South Fork Clearwater River
Subbasin Assessment
and
Total Maximum Daily Loads
Idaho Department of Environmental Quality
U.S. Environmental Protection Agency
October 2003
-------
South Fork Clearwater River
Subbasin Assessment
and
Total Maximum Daily Loads
October 2003
Prepared by:
Tom Dechert
Idaho Department of Environmental Quality
1118 "F" Street
Lewiston, Idaho 83501
Leigh Woodruff
U.S. Environmental Protection Agency
1435 N. Orchard
Boise Idaho 83706
In consultation with the South Fork Clearwater River
Watershed Advisory Group
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
South Fork Clearwater River Subbasin Watershed
Advisory Group
Ranching/Livestock
Bob Rylaarsdam
Grangeville, ID 83530
Wastewater Treatment Plants
Bob Klecha
Grangeville, ID 83530
Family Farms
Jo Ann Mider
Kamiah, ID 83536
Tourism/Travel
Ron Andrews
Kooskia, ID 83539
Preservationist
/Environmentalist
Bonnie Schonefeld
Kooskia, ID 83539
Road Districts
Troy Biesecker
Kidder Harris Hwy Dist.
Kooskia, ID 83539
Outfitters/Guides
Lin Laughy (Vice-Chair)
Kooskia, ID 83539
At Large
Alice Mattson
Kooskia, ID 83538
Local Government
Kelly Frazier
City of Kooskia
Kooskia, ID 83539
Nez Perce Tribe
Rudy Carter
Grangeville, ID 83530
Mining
Pat Holmberg
Grangeville, ID 83530
Timber
Dick Wilhite (Chair)
Shearer Lumber
Elk City, ID 83 525
Agriculture
Ed Stuivenga
Grangeville, ID 83530
Recreation
Borg Hendrickson
Kooskia, ID 83539
At Large
Joy Lee
Kooskia, ID 83539
Federal Land Managers
Kevin Martin
Elk City Ranger Station
Elk City, ID 83 525
Replaced by:
Phil Jahn
Supervisor's Office
Grangeville, ID 83530
Watershed Advisory Group
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Acknowledgments
The Nez Perce Tribe and Ann Storrar from the Nez Perce Tribe Watershed Department
contributed substantially to the development of this subbasin assessment and TMDLs. They
collaborated in the development of this document through a Memorandum of Agreement as
shown in Appendix A. They did many of the many analyses, and wrote several parts for the
document. They contributed substantial amounts of time and money to the effort. We
greatly appreciate all of their input to this project.
This document in its present form would not have been possible without the help received
from personnel of the Nez Perce National Forest. Nick Gerhardt, Forest Hydrologist,
participated at a level equal to the cooperators of the Memorandum of Understanding. Scott
Russell, Forest Fisheries Biologist, provided invaluable input with respect to fisheries
resources and use of the forest databases. Many other forest personnel provided unstinting
help with data acquisition and analysis. Much of the information and data used in this report
came from the Nez Perce National Forest. The forest provided office space and resources as
needed both in Grangeville and Elk City.
The Idaho County Soil and Water Conservation District provided considerable support to the
project, taking the lead in helping us understand and document agricultural practices in the
area. First, Sydney Yuncevich, and later Holly Cotton, from the district provided
administrative support to the Watershed Advisory Group.
The City of Kooskia graciously provided space on a monthly basis for meetings of the
Watershed Advisory Group. Shearer Lumber Company kindly allowed Dick Wilhite the
time to attend and chair the Watershed Advisory Group meetings. Drs. Jan Boll and Erin
Brooks from the University of Idaho devoted numerous hours helping us develop and run the
sediment models. Craig Johnson and the Cottonwood Office of the Bureau of Land
Management provided information on the fisheries and land use resources. Jody Brostrom,
formerly with Idaho Fish and Game and currently with the U.S. Fish and Wildlife Service
shared her wealth of knowledge and data on fish in the subbasin.
The photograph on the cover of this document was taken by Garth Newton from the Idaho
Department of Water Resources.
iii Acknowledgments
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
South Fork Clearwater River Subbasin Watershed Advisory Group i
Acknowledgments iii
Table of Contents v
List of Tables viii
List of Figures xi
List of Appendices xvii
Abbreviations, Acronyms and Symbols xix
Executive Summary xxiii
1. Subbasin Assessment - Watershed Characterization 1
1.1 Introduction 1
Background 1
Idaho and Tribal Roles 2
1.2 Physical and Biological Characteristics 3
Subbasin Characteristics 9
Subwatershed Characteristics 17
Stream Characteristics 23
1.3 Cultural Characteristics 30
Land Ownership 30
Nez Perce Tribe Treaty Rights 31
Communities 32
History and Economics 33
Land Use 34
2. Subbasin Assessment-Water Quality Concerns and Water Quality Status. 39
2.1 Water Quality Limited Segments Occurring in the SF CWR Subbasin 39
2.2 Applicable Water Quality Standards 41
Beneficial Uses 41
Water Quality Criteria 42
2.3 Summary and Analysis of Existing Water Quality Data 45
Subbasin-wide Biological and Other Data 45
Subbasin Flow Characteristics 52
Subbasin-wide Water Column Data 58
Conclusions from the Water Column Data for the SF CWR Subbasin. 72
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Summary and Analysis of Existing Water Quality Data for Threemile
Creek and Butcher Creek 73
Summary and Analysis of Existing Water Quality Data for Lucas Lake
93
2.4 Data Gaps 93
Flow 93
Water Column Data 93
Temperature 94
Biological and Other 95
Beneficial Uses 95
3. Subbasin Assessment - Pollutant Source Inventory 97
3.1 Sources of Pollutants of Concern 97
Point Sources 97
Nonpoint Sources 106
3.2 Data Gaps 124
Point Sources 124
Nonpoint Sources 124
4. Subbasin Assessment - Summary of Past and Present Pollution Control
Efforts 129
4.1 Point Source Control Efforts 129
Wastewater Treatment Facilities 129
Suction Dredge Mining 132
4.2 Nonpoint Source Control Efforts 133
Agriculture 134
Forestry 134
4.3 Watershed Improvement Projects 135
5. Total Maximum Daily Loads 143
5.1 Bacteria TMDL - Threemile Creek 144
Design Conditions 144
Target Selection 145
Monitoring Points 145
Load Capacity 145
Estimates of Existing E. co//Loads 146
Load and Wasteload Allocations 148
Margin of Safety 148
Seasonal Variation/Critical Conditions 148
Background 148
Reserve 151
5.2 Nutrient TMDL - Threemile Creek 151
Design Conditions 152
Target Selection 152
Monitoring Points 154
Load Capacity 154
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Estimates of Existing Total Phosphorus Loads 155
Load and Wasteload Allocations 155
Margin of Safety 158
Background 158
Reserve 158
5.3 Temperature TMDLs 159
In-Stream Water Quality Targets 159
Design Conditions 160
Target Selection 161
Surrogate Water Temperature Targets 168
Heat Loading Capacity 170
Estimates of Existing Heat Loading 170
Heat Load Allocation 177
Margin of Safety 188
Seasonal Variation/Critical Conditions 189
Background 189
Reserve 190
5.4 Sediment TMDLs 190
In-Stream Water Quality Targets for Sediment 190
Design Conditions 190
Target Selection 197
Flow Data and Flow Estimation 198
TSS and Bedload Data 203
Estimates of Existing Sediment Loads 204
Estimates of Background Sediment Loading 206
Sediment Load Capacity 207
Excess Loading 211
Margin of Safety 216
Seasonal Variation 216
Sediment Load Allocations 216
5.5 Implementation Strategy 225
Temperature 226
Sediment 227
Bacteria 230
Nutrients/DO 231
Approach 231
Reasonable Assurance 231
Time Frame 232
Participating Parties 232
Monitoring Strategy 233
5.6 Summary and Conclusions 235
References 239
Glossary 253
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Tables
Table A. Water quality limited water bodies in the SF CWR Subbasin xxiv
Table B. Streams and pollutants for which TMDLs were developed xxix
Table 1. SF CWR Subbasin watersheds, water bodies, and acreages 4
Table 2. Summary of climatic data for various stations in and around the SF
CWR Subbasin 9
Table 3. SF CWR Subbasin landform group characteristics 17
Table 4. Watershed condition indicators 18
Table 5. SF CWR temperatures, 1991-1993 (USFS 1999) 28
Table 6. Acreages of the SF CWR Subbasin land management groups 31
Table 7. Population trends in Idaho County 32
Table 8. Sawlog volume sold from SF CWR Subbasin 35
Table 9. Percent land use in Threemile and Butcher Creeks 37
Table 10. Water quality limited water bodies in the SF CWR Subbasin 40
Table 11. Sources of water quality data 46
Table 12. Salmon, trout, and char species present in the SF CWR Subbasin. 48
Table 13. Other fish species known to occur in the SF CWR Subbasin 48
Table 14. WBAG version 1996 results for 303(d) listed water bodies in the SF
CWR Subbasin 50
Table 15. WBAG version 2002 assessment of the 303(d) listed wadeable
streams in the SF CWR Subbasin 51
Table 16. USGS and Storet Stations in the SF CWR Subbasin 54
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table 17. Flow data (cubic feet per second) for the SF CWR near Grangeville
(#13338000), 1910-1963 55
Table 18. Flow data (cubic feet per second) for the SF CWR near Elk City
(#13337500), 1944-1974 56
Table 19. Flow data (cubic feet per second) for the SF CWR at Stites
(#13338500), 1910-1912, 1964-1998 57
Table 20. Mean monthly flows (cubic feet per second) for the SF CWR at Elk
City and Stites, and for Lapwai Creek at Lapwai 57
Table 21. Magnitude and frequency of instantaneous peak flow at gaging
stations in SF CWR Subbasin 58
Table 22. SF CWR instantaneous peak discharges (cubic feet per second)
during major flood events 58
Table 23. Monitored flows in Threemile Creek from February 22, 2000, to
February 6, 2001 76
Table 24. Ortho-phosphorus concentrations on Threemile Creek (February 22,
2000, to February 6, 2001) 85
Table 25. Total nitrogen data summaries for Threemile Creek (February 22,
2000 to February 6, 2001) 87
Table 26. Total phosphorus, nitrate-nitrogen, and bacteria for all stations and
dates along Threemile Creek 90
Table 27. Range and median of nutrients in the Clearwater aquifer measured
from 1991 through 1993 (Crockett 1995) 91
Table 28. NPDES permitted point sources in the SF CWR Subbasin 98
Table 29. Summary of sample results for suction dredges larger than 5 inches
(USFS 1980a; USFS 2000) 103
Table 30. Turbidity and TSS data for 8 inch section dredges (USFS 1980a;
DEQ2000) 104
Table 31. Land use in each SF CWR Subbasin WBID units 106
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table 32. Sediment loads from nonpoint sources for each of the water bodies
in the SF CWR Subbasin 111
Table 33. Road data for the SF CWR Subbasin 119
Table 34. E. coli load capacities for Threemile Creek 146
Table 35. Average monthly flow, E. coli concentration, and loading in
Threemile Creek 147
Table 36. E. coli nonpoint source allocations and wasteload allocations for
Threemile Creek 150
Table 37. Total phosphorus (TP) load capacities for Threemile Creek 155
Table 38. Average monthly flow, total phosphorus (TP) concentration, and
loading in Threemile Creek 156
Table 39. Total phosphorus (TP) load allocations and wasteload allocations
for Threemile Creek 157
Table 40. Applicable water temperature criteria 159
Table 41. Time periods of salmonid spawning and incubation in the SF CWR
Subbasin 162
Table 42. Salmonid species distribution in the SF CWR Subbasin 163
Table 43. Point sources that may affect stream temperature 177
Table 44. Nonpoint source shade increase summary 183
Table 45. Elk City wastewater treatment plant (WWTP) maximum daily effluent
temperatures (°C)a that would not increase temperatures in Elk Creek by more
than 0.3 °C between June 1 and September 30 when federal bull trout criteria
apply 186
Table 46. Grangeville wastewater treatment plant (WWTP) maximum daily
effluent temperatures (°C)a which would not increase temperatures in
Threemile Creek by more than 0.3 °C between April 1 and May 31 when the
salmonid spawning criteria is applicable 186
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table 47. Grangeville wastewater treatment plant (WWTP) maximum daily
effluent temperature (°C) that would not increase Threemile Creek temperature
more than 0.3 °C between July 15 and September 15 when coldwater aquatic
life temperature criteria apply 187
Table 48. Temperature wasteload allocations for wastewater treatment plants.
187
Table 49. Threemile Creek loading calculations 193
Table 50. Butcher Creek loading calculations 194
Table 51. Stites USGS station loading calculations 195
Table 52. Harpster site loading calculations 196
Table 53. Sediment loads from point sources in the SF CWR Subbasin 204
Table 54. Estimated cumulative sediment loads from nonpoint sources in the
SF CWR Subbasin.3 206
Table 55. Total suspended solids (TSS)-based load capacities for water
bodies in the lower SF CWR Subbasin 208
Table 56. Total sediment loading capacity of water bodies in the upper SF
CWR Subbasin 212
Table 57. Total suspended solids (TSS) excess loading for water bodies in the
lower SF CWR Subbasin 212
Table 58. Sediment wasteload allocations for the SF CWR Subbasin 220
Table 59. Sediment load allocations for nonpoint sources in the SF CWR
Subbasin. a 224
Table 60. Sediment excess loads by management responsibility in the SF
CWR Subbasin 227
Table 61. Sediment load targets by data type in the SF CWR Subbasin 234
Table 62. Streams and pollutants for which TMDLs were developed 237
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Figures
Figure A. The South Fork Clearwater River Subbasin in North-Central Idaho
xxiv
Figure 1. The South Fork Clearwater River Subbasin in North-Central Idaho ...4
Figure 2. Water Bodies and Water Body Numbers in the SF CWR Subbasin ....7
Figure 3. Climatic Stations and Precipitation Zones in the SF CWR Subbasin .8
Figure 4. Monthly Percent of Annual Flow 11
Figure 5. Geology of the SF CWR Subbasin 12
Figure 6. Habitat Type Groups of the SF CWR Subbasin 13
Figure 7. Aquatic Landtype Associations of the SF CWR Subbasin 13
Figure 8. Major Land Managers of the SF CWR Subbasin 31
Figure 9. Water Quality Limited Water Bodies in the SF CWR Subbasin 39
Figure 10. Locations of BURP Sites Throughout the SF CWR Subbasin 49
Figure 11. Recent Annual Maximum Weekly Maximum Temperature (MWMT)
(°F) Temperature Statistic Values Observed in the SF CWR Subbasin 59
Figure 12. Maximum Weekly Maximum Temperatures Measured along the SF
CWR Main Stem in 2000 60
Figure 13. SF CWR Temperatures Derived from Instream Monitors and
Remote Sensed Thermal Infrared Imaging (TIR a.k.a. FLIR) for August 3, 2000
61
Figure 14. Observed Diurnal Temperatures in the Main Stem SF CWR on
Augusts, 2000 62
Figure 15. Maximum Weekly Mean Temperatures Measured along Red River in
2000 63
Figure 16. Observed Diurnal Temperatures in Red River on August 3, 2000 ..63
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Figure 17. Measured Maximum Weekly Mean Temperature (°F) in the American
River System in 2000 64
Figure 18. Diurnal Temperatures Measured in Big Elk Creek and the American
River (mouth) on August 3, 2000 65
Figure 19. Diurnal Temperatures Measured in Little Elk Creek and the
American River (mouth) on August 3, 2000 65
Figure 20. Maximum Weekly Mean Temperatures Measured in Threemile
Creek in 2000 66
Figure 21. Diurnal Temperature Measured in Threemile Creek on August 3,
2000 67
Figure 22. Seasonal Variations in Daily Maximum Temperatures in the SF
CWR (Summer 2000) 67
Figure 23. Seasonal Variations in Daily Maximum Temperatures in Threemile
Creek (Summer 2000) 68
Figure 24. Seasonal Variations in Daily Maximum Temperatures in the Red
River (Summer 2000) 68
Figure 25. Total Suspended Solids Excess Loads for Stites, Threemile Creek,
and Butcher Creek 71
Figure 26. Monitoring Sites on Threemile Creek 74
Figure 27. Stream Flow at Four Monitoring Points on Threemile Creek 75
Figure 28. Flows Monitored in Butcher Creek 76
Figure 29. Measured Monthly Temperature and Precipitation vs. 40 Year
Monthly Averages for Temperature and Precipitation 77
Figure 30. E. coli Bacteria Monitoring Results for Threemile Creek 78
Figure 31. E. coli Monitoring Results for Butcher Creek 79
Figure 32. Dissolved Oxygen Monitoring Results for Threemile Creek 80
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Figure 33. Dissolved Oxygen Monitoring Results for Butcher Creek 81
Figure 34. Total Ammonia Monitoring Results for Threemile Creek 82
Figure 35. Total Ammonia Monitoring Results for Butcher Creek 82
Figure 36. pH Monitoring Results for Threemile Creek 83
Figure 37. pH Monitoring Results for Butcher Creek 83
Figure 38. Ortho-phosphorus Monitoring Results for Threemile Creek 86
Figure 39. Ortho-Phosphorus Monitoring Results for Butcher Creek 86
Figure 40. Total Nitrogen Monitoring Results for Threemile Creek 88
Figure 41. Total Nitrogen Monitoring Results for Butcher Creek 89
Figure 42. Locations of NPDES Permitted Sites in the SF CWR Subbasin 99
Figure 43. Land Use Distribution in the SF CWR Subbasin 109
Figure 44. Sediment Production by Water Body in the SF CWR Subbasin....118
Figure 45. Annual Sediment Production per Square Mile in the SF CWR
Subbasin 118
Figure 46. Fish TAG Assessment of Water Bodies in the SF CWR Subbasin
with Significant Sediment Problems 122
Figure 47. Seasonal Variation in Maximum Water Temperature at Various
Locations along the SF CWR in 2000 171
Figure 48. Diurnal Temperatures Measured Big Elk Creek and the American
River (mouth) on August 3, 2000 172
Figure 49. Current Percent Canopy Closure Determined by Aerial
Photographic Interpretation of the SF CWR Subbasin 173
Figure 50. Current Canopy Closure of Threemile and Butcher Creeks 173
Figure 51. Current Canopy Closure of Big Elk and Little Elk Creeks 174
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Figure 52. Big Elk Creek Current Effective Shade, Lower Reaches 174
Figure 53. Little Elk Creek Current Effective Shade, Lower Reaches 175
Figure 54. Threemile Creek Current Effective Shade 175
Figure 55. South Fork Clearwater River Current Effective Shade 176
Figure 56. Butcher Creek Current Effective Shade 176
Figure 57. Cumulative Watershed Effects (CWE)-Based Target Percent
Canopy Closure for the SF CWR Subbasin 179
Figure 58. Cumulative Watershed Effects (CWE)-Based Target Percent
Canopy Closure for the Threemile/Butcher Creeks Area 179
Figure 59. Cumulative Watershed Effects (CWE)-Based Target Percent
Canopy Closure for the Big and Little Elk Creeks Area 180
Figure 60. Current and System Potential Effective Shade Conditions for the SF
CWR 180
Figure 61. Current and System Potential Effective Shade Conditions for Big
Elk Creek 181
Figure 62. Current and System Potential Effective Shade Conditions for Little
Elk Creek 181
Figure 63. Current and System Potential Effective Shade Conditions for
Threemile Creek 182
Figure 64. Current and System Potential Effective Shade Conditions for
Butcher Creek 182
Figure 65. U.S. Geological Survey (USGS) Flow Record from Stites 199
Figure 66. U.S. Geological Survey (USGS) Flow Data for Lapwai Creek 200
Figure 67. Derived 10-Year Flow for Threemile Creek 202
Figure 68. Derived 10-Year Flow for Butcher Creek 202
Figure 69. Derived 10-Year Flow for the Harpster Site on the SF CWR 203
Figure 70. Average Daily Total Suspended Solids (TSS) Load Capacities for
Stites Site on the SF CWR, Threemile Creek, and Butcher Creek 210
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Figure 71. Excess Sediment Loading for Threemile Creek 213
Figure 72. Excess Sediment Loading for Butcher Creek 214
Figure 73. Excess Sediment Loading at Stites 215
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Appendices
Appendix A. Memorandum of Agreement
Appendix B. Federal Bull Trout Criteria
Appendix C. Assessment Units for the South Fork Clearwater River Subbasin
TMDLs
Appendix D. Fisheries Resources
Appendix E. Agricultural Chemicals
Appendix F. System Potential Vegetation Methods and Results
Appendix G. The Cumulative Watershed Effects Temperature Model Applied
to the South Fork Clearwater River Subbasin
Appendix H. U.S. Forest Service Vegetation Response Unit and Habitat Type
Group Descriptions
Appendix I. Overview of Stream Heating Processes
Appendix J. Stream and River Temperature Data
Appendix K. Summary of Stream Habitat Data
Appendix L. South Fork Clearwater River Subbasin Sediment Budget
Appendix M. Total Suspended Solids and Bedload Data
Appendix N. Reference Watersheds
Appendix O. Wastewater Treatment Plant (WWTP) Effluent Temperature and
Heat Loading Analysis
Appendix P. Lucas Lake, Beneficial Use Assessment and Reconnaissance
Metals Monitoring
Appendix Q. Unit Conversion Chart
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Appendix R. Public Comment Distribution List
Appendix S. Responses to Public Comments
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October 2003
Abbreviations, Acronyms, and Symbols
303(d) Refers to section 303
subsection (d) of the Clean
Water Act, or a list of impaired
water bodies required by this
section
\i micro, one-one thousandth
§ Section (usually a section of
federal or state rules or
statutes)
ACOE Army Corps of Engineers
ALTA aquatic landtype association
ave. average
BA biological assessment
BAG Basin Advisory Group
BLM United States Bureau of Land
Management
BMP best management practice
BOD biological oxygen demand
BPA Bonneville Power
Administration
Btu British thermal unit
BURP Beneficial Use Reconnaissance
Program
C Celsius
CAFO confined animal feeding
operation
CFI Clearwater Forest Industries
CFR Code of Federal Regulations
(refers to citations in the
federal administrative rules)
cfs cubic feet per second
cfu colony forming units
cm centimeters
CRP Cropping Reserve Program
CWA Clean Water Act
CWAL cold water aquatic life
CWE cumulative watershed effects
DEQ Idaho Department of
Environmental Quality
DO dissolved oxygen
DRG digital Raster graphic
ECA equivalent clearcut acres
EMAP Environmental Monitoring and
Assessment Program
EQIP Environmental Quality
Incentive Program
ESA Endangered Species Act
ESU ecologically significant unit
F Fahrenheit
Fish TAG Fisheries Technical Advisory
Group
FLIR forward-looking infra-red
FPA Idaho Forest Practices Act
xix
Abbreviations, Acronyms & Symbols
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
FSA Farm Services Administration
FWS U. S. Fish and Wildlife Service
GIS Geographical Information
Systems
HALT habitat alteration
HI DEQ' s Habitat Index
HTG habitat type groups
HUC Hydrologic Unit Code
ICBEMP Interior Columbia Basin
Environmental Management
Program
IDA Idaho Department of
Agruculture
IDAPA Refers to citations of Idaho
administrative rules
IDC Idaho Department of
Commerce
IDHW Idaho Department of Health
and Welfare
ITD Idaho Transportation Dept.
IDFG Idaho Department of Fish and
Game
IDL
Idaho Department of Lands
IDWR Idaho Department of Water
Resources
INFISH Federal Inland Native Fish
Strategy
km
kilometer
km square kilometer
LA load allocation
LFG landform group
LC load capacity
m meter
m3 cubic meter
M&E monitoring and evaluation
mi mile
mi2 square miles
MBI macroinvertebrate biotic index
MGD million gallons per day
mg/L milligrams per liter
mm millimeter
MMBF million board feet
MOS margin of safety
MOU Memorandum of
Understanding
MWMT maximum weekly maximum
temperature
N nitrogen
n.a. not applicable
NA not assessed
NB natural background
nd no data (data not available)
xx
Abbreviations, Acronyms & Symbols
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
NEPA National Environmental Policy
Act
NEZSED Nez Perce National Forest
sediment model
NFS
not fully supporting
NMFS National Marine Fisheries
Service
NO2
NO3
nitric oxide
nitrous oxide
NPDES National Pollutant Discharge
Elimination System
NPNF Nez Perce National Forest
NPT
Nez Perce Tribe
NRCS Natural Resources
Conservation Service
NTU nephlometric turbidity unit
NWI National Wetlands Inventory
ORW Outstanding Resource Water
P phosphorus
PACFISH The federal Pacific
Anadromous Fish Strategy
PCB polychloro bi-phenols
PCR primary contact recreation
PFC proper functioning condition
ppm part(s) per million
QA quality assurance
QALT flow alteration
QC quality control
RFI DEQ' s river fish index
RHCA riparian habitat conservation
area
RM river mile
RMI DEQ's river macroinvertebrate
index
RUSLE revised universal soil loss
equation
SBA subbasin assessment
SCR secondary contact recreation
SF CWR South Fork Clearwater River
SFI DEQ's stream fish index
SHI DEQ's stream habitat index
SMI DEQ's stream
macroinvertebrate index
SS salmonid spawning
SSOC stream segment of concern
SSURGO Soil Survey Geographic
Database
STATSGO State Soil Geographic
Database
STP sewage treatment plant
TAG technical advisory group
TIN total inorganic nitrogen
xxi
Abbreviations, Acronyms & Symbols
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
TIR thermal infra-red
TKN total Kjeldahl nitrogen
TMDL total maximum daily load
TN total nitrogen
TP total phosphorus
TSS total suspended solids
t/y tons per year
U.S. United States
U.S.C. United States Code
USDA United States Department of
Agriculture
USDI United States Department of
the Interior
USEPA United States Environmental
Protection Agency
USFS
United States Forest Service
USGS United States Geological
Survey
VRU vegetative response units
WAG Watershed Advisory Group
WBAG Water Body Assessment
Guidance
WB
water body
WBID water body identification
number
WEPP Watershed Erosion Prediction
Project sediment model
WLA wasteload allocation
WQS water quality standard(s)
WWTP waste water treatment plant
xxn
Abbreviations, Acronyms & Symbols
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Executive Summary
The federal Clean Water Act (CWA) requires that states and tribes restore and maintain the
chemical, physical, and biological integrity of the nation's waters. States and tribes, pursuant
to Section 303 of the CWA, are to adopt water quality standards (WQS) necessary to protect
fish, shellfish, and wildlife while providing for recreation in and on the waters whenever
possible. Section 303(d) of the CWA establishes requirements for states and eligible tribes to
identify and prioritize water bodies that are water quality limited (i.e., water bodies that do
not meet water quality standards). States and tribes must periodically publish a priority list
of impaired waters, currently every two years. For waters identified on this list, states and
tribes must develop a total maximum daily load (TMDL) for the pollutants, set at a level to
achieve WQS. This document addresses the water bodies in the South Fork Clearwater River
(SF CWR) Subbasin that have been placed on what has come to be known as the "303(d)
list." This document was prepared collaboratively under a Memorandum of Agreement by
the Idaho Department of Environmental Quality (DEQ), the Nez Perce Tribe (NPT), and the
U.S. Environmental Protection Agency (USEPA).
This subbasin assessment and TMDLs have been developed to comply with Idaho's WQS
and TMDL schedule. The first part of this document, the subbasin assessment, is an
important first step in leading to the TMDL. This assessment describes the physical,
biological, and cultural setting; water quality status; pollutant sources; and recent pollution
control actions in the SF CWR Subbasin located in north-central Idaho. The starting point
for the assessment was Idaho's 1998 303(d) list of water quality limited water bodies.
Eighteen stream segments and one lake in the SF CWR Subbasin were included on this list.
The subbasin assessment portion of this document examines the current status of 303(d)
listed waters. It defines the extent of impairment and causes of water quality limitation
throughout the subbasin. The loading analysis, or TMDL, portion of the document quantifies
pollutant sources and allocates responsibility for load reductions needed to return listed
waters to a condition of meeting WQS.
Subbasin Assessment at a Glance
The SF CWR Subbasin is entirely within Idaho County, with the county seat at Grangeville,
Idaho, and partially on the Nez Perce Reservation (Figure A). Total maximum daily loads
were completed in 2000 for the six stream segments in the Cottonwood Creek watershed
within the SF CWR Subbasin. This document addresses the remaining 12 listed stream
segments and Lucas Lake. Their extent, beneficial uses, and suspected pollutants are shown
in Table A. However, at the completion of the assessment of temperature impairment to
water quality, it was concluded that many unlisted stream segments throughout the subbasin
need heat load reductions to meet WQS. Heat load reductions in terms of stream shading
increases were established for stream segments throughout the subbasin.
A new, comprehensive system of water quality accounting is being established by DEQ and
USEPA which uses water quality "assessment units" (AUs). The correlation between AUs
and the water bodies assessed in this report is presented in Appendix C.
xxiii Executive Summary
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
South Fork Clearwater River Subbasin
Major Roacte
@ Cities
{^ ~) NP T Reservation Boundary
SF C!earwaier4ih Field HUC
Figure A. The South Fork Clearwater River Subbasin in North-Central Idaho
Table A. Water quality limited water bodies in the SF CWR Subbasin.
Stream
Name
South Fork
Clearwater
River
Three mile
Creek
Butcher
Creek
Dawson
Creek
Little Elk
Creek
Big Elk
Water Body
Identification
Numbers3
1, 12,22,30,
36
10
11
38
57
58
Boundaries
(1998
303(d) list)b
Red River to
Clearwater
River
Headwaters
to SF CWR
Headwaters
to SF CWR
Headwaters
to Red River
Headwaters
to Elk Creek
Headwaters
Beneficial
Usesc
CW/SS(d)
PCR(d)
SRW (d)
CW/SS(d)
SCR(d)
CW/SS(d)
SCR(d)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
303(d)
Listed
Pollutantd
Halt, Sed,
Temp
Bac, DO,
Qalt, Halt,
NH3, Nut,
Sed, Temp
Bac, DO,
Qalt, Halt,
Sed, Temp
Sed
Temp
Temp
TMDLs
Completed
Sed, Temp
Bac, DO,
Nut, Sed,
Temp
Sed, Temp
Temp
Temp
Temp
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South Fork Clearwater River Subbasin Assessment and TMDLs
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Stream
Name
Creek
Buffalo
Gulch
New-some
Creek
Nugget
Creek
Beaver
Creek
Sing Lee
Creek
Cougar
Creek
Lucas
Lake
58 Other
Water
Bodies6
Water Body
Identification
Numbers3
59
62
64
65
73
79
Boundaries
(1998
303(d) list)b
to Elk Creek
Headwaters
to American
River
Beaver Creek
to SF CWR
Headwaters
to Newsome
Creek
Headwaters
to Newsome
Creek
Headwaters
to Newsome
Creek
Headwaters
to SF CWR
Beneficial
Usesc
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
303(d)
Listed
Pollutantd
Sed
Sed
Sed
Sed
Sed
Sed
Sed
TMDLs
Completed
Temp
Temp
Temp
Temp
Temp
Temp
Temp
a A new accounting system for water quality tracking is being setup using water quality "assessment units"
(AUs). A given water body may contain one or more AUs. The correlation between water bodies
assessed in this document and AUs may be found in Appendix C.
b Refers to a list created in 1998 of water bodies in Idaho that did not fully support at least one beneficial use.
This list is required under section 303 subsection "d" of the Clean Water Act. This list may change in the
future.
c CW = Cold Water, SS = Salmonid Spawning, PCR = Primary Contact Recreation, SCR = Secondary Contact
Recreation, SWR= Special Resource Water, (d) = designated beneficial use, (e) = existing beneficial use
dBac = bacteria, DO = dissolved oxygen, Qalt = flow alteration, Halt = habitat alteration, NH3 = ammonia, Nut
= nutrients, Sed = sediment, Temp = temperature
e Temperature TMDLs were written for the 58 other water bodies in the SF CWR Subbasin, excepting those
water bodies covered by the Cottonwood Creek TMDL.
Pollutant analyses were conducted in four distinct groupings: subbasin-wide analyses for
temperature (heat loading); subbasin-wide analyses for sediment; Threemile and Butcher
Creeks for bacteria, nutrients, dissolved oxygen, and ammonia; and Lucas Lake for sediment.
Subbasin-wide temperature analyses were conducted in light of an extensive database
indicating that no stream in the SF CWR Subbasin, not even ones in relatively pristine
condition, meets the Idaho numeric temperature criteria for salmonid spawning. However,
the Idaho WQS recognize that stream temperatures may naturally exceed numeric criteria
and that pollution control measures should only address the human-caused increases in
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
temperature. The non-point temperature assessments assumed that the human-caused effects
were increased solar insolation, primarily a result of reduced streamside vegetation and,
secondarily a result of increased stream width. Shading and stream width analyses were
conducted on all perennial streams in the subbasin. The human-caused stream temperature
increase was quantified in terms of the percent decrease in stream shade and increase in
stream width. Targets were set based on best estimates of natural conditions for stream shade
and stream width. It was recognized that minor amounts of human-caused heat loading
occur, such as from hatchery facilities or old mining sites, but allocations were limited to the
major source of increased heat loading, reduced stream shading and increased stream width.
Point source temperature loadings were calculated based on temperatures and flows, and
were generally very low except at the Grangeville wastewater treatment plant (WWTP).
Targets for all WWTPs were set to limit temperature increases in receiving waters to less
than 0.3°C (0.5°F) above the temperature criteria, as per the WQS and USEPA temperature
guidance (USEPA 2003).
Subbasin-wide sediment analyses were based on a limited stream turbidity and total
suspended solids (TSS) data set from four locations in the lower subbasin and a sediment
delivery budget to streams from various sources. The sediment budget was developed using
estimates from different models and data sets from the various sediment sources throughout
the subbasin, as follows: NEZSED erosion model estimates of sediment from federally-
managed timber land; RUSLE erosion model estimates of sediment from agricultural and
range land; a stream bank erosion model estimate of in-stream erosion; WEPP erosion model
estimates of sediment from county roads; a Nez Perce National Forest inventory of mass
failures extrapolated to include the complete subbasin; and an estimate based on average
annual rock crush of gravel from State Highway 14 reaching the river. Point sources of
sediment in the subbasin (municipal WWTPs, suction dredges, construction and industrial
stormwater runoff) were found to be insignificant in relation to the nonpoint sources.
Turbidity data were compared directly to the state WQS with loadings calculated using
turbidity to TSS relationships. Sediment targets and allocations in the lower basin were set to
meet the state turbidity criteria. Sediment targets for the upper basin, where no turbidity data
were available, were set based on the percent load reduction needed at the mouth of the SF
CWR, the Stites bridge control location. It was recognized that minor amounts of human-
caused sediment loading occurs, such as from hatchery facilities or old mining sites, but
allocations were limited to the major sources identified in the sediment budget. Point source
allocations were established at required technology based levels, or at levels in existing
National Pollutant Discharge Elimination System (NPDES) permits.
Threemile and Butcher Creeks are 303(d) listed for several other pollutants in addition to
sediment and temperature. They were both also evaluated for nutrients, dissolved oxygen,
bacteria, and ammonia. Threemile Creek is particularly impacted because it receives effluent
from the Grangeville WWTP, which at times makes up more than 50% of the stream flow.
Data for pollutants were collected near the mouth of Butcher Creek and at four locations on
Threemile Creek. Bacteria, dissolved oxygen, and ammonia data were compared to the state
WQS. Nutrient levels were compared to both USEPA guidelines and the state's narrative
WQS to determine impairment. In the case of Threemile Creek, where water quality
xxvi Executive Summary
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
impairment was identified, the target was set for phosphorus based on the USEPA guidelines
and local monitoring results. These targets, and the seasonality of their application, may
require adjustments in the future as additional data and information are collected. The
phosphorus TMDL is expected to result in compliance with the numeric dissolved oxygen
standard as well as the narrative nutrient criteria. A bacteria TMDL was also established for
Threemile Creek to address the seasonally high levels of E. coli.
Lucas Lake, near Elk City, is an old "glory hole" about 2 acres in size from the mining days.
It was 303(d) listed because it was identified in the Idaho 1988 Water Quality Status Report
andNonpoint Source Assessment (DEQ 1989) as not supporting one or more beneficial uses
due to sediment siltation. Turbidity and metals samples were collected for the lake and
compared against the state WQS. No impairment was identified.
Key Findings
The SF CWR subbasin assessment and TMDLs have been written with input from a local
Watershed Advisory Group consisting of 16 members representing a wide range of interests
and land managers. This group met monthly over the course of the project to review
progress and provide input. A Fisheries Technical Advisory Group of professionals
knowledgeable of the fisheries resources in the subbasin met several times and provided
detailed information about the presence and condition of salmonid species in the subbasin.
As a result of the subbasin assessment, temperature TMDLs were written for all 74 water
bodies in the part of the subbasin covered by this document; sediment TMDLs were written
for the main stem SF CWR, Butcher Creek, and Threemile Creek; and nutrient and bacteria
TMDLs were written for Threemile Creek. It is expected that these TMDLs will improve
conditions throughout the subbasin for all aquatic species, including threatened and
endangered fish species such as bull trout, spring chinook salmon, and steelhead.
Water temperatures are elevated above WQS at all monitoring locations throughout the
subbasin. Shading of the water surface has been reduced by logging, reading, mining,
grazing, and agricultural activities near the streams and rivers. To a lesser degree, stream
channel configurations have been altered by the same human activities. Water channels that
have been made wider and shallower, with less vegetative shading, are being heated by solar
insolation. The degree to which shade has been reduced and channels altered was assessed
on a stream reach by stream reach basis. Current stream shading was assessed using aerial
photograph interpretation and other analytical techniques. Potential shade in forested areas
was assumed to be 90%. Channel widths in forested areas were assumed to have been little
altered in relation to the size of coniferous trees and their ability to provide shade. Potential
shade in non-forested areas was calculated from the size and density of an expected natural
vegetation and an expected natural channel width. Targets were set to restore stream shading
and stream channel morphology to conditions representing minimal human impact.
Whereas stream heat load capacity can be described in terms of joules per day, and some
discussion of heat loading in relation to stream shade and channel width is included in this
document, loading for temperature is presented in terms of stream shade and stream width.
xxvii Executive Summary
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
The load capacity of a given stream reach is set at the heat loading that would occur if the reach
were in a relatively undisturbed condition in terms of the channel morphology and streamside
vegetation. In the forested part of the subbasin, 3,640 stream reaches were evaluated, of which
54% need various percentage increases of stream canopy closure. An Arc View shapefile is
included with the TMDL so users can locate stream reaches and identify whether or not a shade
increase is needed, and how much. For the non-forested streams and rivers, more variable
current conditions led to the need to have shade and stream width targets defined on a more site-
specific basis. Any need for increased shade and/or stream width reduction must be calculated
on the ground using a set of graphs which require input of wetted stream width, aspect of the
stream, and one of twelve expected natural vegetation categories.
Point source contributions to water temperature increases are minor throughout the subbasin
except for the effects of the effluent from the Grangeville WWTP on Threemile Creek.
Allocations are established for all WWTPs such that they will not increase stream temperature
more than 0.3°C (0.5°F) above established temperature criteria per IDAPA 58.01.02.401.03.a.v,
and USEPA regional temperature guidance (USEPA 2003).
Sediment loadings to waters of the SF CWR Subbasin fall into two relatively distinct categories:
sediment loadings from agricultural and grazing areas on the order of 10-30 times natural
background (per water body) compared to sediment loadings from forested areas no greater than
twice natural background. For Threemile and Butcher Creeks which are the primary agricultural
areas in the subbasin, TSS based on the turbidity WQS need to be reduced 71% and 46%,
respectively, to meet the state WQS. At Stites on the main stem SF CWR, with dilution from the
forested part of the watershed, TSS loading needs to be reduced by 25%. At the Harpster control
location, which is above the majority of agricultural and grazing areas, turbidity meets the WQS.
Water quality in the upper basin was determined to be degraded by coarse sediment, primarily
sand-sized material, as it affects salmonid spawning. The problem is more-or-less basin-wide
wherever human activities have occurred. In order to meet water quality objectives, sediment
load reduction allocations of 25% were set for the Harpster control location as well as three other
upstream control locations (above Johns Creek, above Tenmile Creek, and above Crooked River)
on the main stem SF CWR. Control locations were set on the main stem with the goal of
directing land managers to reduce sediment from appropriate locations throughout the upper
basin. For example, to meet the load allocated to the main South Fork Clearwater River at
Harpster reductions may occur anywhere in the watershed above Harpster. The 25% load
reduction target was selected as consistent with the load reduction required at the Stites location
at the mouth of the main stem.
Point sources of sediment loading include five municipal WWTPs, suction dredge mining
operations, and construction and industrial stormwater runoff. All of these sources are very
minor in comparison to loading from human-caused nonpoint source runoff. Allocations for
these facilities are based on meeting turbidity and treatment requirements in Idaho WQS, and
technology based limits for WWTPs.
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Bacteria levels in Threemile Creek substantially exceed the E. coll criteria in Idaho WQS.
Limited data are available to assess the source of bacteria loading, but it is believed that
livestock grazing in and around the creek is the most significant source. Other potential
sources include stormwater runoff and leaking sewer lines in Grangeville, failed septic
systems, and waterfowl and other wildlife. A general load reduction of 82% - 93% has been
set for all nonpoint sources. The Grangeville WWTP is a known point source, but due to its
disinfection facilities, it contributes less than allowed by the WQS and its NPDES permit. It
received an allocation equal to the WQS, with no required load reduction.
Nutrient levels in Threemile Creek substantially exceed USEPA's regional guidance for both
nitrogen and phosphorus. The majority of the nutrients are contained in the effluent from the
WWTP; however, a considerable portion is also from nonpoint sources. Required load
reductions are developed for phosphorus as the limiting nutrient for both the WWTP and
non-point sources. Since dissolved oxygen (DO) and nutrient levels are linked, the state
WQS of 6 mg/L of DO is set as a target for DO. In order to attain the targets, phosphorus
load reductions were set at 32% from the headwaters to the WWTP, 32% from the WWTP
outfall to the Nez Perce Reservation boundary, and 0% from the reservation boundary to the
mouth. The WWTP received a 97% phosphorus load reduction.
Table B. Streams and pollutants for which TMDLs were developed.
Stream
South Fork Clearwater River
Threemile Creek
Butcher Creek
Dawson Creek
Little Elk Creek
Big Elk Creek
Buffalo Gulch
Newsome Creek
Beaver Creek
Nugget Creek
Sing Lee Creek
Cougar Creek
58 Other Water Bodies
Pollutant(s)
Sediment, Temperature
Bacteria, Nutrients, DO, Sediment, Temperature
Sediment, Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Timeframe.
Development of the implementation plan has already begun. The plan is expected to be
completed in time to submit for 319 funding in 2004/2005. Wasteload allocations will be
incorporated into NPDES permits when they are reissued or reopened. The Grangeville
permit is expected to be reissued within the next 1-2 years, and the recently reissued permits
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
for Kooskia, Stites, Elk City and Red River Ranger Station will need to be re-opened to
incorporate revised limits.
Implementation of nonpoint source controls has already begun, but is expected to proceed in
earnest once the implementation plan is complete and funds are available. A majority of the
sources of temperature and sediment loading are nonpoint in origin, and realistically it may
take many years if not decades to fully achieve the goals of the TMDL. Certain
improvements such as controlling temperature and nutrients from the Grangeville treatment
facility or controlling nonpoint bacteria sources are likely to occur within a few years. In
order to improve stream temperature, restored riparian communities and stream channels are
needed. In smaller streams and watersheds, for example, the exclosure on Big Elk Creek,
significant improvement may be seen in several years. It is likely to take decades to see such
improvement throughout the watershed given the large scale of needed improvements and the
time needed for riparian vegetation to grow to maturity.
xxx Executive Summary
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
1. Subbasin Assessment - Watershed Characterization
The federal Clean Water Act (CWA) requires that states and tribes restore and maintain the
chemical, physical, and biological integrity of the nation's waters (33 U.S.C. 1251). States
and tribes, pursuant to section 303 of the CWA are to adopt water quality standards (WQS)
wherever attainable necessary to protect fish, shellfish, and wildlife while providing for
recreation in and on the waters. Section 303(d) of the CWA establishes requirements for
states and tribes to identify and prioritize water bodies that are water quality limited (i.e.,
water bodies that do not meet WQS. States and tribes must periodically publish a priority list
of impaired waters, currently every two years. For waters identified on this list, states and
tribes must develop a total maximum daily load (TMDL) for the pollutants, set at a level to
achieve WQS. This document addresses the water bodies in the South Fork Clearwater River
(SF CWR) Subbasin that have been placed on what is known as the "303(d) list."
The overall purpose of this subbasin assessment (SB A) and TMDL is to characterize and
document pollutant loads and set load allocations to meet existing WQS within the SF CWR
Subbasin. The first portion of this document, the SB A, is partitioned into four major
sections: watershed characterization, water quality concerns and status, pollutant source
inventory, and a summary of past and present pollution control efforts (Chapters 1 - 4). This
information is used to develop a TMDL for each pollutant of concern for the SF CWR
Subbasin (Chapter 5).
1.1 Introduction
In 1972, Congress passed public law 92-500, the Federal Water Pollution Control Act, more
commonly called the Clean Water Act. The goal of this act is to "restore and maintain the
chemical, physical, and biological integrity of the Nation's waters" (Water Pollution Control
Federation 1987). The act and the programs it has generated have changed over the years as
experience and perceptions of water quality have changed. The CWA has been amended 15
times, most significantly in 1977, 1981, and 1987. One of the goals of the 1977 amendment
is protecting and managing waters to insure "swimmable and fishable" conditions. This goal,
along with a 1972 goal to restore and maintain chemical, physical, and biological integrity,
relates water quality with more than just chemistry.
Background
The federal government, through the U.S. Environmental Protection Agency (USEPA),
assumed the dominant role in defining and directing water pollution control programs across
the country. The Idaho Department of Environmental Quality (DEQ) implements the CWA
in Idaho, while the USEPA oversees Idaho and certifies the fulfillment of CWA requirements
and responsibilities. The USEPA implements the CWA on the Nez Perce Reservation.
Because this document addresses water quality issues pertaining to the authorities of DEQ,
USEPA and the Nez Perce Tribe (NPT), it has been prepared under the auspices of a
Memorandum of Agreement (Appendix A).
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Section 303 of the CWA requires DEQ and tribes to adopt, with USEPA approval, WQS and
to review those standards every three years. Additionally, DEQ and tribes must monitor
waters to identify those not meeting WQS. For those waters not meeting standards, DEQ and
tribes must establish TMDLs for each pollutant impairing the waters. Further, states and
tribes must set appropriate controls to restore water quality and allow the water bodies to
meet their designated uses. These requirements result in a list of impaired waters, called the
"303(d) list." This list describes water bodies not meeting WQS. Waters identified on this
list require further analysis. A SB A and TMDL provide a summary of the water quality
status and allowable TMDL for water bodies on the 303(d) list. This document, the South
Fork Clearwater River Subbasin Assessment and Total Maximum Daily Loads, provides this
summary for the currently listed waters in the SF CWR Subbasin.
The SB A sections of this report (Chapters 1-4) include an evaluation and summary of the
current water quality status, pollutant sources, and control actions in the SF CWR Subbasin
to date. While the SB A is not a requirement of the TMDL, USEPA, DEQ, and the NPT
completed this assessment to ensure impairment listings are up to date and accurate.
The TMDL is a plan to improve water quality by limiting pollutant loads. Specifically, a
TMDL is an estimation of the maximum pollutant amount that can be present in a water body
and still allow that water body to meet WQS (40 CFR §130). Consequently, a TMDL is
specific to a water body and each of its pollutants. The TMDL also includes pollutant
allocations among various sources of the pollutant. The USEPA considers certain unnatural
conditions, such as flow alteration, a lack of flow, or habitat alteration, that are not the result
of the discharge of a specific pollutant as "pollution." TMDLs are not required for water
bodies impaired by pollution, but not by specific pollutants. In common usage, a TMDL also
refers to the written document that contains the statement of loads and supporting analyses,
often incorporating TMDLs for several water bodies and/or pollutants within a given
watershed.
Idaho and Tribal Roles
Idaho and tribes adopt WQS to protect public health and welfare, enhance the quality of
water, and protect biological integrity. A WQS defines the goals of a water body by
designating the use or uses for the water, setting criteria necessary to protect those uses, and
preventing degradation of water quality through antidegradation provisions.
The state and/or tribe may assign or designate beneficial uses for particular Idaho water
bodies to support. State of Idaho beneficial uses are identified in the Idaho WQS and
include:
• Aquatic life support - cold water, seasonal cold water, warm water, salmonid
spawning, modified
• Contact recreation - primary (swimming), secondary (boating)
• Water supply - domestic, agricultural, industrial
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
• Wildlife habitats, aesthetics, special resource water, and outstanding resource water
The Idaho legislature designates uses for water bodies on state lands. Industrial water
supply, wildlife habitat, and aesthetics are designated beneficial uses for all water bodies in
the state. If a water body is unclassified, then cold water aquatic life and primary or
secondary contact recreation are used as additional default designated uses when water
bodies are assessed (IDAPA 58.01.02.101.01.a).
An SB A entails analyzing and integrating multiple types of water body data, such as
biological, physical/chemical, and landscape data to address several objectives:
• Determine the degree of designated beneficial use support of the water body (i.e.,
attaining or not attaining WQS).
• Determine the degree of achievement of biological integrity.
• Compile descriptive information about the water body, particularly the identity and
location of pollutant sources.
• Determine the causes and extent of the impairment when water bodies are not
attaining WQS.
1.2 Physical and Biological Characteristics
The majority of text and statistics in this section are taken directly from the South Fork
Clearwater River Biological Assessment (USFS 1999), and the South Fork Clearwater River
Landscape Assessment (USFS 1998).
The SF CWR Subbasin is located in north-central Idaho and encompasses an area of
approximately 1,175 square miles (752,000 acres) with a 207 mile perimeter (Figure 1). The
subbasin extends from the headwaters above Elk City (elevation 6,382 feet) to the confluence
with the Middle Fork of the Clearwater River at Kooskia, Idaho (elevation 1,280 feet). The
lower 12.8 miles of the SF CWR main stem flow through the NPT Reservation. The NPT
Reservation encompasses 84,035 acres of the subbasin.
Idaho State Code divides the SF CWR Subbasin into 82 numbered water bodies (IDAPA
58.01.02.120.07). These are the water body units to which the 303(d) list applies and which
this document refers to by name and number. Table 1 lists the major watersheds, their
associated water bodies, water body numbers, and their number of acres. Figure 2 shows the
distribution of the water bodies throughout the SF CWR Subbasin.
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Middle Fork
Clearwater River
Major Roads
0 Cities
/\/ Rivers
C 3 NPT Reservation Boundary
SF Cleat-water4th Field HUC
Figure 1. The South Fork Clearwater River Subbasin in North-Central Idaho
Table 1. SF CWR Subbasin watersheds, water bodies, and acreages.
Watershed/Water Body
South Fork Clearwater River
WB 1 - Lower South Fork Clearwater River
WB 12 - Mid-Lower South Fork Clearwater River
WB 22 - Middle South Fork Clearwater River
WB 30 - Mid-Upper South Fork Clearwater River
WB 36 - Upper South Fork Clearwater River
Threemile Creek
WB 1 0 - Threemile Creek
Butcher Creek
WB 1 1 - Butcher Creek
Mill Creek
WB 13 -Mill Creek
Acreage
115,223
19,723
56,690
18,950
17,165
2,695
21,440
10,000
23,249
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Watershed/Water Body
Johns Creek
WB 14- Lower Johns Creek
WB 15 -Gospel Creek
WB 16 - West Fork Gospel Creek
WB 1 7 - Middle Johns Creek
WB 1 8 - Upper Johns Creek
WB 1 9 - Moores Creek
WB 20 - Square Mountain Creek
WB 21 - Hagen Creek
Wing Creek
WB 23 - Wing Creek
Twentymile Creek
WB 24 -Twentymile Creek
Tenmile Creek
WB 25 - Lower Tenmile Creek
WB 26 - Middle Tenmile Creek
WB 27 - Upper Tenmile Creek
WB 28 - Williams Creek
WB 29 - Sixmile Creek
Crooked River
WB 31 - Lower Crooked River
WB 32 - Upper Crooked River
WB 33 - West Fork Crooked River
WB 34 - East Fork Crooked River
WB 35 -Relief Creek
Red River
WB 37 - Lower Red River
WB 38 -Middle Red River
WB 39 - Moose Butte Creek
WB 40 - Lower South Fork Red River
WB 41 - Middle South Fork Red River
WB 42 - West Fork Red River
WB 43 - Upper South Fork Red River
WB 44 - Trapper Creek
Acreage
72,150
26,300
10,830
4,465
10,180
8,660
3,960
2,270
5,520
5,329
14,545
34,410
2,500
7,230
13,630
5,900
5,150
45,659
9,470
14,470
7,580
6,670
7,470
103,348
10,200
16,000
7,050
3,100
2,700
6,370
4,730
7,060
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Watershed/Water Body
WB 45 - Upper Red River
WB 46 - Soda Creek
WB 47 - Bridge Creek
WB 48 - Otterson Creek
WB 49 - Trail Creek
WB 50 - Siegel Creek
WB 51 - Red Horse Creek
American River
WB 52 - Lower American River
WB 53 - Kirks Fork American River
WB 54 - East Fork American River
WB 55 - Upper American River
WB 56 - Elk Creek
WB 57 - Little Elk Creek
WB 58 - Big Elk Creek
WB 59 - Buffalo Gulch
Whiskey Creek
WB 60 - Whiskey Creek
Maurice Creek
WB 61 Maurice Creek
Newsome Creek
WB 62 - Lower Newsome Creek
WB 63 - Bear Creek
WB 64 - Nugget Creek
WB 65 - Beaver Creek
WB 66 - Middle Newsome Creek
WB 67 - Mule Creek
WB 68 - Upper Newsome Creek
WB 69 - Haysfork Creek
WB 70 - Baldy Creek
WB 71 - Pilot Creek
WB 72 - Sawmill Creek
WB 73 - Sing Lee Creek
WB 74 - West Fork Newsome Creek
Acreage
19,000
3,340
3,260
2,460
4,540
7,760
5,800
58,612
7,216
6,258
11,500
15,275
2,324
5,081
8,821
2,139
1,660
1,094
42,576
4,144
3,831
1,450
3,732
1,134
5,498
6,354
3,170
2,723
3,916
1,768
1,554
3,303
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Watershed/Water Body
Leggett Creek
WB 75 - Leggett Creek
Fall Creek
WB 76 - Fall Creek
Silver Creek
WB 77 - Silver Creek
Peasley Creek
WB 78 - Peasley Creek
Cougar Creek
WB 79 - Cougar Creek
Meadow Creek
WB 80 - Meadow Creek
Sally Ann Creek
WB 81 - Sally Ann Creek
Rabbit Creek
WB 82 - Rabbit Creek
Acreage
4,918
2,334
16,509
9,112
7,731
24,115
8,890
6,190
Idaho Code Designated Water Bodies
for the South Fork Clearwater
River Subbasin
| | Water Body ID watersheds
D «
/\J 303(d) Listed Sti
M,j., Sterns
Other Streams
Figure 2. Water Bodies and Water Body Numbers in the SF CWR Subbasin
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Climate
Northern Idaho is dominated by Pacific maritime air masses and prevailing westerly winds.
Over 85% of the annual precipitation occurs during the fall, winter, and spring months.
Cyclonic storms consisting of a series of frontal systems moving east produce long duration,
low-intensity precipitation during this period of the year. In winter and spring, this inland
maritime regime is characterized by prolonged gentle rains, fog, cloudiness, and high
humidity; with deep snow accumulations at higher elevations. Winter temperatures are often
15 to 25 °F warmer than the continental locations of the same latitude. The climate during
the summer months is influenced by stationary high-pressure systems over the northwest
coast. These warm dry systems result in only 10-15% of the annual precipitation falling
during the summer. Figure 3 shows precipitation distribution and climatic stations. Table 2
summarizes climatic information from several stations in the area of the SF CWR Subbasin.
Precipitation Zones for the South Fork Clearwater River Subbasin
and Location of Climatic Stations
Legend
Major Stream
| | WBID Watershed
| | 4th HUG Boundary
^3 NPT Reservation Boundary
• Climate Stations
Precipitaion (in)
Hi 19-23
23-29
29-33
•• 33 - 37
M 37 - 41
HI 41 - 45
^•45-53
DIXIE
Figure 3. Climatic Stations and Precipitation Zones in the SF CWR Subbasin
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 2. Summary of climatic data for various stations in and around the SF
CWR Subbasin.
Station
Name
Cottonwood
Dixie
Elk City
Fenn
Grangeville
Kooskia
Mountain
Meadows
Elevation
(feet)
3,950
5,620
4,060
1,590
3,360
1,280
6,360
Period of
Record
1950-2000
1952-2000
1950-2000
1948-2000
1948-2000
1908-2000
1989-2000
Mean Annual
Temperature
(°F)
46.5
36.2
41.3
49.1
46.3
50.4
34.5
Mean Annual
Precipitation
(inches)
22.5
28.5
30.2
38.1
23.8
24.2
45.8
Avg. Number
of Days
Above 90°F
Per Year
5.5
1.2
12.2
40.5
14.0
53.2
0.1
Subbasin Characteristics
The subbasin hydrography, hydrology, geology, landforms, and soils are described below.
Hydrography
The SF CWR flow regime reflects the annual precipitation and temperature patterns.
Precipitation in the subbasin ranges from 25 inches at the lower elevations to over 50 inches
at the higher elevations. Ten percent of the annual precipitation in Kooskia falls as snow,
whereas 40% of the precipitation in Elk City is snow. Annual runoff from the SF CWR
Subbasin averages about 12 inches, as measured by the U.S. Geological Survey (USGS)
stream gage at Stites. Mean annual streamflow at Stites, the lower end of the subbasin, is
1,060 cubic feet per second (cfs). Streamflows are highest in May with an average of 3,370
cfs. Flows are lowest in September with an average of 258 cfs.
The SF CWR typically experiences annual flood peaks during late April, early May, or early
June. An average spring runoff peak at Stites is about 5,000 to 7,000 cfs. The largest flood
of record was on June 8, 1964, with an estimated peak of 17,500 cfs. Floods occasionally
result from snowmelt or rain-on-snow between November and March. An analysis of peak
flow records at Stites shows that 15% of flood peaks occurred during this period. Only 5%
of flood peaks occurred during these months upstream near the forest boundary as shown by
historic gaging station records. Further upstream, near Elk City, only 3% of flood peaks
occurred during these months. These differences show the transition of climatic conditions
from the lower to upper parts of the subbasin, as well as the relative dominance of peak flows
during spring runoff.
The major tributaries in the upper reaches of the SF CWR watershed (i.e., American River,
Red River, Crooked River, and Newsome Creek) have a runoff regime very similar to the
main stem. They drain large areas of rolling upland terrain and typically do not have a flashy
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
response to floods due to elevation, climate, relatively deep soils, forest vegetation, and
moderate topography.
The runoff regimes of tributaries between Newsome Creek and the Nez Perce National
Forest (NPNF) boundary in the lower part of the subbasin are relatively complex, and depend
on size, elevation, and landform. For example, Johns Creek and Tenmile Creek drain high
elevation terrain in their headwaters and mid- to low-elevation breaklands in their lower
reaches. Due to the high elevation headwaters, peak flows often occur several weeks later in
the spring than the upper subbasin streams. Medium size, mid-elevation tributaries,
including Silver Creek, Mill Creek, Twentymile Creek, and Meadow Creek have a similar
runoff regime to the major upper basin streams described above. The smaller tributaries in
this reach of the South Fork Canyon often originate on low elevation breaklands that are
subject to winter rain-on-snow events or spring and summer thunderstorms. These events
can produce localized floods and debris torrents.
Butcher Creek, Threemile Creek, and Cottonwood Creek drain the Camas Prairie and have a
significantly different runoff regime. They often have their annual peak flows in the
midwinter, associated with rain-on-snow or rapid snowmelt events. Spring rains can also
produce peak flows in these streams. These streams experience low flows earlier in the
season than upstream tributaries.
Hydrology
Four basic hydrologic zones have been described in the SF CWR Subbasin by the NPNF
(USFS 1999).
Zone 1- High Elevation Mountains. This includes those areas above 6,000 feet, often on
glaciated landforms. Annual precipitation is typically 40-60 inches. High snow
accumulations and relatively late, prolonged snowmelt are common. Stream channels are
highly variable within this zone ranging from very steep, confined headwater streams to
relatively flat channels located in glaciated valleys. Examples in this zone include upper
Johns Creek and Tenmile Creek.
Zone 2- Mid Elevation Rolling Uplands. This zone is typically between 4,000 and 6,000 feet
elevation with relatively low relief rolling hills. Annual precipitation is 30 to 40 inches.
These areas have a moderate annual snow pack and snowmelt in May. Stream channels
range in size and flow through relatively steep confined headwaters to low gradient,
unconfmed alluvial valley bottoms. This zone covers the largest portion of the SF CWR
Subbasin and is best exemplified by the tributaries of Red River, American River, Newsome
Creek, and Crooked River.
Zone 3- Low Elevation Breaklands. This zone is less than 4,000 feet in elevation and is
comprised of steep sideslopes in the major stream and river canyons. Precipitation is
typically 20 to 30 inches per year, with a low to moderate snow pack. The runoff regime is
complex with a mix of snowmelt, rain-on-snow, and heavy rain resulting in peak runoff
events. These occur typically in early spring. Streams are generally confined to steep valley
10 Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
walls with gradients that vary. Debris torrents are relatively common in smaller drainages.
This zone is found all along the South Fork Canyon and up the major drainages.
Zone 4- Low Elevation Plateaus. This zone is less than 4,000 feet in elevation and has a
rolling topography. Annual precipitation is 20 to 30 inches. The snow pack is low to
moderate. The runoff regime is mixed with snowmelt, rain-on-snow, and heavy rain
resulting in peak flows at varying times from midwinter to early spring. This zone is best
exemplified by the Camas Prairie tributaries: Butcher Creek, Threemile Creek, and
Cottonwood Creek.
Figure 4 shows the mean monthly hydrographs as expressed as percent of annual flow from
stream gages representative of the hydrologic zones within the SF CWR Subbasin. The Zone
1 plot is from Johns Creek, Zone 2 is from the SF CWR near Elk City, and Zones 3 and 4 are
from Lapwai Creek. Although it is not in the SF CWR Subbasin, Lapwai Creek was used as
the example for Zones 3 and 4, because it is the only stream draining the Camas Prairie with
a long term gaging record.
Monthly Percent of Annual Flow
by Hydrologic Zone
Zones 3 & 4
Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep
Figure 4. Monthly Percent of Annual Flow
Since the figures are expressed as percentages, the plots do not represent the relative
magnitude of flow, but rather the distribution of flow over the water year (October 1-
September 30). For example, the relatively large percentage of flow in the month of May in
Zone 2 does not necessarily represent a higher peak flow from this zone, but rather that the
peak flow consistently occurs in the month of May. This is in contrast to Zones 3 and 4,
where peak flows commonly occur during any of several months, depending on annual
weather conditions.
11
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Geology, Landforms, and Soils
Landform groups are broad ecological land units that possess unique patterns of landform,
geology (Figure 5), vegetation (Figure 6), climate, soils, and disturbance regimes. The SF
CWR Subbasin is comprised of seven landform groups (LFGs). A summary description of
each of these landforms, soils, erosional hazards, and vegetation follows. Aquatic landtype
associations (ALTAs) have also been used to characterize the SF CWR Subbasin (Figure 7).
The ALTAs emphasize patterns of stream networks and terrestrial-aquatic interactions that
consider landform, geology, elevation, ground water temperatures, and hydrologic
disturbance regimes. The LFG descriptions that follow include the corresponding ALTAs
for reference.
Geology
South Fork Clearwater River
Subbasin
Figure 5. Geology of the SF CWR Subbasin
12
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Legend
| _ | SF C learcudter 4th Field HUC
KP
Habitat Type Groups
Alpine Meadows And Scrub
Cold
Cold And Moderate h/ Dry
CoolAnd Moderate^ Dry
CoolAnd Moist
CoolAnd Wei
Grassland Steppe
Hardwoods
Moderately Cool And Moist
Mod erately C DO! And W et
Moderately W arm And Dry
Moi
ModeratelyWarm And M
Rock
Shrubland Steppe
Warm And Dry
Water
N o D ata
Habitat Type Groups
South Fork Clearwater
River Subbasin
14 Miles
May. 2002
Figure 6. Habitat Type Groups of the SF CWR Subbasin
Legend
SF Clearviater4th Field HUC
•Cl^) Water Body ID watersheds
\^_^ NPT Reservation Boundary
Aquatic Landtype Associations
Alluvial valley, lowelevation
^m^ Alluvial valley, higher elevation
4^^ Breaklands, low elevation, basalt
409 Breaklands, low elevation, granitics
4^P Breaklands, moist, metamorphics
Broad convex ridge, granitic
4V^ Glacial valley bottom, granitic
Glaciated slope, granitic
Low relief hills, low elevation, granitic
jfft Low relief hills, mid elevation, granitic
Low relief hill, weathered granitic
^||^ Low relief hills, moist, metam orphics
Mountain uplands, granitic
4^P Plateaus, low elevation, basalt
Aquatic Landtype Associations |
South Fork Clearwater
River Subbasin
14 Miles
October 2003
Figure 7. Aquatic Landtype Associations of the SF CWR Subbasin
13
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Landform Group 1: Rolling Uplands-Granodiorite (ALTA 9)
This group comprises approximately 0.5% of the total analysis area, with elevations ranging
from 3,800 to 5,000 feet. This LFG occurs on the upper reaches of East Fork Cougar Creek
and Covert Creek and is characterized by rolling uplands derived from moderately well
weathered granodiorite. The erosion hazard is very high for this material, and when it
erodes, it generates mostly sand and small gravel. Sediment delivery efficiency is moderate.
Surface erosional processes dominate in this LFG, but erosion is buffered by a volcanic ash-
influenced soil surface layer. The slopes are moderate at 20-50%.
Cool, moderately moist habitat types are dominant. Aspect and elevation, coupled with
ecological events and processes like fire, competition, herbivory, and pathogen activity are
the primary influences on vegetation composition. Upland habitat types include grand fir
series. Dominant overstory tree species are lodgepole pine, Douglas fir, western larch,
Ponderosa pine, and grand fir. Mid and low shrubs, forbs, and grasses can dominate the
understory. High water tables in sediment-filled valley bottoms favor development of
meadow and meadow/shrub complexes interspersed with forest.
Landform Group 2: Rolling Uplands-Gneiss, Granite, Quartizite, and Schist (ALTAs 1,4,6,
21)
This group comprises approximately 56% of the SF CWR Subbasin, (area east of
Grangeville, except along the main stem and tributary canyons and glaciated headwaters),
with elevations ranging from 2,800 to 8,000 feet. It is characterized by rolling hills and
convex slopes derived from moderately- to well-weathered gneiss, granite, quartzite and
schist. The erosion hazard is moderate to high for these materials, which generate mostly
sands and gravels. The sediment delivery efficiency is moderate. Surface erosional
processes dominate in this LFG, but surface soil erosion is buffered by a volcanic ash
influenced soil surface layer. The slopes are moderate at 20-50%.
Cool and cold, moderately moist habitat types are dominant. Aspect and elevation coupled
with the ecological events and processes like fire, competition, herbivory, and pathogen
activity are the primary influences on vegetation composition. Upland habitat types include
grand fir and subalpine fir series. Dominant overstory tree species are lodgepole pine,
Douglas fir, Engelmann spruce, western larch, grand fir, Ponderosa pine, and subalpine fir.
Shrubs, forbs, and grasses can dominate the understory. Forest habitat types dominate
streamside zones. Upland tree species often grow next to streams on well-drained adjacent
hillslopes. Meadow/shrub complexes occur most extensively along Red River, American
River, Elk Creek, and Meadow Creek.
Landform Group 3: Breaklands-Gneiss, Quartzite, Schist, and Granite (ALTA 3)
This LFG comprises approximately 12% of the SF CWR Subbasin (middle reaches of the SF
CWR and lower reaches of Mill Creek, Johns Creek, Tenmile Creek, Crooked River, and
Peasley Creek), at elevations ranging from 1,600 to 7,000 feet. This LFG is characterized by
stream breaklands, mass wasted slopes, and colluvial slopes derived from moderately well-
weathered granite, quartzite, gneiss, and schist. The erosion hazard is high, with these
materials generating mostly sand to cobble materials. The sediment delivery efficiency is
high. Surface erosion occurs on the steepest south aspects and little volcanic ash remains to
14 Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
buffer against erosion. Channel scour, colluviation, and mass wasting are important
landforming processes. The slopes range from 40-80%.
Habitat types vary from warm and dry to cold and moist depending on aspect and elevation.
Ponderosa pine and Douglas fir series dominate lower elevations; grand fir series dominate
north aspects and higher elevations. Subalpine fir is found at highest elevations. Dominant
species are Ponderosa pine, Douglas fir, grand fir, western larch, lodgepole pine, subalpine
fir, and Engelmann spruce. Streamside vegetation includes shrub complexes along lower
elevation stream bottoms and conifer dominated communities on north aspects or higher
elevations.
Landform Group 4: Glaciated Lands-Quartzite and Dior ite (ALTA 2, 5)
This group comprises approximately 5% of the subbasin (upper reaches of Tenmile Creek
and Johns Creek in the Gospel Hump Wilderness) with elevations ranging from 5,200 to
8,000 feet. It is characterized by steep, ice-scoured cirques and glacial troughs with
inclusions of gently sloping ice scoured ridges, glacial valley bottom, and moraine deposits
derived from poorly weathered Precambrian quartzite and Cretaceous quartz diorite. The
erosion hazard is high, with the quartzite and quartz diorite generating sand to cobble size
material. The sediment delivery efficiency is moderate to high. Sediment movement is
buffered by abundant rock and locally abundant volcanic ash surface soil. Surface erosion
occurs on steep slopes with shallow soils. Debris torrents, colluviation, and mass wasting are
also important landforming processes. The slopes vary from 10-100%.
The vegetation is composed of cold and dry to wet grand fir and subalpine fir habitat types
depending on elevation, soil depth, and aspect. Dominant species are lodgepole pine,
Engelmann spruce, subalpine fir, Douglas fir, grand fir, and whitebark pine. Shrub and
herbaceous communities are intermingled with forest communities in valley bottoms.
Herbaceous communities are found on dry ridges.
Landform Group 5: Rolling Hills and Plateaus-Basalt (ALTA 15)
This LFG comprises approximately 1% of the SF CWR Subbasin with elevations ranging
from 3,600 to 5,400 feet. It occurs primarily along headwater streams south and east of
Grangeville, and is characterized by low rolling hills and plateaus of low to moderate relief,
derived from moderately weathered Columbia River basalt. The erosion hazard from these
materials is only slight in comparison to other geologic materials in the subbasin, generating
clay to cobble size materials. The sediment delivery efficiency is low. The soils have
volcanic ash surface layers, and highly aggregated subsoils with a high rock content that
buffers effectively against erosion. Surface erosional processes dominate in this landform
but are slight in comparison to other LFGs. The slopes are moderate, varying from 10-40%.
Warm to cool and dry to moderately moist habitat types are dominant depending on aspect,
elevation, and ecological processes. Upland habitat types include Douglas fir, grand fir, and
subalpine fir series. Dominant tree species are grand fir, Engelmann spruce, Douglas fir,
lodgepole pine, Ponderosa pine, western larch, and subalpine fir. Mid and low shrubs, forbs,
and grasses dominate the understory. Meadow/shrub complexes occur occasionally.
15 Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Landform Group 6: Steep Mountain Slopes and Stream Breaklands-Basalt andAndesite
(ALTA 7)
This group comprises approximately 6% of the SF CWR Subbasin (along the SF CWR from
Kooskia for 18 miles upstream and along the main canyons of Threemile Creek, Butcher
Creek, and Cottonwood Creek), with elevations ranging from 1,300 to 5,200 feet. Steep
mountain slopes, stream breaklands, and mass wasted slopes derived from poorly to
moderately weathered Columbia River basalt ad Seven Devil volcanics characterize this
LFG. The erosion hazard is slight compared to other geologic materials in the subbasin,
generating mostly silts, clays, gravels, and cobbles. Sediment delivery efficiency is high.
Surface erosion, colluviation, and mass wasting are important landforming processes. Little
volcanic ash is present to buffer surface soils against erosion. Slopes are steep, varying from
40-80%.
Plant community composition is highly dependent on aspect and varies from very dry to
moderately moist. Bunchgrass, ponderosa pine, and Douglas fir series dominate lower
elevations and grand fir series dominate north aspects and higher elevations. Dominant
species are Ponderosa pine, Douglas fir, grand fir, western larch, lodgepole pine, and
Engelmann spruce. Streamside vegetation includes shrub and deciduous tree complexes
along lower elevation stream bottoms and conifer dominated communities on north aspects
or higher elevations. Extensive grazing and development have altered riparian vegetation
along lower gradient reaches. Fish cover and bank stability have been reduced.
Landform Group 7: Plateaus-Basalt, Prairie (ALTA 16)
This LFG comprises approximately 20% of the SF CWR Subbasin (Camas Prairie and area
south of Battle Ridge) with elevations ranging from 1,800 to 4,200 feet. This group is
characterized by plateaus of low relief, derived from Columbia River basalt. The erosion
hazard is only slight compared to other subbasin geology, generating mostly silt, gravel, and
cobble. The sediment delivery hazard is low. Soils have mixed volcanic ash surface layers,
and highly aggregated subsoils that help buffer against erosion. Slopes are gentle, varying
from 5-40%.
Vegetation patterns are influenced by thin soils, low elevations, and warm dry habitat.
Grasslands and open park-like stands of Ponderosa pine and Douglas fir once dominated this
LFG. Upland shrub species occur with scattered trees in stream bottoms. Bunchgrass habitat
types are on uplands. Existing vegetation is now primarily cropland, hay, and pasture with
some remaining forestland that has been heavily impacted by grazing and timber harvest.
Riparian areas were generally shrub-dominated prior to grazing and tillage impacts.
Table 3 shows the characteristics of each of the seven landform groups in the SF CWR
Subbasin as related to potential sediment effects to the SF CWR and downstream areas.
"Sediment Hazard from Substratum Erosion" describes the likelihood that geologic erosion
would occur and that resulting sediment would be transported to a stream channel. "Mass
Erosion Hazard" describes the likelihood that mass sediment delivery from lower slopes
directly into a channel would occur.
16 Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 3. SF CWR Subbasin landform group characteristics.
Landform
Group
1
2
3
4
5
6
7
Description
Rolling Uplands
Rolling Uplands
Breaklands
Glaciated Lands
Forested Rolling
Hills and Plateaus
Steep Mountain
Slopes and
Stream
Breaklands
Rolling Plateaus-
Prairie
Parent
Material
Granodiorite
Granite, Gneiss,
Schist, Quartzite
Granite, Gneiss,
Schist, Quartzite
Quartzite, Diorite
Basalt
Basalt, Andesite
Basalt
Sediment
Hazard from
Substratum
Erosion
Very High
Moderate to High
Moderate
Low to High
Low
Low
Low
Mass Wasting
Hazard
Low to Moderate
Low to Moderate
Moderate to High
Low to Moderate
Low to Moderate
Moderate
Low
Fisheries and Aquatic Fauna
The fisheries resources in the SF CWR Subbasin are thoroughly described in Appendix D. A
fisheries technical advisory group (Fish TAG) was convened to develop a complete
description of the fisheries resources in the SF CWR system.
Subwatershed Characteristics
The SF CWR Subbasin 303(d) listed segments are described below in the context of the
subwatershed in which they are located. These were compiled from the NPNF South Fork
Clearwater River Landscape Assessment (USFS 1998), Ecological Reporting Units.
Although this discussion is limited to those subwatersheds containing 303(d) listed segments,
Table 4 is included to allow comparison of the watershed condition within the SF CWR
Subbasin as a whole. Channel types are described using the Rosgen (1994) classification
system based on channel thread, channel entrenchment, sinuosity, bankfull width-to-depth
ratio, stream gradient, and stream substrate. The primary A, B, and C channel types are
broadly characterized by decreasing stream gradient and increasing sinuosity, with A channel
types being characteristic of steep mountain streams, and C channel types being
characteristic of meandering streams flowing across plains.
17
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 4. Watershed condition indicators.
Watershed
Mill Creek
Johns Creek
Twentymile Creek
Tenmile Creek
Crooked River
Red River
American River
Newsome Creek
Silver Creek
Peasley Creek
Cougar Creek
Meadow Creek
Area
(acres)
23,249
72,150
14,545
34,410
45,659
103,348
58,612
42,576
16,509
9,112
7,731
24,115
Roads
(miles)
94
60
17
24
137
588
213
220
27
55
48
164
Road
Density
(mi/mi2)
2.6
0.5
0.7
0.4
2.0
3.6
2.3
3.3
1.1
3.8
4.0
4.4
Timber
Harvest
(acres)
4,586
1,198
153
336
4,616
22,939
8,129
8,010
1,097
2,016
1,750
7,684
Timber
Harvest
(%)
20
3
1
1
10
22
14
19
7
22
23
32
EGA1
(%)
8
<1
1
1
6
12
10
7
5
13
12
11
Sed.
Yield
(%)2
8
1
4
1
8
24
14
13
3
20
15
16
Equivalent Clearcut Acres
2 Sediment Yield percent over background
Source: USFS 1998
American River Watershed
The 303(d) listed water bodies in this watershed are Big Elk Creek, Little Elk Creek, Buffalo
Gulch, and Lucas Lake. This watershed (58,612 acres) is almost entirely composed of mid-
to upper-elevation low relief hills and alluvial valleys (ALTAs 6, 18) with some mountain
uplands (ALTA 21) on the western and eastern edges. The watershed is located in
Hydrologic Zone 2, characterized by mid-period snowmelt and moderate to low gradient
channels.
Stream channels are predominantly low to moderate gradient B and C channel types (Rosgen
1994) with higher gradient channels in the mountain uplands. Along with the Red River, this
watershed has a large amount of mid- to upper-elevation alluvial valleys (ALTA 18), and
these features are spread more evenly throughout the watershed than is typical of the
subbasin, where this ALTA is a linear feature along the tributary main stem. ALTA 18 is
composed predominantly of C channel typess (Rosgen 1994).
The American River has been significantly affected by human activity. Historic mining
occurred along significant portions of the higher order streams in the lower basin. Grazing
has affected stream/riparian processes. There have been about 8,000 acres of timber harvest
in the watershed (14% of the area); about 925 acres of this has been in a Riparian Habitat
Conservation Area (RHCA). The RHCA's are portions of watersheds in national forests
where riparian dependent resources receive primary emphasis, and federal management
18
Chapter 1
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
activities are subject to specific standards and guidelines. They include riparian corridors,
wetlands, intermittent streams, and other areas that help maintain the integrity of aquatic
ecosystems by: 1) influencing the delivery of coarse sediment, organic matter, and woody
debris to streams, 2) providing root strength for channel stability, 3) shading the stream, and
4) protecting water quality (USFS and BLM 1995). There are about 200 miles of existing
roads in the watershed (2.3 mi/mi2), and about 60 miles in the RHCA. Some sections of road
encroach on stream/riparian processes. The NPNF considers about half this watershed to
have a low level of human development. The current equivalent clearcut area (EGA) is 10%,
and the current sediment yield is 14% over natural base. Big and Little Elk Creeks are part
of the Elk City municipal watershed.
The overall condition for this watershed is considered low, with some subwatersheds within
it in moderate condition. Stream and riparian processes have been altered principally by
historic dredge mining, as well as by road encroachment and grazing. These activities have
affected channel patterns, floodplain connectivity, and habitat conditions. The alteration in
sediment regimes is a result of change from infrequent, large-scale disturbance events to
frequent disturbances. These changes are significant in terms of aquatic processes and
aquatic species, and the viability offish populations in this watershed, including resilience to
natural disturbance events, has been reduced as a consequence.
Red River Watershed
The 303(d) listed stream in this watershed is Dawson Creek. Red River is a large (103,348
acres) watershed with the largest alteration of historic sediment regimes in the SF CWR
Subbasin. The lower area of the watershed is comprised of ALTA 6, mid- to upper-elevation
low relief hills, with areas of ALTA 18, mid- to upper-elevation alluvial valleys. The mid-
elevation subwatershed is mostly ALTA 4, low relief hills generally associated with lower
elevations, along with some ALTA 18. The upper watershed is composed of ALTA 1, high
elevation broad ridges. Red River is predominantly in Hydrologic Zone 2, mid-elevation
rolling uplands, with the upper subdivision in Hydrologic Zone 1, high elevation mountains.
Streams in this watershed have a high frequency of B and C channel types (Rosgen 1994),
and have a branched channel pattern.
Management activity in this watershed has included historic mining, roads encroaching on
the stream corridors, and grazing on the main stem. About 23,000 acres of timber have been
harvested (22% of the subwatershed). Approximately 5,000 acres of this harvest occurred in
the RHCA. There are approximately 588 miles of existing road (3.6 mi/mi2) in the
watershed, and about 175 miles in the RHCA. There are few large areas with low levels of
human development, although those areas that do exist are found in the upper basin. The
current EGA for the watershed is 12% and the current sediment yield is estimated at 24%
over natural base.
The overall condition for this watershed is considered low, with a portion of the upper
watershed considered moderate condition. The current sediment yield is the highest percent
over base for the SF CWR Subbasin, with the stream channels sensitive to these effects. As a
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result of management over several decades, this watershed has been subjected to one of the
highest frequencies of disturbance and a reduction in habitat condition. The watershed
condition has changed from patches of active disturbance and recovery, surrounded by areas
of stable, high quality habitat, to homogeneously degraded habitat. The ability of aquatic
species to persist as well as rebuild or repopulate areas from local stronger populations has
been reduced.
Newsome Creek Watershed
The 303(d) listed water bodies in this watershed are lower Newsome Creek (Beaver Creek to
SF CWR), Beaver Creek, Nugget Creek, and Sing Lee Creek. The Newsome/Leggett Creek
watersheds (47,809 acres) are comprised primarily of mid- to upper-elevation low relief hills
(ALTA 6), with a ring of mountain uplands (ALTA 21) on three sides. There are small
patches of steep breaklands (ALTA 3) along the main stem channel. Narrow alluvial valleys
(ALTA 18) are found along portions of the main stem and major tributary streams. The
watersheds lie primarily in Hydrologic Zone 2.
The Newsome Creek main stem is predominantly a B3/B4 channel type (Rosgen 1994). The
tributary streams have a wide range of conditions, ranging from A through E channel types
with most of the lower gradient, higher quality fish habitat (B and C channel types) occurring
in conjunction with ALT As 18 and 6.
The Newsome Creek area has had a considerable amount of management activity. Most of
the main stem channels and some tributaries had historic mining that affected stream and
riparian processes. Additionally, a road parallels the main stem, encroaching on the riparian
area and stream floodplain. Approximately 8,000 acres have been harvested for timber (19%
of the area) with about 1,300 of these acres in the RHCA. The current EGA for Newsome
Creek is 7%. There are approximately 220 miles of existing road in the Newsome Creek
watershed (3.3 mi/mi2); 55 miles in the RHCA. About one third of the watershed is
considered to have a low level of human development by the NPNF. Current sediment yield
is estimated at!3% over natural base.
The Newsome Creek watershed condition is considered to be low quality by the NPNF.
Stream/riparian processes have been altered by historic mining and road impacts. Sediment
yields have been influenced from an infrequent disturbance regime changing to a frequent
disturbance regime. Connectivity with the SF CWR main stem (the movement of aquatic
species up or downstream) has also been reduced by unsuitable habitat conditions.
Cougar Creek Watershed
Cougar Creek is considered water quality limited (303(d) listed) from its headwaters to the
confluence with the SF CWR. The watershed (7,731 acres) is composed predominantly of
ALTAs 3 and 4, with some ALTA 21 in the upper end. It is located primarily in Hydrologic
Zone 3. The main stem is predominantly B channel, with higher gradient A channels in
tributaries.
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Approximately 2,309 acres of timber have been harvested (29% of the watershed). There are
2
48 miles of existing roads, with a watershed road density of 5.1 mi/mi . The current EGA is
12%, and sediment yields are estimated at 15% over natural base levels.
The Cougar Creek watershed is considered to be low quality by the NPNF. Accelerated
sediment yields have led to a reduction in aquatic habitat diversity and a deteriorated
condition.
South Fork Clearwater River Canyon
The SF CWR is considered water quality limited (303(d) listed) from its headwaters at the
confluence of Red River and American River to the mouth at Kooskia. The South Fork
Canyon watershed (90,058 acres) includes the main stem South Fork River and the face
drainage tributaries. This area is primarily ALTA 3, low elevation breaklands, with upper
portions of the canyon considered ALTA 6. The canyon is in Hydrologic Zone 3. Most of
the land area below the NPNF boundary is assigned to the Camas Prairie Watershed for
descriptive purposes.
Historic mining has affected portions of the main stem and some tributaries, primarily in
upper river areas. Timber harvest has occurred on 19,545 acres (22% of the area) with about
3,300 acres in the RHCA. The majority of timber harvests occurred between 1960 and 1990,
mainly as clearcuts. There are approximately 487 miles of existing roads, with about 160
miles located in the RHCA. Many roads, including the highway along the river, encroach on
stream/riparian processes. About one third of the area is considered to have a low level of
human development. Management activity has also affected the sediment regime, although
the precise effects on the main stem are unknown.
The lower reaches of the SF CWR have been affected to various degrees by aggradation,
channelization, diking, riparian vegetation removal, and encroachment by roads and
buildings. Aggradation of the river is associated with bedload from upstream sources, most
noticeably from the major Camas Prairie tributaries (Butcher Creek, Threemile Creek, and
Cottonwood Creek), and localized bank erosion. In the unconfmed reaches of the South
Fork, this has resulted in a wider, shallower channel with fewer large pools. Fish habitat has
been affected by less cover, fewer deep holding areas, elevated sediment yields, and warmer
summer water temperatures. These conditions have resulted in reduced connectivity and
rearing capability.
Camas Prairie Watersheds
The 303(d) listed water bodies on the Camas Prairie are Cottonwood Creek, Threemile
Creek, and Butcher Creek. This area of the SF CWR Subbasin (199,000 acres) includes the
basalt plateau and the steep canyons at lower elevations along the large streams and SF
CWR. Most of the area to the west of the NPNF boundary was assigned to these watersheds.
Cottonwood, Grangeville, Harpster, Kooskia, Stites, and Clearwater are centers of residential
development. This SBA will focus on Threemile Creek and Butcher Creek subwatersheds.
The Cottonwood Creek TMDL was completed in 2000 by DEQ, USEPA, and the NPT.
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The Camas Prairie watersheds are comprised of silt-loam soils overlying the Mafic (99%)
and Calc-Alkaline (1%) volcanic flows. The Brody-Wapshilla association and the Telcher-
Suloaf silt loams dominate the mountain soils. The Nez Perce, Ferdinand, and Shebang silt
loams are the dominant soil series on the plateau. The Klickson-Suloaf complex is the
dominant soil series on the canyon side slopes, and the Typic Xerofluvents comprise the
flood plains and stream channels (Barker 1982).
The Camas prairie streams are among the most heavily impacted in the subbasin. Most
streams on agricultural land have been modified by riparian tree and shrub removal, field
plowing, and channelization. This has resulted in channel erosion, channel destabilization,
and sediment deposition. Livestock feedlots and season-long grazing have impacted certain
reaches. As the streams flow from the prairie via breaklands to the main stem SF CWR,
erosion of channels is common due to steeper gradients and altered upstream conditions. As
these streams reach the SF CWR valley floor, their gradients drop considerably, causing
deposition of bedload sediment. This has resulted in aggraded channels. Impacts of the
increased sediment yields to tributary channels include wider, shallower channels, loss of
pools, loss of riparian shading, and warmer summer water temperatures.
Threemile Creek originates in forested headwaters (5,000 feet elevation), four miles south of
Grangeville and flows approximately 16 miles to its confluence with the SF CWR at river
mile 7.6. The watershed is approximately 24,966 acres in size and 99% privately owned (less
than 0.5% owned by the Bureau of Land Management (BLM 1999). The lower 5 miles flow
through the NPT Reservation.
The upper reaches of Threemile Creek flow through dryland farming and livestock grazing
areas. As the stream passes through the city of Grangeville it is impacted by storm water
runoff, domestic livestock grazing, and the Grangeville waste water treatment plant
(WWTP). Additional dryland farms are situated along the stream for approximately 4 miles
north of Grangeville before it flows through a steep canyon for approximately 8 miles and
into the SF CWR. The Threemile Creek drainage is in poor condition due to agricultural
activities, riparian degradation from grazing, and sewage effluent. Logging and roads in the
canyon reaches have also resulted in localized adverse effects to the stream (BLM 1999).
Butcher Creek originates 1 mile south of Mt. Idaho in forested headwaters (5,000 feet
elevation) and flows 11.9 miles to its confluence with the SF CWR at river mile 11.7. The
watershed is approximately 11,203 acres, and is 98% privately owned, 2% state-owned, and
less than 0.001% BLM-owned (BLM 1999). The lower 1.8 miles of Butcher Creek flow
within the NPT Reservation boundary.
The headwater area consists of moderately sloped rolling hills with agriculture and wood lot
areas. During the past years the number of residences and ranchettes has increased in the
headwater areas. The stream flows through a moderately steep canyon from the town of Mt.
Idaho to the mouth. Cattle grazing occurs over the entire length of the creek, but
predominantly in the extreme upper and lower reaches (Fuller et al. 1985). Fuller et al.
(1985) found sparse riparian vegetation at the two extremes but dense vegetation in the
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canyon proper. High annual runoff was evident and indications of past flooding were
identified in the lower reaches. Logging has occurred in the past throughout the drainage.
Stream Characteristics
Stream characteristics for the 303(d) listed segments discussed below are compiled from the
South Fork Clearwater River Biological Assessment (USFS 1999). Ratings for habitat
parameters refer to the Matrix of Pathways and Indictors of Watershed Condition for
Chinook, Steelhead, and Bull Trout- Local adaptation for the Clearwater Basin and Lower
Salmon (NMFS et al. 1998). This matrix is used by federal land management agencies to
describe watershed conditions as high, moderate, or low condition for endangered species
consultation. Stream and watershed parameters (temperature, cobble embeddedness, road
density, etc.) are evaluated using quantitative and qualitative indicators.
American River Watershed
The 303(d) listed segments/water bodies occurring within American River watershed
include: Buffalo Gulch, Big Elk Creek, Little Elk Creek, and Lucas Lake.
Buffalo Gulch
Buffalo Gulch flows into the American River at river mile 0.7, and provides habitat for
steelhead, westslope cutthroat trout, brook trout, and sculpin. Spring chinook salmon may
use the stream for rearing; however, such use has not been documented. The lower reaches
of the creek have been dredge mined; and roads, logging, and grazing have impacted the
stream. Monitoring by the BLM measured 65% cobble embeddedness and spawning gravels
had 48% fine sediment less than 6.3 mm (BLM 1995a). Rosgen (1994) B type channels
dominate in the lower reaches, while A channel types (Rosgen 1994) dominate the upper
reaches (BLM 1995a). The average gradients ranged from 2-9%, and unstable stream banks
ranged from 2-30%. Limiting habitat factors include high levels of deposited sediment, high
summer water temperatures, and a lack of good quality pools (USFS 1999).
Big Elk Creek
Big Elk Creek provides habitat for steelhead, spring chinook, salmon, westslope cutthroat
trout, brook trout, mountain whitefish, sculpin, and dace. Bull trout may use Big Elk Creek
for adult and subadult rearing; however, an Idaho Department of Fish and Game (IDFG)
survey in 1998 did not document the presence of bull trout. The lower reaches meander
through a broad meadow, while the middle reaches flow through stringer meadows and
forested stream bottoms. Grazing is light in the stream bottoms and moderate in the meadow
areas. Land use impacts include grazing, roads, and logging. Cobble embeddedness was
52%, and spawning gravels had 40% fines less than 6.3 mm (USFS 1999). A 1991 BLM
survey identified C channels as dominant in the lower reaches, and B channel types (Rosgen
1994) in the upper reaches. Average gradient ranged from 1-3 %, and unstable stream banks
varied from 2-10%. The seven-day running average maximum temperature during steelhead
and cutthroat trout spawning periods was 11.5 °C (52.7 °F) (rated high quality). The seven-
day running average maximum temperature for the bull trout spawning interval was 13.4 °C
(56.1 °F) (rated low quality). Primary limiting habitat factors include high levels of
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
deposited sediment, high summer water temperatures, and lack of good quality pools. Water
temperatures are cooler in upstream reaches (USFS 1999).
Little Elk Creek
Little Elk Creek provides habitat for steelhead, spring chinook salmon, westslope cutthroat
trout, brook trout, mountain whitefish, sculpin, and dace. Bull trout may use Little Elk Creek
for adult and subadult rearing; however, an IDFG survey in 1998 did not document the
presence of bull trout (USFS 1999). The upper reaches flow through stringer meadows and
forested stream bottoms, while the lower reaches meander through a broad meadow. Grazing
is light in the stream bottoms and moderate in the meadow areas. Land use impacts include
grazing, mining, roads, and logging. BLM monitoring in 1986 showed cobble
embeddedness to be 56% (rated low condition), while spawning gravels had 37% fines less
than 6.3 mm surveyed (rated low condition) (USFS 1999). A BLM survey conducted in 1992
(USFS 1999) identified C channel types as dominant in the lower reaches, and B channel
types (Rosgen 1994) in the upper reaches. The average gradient ranged from 1-2 %, and
unstable stream banks varied from 10-25% in the lower reaches downstream from the NPNF
boundary. The seven-day running average maximum temperature during steelhead and
cutthroat trout spawning periods was 14.1 °C (57.4 °F) at stream mile 0.01 and 10.6 °C (51.1
°F) at stream mile 4.2. The seven-day running average maximum temperature for the bull
trout spawning interval was 19.6 °C (67.3 °F) at stream mile 0.01 (rated low condition) and
15.2 °C (59.4 °F) at stream mile 4.2 (rated low condition). Primary limiting habitat factors
include high levels of deposited sediment, high summer water temperatures, and lack of good
quality pools. Water temperatures are cooler in upstream reaches.
Lucas Lake
Lucas Lake is currently listed on Idaho's 303(d) list for sediment pollution. It is a sink or
depression that may be an old "glory hole," (pit left by hydraulic mining) or it may be a
natural feature. Lucas Lake has steep underwater banks, and appears to maintain full pool
conditions throughout the year. The lake is surrounded by a very small, steep, contributing
watershed composed of small-grained sedimentary deposits. Many raw outcroppings of this
erosive sedimentary rock are visible. The riparian area appears healthy. There is a distinct
blue-green color to the water, probably colloidal in nature, which may have been mistaken
for toxic substances in past assessments. Abundant water boatman (Hemiptera corixidae)
and backswimmer (Hemiptera notonectidae) aquatic insects were observed, and there have
been reports offish (Appendix N).
Riparian Characteristics of the American River Watershed
The riparian vegetation includes grand fir/arrowleaf groundsel, subalpine fir/twisted stalk,
subalpine fir/bluejoint, sedge meadows, shrub/sedge complexes, and riparian shrubs (e.g.
willow, alders etc.). Many of the low gradient reaches in the Elk City township have been
dredge mined and lack grass/sedge meadow vegetation. The shrub component is lacking or
reduced due to browsing by domestic animals and wildlife and the mining impacts.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Red River Watershed
Dawson Creek discussed below is the only 303 (d) listed water body in the Red River
Watershed.
Dawson Creek
Dawson Creek provides habitat for steelhead, spring chinook salmon, and westslope
cutthroat trout. Bull trout presence is not documented (DEQ 1998). The NPNF classifies the
Red River watershed as a stronghold for these four fish species. Reconnaissance-level
surveys conducted of the lower reach (DEQ 1995, BLM 2001) identified a B type channel
with a gradient of 1-2 %. The dominant substrate particle size was small gravel while the
subdominant substrate was sand/silt size. The average width was 2-4 feet and the average
depth 0.3 feet. Stream bank stability was rated 95-100% for the reaches surveyed. Percent
surface fines ranged 15-25% (BLM 2001) to 49% (DEQ 1995). Cobble embeddedness was
rated 40-50% (BLM 2001). The instantaneous temperature was 13°C, and discharge ranged
from 0.3 cfs (BLM 2001) to 0.6 cfs (DEQ 1995). The BLM survey noted the presence of 6-
inch trout and spotted frogs. Land use observed at the time included livestock grazing
(horses), timber harvest, roads, and a private residence. Localized logging was noted along
the stream/riparian area on private lands.
Common Riparian Vegetation of the Dawson Creek Watershed
Common riparian vegetation includes alder, Carex sp., western yarrow, grand fir, menziesia
(fool's huckleberry), and arrowleaf groundsel (BLM 2001).
Newsome Creek Watershed
The Newsome Creek watershed provides habitat for steelhead, spring chinook salmon,
westslope cutthroat trout, bull trout, and several other species including long nose dace,
suckers, sculpin, and whitefish. The four 303(d) listed water bodies include: Newsome
Creek (Beaver Creek to SF CWR), Beaver Creek, Nugget Creek, and Sing Lee Creek.
Newsome Creek
Newsome Creek width-to-depth ratios rate high condition for B and C channel types (Rosgen
1994) and low condition for A channels. The first mile upstream from the mouth (B channel)
rates as low condition due to a very high width-to-depth ratio. Some channel reaches have
been altered by dredge mining. Stream bank stability is rated low condition for main stem
Newsome Creek. Floodplain connectivity is rated low condition due to extensive dredging
and road encroachment.
Cobble embeddedness exceeded 30% (low condition) throughout all measured reaches in the
watershed, and ranged from 34-94% (USFS 1999). Percent surface fines rated low condition,
with 18% fines for riffles and 31% for pools (USFS 1999). Fines by depth rated low
condition (36%) as measured by McNeil core sampling in 1984. The acting woody debris is
rated low condition, ranging from 0-5 pieces per 100 meters. The pool frequency is rated
low condition with no reaches meeting pool frequency standards, but the pool quality is rated
high in the main stem from habitat improvement structures (USFS 1999).
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Temperatures rated low condition for steelhead and bull trout, exceeding 18°C in surveys
conducted in 1995 and 1996 (USFS 1999).
Beaver Creek
Surveys conducted of Beaver Creek, one reach BURP (DEQ 1995), and two reaches NPNF
(USFS 1996b) identified predominantly B channel type (Rosgen 1994) with a gradient
ranging from 3-7 %. The average wetted width was 2.7 meters and the average wetted depth
was 0.2 meters. Stream bank stability was rated 70-100% for the reaches surveyed. Percent
surface fines were 46% (DEQ 1995). Cobble embeddedness was rated at 50-75% (DEQ
1995). Instantaneous temperatures were 10°C and 12°C, and discharge was 6.7 cfs (DEQ
1995).
Nugget Creek
Two surveys conducted of Nugget Creek (DEQ 1995, USFS 1996b) identified predominantly
B channel type (Rosgen 1994) with a gradient of 3.3-3.5%. The average wetted width was
2.13 meters and the average wetted depth was 0.05 meters. Stream bank stability was rated
99-100% for the reaches surveyed. Percent surface fines were 35% (DEQ 1995). Cobble
embeddedness was rated 48% (USFS 1996b). The instantaneous temperature was 11°C
(USFS 1996b) and discharge was 1.0 cfs (DEQ 1995).
Sing Lee Creek
The survey conducted of lower Sing Lee Creek (DEQ 1995) identified predominantly B
channel types (Rosgen 1994) with a gradient of 3.5%. The average wetted width was 1.6
meters and the average wetted depth was 0.04 meters. Stream bank stability was rated 90%
for the reach surveyed. Percent surface fines were 50%. Discharge was 1.8 cfs.
Riparian Characteristics of the New some Creek Watershed
Streamside vegetation includes grand fir/arrow leaf groundsel, subalpine fir/twisted stalk,
subalpine fir/bluejoint, sedge meadows, and shrub/sedge complexes.
Cougar Creek Watershed
Cougar Creek is 303(d) listed as impaired by sediment. Its stream characteristics are
discussed below.
Cougar Creek
The bottom substrate of Cougar Creek consists mainly of boulders and bedrock. The main
stem is predominantly a B-l channel, with short sections of B-2 and C-2 channel types
(Rosgen 1994). Stream gradients average 4-5% although a few reaches vary between 7-8%.
Cobble embeddedness estimates are high and are thought to be limiting fish production.
Cobble embeddedness averaged 65% in 1989 surveys (USFS 1999) and 58% and 64% at two
locations in 1996 surveys (USFS 1999). There are very low levels of acting and potential
large woody debris. Pool frequency is rated low. Pools per mile ranged from 46.7 to 91.9 in
1989 surveys. Flood plain connectivity is considered low due to roads paralleling the stream.
Stream bank stability is moderate, with B channel types rated 94-95% stable. The stream
bankfull width-to-depth ratio is considered low condition. Thermographs in the summer of
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
1996 recorded a high of 19.8 °C (67.6 °F) and a daily average of 17.6 °C (63.7 °F) (USFS
1999).
Riparian Vegetation Characteristics of the Cougar Creek Watershed
The riparian condition is rated as moderate due to poor bank cover in lower reaches. Upper
reaches have relatively good bank cover. Livestock grazing has also degraded riparian and
stream bank conditions.
South Fork Clearwater River Canyon
Chinook salmon, steelhead, westslope cutthroat trout, and bull trout are present in the main
stem of the SF CWR. The face drainages currently are rated low condition for road density
and streamside road density. There are an average of 3.51 miles of roads per square mile of
watershed, and an average streamside road density of 4.36 miles per square mile. Landslide
prone road density is considered moderate at 1.1 miles per square mile throughout the face
drainages. Potential changes in peak/base flow and water yield rate as low condition. The
average ECA for the face drainages (9.6%) suggests that there should not be significant
effects on peak/base flow related to fires or logging. However the moderately high ECA
values in some watersheds (15-30%) and extremely high ECA values in Nelson Creek
(48.2%) and Earthquake Creek (36.1%) may be causing localized impacts in individual
watersheds and on the main stem SF CWR (USFS 1999).
Sediment yield from the face drainages and SF CWR main stem is currently 9% over base,
rating as moderate condition. Stream bank stability of the main stem is rated high condition
due to armoring along Highway 14. The opposite bank is primarily composed of bedrock
and large boulders. Suspended sediment levels are fairly low, rating high condition for
habitat. Main stem suspended sediment averages exceeded 25 milligrams per liter (mg/L) for
8 days and 80 mg/L for one day during years 1988-1992 (USFS 1999).
The main stem SF CWR begins at the confluence of the American River and the Red River.
From this point to about Tenmile Creek, the river is relatively low-gradient (C channel)
riffle/pool habitat dominated by gravel and cobble substrate. The channel has been altered
by dredge mining and the placement of State Highway 14. From Tenmile Creek to Mill
Creek, the river becomes steeper and more confined with the substrate dominated by
boulders and cobbles. The channel type is typically A, B, or G (Rosgen 1994). This is a
high-energy reach through which the sediment is readily transported. From Mill Creek to
just above Threemile Creek, the river alternates between relatively flat, unconfmed reaches
and steep, narrow, confined reaches. The Rosgen (1994) channel type varies widely (A, B,
C, or G). The river also changes direction near the forest boundary and begins to flow nearly
due north. From Butcher Creek to its confluence with the Clearwater River at Kooskia, the
SF CWR is a relatively flat, unconfmed, C channel, dominated by riffle/pool habitat with
gravel and cobble substrate. This lowest reach of the river has been partially confined by
dikes in the vicinity of Stites and Kooskia.
Cobble embeddedness (40%) is rated low condition for the upper SF CWR. Percent surface
fines were 12% in the upper SF CWR and were rated moderate condition. Percent fines by
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
depth for spawning gravels are rated poor condition for the upper SF CWR and 40% were
less than 6.3 mm (USFS 1999).
Temperature is rated low condition for bull trout and steelhead spawning, rearing, and
migration. The highest mean weekly temperature was 26.6 °C (80.0 °F) at Mount Idaho, and
temperatures exceeded 15.5 °C (59.9 °F) during the steelhead spawning interval (USFS
1999).
Generally temperatures in the SF CWR main stem are too warm for native fish and
temperatures increase after the river leaves the NPNF. Several factors contribute to this
temperature increase including stream aspect (north-south), elevation, warmer ambient air
temperature, and a high width-to-depth ratio. Data collected in the SF CWR between 1991
and 1993 by the NPNF, BLM, and USGS (USFS 1999) show temperatures exceeding levels
conducive to chinook, steelhead/rainbow, cutthroat, and bull trout optimal growth, migration,
and survival (Table 5).
Table 5. SF CWR temperatures, 1991-1993 (USFS 1999).
Site
Mt. Idaho
Mt. Idaho
Stites
Mt. Idaho
Stites
Year
1991
1992
1992
1993
1993
Days >20 °C (68 °F)
44 (24 consecutive days)
14 (9 consecutive days)
34
0
32
Maximum Temperature
24.1 °C(75.4°F)
22. 3 °C (72.1 °F)
27.1 °C(80.8°F)
1 9.0 °C (66.2 °F)
22.6 °C (72.7 °F)
Data collected by the BLM just upstream of the Crooked River Bridge (approximately 27
miles upstream from the Mt. Idaho Bridge) suggest that the temperatures recorded at the Mt.
Idaho site are indicative of those found throughout the upper SF CWR basin (USFS 1999).
Water Temperature Conditions Summarized in 1999 NPNF Biological Assessment (USFS
1999):
1. Summer maximum water temperatures in the upper reaches of the main stem are probably
significantly elevated above natural, since the river there is primarily composed of inflows
from impacted tributaries such as the American River, Red River, Newsome Creek, and
Crooked River.
2. The main stem may become relatively cooler as it flows through the steep narrow reaches
from Golden Canyon to the Mt. Idaho Bridge as a result of topographic shading and inflow
from large cool tributaries such as Tenmile Creek and Johns Creek.
3. Below the NPNF boundary, the main stem warms considerably for the reasons discussed
above.
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Riparian Characteristics ofSF CWR Main Stem
Riparian vegetation has been severely reduced for the entire length of the main stem by State
Highway 14. Invasions of knapweed have occurred along both banks. Herbicides are
routinely applied by the Idaho Transportation Department (ITD). A number of different
compounds have been approved for use in the SF CWR watershed including Amine 4,
Garlon 3 A, Karmex DF, Oust XP, Transline, and Krovar I (Funkenhouser 2002). These
products are applied according to the manufacturer's recommendations, and if applied
correctly are acceptable for use near water bodies.
Floodplain connectivity is rated low condition. The location of the highway has led to a
reduction in riparian and wetland areas and a significant change in riparian
vegetation/succession.
Camas Prairie
Threemile Creek and Butcher Creek headwater areas have gravel and cobble substrate. As
the streams flow through upper prairie areas, the channel types (Rosgen 1994) are typically B
and the dominant substrate changes to silt and sand. These streams become steeper and their
valleys more confined as they cut into low elevation breaklands, with the substrate changing
to predominantly gravel and cobble. Significant amounts of bedload from these streams are
delivered to the lower main stem SF CWR, as evidenced by the accumulation of alluvial fans
at their mouths. These systems respond quickly to midwinter snowmelt and rain-on-snow
events, frequently resulting in localized flooding.
Threemile Creek
Threemile Creek provides spawning and juvenile rearing habitat for steelhead trout, and
historically chinook salmon. Surveys conducted in 1982 collected 6 young of the year
(YOY) rainbow/steelhead and one YOY chinook salmon at stream mile 0.8. (Kucera et al.
1983). Adult steelhead have been observed during the past in the segment of the creek
flowing through Grangeville (BLM 1999). Bull trout use of this creek has not been
documented. Spring/summer chinook salmon use the creek for rearing (Kucera et al. 1983);
however, spring chinook salmon use of the creek is at very low levels. A 1996 flood event
resulted in severe channel and stream bank scouring. Previous flood events have also
resulted in severe channel scouring. Large woody debris is lacking in-stream. The primary
limiting factors for fish production include low flows, high summer water temperatures, poor
riffle/ pool ratios, lack of good quality pools, and lack of in-stream cover (BLM 1999).
Kucera et al.'s (1983) survey found cobble embeddedness ranged from 40-60%, with
substrates ranging from small rubble and loose gravels to small boulder at the three stations.
Butcher Creek
Butcher Creek provides spawning and juvenile rearing habitat for steelhead. Spring/summer
chinook salmon use Butcher Creek for rearing; however, such use is at very low levels. Bull
trout use of this creek has not been documented. In 1982 rainbow/steelhead trout and young
of the year spring/summer chinook salmon were sampled in Butcher Creek (Kucera et al.
1983). Recent electrofishing conducted by the NPT, June 27, 2002, documented 7 age one
rainbow/steelhead and 3 juveniles (NPT 2002b). The primary limiting factors for fish
29 Chapter 1
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production include low summer stream flow, high summer water temperatures, extreme
variations in stream flow, and lack of in-stream cover (BLM 1999). Kucera et al.'s (1983)
survey found cobble embeddedness ranged from 25-60%, with substrates varying from small
to large rubble at the three stations.
Vegetation Characteristics of Lower SF CWR Tributaries
Plant community composition is dependent of aspect, elevation, and soils. Habitat types vary
from warm and dry (15 inches precipitation) to cool and moist (30 inches of precipitation).
Common vegetation types include conifer, Palouse/canyon grasslands, and agriculture (dry
farming-wheat, barley). The Palouse/canyon grasslands vegetation includes bluebunch
wheatgrass, Idaho fescue, arrowleaf balsamroot, cheat grass, and shrubs/trees associated with
some aspects. Good examples of relic Palouse grasslands are very rare, as agricultural
activity and livestock grazing have altered these habitats significantly. Canyon grasslands in
poor ecological condition generally are heavily infested with noxious weeds; yellow star
thistle is the most common weed infesting range lands in the area. Common timber types
include Douglas fir and ponderosa pine; grand fir occurs at higher elevations and areas with
higher moisture regimes (BLM 1999)
1.3 Cultural Characteristics
Land ownership, land use, and cultural aspects of the SF CWR Watershed are discussed
below.
Land Ownership
The SF CWR Subbasin includes a mixture of private and public lands covering
approximately 752,000 acres (Figure 8). Table 6 lists the acreage of the major management
groups. The Camas Prairie portion of the watershed contains approximately 199,000 acres
and is comprised of private, BLM, state of Idaho, and NPT ownership.
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October 2003
' Kooskia
Land Management
South Fork Clearwater
River Subbasin
I **
14 Miles
April 2003
Legend
] SF Clearwater 4ih Field HUC
Water Body I D watersheds
| NPT Reservation Boundary
/\/ 3Q3fd) Listed Stream s
Ownership
Q B.L.M.
n NMP
Forest Service
Open Water
Private
State of Idaho
Figure 8. Major Land Managers of the SF CWR Subbasin
Table 6. Acreages of the SF CWR Subbasin land management groups.
Land Ownership/Management Agency
Nez Perce National Forest
Bureau of Land Management
Private
Nez Perce Tribe
Idaho State Department of Lands
Acres
516,262
14,906
218,316
564
3,330
Percent
68
2
29
<1
<1
Nez Perce Tribe Treaty Rights
Members of the Nez Perce Tribe have used and occupied the SF CWR Subbasin and
surrounding area since time immemorial. Prior to the Treaty of 1855, the Nez Perce had
exclusive use and occupancy over an area of approximately 13 million acres in central Idaho,
northeastern Oregon, and southeastern Washington. Nez Perce members have and continue
to use much of this territory, including the SF CWR Subbasin for hunting, fishing, gathering,
and pasturing.
By virtue of the Treaties of 1855 and 1863, the Nez Perce Tribe reserved to itself certain
rights, which are described in the treaties referenced below.
Treaty with the Nez Perce of 1855, Article 3: "The exclusive right of taking fish in all
streams where running through or bordering said Reservation is further secured to said
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Indians; as also the right of taking fish in all usual and accustomed places in common with
citizens of the Territory; and of erecting temporary buildings for curing, together with the
privilege of hunting, gathering roots and berries, and pasturing their horses and cattle upon
open and unclaimed land."
Treaty with the Nez Perce of 1863, Article 8: "The United States also agrees to reserve all
springs or fountains not adjacent to, or directly connected with, the streams or rivers within
the lands hereby relinquished, and to keep back from settlement or entry so much of the
surrounding land as may be necessary to prevent the said springs or fountains being enclosed;
and, further, to preserve a perpetual right of way to and from the same, as watering places,
for the use in common of both whites and Indians."
Communities
The largest town in the SF CWR Subbasin and the Idaho County seat is Grangeville
(population 3,208). Other towns in the watershed include Kooskia (population 708),
Cottonwood (population 852), Stites (population 215), Elk City (population 670), Mt. Idaho
(population 75), Greencreek (population 50), Clearwater (population 35), Orogrande
(population 10), Harpster, Big Butte, and Golden.
The current population estimate for Idaho County is 15,311. As the population of the Idaho
County towns (Table 7) is only 5,693, approximately 10,000 residents live in rural areas.
Growth trends in north-central Idaho show rural areas experiencing an influx of new
residents. An analysis for Clearwater Economic Development Association (USFS 1998)
showed nine communities with populations less than 1,000 growing in excess of 4% per year
since 1991. In addition, unincorporated areas in Idaho County are attracting a greater share
of new residents and exceeding city population growth. Many of the people locating in the
rural areas are self-employed or retirees. Retirees tend to spend more of their income locally
than other groups, and individuals who are self employed are not competing for jobs that
others can fill. Table 7 shows population trends in Idaho County.
Table 7. Population trends in Idaho County.
Location
Cottonwood
Ferdinand
Grangeville
Kooskia
Riggins
Stites
White Bird
1970
867
157
3636
809
533
263
185
1980
941
144
3666
784
527
253
154
1990
822
135
3226
692
443
220
108
1992
852
141
3208
708
460
215
109
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History and Economics
The SF CWR was once a major producer of steelhead and spring chinook salmon. The main
stem and almost all tributaries with adequate access and discharge supported spawning and
rearing for steelhead. Cutthroat and bull trout populations are also believed to have thrived
throughout the subbasin. The lower SF CWR may have supported runs of coho and fall
chinook salmon. The productivity of the subbasin is believed to have been historically
higher as a function of nutrient supplementation from the Pacific Ocean when large numbers
of anadromous salmonids provided nutrients both in the form of thousands of decaying
carcasses from returning adults and the millions of eggs laid annually. In addition, the
rearing juveniles provided a large prey base for resident salmonids.
The decline of the fishery and habitat in the SF CWR Subbasin probably began in 1861 when
gold was discovered in the basin. Early mining, along with the associated grazing and timber
harvest, is likely to have created only localized degradation. The decline accelerated in 1900
when large-scale hydraulic and dredge mining began. Road construction, primarily to access
mining claims, also increased. A lull in large-scale mining occurred between about 1910
and 1930. In 1930, large-scale mining projects resumed and continued through the late
1950s. Newsome Creek, American River, Red River, and Crooked River were among the
most heavily impacted. Between 40 and 50 miles of prime spawning and rearing habitat
were drastically altered and heavily degraded by dredge mining, and large amounts of
sediment were released into the tributaries and the SF CWR main stem.
As hydraulic and dredge mining activity declined, commercial timber harvest and road
construction activity increased, most dramatically during the 1960s. This increase created
another large, sustained peak in sediment levels. Harvest units typically did not have riparian
buffers, and roads were poorly constructed. Streams were frequently straightened to
accommodate roads, and the reconstruction of the South Fork Highway (Highway 14)
resulted in constriction, steepening of the channel, and direct sediment delivery.
Grazing probably peaked in the 1920s and currently occurs at a lower level. Grazing impacts
have been most severe in some of the important anadromous spawning and rearing areas in
the Red River, American River, and Meadow Creek. Grazing has also impacted a number of
smaller tributaries and has had severe impacts in many of the lower mainstem tributaries as
well.
In 1911, a dam was constructed on the lower SF CWR main stem below the NPNF boundary
near Harpster, near river mile 22 (upstream from the mouth), to provide power to the city of
Grangeville. A fish ladder was installed in 1935 and remained until 1949, when it was
destroyed by high water. Thus, the dam was a complete barrier to fish migration, and
anadromous salmonids (chinook, coho, steelhead) and Pacific lamprey were excluded from
the upper watershed from 1911 to 1935, and from 1949 until 1963, when the dam was
removed. A second dam was constructed on the Clearwater River main stem near Lewiston
in 1927 and was removed in 1974. This dam's fish ladder was remodeled around 1939
because the original ladder functioned poorly. Even though run sizes were sharply reduced,
some passage of anadromous fish is believed to have occurred during 1927-1939. Two
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potential fish barriers on the SF CWR include the Kooskia Flower Mill Dam and the Dewey
Mine Dam. Fish passage conditions from these dams are not fully known, but they don't
appear to have been complete migration barriers (N. Gerhardt 2002d). These two dams no
longer exist. Construction of downstream dams on the main stem of the Snake and Columbia
Rivers has also contributed to the decline of anadromous fisheries in the SF CWR Subbasin.
The exclusion of anadromous salmonids from the upper watershed caused a major decrease
in the availability of forage fish for cutthroat and bull trout. This decrease coupled with
habitat degradation is believed to have caused sharp reductions in cutthroat and bull trout
populations beginning in the 1930s. Increased fishing pressure following completion of a
road adjacent to the SF CWR in 1932 may have also contributed to the decline (Appendix
D)
Anadromous salmonids returned to the upper SF CWR watershed through a combination of
natural straying and reintroduction efforts after the Harpster dam was removed. However, by
this time, prime spawning and rearing areas were heavily degraded. Populations of
anadromous and resident fish have never recovered, and current population levels represent
only a small percentage of their original levels. Even in the current degraded condition,
under-utilized spawning and rearing habitat is available in the watershed. Thus the potential
remains for the SF CWR to play a significant role in the recovery of anadromous salmonids
if escapement at downstream dams can be improved.
Land Use
Primary land uses and economic interests within the subbasin include timber harvesting,
mining, grazing, outfitting and guiding, recreation, and agriculture.
Timber Harvest
Timber harvest was associated with early mining activity between 1860 and 1910, and with
homesteading from 1910-1920. In 1863, a sawmill was built in the vicinity of Elk City. By
the turn of the century, as many as seven sawmills were producing lumber in the Elk City
mining district. Commercial timber harvest began in the 1940s. During the 1940s and the
1950s, the rate of timber harvest was relatively low. The sawlog timber volumes sold in the
subbasin since 1971 are shown in Table 8. The volume peaked in 1972 at 83.4 million board
feet (MMBF). The lowest level was in 1992 with a figure of 0.3 MMBF.
In 1958, the Shearer Lumber Products sawmill near Elk City opened. This mill, as well as
other mills which opened about the same time, created a large demand for timber. As a result
the rate of harvest increased during the 1960s and 1970s. Clearcutting was the dominant
silvicultural system used. Since the 1980s, the rate of timber harvest has been decreasing, as
well as the amount of clearcutting.
In 1974, the state of Idaho adopted the Forest Practices Act (FPA), which oversees forest
practices. Inspections are made by the state to ensure compliance with these rules and
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regulations. From 1991 to 1993, the number of harvest activities on private land increased
from 107 to 234. The size of individual harvests is also increasing.
Table 8. Sawlog volume sold from SF CWR Subbasin.
5 Year Intervals
1971-75
1976-80
1981-85
1986-90
1991-95
1996-2000
Total MMBFa
289.3
284.3
224.4
221.0
91.8
72.4
Average MMBF/Year
57.9
56.9
44.9
44.2
18.4
14.5
""Million board feet
Mining
The first major gold discovery in the subbasin was in June 1861, near Elk City. A placer
mining boom followed, concentrated in the upper part of the basin. Hydraulic mining began
in the mid-1860s resulting in thousands of cubic yards of sediment being washed into stream
channels and rivers. The first dredge operated in the Elk City area in 1891. In 1902, the first
ore processing mill, the "American Eagle," was built and full scale lode mining began. In
upland areas, lode mines averaged a few acres in size and most work was completed with
hand tools, which limited watershed impacts. However, the mills were located near streams
for water and power supply, and it is likely that cyanide and mercury contaminated tailings
were discharged into them.
The 1930s depression era brought a revival of placer mining and some lode mining. Most of
the heavy dredging occurred in the tributaries (Newsome Creek, American River, Red River,
and Crooked River), and in the upper section of the SF CWR main stem extending from the
mouth of Newsome Creek to the upper reaches. Most of these impacts occurred in the lower
gradient sections, which provide the richest spawning and rearing habitat.
Hydraulic mining of hillsides also revived in the 1930s. Large amounts of sediment caused
changes in stream morphology as the volume was too great to be washed downstream. The
pits left by hydraulic mining, called "glory holes" continue to be a focus of current
restoration efforts. Their large, unvegetated, unstable banks are constantly eroding and
contributing sediment to the system.
By 1960, more than 24 million cubic yards of material had been dredged in the subbasin,
affecting approximately 30 miles of stream. Recent mining activity consists mostly of small
scale suction dredging, placer and lode operations, and aggregate sources (rock pits).
Approximately 70 aggregate sources have been developed in the subbasin over the years.
Most are bank excavations above an entry road, and others utilize existing dredge tailings.
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The USFS mining regulations have led to a reduction in mining impacts since 1974. One
provision in these regulations requires that the operator furnish a bond to ensure that
reclamation occurs. Environmental laws passed in the 1970s and 1980s have also reduced
mining impacts.
Grazing
Domestic sheep and cattle arrived in the mid-1860s, with the gold rush and the movement of
people to the area. It is estimated that more grazing by domestic livestock occurred at the
turn of the century than occurs now. The NPT pastured large bands of horses throughout the
area. It is also known that the NPT practiced prescribed fire management.
Livestock management increased with the number of settlers, and operations were
concentrated in suitable areas around major trailheads leading to the large mining camps.
Grazing laws were enacted in 1908 with the establishment of the NPNF. The livestock
industry thrived on the range land of the area. Stites was the major livestock shipping
location for the county.
Currently there are twelve active NPNF cattle allotments in the subbasin. The allotments are
designated areas of land upon which a specified number of livestock may be grazed under a
range allotment management plan. Grazing allotments total approximately 222,100 acres of
the 515,000 acres within the NPNF portion of the subbasin. Approximately 105,450 of the
allotment acreage have forage and are suitable for grazing. The rest is forested.
The degree of impact from grazing has fluctuated over the years. Recent monitoring
indicates that the NPNF allotments are not major contributors to degraded fish habitat or
water quality. However, about one third of the allotments have localized areas of overuse,
which cause damage to stream banks and reduce riparian vegetation (USFS 1998).
Private, BLM, state, and tribal lands have been grazed by domestic livestock since the mid-
1800s. The extent, location, and effects of the early grazing are not known. The earliest
surveys done in Cottonwood Creek in 1962 documented riparian zones in poor condition and
high water temperatures. Subsequent studies (1974, 1980, 1982, 1987, and 1992) all indicate
a lack of riparian vegetation, lack of vegetative diversity, and severe channelization of the
stream (USFS 1999). It is not known to what extent these impacts are attributable to grazing.
Outfitting/Guiding
There are currently seven different outfitters who utilize portions of the watershed for big
game hunting (elk, deer, black bear, and cougar), fishing, and pack trips. There are currently
no outfitter-guide permits for water related activities, such as rafting or kayaking.
Recreation
Recreation use includes big game hunting, fishing, horseback riding, hiking, cross-country
skiing, swimming, Whitewater kayaking, snorkeling and scuba diving, camping,
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photography, wildlife viewing, picnicking, arts and craft activities, outdoor learning, berry
picking, wood cutting, off-road vehicle use, sight seeing, and recreational dredge-mining.
The early trails and wagon roads provided access for the nearby prairie and river
communities to hunt, fish, and camp in the NPNF. The main stem of the SF CWR and the
Red River have most of the developed campgrounds on the forest. In 2001, the north-central
Idaho chinook fishing season brought $46 million dollars to the region (IDC 2002).
Recreation/tourism has been a traditional and historic use of the SF CWR area for as long as
110 years. The gravesite of G. Colgate lies alongside Highway 12 in the nearby Lochsa
River subbasin. In 1893, Colgate was cook for a group of easterners engaged in a guided
hunt along the Lochsa River (Hendrickson 2002). According to 1999-2000 Idaho
Department of Commerce (IDC) figures, tourism is second only to lumber in north-central
Idaho in revenue generated. Agriculture is third. In Idaho County, the gap between lumber
and tourism is smaller than in north-central Idaho as a whole (Laughy 2002). In 1997, travel
and tourism expenditures were 47.4 million dollars and agricultural sales were 32.6 million
dollars. The lumber industry (all sales of manufactured lumber products, including logging,
trucking, milling, etc.) was estimated to have generated 50.5 million dollars in 2000.
According to IDC, travel and tourism figures do not reflect the income of proprietors and
thus is underestimated. In summary, the three major industries in Idaho County are
agriculture, lumber/milling, and tourism. They are all of similar size, with agriculture being
the smallest. Travel and tourism is the most rapidly growing industry, while the others are
declining.
Agriculture
In the mid-1800s settlers began moving into the area and established homesteads and
ranches. Larger tracts were put into crop production with the development of mechanized
equipment, resulting in the loss of riparian areas and wetlands. Predominantly agricultural
land use occurs in the Threemile Creek and Butcher Creek watersheds (Table 9).
Table 9. Percent land use in Threemile and Butcher Creeks.
Water body
Segment
Threemile Creek
Butcher Creek
Cropland
63.5
53.9
Pasture and Range
12.3
35.2
Forest
4.7
2.0
Steep
Canyons
14.6
8.7
Urban
0.3
0.2
The majority of cropland is devoted to dryland agriculture. About 10% of area farmers are
now using direct seed and no-tilling practices, with the trend on the increase (Rowan,
September 23, 2002). The major crops are winter wheat, spring wheat, barley, peas, lentils,
and canola. Most of the cropland is on gently sloping, well-drained soils. Farming practices
include conventional tillage for seedbed preparation, plow, disc, harrow, fertilization of
inorganic nitrogen (on average 100 pounds per acre for winter wheat) and phosphorus, and
pesticide application for control of weeds and insects. Crops are generally grown in rotation
with winter wheat following a legume or canola.
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Range and grazing lands tend to be on the steeper slopes or areas with soils unsuitable for
crop production. Some areas have large numbers of animals confined to relatively small
areas with direct access to the creek. Currently none of these areas are officially designated
as "confined animal feeding operations" (CAFOs) (Rowan, September 23, 2002).
Approximately 60% of all private agricultural land has had riparian vegetation removed
according to Idaho Soil and Water Conservation District representatives (USFS 1999).
During spring runoff, flooding of cropland, pasture, and hay land adjacent to streams occurs.
Little vegetation is left to trap sediments during these periods of runoff. Severe stream bank
erosion has also occurred in some areas resulting from the high velocity flows associated
with seasonal flooding.
The majority of cropland is left in a tilled condition going into winter. Soil erosion occurs
following winter rains (November to March) on snow and frozen soil resulting in rapid
runoff. When the soil is partially frozen, the surface water infiltration is greatly reduced and
runoff erodes topsoil down to the frozen layer, carrying sediment onto lower lands and into
stream systems. Localized high intensity rainstorms, which may occur at any time during the
year, also contribute to soil erosion.
Agricultural chemical use on private land is widespread, and approximately two thirds of the
cropland area receives at least one chemical application per year. Appendix E lists chemicals
identified as being used in support of agriculture and grazing on the Camas Prairie.
Approximately 46 different herbicides and pesticides are used on the Camas Prairie for weed
and insect control (Sandlund 2002).
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2. Subbasin Assessment-Water Quality Concerns and
Water Quality Status
This section identifies the 13 water quality limited segments in the SF CWR Subbasin, the
applicable WQS for these water bodies, existing water quality data, and data gaps. The SF
CWR Subbasin, HUC 17060305, is comprised of the 82 water body units defined by Idaho
Code (IDAPA 58.01.02.120.07) (see Table 1).
2.1 Water Quality Limited Segments Occurring in the SF CWR Subbasin
The water quality limited water bodies (DEQ 1999), beneficial uses, and pollutants are
shown in Table 10. Figure 9 shows the water quality limited stream and river segments and
their associated watersheds.
303(d) Listed Water Quality Limited
Stream and River Segments in the
South Fork Clearwater River Subbasin
18 Miles
Cottonwood
o
Legend
SF Clearwater HUC
NPT Reservation Boundary
303(d) Listed Streams
303d Listed Water Body
Major Streams
Other Streams
Cottonwood Creek
October 2003
Figure 9. Water Quality Limited Water Bodies in the SF CWR Subbasin
The CWA requires the restoration and maintenance of the chemical, physical, and biological
integrity of the nation's waters (33 USC §§ 1251 - 1387). States and qualified Tribes,
pursuant to Section 318 of the CWA, are to adopt WQS necessary to protect fish, shellfish,
and wildlife while providing recreation in and on water whenever attainable. Section 303(d)
of the CWA establishes requirements for states and qualified Tribes to identify and prioritize
water bodies that are water quality limited. States and qualified Tribes must publish a
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priority list of impaired waters every two years. For waters identified on this list, states and
qualified Tribes must develop a TMDL set at a level to achieve WQS.
Table 10. Water quality limited water bodies in the SF CWR Subbasin.
Stream
Name
Threemile
Creek
Butcher
Creek
Newsome
Creek
Lucas
Lake
Beaver
Creek
Buffalo
Gulch
Dawson
Creek
Nugget
Creek
Sing Lee
Creek
South Fork
Clearwater
River
Cougar
Creek
Little Elk
Creek
Big Elk
Creek
Water Body
ID(s)
10
11
62
52
65
59
38
64
73
1, 12,22,30,
36
79
57
58
Boundaries
(1998303(d)
list)3
Headwaters to
SFCWR
Headwaters to
SFCWR
Beaver Creek to
SFCWR
Headwaters to
Newsome Creek
Headwaters to
American River
Headwaters to
Red River
Headwaters to
Newsome Creek
Headwaters to
Newsome Creek
Red River to
Clearwater River
Headwaters to
SFCWR
Headwaters to
Elk Creek
Headwaters to
Elk Creek
Beneficial
Uses"
CW/SS(d)
SCR(d)
CW/SS(d)
SCR(d)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(d)
PCR(d)
SRW (d)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
CW/SS(e)
PCR/SCR(e)
Stream
Miles
49.8
18.9
12.4
.00
6.7
6.5
2.3
4.6
4.5
248.8
17.1
12.7
19.7
Pollutant0
Bac, DO, Qalt,
Halt, NH3, Nut,
Sed, Temp
Bac, DO, Qalt,
Halt, Sed, Temp
Sed
Sed
Sed
Sed
Sed
Sed
Sed
Halt, Sed, Temp
Sed
Temp
Temp
aRefers to a list created in 1998 of water bodies in Idaho that did not fully support at least one beneficial use.
This list is required under section 303 subsection "d" of the Clean Water Act.
bCW = Cold Water, SS = Salmonid Spawning, PCR = Primary Contact Recreation, SCR = Secondary Contact
Recreation, SWR= Special Resource Water
(d) = designated beneficial use, (e) = existing beneficial use
°Bac = bacteria, DO = dissolved oxygen, Qalt = flow alteration, Halt = habitat alteration, NH3 = ammonia, Nut
= nutrients, Sed = sediment, Temp = temperature
As a result of the court-ordered 303(d) listing by USEPA in 1994 (DEQ 1999), the entire
main stem SF CWR and 49 tributaries were listed as water quality-limited, not including the
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Cottonwood Creek drainage, which was addressed by a separate TMDL effort (DEQ, NPT,
USEPA 2000). Streams were listed for numerous reasons, not only WQS violations. Nine
streams came to the 303(d) list as a result of being identified in Appendix D of DEQ's 1992
305(b) report (DEQ 1992). The remaining 40 tributaries and the main stem SF CWR itself
were listed because of information accumulated from the NPNF plan (USFS 1987), other
NPNF studies, and Idaho's water quality status report (DEQ 1989).
Waters identified in Appendix D of the 1992 305(b) report were listed as potentially impaired
sites needing further assessment to verify any actual WQS violations (including impaired
beneficial uses) (DEQ 1989). Waters identified in USFS plan and other studies as not
meeting forest plan objectives are not necessarily violating state WQS, as forest plan
objectives may be quite different from state WQS. Idaho's Stream Segment of Concern
(SSOC) listing process was a mechanism for the public to voice concerns about particular
water bodies. Unfortunately, these lists likewise had little evidence of actual water quality
problems or impaired uses. The SSOC waters were often identified as impaired simply
because they were favored by the interested public. In all these cases, little actual data were
available to assess whether or not these waters were violating WQS or impairing beneficial
uses.
In 1998, DEQ attempted to rectify that situation by processing several years worth of
Beneficial Use Reconnaissance Program (BURP) data in order to assess the status of
beneficial uses and record WQS violations for these 303(d) listed streams. The 1998 DEQ
303(d) list (DEQ 1999) removed 39 of the original 49 tributaries listed under the court order.
Section 3.2 discusses the analyses of the BURP data. The tributaries remaining on the 303(d)
list are shown in Table 10. For waters within the Nez Perce Reservations, the 1994 303(d)
list remains in effect.
2.2 Applicable Water Quality Standards
The water quality criteria (narrative and numeric) that are relevant for the designated and
existing beneficial uses for the SF CWR Subbasin are discussed below. Designated
beneficial uses listed for the main stem SF CWR include salmonid spawning, primary contact
recreation, and special resource water (IDAPA 58.01.02). The beneficial uses of the 303(d)
tributaries are listed above in Table 10. For undesignated 303(d) listed tributaries, the
existing beneficial use for aquatic life in the SF CWR Subbasin is salmonid spawning and the
existing beneficial use for recreation is primary or secondary contact recreation (IDAPA
58.01.02.101.01).
Beneficial Uses
Idaho WQS require that surface waters of the state be protected for beneficial uses, wherever
attainable (IDAPA 58.01.02.050.02). These beneficial uses are interpreted as existing uses,
designated uses, and "default" uses as briefly described in the following paragraphs. The
Water Body Assessment Guidance., second edition (Grafe et al. 2002) gives a more detailed
description of beneficial use identification for use assessment purposes.
41 Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Existing Uses
Existing uses under the CWA are "those uses actually attained in the water body on or after
November 28, 1975, whether or not they are included in the water quality standards." The
existing beneficial uses and the level of water quality necessary to protect the uses shall be
maintained and protected (IDAPA 58.01.02.003.35, .050.02, and 051.01 and .053). Existing
uses include uses which have occurred since 1975, whether or not the level of water quality
to fully support the uses exists.
Designated Uses
Designated uses under the CWA are "those uses specified in WQS for each water body or
segment, whether or not they are being attained." Designated uses are simply uses officially
recognized by the state. In Idaho these include things like aquatic life support, recreation in
and on the water, domestic water supply, and agricultural use. Water quality must be
sufficiently maintained to meet the most sensitive use. Designated uses may be added or
removed using specific procedures provided for in state law, but the effect must not be to
preclude protection of an existing higher quality use such as cold water aquatic life or
salmonid spawning. Designated uses are specifically listed for water bodies in Idaho in
tables in the Idaho WQS (see IDAPA 58.01.02.003.22 and .100, and IDAPA 58.01.02.109-
160).
Presumed Uses
In Idaho, most water bodies listed in the tables of designated uses in the WQS do not yet
have specific use designations. Until such time as specific uses are designated, and absent
information on existing uses, DEQ presumes that most waters in the state will support cold
water aquatic life and either primary or secondary contact recreation (IDAPA
58.01.02.101.01). To protect these so-called "presumed uses," Idaho WQS indicate that the
numeric criteria for cold water aquatic life and primary or secondary contact recreation
criteria will be applied to undesignated waters. If other more restrictive existing use occur in
the water body (e.g., salmonid spawning), then the criteria for those uses would apply as well
(e.g., intergravel dissolved oxygen, temperature). However, if for example, cold water
aquatic life is not found to be an existing use, a use designation to that effect is needed before
some other aquatic life criteria (such as seasonal cold) can be applied in lieu of cold water
criteria (IDAPA 58.01.02.101.01).
Water Quality Criteria
Details of Idaho WQS may be seen in the state of Idaho Web site
(www2.state.id.us/adm/adminrules/rules/IDAPD581/0102.pdf) or obtained from DEQ's
Lewiston Regional Office. Idaho WQS include criteria necessary to protect designated
beneficial uses. The standards are divided into three sections: General Surface Water
Criteria, Surface Water Quality Criteria for Use Designations, and Site-Specific Surface
Water Quality Criteria (IDAPA 58.01.02). The numeric standards that exist in these rules for
Escherichia coli (E. coli) bacteria, temperature, turbidity, ammonia, and dissolved oxygen
42 Chapter 2
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will be used in the TMDL. The standards for nutrients and sediment are narrative standards.
A narrative standard states that the level of a pollutant cannot exceed quantities above natural
background that impair beneficial uses. Because these pollutants do not have numeric
standards, surrogate numeric targets are proposed in the TMDL (Sections 5.2 and 5.3).
According to IDAPA 58.01.02.070.07, numeric WQS are to apply to intermittent waters
during optimum flow periods sufficient to support the uses for which the water body is
designated. Optimum flows are defined as 5.0 cfs for recreation and water supply uses and
1.0 cfs for aquatic life uses.
These WQS pertain to those times and locations where stream flow is non-intermittent.
Idaho rule (IDAPA 58.01.02.003.50) defines an intermittent stream as "A stream which has
a period of zero flow for at least one week during most years. Where flow records are
available, a stream with a 7Q2 (seven day, 2 year low flow) hydrologic-based design flow of
less than one-tenth (0.1) cfs is considered intermittent. Streams with perennial pools which
create significant aquatic life uses are not intermittent." Stream segments of zero flow occur
between perennial pools within portions of the Threemile Creek and Butcher Creek
watersheds.
Idaho WQS pertaining to point source discharges stipulate "the width of the mixing zone is
not to exceed more than twenty five percent (25%) of the stream width, and more than
twenty five percent (25%) of the volume of the stream flow" (IDAPA 58.01.02.060.01).
Also, in the case of permitted point source discharges, additional stipulations for the mixing
of wastewater discharge may be applied. For example, unless specific exemptions are made,
"the temperature of the wastewater must not affect the receiving water outside the mixing
zone so that: (i) the temperature of the receiving water or of downstream waters will interfere
with designated beneficial uses, (ii) daily and seasonal temperature cycle characteristics of
the water body are not maintained, ... (iv) if the water is designated for cold water aquatic
life or salmonid spawning, the induced variation is more than plus one (+1) degrees C"
(IDAPA 58.01.02.401.03.a). The wastewater may not increase turbidity of receiving water
outside the mixing zone by more than 5 nephlometric turbidity units (NTU) over background,
when background turbidity is 50 NTU or less, or by more than 10% when background is
more than 50 NTU, not to exceed a maximum increase of 25 NTU (IDAPA
58.01.02.401.03.b). These and other considerations specific to the WWTP point source
discharge will be determined by the local DEQ permitting engineer during 401 permit
certification.
A subset of the Idaho WQS as defined in Idaho Code 58.01.02 that pertains to the SF CWR
Subbasin follows below. All surface water quality criteria are subject to the clause, "Surface
waters are not to vary from the following characteristics due to human activities.".
Temperature Idaho State Standard for Cold Water Aquatic Life: Water temperatures of
twenty-two(22) degrees C (71.6 °F)or less with a maximum daily average of
no greater than nineteen (19) degrees C (66.2 °F) (IDAPA 58.01.02.250.02b).
43 Chapter 2
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Idaho State Standard for Salmonid Spawning: Water temperatures of thirteen
(13) degrees C (55.4 °F)or less with a maximum daily average no greater than
nine (9) degrees C (48.2 °F) (IDAPA 58.01.02.250.02e). (See Appendix D for
SF CWR fish varieties spawning intervals.)
Federal Bull Trout Standard: 10°C (50 °F)expressed as an average of daily
maximum temperatures over a seven-day period, referred to as the "mean
weekly maximum temperature (MWMT). Applies during months of June,
July, August, and September to water bodies identified in Appendix B of the
July 1997 Federal Register.
Sediment Idaho State Standard for Sediment: Sediment shall not exceed quantities
specified in Sections 250 and 252, or in the absence of specific sediment
criteria, quantities which impair designated beneficial uses. Determinations of
impairment shall be based on water quality monitoring and surveillance and
the information utilized as described in Section 350 (IDAPA
58.01.02.200.08).
Turbidity standard for Cold Water Aquatic Life: Turbidity below any
applicable mixing zone set by the Department, shall not exceed background
turbidity by more than fifty (50) NTU instantaneously or more than twenty-
five (25) NTU for more than ten (10) consecutive days (IDAPA
58.01.02.250.02d).
Nutrients Idaho State Standard for Excess Nutrients: Surface waters shall be free from
excess nutrients that can cause visible slime growth or other nuisance aquatic
growths impairing designated beneficial uses (IDAPA 58.01.02.200.06).
Pathogens Idaho State Standard for Primary and Secondary Contact Recreation.
Primary Contact Recreation: Waters designated for primary contact
recreation are not to contain E. coli bacteria significant to public health in
concentrations exceeding:
a. A single sample of four hundred six (406) E. coli organisms per one
hundred (100) ml; or
b. A geometric mean of one hundred twenty-six (126) E. coli organisms per
one hundred (100) ml based on a minimum of five (5) samples taken every
three (3) to five (5) days over a thirty (30) day period (IDAPA
58.01.02.251.01).
Secondary Contact Recreation: Waters designated for secondary contact
recreation are not to contain E. coli bacteria significant to public health in
concentrations exceeding:
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October 2003
Ammonia
Dissolved
Oxygen
a. A single sample of five hundred seventy-six (576) E. coll organisms per
one hundred (100) ml; or
b. A geometric mean of one hundred twenty-six (126) E. coli organisms per
one hundred (100) based on a minimum of five (5) samples taken every three
(3) to five (5) days over a thirty (30) day period (IDAPA 58.01.02.251.02).
Idaho State Standard for Cold Water Aquatic Life and Salmonid Spawning
As defined in tables in 58,01.02.250.02.c.i. and ii.; pH dependent.
Idaho State Standard for Cold Water Aquatic Life:
Waters designated for cold water aquatic life are not to vary from the
following characteristics due to human activities:
a. Dissolved oxygen concentrations exceeding 6 mg/L at all times.
Idaho State Standard for Salmonid Spawning:
(1) Intergravel dissolved oxygen
(a) One (1) day minimum of not less than five point zero (5.0) mg/L.
(b) Seven day average mean of not less than six point zero (6.0) mg/L.
(2) Water Column dissolved oxygen
(a) One (1) day minimum of not less than six point zero (6.0) mg/L or
ninety percent (90%) of saturation, whichever is greater (IDAPA
58.01.02.250.02).
2.3 Summary and Analysis of Existing Water Quality Data
Table 12 displays sources of existing water quality and stream habitat data obtained from
local agencies used in the development of the temperature and sediment TMDLs.
Subbasin-wide Biological and Other Data
The stream habitat data, reference stream data, and fish data assembled for this analysis is
discussed below. Sources for the data are shown in Table 11.
Stream Habitat Data
The BLM (Johnson 1999) completed the Biological Assessment of the Lower South Fork
Clearwater River and Tributaries as part of its biological assessment of ongoing and
proposed BLM activities on Endangered Species Act (ESA) listed salmonids. The main stem
SF CWR below the NPNF, and tributaries including Threemile Creek, Butcher Creek, Mill
Creek, and Sally Ann Creek, were assessed using the Matrix of Pathways and Indicators of
Watershed Condition -Local Adaptation for the Clearwater Basin (NMFS et al. 1998). For
most of the criteria evaluated, conditions in the lower SF CWR and tributaries were
suboptimal, rating "low" for habitat condition.
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 11. Sources of water quality data.
Data Type3
Stream Habitat Data
Reference Stream Data
Fisheries Resources Report
Fish TAG Report
BURP Data
Flow Data
Temperature Data
Sediment Data:
TSS and Bedload
Sediment Loading Calculations
Stream Erosion Inventory
Sediment Budget
Source"
Lower SF CWR and tributaries
Biological Assessment
SF CWR Biological Assessment
NPNF
Wallowa-Whitman National Forest
Fish TAG Report
SF CWR Fish TAG
DEQ
1995 Earthinfo compact disc
USGS (Boise office)
USEPA Storet database
Clearwater Subbasin summary,
NWPP Council (2001)
NPNF, NPT, BLM, IDFG, and DEQ
thermographs
Thermal Infrared Imaging
NPNF, NPT and DEQ
TMDL
DEQ, NPT, USEPA (TMDL)
TMDL
Location
BLM
NPNF
Appendix N
Appendix N
Appendix D
Appendix D
Appendix K
Section 2.3.2
Appendix J
DEQ Report (2001)
Appendix M
Chapter 5
Appendix L
Appendix L
aFish TAG = fisheries technical advisory group, BURP = Beneficial Use Reconnaissance Program, TSS = total
suspended solids
bNPNF - Nez Perce National Forest, DEQ = Department of Environmental Quality, USGS = U.S. Geological
Survey, USEPA = U.S. Environmental Protection Agency, NWPP = Northwest Power Planning Council, NPT
= Nez Perce Tribe, BLM = Bureau of Land Management, IDFG = Idaho Department of Fish and Game
The South Fork Clearwater River Biological Assessment (USFS 1999) rates the biological
condition of 15 major watersheds in the SF CWR Subbasin for ESA listed species using the
Matrix of Pathways and Indicators of Water shed Condition - Local Adaptation for the
Clearwater Basin (NMFS et al. 1998). The watersheds assessed include the Red River,
American River, Crooked River, Newsome Creek, Leggett Creek, Tenmile Creek,
Twentymile Creek, Wing Creek, Silver Creek, Peasley Creek, Cougar Creek, Johns Creek,
Meadow Creek, Mill Creek, and the SF CWR main stem and face drainages. Summarized at
a watershed scale, the majority of water quality and habitat elements rate as "low" condition,
while watershed condition (road parameters), channel conditions, and species take
(harassment, redd disturbance, juvenile harvest) rate as "moderate" condition. Appendix K
contains the Environmental Baseline/Habitat Condition rating. Water quality and stream
46
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
habitat results for the 303(d) listed segments are discussed in Chapter 1, Stream
Characteristics.
Reference Stream Habitat Data
To better assess the condition of streams and rivers of the SF CWR Subbasin as they are
affected by sediment, we acquired two data sets for hydrologic systems considered to be in
good to near pristine condition. We acquired data sets that consisted of measures of cobble
embeddedness, percent pools, residual pool volumes, pool filling, bank full width, and
Rosgen channel type. Stream habitat data were acquired from the NPNF for Meadow Creek
in the Selway basin and Bargamin Creek that drains into the Salmon River. These two
systems lie immediately to the east of the SF CWR Subbasin, are largely unroaded or
otherwise disturbed, have similar geology and geomorphology to the forested streams of the
upper SF CWR, and have reasonable data sets because they are recognized by the NPNF as
being systems in good condition that can be used as reference. As a reference for the lower
SF CWR main stem, particularly within the basalts, we acquired data from the Wallowa-
Whitman National Forest for the Imnaha River above the Forest Service boundary. The
Imnaha River lies about 50 miles to the west of the SF CWR Subbasin in Oregon. It flows
down out of the Eagle Cap Wilderness through some relatively undisturbed basalt forest
lands into the Snake River.
To compare these reference data to streams and rivers in the SF CWR Subbasin, we acquired
two different data sets for the subbasin. We acquired the set of stream habitat data from the
NPNF, which covered portions of the upper basin streams. We also contracted with a private
company to collect these same data for the main stem SF CWR. The reference data are
presented in Appendix N.
Fish Data
Pertinent fish data including IDFG snorkeling surveys conducted for the SF CWR main stem
in 2000, historic influences on fisheries resources, and current status of salmonid populations
in the subbasin are discussed in Appendix D, Fisheries Resources. Tables 12 and 13 list
species known to be present in the SF CWR Subbasin.
A Fish TAG was convened to provide professional judgement regarding the status of local
fish populations, the habitat quality in the subbasin, and the effects of nonpoint source
pollutants. The group was comprised offish biologists and hydrologists from the National
Marine Fisheries Service (NMFS), NPT, NPNF, IDFG, USEPA, and BLM. In order to
prioritize restoration needs for fisheries in the subbasin, the group ranked the quality of the
82 water bodies for each species.
Water bodies were ranked for current fish population presence, current condition of habitat,
natural inherent water body potential, pollutant severity, and conservation/preservation
priority. Areas ranked "conserve" are areas currently considered to be of high habitat quality.
Appendix D shows the Fish TAG water body ranking chart and maps illustrating current
habitat condition by species, water body potential by species, and restoration potential.
47 Chapter 2
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Table 12. Salmon, trout, and char species present in the SF CWR Subbasin.
Common Name
Bull trout
Spring Chinook salmon
Snake River fall Chinook
Steelhead rainbow /redband trout
Westslope cutthroat trout
Brook trout (introduced species)
Scientific Name
Salvelinus confluentus
Oncorhynchus tschawytscha
Oncorhynchus tschawytscha
Oncorhynchus mykiss
Oncorhynchus clarki lewisi
Salvelinus fontinalis
Table 13. Other fish species known to occur in the SF CWR Subbasin.
Common Name
Pacific lamprey
Mountain whitefish
Northern pikeminnow
Chiselmouth
Bridgelip sucker
Sculpin
Black bullhead
Redside shiner
Speckled dace
Longnose dace
Smallmouth bass
Scientific Name
Lampetra tridentatus
Prosopium Williamson!
Rychocheilus oregonensis
Acrocheilus alutaceus
Catostomus columbianus
Cottus sp.
Ictalurus melas
Richardson/us balteatus
Rhinichthys osculus
Rhinichthys cataractae
Micro pterus dolomieui
Origin
Native
Native
Native
Native
Native
Native
Introduced
Native
Native
Native
Introduced
BURP Data and WBAG Assessment
IDAPA 58.01.02.053 establishes a procedure to determine whether a water body fully
supports designated and existing beneficial uses. The procedure detailed in the 1996 Water
Body Assessment Guidance (WBAG) (DEQ 1996a) and revised in 2002 (Grafe et al. 2002)
relies on physical, chemical, and biological parameters to identify water quality limited
segments that require TMDL development.
The General Surface Water Quality Criteria (IDAPA 58.01.02.200) for Idaho set forth
general guidance for surface water quality. The Surface Water Quality Criteria for Aquatic
Life Use Designations (IDAPA 58.01.02.250) set forth specific numeric criteria to be met for
particular beneficial uses. It also sets forth "narrative" standards that require a logical
accumulation of
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South Fork Clearwater River Subbasin Assessment and TMDLs
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evidence to determine whether a water body is supporting its beneficial uses. The WBAG
sets forth a methodology whereby a water body is first assessed using the numeric criteria for
a particular beneficial use, then identifies indices and methods for "narrative" assessment of
pollutants for which numeric criteria do not apply or are not available (DEQ 1996a; Grafe et
al. 2002). Sediment is the primary pollutant addressed by narrative means in the WBAG.
Idaho determines if its narrative sediment criteria are being met by collecting BURP data to
verify if viable communities of aquatic organisms are present and if evidence of beneficial
use exists in the stream. The BURP is a consistent scientific process used statewide for
collecting this data. The evaluatation of the BURP data using WBAG results in indices used
to compare water quality with the standards to determine beneficial use support status.
Figure 10 shows all of the BURP locations in the SF CWR Subbasin.
South Fork Clearwater River
Subbasin BURP sites
and 303(d) Listed Streams
Figure 10. Locations of BURP Sites Throughout the SF CWR Subbasin
BURP surveys were completed on the 303(d) streams in the SF CWR Subbasin during the
summer monitoring seasons of 1995, 1996, and 2000. The BURP surveys collected data on
fish, macroinvertebrates, and stream habitat. The data were analyzed through a systematized
and statistical process to determine whether a particular water body supports its beneficial
uses as described in the WBAG. The WBAG results using the 1996 version for the 303(d)
listed water bodies are presented in Table 14. Several streams have two BURP sites; and
therefore, two sets of results. These are the WBAG results that were used in the development
of the 1998 303(d) list (DEQ 1999). Table 15 presents the results of analyzing the same data
for the 303(d) listed water bodies using the 2002 version of WBAG.
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Table 14. WBAG version 1996 results for 303(d) listed water bodies in the SF
CWR Subbasin.
Water Body
Threemile Creek (L)c
Threemile Creek (U)d
Butcher Creek (L)
Butcher Creek (U)
Newsome Creek (L)
Newsome Creek (U)
Beaver Creek
Buffalo Gulch
Dawson Creek
Nugget Creek
Sing Lee Creek
SF Clearwater
Cougar Creek (L)
Cougar Creek (U)
Macro-
invertebrate
Biotic Index
(MBI)
3.30
2.61
3.04
3.42
3.79
3.71
2.18
2.93
4.13
4.23
3.22
*e
4.12
3.61
Salmonid
Age
Classes3
1
0
1
0
5+j
5?
3+j
1+j
1
1
2
*
0
Fish barrier
1/2 mi below
BURPf
reach
Temper-
ature
(°C)
16
15
23
18
19
16
13
9
9
11
15
*
13
12
Habitat
Index
(HI)
104
75
85
85
104
89
104
98
99
106
141
*
101
99
Support
Status"
NFS
NFS
NFS
NV
NFS
NV
NFS
NFS
NFS
NFS
NFS
*
NFS
FS
a+j = including juveniles
bFS = Full support, NFS = Not Ml support, NV = Needs verification, from 1998 303(d) list (DEQ 1999)
°L = Lower
dU = Upper
eTo be assessed using the Large River Protocol, which is not yet available
fBeneficial Use Reconnaissance Program
Within the 1996 WBAG protocol, the macroinvertebrate biotic index (MBI) is the primary
indices used to confirm beneficial uses support status. The MBI score is generated from
seven different qualities about macroinvertebrates (aquatic insects). Examples of the
qualities include diversity of species, richness of species diversity, species guilds, and
pollutant tolerance of insects present. An MBI score of 3.5 or more indicates that the
macroinvertebrate community is not impaired, a score between 2.5 and 3.5 indicates that
more information is needed, and a score of 2.5 or less indicates that the macroinvertebrate
community is impaired. Newsome Creek, Dawson Creek, Nugget Creek, and Cougar Creek
MBI scores indicate that these water bodies are supporting their beneficial uses.
The second indicator of full supprt of beneficial uses is the presence of salmonid species and
their young of the year in a stream. If three age classes offish, including juveniles (fish <100
mm in length) are present, then a water body is considered to be fully supporting salmonid
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spawning. If only two age classes including juveniles are present, then the habitat index (HI)
is considered. The HI utilizes both quantitative and qualitative stream data to determine the
level of habitat impairment within three ranges as compared to the ecoregion reference
condition. If the HI is 73 or greater, the water body is considered to be fully supporting its
beneficial uses. Less than two age classes of salmonids, including juveniles, indicates that
the water body is not fully supporting its beneficial uses. If no fish length data or no fish data
exist at all, then salmonid spawning beneficial use is not assessed (DEQ 1996a). The HI
scores and presence of salmonids in Beaver Creek and Sing Lee indicate that these water
bodies are supporting their beneficial uses.
Following a literal interpretation of the WBAG 1996 version, only Threemile Creek and
Butcher Creek data are not fully supporting their beneficial uses, with Buffalo Gulch needing
verification. The reasoning for maintaining the other water bodies on the 1998 303(d) list is
unknown at this time.
Table 15. WBAG version 2002 assessment of the 303(d) listed wadeable
streams in the SF CWR Subbasin.
Water Body
Threemile
Butcher
Dawson
Buffalo Gulch
Newsome
Nuggett
Beaver
Sing Lee
Cougar
SMI
MS
1.0
2.0
2.0
3.0
3.0
1.0
1.0
2.0
SHI
MS
1.0
2.0
3.0
3.0
3.0
3.0
3.0
3.0
SFI
MS
MS
2.0
3.0
ND
3.0
3.0
ND
ND
WB Score
1.6
1.0
2.0
2.7
3.0
3.0
2.3
2.0
2.5
SMI = Stream Macrobiotic Index; SHI = Stream Habitat Index; SFI = Stream Fish Index; MS = Multiple Sites;
ND = No Data.
In the WBAG version 2002, a Water Body Score of 2 or greater is passing. All of the water
bodies except Threemile Creek and Butcher Creek in the SF CWR have scores of 2 or
greater. Note that Sing Lee Creek, Cougar Creek, Beaver Creek, Dawson Creek, and Buffalo
Gulch, though passing, have the lowest scores.
These WBAG assessment results of the 303(d) listed water bodies above Harpster indicate
that sediment may not be significantly impairing water quality in the upper basin water
bodies. However, in the context of the narrative sediment WQS, we need to look at other
data types and reach a conclusion based on all of them. Using WBAG version 2002, these
BURP data by themselves cannot be used to make the status call because they are more than
5 years old and were collected using somewhat different methods. Also, WBAG version
2002 requires consideration of qualified non-BURP data, which is not shown in Table 15.
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For all the other BURP sites in the SF CWR Subbasin shown in Figure 10, assessments using
either the WBAG version 1996 or version 2002 indicate full support of beneficial uses.
Subbasin Flow Characteristics
The following gauging station data were obtained from a variety of sources including a 1995
Earthinfo® compact disc, the USGS, and a 1998 USEPA Storet compact disc (Table 16).
There are a number of active gauging stations in the subbasin, perhaps more than the typical
subbasin (Table 16). The USGS maintains an active gage on the SF CWR at Stites
(#13338500). Flow data have been collected here since 1964. The USGS also collects water
quality trend monitoring data at this site. The USGS has had two other gages on the SF
CWR in the past, one near Elk City (#13337500) at the confluence of the American and Red
Rivers (1944 to 1974), and one near Grangeville (#13338000, 1910 to 1963). The
Grangeville station was moved to Stites just prior to the removal of a dam that existed on the
SF CWR near the NPNF boundary. The NPNF has four active gauging stations in the
subbasin that have operated since 1986; on Red River, South Fork Red River, Trapper Creek,
and Johns Creek. Summary statistics are provided for the SF CWR stations in Tables 17-19.
Additionally, there were several stations across the basin that operated for very short periods
of time. Two stations established and operated in the late 1980s on Crooked River, one near
Orogrande (#13337510) and the other near the river mouth near Elk City (#13337520).
Station #13337200, at Red Horse Creek near Elk City, collected a few discharge
measurements in the late 1970s, as did stations on Leggett Creek near Golden (#13337540),
Peasley Creek near Golden (#13337700), and Sally Ann Creek near Stites (#13338200).
These data are of limited value due to their small amount.
USGS Station Information
Station #13338500 SF CWR at Stites
Drainage area = 1,150 square miles
• Elevation = 1,311 feet
• Latitude and Longitude = 46°05'12" 115°58'32"
• Location = ME 1/4 SE1/4 ME 1/4 sec.29 T32N R4E, Idaho County, on left bank 0.4 mile
upstream from county road bridge, 0.4 mile downstream from Cottonwood Creek, at river
mile 4.0.
• Extremes of Record = Maximum discharge 12,100 cfs, gage height 8.82 feet, on February
7, 1996; minimum discharge 48 cfs, gage height 2.39 feet, on November 30, 1987.
• Period of Record = October 1910 - April 1912, October 1964 - present.
• Extremes Outside of Record = 17,500 cfs, gage height 10.3 feet, on June 8, 1964.
Station #13337500 SF CWR near Elk City
• Drainage area = 261 square miles
• Elevation = 3,816 feet
• Latitude and Longitude = 45°49'29" 115°31'36"
• Period of Record = 1945 - 1974
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Station #13338000 SF CWR near Grangeville
• Drainage area = 865 square miles
• Elevation (Datum) = 1,830 feet
• Latitude and Longitude = 45°54'49" 116°00'17"
• Period of Record = 1911 - 1963, 2000 -- present
Station #13342450 Lapwai Creek near Lapwai
• Drainage Area = 235 square miles
• Elevation = 865 feet
• Latitude and Longitude = 46°25'36"'116°48'15"
• Period of Record = 1974 - present
The SF CWR has a snowmelt runoff dominated flow pattern. Highest mean monthly flows
occur in spring (April-June) and lowest flows occur in the fall and winter. It is likely that
April high flows are predominantly prairie and other lower elevation snowmelt runoff events,
whereas June high flows are predominantly high country snowmelt runoff. An average
spring runoff peak at Stites is about 5,000 to 7,000 cfs. The annual runoff from the subbasin
as measured at Stites averages about 12 inches. The largest flood had an estimated peak of
17,500 cfs. Floods occasionally result from snowmelt or rain-on-snow events between
November and March.
The major tributary streams in the upper forested region (American, Red, and Crooked
Rivers, and Newsome Creek) have runoff regimes very similar to the SF CWR (USFS 1999).
These streams typically do not have a flashy response to storms. Their moderately rolling
topography, relatively deep soils, forest vegetation, and cooler climate ameliorate rapid
runoff. Further down the drainage below Newsome Creek to the NPNF boundary the
tributary runoff regimes become more complex. High elevations in Johns and Tenmile
Creeks create later runoff peaks and cooler water inputs into the SF CWR later in the summer
(USFS 1999). Smaller tributaries in the canyon breaklands can be more flashy in response to
rain-on-snow events and thunderstorms that create localized flooding and debris torrents.
Tributaries on the prairie have very different runoff patterns than those in the forested region.
Peak flows can occur in mid-winter in addition to spring peaks due to rain-on-snow and/or
rapid snowmelt (USFS 1999). Low flows are reached earlier in the season and last longer
through the year than up-river tributaries.
Because the TMDLs developed in this document are heavily dependent on understanding the
flows in Threemile and Butcher Creeks, as well as Cottonwood Creek, we have estimated
flow patterns in these drainages based on flow data from Lapwai Creek. Lapwai Creek
drains the Camas prairie, at the same elevations as Threemile and Butcher Creeks, and has
many of the same vegetative, geologic, landform, and land use characteristics. We
constructed stochastic flow regimes for Threemile and Butcher Creeks based on the flow
patterns from Lapwai Creek following roughly the same procedure used in the Cottonwood
Creek TMDL (DEQ, NPT, USEPA 2000).
53 Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 16. USGS and Storet Stations in the SF CWR Subbasin.
Station #
13337500
13337510
13337520
13338000
13338500
13338500
13337200
13337540
13337700
13338200
209 Storet
Stations
Location
SF CWR near Elk
City
Crooked River
nearOrogrande
Crooked River
near mouth
SF CWR near
Grangeville
SF CWR at Stites
SF CWR at Stites
Red Horse Creek
near Elk City
Leggett Creek
near Golden
Peasley Creek
near Golden
Sally Ann Creek
near Stites
Throughout the
subbasin
Parameters
Discharge, monthly
and annual means
Discharge, water
temperature
Discharge, water
temperature
Discharge, monthly
and annual means
Discharge, monthly
and annual means,
peaks
WQ parameters,
summary statistics
Instant discharge,
temperature, specific
conditions
Instant discharge,
temperature, specific
conditions
Instant discharge,
temperature, specific
conditions
Instant discharge,
temperature, specific
conditions
WQ parameters,
summary statistics,
most very limited
Source3
Earth info
USGS, Boise
USGS, Boise
Earth info
USGS, Web site
Storet CD
Earth info
Earth info
Earth info
Earth info
Storet CD
Time Period
1911-1963
2000-present
1986-1989
1984-1988
1914-1963
1965-present
1972-1992
5 days in 1970s
11 days in 1973-
1981
11 days in 1973-
1981
5 days in 1970s
Limited, ending in
1998
aThese sources are where data were found. They are not necessarily the only location or the most complete set
of data for these stations. Earthinfo = http://www.earthinfo.com/, USGS = U.S. Geological Survey, USGS
Web site = http://waterdata.usgs.gov/nwis/sw/, Storet = USEPA computerized data base (USEPA undated).
Table 20 shows that maximum flows in Lapwai Creek generally occur in April, while in the
SF CWR Subbasin in general the maximum flows occur in May. The flows and sediment
delivery calculations from Cottonwood Creek figure prominently in understanding flows and
sediment in the SF CWR Subbasin. The mean daily flows for the 10 years (1992 through
2001) for Stites and Lapwai Creek (USGS data) and Threemile, Butcher, and Harpster
Creeks (derived data) were used for the sediment TMDL calculations. The plots of those
flows are presented in Chapter 5 as part of the sediment loading calculations.
54
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 17. Flow data (cubic feet per second) for the SF CWR near Grangeville
(#13338000), 1910-1963.
Month
October
November
December
January
February
March
April
May
June
July
August
September
Annual Mean
Ave. Mean Monthly
(cfs)
263
320
322
283
312
566
1945
3225
2197
654
218
191
875
Max. Mean Monthly
(cfs) (year)
1,032(1960)
1,319(1928)
1,161 (1928)
1,260(1928)
661 (1928)
1,443(1934)
3,390(1943)
6,489(1948)
4,821 (1948)
1,716(1955)
413(1948)
386(1959)
1,474(1948)
Min. Mean Monthly
(cfs) (year)
104(1937)
101 (1937)
117(1936)
94(1937)
119(1937)
197(1955)
714(1955)
932(1934)
510(1934)
175(1934)
88(1931)
93(1935)
494(1937)
From a sediment loading and sediment loading exceedance point of view, the mean monthly
flow rates are not the correct indicators of the major periods of sediment movement. As
discussed in detail in Chapter 5, it is the few days of extreme high flows that occur at a five-
year interval or less when the majority of sediment is moved in the SF CWR Subbasin.
Table 21 shows the statistical frequency of these extreme high flows based on the complete
records and USGS calculations (NWPP Council 2001), while Table 22 shows the dates and
magnitudes of extreme events at the Stites and Harpster USGS stations.
55
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 18. Flow data (cubic feet per second) for the SF CWR near Elk City
(#13337500), 1944-1974.
Month
October
November
December
January
February
March
April
May
June
July
August
September
Annual Mean
Ave. Mean Monthly
(cfs)
70
90
97
99
109
176
662
1137
585
146
57
53
274
Max. Mean Monthly
(cfs) (year)
263(1960)
247(1969)
285(1959)
428(1969)
373(1968)
479(1972)
1,216(1969)
2,001 (1948)
1,622(1964)
364(1955)
106(1964)
117(1968)
401 (1965)
Min. Mean Monthly
(cfs) (year)
25(1953)
29(1953)
31 (1953)
37(1955)
31 (1966)
49(1955)
226(1955)
413(1973)
207(1973)
74(1966)
27(1961)
25(1953)
133(1973)
The only high flow event at Lapwai that corresponds directly with the record at Stites is
1996, when the high flow at Lapwai was 5,010, the highest flow on record for the site. Other
high flows at Lapwai were 2,200 cfs in December 1976; 2,050 cfs in February 1982; 3,380
cfs in February 1986; and 3,190 cfs in January 1997.
Not evident in the flow data presented above, but discussed in Chapter 5, is the timing and
magnitude of extreme flows from Cottonwood, Butcher, and Threemile Creeks on sediment
loading to the lower main stem of the SF CWR. The discordance between the flow regimes
of Cottonwood, Butcher, and Threemile Creeks in relation to the rest of the subbasin leads to
a special set of problems for sediment delivered into the main stem from these three
tributaries.
Other flow data used in the TMDL calculations are those flow data collected at the time and
location of the total suspended solids (TSS), bedload, biological, and chemical sampling.
Those instantaneous flow data are presented in Appendix M with their associated water
quality monitoring data.
56
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 19. Flow data (cubic feet per second) for the SF CWR at Stites
(#13338500), 1910-1912, 1964-1998.
Month
October
November
December
January
February
March
April
May
June
July
August
September
Annual Mean
Ave. Mean Monthly
(cfs)
282
358
460
540
655
996
2089
3312
2507
831
292
247
1046
Max. Mean Monthly
(cfs) (year)
677(1976)
893(1969)
2,365(1976)
1,665(1969)
2,211 (1996)
2,387(1978)
3,549(1978)
5,528(1976)
5,706(1975)
2,063(1975)
528(1975)
473(1968)
1,711 (1976)
Min. Mean Monthly
(cfs) (year)
108(1988)
139(1988)
167(1988)
144(1988)
227(1994)
312(1977)
807(1973)
947(1992)
463(1992)
314(1973)
137(1973)
115(1987)
451 (1992)
Table 20. Mean monthly flows (cubic feet per second) for the SF CWR at Elk
City and Stites, and for Lapwai Creek at Lapwai.
Month
January
February
March
April
May
June
July
August
September
October
November
December
Elk City (cfs)
99
109
176
662
1,140
585
146
57
53
70
90
97
Stites (cfs)
556
663
994
2070
3,420
2,660
821
289
262
292
354
463
Lapwai (cfs)
72
124
208
223
136
54
17
8.2
12
17
24
61
57
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 21. Magnitude and frequency of instantaneous peak flow at gaging
stations in SF CWR Subbasin.
Station
SFCWR
Near Elk
City
SFCWR
Near
Grange-
ville
SFCWR
Near
Stites
Lapwai
Cr. at
Spalding
Period of
Record
1945-74
1911-20
1923-63
1964-99
1975-97
Daily discharge (cubic feet per second) recurrence interval
(years) and exceedance probability (%) based on indicated
period of record
2yr
50%
1,940
5,040
6,470
798
5yr
20%
2,610
6,800
9,480
1,880
10 yr
10%
3,050
7,990
11,600
2,960
25 yr
4%
3,610
9,540
14,400
4,800
50 yr
2%
4,030
10,700
16,500
6,590
100yr
1%
4,440
11,900
18,800
8,770
200 yr
0.5%
4,870
13,200
21,100
11,400
500 yr
0.2%
5,430
14,900
24,300
15,700
Table 22. SF CWR ini
during ma
Location
SF CWR near
Grangeville
SF CWR near
Stites
1933
6,090
NA
stantaneous peak discharges (cubic feet per second)
or flood events.
1934
2,380
NA
1938
6,740
NA
1948
12,600
NA
1957
8,910
NA
1964
NA
17,500
1974
NA
6.750
1996
NA
8,010
Subbasin-wide Water Column Data
Subbasin-wide water quality data is presented and discussed below.
Temperature
The temperature of stream water usually varies on seasonal and daily time scales, and differs
by location according to climate, elevation, extent of streamside vegetation, and the relative
importance of ground water inputs. Other factors affecting stream temperatures include solar
radiation, cloud cover, evaporation, humidity, air temperature, wind, inflow of tributaries,
and width to depth ratio. Diurnal temperature fluctuations are common in small streams,
especially if unshaded, due to day versus night changes in air temperature and absorption of
solar radiation during the day.
58
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Aquatic species are restricted in distribution to a certain temperature range, and many
respond more to the magnitude of temperature variation and amount of time spent at a
particular temperature rather than an average value (MacDonald et al. 1991). Although
species have adapted to cooler and warmer extremes of most natural waters, few taxa are able
to tolerate very high temperatures. Reduced oxygen solubility at high water temperatures can
compound the stress on fish caused by marginal dissolved oxygen concentrations.
Hourly stream temperatures were measured at various locations throughout the watershed
during the summers of 1999 through 2001. Summary statistics for these data are presented in
Appendix J. Water temperature criteria were exceeded in all streams monitored in at least
one of the three years when monitoring was conducted. Figure 11 illustrates the most recent
maximum weekly maximum temperature (MWMT) statistics for each site. Since the year
that these data were collected may vary from site to site, this information should not be used
to draw reach-by-reach comparisons; however, it is useful to illustrate the general pattern of
stream temperature across the subbasin.
Temperature Statistic (MWMT) (*F)
Less Than 50.0*F
50.0*F to 53.6*F
53.6*F to 57.2*F
57.2*F to 60.8*F
60.8*F to 64.4*F
64.4*F to 68.0*F
68.0*Fto71.6*F
Greater Than 71.6*F
Figure 11. Recent Annual Maximum Weekly Maximum Temperature (MWMT)
(°F) Temperature Statistic Values Observed in the SF CWR
Subbasin
Main Stem Temperature Condition
Stream temperatures within the main stem SF CWR generally follow two distinct
longitudinal (downstream) heating patterns: 1) water temperatures remain relatively stable in
the upper reaches (river mile [RM] 65 through 23.1); and 2) water temperatures increase
dramatically in bottom reaches (Figure 12). Tributary temperatures presented on this figure
are generally less than main stem temperatures. Tributary temperatures presented in this
figure are values observed at the mouth.
59
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
It is important to point out that water temperatures are already elevated at the headwaters
(beginning) of the SF CWR, which originates from the combined flows of the American
River and the Red River. Stream temperatures appear to decrease slightly as the river travels
immediately downstream from the confluence. This indicates that factors influencing stream
temperature conditions are dramatically different between the headwater reach of the
Clearwater River (RM 65 through 23.1), and the American River and Red River systems.
90 !
o 85 H
o
CM
.80 -
75 -
70 -
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
was a discrepancy between instream calibration temperature data and stream temperatures
calculated from the TIR data. Regardless, afternoon TIR data presented in Figure 13 can still
be used to illustrate relative temperature trends along the main stem of the SF CWR. These
trends correspond closely with heating trends observed in ground level data (Figure 12).
As can be seen in this image, stream temperatures increase dramatically downstream of the
Mt. Idaho Bridge. In addition, the diurnal variability (i.e., the difference between morning
and afternoon temperature) increased dramatically in these downstream areas. These results
indicate that factors that influence stream temperature conditions, such as vegetative and
topographic shade, width-to-depth ratio, and aspect, are dramatically different between these
two sections of the SF CWR.
90 n
:, FUR Temperature (6:00-7.06PM - 8/3/00)! (*F)
- FLIR Temperature (7:47-8.47AM - 8/3/00)) (*F)
Probe Data (6 PM - 8/3/00)
Probe Data (8 AM - 8/3/00)
0 5 10 15 20 25 30 35 40 45 50 55 60 65
River Mile (South Fork Clearwater River)
Figure 13. SF CWR Temperatures Derived from Instream Monitors and
Remote Sensed Thermal Infrared Imaging (TIR a.k.a. FLIR) for
August 3, 2000
Main Stem Diurnal Temperature Pattern
Measured stream temperatures within the main stem SF CWR on August 3, 2000, are
presented in Figure 14. This is the same period of forward-looking infrared (FLIR)/TIR data
collection (Figure 13). The diurnal profile presented in Figure 13 shows that temperatures
remain relatively constant throughout the course of the entire day in the upper portions of the
river. This indicates that very little stream heating (i.e., net energy input) is occurring within
this section of the river. Water temperatures measured at the Mt. Idaho Bridge (RM 24.4)
indicate that daily minimum water temperatures are elevated from values measured in
61
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
upstream sites. This can indicate a gradient change between this site and upper sites, which
would affect the amount of heat energy dissipation from the river into the surrounding
environment during the non-daylight periods. It is important to point out that daily
maximum temperatures are similar to upstream locations, indicating that stream heating
processes between these locations are similar.
Daily maximum water temperatures increase dramatically on the SF CWR at the Stites
monitoring location (RM 4.3). However, it is important to note that nighttime temperatures
are identical to the upstream location at the Mt. Idaho Bridge (RM 24.4), indicating that these
two sites are exposed to similar stream heating conditions during non-daylight periods.
Daytime temperatures measured at the Stites location illustrate a dramatic heating profile,
indicating large energy loads.
84 -,
80 -
76 -
72 -
68 -
64 -
60
Diurnal Stream Temperature (*F)
-A- Above Crooked Creek (RM 58.8)
-m- Above Leggett Creek (RM 47.9)
HX- Below 20 Mile Creek (RM 42.4)
-B- At Mt Idaho Bridge (RM 24.4)
-A- At Stites (RM 4.3)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Time of Day (8/3/2000)
Figure 14. Observed Diurnal Temperatures in the Main Stem SF CWR on
August 3, 2000
Red River Temperature Condition
As mentioned above, the SF CWR originates from the confluence of the American and Red
River systems. Accordingly, upstream temperatures of the SF CWR are directly dependent
on the temperature conditions within these two rivers. Measured stream temperatures
observed within Red River are illustrated in Figure 15. This profile indicates a large increase
in stream temperature within the upper reaches of this system (approximately RM 18 - 26),
which are maintained until the mouth (i.e., confluence with the American River) and
ultimately many miles downstream in the SF CWR (Figure 12). Figure 16 presents diurnal
temperatures measured within Red River on August 3, 2000. The shape of the diurnal
temperature profile remains relatively constant at all locations. However the diurnal range
62
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
(i.e., minimum and maximum temperatures) increases as the river travels downstream,
indicating greater heating conditions within these downstream reaches. Once again, elevated
stream temperatures within this tributary are maintained throughout the entire length of the
SF CWR.
85
80 -
• 75
'70 -
.65 -
60
66
50 ~
\
Qtteraon
Creek
Little Moose
Crftsk Creak
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32
River Mile (Red River)
Figure 15. Maximum Weekly Mean Temperatures Measured along Red River in
2000
80.0 -,
75.0 -
70.0 -.
iT 65.0 -
* L
t
D
«3 60.0 J
a
H 55.0 -
50.0 -
45.0 -
AC\ n
'I-U.U
C
• Red Rive abv Shissler Cr (RM 28.3)
A Red Rive abv Qtterson Cr (RM 263)
•Red Rive abv Trail Cr(RM 235)
A Red Rive abv Ditch Cr(RM 195) x ^
X Red Rive @ mouth X X X
*- X v
X X
x
X A A
X x x '-•'•AAA
! A A 4 A •
_ A • . . A
A A A . * ^ *
"" AA*A. *' '••
. * • •
• * A 4 * • "
" • t . "
2 4 6 8 10 12 14 16 18 20 22 0
Time of Day (August 3, 2000)
Figure 16. Observed Diurnal Temperatures in Red River on August 3, 2000
63
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
American River Temperature Condition
The American River is one of the two river systems that combine to form the main stem SF
CWR. Accordingly, upstream temperatures of the SF CWR are directly dependent on the
temperature conditions within the American River. Ultimately, American River water that
enters the SF CWR is comprised of several tributary streams within the American River
system (Figure 17). Temperatures illustrated on this figure show that water temperatures
increase dramatically within lower meadow reaches of the river system. These elevated
temperatures are maintained throughout the entire length of the SF CWR. Figures 18 and 19
illustrate that the diurnal temperature range increases dramatically within these lower reaches
of this river system.
€>
72.9
J^
South Fork Clearwater
MWMT (*F)(2000)
I Less Than 50.0*F
50.0*F to 53.6*F
53.6*F to 57.2*F
57.2*Fto 60.8*F
60.8*F to 64.4*F
64.4*F to 68.0*F
68.0*F to 71.6*F
Greater Than 71.6*F
American River
76.1
Red River
Figure 17. Measured Maximum Weekly Mean Temperature (°F) in the American
River System in 2000
64
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
82
78
i_ 74
£
g 70
0)
Q.
I 66
62 -
58
54
50
Big Elk Creek
-*- Big Elk Creek at USFS Boundary (Relative RM 10.3)
-•— Big Elk Creek above Little Elk Confluence (Relative RM 4.7)
-*- American River at Mouth (RM 0.0)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Time of Day (8/3/2000)
Figure 18. Diurnal Temperatures Measured in Big Elk Creek and the American
River (mouth) on August 3, 2000
5b^
82 -
78 -
£ 74-
0)
3
70 -
66 -
62 -
58 -
54 -
50
Little Elk Creek
- Little Elk Creek at USFS Boundary (Relative RM 9.1)
- Little Elk Creek above Little Elk Confluence (Relative RM 4.5)
-American River at Mouth (RM 0.0)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Time of Day (8/3/2000)
Figure 19. Diurnal Temperatures Measured in Little Elk Creek and the
American River (mouth) on August 3, 2000
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Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Threemile Creek Temperature Condition
Threemile Creek is an important tributary in the lower reaches of the SF CWR Subbasin.
Figure 20 illustrates calculated MWMT temperature statistics for three sites on this stream
system in 2000. As can be seen in this image, water temperatures are elevated throughout the
system. It is impossible to determine water temperature conditions within headwater reaches
of this creek because no data are available for this section of the stream. It could be assumed
that stream temperatures in the forested headwater reach are lower than values measured near
the city of Grangeville. This relationship was observed in other parts of the subbasin with
"headwaters" data (Figure 11).
The diurnal temperature pattern within this stream shows that the Grangeville WWTP
effluent discharging to the stream increased daily maximum temperatures on August 3, 2000,
but more significantly, daily minimum temperatures were dramatically elevated at this
downstream location on this date (Figure 21). The only conclusion that can be made from
these three data sets is that river temperature was already elevated upstream from the WWTP
effluent site (RM 12.9).
85
80
75
70 •
65
60 -
55
Start of
C.nyan
6 8 10 12 14
River Mile (Three Mile Creek)
16
18 20
Figure 20. Maximum Weekly Mean Temperatures Measured in Threemile
Creek in 2000
Seasonal Variation
Stream reaches within the SF CWR Subbasin experience prolonged warming starting in late
spring and extending into the fall. Maximum temperatures typically occur in July and
August (Figures 22, 23, and 24). The longitudinal downstream heating pattern described
above is maintained throughout the summer period, as can be seen in these figures.
66
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
86 -,
82
78
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a.
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58
54
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-A- Three Mile Creels Above STP (RM 12.9)
• Three Mils Creek Bebw STP (RM 12.8)
» Trree Mile Creek @ mouth
01 234567
9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Time of Day i8/3/2000)
Figure 21. Diurnal Temperature Measured in Threemile Creek on August 3,
2000
85
80
75
S. 60 •
? 55 -)*
1 50-
45
40
35
-if- Above Crooked Creek (RM 58.8)
-*- Above lejgett Creek (RM 47.9)
• Below20 Mile Creek (RM 42.4)
G At Ml Idaho Bridge (RM 24.4)
South Fork Clearwater
• ^ h3 N> cS ^* fo
ro o os w ^
Date (2000)
000
^2 fy t3
01
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
80 -i
75 -
£• 70
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g 65
Tfiree Mile Creek Above STP (12-9)
••'• TlireeMileCreekbelowSTP(12.8)
-*- TTiree Mile Creek (moulh)
.** A: *•/
*f if* rV
Three Mile Creek
s s
^ i K3
-l CD --J
s s
Date (2000)
to co
^ K>
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-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
are particularly sensitive to suspended sediment, although at high enough concentrations
adult fish are affected as well.
Turbidity is a measure of the extent to which light passing through water is scattered due to
suspended material. The Idaho turbidity standard states that turbidity shall not exceed
background by more than 50 NTU instantaneously or 25 NTU for more than 10 consecutive
days.
Total suspended solids concentrations include the amount of solids suspended in the water,
whether mineral (such as soil particles) or organic (such as algae). The TSS test measures
the actual weight of material per volume of water. A comprehensive review of TSS criteria
conducted by DEQ and USEPA (Rowe et al. 1998) suggests that 25 mg/L is a highly
protective threshold for salmonids. This threshold can be variable but likely ranges from
about 25 mg/L to 80 mg/L, depending on duration.
Bedload is material generally of sand size or larger that is carried by the stream on or
immediately above its bed. Excessive bedload causes the loss of spawning and rearing
habitat (i.e., cobble embeddedness, filling of pools, bed aggradation) and can lead to changes
in channel width that then lead to increased temperature and reduction in aquatic habitat.
The percentage of small gravel and finer particles less than 6.35 mm is often used as an
indicator of habitat quality for salmonid fishes. Deposition of fine sediments in spawning
substrate has been shown to be a major cause of embryo and larval mortality. Survival is
high only if the eggs receive an adequate supply of DO, an adequate flow of water through
the gravel to supply this oxygen, and necessary flows to remove metabolic wastes (Beschta
and Platts 1986). Percent emergence of swim-up fry has also been shown to be reduced by
fine sediment by a number of researchers. When particle sizes less than 6.35 mm reach 20-
25% of the total substrate, embryo survival and emergence of swim-up fry is reduced by 50%
(Bjornn and Reiser 1991).
When the fine textured bedload sediment is in excess of transport capacity, coarser particles
on the stream substrate tend to become surrounded or partially buried (embedded) by sand
and silt. Embeddedness quantitatively measures the extent to which the larger particles are
embedded or buried by fine sediment. Areas with high embeddedness have very little space
for invertebrates or juvenile fish to hide or seek protection from the current. Research has
noted lower aquatic insect and salmonid fish densities in areas with high levels of cobble
embeddedness. Levels above 30% are considered to indicate poor habitat conditions in the
Clearwater River Basin (NMFS et al. 1998).
It is generally believed that many of the streams 303(d) listed as impaired by sediment may
be impaired by both suspended sediment and bedload sediment, as they both affect salmonid
spawning. However, at the beginning of our analyses, we found that water column data
related to the hypothesized sediment pollution were few and disparate, and would have been
very difficult to use for a systematic analysis. Therefore, the NPT, DEQ, and USEPA
launched a monitoring effort to collect data on both TSS and bedload for the main stem of
the SF CWR, Threemile Creek, and Butcher Creek. A reasonable data set had been collected
and was available for Cottonwood Creek as a result of the TMDL there (DEQ, NPT, USEPA
69 Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
2000). The additional monitoring effort for this TMDL resulted in bedload and TSS data for
the SF CWR main stem at Stites and at a private bridge above Harpster, and TSS data for
Butcher and Threemile Creeks. These data, along with the derived rating curves, are
presented in Appendix M. Reasonable sediment rating curves were developed for both
bedload and TSS for the Harpster and Stites locations, and for TSS at the Butcher and
Threemile locations. The total bedload for Threemile and Butcher Creeks was derived from
instream erosion data and is discussed in Chapter 3 as a pollution source.
Chapter 5 presents the sediment loading calculations, wherein the sediment rating curves are
coupled with the daily flow records to identify whether turbidity exceeds the state WQS.
Appendix M shows the development of the relationship at each site between turbidity and
TSS. This sets the stage for relating the WQS of 25 NTU above background over 10 days to
loading calculations of TSS. The excess TSS loads plotted in Figure 25 are the sediment
loads above the load capacities based on the 25 NTU standard. Generally, the exceedances
occur in the January through May time period during the times when extreme high flows
occur. Figure 25 also includes blow-ups of two years' data to show that the exceedances do
occur in relatively narrow time frames in the January through May critical time period.
These are episodic events so they cannot be predicted any more closely.
The data indicate that TSS exceedances do not occur at Harpster. Based on these limited
data, it appears that TSS is not a pollutant of concern above Harpster. The TSS-based
loading allocations are indicated for Threemile and Butcher Creeks, and the lower main stem
water body of the SF CWR
70 Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
4500
f 400°
g 3500
iT 3000
8 2500
Jj 2000
% 1500
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Stites Bridge Excess Load
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c
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Butcher Creek Excess Load for Two Years
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Figure 25. Total Suspended Solids Excess Loads for Stites, Threemile Creek, and Butcher Creek
71
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Conclusions from the Water Column Data for the SF CWR Subbasin
The temperature data presented in Appendix J clearly show that all of the water bodies in the
SF CWR Subbasin monitored for temperature exceed the state WQS. It is likely that most if
not all, of the water bodies in the subbasin exceed the temperature standards. A temperature
loading analysis is warranted for the whole subbasin. The loading analysis will include point
sources for temperature problems. It will also include consideration that some level of
temperature standards exceedance is probably a natural condition in the SF CWR Subbasin.
The critical time period for the water temperature analysis is during the months of July and
August when air temperatures and water temperatures are highest, and when water flows are
lowest. Although stream temperature problems occur throughout the subbasin, the Fish TAG
identified those water bodies with the most critical temperature problems (Appendix D).
Turbidity, TSS, and flow data for Threemile Creek, Butcher Creek, and the lower main stem
SF CWR show exceedances of the WQS during periods of high flows throughout the three
water bodies. The periods of high flows occur episodically during January through May.
The exceedances occur with both fine and coarse sediment. Indicators of use impairment are
cobble embeddedness, bank instability, and a lack of pools in Threemile and Butcher Creeks,
and a lack of pools and cobble embeddedness in the main stem SF CWR. Sediment TMDLs
need to be developed for Threemile Creek, Butcher Creek, and the lower main stem SF
CWR.
For the 303(d) listed water bodies upstream from the mouth of Butcher Creek, water quality
limitations in relation to the WQS are much less clearly indicated by the data. Existing TSS
data coupled with flow data, presented in Chapter 5, indicate that the main stem and streams
upstream from Harpster are meeting the turbidity water quality standards. The general
consensus is that any water quality impairment upstream from Harpster is the result primarily
of sand-sized material.
Overall, the evidence is mixed whether a sediment loading analysis and TMDL is warranted
for the water bodies upstream from Harpster. WBAG assessments of BURP data from the
303(d) listed as well as all other water bodies above Harpster indicate that beneficial uses are
being supported. WBAG assessments are not available for the main stem water bodies for
lack of an appropriate data set and/or approved assessment tools. The sediment budget
developed in Appendix L identifies some of the 303(d) listed tributaries as having above
average sediment loading rates for the subbasin. However, the highest sediment loading
rates are for the main stem water bodies, and some non-303(d) listed tributaries. Except for
the main stem and middle Red River water bodies, all others in the upper basin have
sediment loadings less than 50% over natural background. Average cobble embeddedness
rates throughout the upper basin and main stem are elevated both in relation to reference
watersheds and generally accepted levels of cobble embeddedness for good salmonid
spawning. The Fish TAG identified self-supporting populations of salmonids throughout the
upper basin, but also identified about half the water bodies in the upper basin as being limited
by sediment.
72 Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
In the final analysis, the three parties considered all lines of evidence, including information
and input from the WAG and resource professionals, in relation to the state WQS. The three
parties could not agree on the need to write sediment TMDLs for the upper tributaries. The
parties did agree, however, that a sediment TMDL is warranted for the upper SF CWR main
stem and that land managers should be encouraged to reduce sediment loading throughout
most of the managed portions of the subbasin, including tributaries, to improve salmonid
habitat in the upper basin and contribute to the load reductions needed for the upper and
lower reaches of the main stem. To accomplish these goals, loading analyses should be
completed for control locations at the pour points for each of the four main stem water bodies
upstream from Butcher Creek. Load reductions of human-caused sediment for each of these
control locations should be proportionate to the load reduction calculated for the Stites
control location. Sediment load reduction allocations for each of the four locations will be
gross load reduction allocations, leaving the where and how of the load reductions to the
discretion of the WAG and local land managers.
For the sediment analysis of the upper main stem water bodies, the critical flow period is the
same as downstream water bodies: those episodic times of very high flow conditions that
occur from January through May. While it is generally believed that the primary impairment
to salmonid spawning is sand-sized bedload sediment, loading analyses will be for the whole
sediment load with the assumption that reducing the whole sediment load will result in the
necessary reduction of bedload.
Summary and Analysis of Existing Water Quality Data for Threemile Creek and
Butcher Creek
Threemile Creek and Butcher Creek are 303 (d) listed for a number of pollutants in addition
to sediment and temperature, including bacteria, dissolved oxygen, nutrients, and ammonia
(Threemile Creek only). These additional pollutants are discussed below for each of these
two water bodies.
Threemile Creek
Threemile Creek has been designated by the state of Idaho for salmonid spawning and
secondary recreation beneficial uses. The salmonid spawning WQS apply over the entire
reach of the creek. There are portions of the creek not far from the mouth blocked by
landslides, where the creek travels subsurface, which restricts fish migration during low
flows. In addition, a series of 2-meter falls occurs approximately 9.5 kilometers upstream
from the mouth, which may limit fish passage on a seasonal basis. Fuller et al. (1984)
documented rainbow/steelhead above this potential barrier at stream kilometer 10.3.
Threemile Creek data were collected biweekly (February 2, 2000, through January 22, 2001)
by DEQ at the six monitoring sites shown in Figure 26. Parameters sampled included
continuous temperature at the mouth, flow, pH, DO, turbidity, TSS, total and ortho-
phosphorous, nitrates and ammonia, and E. coli and coliform bacteria. Sporadic
measurements were taken at sites called "Big Barn" and "Headwaters."
73 Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Butcher Creek
Butcher Creek beneficial uses are currently undesignated by the state of Idaho. Prior to
designation, according to Idaho Code, "undesignated waters shall be protected for beneficial
uses, which includes all recreational use in and on the water and the protection and
propagation offish, shellfish, and wildlife, wherever attainable" (IDAPA 58.01.02.101).
Studies by the NPT and DEQ (Fuller et al. 1984, DEQ 1995, NPT 2002) have established
salmonid spawning as an existing beneficial use. Butcher Creek also has the beneficial uses
of primary and/or secondary contact recreation.
The salmonid spawning water quality criteria apply over the entire length of the Butcher
Creek, although there is a series of falls approximately 6 miles upstream from the mouth that
may limit fish movement upstream. This TMDL will use the mouth of the creek as the point
of compliance for meeting salmonid spawning water quality criteria.
Butcher Creek data were collected by the NPT monthly (February 27, 2001, through
February 26, 2002) approximately 1 mile upstream from its confluence with the SF CWR.
Parameters sampled included continuous temperature at the mouth, flow, pH, DO, turbidity,
TSS, total and ortho-phosphorous, nitrates and ammonia, andE. coli and coliform bacteria.
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STP Outlet
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Below STP
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December, 2001
Figure 26. Monitoring Sites on Threemile Creek
74
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Flow Characteristics
Instantaneous flows collected while monitoring Threemile Creek and Butcher Creek are
shown in Figures 27 and 28. Appendix M shows flow curves for the two creeks based on
extrapolation of these data and flow data from Lapwai Creek.
The minimum flow for all sites on Threemile Creek was measured on August 8, 2000, and
the maximum flow was measured on May 16, 2000 (Table 23). Although there was
consistent flow above the WWTP outfall, on two occasions the flow at the WWTP outfall
was greater than or equal to the flow below the outfall. On the average, the outfall
contributed 43% of the flow below the outfall. It contributed 30% of the flow, 50% of the
time.
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75
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
25
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Table 23. Monitored flows in Threemile Creek from February 22, 2000, to
February 6, 2001.
Mean (cfs)a
Maximum (cfs)
Minimum (cfs)
Above Outfall
2.01
7.60
0.14
Outfall
0.90
1.38
0.49
Below Outfall
3.32
10.35
0.49
Mouth
5.51
17.09
0.81
a cubic feet per second
During the entire monitoring period (February 2000 through February 2001) the area
received near average precipitation, and temperatures were slightly higher than normal
(Figure 29). However, during the summer, the region experienced lower than normal
precipitation and higher temperatures.
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Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
120
100
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FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC JAN FEB
Figure 29. Measured Monthly Temperature and Precipitation vs. 40 Year
Monthly Averages for Temperature and Precipitation
Peak flows occurred during the spring due to snowmelt. The WWTP outfall volume is nearly
constant year round, with an average of 0.90 cfs. The flow at the mouth was greater than 1.0
cfs during most of the year, except during late July and early August when the discharge
measured only 0.81 cfs. Immediately below the WWTP outfall, stream flows were above 1.0
cfs except for one June day when the discharge measured 0.76 cfs. However, the monitoring
point below the outfall may not be representative of upper Threemile Creek. The WWTP is a
constant source of water and adds a significant portion of the flow during the summer and
fall months.
Pathogens
Pathogens are a small subset of microorganisms (e.g., certain bacteria, viruses, and protozoa),
which if taken into the body through contaminated water or food, can cause sickness or even
death. Some pathogens are also able to cause illness by entering the body through the skin or
mucous membranes.
Direct measurement of pathogen levels in surface water is difficult because pathogens
usually occur in very low numbers and analysis methods are unreliable and expensive.
Consequently, indicator bacteria which are often associated with pathogens, but which
generally occur in higher concentrations and are thus more easily measured, are assessed. E.
co//', a type of fecal coliform bacteria, are used by the state of Idaho as the indicator for the
presence of pathogenic microorganisms.
77
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
The major sources of pathogens in the watershed include livestock grazing, confined
livestock management, wild game and waterfowl, and failing septic systems. Animals
dependent on the stream as a water source contribute bacteria directly to the stream in
addition to breaking down stream banks and grazing on streamside vegetation. This results
in reduced stream buffering and a increased likelihood of wastes entering the stream.
Because fecal coliform can survive for long periods of time in the stream substrate, bacterial
numbers may be influenced by past activities and can be resuspended by stream flow or
animal disturbance. E. coli counts may also increase with storm and runoff events, as
pathogens are washed into the stream. Figure 30 shows the measured E. coli bacteria
collected from Threemile Creek during the 2000-2001 monitoring period.
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The state of Idaho criteria for E. coli are not to exceed 126 colony forming units (cfu) per
100 ml as a monthly mean or 406 cfu per 100 ml as an instantaneous sample for primary
contact recreation. The secondary contact recreation criteria are the same as primary contact
recreation for the monthly mean, and not to exceed 576 cfu per 100 ml for an instantaneous
sample.
Threemile Creek is designated for secondary contact recreational use by the state of Idaho.
The instantaneous criterion for E. coli concentrations is not to exceed 576 organisms per 100
ml at any time. Eighteen exceedances of secondary contact criteria were documented at the
Threemile Creek monitoring sites: eight located at the site above the WWTP outfall, one at
the WWTP outfall, seven below the WWTP outfall, one at the Big Barn, and one at the
mouth. Generally high bacterial counts occurred during high stream flow (storm events).
Potential bacteria sources include storm water runoff from the city of Grangeville, livestock
78
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
grazing and/ or confinement adjacent to the creek, waterfowl and wild game, and failing
septic systems.
The WWTP is also a source of bacteria, but the concentrations are generally low.
Historically, a few exceedances of the fecal coliform permit limits occurred, but in recent
years fecal coliform concentrations have been well within the permit compliance limits of
100 cfu/lOOml. Low levels of fecal coliform are routinely detected in the WWTP effluent
although it is chlorinated.
Butcher Creek had no instantaneous exceedances of either primary or secondary contact
recreation during the 15-month sampling period (Figure 31). The highest E. coli levels
(instantaneous counts of 250 and 160) were associated with high flows and exceeded the
monthly average target of 126 cfu perlOO ml. This may indicate bacteria entering the stream
as a result of overland flow from rain events. Best management practices (BMPs) that reduce
sediment and heat loading in Butcher Creek may also reduce levels of bacteria. These
activities may include the removing cattle from areas of the creek, fencing, and re-
establishing riparian buffer zones. Although a TMDL is not warranted at this time for
pathogens, monitoring should continue to observe for potential exceedances.
300
250
200
150
HI
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§ 100
111
50
NM
E. coli monthly mean
NM
Figure 31. E. coli Monitoring Results for Butcher Creek
79
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Dissolved Oxygen
The Idaho criteria for DO in the water column for cold water aquatic life and salmonid
spawning is a one-day minimum of not less than 6.0 mg/L or 90% saturation, whichever is
greater. The criteria for intergravel DO for salmonid spawning is 6.0 mg/L or greater for a
weekly mean and 5.0 mg/L or greater for a daily minimum. The DO levels in a stream may
be reduced by excessive nutrient loading and consequent algae growth. The biological
decomposition of algae utilizes oxygen and may deplete it under low flow conditions.
Instantaneous DO levels in Threemile Creek were very close to a criteria deficiency during
three sampling events at the mouth (July 25, 2000 - 6.07 mg/L; August 8, 2000 - 6.03 mg/L;
and August 22, 2000 - 6.40 mg/L) (Figure 32). The results from this study are inconclusive
and follow-up studies will be undertaken in the future.
on
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-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
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Figure 33. Dissolved Oxygen Monitoring Results for Butcher Creek
Ammonia
Ammonia was measured in Threemile Creek and Butcher Creek as total ammonia, which
combines the forms of dissolved gas, ammonium hydroxide, and the ammonium ion.
Ammonia can be both toxic to aquatic animal life and provide a source of nitrogen to plants.
As temperature and pH increase in the stream so will the total ammonia level. The critical
period for salmonid spawning is April through October. The Idaho criteria establishes
ammonia limits depending on pH and water temperature. None of the ammonia
concentrations shown in Figure 34 exceed the WQS.
The Grangeville WWTP National Pollution Discharge Elimination System (NPDES) permit
allows releases up to 5.0 mg/L total ammonia as N into Threemile Creek. The WWTP
exceeded its limit once during the monitoring period.
The ammonia criteria were never exceeded in Butcher Creek (Figure 35), although during
August the temperature, pH, and ammonia levels were high (See Figures 35 and 37).
Both Threemile and Butcher Creeks, therefore, appear to be in compliance with the WQS for
ammonia and no TMDLs for ammonia will be developed. It is recommended that Threemile
Creek be removed from the 303(d) list for ammonia.
81
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Ofi
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0.035
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en
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0.015
0.01
0.005
Standard for high pH and temperature = 0.16 mg/L
NM
NM
NM
NM
Figure 35. Total Ammonia Monitoring Results for Butcher Creek
82
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
PH
Threemile Creek pH levels ranged from 6.21 to 8.88 at the mouth. Generally, pH averaged
7.6 for all the Threemile Creek sites at all times of the year with little seasonal fluctuation
(Figure 36). Butcher Creek's pH ranged from 7.5 to 8.64 for the sampling period (Figure
37). Generally the pH averaged 8.1 at all times of the year with little seasonal fluctuation.
10
7 -
DAbove Outfall
D Outfall
• Below Outfall
DMouth
Figure 36. pH Monitoring Results for Threemile Creek
10 -,
9
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Figure 37. pH Monitoring Results for Butcher Creek
83
Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Nutrients
Nuisance aquatic growth can adversely impact aquatic life and recreation. Algae of various
types grow in the water and on the beds of streams. Algae provide a food source for many
aquatic insects, which in turn serve as food for fish. Algae grow where the substrate is
suitable and sufficient nutrients (nitrogen and phosphorus) are available to support growth.
Flow, temperature, and sunlight penetration into the water all must combine with nutrient
availability to produce conditions suitable for photosynthetic growth. When nutrients exceed
the quantities needed to support primary productivity, algae blooms may develop.
Subsequent death and decay of algae creates an oxygen demand. If the demand is high
enough due to large algae blooms, DO concentrations in the water body may decline to low
levels that harm fish. Algae blooms and excessive rooted macrophytes can also physically
interfere with recreational activities such as swimming and wading and directly alter fish
habitat. In addition, decomposing algae can create objectionable odors, and some species
produce toxins that impair the agricultural water supply.
Nutrient limitations occur when a nutrient, usually phosphorus or nitrogen, is below the level
needed for algal growth in the water column. Influxes of these nutrients will stimulate algal
growth if other factors, such as light, temperature, and flow, are conducive to growth.
Alternatively, a system can have high enough levels of nutrients that growth is limited by
other factors besides nutrients, and nutrient levels must be decreased to limiting levels to
have an effect on algal biomass.
Idaho's narrative standard for nutrients states: "surface waters shall be free from excess
nutrients that can cause visible slime growth or other aquatic growths impairing beneficial
uses" (IDAPA 58.01.02.200.06). Salmonid spawning beneficial uses can be impaired when
excess algae decompose, resulting in depleted dissolved oxygen levels. Primary/secondary
contact recreation can be also impacted by visible slime and algae growth caused by
excessive nutrients when temperature and sunlight are not limiting. Salmonid spawning can
be impaired when excess algae decompose, resulting in depleted DO levels.
Phosphorus Compounds
Total phosphorus (TP) consists of both particulate and dissolved fractions of both organic
and inorganic phosphorus compounds. Dissolved phosphorus consists of all forms of
phosphorus in solution, whether organic or inorganic. Phosphorus in solution in surface
waters occurs almost solely as phosphates. Orthophosphate (PO4 3) is the form that plants
can use, and thus best correlates to short-term stimulation of growth.
In order to prevent nuisance algae growth and dissolved oxygen problems, USEPA (1986)
developed a national guideline for streams of 0.1 mg/L TP. More recently USEPA (2000)
developed a nutrient criteria for total phosphorus of 0.030 mg/L TP specific to Columbia
Plateau subecoregion streams. These criteria provide USEPA's most recent
recommendations to states and authorized tribes for use in establishing their water quality
standards. USEPA further recommends that, wherever possible, states develop nutrient
criteria that fully reflect localized conditions and protect specific designated uses.
84 Chapter 2
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Total phosphorus in Threemile Creek ranged from 0.06 mg/L (headwaters) to 4.55 (WWTP
outfall). Ortho-phosphorus concentrations ranged from 0.04 mg/L above the WWTP outfall
to 3.72 mg/L at the outfall, with an overall average of 0.93 mg/L (Table 24). The WWTP
outfall had the largest range in values, while the mouth had the lowest range. The ratio of
ortho-phosphorus to total P ranged from 0 to 1 and averaged 0.47 (above outfall), 0.82
(outfall), 0.85 (below outfall), and 0.72 (mouth).
Table 24. Ortho-phosphorus concentrations on Threemile Creek (February 22,
2000, to February 6, 2001).
Mean (mg/L)
Maximum (mg/L)
Minimum (mg/L)
Above Outfall
0.05
0.09
0.02
Outfall
1.79
3.72
0.15
Below Outfall
1.03
2.87
0.30
Mouth
0.22
0.31
0
Concentrations of P in ground water ranged from 0.01 to 0.28mg/L on the Camas Prairie
with a median of 0.05 mg/L (Crockett 1995). A well sampled in the Threemile Creek
watershed had average P levels of 0.03 mg/L (Hagen 2002).
Grangeville's WWTP contributes 43% of the flow to the creek and a concentration of 1.79
mg/L P on an annual average with peak concentrations in the spring and summer. At the
WWTP outfall monitoring point, the concentration of ortho-phosphorus is high in the late
winter and summer and low in spring and late fall/early winter (Figure 37). The facility
controls concentrations of P entering the creek using holding tanks, which settle out solids
containing P. High P levels from the WWTP in the late winter and early spring may be a
result of sediment entering the city's sewage system through leaks in pipes during times of
high precipitation. The city of Grangeville has recently begun a program of maintaining the
sewer pipes to reduce inflow.
There is no seasonal change in ortho-phosphorus above the outfall or at the mouth of
Threemile Creek (Figure 38). Above the outfall, P concentrations in the creek may be
influenced by storm water runoff from Grangeville, the natural background levels in soils,
geological sources, and land management activities such as livestock grazing. The mouth of
Threemile Creek has a fairly constant concentration of P.
Total phosphorus in Butcher Creek ranged from 0.1 to 0.49 mg/L, and averaged 0.16 mg/L.
There were three exceedances of USEPA recommended levels for TP during the 15 months
monitored (0.49 mg/L, 0.23 mg/L, and 0.24 mg/L). Ortho-phosphorus, the form of P most
readily available for plant uptake, ranged from 0.054 mg/L to 0.109 mg/L, and averaged
0.094 mg/L (Figure 39). Five samples exceeded 0.1 mg/L ortho-phosphorus at the mouth of
Butcher Creek.
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
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October 2003
Nitrogen Compounds
In surface waters, nitrogen (N) occurs as nitrate (NOs), nitrite (NO2), ammonia, and organic
N. Nitrate-nitrite covers most of the nitrogen available in surface waters. Ammonia is also
available for plant uptake. Total Kjeldahl nitrogen (TKN) is the fraction of organic N bound
in the aquatic organisms and unavailable for plant growth. Upon decomposition, organic N
can be converted to inorganic N and become available for plant uptake. Total nitrogen (TN)
is composed of inorganic and organic nitrogen.
In order to prevent nuisance algae growth, USEPA (1993) developed a national guideline for
streams of 0.3 mg/L TN. More recently, USEPA (2000) developed a recommended nutrient
criterion of 0.22 - 0.36 mg/L TN specific to the Columbia Plateau subecoregion streams.
A ground water well monitored by the Idaho Department of Water Resources (IDWR) within
the Threemile Creek watershed contained very low levels of NOs. Nitrate concentrations
were less than 0.05 mg/L in seven out of eight years, with a maximum concentration of 0.074
in!996(Hagen2002).
Threemile Creek average annual TN levels exceeded 0.30 mg/L at each monitoring point
along Threemile Creek, except at the headwaters. The TN concentrations ranged from 0.16
mg/L above the outfall to 24.95 mg/L at the outfall, with an overall average of 7.14 mg/L
(Table 25). The largest range in values was seen below the outfall and the lowest range was
above the outfall. The ratio of inorganic N to TN ranged from 0-1 and averaged 0.25 (above
outfall), 0.91 (at outfall), 0.88 (below outfall), and 0.86 (mouth).
Table 25. Total nitrogen data summaries for Threemile Creek (February 22,
2000 to February 6, 2001).
Mean (mg/L)
Maximum (mg/L)
Minimum (mg/L)
Above Outfall
0.35
1.16
0.16
Outfall
17.4
24.95
12.37
Below Outfall
8.72
22.22
2.47
Mouth
2.31
8.33
0.23
Concentrations of TN above the WWTP outfall after the creek has passed through some
grazing land, farmland, and the city of Grangeville averaged 0.35 mg/L and had a maximum
of 1.16 mg/L. However, the summer month values were lower than 0.30 mg/L.
At the outfall monitoring point, the concentration of TN is highest in the late winter and
summer and lowest in the spring and late fall/early winter (Figure 40). The WWTP outfall
appears to influence levels downstream. Although there is no seasonal change in TN above
the outfall, at the mouth TN concentrations are greater in the winter and spring than in the
summer and early fall.
Sources of N in the watershed include the WWTP, livestock management, and agricultural
practices, including fertilizer application.
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30
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Figure 40. Total Nitrogen Monitoring Results for Threemile Creek
The TN concentrations in Butcher Creek averaged 1.24 mg/L (Figure 41). The highest levels
occurred in January, February, and March and correlated with high stream flows. The TN
levels exceeded 0.30 mg/L for 11 out of 14 samples. However, during the summer growing
season, values were near or just above this target (0.33 mg/L on June 26 and August 1,
2001).
The concentrations of TN at the mouth of Butcher Creek show a high degree of seasonality
and relationship with flow: highest levels in the spring, then decreasing in the summer. Due
to the N levels approaching 0.3 mg/L during the summer growing season/critical time
period, and no violations of the DO criteria, it is concluded that beneficial uses are currently
being met. Although no TMDL is established for N at this time, consistently high fall and
winter values (ranging from 0.5 to 5.01 mg/L) warrant further observation. Best
management practices that reduce temperature and sediment pollution in the watershed (i.e.,
vegetative buffers, fences, livestock exclosures, and grazing management) should also
effectively reduce levels of N. Follow-up implementation effectiveness monitoring is
recommended to ensure an overall reduction in N loading.
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
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Figure 41. Total Nitrogen Monitoring Results for Butcher Creek
Other Water Quality Studies
An Idaho Division of Environmental Quality report (DEQ 1979) summarized a study
conducted on Threemile Creek in 1976 and 1977. The purpose was to assess the effect of
Grangeville's WWTP on the stream and develop effluent limitations for the discharge as
required for an NPDES permit. A secondary purpose was to determine if Threemile Creek
met requirements for Class A waters. Five sampling stations were selected and monitored
during high and low flow periods. Field and laboratory analyses were carried out for each
site and date. Bacteria levels were well above the standard and both P and N levels were
found in high concentrations (Table 26).
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Table 26. Total phosphorus, nitrate-nitrogen, and bacteria for all stations and
dates along Threemile Creek.
Total P (mg/L)a
NO3-N
(mg/L)b
£. co//
(cfu/100ml_)c
Above Grangeville
November 17, 1976
November 18, 1976
June 7, 1977
JuneS, 1977
0.18
0.15
0.14
0.17
0.01
0.02
0.03
0.01
200
200
900
740
Above Outfall
November 17, 1976
November 18, 1976
June 7, 1977
JuneS, 1977
0.13
0.20
0.19
0.25
0.10
0.01
0.02
0.11
200
400
680
4500
1 00 feet Below Outfall
November 17, 1976
November 18, 1976
June 7, 1977
JuneS, 1977
6.55
5.44
3.55
2.44
11.41
10.20
4.33
4.52
200
200
855
5400
1 .25 miles Below Outfall
November 17, 1976
November 18, 1976
June 7, 1977
JuneS, 1977
5.75
6.55
2.24
2.98
12.60
9.56
4.55
4.64
200
200
3100
780
3 miles Below Outfall
November 17, 1976
November 18, 1976
June 7, 1977
JuneS, 1977
3.54
5.51
1.84
2.55
8.85
10.25
1.62
4.52
200
200
380
520
a Total phosphorus in milligrams per liter
b Nitrate-nitrogen in milligrams per liter
0 Colony forming units per 100 milliliters
The study concluded that the WWTP contributed to the pollution of the creek through
additions of nutrients, and that the bacterial problem was caused by nonpoint source pollution
from livestock and poor private septic facilities upstream of the WWTP. The
recommendations at the time were to upgrade the WWTP to reduce nutrients and revise the
chlorinating procedure to maintain acceptable bacteria levels. Best management practices for
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the nonpoint sources were identified for agricultural runoff, summer livestock grazing, and
winter livestock holding areas.
On the Clearwater Plateau continued sampling for nutrients and pesticides by IDWR and the
Idaho Department of Agriculture (IDA) have documented significant zones of ground water
contamination exceeding the 10 mg/L drinking water standard for NOs-N, with a maximum
80 mg/L NOs-N measured in the sampling. This contamination appears to be located in
geologic environments where granitic outcrops exist as islands surrounded by basalt.
In April 1995, IDWR produced a Water Information Bulletin (Crockett 1995) that
summarized the results of a ground water monitoring program carried out from 1991 through
1993. One of the objectives of the study was to determine the background levels in ground
water in the aquifers of Idaho. The results indicate that the Clearwater aquifer contains
elevated background levels of TP and NOs (Table 27).
Table 27. Range and median of nutrients in the Clearwater aquifer measured
from 1991 through 1993 (Crockett 1995).
Range
Median
Nitrate
(mg/L)a
0.05-19.00
0.38
Ammonia
(mg/L)
0.01 -0.29
0.01
Phosphorus
(mg/L)
0.01 -0.28
0.05
a milligrams per liter
In 1998 DEQ produced a report on the reconnaissance of NO2 and NO3 in the Camas Prairie
ground water. Although the report indicates elevated levels of NOs on the prairie, the single
well within the Threemile Creek watershed contained very low levels of NOs. Nitrate
concentrations were less than 0.05 mg/L in seven of eight years (maximum was 0.074 mg/L
in 1996), while concentrations of P averaged 0.03 mg/L (Hagen 2002).
Threemile Creek Conclusions
Flow was below normal and air temperatures were higher than normal during the summer
months that Threemile Creek was monitored. The low flow and high temperatures could
indicate a year where there may have been less recreational use and higher than normal
concentrations of pollutants in the creek.
Pathogen levels in the creek are above the secondary contact criteria set by the state.
Potential sources include grazing/livestock operations, septic systems, and waterfowl and
animals.
Dissolved oxygen levels were borderline at the mouth on two occasions and no data were
available to evaluate diurnal DO sags. Further monitoring to verify DO levels at critical
times is warranted
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In-stream ammonia concentrations were below the criteria set by the state of Idaho. The
Grangeville WWTP discharges ammonia and is well within its permit limit. Since ammonia
levels are below criteria, a TMDL will not be written. It is recommended that Threemile
Creek be delisted for ammonia.
The nutrient levels in Threemile Creek are generally an order of magnitude or more higher
than the USEPA "Goldbook" guidelines (USEPA 1986). Nitrogen levels above the WWTP
outfall are lower than the 0.3 mg/L guideline. At the WWTP outfall and below it, the TN
concentrations are much higher and are a cause for concern. At the mouth of the creek the
level of TN tends to be seasonal, decreasing in the summer when the concentration at the
outfall reaches its maximum. This may indicate that plants are taking up the TN.
Phosphorus concentrations are at or below the USEPA guidelines above the WWTP outfall,
but are higher than the guidelines at and below the outfall. The TP concentrations at and
below the outfall also increase in the spring and summer. The WWTP outfall directly
influences the site below it. There are no indications that the concentration of TP has any
seasonality at the mouth; the concentration of TP remains at a steady 0.30 mg/L regardless of
flow, temperature, or any other parameter measured during this monitoring period.
Due to the significantly elevated levels of TN and TP, these nutrients were considered for the
development of TMDLs. The deleterious effects of high and/or unbalanced nutrient levels,
i.e., nuisance algal growth and/or low DO, can be controlled if nutrient levels are returned to
levels that limit algal growth.
Butcher Creek Conclusions
There were no instantaneous exceedances of either primary or secondary contact recreation
E. coli criteria during the 15-month sampling period, although on two occasions levels
exceeded 126 cfu. Since E. coli concentrations were below criteria on all sampling dates, a
TMDL will not be written. It is recommended that Butcher Creek be delisted for bacteria.
Dissolved oxygen levels were never low enough to cause a concern and may indicate the lack
of excessive algae growth in the creek at the monitoring site. Since the DO concentrations
were above the criteria on all the sampling dates, a TMDL will not be written. It is
recommended that Butcher Creek be delisted for DO.
The nitrogen levels in Butcher Creek are generally higher than the USEPA guidelines, and
generally occur in winter during periods of high flow. Phosphorus levels were generally
within the guidelines set by USEPA. Nitrogen levels are elevated, but there is no indication
that there is a DO or nuisance algae problem. A TMDL for nutrients will not be written;
however, the implementation of the TMDLs being written for temperature and sediment is
expected to lower the N levels.
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Summary and Analysis of Existing Water Quality Data for Lucas Lake
Lucas Lake is a small, locally named water body that is 303(d) listed for sediment. Based on
a DEQ report by Steed (2002), Appendix P, Lucas Lake supports beneficial uses of primary
contact recreation and cold water aquatic life.
Lucas Lake was originally listed in 1994, based on earlier BLM reports that indicated
possible problems with sediment. Since the lake lies in a placer mining zone, DEQ
monitoring included a screening for toxic substances (metals). DEQ sampled the lake in
December 2001 and again in June 2002. The results from the sampling are shown in
Appendix N.
The TSS concentrations from both sampling periods are below the 4 mg/L detection limit.
Although turbidity is not reported, it is unlikely that 4 mg/L could correlate to anything close
to the WQS of 50 NTU above background. (A handwritten note of the lab sheet indicates an
NTU reading of 0.80 NTU.)
The metal screening did not indicate any problems with toxic metals.
It is recommended that Lucas Lake be removed from the 303(d) list for sediment.
2.4 Data Gaps
Data gaps identified in this section provide readers with an idea of the amount of error
involved in the analyses, and set the stage for research and data development necessary to
improve the quality of these analyses.
Flow
In order to do flow-based analyses for sediment TMDLs, it would be helpful to have actual
flow measurements, rather than extrapolating from existing data sets. While the level of
error introduced by extrapolated flow is probably less that the error in the sediment yield
curves, better flow data is important to understanding water quality.
We did not have continuous flow data for the points above and below the WWTP at
Grangeville, and virtually no flow data for any of the other point sources. The effects of
point sources for nutrients, temperature, and sediment are all dependent on some kind of flow
estimation that corresponds to water quality data of the effluent.
Water Column Data
Diurnal DO monitoring is needed to determine the effects of the Grangeville WWTP on DO
levels in Threemile Creek.
Intergravel DO data would be helpful in determining if the criteria are being met for
salmonid spawning in Threemile Creek and Butcher Creek.
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Increased frequency of sampling for E. coli to more accurately determine criteria
exceedances and genetic fingerprinting to determine the source of pathogens would be
helpful in Threemile Creek and Butcher Creek.
An analysis of streambed and bank sediments is recommended to determine exchange
coefficients for phosphorus in order to evaluate effects of phosphorus in the system.
There are no good data sets for background turbidity and TSS to relate to the state WQS.
Our estimates of background are based on the sediment budget and; therefore, incorporate the
huge errors involved in translating sediment source data to in-stream sediment results.
Similarly, more extensive turbidity and TSS data throughout at least the lower part of the
basin, over several years, would improve the reliability of our sediment loading analyses.
For the most part, the data set we have applied to the loading analysis would be considered
below the minimum necessary by most professionals.
We attempted to collect and model bedload data, realizing that some sort of quantification
would be necessary to write the TMDLs. We were only able to collect a minimal amount of
bedload data for the Stites and Harpster sites, yet the impairment we are trying to address
throughout the subbasin above Harpster is bedload. Bedload data for all of the 303(d) listed
water bodies would have been helpful. We failed in our modeling effort because we were
unable to collect enough data to get the model to work reliably.
More systematic monitoring on an annual basis of the effects of suction dredging on water
column and substrate sediment levels would allow better quantification of sediment loading
impacts from this industry.
Temperature
Continuously recorded stream temperature data exist for a large number of sites in the SF
CWR Subbasin. Many of these sites are at the mouths of streams—the warmest locations.
A few streams have several temperature recording sites such that the beginning of a linear
temperature profile can be developed. However, for the most part, we lack information about
stream temperatures along the full lengths of any stream. We have neither recorded data for
temperature profiles, nor stream parameter and heat loading data to be able to model the
profiles. We assume that the stream temperature data from one or a few sites within a given
water body represent the temperature profile for the whole water body.
The narrative part of the Idaho WQS identifies temperature (heat) pollution to be controlled
and regulated as that part of heat loading which has resulted from human activity, as opposed
to the level of heat loading or stream temperature that existed prior to human intervention.
We do not have data or models that quantify the level of heat loading or stream temperatures
prior to human intervention.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Biological and Other
We have no baseline data for the condition offish populations and their spawning habitat, or
other physical/hydrologic data prior to human intervention in the subbasin. We attempt to
overcome this deficiency with data from reference sites, modeling, and professional
judgement.
We acquired stream habitat data sets from reference watersheds and compared them to
streams in the SF CWR Subbasin. Cobble embeddedness is the primary parameter for which
we could quantify the differences, but we were unable to determine the relationship between
percent cobble embeddedness and sediment loading. Much better reference data would be
useful to be able to fully assess the impact of human activity in any particular water body.
Currently data is lacking in order to quantify the effects of agricultural chemicals on stream
biota and their accumulation in fish tissue. A study conducted by USEPA and the Columbia
River Inter-tribal Fish Commission in 1996-97 detected 92 chemicals in fish tissues collected
in the Columbia Basin, including the Clearwater River (USEPA 2002). The concentrations
of pesticides were higher in the resident species, especially mountain whitefish, white
sturgeon, largescale sucker, and whole body walleye than in anadromous species. Of the
anadromous fish species, Pacific lamprey had higher levels of poly chlorinated biphenyls
(PCBs). This appears to be associated with the high amount of fat in these fish types since
PCBs and pesticides are readily absorbed by fats. The NPT will begin assessing fish tissue
for heavy metals and volatile organic compounds (including pesticides) as part of their
Environmental Monitoring Assessment Program (EMAP) in 2003. Studies of the effects of
agricultural chemicals on stream macroinvertebrates (insects) have not been done.
Beneficial Uses
Beneficial use support status assessment for the main stem SF CWR is not available at this
time. The assumption was made that the main stem is not fully supporting its beneficial uses,
but data are largely nonexistent to support this assumption.
While there is ample information in the literature relating sediment and/or temperature to fish
spawning and reproductive health, there is little site-specific data linking sediment and/or
temperature in the SF CWR Subbasin to its beneficial uses.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
3. Subbasin Assessment - Pollutant Source Inventory
This section summarizes point and nonpoint sources of pollutants in the SF CWR Subbasin.
3.1 Sources of Pollutants of Concern
The primary nonpoint pollution sources in the SF CWR Subbasin are forestry, grazing,
agriculture, mining, roads, and storm water runoff. Additional sources include natural and
road-related mass failures. Agricultural related nonpoint source pollution is caused by tillage
practices and livestock management. Potential impacts to water quality also stem from
livestock grazing. Forestry related nonpoint pollution sources include forest roads, skid
trails, stream crossings, and loss of stream shade within riparian areas.
Storm water related pollution is caused by construction activities, residential and business
activities, roadways, and parking lots. Discrete facilities within the watershed such as mills
and gravel pits also contribute storm water runoff. For the sites not currently managed under
the USEPA NPDES Storm Water Program, the TMDL pollutant loads and allocations have
been grouped with nonpoint storm water discharge activities. Activities that are covered by
the storm water program are addressed under point source discussions.
Point Sources
Several types of point sources exist within the SF CWR Subbasin, including municipal
WWTPs, suction dredge mining operations, and storm water runoff. Point sources are
generally minor contributors to the loading of the most significant pollutants in the SF CWR
Subbasin (temperature, sediment, nutrients and bacteria), when compared to nonpoint source
loading. However, the Grangeville wastewater treatment plant (WWTP) is a significant
contributor to nutrient and heat loading in Threemile Creek.
Municipal Wastewater Treatment Plants
Five municipal WWTPs exist within the SF CWR Subbasin: Kooskia, Stites, Grangeville,
Elk City, and Red River Ranger Station. Each of these facilities has been issued an NPDES
permit by USEPA to discharge wastewater to waters of the United States. These permits
contain conditions and limits for certain pollutants based on the design flow for each facility
and have a five-year life. The USEPA reissued NPDES permits for Kooskia, Stites, Elk City
and Red River Ranger Station in October 2002. Typically, reissuance of NPDES permits
should occur immediately following completion of a TMDL, so that wasteload allocations
for point sources in the TMDL can be incorporated into the permit. However, due to delays
in initiating work on the SF CWR TMDL, the NPDES permits for all facilities except
Grangeville have already been reissued. Table 28 lists the five municipal WWTPs, and
identifies existing permit limits and the design flows. Figure 42 shows their locations in the
SF CWR Subbasin
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South Fork Clearwater River Subbasin Assessment and TMDLs
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Table 28. NPDES permitted point sources in the SF CWR Subbasin.
Source
City of
Kooskia
City of
Stites
Elk City
Red
River
Ranger
Station
City of
Grange-
ville
Permit #
ID-002181-4
ID-002034-6
ID-002201-2
ID-002069-9
ID-002003-6
Expiration
Date
9/30/07
9/30/07
9/30/07
9/30/07
12/29/92
Location
Kooskia
Stites
Elk City
S.F. Red
River
Grangeville
Receiving
Water
SFCWR
SFCWR
Elk Creek
South Fork
Red River
Threemile
Creek
Permit
Limits
BODb
TSSC
TRCd
Fecal6
BOD TSS
TRC,
Fecal
BOD TSS
TRC
Fecal
BOD
TSS
BOD TSS
TRC
Fecal TAf,
PH
Discharge
Volume
(MGDa)
0.20
0.070
0.12
0.0063
0.88
aMillion gallons per day
bBiological oxygen demand
°Total suspended solids
dTotal residual chlorine
Tecal coliform bacteria
fTotal ammonia
The most significant pollutants discharged from WWTPs include nutrients (N and P),
bacteria (E. coli, fecal coliform, etc.), sediment (TSS), oxygen demanding materials
(biological oxygen demand [BOD]), and heat. Depending on the concentrations of these
pollutants in the effluent, and the magnitude of the discharge compared to the stream flow,
WWTP discharge can be an exceedingly minor contributor or a major contributor. Kooskia,
Stites, Elk City, and the Red River Ranger Station discharges are relatively small in
comparison to stream flow. However, the discharge from the Grangeville WWTP can be
quite significant in comparison to the flow in Threemile Creek, particularly during the
summer and fall. More specific discussions of pollutant loading from these facilities are
included in later sections.
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NPDES Locations in the
South Fork Clearwater River Subbasin
NPDES Sites
NPDES Locations
SF Clearwater 4th Field HUC
303(d) Listed Streams
Ownership
| | B.L.M.
NezPerce Tribe
Forest Service
Open Water
| | Private
State of Idaho
Red River R.S.
5 10 Miles
April 2003
Figure 42. Locations of NPDES Permitted Sites in the SF CWR Subbasin
Suction Dredge Mining
Gold was discovered in the SF CWR Subbasin in 1861, with relatively active and intense
hydraulic and dredge mining occurred off and on until World War II. Since that time, there
has been far less mining activity, although there was a surge in suction dredge mining in the
1970s as a result of increasing gold prices.
A suction dredge typically consists of a floating platform on which a pump and sluice box are
mounted, with a 2" to 12" flexible suction hose that reaches the bottom of the stream. The
gasoline-powered pump is used to lift gravel from the stream bottom through the hose onto
the sluice box mounted on a floating platform for gold recovery. The objective is to get to
bedrock where it is most common to find the largest deposits of gold. The intake size of the
hose and the horsepower of the engine driving the pump determine the volume of gravel that
a dredge can potentially move. The amount of material actually moved depends on the skill
of the operator and the conditions in which the operator is working (USEPA 1993).
Large gravel and cobble discharged to the stream is typically deposited immediately behind
the sluice box. Finer material such as fine gravel and sand may move some distance
downstream as bedload, and silt and finer materials are carried further downstream in the
99
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
water column. Large rock and boulder piles can form where dredges have remained in one
place for a long time. Large pools may also be formed by this process.
The IDWR regulates suction dredging through the Idaho Stream Channel Protection Act
(TDAPA 37.03.07.064). Under this statute, dredge miners are required to obtain a permit
from IDWR (IDWR 2003). Small-scale operations (<5" nozzle; < 15 horsepower) are
covered under the Individual Recreational Dredging Application permit process (a.k.a.
General Permit). In the SF CWR Subbasin, dredging is only allowed from July 15 through
August 15 each year, in order to avoid periods when chinook, cutthroat, and steelhead are
spawning and eggs are incubating. The USEPA reviewed the IDWR General Permit for
suction dredge mines in 1998, and found that it adequately addressed environmental concerns
from these operations (USEPA 1998). Although there is currently no limit on the number of
facilities which can operate in the SF CWR Subbasin under the General Permit, the actual
number of permits issued in recent years has been limited to 15 in 2000, seven in 2001, and
eight in 2002 (IDWR 2002).
Larger scale operations, or facilities that operate in waters not listed under the IDWR General
Permit, must obtain permits from IDWR and the Army Corps of Engineers (ACOE) under
the Joint Application Permit process. In 2000, the USFS received three applications to
operate suction dredges within the NPNF which did not fall within the General Permit. The
Genesis Placer proposal is to operate two dredges (5 and 8 inch diameter nozzles) year
around in the Red River. A draft environmental impact statement was issued for this
proposal in July 2000. The El Luky Duk proposal is to operate four different dredges of 3, 5,
6 and 8 inch diameter nozzles from July to October on the SF CWR. The Booger Placer
proposal is to operate an 8 inch dredge on Little Elk Creek. Within the past five years, the
only known operation of dredges >5 inch was a test run of the 8 inch Booger Placer dredge
on July 6-7, 2000.
When compared to other sediment sources in the subbasin including roads and natural
erosion processes, sediment loading from current recreational suction dredge operations
appears to be minimal given their limited number, size, and 30 day annual operating window
allowed under the current IDWR general permit. This is consistent with Harvey and Lisle
(1998) who indicate that single dredging operations cannot mobilize significant volumes of
fine sediment compared with the volume mobilized during high seasonal flows from
throughout a watershed, when large portions of the streambed are entrained.
Suction dredges are considered to be point sources, and therefore are required to obtain an
NPDES permit to discharge (USEPA 1998). Currently no NPDES permits have been issued
for suction dredges within the SF CWR Subbasin, and an application for permit coverage has
only been received for the Genesis dredge on Red River.
A great deal of literature exists on the effects of suction dredge mining on water quality and
stream habitat. While the literature is mixed in terms of the nature and severity of effects
from dredge mining operations, serious impacts to water quality and habitat have been
documented, depending on the size, location and manner in which dredges are operated. For
a recent summary of suction dredge impacts, see Harvey and Lisle (1998).
100 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
The NPNF began tracking, inspecting, and monitoring suction dredges in the SF CWR in
1980, with a more concentrated effort since 1995. The focus has been primarily on
recreational dredging (5" or less diameter nozzle), but also to some extent on commercial
dredging (greater than 5" diameter nozzle). The NPNF requires a Notice of Intent (NOT)
from recreational suction dredgers which indicates the dates and locations of proposed
mining. Inspections of these operations and instream monitoring are performed seasonally
(DeRito 2000). The monitoring system is still being refined.
While turbidity and streambed composition data have been collected from some of these
facilities off and on since 1980, there is little information available from which to estimate
loading from an individual operation, or the industry as a whole. Monitoring results overall
are mixed. Turbidity data that have been processed to date generally show turbidity levels
below the mixing zone of small facilities (<5 inch nozzle) to be less than 50 NTU above
upstream measurements. The most recent published monitoring in the SF CWR (DEQ 2003)
indicates that such facilities operating properly under IDWR permits meet the ambient
turbidity criteria, but it is not clear if they would meet the turbidity treatment requirements
for point sources of 5 NTU above background outside any applicable mixing zone (IDAPA
58.01.02.401.03.b.i.). Surface fines data have been difficult to interpret due to a lack of pre-
dredge data, limited sample numbers, and relatively little information (DeRito 2000).
Although data from larger facilities is sparse and largely unpublished in draft reports, it
suggests that these facilities have a greater impact on water column and substrate sediment
levels than recreational dredges. Table 29 summarizes all available results of bedload,
surface sediment and suspended sediment from dredges greater than 5 inches in the SFCWR.
Surface fine sediment data from the Mendenhall and McCroskey facility suggest that surface
fine sediment increases significantly in tailings below each facility (statistically significant at
a 95% confidence level), but appear to return to pre-dredge levels by the following year.
Bedload movement below Richardson's facility increases several-fold while the dredge is
operating. Although the bedload rates are not as high as would be expected naturally at other
times of year, they are cause for concern since the primary form of sediment causing
impairment in the upper SF CWR is elevated substrate sediment levels thought to be due to
bedload movement. Further increasing bedload sediment transport may cause additional
impacts to cutthroat, chinook and bull trout spawning and incubation which occur prior to
increased substrate fines levels being flushed out by high spring flows. Table 29 also clearly
indicates that suspended sediment levels increase significantly below these operations, in
some cases by an order of magnitude or more.
Available turbidity data is summarized in Table 30. Turbidity data for the Richardson
facility on Newsome Creek are estimated based on TSS levels reported in a USFS (1980b)
report, and the TSS to turbidity relationship for the Harpster location from Appendix M, page
M-15. While none of the data indicates levels exceeding the 25 or 50 NTU ambient criteria,
turbidity remains more than 5 NTU above background from 400 to greater than 600 feet
below the dredge. This is consistent with statements in the report that turbidity plumes
remain noticeable for the entire length of Newsome Creek below the dredge. Downstream
mixing zone boundaries below smaller dredges in DEQ 2000 ranged from 130-360 feet
101 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
below the dredge. While mixing zones are quite site specific, and may be smaller in
Newsome Creek due to its smaller flow, it appears likely that the Richardson facility would
have exceeded 5 NTU above background outside the mixing zone.
Turbidity was only measured at one other large facility, a test of the Booger Placer dredge on
Little Elk Creek in July 2000. As indicated in Table 30, turbidities significantly exceeded the
50 NTU instantaneous ambient turbidity criteria. It is also highly likely that the 5 NTU
treatment technique requirement was exceeded, although the boundaries of a mixing zone
were not established. The magnitude of these results is most likely due to the relatively large
size of the dredge, and small size of the water body.
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October 2003
Table 29. Summary of sample results for suction dredges larger than 5 inches (USFS 1980a; USFS 2000).
Dredge
Mendenhall
McCroskey
Richardson
Richardson
Location
Newsome
Creek
Newsome
Creek
Newsome
Creek
Newsome
Creek
Dredge
Size
(inches)
8
8
Sand 6
8
8
Date
Aug. 17-18,
1980
Aug. 4-5,
1980
(prior to
dredge
operating)
Aug. 15-16,
1979
July 24-27,
1980
Aug. 7,
1980
Flow
(cfs)
Percent Surface
Fine Sediment
Control
14%
20%
14%
Dredge
tailings
34%
14%
26%
Bedload Movement
Below Dredge
Control
(Ib/hr)
0.13
0.11
Below
(Ib/hr)
0.31 -2.39
0.12-0.74
Suspended
Sediment and
Turbidity
Control
(Ib/hr)
49
23
17
Below
(Ib/hr)
140-340
93 - 385
26-142
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October 2003
Table 30. Turbidity and TSS data for 8 inch section dredges (USFS 1980a; DEQ 2000).
Facility
Richard-
son
Richard-
son
Booger
Placer
Date
7/24/80
8/7/80
7/6/00
7/7/00
Stream
Newsome
Creek
Newsome
Creek
Little Elk
Creek
Little Elk
Creek
TSS (mg/L)
Estimated Turbidity
(NTU)
Turbidity Increase
above Background
(NTU)
TSS (mg/L)
Estimated Turbidity
(NTU)
Turbidity Increase
above Background
(NTU)
Turbidity (NTU)
Turbidity (NTU)
Above
1.87
0.91
—
1.98
0.95
1.9
2.0
Below
25
feet
30
12.49
11.59
50
feet
26
10.85
9.94
20.8-
230
135-
>1,000
100
feet
16
6.73
5.82
200
feet
15.30
6.44
5.53
400
feet
14.20
5.99
5.08
16.54
6.95
5.99
600
feet
7.40
3.19
2.28
16.54
6.95
5.99
0.6
miles
5.05
2.22
1.26
2.0
miles
1.90
0.92
-0.03
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Confined Animal Feeding Operations
Confined animal feeding operations are facilities which confine, maintain, or feed animals
for at least 45 days per year, and which harbor a minimum number of animals as defined in
federal regulations (40 CFR §122.23). Smaller operations can also be classified as CAFOs if
they are determined by USEPA or IDA to be significant contributors of pollution. A CAFO
is considered to be a point source and therefore is subject to NPDES permits. While quite a
number of animal feeding operations exist in the subbasin, particularly in the Threemile and
Butcher Creek watersheds, there is no record that any of these operations are large enough
outright to be considered a CAFO, nor have any animal feeding operations yet been
determined to be significant contributors of pollution. Pollutant loading and allocations for
existing animal feeding operations will therefore be addressed through the nonpoint source
loading and allocation.
Storm Water
Storm water discharges from certain municipalities, construction activities, and industrial
operations are considered to be a point sources of pollution under federal regulations (40
CFR 122.26).
There are currently no municipal separate storm sewer systems within the SF CWR Subbasin
meeting the definitions of 40 CFR 122.26 and which are required to obtain an NPDES storm
water discharge permit. As a result, storm water discharges from these are addressed as a
component of the nonpoint source loading and allocation.
Construction activities disturbing one or more acres must obtain NPDES storm water permit
coverage from USEPA for discharges occurring during the active construction phase;
however, within the SF CWR, there is no information available to determine current
sediment contribution from construction-related storm water runoff to the SF CWR drainage.
However, construction sites and activities are generally not extensive and are widely
dispersed throughout the watershed, therefore, construction activity is not considered to be a
significant anthropogenic sediment contribution at this time.
Twenty-nine categories of industrial operations (determined by Standard Industrial
Classification code) are required to obtain coverage under USEPA's general storm water
NPDES permit for any storm water discharges associated with industrial activities. Within
the SW CWR, no industrial facilities are currently authorized to discharge under USEPA's
Multi Sector General Permit for Storm Water Associated with Industrial Activity, according
to USEPA's list of permitted storm water facilities in February 2003. Such facilities may
exist in the SF CWR, and yet be unaware of their obligation to apply for NPDES permit
coverage.
Two facilities that have greater potential for impact due to their size and proximity to surface
water are the Clearwater Forest Industries (CFI) timber processing facility in Kooskia and the
Shearer Lumber Mill near Elk City. Historically Clearwater Forest Industries discharged
105 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
storm water, log deck sprinkling water, and process water through a series of seven outfalls.
Process water (e.g., boiler blowdown) may be a source of excess heat loading, and storm
water and log deck runoff could be sources of sediment loading.
An application for an NPDES permit was received by USEPA on March 29, 1996. The
facility was contacted in August 2001 to determine if there were any updates in the
application. At that time the facility indicated that they were attempting to contain all
process (non-storm water) wastewater on-site, in order to avoid the need for NPDES permit
coverage, and instead apply for coverage under USEPA's Multi-Sector General Permit for
industrial stormwater. Since that time, CFI has determined that there are times when they
cannot contain process wastewater on-site and must discharge to the SF CWR, primarily
during the spring when the source of their raw water (SF CWR) is of low quality (CFI 2003).
As a result, it appears that renewal of their NPDES wastewater permit is required. More
information can be obtained by visiting the Region 10 USEPA Web site at
www.epa.gov/rlOearth.
Shearer Lumber Mill is located on the SF CWR just below the confluence of Red River and
American River. Runoff from the mill is collected through surface and underground
collection systems and disposed in an underground infiltration gallery (Wilhite 2002).
Shearer Lumber was covered by the NPDES General Storm Water Permit from May 1997
through September 2000, but is not currently included in the permit.
There is no information available to determine current sediment contribution from municipal,
industrial or construction related storm water to the SF CWR drainage, although it is
generally believed to be quite low compared to other anthropogenic sources, and the overall
nonpoint source sediment load.
Nonpoint Sources
Land use practices (mining, timber harvesting, agricultural practices, and grazing)
contributing nonpoint pollutants to the SF CWR Subbasin were discussed in Section 1.3.
Table 31 identifies acres of land use within each water body in the subbasin. Figure 43
shows the distribution of land use throughout the SF CWR Subbasin.
Table 31. Land use in each SF CWR Subbasin WBID units.
Water
Body ID
1
2
3
4
5
6
7
Water Body Name
Lower SF CWR
Lower Cottonwood Creek
Upper Cottonwood Creek
Lower Red Rock Creek
Upper Red Rock Creek
Stockney Creek
Shebang Creek
Agriculture
(acres)
6,758
6,195
16,303
1,499
21,080
18,793
16,713
Grazing
(acres)
8,513
8,088
3,100
1,279
1,821
589
684
Forestry
(acres)
4,129
2,017
1,494
200
75
190
175
Urban
(acres)
0
0
248
0
0
0
0
Water
(acres)
0
0
2
0
0
0
0
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Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body ID
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
Water Body Name
S.F. Cottonwood Creek
Long Haul Creek
Threemile Creek
Butcher Creek
Mid-Lower SF CWR
Mill Creek
Lower Johns Creek
Gospel Creek
West Fork Gospel Creek
Middle Johns Creek
Upper Johns Creek
Moores Creek
Square Mountain Creek
Hagen Creek
Middle SF CWR
Wing Creek
Twentymile Creek
Lower Tenmile Creek
Middle Tenmile Creek
Upper Tenmile Creek
Williams Creek
Sixmile Creek
Mid-Upper SF CWR
Lower Crooked River
Upper Crooked River
West Fork Crooked River
East Fork Crooked River
Relief Creek
Upper SF CWR
Lower Red River
Middle Red River
Moose Butte Creek
Lower S.F. Red River
Agriculture
(acres)
12,218
7,356
14,235
6,432
3,025
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Grazing
(acres)
192
519
4,146
2,393
12,551
1,127
1,145
1,462
377
316
232
315
216
215
1,335
31
198
69
25
810
71
72
486
421
434
533
18
355
105
720
1,682
339
260
Forestry
(acres)
10
137
2,671
1,921
40,063
21,977
25,225
9,291
4,023
9,879
8,442
3,546
2,051
5,225
17,591
5,298
14,422
2,377
7,200
12,626
5,810
5,054
16,655
9,060
14,050
7,044
6,429
7,129
2,586
9,610
14,362
6,748
2,892
Urban
(acres)
0
255
391
0
0
0
0
0
0
0
0
0
0
0
0
0
1
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Water
(acres)
0
0
0
0
44
0
10
32
16
5
0
0
0
22
28
0
13
0
4
18
4
0
28
1
0
13
0
0
5
3
0
0
0
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Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body ID
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
Water Body Name
Middle S.F. Red River
West Fork Red River
Upper S.F. Red River
Trapper Creek
Upper Red River
Soda Creek
Bridge Creek
Otterson Creek
Trail Creek
Siegel Creek
Red Horse Creek
Lower American River
Kirks Fork
East Fork American River
Upper American River
Elk Creek
Little Elk Creek
Big Elk Creek
Buffalo Gulch
Whiskey Creek
Maurice Creek
Lower Newsome Creek
Bear Creek
Nugget Creek
Beaver Creek
Middle Newsome Creek
Mule Creek
Upper Newsome Creek
Haysfork Creek
Baldy Creek
Pilot Creek
Sawmill Creek
Sing Lee Creek
Agriculture
(acres)
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Grazing
(acres)
149
147
342
495
940
263
10
6
65
164
144
284
137
178
290
662
475
910
105
15
18
119
101
78
76
38
143
74
92
113
76
14
36
Forestry
(acres)
2,640
6,258
3,912
6,501
18,216
3,071
2,150
2,380
4,472
7,579
5,540
6,928
6,067
11,059
14,628
1,639
4,605
7,901
2,034
1,645
1,074
4,024
3,730
1,372
3,567
1,096
5,217
5,818
3,012
2,534
3,816
1,757
1,516
Urban
(acres)
0
2
2
0
0
1
0
0
0
0
0
0
1
0
0
24
0
3
0
0
0
0
0
0
0
0
0
0
0
1
1
0
0
Water
(acres)
0
0
0
0
0
0
0
0
0
0
0
2
0
0
0
0
2
0
0
0
0
3
0
0
0
0
0
0
0
0
0
0
0
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Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body ID
74
75
76
77
78
79
80
81
82
Water Body Name
West Fork Newsome Creek
Leggett Creek
Fall Creek
Silver Creek
Peasley Creek
Cougar Creek
Meadow Creek
Sally Ann Creek
Rabbit Creek
Agriculture
(acres)
0
0
0
0
0
0
0
2,370
2,464
Grazing
(acres)
139
203
111
222
301
379
844
1,365
828
Forestry
(acres)
3,167
4,789
2,223
16,172
8,793
7,353
23,002
5,148
1,945
Urban
(acres)
1
0
0
2
1
0
0
0
0
Water
(acres)
0
1
1
0
0
0
0
0
0
I I SF Cleanjjater4th Field HUC
^J Water Body ID ui atersheds
] MPT Reservation Boundary
Landuse
Q Bare Rook/Sand
• r- fc,
Coniferous
| Deo
• F,l,
D <=-
D 01
D oi
Q WoodyWatlHn
fj No D.t,
Land Use Classification of the
South Fork Clearwater
River Subbasin
20000
Figure 43. Land Use Distribution in the SF CWR Subbasin
Sediment
As early settlers began moving into the SF CWR Subbasin, surface erosion rates increased
due to road construction, mining, timber harvest, building construction, agriculture, and
grazing. This SB A identifies the major sources of sediment as road erosion, stream bank
erosion, mass failures, agricultural field erosion, and grazed land erosion. Using various
methods in a Geographical Information Systems (GIS) environment, we calculated estimates
109
Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
of the magnitude of the erosion from each source and created a sediment budget from the
results. Summary results from the sediment budget on a water body by water body basis are
presented in Table 32.
The largest nonpoint sources of sediment in the subbasin are the agricultural lands in the
Threemile, Butcher, Sally Ann, and Rabbit Creek drainages and the lower main stem
sidewalls (Table 32). Another large source is erosion caused by livestock grazing, from
grazed lands and from increased in-stream erosion as the result of reduced vegetative cover.
Surface erosion from agricultural, grazing, and forestlands outside the federal ownership
perimeter was modeled using the RUSLE model (Renard et al. 1997) in a GIS environment
(Engel 1999). The modeling was done by staff from the University of Idaho Biological and
Engineering Department following methods reported in Boll et al. (2001), with an updated
land use map for the SF CWR area.
Lands within the outside perimeter of the NPNF, including BLM and private inclusions, were
evaluated for sediment production using the NEZSED sediment model (USFS 1981). This
model estimates sediment produced by forest practices and then routes it through the
hydrologic system. The most important source of estimated sediment in this model is from
forest roads. Less important sources are logging areas, burned areas, logging decks, and
other forest practice impacted areas. The NEZSED model does not estimate sediment from
grazing or mining practices that occur within the federal perimeter, nor does it include
estimates of human activity-related mass failures.
Mass failures within the federal perimeter were accounted for by an inventory conducted by
the NPNF and the BLM. We extrapolated those results to estimate sediment from mass
failures throughout the SF CWR Subbasin.
The primary effect of grazing on sediment is increased stream bank erosion as the cattle
access the stream. We conducted an inventory of stream bank erosion to quantify sediment
from this source. We inventoried all of the known eroding streams in the subbasin. The
inventory method is presented in Appendix L.
Using the WEPP road model, the University of Idaho developed a database to model
sediment from county roads outside the federal perimeter (Flanagan and Livingston 1995).
For gravel and other sediment coming from State Highway 14 that follows the main stem
from Kooskia to Elk City, we estimated the amount of sediment being delivered to the river
based on the amount of rock ITD crushes on a yearly basis. The estimate was adjusted for
delivery, as were other sediment sources (Appendix L).
All of these sources of sediment and our calculations are presented in Appendix L, Sediment
Budget. Summary sediment delivery results for all subbasin water bodies are shown in Table
32.
110 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 32. Sediment loads from nonpoint sources for each of the water bodies in the SF CWR Subbasin.
Water
Body
No.
1
2
3
4
5
6
7
8
9
10
11
12NFM
12 FM
13
14
15
16
17
18
Area
(mi2)
30.8
26.5
33.2
4.6
36.7
31.2
28.7
19.8
13.8
33.6
16.8
27.6
61.0
36.6
41.2
16.9
7.0
15.9
13.6
WEPP&
Highway
14
(t/WB/yr)
72
MD
MD
MD
MD
MD
MD
MD
MD
205
137
177
948
NEZSED
(t/yr/WB)
2,651
1,050
1,248
1,207
346
510
544
RUSLE
(t/WB/yr)
2638
12572
19807
2633
25261
19898
11691
10108
6194
11632
1708
4817
Mass
Failures
(t/WB/yr)
21
MD
MD
MD
MD
MD
MD
MD
MD
43
21
21
381
180
8
Instream
Erosion
(t/WB/yr)
MD
MD
MD
MD
MD
MD
MD
MD
616
211
Total
Sediment
(t/WB/yr)
2,732
12,572
19,807
2,633
25,261
19,898
11,691
10,108
6,194
12,496
2,078
5,015
3,980
1,230
1,256
1,207
346
510
544
Background
Sediment
Rate
(t/miA2)
30E
30E
30E
30E
30E
30E
30E
30E
30E
30E
30E
30E
38
27
29
72
50
32
40
Total
Background
Sediment
(t/WB/yr)
925
794
995
139
1,101
937
862
594
413
1,007
503
694
2,503
971
1,212
1,207
346
509
544
Routing
Coeffic-
ient
0.54
0.55
0.53
0.76
0.52
0.54
0.55
0.58
0.62
0.53
0.60
0.55
0.55
0.52
0.51
0.60
0.70
0.61
0.63
Routed
Activity
Sediment
(t/WB/yr)
975
6,532
10,017
1,892
12,632
10,207
5,918
5,558
3,606
6,105
948
2,379
813
136
23
0
0
1
0
111
Chapter 3
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October 2003
Water
Body
No.
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
Area
(mi2)
6.2
3.6
8.7
29.6
8.3
22.9
3.8
11.3
21.3
9.2
8.0
26.8
14.8
22.6
11.9
10.5
11.7
4.2
16.1
25.1
WEPP&
Highway
14
(t/WB/yr)
468
472
148
NEZSED
(t/yr/WB)
551
316
417
1,167
256
476
120
313
998
262
152
848
418
460
270
287
226
147
376
680
RUSLE
(t/WB/yr)
Mass
Failures
(t/WB/yr)
23
49
Instream
Erosion
(t/WB/yr)
210
Total
Sediment
(t/WB/yr)
551
316
417
1,658
256
476
120
313
998
262
152
1,320
418
460
270
287
226
295
425
891
Background
Sediment
Rate
(t/miA2)
89
89
48
36
30
20
30
27
47
29
17
28
25
19
23
27
17
26
17
20
Total
Background
Sediment
(t/WB/yr)
551
316
417
1,073
251
458
115
303
998
262
135
752
371
425
267
280
196
109
281
503
Routing
Coeffic-
ient
0.72
0.80
0.68
0.54
0.68
0.57
0.79
0.65
0.58
0.67
0.69
0.55
0.62
0.57
0.64
0.66
0.64
0.77
0.61
0.56
Routed
Activity
Sediment
(t/WB/yr)
0
0
0
318
3
10
4
7
0
0
11
314
29
20
2
4
19
144
87
217
112
Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body
No.
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
Area
(mi2)
11.1
4.9
4.4
10.0
7.4
11.1
30.1
5.2
3.7
3.9
7.1
12.2
9.1
11.3
9.8
17.9
23.9
3.6
7.9
13.8
WEPP&
Highway
14
(t/WB/yr)
NEZSED
(t/yr/WB)
261
112
108
186
136
215
745
115
90
81
160
266
217
281
235
413
622
128
190
416
RUSLE
(t/WB/yr)
Mass
Failures
(t/WB/yr)
28
Instream
Erosion
(t/WB/yr)
12
62
3
15
39
124
25
63
Total
Sediment
(t/WB/yr)
273
112
108
186
136
215
807
115
90
81
163
282
217
281
235
413
689
252
215
479
Background
Sediment
Rate
(t/miA2)
17
18
19
17
17
18
20
18
21
21
20
18
21
17
23
18
24
29
18
24
Total
Background
Sediment
(t/WB/yr)
192
88
82
170
124
193
593
95
80
81
142
216
192
196
225
329
560
105
144
337
Routing
Coeffic-
ient
0.65
0.75
0.77
0.66
0.70
0.65
0.54
0.74
0.79
0.78
0.70
0.64
0.67
0.65
0.66
0.60
0.56
0.79
0.69
0.62
Routed
Activity
Sediment
(t/WB/yr)
53
18
20
10
8
14
116
15
8
0
15
42
17
55
7
50
73
116
49
88
113
Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body
No.
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
Area
(mi2)
3.3
2.6
1.7
6.5
6.0
2.3
5.8
1.8
8.6
9.9
5.0
4.3
6.1
2.8
2.4
5.2
7.8
3.6
25.8
14.2
WEPP&
Highway
14
(t/WB/yr)
NEZSED
(t/yr/WB)
86
62
39
189
143
44
122
52
190
224
135
119
163
77
73
151
231
108
639
440
RUSLE
(t/WB/yr)
Mass
Failures
(t/WB/yr)
11
8
Instream
Erosion
(t/WB/yr)
4
36
0
Total
Sediment
(t/WB/yr)
90
62
39
225
143
44
122
52
190
224
135
119
163
77
73
151
231
108
650
448
Background
Sediment
Rate
(t/miA2)
21
21
20
24
20
16
19
24
18
21
23
25
26
28
27
28
26
26
24
27
Total
Background
Sediment
(t/WB/yr)
69
53
33
157
117
37
112
43
152
209
114
107
158
77
66
143
205
95
623
378
Routing
Coeffic-
ient
0.80
0.84
0.91
0.71
0.72
0.86
0.73
0.90
0.68
0.66
0.75
0.77
0.72
0.83
0.85
0.74
0.69
0.79
0.56
0.62
Routed
Activity
Sediment
(t/WB/yr)
17
8
5
49
19
6
7
8
26
10
15
9
4
0
6
6
18
10
15
44
114
Chapter 3
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October 2003
Water
Body
No.
79
80
81-NFM
81 -FM
82-NFM
82-FM
Totals
Area
(mi2)
12.1
37.5
9.8
4.1
9.0
0.7
WEPP&
Highway
14
(t/WB/yr)
53
28
2,708
NEZSED
(t/yr/WB)
343
1,164
129
0
13
26,210
RUSLE
(t/WB/yr)
1205
784
130947
Mass
Failures
(t/WB/yr)
15
12
822
Instream
Erosion
(t/WB/yr)
53
1
0
1,473
Total
Sediment
(t/WB/yr)
357
1,229
1,258
129
812
13
162,160
Background
Sediment
Rate
(t/miA2)
23
27
30E
28
30E
18
Total
Background
Sediment
(t/WB/yr)
279
1,003
294
114
270
12
33,378
Routing
Coeffic-
ient
0.64
0.52
0.66
0.66
0.67
0.66
Routed
Activity
Sediment
(t/WB/yr)
50
118
639
10
365
1
71,169
Explanation of Table 32 (A complete discussion is presented in Appendix L, Sediment Budget.)
"t/WB/yr" means tons per water body per year.
"E" is the estimated background erosion rate.
"MD" is missing data from the water bodies covered in the Cottonwood Creek TMDL for which we did not allocate resources to complete.
"FM" means federally managed lands
"NFM" means not federally managed lands
"Area" is the area of each water body in square miles.
"WEPP & Highway 14" is a combination of sediment production from roads outside the federally managed area estimated using the WEPP model
and estimates of sediment from Highway 14.
"NEZSED" is sediment production from lands within the overall boundary of federal ownership estimated using the NEZSED model.
"RUSLE" is sediment production from agriculture and grazing lands predicted by the RUSLE model.
"Mass Failures" are estimates of sediment from road related mass failures delivered to streams based on data from the NPNF.
"Instream Erosion" is sediment estimated using the Natural Resources Conservation Service (NRCS) field methods described in the Sediment
Budget (Appendix L).
(Continued on next page)
115
Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Explanation of Table 32 (continued)
"Total Sediment" is the total estimated sediment produced from the landscape in a water body, on an
annual basis. These numbers are for the water body per se, and, in this table, are not
cumulative from all water bodies upstream.
"Background Sediment Rate" is the rate derived by the NPNF for NEZSED, or our estimated rate
based on the literature.
"Total Background Sediment" is the total amount of sediment from the water body landscape that is
estimated to be background.
"Routing Coefficient" is that of Roehl (1962) and is an estimate of what proportion of sediment
produced on the landscape is routed through the streams.
"Routed Activity Sediment" is the Total Sediment minus the Background Sediment multiplied by the
Routing Coefficient, resulting an estimate of human-caused sediment being delivered by the
stream at the mouth of each water body.
Water bodies 1, 10, 11, 12, 22, 30, 36, 59, 62, 64, 65, 73, and 79 are the 303(d) listed water bodies.
Water bodies 12, 81, and 82 are reported in two parts, that part managed by federal agencies, and that
part in private ownership.
Water bodies 2 through 9 are those that were covered in the Cottonwood Creek TMDL.
Sediment Transport
One of the major issues with the sediment budget approach to sediment loading analysis is
the question of sediment yield, or sediment routing, as we have chosen to term it in this
document. There are methods for validating estimates of sediment production from the
landscape and we have looked at various sources of information to be relatively sure that our
estimates of sediment production make sense. However, what happens to sediment once it
enters a stream network is highly uncertain in terms of being able to predict and quantify. At
a conceptual level, we know that some portion of sediment delivered to a stream is actually
stored within a watershed in such places as bars, floodplains, outwash fans, etc. The steeper
and more energetic a stream, the higher the likelihood that sediment will be flushed through
rather than stored. And, in general, the larger the water body being analyzed, the greater the
amount of sediment that will be stored.
In consultation with several hydrologists in the region, we concluded that it would be nearly
impossible to predict sediment routing in any sort of a reliable way. We decided, therefore,
to use the routing coefficient developed by Roehl (1962), which simply relates the amount of
sediment routed through a watershed to the size of the watershed. The R1/R4 suite of models
(USFS 1981) for sediment estimation from forestlands uses this equation. We decided to
apply it to all of our sediment sources on a uniform, water body basis, i.e., it was applied to
each water body independently based on the area of that water body. However, consistent
with USFS use, it was not applied at a cumulative water body level, or at the level of the total
SF CWR subbasin. The sediment budget summary in Table 32, above, shows the use of the
routing coefficient. Appendix L, Sediment Budget, explains its use further.
While we have very poor bedload data to use to draw any reliable conclusions about our use
of the routing coefficient, the data we do have indicate that somewhat more sediment is being
produced in the landscape than we have been able to account for in our TSS and bedload
data. In other words, it appears that there is more storage in the watersheds than the Roehl
equation predicts, especially for Threemile and Butcher Creeks. Since we switch from
116 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
instream-based, TSS sediment estimation to sediment-budget-based, total sediment
estimation from the non-federal to the federal part of the subbasin, we have had to make
adjustments in our calculations to account for problems in our routing estimates. These are
explained more fully in Appendix L.
Human Caused Sediment
For the water bodies above Harpster, the total amount of human-caused (activity) sediment
being routed through the water bodies ranges from zero for those water bodies in the
wilderness to a high of 3,191 t/year for the water body around Harpster (WB 12). The next
two highest sediment producing water bodies are the next two water bodies upstream from
Harpster on the main stem (WB 22 and WB 30). Aside from these main stem water bodies,
the following water bodies upstream from Harpster are producing greater than 100 tons of
sediment per year: Mill Creek, Middle Red River (which includes Dawson Creek), Upper
Red River, Lower Elk Creek, and Meadow Creek. Water bodies producing between 50 and
100 tons of sediment per year include: Lower Red River, Moose Butte Creek, Lower
American River, East Fork American River, Upper American River, Big Elk Creek, and
Cougar Creek. Figure 44 shows the distribution of human-caused sediment by water body.
To account for the varying sizes of the water bodies, another way of looking at sediment
production is on a per unit area basis. Apart from the main stem water bodies which produce
the most sediment on a per unit area basis, the following water bodies are producing the most
sediment: Lower Elk Creek at 32 t/mi2/yr, Middle Red River at 9 t/mi2/yr (which includes
Dawson Creek), Lower Newsome Creek at 8 t/mi2/yr, Big Elk Creek at 6 t/mi2/yr, Little Elk
Creek at 6 t/mi2/yr, Lower Red River at 5 t/mi2/yr, and Buffalo Gulch at 5 t/mi2/yr. Water
bodies in the 3-5 t/mi2/yr range include Mill Creek, Meadow Creek, Cougar Creek, Peasley
Creek, Haysfork Creek, Mule Creek, Bear Creek, Middle Newsome Creek, Maurice Creek,
Lower and Upper American River, Siegel Creek, Moose Butte Creek, Lower and Middle
South Fork Red River, and Upper Red River. The other 303(d) listed water bodies, Sing Lee
Creek, Nugget Creek, and Beaver Creek, are producing in the range of 1 to 3 t/mi2/yr of
human caused sediment. Figure 45 shows the distribution of human-caused sediment per
unit area.
117 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Routed Activity Sediment for the
South Fork Clearwater River Subbasin
in Tons per Water body per Year
Routed Activity Sadmenl (t/w6/yr)
O '»
50 100
100.300
Figure 44. Sediment Production by Water Body in the SF CWR Subbasin
Routed Activity Sediment for the
South Fork Clearwater River Subbasin
in Tons per Square Mile per Year
^ _ ^ Npl Resftvanai Snunctafy
/\/ 303HJI Ltsu-d Slrsans
/\/ Major Streams
Glhfrr ^bearra
Routed Activity Sediment (t/m.11?)
O> 3-5
O> 5-50
October 2003
Figure 45. Annual Sediment Production per Square Mile in the SF CWR
Subbasin
118
Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Sediment from Roads
The sediment budget is based on a number of data sources as presented in Appendix L and
summarized in Table 32. The NEZSED model predicts sediment delivery from all forest
practices, but beyond the first few years after a fire or harvest activity, the largest amount of
sediment comes from roads. Table 33 shows the distribution of roads in the subbasin in
relation to streams. Shaded cells show water bodies that have the highest road densities, road
stream crossings, or miles of roads close to streams. Most of the 303(d) listed water bodies
have high road densities and/or a large number of stream crossings.
Table 33. Road data for the SF CWR Subbasin.
WB
ID
1
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
Water Body Name
Lower SF CWR
Threemile Cr.
Butcher Cr.
Mid-Lower SF CWR
Mill Cr.
Lower Johns Cr.
Gospel Cr.
WF Gospel Cr.
Middle Johns Cr.
Upper Johns Cr.
Moores Cr.
Square Mntn. Cr.
Hagen Cr.
Middle SF CWR
Wing Cr.
Twentymile Cr.
Lower Tenmile Cr.
Middle Tenmile Cr.
Upper Tenmile Cr.
Williams Cr.
Sixmile Cr.
Mid-Upper SF CWR
Lower Crooked R.
Area
(mi2)
30.8
33.6
16.8
89.0
36.6
41.2
16.9
7.0
15.9
13.6
6.2
3.6
8.7
29.6
8.3
22.9
3.8
11.3
21.3
9.2
8.0
26.8
14.8
Miles
of
Stream
38.3
49.8
18.9
114.2
44.7
52.1
21.3
5.9
18.9
21.3
8.8
5.0
11.3
49.8
11.0
27.9
6.4
15.0
21.7
11.7
13.8
40.2
19.9
Road
Miles per
Water
Body
(mi/WB)
62.3
70.7
32.2
344
108.0
77.3
6.2
3.0
9.8
9.4
9.1
1.4
3.5
79.2
13.9
35.7
2.4
17.6
21.3
2.2
15.5
93.4
46.8
Road
Density
(mi/mi2)
2.0
2.1
1.9
3.9
3.0
1.9
0.4
0.4
0.6
0.7
1.5
0.4
0.4
2.7
1.7
1.6
0.6
1.6
1.0
0.2
1.9
3.5
3.2
Road
Crossings
24
62
13
132
40
24
4
1
3
5
6
0
0
45
2
12
0
5
6
1
6
36
11
Miles of
Road
Within
100 Feet
of Stream
4.1
3.9
0.7
12.4
5.0
3.1
0.2
0.1
0.3
0.4
1.5
0.0
0.0
8.4
0.2
1.1
0.0
0.4
0.4
0.1
0.6
7.9
1.4
119
Chapter 3
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
ID
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
Water Body Name
Upper Crooked R.
WF Crooked R.
EF Crooked R.
Relief Cr.
Upper SFCWR
Lower Red R.
Middle Red R.
Moose Butte Cr.
Lower SF Red R.
Middle SF Red R.
WF Red R.
Upper SF Red R.
Trapper Cr.
Upper Red R.
Soda Cr.
Bridge Cr.
Otterson Cr.
Trail Cr.
Siegel Cr.
Red Horse Cr.
Lower American R.
Kirks Fork
East Fork American R.
Upper American R.
ElkCr.
Little Elk Cr.
Big Elk Cr.
Buffalo Gulch
Whiskey Cr.
Maurice Cr.
Lower Newsome Cr.
Area
(mi2)
22.6
11.9
10.5
11.7
4.2
16.1
25.1
11.1
4.9
4.4
10.0
7.4
11.1
30.1
5.2
3.7
3.9
7.1
12.2
9.1
11.3
9.8
17.9
23.9
3.6
7.9
13.8
3.3
2.6
1.7
6.5
Miles
of
Stream
33.7
13.5
12.0
13.5
6.5
24.9
43.6
15.2
6.4
7.8
14.9
7.9
13.8
43.4
8.0
7.2
6.2
9.4
13.6
14.0
20.1
17.1
33.1
39.3
4.4
12.7
19.7
6.5
4.2
2.6
12.4
Road
Miles per
Water
Body
(mi/WB)
46.2
11.4
6.9
43.2
12.2
93.4
129.6
57.0
20.5
18.8
23.7
27.1
34.1
113.9
19.2
7.3
3.0
16.7
43.9
21.9
38.0
16.7
53.0
61.4
10.0
26.8
40.5
14.5
9.0
5.1
31.0
Road
Density
(mi/mi2)
2.0
1.0
0.7
3.7
2.9
5.8
5.2
5.1
4.2
4.3
2.4
3.7
3.1
3.8
3.7
1.9
0.8
2.3
3.6
2.4
3.4
1.7
3.0
2.6
2.8
3.4
2.9
4.3
3.5
3.0
4.8
Road
Crossings
23
1
1
5
4
31
58
19
4
9
7
4
7
42
10
3
0
6
16
12
18
4
27
29
6
12
19
9
3
0
12
Miles of
Road
Within
100 Feet
of Stream
2.3
0.1
0.0
0.6
0.3
4.0
6.0
4.5
0.9
0.8
0.5
0.5
0.5
6.3
0.5
0.6
0.0
0.5
3.0
1.8
3.7
1.3
6.5
4.6
0.3
1.3
1.3
0.8
0.2
0.0
1.1
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October 2003
WB
ID
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
Water Body Name
BearCr.
Nugget Cr.
Beaver Cr.
Middle Newsome Cr.
Mule Cr.
Upper Newsome Cr.
Haysfork Cr.
Baldy Cr.
Pilot Cr.
Sawmill Cr.
Sing Lee Cr.
WF Newsome Cr.
Leggett Cr.
Fall Cr.
Silver Cr.
Peasley Cr.
Cougar Cr.
Meadow Cr.
Sally Ann Cr.
Rabbit Cr.
Area
(mi2)
6.0
2.3
5.8
1.8
8.6
9.9
5.0
4.3
6.1
2.8
2.4
5.2
7.8
3.6
25.8
14.2
12.1
37.5
18.0
10.0
Miles
of
Stream
8.0
4.6
6.7
2.3
13.8
15.7
9.5
8.0
10.4
6.0
4.5
7.2
11.9
7.8
41.0
22.3
17.1
47.8
18.3
11.2
Road
Miles per
Water
Body
(mi/WB)
32.7
10.4
14.9
7.8
44.4
22.9
24.7
19.9
6.9
0.3
10.3
14.5
34.7
12.2
38.6
66.1
51.4
168.1
71.0
19.0
Road
Density
(mi/mi2)
5.5
4.6
2.6
4.4
5.2
2.3
5.0
4.7
1.1
0.1
4.2
2.8
4.4
3.3
1.5
4.7
4.3
4.5
4.0
2.0
Road
Crossings
4
4
1
6
8
16
7
3
2
0
3
6
12
7
12
24
26
47
19
10
Miles of
Road
Within
100 Feet
of Stream
0.2
0.2
0.0
0.6
0.8
2.6
0.4
0.3
0.2
0.0
0.2
1.0
1.6
0.4
0.7
1.9
5.1
6.2
2.4
0.9
*Road Density Greater than 4.2
**Road Crossings Greater than 20 per water body
***Stream Miles Within 100 feet of Stream Greater than 2
Fisheries Technical Advisory Group Assessment of Sediment
Sediment production and delivery to a stream network, or even documented sediment in a
stream channel, does not lead directly to the conclusion that the Idaho sediment WQS are
being exceeded, or that beneficial uses are being impaired beyond a level acceptable under
the narrative conditions of the WQS. The Fish TAG of fisheries professionals
knowledgeable offish conditions in the SF CWR Subbasin was created and asked for its best
professional judgement.
The results of Fish TAG deliberations are presented in Appendix D. Whereas the Fish TAG
had access to the results presented above, as well as numerous other sources of information,
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October 2003
its deliberations included the whole SF CWR Subbasin and did not focus to any degree on
the 303(d) listed water bodies. The conclusions about sediment problems (Figure 46) are
relevant to the question of importance of sediment to salmonid spawning. Generally, the
fisheries biologists think there are sediment problems in all the water bodies where any
significant human activity has taken place. However, among those with sediment problems
above Harpster, the biologists think that fish habitat conditions are poor in Cougar Creek,
Lower and Middle Newsome Creek, Buffalo Gulch, Maurice Creek, Lower Crooked River,
Lower and Middle Red River (which includes Dawson Creek), Lower Elk Creek, and Lower
American River.
Fish TAG Identification of
Sediment Problems in the
South Fork Clearwater Subbasin
C»
Fisld HUC
NPT Reswvatwn Boundary
Walsr EtaJy ID n«l«rW«ds
\/ 303td) Listed breams
Figure 46. Fish TAG Assessment of Water Bodies in the SF CWR Subbasin
with Significant Sediment Problems
The significant point of the Fish TAG identification of water bodies impacted by sediment is
that they correspond relatively well with those identified by the sediment budget as having
the highest sediment load (see Figure 46).
Temperature
Stream temperatures are primarily controlled by channel morphology, stream flow, shading,
and air temperature. Wide, shallow streams with little shade will heat most quickly. In
tributaries, forestry, mining, grazing, and other activities that cause widening of the channel,
reduced depth, or reduced shade can increase stream temperatures and adversely affect
salmonids. The introduction of bedload sediment resulting in increased surface area of
streams may occur through overland flow from sources such as roads, agricultural practices,
bank slumping, and erosion.
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The lower SF CWR is naturally warm during the summer due to high air temperatures and
local reach characteristics. Thermal refugia, or cold spots, in the main stem represent
important areas for the survival and growth of salmonids, especially for adult fluvial bull
trout. The cool water plumes at the mouths of tributaries represent another type of thermal
refuge, so any activity that affects the associated tributary's temperature has the potential to
degrade the quality of these areas (USFS 1999). Appendices G, H, and I present more details
of water heating processes in the subbasin and our approaches to analyzing the situation.
Aquaculture Facilities
Two aquaculture facilities (hatcheries) exist in the SF CWR Subbasin, the Lukes Gulch
hatchery discharging up to 1.8 cfs to the SF CWR approximately 5 miles south of Stites, and
the Newsome Creek hatchery discharging up to 1 cfs to Newsome Creek approximately 3
miles upstream from the mouth. The Lukes Gulch hatchery operates from March until June
15 and rears fall chinook fmgerlings (NPT 2003b). Maximum annual production is estimated
to be 4,167 pounds. The Newsome Creek hatchery raises spring chinook fmgerlings, and
operates from May until October (NPT 2003a). Maximum annual production is estimated to
be 2,601 pounds. Because the annual production from both of these facilities is less than
20,000 pounds per year, they are considered to be nonpoint sources (40 CFR §122.24
Appendix C).
These facilities are potential contributors of sediment and heat loading to their receiving
waters. TSS levels in the Newsome Creek facility effluent are expected to range from 0.44 -
1.97 mg/L (NPT 2003a), and from 1.1-1.54 mg/L in effluent from the Lukes Gulch facility
(NPT 2003b). These levels are generally well below ambient levels in the receiving water
for each facility, and well below any TSS levels that would correspond to the state's turbidity
WQS, i.e., TSS levels would have to be >20 mg/L before one would start to be concerned
that the turbidity criteria would be exceeded.
The Newsome Creek facility uses Newsome Creek as its sole source of water, and since
temperature does not increase as it passes through the facility (NPT 2003a), it is not
considered to be a source of heat loading to Newsome Creek.
The Lukes Gulch facility uses a mix of SF CWR water and well water, the proportions
varying between March and June. The well water is warmer than river water during this
time, so effluent from the facility exceeds the temperature of SF CWR by up to 8.9 °F. SF
CWR flows during this time period are approximately 1,000 - 2,500 cfs, so the 1.8 cfs
discharge from the hatchery is expected to increase SF CWR temperature by no more than
0.07 °F. The SF CWR currently meets applicable temperature criteria between March and
June, and this very minor increase in temperature is not expected to cause any exceedances of
temperature criteria in the SF CWR.
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3.2 Data Gaps
This assessment has identified several data gaps that limit full assessment of the effects of
303(d) listed pollutants on beneficial uses. Some of the data gaps will be filled with
additional sampling efforts. As part of the TMDL implementation phase, a long-term
monitoring plan will be developed that will address data gaps. Data limitations are also
indicated in the TMDL loading analysis (Sections 5.1 through 5.3).
Point Sources
Additional nutrient monitoring and diurnal DO monitoring is needed to determine the effects
of the Grangeville WWTP on Threemile Creek, particularly during the April - June time
frame.
Nutrient monitoring is also recommended for Elk Creek. Observations indicate there are
areas with potential excess algae growth which could result in low DO. Diurnal DO
monitoring is recommended to evaluate effects of the Elk City WWTP.
Given the lack of consistent monitoring of the effects of suction dredging, a monitoring plan
should be established to further characterize and assess the sediment and habitat impacts of
this industry on an ongoing basis.
There is a need to collect temperature data from the outflow of each of the WWTPs.
Similarly, there is a need to collect flow data in the recipient streams at the point of discharge
for each of the WWTPs.
Nonpoint Sources
The nature of the problem of nonpoint source pollution is that there are always significant
data gaps resulting from extrapolation of data points across a landscape. Nonpoint source
pollutant analysis can always benefit from a greater density of sampling, such sampling being
limited by time and money.
Bacteria
Data are generally lacking altogether for bacteria in the upper part of the basin upstream from
Harpster. Monitoring in other areas of north Idaho of grazed forest and meadow systems has
shown elevated levels of bacteria. For the SF CWR SB A, this type of data was not available.
Temperature
For the purposes of this TMDL, we assume that the majority of human caused nonpoint
source heat loading over background is the result of streamside vegetative alteration causing
reduced shading of the streams and increased stream widths. We set our heat loading
reduction targets based on this assumption. However, we lack data or models that describe
pre-human vegetative condition/shading or stream channel morphology. We have used the
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results of various studies and models to arrive at a best approximation of desired streamside
vegetative conditions and assume that these conditions will mitigate the effects of human
activity with regard to stream temperature.
Sediment
Nonpoint source sediment is identified as bedload and TSS coming from a number of
sources. Various models and direct monitoring techniques have been used to quantify the
amounts of sediment from different sources and the fate of the sediment as it is transported
through the system. Clearly, a high level of uncertainty exists when mixing and matching so
many different technical approaches and models. A more unified and quality controlled
system of measuring or modeling sediment production, routing, fate, and transport
throughout the subbasin could add substantially to the reliability of the results of this
analysis.
Probably the largest source of uncertainty in the overall sediment budget analysis is the
routing of the bedload. It is recognized that sediment produced by various sources on the
landscape is not all routed directly through the hydrologic system. Differing percentages of
sediment are stored at various locations in the system (depositional areas, alluvial fans,
floodplains, etc.), depending on the nature of the watershed and the events producing the
sediment. As a generality, the larger the watershed under consideration, the higher
percentage of the sediment that is stored, rather than transported through the system. With
our various models and measurements, we are getting better at calculating sediment
production on the landscape. However, we have relatively little ability to quantify the
routing of such sediment. For the purposes of this TMDL, we used the Roehl (1962) routing
equation for all particle sizes except the coarse bedload. For coarse bedload, we applied the
results of a study by Beechie (2001). Both of these methods provide coarse generalities, and
a method for quantifying sediment routing through any particular hydrologic system would
add greatly to the sediment budget analysis.
The single largest source of sediment in the subbasin appears to be surface erosion from
agricultural and grazing lands. Numbers for this source were generated using the RUSLE
(Renard, et al. 1997) model in a GIS environment (Engle 1999). The largest source of error,
as this model was applied to the private lands of the subbasin, was the land use map. An up-
to-date land use map could change the results from this model. Similarly, the C-factor for
erosion from the different land uses needs to be validated for the different land uses of the
subbasin.
The largest portion of sediment in the SF CWR Subbasin is shown in this TMDL to move in
pulses associated with high rainfall, rapid snowmelt, or large rain-on-snow events. In the
largest of these, rain-on-snow events such as occurred in 1996, a significant portion of the
sediment is generated by mass failures. The NPNF inventoried mass failures from the 1996
events; however, no similar inventory exists for the private lands. We extrapolated the
results from the federally managed lands to the private lands, coupled with an aerial photo
investigation. Several assumptions had to be made about percent delivery and whether the
mass failure was natural or road related. A complete inventory of mass failures over the
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whole subbasin describing date of occurrence, size, percent delivery, particle size
distribution, and cause would significantly improve the reliability of information about this
sediment source. Alternatively, a model could be developed to predict sediment delivery
from mass failures over time, but these events are so episodic as to be hard to predict except
over a very long time frame.
To develop this TMDL, we collected data on in-stream erosion rates using a methodology
developed by the NRCS (Appendix L). The field measurements for the methodology are
fairly well set out, but the final calculation requires an estimation of bank recession rate,
based largely on best professional judgement. While we conducted considerable field
correlation and quality control of these estimates in the field, a better method for developing
these estimates would increase the reliability of this method and confidence in its results.
We were able to better quantify sediment from roads. We developed estimates of sediment
from the State Highway 14 that runs from Kooskia to Elk City based on the amount of gravel
that is crushed each year and distributed on the road. We reduced the sediment load through
estimates of percent roads delivering and the routing coefficient. Above the NPNF
boundary, NEZSED was applied to Highway 14. Better collaboration with ITD could result
in a much better understanding and quantification of this sediment load.
For the roads outside the federal boundary, we estimated sediment from the county roads
using the WEPP model. However, we have no data for sediment coming from private forest
practice or agricultural roads. The Forest Practices Cumulative Watershed Effects Process
for Idaho (IDL 2000) identifies roads as the major source of sediment from forest practices.
Similarly, NEZSED shows that sediment from roads is usually the major component. An
equivalent rate of sediment production could be assumed for private agriculture and grazing
use roads. However, we do not have an inventory of these roads, or any reasonable way to
estimate their contribution to the sediment budget. It is unlikely that privately owned roads
produce a greater magnitude of sediment than the WEPP modeled roads, so would be fairly
insignificant in the larger picture of sediment production from this landscape. We assume
that the nonpoint source sediment load reductions allocated to these water bodies will result
in any needed sediment reductions from private roads as well.
The NEZSED model does not estimate surface erosion coming from cattle grazing. We
estimated the effects of livestock as they affect stream bank stability, but we have no data to
estimate the amount of sediment that is being delivered from cattle trails and from other
effects of livestock grazing. This is a data gap for the federally managed lands only. For the
private lands, the RUSLE model estimates sediment coming from grazing in the land use and
land cover parameters.
We lack data on the legacy effects of sediment left in place from the dredge and placer
mining that took place in this subbasin 50 to 100 years ago. Relatively large portions of the
stream channels were altered significantly by these operations. Today they appear relatively
stable, with the dredge mining spoils appearing much the same as they have historically.
While these dredge-mined areas are considered to be poor salmonid habitat, we have not
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been able to differentiate between historic and more recent sediment effects. Studies and
data are limited on the effects of suction dredging taking place in the SF CWR Subbasin.
While the NEZSED model as part of the R1/R4 suite of models has estimated the
background sedimentation rate for forested landscapes, a similar estimation of background
erosion rates for agricultural and grazing lands is largely nonexistent. While it would take a
significant change in the estimate of background erosion rates for private lands to change
their load reduction allocations very much, the fact remains that this parameter is estimated
with limited information.
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4. Subbasin Assessment - Summary of Past and Present
Pollution Control Efforts
4.1 Point Source Control Efforts
Of the point sources of pollution in the SF CWR Subbasin, the community WWTPs are
among the largest in the subbasin, however they have a relatively strong record for treatment
before discharging to waters of the subbasin. Other point sources of interest are wood
products industrial plants and recreational suction dredge mining operations.
Wastewater Treatment Facilities
Red River
The Red River Ranger Station is located near the confluence of the South Fork Red River
and the main stem of Red River. The WWTP, operated by the NPNF, consists of secondary
treatment and chlorine disinfection. Sewage flows to a waste stabilization pond followed by
passage through a sand filter for treatment. This is followed by chlorine disinfection prior to
release into the South Fork Red River at the confluence with Red River proper (USEPA
2002e). Exceedances listed in discharge monitoring reports between 1995 and 2000,
according to the USEPA fact sheet for plans to reissue the NPDES permit to the Red River
Ranger Station (USEPA 2002e), included exceedances of the following parameters:
• BOD (1995-2000)
• TSS (1995-1997, 1999)
• Fecal coliform (1995)
• pH(1995)
The NPDES permit for the Red River Ranger Station WWTP expired on December 31, 1978,
and was administratively extended on October 29, 1979. A renewal application was received
by USEPA on June 25, 2001, and USEPA reissued the permit on October 1, 2002. The new
permit includes the stipulation that the permittee develop a facility plan and schedule in the
event that average annual input exceeds capacity for three consecutive months. More
information is available on the Region 10 USEPA Web site at www.epa.gov/rlOearth
(USEPA 2002e).
Elk City
Elk City is located in the American River watershed. The Elk City Water and Sewer
Association municipal WWTP uses treatment equivalent to secondary treatment and chlorine
disinfection. The facility collects wastewater through a gravity sewer collection system and
treats it in an aerated waste stabilization pond. It is then disinfected using chlorine prior to
release into Elk Creek, a tributary of the American River (USEPA 2002d). Exceedances
listed in discharge monitoring reports between 1995 and 2000, according to the USEPA fact
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sheet for plans to reissue the NPDES permit to the Elk City Water and Sewer Association
(USEPA 2002d), included exceedances of the following parameters:
• BOD (1995, 1998)
• Total residual chlorine (1995-1998)
• BOD percent removal (1995-2000)
• pH (1996-1998)
The NPDES permit for the Elk City Water and Sewer Association expired on May 31, 1993.
The initial renewal application was received by USEPA in December 1992. An updated
renewal application was filed on July 9, 2001. The USEPA reissued the permit on October
1, 2002. The new permit includes the stipulation that the permittee develop a facility plan
and schedule in the event that average annual values exceed capacity for three consecutive
months. More information can be obtained by visiting the Region 10 USEPA Web site at
www.epa.gov/rlOearth (USEPA 2002d).
Grangeville
The city of Grangeville operates a municipal WWTP that discharges into Threemile Creek.
Originally the system consisted of a trickling filter and primary clarifier with anaerobic
digestion, followed by drying beds and treatment in a single chlorine tank before discharge.
This system was ineffective, as high flows in the spring often overloaded the system.
In 1989, the City of Grangeville upgraded with a new $3 million system designed to handle
0.88 million gallons per day (MGD). The new system consists of activated sludge and a boat
clarifier inside oxidation ditches, followed by a clear water weir and three chlorine contact
tanks. The treated effluent is discharged into Threemile Creek via an underground pipe
(Klecha 2002). Inspections in 1996 (USEPA 1997) and 2002 (DEQ 2003) found the facility
to be generally in compliance. An NPDES permit was issued to Grangeville on December 30,
1987, and expired on December 29, 1992. The USEPA will initiate reissuance of the permit
once the SF CWR TMDL is complete.
Stites
The City of Stites is located on the main stem SF CWR. The municipal WWTP for the City
of Stites uses treatment equivalent to secondary treatment and chlorine disinfection. Sewage
is moved through a pump station to a lagoon cell where it is treated. It then undergoes
chlorine disinfection before release into the SF CWR (USEPA 2002b). Exceedances listed in
discharge monitoring reports between 1995 and 2000, according to the USEPA fact sheet for
plans to reissue an NPDES permit to the City of Stites (USEPA 2002b), included
exceedances of the following parameters:
• BOD (1995)
• TSS (1995-2000)
• Fecal coliform (1995-1999)
• BOD percent removal (1995-1999)
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The NPDES permit for the City of Stites municipal WWTP expired on January 9, 1991. The
renewal application was received by USEPA on July 31, 2001. Upon completing an anti-
degradation analysis, USEPA concluded that continued discharge will not reduce water
quality beyond the mixing zone. The USEPA reissued the permit on October 1, 2002. The
new permit includes the stipulation that the permittee develop a facility plan and schedule in
the event that average annual values exceed the capacity for three consecutive months. More
information can be obtained by visiting the Region 10 USEPA Web site at
www.epa.gov/rl Dearth (USEPA 2002b).
Terry Nab, the engineer developing the facility plan for the City of Stites, is recommending
as part of this plan that the City of Stites connect with the City of Kooskia's WWTP. The
City of Stites recently applied for financial assistance with the U.S. Department of
Agriculture's Rural Utilities Service, which has prepared an Environmental Assessment
evaluating the effects of connecting the City of Stites to the City of Kooskia's sewage
system. The proposed project would additionally make improvements to the City of Stites'
sewage collection system. The comment period required under the National Environmental
Policy Act (NEPA) process ended July 19, 2002. As of this time, the cities have decided to
move forward with project, but have not yet begun construction.
Clearwater Forest Industries
Clearwater Forest Industries (CFI) is located off State Highway 12 between Stites and
Kooskia. The timber processing operation has a total of seven outfalls discharging to the
main stem SF CWR. Outfalls 1, 3, and 7 combine wastewater from log deck sprinkling
during April through October, and storm water. Outfalls 2, 5, and 6 are for storm water only.
Outfall 4 is for a combination of storm water and boiler blowdown with recycled kiln
condensate. Treatment of outfalls 3, 4, and 7 is provided through the use of settling ponds,
while outfalls 1, 2, 5, and 6 receive no treatment prior to release to the SF CWR (USEPA
2002c).
An application for an NPDES permit was received by USEPA on March 29, 1996. The
facility was contacted in August 2001 to determine if there were any updates in the
application. At that time the facility indicated that they were attempting to contain all
process (non-storm water) wastewater on-site, in order to avoid the need for NPDES permit
coverage, and instead apply for coverage under USEPA's Multi-Sector General Permit for
industrial stormwater. Since that time, CFI has determined that there are times when they
cannot contain process wastewater on-site and must discharge to the SF CWR, primarily
during the spring when the source of their raw water (SF CWR) is of low quality (CFI 2003).
As a result, it appears that renewal of their NPDES wastewater permit is required. More
information can be obtained by visiting the Region 10 USEPA Web site at
www.epa.gov/rlOearth.
Kooskia
The City of Kooskia is located on the main stem SF CWR near the confluence with the
Middle Fork Clearwater River. The City of Kooskia operates a municipal WWTP that uses
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treatment equivalent to secondary treatment and disinfection. Sewage is treated in a two-cell
aerated lagoon, followed by a settling contact chamber. Wastewater is then disinfected by
chlorination prior to discharge to a polishing ditch prior to release into the SF CWR at river
mile 0.5 (USEPA 2002a). Exceedances listed in discharge monitoring reports between 1995
and 2000, according to the USEPA fact sheet for plans to reissue an NPDES permit to the
City of Kooskia (USEPA 2002a), included exceedances of the following parameters:
• TSS (1995-1999)
• Fecal coliform (1995-2000)
• BOD percent removal (1995-1999)
• pH(1996)
The NPDES permit for the City of Kooskia expired on March 20, 1991. A renewal
application was received by USEPA on May 24, 2001. Upon completing an anti-degradation
analysis, USEPA concluded that continued discharge will not reduce water quality beyond
the mixing zone in the SF CWR and reissued the permit on June 26, 2002. The new permit
includes the stipulation that the permittee develop a facility plan and schedule in the event
that average annual values exceed capacity for three consecutive months. More information
is available on the Region 10 USEPA Web site at www.epa.gov/rlOearth (USEPA 2002a).
Suction Dredge Mining
The IDWR regulates suction dredging through the Idaho Stream Channel Protection Act
(IDAPA 37.03.07.064). Under this statute, dredge miners are required to obtain a permit
from IDWR (IDWR 2003). Small-scale operations (less than or equal to 5 inch nozzle; less
than or equal to 15 horsepower) are covered under the One Stop Recreational Dredging
Application permit process (a.k.a. General Permit). The U.S. Army Corps of Engineers
(ACOE) has determined that recreational suction dredge mining activities that meet the
criteria established by IDWR for their One-Stop Recreational Dredging Permit do not require
a CWA Section 404 permit (ACOE 2003).
In the SF CWR Subbasin, dredging is only allowed in the SF CWR mainstem, and only from
July 15 through August 15 each year, in order to avoid periods when chinook, cutthroat, and
steelhead are spawning and eggs are incubating. The USEPA reviewed the IDWR General
Permit for suction dredge mines in 1998, and found that it adequately addresses
environmental concerns from these operations (USEPA 1998). Although there is currently
no limit on the number of facilities which can operate in the SF CWR Subbasin under the
General Permit, the actual number of permits issued in recent years was 15 in 2000, seven in
2001, and eight in 2002 (IDWR 2002).
Larger scale operations, or facilities that operate in waters or time frames not listed under the
IDWR General Permit, must obtain permits from IDWR and the ACOE under the Joint
Application Permit process. In 2000, the USFS received applications to operate suction
dredges within the NPNF which did not fall within the General Permit. The Genesis Placer
proposal is to operate two dredges (5 and 8 inch diameter nozzles) year around in the Red
River. A draft environmental impact statement was issued for this proposal in July 2000.
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The El Luky Duk proposal is to operate four different dredges of 3, 5, 6 and 8 inch diameter
nozzles from July to October on the SF CWR. The Booger Placer proposal is to operate an 8
inch dredge on Little Elk Creek. The Clearwater #1 proposal by Daniel Templeton plans to
operate an 8 inch dredge powered by three 8 horsepower engines in the SF CWR just
upstream of the confluence with Johns Creek. Within the past five years, the only known
operation of dredges greater than 5 inch was a test run of the 8 inch Booger Placer dredge on
July 6-7, 2000.
When compared to other sediment sources in the subbasin including roads and natural
erosion processes, sediment loading from current recreational suction dredge operations
appears to be minimal given their limited number, size, and 30 day annual operating window
allowed under the current IDWR general permit. This is consistent with Harvey and Lisle
(1998) who indicate that single dredging operations cannot mobilize significant volumes of
fine sediment compared with the volume mobilized during high seasonal flows from
throughout a watershed, when large portions of the streambed are entrained.
Suction dredges are considered to be point sources, and therefore are required to obtain an
NPDES permit to discharge (USEPA 1998). Currently no NPDES permits have been issued
for suction dredges within the SF CWR, but an application for permit coverage has been
received for the Genesis dredge on Red River.
A great deal of literature exists on the effects of suction dredge mining on water quality and
stream habitat. While the literature is mixed in terms of the nature and severity of effects
from dredge mining operations, serious impacts to water quality and habitat have been
documented, depending on the size, location and manner in which dredges are operated. For
a recent summary of suction dredge impacts, see Harvey and Lisle (1998).
The NPNF began tracking, inspecting, and monitoring suction dredges in the SF CWR in
1980, with a more concentrated effort since 1995. The focus has been primarily on
recreational dredging (5 inch or less diameter nozzle), but also to some extent on commercial
dredging (greater than 5 inch diameter nozzle). The NPNF requires a Notice of Intent (NOT)
from recreational suction dredgers which indicates the dates and locations of proposed
mining. Between 1995 and 2000 inspections of these operations and instream monitoring
were performed seasonally (DeRito 2000). The NPNF and DEQ have discussed additional
monitoring of these operations, but there are no firm plans at this time.
4.2 Nonpoint Source Control Efforts
Nonpoint source pollution control efforts in the SF CWR Subbasin are numerous and
widespread. For the most part, they come from the implementation of standardized BMPs
for forestry and agriculture. Several specially funded projects have been implemented in the
subbasin since passage of the CWA.
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Agriculture
State, tribal, federal, and private lands in the subbasin have been cultivated and grazed since
the mid-1800s (USFS 1998). Records are kept only on current contracts with private
landowners for land enrolled in the Conservation Reserve Program through the Farm
Services Agency. Currently, the records show contracts as early as 1992 and extending
through 2011. Land enrolled in the program in the SF CWR drainage as a whole totals
1,743.7 acres, which includes the Cottonwood Creek watershed. Most of the land is enrolled
as permanent wildlife habitat. There are some lands under contract to maintain existing
vegetative cover, others to maintain permanent grasses and lagoons, some to provide wildlife
food plots, two to maintain shallow water areas, one to establish a shelter belt (windbreak
adjacent to a stream), and one to establish a tree planting plot (Sickels 2002).
The NRCS in Grangeville has treated, or is currently treating, approximately 320 acres of
cropland, pasture, and hay land under the NRCS Environmental Quality Incentives Program
in the SF CWR Subbasin. The program encourages using no-till agriculture, planting grass
waterways, and seeding pastures and hay lands (Spencer 2002). Cottonwood Creek has had a
significant amount of land treated through Cottonwood Creek TMDL implementation efforts,
including a large number of acres seeded using no-till/direct-seed methods and several acres
managed under nutrient management plans. An off-site water facility and some filter strips
have also been installed. Additionally, more areas are expected to receive treatment in the
near future. For more information, refer to the Cottonwood Creek TMDL Implementation
Plan available at the NRCS office in Grangeville.
The NPT Land Services Division is responsible for writing conservation plans of operations
for agriculture leases on Indian-owned land, based on wise land use practices and owner
input. The conservation plans of operations requirements include residue management and
specific tilling requirements. Residue is not to be burned and, except for harvested grass
seed, must be returned to the soil. Residue cannot be grazed or baled without authorization.
Residue requirements are additionally in place specifying percent coverage for various low
and high-residue crops. Tilling and seeding operations are to be performed across slope or as
close as possible to contour. These operations must be performed parallel to diversions or
terraces, where present (NPT 2002a).
Grazing regulations in the NPNF were enacted when the forest was established in 1908.
Currently, there are 12 grazing allotments active in the subbasin (USFS 1998).
Forestry
Timber harvest in the SF CWR Subbasin began in the mid- to late-1800s in association with
mining activities. Commercial harvest began in the 1940s. From this time until the 1960s,
harvest was largely selective, removing only high-value species. At this time ground
skidding, even on steep slopes, was not considered problematic. As a result, skid trail
density was higher than that of the present (USFS 1998). Since 1970, cable yarding has been
required on steep slopes, reducing the amount of skid trails necessary. In addition, it has
become common practice to obliterate these trails when they are no longer necessary. Fuels
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abatement practices and site preparation activities have also been changed to reduce the
amount of soil disturbances on harvested areas. In the 1960s and 1970s, clearcutting became
the dominant harvest method, but decreased in the mid-1980s (USFS 1998).
In 1974, rules and regulations were adopted under the FPA, giving oversight of all forest
practices on forest land to the state of Idaho. Inspections are made by the DDL and the
federal land management agencies to ensure compliance (USFS 1998). The NPNF, through
the federal Pacific Anadromous Fish Strategy (PACFISH), generally does not permit timber
harvest in riparian habitat conservation areas and other areas where the activity would pose
an unacceptable risk to aquatic or riparian habitat (USFS and BLM 1995).
The NPT's Forest Management Plan (1999) outlines BMPs that are to be implemented on
tribal-owned lands during harvest activities. These include planting riparian buffer strips,
following yarding practice requirements, following road design stipulations, and allowing
revegetation time prior to beginning grazing activities (NPT 1999).
4.3 Watershed Improvement Projects
The USFS administers approximately two-thirds of the land in the SF CWR Subbasin as the
NPNF. The NPNF, in conjunction with the BLM and the NPT, has been involved in
numerous watershed improvement activities in the SF CWR Subbasin. Pollution control
efforts have been a regular part of forestry operations. In the 1980s the Bonneville Power
Administration (BPA) funded a habitat improvement project. The BPA and the NPNF
entered into an agreement in 1984 (Project 84-5) to improve fish habitat in accordance with
the Pacific Northwest Electric Power Planning and Conservation Act of 1980 (Siddall 1992).
The act stipulated mitigation and enhancement offish populations affected by hydroelectric
power development in the Pacific Northwest. The original agreement included plans to
improve the Crooked and Red Rivers. A series of amendments subsequently resulted in the
plan including improvements in four glory holes. These massive holes left in hillsides from
hydraulic mining from 1852 through the 1950s exposed large areas of bare soil on extremely
steep slopes. Some efforts were executed in an attempt to reduce erosion prior to Project 84-
5 at some of these glory holes, but they were largely ineffective.
The USFS and BLM produced a land management plan, PACFISH (USFS and BLM 1995),
in response to the declining salmon populations in the subbasin and the listing of Snake River
fall chinook (Oncorhynchus tshawhytscha) as threatened in the Clearwater Basin under the
ESA of 1973 (Federal Register 1992). The plan's strategies and goals aim to slow
degradation and begin the restoration of habitat for anadromous fish. The plan sets forth
management measures for proposed and new activities involving resource management and
land use decisions that pose an unacceptable risk to anadromous fish. The strategy is applied
to all proposed projects (including recreation, mining, timber, roads, and grazing
management projects) required to comply with the ESA, NEPA, the National Forest
Management Act, the Federal Land Policy and Management Act, and any other applicable
environmental law. It additionally outlined measures for restoration of watersheds and fish
and wildlife habitat within anadromous fish habitat. This was adopted as an interim plan
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prior to the decisions resulting from the Interior Columbia Basin Ecosystem Management
Project (ICBEMP) (USFS and BLM 2000). The PACFISH policy is still in place.
In 1994, BLM and USFS, in order to determine the status of the whole Columbia Basin
ecosystem upstream from The Dalles, OR, commenced the ICBEMP (USFS and BLM 2000).
Findings from this project were considered for the South Fork Clearwater River Landscape
Assessment completed by the NPNF in 1998 (USFS 1998). This document characterized
both social and ecological conditions within the subbasin on which to base forest
management decisions. It identified water quality as one of the key issues to be addressed.
Resulting recommendations from this document included road maintenance and fish habitat
conservation. Road decommissioning activities in the NPNF increased after 1995, and
currently forest improvements focus on road decommissioning and instream improvements
(Gerhardt 2002b).
The NPNF released the South Fork Clearwater River Biological Assessment (BA) in April
1999 (USFS 1999). In accordance with the ESA, this assessment presents the existing
conditions in the subbasin using the best available data. Screening of ongoing and proposed
activities was presented on a watershed basis. The BA is used to assess all ongoing and
proposed activities that affect listed species, including Snake River steelhead (Oncorhynchus
mykiss\ bull trout (Salvelinus confluentus\ and fall chinook salmon (O. tshawhytscha)
(USFS 1999). The NPNF conducts regular monitoring of forest practices. The results are
reported annually in forest plan monitoring and evaluation reports.
The Clinton administration's Roadless Area Conservation Rule (USFS 2002b), issued on
January 12, 2001, established prohibitions on road construction and reconstruction and
timber harvest in inventoried roadless areas on National Forest System lands. In the NPNF,
127,000 acres of current inventoried roadless areas (6% of the NPNF) are potentially affected
by this rule (USFS 2002b).
The NPT Fisheries Watershed Division has constructed exclosures in meadows and riparian
areas, implemented channel alignment improvements, and performed plantings on stream
banks and meadows throughout the watershed. Monitoring of these projects has been on-
going to assess effectiveness. Project areas have included Red River, Newsome Creek, Johns
Creek, McComas Meadows (Meadow Creek), and Mill Creek (McRoberts 2002). The NPT
is currently planning road decommissioning in several watersheds in the subbasin.
Specific pollution control activities are presented in the following text by watershed. In
addition to these specific projects, the BA presents road and trail maintenance and
stabilization activities as well as outfitter, timber sale, and grazing allotment controls as they
contribute to the mitigation efforts throughout the SF CWR Subbasin (USFS 1999).
Red River
Road building, logging, grazing, and dredge mining have heavily impacted the Red River
drainage. Much of the riparian vegetation has been eliminated and the river channel has been
straightened as a result of these activities. Project 84-5, a product of the agreement between
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BPA and the NPNF in 1984, involved the installation of instream structures, re-establishment
of vegetation, installation of streamside fencing to alleviate grazing impacts, and stabilization
of areas previously disturbed by dredging activities. From 1985 to 1989, six sediment traps
were constructed in the Red River drainage to reduce sediment reaching fish rearing and
spawning areas (Siddall 1992).
The Cal-Idaho glory hole, the largest in the SF CWR Subbasin, is located on private land
(Stewart 2002). Runoff from this pit transports sediment to the Red River. In 1990, as part
of Project 84-5, a rock crib check dam to trap sediment was installed in a small canyon that
drains the majority of the glory hole (Siddall 1992). The dam was effective; however its
storage capacity proved to be too small and it was soon filled with sediment (Gerhardt
2002c). Further projects focusing on the Cal-Idaho glory hole were discussed in the mid-
1990s, but actions were not initiated. The NPNF had a completed design for a more elaborate
trap at the outlet to Red River. The trap was to be constructed busing BPA funds, but the
landowner did not grant permission (Gerhardt 2002c). Shearer Lumber started using the Cal-
Idaho glory hole as a wood waste disposal site, covering the eroding banks with wood waste.
This, in fact, has been successful in halting the erosion. Unfortunately, the owner of the site
could not be convinced to continue with this operation (Wilhite 2002).
Many improvement activities had been complicated due to the large amount of degraded land
being privately owned. There were difficulties in acquiring riparian easements and providing
long-term maintenance offence and instream structures throughout the execution of Project
84-5. Permission to perform work on private land was often delayed or not granted (Siddall
1992).
Activities in 1990 and 1991, however, focused on private land just below the confluence of
the South Fork Red River and the Red River proper. These activities were collectively
known as the "Mullins Project," named after the private landowner, E. Mullins. The BPA-
funded project was largely the result of cooperation from the Idaho National Guard, the Red
River Ranger District, Shearer Lumber Company, Kelly Creek Flycasters, Potlatch
Corporation, IDFG, and the U.S. Fish and Wildlife Service. Within this meadow area of
approximately 0.75 mile in stream length, the channel was realigned, banks stabilized, and
width to depth ratio decreased. Instream structures were also installed, and riparian
vegetation was planted. As of April 1992, the project was considered successful (Siddall
1992).
In 1993, the BPA, the National Fish and Wildlife Foundation, IDFG, Rocky Mountain Elk
Foundation, and Trout Unlimited purchased a 314-acre parcel in the lower Red River
drainage. This parcel became the Red River Wildlife Management Area and was deeded to
IDFG to manage with the goal of restoring the lower Red River Meadow ecosystem to high
quality habitat for bull trout (Salvelinus confluentus\ steelhead trout (Oncorhynchus mykiss\
chinook salmon (Oncorhynchus tshawytscha), and other fish species (LRK Communications
2001). Project planning began in 1994 and implementation began in 1996. Monitoring was
initiated in 1997 to assess the effectiveness of the project. As of 2001, channel length in the
project area had been increased by 5,045 feet compared to pre-restoration conditions. Slope
had been decreased by 40 percent, and sinuosity had been increased by 60 percent. These
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efforts have resulted in a decreased water velocity at bankfull, alleviating areas of bank
erosion. Channel width and depth characteristics have additionally been improved in the
project area (LRK Communications 2001). More information on the project can be accessed
at http://boise.uidaho.edu/hosted/redriver (LRK Communications 2001).
The 1999 NPNF BA summarized proposed activities that may have affects on the Red River
drainage (USFS 1999). Included in the summary was a discussion of the proposed Hercules
Mine reclamation and Soda Creek 1 and 2 Rock Pit restorations. The Hercules Mine, a lode
gold mine, is located in the Ditch Creek drainage. Reclamation would involve removing
trash and mining structures, breaking-up the road surface over roughly 20 acres, and seeding
trees. Reclamation of Soda Creek 1 and 2 Rock Pits would include reshaping pits, replacing
topsoil, creating water bars, and planting vegetation to reduce erosion (USFS 1999). Neither
of these projects started prior to the drafting of this document (USFS 2002a). Improvements
were made in the Bridge Creek Campground near Red River Hot Springs to alleviate
sediment input and fish harassment as recommended by the 1999 BA (USFS 1999).
Campsites adjacent to a tributary of Bridge Creek were blocked and tables removed to
decrease traffic in the area (Sherwood 2002).
In 2001, the NPT, in cooperation with the NPNF, initiated a road and culvert inventory,
which will be used to develop a transportation plan and prioritize upgrades in the watershed
(McRoberts 2002). Currently, several vegetation treatment projects with associated aquatic
improvement are being analyzed for the Red River basin, including the Red River Salvage
and Red Pines projects.
Crooked River
The agreement between BPA and the NPNF (Project 84-5) for the Crooked River included,
among others, goals of improving fish and riparian habitat. The project area extended from
the confluence with the SF CWR to Fivemile Creek. Primary focus was placed on riparian
revegetation, creation of floodplains where tailings piles had confined flow, and cover
installation in the existing channel. Bank stabilization also occurred in areas where sharp
bends in the channel had caused unstable and eroding banks (Siddall 1992).
The NPNF's 1999 BA summarized projects with potential watershed affects in the Crooked
River drainage (USFS 1999). According to the BA, drilling exploration (Petsite III mine
exploration) and resulting road construction (approximately 2.5 miles of road) occurred
southeast of the Old Orogrande town site in 1996 and 1997. Some restoration occurred
following these activities (USFS 1999). Three additional planned restoration projects (two
road obliterations, one road closure, and some fish habitat structures in Crooked River) were
not completed.
The NPNF and DEQ are working with the proponent of the Golden Eagle Mine, which was
established in 1974, to minimize potential watershed affects. The only impact from this mine
at the time of the BA was a road that was to be repaired by the end of the 2000 field season
by the NPNF (USFS 1999).
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American River
Elk City is located in the American River watershed. The BLM administers approximately
14,000 acres of land in the SF CWR Subbasin, primarily in the Elk City township. In the
mid-1990s, the BLM prepared an aquatic habitat management plan for fish-bearing streams
in the Elk City township. Activities outlined in the plan include riparian and wetland
restoration, installation of instream fish habitat structures, relocation of stream channels, and
construction of rearing ponds and channels (USFS 1999). Activities have been focused
primarily on the dredged areas of American River. Implementation has been slowed by
issues arising with mining claims. To date, the plan is roughly 30 percent implemented
(Johnson 2002b). The BLM has recently closed problem roads under its jurisdiction to
motorized vehicles in an effort to reduce erosion. The BLM has made road improvements,
such as culvert removal and replacement, and is currently in the process of finalizing plans to
further survey and improve existing roads (Johnson 2002b).
In addition to road closures and improvements, BLM has been involved with riparian
exclosures and stream channel restoration efforts throughout the watershed. Instream
structures and some riparian plantings have been the primary focus of restoration efforts. A
total of 5 miles of instream structures/improvements have been completed on the American
River by BLM. Approximately 0.3 miles of the East Fork American River have received
improvements (Johnson 2002b). Grazing plans have been developed to reduce grazing
impacts along stream banks and include restrictions on seasonal use, standards for utilization,
and riparian grazing restrictions. Streams with overgrazing problems, including Elk Creek
and Big Elk Creek, have had riparian exclosures constructed. The BLM Elk Creek and Big
Elk Creek riparian pasture exclosures have been put in place for a total of 1 mile in stream
length (Johnson 2002b). Section 7 ESA consultations with NMFS have been completed for
all BLM grazing allotments (Johnson 2002b).
Newsome Creek
The Haysfork glory hole is a result of hydraulic mining activities in the early 1900s. This
glory hole has contributed high levels of sediment into the Newsome Creek system. Efforts
to rehabilitate the area began in the mid-1980s and continue today. Efforts in the mid-1980s
proved ineffective, as slope failure returned the pit to the steep-sloped condition that had
existed prior to rehabilitation. The glory hole was scheduled for work under the Project 84-5,
but following concerns from contractors, engineers, and hydrologists, activities did not
commence until 1991. At this time, the top of the glory hole was seeded with grass and
fertilized. The drainage system in the hole was improved and the area was lined with erosion
control material. Existing sediment traps were emptied on the stream side of the hole, and a
third trap was installed above the two existing traps (Siddall 1992). In 1997, a large settling
pond with a 40-year storage capacity was created at the mouth of the draw which drains the
glory hole in an effort to reduce sediment input to Newsome Creek from the glory hole
(USFS 1999). Efforts to date have been partially effective. The upper slopes and portions of
the lower slopes have been stabilized. However, oversteepened and unstable slopes still exist
on the site.
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In addition to these efforts, the NPT, in collaboration with the NPNF, has set the goal of
decommissioning approximately 7 miles of roads in the Newsome Creek drainage and is
initiating a feasibility study to determine the destiny of the dredge mine tailings and their
effect on the stream channel (McRoberts 2002). Also, an EAWS for Newsome Creek is in
the final stages of completion, which makes recommendations for instream, riparian, and
upland improvements.
Leggett Creek
Two projects were initiated in the Leggett Placer glory hole by the NPNF as part of Project
84-5. Trees and shrubs were planted in the glory hole in 1987, and a sediment trap was
constructed adjacent to the road below Leggett Placer. Runoff was also diverted from
Leggett Placer through the pond (Siddall 1992).
There were no records of glory hole planting success as of 1991, and in his Project 84-5
report, Siddall stated that further planting would be ineffective (Siddall 1992). The sediment
trap was reported to be 50 percent effective at best early on, delivering sediment to Leggett
Creek in major storm events (Siddall 1992). Sediment is currently removed from the trap
every year and relocated to a flat area near the mouth of Leggett Creek, where it is contoured
and seeded. This has reportedly worked well (USFS 1999).
Johns Creek
The NPNF has rehabilitated several roads and trails and obliterated various roads in the Johns
Creek watershed (USFS 1999). In addition, the 1999 BA outlined plans to stabilize a slide
on Road 9429, although work had not begun as of 2002 (USFS 2002a).
The NPT Fisheries Watershed Division installed approximately 2.5 miles offence in the
Johns Creek watershed. The resulting exclosure protects approximately 1 mile of stream
length along Johns Creek from the effects of grazing. This work was accomplished with
funds from the National Atmospheric and Oceanic Administration's Pacific Coastal Salmon
Recovery Fund (McRoberts 2002).
Meadow Creek
Fisher Placer activities utilized water from Meadow Creek for mining operations using a 4-
mile flume. Since mining ended in 1918, some revegetation has occurred naturally in the
Fisher Placer. Heavy erosion has prevented vegetative growth on the steep west and north
sides of the glory hole, and erosion still occurs throughout the placer. From 1982 to 1987,
seeding with grasses and clover took place along the slopes. This was successful in some
areas, but did not take hold in more heavily eroding areas. In 1988, BPA funds were used to
plant trees on the slopes of the main glory hole as well as on two test plots to determine
success. At 3.5 months, erosion was determined to be quite significant at both plots (Siddall
1992). Erosion of the slopes has continued, with significant movement in 2000. The glory
hole is currently located on private land (Paradis 2002) in the Meadow Creek watershed on a
hillside. It is not immediately adjacent to Meadow Creek or a tributary (Lewis 2002).
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As a part of Project 84-5, a partial fish barrier was removed from Meadow Creek in 1986.
Prior attempts had been made to modify barriers-once in the late 1970s using explosives and
again in 1984 with further blasting. Both attempts were ineffective at improving passage.
With annual maintenance efforts, though, the 1986 effort has proved successful (Siddall
1992).
The Meadow Face EIS and Record of Decision have been completed. This project contains a
large component of watershed improvement work, including soils restoration, road
decommissioning, road improvements, landslide stabilization and instream improvements.
The NPT Fisheries Watershed Division has been involved in fence installation, riparian and
stream channel improvements, and road decommissioning activities in the Meadow Creek
drainage since 1997 with funding from BPA and in conjunction with the NPNF. Fencing
activities began in 1997 in McComas Meadows, protecting the area from the impacts of
grazing. A total of approximately 600 acres is currently protected in this area. In addition,
riparian plantings, channel redirection, and removal of a constructed ditch have further
improved the habitat of Meadow Creek. Culvert replacements are planned for the watershed
as is decommissioning of approximately 20 miles of roads (McRoberts 2002). The NPNF
performed channel restoration activities on Swede Creek, a tributary of Meadow Creek, in
2001 (USFS 2002a).
A stabilization plan was developed for a large slide area near the mouth of Meadow Creek.
The slide contributes large quantities of sediment to Meadow Creek and the SF CWR. The
plan involves a relief ditch to partially drain ponds at the head of the slide, but has not yet
been implemented (USFS 1999).
South Fork Main Stem
Watershed improvement recommendations for the SF CWR main stem are summarized in the
1999 NPNF BA (USFS 1999). These improvements include the obliteration and
rehabilitation of roads and the removal of sediment from the Leggett Placer (mentioned
previously). Additionally, the document recommended reclamation activities on a small
portion of the Prospector Bunny Mine. Seeding and mulching activities were suggested to
rehabilitate deep gullies and unstable slopes at this site (USFS 1999).
Road rehabilitation activities on the Fisher Placer Road and Road 279L were completed by
the NPNF by 2001. These resulted in improved drainage and stabilized road surfaces, which
will reduce erosion. In addition, Bully Creek Road rehabilitation activities were completed
in 2001, resulting in road stabilization in an area that had experienced past failures and had
the potential for a number of future ones. These failures had restricted access for
maintenance and resulted in a number of plugged culverts. Areas disturbed during
rehabilitation activities were reseeded and mulched (USFS 2002a).
The Starbucky EIS in the Santiam, Buckhorn and several smaller face watersheds is currently
being implemented. In includes road improvements, road decommissioning, and mine
stabilization.
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5. Total Maximum Daily Loads
A load is fundamentally a quantity of a pollutant discharged over some period of time and is
the product of concentration and flow. A TMDL prescribes an upper limit, called the load or
load capacity (LC), on the pollutant load discharged from all sources so as to assure water
quality standards are met. The load capacity is allocated among the various sources of the
pollutant. Pollutant sources fall into two broad classes: point sources, each of which receives
a wasteload allocation (WLA); and nonpoint sources, which receive a load allocation (LA).
Natural background (NB), when present, is considered part of the LA, but is often broken out
on its own because it represents a part of the load not subject to control. The magnitude of
the natural background load determines the amount of the LC that is available for allocation
to human-made pollutant sources.
Because of uncertainties regarding quantification of loads and the relation of specific loads to
attainment of water quality standards, the rules regarding TMDLs (40 CFR § 130) require
that a margin of safety (MOS) be a part of the TMDL. The MOS may be implicit, as in
conservative assumptions used in calculating the LC, WLA, and LAs. The MOS may also be
explicitly stated as an added, separate, quantity in the TMDL calculation
The TMDL components presented above can be summarized symbolically as:
LC = MOS + NB + LA + WLA = TMDL
The equation is written in this order because it represents the logical order in which a loading
analysis is conducted. First the LC is determined. Then the LC is broken down into its
components: taking into consideration the MOS and NB, the remaining portion of the LC is
then allocated among point and nonpoint pollution sources.
Another step in a loading analysis is the quantification of current pollutant loads by source.
This allows the specification of load reductions as percentages from current conditions,
considers equities in load reduction responsibility, and is necessary in order for pollutant
trading to occur. Also a required part of the loading analysis is that the LC be based on
critical conditions - the conditions when water quality standards are most likely to be
violated. If protective under critical conditions, a TMDL will be more than protective under
other conditions. Because both LC and pollutant source loads vary, and not necessarily in
concert, determination of critical conditions can be more complicated than it may appear.
Due to the diverse nature of various pollutants, and the difficulty of strictly dealing with
loads, the federal rules allow for "other appropriate measures" to be used when necessary.
These "other measures" must still be quantifiable, and relate to water quality standards, but
they allow flexibility to deal with pollutant loading in more practical and tangible ways. The
rules also recognize the particular difficulty of quantifying nonpoint loads and allow "gross
allotment" as a LA where available data or appropriate predictive techniques limit more
accurate estimates. For certain pollutants whose effects are long term, such as sediment and
nutrients, seasonal or annual loads are allowed.
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This document has four types of TMDLs: a bacteria TMDL for Threemile Creek, nutrient
and associated dissolved oxygen TMDLs for Threemile Creek, a set of temperature TMDLs
that cover all of the water bodies in the subbasin, and a set of sediment TMDLs for
Threemile Creek, Butcher Creek and the main stem SF CWR. The Threemile Creek bacteria
TMDL is presented in Section 5.1, the nutrient TMDLs for Threemile Creek in Section 5.2,
the temperature TMDLs in Section 5.3, and the sediment TMDLs in Section 5.4.
5.1 Bacteria TMDL-Threemile Creek
Threemile Creek is listed for bacteria, and data discussed in Chapter 2 indicate that
development of a bacteria TMDL is warranted. Threemile Creek has been designated by the
state of Idaho for secondary contact recreation. A secondary contact recreation designation is
for waters in which only incidental human contact with the water is expected. It is not likely
that such water bodies would be used for swimming, but some water contact, such as from
fishing or other activities may occur. Idaho WQS include criteria for E. coli that is intended
to provide protection from microbiological illnesses that may be caused by incidental water
contact. The purpose of this TMDL is to reduce bacteria levels in order to meet these criteria
and fully support the secondary contact recreation beneficial use.
Design Conditions
Numeric criteria to protect recreational beneficial uses apply to all perennial reaches of
Threemile Creek and to intermittent reaches of Threemile Creek during periods of optimum
flow (defined as 5 cfs or greater in Idaho WQS). Four sampling points in Threemile Creek
were monitored twice per month for one year to estimate bacteria concentrations. At all four
of these locations (above the Grangeville WWTP outfall, at the outfall, below the outfall, and
at the mouth), flow was measured throughout the year. While there may be locations in the
headwaters and in the canyon reach of the Threemile Creek that are intermittent in nature, the
locations sampled were all perennial. As a result, the numeric bacteria criteria are applicable
at these locations, and the TMDL was developed based on flow and concentration data
collected from these sites.
Data shown in Table 34 indicate that bacteria WQS are exceeded consistently from May
through September, with fewer violations from October through January. Peak
concentrations appear to occur in August and September, which is also the period of lowest
flow. In order to address critical conditions, the LC and allocations were developed based on
the flows and concentrations that occur during this time. It is expected that reductions driven
by these allocations will be protective other times of the year when E. coli concentrations are
lower.
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Target Selection
The criteria for E. coli concentrations in Idaho WQS intended to protect the secondary
contact recreation beneficial use are:
• not to exceed 576 cfu per 100 ml at any time, and
• not to exceed a geometric mean of 126 cfu per 100 ml based on a minimum of 5 samples
taken every 3 to 5 days over a 30-day period.
These criteria are the targets of the TMDL and have been used to establish the LC and
allocations.
Monitoring Points
A comprehensive monitoring plan for bacteria should be implemented to assure planners that
mitigation practices are sufficiently addressing the pollution problems. It is recommended
that additional sites be monitored and that more frequent monitoring occur during times
when elevated concentrations are expected in order to evaluate compliance with the 126
cfu/100 ml monthly E. coli criteria. In addition to existing sites, a site near the headwaters
would enable planners to determine the NB concentration of bacteria. Continued monitoring
above the WWTP outfall, at the outfall, and below the outfall would enable planners to
monitor the city improvements to the sewer lines and WWTP modifications. A site at the
head of the canyon would identify contributions from farmland below the WWTP.
Load Capacity
The LC is the greatest amount of pollutant loading a water body can receive and still meet
WQS. The LC will vary with flow, that is, at higher flows a water body can accept greater
loading and still comply with criteria. The LCs were estimated for the four sampling
locations using the average flow recorded during August and September multiplied by the
monthly mean E. coli criteria of 126 cfu/100 ml. While elevated concentrations of E. coli
occur during periods of high runoff (e.g., in May), the LC was established utilizing the low
flow period because a much lower bacteria loading is necessary in order to remain in
compliance with established criteria.
Table 34 lists LCs at the three sampling locations used to establish the monthly criteria. The
loading is presented in terms of colony forming units per day. This is not a very practical
measure as there is seldom information from which to estimate such daily loads. As a result,
the allocations include the percent reduction in bacteria loading needed to achieve the LC in
addition to the numeric criteria.
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October 2003
Table 34. E. coli load capacities for Threemile Creek.
Location
Above Outfall
Below Outfall
Mouth
Target (cfu/1 00 ml)
126
126
126
Critical Flow (cfs)
0.7
1.5
2.6
Load Capacity
(cfu/day)
2.1E+12
4.7E+12
7.9E+12
Estimates of Existing E. coli Loads
Estimates of the current concentrations and loading are presented in Table 35. Concentration
data were collected during the February 2000 through February 2001 time period, with two
samples collected during most months. Flow, concentration, and loading are presented by
month, and are averages of the two monthly measurements. As discussed in Chapter 2, flows
during this time period were somewhat below average for the time period.
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October 2003
Table 35. Average monthly flow, E. coli concentration, and loading in
Threemile Creek.
Above
Outfall
Grange-
ville
WWTP
(at
outfall)
Below
Outfall
At Mouth
Flow
(cfs)a
Measured £.
coli
(cfu/100ml)b
Measured
load
(cfu/day)c
Flow
(cfs)
Measured £.
coli
(cfu/100ml)
Measured
load
(cfu/day)
Flow
(cfs)
Measured £.
coli
(cfu/100ml)
Measured
load
(cfu/day)
Flow
(cfs)
Measured £.
coli
(cfu/100ml)
Measured
load
(cfu/day)
Jan
1.8
28
1.13
E+12
1.4
9
1.97
E+11
2.9
690
4.39
E+13
4.0
5
7.63
E+11
Feb
1.4
86
5.07
E+12
1.9
17
3.73
E+11
1.5
62
5.24
E+12
9.9
17
3.81
E+12
Mar
2.2
95
7.52
E+12
2.5
38
8.34
E+11
3.4
110
1.18
E+13
8.5
6
1.81
E+12
Apr
3.4
82
7.18
E+12
1.8
43
9.44
E+11
4.6
89
1.03
E+13
7.5
6
2.00
E+12
May
5.3
903
5.44
E+13
1.2
375
8.23
E+12
7.0
767
6.59
E+13
11.4
38
8.71
E+12
Jun
2.0
370
1.13
E+13
1.5
4
8.78
E+10
2.6
245
1.29
E+13
5.9
67
7.75
E+12
Jul
0.7
710
1.33
E+13
3.8
208
4.56
E+12
1.3
690
2.74
E+13
1.6
200
1.42
E+13
Aug
0.2
1750
2.84
E+13
3.3
51
1.12
E+12
1.0
605
2.23
E+13
1.2
77
4.72
E+12
Sep
1.3
1350
2.30
E+13
2.7
56
1.23
E+12
1.7
1201
4.54
E+13
1.9
691
4.45
E+13
Oct
0.7
300
5.65
E+12
2.0
4
8.78
E+10
1.4
130
5.17
E+12
3.8
120
8.54
E+12
Nov
0.3
400
9.03
E+12
1.9
0
0.00
E+00
1.3
20
8.80
E+11
2.8
26
2.22
E+12
Dec
0.7
41
1.35
E+12
1.7
1
2.19
E+10
1.1
1400
7.78
E+13
2.6
38
4.76
E+12
a cubic feet per second
b colony forming units per one-hundred milliliters
0 colony forming units per day
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Load and Wasteload Allocations
Nonpoint source allocations and WLAs are presented in Table 36, and include a WLA for the
Grangeville WWTP and allocations for the other three monitoring stations. Because source-
specific loading information was not available, the nonpoint allocations are gross allotments
to all nonpoint sources within the reach upstream of each point, and include all sources, such
as storm water runoff, animal feeding operations, septic systems, etc.
Allocations were established at the same loading and concentration as the LC in Table 34,
without an explicit margin of safety. Due to the lack of sufficient information, it was not
possible to differentiate background loading from anthropogenic loading, so background
loading is included within the gross allocation to nonpoint sources. The percent reduction
needed to achieve nonpoint source LAs is also shown, in order to provide some perspective
on the magnitude of source control needed during the critical period.
The WLA for the Grangeville WWTP is established at the level of the applicable water
quality criteria for E. coli. The monthly geometric mean limit of 126 cfu/100 ml is the same
as in NPDES permits for other wastewater facilities in the SF CWR Subbasin (USEPA
2002a-d). The maximum daily limit of 576 cfu/100 ml is somewhat higher than for other
regional WWTPs because Threemile Creek is designated for secondary contact recreation
rather than primary contact recreation. These limits are expected to be incorporated into
Grangeville's permit when it is reissued.
Margin of Safety
An implicit MOS has been incorporated into the TMDL by utilizing conservative
assumptions. The period of lowest flows was used to estimate the LC. This results in a LC
far below that needed to achieve criteria during 10 months of the year. The LC is also
somewhat conservative during the critical August and September period, since the flows
measured during the year used to derive the allocations were somewhat below normal
(Chapter 2). The resulting allocations range from 36% to 92% reductions for nonpoint
sources and send a clear message that major reductions are needed in order to meet criteria.
Seasonal Variation/Critical Conditions
Although the TMDL does not include seasonal allocations, it does consider seasonal
variations in loading. Table 35 lists concentrations and loading by month, and the annual
variation and peak in concentration in August and September is apparent. The TMDL
addresses critical conditions by deriving allocations from the period of highest concentration
and lowest flow, which both occur in August and September.
Background
As discussed previously, it was not possible to differentiate background from anthropogenic
loading, so background has been included with other sources in the gross nonpoint source
allocation. This has been identified as a data gap, and in the future it may be possible to
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refine relative source contributions and refine allocations if more definitive monitoring is
conducted.
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Table 36. E. coli nonpoint source allocations and wasteload allocations for Threemile Creek.
Location
Headwaters
to
Grangeville
WWTP
Outfalld
Grangeville
WWTP
Outfall to
Nez Perce
Reservation
Nez Perce
Reservation
Boundary to
mouth
Target
(cfu/100ml)a
126
126
126
126
Allocation
Type
NPS - LAe
NPS - LA
PS - WLAf
Grangeville
WWTP
NPS - LA
Critical
Flow
(cfs)b
0.71
0.71
0.89
1.54
E. coli
cone.
(cfu/100ml)
1530
903
53
196
E. coli
Current
Load
(cfu/day)c
2.7E+10
1.6E+10
1.2E+09
7.4E+09
E. coli Load
Capacity
(cfu/day)
2.2E+09
2.2E+09
2.7E+09
4.7E+09
£. coli
Allocation
(cfu/day)
2.2E+09
2.2E+09
2.7E+09
4.7E+09
£. coli
Allocation
(cfu/100ml)
126- monthly
geo. Mean
576 - daily max.
126- monthly
geo. Mean
576 - daily max.
126- monthly
geo. Mean
576 - daily max.
126- monthly
geo. Mean
576 - daily max.
£. coli
Load
Reduction
92%
86%
0.0%
36%
acfu/100 ml = colony forming units per 100 milliliters
b cfs = cubic feet per second
0 cfu/day = colony forming units per day
d WWTP = wastewater treatment plant
e NPS-LA = nonpoint source load allocation
PS-LA = point source waste load allocation
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Reserve
An explicit reserve for future growth has not been set aside within the TMDL. Any
increased discharge from future growth or development within the Threemile Creek
watershed would need to be consistent with these allocations. In other words, it could not
increase E. coli concentrations above target criteria identified above.
5.2 Nutrient TMDL - Threemile Creek
Threemile Creek has been designated by the state of Idaho for salmonid spawning and
secondary contact recreation. Idaho's narrative standard states: "surface waters shall be free
from excess nutrients that can cause visible slime growth or other aquatic growths impairing
beneficial uses" (IDAPA 58.01.02.200.06). Salmonid spawning aquatic life beneficial uses
can be impaired when excess algae decompose, depleting DO in the water column. Primary
and secondary contact recreation can be also impacted by visible slime and algae growth
resulting from excess nutrients when temperature and sunlight are not limiting.
Threemile Creek is listed for nutrients and data discussed in Chapter 2 indicate that
development of a nutrient TMDL is warranted. Nitrogen and phosphorus are nutrients that
are essential to the growth of algae in streams. By examining the concentrations and ratios of
these nutrients, it can be determined whether one or both of these nutrients must be
controlled in order to prevent excess algae growth, and low dissolved oxygen levels which
may result from excess algae growth and decomposition.
Nitrogen to phosphorus ratios (mole to mole) of less than 7 generally indicate systems in
which nitrogen is the limiting nutrient (Reynolds 1984). Ratios of greater than 7 generally
indicate systems which are limited by phosphorus. Data collected above the Grangeville
WWTP indicate the system is usually nitrogen limited during the summer months. Total
nitrogen levels during the summer average 0.39 mg/L, just slightly above the USEPA
Ecoregional nutrient target range of 0.22 - 0.36 mg/L (USEPA 2000), and are more than an
order of magnitude below nitrogen levels below the WWTP. Although the reach above the
WWTP is theoretically nitrogen limited, since nitrogen levels are so close to ecoregional
nutrient target levels, further controlling nitrogen appears to be of minimal benefit.
The reach below the WWTP is phosphorus limited at all times of the year, and is the area of
greatest concern due to the relatively low gradient, high nutrient concentrations, and low
shade, conditions which tend to promote algae growth.
Results at the mouth are mixed, with both nitrogen and phosphorus limiting conditions
occurring. These results are difficult to interpret, since the subsurface flow at the mass
failure above this sampling location appears to be controlling phosphorus levels.
Controlling nitrogen appears to be of limited value above the WWTP, and in the canyon
reach above the mouth. Since phosphorus is the limiting nutrient in the reach of greatest
concern immediately below the WWTP, and since the costs of controlling nitrogen in
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wastewater treatment plant effluent are quite high, the TMDL will only focus on controlling
phosphorus.
Reducing levels of phosphorus is expected to result in decreased algae growth, thus meeting
the narrative nutrient standard. Due to the very low flows in Threemile Creek during the
summer, it was infeasible to model the relationship between phosphorus and DO. However,
it is expected that achieving the phosphorus reductions identified in the TMDL will result in
compliance with the DO standard, and phosphorus is considered to be a surrogate measure
for the DO TMDL.
Design Conditions
Numeric criteria and narrative standards to protect salmonid spawning and recreational
beneficial uses apply to all perennial reaches of Threemile Creek and to intermittent reaches
of Threemile Creek during periods of optimum flow (defined as 5 cfs or greater in Idaho
WQS). Four sampling points in Threemile Creek were monitored twice per month for one
year to estimate phosphorus and nitrogen concentrations. At all four of these locations
(above the Grangeville WWTP outfall, at the outfall, below the outfall, and at the mouth),
flow was measured throughout the year. While there may be locations in the headwaters and
in the canyon reach of the Threemile Creek that are intermittent in nature, the locations
sampled were all perennial. As a result, the numeric salmonid spawning criteria and
narrative nutrient standards are applicable at these locations, and the TMDL was developed
based on flow and concentration data collected from these sites.
Data shown in Table 37 indicate that levels of TP consistently exceeded USEPA (2000)
regional guidance of 0.030 mg/L TP for the Columbia Plateau streams and frequently
exceeded USEPA guidance commonly known as the "Goldbook" (USEPA 1986)
recommendations (0.1 mg/L). The headwaters had a consistent TP level of 0.056 mg/L.
Above the WWTP outfall, TP ranged from 0.038 to 0.166 mg/L. Below the WWTP, TP
ranged from 0.24 to 3.14 mg/L. The mouth had a fairly constant level of TP, ranging from
0.272 to 0.336 mg/L.
The critical time period for algae growth, and the time frame in which TMDL allocations
have been typically applied in the Clearwater River basin, is April through September.
However, within this window, it is expected that most growth occurs during the warmest
months, July through mid-September, which is also the period of lowest flow with increased
risk of low DO levels. In order to address the critical time period for algae growth, the LC
and allocations were developed based on the flows and concentrations which occur during
this time. It is expected that reductions driven by these allocations will be protective of
beneficial uses during other times of the year.
Target Selection
Targets were selected for TP based on site specific characteristics of the Threemile Creek
watershed and regional guidance levels discussed above. The targets are set to avoid
promoting nuisance algae growth. Grangeville is still considering options for the WWTP,
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including land application of its wastewater during the critical time period for excessive
algae growth (July through mid-September). A waste load allocation has been established
for the WWTP which will ensure compliance with the TP target set for the segment
immediately downstream from the outlet. The three TP targets described below have been
used to establish the LC and allocations of the TMDL.
A TP target of 0.08 mg/L was set for the segment of Threemile Creek beginning at the
headwaters and ending upstream of the WWTP outfall. This target was selected based on
averaging the level of TP (0.056 mg/L) in the forested headwaters with the USEPA
"Goldbook" (USEPA 1986) value of 0.1 mg/L, recommended to prevent nuisance algae
growth in streams. The TP background value was averaged with the USEPA (1986) value to
derive a target for this portion, due to this segment's location. The segment begins in the
relatively nutrient-poor forested headwater soils and progresses downstream to more nutrient
rich prairie soils. The USEPA (1986) guidance was utilized because the local reference
values for background TP exceeded the USEPA (2000) eco-regional guidance value of 0.030
mg/L, and the nutrient rich soils in agricultural lands are expected to further increase nutrient
levels in Threemile Creek naturally. In addition, the "Goldbook" (USEPA 1986) value has
been used in previously developed regional TMDLs, including the adjacent Cottonwood
Creek TMDL.
A TP target of 0.1 mg/L was selected for the segment beginning at the WWTP outfall and
ending at the Nez Perce Reservation boundary in the canyon. This target is based on the
USEPA "Goldbook" (USEPA 1986) and reflects a slight increase from the upstream target
due to natural enrichment anticipated with the change in soil type and the distance
downstream from headwater areas.
A TP target of 0.3 mg/L was selected for the segment beginning at the Nez Perce Reservation
boundary and ending at the mouth. Monitoring has demonstrated that the TP concentration
at the mouth does not vary substantially with flow, season, or short duration changes in
WWTP discharge. It is consistently near 0.3 mg/L. The exact mechanism causing these
stable concentrations regardless of flow, loading and season is unknown, but it is suspected
that phosphorous is taken up and released in an equilibrium reaction with soil particles as the
stream flows subsurface through a large landslide for a distance of approximately 0.75 mile,
1 mile upstream from the mouth. Approximately 2 cfs continually flow subsurface at all
flow rates. During the critical time period for which targets are designated, flows ranged
from 1.2 cfs to 1.9 cfs at the mouth. Thus, during this interval, all flow was subsurface
through the landslide. Although a detailed research study of the effects of the mass failure on
TP concentrations is recommended, it is beyond the scope of this analysis. Without such
information, at this time it is not reasonable to establish a TP target that would drive further
phosphorus reductions upstream because it appears that it would have no benefit below the
landslide. However, as nonpoint and point source treatments are implemented, targets may
be re-evaluated.
A DO target based on the Idaho WQS of 6.0 mg/L was established.
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Monitoring Points
A comprehensive monitoring plan for nutrients should be implemented to assure planners
that mitigation practices are sufficiently addressing the pollution problems. It is
recommended that three sites be monitored: one above the WWTP outfall; a second at the
county road (known as Butcher Creek Road) crossing on the canyon rim (a.k.a. "Big Barn"
site): and the third at the mouth. Monitoring will continue at the WWTP outfall as required
by the NPDES permit.
Load Capacity
The LC is the greatest amount of pollutant loading a water body can receive and still meet
WQS. The LC will vary with flow, i.e., at higher flows a water body can accept greater
loading and still comply with standards. The LCs were estimated for the three segments
(above the WWTP, from the WWTP to the Nez Perce Reservation boundary, from the Nez
Perce Reservation boundary to the mouth) using the average flows recorded during July,
August, and September, multiplied by the TP target for that site. Average flows during this
time were determined to be adequately protective, because the TMDL focuses only on the
critical portion of the year, which coincides with the annual period of low flow, and because
flows in the subbasin in 2000 were well below average flows based on historical records in
the SF CWR. While elevated concentrations of TP occur during periods of high runoff (e.g.,
in May), the LC was established utilizing the critical growing season for aquatic vegetation.
Nutrient levels greater than the LC at this time may result in excess algae growth and
depleted oxygen in the water column, thus impairing beneficial uses. Table 37 lists the LC
for the critical time period at three sampling locations presented in kilograms per day. The
LC for the "below outfall" site does not include WWTP loading.
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Table 37. Total phosphorus (TP) load capacities for Threemile Creek.
Location
Headwater to Grangeville WWTP Outfall
Grangeville WWTP Outfall to Nez Perce
Reservation Boundary
Nez Perce Reservation Boundary to Mouth
TP Target
(mg/L)
0.08
0.10
0.30
Critical Flow
(cfs)a
0.7
1.6
1.5
TP Load Capacity
(kg/day)b
0.14
0.39
1.13
a cubic feet per second
b kilograms per day
Estimates of Existing Total Phosphorus Loads
Estimates of the current concentrations and loading are presented in Table 38. Flow,
concentration, and loading are presented by month, and are averages of the two monthly
measurements. As discussed in Chapter 2, flows were somewhat below average for the time
period.
Monthly variations in TP concentrations and loading are shown in Table 38. Below the
WWTP outfall, TP concentrations vary considerably throughout the year, with the highest
concentrations and lowest in-stream flows occurring in July and August.
Above the outfall, concentrations and flows are highest in the spring (March, April, and
May). Flows from the Grangeville WWTP are relatively stable year around. While total
loading increases for TP at the mouth during the spring, concentrations remains fairly
constant at 0.3 mg/L. This may be due to an interaction of P with soils in the landslide area as
described above.
Load and Wasteload Allocations
Nonpoint source allocations for TP and a WLA for the Grangeville WWTP are presented in
Table 39. Because source-specific loading information was not available, the nonpoint
allocations are gross allocations to all nonpoint sources within each reach, and include all
sources, such as unregulated storm water runoff, farming practices, animal feeding
operations, septic systems, etc.
Allocations were established at the same loading and concentration as the LC in Table 37,
without an explicit margin of safety. Due to the lack of sufficient information, it was not
possible to differentiate background loading from anthropogenic loading, so background
loading is included within the gross allocation to nonpoint sources. The percent reduction
needed to achieve nonpoint source load allocations is also shown, in order to provide some
perspective on the magnitude of source control needed during the critical period.
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October 2003
Table 38. Average monthly flow, total phosphorus (TP) concentration, and loading in Threemile Creek.
Above
Outfall
Grange-
ville
WWTP(at
outfall)
Below
Outfall
At Mouth
Flow (cfs)a
Measured TP
(mg/L)b
Measured Load
(kg/day)c
Flow (cfs)
Measured TP
(mg/L)
Measured Load
(kg/day)
Flow (cfs)
Measured TP
(mg/L)
Measured Load
(kg/day)
Flow (cfs)
Measured TP
(mg/L)
Measured Load
(kg/day)
Jan
1.8
0.058
0.255
1.4
0.896
3.095
2.9
0.922
6.564
4.0
0.306
2.957
Feb
1.4
0.142
0.486
1.9
0.741
4.170
1.5
0.909
3.225
9.9
0.330
8.017
Mar
2.2
0.108
0.581
2.5
0.876
5.399
3.4
0.985
8.218
8.5
0.321
6.699
Apr
3.4
0.094
0.782
1.8
0.799
3.973
4.6
0.482
5.377
7.5
0.326
5.974
May
5.3
0.112
1.452
1.2
1.100
2.656
7.0
0.369
6.329
11.4
0.283
7.879
Jun
2.0
0.091
0.445
1.5
0.99
3.226
2.6
0.591
3.803
5.9
0.282
4.078
Jul
0.7
0.112
0.186
3.8
0.737
8.384
1.3
2.130
6.879
1.6
0.277
1.071
Aug
0.2
0.115
0.048
3.3
0.876
7.210
1.0
2.820
6.830
1.2
0.298
0.860
Sep
1.3
0.137
0.436
2.7
1.056
6.014
1.7
16.69
70.233
1.9
0.305
1.388
Oct
0.7
0.078
0.128
2.0
0.869
4.324
1.4
12.84
44.922
3.8
0.336
3.148
Nov
0.3
0.038
0.032
1.9
0.735
4.258
1.3
7.01
21.781
2.8
0.316
2.165
Dec
0.7
0.064
0.102
1.7
0.740
3.775
1.1
1.82
4.809
2.6
0.311
1.955
a cubic feet per second
b milligrams per liter
0 kilograms per day
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October 2003
Table 39. Total phosphorus (TP) load allocations and wasteload allocations for Threemile Creek.
Location
Headwaters to Grangeville
WWTP Outfall ?
Grangeville WWTP Outfall to
Nez Perce Reservation
Boundary
Nez Perce Reservation
Boundary to Mouth
Applicable Period
TP
Target
(mg/L)a
0.08
0.10
0.30
Allocation
Type
NPS-LA6
NPS-LA
r
PS-WLA
Grangeville
WWTP
NPS-LA
Critical
Flow
(cfs)b
0.71
0.71
0.89
1.54
Peak
Concen-
tration
(mg/L)
0.13
0.13
4.6
0.31
Average
Current
Load
(kg/day)c
0.24
0.12
7.3
1.10
TP Load
Capacity
(kg/day)
0.14
0.17
0.22
1.13
TP Load
Allocation
(kg/day)
0.14
0.17
0.22
1.13
TP Load
Reduction
(%)
32
32
97
0
July1-Sept15
a milligrams per liter
b cubic feet per second
0 kilograms per day
d WWTP = wastewater treatment plant,
e NPS-LA = nonpoint source load allocation
f PS-WLA = point source waste load allocation
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The WLA for the Grangeville WWTP was established based on the 0.1 mg/L TP target
during the critical time period (July through mid- September), and average WWTP flows
measured by DEQ during July-September 2000. The WLA does not apply during the
remainder of the year. These limits are expected to be incorporated into Grangeville's
NPDES permit when it is reissued, as monthly average limits. If further studies being
conducted by DEQ and Grangeville indicate that DO or other nutrient impairments occur
earlier in the summer (e.g., June), then the Grangeville WWTP and nonpoint source
allocations will be revised to include this new time period.
Margin of Safety
An implicit margin of safety has been incorporated into the TMDL by utilizing conservative
assumptions. The period of greatest aquatic plant growth and lowest flows was used to
estimate the LC. The LC is also conservative during the critical time of July through mid-
September, since the flows measured during the year used to derive the allocations were
somewhat below normal (Chapter 2). The resulting TP allocations range from 32% to 90%
reductions for nonpoint sources. These percentages indicate that major reductions are needed
in order to meet targets set for standards attainment.
Seasonal Variation/Critical Conditions
The TP TMDL includes seasonal allocations in order to address the growing season when
nutrient enrichment may result in nuisance algae growth and lower DO levels. The period in
which allocations apply is also believed to encompass critical conditions for nutrient
impairments, because it includes the periods of lowest flows and highest stream
temperatures, which are the most conducive to rapid algae growth and depressed DO levels.
Background
As discussed previously, it was not possible to differentiate background from anthropogenic
loading, so background has been included with other sources in the gross nonpoint source
allocation. This has been identified as a data gap, and in the future it may be possible to
refine relative source contributions and refine allocations if more definitive monitoring is
conducted.
Reserve
An explicit reserve for future growth has not been set aside within the TMDL. Discharge
from future growth or development within the Threemile Creek watershed would need to be
consistent with the allocations, and could not increase TP concentrations above the target
criteria identified.
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October 2003
5.3 Temperature TMDLs
In-Stream Water Quality Targets
Nine water bodies were identified in Chapter 2 (Table 10) as water quality limited due to
temperature. In addition, all other streams in the subbasin that have been monitored have
been found to exceed temperature criteria (Appendix J), even though they are not currently
303(d) listed for temperature. The goal of the temperature TMDLs is to achieve applicable
temperature criteria and restore all of the temperature-impaired water bodies (listed or not) to
"full support of designated beneficial uses" (Idaho Code 39.3611, 3615).
The five water bodies that make up the SF CWR main stem and Three Mile Creek have
designated beneficial uses of cold water aquatic life and salmonid spawning. Little Elk
Creek, Big Elk Creek and Butcher Creek have existing beneficial uses of cold water aquatic
life and salmonid spawning. All these streams must meet the cold water aquatic life
temperature criteria, and the salmonid spawning temperature criteria when spawning occurs
(Table 40). In addition, USEPA has established temperature criteria for bull trout for a
number of water bodies in the subbasin, including two that are 303(d) listed: Big Elk and
Little Elk Creeks. Appendix B shows the complete list of streams in the SF CWR Subbasin
for which USEPA has established bull trout temperature criteria. These streams must meet
the federally-promulgated bull trout temperature standard of 10 °C (50 °F) as an average of
daily maximum temperatures over a seven-day period (MWMT) for the months of June
through September.
Table 40. Applicable water temperature criteria.
Beneficial use
Cold Water Aquatic Life
Salmonid Spawning
Bull Trout
Criteria
19°C(66.2°F)
daily average
9 °C (48.2 °F)
daily average
22 °C(71 .6 °F)
daily maximum
13°C(55.4°F)
daily maximum
10°C(50°F)MWMTa
Reference
IDAPA 58.01 .02.250.02.D
IDAPA58. 01. 02.250.02.6. ii
40 CFR Part 131 .33(a)
maximum weekly maximum temperature
Idaho water quality standards include a provision (IDAPA 58.01.02.401.03.a.v) that
addresses point source discharges in circumstances where natural temperature conditions
exceed existing criteria, as follows:
"If temperature criteria for the designated aquatic life use are exceeded in the
receiving waters upstream of the discharge due to natural background
conditions, then Subsections 401.03.a.iii. and 401.03.a.iv. do not apply and
instead wastewater must not raise the receiving water temperatures by more
than three tenths (0.3) degrees C."
159
Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Design Conditions
Heat loading sources on the main stem SF CWR were evaluated through an assessment of
measured temperature data with support from model analysis (Appendix I and J).
Temperature data indicate that much of the excess heat loading in the upper main stem is the
result of loading from the headwater tributaries, from both natural and human caused
processes. Human caused heat loading measured in the tributaries is largely a result of the
loss of shade from riparian vegetation from such activities as grazing, road construction,
dredge mining, and timber harvest. The influence of shade on stream temperature is much
more significant on smaller streams with smaller water volumes than larger streams. In
addition, tributaries are often locations of lower observed stream temperatures within the SF
CWR Subbasin; therefore, protecting these tributary source areas, even if they are currently
below the criteria, will reduce the cumulative temperature effects on the main stem. The
management of tributary conditions is the most effective method to reduce stream
temperature in the main stem.
Analysis also showed that main stem heat loading conditions increased dramatically in lower
reaches of the SF CWR main stem, which resulted in a large rise in stream temperatures.
Once again, landuse activities occurring within this portion of the basin have resulted in very
low shade conditions. Reach scale dynamics (aspect, width/depth ratio, flow, etc.) become
more dominant components of the heat loading process in this section of the river, and when
coupled with the low shade conditions, have resulted in very high water temperatures.
Heat loading and final nonpoint source heat load allocations, i.e., stream shade and stream
channel configuration, focus on the predominant sources of human-caused heat loading in the
subbasin. Many minor sources of human-caused heat loading exist throughout the subbasin.
Some like old mines, developments, and the like are discussed in chapter 3, while others are
largely unidentifiable or unquantifiable. Load allocations are designed and set for the major
human-caused addition of heat, with the assumption that the minor and unmeasureable
sources are included within these allocations, and reductions from these minor sources will
not be necessary in order to meet the goals of the TMDLs and Idaho WQS.
Although criteria are also exceeded at other times of the year, the critical time period for
water temperature has been determined to be the months of July and August when air and
water temperatures are at their peak and the most dramatic exceedances of criteria occur. As
a result, the TMDLs focus on achieving temperature targets for these months. If the
temperature standards are attained during July and August, when water flows are low and air
temperatures are high, it is expected that temperature criteria will be met throughout the rest
of the year.
The SF CWR Subbasin is predominantly forested and managed for various forest practices
(Figure 8). Under the auspices of the Idaho FPA (IDAPA 20.02.01), the Forest Practices Act
Advisory Committee developed a Cumulative Watershed Effects (CWE) methodology for
assessing stream temperature problems on lands covered under the FPA (IDL 2000,
Appendix G). A modified version of this methodology is applied to the streams in the
160 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
subbasin that are primarily influenced by forest practices. All other streams and rivers in the
SF CWR Subbasin are assessed using a methodology developed by the USEPA (Appendix
F). While the two methods have the same goals, the actual results in terms of TMDL
development are somewhat different for the two parts of the SF CWR Subbasin.
Target Selection
The cold water aquatic life criteria of 19 °C (66.2 °F) daily average and 22 °C (71.6 °F) as a
daily maximum apply to all waters year around. In addition, more restrictive salmonid
spawning criteria of 9°C (48.2 °F) daily average and 13 °C (55.4 °F) daily maximum apply to
most streams in the subbasin on a seasonal basis depending on which salmonid species are
present (Table 41). The criterion for bull trout waters identified in federal regulations is 10
°C (50 °F) MWMT or less during the months of June through September (Appendix B
includes a list of streams in the SF CWR Subbasin covered by the federal bull trout criteria).
Using a conversion factor developed by Sugden et al. (1998) for northern Idaho and western
Montana, 9 °C (48.2 °F) daily average temperature is equivalent to 9.7 °C (49.5 °F) MWMT,
such that the federal bull trout temperature standard and Idaho's salmonid standrad are
roughly equivalent in terms of MWMT. Therefore, we assume they are equivalent and use
10°C (50°F) MWMT for both standards in the FPA CWE analysis discussed in Appendix G.
The cold water biota aquatic life standard of 19 °C (66.2°F) can be converted to 21 °C (69.8
°F) MWMT.
The time periods when salmonid spawning numeric criteria are applicable for different
salmonid species found in the SF CWR are listed in Table 41, and are based on the findings
of the Fish TAG (Appendix D) and federal regulations for bull trout. The distribution of
salmonid species within the SF CWR Subbasin is listed in Table 42 (and shown in a series of
maps at the end of Appendix D), which indicates that salmonids are present in all water
bodies covered by the SF CWR TMDLs; hence, the salmonid spawning criteria are
applicable in all these waterbodies. Reviewing the spawning and incubation windows in
Table 41, if bull trout, cutthroat trout, spring/summer chinook salmon, brook trout or
steelhead, (mid-upper reaches and tributaries) are present, the salmonid spawning window
includes the critical July-August time period, and hence the salmonid spawning criteria are
applicable for all the temperature TMDLs. Reviewing the species distribution information in
Table 42, all streams included in the SF CWR Subbasin TMDL have one or more of these
species present; therefore, the salmonid spawning criteria are applicable.
Application of the Idaho WQS for the development of TMDL targets, however, requires
consideration of human causation. Many streams in the SF CWR Subbasin that exceed the
numeric temperature criteria are relatively undisturbed by human intervention and, therefore,
meet the WQS for temperature. It can be assumed then that many, if not most, other streams
in the SF CWR Subbasin probably exceed the numeric temperature criteria naturally.
Targets for TMDLs need to be designed to address heat loading that is human caused. The
most important human-caused effects on increased stream heat loading are increased direct
insolation and streamside heating as a result of the removal or diminishment of streamside
vegetation and the widening of stream channels. The temperature TMDLs herein, therefore,
161 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
set shading targets and stream channel width targets as those parameters needed to be
modified or managed to meet the Idaho WQS.
Table 41. Time periods of salmonid spawning and incubation in the SF CWR
Subbasin.
Salmonid Species
Bull Trout
Cutthroat Trout
Spring/Summer Chinook Salmon
Steelhead/Rainbow Trout (lower SF CWR and tributaries)
Steelhead/Rainbow Trout (middle and upper SF CWR and
tributaries)
Whitefish
Brook Trout
Dates Criteria Are Applicable
June 1 -September 30
March 15 -August 15
August 15 -April 30
February 1 -June 1
February 1 -July 15
October 1 - February 28
August 1 5 - February 28
162
Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 42. Salmonid species distribution in the SF CWR Subbasin.
South Fork Clearwater River Subbasin
WB
IDa
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
Water Body Name
Lower SF CWR
Lower Cottonwood Cr.
Upper Cottonwood Cr.
Lower Red Rock Cr.
Upper Red RockCr.
Stockney Cr.
Shebang Cr.
S.F. Cottonwood Cr.
Long Haul Cr.
Threemile Cr.
Butcher Cr.
Mid-Lower SF CWR
Mill Cr.
Lower Johns Cr.
Gospel Cr.
W. F. Gospel Cr.
Middle Johns Cr.
Acres
19,723
16,929
21,223
2,969
23,481
19,978
18,380
12,676
8,812
21,475
10,723
56,691
23,410
26,378
10,832
4,467
10,200
Current Fish Population
Presence13
BUT
Y
N
N
N
N
N
N
N
N
N
N
Y
Y
Y+
Y
Y
Y+
CUT
Y
N
N
N
N
N
N
N
N
N
N
Y
Y
Y
Y
Y
Y
SCH
Y
N
N
N
N
N
N
N
N
Y
Y
Y+
Y+
Y
N
N
Y
ST
RBT
Y
Y
Y
N
N
N
N
N
N
Y
Y
Y
Y
Y
Y
N
Y
BRT
Y
N
N
N
N
N
N
N
N
N
N
Y
N
N
N
N
N
Current
Habitat
Condition0
Salmonids
P
P
P
P
P
P
P
P
P
P
P
P
F
G
G
G
G
Natural Inherent
Conditions
BUT
F
P
P
P
P
P
P
P
P
P
P
F
F
G
G
G
G
CUT
F
P
P
P
P
P
P
P
P
P
P
F
G
G
G
G
G
SCH
F
P
P
P
P
P
P
P
P
P
P
F
F
F
P
P
F
ST
RBT
F
G
F
G
F
F
F
F
F
F
F
F
G
G
G
F
G
Pollutant Problemsd
SED
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
N
N
N
TEMP
Y
Y
N
N
N
N
N
N
N
Y
Y
Y
Y
N
N
N
N
NUTR
Y?
N
N
N
N
N
N
N
N
Y
Y
N
N
N
N
N
N
Conservation
Preservation
Priority6
M (main stem)
L
L
L
L
L
L
L
L
L
M
M (main stem)
M
C/H
C/H
C/H
C/H
163
Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
South Fork Clearwater River Subbasin
WB
IDa
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
Water Body Name
Upper Johns Cr.
Moores Cr.
Square Mountain Cr.
Hagen Cr.
Middle SF CWR
Wing Cr.
Twentymile Cr.
Lower Tenmile Cr.
Middle Tenmile Cr.
Upper Tenmile Cr.
Williams Cr.
Sixmile Cr.
Mid-Upper SF CWR
Lower Crooked R.
Upper Crooked R.
W. F. Crooked R.
E. F. Crooked R.
Reliefer.
Acres
8,674
3,987
2,289
5,537
18,952
5,329
14,641
2,447
7,227
13,617
5,891
5,130
17,165
9,481
14,488
7,594
6,689
7,484
Current Fish Population
Presence13
BUT
Y+
Y+
Y
Y
Y
N
Y
Y+
Y+
Y+
Y
Y
Y
Y
Y+
Y+
Y+
Y
CUT
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
SCH
N
N
N
N
Y+
N
N
Y
Y+
Y
N
Y
Y+
Y+
Y+
Y
Y
Y+
ST
RBT
Y
Y
Y
Y
Y
N
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
BRT
N
N
N
N
Y
N
N
N
N
N
N
N
Y
Y
Y
Y+
N
N
Current
Habitat
Condition0
Salmonids
G
G
G
G
F
F
G
G
G
G
G
F
F
P
F
G
G
F
Natural Inherent
Conditions
BUT
G
G
G
G
F
P
F
F
G
G
F
F
F
F
G
G
G
F
CUT
G
G
G
G
F
F
G
F
G
G
G
G
F
G
G
G
G
G
SCH
P
P
P
P
F
P
P
F
F
F
F
F
G
G
G
G
G
G
ST
RBT
G
G
F
F
G
F
F
G
G
G
G
G
G
G
G
G
G
G
Pollutant Problemsd
SED
N
N
N
N
Y
N
N
N
N
N
N
Y
Y
Y
Y
N
N
Y
TEMP
N
N
N
N
Y
N
N
N
N
N
N
N
Y
Y
Y
N
N
Y
NUTR
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
Conservation
Preservation
Priority6
C/H
C/H
C/H
C/H
M (main stem)
L
C/M
C/H
C/H
C/H
C/H
M
M
H
H
C/H
C/H
M
164
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October 2003
South Fork Clearwater River Subbasin
WB
IDa
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
Water Body Name
Upper SF CWR
Lower Red R.
Middle Red R.
Moose Butte Cr.
Lower S.F. Red R.
Middle S.F. Red R.
W. F. Red R.
Upper S.F. Red R.
Trapper Cr.
Upper Red R.
Soda Cr.
Bridge Cr.
Otterson Cr.
Trail Cr.
Siegel Cr.
Red Horse Cr.
Lower American R.
Kirks Fork
Acres
2,695
10,333
16,042
7,087.55
3,154
2,791
6,406
4,744
7,077
19,250
3,353
2,380
2,488
4,560
7,784
5,806
7,215
6,257
Current Fish Population
Presence13
BUT
Y
Y
Y
Y
Y+
Y+
Y+
Y+
Y
Y
N
N
Y
Y
Y
Y
Y
Y
CUT
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
SCH
Y+
Y+
Y+
Y+
Y+
Y+
Y
Y
N
Y+
N
N
Y
Y
Y
Y
Y+
Y
ST
RBT
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
N
N
N
Y
Y
Y
Y
BRT
Y
Y
Y
Y
Y
Y
Y
Y
Y+
Y+
Y+
Y+
Y+
Y+
Y+
Y+
Y
Y
Current
Habitat
Condition0
Salmonids
P
P
P
F
F
F
G
F
F
F
F
G
G
F
F
F
P
F
Natural Inherent
Conditions
BUT
F
F
F
F
G
G
G
G
G
G
F
F
F
F
F
F
F
F
CUT
F
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
SCH
G
G
G
G
G
G
G
G
F
G
F
F
F
F
G
G
G
G
ST
RBT
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Pollutant Problemsd
SED
Y
Y
Y
Y
Y
Y
N
Y
Y
Y
Y
N
N
Y
Y
Y
Y
Y
TEMP
Y
Y
Y
Y
Y
N
N
N
N
Y
N
N
N
N
Y
Y
Y
Y
NUTR
N
N
Y?
N
N
N
N
N
N
N
N
N
N
N
N
N
Y?
N
Conservation
Preservation
Priority6
H
M
H
H
H
H
C/H
H
H
H
H
C/M
C/M
H
H
H
H
H
165
Chapters
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October 2003
South Fork Clearwater River Subbasin
WB
IDa
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
Water Body Name
E.F. American R.
Upper American R.
ElkCr.
Little Elk Cr.
Big Elk Cr.
Buffalo Gulch
Whiskey Cr.
Maurice Cr.
Lower Newsome Cr.
BearCr.
Nugget Cr.
Beaver Cr.
Middle Newsome Cr.
Mule Cr.
Upper Newsome Cr.
Haysfork Cr.
Baldy Cr.
Pilot Cr.
Acres
1 1 ,445
15,275
2,324
5,081
8,821
2,139
1,659
1,094
4,145
3,832
1,451
3,733
1,135
5,497
6,356
3,172
2,724
3,918
Current Fish Population
Presence13
BUT
Y
Y
Y
Y
Y
N
Y
N
Y
Y
Y
Y
Y
Y
Y
N
Y+
Y+
CUT
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
SCH
Y+
Y+
Y+
Y
Y+
N
Y
N
Y+
Y
N
N
Y+
Y
Y+
Y
Y
Y
ST
RBT
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
Y
Y
Y
Y
Y
Y
Y
BRT
Y+
Y+
Y+
Y+
Y+
N
Y
N
Y
N
N
N
N
N
N
N
N
N
Current
Habitat
Condition0
Salmonids
F
F
P
F
F
P
F
P
P
F
F
F
F
F
F
F
F
G
Natural Inherent
Conditions
BUT
G
F
F
F
F
P
F
P
F
F
F
F
F
F
F
F
G
G
CUT
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
SCH
G
G
G
G
G
F
F
F
G
G
F
F
G
G
G
G
G
G
ST
RBT
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Pollutant Problemsd
SED
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
TEMP
N
Y
Y
Y
Y
Y
Y
Y
Y
Y?
Y?
Y?
Y
Y?
Y
Y?
Y?
Y?
NUTR
N
N
Y
V
V
N
N
N
N
N
V
V
N
N
N
N
N
N
Conservation
Preservation
Priority6
H
H
H
H
H
M
M
M
H
H
M
H
H
H
H
H
H
C/H
166
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
South Fork Clearwater River Subbasin
WB
IDa
72
73
74
75
76
77
78
79
80
81
82
Water Body Name
Sawmill Cr.
Sing Lee Cr.
W.F. Newsome Cr.
Leggett Cr.
Fall Cr.
Silver Cr.
Peasley Cr.
Cougar Cr.
Meadow Cr.
Sally Ann Cr.
Rabbit Cr.
Acres
1,769
1,556
3,305
4,992
2,334
16,517
9,093
7,737
24,010
8,891
6,191
Current Fish Population
Presence13
BUT
Y
N
Y
N
N
Y
N
N
Y
Y
Y
CUT
Y
Y
Y
Y
Y
N
Y
Y
Y
Y
Y
SCH
Y
Y
Y
Y
N
N
N
N
Y+
N
N
ST
RBT
Y
Y
Y
Y
N
Y
Y
N
Y
Y
Y
BRT
N
N
N
N
N
Y+
N
N
Y+
N
Y
Current
Habitat
Condition0
Salmonids
G
F
F
F
F
G
F
P
P
P
P
Natural Inherent
Conditions
BUT
F
F
F
F
P
F
F
P
F
F
F
CUT
G
G
G
G
F
G
G
F
G
F
F
SCH
G
G
G
F
P
P
F
P
F
P
P
ST
RBT
G
G
G
G
G
F
G
F
G
F
F
Pollutant Problemsd
SED
N
N
N
Y
Y
N
Y
Y
Y
Y
Y
TEMP
Y?
Y?
Y
Y
N
N
Y?
Y?
Y
Y
Y
NUTR
N
N
N
N
N
N
N
N
N
N
N
Conservation
Preservation
Priority6
C/M
M
H
M
L
C/L
M
L
M
M
L
a water body identification number
b Y+ = known spawning and rearing population
BUT = bull trout, CUT = cutthroat trout, SCH = spring chinook salmon, ST RBT = steelhead/rainbow trout, BRT = brook trout
0 G = good, F = fair, P = poor
d SED = sediment, TEMP = temperature, NUTR = nutrients
e C/G or C/F or C/P = ratings for conservation rather than restoration. All other ratings in this column are priorities for restoration
167
Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Surrogate Water Temperature Targets
Shade is one of the most important factors affecting stream temperature. As mentioned
previously, two approaches for evaluating shade were used to develop surrogate targets for
the TMDL: CWE and System Potential Vegetation (SPY). Percent effective shade and
percent canopy closure have been identified as surrogate targets for achieving the
temperature standards. Percent effective shade over a stream, or percent canopy closure,
depending on the approach, are practical targets because they are the primary factors that can
be managed to alter heat loading and stream temperature. Such targets also allow detailed
monitoring of streamside conditions affected by management and progress towards target
attainment.
While it is recognized that there are some technical differences between "percent effective
shade" of the SPV method and "percent canopy closure" of the CWE method, both
approaches address near-stream vegetation conditions, and the two terms are used
interchangeably in the discussions to follow. The technical differences between the two do
not translate into significant differences in the amount or location of vegetation needed to
protect stream temperatures.
For the portions of the SF CWR Subbasin with the potential for a largely complete conifer
canopy cover over the stream, the CWE temperature model developed for north Idaho under
the auspices of the FPA (IDL 2000) is used. The CWE model is an empirical, reach-based
model that predicts the amount of stream canopy closure required in a given 200-foot
elevation range empirically predicted to maintain a given stream temperature. Each elevation
reach has a predicted percent canopy closure target. Canopy closure requirements increase
with decreasing elevation (as would be expected to account for cumulative effects) increased
exposure times to energy inputs, and increased air temperatures at lower elevations. The
CWE model and its results are discussed in more detail in Appendix G.
The CWE temperature model relationship was developed from data collected in north Idaho,
where the MWMT is predicted by elevation and percent canopy closure. The model assumes
that water temperature has been protected upstream. It accounts for three of the primary
environmental factors affecting stream temperature: local air temperature as it varies by
elevation, micro-environmental modification by the vegetation and its canopy, and shade of
the stream surface by the riparian canopy. Thus, the CWE model predicts the amount of
canopy closure required at a given elevation to maintain stream temperatures within the
water quality standards. In applying the model, the amount of required shade has been
limited to that determined to be the maximum possible for coniferous sites in the SF CWR
Subbasin, or approximately 90% canopy closure.
In non-forested areas in the subbasin, and for large streams where the CWE approach is not
applicable (e.g., SF CWR main stem), an approach that estimates the effective shade
produced by a mature native vegetation community (SPV) has been utilized.
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"System potential land cover" is necessary to achieve "system potential effective shade," and
is defined for purpose of the TMDL as "the potential near-stream vegetation that can grow
and reproduce on a site, given the climate, elevation, soil properties, plant biology, and
hydrologic processes." System potential does not consider management or land use as
limiting factors. In essence, system potential is the design condition used for TMDL analysis
that meets the temperature standard by minimizing human-related warming.
System potential is an estimate of the condition where anthropogenic activities that cause
stream warming are minimized. System potential is not an estimate of pre-settlement
conditions. Although it is helpful to consider historic land cover patterns, channel conditions,
and hydrology, many areas have been altered to the point that the historic condition is no
longer attainable given drastic changes in stream location and hydrology (channel armoring,
wetland draining, urbanization, etc.).
Loading capacity in the SF CWR Subbasin is largely controlled by nonpoint source
influences of heat to the system. Heat accumulates through much of the watershed by direct
solar radiation loading. System potential was estimated as August solar radiation levels that
would reach the stream surface under conditions where anthropogenic activities would not
measurably increase temperature. Similarly, the CWE model estimates percent canopy
closure conditions required during the hottest time of the year, late July and early August, to
protect stream temperatures.
Current effective shade conditions were modeled using Heat Source 6.5 (Boyd 1996; ODEQ
2002) using recently collected field data and other spatial data (i.e., bank full width, digital
elevation models, digital orthophoto quads, and streamside vegetation). These features were
measured on a fine scale using existing GIS databases and digital orthophoto quads (Chapter
3). Simulations were performed for all currently 303(d) listed streams including the SF CWR
main stem, Big Elk Creek, Little Elk Creek, Butcher Creek, and Threemile Creek. The Red
River was also analyzed because it is a meadow-dominated system that dramatically
influences the temperature profile translated downstream.
"System potential effective shade" was simulated by increasing tree heights and densities to
those expected at "system potential land cover." System potential land cover was calculated
for various forested, non-forested, and wetland plant communities. The output of this effort is
a series of curves and graphs that identify effective shade targets given different vegetation
types, channel widths, and aspect (north, south, east, and west). The details of this approach
may be found in Appendix F.
Using the CWE and the SP V methods, surrogate measures of percent stream shading have
been developed. The target percent stream shading is the necessary percent stream shading
needed to achieve temperature standards during the period of the year with highest ambient
air temperatures (late July and early August), which is the critical time period for stream
temperatures.
Using the approach of percent shade targets distributed throughout the SF CWR Subbasin,
shading conditions were established under which stream temperature criteria have the highest
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probability of being achieved throughout the subbasin. While it is recommended that
progress towards attainment of stream temperature targets be monitored using continuous in-
stream temperature monitoring devices, evaluation by land managers of progress towards the
reach-by-reach shade targets should help guide decisions regarding methods to increase
stream shade.
Heat Loading Capacity
The heat load needed to achieve state and federal temperature criteria during the critical time
of the year is used as the loading capacity for all water bodies. The actual heat loading, in
Langleys per day or British thermal units (Btu) per day, needed to achieve temperature
criteria in each waterbody can be derived. Examples of this are shown in graphs of shade
levels and corresponding Langley loadings in Appendix F. Wastewater treatment plant heat
loading in Btus per day which would achieve applicable temperature criteria are listed in a
series of tables in Appendix O. Given that the heat energy (Langley or Btu) loading is not
very useful in guiding nonpoint or point source management practices, we have instead
focused on the temperature criteria and the surrogate target of percent shade in addressing
point and nonpoint sources respectively.
Estimates of Existing Heat Loading
Increased stream temperatures in the SF CWR Subbasin are primarily the result of increased
heat loading from increased solar radiation reaching the water surface and increased local
environmental temperatures as a result of the removal of riparian shading. Logging, road
building, mining, agriculture, livestock grazing, fire, and residential construction are the
primary anthropogenic causes of riparian shade reduction over the last century. In some
cases, lack of shade beyond that which will maintain stream temperatures within the
applicable standard is natural and/or may be the result of forest fires and other natural
disturbance processes. Solar radiation and resultant heat loading have also been increased in
numerous locations around the SF CWR Subbasin through widening of the stream channel
(an increase in the width-to-depth ratio). This is the result of dredge mining, deterioration
and/or removal of the streamside vegetation, channelization, and sediment accumulation
resulting in stream aggradation.
Increasing net heat loading to the surface of a stream segment will result in higher stream
temperatures. Heat loading to a stream surface, however, has both temporal and spatial
variability within the water bodies for which TMDLs are being developed. Predicting the
stream temperature at any location and time in a water body requires an understanding of
how heat is distributed through space and time. In reality, it is most useful to describe heat
loading throughout a water body in a way that provides information about maintaining water
temperatures that supports the water body's beneficial uses.
In terms of timing, heat loading in the SF CWR Subbasin is at its greatest during late July
and early August and is reflected in the high stream temperatures at this time (see Figure 13
and Appendix J stream temperature plots). July and August are the critical months for
temperature exceedances, though exceedances can occur from April through October,
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depending on the water body. Water temperatures increase in April through June, but are
consistently at their peaks during late July and early August. Water temperatures decrease
rapidly after the first wet cold fronts of late August or early September. Heat loading and
stream temperature are analyzed for the critical period of July through August, and it is
assumed that if stream temperatures are in compliance with the temperature WQS during this
period, they will be in compliance throughout the rest of the year.
The effects of heat loading on stream temperature were evaluated using measured in-stream
and remotely sensed water temperature data, calculated percent shade (the most significant
factor influencing heat loading), and stream temperature. The in-stream temperature data in
Section 2.3 and Appendix J show the stream temperatures for specific locations in each water
body. These data are often collected near the mouth where temperatures are likely to be the
highest and can be assumed to integrate all the heat loading and unloading occurring
upstream from the monitoring site. These data indicate that all streams monitored exceeded
applicable temperature criteria between 1999 through 2001. Exceedances of the criteria
occurred as early as April in water bodies at lower elevations in the watershed (e.g.,
Threemile Creek) and continue into early October in some other water bodies (e.g., lower SF
CWR). Standards are usually exceeded by the greatest amount in late July and early August,
which corresponds with the highest air temperatures. An example of water temperature data,
showing peaks in July and August, can be seen in Figure 47.
A Above Crooked Creek (RM 588)
• Above Leggett Creek (RM 47.9)
- Below20 Mile Creek (RM 42.4)
-e- At Mt Idaho Bridge (RM 24.4)
A AtSttes(RM4.3)
S <£.
Date (2000)
Figure 47. Seasonal Variation in Maximum Water Temperature at Various
Locations along the SF CWR in 2000
Water temperature criteria apply throughout all water bodies and at all times. Spatial and
temporal variations in heat loading can be evaluated using remotely sensed surface water
temperatures or a series of in-stream temperature monitors. A number of factors influence
these patterns (Appendix I), but in general, the common pattern is that stream temperatures
increase in a downstream direction and significant diurnal fluctuations can occur. Section
2.3 discusses patterns of heat loading in the SF CWR and several tributaries in more detail.
The main stem SF CWR temperatures are already significantly elevated at the confluence of
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the American and Red Rivers, but remain relatively stable until the Mt. Idaho bridge, where
temperatures begin to increase dramatically. Similarly, an evaluation of data from Red
River, Big and Little Elk Creeks, and Threemile Creek indicate that temperatures increase
dramatically in the lower reaches of these tributaries as well.
Figure 48 illustrates the diurnal temperature pattern in Big Elk Creek. The temperatures at
the NPNF boundary, reflecting largely forested conditions, are much lower than temperatures
at a point 5 miles downstream (RM 4.7). The primary difference between these two
monitoring stations is that a series of meadows occur between the two, in which much of the
riparian vegetation (shading) has been removed as a result of long-term grazing. Measured
data for Big Elk Creek clearly show the effect of shade on heat loading and stream
temperature that occurs in the SF CWR Subbasin.
82
78
E 74
at
5
»| 70
V
CL
I 66
H
& „
re 62
58
54
50
Big Elk Creek
A Big Elk Creek at USFS Boundary (Relate RM 10.3)
• Big Bk Creek above Little Elk Confluence (Relative RM 4.7)
— Ametkan Riwr at Mould (RM 0.0)
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Time of Day (8/3/2000)
Figure 48. Diurnal Temperatures Measured Big Elk Creek and the American
River (mouth) on August 3, 2000
Current shade conditions were estimated using CWE (percent canopy closure) and SPY
(percent effective shade) methods for forested and non-forested areas, respectively
(Appendices F and G). The CWE determination of current percent canopy closure for the SF
CWR Subbasin is presented in Figure 49. Focusing on water bodies currently 303(d) listed
for temperature, Figures 50 and 51 show current CWE percent canopy closure data for the
Threemile Creek/Butcher Creek area and the Big Elk Creek/Little Elk Creek area. Figures
52 - 56 list current effective shade for Threemile Creek, Big and Little Elk Creeks (meadow
areas), the main stem SF CWR, and Butcher Creek. The line presented on these figures
represents the 0.25-mile moving average condition, which was calculated at 100-foot
intervals along the stream segments.
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OWE Percent Existing Shade
in the South Fork
Clearwater Subbasin
May. 2002
Figure 49. Current Percent Canopy Closure Determined by Aerial
Photographic Interpretation of the SF CWR Subbasin
NPT Reservation Bound
Cottonwood TMDLArea
Water Body ID watershe
C ^ Threemiie Creek
utcherCreek
Existing % Canopy Closure
D
A/ »-«
'N/ 25 - SD
A/
/\/ 75-100
October 2003
Figure 50. Current Percent Canopy Closure of Threemiie and Butcher Creeks
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Figure 51. Current Percent Canopy Closure of Big Elk and Little Elk Creeks
100% -,
90% -
80% -
V 70% -
•O
ra
W 60% -
I
« 50% -
It
LU
•o 40%
•s
20% 7
10%
0%
Forest
Boundary
12345678
River Mile (Big Elk Creek)
9 10 11
Figure 52. Big Elk Creek Current Effective Shade, Lower Reaches
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100% -
90% -
_ 80% -
£
* 70% •
(B
" 60% •
I
I 50%
•n 40%
*S
| 30%
° 20% •
10% .
0% -
0
234567
River Mile (Little Elk Creek)
Figure 53. Little Elk Creek Current Effective Shade, Lower Reaches
100% -i
90% J
„ 80% J
« 70%
ro
« 60%
s 50%
•o 40%
£
= 30%
'ro
° 20%
10% I
0% I-
0
1
y1 (* ¥
r J St>rt of
245
10 12 14 16 18 20
River Mile (Three Mile Creek)
Figure 54. Threemile Creek Current Effective Shade
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100% •
10 15 20 25 30 35 40 45 50 55 60 65
River Mile (South Fork Clearwater River)
Figure 55. South Fork Clearwater River Current Effective Shade
23456789
River Mile {Butcher Creek)
10 11 12
Figure 56. Butcher Creek Current Effective Shade
Point sources are another source of heat loading in the subbasin. While Section 3.1 identifies
a number of point sources known to exist in the SF CWR Subbasin, only the five municipal
WWTPs listed in Table 43 are expected to have a significant effect on stream temperature.
Other point sources in the subbasin include suction dredge operations and industrial and
construction related stormwater. The heat of water and sediment is not believed to increase
significantly as it passes through the pumps and piping of suction dredge operations, and
stormwater runoff during the critical time period for temperature (July-August) is minimal or
nonexistent since precipitation during these months is the lowest for the year (WRCC 2003).
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Table 43. Point sources that may affect stream temperature.
Facility
Location
Grangeville
Kooskia
Stites
Elk City
Red River
Ranger Station
NPDES
Permit
Number3
ID-002003-6
ID-002181-4
ID-002034-6
ID-002201-2
ID-002069-9
Type of Facility
Wastewater
Treatment Plant
Wastewater
Treatment Plant
Wastewater
Treatment Plant
Wastewater
Treatment Plant
Wastewater
Treatment Plant
Receiving Water
Threemile Creek
South Fork
Clearwater River
South Fork
Clearwater River
Elk Creek
South Fork Red River
Design
Flow
(MGD)b
0.88
0.2
0.07
0.12
0.0063
National Pollution Discharge Elimination system
million gallons per day
Heat Load Allocation
Allocation of heat load is the process in which the heat loads necessary to achieve the load
capacity (i.e., water temperature criteria) are assigned to the various nonpoint and point
sources and background. Shade conditions for nonpoint sources are used as a surrogate to
achieve in-stream temperature criteria in the SF CWR Subbasin. The allocation process for
point sources must explicitly identify a heat load (i.e., a temperature or range of
temperatures), also known as a WLA, which will be subsequently incorporated into NPDES
permits.
Shade targets were established for the SF CWR and all tributaries, whether or not they are
included on the current 303(d) list, for two reasons. First, the entire SF CWR main stem is
303(d) listed for temperature. As discussed in Section 2.3, a significant portion of heat
loading to the SF CWR is from tributaries, and it is necessary to address elevated
temperatures in the tributaries in order to reduce main stem SF CWR temperatures. Second,
as also pointed out in Section 2.3, the applicable temperature criteria are exceeded at some
time in all streams monitored within the SF CWR Subbasin. While most of these streams are
not currently on the 303(d) list, including shade targets for them in the TMDL will address
human-caused temperature problems measured in the main stem, as well as in these streams,
and preclude the need to include them in future 303(d) lists and TMDLs.
To the extent possible, the allocation process should also identify what portion of the total
load allocation is natural background. Clearly there is significant natural solar radiation
loading to all SF CWR Subbasin streams. Some streams have significant human influences
that have elevated stream temperature (e.g., Red River, Big Elk Creek). Also, as mentioned
previously, some streams that have very little human influence, such as Johns and Silver
Creeks, also exceed applicable temperature criteria. In all cases it is difficult to quantify
what portion of the loading is from background and what portion is human caused. Rather
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
than attempting to identify the specific natural background heat load, it is assumed that by
establishing and achieving shade targets, and correcting channel problems in some locations,
the majority of human caused heat loading will be addressed. What remains will largely be
natural heat loading (background). Temperature in some streams may still exceed numeric
criteria, but if human-caused sources of heat loading have been addressed, these streams will
be in compliance with Idaho WQS (IDAPA 58.01.02.250.02).
Nonpoint source allocations (shade targets) have been assigned independent of land use or
land ownership. Reductions in stream shade have occurred as a result of a variety of land use
activities, and on private, state, and federal lands. In order to resolve temperature problems,
improvements will need to be made across all land use and ownership categories. The
location and degree of shade loss and channel alteration are the major factors that must be
considered in restoration. As a result, allocations were established based on conditions at a
given location, regardless of land use or land ownership.
Non-point source load allocation
Nonpoint source load allocations consist of a series of shade targets established for each
stream in the SF CWR Subbasin. As discussed in Section 3.1 and Appendix G, shade targets
for forested areas have been developed utilizing the CWE process. Specific percent canopy
closure targets for each 200-foot elevation reach have been developed. Due to the sheer
number of stream segments evaluated, these are included as a map in Appendix G
accompanied by an Arc View shapefile on CD or diskette. For illustration, targets for
forested areas in currently 303(d) listed streams are shown Figures 57, 58, and 59.
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CWE Temperature Model Modified /^"\
by USEPA Policy Target Percent \ ""• |
Canopy Closure in the South Fork
Clearwater Subbasin
May, 2002
Figure 57. Cumulative Watershed Effects (CWE)-Based Target Percent
Canopy Closure for the SF CWR Subbasin
CWE % Canopy Closure Target
A/ «-•*
25-50 A
60-75 «'XI>E
SPY Analysis
NPT Reservation Boundary
Cottonwood TMDL
BulcherCreek
Threemile Creek
Water Body ID Watershed
October 2003
Figure 58. Cumulative Watershed Effects (CWE)-Based Target Percent
Canopy Closure for the Threemile/Butcher Creeks Area
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Target Percent Canopy
Closure Predicted by the
CWE Temperature Model
Modified by USEPA Policy
-
Legend
CWE % Canopy Closure Target
A/ »-»
25-50
75-90 S
Not Assessed
SPV Analyse
303D TOTpcrature USKO WB5
water Body ID raenrMiK
Figure 59. Cumulative Watershed Effects (CWE)-Based Target Percent
Canopy Closure for the Big and Little Elk Creeks Area
In non-forested areas the allocation consists of effective shade targets established through the
SPV process outlined in Appendix F. A series of curves has been developed for 12 different
vegetative response units (VRUs) and three wetland types (Appendix F). Reach-specific
targets may be derived from these curves using site-specific information on channel width
and aspect. Effective shade targets for currently listed 303(d) streams based on existing
vegetation and channel width information were estimated and are shown in Figures 60-64.
Target conditions (gray lines) are plotted against the current shade conditions (dark lines).
System Potential Effective Shade (%)-1/4 Mile Moving Average
Current Effective Shade -1/4 Mile Moving Average
10 15 20 25 30 35 40 45 50 55 60 65
River Mile (South Fork Clearwater River)
Figure 60. Current and System Potential Effective Shade Conditions for the SF
CWR
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f
234567
River Mile (Big Elk Creek)
9 10 11
Figure 61. Current and System Potential Effective Shade Conditions for Big
Elk Creek
£
a
•o
n
!
1
•q
0]
1
"3
I
TO
0
100% -i
30%
80% ^
70%
60%
50%
40% -
30% -
20%
10%
0%
^ n i\ A
rurJiJS A
\
I
I I
I
n /v^~v «—
\ j W^^ asunrtaly
[j
" ^_IM M.lfMowMJ A^fifle . &fcre*B Shade JH)
lf4U
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Figure 63. Current and System Potential Effective Shade Conditions for
Threemile Creek
100%
90%
_ 80% J
S*
| "*-
« 60%-
§ 50% -
B
•D 40%
fi
1 30%
5 20%
10% '
0%-
(
I'll
y
IH UK MMtvj ttnge . Cunr> MIEIM SIUK Kl
l.fl Utt McMng Astlrags - Sy'.ferll Potvrll* f rUD'*
I
(I
JAn
> (r-^ y '
nJ^iv 1 Ur^
V
1 '
11 2 3 4 5 6 7 8 9 10 11 12
River M lie {Butcher Creek)
Figure 64. Current and System Potential Effective Shade Conditions for
Butcher Creek
The nonpoint source shade allocations result in the need to increase shade in most of the
watershed historically managed by man. Increases in shade are not needed in areas that have
natural vegetation and channel conditions. These areas primarily occur in high elevation
forests, and portions of lightly managed watersheds, such as Johns and Silver Creeks. A
summary of the general increases in shaded needed throughout the SF CWR subbasin is
listed in Table 44.
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Current shade levels are highly variable in all land use types, and reflect a wide range of
natural and man-induced disturbance conditions, and variability in vegetation types. For
example, mapped meadow areas often contain small patches of coniferous trees, resulting in
a naturally wide range of shade. The summary of needed shade increases shown in the last
column of Table 44 provides a general impression of the average difference between currnt
and target shade levels needed. However, landowners and land managers must consult
detailed allocations within the TMDL, coupled with on-site field verification, in order to
establish site specific targets.
Table 44. Nonpoint source shade increase summary.
Land Use Type
SF CWR Mainstem
Forested areas
Upper Meadow areas
Agricultural areas
Current shade
0 - 95%
0 - 90%
0 - 97%
0 - 83%
Average Percent Shade
Increase Needed
19%
21%
24%
19%
Point Source Wasteload Allocations
As indicated in Chapter 3, point sources in the SF CWR include WWTPs, storm water
runoff, and suction dredging. Of these, only WWTPs are known to be contributors of heat to
the SF CWR and are the focus of WLAs in this TMDL.
It has been established that temperatures in all SF CWR streams monitored in recent years
exceed established water quality criteria, primarily during the summer months. Since even
streams at high elevations with little or no human impact exceed temperature criteria, it has
been concluded that streams temperatures naturally exceed criteria throughout the subbasin,
primarily during the warmest months of the year. The temperature exception for natural
conditions in the Idaho WQS (IDAPA 58.01.02.401.OS.a.v) provides that:
"If temperature criteria for the designated aquatic life use are exceeded in the receiving
waters upstream of the discharge due to natural background conditions, then Subsections
401.03.a.iii. and 401.03.a.iv. do not apply and instead wastewater must not raise the
receiving water temperatures by more than three tenths (0.3) degrees C."
This standard is consistent with recently issued temperature guidance (USEPA 2003), which
supports allowance of "de-minimis" increases.
The natural stream temperature at each of the treatment facilities will vary daily, seasonally,
and from year to year, and is clearly the most difficult of these variables to establish.
Further, at each of the facilities, upstream human activities likely have increased stream
temperature above background levels, so stream temperatures upstream of each outfall are
not considered to be natural. Natural stream temperatures may be modeled, but such
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modeling is beyond the scope of this TMDL, and likely is not feasible for very small streams
such as Elk Creek, Threemile Creek, and the South Fork Red River.
It is not necessary to know natural background temperatures in order to establish effluent
limits that will not increase temperature by more than 0.3°C (0.5 °F). If the calculation is
made at criteria temperatures, the resulting heat load will also meet the limit at higher
receiving water temperatures. If natural temperatures are actually lower than the criteria, the
effluent limit so calculated will still more than meet standards, as a greater increase would be
allowed (1.0 °C = 1.8 °F) in such circumstances. So the conservative approach taken here is
to calculate the allowable heat load as if the natural background temperature was equal to the
applicable numeric criterion.
Given the lack of natural stream temperature data, for the purposes of calculating effluent
limits, it has been conservatively assumed that the in-stream temperature upstream of a
treatment facility does not exceed the applicable temperature criteria. Effluent temperatures
that would increase the stream temperature by 0.3°C are then calculated using a mass balance
equation and provisions in Idaho WQS which allow mixing zones of up to 25% by volume of
the stream flow (IDAPA 58.01.02.060). This approach is consistent with recommendations
in the USEPA temperature guidance (USEPA 2003). The mass balance equation is as
follows:
TE = [QK + (0.25 *QsD1 * [Tr + 0.3C1 - [(0.25 * (V) * T£1
QE
Where:
TE = effluent temperature (°C)
QE = effluent flow (cfs)
Qs = stream flow (cfs)
Tc = applicable temperature criteria (cfs)
0.25 = 25% by volume mixing zone allowance (unitless)
Based on these calculations, very high effluent temperatures at Kooskia, Stites, Red River
Ranger Station, and, to some degree, Elk City would not significantly increase in-stream
temperatures below the mixing zone (See Appendix O). However, since all of the receiving
waters for these facilities naturally exceed temperature criteria, and since other anthropogenic
sources in these watersheds are also increasing stream temperatures, it is not reasonable to
allow treatment facilities to further increase their effluent temperatures. USEPA enforces
this concept with their anti-backsliding provisions of the NPDES permitting process.
Consequently, allocations for these facilities will be based on current maximum
temperatures, as recommended in the temperature guidance (USEPA 2003).
Local data to estimate maximum effluent temperatures are sparse; only Grangeville, and
more recently, Kooskia, have monitored and reported effluent temperatures historically.
Effluent data collected by Grangeville between 1989 and 2001 and included in USEPA's
Permit Compliance System database (USEPA 2003b) were reviewed, and a maximum
temperature of 23 °C (73.4 °F)was reached during six different months (typically August)
over the 12-year period. This is consistent with data reported in TMDLs in eastern Oregon
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for other small community WWTPs: Pendleton, OR - 22 °C; Hermiston, OR - 23°C; La
Grande, OR - 23°C (ODEQ 2000, ODEQ 2001). Therefore, establishing a maximum daily
limit of 23°C, which would apply at times when temperature criteria are expected to be
exceeded, appears to be reasonable for Kooskia, Stites, Red River Ranger Station, and
portions of the year for Elk City.
Kooskia began monitoring effluent temperature in May of 2003. Peak temperatures were
reached during July 2003, with a maximum daily temperature of 26 °C (78.8 °F) recorded on
July 31 (Kooskia 2003). Based on these data, a maximum daily limit of 26 °C (78.8 °F) will
be established as the wasteload allocation for Kooskia and Stites, which is in close proximity.
This allocation will apply from July 15 - August 31, and from October 1-15, when
temperature criteria in the SF CWR are expected to be exceeded.
The wasteload allocation for the Red River Ranger Station and Elk City will include a
maximum daily limit of 23 °C (73.4 °F), based on data from Grangeville and eastern Oregon
communities. While Elk City and the Red River Ranger Station have thus far not reported
the temperature of their effluent, these facilities are located at 4,060 and 4,330 feet elevation
respectively, whereas Kooskia and Grangeville lie at 1,280 and 3,360 feet elevation
respectively. While the surface area and shape of the waste treatment ponds at these facilities
will likely affect effluent temperature, for purposes of this allocation it is expected that
temperatures of the Grangeville effluent are more comparable to that of Elk City and the Red
River Ranger Station due to the relatively low elevation of Kooskia. This allocation may be
adjusted in the future if effluent monitoring at Elk City and the Red River Ranger Station
indicates that effluent temperature from these facilities exceeds 23 °C (73.4 °F).
Effluent temperatures for Grangeville, and Elk City under low stream flow conditions, may
have a significant impact on stream temperature. Wasteload allocations for these facilities
will be based on mass balance calculations in Tables 45 - 47 to ensure that permit limits do
not result in greater than a 0.3°C increase in stream temperature.
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Table 45. Elk City wastewater treatment plant (WWTP) maximum daily effluent
temperatures (°C)a that would not increase temperatures in Elk Creek
by more than 0.3 °C between June 1 and September 30 when federal
bull trout criteria apply.
Elk Creek
Flow Above
WWTP (cfs)b
3
5
10
15
20
25
30
35
>35
WWTP Effluent Discharge (cfs)
0.01
23.0
23.0
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.02
20.6
23.0
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.03
16.8
21.8
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.04
14.9
18.7
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.05
13.8
16.8
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.10
11.6
13.1
16.8
20.6
23.0
23.0
23.0
23.0
23.0
0.15
10.8
11.8
14.3
16.8
19.3
23.0
23.0
23.0
23.0
0.20
10.4
11.2
13.1
14.9
16.8
18.7
20.6
22.4
23.0
Applicable between June 1 and September 30 when federal bull trout temperature criteria apply
cubic feet per second
Table 46. Grangeville wastewater treatment plant (WWTP) maximum daily
effluent temperatures (°C)a which would not increase temperatures
in Threemile Creek by more than 0.3 °C between April 1 and May 31
when the salmonid spawning criteria is applicable.
Threemile Creek Flow Above
WWTPOutfall(cfs)b
0.1
1
3
5
7
9
10
WWTP Effluent Discharge (cfs)
0.4
9.3
9.5
9.9
10.2
10.6
11.0
11.2
1.0
9.3
9.4
9.5
9.7
9.8
10.0
10.1
1.5
9.3
9.4
9.5
9.6
9.7
9.8
9.8
2.0
9.3
9.3
9.4
9.5
9.6
9.6
9.7
2.5
9.3
9.3
9.4
9.5
9.5
9.6
9.6
Applicable between April 1 and May 31 when salmonid spawning temperature criteria apply
' cubic feet per second
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Table 47. Grangeville wastewater treatment plant (WWTP) maximum daily
effluent temperature (°C) that would not increase Threemile Creek
temperature more than 0.3 °C between July 15 and September 15
when coldwater aquatic life temperature criteria apply.
Threemile Creek Flow
Above WWTP Outfall
(cfs)
0.1
1.0
2.0
3.0
WWTP Effluent Discharge (cfs)
0.3
19.3
19.6
19.8
20.1
0.5
19.3
19.5
19.6
19.8
1.0
19.3
19.4
19.5
19.5
1.5
19.3
19.4
19.4
19.5
2.0
19.3
19.3
19.4
19.4
Specific WLAs for all WWTPs are listed in Table 48. Heat loads (Btu/day) that correspond
to these allocations are listed in tables in Appendix O. These allocations are intended to
apply only during times when it is expected that the receiving waters will exceed numeric
temperature criteria, based on historic data in Appendix J. It is expected that these limits will
be incorporated directly into NPDES permits, since a 25% mixing zone provision has already
been included in WLAs for Grangeville and Elk City. For Kooskia, Stites, and Red River
Ranger Station, the WLAs should be interpreted as an end-of-pipe limit (i.e., no mixing
zone), since it represents the reasonable maximum end-of-pipe temperature.
Table 48. Temperature wasteload allocations for wastewater treatment plants.
Facility
Kooskia Wastewater
Treatment Plant
Stites Wastewater
Treatment Plant
Red River Ranger Station
Wastewater Treatment
Plant
Elk City Wastewater
Treatment Plant
Grangeville
Wasteload Allocation
26 °C (78.8 °F), daily
maximum
26 °C (78.8 °F), daily
maximum
23 °C (73.4 °F), daily
maximum
23 °C (73.4 °F), daily
maximum
See 45
See Table 46
See Table 47
Applicable Period
July 15 -August 31
October 1-15
July 15 -August 31
October 1-15
July 15 -August 31
May 15 -31
June 1 - September 30
April 1 - May 31
July 15 - September 15
An evaluation of localized impacts of thermal plumes on salmonids, as recommended in the
temperature guidance, was not conducted as part of this TMDL. The guidance describes
potential adverse impacts from thermal plumes, which may occur at different temperatures
ranging from 13 °C to 32 °C (55.4 °F to 89.6 °F), for different exposure periods. The
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evaluation in the TMDL supporting allocations for all facilities focused on achieving
salmonid spawning (9 °C (48.2 °F) daily average), bull trout (10 °C (50 °F) MWMT), or the
cold water aquatic life criteria (19 °C (66.2 °F) daily average) at the edge of a 25% by
volume mixing zone. Given the nature of this evaluation, and the size and location of the
WWTPs, the only scenario in the temperature guidance which would appear to warrant
further impacts analysis is whether the WWTP effluent causes stream temperature to exceed
13°C, or cause increases in stream temperature of more than 0.25 °C (0.45 °F), in the vicinity
of active salmonid spawning and egg incubation areas. Prior to issuing NPDES permits
based on these WLAs, it is recommended that stream channels in the vicinity and
downstream of these outfalls be surveyed by fisheries biologists to establish the nearest
downstream spawning areas. Mixing zone calculations should then be conducted to
determine if the wasteload allocations would cause stream temperature to exceed 13°C, or
cause stream temperature to increase more than 0.25°C in these spawning areas. If so,
wasteload allocations and NPDES permit limits should be adjusted to avoid these conditions.
Margin of Safety
The CWA requires that each TMDL be established with an MOS. The statutory requirement
that TMDLs incorporate an MOS is intended to account for uncertainty in available data or in
the actual effect controls will have on loading reductions and receiving water quality. An
MOS is expressed as unallocated assimilative capacity or conservative analytical
assumptions used in establishing the TMDL (e.g., derivation of numeric targets, modeling
assumptions, or effectiveness of proposed management actions).
The MOS may be implicit, as in conservative assumptions used in calculating the LC, WLA,
and LA. The MOS may also be explicitly stated as an added, separate quantity in the TMDL
calculation. In any case, assumptions should be stated and the basis behind the MOS
documented. The MOS is not meant to compensate for a failure to consider factors that
affect water quality.
A TMDL and associated MOS, which result in an overall allocation, represent the best
estimate of how standards can be achieved. The TMDL process accommodates the ability to
track and ultimately refine assumptions within the TMDL implementation-planning
component.
The following factors may be considered in evaluating and deriving an appropriate MOS:
• The analysis and techniques used in evaluating the components of the TMDL process
and deriving an allocation scheme.
• The characterization and estimates of source loading (e.g., confidence regarding data
limitation, analysis limitation, or assumptions).
• An analysis of relationships between the source loading and in-stream impact.
• The prediction of the response of receiving waters under various allocation scenarios
(e.g., the predictive capability of the analysis and simplifications in the selected
techniques).
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• The implications of the MOS on the overall load reductions identified in terms of
reduction feasibility and implementation time frames.
A number of areas of uncertainty exist in the SF CWR Subbasin temperature TMDL.
Among the more significant are:
• The relationship between stream temperature and shade levels.
• Estimating CWE and system potential shade levels.
• Estimating point source effluent temperatures.
The TMDL accounts for these uncertainties by incorporating implicit MOS. The procedure
to develop shade targets utilizing the CWE methodology is based on achieving existing
temperature criteria. Analysis above indicates that temperatures naturally exceed criteria
throughout the subbasin; therefore, shade targets and WLAs that are developed to meet the
criteria are inherently conservative. In addition, by definition SPV targets represent riparian
vegetation conditions absent human disturbance, and are therefore the best achievable.
Seasonal Variation/Critical Conditions
Temperature varies seasonally due to changes in solar radiation loading, air temperature, and
other factors, as illustrated in Section 2.3. Water temperatures peak in the July - August time
period, which coincides with spawning and incubation periods for key sensitive aquatic
species including spring/summer chinook salmon, cutthroat trout, bull trout, and steelhead.
Egg and larval stages of salmonids are the most sensitive to elevated temperatures, so the
July - August time period, when the magnitude of temperature exceedances is the greatest
and flows are the lowest, is the most critical period for temperature.
The TMDLs have addressed the seasonal nature and this critical time period by developing
shade targets (CWE and SPV) and WLAs specifically for this period. The CWE analysis
targets early August in deriving canopy closure targets that have been associated with water
temperature compliance, and the heat loading resulting from system potential vegetation
targets is estimated for the August time frame. Seasonal WLAs apply only during the time
period when violations are expected to occur, and have been established to meet Idaho
temperature criteria, including natural condition provisions, during the critical low flow
summer months. By developing targets for the most critical time period, it is expected that
shade targets will be protective at other times of the year as well.
Background
The natural background heat loading is an important component of the TMDL, because
temperatures throughout the subbasin appear to naturally exceed existing water quality
criteria at certain times. The TMDL does not attempt to quantify the natural background heat
loading or establish the natural thermal regime of individual water bodies. Rather, the
TMDL allocations incorporate natural background by setting shade targets that are expected
to achieve natural background temperatures. This is consistent with direction provided in
Idaho WQS (TDAPA 58.01.02.200.09), which say that when natural background conditions
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exceed any applicable water quality criteria, the water quality criteria shall not apply; instead,
pollutant levels shall not exceed natural background conditions.
Reserve
A reserve capacity for future growth has not been specifically identified or incorporated
within these temperature TMDLs. Future management activities and growth of
municipalities is expected to be possible within the allocations and WLAs established.
5.4 Sediment TMDLs
Sediment TMDLs are developed below for seven water bodies in the SF CWR Subbasin:
Threemile Creek, Butcher Creek, and the five water bodies of the main stem SF CWR. Point
sources of sediment within the subbasin are relatively minor in relation to the nonpoint
sources. However, all known point sources are evaluated and WLAs set.
The details of the data sets and some of the calculations for the nonpoint source of sediment
are presented in Appendix M. A sediment budget (Appendix L) was developed for all the
major nonpoint sediment sources in the SF CWR Subbasin; the results of which are used to
calibrate and validate the sediment loadings calculations.
In-Stream Water Quality Targets for Sediment
The goal of a sediment TMDL is to restore "full support of designated beneficial uses"
(Idaho Code 39.3611). A part of the analysis discussed herein uses a TSS target derived
from the turbidity WQS based on equations found in Appendix M. Other parts of the analysis
use the narrative sediment standard and are driven by reasoning processes rather than hard
numbers. Setting the targets for the narrative-derived TMDLs involved the WAG and other
interest groups to arrive at a method that would address the sediment impairment in the
subbasin and not adversely affect one economic interest over another.
In general, in-stream TSS targets are set for Threemile Creek, Butcher Creek, and the lower
main stem SF CWR at Stites. The sediment targets for the main stem SF CWR above
Butcher Creek are set at the targeted percent sediment load reduction from the Stites location,
(i.e., 25% of the total human-caused sediment load). The human-caused loads and targets for
the locations upstream from Butcher Creek are based on the sediment budget presented in
Appendix L.
Design Conditions
The 303(d) listed streams in the SF CWR Subbasin for which sediment TMDLs were
developed are Threemile Creek and Butcher Creek in the lower end of the subbasin and the
whole of the main stem SF CWR from Kooskia up to the confluence of the Red and
American Rivers. The main stem SF CWR is divided into five water bodies in state code
(IDAPA 58.01.02.120.07) and sediment TMDLs are developed for each one of them.
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Salmonid spawning aquatic life use is the most limiting designated or existing beneficial use
for all of these water bodies.
Sediment loading to streams and rivers in the SF CWR Subbasin is dominated by spring
runoff events, particularly those extreme events that have a recurrence of once every five
years or longer. Sediment loadings for the SF CWR TMDLs are calculated on an annual
basis. However, it is clear that only significant load reductions during the extreme events
will result in attainment of the water quality targets. The majority of sediment load
reductions for the SF CWR Subbasin must come from Cottonwood Creek if the subbasin is
to meet WQS. The sediment TMDL for Cottonwood Creek has been written (DEQ, NPT,
USEPA 2000) and the SF CWR Subbasin TMDLs rely on some of its calculated loadings to
balance the sediment budget.
Sediment loading calculations focus on the large and predominant sources of sediment in
the subbasin. Many other minor sources of sediment exist throughout the subbasin, such as
the fish hatchery facilities, old mines, and other largely unidentifiable and unquantifiable
sources (see Chapter 3). Gross sediment load allocations are established at key control
locations within the watershed, and include all nonpoint sources of sediment. It is expected
that a majority of the sediment reductions needed to achieve the allocations will come from
the major anthropogenic sources, principally agriculture, roads, and stream bank erosion
control.
The sediment loading analyses and target development are driven by the turbidity standard
which states that waters shall not exceed 25 NTU over background for greater than 10 days
and shall not exceed 50 NTU over background at any time. The turbidity measurements used
in the calculations are instantaneous samples. Similarly, the extreme flows which generate
the greatest amount of sediment are in effect instantaneous, or at least do not last for 10 days.
To transform the instantaneous turbidity data to produce continuous sediment loading
numbers, a stochastic flow model of daily average flow for 10 years is developed. The
resulting continuous flow/turbidity/TSS model results are then compared to the 25 NTU over
background criterion to develop daily loading, daily load capacity, daily natural background
loading, and daily excess sediment loading. These results are then annualized to produce the
loading figures presented in this report. Doing all the calculations on a daily, essentially
continuous basis, using the 25 NTU criterion automatically includes all times when the 50
NTU criterion is exceeded. Subsequent discussions of the loading calculations for these
TMDLs refer to achieving the 25 NTU criterion. It is to be understood that the methods used
for the calculations automatically include the times when the 50 NTU criterion applies, and
will also ensure this portion of the turbidity standard is met.
The narrative sediment WQS states that sediment "shall not exceed quantities ... which
impair designated beneficial uses" (IDAPA 58.01.02.200.08). Sediment load reduction
calculations for the main stem SF CWR above Butcher Creek are based on restoring
beneficial uses that are impaired in this part of the river. DEQ's protocol for assessing
beneficial use support status for large rivers has not been applied to the main stem SF CWR
for lack of adequate data. However, sediment loading, coupled with the Fish TAG
conclusions (Appendix D), cobble embeddedness data, and other reference watershed data
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(Appendix N) have led to the conclusion that beneficial uses are impaired in the main stem
and that TMDLs are required. The requirement for load reductions in the main stem will
likely result in load reductions from water bodies flowing into the main stem. Targets are set
at four main stem SF CWR control points upstream from the mouth of Butcher Creek.
Bedload in the form of sand-sized particles is considered to be the primary pollutant of
interest in the main stem SF CWR water bodies above Butcher Creek. Bedload is also
considered to be a problem in Butcher Creek, Threemile Creek, and the lower reach of the
main stem. While we do have some bedload data, there are insufficient data to calculate
loads and set targets for bedload. Therefore, it is assumed that sediment load reductions to
meet TSS-based targets will result in adequate bedload reductions as well. The basis for this
assumption is discussed in the sections to follow.
Sediment loading calculations for these SF CWR TMDLs are based on daily average flows
and monitoring results of associated in-stream TSS. The calculated results are then
annualized so sediment LAs can be made. The following sections of this report present the
calculations in the order they come into play: development of the stochastic flow models;
development of the flow to TSS and bedload relationships; estimations of current sediment
loading; estimations of the proportions of current sediment loading that are natural
background; estimations of loading capacities based on the WQS, flow, and background;
calculations of excess sediment loading from the current loading and loading capacities;
determination of a MOS; and estimation of a required sediment load reduction to meet WQS.
The summary results of all the calculations and estimations are presented for control
locations for Butcher and Threemile Creeks and the main stem SF CWR at Stites and
Harpster in Tables 49 through 52.
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Table 49. Threemile Creek loading calculations.
Parameter3
Daily Flow for Last 1 0 Years (cfs)
Existing TSS, Daily Average (mg/L)c
Existing TSS (t/day)
Existing TSS, Yearly Average (t/y)
Existing Turbidity (NTU)
Background Ratio
Background TSS (mg/L)
Background TSS (t/day)
Load Capacity (t/day)
Excess Load (t/day)
Excess Load (t/y)
Load Reduction (%)
Equation"
Derived from Lapwai Creek and Lipscomb (1998)
correction
(flow) * (0.9779)
(TSS) * (flow) * (0.0027)
(flow)* (1.81 82)
(535 t/y/WB) / (6640 t/y/WB)
(TSS daily average) * (background ratio)
TSS (t/day) * background ratio
((17 mg/L) * daily flow * 0.0027) + background
TSS (t/day)
If load capacity > TSS (t/day)
Else, TSS (t/day) - load capacity
Excess load / (TSS - background TSS) yearly
average
Minimum
0.19
0.19
0.0001
18
0.25
0.02
0
0.008
0
0
Maximum
411
402
446
3,992
542
35
38
57.8
0
388
Average
16
16
3.0
1,112
21
0.08 (8%)
1.3
0.27
1.0
0
2.1
775
0.77 (77%)
a cfs = cubic feet per second, TSS = total suspended solids, mg/L - milligrams per liter, t/day = tons per day, t/y = tons per year, NTU
= nephlometric turbidity units
b t/y/WB = tons per year per water body
c From sediment yield curves in Appendix M
Threemile Creek watershed area = 21, 478 acres or 33.5 square miles
Threemile Creek sediment yield equation: 25 NTU Idaho WQS criterion = 17 mg/L = (25 NTU * 0.674)
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Table 50. Butcher Creek loading calculations.
Parameter3
Daily Flow for Last 10 Years (cfs)
Existing TSS, Daily Average (mg/L)
Existing TSS (t/day)
Existing TSS, Yearly Average (t/y)
Existing Turbidity (NTU)
Background Ratio
Background TSS (mg/L)
Load Capacity (mg/L)
Background TSS (t/day)
Load Capacity (t/day)
Excess Load (t/day)
Excess Load (t/y)
Load Reduction (%)
Equation"
Derived from Lapwai Creek and Lipscomb (1998)
correction
(flow)* (2.381) + 5.89 c
(TSS) * (flow) * (0.0027)
((flow)* (2.61 18)) + 3.731 7
(303 t/y/WB) / (1 ,251 t/y/WB)
(TSS daily average) * (background ratio)
Background + 25.25 mg/L
TSS (t/day) * background ratio
((25.25 mg/L) * daily flow * (0.0027)) +
background TSS (t/day)
If load capacity > TSS (t/day)
Else, TSS (t/day) - load capacity
Excess load / (TSS - background TSS) yearly
average
Minimum
0.07
6.1
0.001
13.8
3.9
1.5
26.7
0.0003
0.005
0
0
Maximum
159
384
165
1,537
418
92.7
117.98
39.8
50.6
0
114
Average
6.2
20.6
1.2
435.6
19.9
0.24 (24%)
5.0
30.2
0.29
0.71
0
0.55
199.4
0.61 (61%)
a cfs = cubic feet per second, TSS = total suspended solids, mg/L - milligrams per liter, t/day = tons per day, t/y = tons per year, NTU = nephlometric turbidity
units
b t/y/WB = tons per year per water body
0 From sediment yield curves in Appendix M
Butcher Creek watershed area = 10,723 acres or 16.8 square miles
Butcher Creek sediment yield equation: 25 NTU Idaho WQS standards = 25.25 mg/L = ((25 NTU) * 0.9056) + 2.6113
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Table 51. Stites USGS station loading calculations.
Parameter3
Daily Flow for Last 10 Years (cfs)
Existing TSS, Daily Average (mg/L)
Existing TSS (t/day)
Existing TSS, Yearly Average (t/y)
Existing Bedload, (t/y)
Existing Turbidity (NTU)
Background Ratio
Background TSS (mg/L)
Load Capacity (mg/L)
Background TSS (t/day)
Load Capacity (t/day)
Excess Load (t/day)
Excess Load (t/y)
Load Reduction (%)
Equation"
Stites USGS station and Lipscomb (1998)
correction
(flowA1. 953)* (0.00005) c
TSS (mg/L) * flow * (0.0027)
3 * (10A(-12)) * (flowA3.6237)
(flow) * (0.0058)
(1 9,884 t/y/WB) / (91 ,052 t/y/WB)
(TSS daily average) * (background ratio)
Background TSS (mg/L) + 45 mg/L
TSS (t/day) * background ratio
((46.9 mg/L) * daily flow * (0.0027) + (background
TSS (t/day))
If load capacity > TSS (t/day)
Else, TSS (t/day) - load capacity
Excess load / (TSS - background TSS) yearly
average
Minimum
90
0.03
.008
NA
NA
0.5
0.007
45
0.002
11.4
0
0
Maximum
9,140
272
6,715
NA
NA
53
60.2
1,05.2
1,485
2,842
0
3,873
Average
1,099
9.7
104
38,157
2,542
6.4
0.22 (22%)
2
47
23
186
0
21
7,574
0.25 (25%)
a cfs = cubic feet per second, TSS = total suspended solids, mg/L - milligrams per liter, t/day = tons per day, t/y = tons per year, NTU = nephlometric turbidity
units
b t/y/WB = tons per year per water body
c From sediment yield curves in Appendix M
Watershed area = 1,150 square miles
Stites sediment yield equation: 25 NTU Idaho WQS standards = 45 mg/L = (25 NTU) * 1.8074
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Table 52. Harpster site loading calculations.
Parameter3
Daily Flow for Last 10 Years (cfs)
Existing TSS, Daily average (mg/L)
Existing TSS (t/day)
Existing TSS, Yearly Average (t/y)
Existing Bedload, (t/y)
Existing Turbidity (NTU)
Background Ratio
Background TSS (mg/L)
Load Capacity (mg/L)
Background TSS (t/day)
Load Capacity (t/day)
Excess Load (t/day)
Excess Load (t/y)
Load Reduction (%)
Equation"
(Stites USGS station) - (Prairie flow) and
Lipscomb (1998) correction
(Flow)* (0.0066) + 6.721 9 c
(TSS) * (flow) * (0.0027)
6*(10A(-9))*(flowA2.713)
(TSS-3.8524) / 2.0474
(14,856 t/y/WB) / (20,621 t/y/WB)
(TSS daily average) * (background ratio)
(Background TSS) + (60 mg/L)
TSS (t/day) * (background ratio)
(60 mg/L) * daily flow * (0.0027) + (background
TSS (t/day))
If load capacity > TSS (t/day)
Else, TSS (t/day) - load capacity
Excess load / TSS, yearly average
Minimum
42
4.5
0.5
NA
NA
0.3
3.1
63.1
0.4
7.2
0
0
Maximum
7,479
52.8
1,067
NA
NA
23.9
36.6
96.6
739
1,958
0
0
Average
860
9.8
45.3
15,053
1,212
2.9
0.72 (72%)
6.8
66.8
31.4
186
0
0
0
0
a cfs = cubic feet per second, TSS = total suspended solids, mg/L - milligrams per liter, t/day = tons per day, t/y = tons per year, NTU = nephlometric turbidity
units
b t/y/WB = tons per year per water body
GFrom sediment yield curves in Appendix M
Watershed area = 880 square miles
Harpster sediment yield equation: 25 NTU Idaho WQS standards = 60 mg/L = ((25 NTU) * (2.4281)) - 0.3334
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Discussion of Tables 49 through 52
For Threemile Creek, the sediment budget calculations (Appendix L) indicate that 6,640 t/y
of sediment are produced, whereas these TSS data (Table 49) indicate that only about 1,112
t/y of TSS are being output at the mouth. If one adds in the estimate of bedload for
Threemile Creek, 615 t/y, this results in an estimate of 1,727 t/y of sediment discharged from
the mouth, or only about 26% of the total from the sediment budget calculations. This 74%
discrepancy may be the result of much more storage in this watershed than we have
accounted for in the routing coefficient. There is an old mass failure about 1 mile above the
mouth, above which sediment is accumulating. At the lower flows over most of the year, the
stream goes subsurface above the mass failure, which probably accounts for the consistently
low TSS and turbidity at low flows. The effect of the mass failure on sediment throughput,
however, is not well understood. Another real possibility for the discrepancy would be that
bedload is poorly estimated.
The sediment budget calculations (Appendix L) for Butcher Creek indicate that 1,251 t/y of
sediment are produced, whereas these TSS data (Table 50) indicate that only about 435 t/y of
TSS are being output at the mouth. If one adds in the estimate of bedload for Butcher Creek,
211 t/y, this results in an estimate of 646 t/y of sediment discharged from the mouth, which is
only 52% of the sediment predicted by the sediment budget. This 48% discrepancy is
consistent with the data from Stites and may be the result of more storage in the watershed
than accounted for in the routing coefficient. Also, the estimate for has a large level of
uncertainty.
The sediment budget calculations (Appendix L) for the mouth of the SF CWR at Stites
indicate that 91,052 t/y of sediment are produced in the SF CWR watershed, whereas the
TSS data indicate that only about 38,157 t/y of TSS (Table 51) are being output at the mouth.
If one adds in the estimate of bedload for the South Fork, 2,541 t/y, this results in an estimate
of 40,698 t/y of sediment discharged from the mouth, which is only 45% of the calculated
sediment budget. This 55% discrepancy may be the result of more storage in the watersheds
than accounted for in the routing coefficient, or could as well be the result of poor estimation
of bedload, given the few data available.
For the Harpster site, the sediment budget calculations (Appendix L) indicate that 19,624 t/y
of sediment are produced in the SF CWR watershed above Harpster, whereas these TSS data
(Table 52) indicate that about 15,053 t/y of TSS are being output. If one adds in the estimate
of bedload at Harpster, 1,212 t/y, this results in an estimate of 16,265 t/year of sediment
discharged from the mouth. This <10 percent discrepancy is somewhat surprising giving the
level of reliability of the data and the relationships being used. However, it is noted that
these numbers are very close to numbers generated in the past by the NPNF for sediment
loading at the Mt. Idaho bridge (Kenny 1995).
Target Selection
The targets for Threemile Creek, Butcher Creek and lowest reach of the main stem SF CWR
(water body #1) are derived using TSS data collected at bridges near the mouths of
Threemile and Butcher Creeks and at the bridge at Stites over the SF CWR (near the USGS
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gaging station at Stites). Loading calculations and targets are set using the state WQS of 25
NTU over background with the assumption that the duration of excursions greater than 25
NTU is greater than 10 days.
The sediment targets for the four main stem water bodies upstream from the mouth of
Butcher Creek (i.e., water bodies #12, #22, #30, and #36) are set based on the percent load
reduction required at Stites, the pour point for the basin. The data suggest that bedload
sediment in the SF CWR Subbasin above Butcher Creek is impacting the beneficial uses of
the waters above this point. However, bedload data at hand are insufficient to set bedload
targets. It is assumed that targets based on total sediment loads will address the bedload
issue. Targets for the main stem above Butcher Creek are set as a percentage of the total
human-caused sediment load. The percentage is the same as that calculated for the Stites
location. The human-caused sediment load is that calculated in the sediment budget in
Appendix L.
Flow Data and Flow Estimation
Mean daily flow data recorded by the USGS are available for the lower main stem SF CWR
ranging back to 1911. For the period of 1923-1963, the recording station was relocated at a
site above the dam at Harpster. Since 1965, the recording station has been at Stites. Daily
flow data from the USGS site at Stites are shown in Figure 65. The flow data for 10 years,
from 1991 through 2001, were selected for the calculations. Examination of the flow chart
shows that this is a reasonably representative time period. It includes the 1995 and 1996 high
flow events, but as can be seen, these were not unusually high flow years. The USGS
predicts that the 8,000 cfs flows of 1995 and 1996 have a return period of five years (see
Table 21). The other major feature to note about the USGS plot is the variation in flow on an
annual basis, almost two orders of magnitude.
Flow and loading calculations for each watershed were accomplished in a spreadsheet format
with 3,658 daily mean flow records, one for each day of the 10 years of record used.
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uses
U8G8 1333B500 8F CLEflRUflTER RIVER flT STITES ID
1965 1970 1975 1988 1985 1990 1995 2808
DHTES: 01/81/1965 to 12/31/2801
EXPLRNRTION
DRILY HERN STRERHFLOH X HERSURED STRERHFL8H
ESTIMHTED STRERHFLOH
Figure 65. U.S. Geological Survey (USGS) Flow Record from Stites
It is generally recognized by local residents and hydrologists working in the area that the
flow patterns from the watersheds in the lower subbasin, those watersheds to the west of the
federal lands, are significantly different from those in the upper basin both in terms of the
timing and duration of peak flows and the duration of minimum flows. The nearest USGS
gaging station with similar flow patterns to the lower elevation streams flowing off the
Camas Prairie is on Lapwai Creek. Of particular interest for the analyses are the flows of
Cottonwood Creek, Threemile Creek, and Butcher Creek. Flows for Cottonwood Creek were
calculated for the Cottonwood Creek TMDL based on flows from Lapwai Creek (DEQ, NPT,
USEPA 2000). A similar procedure as used in the Cottonwood Creek TMDL using USGS
measured flow from Lapwai Creek over the same 10-year time period from 1991 through
2001 was followed to calculate flows for Threemile Creek and Butcher Creek. The USGS
chart of flows for Lapwai Creek is presented in Figure 66.
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ZUSGS
USGS 13342450 LflPWfll CREEK NR LflPUfll ID
1975
1980 1985 1990 1995
DRIES: 18/81/1974 to 89/38/2881
2800
EXPLRNRTI8N
DRILY HERN STRERHFLOH
X HERSURED STRERHFL8H
ESTIhflTED STRERHFLOH
Figure 66. U.S. Geological Survey (USGS) Flow Data for Lapwai Creek
The flow at Lapwai Creek is much more variable from year to year compared to the flow at
Stites, and the annual range of flow rates approaches three orders of magnitude.
Of particular concern about transposing the Lapwai Creek flow data to other watersheds is
the single extreme flow event of February 1996. The flow rates for the three days when this
flow occurred were reduced before using these flow data to calculate the stochastic flow
models for Threemile, Cottonwood, and Butcher Creeks. It did not seem reasonable to
extrapolate such an extreme event from Lapwai Creek to other watersheds where anecdotal
evidence suggests that while the event was very large, it was not of the extreme nature as
occurred in Lapwai Creek. In Figures 67 and 68 showing the graphs of the calculated flows
for Threemile and Butcher Creeks, the February 1996 flows have been reduced to only
slightly greater than other high flows that occurred in 1996 and 1997.
Daily flows for Threemile and Butcher Creeks were calculated in a two-step process. Since
the volume of runoff from a watershed is proportional to the size of the watershed,
everything else being equal, daily flow from Lapwai Creek was multiplied the values
33.5/235 for Threemile Creek and 16.8/235 for Butcher Creek (33.5, 16.8, and 235 are areas
in square miles of Threemile, Butcher and Lapwai Creeks, respectively).
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
However, everything else is not equal between Threemile, and Butcher, and Lapwai Creeks,
especially the precipitation. They all also have somewhat different geology, soils,
physiography, land cover, and other features. Most notably, Threemile Creek and Butcher
Creek receive more precipitation than Lapwai Creek. The USGS (Lipscomb 1998) provides
statistically derived estimates of mean annual and mean monthly discharge for water bodies
in central Idaho. The proportion of the mean annual flow from the USGS estimates were
compared against the area adjusted mean annual flows to calculate daily flows over the 10
years, such that the mean annual flow over the 10 years equaled the USGS developed
discharge rate for the two watersheds. This then is assumed to be a daily flow pattern
representative of each watershed over the long term. The derived 10-year flow patterns for
Threemile and Butcher Creeks are shown in Figures 67 and 68. The same calculations for
were performed for Cottonwood Creek so the data would be available to calculate the flow
pattern at Harpster, based on removal of high flows from these prairie streams.
For daily flow at Stites, the flow record from the USGS station was used and adjusted
upwards to meet the long term annual discharge calculated by the USGS (Lipscomb 1998),
resulting in a flow curve representative of the long term flow at the site. For daily flow at
Harpster, the daily flows for Cottonwood, Threemile, and Butcher Creeks were subtracted
from the Stites daily flow to account for the change in flow pattern as result of the different
timing of peak flows from these three major tributaries. The flow was then adjusted to match
the USGS estimate (Lipscomb 1998).
These calculations result in an estimate mean daily discharge based on the flow pattern over
the last 10 years for Threemile Creek, Butcher Creek, and the Harpster site on the SF CWR
(Figures 67, 68, and 69) and are assumed to be representative of long term flows in the
respective watersheds. These flow estimates form the basis from which sediment movement
in the basin can be calculated.
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Threemile Creek Daily Flow
42
3-
_o
Li.
Figure 67. Derived 10-Year Flow for Threemile Creek
Butcher Creek Daily Flow
Figure 68. Derived 10-Year Flow for Butcher Creek
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Harpster Daily Flow
Figure 69. Derived 10-Year Flow for the Harpster Site on the SF CWR
TSS and Bedload Data
TSS and bedload data reported herein are the results of several different efforts on the part of
DEQ, NPT, and USEPA. The USEPA provided funding for some of these efforts. DEQ
collected instantaneous flow, TSS, and turbidity data for Threemile Creek as part of its
detailed monitoring of that water body. The NPT collected instantaneous flow, TSS,
turbidity, and bedload data for Butcher Creek as part of its monitoring of that water body.
DEQ contracted with Western Watershed Analysts of Lewiston, Idaho, to provide flow and
bedload data for the main stem SF CWR and Threemile Creek.
Unfortunately, flows in Threemile Creek and Butcher Creek over the sample period were
below the level where significant bedload moved or could be sampled. Therefore, bedload
for these streams is estimated from the sediment budget. Similarly, for the year when the
contractor was to sample bedload in the upper main stem SF CWR, flows did not allow the
bedload to be sampled. The result is that sampled bedload data exist only for the Stites and
Harpster sites.
Other TSS and turbidity data exist for the SF CWR Subbasin, but come from such diverse
locations and time periods as to make them difficult to use for a subbasin-wide analysis.
DEQ collected turbidity and flow data for a number of streams in the SF CWR Subbasin
(Thomas 1991) and these data provide a comparison for the results of the calculations. The
NPNF collected TSS, turbidity, and flow data at the Mt. Idaho bridge from 1988-1992,
analyzed these data, and extrapolated them using the data from Thomas (1991). These
results were used to help validate the results from the 1991-2001 time frame of the analyses.
Sediment yield curves are developed from the TSS and bedload data. The data and sediment
yield curves for the Threemile, Butcher, Stites, and Harpster sites are presented in Appendix
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M. The sediment yield curves for each site are presented in the summary sediment loading
calculations Tables 49 through 52.
Estimates of Existing Sediment Loads
Regulations allow that loadings ".. .may range from reasonably accurate estimates to gross
allotments, depending on the availability of data and appropriate techniques for predicting
the loading," (Water quality planning and management, 40 CFR 130.2(1)). An estimate must
be made for each point source. Nonpoint sources are typically estimated based on the type of
sources (land use) and area (such as a subwatershed), but may be aggregated by type of
source or land area. To the extent possible, background loads should be distinguished from
human-caused increase in nonpoint loads.
Point Sources
Existing sediment loads from the point sources in the SF CWR Subbasin are presented in
Table 53
Table 53. Sediment loads from point sources in the SF CWR Subbasin.
Facility
Kooskia Wastewater
Treatment Plant
Grangeville
Wastewater
Treatment Plant
Elk City Wastewater
Treatment Plant
Stites Wastewater
Treatment Plant
Red River Ranger
Station Wastewater
Treatment Plant
Clearwater Forest
Industries
Storm Water
Sources
Suction Dredge
Industry
NPDES
Permit3
ID-002181-4
ID-002003-6
ID-002201-2
ID-002034-6
ID-002069-9
ID-002770-7
None
currently
None
currently
Design
Flow
(MGD)b
0.20
0.88
0.12
0.07
0.0063
0.0019
NA
NA
Current
Monthly
TSS
Permit
Limit
(mg/L)c
70
30
70
70
30
None
currently
None
currently
None
currently
Current
TSS
Concentra
-tion
(mg/L)d
34
11
21.6
45.6
5.0
Data not
available
Data not
available
Data not
available
Current TSS
Load
(t/y)d
4.3
12.3
1.5
3.0
0.08
Data not
available
Data not
available
Unknown (see
discussion)
a National Pollution Discharge Elimination Permit number
b million gallons per day
0 TSS = total suspended solids, mg/L - milligrams per liter
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d Based on data from March 1999 through February 2002, t/y = tons per year
Estimates of loading from WWTPs are averages based on flow and TSS monitoring data
collected by each facility and reported to USEPA in monthly discharge monitoring reports
for the period from March 1999 through February 2002.
Estimates for Clearwater Forest Industries, storm water sources and suction dredging are not
available due to the lack of monitoring data from which to quantify annual loads. As
explained in Section 3.1, sediment loading from these sources is expected to be minor when
compared to nonpoint sources of sediment.
Nonpoint Sources
For Threemile Creek, Butcher Creek, and the Stites location on the lower main stem SF
CWR, sediment loads are calculated from in-stream TSS and bedload data. The TSS and
bedload yield curves (Appendix M) were coupled with daily flow data in a spreadsheet to
predict TSS loads and bedloads on a daily basis. The average daily TSS sediment loads in
mg/L were then converted to tons of sediment per day and tons of sediment per year.
Average daily NTUs were calculated from a similarly developed relationship. The
summaries of these results for the Threemile, Butcher, Stites, and Harpster locations are
presented in Tables 49 through 52.
For the water bodies above Harpster, estimates of existing nonpoint source sediment loads
are from the sediment budget presented in Appendix L. Table 30 in Section 3.1 summarizes
the results from Appendix L. The TSS-based method for the downstream water bodies and
the sediment budget-based method for the upstream water bodies are quite different and
produce results that should only be compared in light of the different methods. When
compared, the results of the two methods compare reasonably well, lending confidence to
both methods.
Table 54 shows the total nonpoint source sediment load, the background sediment load, and
the human-caused sediment load for each control location. Both methods include
assessments of which parts of the loads are human-caused and which parts are estimated
background loads. Each number is the sum of all the sediment yields upstream from that
control location. Human-caused sediment is the total sediment load minus the background
sediment load.
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Table 54. Estimated cumulative sediment loads from nonpoint sources in the
SF CWR Subbasin.3
Water Body Name
Lower SF CWR
Threemile Creek
Butcher Creek
Mid-Lower SF CWR
Middle SF CWR
Mid-Upper SF CWR
Upper SF CWR
Water
Body
ID
1
10
11
12
22
30
36
Control Location
Stites Bridge
Mouth
Mouth
Harpster Bridge
Above Johns Creek
Above Tenmile
Creek
Above Crooked
River
Total
Load
(ton/year)
38,157
1,112
441
20,622
11,185
7,827
4,527
Background
Load
(ton/year)
8,439
97
106
14,856
8,898
5,993
3,279
Human-
Caused
Load
(ton/year)
29,718
1,015
335
5,736
2,297
1,835
1,248
a Loads presented for these sites are cumulative of all areas upstream of the control location. Loads for water
bodies 1, 10, and 11 are total suspended solids loads, while loads for water bodies 12, 22, 30, and 36 are total
sediment loads, calculated using different methods.
Estimates of Background Sediment Loading
The background sediment loading for each of the control locations in the subbasin (Table 54)
is calculated from background loading rates for each of the water bodies or rates for
groupings of water bodies. Background sediment loading was developed from the sediment
budget (Appendix L). The background ratio for each control location was calculated using
the routed background erosion for all areas upstream of the control location divided by the
total tons of sediment routed from a watershed. The background loads in Table 54 are
cumulative for all the water bodies upstream from the control locations.
Background erosion rates have been developed for all federally managed watersheds and
range from 16 to 90 tons per square mile per year. After reviewing the range of background
figures from the federally-managed lands, background figures used in other TMDLs, erosion
studies at Washington State University, predictions by the RUSLE model, and best
professional judgement, a background erosion rate of 30 tons per square mile per year was
assigned for the non-federal lands. The routing coefficient was that used by the NPNF to
route sediment using the NEZSED model (Roehl 1962) and that used throughout the
sediment budget calculations in this TMDL. The background ratios developed from the
sediment budget for the Threemile, Butcher, Stites, and Harpster sites are presented Tables
49 through 52.
For the Threemile, Butcher, and Stites locations, the amount of daily load that is attributed to
background was calculated by multiplying the daily load by the background ratio. This
results in different background loads depending on flow, as would be expected naturally, as
higher flows naturally would have resulted in greater movement of sediment. For the control
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locations upstream from Butcher Creek, including the Harpster site, the background loading
rate is simply the yearly rate based on the sums from the sediment budget.
Results for the Stites, Threemile, and Butcher locations are not directly comparable to those
of the other four water bodies because of different methods used for the calculations. This is
especially noticeable in the background loads shown in Table 54. The background load for
Stites would be approximately 20,000 t/y if calculated from the sediment budget, and the
total sediment load would be in the range of 90,000 t/y if calculated from the sediment
budget (the TSS-based estimates for Stites are 8,439 t/y background load and 38,157 t/y total
load [Table 54]). This magnitude of difference between the TSS-based calculations and the
sediment budget-based calculations is noticeable throughout these sediment loading
calculations. Part of the difference is that TSS-based estimates do not include bedload,
whereas the sediment budget does. More importantly, however, current sediment routing
models do not adequately account for sediment storage in a watershed. The sediment budget
adds up eroded sediment from numerous sources, but does not adequately account for where
that sediment goes once detached from its location. It is likely that much more of it is being
stored in floodplains, low slope areas, and other locations than is being moved through the
active waterways.
Sediment Load Capacity
The goal of the sediment TMDLs is to achieve both the numeric turbidity standard and the
narrative sediment standard. Calculations of the fine sediment load capacities needed to
achieve the numeric turbidity WQS relate the turbidity to TSS levels at the Threemile,
Butcher, Stites, Harpster, and Mt. Idaho monitoring locations. The fine sediment load
capacity calculations are based on daily flow records coupled with sediment yield curves
developed from TSS and bedload monitoring data collected at these sites. The load capacity
for Cottonwood Creek as it empties into the SF CWR is quoted from the Cottonwood Creek
TMDL (DEQ, NPT, USEPA 2000).
Total suspended solids sediment load capacity and excess load capacity were calculated
based on the Idaho WQS of "turbidity ... shall not exceed background turbidity by more than
fifty NTU instantaneously or more than twenty-five NTU for more than ten consecutive
days" (IDAPA 58.01.02.250.02.d). Using the daily flow method for the loading calculations,
all exceedances over 25 NTU are included in the calculations, including exceedances over
the 50 NTU criterion. Plots of the sediment loadings at Threemile Creek and Butcher Creek
showed that turbidity is elevated for periods of considerably greater than 10 days. Loading
calculations are based, therefore, on the 25 NTU above background WQS. As sediment
loading reductions are accomplished, using this standard to make the loading calculations
will result in a large MOS for loading reductions as turbidity begins to be reduced to less
than 10 consecutive days of exceedances.
The load capacity was calculated based on the relationship between turbidity in NTUs and
the TSS in milligrams per liter (mg/L), resulting in a calculation of the amount of TSS in
milligrams per liter that 25 NTUs from the state WQS represents. For example, in Threemile
Creek, 25 NTUs is equivalent to 17 mg/L TSS. For each day then, the load capacity is the 17
207 Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
mg/L plus the percentage of the load that is background. Since the background load varies
with flow, the load capacity varies with flow as well.
The annualized TSS load capacities for five locations are presented in Table 55. However,
these numbers are relatively meaningless for loading calculations based on daily flows. They
are shown here because they are expected as part of a TMDL. The useful numbers for
calculations using the daily flow method are those for excess loading shown in the next
section.
Table 55. Total suspended solids (TSS)-based load capacities for water
bodies in the lower SF CWR Subbasin.
Water Body Name
Lower SF CWR
Cottonwood Creek
Threemile Creek
Butcher Creek
Mid-lower SF CWR
Water
Body
ID
1
2
10
11
12
Sampling
Location
Stites Bridge
At the mouth
At the mouth
At the mouth
Harpster Bridge
TSSa
(t/y)
68,095
5,110
366
261
61,631
aBased on daily flow calculations summed and averaged for 10 years.
In the absence of a numeric standard for coarse sediment, or any particular knowledge about
the level of loading that might impair beneficial uses, the coarse sediment load capacities for
these same sites are assumed to be proportional to the total coarse sediment loading for the
lower main stem, or about 7%. This is consistent with USGS data for the Clearwater River
indicating that bedload is in the range of 5-10% of total sediment load (Jones and Seitz
1980).
The load capacity for the five lower water bodies is dependant on flow on a day-to-day basis,
or even hour-to-hour basis for extremely flashy streams like Threemile and Butcher Creeks.
In general, the highest load capacities occur during the highest flows, which occur
episodically January through May. The load capacities in Table 55 are based on load
capacities calculated on a daily basis and averaged over 10 years to arrive at a yearly rate.
Since on most days the existing load is less than the load capacity, the average load capacity
may be far greater than the existing load over a year. However, load capacity exceedances
also occur on a daily basis and when these are summed and averaged, load exceedances
summed over a year occur even when yearly average load capacity is greater than yearly
average existing load.
A good example of this can be found in the data set for Stites. The average annual load at
Stites is about 38,000 t/y (Table 54). The average annual load capacity at Stites is 69,000 t/y
(Table 55). However, the average annual load exceedance at Stites is about 7,500 t/y because
there are days of high flow and heavy erosion every year when the actual loading on a daily
basis exceeds the load capacity. It is during these few days of extreme high flows, such as
the 1996 events, when excess loading adds up significantly. These are the sediment loading
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
events that really exceed the capacity of the system to handle sediment, and these are the
events that need to be managed if sediment in the SF CWR system is to be reduced to meet
WQS.
Figure 70 shows the variability of load capacity over the 10-year period that these
calculations were based on. Also in Figure 70 is an associated graph for each one of the
three sites showing the load capacity in more detail, for two years.
209 Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Stites Brdige Load Capacity
'o
CO
O
« 1000 -
o
W 500 -
« °UU
1-
1
—
^JUu
^ ^ so? ^ f
^ ^ ^ ^ ^
U
1
1
1 li 1 1
flwlJuAjJV
•^ ^x ^x ^x ^x
TSS Loading Capacity (t/day)
^- -^rOCO-t^Cna)^!
iS^-OO OOOO OO
Threemile Creek Load Capacity
.... 1 , A J
TSS Load Capacity (t/day)
%7 0 0 B g S g §
i
| 1 JL j, Ll
Butcher Creek Load Capacity
a L»
J
ll
1 .J. Jk .^ .k
/- /" / / / / /" /" /
TSS Load Capacity (t/day)
Stites Bridge Load Capacity for Two Years
^^A^^K^^^^JW
J
1
V__^
/ A/ / /• / ,/ /
Threemile Creek Load Capacity for Two Years
CO
o
CO
O
c
ro 20 -
o
-" in
Vjw
& & & <(& dP dP
\N- \V ,\V vV \V \V
v V- -v ^ v V-
vV
* /
Butcher Creek Load Capacity for Two Years
CO
CO
O
o
K. .. JSJvJ'V , _JUsjJv
vj
VrV
AN""
* /•
Figure 70. Average Daily Total Suspended Solids (TSS) Load Capacities for the Stites Site on the SF CWR,
Threemile Creek, and Butcher Creek for the 10-Year Analysis Period and Enlarged Showing Details for
1995 and 1996
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Upstream from the mouth of Butcher Creek (water body #12 and upstream), from the control
location called the Harpster site, load capacities are calculated in a different manner based on
the available data. Below Harpster, load capacities were calculated on a daily basis, but
above Harpster, they were calculated on an annual basis. The daily and annual load
capacities are not very comparable. Above the Mt. Idaho bridge, TSS and flow coupled data
for the rest the subbasin are not adequate to support making estimates of daily loading and
daily loading exceedances. The private bridge above Harpster was set as the control location
for the entire subbasin above the confluence of Butcher Creek with the main stem because it
is a good sampling site.
Upstream from Harpster we do not differentiate between fine and coarse sediment. Nez
Perce National Forest data show that bedload may represent anywhere from 2% to 60% of
the total loading from any particular stream, depending on watershed area, geology, and
stream type (Gloss 1995). Therefore, load capacity is based on total sediment load, with the
assumption that load reductions will result in both fine and coarse sediment loading
reductions proportional to the total load.
Lacking specific in-stream data to calculate load capacities for the 303(d) listed water bodies,
load capacities are calculated based on the sediment budget and the target load reduction.
For example, the load capacity for the control location on the main stem SF CWR above the
mouth of Johns Creek is calculated from sum of total sediment for all the water bodies above
Johns Creek (water bodies #22-79) minus 25% of the sum of the human-caused sediment for
the same set of water bodies. This change from in-stream sediment estimates to sediment
source estimates is partially justified by the fact that estimates of human caused in-stream
and sediment sources at the Harpster control location are essentially equal, in the 19,000-
20,000 t/y range. The NPNF came up with similar figures (16,100 t/y) with their analyses of
NEZSED data (Kenny 1995) for the area above the Mt. Idaho bridge. The NPNF
calculations did not include estimates for in-stream erosion, sand and gravel applied to the
highway, mining, or mass failures greater then 10 yd3.
The loading capacities for the 303(d) listed water bodies above Harpster/Butcher Creek are
presented in 56. Again, these numbers are not directly comparable to the numbers in Table
54 above because different calculation methods were used. The numbers in Table 56 are
truly annually based, rather than daily data averaged over a year (Table 55). The load
capacity at Harpster calculated using the sediment budget method is 19,180 t/day, vs. the
62,000 t/day shown in Table 55. The difference is as discussed above for the example at
Stites. Numbers calculated for the table below (Table 56) correspond better to the conceptual
framework for TMDL loading calculations presented earlier.
Excess Loading
Excess loading occurs when the current loading is greater than the load capacity. Excess
loading on a daily basis is the current load minus the load capacity. The excess loads
addressed by the TMDLs for Threemile Creek, Butcher Creek, and the Stites site are shown
211 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 56. Total sediment loading capacity of water bodies in the upper SF
CWR Subbasin.
Water Body Name
Mid-lower SF CWR
(Johns Cr. to Butcher Cr.)
Middle SF CWR
(Tenmile Cr. to Johns Cr.)
Mid-upper SF CWR
(Crooked R. to Tenmile Cr.)
Upper SF CWR
(Confluence to Crooked R.)
Water
Body
ID
12
22
30
36
Control Location
Harpster Bridge
Above mouth of Johns Cr.
Above mouth of Tenmile Cr.
Above mouth of Crooked R.
Load Capacity
(t/y)
19,180
10,621
7,369
4,215
in Figures 71, 72, and 73. The first figure in each of these sets of figures shows the
distribution and magnitude of excess loads over thelO years used in the calculations, and the
subsequent figure shows more detail of only two years of those same data. The figures show
that excess loading only occurs over short time frames, the same time frames as high flows,
and that the episodes of excess loading are limited to January through May each year.
The excess load is summed over the 10 years of data and divided by 10 to calculate an
average amount of excess loading on a yearly basis. When this figure is divided by the
average annual human-caused TSS yield, the result is the percent reduction of human-caused
TSS needed for a given water body. The summaries of these calculations are presented in
Tables 49 through 52 and Table 57. These calculations indicate that significant load
reductions in TSS are needed for Threemile Creek, Butcher Creek, and for the main stem SF
CWR at Stites.
Table 57. Total suspended solids (TSS) excess loading for water bodies in the
lower SF CWR Subbasin.
Water Body Name
Lower SF CWR
Threemile Creek
Butcher Creek
Mid-lower SF CWR
Water
Body
ID
1
10
11
12
Control
Location
Stites Bridge
At the mouth
At the mouth
Harpster Bridge
Human
Caused
Loading
(t/y)
29,718
1,015
335
4,632
Excess TSS
Loading a
(t/y)
7,574
780
203
0
Excess TSS
Loading
(%)
25
77
61
0
"Based on daily flow calculations summed and averaged for 10 years.
One could subtract the excess TSS loading from the human caused loading to arrive at
another sort of estimate of load capacity on an annual basis. However, based on the daily
212
Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
flow and loading approach used in these calculations, that figure does not have much
meaning.
These data indicate that TSS does not exceed that state WQS at Harpster. However,
application of the narrative standard, as discussed in Chapter 2, results in a conclusion that
the four main stem water bodies above Butcher Creek are impaired by coarse sediment. For
lack of any other data, the excess load for these water bodies is set at the 25% excess load
calculated for the Stites location.
Threemile Creek Excess Load for Ten Years
450
a
•H
5. -350
51 Qnn -
_C OUU
5
g 250
_i
in 200
«
8 icn
o 150
X
111 1nn
« 100
£ ^n
r- 50
T
/
NQN
J ,J .1
1
1 .,lL ,. Li
<&<£>(&(&<&(& d?*d?r?:'
Nf> ^ ^ Nf> ^ ^ *^> V? V?
Nox Nox NoN NoN Nox NoN NoN Nox Nox
Threemile Creek Excess Load for Two Years
4UU
c
^ 300
TO
S onn
« zUU
©
o
x 150
w 100
K Rn
^
/
V
i ^ ^ JV . . rAA.
VO^
U
cft> cft> r& (^> (^O i&l ,&
N^ N^ ^> N N0N NN ^ -\\ N0N
Figure 71. Excess Sediment Loading for Threemile Creek for the 10-Year
Analysis Period and Enlarged Showing Detail for 1995 and 1996
213
Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Butcher Creek Excess Load for Ten Years
A on
IzO
"T"* 'i nn
>, 1 UU
(0
•O
33
*"""" on
•o 80
re
5 GO
0 60
(0
(D
o
x A n
Uj 40
(0
2 on
(_ 2\)
T
N^
N^N
.1 ,J .1
ll
II 1 ..ill .. Ll
1 1 1 1 1 1 1 1 1
,/ /• / £ / / ^ / v^
O\ CV CV CV CV CV CV Cv CV
.N N^N^N^NVJf^N^f^Nv)
Butcher Creek Excess Load for Two Years
A on
IzO
*^ * nn
— 1 00
Cw
•o
s.
on
"D oO
n
O
en
» DO
(0
o
o
X A n
UJ 4U
(A
(/}
h— on
r^ zO
T
/
V
i «^ n. _A « . ,.AJL
vuu
u
i i i i i
e& e& o& r& riSo rS> riS>
^ VN^ \^ ^ \^ ^ \^
(x\ Ax N0X \x txx Ax N0N
Figure 72. Excess Sediment Loading for Butcher Creek for the 10-Year
Analysis Period and Enlarged Showing Detail for 1995 and 1996
214
Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Stites Bridge Excess Load for Ten Years
A cnn
4o(JU
A r\r\r\
4UUU
re ooUU
•a
^ onnn
-— 'oDDD
TJ
re 250Q
Wonnn
„. ZUUU
0)
g IbOO
UJ
._ A nnn
{/J 1UUU
V)
II
||
1 1 1 1
1 1
f / X X X
Stites Bridge Excess Load
A cnn
4oUU
reoj-nn
^ OOUU
re
v)
0)
u
UJ1500
W1000
oOO
for Two Years
^
i i i i
N,
Figure 73. Excess Sediment Loading at Stites for the 10-Year Analysis Period
and Enlarged Showing Detail for 1995 and 1996
215
Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Margin of Safety
Loading calculations using 25 NTU over background as the WQS above which loading is
treated as an exceedance results in a significant MOS. As sediment reduction activities
proceed to the point where the 25 NTU over background loadings no longer exceed 10 days,
the standard becomes 50 NTU over background. All exceedance loading calculations for
nonpoint source sediment in these TMDLs have this MOS built into them. Therefore, no
further load allocation to MOS has been built into the TMDLs.
For example, at Stites, the 25 NTU over background for more than 10 days standard has only
been exceeded during one event during the last 10 years. So, one can conclude that the Stites
location is close to the threshold where the 50 NTU over background standard should be in
effect. Using the 50 NTU over background standard in the same calculations as above, the
excess load at Stites is only 3,578 t/y, compared to 7,754 t/y at 25 NTU, and the percent load
reduction required would be 9% compared to 25%. Similar calculations could be done for
Threemile Creek and Butcher Creek. However, the point is that use of the 25 NTU over
background as the basis for the loading calculations provides a very large MOS in the
loading calculations. The use of the 25 NTU standard in the loading calculations is justified
because that is the standard that should be applied for the current situation, but as compliance
with the TMDL is accomplished, the 50 NTU over background instantaneous criterion is the
only one that can be applied if there are no exceedances greater than 10 days duration.
Seasonal Variation
Calculations for sediment TMDLs of the SF CWR Subbasin have focused on the seasonality
and episodic nature of sediment loading to the 303(d) water bodies. Clearly, almost all of the
loading occurs between January and May (Figures 71, 72 and 73), but more importantly, the
problem loadings occur during extreme, five-year (or longer) recurring episodic events.
These episodic events are not predictable by nature, they have been accounted for by running
the calculations over a 10-year period. An examination of the flow regime data indicated that
a 10-year time frame for the calculations was adequate to capture the effects of these major
sediment-producing episodes.
Sediment Load Allocations
Sediment loading in the SF CWR Subbasin is dominated by nonpoint sources. A number of
nonpoint sources have been identified, coming from lands with a number of different owners
and management agencies. While sediment from point sources is relatively insignificant in
the overall picture of the subbasin, WLAs are set for the purposes of NPDES permitting, and
will be incorporated into these permits by the USEPA.
Wasteload Allocations for Wastewater Treatment Plants and Clearwater Forest
Industries
As can be seen by comparing sediment loading in Table 58 with total sediment loading in the
various watersheds in Table 59, WWTPs and CFI contribute only a very minor amount to the
216 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
overall sediment loading, so it is not necessary to require load reductions from these
facilities. Currently permitted facilities include the Kooskia, Stites, Grangeville, Elk City,
and Red River Ranger Station WWTPs. Federal technology standards outlined in 40 CFR
133.105 (Treatment Equivalent to Secondary Treatment) apply to facilities treating domestic
sewage, and vary based on the type of treatment process used by that facility. For those
facilities using stabilization ponds/lagoons (i.e., Kooskia, Stites, Elk City, and Red River
Ranger Station), federal regulations specify monthly and weekly average TSS limits of 45
and 65 mg/L respectively. For other treatment types (i.e., Grangeville), the monthly and
weekly average TSS limits are 30 and 45 mg/L respectively.
The state of Idaho also has technology standards for facilities that treat domestic sewage
using stabilization ponds/lagoons of 70 and 105 mg/L as monthly and weekly averages,
respectively. These limits have not been approved by USEPA, and therefore the federal
requirements specified above apply.
In the case of Red River Ranger Station, federal regulations that address anti-backsliding
prohibit new effluent limits from being less stringent than previous limits in an NPDES
permit. The previous and current limits in the NPDES permit are 30 and 45 mg/L TSS as
monthly and weekly averages. Therefore, the Red River Ranger Station limits must remain
at 30 and 45 mg/L. After reviewing effluent data from Red River Ranger Station, the facility
appears to be meeting the current limits.
Clearwater Forest Industries is in the process of obtaining an NPDES discharge permit for
stormwater and approximately 1,900 gallons per day of boiler blowdown and kiln
condensate. The stormwater component of their wasteload allocation is discussed further in
the section below. No monitoring of the non-contact cooling water has been conducted, but
review of monitoring of other industrial facility non-contact cooling water suggests that TSS
levels are likely to be less than 10 mg/L. Given the exceedingly small flow in comparison to
the SF CWR and expected low TSS and turbidity levels, no reduction in this loading is
needed in order to achieve the turbidity targets in the SF CWR. The ambient turbidity
criteria, which is the overall goal of the sediment TMDL in this reach, will be established as
the wasteload allocation for the boiler blowdown and kiln condensate portion of CFFs
discharge.
Wasteload allocations for the Kooskia, Stites, Elk City, and Grangeville WWTPs will be the
technology based TSS limits described above. The Red River Ranger Station WWTP's
WLA will be based on the current NPDES limits and anti-backsliding provision (Table 58).
Wasteload Allocations for Storm Water Discharge.
A comprehensive inventory of storm water sources subject to NPDES permit requirements1
has not been established, but these sources are not considered to be significant components of
1 NPDES permits are required for storm water discharges from a) construction activities disturbing one or more
acres, b) certain categories of industrial activities, and c) municipal storm drainage systems located in Census
Bureau - defined "urbanized areas". For further information regarding stormwater permit requirements, see the
Region 10 USEPA web site at www.epa.gov/rlOearth.
217 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
the anthropogenic sediment load either individually or cumulatively (Section 3.1). Due to
the lack of facility specific information, a single generalized WLA covering both the
industrial and construction stormwater categories has been established. Currently there are
no municipal storm water sources in the SF CWR subject to NPDES permit requirements, so
these sources are included in the nonpoint source allocations.
The overall goal of the sediment TMDL in the mid-lower watershed, where most industrial
and/or construction storm water discharges are likely to exist, is to achieve Idaho's 25 NTU
above background turbidity criteria (50 NTU above background instantaneous)(IDAPA
58.01.02.250.02.d.). Therefore, the allocation for regulated industrial/construction storm
water discharges is compliance with this turbidity criteria, or compliance with appropriate
BMPs to control sediment as required by the applicable NPDES storm water permit. It is
recognized that monitoring compliance with a turbidity allocation may be difficult or
impossible. As a result, if during the course of applying for NPDES permit coverage, it is
determined to be infeasible to conduct compliance monitoring for any facility, the allocation
is interpreted to be the installation of appropriate storm water BMPs as described in local
ordinances or the Idaho Catalogue of Storm Water Best Management Practices (DEQ
2003c), whichever is more stringent, in lieu of the turbidity allocation.
Storm water sources that are not subject to NPDES permit requirements, including all
municipal sources of storm water, are included within the general load allocation for
nonpoint sources.
Wasteload Allocations for Suction Dredge Mining.
As indicated in Chapter 3, suction dredging may have adverse effects on both water column
and substrate sediment levels. A two-part allocation will be established to address these
impacts.
Turbidity, as a surrogate for sediment, is a parameter which can be measured easily and
reliably in the field, directly relates to the water column impacts of suction dredges, and for
which specific ambient and treatment criteria are included in Idaho WQS. The water column
portion of the interpretation of the narrative sediment standard is based upon treatment
requirements for point sources in the Idaho WQS (IDAPA 58.01.02.401.03.b). In essence,
the standard requires that turbidity below any applicable mixing zone must not exceed
background turbidity by more than 5 NTU, or by more than 10% if background turbidity is
50 NTU or higher.
Substrate sediment problems caused by increased bedload movement are more difficult to
measure and quantify in the field, and incorporate in a WLA or NPDES permit. As
indicated in Chapter 3, increased bedload or surface fine sediment has been observed
hundreds of feet below 5 and 8 inch dredges (USFS 1980b). However, the current operation
of a limited number of recreational dredges appears to result in minimal downstream
increases in bedload or surface fine sediment levels below the area of active mining. The
daily volume of sediment processed by these existing operations therefore appears to be a
218 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
reasonable surrogate measure to prevent increased bedload movement and surface fine
sediment downstream of suction dredges.
Since 2000, up to 15 recreational suction dredges/year have applied for coverage under the
IDWR General Permit (IDWR 2002). The General Permit allows these dredges to operate
only in the main stem SF CWR, between July 15 - August 15, and to process no more than
2 cubic yards of material per hour as averaged over the period of operation for the entire
day. Based on available data, for the purpose of this allocation it is assumed that 15 such
operations could operate each year during the July 15 - August 15 window without resulting
in increased bedload movement or surface fine sediment levels downstream of active mining.
Assuming these dredges move no more than 2 cubic yards of material per hour, and further
assuming a normal 8 hour work day, an allowable daily mass sediment loading from dredgers
is:
15 dredges x 2 yd3/hour x 8 hr/day = 240 yd3/day
1 yd3 = 27 ft3
Sediment density = 96.8 lbs/ft3 x 27 ft3= 2614 lbs/yd3 (Hausenbuiller 1985)
240 yd3 x 2614 lbs/yd3 = 627,360 Ibs = 314 tons/day
This is an industry wide WLA which applies to dredges of all sizes. Furthermore, suction
dredge mining has historically occurred in the upper SF CWR and tributaries. Accordingly,
the WLA will be established for the entire SF CWR watershed above the Harpster Bridge,
including tributaries.
The effectiveness of this allocation in controlling bedload related problems is also contingent
upon the following two key assumptions:
• Each facility complies with all applicable permitting processes, including those of
USEPA (NPDES permit), IDWR (Stream Channel Alteration Permit), USFS (Plan of
Operations approval; Decision Notice and Finding of No Significant Impact), BLM
(Decision Notice and Finding of No Significant Impact), and ACOE (Clean Water
Act Section 404 permit), which include important operational considerations to
minimize substrate problems.
• The location of permitted facilities is such that mixing zones do not overlap, in order
to avoid localized excessive impacts from suspended and bedload sediment mobilized
by these operations, and in no case are individual dredges separated by less than 100
feet, consistent with IDAPA 37.03.07.064.
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Recommended implementation procedures
As indicated in Chapter 3, suction dredges are considered to be point sources and are
therefore required to obtain NPDES permits from the USEPA. In order to most easily mesh
with current IDWR permitting processes, in implementing this WLA it is recommended that
USEPA adopt a similarly tiered NPDES permit process. Specifically, it is recommended that
a general permit process be established for dredges of less than or equal to 5 inch nozzle size
and less than or equal to 15 hp, and that each dredge be limited to discharge no more than 2
yd3 /hour, as averaged over the period of operation for the entire day. Should the IDWR
permitting process be terminated, it is recommended that the general permit conditions of,
and attachments to, the IDWR permit be incorporated into the USEPA general NPDES
permit.
Given the greater volume of material discharged, and greater chance of causing sediment
related problems, it is recommended that larger dredges be required to apply for an individual
NPDES permit. Finally, since the WLA applies to the entire industry, it should be available
for allocation on a first come-first served basis, with first opportunity given to facilities
currently permitted by IDWR.
It is expected that achieving the wasteload allocation will ensure compliance with the
numeric turbidity criteria and the narrative sediment standard. Given the lack of consistent
monitoring of the effects of this industry in the SF CWR watershed, it is recommended that
the USFS, IDEQ and USEPA establish a monitoring plan to further characterize and assess
these impacts on an ongoing basis.
Table 58. Sediment wasteload allocations for the SF CWR Subbasin.
Facility3
Kooskia
WWTP
Grangeville
WWTP
Elk City
WWTP
Stites WWTP
Red River
Ranger
Station
WWTP
NPDES
Permit
Number
ID-002181-4
ID-002003-6
ID-002201-2
ID-002034-6
ID-002069-9
Design
Flow
(MGD)b
0.20
0.88
0.12
0.07
0.0063
Wasteload Allocation0
Monthly
Average TSS
Concentration
(mg/L)
45
30
45
45
30
Weekly
Average TSS
Concentration
(mg/L)
60
45
60
60
45
Annual
TSS
Load
(t/y)
13.7
40.3
8.2
4.8
0.29
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Facility3
NPDES
Permit
Number
Design
Flow
(MGD)b
Wasteload Allocation0
Monthly
Average TSS
Concentration
(mg/L)
Weekly
Average TSS
Concentration
(mg/L)
Annual
TSS
Load
(t/y)
Clearwater
Forest
Industries
ID-002770-7
0.0019
Turbidity shall not exceed background turbidity by
more than 50 NTU instantaneously, or by more
than 25 NTU for more than 10 consecutive days.
Storm Water
Industrial and
Construction
Activities
ID-R050000
ID-R100000
NA
Turbidity shall not exceed background turbidity by
more than 50 NTU instantaneously, or by more
than 25 NTU for more than 10 consecutive days.f
Suction
Dredge
Industry
None
currently
SF Clearwater River above Harpster Bridge, including tributaries
July 15 -August 15:
• Turbidity below any applicable mixing zone shall not exceed
background turbidity by more than 5 NTU when background
turbidity is 50 NTU or less, and
• Turbidity below any applicable mixing zone shall not exceed
background turbidity by more than 10% when background
turbidity is more than 50 NTU, and shall not exceed a
maximum increase of 25 NTU, and
• 314 tons/day total sediment discharge.e
August 16-July 14:
• Zero wasteload allocation.
SF Clearwater River below Harpster Bridge:
• Zero wasteload allocation.
a WWTP = wastewater treatment plant, CAFO = confined animal feeding operation
b MOD = million gallons per day
0 TSS = total suspended solids, mg/L = milligrams per liter, t/y = tons per year, NTU = nephelometric turbidity
unit, BMP = best management practice
d Each facility must comply with all other applicable permitting processes, including those of the Idaho
Department of Water Resources, U.S. Forest Service, Bureau of Land Management, Army Corps of Engineers,
and U.S. Environmental Protection Agency, which include important operational considerations to minimize
substrate problems.
e This WLA only allows discharge of sediment which occurs on the bed of the stream, and does not allow the
discharge of sediment which occurs above the high water mark either directly or through undercutting of stream
banks.
flf it is determined as part of the NPDES permitting process that monitoring compliance with this wasteload
allocation is infeasible, the allocation is interpreted to be the installation of appropriate storm water BMPs as
described in local ordinances or the Idaho Catalogue of Storm Water Best Management Practices (DEQ 2003c),
whichever is more stringent, in lieu of the turbidity allocation.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Nonpoint Source Sediment Load Allocations
The excess load of nonpoint source sediment in Table 59 is calculated using the two methods
discussed above. The excess loads for the Stites, Threemile Creek, and Butcher Creek
control locations are based on TSS daily loading calculations, while the excess loads for
Harpster and upstream are based on yearly loading calculations from the sediment budget. In
the case of the daily calculations, those days when the existing load exceeds the daily load
capacity are summed and averaged over the 10 years. For Harpster and above, the excess
load is calculated by subtracting the yearly background load from the load capacity and
comparing the result to the activity load. For Harpster and above the load capacity was fixed
based on the current activity load and the percent load reduction needed at Stites (the pour
point for the basin). The discussion used to justify the 25% load reduction for all water
bodies above Stites is presented in Appendix M, Loading Calculations.
Surrogate Sediment Target
A number of instream measures exist which characterize substrate fine sediment including:
cobble embeddedness, percent depth fines, percent surface fines, residual pool volume,
width-to-depth ratios, etc. Target or threshold values have been set for a number of these by
various entities to evaluate habitat quality. The NPNF has established Desired Future
Conditions for different fish species as part of their integrated Forest Planning Process
(USFS 1992). The Desired Future Conditions for steelhead and chinook rearing habitat in B
and C channel types, for 3rd to 5th order streams, includes cobble embeddedness <25 % and
fines by depth <19% to attain 100% habitat capability. NMFS uses similar values to evaluate
habitat quality in ESA biological assessments (NMFS 1998). Habitat quality is rated as
"high" condition with cobble embeddedness levels <20%; percent surface fines <=20 (C
channels); and percent fines by depth <20. The Columbia River Inter-Tribal Fish
Commission (CRITFC 1995) sets the following goals for salmonid rearing habitat: <=30
percent cobble embeddedness, and <=20 percent surface fines, in order to meet desired
fishery production levels.
Reference watershed data may also be used to evaluate decreasing trends in sedimentation
(see Appendix N). Meadow Creek and Bargamin Creek are recognized as being relatively
undisturbed and have similar geology, rainfall, and topography as the upper basin of the SF
CWR. Lower Meadow Creek cobble embeddedness of 32% may be used as a reference
value to compare to the main stem SF CWR (48% cobble embeddedness), although the data
exhibits variability and lower Meadow Creek is somewhat steeper and more confined. Data
for similarly sized streams for upper Meadow Creek and Bargamin Creek was also compared
with the data set from the SF CWR. In almost all cases, cobble embeddedness in the SF
CWR is significantly higher than in upper Meadow Creek and Bargamin Creek (refer to
graphs and/or values), and these comparisons may be used to establish decreasing trends in
cobble embeddedness.
In light of the reference watershed data showing that cobble embeddedness in the SF CWR is
higher than that of lower Meadow Creek, a surrogate target of a decreasing trend in substrate
fine sediment levels (cobble embeddedness, depth fines, surface fines) is being set for the
222 Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
main stem SF CWR above Harpster. This surrogate target is set as a monitoring tool to
verify that sediment reduction activities in the main stem face drainages and in other
contributing watersheds are reducing substrate sediment in the river. The NPNF and the
BLM may choose to continue monitoring at established river monitoring sites, or they may
choose to continue monitoring the sites established at the control locations for this TMDL.
In either case, the intent of the decreasing trend target is to provide an indicator of the
effectiveness of the BMPs or other sediment reduction activities of implementation.
It is recognized that uncertainty exists in establishing the most appropriate substrate sediment
level for comparison; therefore, the goal of TMDL is a statistically significant decreasing
trend in substrate fine sediment levels (cobble embeddedness, depth fines, surface fines). A
detailed monitoring plan will be developed as part of the implementation plan in order to
evaluate effectiveness of BMPs in reducing instream sediment levels. This plan will identify
the specific entities responsible for collecting the data, which parameters will be sampled,
and the locations and frequencies of sampling.
223 Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table 59. Sediment load allocations for nonpoint sources in the SF CWR Subbasin.
Water Body Name
Lower SF CWR
Threemile Creek
Butcher Creek
Mid-Lower SF CWR
Middle SF CWR
Mid-Upper SF CWR
Upper SF CWR
Water
Body
ID
1
10
11
12
22
30
36
Control Location
Stites Bridge
Mouth
Mouth
Harpster Bridge
Above Johns Creek
Above Tenmile
Creek
Above Crooked
River
Total
Load
(t/y)b
38,157
1,112
441
20,622
11,185
7,827
4,527
Background
Load
(t/y)b
8,439
97
106
14,856
8,898
5,993
3,279
Human
Caused
Load
(t/y)b
29,718
1,015
335
5,736
2,297
1,835
1,248
Excess
Load
(t/y)b
7,754
780
203
1,434
574
456
312
Target
Load
(t/y)b
21,964
235
132
4,302
1,723
1,379
936
Load
Reduction
(%)
25
77
61
25
25
25
25
a Loads presented for these sites are cumulative of all areas upstream of the control location. Loads for water bodies 1, 10, and 11 are total suspended solids
loads, while loads for water bodies 12, 22, 30, and 36 are total sediment loads.
t/y = tons per year
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5.5 Implementation Strategy
"An implementation plan identifies and describes the specific pollution controls or
management measures to be undertaken, the mechanisms by which the selected pollution
control and management measures will be put into action, and describes the authorities,
regulations, permits, contracts, commitments, or other evidence sufficient to ensure that
implementation will take place. The plan also describes when implementation will take
place, identifies when various tasks or action items will begin and end, when mid-term and
final objectives will be met, and establishes dates for meeting water quality targets." (Dailey
etal. 1999, p 67)
Development of the SF CWR Subbasin implementation plan will occur through a
collaborative process involving a number of entities and interest parties, including the SF
CWR WAG, landowners, land managers (private, state, federal and tribal), and resource
agencies. Further details on the parties involved, contents, and the timeframe for
development of the plan are included in later sections of this strategy.
Implementation of the TMDLs presented in this document should occur in an integrated
fashion to address the pollutants in a cost effective manner. The major human-caused
pollutant sources that have been identified in the SF CWR Subbasin include roads, forestry,
livestock grazing, agriculture, mining, eroding streambanks, mass failures, and highway
gravel. In the upper basin above Harpster, sediment and temperature problems are
widespread and occur in many of the same areas with many of the same causes. Similarly, in
the lower basin, especially Threemile Creek, the sediment, temperature, bacteria and nutrient
problems are all closely related and should be addressed with a comprehensive
implementation strategy. It is recommended that the implementation strategy be broadly
based to address as many of the pollutants as possible with any particular project or BMP.
This will likely be the most cost effective way to address the problems.
"Application of effective BMPs is crucial to achieving the pollutant load reductions and
targets of the TMDLs. Consequently, the implementation plan, to the extent practicable,
must be explicit about which BMPs or systems of BMPs will be employed to achieve the
targets, where and when the BMPs will be employed, and how application of the BMPs
will achieve the stated targets. USEPA guidance specifically identifies several criteria by
which BMPs will be judged:
• A data-based analysis showing that the selected BMPs have been demonstrated to be
effective in addressing the issue or pollutant in question (i.e., a history of successful
application in similar situations);
• An explanation of the mechanisms by which application of the BMPs will be assured;
and
• A plan for tracking the implementation and effectiveness of the BMPs." (Dailey et al.
1999. p 67)
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As implementation progresses, pollutant reductions may be accomplished in a variety of
ways at the discretion of the implementing landowners, managers, and agencies. Over time,
implementation strategies for the TMDLs may need to be modified if monitoring shows that
the TMDL goals are not being met, or that significant progress is not being made toward
achieving the goals.
The following are issues with each one of the TMDL pollutants that should be kept in mind
while developing an implementation plan:
Temperature
Shade targets are established in the TMDL (CWE percent canopy closure and SPY percent
effective shade) as surrogate measures necessary to achieve temperature criteria. While
specific information and direction regarding how these targets are to be implemented will be
established in the implementation plan, certain general considerations accompany these
targets.
The overall intent is to meet temperature criteria by increasing shade, or in areas where shade
targets are already met, to maintain natural shade levels, which incorporate natural
disturbance regimes (e.g., fire, mass wasting, insects, disease, etc). While these shade targets
do not preclude management of the riparian zone, only activities that will result in negligible
shade reduction, or through careful evaluation, will result in long term benefits in terms of
stream temperature, are consistent with the targets.
Application of these targets is expected to be carried out at a stream reach scale, as defined in
the NPNF Basinwide Survey Methodology (USFS 1996) or similar guidance. Typically the
stream reaches are 0.5 mile in length, but this may vary considerably given the nature and
size of the stream. In all cases (both SPY and CWE), a site evaluation will be essential in
order to 1) confirm current shade conditions, 2) confirm channel conditions, 3) determine
why shade is above or below target values, and 4) establish appropriate BMPs. While the
shade targets provide a useful goal for restoration, the key to implementation is to tailor
management to the problems unique to each stream reach.
In much of the watershed it is expected that shade targets will be achieved through passive
restoration, that is, allowing vegetation to grow to a mature state. In some locations (e.g.,
dredge mined areas, grazed areas), active restoration through plantings and channel
modification will likely be warranted.
There may be circumstances in which it is necessary to temporarily reduce shade in order to
achieve increased shade and ecological health in the long term. For example, active channel
restoration or prescribed fire may temporarily reduce existing shade, but lead to long-term
temperature benefits. These activities would be consistent with TMDL targets, provided they
are carefully evaluated to establish whether or not the long-term temperature benefits
outweigh the short-term loss of shade.
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In still other areas, it is recognized that it may not be possible to achieve the desired shade
due to essentially irreversible human caused changes, such as major roads or railroads
adjacent to the stream. In these areas, it is expected that the implementation plan will
identify local or other offsetting measures (e.g., plantings along the stream) that would
minimize the effects of permanent human-caused shade loss.
Sediment
Sediment targets (Table 59) are set based on loading from various sources on the landscape
shown in Table 30. Implementation of the sediment TMDLs should be based on the various
data types and assumptions that went into developing the targets as described in Appendix L.
Nonpoint source sediment load reductions are divided for each control location by
management responsibility in Table 60. This is provided as guidance for locations of
implementation efforts. Management responsibilities were divided as follows: NPNF, BLM,
the state (state highway), Idaho County (county roads), and private individuals. Small
amounts of land managed by the NPT and IDL are too small to be broken out. Generally, the
loading division by management responsibility used the following scheme: all RUSLE
results were identified as private; all WEPP results were identified as county roads; mass
failures were divided between the NPNF and private based on locations in the GIS, since we
had no data that any occurred on BLM land; in-stream erosion results were divided between
the NPNF, BLM, and private based on locations; and NEZSED results were divided between
NPNF, BLM, and private based on percentage of ownership.
Table 60. Sediment excess loads by management responsibility in the SF
CWR Subbasin.
Control
Location
Stitesc
Threemile Greek0
Butcher Creekc
Management
Responsibility3
All
NPNF
State Highway
County Roads
BLM
Private
Cottonwood TMDLd
All
County Roads
Private
All
Private
County Roads
Human-
Caused Load
(tons/year) b
29,718
2,009
1,151
516
250
11,006
22,300
1,015
134
881
335
325
111
227
Target
Sediment Load
(tons/year) b
21,964
1,391
863
387
187
8,254
6,640
235
39
196
132
128
60
Excess
Sediment Load
(tons/year) b
7,754
618
288
129
63
2,752
15,660
780
95
685
203
197
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Control
Location
Harpster
(Johns Creek to
Threemile Creek) e
Tenmile Creek to
Johns Creek6
Crooked River to
Tenmile Creek6
American and Red
Rivers Confluence
to Crooked River6
Management
Responsibility3
BLM
All
NPNF
State Highway
County Roads
BLM
Private
All
NPNF
State Highway
BLM
Private
All
NPNF
State Highway
BLM
Private
All
NPNF
State Highway
BLM
Private
Human-
Caused Load
(tons/year) b
6
5,736
1,658
1,151
98
135
2,792
2,297
1,168
630
135
306
1,835
1,003
375
135
301
1,248
708
114
135
284
Target
Sediment Load
(tons/year) b
3
4,302
1,243
863
74
101
2,094
1,723
876
473
101
230
1,376
752
281101
101
226
936
531
86
101
213
Excess
Sediment Load
(tons/year) b
3
1,434
415
288
25
34
698
574
292
156
34
77
459
251
94
34
75
312
177
29
34
71
aNPNF = Nez Perce National Forest, BLM = Bureau of Land Management
b Totals for Stites do not equal the sum of the parts because of different estimation methods used in the
Cottonwood Creek TMDL; other totals do not all add up due to rounding
0 Total suspended solids (TSS)-based loading calculations
d Derived from the Cottonwood Creek TMDL
e Sediment budget-based calculations
Site specific treatments and BMPs for sediment reductions will be identified in the
implementation plan. The following are a few examples of the many forest and agricultural
practices which could be implemented to reduce sediment.
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• Road improvements including: culvert and stream crossing upgrades, sidecast removal or
reduction, road removal or closure, stabilizing cut and fill banks, hardening surfaces, and
improving maintenance.
• Stabilizing mass failures.
• Grazing management including: reducing concentration of animals, fencing and off-site
water installation, and rotational grazing systems.
• Agricultural BMPs including: nutrient management, grassed waterways, Conservation
Reserve Program (CRP) vegetative plantings, filter and riparian buffer strips, reduced
channel straightening, road buffers, and direct seeding.
• Land management activities which attenuate water yield are also recommended and may
include: wetland and riparian buffer enhancement/development, and no-till agriculture.
• Instream habitat restoration in intensively mined areas including: re-establishing historic
fluvial processes, pool frequency, pool depth etc. through channel reconstruction (ie. Red
River project).
The following data sets may be monitored as implementation proceeds:
Threemile and Butcher Creeks
Percent Eroding Banks
SCC, Soil and Water Conservation District (SWCD), NRCS, NPT
RUSLE model for changed farming practices
SCC, SWCD, NRCS
Road Erosion Buffering
ITD, Road District
Main Stem SF CWR
In-channel habitat and substrate conditions
NPT, NPNF, BLM
Highway Gravel
ITD
Percent Eroding Stream Banks
NPNF, BLM, SWCD, SCC, NRCS
NEZSED model results to track forest activity sediment reductions
NPNF, BLM
Cobble embeddedness, percent surface fines, percent fines by depth, residual
pool volume, width to depth ratios
NPNF, BLM
As BMPs and other management practices are designed to reduce sediment, modeled or
expected results need to include the routing coefficient used in the sediment budget.
Generally, sediment sources on the land need to be reduced by about twice the amount
specified in the targets in order to account for routing. In other words, the sediment targets
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are instream targets set for the instream control locations. Sediment reduction activities on
the land must reduce sediment by both the amount lost during routing and the amount
required by the target. For example, the 29 t/y sediment reduction target for gravel from
Highway 14 between the confluence and Crooked River is a target reduction for gravel in the
river channel. Actual reduction of gravel applied to the road surface should be back
calculated using the routing coefficient shown in Table 32, e.g., (29 t/y)/(0.77)=38 t/y.
In addition, estimations of potential sediment reduction need to consider any assumptions
built into the sediment budget (Appendix L). To continue the example of gravel applied to
Highway 14 between the confluence and Crooked River, loading calculations were based on
an assumption that only 80% of the highway delivers to the river. Further back calculations
to account for this assumption results in a needed reduction of gravel delivery from the road
surface to the stream channel on the order of 47 t/y [(38 t/y)/(0.8) = 47 t/y].
Another way that any particular management group might look at the needed sediment
reduction from their operations is simply to reduce their sediment contribution by 25%. In
the case of operations in Butcher Creek, the sediment reduction is 61%, and in Threemile
Creek, it is 77%. However, if a method of estimation different from that used in the TMDL
is used, it should be clearly shown in the implementation plan how the target will be attained.
Since the sediment budget for the upper basin indicates that sediment is coming from
dispersed sources, it is expected that sediment reductions will come from throughout the
upper basin as well. Table 31 provides a guide to the sediment sources throughout the
subbasin and can be used to help prioritize where action needs to take place. Activities
designed to restore streamside vegetation will work toward achieving both sediment and
temperature targets. For example, the most cost-effective way to address the temperature
TMDL is reestablishment of streamside vegetation, which at the same time will reduce in-
stream erosion. In some areas, in-stream erosion would be reduced to virtually zero by the
reestablishment of streamside vegetation. For the control location above Crooked River, in-
stream erosion reduced to zero would result in almost two-thirds of the total sediment load
reduction needed. Those areas with in-stream erosion problems are also those contributing
most to the heat loading problem.
Bacteria
Levels of bacteria that exceed the state WQS were identified at several times throughout the
year and at several locations in Threemile Creek. The target is set at the state WQS of a
geometric mean of 126 cfu/100 ml. Available data indicate that effluent from the
Grangeville WWTP is not contributing to the problem beyond its permitted level of 100
cfu/100 ml. Probable causes are livestock defecation near and in the creek, stormwater
runoff from the city of Grangeville, wildlife defecation near and in the creek, and possibly
failing sewage disposal systems.
While the precise sources of bacteria in Threemile Creek have not been identified, sources
that are the result of human activity are known to exist and should be addressed in the
implementation plan. BMPs that reduce sediment and heat loading may also reduce levels of
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bacteria. These activities may include the removal of cattle from areas of the creek, fencing,
re-establishing riparian buffer zones, and improving stormwater management. Continued
monitoring of bacteria as described below will better isolate the sources of bacteria.
Nutrients/DO
Monitored levels of nitrogen and phosphorus in Threemile Creek exceed USEPA
recommended levels by as much as 2 orders of magnitude. A TMDL was developed for
phosphorus with the assumption that limiting P will result in decreased nuisance algal growth
and/or DO deficiencies. Targets are set at 0.08 mg/L TP above the WWTP outfall, 0.10
mg/L TP from the WWTP outfall to the Big Barn site at the head of the canyon, and 0.30
mg/L TP at the mouth.
Sources of P in the watershed include: urban runoff, agriculture and grazing practices, stream
bank instability, sediment from roads, and the WWTP. The City of Grangeville is working to
reduce P from the WWTP and the wasteload allocation for the WWTP will be incorporated
into Grangeville's NPDES permit by the USEPA. It can be expected that BMPs effective in
dealing with bacteria, temperature and sediment issues in Threemile Creek will also be
effective in reducing nonpoint nutrient loading to the creek. Examples include: stormwater
management, minimum till farming, riparian buffer planting and enhancement, stream bank
stabilization, fencing with off-site watering for livestock, and road/culvert maintenance.
Approach
The implementation plan will be developed jointly through a collaborative process involving
the WAG, landowners, land managers, and responsible resource agencies. Contents of the
implementation plan are expected to include:
A description of how targets are to be attained (e.g., explains details of how to implement
SPY and CWE targets).
An identification of BMPs and BMP locations.
An identification of existing efforts that will help achieve TMDL goals.
An implementation schedule with milestones based on restoration priorities.
Provisions to seek funding sources and sponsoring agencies.
Reasonable Assurance
Reasonable assurance of the implementation of nonpoint source control actions is required in
a TMDL when point source WLAs are made less restrictive as a result of expected reductions
from nonpoint source allocations. Where there are not reasonable assurances, the entire load
reduction must be assigned to point sources (USEPA 1991). Wasteload allocations in these
TMDLs are not less restrictive than current NPDES limits. In addition, except for the case of
nutrients in Threemile Creek, point source loading compared to the overall load capacity is
very minor. As a result, assigning the entire load reduction to point sources would result in
essentially no improvement in conditions in the SF CWR. The implementation plan will
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address many aspects of reasonable assurance for nonpoint sources as summarized above
under the section titled "Approach."
Nonetheless, for forested areas in the SF CWR Subbasin, water quality problems caused by
nonpoint sources of sediment and heat are improving as a result of work by land managers,
federal policies, and the Idaho's FPA. There is no reason to expect that the trend will not
continue. The TMDLs identify areas of highest pollutant input and should allow for
prioritization of areas for additional work.
In the agricultural and grazing areas of the subbasin, no-till and minimum-till farming have
been making an impact in the Cottonwood drainage, and there is reason to expect that
farmers in the Threemile and Butcher Creek watersheds will adopt these practices as well.
Similarly, there are programs being put in place by the SCC to limit livestock access to
stream banks, which would allow vegetation to regrow along the streams. The Idaho
Department of Agriculture has an active program working with AFOs to eliminate water
pollution from these operations.
Time Frame
Implementation plans are to be developed within 18 months of USEPA approval of the
TMDL, and are intended to achieve the water quality goals provided in a TMDL package.
Development of the implementation plan has already begun and is expected to be completed
in time for submittal of nonpoint source projects for CWA Section 319 funding in
2004/2005. Wasteload allocations will be incorporated into NPDES permits when they are
reissued or reopened. The Grangeville NPDES permit is expected to be reissued within the
next 1-2 years, and the recently reissued permits for Kooskia, Stites, Elk City, and Red River
Ranger Station will need to be reopened to incorporate revised limits.
Implementation of nonpoint source controls has already begun, but is expected to proceed
more rapidly once the implementation plan is complete and funds are available. A majority
of the sources of pollutant loading are nonpoint in origin, and realistically it may take many
years if not decades to fully achieve the goals of the TMDL. Certain improvements, such as
controlling temperature and nutrients from the Grangeville WWTP or controlling nonpoint
bacteria sources, are likely to occur fairly rapidly, within a few years. In order to
substantially improve stream temperatures, mature riparian communities and a stable
hydrologic regime and stream channel are needed. In smaller streams and watersheds, for
example at an exclosure on Big Elk Creek, significant improvement may be seen in a few
years. Realistically though, it is likely to take decades to see such improvement throughout
the watershed given the large scale of needed improvements and the time frame needed to for
riparian vegetation to grow to maturity.
Participating Parties
Responsible agencies and interest groups expected to play an important role in developing
and implementing restoration measures include: the SF CWR WAG, NPNF, NPT, IDL,
ISWCD, SCC, BLM, ITD, IDWR, BIA, Idaho Department of Agriculture, NRCS, DEQ,
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NMFS, USEPA, IDFG, U.S. Fish and Wildlife Service, Idaho County, local highway
districts, municipalities, industries, and local landowners.
Monitoring Strategy
Monitoring needs include continued monitoring of in-stream temperatures, determining point
source discharge temperatures, and monitoring to establish reach-specific shade targets.
Monitoring for stream temperature trends and standards attainment should occur near the
mouths of each of the water bodies 303(d) listed for temperature, as well as those other
303(d) listed streams that are protected for bull trout. A total of 13 monitoring points should
be established in the SF CWR Subbasin: five on the main stem near the lower ends of the
water bodies, and one each near the mouths of Threemile Creek, Butcher Creek, Newsome
Creek, American River, Big Elk Creek, Little Elk Creek, Red River and Crooked River.
Stream temperature should be monitored using a device that at a minimum can make hourly
recordings over the course of six months, encompassing the critical months of July and
August. Monitoring should occur every summer until such time as the WQS are attained, or
until this TMDL is revised and another plan established.
Monitoring of point source temperatures is needed so that the facilities can verify compliance
with WLAs using current operations or determine if treatment revisions will be necessary.
Monitoring requirements will be included in revised NPDES permits, but point sources are
encouraged to begin collecting data immediately.
Determining reach-specific channel width, aspect, and current effective shade is needed in
order to verify SPY shade targets and determine whether increases in shade are needed. A
systematic procedure and time frame for collecting these data across federal, state, and
private land is needed.
As with temperature, improvements in sediment condition throughout the basin should be
monitored. For each of the control locations, one to several types of data are identified to
monitor whether control measures are being put in place. Table 61 presents the targets for
the different data types for the areas upstream from each of the control locations. The targets
are the cumulative sediment from all portions of the subbasin upstream from the control
locations. The current condition and targets are set based on the data type. As noted above,
where both TSS and sediment budget methods of calculating the sediment loading are used,
the sum of the different targets do not add to the total sediment load target at any particular
control location.
In Table 61, methods are described by which sediment implementation results could be
monitored. Monitoring of sediment reduction should be designed to measure against the
TSS-based targets or the sediment load-based targets. Implementing agencies should collect
data to track progress. The implementation plan will identify how monitoring data will be
acquired, organized and maintained for each of the control locations.
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Table 61. Sediment load targets by data type in the SF CWR Subbasin.
Control
Location
Stitesc
Threemile Greek0
(mouth)
Butcher Creekc
(mouth)
Johns Creek to
Threemile Creek6
(Harpster Bridge)
Tenmile Creek to
Johns Creek6
Crooked River to
Tenmile Creek6
Confluence to
Crooked River6
Data Type
Sediment Load
Cottonwood TMDLd
Sediment Load
In-stream Erosion Model
RUSLE Model (ag and grazing)
WEPP Model (roads)
Sediment Load
RUSLE Model (ag and grazing)
WEPP Model (roads)
In-stream Erosion Model
Sediment Load
RUSLE Model (ag and grazing)
NEZSED (forestry and grazing)
Highway Gravel
In-stream Erosion Model
Sediment Load
NEZSED (forestry and grazing)
Highway Gravel
Sediment Load
NEZSED (forestry and grazing)
Highway Gravel
In-stream Erosion Model
Sediment Load
NEZSED (forestry and grazing)
Highway Gravel
In-stream Erosion Model
Target Type3
TSS tons/year
TSS tons/year
TSS tons/year
Tons/year
Tons/year
Tons/year
TSS tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Tons/year
Current
Condition13
29,718
22,300
1,015
357
5,632
134
335
723
111
131
5,736
2,268
1,439
1,151
405
2,297
1,292
630
1,835
1,083
375
376
1,248
903
114
231
Targetb
22,144
6,640
235
103
1,633
39
132
390
60
71
4,302
1,701
1,079
863
304
1,723
969
474
1,376
812
281
282
936
677
85
173
'TSS = total suspended solids
All numbers for the control locations on the main stem are cumulative for all areas upstream
c Total suspended sediment (TSS)-based loading calculations
d Derived from the Cottonwood Creek TMDL
6 Sediment budget-based calculations
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A surrogate target for sediment has been set as an improving trend for in-stream habitat. It is
expected that the management agencies will establish long term monitoring sites for cobble
embeddedness and/or several habitat parameters at no less than one for each of the control
locations. In addition to reduced loading as calculated against the above targets, the TMDL
will be successful only if a statistically significant improving trend of river habitat is
demonstrated. This trend monitoring is a measure of BMP effectiveness and would need to
be carefully designed if there is any intent to measure the effectiveness of one suite of BMPs
vs. another.
For suction dredging, it is expected that achieving the wasteload allocation will ensure
compliance with the numeric turbidity criteria and the narrative sediment standard.
Monitoring required as part of the NPDES permitting process, will be an important tool to
evaluate ongoing compliance with this allocation. Given the lack of consistent monitoring of
the effects of this industry in the SF CWR watershed, it is also recommended that the NPNF,
DEQ and USEPA establish a monitoring plan to further characterize and assess these impacts
on an ongoing basis.
For the bacteria and nutrient/DO TMDLs in Threemile Creek, it is recommended that a
monitoring network be established to determine background loading and the distribution of
nonpoint source loading of these pollutants. Specifically, it is recommended that monitoring
locations be established in the forested headwaters for background, a location above the city
and one below the city but above the WWTP to identify problems with runoff from the city,
below the WWTP to capture effects of the WWTP, at the top of the canyon above the falls to
capture the effects from the agricultural lands, above the mass failure in the lower end of the
canyon, and one and the mouth of the creek. The critical time periods when these sites
should be sampled are July, August and September on a bi-weekly basis. If these sites were
monitored each year during implementation, trend analysis could lead to conclusions about
BMP effectiveness. A more detailed research study of the effects of the mass failure on
phosphorus concentrations is also recommended, but is likely beyond the scope of routine
follow up monitoring during implementation.
5.6 Summary and Conclusions
This subbasin assessment and TMDLs have been developed to comply with Idaho's WQS
and TMDL schedule. The first part of this document, the subbasin assessment describes the
physical, biological, and cultural setting; water quality status; pollutant sources; and recent
pollution control actions in the SF CWR Subbasin located in north-central Idaho. The
starting point for the assessment was Idaho's 1998 303(d) list of water quality limited water
bodies. Eighteen stream segments and one lake in the SF CWR Subbasin were included on
this list. The subbasin assessment portion of this document examines the current status of
303(d) listed waters. It defines the extent of impairment and causes of water quality
limitation throughout the subbasin.
Subbasin-wide temperature analyses were conducted in light of an extensive database
indicating that no stream in the SF CWR Subbasin, not even those in relatively pristine
condition, meets the Idaho numeric temperature criteria for salmonid spawning. However,
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the Idaho WQS recognize that stream temperatures may naturally exceed numeric criteria
and that pollution control measures should only address the human-caused increases in
temperature. The non-point temperature assessments assumed that the human-caused effects
were increased solar insolation, primarily a result of reduced streamside vegetation and,
secondarily a result of increased stream width. Shading and stream width analyses were
conducted on all perennial streams in the subbasin. The human-caused stream temperature
increase was quantified in terms of the percent decrease in stream shade and increase in
stream width. Targets were set based on best estimates of natural conditions for stream shade
and stream width. Heat loadings were calculated based on current temperatures and flows,
and were generally very low except at the Grangeville WWTP. Targets for all WWTPs were
set to limit temperature increases in receiving waters to less than 0.3 °C (0.5 °F) above the
temperature criteria, as per the WQS.
Subbasin-wide sediment analyses were based on a limited stream turbidity data set from four
locations in the lower subbasin and a sediment delivery budget to streams from various
sources. The sediment budget was developed using estimates from different models and data
sets from the various sediment sources throughout the subbasin, as follows: NEZSED
erosion model estimates of sediment from federally-managed timber land; RUSLE erosion
model estimates of sediment from agricultural and range land; a stream bank erosion model
estimate of in-stream erosion; WEPP erosion model estimates of sediment from county
roads; a NPNF inventory of mass failures extrapolated to include the complete subbasin; and
an estimate based on average annual rock crush of gravel from State Highway 14 reaching
the river. Current discharge of sediment from point sources in the subbasin (municipal
WWTPs, suction dredges, construction and industrial stormwater runoff) were found to be
very minor in relation to the nonpoint sources.
Turbidity data were compared directly to the state WQS with loadings calculated using
turbidity to total suspended solids (TSS) relationships. Sediment targets and allocations in
the lower basin were set to meet the state turbidity criteria. Sediment targets for the upper
basin, where no turbidity data were available, were set based on the percent load reduction
needed at the mouth of the SF CWR, the Stites bridge control location. Point source
allocations were established at required technology based levels in State or federal
regulations, or at levels in existing NPDES permits.
Threemile and Butcher Creeks are 303(d) listed for several other pollutants in addition to
sediment and temperature. They were both also evaluated for nutrients, dissolved oxygen,
bacteria, and ammonia. Threemile Creek is particularly impacted because it receives effluent
from the Grangeville WWTP, which at times makes up more than 50% of the stream flow.
Data for pollutants were collected near the mouth of Butcher Creek and at four locations on
Threemile Creek. Bacteria, dissolved oxygen, and ammonia data were compared to the state
WQS. Nutrient levels were compared to both USEPA guidelines and the state's narrative
WQS to determine impairment. In the case of Threemile Creek, where a water quality
impairment was identified, the target was set for phosphorus based on the USEPA guidelines,
and data collected in the watershed. These targets, and the seasonality of their application,
may require adjustments in the future as additional data and information are collected.
236 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Lucas Lake, near Elk City, is an old "glory hole" from the mining days of about 2 acres in
size. It was originally 303(d) listed in 1994 based on data from the Idaho 1988 Water
Quality Status Report and Nonpoint Source Assessment which indicated that it did not
support one or more beneficial uses due to sediment/siltation. Turbidity and metals samples
were collected for the lake and compared against the state WQS. No impairment was
identified.
As a result of the subbasin assessment, temperature TMDLs were written for all 74 water
bodies in the subbasin; sediment TMDLs were written for the SF CWR watershed, Butcher
Creek, and Threemile Creek; and nutrient and bacteria TMDLs were written for Threemile
Creek (Table 62). It is expected that these TMDLs will improve conditions throughout the
subbasin for all aquatic species, including threatened and endangered fish species such as
bull trout, fall chinook salmon, and steelhead.
Table 62. Streams and pollutants for which TMDLs were developed.
Stream
South Fork Clearwater River
Threemile Creek
Butcher Creek
Dawson Creek
Little Elk Creek
Big Elk Creek
Buffalo Gulch
Newsome Creek
Beaver Creek
Nugget Creek
Sing Lee Creek
Cougar Creek
58 remaining water bodies
Pollutant(s)
Sediment, Temperature
Bacteria, Nutrients, DO, Sediment, Temperature
Sediment, Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Temperature
Development of the implementation plan has already begun. The plan is expected to be
completed in time to submit for 319 funding in 2004/2005. Wasteload allocations will be
incorporated into NPDES permits when they are reissued or reopened. The Grangeville
permit is expected to be reissued within the next 1-2 years, and the recently reissued permits
for Kooskia, Stites, Elk City and Red River Ranger Station will need to be re-opened to
incorporate revised limits.
Implementation of nonpoint source controls has already begun, but is expected to proceed in
earnest once the implementation plan is complete and funds are available. A majority of the
sources of temperature and sediment loading are nonpoint in origin, and realistically it may
take many years if not decades to fully achieve the goals of the TMDL. Certain
237
Chapter 5
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
improvements such as controlling temperature and nutrients from the Grangeville treatment
facility or controlling nonpoint bacteria sources are likely to occur within a few years. In
order to improve stream temperature, restored riparian communities and stream channels are
needed. In smaller streams and watersheds, for example, the exclosure on Big Elk Creek,
significant improvement may be seen in several years. It is likely to take decades to see such
improvement throughout the watershed given the large scale of needed improvements and the
time needed for riparian vegetation to grow to maturity.
It is expected that implementation of the TMDLs as presented in this document will result in
full restoration of the waters of the SF CWR Subbasin to meet the Idaho WQS. Further, this
restoration will contribute substantially to improved habitat for threatened and endangered
aquatic species in the subbasin.
238 Chapters
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
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Division of Environmental Quality, Boise, ID. 14 pp + app.
USACOE (U.S. Army Corps of Engineers). 2003. Recreational Suction Dredge Mining
Information Paper. U.S. Army Corps of Engineers, Walla Walla District. January 7,
2003.
USEPA (U.S. Environmental Protection Agency). Undated. Storet: EPA's computerized
water quality data base. Storet User Assistance. USEPA, Washington DC.
USEPA (U.S. Environmental Protection Agency). 1986. Quality criteria for water 1986.
EPA440/5-86-001. USEPA Office of Water Regulations and Standards, Washington.
DC.
USEPA (U.S. Environmental Protection Agency). 1991. Guidance for water quality-based
decisions: The TMDL process. EPA 440/4-91-001. U.S. Environmental Protection
Agency, Office of Water: Washington, DC. April 1991.
USEPA (U.S. Environmental Protection Agency). 1993a. A review of the regulations and
literature regarding the environmental impacts of suction gold dredges. U.S.
Environmental Protection Agency, Region 10, Alaska Operations Office.
USEPA (U.S. Environmental Protection Agency). 1993b. Biological criteria: technical
guidance for streams and small rivers. EPA 822-B-96-001. U.S. Environmental
Protection Agency, Office of Water, Washington, DC. 162 pp.
USEPA (U.S. Environmental Protection Agency). 1996. Monitoring protocols to evaluate
water quality effects of grazing management on western rangeland streams.
USEPA910/R-93-017. USEPA Region 10, Water Division, Surface Water Branch,
Seattle WA.
USEPA (U.S. Environmental Protection Agency). 1997'a. Guidelines for preparation of the
comprehensive state water quality assessments (305(b) reports) and electronic
updates: supplement. EPA-841-B-97-002B. U.S. Environmental Protection Agency,
Washington DC. 105pp.
249 References
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
USEPA (U.S. Environmental Protection Agency). 1997b. Memorandum From: Michael
Hoyles, USEPA , To: Sylvia Kawabata, USEPA , Re: Compliance Inspection - City
of Grangeville, Idaho. U.S. Environmental Protection Agency, Region 10, Seattle,
WA. April 24, 1997.
USEPA (U.S. Environmental Protection Agency). 1998. Letter from: William M. Riley,
Administrator, USEPA Region 10, Seattle. WA. to Jack A. Blackwell, U.S. Forest
Service, Intermountain Region, Denver, CO, and Dale N. Bosworth, U.S. Forest
Service Northern Region, Mis soul a, MT.
USEPA (U.S. Environmental Protection Agency). 2000. Ambient water quality criteria
recommendations: rivers and streams in nutrient Ecoregion III. U.S. Environmental
Protection Agency. EPA 822-B-00-016. Seattle, WA.
USEPA (U.S. Environmental Protection Agency). October 2002a. National pollutant
discharge elimination system (NPDES) permit. City of Kooskia, ID. NPDES Permit
No.: ID-002181-4. USEPA Region 10, Seattle, WA.
USEPA (U.S. Environmental Protection Agency). October 2002b. National pollutant
discharge elimination system (NPDES) permit. City of Stites, ID. NPDES Permit
No.: ID-002034-6. USEPA, Region 10, Seattle, WA.
USEPA (U.S. Environmental Protection Agency). October 2002c. National pollutant
discharge elimination system (NPDES) Permit. Clearwater Forest Industries,
Kooskia, ID. NPDES Permit No.: ID-002770-7. USEPA Region 10, Seattle, WA.
USEPA (U.S. Environmental Protection Agency). October 2002d. National pollutant
discharge elimination system (NPDES) Permit. Elk City Water and Sewer
Association, Elk City, ID. NPDES Permit No.: ID-002201-2. USEPA Region 10,
Seattle, WA.
USEPA (U.S. Environmental Protection Agency). October 2002e. National pollutant
discharge elimination system (NPDES) Permit. Red River Ranger Station NPDES
Permit No.: ID-002069-9. USEPA Region 10, Seattle, WA.
USEPA (U.S. Environmental Protection Agency). 2002f Columbia River fish contaminant
survey 1996-1998. USEPA 910/R-02-006.
USEPA (U.S. Environmental Protection Agency). 2003. EPA Region 10 guidance for
Pacific Northwest state and tribal temperature water quality standards. EPA 910-B-
03-002. U.S. Environmental Protection Agency, Region 10, Office of Water. Seattle,
WA. April 2003.
USFS (USDA Forest Service). 1980a. Analysis of suction dredge mining on forest stream
habitats on the Nez Perce National Forest. Nez Perce National Forest, Grangeville,
ID.
250 References
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
USFS (USDA Forest Service). 1980b. Suction Dredge Mining on the Nez Perce Forest.
Nez Perce National Forest, Grangeville, ID.
USFS (USDA Forest Service). 1981. Guide for predicting sediment yields from forested
watersheds. Northern and Intermountain Regions, Missoula, MT. 40 pp + app.
USFS (USDA Forest Service). 1987. Nez Perce National Forest Plan. Nezperce National
Forest, Grangeville, ID.
USFS (USDA Forest Service). 1992. DFC fisheries model and analysis procedures: a
training module. Clearwater National Forest fish habitat relationships. Clearwater
National Forest, Orofmo, ID. 9 pp + 2 app.
USFS (USDA Forest Service). 1995a. Biological assessment South Fork Clearwater River.
Nez Perce National Forest, Grangeville, ID.
USFS (USDA Forest Service). 1995b. Nez Perce National Forest - 1995 basinwide survey
methods. Nez Perce National Forest, Grangeville, ID.
USFS (USDA Forest Servie). 1996a. Meadow-Lightning environmental assessment. Nez
Perce National Forest, Grangeville, ID.
USFS (USDA Forest Service). 1996b. Unpublished data. Nez Perce National Forest,
Grangeville, ID.
USFS (USDA Forest Service). 1998. South Fork Clearwater River landscape assessment.
Volume 1 -Narrative. Nez Perce National Forest, Grangeville, ID. 210 pp.
USFS (USDA Forest Service). 1999. South Fork Clearwater River biological assessment.
Nez Perce National Forest, Grangeville, ID. 603 pp. +app.
USFS (USDA Forest Service). 2002a. Draft addendum to South Fork Clearwater River
biological assessment. Nez Perce National Forest, Grangeville, ID.
USFS (USDA Forest Service). 2002b. Inventoried roadless areas by state.
http://roadless.fs.fed.us/states/id/state3.shtml. Data from September 2000.
USFS and BLM (USDA Forest Service and USDI Bureau of Land Management). 1995.
PACFISH decision notice/decision record. Environmental assessment for interim
strategies for managing anadromous fish-producing watersheds in Eastern Oregon,
Washington, Idaho, and portions of California. Portland, OR. 72 pp.
USFS and BLM (USDA Forest Service and USDI Bureau of Land Management). 2000.
Interior Columbia Basin Ecosystem Management Project. Portland OR.
http://www.icbemp.gov/html/proiectinfo/web/int-dir.htm.
251 References
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
USGS (U.S. Geological Survey). 1987. Hydrologic unit maps. Water supply paper 2294.
USGS, Denver, CO. 63 p.
USGS (U.S. Geological Survey), http://waterdata.usgs.gov/nwis/sw/.
Vallett, H.M., S.G. Fisher, and E.H. Stanley. 1990. Physical and chemical characteristics of
the hyporheic zone of a sonoran desert stream. Journal of American Benthological
Society 25(3):201-215.
Water Pollution Control Federation. 1987. The Clean Water Act of 1987. Water Pollution
Control Federation, Alexandria, VA. 318 p.
Water Quality Act of 1987, Public Law 100-4 (1987).
Water quality planning and management, 40 CFR 130.
Wilhite, D. 2002. Personal communication. Company efforts to use the glory hole for wood
waste disposal. Shearer Lumber Company, Elk City, ID.
WRCC (Western Regional Climate Center). 2003 Kooskia, Idaho; 1908 - 1987.
http://www.wrcc.dri.edu/cgi-bin/cliRECtM.pl7idkoos. May, 2003.
GIS Coverages:
Restriction of liability: Neither the state of Idaho nor the Department of Environmental
Quality, nor any of their employees make any warranty, express or implied, or assume any
legal liability or responsibility for the accuracy, completeness or usefulness of any
information or data provided. The data could include technical inaccuracies or typographical
errors. The Department of Environmental Quality may update, modify, or revise the data
used at any time, without notice.
252 References
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October 2003
Glossary
305(b)
§303(d)
Acre-Foot
Adsorption
Aeration
Aerobic
Assessment Database (ADB)
Refers to section 305 subsection "b" of the Clean Water
Act. 305(b) generally describes a report of each state's
water quality, and is the principle means by which the
U.S. Environmental Protection Agency, Congress, and the
public evaluate whether U.S. waters meet water quality
standards, the progress made in maintaining and restoring
water quality, and the extent of the remaining problems.
Refers to section 303 subsection "d" of the Clean Water
Act. 303(d) requires states to develop a list of water
bodies that do not meet water quality standards. This
section also requires total maximum daily loads (TMDLs)
be prepared for listed waters. Both the list and the
TMDLs are subject to U.S. Environmental Protection
Agency approval.
A volume of water that would cover an acre to a depth of
one foot. Often used to quantify reservoir storage and the
annual discharge of large rivers.
The adhesion of one substance to the surface of another.
Clays, for example, can adsorb phosphorus and organic
molecules.
A process by which water becomes charged with air
directly from the atmosphere. Dissolved gases, such as
oxygen, are then available for reactions in water.
Describes life, processes, or conditions that require the
presence of oxygen.
The ADB is a relational database application designed for
the U.S. Environmental Protection Agency for tracking
water quality assessment data, such as use attainment and
causes and sources of impairment. States need to track
this information and many other types of assessment data
for thousands of water bodies, and integrate it into
meaningful reports. The ADB is designed to make this
process accurate, straightforward, and user-friendly for
participating states, territories, tribes, and basin
commissions.
253
Glossary
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Adfluvial
Adjunct
Alevin
Algae
Alluvium
Ambient
Anadromous
Anaerobic
Anoxia
Anthropogenic
Describes fish whose life history involves seasonal
migration from lakes to streams for spawning.
In the context of water quality, adjunct refers to areas
directly adjacent to focal or refuge habitats that have been
degraded by human or natural disturbances and do not
presently support high diversity or abundance of native
species.
A newly hatched, incompletely developed fish (usually a
salmonid) still in nest or inactive on the bottom of a water
body, living off stored yolk.
Non-vascular (without water-conducting tissue) aquatic
plants that occur as single cells, colonies, or filaments.
Unconsolidated recent stream deposition.
General conditions in the environment. In the context of
water quality, ambient waters are those representative of
general conditions, not associated with episodic
perturbations, or specific disturbances such as a
wastewater outfall (Armantrout 1998, EPA 1996).
Fish, such as salmon and sea-run trout, that live part or
the majority of their lives in the salt water but return to
fresh water to spawn.
Describes the processes that occur in the absence of
molecular oxygen and describes the condition of water
that is devoid of molecular oxygen.
The condition of oxygen absence or deficiency.
Relating to, or resulting from, the influence of human
beings on nature.
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Glossary
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Anti-Degradation
Aquatic
Aquifer
Assemblage (aquatic)
Assimilative Capacity
Autotrophic
Batholith
Bedload
Beneficial Use
Refers to the U.S. Environmental Protection Agency's
interpretation of the Clean Water Act goal that states and
tribes maintain, as well as restore, water quality. This
applies to waters that meet or are of higher water quality
than required by state standards. State rules provide that
the quality of those high quality waters may be lowered
only to allow important social or economic development
and only after adequate public participation (IDAPA
58.01.02.051). In all cases, the existing beneficial uses
must be maintained. State rules further define lowered
water quality to be 1) a measurable change, 2) a change
adverse to a use, and 3) a change in a pollutant relevant to
the water's uses (IDAPA 58.01.02.003.56).
Occurring, growing, or living in water.
An underground, water-bearing layer or stratum of
permeable rock, sand, or gravel capable of yielding of
water to wells or springs.
An association of interacting populations of organisms in
a given water body; for example, a fish assemblage, or a
benthic macroinvertebrate assemblage (also see
Community) (EPA 1996).
The ability to process or dissipate pollutants without ill
effect to beneficial uses.
An organism is considered autotrophic if it uses carbon
dioxide as its main source of carbon. This most
commonly happens through photosynthesis.
A large body of intrusive igneous rock that has more than
40 square miles of surface exposure and no known floor.
Abatholith usually consists of coarse-grained rocks such
as granite.
Material (generally sand-sized or larger sediment) that is
carried along the streambed by rolling or bouncing.
Any of the various uses of water, including, but not
limited to, aquatic biota, recreation, water supply, wildlife
habitat, and aesthetics, which are recognized in water
quality standards.
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Beneficial Use Reconnaissance
Program (BURP)
Benthic
Benthic Organic Matter.
Benthos
Best Management Practices (BMPs)
Best Professional Judgment
Biological Oxygen Demand (BOD)
Biological Integrity
Biomass
Biota
A program for conducting systematic biological and
physical habitat surveys of water bodies in Idaho. BURP
protocols address lakes, reservoirs, and wadeable streams
and rivers.
Pertaining to or living on or in the bottom sediments of a
water body.
The organic matter on the bottom of a water body.
Organisms living in and on the bottom sediments of lakes
and streams. Originally, the term meant the lake bottom,
but it is now applied almost uniformly to the animals
associated with the lake and stream bottoms.
Structural, nonstructural, and managerial techniques that
are effective and practical means to control nonpoint
source pollutants.
A conclusion and/or interpretation derived by a trained
and/or technically competent individual by applying
interpretation and synthesizing information.
The amount of dissolved oxygen used by organisms
during the decomposition (respiration) of organic matter,
expressed as mass of oxygen per volume of water, over
some specified period of time.
1) The condition of an aquatic community inhabiting
unimpaired water bodies of a specified habitat as
measured by an evaluation of multiple attributes of the
aquatic biota (EPA 1996). 2) The ability of an aquatic
ecosystem to support and maintain a balanced, integrated,
adaptive community of organisms having a species
composition, diversity, and functional organization
comparable to the natural habitats of a region (Karr
1991).
The weight of biological matter. Standing crop is the
amount of biomass (e.g., fish or algae) in a body of water
at a given time. Often expressed as grams per square
meter.
The animal and plant life of a given region.
256
Glossary
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Biotic
Clean Water Act (CWA)
Coliform Bacteria
Colluvium
Community
Conductivity
Cretaceous
Criteria
Cubic Feet per Second
A term applied to the living components of an area.
The Federal Water Pollution Control Act (commonly
known as the Clean Water Act), as last reauthorized by
the Water Quality Act of 1987, establishes a process for
states to use to develop information on, and control the
quality of, the nation's water resources.
A group of bacteria predominantly inhabiting the
intestines of humans and animals but also found in soil.
Coliform bacteria are commonly used as indicators of the
possible presence of pathogenic organisms (also see Fecal
Coliform Bacteria).
Material transported to a site by gravity.
A group of interacting organisms living together in a
given place.
The ability of an aqueous solution to carry electric
current, expressed in micro (u) mhos/cm at 25 °C.
Conductivity is affected by dissolved solids and is used as
an indirect measure of total dissolved solids in a water
sample.
The final period of the Mesozoic era (after the Jurassic
and before the Tertiary period of the Cenozoic era),
thought to have covered the span of time between 135 and
65 million years ago.
In the context of water quality, numeric or descriptive
factors taken into account in setting standards for various
pollutants. These factors are used to determine limits on
allowable concentration levels, and to limit the number of
violations per year. The U.S. Environmental Protection
Agency develops criteria guidance; states establish
criteria.
A unit of measure for the rate of flow or discharge of
water. One cubic foot per second is the rate of flow of a
stream with a cross-section of one square foot flowing at
a mean velocity of one foot per second. At a steady rate,
once cubic foot per second is equal to 448.8 gallons per
minute and 10,984 acre-feet per day.
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Glossary
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Cultural Eutrophication
Culturally Induced Erosion
Debris Torrent
Decomposition
Depth Fines
Designated Uses
Discharge
Dissolved Oxygen (DO)
Disturbance
E. coli
The process of eutrophication that has been accelerated
by human-caused influences. Usually seen as an increase
in nutrient loading (also see Eutrophication).
Erosion caused by increased runoff or wind action due to
the work of humans in deforestation, cultivation of the
land, overgrazing, and disturbance of natural drainages;
the excess of erosion over the normal for an area (also see
Erosion).
The sudden down slope movement of soil, rock, and
vegetation on steep slopes, often caused by saturation
from heavy rains.
The breakdown of organic molecules (e.g., sugar) to
inorganic molecules (e.g., carbon dioxide and water)
through biological and nonbiological processes.
Percent by weight of particles of small size within a
vertical core of volume of a streambed or lake bottom
sediment. The upper size threshold for fine sediment for
fisheries purposes varies from 0.8 to 6.5 mm depending
on the observer and methodology used. The depth
sampled varies but is typically about one foot (30 cm).
Those water uses identified in state water quality
standards that must be achieved and maintained as
required under the Clean Water Act.
The amount of water flowing in the stream channel at the
time of measurement. Usually expressed as cubic feet per
second (cfs).
The oxygen dissolved in water. Adequate DO is vital to
fish and other aquatic life.
Any event or series of events that disrupts ecosystem,
community, or population structure and alters the physical
environment.
Short for Escherichia Coli, E. coli are a group of bacteria
that are a subspecies of coliform bacteria. Most E. coli
are essential to the healthy life of all warm-blooded
animals, including humans. Their presence is often
indicative of fecal contamination.
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Glossary
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Ecology
Ecological Indicator
Ecological Integrity
Ecosystem
Effluent
Endangered Species
Environment
Eocene
Eolian
Ephemeral Stream
Erosion
The scientific study of relationships between organisms
and their environment; also defined as the study of the
structure and function of nature.
A characteristic of an ecosystem that is related to, or
derived from, a measure of a biotic or abiotic variable that
can provide quantitative information on ecological
structure and function. An indicator can contribute to a
measure of integrity and sustainability. Ecological
indicators are often used within the multimetric index
framework.
The condition of an unimpaired ecosystem as measured
by combined chemical, physical (including habitat), and
biological attributes (EPA 1996).
The interacting system of a biological community and its
non-living (abiotic) environmental surroundings.
A discharge of untreated, partially treated, or treated
wastewater into a receiving water body.
Animals, birds, fish, plants, or other living organisms
threatened with imminent extinction. Requirements for
declaring a species as endangered are contained in the
Endangered Species Act.
The complete range of external conditions, physical and
biological, that affect a particular organism or
community.
An epoch of the early Tertiary period, after the Paleocene
and before the Oligocene.
Windblown, referring to the process of erosion, transport,
and deposition of material by the wind.
A stream or portion of a stream that flows only in direct
response to precipitation. It receives little or no water
from springs and no long continued supply from melting
snow or other sources. Its channel is at all times above
the water table. (American Geologic Institute 1962).
The wearing away of areas of the earth's surface by
water, wind, ice, and other forces.
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Glossary
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Eutrophic
Eutrophication
Exceedance
Existing Beneficial Use or Existing
Use
Exotic Species
Extrapolation
Fauna
Fecal Coliform Bacteria
Fecal Streptococci
Feedback Loop
Fixed-Location Monitoring
Flow
From Greek for "well nourished," this describes a highly
productive body of water in which nutrients do not limit
algal growth. It is typified by high algal densities and low
clarity.
1) Natural process of maturing (aging) in a body of
water. 2) The natural and human-influenced process
of enrichment with nutrients, especially nitrogen and
phosphorus, leading to an increased production of
organic matter.
2)
A violation (according to DEQ policy) of the pollutant
levels permitted by water quality criteria.
A beneficial use actually attained in waters on or after
November 28, 1975, whether or not the use is designated
for the waters in Idaho's Water Quality Standards and
Wastewater Treatment Requirements (IDAPA 58.01.02).
A species that is not native (indigenous) to a region.
Estimation of unknown values by extending or projecting
from known values.
Animal life, especially the animals characteristic of a
region, period, or special environment.
Bacteria found in the intestinal tracts of all warm-blooded
animals or mammals. Their presence in water is an
indicator of pollution and possible contamination by
pathogens (also see Coliform Bacteria).
A species of spherical bacteria including pathogenic
strains found in the intestines of warm-blooded animals.
In the context of watershed management planning, a
feedback loop is a process that provides for tracking
progress toward goals and revising actions according to
that progress.
Sampling or measuring environmental conditions
continuously or repeatedly at the same location.
See Discharge.
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Fluvial
Focal
Fully Supporting
Fully Supporting Cold Water
Fully Supporting but Threatened
Geographical Information Systems
(CIS)
Geometric Mean
Grab Sample
Gradient
Ground Water
In fisheries, this describes fish whose life history takes
place entirely in streams but migrate to smaller streams
for spawning.
Critical areas supporting a mosaic of high quality habitats
that sustain a diverse or unusually productive complement
of native species.
In compliance with water quality standards and within the
range of biological reference conditions for all designated
and exiting beneficial uses as determined through the
Water Body Assessment Guidance (Grafe et al. 2002).
Reliable data indicate functioning, sustainable cold water
biological assemblages (e.g., fish, macroinvertebrates, or
algae), none of which have been modified significantly
beyond the natural range of reference conditions (EPA
1997).
An intermediate assessment category describing water
bodies that fully support beneficial uses, but have a
declining trend in water quality conditions, which if not
addressed, will lead to a "not fully supporting" status.
A georeferenced database.
A back-transformed mean of the logarithmically
transformed numbers often used to describe highly
variable, right-skewed data (a few large values), such as
bacterial data.
A single sample collected at a particular time and place.
It may represent the composition of the water in that
water column.
The slope of the land, water, or streambed surface.
Water found beneath the soil surface saturating the layer
in which it is located. Most ground water originates as
rainfall, is free to move under the influence of gravity,
and usually emerges again as stream flow.
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Glossary
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Growth Rate
Habitat
Headwater
Hydrologic Basin
Hydrologic Cycle
Hydrologic Unit
Hydrologic Unit Code (HUC)
Hydrology
Impervious
Influent
A measure of how quickly something living will develop
and grow, such as the amount of new plant or animal
tissue produced per a given unit of time, or number of
individuals added to a population.
The living place of an organism or community.
The origin or beginning of a stream.
The area of land drained by a river system, a reach of a
river and its tributaries in that reach, a closed basin, or a
group of streams forming a drainage area (also see
Watershed).
The cycling of water from the atmosphere to the earth
(precipitation) and back to the atmosphere (evaporation
and plant transpiration). Atmospheric moisture, clouds,
rainfall, runoff, surface water, ground water, and water
infiltrated in soils are all part of the hydrologic cycle.
One of a nested series of numbered and named
watersheds arising from a national standardization of
watershed delineation. The initial 1974 effort (USGS
1987) described four levels (region, subregion,
accounting unit, cataloging unit) of watersheds
throughout the United States. The fourth level is uniquely
identified by an eight-digit code built of two-digit fields
for each level in the classification. Originally termed a
cataloging unit, fourth field hydrologic units have been
more commonly called subbasins. Fifth and sixth field
hydrologic units have since been delineated for much of
the country and are known as watershed and
sub watersheds, respectively.
The number assigned to a hydrologic unit. Often used to
refer to fourth field hydrologic units.
The science dealing with the properties, distribution, and
circulation of water.
Describes a surface, such as pavement, that water cannot
penetrate.
A tributary stream.
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Glossary
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Inorganic
Instantaneous
Intergravel Dissolved Oxygen
Intermittent Stream
Interstate Waters
Irrigation Return Flow
Key Watershed
Knickpoint
Land Application
Limiting Factor
Limnology
Materials not derived from biological sources.
A condition or measurement at a moment (instant) in
time.
The concentration of dissolved oxygen within spawning
gravel. Consideration for determining spawning gravel
includes species, water depth, velocity, and substrate.
1) A stream that flows only part of the year, such as
when the ground water table is high or when the
stream receives water from springs or from surface
sources such as melting snow in mountainous areas.
The stream ceases to flow above the streambed when
losses from evaporation or seepage exceed the
available stream flow. 2) A stream that has a period
of zero flow for at least one week during most years.
Waters that flow across or form part of state or
international boundaries, including boundaries with
Indian nations.
Surface (and subsurface) water that leaves a field
following the application of irrigation water and
eventually flows into streams.
A watershed that has been designated in Idaho Governor
Batt's State of Idaho Bull Trout Conservation Plan (1996)
as critical to the long-term persistence of regionally
important trout populations.
Any interruption or break of slope.
A process or activity involving application of wastewater,
surface water, or semi-liquid material to the land surface
for the purpose of treatment, pollutant removal, or ground
water recharge.
A chemical or physical condition that determines the
growth potential of an organism. This can result in a
complete inhibition of growth, but typically results in less
than maximum growth rates.
The scientific study of fresh water, especially the history,
geology, biology, physics, and chemistry of lakes.
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Glossary
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Load Allocation (LA)
Load(ing)
Loading Capacity (LC)
Loam
Loess
Lotic
Luxury Consumption
Macroinvertebrate
Macrophytes
A portion of a water body's load capacity for a given
pollutant that is given to a particular nonpoint source (by
class, type, or geographic area).
The quantity of a substance entering a receiving stream,
usually expressed in pounds or kilograms per day or tons
per year. Loading is the product of flow (discharge) and
concentration.
A determination of how much pollutant a water body can
receive over a given period without causing violations of
state water quality standards. Upon allocation to various
sources, and a margin of safety, it becomes a total
maximum daily load.
Refers to a soil with a texture resulting from a relative
balance of sand, silt, and clay. This balance imparts many
desirable characteristics for agricultural use.
A uniform wind-blown deposit of silty material. Silty
soils are among the most highly erodible.
An aquatic system with flowing water such as a brook,
stream, or river where the net flow of water is from the
headwaters to the mouth.
A phenomenon in which sufficient nutrients are available
in either the sediments or the water column of a water
body, such that aquatic plants take up and store an
abundance in excess of the plants' current needs.
An invertebrate animal (without a backbone) large
enough to be seen without magnification and retained by
a SOOum mesh (U.S. #30) screen.
Rooted and floating vascular aquatic plants, commonly
referred to as water weeds. These plants usually flower
and bear seeds. Some forms, such as duckweed and
coontail (Ceratophyllum sp.), are free-floating forms not
rooted in sediment.
264
Glossary
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Margin of Safety (MOS)
Mass Wasting
Mean
Median
Metric
Milligrams per Liter (mg/L)
Million Gallons per Day (MGD)
Miocene
Monitoring
Mouth
An implicit or explicit portion of a water body's loading
capacity set aside to allow the uncertainly about the
relationship between the pollutant loads and the quality of
the receiving water body. This is a required component
of a total maximum daily load (TMDL) and is often
incorporated into conservative assumptions used to
develop the TMDL (generally within the calculations
and/or models). The MOS is not allocated to any sources
of pollution.
A general term for the down slope movement of soil and
rock material under the direct influence of gravity.
Describes the central tendency of a set of numbers. The
arithmetic mean (calculated by adding all items in a list,
then dividing by the number of items) is the statistic most
familiar to most people.
The middle number in a sequence of numbers. If there
are an even number of numbers, the median is the average
of the two middle numbers. For example, 4 is the median
of 1, 2, 4, 14, 16; and 6 is the median of 1, 2, 5, 7, 9, 11.
1) A discrete measure of something, such as an
ecological indicator (e.g., number of distinct taxon).
2) The metric system of measurement.
A unit of measure for concentration in water, essentially
equivalent to parts per million (ppm).
A unit of measure for the rate of discharge of water, often
used to measure flow at wastewater treatment plants. One
MGD is equal to 1.547 cubic feet per second.
Of, relating to, or being an epoch of, the Tertiary between
the Pliocene and the Oligocene periods, or the
corresponding system of rocks.
A periodic or continuous measurement of the properties
or conditions of some medium of interest, such as
monitoring a water body.
The location where flowing water enters into a larger
water body.
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National Pollution Discharge
Elimination System (NPDES)
Natural Condition
Nitrogen
Nodal
Nonpoint Source
Not Assessed (NA)
Not Attainable
Not Fully Supporting
Not Fully Supporting Cold Water
Nuisance
A national program established by the Clean Water Act
for permitting point sources of pollution. Discharge of
pollution from point sources is not allowed without a
permit.
A condition indistinguishable from that without human-
caused disruptions.
An element essential to plant growth, and thus is
considered a nutrient.
Areas that are separated from focal and adjunct habitats,
but serve critical life history functions for individual
native fish.
A dispersed source of pollutants, generated from a
geographical area when pollutants are dissolved or
suspended in runoff and then delivered into waters of the
state. Nonpoint sources are without a discernable point or
origin. They include, but are not limited to, irrigated and
non-irrigated lands used for grazing, crop production, and
silviculture; rural roads; construction and mining sites;
log storage or rafting; and recreation sites.
A concept and an assessment category describing water
bodies that have been studied, but are missing critical
information needed to complete an assessment.
A concept and an assessment category describing water
bodies that demonstrate characteristics that make it
unlikely that a beneficial use can be attained (e.g., a
stream that is dry but designated for salmonid spawning).
Not in compliance with water quality standards or not
within the range of biological reference conditions for any
beneficial use as determined through the Water Body
Assessment Guidance (Grafe et al. 2002).
At least one biological assemblage has been significantly
modified beyond the natural range of its reference
condition (EPA 1997).
Anything which is injurious to the public health or an
obstruction to the free use, in the customary manner, of
any waters of the state.
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Nutrient
Nutrient Cycling
Oligotrophic
Organic Matter
Orthophosphate
Oxygen-Demanding Materials
Parameter
Partitioning
Pathogens
Perennial Stream
Periphyton
Any substance required by living things to grow. An
element or its chemical forms essential to life, such as
carbon, oxygen, nitrogen, and phosphorus. Commonly
refers to those elements in short supply, such as nitrogen
and phosphorus, which usually limit growth.
The flow of nutrients from one component of an
ecosystem to another, as when macrophytes die and
release nutrients that become available to algae (organic
to inorganic phase and return).
The Greek term for "poorly nourished." This describes a
body of water in which productivity is low and nutrients
are limiting to algal growth, as typified by low algal
density and high clarity.
Compounds manufactured by plants and animals that
contain principally carbon.
A form of soluble inorganic phosphorus most readily used
for algal growth.
Those materials, mainly organic matter, in a water body
that consume oxygen during decomposition.
A variable, measurable property whose value is a
determinant of the characteristics of a system, such as
temperature, dissolved oxygen, and fish populations are
parameters of a stream or lake.
The sharing of limited resources by different races or
species; use of different parts of the habitat, or the same
habitat at different times. Also the separation of a
chemical into two or more phases, such as partitioning of
phosphorus between the water column and sediment.
Disease-producing organisms (e.g., bacteria, viruses,
parasites).
A stream that flows year-around in most years.
Attached microflora (algae and diatoms) growing on the
bottom of a water body or on submerged substrates,
including larger plants.
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Pesticide
PH
Phased TMDL
Phosphorus
Physiochemical
Plankton
Point Source
Pollutant
Substances or mixtures of substances intended for
preventing, destroying, repelling, or mitigating any pest.
Also, any substance or mixture intended for use as a plant
regulator, defoliant, or desiccant.
The negative logio of the concentration of hydrogen ions,
a measure which in water ranges from very acid (pH=l)
to very alkaline (pH= 14). A pH of 7 is neutral. Surface
waters usually measure between pH 6 and 9.
A total maximum daily load (TMDL) that identifies
interim load allocations and details further monitoring to
gauge the success of management actions in achieving
load reduction goals and the effect of actual load
reductions on the water quality of a water body. Under a
phased TMDL, a refinement of load allocations,
wasteload allocations, and the margin of safety is planned
at the outset.
An element essential to plant growth, often in limited
supply, and thus considered a nutrient.
In the context of bioassessment, the term is commonly
used to mean the physical and chemical factors of the
water column that relate to aquatic biota. Examples in
bioassessment usage include saturation of dissolved
gases, temperature, pH, conductivity, dissolved or
suspended solids, forms of nitrogen, and phosphorus.
This term is used interchangeable with the terms
"physical/chemical" and "physicochemical."
Microscopic algae (phytoplankton) and animals
(zooplankton) that float freely in open water of lakes and
oceans.
A source of pollutants characterized by having a discrete
conveyance, such as a pipe, ditch, or other identifiable
"point" of discharge into a receiving water. Common
point sources of pollution are industrial and municipal
wastewater.
Generally, any substance introduced into the environment
that adversely affects the usefulness of a resource or the
health of humans, animals, or ecosystems.
268
Glossary
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Pollution
Population
Pretreatment
Primary Productivity
Protocol
Qualitative
Quality Assurance (QA)
Quality Control (QC)
Quantitative
Reach
A very broad concept that encompasses human-caused
changes in the environment which alter the functioning of
natural processes and produce undesirable environmental
and health effects. This includes human-induced
alteration of the physical, biological, chemical, and
radiological integrity of water and other media.
A group of interbreeding organisms occupying a
particular space; the number of humans or other living
creatures in a designated area.
The reduction in the amount of pollutants, elimination of
certain pollutants, or alteration of the nature of pollutant
properties in wastewater prior to, or in lieu of, discharging
or otherwise introducing such wastewater into a publicly
owned wastewater treatment plant.
The rate at which algae and macrophytes fix carbon
dioxide using light energy. Commonly measured as
milligrams of carbon per square meter per hour.
A series of formal steps for conducting a test or survey.
Descriptive of kind, type, or direction.
A program organized and designed to provide accurate
and precise results. Included are the selection of proper
technical methods, tests, or laboratory procedures; sample
collection and preservation; the selection of limits; data
evaluation; quality control; and personnel qualifications
and training. The goal of QA is to assure the data
provided are of the quality needed and claimed (Rand
1995, EPA 1996).
Routine application of specific actions required to provide
information for the quality assurance program. Included
are standardization, calibration, and replicate samples.
QC is implemented at the field or bench level (Rand
1995, EPA 1996).
Descriptive of size, magnitude, or degree.
A stream section with fairly homogenous physical
characteristics.
269
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Reconnaissance
Reference
Reference Condition
Reference Site
Representative Sample
Resident
Respiration
Riffle
Riparian
Riparian Habitat Conservation Area
(RHCA)
An exploratory or preliminary survey of an area.
A physical or chemical quantity whose value is known,
and thus is used to calibrate or standardize instruments.
1) A condition that fully supports applicable beneficial
uses with little affect from human activity and
represents the highest level of support attainable. 2)
A benchmark for populations of aquatic ecosystems
used to describe desired conditions in a biological
assessment and acceptable or unacceptable departures
from them. The reference condition can be
determined through examining regional reference
sites, historical conditions, quantitative models, and
expert judgment (Hughes 1995).
A specific locality on a water body that is minimally
impaired and is representative of reference conditions for
similar water bodies.
A portion of material or water that is as similar in content
and consistency as possible to that in the larger body of
material or water being sampled.
A term that describes fish that do not migrate.
A process by which organic matter is oxidized by
organisms, including plants, animals, and bacteria.
process converts organic matter to energy, carbon
dioxide, water, and lesser constituents.
The
A relatively shallow, gravelly area of a streambed with a
locally fast current, recognized by surface choppiness.
Also an area of higher streambed gradient and roughness.
Associated with aquatic (stream, river, lake) habitats.
Living or located on the bank of a water body.
A U.S. Forest Service description of land within the
following number of feet up-slope of each of the banks of
streams:
- 300 feet from perennial fish-bearing streams
- 150 feet from perennial non-fish-bearing streams
- 100 feet from intermittent streams, wetlands, and
ponds in priority watersheds.
270
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River
Runoff
Sediments
Settleable Solids
Species
Spring
Stagnation
Stenothermal
Stratification
Stream
Stream Order
A large, natural, or human-modified stream that flows in a
defined course or channel, or a series of diverging and
converging channels.
The portion of rainfall, melted snow, or irrigation water
that flows across the surface, through shallow
underground zones (interflow), and through ground water
to creates streams.
Deposits of fragmented materials from weathered rocks
and organic material that were suspended in, transported
by, and eventually deposited by water or air.
The volume of material that settles out of one liter of
water in one hour.
1) A reproductively isolated aggregate of interbreeding
organisms having common attributes and usually
designated by a common name. 2) An organism
belonging to such a category.
Ground water seeping out of the earth where the water
table intersects the ground surface.
The absence of mixing in a water body.
Unable to tolerate a wide temperature range.
A Department of Environmental Quality classification
method used to characterize comparable units (also called
classes or strata).
A natural water course containing flowing water, at least
part of the year. Together with dissolved and suspended
materials, a stream normally supports communities of
plants and animals within the channel and the riparian
vegetation zone.
Hierarchical ordering of streams based on the degree of
branching. A first-order stream is an unforked or
unbranched stream. Under Strahler's (1957) system,
higher order streams result from the joining of two
streams of the same order.
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Storm Water Runoff
Stressors
Subbasin
Subbasin Assessment (SBA)
Subwatershed
Surface Fines
Surface Runoff
Surface Water
Suspended Sediments
Rainfall that quickly runs off the land after a storm. In
developed watersheds the water flows off roofs and
pavement into storm drains that may feed quickly and
directly into the stream. The water often carries
pollutants picked up from these surfaces.
Physical, chemical, or biological entities that can induce
adverse effects on ecosystems or human health.
A large watershed of several hundred thousand acres.
This is the name commonly given to 4th field hydrologic
units (also see Hydrologic Unit).
A watershed-based problem assessment that is the first
step in developing a total maximum daily load in Idaho.
A smaller watershed area delineated within a larger
watershed, often for purposes of describing and managing
localized conditions. Also proposed for adoption as the
formal name for 6th field hydrologic units.
Sediments of small size deposited on the surface of a
streambed or lake bottom. The upper size threshold for
fine sediment for fisheries purposes varies from 0.8 to
605 mm depending on the observer and methodology
used. Results are typically expressed as a percentage of
observation points with fine sediment.
Precipitation, snow melt, or irrigation water in excess of
what can infiltrate the soil surface and be stored in small
surface depressions; a major transporter of nonpoint
source pollutants in rivers, streams, and lakes. Surface
runoff is also called overland flow.
All water naturally open to the atmosphere (rivers, lakes,
reservoirs, streams, impoundments, seas, estuaries, etc.)
and all springs, wells, or other collectors that are directly
influenced by surface water.
Fine material (usually sand size or smaller) that remains
suspended by turbulence in the water column until
deposited in areas of weaker current. These sediments
cause turbidity and, when deposited, reduce living space
within streambed gravels and can cover fish eggs or
alevins.
272
Glossary
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Taxon
Tertiary
Thalweg
Threatened Species
Total Maximum Daily Load (TMDL)
Total Dissolved Solids
Total Suspended Solids (TSS)
Any formal taxonomic unit or category of organisms
(e.g., species, genus, family, order). The plural of taxon
is taxa (Armantrout 1998).
An interval of geologic time lasting from 66.4 to 1.6
million years ago. It constitutes the first of two periods of
the Cenozoic Era, the second being the Quaternary. The
Tertiary has five subdivisions, which from oldest to
youngest are the Paleocene, Eocene, Oligocene, Miocene,
and Pliocene epochs.
The center of a stream's current, where most of the water
flows.
Species, determined by the U.S. Fish and Wildlife
Service, which are likely to become endangered within
the foreseeable future throughout all or a significant
portion of their range.
A TMDL is a water body's loading capacity after it has
been allocated among pollutant sources. It can be
expressed on a time basis other than daily if appropriate.
Sediment loads, for example, are often calculated on an
annual bases. TMDL = Loading Capacity = Load
Allocation + Wasteload Allocation + Margin of Safety.
In common usage, a TMDL also refers to the written
document that contains the statement of loads and
supporting analyses, often incorporating TMDLs for
several water bodies and/or pollutants within a given
watershed.
Dry weight of all material in solution in a water sample as
determined by evaporating and drying filtrate.
The dry weight of material retained on a filter after
filtration. Filter pore size and drying temperature can
vary. American Public Health Association Standard
Methods (Greenborg, Clescevi, and Eaton 1992) call for
using a filter of 2.0 micron or smaller; a 0.45 micron filter
is also often used. This method calls for drying at a
temperature of 103-105 °C.
273
Glossary
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Toxic Pollutants
Tributary
Trophic State
Total Dissolved Solids
Total Suspended Solids (TSS)
Toxic Pollutants
Tributary
Trophic State
Turbidity
Vadose Zone
Materials that cause death, disease, or birth defects in
organisms that ingest or absorb them. The quantities and
exposures necessary to cause these effects can vary
widely.
A stream feeding into a larger stream or lake.
The level of growth or productivity of a lake as measured
by phosphorus content, chlorophyll a concentrations,
amount (biomass) of aquatic vegetation, algal abundance,
and water clarity.
Dry weight of all material in solution in a water sample as
determined by evaporating and drying filtrate.
The dry weight of material retained on a filter after
filtration. Filter pore size and drying temperature can
vary. American Public Health Association Standard
Methods (Greenborg, Clescevi, and Eaton 1995) call for
using a filter of 2.0 micron or smaller; a 0.45 micron filter
is also often used. This method calls for drying at a
temperature of 103-105 °C.
Materials that cause death, disease, or birth defects in
organisms that ingest or absorb them. The quantities and
exposures necessary to cause these effects can vary
widely.
A stream feeding into a larger stream or lake.
The level of growth or productivity of a lake as measured
by phosphorus content, chlorophyll a concentrations,
amount (biomass) of aquatic vegetation, algal abundance,
and water clarity.
A measure of the extent to which light passing through
water is scattered by fine suspended materials. The effect
of turbidity depends on the size of the particles (the finer
the particles, the greater the effect per unit weight) and
the color of the particles.
The unsaturated region from the soil surface to the ground
water table.
274
Glossary
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Wasteload Allocation (WLA)
Water Body
Water Body Identification Number
(WBID)
Water Column
Water Pollution
Water Quality
Water Quality Criteria
Water Quality Limited
The portion of receiving water's loading capacity that is
allocated to one of its existing or future point sources of
pollution. Wasteload allocations specify how much
pollutant each point source may release to a water body.
A stream, river, lake, estuary, coastline, or other water
feature, or portion thereof.
A number that uniquely identifies a water body in Idaho
and ties in to the Idaho Water Quality Standards and GIS
information.
Water between the interface with the air at the surface and
the interface with the sediment layer at the bottom. The
idea derives from a vertical series of measurements
(oxygen, temperature, phosphorus) used to characterize
water.
Any alteration of the physical, thermal, chemical,
biological, or radioactive properties of any waters of the
state, or the discharge of any pollutant into the waters of
the state, which will or is likely to create a nuisance or to
render such waters harmful, detrimental, or injurious to
public health, safety, or welfare; to fish and wildlife; or to
domestic, commercial, industrial, recreational, aesthetic,
or other beneficial uses.
A term used to describe the biological, chemical, and
physical characteristics of water with respect to its
suitability for a beneficial use.
Levels of water quality expected to render a body of
water suitable for its designated uses. Criteria are based
on specific levels of pollutants that would make the water
harmful if used for drinking, swimming, farming, or
industrial processes.
A label that describes water bodies for which one or more
water quality criterion is not met or beneficial uses are not
fully supported. Water quality limited segments may or
may not be on a §303(d) list.
275
Glossary
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Water Quality Limited Segment
(WQLS)
Water Quality Management Plan
Water Quality Modeling
Water Quality Standards
Water Table
Watershed
Wetland
Young of the Year
Any segment placed on a state's §303(d) list for failure to
meet applicable water quality standards, and/or is not
expected to meet applicable water quality standards in the
period prior to the next list. These segments are also
referred to as "§303(d) listed."
A state or area-wide waste treatment management plan
developed and updated in accordance with the provisions
of the Clean Water Act.
The prediction of the response of some characteristics of
lake or stream water based on mathematical relations of
input variables such as climate, stream flow, and inflow
water quality.
State-adopted and U.S. Environmental Protection
Agency-approved ambient standards for water bodies.
The standards prescribe the use of the water body and
establish the water quality criteria that must be met to
protect designated uses.
The upper surface of ground water; below this point, the
soil is saturated with water.
1) All the land which contributes runoff to a common
point in a drainage network, or to a lake outlet.
Watersheds are infinitely nested, and any large
watershed is composed of smaller "subwatersheds."
2) The whole geographic region which contributes
water to a point of interest in a water body.
2)
An area that is at least some of the time saturated by
surface or ground water so as to support with vegetation
adapted to saturated soil conditions. Examples include
swamps, bogs, fens, and marshes.
Young fish born the year captured, evidence of spawning
activity.
276
Glossary
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Appendix A. Memorandum of Agreement
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
MEMORANDUM OF AGREEMENT AMONG
THE U.S. ENVIRONMENTAL PROTECTION AGENCY
THE IDAHO DEPARTMENT OF ENVIRONMENTAL QUALITY AND
THE NEZ PERC E TRIBE RELATING TO THE
DEVELOPMENT OF A TMDL FOR 1 HE SOUTH FORK OF THE CLEARWATER RIVER
HYDROLOGIC UNIT
WHEREAS, the U.S. Environmental Protection Agency (EPA), the State of Idaho Department of Environmental
Quality (DEQ), and the Nez Perce Tribe (collectively "the Parties") each desire to develop a government to
government agreement for the development of a total maximum daily load (TMDL) for the South Fork of the
Clearwater River hydrologic unit code (HUC # ; 7060305).
WHEREAS, the Parties wish to work together to restore water quality, build, support, and promote cooperation
among citizens, business, and governments at the community level for purposes of formulating effective
community support and a South Fork of the Cleai-water River HUC TMDL (hereinafter "the TMDL").
THEREFORE, the parties enter into this Memorandum of Agreement (the Agreement), and agree as follows:
1, The Parties will each provide staff to coordinate and to provide technical advice to draft the TMDL, in
addition to any other assistance each respective agency desires to provide.
2. The TMDL produced by the technical staff will be jointly presented to the Parties on or before December 31,
2001, or other deadline consistent with the court approved schedule, for approval under their respective
authorities. This agreement does not constitute approval by any Party of any TMDL.
3. For purposes of developing this TMDL, the Pa»1ies agree that the water quality standards as determined by 40
C.F.R. § 131.21, including those which EPA has approved or promulgated for the State of Idaho, are an
appropriate measure for calculating the TMDL.
4. Communications between the Parties while implementing this Agreement generally will be at the staff level. If
a dispute arises the issue will be presented to immediate supervisors and the staffs will present the matter to
progressively higher levels of management until consensus is reached. Alternative methods of dispute resolution
may be utilized, if consented to by all Parties.
5. The Parties recognize that each Party reserves 211 rights, powers, and remedies now or hereafter existing in law
or in equity, by statute, treaty, or otherwise. Nothing in this Agreement is or shall be construed to be a waiver of
the sovereignty of the Nez Perce Tribe, the State of Idaho, or the United States. By entering into this
Agreement, the Parties reserve, and do not waive, their claims to jurisdiction over all or parts of the South Fork
of the Clearwater River and sources of pollution affecting the South Fork of the Clearwater River. This
Agreement is intended solely for the purposes of facilitating inter-governmental cooperation between the Parties,
and creates no rights in third parties or the right to judicial review.
A-l Appendix A
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
6. This Agreement shall be effective upon the date of signature by all of the Parties. Any Party may voluntarily
withdraw from this Agreement by providing thirty (30) days written notice to the other Parties
NEZ PERCE TRIBE
BY;
BY:
Samuel N. Penney, Chairmarf
Arthur M. Taylor, Secnsfafy
Date
Date
NMENTAL QUALITY
IDAHO
BY:
U.S. EhTVIRONMENTAL PROTECTION AGENCY
BY:
Chuck Findley, Acting Regional Administrator
Dat? 7
Date
A-2
Appendix A
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Appendix B. Federal Bull Trout Criteria
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Federal Bull Trout Criteria
Federal Register
§ 131.33 Idaho.
(a) Temperature criteria for bull trout.
(1) Except for those streams or portions of streams located in Indian country, or as may
be modified by the Regional Administrator, EPA Region X, pursuant to paragraph (a)
(3) of this section, a temperature criterion of 10 °C, expressed as an average of daily
maximum temperatures over a seven-day period, applies to the waterbodies identified
in paragraph (a) (2) of this section during the months of June, July, August, and
September.
(2) The following waters are protected for bull trout spawning and rearing:
(xviii) SOUTH FORK CLEARWATER BASIN: American River, Baker Gulch,
Baldy Creek, Bear Creek, Beaver Creek, Big Canyon Creek, Big Elk Creek, Blanco
Creek, Boundary Creek, Box Sing Creek, Boyer Creek, Cartwright Creek, Cole
Creek, Crooked River, Dawson Creek, Deer Creek, Ditch Creek, East Fork American
River, East Fork Crooked River, Elk Creek, Fivemile Creek, Flint Creek, Fourmile
Creek, Fox Creek, French Gulch, Galena Creek, Gospel Creek, Hagen Creek,
Haysfork Creek, Johns Creek, Jungle Creek, Kirks Fork American River, Little Elk
Creek, Little Moose Creek, Little Siegel Creek, Look Creek, Mackey Creek, Meadow
Creek, Melton Creek, Middle Fork Red River, Mill Creek, Monroe Creek, Moores
Creek, Moores Lake Creek, Moose Butte Creek, Morgan Creek, Mule Creek,
Newsome Creek, Nuggett Creek, Otterson Creek, Pat Brennan Creek, Pilot Creek,
Quartz Creek, Queen Creek, Rabbit Creek, Rainbow Gulch, Red River, Relief Creek,
Ryan Creek, Sally Ann Creek, Sawmill Creek, Schooner Creek, Schwartz Creek,
Sharmon Creek, Siegel Creek, Silver Creek, Sixmile Creek, Sixtysix Creek, Snoose
Creek, Sourdough Creek, South Fork Red River, Square Mountain Creek, Swale
Creek, Swift Creek, Taylor Creek, Tenmile Creek, Trail Creek, Trapper Creek, Trout
Creek, Twentymile Creek, Twin Lakes Creek, Umatilla Creek, West Fork Big Elk
Creek, West Fork Crooked River, West Fork Gospel Creek, West Fork Newsome
Creek, West Fork Red River, West Fork Twentymile Creek, Whiskey Creek,
Whitaker Creek, Williams Creek.
B-l Appendix B
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Appendix C. Assessment Units for the South Fork
Clearwater River Subbasin TMDLs
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Appendix C. Assessment Units for the South Fork
Clearwater River Subbasin TMDLs
The South Fork Clearwater River Subbasin TMDLs are written for water bodies as defined in
the Idaho code (IDAPA 58.01.02.120.07). However, the state of Idaho and USEPA are
moving towards a water quality accounting system based on assessment units. One water
body may contain one or more assessment units. Table C-l shows the assessment units
accounted for by the TMDLs in this document and their relation to the 303(d) list.
The Assessment Unit code contains information that can be used to relate the assessment
units to water bodies, hydrologic units, and the state as follows: The ID prefix indicates the
state of Idaho; the numbers 17060305 is the hydrologic unit code for the South Fork
Clearwater River Subbasin; CL001 through CL082 are the water bodies in the South Fork
Clearwater River Subbasin (the numbers here are the water body numbers used in tables
throughout this document); and the last numbers identify the assessment unit within the water
body.
For the individual assessment unit identifiers, the rationale for the particular numbers and
letters are as follows: 02 indicates first and second order streams; 03 indicates third order
streams, 04 indicates fourth order streams, 05 indicates fifth order streams; "T" indicates a
tribal water within the boundaries of the NPT reservation; and "a" indicates a subdivision of
the water body for any characteristic thought to be important to water quality assessment.
The Lucas Lake assessment unit appears at the end of the table, with its unique code showing
that it is a lake in water body 52 (CL052L_00), the lower American River water body.
Table C-1. Assessment units correlated to the 1998 303(d) list and water
bodies with completed TMDLs in the SF CWR Subbasin.
Assess-
ment Unit
ID1 7060305
CL001_02
ID1 7060305
CL001_02T
ID1 7060305
CL001_05T
ID1 7060305
CL010_02
ID1 7060305
CL010_02T
ID1 7060305
CL010_03T
ID1 7060305
CL011_02
Water Body Description
South Fork Clearwater R. - Butcher Cr.
to mouth
South Fork Clearwater R. - Butcher Cr.
to mouth
South Fork Clearwater R. - Butcher Cr.
to mouth
Threemile Cr. - source to mouth
Threemile Cr. - source to mouth
Threemile Cr. - source to mouth
Butcher Cr. - source to mouth
303(d) Listed
Pollutants3'13
Halt, Sed, Temp
Halt, Sed, Temp
Halt, Sed, Temp
Bac, DO, Nut, NH3,
Qalt, Halt, Sed, Temp
Bac, DO, Nut, NH3,
Qalt, Halt, Sed, Temp
Bac, DO, Nut, NH3,
Qalt, Halt, Sed, Temp
Bac, DO, Qalt, Halt,
Sed, Temp
TMDLs
Completed13
Sed, Temp
Sed, Temp
Sed, Temp
Sed, Temp,
Bac, DO, Nut
Sed, Temp,
Bac, DO, Nut
Sed, Temp,
Bac, DO, Nut
Sed, Temp
C-l
Appendix C
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Assess-
ment Unit
ID1 7060305
CL011_02T
ID1 7060305
CL012_02
ID1 7060305
CL012_02a
ID1 7060305
CL012_05
ID1 7060305
CL012_05T
ID1 7060305
CL013_02
ID1 7060305
CL013_03
ID1 7060305
CL014_02
ID1 7060305
CL014_04
ID1 7060305
CL015_02
ID1 7060305
CL015_03
ID1 7060305
CL016_02
ID1 7060305
CL017_02
ID1 7060305
CL017_03
ID1 7060305
CL018_02
ID1 7060305
CL018_03
ID1 7060305
CL019_02
ID1 7060305
CL020_02
ID1 7060305
CL021_02
ID1 7060305
CL022_02
ID1 7060305
Water Body Description
Butcher Cr. - source to mouth
South Fork Clearwater R. - Johns Cr. to
Butcher Cr.
South Fork Clearwater R. - Johns Cr. to
Butcher Cr.
South Fork Clearwater R. - Johns Cr. to
Butcher Cr.
South Fork Clearwater R. - Johns Cr. to
Butcher Cr.
Mill Cr. - source to mouth
Mill Cr. - source to mouth
Johns Cr. - Gospel Cr. to mouth
Johns Cr. - Gospel Cr. to mouth
Gospel Cr. - source to mouth
Gospel Cr. - source to mouth
West Fork Gospel Cr. - source to mouth
Johns Cr. - Moores Cr. to Gospel Cr.
Johns Cr. - Moores Cr. to Gospel Cr.
Johns Cr. - source to Moores Cr.
Johns Cr. - source to Moores Cr.
Moores Cr. - source to mouth
Square Mountain Cr. - source to mouth
Hagen Cr. - source to mouth
South Fork Clearwater R. - Tenmile Cr.
to Johns Cr.
South Fork Clearwater R. - Tenmile Cr.
303(d) Listed
Pollutants3'13
Bac, DO, Qalt, Halt,
Sed, Temp
Halt, Sed, Temp
Halt, Sed, Temp
Halt, Sed, Temp
Halt, Sed, Temp
None
None
None
None
None
None
None
None
None
None
None
None
None
None
Halt, Sed, Temp
Halt, Sed, Temp
TMDLs
Completed13
Sed, Temp
Sed, Temp
Sed, Temp
Sed, Temp
Sed, Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Sed, Temp
Sed, Temp
C-2
Appendix C
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Assess-
ment Unit
CL022_02a
ID1 7060305
CL022_05
ID1 7060305
CL023_02
ID1 7060305
CL023_03
ID1 7060305
CL024_02
ID1 7060305
CL024_03
ID1 7060305
CL025_02
ID1 7060305
CL025_04
ID1 7060305
CL026_02
ID1 7060305
CL026_03
ID1 7060305
CL027_02
ID1 7060305
CL028_02
ID1 7060305
CL029_02
ID1 7060305
CL029_03
ID1 7060305
CL030_02
ID1 7060305
CL030_05
ID1 7060305
CL031_02
ID1 7060305
CL031_03
ID1 7060305
CL032_02
ID1 7060305
CL032_03
ID1 7060305
CL033_02
Water Body Description
to Johns Cr.
South Fork Clearwater R. - Tenmile Cr.
to Johns Cr.
Wing Cr. - source to mouth
Wing Cr. - source to mouth
Twentymile Cr. - source to mouth
Twentymile Cr. - source to mouth
Tenmile Cr. - Sixmile Cr. to mouth
Tenmile Cr. - Sixmile Cr. to mouth
Tenmile Cr. - Williams Cr. to Sixmile Cr.
Tenmile Cr. - Williams Cr. to Sixmile Cr.
Tenmile Cr. - source to Williams Cr.
Williams Cr. - source to mouth
Sixmile Cr. - source to mouth
Sixmile Cr. - source to mouth
South Fork Clearwater R. - Crooked R.
to Tenmile Cr.
South Fork Clearwater R. - Crooked R.
to Tenmile Cr.
Crooked R. - Reliefer, to mouth
Crooked R. - Reliefer, to mouth
Crooked R. - confluence of West and
East Fork Crooked R.s to Relief Cr.
Crooked R. - confluence of West and
East Fork Crooked R.s to Relief Cr.
West Fork Crooked R. - source to mouth
303(d) Listed
Pollutants3'13
Halt, Sed, Temp
None
None
None
None
None
None
None
None
None
None
None
None
Halt, Sed, Temp
Halt, Sed, Temp
None
None
None
None
None
TMDLs
Completed13
Sed, Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Sed, Temp
Sed, Temp
Temp
Temp
Temp
Temp
Temp
c-
Appendix C
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Assess-
ment Unit
ID1 7060305
CL034_02
ID1 7060305
CL035_02
ID1 7060305
CL036_02
ID1 7060305
CL036_05
ID1 7060305
CL037_02
ID1 7060305
CL037_04
ID1 7060305
CL038_02
ID1 7060305
CL038_02a
ID1 7060305
CL038_04
ID1 7060305
CL039_02
ID1 7060305
CL039_03
ID1 7060305
CL040_02
ID1 7060305
CL040_03
ID1 7060305
CL041_02
ID1 7060305
CL041_03
ID1 7060305
CL042_02
ID1 7060305
CL042_03
ID1 7060305
CL043_02
ID1 7060305
CL044_02
ID1 7060305
CL045_02
ID1 7060305
Water Body Description
East Fork Crooked R. - source to mouth
Relief Cr. - source to mouth
South Fork Clearwater R. - confluence of
American R. and Red R. to Crooked R.
South Fork Clearwater R. - confluence of
American R. and Red R. to Crooked R.
Red R.- Siegel Cr. to mouth
Red R.- Siegel Cr. to mouth
Red R. - South Fork Red R. to Siegel Cr.
Red R. - South Fork Red R. to Siegel Cr.
Red R. - South Fork Red R. to Siegel Cr.
Moose Butte Cr. - source to mouth
Moose Butte Cr. - source to mouth
South Fork Red R. - Trapper Cr. to
mouth
South Fork Red R. - Trapper Cr. to
mouth
South Fork Red R. - West Fork Red R. to
Trapper Cr.
South Fork Red R. - West Fork Red R. to
Trapper Cr.
West Fork Red R. - source to mouth
West Fork Red R. - source to mouth
South Fork Red R. - source to West Fork
Red R.
Trapper Cr. - source to mouth
Red R. - source to South Fork Red R.
Red R. - source to South Fork Red R.
303(d) Listed
Pollutants3'13
None
None
Halt, Sed, Temp
Halt, Sed, Temp
None
None
Sed
None
None
None
None
None
None
None
None
None
None
None
None
None
None
TMDLs
Completed13
Temp
Temp
Sed, Temp
Sed, Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
C-4
Appendix C
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Assess-
ment Unit
CL045_03
ID1 7060305
CL046_02
ID1 7060305
CL047_02
ID1 7060305
CL048_02
ID1 7060305
CL049_02
ID1 7060305
CL050_02
ID1 7060305
CL051_02
ID1 7060305
CL052_02
ID1 7060305
CL052_04
ID1 7060305
CL053_02
ID1 7060305
CL053_03
ID1 7060305
CL054_02
ID1 7060305
CL054_03
ID1 7060305
CL055_02
ID1 7060305
CL055_03
ID1 7060305
CL056_02
ID1 7060305
CL056_03
ID1 7060305
CL057_02
ID1 7060305
CL058_02
ID1 7060305
CL058_03
ID1 7060305
CL059_02
Water Body Description
Soda Cr. - source to mouth
Bridge Cr. - source to mouth
Otterson Cr. - source to mouth
Trail Cr. - source to mouth
Siegel Cr. - source to mouth
Red Horse Cr. - source to mouth
American R. - East Fork American R. to
mouth
American R. - East Fork American R. to
mouth
Kirks Fork - source to mouth
Kirks Fork - source to mouth
East Fork American R. - source to mouth
East Fork American R. - source to mouth
American R. - source to East Fork
American R.
American R. - source to East Fork
American R.
Elk Cr. - confluence of Big Elk and Little
Elk Cr.s to mouth
Elk Cr. - confluence of Big Elk and Little
Elk Cr.s to mouth
Little Elk Cr. - source to mouth
Big Elk Cr. - source to mouth
Big Elk Cr. - source to mouth
Buffalo Gulch - source to mouth
303(d) Listed
Pollutants3'13
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
None
Temp
Temp
Temp
Sed
TMDLs
Completed13
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
C-5
Appendix C
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Assess-
ment Unit
ID1 7060305
CL060_02
ID1 7060305
CL061_02
ID1 7060305
CL062_02
ID1 7060305
CL062_04
ID1 7060305
CL063_02
ID1 7060305
CL064_02
ID1 7060305
CL065_02
ID1 7060305
CL066_04
ID1 7060305
CL067_02
ID1 7060305
CL067_03
ID1 7060305
CL068_02
ID1 7060305
CL068_03
ID1 7060305
CL069_02
ID1 7060305
CL070_02
ID1 7060305
CL071_02
ID1 7060305
CL071_03
ID1 7060305
CL072_02
ID1 7060305
CL073_02
ID1 7060305
CL074_02
ID1 7060305
CL074_02a
ID1 7060305
Water Body Description
Whiskey Cr. - source to mouth
Maurice Cr. - source to mouth
Newsome Cr. - Beaver Cr. to mouth
Newsome Cr. - Beaver Cr. to mouth
Bear Cr. - source to mouth
Nugget Cr. - source to mouth
Beaver Cr. - source to mouth
Newsome Cr. - Mule Cr. to Beaver Cr.
Mule Cr. - source to mouth
Mule Cr. - source to mouth
Newsome Cr. - source to Mule Cr.
Newsome Cr. - source to Mule Cr.
Haysfork Cr. - source to mouth
Baldy Cr. - source to mouth
Pilot Cr. - source to mouth
Pilot Cr. - source to mouth
Sawmill Cr. - source to mouth
Sing Lee Cr. - source to mouth
West Fork Newsome Cr. - source to
mouth
West Fork Newsome Cr. - source to
mouth
Leggett Cr. - source to mouth
303(d) Listed
Pollutants3'13
None
None
Sed
Sed
None
Sed
Sed
None
None
None
None
None
None
None
None
None
None
Sed
None
None
None
TMDLs
Completed13
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
C-6
Appendix C
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Assess-
ment Unit
CL075_02
ID1 7060305
CL076_02
ID1 7060305
CL077_02
ID1 7060305
CL077_02a
ID1 7060305
CL077_03
ID1 7060305
CL078_02
ID1 7060305
CL079_02
ID1 7060305
CL080_02
ID1 7060305
CL080_03
ID1 7060305
CL081_02
ID1 7060305
CL081_03
ID1 7060305
CL081_03T
ID1 7060305
CL082_02
ID1 7060305
CL052L_00
Water Body Description
Fall Cr. - source to mouth
Silver Cr. - source to mouth
Silver Cr. - source to mouth
Silver Cr. - source to mouth
Peasley Cr. - source to mouth
Cougar Cr. - source to mouth
Meadow Cr. - source to mouth
Meadow Cr. - source to mouth
Sally Ann Cr. - source to mouth
Sally Ann Cr. - source to mouth
Sally Ann Cr. - source to mouth
Rabbit Cr. - source to mouth
Lucas Lake
303(d) Listed
Pollutants3'13
None
None
None
None
None
Sed
None
None
None
None
None
None
Sed
TMDLs
Completed13
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
Temp
None
aRefers to a list created in 1998 of water bodies in Idaho that did not fully support at least one beneficial use.
This list is required under section 303 subsection "d" of the Clean Water Act.
bBac = bacteria, DO = dissolved oxygen, Qalt = flow alteration, Halt = habitat alteration, NH3 = ammonia, Nut
= nutrients, Sed = sediment, Temp = temperature
C-7
Appendix C
-------
Appendix D. Fisheries Resources
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
Appendix D. Fisheries Resources D-1
Table of Contents D-i
List of Tables D-ii
List of Figures D-iv
Introduction D-3
Historic Influences on Fisheries Resources D-4
Salmon, Trout, and Char Species of the SF CWR D-6
Extirpated Species D-7
Non-Game Species Presence D-8
Other Aquatic Species of Concern D-10
Salmonid Resources D-11
Spring Chinook Salmon D-11
Fall Chinook Salmon D-15
Steelhead Trout D-17
Rain bow/Red band Trout D-21
Bull Trout D-22
Westslope Cutthroat Trout D-25
Fisheries Management D-27
Hatchery Facilities in the SF CWR Subbasin D-28
Nez Perce Tribe Fish Facilities D-28
Idaho Department of Fish and Game/Lower Snake River Compensation
Program Facilities in the Subbasin D-29
Conclusions D-29
References D-47
Attachments D-50
D- i Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Tables
Table D-1. Salmon, trout, and char species known to be present in the SF
CWRmain stem D-6
Table D-2. Salmon, trout, and char species known to be present in the SF
CWR tributaries D-7
Table D-3. Non-game fish species known to occur in the SF CWR subbasin.
D-8
Table D-4. Pacific lamprey life history timing in the SF CWR subbasin D-9
Table D-5. Mountain whitefish life history timing in the SF CWR subbasin... D-9
Table D-6. Spring Chinook salmon life history timing in the SF CWR subbasin.
D-12
Table D-7. Fall Chinook life history timing in the SF CWR subbasin D-16
Table D-8. Steelhead life history timing in the SF CWR subbasin D-18
Table D-9. Bull trout life history timing in the SF CWR subbasin D-22
Table D-10. Westslope cutthroat trout life history timing in the SF CWR
subbasin D-26
Table D-11. Results offish tag assessments of salmonid and habitat
conditions in the SF CWR subbasin D-30
Attachment D-1. Timing of life history stages of salmonids within the SF CWR
Subbasin D-50
Attachment D-2. Spring Chinook redd counts from the SF CWR subbasin
based on observations in several locations, 1974-1997 D-52
Attachment D-3. Adult spring Chinook returns to the Red River pond hatchery,
1969-1996 D-53
D-ii Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Attachment D-4. Number of fall Chinook salmon redds counted in the
Clearwater River subbasin, 1988-2000 D-53
Attachment D-5. Steelhead redd count data from the Crooked and Red Rivers.
D-54
Attachment D-6. Number of steelhead adults returning to the Crooked River
fish trap, 1991-1996 D-54
Attachment D-7. Summary of SF CWR main stem snorkel data collected
summer 2000 D-55
D-iii Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Figures
Figure D-1. Spring Chinook Salmon Density in the Main Stem SF CWR Based
on 2000 Snorkel Surveys D-12
Figure D-2. Spring Chinook Redd Counts from the SF CWR Subbasin Based
on Observations at Several Locations, 1974-2000 D-14
Figure D-3. Spring Chinook Adult Returns to Red River Pond and Crooked
River Hatcheries of the SF CWR, 1969 and 1987-1997 D-14
Figure D-4. Steelhead Redds per Mile from Surveys in the Crooked (1990-
1997) and Red Rivers (1990, 1993-1997) D-19
Figure D-5. Total Number of Steelhead Adults Returning to the Crooked River
Fish Trap, 1990-2000 D-20
Figure D-6. Steelhead Density in the Main Stem SF CWR Based on 2000
Snorkel Surveys D-20
Figure D-7. Bull Trout Density in the Main Stem SF CWR Based on 2000
Snorkel Surveys D-23
Figure D-8. Cutthroat Trout Density in the Main Stem SF CWR Based on 22
June through 8 August 2000 Snorkel Surveys D-26
Figure D-9. Fish TAG Assessment of the Presence of Spring Chinook in the
SF CWR Subbasin D-33
Figure D-10. Fish TAG Assessment of Potential Spring Chinook in the SF CW
Subbasin D-34
Figure D-11. Fish TAG Assessment of the Presence of Cutthroat Trout in the
SF CWR Subbasin D-35
Figure D-12. Fish TAG Assessment of Potential Cutthroat Trout in the SF CWR
Subbasin D-36
Figure D-13. Fish TAG Assessment of the Presence of Bull Trout in the SF
CWR Subbasin D-37
Figure D-14. Fish TAG Assessment of Potential Bull Trout in the SF CWR
Subbasin D-38
Figure D-15. Fish TAG Assessment of the Presence of Steelhead/Rainbow
Trout in the SF CWR Subbasin D-39
Figure D-16. Fish TAG Assessment of Potential Steelhead/Rainbow Trout in
the SF CWR Subbasin D-40
Figure D-17. Fish TAG Assessment of the Presence of Brook Trout in the SF
CWR Subbasin D-41
Figure D-18. Fish TAG Classification of Current Fish Habitat Conditions in the
SF CWR Subbasin D-42
Figure D-19. Fish TAG Identification of Sediment Problems in the SF CWR
Subbasin D-43
Figure D-20. Fish TAG Identification of Temperature Problems in the SF CWR
Subbasin D-44
Figure D-21. Fish TAG Restoration and Conservation Recommendations for
the SF CWR Subbasin D-45
D-iv Appendix D
-------
South Fork Clearwater River
Subbasin Assessment and TMDLs
Fisheries Resources
October 2002
Fisheries Technical Advisory Group
Report prepared by:
Lillian Herger, U.S. Environmental Protection Agency
Ann Storrar, Nez Perce Tribe
Tom Dechert, Department of Environmental Quality
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Fisheries Resources
Introduction
In order to acquire the most up-to-date and professional information about the fisheries
resources in the South Fork Clearwater River (SF CWR) Subbasin, a Fisheries Technical
Advisory Group (Fish TAG) was assembled to provide input to the subbasin assessment
(SBA) and Total Maximum Daily Load (TMDL) process. The following individuals made
up the SF CWR Fish TAG:
Lillian Herger U.S. Environmental Protection Agency Seattle
Bob Ries/Gary Kedish National Marine Fisheries Service Moscow
Daniel Stewart Idaho Department of Environmental Quality Grangeville
Ann Storrar Nez Perce Tribe Lapwai
Heidi McRoberts Nez Perce Tribe Lapwai
JoeDuPont Idaho Department of Lands Coeurd'Alene
Jody Brostrom Idaho Department of Fish and Game Lewiston
Craig Johnson U.S. Bureau of Land Management Cottonwood
Scott Russell U.S. Forest Service Grangeville
Nick Gerhardt U.S. Forest Service Grangeville
Fish TAG meetings were held on March 1 and March 29, 2001, where general information
about the fisheries resources in the subbasin was discussed. In addition, a report was
prepared by Lillian Herger and Ann Storrar documenting the known information regarding
aquatic species in the SF CWR Subbasin. That report forms the majority of this appendix.
A third meeting of the Fish TAG was held as a field trip through the SF CWR Subbasin on
July 9, 2001, where factors impacting fishery resources were discussed.
On June 14, 2002, the Fish TAG met one final time to draw conclusions about the conditions
of the salmonid populations and their aquatic habitat in the SF CWR Subbasin. At that
meeting, Gary Kedish replaced Bob Ries from National Marine Fisheries Service. For that
meeting, the Fish TAG members were provided with summaries of most of the data that had
been collected for the SBA to that date. The conclusions from that final meeting have been
inserted in this document as "Conclusions" sections for each of the salmonid species
discussed, and as Table D-l 1 and Figures D-9 through D-21 at the end of this document.
Data and information regarding the aquatic species in the SF CWR Subbasin have been
thoroughly reviewed and reported in the following documents. Much of the information in
these reports is from Quigley and Arbelbide (1997).
• Biological Assessment of South Fork Clearwater River (chinook), (USFS 1995)
• South Fork Clearwater River Subbasin Landscape Assessment (USFS 1998)
• South Fork Clearwater River Subbasin Bull Trout Problem Assessment (DEQ 1998)
• Biological Assessment of the South Fork Clearwater River Subbasin (steelhead/bull trout)
(USFS 1999)
D- 3 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
• Lower South Fork Clearwater River and Tributaries Biological Assessment (BLM 1999)
• Cottonwood Creek Total Maximum Daily Load (DEQ, NPT, and USEPA 2000)
• Clearwater River Subbasin Salmon and SteelheadProduction Plan (NPT and IDFG
1990)
Based on the information in these documents the following sections provide a brief overview
description of most aquatic species within the SF CWR Subbasin, including their
distribution, life history, status, and reasons for decline. Also, newly available data on
species abundance in the watershed are presented. Communications with local biologists
were used to generate life history phase timelines for each salmonid species (Attachment D-
1). Although the presence and distribution of most fish species in the subbasin are commonly
known, consistent long-term fisheries abundance data are not available.
Historic Influences on Fisheries Resources
Historically, land management in the subbasin has altered fish habitat. The most far-reaching
activities have been in-channel placer mining and hydraulic mining on the hill slopes. These
practices, which were common and widespread during the early 1900s, contributed to
extreme alterations in channel morphology, particularly with respect to altered sediment
loads. The signature of these practices is still evident today. Other land management
practices that have influenced aquatic habitat quality include timber harvest, road system
development, and agriculture. Direct human influence on habitat will be the main issue
addressed in the TMDL, yet, in discussing salmonid status, it is important to recognize other
human related practices that broadly influence the fish populations in the SF CWR Subbasin.
These include construction/operation of dams and hatchery facilities, introduction of non-
native species, and hatchery stocking.
Dams
Construction and operation of mainstem dams on the Columbia and Snake Rivers are
considered the major cause of the decline of anadromous fish (USFS 1998). Upstream
migrations offish are delayed and smolts may be killed by turbines or become injured and
disoriented, making them more susceptible to predation. Migration also may be delayed in
the impoundments behind dams.
Other dams, built in the early 1900s, are believed to have had a major effect on anadromous
species in the subbasin. On the main stem SF CWR, the earliest known dam was the Dewey
Dam, built in about 1895 approximately 0.1 miles above the mouth of Mill Creek (Gerhardt
1999). It was approximately 6-8 feet high. There is no known documentation offish
passage conditions at this dam and it washed out after only a few years. The Harpster Dam,
built on the SF CWR in 1911 (at river mile 22), completely excluded anadromous salmonids
from the upper watershed until 1935, when a fish ladder was installed. The ladder was
destroyed in 1949, once more eliminating anadromous fish passage until the dam was
removed in 1963 (USFS 1995).
D-4 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Dams were also located on the Clearwater River main stem. The Kooskia Flour Mill Dam,
located on the Clearwater River about 1 mile above the mouth of the SF CWR, was built
prior to 1910 and was in place until sometime in the 1930s (Gerhardt 1999). The dam is
estimated to have been about 6 feet high. Although fish passage is not documented, it has
been suggested that upstream migration of anadromous salmonids was probably not impaired
by this structure (Gerhardt 1999). A second dam was constructed on the main stem
Clearwater River near Lewiston in 1927 and was removed in 1974. A fish ladder was
installed on this dam in 1939, but the dam completely blocked adult chinook salmon passage
(NPT and IDFG 1990).
Following dam construction, numbers of anadromous fish were typically drastically reduced.
Hatchery stocking was used to supplement the fish stocks to help with their recovery
following the removal of these dams. Naturally spawning stocks did eventually return to the
system. The dams are believed to have contributed to a sharp decline of cutthroat and bull
trout populations from the 1930s through the 1960s by eliminating their prey base and
reducing connectivity of resident fish populations (USFS 1995).
Mitigation Efforts Using Hatcheries
To mitigate the effects of dam construction/operation on migration and the subsequent
decline of anadromous fish stocks, hatchery produced fish were planted in the subbasin.
Chinook brood stock come from the Rapid River Hatchery and the Dworshak National Fish
Hatchery, and steelhead come from the Dworshak National Fish Hatchery (North Fork B-run
stock). Parr and smolts are produced to mitigate fish harvest and to supplement natural
production. While supplementation is a viable method to insure the continuance of a stock,
hatchery production can cause problems that can further the decline of a stock in the long
term. These problems include: 1) genetic introgression and associated loss of fitness and loss
of local adaptations of the native stock, 2) reduced wild spawning escapement for collection
of brood stock, 3) ecological interactions between hatchery and wild fish, and 4) transmission
of disease. Since endemic chinook stocks were eliminated in the SF CWR Subbasin, genetic
risk to the local stock was not considered an issue. Currently, stocking of chinook and
steelhead occurs in areas with past out planting activity to minimize risk to locally adapted
and naturally reproducing populations. Hatchery supplementation has clouded the lines of
genetic distinction between stocks throughout the subbasin (USFS 1998).
Introduced Non-Native Species (Brook Trout)
Introduction of non-native eastern brook trout can present a significant negative influence on
native trout species. In the SF CWR Subbasin, the primary species of concern for brook trout
interaction are cutthroat and bull trout. Brook trout introduction often results in
encroachment/competition with native westslope cutthroat trout that is detrimental to the
native species. Introduced brook trout are a known risk to the persistence of cutthroat trout,
particularly where populations are isolated (Griffith 1988, Behnke 1992). Brook trout can
replace bull trout populations by hybridizing with bull trout, leading to a net reduction in bull
trout numbers via reduced breeding success. Also, brook trout have demonstrated a
competitive advantage over bull trout resulting in bull trout displacement. Brook trout have
D- 5 Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
been recognized as a significant threat to the persistence of bull trout populations (Reiman
and Mclntyre 1993).
In the SF CWR Subbasin, brook trout were stocked in the American River, Red River, and
Crooked River, and Meadow, Mill, Johns, Cottonwood, Cougar, Peasley, Rabbit, Silver,
Threemile, Sixmile, and Twentymile Creeks. Brook trout are present in the main stems of
Crooked River, American River, and Newsome Creek, and in smaller tributaries to the Red,
American, and Crooked Rivers. Brook trout are also strongly established in Silver Creek,
both upstream and downstream of a natural barrier 0.25 miles above the mouth. Figure D-17
shows the current distribution of brook trout in the SF CWR Subbasin.
Other Trout Introductions
Yellowstone cutthroat trout have been stocked in some high lakes and tributaries in the
subbasin in the past, and some loss of genetic integrity of native westslope cutthroat trout
may have resulted. Since the late 1970s, only westslope cutthroat have been stocked in
mountain lakes, and tributary stocking is no longer practiced. The extent of the loss of
genetic integrity, if any, is unknown. Hatchery rainbow trout have also been planted in the
subbasin and, likewise, the effects are unknown. Steelhead fry were planted in Silver Creek
in 1996 and 1999 by U.S. Geological Service (Rubin 2001).
Salmon, Trout, and Char Species of the SF CWR
Salmon, trout, and char species that inhabit the main stem of the SF CWR are listed in Table
D-l and their known presence in selected tributary streams of the subbasin are listed in Table
D-2. All are native to the subbasin except for brook trout.
Table D-1. Salmon, trout, and char species known to be present in the SF
CWR main stem.
Common Name
Bull trout
Spring Chinook salmon/Snake River fall
Chinook salmon
Steelhead/rainbow/redband trout*
Redband trout
Westslope cutthroat trout
Yellowstone cutthroat trout
Brook trout
Scientific Name
Salvelinus confluentus
Oncorhynchus tschawytscha
Oncorhynchus mykiss
Oncorhynchus mykiss gibbsi
Oncorhynchus clarki lewisi
Oncorhynchus clarki bouveri
Salvelinus fontinalis
*Redband trout or rainbow are the non-anadromous form of this species.
D- 6 Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table D-2. Salmon, trout, and char species known to be present in the SF
CWR tributaries.
Subwatershed
SF CWR main stem
Cottonwood Creek
Threemile Creek
Sally Ann Creek
Butcher Creek
Sears Creek
Green Creek
Lightening Creek
Mill Creek
(off forest)
Schwartz Creek
Meadow Creek
Mill Creek
Johns Creek
Cougar Creek
Peasley Creek
Silver Creek
Twenty Creek/
Wing Creek
Tenmile Creek
Newsome Creek/
Leggett Creek
Crooked River
American River
Red River
Bull
Trout
X
-
X
X
-
-
Lower
Lower
X
X
X
X
X
Spring
Chinook
Salmon*
X
X
X
X
X
X
X
-
-
-
-
X
X
X
X
X
Steel head/
Rainbow/
Redband
Trout
X
X
X
X
X
X
X
X
X
X
X
X
Lower
-
Lower
-
X
X
X
X
X
Wests lope
Cutthroat
Trout
X
X
X
X
X
X
Lower
-
-
X
X
X
X
X
X
Snake
River Fall
Chinook
Salmon**
X
Brook
Trout
X
X
X
X
X
X
X
X
X
X
* Spring Chinook salmon are considered a "stream" species type.
** Fall Chinook Salmon are considered "ocean type" and are found in a more restricted range
tied principally to mainstem rivers and larger tributary systems.
Extirpated Species
Coho salmon historically used the Clearwater River basin for spawning and rearing.
However, coho became extirpated from Idaho in the mid-1980s, with adult fish no longer
returning to Idaho waters. Reports verify that historic runs of coho utilized the Clearwater
D-7
Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
River and Lochsa River and there are anecdotal accounts of coho use of the SF CWR
(Johnson 2001). In recent years the Nez Perce Tribe has been involved in supplementation
releases of coho salmon. Returning adults were documented in the lower Clearwater River
basin (Potlatch River and Lapwai Creek) in 1999 and 2000. Coho have not been observed or
documented in the SF CWR Subbasin in recent times.
Non-Game Species Presence
The presence of many non-game fish species in the subbasin has been determined (Table D-
3), but the distribution of these species has not been summarized or is not well known.
Below are brief descriptions of each species that has been observed in the subbasin from
Simpson and Wallace (1978). The remainder of this document will focus on the salmon,
trout, and char species.
Table D-3. Non-game fish species known to occur in the SF CWR subbasin.
Common Name
Pacific lamprey
Mountain whitefish
Northern pikeminnow
Chiselmouth
Bridgelip sucker
Sculpin
Black bullhead
Redside shiner
Speckled dace
Longnose dace
Smallmouth bass
Scientific Name
Lampetra tridentatus
Prosopium williamsoni
Rychocheilus oregonensis
Acrocheilus alutaceus
Catostomus columbianus
Cottus sp.
Ictalurus melas
Richardsonius balteatus
Rhinichthys osculus
Rhinichthys cataractae
Micro pterus dolomieui
Origin
Native
Native
Native
Native
Native
Native
Introduced
Native
Native
Native
Introduced
The Pacific lamprey is an anadromous and parasitic lamprey widely distributed along the
Pacific coast. It is found in all areas accessible to salmon and steelhead (Simpson and
Wallace 1978). Waters used by Pacific lamprey in the SF CWR Subbasin include the main
stem SF CWR, Red River, American River, Crooked River, Mill Creek, Meadow Creek,
Johns Creek, and Tenmile Creek. The Pacific lamprey is listed as a state of Idaho
endangered species and was traditionally an important ceremonial and subsistence species for
native peoples. Recently, eleven conservation organizations in Oregon, California, and
Washington have petitioned the U.S. Fish and Wildlife Service, under the federal
Endangered Species Act, to list four species of lamprey as threatened or endangered
(www.onrc.org/info/lamprey/petition.pdf). Pacific lamprey adults enter freshwater between
July and September and migrate inland. They spawn in sandy gravel immediately upstream
from riffles in the spring of the following year and die soon after. The juvenile lampreys
(ammocoetes) remain in freshwater for up to the next six years in soft substrate as filter-
D-8
Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
feeders before emigrating to the ocean. The timing of life history stages of the Pacific
lamprey in the SF CWR is outlined in Table D-4 (Brostrom 2001).
Table D-4. Pacific lamprey life history timing in the SF CWR subbasin.
Life History Stage
Residence
Adult Migration
Spawning
Incubation and Emergence
Rearing
SF CWR Main
Stem
All Year
May 1 -Sept 30
Feb1-May31
Feb 1-June 30
All Year
Major Creeks and
Rivers
All Year
May 1 -Sept 30
Feb 1 -May 31
Feb 1-June 30
All Year
Other Perennial
Streams
All Year
May 1 -Sept 30
Feb 1 -May 31
Feb 1-June 30
All Year
Mountain whitefish prefer cold mountain streams with deep pools. They are well distributed
in most of the larger tributaries and in the main stem SF CWR. These fish mature in three
years and spawn in the fall when temperatures approach 6 °C (October through November).
Extensive downstream movement by pre- and post-spawning whitefish has been documented
in the Clearwater River basin (Pettit and Wallace 1975, Rockhold and Berg 1995). Eggs are
laid in riffles and hatch in March. The desired spawning substrate is gravel and small cobble
with an adequate current to keep silt removed from the eggs. Mountain whitefish eat
primarily aquatic and terrestrial insects. Waters inhabited by whitefish in the SF CWR
Subbasin include Red River, American River, Crooked River, Mill Creek, Meadow Creek,
Johns Creek, and Tenmile Creek. The timing of life history stages for mountain whitefish in
the SF CWR is outlined in Table D- 5 (Brostrom 2001).
Table D-5. Mountain whitefish life history timing in the SF CWR subbasin.
Life History Stage
Residence
Adult Migration
Spawning
Incubation and Emergence
Rearing
SF CWR Main
Stem
All Year
May 1-Nov30
Oct 1-Dec 15
Oct1-Feb28
All Year
Major Creeks and
Rivers
All Year
May 1-Nov30
Oct 1 -Dec 1 5
Oct 1 -Feb 28
All Year
Other Perennial
Streams
All Year
May 1-Nov30
Oct 1-Dec 15
Oct 1 -Feb 28
All Year
Northern pikeminnows spawn in shallow water on gravel substrate in late May to early June.
They feed on aquatic invertebrates and fish.
Chiselmouths spawn in spring and early summer when water temperatures reach 60 °F.
Spawning occurs in streams over gravel or small rubble. Adults feed exclusively on algae
although the young will feed on the surface and consume insects.
Bridgelip suckers prefer the colder water of small, fast flowing rivers with gravel to rocky
substrates. Spawning occurs in late May to Jane.
D-9
Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Sculpin species are thought to be indicators of high water quality (high dissolved oxygen,
cold temperatures, and low pollution levels). Generally sculpin spawn in May and early June
with adhesive eggs deposited in rock crevices and under rocks. A single male usually
protects the nest until the eggs hatch after 30 days at 50 °F. Sculpin eat insects and small fish
and are an important food source for trout.
Speckled dace live in a variety of habitats, but normally prefer shallow, cool, and quiet
waters. They spawn in spring and are omnivorous feeders.
Longnose dace primarily live in stream riffle areas and spawn over gravel in the spring when
water temperatures reach 53 °F. Their diet consists of immature aquatic insects. They are an
important forage fish for trout.
Redside shiners prefer lakes, ponds, or rivers with slow-moving currents. Spawning occurs
in June or July with adults moving into spawning areas when the water temperature reaches
at least 50 °F. The eggs are adhesive and attach to the substrate or submerged vegetation.
The fry feed on small planktonic organisms, but by the second year of life the young fish
switch to a diet of insects (mostly terrestrial).
Black bullheads (found in upper Cottonwood Creek) have a high tolerance for turbid water
with low oxygen and warm temperatures as high as 85 °F. Spring spawning occurs when
water temperatures reach 65 °F. They eat primarily snails, aquatic insects, crustaceans, and
plant material.
Other Aquatic Species of Concern
Amphibians, crayfish, and bivalves are additional aquatic species found in the SF CWR.
Amphibians
The following amphibians have been observed during surveys of tributaries throughout the
SF CWR Subbasin: spotted frogs (Ranapretiosa), tailed frogs (Ascaphus truei), Pacific
giant salamanders (Dicamptodon tenabrosus), long-toed salamanders (Ambystoma
macrodactylum), and western toads (Bufo boreas). Spotted frogs are fairly common
throughout the subbasin, but evidence of other frog species is limited. The current amphibian
distribution has probably been altered from the historical distribution due to land
management effects on aquatic habitat in the (Blair 2001). Long-toed salamanders are
relatively common in many areas including timber harvest sites, but trend information is not
available.
Spotted frogs are found in mountainous areas near cold streams and lakes. They breed from
March to June and release free egg clusters. Tailed frogs breed from May to September with
eggs attached to the downstream side of rocks in cold, swift-flowing mountain streams.
Tailed frog tadpoles have sucking mouth parts used to cling to rocks. They feed on algae and
invertebrates and transform in 1-3 years. Pacific giant salamanders breed in the spring in
D-10 Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
river headwaters and lay eggs on submerged timber. Larvae transform during their second or
third year.
Crayfish
Freshwater crayfish are present in the SF CWR watershed and have been documented by
surveys in the American River (IDFG 2000) and Butcher Creek (DEQ 1995).
Bivalves
Freshwater mussels are have been found in the main stem SF CWR as well as the American
River, Crooked River, and Red River by IDFG (IDFG 2000).
Salmonid Resources
Salmonid distribution, life history, stock description, population status, and factors
influencing current status are discussed below.
Spring Chinook Salmon
Spring chinook salmon distribution, life history, stock description, population status, and
factors influencing current status are discussed below.
Distribution
The current distribution of spring chinook salmon is probably similar to the historic
distribution in the subbasin. Areas with very high habitat potential are Red River, Crooked
River, American River, and the lower reaches of Newsome Creek. Areas with high habitat
potential are lower Johns Creek and Tenmile Creek. Spring chinook have been documented
in all of these drainages as well as Meadow Creek, Mill Creek, and Johns Creek (USFS
1998). Spring chinook use the main stem SF CWR for juvenile and adult migration and, to a
limited extent, for spawning and juvenile rearing (Figure D-l). The larger tributaries are
used for spawning and juvenile rearing.
D-ll Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Spring/summer Chinook density, 2000
0.60
0.50
0.40
0.30
0.20
0.10
0.00
Segment
Figure D-1. Spring Chinook Salmon Density in the Main Stem SF CWR Based
on 2000 Snorkel Surveys
Life History
The timing of life history stages of spring chinook within the SF CWR Subbasin are shown
in Table D-6 (Brostrom 2001).
Table D-6. Spring chinook salmon life history timing in the SF CWR subbasin.
Life History Stage
Adult Migration
Spawning
Incubation and
Emergence
Rearing
Juvenile Out Migration
SF CWR Main Stem
April 15-Sept 15
Aug 15-Sept 30
Aug 15-April 30
All Year
Sept 1-June 30
Major Creeks and
Rivers
April 15-Sept 15
Aug 15-Sept 30
Aug 15-April 30
All Year
Sept 1-June 30
Other Perennial
Streams
Aug 1 5-Sept 30
Aug 15-April 30
All Year
Sept 1-June 30
Stock Description
-Stock origin and hatchery supplementation
Historically, it is likely that spring chinook of the SF CWR were a separate stock from others
occurring in the Clearwater Subbasin. Currently, spring chinook have mixed hatchery and
natural origin. Hatchery plants (mostly Rapid River hatchery stock) were used to mitigate the
loss of spring chinook caused by dam construction/operation. Stocking for harvest
mitigation and supplementation for natural production is ongoing, with satellite hatcheries
with weirs and acclimation ponds at Red River and Crooked River (operated by the Idaho
D-12
Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Department of Fish and Game), and direct releases into Newsome Creek, Mill Creek and
Meadow Creek. In most years hundreds of thousands of sub-yearlings are released in the
subbasin (Stream Net 2000). Another satellite facility is being built on Newsome Creek as
part of the Nez Perce Tribal Hatchery. This facility will be online in 2002. All facilities
have monitoring and evaluation programs in place. Naturally produced chinook salmon
return to spawn, and it is likely they have developed local adaptations.
-Population status
The spring chinook population is maintained tenuously through the use of hatchery
supplementation. Although Snake River chinook salmon have been listed under the
Endangered Species Act, spring chinook of the Clearwater Basin are not included in the
listing. This portion of the population is exempt because the Lewiston Dam blocked all
indigenous chinook from the Clearwater Basin, and mixed broodstock were used for
reintroduction, thus, the genetic origin of the Clearwater stocks is questionable (see above)
and probably exclusively of hatchery origin. Nevertheless, SF CWR spring chinook are
considered an important meta-population within the Clearwater basin, and are listed as a
species of special concern by the state of Idaho and a sensitive species by the U.S. Forest
Service and Bureau of Land Management.
-Current abundance
Spring chinook numbers are severely reduced from their historic pre-dam abundance. There
is a decreasing trend in the abundance of SF CWR spring chinook and the population has a
high risk of extirpation. Data from trend redd surveys in Red River, American River,
Crooked River, and Newsome Creek indicate low spawning activity in the SF CWR with
fewer than 150 total redds in most years (Figure D-2, Attachment D-2). Hatchery return
counts are also low, with less than 400 adults in most years (Figure D-3, Attachment D-3).
Despite large numbers in 1997, the overall trend has declined (Stream Net 2000, Elms-
Cockrum In Press).
Factors Influencing Current Status
The following factors have been identified as effecting current status of spring chinook
salmon.
-Subbasin factors
• Fine sediment and channel alteration from in-channel placer mining in the areas of
high habitat potential including Crooked River, American River, and Newsome
Creek, and to a lesser degree Red River and the main stem SF CWR.
• High water temperatures.
• Lack of instream cover.
• Issues associated with hatchery supplementation.
-Downstream factors
• Construction and operation of the main stem dams on the Columbia and Snake River
system which result in: 1) delays in both upstream and downstream migration; 2)
death, injury, or disorientation of smolts passing through turbines; and 3) large-scale
D-13 Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
riverine habitat alteration (conversion of flowing system to series of lacustrine
habitats).
Harvest of adults in Columbia River system and the ocean (coded wire tag data show
less than 1% of Idaho chinook are harvested in the ocean) (IDFG 2001).
Predation by introduced species.
Downstream habitat degradation.
Chinook redd counts, 1974-2000.
tn tn
Year
Figure D-2. Spring Chinook Redd Counts from the SF CWR Subbasin Based
on Observations at Several Locations, 1974-2000
Chinook return to hatchery weirs, 1969 and 1987-1997
1200
1000
800
600
400
200
1969 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997
Year
Figure D-3. Spring Chinook Adult Returns to Red River Pond and Crooked
River Hatcheries of the SF CWR, 1969 and 1987-1997
D-14
Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Conclusions
Conclusions of the Fish TAG with respect to spring chinook salmon current distribution and
potential distribution in the SF CWR Subbasin are shown in Figures D-9 and D-10,
respectively. Table D-l 1 summarizes the conclusions for all salmonids of concern. Figure
D-18 shows the general conclusions about current fish habitat conditions throughout the
subbasin, while Figures D-l9 and D-20 identify watersheds exhibiting sediment and
temperature problems, respectively. Figure D-21 identifies areas recommended for
conservation and others prioritized for restoration of salmonid habitat in the SF CWR
Subbasin.
Fall Chinook Salmon
Snake River fall chinook salmon are listed as "threatened" under the Endangered Species
Act. The listed population includes all natural populations of fall-run chinook salmon in the
main stem Snake River and several tributaries, including the Clearwater basin. Critical
habitat for the listed environmentally significant unit (ESU) is designated to include river
reaches presently or historically accessible to Snake River fall chinook. In the Clearwater
system, this encompasses the main stem Clearwater River from its confluence with the Snake
River upstream to its confluence with Lolo Creek and the North Fork Clearwater River from
its confluence with the Clearwater River upstream to Dworshak Dam.
Anecdotal evidence suggests that fall chinook salmon were historically present in the lower
portion of the SF CWR (up to Harpster). Nez Perce tribal elders reported seeing adult fall
chinook in the lower section of the SF CWR. These observations suggest that many fish
were seen prior to the Lewiston Dam construction and few fish were seen in the years
immediately following. Currently, observations of fall chinook in the SF CWR have been
very rare.
Distribution
The majority of fall chinook redds have been down river from the North Fork Clearwater
River. Limited spawning occurs in the North Fork Clearwater River and SF CWR. Aerial
surveys have not found any redds in the Middle Fork Clearwater River; however, historical
reports have documented the occurrences of fall chinook salmon in the Middle Fork
Clearwater River and Selway River. During 1999 and 2000, fall chinook salmon were
documented in the Potlatch River, a tributary to Clearwater River tributary at river mile 15.1.
Nez Perce tribal elders reported seeing adult fall chinook in the lower section of the SF CWR
in the past.
Life History
The timing of life history stages of fall chinook within the SF CWR Subbasin are outlined in
Table D-7 (Brostrom 2001).
D-l 5 Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table D-7. Fall Chinook life history timing in the SF CWR subbasin.
Life History Stage
Adult Migration
Spawning
Incubation and Emergence
Juvenile Out Migration
SF CWR Main Stem
Sept 15-Nov30
Oct 1-Dec 15
Oct 1-May 15
May 1-Aug 31
Fall chinook salmon begin entering the Columbia River in August and continue through
October, with the peak occurring in early September. Returning adults generally have spent
three to four years in the ocean. Adults generally arrive in the Lower Clearwater River in
October and are present through mid-December; peak spawning activity occurs during
November. Spawning fall chinook salmon use shallow (e.g., 0.2 meter) to deep (e.g., 6.5
meters) waters with velocities ranging from 0.4 to 2.1 meters per second and relatively
homogenous substrate, ranging in size from 2.5 to 15.0 cm (Groves and Chandler 1999).
Fry emerge in April and May. After emergence, fry concentrate in shallow, slow water near
the riverbanks, which provide cover. These areas are often associated with narrow bands of
riparian vegetation along the margins of the rivers during high flow periods. The salmon rear
in the main stem rivers before emigrating to the ocean from June through August the
following year as sub-yearlings.
Abundance
Current fall chinook use of the SF CWR is very low. A total of nine redds have been
observed during annual aerial surveys of the lower SF CW, which began in 1992 (mouth to
Harpster). One carcass has also been found. Survey data for various portions of the
Clearwater basin are in Attachment D-4.
Hatchery Supplementation
In 1997, the Nez Perce Tribe started the operation of a fall chinook satellite facility along the
Clearwater River immediately down river from the mouth of Big Canyon Creek. The facility
operation includes the acclimation and release of yearling smolts (from Lyons Ferry
Hatchery, Washington). During 1997 and 1998, approximately 150,000 smolts were released
each year, and during 1999 approximately 300,000 smolts were released. Aerial surveys
conducted during 1999 and 2000 have documented high redd counts in the lower Clearwater
River, which can partially be attributed to operation of this satellite facility.
Factors Influencing Current Status in the Clearwater Basin
• Construction and operation of the main stem dams on the Columbia and Snake River
system which result in: 1) delays in both upstream and downstream migration; 2) death
injury, or disorientation of smolts passing through turbines; and 3) large-scale riverine
habitat alteration (conversion of flowing system to series of lacustrine habitats).
D-16 Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
• Fine sediment deposition in the substrate adversely impacts spawning and rearing
habitats, while land uses that encroach on floodplains, riparian areas, and channels
impacts rearing and spawning habitats.
• River-based recreation (e.g., power and float boating and steelhead fishing), a major
activity occurring in the Clearwater River during the fall chinook spawning period (down
river from the North Fork Clearwater River), can disturb spawning fish and redds.
• The lower Clearwater River altered flow regimes as a result of the operation of Dworshak
Dam. These altered flow regimes can result in elevated water temperatures in the main
stem rivers, particularly the SF CWR during the summer, which adversely impacts sub-
yearling rearing habitat.
Steelhead Trout
Distribution
Steelhead use the lower main stem and its tributaries as spawning, early rearing, and
overwintering habitat. The canyon reaches of tributaries such as Johns Creek, Newsome
Creek, Tenmile Creek, and Crooked River are considered the best spawning and rearing
habitat. Habitat quality varies in American River, Red River, Newsome Creek, Mill Creek,
and Meadow Creek due to human activities that have degraded sections of each stream.
Currently, Johns Creek and Tenmile Creeks are considered areas with strong steelhead
populations.
Life History
There are two runs (A-run and B-run) of steelhead that occur in the SF CWR Subbasin. The
following description of these runs is from the Clearwater Subbasin Summary (NW Power
Planning Council 2001). A-run steelhead occupy the lower Clearwater River, including the
Middle Fork Clearwater River, Lower SF CWR, and tributaries (Kiefer et al. 1992). B-run
steelhead occupy the Lochsa, Selway, upper SF CWRs, and were extirpated by Dworshak
Dam on the North Fork Clearwater (Kiefer et al. 1992). B-run steelhead have been
documented in only two subbasins in the Columbia River system, the Clearwater and Salmon
(NPT and IDFG 1990). A-run steelhead trout from the Clearwater basin have typically spent
one year in saltwater environments; B-run steelhead trout will have spent 1-3 years in
saltwater environments before returning to spawn, with over 90% having spent two years
there (Miller 2001). Due to differing lengths of ocean residence, differentiation of the two
forms of Clearwater steelhead trout can be based on size; B-run fish average 75-100 mm
larger than A-run fish (Columbia Basin Fish and Wildlife Authority 1991). B-run steelhead
enter the Columbia River later in the year than A-run and benefit from the extra ocean time
to rear, resulting in a two ocean (two years in the ocean prior to returning to spawn) A-run
fish being smaller than a two ocean B-run fish (Miller 2001). The timing of life history
stages of steelhead runs within the SF CWR are outlined in Table D-8 (Brostrom 2001).
D-17 Appendix D
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table D-8. Steelhead life history timing in the SF CWR subbasin.
Life History Stage
SF CWR Main
Stem
Major Creeks and
Rivers
Other Perennial
Streams
A-Run (Lower SF Main Stem and its Tributaries)
Residence
Migration to Tributaries
Spawning
Incubation and Emergence
Rearing
Juvenile Out Migration
Sept1-Feb1
Feb1-May 15
All Year
Feb 1-June 1
Feb 1 -May 15
Feb 1 -May 15
Feb 1-June 1
All Year
Feb 1-June 1
Feb 1-May 15
Feb 1-June 1
All Year
Feb 1-June 1
B-Run (Middle and Upper SF Main Stem and its Tributaries)
Residence
Migration to Tributaries
Spawning
Incubation and Emergence
Rearing
Juvenile Out Migration
Dec 1-July 15
Feb 1 -May 15
Feb 1 -May 31
Feb 1 -July 15
All Year
Feb 1 -June 30
Jan 1-May 31
Feb 1 -May 31
Feb 1 -July 15
All Year
Feb 1-June 30
Feb 1-May 31
Feb 1 -July 15
All Year
Feb 1-June 30
Stock Description
-Stock origin and hatchery supplementation
Historically, it is likely that the SF CWR steelhead were a separate stock (adapted to local
conditions) from others in the Clearwater system. The present population is of mixed
hatchery, natural, and wild origin.
As with chinook salmon, hatchery supplementation has been used in the subbasin to mitigate
the decline of steelhead populations caused by dam construction and operation. Following
the removal of the Harpster dam, steelhead broodstock from the Lewiston dam and the North
Fork Clearwater River were planted in the upper main stem SF CWR and tributaries of Red
River, American River, Crooked River, and Newsome Creek. Smolt stocking was
discontinued in the late 1980s in the upper river and tributaries with the exception of research
releases. Beginning again in 2000, unmarked smolts of Dworshak (North Fork) B-run
steelhead have been released in Red River, Crooked River, American River, Newsome
Creek, Meadow Creek, and Mill Creek. Returning hatchery origin adults in excess of
hatchery needs have also been planted in Newsome Creek, Mill Creek, Meadow Creek and
American River. Genetic sampling of steelhead from Johns Creek and Tenmile Creek
indicate that a portion of what might have been the endemic population remains; those creeks
will be managed without hatchery supplementation (J. Brostrom 2001).
D-18
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
-Population status
Both A-run and B-run steelhead of the Clearwater Basin are included in the Snake River
ESU of west coast steelhead (Busby et al. 1996). Declines of wild/natural adult steelhead in
the ESU (including the SF CWR) are well documented and have resulted in their listing as
"threatened" under the Endangered Species Act. They are considered a species of special
concern by the state of Idaho and considered a sensitive species by the U.S. Forest Service.
The SF CWR steelhead are an important metapopulation of the Clearwater basin.
-Current abundance
Steelhead populations in the SF CWR are considered depressed (Quigley and Arbelbide
1997). Their abundance has declined over the past seven decades through a combination of
downstream and local activities. Generally, abundance of steelhead correlates with numbers
of returning adults and numbers of hatchery steelhead planted in the SF CWR. Wild
steelhead populations have declined in the subbasin even though hatchery supplementation
has increased. Redd counts conducted in Crooked River and Red River have been relatively
stable, yet low (Figure D-4, Attachment D-5) (Stream Net 2000). Data from recent years
indicate a decline in returns to the Crooked River fish trap (Figure D-5, Attachment D-6)
(Stream Net 2000, IDFG 2001). Steelhead were relatively numerous in the SF CWR main
stem compared to other species observed during 2000 snorkel surveys (Attachment D-7), but
most of the steelhead observed were likely residual unmarked hatchery steelhead (Figure D-
6, Attachment D-7) (IDGF 2001).
Steelhead Redd Counts
1
30.0
25.0
20.0
15.0
10.0
5.0
0.0
I
90 91 92 93 94 95 96 97
Year
Figure D-4. Steelhead Redds per Mile from Surveys in the Crooked (1990-
1997) and Red Rivers (1990, 1993-1997)
D-19
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Steelhead Returns to Crooked R. trap
90 91 92 93 94 95 96 97 98 99 00
Figure D-5. Total Number of Steelhead Adults Returning to the Crooked River
Fish Trap, 1990-2000
Steelhead density, 2000
• Steelhead
• hatchery Steelhead
Figure D-6. Steelhead Density in the Main Stem SF CWR Based on 2000
Snorkel Surveys
D-20
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Factors Influencing Current Status
-Subbasin factors
• Fine sediment and channel alteration in the main stem SF CWR, Crooked River,
American River, Red River, and Newsome Creek. Exceptions are Johns Creek and
Tenmile Creek, which have not had significant mining. The extensive road network
also contributes to the increased sediment yield. An altered sediment regime has been
noted in American River, Miller Creek, Newsome Creek, and Meadow Creek.
• High water temperature.
-Downstream factors
• Construction and operation of the main stem dams on the Columbia and Snake River
system which result in: 1) delays in both upstream and downstream migration; 2)
death, injury, or disorientation of smolts passing through turbines; and 3) large-scale
riverine habitat alteration (conversion of flowing system to series of lacustrine
habitats).
• Barriers to migration.
• Predation.
• Hatchery supplementation issues.
• Commercial fishing in the Columbia River, along the coast, and in the ocean.
Conclusions
Conclusions of the Fish TAG with respect to the current distribution and potential
distribution of steelhead/rainbow trout in the SF CWR Subbasin are shown in Figures D-15
and D-16, respectively. Table D-l 1 summarizes the conclusions for all salmonids of
concern. Figure D-l8 shows the general conclusions about the current fish habitat condition
throughout the subbasin, while Figures D-l9 and D-20 identify watersheds exhibiting
sediment and temperature problems, respectively. Figure D-21 identifies areas recommended
for conservation and others prioritized for restoration of salmonid habitat in the SF CWR
Subbasin.
Rainbow/Redband Trout
Rainbow or redband trout are the non-anadromous form of steelhead. Non-anadromous
rainbow trout in the Upper Columbia River basin have been further divided into two groups.
One group evolved in sympatry with steelhead and the other group is allopatric with
steelhead, or evolved outside the historical range of steelhead. Sympatric rainbow/redband
trout (termed "residuals") are considered the non-anadromous form that is historically
derived or associated with steelhead. Both anadromous and non-anadromous forms exist in
sympatry in most populations. Morphologically, juveniles of both forms are
indistinguishable and cannot be differentiated, especially while snorkeling.
Rainbow/redband trout use the main stem SF CWR for migration and rearing (both juveniles
and adults). Spawning and rearing generally occur in the tributary streams. In the main
stem, rainbow/redband density ranged from 0 to 0.03 fish per 100m2 based on snorkel studies
conducted in summer 2000 (Attachment D-7). Rainbow/edband and steelhead juveniles
D-21 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
cannot be differentiated while snorkeling. The distribution and status of rainbow/redband
populations in the SF CWR drainage is not known.
Bull Trout
Distribution
Historically, migratory bull trout are believed to have been distributed throughout the
subbasin, particularly in tributary main stems. Currently, bull trout are still broadly
distributed in the SF CWR. Most of the migratory fish are found in the lower portion of the
subbasin, and resident fish are mostly at higher elevations. Although the residents are
broadly distributed, their numbers are low.
Current important bull trout areas include Tenmile Creek and upper Johns Creek, which hold
the highest populations and are considered population strongholds. Crooked River also has
high habitat condition. Newsome Creek and Red River were historic strongholds that
currently have good bull trout density in a few of their tributaries. The American River was
also a historic stronghold but current bull trout density is low. There is abundant good
habitat available at high elevations, but habitat quality is greatly reduced in the middle and
low elevation areas, particularly due to increased water temperature. These are the areas that
are most important to the larger migratory portion of the population.
Life History
The SF CWR Subbasin has historically supported two types of bull trout life history
strategies. The large migratory component of the population uses the main stem and the
larger tributaries for sub adult/adult rearing. These fish migrate to smaller tributaries to
spawn. Bull trout with a resident life history strategy are found in the upper reaches of the
subbasin. The timing of the life history stages of bull trout within the SF CWR Subbasin are
outlined in Table D-9 (Brostrom 2001).
Table D-9. Bull trout life history timing in the SF CWR subbasin.
Life History Stage
Residence
Adult Migration (pre spawn)
Adult Migration (post spawn)
Spawning
Incubation and Emergence
Rearing
SF CWR Main
Stem
All Year
April 1-July 15
Sept1-Oct31
All Year
Major Creeks and
Rivers
All Year
April 1-July 15
Sept 1-Oct31
Aug 15-Nov30
Aug 15-Mar31
All Year
Other Perennial
Streams
All Year
April 1-July 15
Sept 1-Oct31
Aug 15-Nov30
Aug 15-Mar31
All Year
D-22
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Stock Description
-Stock origin
The bull trout population is native and wild. There is no hatchery supplementation that
would affect the bull trout stock. The extent of hybridization with introduced brook trout has
not been documented (see below).
-Population status
Bull trout in the SF CWR Subbasin are listed as "threatened" under the Endangered Species
Act and the SF CWR is identified as a key watershed for the Idaho Bull Trout Conservation
Plan (Batt 1996). Overall, the bull trout population in the SF CWR is considered weak and
depressed.
-Historic/current abundance
There is no historic data on bull trout densities, but anecdotal accounts support that large
numbers of migratory bull trout used the upper subbasin. Compared to these historic
accounts the current abundance is dramatically reduced and very low. While bull trout
abundance in the main stem SF CWR is generally low, there is greater abundance in the
upper reaches (Figure D-7, Attachment D-7) (IDGF 2001).
Bull Trout Density, 2000
234
Mainstem segment #
Figure D-7. Bull Trout Density in the Main Stem SF CWR Based on 2000
Snorkel Surveys
Factors Influencing Current Status
Effects to the bull trout population of the watershed from downstream activities are minor
compared to effects from activities within the subbasin because bull trout do not range far
D-23
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
downstream from the SF CWR. Subbasin factors that have contributed to the decline of bull
trout in the SF CWR Subbasin include the following:
• Habitat degradation. Although the subbasin has an inherently high capacity to support
migratory bull trout, human uses (mining, roads, grazing, and timber harvest) have
reduced habitat quality in the lower and middle reaches, which are most important to the
migratory portion of the population. Major habitat concerns are high summer water
temperatures and fine sediment intrusion that result in loss of rearing space and loss of
pool habitat. Channel simplification results in low habitat complexity and reduced woody
debris retention. Currently, Johns Creek and Tenmile Creek are exceptions within the
watershed and have relatively high habitat quality.
• Angling. Roads adjacent to the river make the main stem accessible to anglers and
poachers. Bull trout have been closed to sport harvest since 1994, but are still caught
incidentally during seasons open for other species.
• Interactions with introduced brook trout. Brook trout have been recognized as a
significant threat to the persistence of bull trout populations (Reiman and Mclntyre
1993). In the SF CWR Subbasin, brook trout are present in almost every subwatershed
except Johns Creek and Twentymile Creek. Brook trout have the ability to hybridize
with bull trout, and hybridization leads to net reductions in bull trout numbers via
reduced breeding success. In addition, brook trout have a competitive advantage over
bull trout, which results in bull trout displacement.
• Population isolation. The loss of the migratory component of the population due to
harvest (angling/poaching) and habitat degradation in the middle and low elevation
reaches of the river results in long distances between resident population strongholds.
This loss of connection by the migratory component results in isolation of resident
populations, which increases the extinction risk to the overall population.
Conclusions
Conclusions of the Fish TAG with respect to bull trout current distribution and potential
distribution in the SF CWR Subbasin are shown in Figures D-13 and D-14, respectively.
Table D-l 1 summarizes the conclusions for all salmonids of concern. Figure D-18 shows the
general conclusions about current fish habitat conditions throughout the subbasin, while
Figures D-l9 and D-20 identify watersheds exhibiting sediment and temperature problems,
respectively. Figure D-21 identifies areas recommended for conservation and others
prioritized for restoration of salmonid habitat in the SF CWR Subbasin.
D-24 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Westslope Cutthroat Trout
Distribution
Westslope cutthroat trout historically ranged throughout western Montana, central and
northern Idaho, the southern Canadian provinces, and a small portion of Wyoming. They
were also found in isolated populations in Washington (Lake Chelan) and Oregon (John Day
basin) (Behnke 1992). The current range and abundance of this interior cutthroat stock have
been drastically reduced over the past 100 years, and it is estimated that only 2.5% of the
historic range is still occupied by genetically pure westslope cutthroat trout (Liknes and
Graham 1988).
Historically, westslope cutthroat were the dominant salmonid in streams of central Idaho
(Likens and Graham 1988). In the SF CWR they are the most widely distributed salmonid
species, using a range of habitats including both main stem and smaller high gradient
reaches. The current distribution in the subbasin is thought to be similar to the historic
distribution, but current abundance is reduced from historic levels. Although there are
numerous sub-populations, the migratory portion of the population that used to inhabit the
main stem and larger tributaries (Newsome Creek and Crooked River) has probably been
extirpated. Resident populations in many of the upper reaches persist with varying
population strengths. Currently, the upper portions of Johns Creek, Tenmile Creek, Crooked
River, Meadow Creek and Mill Creek are considered population strongholds.
Life History
The westslope cutthroat trout in the SF CWR Subbasin exhibit two general life history
patterns. The migratory component of the population uses the main stem as adults year-
round, and only moves to smaller tributaries for spawning (Behnke 1992). Conversely, the
resident component spends its entire life in tributaries. Use of different areas of the
watershed by life history phase is not distinct for westslope cutthroat trout as the majority of
these fish are residents and use the drainages where they occur for all life history phases. In
contrast, the migratory component of the population use the main stem of the SF CWR and
larger tributaries to rear and grow, and then migrates to smaller tributaries for spawning. The
timing of the life history stages of westslope cutthroat trout within the SF CWR Subbasin are
outlined in Table D-10 (Brostrom 2001).
Stock Description
-Stock origin
Westslope cutthroat trout of the SF CWR are considered to be mostly a native
(nonintroduced) and wild population. Some hybridization has occurred due to the planting of
hatchery Yellowstone cutthroat trout in Johns Creek, Tenmile Creek, Mill Creek, Meadow
Creek, and Crooked River. This hatchery stocking may have resulted in some genetic
introgression (repeated back-crossing of hybrid descendants with a parental species), which
can lead to decreased population of native cutthroat trout populations in these drainages.
D-25 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table D-10. Westslope cutthroat trout life history timing in the SF CWR
subbasin.
Life History Stage
Residence
Adult Migration
Spawning
Incubation and
Emergence
Rearing
SF CWR Main
Stem
All Year
March 1-June 30
All Year
Major Creeks and
Rivers
All Year
Marl-July 15
Mar15-June30
Mar 15-Aug 15
All Year
Other Perennial
Streams
All Year
Marl-July 15
Mar15-June 30
Mar 15-Aug 15
All Year
-Population status
Currently, westslope cutthroat trout are not listed under the federal Endangered Species Act.
This species is considered a sensitive species by the U.S. Forest Service (Region 1) and is a
species of special concern in the state of Idaho.
-Current abundance
Year 2000 sampling verified that westslope cutthroat trout are distributed throughout the
main stem CWR. Larger, migratory fish appear to be rare based on these data (Figure D-8,
Attachment D-7) (IDGF 2000).
Cutthroat trout density, 2000
o
o
Segments
Figure D-8. Cutthroat Trout Density in the Main Stem SF CWR Based on 22
June through 8 August 2000 Snorkel Surveys
D-26
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Factors Influencing Current Status
Because westslope cutthroat trout are not anadromous, downstream activities only indirectly
influence their population (e.g., reduced forage source and reduced nutrients to stream due to
a reduced number of migration to the subbasin). Subbasin factors that have contributed to
the decline of westslope cutthroat trout include the following:
• Habitat degradation. Loss of stream riparian area integrity results in high summer water
temperatures. Fine sediment intrusion results in loss of rearing space and loss of pool
habitat. Channel simplification results in low habitat complexity and reduced woody
debris retention. Habitat degradation is most profound in Red River, American River,
Newsome Creek, and Crooked Creek.
• Angling. Angling has reduced the large migratory component of the population due to
easy access to the middle and lower portions of the watershed (river adjacent road) and
the vulnerability of these fish to angling efforts.
• Competition with introduced species. Introduction of non-native brook trout has led to
the displacement of westslope cutthroat trout. Brook trout strongholds in the watershed
are the Red River and Silver Creek drainages. They are also present in Crooked River,
Newsome Creek, and American River.
• Hybridization. This is a risk where Yellowstone cutthroat trout have been stocked (Johns
Creek, Tenmile Creek, and Crooked River).
• Population isolation. Loss of the migratory component of the population due to harvest
(angling/poaching) and habitat degradation in the middle and low elevation reaches
results in long distances between resident population strongholds. This loss of
connection by the migratory component results in isolation of resident populations, which
increases the risk to the overall population.
Conclusions
Conclusions of the Fish TAG with respect to westslope cutthroat trout current distribution
and potential distribution in the SF CWR Subbasin are shown in Figures D-l 1 and D-12,
respectively. Table D-l 1 summarizes the conclusions for all salmonids of concern. Figure
D-l8 shows the general conclusions about the current fish habitat condition throughout the
subbasin, while Figures D-l9 and D-20 identify watersheds exhibiting sediment and
temperature problems, respectively. Figure D-21 identifies areas recommended for
conservation and others prioritized for restoration of salmonid habitat in the SF CWR
Subbasin.
Fisheries Management
The SF CWR main stem and most tributaries are currently managed under a six-trout catch
limit throughout the Memorial Day to November 30 general fishing season. Streams known
D-27 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
to have wild steelhead populations (Crooked River, Johns Creek, and Tenmile Creek) have a
two-trout limit. In addition, the SF CWR main stem is managed for exploitation of hatchery
steelhead and surplus hatchery chinook when the numbers of returning adults are high
enough to allow a season.
The Idaho Department of Fish and Game has established programs and management
objectives that pertain to the SF CWR (TDFG 2001). Program directions include increasing
emphasis on habitat protection, continuing emphasis on protection and enhancement of wild
trout, and continuing emphasis on protection and enhancement of salmon and steelhead.
Objectives that pertain to the SF CWR Clearwater include:
• Maintain and improve fish habitat and water quality.
• Maintain a diversity of fishing opportunity to meet angler demand.
• Increase fishing access.
• Maintain existing populations of chinook salmon and steelhead trout.
• Maintain or restore wild native populations offish in suitable waters.
• Fully utilize fish habitat capabilities by increasing populations of suitable fish species
to carrying capacity of the habitat.
Hatchery Facilities in the SF CWR Subbasin
Nez Perce Tribe Fish Facilities
The following facilities are managed by the Nez Perce Tribe in the SF CWR subbasin with
the goal of increasing production of spring and fall chinook.
Newsome Creek
A smolt trap at the mouth of Newsome Creek is operated by the Nez Perce Tribal Hatchery
Monitoring and Evaluation (NPTH M&E) Project. The trap is a rotary screw trap and its
function is to monitor the out migration of juvenile spring chinook. The trap is operated
from late spring to early fall, dependent on stream flows and fish movements. Upstream
approximately 300 yards, NPTH M&E also operate a temporary fish weir and trap. It is a
picket style weir and its function is to monitor adult spring chinook upstream passage.
Beginning in 2002, this trap will also collect spring chinook broodstock to be held and
spawned at the NPTH Newsome Creek Acclimation Facility. Information collected from the
smolt trap and weir will be used to improve the management and operation of the acclimation
facility now under construction near the Newsome town site. This facility will be operational
May through mid-October and will contain two flow- through ponds: an adult holding
raceway and a juvenile acclimation pond with a total water requirement of 1.24 cubic feet per
second (cfs). The acclimation pond will rear 75,000 parr and the adult holding pond will
contain up to 84 fish. The overall goal of these projects is to establish a self-perpetuating
population of spring chinook in Newsome Creek.
D-28 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Lukes Gulch
The Lukes Gulch facility will be operational in early 2002. Portable, circular tanks will be
installed for acclimation of 200,000 sub-yearling fall chinook smolts, February through mid-
June, with a total surface water requirement of 2.5 cfs. Up to 1.0 cfs of ground water will be
pumped from one well to raise the water temperature to 54 °F in the rearing pond. Pumping
will cease once the river water temperature reaches 54 °F.
The number offish held at these satellite facilities is below the threshold limit for state and
federal regulations that require water quality monitoring. However, the tribe will monitor
influent and effluent bimonthly during the operating period for total suspended solids, settled
solids, and dissolved oxygen. Additional sampling for nutrients may be implemented based
on water quality concerns.
Idaho Department of Fish and Game/Lower Snake River Compensation Program
Facilities in the Subbasin
Extensive descriptions of hatchery facilities in the Clearwater Basin are given in the
Clearwater Subbasin Summary (NW Power Planning Council 2001). This information can
be reviewed at the following Web site: http://www.cbfwf.org.
Conclusions
Conclusions by the Fish TAG are displayed in Table D-l 1 and a series of maps (Figures D-9
through D-21) showing the distribution of salmonid species throughout the SF CWR
Subbasin.
D-29 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table D-11. Results offish tag assessments of salmonid and habitat conditions in the SF CWR subbasin.
WB
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
WATER BODY
NAME
Lower SF CWR
L. Cottonwood Creek
U. Cottonwood Creek
L. Red Rock Creek
U. Red Rock Creek
Stockney Creek
Shebang Creek
SF Cottonwood Cr.
Long Haul Creek
Threemile Creek
Butcher Creek
Mid-Lower SF CWR
Mill Creek
Lower Johns Creek
Gospel Creek
West Fork Gospel Cr.
Middle Johns Creek
Upper Johns Creek
Moores Creek
Square Mountain Cr.
Hagen Creek
Middle SF CWR
Wng Creek
Twentymile Creek
Lower Tenmile Creek
Middle Tenmile Creek
Upper Tenmile Creek
Wlliams Creek
Sixmile Creek
Mid-Upper SF CWR
ACRES
19,722.51
16,928.92
21,222.86
2,968.83
23,480.76
19,977.77
18,380.20
12,676.30
8,811.76
21,474.81
10,723.48
56,691.11
23,410.24
26,377.99
10,831.77
4,467.34
10,199.89
8,673.57
3,987.19
2,289.02
5,537.44
18,952.46
5,329.18
14,640.67
2,447.18
7,227.17
13,617.29
5,890.59
5,129.97
17,165.37
Current Fish Population
Presence*
BUT
Y
N
N
N
N
N
N
N
N
N
N
Y
Y
Y+
Y
Y
Y+
Y+
Y+
Y
Y
Y
N
Y
Y+
Y+
Y+
Y
Y
Y
CUT
Y
N
N
N
N
N
N
N
N
N
N
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
SCH
Y
N
N
N
N
N
N
N
N
Y
Y
Y+
Y+
Y
N
N
Y
N
N
N
N
Y+
N
N
Y
Y+
Y
N
Y
Y+
ST
RBT
Y
Y
Y
N
N
N
N
N
N
Y
Y
Y
Y
Y
Y
N
Y
Y
Y
Y
Y
Y
N
Y
Y
Y
Y
Y
Y
Y
BRT
Y
N
N
N
N
N
N
N
N
N
N
Y
N
N
N
N
N
N
N
N
N
Y
N
N
N
N
N
N
N
Y
Current
Habitat
Condition**
Salmonids
P
P
P
P
P
P
P
P
P
P
P
P
F
G
G
G
G
G
G
G
G
F
F
G
G
G
G
G
F
F
Natural Inherent
Conditions**
BUT
F
P
P
P
P
P
P
P
P
P
P
F
F
G
G
G
G
G
G
G
G
F
P
F
F
G
G
F
F
F
CUT
F
P
P
P
P
P
P
P
P
P
P
F
G
G
G
G
G
G
G
G
G
F
F
G
F
G
G
G
G
F
SCH
F
P
P
P
P
P
P
P
P
P
P
F
F
F
P
P
F
P
P
P
P
F
P
P
F
F
F
F
F
G
ST
RBT
F
G
F
G
F
F
F
F
F
F
F
F
G
G
G
F
G
G
G
F
F
G
F
F
G
G
G
G
G
G
Pollutant
Problems
SED
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
N
N
N
N
N
N
N
Y
N
N
N
N
N
N
Y
Y
TEMP
Y
Y
N
N
N
N
N
N
N
Y
Y
Y
Y
N
N
N
N
N
N
N
N
Y
N
N
N
N
N
N
N
Y
NUTR
Y?
Y
Y
Conservation
Preservation
Priority***
M (main stem)
L
L
L
L
L
L
L
L
L
M
M (main stem)
M
C/H
C/H
C/H
C/H
C/H
C/H
C/H
C/H
M (main stem)
L
C/M
C/H
C/H
C/H
C/H
M
M
D-30
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table D-11. Results offish tag assessments of salmonid and habitat conditions in the SF CWR subbasin.
WB
ID
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
WATER BODY
NAME
Lower Crooked River
Upper Crooked River
West Fork Crooked R.
East Fork Crooked R.
Relief Creek
Upper SF CWR
Lower Red River
Middle Red River
Moose Butte Creek
Lower Red River
Middle Red River
West Fork Red River
Upper Red River
Trapper Creek
Upper Red River
Soda Creek
Bridge Creek
Otterson Creek
Trail Creek
Siegel Creek
Red Horse Creek
Lower American R.
Kirks Fork
EF American River
Upper American R.
Elk Creek
Little Elk Creek
Big Elk Creek
Buffalo Gulch
Whiskey Creek
ACRES
9,480.90
14,487.38
7,594.45
6,688.73
7,484.49
2,695.17
10,333.34
16,041.61
7,087.55
3,153.83
2,791.15
6,405.94
4,744.28
7,076.77
19,249.68
3,353.28
2,380.29
2,488.27
4,560.11
7,783.69
5,806.21
7,215.12
6,257.49
11,444.75
15,275.05
2,323.89
5,081.05
8,820.95
2,138.81
1,659.19
Current Fish Population
Presence*
BUT
Y
Y+
Y+
Y+
Y
Y
Y
Y
Y
Y+
Y+
Y+
Y+
Y
Y
N
N
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
Y
CUT
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
SCH
Y+
Y+
Y
Y
Y+
Y+
Y+
Y+
Y+
Y+
Y+
Y
Y
N
Y+
N
N
Y
Y
Y
Y
Y+
Y
Y+
Y+
Y+
Y
Y+
N
Y
ST
RBT
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
N
N
N
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
BRT
Y
Y
Y+
N
N
Y
Y
Y
Y
Y
Y
Y
Y
Y+
Y+
Y+
Y+
Y+
Y+
Y+
Y+
Y
Y
Y+
Y+
Y+
Y+
Y+
N
Y
Current
Habitat
Condition**
Salmonids
P
F
G
G
F
P
P
P
F
F
F
G
F
F
F
F
G
G
F
F
F
P
F
F
F
P
F
F
P
F
Natural Inherent
Conditions**
BUT
F
G
G
G
F
F
F
F
F
G
G
G
G
G
G
F
F
F
F
F
F
F
F
G
F
F
F
F
P
F
CUT
G
G
G
G
G
F
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
SCH
G
G
G
G
G
G
G
G
G
G
G
G
G
F
G
F
F
F
F
G
G
G
G
G
G
G
G
G
F
F
ST
RBT
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
Pollutant
Problems
SED
Y
Y
N
N
Y
Y
Y
Y
Y
Y
Y
N
Y
Y
Y
Y
N
N
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
TEMP
Y
Y
N
N
Y
Y
Y
Y
Y
Y
N
N
N
N
Y
N
N
N
N
Y
Y
Y
Y
N
Y
Y
Y
Y
Y
Y
NUTR
Y?
Y?
Y
Conservation
Preservation
Priority***
H
H
C/H
C/H
M
H
M
H
H
H
H
C/H
H
H
H
H
C/M
C/M
H
H
H
H
H
H
H
H
H
H
M
M
D-31
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table D-11. Results offish tag assessments of salmonid and habitat conditions in the SF CWR subbasin.
WB
ID
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
WATER BODY
NAME
Maurice Creek
Lower Newsome Cr.
Bear Creek
Nugget Creek
Beaver Creek
Middle Newsome Cr.
Mule Creek
Upper Newsome Cr.
Haysfork Creek
Baldy Creek
Pilot Creek
Sawmill Creek
Sing Lee Creek
WF Newsome Creek
Leggett Creek
Fall Creek
Silver Creek
Peasley Creek
Cougar Creek
Meadow Creek
Sally Ann Creek
Rabbit Creek
ACRES
1,093.79
4,145.33
3,832.48
1,451.46
3,733.24
1,135.41
5,497.49
6,355.59
3,171.89
2,724.18
3,917.87
1,769.33
1,555.92
3,304.66
4,992.17
2,333.69
16,516.61
9,092.74
7,737.01
24,009.74
8,891.48
6,190.89
Current Fish Population
Presence*
BUT
N
Y
Y
Y
Y
Y
Y
Y
N
Y+
Y+
Y
N
Y
N
N
Y
N
N
Y
Y
Y
CUT
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
Y
Y
Y
Y
Y
SCH
N
Y+
Y
N
N
Y+
Y
Y+
Y
Y
Y
Y
Y
Y
Y
N
N
N
N
Y+
N
N
ST
RBT
Y
Y
Y
N
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
Y
Y
N
Y
Y
Y
BRT
N
Y
N
N
N
N
N
N
N
N
N
N
N
N
N
N
Y+
N
N
Y+
N
Y
Current
Habitat
Condition**
Salmonids
P
P
F
F
F
F
F
F
F
F
G
G
F
F
F
F
G
F
P
P
P
P
Natural Inherent
Conditions**
BUT
P
F
F
F
F
F
F
F
F
G
G
F
F
F
F
P
F
F
P
F
F
F
CUT
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
F
G
G
F
G
F
F
SCH
F
G
G
F
F
G
G
G
G
G
G
G
G
G
F
P
P
F
P
F
P
P
ST
RBT
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
F
G
F
G
F
F
Pollutant
Problems
SED
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
N
N
N
N
Y
Y
N
Y
Y
Y
Y
Y
TEMP
Y
Y
Y?
Y?
Y?
Y
Y?
Y
Y?
Y?
Y?
Y?
Y?
Y
Y
N
N
Y?
Y?
Y
Y
Y
NUTR
Conservation
Preservation
Priority***
M
H
H
M
H
H
H
H
H
H
C/H
C/M
M
H
M
L
C/L
M
L
M
M
L
Cutthroat Trout
Brook Trout
SCH = Spring Chinook
* Y+ = known spawning and rearing population
BUT = Bull Trout CUT =
ST RBT = Steelhead/Rainbow Trout BRT =
** G = Good, F = Fair, P = Poor
*** L = Low, M = Medium, H = High; C/L, C/M, and C/H = ratings for conservation rather than restoration. All other ratings in this
column are priorities for restoration
D-32
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
4%
Fish TAG Assessment of the
Presence of Spring Chinook in the
South Fork Clearwater Subbasin
May, 2002
Legend
SFCIearwater 4th Field HUC
NPT Reservation Boundary
_j| Water Body ID watersheds
/\/ 303(d) Listed Streams
/\/ Major Streams
/Ay' Other Streams
Spring Chinook Presence
Q Yes
(HI No
Breeding Populations
Figure D-9. Fish TAG Assessment of the Presence of Spring Chinook in the SF CWR Subbasin
D-33
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Assessment of
Potential Spring Chinook in the
South Fork Clearwater Subbasin
^£0 si,v
Legend
SF Clearwater 4th Field HUG
NPT Reservation Boundary
|| I Water Body ID watersheds
/\/ 303(d) Listed Streams
/\/ Major Streams
/\J Other Streams
Spring Chinook Potential
I Good
Fair
I I Poor
May, 2002
Figure D-10. Fish TAG Assessment of Potential Spring Chinook in the SF CW Subbasin
D-34
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
^£0 si,v
Fish TAG Assessment of the
Presence of Cutthroat Trout in the
South Fork Clearwater Subbasin
Legend
SF Clearwater 4th Field HUC
NPT Reservation Boundary
|| I Water Body ID watersheds
/\/ 303(d) Listed Streams
/\/ Major Streams
/\J Other Streams
Cutthorat Trout Presence
Q Yes
No
May, 2002
Figure D-11. Fish TAG Assessment of the Presence of Cutthroat Trout in the SF CWR Subbasin
D-35
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Assessment of
Potential Cutthroat Trout in the
South Fork Clearwater Subbasin
^£0 si,v
Legend
SF Clearwater 4th Field HUC
NPT Reservation Boundary
|| I Water Body ID watersheds
/\/ 303(d) Listed Streams
/\/ Major Streams
/\J Other Streams
Cutthroat Potential
Good
1 Fair
Poor
May, 2002
Figure D-12. Fish TAG Assessment of Potential Cutthroat Trout in the SF CWR Subbasin
D-36
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
^£0 si,v
Fish TAG Assessment of the
Presence of Bull Trout in the
South Fork Clearwater Subbasin
Legend
SF Clearwater 4th Field HUG
NPT Reservation Boundary
|| I Water Body ID watersheds
/\/ 303(d) Listed Streams
/\/ Major Streams
f\t Other Streams
Bull Trout Presence
Q Yes
EH No
Breeding Populations
May, 2002
Figure D-13. Fish TAG Assessment of the Presence of Bull Trout in the SF CWR Subbasin
D-37
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Assessment of
Potential Bull Trout in the
South Fork Clearwater Subbasin
^£0 si,v
Legend
SF Clearwater 4th Field HUC
NPT Reservation Boundary
|| I Water Body ID watersheds
/\/ 303(d) Listed Streams
/\/ Major Streams
/\/ Other Streams
Bull Trout Potential
! Good
Fair
Poor
May, 2002
Figure D-14. Fish TAG Assessment of Potential Bull Trout in the SF CWR Subbasin
D-38
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Assessment of the
Presence of Steelhead/Rainbow
Trout in the South Fork
Clearwater Subbasin
Legend
SF Clearwater 4th Field HUC
NPT Reservation Boundary
Water Body ID watersheds
/\/ 303(d) Listed Streams
/\f Major Streams
f\J Other Streams
Steelhead / Rainbow
Trout Presence
Figure D-15. Fish TAG Assessment of the Presence of Steelhead/Rainbow Trout in the SF CWR Subbasin
D-39
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Assessment of Potential
Steelhead/Rainbow Trout in the
South Fork Clearwater Subbasin
Legend
SF Clearwater 4th Field HUG
NPT Reservation Boundary
|| I Water Body ID watersheds
/\/ 303(d) Listed Streams
/\/ Major Streams
/ \/ Other Streams
Steelhead / Rainbow Potential
Good
D
May, 2002
Figure D-16. Fish TAG Assessment of Potential Steelhead/Rainbow Trout in the SF CWR Subbasin
D-40
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Assessment of the
Presence of BrookTrout in the
South Fork Clearwater Subbasin
^£0 si,v
Legend
SF Clearwater 4th Field HUC
NPT Reservation Boundary
|| I Water Body ID watersheds
/\/ 303(d) Listed Streams
/\/ Major Streams
/\J Other Streams
BrookTrout Presence
'~^\ Yes
EH N°
Breeding Populations
May, 2002
Figure D-17. Fish TAG Assessment of the Presence of Brook Trout in the SF CWR Subbasin
D-41
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Classification of Current
Fish Habitat Conditions in the
South Fork Clearwater Subbasin
Legend
SF Clearwater4th Field HUC
NPT Reservation Boundary
Water Body ID watersheds
/\/ 303(d) Listed Streams
/\f Major Streams
f\J Other Streams
Current Habitat Conditions
Good
Fair
Poor
Figure D-18. Fish TAG Classification of Current Fish Habitat Conditions in the SF CWR Subbasin
D-42
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Identification of
Sediment Problems in the
South Fork Clearwater Subbasin
Legend
SF Clearwater 4th Field HUG
NPT Reservation Boundary
Water Body ID watersheds
303(d) Listed Streams
/\/ Major Streams
/\/ Other Streams
Sediment Problems
Yes
No
Figure D-19. Fish TAG Identification of Sediment Problems in the SF CWR Subbasin
D-43
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Identification of
Temperature Problems in the
South Fork Clearwater Subbasin
Legend
SF Clearwater 4th Field HUG
NPT Reservation Boundary
Water Body ID watersheds
303(d) Listed Streams
/\f Major Streams
t\J Other Streams
Temperature Problems
Yes
No
Uncertain
Figure D-20. Fish TAG Identification of Temperature Problems in the SF CWR Subbasin
D-44
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Fish TAG Restoration and
Conservation Priorities for the
South Fork Clearwater Subbasin
Legend
SF Clearwater 4th Field HUC
NPT Reservation Boundary
Water Body ID watersheds
303(d) Listed Streams
Major Streams
Other Streams
Conservation Restoration Priority
|~~] Conservation/Good
Q Conservation/Fair
Conservation/Poor
Restoration/Good
| Restoration/Fair
| Restoration/Poor
Restoration/Fair- Main Stem
Figure D-21. Fish TAG Restoration and Conservation Recommendations for the SF CWR Subbasin
D-45
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
References
Batt, P.E. 1996. Governor Philip E. Batt's Idaho bull trout conservation plan. State of
Idaho, Office of the Governor, Boise, ID. 20 pp + appendices.
Behnke, RJ. 1992. Native trout of western North America. American Fisheries Society
Monograph 6.
Brostrom, J. 2001. Personal communication with Lillian Herger, U.S. Environmental
Protection Agency, regarding Idaho Department of Fish and Game unpublished data.
Blair, S. 2001. Nez Perce National Forest. Personal communication with Ann Storrar, Nez
Perce Tribe, regarding aquatic species (non-fish) in the SF CWR Subbasin.
BLM (Bureau of Land Management). 1999. Lower South Fork Clearwater River and
tributaries biological assessment. BLM, Cottonwood Resource Area Office,
Cottonwood, Idaho.
Busby, P.J., T.C. Wainwright, GJ. Bryant, LJ. Lierheimer, R.S. Waples, F.W. Waknitz, and
IV. Lagomarsino. 1996. Status review of west coast steelhead from Washington,
Idaho, Oregon, and California. National Marine Fisheries Service. Seattle,
Washington.
Elms-Cockrum, T. In Press. Salmon spawning ground surveys, 2001. Idaho Department of
Fish and Game. Pacific Salmon Treaty Program: Award No. NA47FP0346.
Gerhardt, N. 1999. A brief history of dams on the South Fork Clearwater River. Nez Perce
National Forest, Grangeville, Idaho.
Griffith, J.S. 1988. Review of competition between cutthroat trout and other salmonids.
American Fisheries Society Symposium 4:134-140.
Groves, P. A. and J.A. Chandler. 1999. Spawning habitat used by fall chinook salmon in the
Snake River. North American Journal of Fisheries Management 19:912-922.
DEQ (Idaho Division of Environmental Quality). 1995. Beneficial Uses Reconnaissance
Project unpublished data. Idaho Division of Environmental Quality, Lewiston
Regional Office, Lewiston, Idaho.
DEQ (Idaho Division of Environmental Quality). 1998. South Fork Clearwater River
Subbasin bull trout problem assessment. By the Clearwater Basin Bull Trout
Technical Advisory Team, Idaho Division of Environmental Quality, Lewiston,
Idaho.
D-47 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
DEQ, NPT, and USEPA (Idaho Department of Environmental Quality, Nez Perce Tribe, and
Environmental Protection Agency). 2000. First Revision. Cottonwood Creek total
maximum daily load (TMDL). Idaho Department of Environmental Quality,
Lewiston, Idaho.
IDFG (Idaho Department of Fish and Game). 2000. Snorkeling surveys unpublished data.
Idaho Department of Fish and Game. Lewiston, Idaho.
IDFG (Idaho Department of Fish and Game). 2001. Fisheries management plan 2001-2006.
Idaho Department of Fish and Game. Boise, Idaho.
Johnson, C. 2001. BLM, Cottonwood. Personal communication regarding SF CWR
fisheries.
Kiefer, S., M. Rowe, and K. Hatch. 1992. Stock summary reports for Columbia River
anadromous salmonids, Volume V: Idaho final draft for the coordinated information
system. Idaho Department of Fish and Game.
Liknes, G.A. and PJ. Graham. 1988. Westslope cutthroat trout in Montana: life history,
status, and management. American Fisheries Society Symposium. 4:53-60.
Miller, W. 2001. US Fish and Wildlife Service. Personal communication.
Northwest Power Planning Council. 2001. Clearwater subbasin summary. Prepared by
Ecovista, Pullman, WA. 115 pp.
NPT and IDFG (Nez Perce Tribe and Idaho Department of Fish and Game). 1990.
Clearwater River Subbasin salmon and steelhead production plan. Funded by the
Northwest Power Planning Council; Columbia Basin Fish and Wildlife Authority.
Pettit, S.W. and R.L. Wallace. 1975. Age, growth, and movement of mountain whitefish,
(Prosopium williamsoni) (Girard), in the North Fork Clearwater River, Idaho.
Transactions of the American Fisheries Society 104(1): 68-76.
Quigley, T.M. and S. J. Arbelbide, technical editors. 1997. An assessment of ecosystem
components in the interior Columbia Basin. Volumes I-IV. U.S Department of
Agriculture Forest Service, Pacific Northwest Research Station. General Technical
Report. PNW-GTR-405.
Rieman, B.E. and J.D. Mclntyre. 1993. Demographic and habitat requirements for
conservation of bull trout. U.S. Department of Agriculture, Forest Service,
Intermountain Research Station. Ogden, Utah.
Rockhold, A. and J.D. Berg. 1995. Mountain Whitefish monitoring program in the Lochsa
River drainage of Northern Idaho. Comprehensive Report 1992-1994. U.S. Fish and
Wildlife Service, Idaho Fishery Resource Office, Ahsahka, Idaho.
Rubin, S. 2001. Personal communication. USGS
D-48 Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Simpson, J.C. and R.L. Wallace 1978. Fishes of Idaho. University Press of Idaho. Moscow,
Idaho.
Stream Net. 2000. Fish distribution [online data]. Gladstone, Oregon.
URL
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Attachments
Attachment D-1. Timing of life history stages of salmonids within the SF CWR
Subbasin.
Life History Stage
SF CWR Main Stem
Major Creeks and
Rivers
Other Perennial
Streams
A-Run Steelhead (Lower SF Main Stem and its Tributaries)
Residence
Migration to
Tributaries
Spawning
Incubation and Emergence
Rearing
Juvenile Out Migration
Sept 1-Feb1
Feb1-May15
All Year
Feb 1-June 1
Feb 1 -May 15
Feb 1 -May 15
Feb 1-June 1
All Year
Feb 1-June 1
Feb 1-May 15
Feb 1-June 1
All Year
Feb 1-June 1
B-Run Steelhead (Middle and Upper SF Main Stem and its Tributaries)
Residence
Migration to Tributaries
Spawning
Incubation and Emergence
Rearing
Juvenile Out Migration
Dec 1-July 15
Feb 1 -May 15
Feb 1 -May 31
Feb 1 -July 15
All Year
Feb 1-June 30
Jan 1-May 31
Feb 1 -May 31
Feb 1 -July 15
All Year
Feb 1-June 30
Feb 1-May 31
Feb 1 -July 15
All Year
Feb 1-June 30
Fall Chinook
Adult Migration
Spawning
Incubation and Emergence
Juvenile Out Migration
Sept15-Nov30
Oct 1 -Dec 15
Oct1-May 15
May 1-Aug 31
Spring Chinook
Adult Migration
Spawning
Incubation and Emergence
Rearing
Juvenile Out Migration
April 15-Sept 15
Aug 15-Sept 30
Aug 15-April 30
All Year
Sept 1-June 30
April 15-Sept 15
Aug 15-Sept 30
Aug 1 5-April 30
All Year
Sept 1-June 30
Aug 15-Sept 30
Aug 15-April 30
All Year
Sept 1-June 30
Bull Trout
Residence
All Year
All Year
All Year
D-50
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Life History Stage
Adult Migration (pre spawn)
Adult Migration (post spawn)
Spawning
Incubation and Emergence
Rearing
SF CWR Main Stem
April 1-July 15
Sept 1-Oct31
All Year
Major Creeks and
Rivers
April 1-July 15
Sept 1 -Oct 31
Aug 15-Nov30
Aug 15-Mar31
All Year
Other Perennial
Streams
April 1-July 15
Sept 1 -Oct 31
Aug 15-Nov30
Aug 15-Mar31
All Year
Westslope Cutthroat Trout
Residence
Adult Migration
Spawning
Incubation and Emergence
Rearing
All Year
March 1-June 30
All Year
All Year
Mar 1-July 15
Mar15-June30
Mar 15-Aug 15
All Year
All Year
Mar 1-July 15
Mar15-June 30
Mar 15-Aug 15
All Year
Mountain Whitefish
Residence
Adult Migration
Spawning
Incubation and Emergence
Rearing
All Year
May 1-Nov30
Oct 1 -Dec 15
Oct 1-Feb28
All Year
All Year
May 1-Nov30
Oct 1 -Dec 15
Oct 1 -Feb 28
All Year
All Year
May 1-Nov30
Oct 1 -Dec 15
Oct 1 -Feb 28
All Year
Pacific Lamprey
Residence
Adult Migration
Spawning
Incubation and Emergence
Rearing
All Year
May 1 -Sept 30
Feb1-May31
Feb 1-June 30
All Year
All Year
May 1 -Sept 30
Feb 1 -May 31
Feb 1-June 30
All Year
All Year
May 1 -Sept 30
Feb1-May31
Feb 1-June 30
All Year
Brook Trout
Residence
Spawning
Incubation and Emergence
All Year
All Year
Aug 15-Oct31
Aug 15-Feb28
All Year
Aug 15-Oct31
Aug 15-Feb28
(Source: Brostrom 2001).
Note: Major creeks and rivers include the Red, American, and Crooked Rivers, and Mill,
Meadow, Johns, and Tenmile Creeks.
D-51
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Attachment D-2. Spring Chinook redd counts from the SF CWR subbasin
based on observations in several locations, 1974-1997.
Year
1974
1975
1976
1977
1978
1979
1980
1981
1982
1983
1984
1985
1986
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
#of
Observation
Locations
3
3
3
4
4
4
4
5
5
5
5
5
5
5
5
5
5
5
5
5
5
5
5
5
Total
20
59
33
138
109
39
53
124
269
234
200
264
192
208
170
83
133
6
98
209
17
6
44
187
Mean
6
19
11
34
27
9
13
24
53
46
40
52
38
41
34
16
26
1
19
41
3
1
8
37
(Source: Stream Net 2000)
Attachment D-2. Cont. Observation locations for spring Chinook redd
surveys.
Years
1974-1997
1974-1997
1977-1997
1981-1997
1974-1997
Location
Crooked River
Red River
SF of Red River
American River
Newsome Creek
River Mile
0-11.7
0-28.5
0-11.7
0-21 .6
0-15.7
(Source: Stream Net 2000)
D-52
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Attachment D-3. Adult spring Chinook returns to the Red River pond hatchery,
1969-1996.
Red River Pond Hatcher
Year
1969
1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
Unknown
215
Females
~
220
209
49
16
7
16
65
13
2
14
/Trap
Males
~
299
185
55
37
11
23
74
18
2
48
Total
Returns
215
519
394
104
53
18
39
139
31
4
62
Crooked River Hatchery Trap
Year
1990
1991
1992
1993
1994
1995
1996
1997
Unknown
1034
Females
10
5
94
211
18
0
94
Males
19
15
134
191
8
6
205
Total
Returns
29
20
228
402
26
6
299
1034
(Source: Stream Net 2000)
Attachment D-4. Number of fall Chinook salmon redds counted in the
Clearwater River subbasin, 1988-2000.
River
Clearwater
(RMO-41)
Clearwater
(RM41-74)
M.F. Clearwater
(RM 74-98)
N.F. Clearwater
S.F. Clearwater
Totals
1988
21
21
1989
10
10
1990
4
4
1991
4
4
1992
25
1
0
0
26
1993
36
0
0
0
36
1994
30
0
0
7
0
37
1995
20
0
0
0
0
20
1996
66
0
0
2
1
69
1997
58
0
0
14
0
72
1998
78
0
0
0
0
78
1999
179
2
0
1
2
184
2000
163
8
0
0
1*
172
2001
285
16
0
1
5
307
* A fall chinook salmon carcass was found in the SF CWR
An empty cell indicates no searches were conducted in the corresponding river segments during a specific year.
D-53
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Attachment D-5. Steelhead redd count data from the Crooked and Red Rivers.
Year
90
91
92
93
94
95
96
97
90
93
94
95
96
97
Stream
Crooked
Crooked
Crooked
Crooked
Crooked
Crooked
Crooked
Crooked
Red
Red
Red
Red
Red
Red
Count
219
50
2
4
3
4
0
0
2
5
6
6
2
0
Survey
River Mile
8.3
10.8
10.8
10.4
10.4
10.4
10.4
12.8
9.8
16.3
6.5
6.5
6.5
6.5
Redd/mile
26.4
4.6
0.2
0.4
0.3
0.4
0.0
0.0
0.2
0.3
0.9
0.9
0.3
0.0
(Source: Stream Net 2000)
Attachment D-6. Number of steelhead adults returning to the Crooked River
fish trap, 1991-1996.
Year
90
91
92
93
94
95
96
97
98
99
00
Weir
Catch
49
49
53
49
6
16
3
3
4
10
16
Wild
17
5
19
17
5
15
2
3
2
3
6
Hatchery
32
44
34
22
1
2
1
0
2
7
10
(Source: Stream Net 2000)
D-54
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
May 2003
Attachment D-7. Summary of SF CWR main stem snorkel data collected summer 2000.
Segment
1
2
3
4
5
SECTION
(KM)*
end 18.2
end 56.4
end 75.7
end 95.3
end 103.2
TYPE
mix b-c
C-Meadow
B-Canyon
B-Canyon
B-Canyon
AREA_m2
35,622.626
63,570.987
27,558.280
34,355.668
14,237.941
sum_sthd
0.10
2.24
4.32
2.76
2.35
sum_stac
0.02
0.39
0.00
0.00
0.01
sum_RBT
0.00
0.03
0.02
0.01
0.02
sum_ct<=12
0.01
0.04
0.08
0.02
0.05
sum_ct>12
0.00
0.00
0.00
0.00
0.01
sum_ct_all
0.01
0.04
0.08
0.02
0.06
sum_bkt
0.00
0.00
0.01
0.00
0.01
Segment
1
2
3
4
5
SECTION*
end 18.2
end 56.4
end 75.7
end 95.3
end 103.2
TYPE
mix b-c
C-Meadow
B-Canyon
B-Canyon
B-Canyon
AREA m2
35,622.626
63,570.987
27,558.280
34,355.668
14,237.941
bull sum<=12
0.00
0.00
0.03
0.01
0.03
bull sum>12
0.00
0.00
0.01
0.00
0.01
sum bull all
0.00
0.00
0.03
0.01
0.04
sum wht
0.19
0.98
0.76
0.59
0.67
sum ch_juv
0.01
0.33
0.48
0.21
0.01
sum ch adult
0.00
0.00
0.03
0.01
0.04
sum coho
0.00
0.00
0.00
0.00
0.00
(Source: IDFG 2000)
RBT= hatchery origin rainbow trout (as determined by fin erosion)
Sthd= wild/natural steelhead/rainbow trout
Stac=adipose fin-clipped steelhead
Ct= cutthroat trout
Bkt= brook trout
Bull= bull trout
Wht= whitefish
Ch= chinook
D-55
Appendix D
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
May 2003
SF CWR Main Stem Segment Designations
Segment #
1
2
3
4
5
Start Landmark
SF CWR Mouth
Butcher Creek Confluence
Johns Creek Confluence
Ten Mile Creek Confluence
Crooked River Confluence
End Landmark
Butcher Creek Confluence
Johns Creek Confluence
Ten Mile Creek Confluence
Crooked River Confluence
Beginning of SF CWR
Start River km
0
18.2
56.4
75.7
95.3
End River km
18.2
56.4
75.7
95.3
103.2
D-56
Appendix D
-------
Appendix E. Agricultural Chemicals
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Agricultural Chemicals
Chemicals used in agriculture on the Camas Prairie
Source: B. Sandlund, NRCS, Grangeville, 2002
The Web site: contains information on these chemicals
2-4, D ester and amine
Acclaim
Achieve
Aim
Ally
Amber
Arsenal
Assert
Assure
Avenge
Banvel
Basagram
Beacon
Bromate
Buctril
Capture
Cassaron
Crossbow
Curtail
Diuron
Farge
Finesswe
Glean
Gramoxone
Harmony Extra and GT
Hoelon
Karmex
Kerb
Landmaster
Malathion
Maverick
MCPA
Oast
Poast
Puma
Pursuit
Roundup
Sencor
Singer
Starne
Tordon 22K
Transline
Treflan
Velpar
Weedmaster
E- 1
Appendix E
-------
Appendix F. System Potential Vegetation Methods and
Results
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
List of Tables F-ii
List of Figures F-iii
System Potential Vegetation Methods and Results F-1
Overview F-1
Current Condition Assessment F-1
Summary - Stream Parameters that Control Temperature Change F-1
Riparian Vegetation - Current Condition F-2
Effective Shade - Current Condition F-15
Stream Side Activities Influencing Riparian/Stream Side Processes F-25
System Potential Vegetation TMDL Components F-26
Vegetation Response Units and Habitat Type Groups F-34
Site Specific Calculation of "System Potential Effective Shade" F-51
Temperature Impairments F-54
Water Quality Standard Identification F-54
Seasonal Variation - Clean Water Act §303(d)(1) F-55
Nonpoint Source Component of Loading Capacity F-55
Surrogate Measures and Nonpoint Source Load Allocations - 40 CFR §
130.2(i) F-55
Effective Shade Surrogate Measures F-57
Margins of Safety -Clean Water Act §303(d)(1) F-60
References F-62
F-i Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Tables
Table F-1. Nez Perce Pi_stratum codes legend (NPNF 2001) F-4
Table F-2. Current condition percentile summary for the Nez Perce National
Forest F-8
Table F-3. Calculated regression coefficients and model information F-9
Table F-4. Factors that influence stream shade F-15
Table F-5. Percent distribution of Vegetation Response Units (VRUs) within a
300-meter buffer surround the South Fork Clearwater River and several major
tributaries F-30
Table F-6. Vegetation composition within "forested" Vegetation Response
Units (VRUs) F-32
Table F-7. Relative proportion (percentage) of vegetation size classes for
Vegetation Response Units (VRUs) F-32
Table F-8. Percent distribution of Habitat Type Groups (HTGs) for each
classified Vegetation Response Units (VRUs) zone within a 300-meter buffer
surrounding the South Fork Clearwater River and major tributaries F-36
Table F-9. Mature vegetation height condition (U.S. Department of Agriculture
Fire Effects Information System [fs.fed.us/database/feis]) F-39
Table F-10. Water bodies included in Idaho 1998 303(d) list for temperature
F-54
Table F-11. Applicable temperature criteria F-54
Table F-12. Temperature allocation summary F-55
Table F-13. Approaches for incorporating a margin of safety into a TMDL. F-61
F-ii Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Figures
Figure F-1. Example of Pi_stratum Vegetation Land Cover Classification F-3
Figure F-2. Current Vegetation Species Composition within the South Fork
Clearwater River Subbasin F-5
Figure F-3. Near-Stream Vegetation Size Classes within a 300-Meter Buffer of
the South Fork Clearwater River within Nez Perce National Forest Lands
(upper) and Below Nez Perce National Forest Lands (lower) F-6
Figure F-4. Measured Tree Heights and Diameter at Breast Height Conditions
within the Nez Perce National Forest (NPNF 2002) F-7
Figure F-5. Example of TTools Automated Vegetation Sampling Methodology
F-10
Figure F-6. South Fork Clearwater River and Red River Current Near-Stream
Vegetation Condition F-11
Figure F-7. Stream Aspect F-16
Figure F-8. Stream Elevation and Gradient F-18
Figure F-9. Topographic Shade Angle F-19
Figure F-10. Calculated Near-Stream Disturbance Zone (NSDZ) Width and
Measured Bankfull Width Data F-20
Figure F-11. Seasonal Variations in Temperature (Daily Maximum) in the
South Fork Clearwater River, Threemile Creek, and Red River in the Summer
of 2000 F-21
Figure F-12. Calculated Current Effective Shade for 303(d) listed streams and
Red River F-22
Figure F-13. SF Clearwater River Main Stem - Calculated Maximum Weekly
Maximum Temperatures in 2000 and Observed Diurnal Temperatures on
Augusts, 2000 F-23
Figure F-14. Maximum Weekly Maximum Temperatures Measured along the
Red River in 2000 F-24
Figure F-15. Stream Side Activities Influencing Riparian and Stream Side
Processes in the South Fork Clearwater River Subbasin F-25
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Figure F-16. Calculated Effective Shade (ES) Reduction Resulting from Road
Encroachment (Measured as Percent Shade) F-26
Figure F-17. Vegetation Response Units (VRUs) for the South Fork Clearwater
River Subbasin F-31
Figure F-18. Habitat Type Groups Within the South Fork Clearwater River
Subbasin F-35
Figure F-19. National Wetlands Inventory for the South Fork Clearwater River
Subbasin F-38
Figure F-20. Shade Curves Developed for Vegetation Response Units (VRUs)
F-42
Figure F-21. Vegetation Composition Application Rule Set- South Fork
Clearwater River Main Stem F-50
Figure F-22. Vegetation Composition Application Rule Set - Areas Other than
the South Fork Clearwater River Main Stem F-50
Figure F-23. Current and System Potential Effective Shade Conditions - South
Fork Clearwater River and Major Tributaries F-51
Figure F-24. System Potential Effective Shade and Loading Capacity - South
Fork Clearwater River, Red River and Three Mile Creek F-58
F4v Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Appendix F. System Potential Vegetation Methods and
Results
Report prepared by:
Peter Leinenbach, Landscape Ecologist, Region 10, USEPA
and
Leigh Woodruff, Environmental Scientist, Region 10, USEPA
Overview
Appendix F is divided into two sections. The first section provides information and analysis
about factors associated with the current stream temperature conditions in the South Fork
Clearwater River Subbasin. The second section presents potential land cover condition
information and data previously developed for this subbasin. This section also presents the
methods utilized in this total maximum daily load (TMDL) to develop an understanding of
expected (or potential) vegetation land cover conditions, which included an accounting of
natural disturbance processes. The final section of this appendix illustrates the methods used
to develop "system potential effective shade" estimates, which are applied in this TMDL as
"surrogate measures."
Current Condition Assessment
Summary - Stream Parameters that Control Temperature Change
Riparian vegetation, stream morphology, hydrology, point source discharge, climate, and
geographic location influence stream temperature. While climate and geographic location
are outside of human control, riparian condition, channel morphology, hydrology, and point
source discharges are affected by human activities. Specifically, the elevated summertime
stream temperatures attributed to anthropogenic sources within the South Fork Clearwater
River Subbasin result from the following:
• Riparian vegetation disturbance reduces stream surface shading via decreased riparian
vegetation height, width, and/or density, thus increasing the amount of solar radiation
reaching the stream surface.
• Riparian vegetation disturbance results in increased temperatures in the microclimate
around the stream resulting in increased heating of the water.
• Localized channel widening (increased wetted width to depth ratios) increases the stream
surface area exposed to energy processes, namely solar radiation and long-wave
radiation.
• Point source discharges directly increase instream temperatures via mass transfer.
F-l Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Ultimately, these factors affect the energy (thermodynamic) processes within the river. A
brief description of stream thermodynamic processes that control temperature change is
presented in Appendix I.
Riparian Vegetation - Current Condition
A summary of current vegetation conditions for the South Fork Clearwater River Subbasin is
discussed in the South Fork Clearwater River Landscape Assessment, Volume I -Narrative
(USDA 1998) and is presented below. These conclusions were developed from the review of
historical and existing data and were intended to provide a brief summary of landscape
conditions and associated trends.
"The summary of vegetation conditions can best be addressed by identifying the
ecological processes that have most changed: alteration of terrestrial disturbance
regimes and introduction of nonnative species.
Fire suppression has resulted in more advanced successional states in the
subbasin. This is shown by increases in medium and large tree classes in most
settings, and reductions in young tree classes and shrublands or montane
parkland. Shade tolerant species like grand fir and subalpine fir have increased,
while early serai species like lodgepole pine, ponderosa pine, and whitebark pine
have decreased. Stand densities have probably increased over historic in some
settings (VRU 3 and 4) with consequent increased risk of insect and disease
activity and more severe fire. Old growth is probably more abundant than
historically, basin-wide, but has declined in ponderosa pine types and increased in
mixed conifer and spruce-fir types. In moist grand fir settings (VRU 7 and 10),
some fragmentation and isolation of old growth has occurred.
Timber harvest has not replicated the frequency, scale, or kind of historic
disturbance. Across watersheds, vegetation conditions are more uniform. Within
stands, vegetation structure has been simplified through clearcutting and removal
of fire tolerant ponderosa pine and larch. Heterogeneity of disturbance size and
stand structure have been lost in many harvested areas. Harvest and fire
suppression have resulted in loss of large patches of fire-killed trees, and large
snags of long lasting species like larch.
The introduction of nonnative species has highly altered grassland steppe
communities. Annual grasses and noxious weeds are well established at low
elevations. Fire behavior and soil productivity may change in response to these
altered plant communities."
The follow points describing current vegetation conditions were included in the South Fork
Clearwater River Landscape Assessment (USDA 1998):
• Conversion of foothills grassland on prairie and hill slopes to cropland, hay land, and
pasture has been extensive on private lands.
F-2 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
• Annual grasses and noxious weeds have become established on grassland habitat types on
low elevation steep south facing slopes.
• Forest succession, fire suppression, and timber harvest have resulted in declines in large
open-growth ponderosa pine. Early serai, intolerant species like lodgepole pine and
western larch have also declined with fire suppression.
• Patch sizes are smaller on lodgepole sites and larger on moist grand fir sites, when
compared to historic conditions.
• Whitebark pine is in serious decline from blister rust, fire exclusion, and mountain pine
beetle. Western white pine, never abundant in the subbasin, has also declined from
blister rust.
• Grand fir, Douglas fir, and subalpine fir have increased.
• Early serai structural stages, including forest openings, seedling and sapling, and pole
stands with snags and down wood, have decreased because of fire suppression. Medium
and large tree classes have increased in most areas, except for larch and ponderosa pine
forests.
• Large patches of fire-killed snags have declined with fire suppression. Numbers of large
diameter snags have declined where timber harvest has occurred.
Current Vegetation Land Cover Condition Data
A geographical information systems (GIS) coverage of the current vegetation land cover
condition, called Pi_stratum, was obtained from the Nez Perce National Forest (NPNF).
Specifically, the Pi_stratum is a six-digit code designed to stratify timber stands based on
aerial photo interpreted properties for timber stand sampling and extrapolation. Figure F-l
illustrates an example area along the South Fork Clearwater River main stem, where the
Pi_stratum coverage was overlaid onto a digital ortho quad photograph. The specific codes
associated with the Pi_stratum are presented in Table F-l and the six-digit code is illustrated
in Figure F-l. This coverage is available for the entire subbasin. Figure F-2 illustrates
assigned species composition within the Pi_stratum data set.
Figure F-1. Example of Pi_stratum Vegetation Land Cover Classification
F-3
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Pi_stratum current land cover data are coded for species type, canopy density, and
size/structure. Species type is coded according to the dominant existing over-story species.
Canopy density is presented as the percentage of ground that is covered by over-story
vegetation when viewed from directly above or measured by a densiometer at ground level.
Size/structure classes are divided by diameter at breast height (dbh) for woody vegetation.
Vegetation Size Class Distribution Summary from the Pi_stratum Data Set
Figure F-3 illustrates the land cover distribution by vegetation size class for a 300-meter
buffer surrounding the South Fork Clearwater River within the NPNF (approximately river
miles 63.9 through 24.4) and areas below the NPNF boundary. These areas roughly
correspond with the two different temperature regimes observed in this river (see Chapter 2).
A much higher proportion of larger trees (expressed as dbh) are present within the NPNF
reach. This area of the river does not exhibit a large temperature increase. The greater
percentage of smaller trees within the non-NPNF areas results in lower shade potential (i.e., a
shorter object will tend to produce a lower shade horizon.) Similarly, a higher proportion of
the "non-stocked with trees" category is present within the lower reach. The percentage of
roads within the 300-meter buffer is approximately similar between the two reaches. A very
large percentage (>50%) of near-stream areas in the lower reach are covered with "tree"
vegetation.
Table F-1. Nez Perce Pi_stratum codes legend (NPNF 2001).
Digit 1 - Status
1 - non-forest (potential)
2 - forest
Digit 3 - Species Composition
0 - not stocked with trees
1 - ponderosa pine/Douglas fir
2 - lodgepole pine
3-subalpine fir
4 - mixed conifer
5 - white bark pine
6 - bracken/coneflower
Digit 5 - Vertical Structure
0 - single storied stand
1 - two storied stand
Digit 2 - Condition
0 - water
1 - land (unproductive)
2 - incapable (forest but can't produce
marketable products)
3 - Capable (forest and can produce
marketable products)
Digit 4 - Size Class
0 - not stocked or not applicable
1 - seedling/sapling (to 4.9 inch dbh)*
2 - poles (5.0 - 8.9 inch dbh)
3 - small saw (9 - 13.9 inch dbh)
4 - large saw (14.0 - 20.9 dbh)
5 - big tree (21 inch or greater dbh)
Digit 6 - Crown Closure
0-0-10%
1 - 1 0-40%
2 - 40-70%
3 - >70%
*diameter at breast height
F-4
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Species Composition
(Pi_stratum)
NonStocked
^^ PP/DF
^B Mixed Conifer
Grand Fir/Alder
No Data
WBP
Figure F-2. Current Vegetation Species Composition within the South Fork Clearwater River Subbasin
F- 5
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
NPNF Lands (Approximately RM 63.9 through RM 24.4)
100% n
5 90% -
i
? 80% -
13
£ 70% -
o
o
" 60% -
c
| 50% -
ra
o
<
3
° 30% -
'o
£ 20% -
0)
u
£ 10% -
no/
U% -4
n Road
• Nonstocked with Trees
• Big Tree (> 21 "dbh)
0 Large Saw ( 1 4.0" to 20.9" dbh)
0 Small Saw (9.01 to 1 3.9' dbh)
• Pole (5.0" to 8.9" dbh)
D Seed/Sap (< 4.9" dbh)
50,4%
39.9%
4.8%
pn
m
•w/i
mi
ill
HP
^ywv
iH?
Up
w/,
0.8%
iH
n
mi
in
m
^P
^^
^
^
IP
4.1%
I I
N on stocked Ponderosa Lodge pole Sub alpine Fir Mixed Conifer Wiitebark Cedar/Grand Grand Fir/Alder Road
with Trees PineClouglas Pme Pine Fir
Fir
Species Composition
Non-NPNF Lands (Approximately RM 24.4 through mouth)
100% -I
o 90% -
3
? 80% -
o
E 70% -
o
o
" 60% -
c
'sz
1 50% -
cs
21" dbh)
B Large Saw ( 1 4.0" to 20.9" dbh)
n Small Saw (9.01 to 1 3.9' dbh)
• Pole (5.0" to 8.9" dbh)
D Seed/Sap (< 4.9" dbh)
36.9%
• I
f
f;
r'
ill
if
m
S
8.3%
P=J 5.5%
Nonstocked Ponderosa Lodgepole Subalpine Fir Mixed Conifer Wistebark Cedar/Grand Grand Fir/Alder Road
with Trees PineDouglas Pine Pine Fir
Fir
Species Composition
Figure F-3. Near-Stream Vegetation Size Classes within a 300-Meter Buffer of
the South Fork Clearwater River within Nez Perce National Forest
Lands (upper) and Below Nez Perce National Forest Lands (lower)
F- 6
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Field Measured Vegetation Condition
Near-stream vegetation conditions were measured by the NPNF during the past decade.
Diameter at breast height, vegetation height, and condition were measured for 1,870 trees.
Figure F-4 illustrates the distribution of observed tree height and dbh, separated by species,
for all observed (non-snag) trees included in this study. Table F-2 presents calculated
percentile information for this data.
'#
^ I
i
"i
T V
Figure F-4. Measured Tree Heights and Diameter at Breast Height Conditions
within the Nez Perce National Forest (NPNF 2002)
F- 7
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table F-2. Current condition percentile summary for the Nez Perce National
Forest.
Tree Height Percentile Summary
Vegetation Type
Douglas Fir
Engelmann Spruce
Grand Fir
Lodgepole Pine
Ponderosa Pine
Western Red Cedar
Subalpine Fir
Whitebark Pine
Western Larch
N
258
208
474
392
78
175
216
36
30
1%
27
16
17
24
17
17
20
30
55
5%
40
30
27
30
28
39
29
30
63
10%
50
37
36
35
45
47
34
31
70
20%
60
45
48
40
74
60
40
38
76
50%
78
75
69
60
99
95
60
45
91
80%
100
108
104
80
131
133
81
50
117
90%
120
118
121
87
144
147
88
53
130
95%
138
124
140
92
150
151
95
55
141
99%
153
139
161
109
165
177
142
55
148
-Diameter at Breast Height Percentile Summary (inches)
Vegetation Type
Douglas Fir
Engelmann Spruce
Grand Fir
Lodgepole Pine
Ponderosa Pine
Western Red Cedar
Subalpine Fir
Whitebark Pine
Western Larch
N
258
208
474
392
78
175
216
36
30
1%
4.2
1.1
3.3
4.4
3.3
4.2
1.8
5.1
6.9
5%
5.6
4.1
5
5.1
5.4
5
4.8
5.3
7.2
10%
7.1
5.5
5.4
5.5
6.9
6.6
5.2
5.7
7.7
20%
9
7.2
6.8
6.2
12.5
9
5.9
7.4
8.4
50%
13.4
13
10.7
9.1
25
19.5
8.6
8.9
12.6
80%
22.3
20.4
20.5
12.3
39
30
13
13
26.1
90%
27.7
24.2
26
14.3
42.2
42.3
15.4
15.1
35
95%
33
30
30.1
16
45.1
51.4
17.7
18.4
39.6
99%
42.5
33.3
37.7
24.4
50.2
66.8
27.5
19.4
42.8
*N = number of trees sampled
Species Specific Growth Curves
The ground level data were used to develop species-specific growth curves. Specifically, the
data were used to develop second-order polynomial equations for each tree species sampled
during these monitoring activities. Calculated second-order polynomial equations provide a
reasonable prediction during tree height modeling where tree size (i.e., dbh) falls within the
diameter range of the data used to generate equation coefficients (Garman et al. 1995). Table
F-3 presents a summary of calculated regression coefficients. It is important to note that snag
trees were not included in model development.
Vegetation Height = (a*dbh2)+(b*dbh)+(c)
F- 8
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table F-3. Calculated regression coefficients and model information.
Engelmann Spruce
Douglas Fir
Grand Fir
Ponderosa Pine
Subalpine Fir
Lodgepole Pine
Western Red Cedar
Western Larch
Whitebark Pine
a
15.097
10.765
7.326
26.414
9.955
10.728
18.63
56.778
20.955
b
5.4849
6.4305
6.6186
3.8410
6.3610
6.5604
5.0542
2.9801
3.2703
c
-0.0658
-0.0991
-0.0857
-0.0327
-0.0872
-0.1190
-0.0497
-0.0276
-0.0888
R2
0.68
0.65
0.77
0.65
0.64
0.49
0.70
0.66
0.37
N
208
258
474
78
218
393
175
30
36
Sampling/Measuring Current Riparian Land Cover
Streams were obtained from GIS coverages at a 1:24K scale. These stream layers were then
segmented into data sampling locations (points) at 100-foot intervals. These point data layers
form the basis for automated sampling performed using the GIS tool "Ttools1". At every
distance node (i.e., every 100 feet) along the stream longitudinally, land cover was sampled
at 15-foot intervals out to 120 feet from the channel edge on both stream banks. Sampling
was conducted at a perpendicular angle from the calculated stream aspect. A total of 18
vegetation samples were taken at each stream distance node (Figure F-5).
The species-specific growth curves presented in Table F-3 were used to assign tree heights
based upon the dbh value reported within the P-stratum data set. roads were included in the
analysis and locations were obtained from a GIS data layer.
F- 9
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Hardwood/Conifer
Mix
Cultivated
Agriculture
Cottonwood
Hardwood/Conifer
Mix
Figure F-5. Example of TTools Automated Vegetation Sampling Methodology
Using the methodology discussed above, current near-stream land cover conditions, as
established from the Pi_stratum data set, were sampled for the South Fork Clearwater River,
Threemile Creek, Butcher Creek, Little Elk Creek, Big Elk Creek, Elk Creek, Newsome
Creek, and Red River. These river systems were chosen for analysis because they are on the
303(d) list and represent examples of a large main stem river system, upper meadow
dominated systems, and lower subbasin tributary systems. Current riparian conditions
measured within 240 feet of near-stream area (120 feet of each side of the stream) are
presented in Figure F-6. Although not included in these images, canopy density of the
vegetation cover was included in the Pi-stratum data set and was sampled during this
analysis.
F-10
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
100-5
South Fork
Clearwater River
Vegetation
Height (ft)
Red River
Vegetation
Height (ft)
River Mile
, Left
Bant
30'
'mm Vegetation
Width (ft)
Right
Bait*
Figure F-6. South Fork Clearwater River and Red River Current Near-Stream
Vegetation Condition
F-ll
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Three Mile Creek
Vegetation
Height (ft) 40,
River Mile
Right
Bank
Newsome Creek
Vegetation
Height (ft)
RiverMile
Vegetation
Width (ft)
Right
Bank
Figure F-6 (continued). Threemile Creek and Newsome Creek Current Near-
Stream Vegetation Condition
F-12
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Little Elk Creek
Vegetation
Height (ft)
River Mile
i»uti Vegetation
Width (ft)
Right
Bank
Lett
Bank
Elk Creek
Vegetation
Height (ft)
Left
Bank
Vegetation
Width ittj
Right
Ban*
Figure F-6 (continued). Little Elk Creek and Elk Creek Current Near-Stream
Vegetation Condition
F-13
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Big Elk Creek
Vegetation
Height (ft)
Right
Banff
Butcher Creek
Vegetation
Height (ft)
River Mile
Right
Bank
Figure F-6 (continued). Big Elk Creek and Butcher Creek Current Near-Stream
Vegetation Condition
F-14
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Effective Shade - Current Condition
As described in Appendix I, stream shade is defined as the amount of solar energy that is
obscured or reflected by vegetation or topography above a stream. Effective shade is defined
as the amount of potential solar radiation not reaching the stream surface. Spatial GIS data
and point measurements of current vegetation conditions (presented above) were used to
calculate current effective shade conditions along streams within the South Fork Clearwater
River Subbasin. Current effective shade conditions were calculated using the "Heat Source"
shade calculator2. This method allows for the incorporation of GIS-derived information to
increase the spatial resolution of calculated values.
GIS-Derived Information Used for Effective Shade Calculation
Factors that influence stream shade production along a river are presented in Table F-4.
Many of these are directly influenced by human activities, while others are not. Along with
topographic shade angle, the parameters listed in this table were used to estimate current
effective shade conditions along the South Fork Clearwater River and several tributaries.
Using information present within the spatially-explicit GIS data sets dramatically increased
the spatial resolution of estimated current effective shade conditions over levels developed
from just using point measurements alone.
Table F-4. Factors that influence stream shade.
Description
Season/Time
Stream Characteristics
Geographic Position
Vegetative Characteristics
Solar Position
Parameter
Date/Time
Aspect, Channel Width
Latitude, Longitude
Near Stream Land Cover Height, Width, and
Density
Solar Altitude, Solar Azimuth
Bold type - influenced by human activities
Stream Aspect - Stream aspect was sampled at every stream data
node (every 100 feet) using the T-tools (Figure F-7). The stream
aspect was calculated as the downstream angle between two stream
nodes and north. The units are recorded as degrees from north in
the downstream direction. Stream aspect data are used to:
Reference the longitudinal direction and allow the calculation of
the transverse direction at each stream data node.
Position the stream relative to simulated surrounding features such
as the sun, surrounding near stream land cover, and shade-
producing topographic features.
Stream taped Sampling
This shade calculator has been used by Oregon Department of Environmental Quality and Washington Department of
Ecology during the development of temperature TMDLs during the past several years.
F-15
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
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-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Stream Elevation and Gradient - Stream elevation and
gradient were sampled from digital elevation models (DEMs)
at each 100-foot model data node using the Ttools. In order
to find the lowest pixel nearest to the stream segment node,
T-tools samples nine pixels: the pixel that falls directly on the
stream segment node and the eight surrounding pixels. The
lowest elevation sampled is assigned to the stream segment
node. Stream elevation data are used to calculate stream
gradients. Both sampled elevation and gradient data are
plotted for the aerial extent displayed (Figure F-8). In this
fashion, stream elevation and gradient were derived for all
stream reaches analyzed. Stream elevation data were used
for calculating solar radiation loading and solar position.
Stream El*vation Sampling
DEM
Changs in Stream Elevation
Stream
ei^t Letvgtii
Change in Stream Elevation
(* of Stream Nodes K$egm«rvt Interval!
Chanel Width Sampling
Topography and Topographic Shade -Topographic features produce shade to the stream
system that controls the time of the local sunrise and sunset. Such features include distant
mountain ranges, canyons, or other near-stream relief. At each stream data node (every 100
feet), the topographic shade angle was sampled from DEMs to the west, south, and east using
TTools. Calculated values are presented in Figure F-9.
Channel Near-Stream Disturbance Zone and Bankfull Width - Near-stream disturbance
zone width (NSDZ) is defined for purpose of the TMDL as the width, from left bank to right
bank, between shade-producing near-stream vegetation. This
distance is often similar to bankfull width. The NSDZ can be
measured from digitized channel edge polylines developed from
DOQ photographs. At each stream segment node, Ttools
measured the distance between the left and right channel edge
polylines in the transverse direction (i.e., perpendicular to the
aspect). The NSDZ sampling was used for the South Fork
Clearwater River (Figure F-10). The bankfull width data were
obtained from Department of Environmental Quality sampling
of other rivers within the South Fork Clearwater River Subbasin
in the summer of 2000 (Figure F-10), where available.
The NSDZ data were used to approximate bankfull width and serve as inner boundaries
where transverse near-stream land cover sampling started within Ttools.
The bankfull width and NSDZ width data were used to establish distance between shade-
producing features during effective shade calculations.
F-17
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
r™
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Mife Movs-g Average)
R!v?rM!J« [R«ri RlvcrJ
I
10* ffi
^ 3500 •
| 3000 -
1 2500
20*30
1500
"——"*' • 0%
River Mile (B*g Elk Creek)
Figure F-8. Stream Elevation and Gradient
F-18
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
2Q 25 3% 35 *Q 45 50 55 Ki 65
Rlvtr m\v JSwuth F#ek Clear wfttw RIvcO
Rtv*f Mite {Three Mite Creek)
J We tov».ftg Averages
W!e Sto-rt«ig A^rs^es
i3 Mile Movwsg Awrsgei
Rives Mtle |K«wso«i* Creek)
456
Rivet Mile f84g Elfe C
Figure F-9. Topographic Shade Angle
F-19
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Mile (Soulh Fork Ctearwaler River)
6 8 10 12
Rjve; Mil* {Thre* Mile c*e
ID 12 14 16
•E Cirelkl
River Miiel Little Elfe C-teck)
Rivet Mil« (Elk C
§
1 15
4 S S 7 3 9 SO
RiVfi Malt ^Big Elk Cretkj
Q123456789501112
R iver :f*sle ^Butcher Creek!
Figure F-10. Calculated Near-Stream Disturbance Zone (NSDZ) Width and
Measured Bankfull Width Data
F-20
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Calculated Current Effective Shade Levels
Near-stream land cover information sampled from the Pi_stratum data set (see Figure F-6)
was used to calculate current effective shade levels in 303(d) listed streams in the South Fork
Clearwater River subbasin, and Red River. Specifically, effective shade was calculated for
each 100-foot model node, taking into account: 1) stream elevation (see Figure F-8), 2)
stream aspect (see Figure F-7), 3) topographic shade angle (see Figure F-9), and 4) NSDZ or
bankfull width (see Figure F-10).
In addition, the stream location on the earth's surface was calculated in GIS, and the sun's
position (i.e., solar altitude and solar azimuth) and movement through the sky were
calculated for August 3, 2000. This day corresponds with the FLIR data collection and with
the period of the year with maximum river temperatures (Figure F-l 1).
Calculated current effective shade levels for 303(d) listed streams and Red River are
presented in Figure F-12. Current effective shade conditions could only be calculated for
areas with an assigned bankfull width or NSDZ (see Figure F-10).
.
*il '
il
0 ' Three Mile Creek
5 ' •
S? fii 15 S? ~! z*
\
45 • R«<] River
Figure F-11. Seasonal Variations in Temperature (Daily Maximum) in the
South Fork Clearwater River, Threemile Creek, and Red River in
the Summer of 2000
F-21
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
10 15 20 25 30 35 4& 45 S*& 55 60 65
River Mlie (South Fork Cleanwater River)
River Mile (Mewsocne Creek>
» W4 A
tef
3-556
RSvur Mile (Big Em C
0 1 2
4 5 6 7 & & 1!) 11 12
Rivsf Mile (BsJtehef Cretik)
Figure F-12. Calculated Current Effective Shade for 303(d) listed streams and
Red River
F-22
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Current Effective Shade and Stream Temperature
When compared with effective shade levels, measured temperatures within the South Fork
Clearwater River Subbasin (Figure F-13), illustrate that energy loading from solar radiation
is a dominant factor causing elevated stream temperature in the lower reaches of this river
system. In addition, the consequences of cumulative effects of frequent, but spatially minor,
low shade areas are clearly presented within the lower Clearwater River (downstream of
approximately river mile 24.4), resulting in great temperature increases (the cumulative
effects principle is described in Appendix I). Temperatures are already relatively elevated at
the beginning of the main stem South Fork Clearwater River, which is the confluence of Red
and American River systems. These elevated temperatures reduce slightly as the river travels
through the forested areas of the NPNF. The diurnal temperature pattern within this upper
reach is maintained throughout the reach, but the diurnal variation increases dramatically in
the lower sections of the river (Figure F-13). This downstream area corresponds with
periodically low effective shade conditions.
I 35
?«
i ?0 ;'*> 30 35
Ksvcf Mile fSou!h Fork Cle
-4 • Dtama] Stream TtrnperaSuRS L'FJ
i_ "*i!J
1
Tim* of Day (KMOOOj
Figure F-13. SF Clearwater River Main Stem - Calculated Maximum Weekly
Maximum Temperatures in 2000 and Observed Diurnal
Temperatures on August 3, 2000
As mentioned above, stream temperatures are elevated in the South Fork Clearwater River at
the confluence of the Red and American Rivers. Elevated stream temperatures in the Red
River illustrate a similar pattern of stream temperature increase within areas of infrequent,
low effective shade conditions (Figure F-14). These elevated temperatures developed in the
Red River (along with the other headwater streams) affect temperature conditions for many
miles downstream in the South Fork Clearwater (Figure F-13).
F-23
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
V
Figure F-14. Maximum Weekly Maximum Temperatures Measured along the
Red River in 2000
F-24
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Stream Side Activities Influencing Riparian and Stream Side Processes
Areas where current and/or historic stream side activities influence riparian and stream side
processes are presented within the NPNF South Fork Clearwater River Landscape
Assessment (USDA 1998). Stream side activities were separated into three categories within
this analysis: 1) historic mining activities near the stream, 2) road encroachment on stream
channels, and 3) current or historic grazing effects on stream or riparian processes (Figure F-
15). These disturbance processes can have a tremendous effect on the parameters that
influence temperature conditions within these rivers. For example, Figure F-16 illustrates
that road encroachment along the South Fork Clearwater River Subbasin can result in great
reduction of localized stream surface shade conditions in the river.
Areas of Current or Historical Grazing Effects on Stream or Riparian Processes
oad Encroachment on Stream Channels
Figure F-15. Stream Side Activities Influencing Riparian and Stream Side
Processes in the South Fork Clearwater River Subbasin
F-25
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
100% -
90%
HI 20% -
10%
0% -
10 •: ZD ;* x :r 40 ^ 50 55 eo 65
River Mile (South Fork Clearwater Rjver)
Figure F-16. Calculated Effective Shade (ES) Reduction Resulting from Road
Encroachment (Measured as Percent Shade)
System Potential Vegetation TMDL Components
Temperature Nonpoint Sources - Clean Water Act §303(d)(1)
Riparian vegetation, stream morphology, hydrology, climate, and geographic location all
influence stream temperature. While climate and geographic location are outside of human
control, riparian condition, channel morphology, and hydrology are affected by land use
activities. Human activities that can degrade thermal water quality conditions in the South
Fork Clearwater River Subbasin watersheds are associated with agriculture, forestry, roads,
urban development, and rural residential related riparian disturbance. Specifically, the
elevated summertime stream temperatures attributed to anthropogenic nonpoint sources
result from the first two items discussed below. Non-anthropogenic sources are also
discussed.
Near-Stream Vegetation Disturbance and Removal
This reduces stream surface shading via decreased riparian vegetation height, width, and/or
density, thus increasing the amount of solar radiation reaching the stream surface (shade is
commonly measured as percent effective shade or percent open sky). Riparian vegetation
also plays an important role in shaping the channel morphology, resisting erosive high flows,
and maintaining floodplain roughness.
Channel Modifications and Widening (Increased Width to Depth Ratios)
Channel modifications and widening increase the stream surface area exposed to energy
processes, namely solar radiation. Bankfull width or NSDZ widening decreases the potential
shading effectiveness of shade-producing near-stream vegetation.
F-26
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Natural Sources and Stream Temperature Natural Conditions
Natural conditions that may impact riparian vegetation and result in elevated stream
temperatures include drought, fires, insect damage to riparian vegetation, diseased riparian
vegetation, and wind throw and blow down in riparian areas. The processes through which
natural conditions affect stream temperatures include increased stream surface exposure to
solar radiation and decreased summertime flows.
It was reported within the South Fork Clearwater River Landscape Assessment (USD A 1998)
that:
"Pre-settlement disturbances like fire affected the pattern of vegetation
because fires tended to vary in size, frequency, severity, and distribution; both
randomly and in response to terrain and conditions before the fire. This
pervasive disturbance produced both some predictable patterns and great
heterogeneity. Fire suppression has reduced this heterogeneity. Timber
harvest has created some age class diversity, but not to the degree that fire did.
Further, the uniformity of harvest treatments and harvest unit size has resulted
in less diversity at the landscape and stand level."
This document goes on to make the following conclusions:
"Historical sediment delivery and water yield were highly dependent on
natural fire regimes. Current sediment delivery and water yield are more
closely aligned with disturbances associated with road construction, timber
harvest, mining, and grazing." (USDA 1998, p. )
"Timber harvest has replaced fire as the dominant vegetation disturbance
process, but this harvest has not sustained landscape pattern; specifically for
elements like large pine, larch, and snags. Susceptibility to certain pathogens
(root rots and spruce budworm) has increased with increases in grand fir and
subalpine fir." (USDA 1998, p. )
"Predominantly pulse disturbances of fire and flood have been supplanted by
wide scale press disturbances of harvest and road-related sediment regimes
that have impacted aquatic integrity." (USDA 1998, p. )
Loading Capacity - 40 CFR 130.2(f)
The loading capacity provides a reference for calculating the amount of pollutant reduction
needed to bring water into compliance with standards. The U.S. Environmental Protection
Agency's (USEPA)'s current regulation defines loading capacity as "the greatest amount of
loading that a water can receive without violating water quality standards." (40 CFR §
130.2(f)).
The approach used to calculate the temperature loading capacity for this portion of the South
Fork Clearwater River Subbasin TMDL is "system potential." System potential is achieved
F-27 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
when nonpoint source solar radiation loading is representative of near stream vegetation and
channel morphology conditions without human disturbance and point source discharges
cause no measurable temperature increases in surface waters.
System Potential Effective Shade - Defined
The primary factors that affect shade are near-stream vegetation height and channel width
(i.e., bankfull width). The maximum level of shade practical at a particular site is termed the
"system potential" effective shade level. System potential effective shade occurs when:
1. Near-stream vegetation is at a mature life stage
• Vegetation community is mature and undisturbed from anthropogenic sources
• Vegetation height and density are at or near the potential expected for the given plant
community
• Vegetation is sufficiently wide to maximize solar attenuation
• Vegetation width accommodates channel migrations
2. Channel width reflects a suitable range for hydrologic process given that near-stream
vegetation is at a mature life stage
• Stream banks reflect appropriate ranges of stability via vegetation rooting strength
and floodplain roughness
• Sedimentation reflects appropriate levels of sediment input and transport
• Substrate is appropriate to channel type
• Local high flow shear velocities are within appropriate ranges based on watershed
hydrology and climate
System Potential Land Cover
As listed above, "system potential land cover" is necessary to achieve "system potential
effective shade" and is defined for purposes of the TMDL as "the potential near-stream land
cover condition which can grow and reproduce on a site, given climate, elevation, soil
properties, plant biology, and hydrologic processes." System potential does not consider
management or land use as limiting factors. In essence, system potential is the design
condition used for TMDL analysis that meets the temperature standard by minimizing human
related warming.
System potential is an estimate of the condition where anthropogenic activities that cause
stream warming are minimized. System potential is not an estimate of pre-settlement
conditions. Although it is helpful to consider historic land cover patterns, channel conditions,
and hydrology, many areas have been altered to the point that the historic condition is no
longer attainable given drastic changes in stream location and hydrology (channel armoring,
wetland draining, urbanization, etc.).
F-28 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
System Potential Simulation
Loading capacity in the South Fork Clearwater River Subbasin is largely controlled by
nonpoint source influences of heat to the system. Temperatures rise throughout much of the
watershed due to accumulated heat energy. The greatest change in the heat budget has been
an increase in direct solar radiation loading due to human-caused reductions in shade.
System potential was estimated as the August solar radiation levels that would reach the
stream surface under conditions where anthropogenic activities would not measurably
increase temperature. The system potential radiation load is the loading capacity.
Current conditions were modeled using an effective shade calculator (Heat Source 6.5 [Boyd
1996]), using recently collected field data and other spatial data sources (i.e., bankfull width
data, DEM, DOQ, and Pi_stratum). These features were measured on a very fine scale using
existing GIS databases and by digitizing with digital orthophoto quadrats. Specifically,
"system potential effective shade" was simulated by incorporating expected vegetation stand
height and density conditions at "system potential land cover."
It is important to distinguish between site potential shade and system potential shade, the
latter being a broad scale view. For a given location, it is expected that site potential shade
could be greater than system potential shade. Over a large area (e.g., a river reach), it is
unlikely that all sites will be at their site potential due to localized natural disturbances (e.g.,
fire, flood, landslide, disease, etc.) causing some fraction of the area to be in a less than
"mature" state. Accordingly, "system potential land cover" used to calculate "system
potential effective shade" incorporates a disturbance component that was developed from
available land cover data sets.
Land Cover Classification
Vegetation Response Units (VRUs), Habitat Type Groups (HTGs), and the National Wetland
Inventory (NWI) are three land cover classifications available for the South Fork Clearwater
River Subbasin. Land cover classifications from these sources are spatially explicit and are
mapped out for the basin.
The VRUs and HTGs emphasize the vegetation component of land cover and differentiate
between forest and non-forest land cover types. These were used, along with NWI data, to
establish the vegetative community descriptions used in to develop appropriate shade targets
for the South Fork Clearwater River Subbasin. Brief descriptions of VRUs, HTGs, and the
NWI are presented below, and detailed information about VRU and HTG is presented in
Appendix H.
Vegetation Response Units
The VRUs are broad ecological land units that display unique patterns of habitat type groups
(potential vegetation) and terrain. The VRU classification and delineation was developed for
the South Fork Clearwater River Subbasin and was reported within the South Fork
Clearwater River Landscape Assessment (USDA 1998) (Figure F-17). The components used
F-29 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
to build the VRU classification system are habitat type groups (potential vegetation),
landform, and pre-settlement disturbance processes (like fire regimes). The VRUs are
basically a product of geology, landform, climate, and soil. Individual VRUs have similar
patterns of disturbance and successional processes. Patterns of plant community composition,
age class structure, and patch size will tend to fall within certain ranges for each VRU. The
VRUs are intended to provide a means to estimate resource capabilities, ecological integrity,
and responses to natural and human-caused disturbances. Ultimately, VRUs are intended to
be templates for assessing historic and current condition and developing target or desired
landscapes.
Table F-5 illustrates the percent distribution of VRU classes within a 300-meter buffer
surrounding the South Fork Clearwater River and several major tributaries. As can be seen
in this table, riparian areas are often dominated by a few VRU classes, and the total number
of VRU classes for each river system is limited. A detailed description of the 13 individual
VRU habitat types within the South Fork Clearwater River Subbasin are provided in
Appendix H.
Table F-5. Percent distribution of Vegetation Response Units (VRUs) within a
300-meter buffer surround the South Fork Clearwater River and
several major tributaries.
VRU
#
1
2
3
4
5
6
7
8
9
10
12
16
17
98
SF
CWR
88.0
6.8
0.4
4.4
0.4
Three-
mile
Creek
39.0
8.7
52.3
Crooked
Creek
20.4
5.4
50.9
13.2
10.1
Red
River
1.5
2.1
12.7
83.7
0.0
American
River
79.7
6.0
14.3
0.1
Little Elk
Creek
54.7
37.8
0.2
7.2
Big
Elk/Elk
Creek
3.0
1.4
69.8
14.0
0.3
11.5
0.0
Newsome
Creek
0.3
21.8
29.8
41.1
7.1
(VRU #98 signifies "no code")
F-30
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
Vegetation Responce Units
I | VRU 1 - Convex Slopes, Subalpine Fir
VRU 2 - Glaciated Slopes, Subalpine Fir
VRU 3 - Breaklands, Grand Fir and Douglas Fir
^| VRU 4 - Rolling Hills, Grand Fir
I | VRU 5 - Moraines, Subalpine Fir and Grand Fir
| | VRU 6 - Cold Basins, Grand Fir and Subalpine Fir
| | VRU 7 - Moist uplands, grand fir and Pacific Yew
| | VRU 8 - Breaklands, Cedar and Grand Fir
| | VRU 9 - Glaciated Ridges, Subalpine Fir and Whitebark Pine
| | VRU 10 - Uplands, Alder, Grand Fir and Subalpine Fir habitat type
| | VRU 12 -Stream Breaklands, Bunchgrass and Shrublands
| | VRU 16 - Plateaus, Bunchgrass and Shrublands habitat types
| | VRU 17 - Rolling Hills, Cedar and Grand Fir
Figure F-17. Vegetation Response Units (VRUs) for the South Fork Clearwater River Subbasin
F-31
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
Forested Vegetation Response Units - Vegetation communities listed for each "forested"
VRU are presented in Table F-6. Vegetation is separated into dominant vegetation and
"other overstory" vegetation. The relative proportion of vegetation size class composition
for each "forested" VRU is summarized in Table F-7.
Table F-6. Vegetation composition within "forested" Vegetation Response
Units (VRUs).
VRU#
1
2
3 - South
3 - North
4
5
6
7
8
9
10
17
Convex slopes, subalpine fir
Glaciated slopes, subalpine fir
Breaklands, grand fir and Douglas fir
Breaklands, grand fir and Douglas fir
Rolling hills, grand fir
Moraines, subalpine fir and grand fir
Cold basins, grand fir and subalpine
fir
Moist uplands, grand fir and Pacific yew
Breaklands, cedar and grand fir
Glaciated ridges, subalpine fir and
whitebark pine
Uplands, alder, grand fir and
subalpine fir
Rolling hills, cedar and grand fir
Dominant
Vegetation*
GF, SAF, LP
SAF, LP, ES
DF, PP
GF, DF
GF, DF, PP, WL
LP, ES
LP, WL, DF, ES,
GF
GF, DF, PY
GF, DF
WBP, SAF, ES, LP
GF, SAF, ES, Sitka,
Alder
GF, DF
Other Overstory*
ES, WL, DF, WBP
PP, WL, ES, LP
LP, ES
GF, DF, SAF, WL
WBP
WL, ES, LP
WL, WRC, WWP,
ES, PY, PP, LP
WRC, WWP, WL,
ES, PP
*GF, Grand Fir; SAF, Subalpine Fir; LP, Lodgepole Pine; ES, Engelmann Spruce; WL, Western Larch; DF,
Douglas Fir; WBP, Whitebark Pine; PP, Ponderosa Pine; PY, Pacific Yew; WRC, Western Red Cedar; WWP,
Western White Pine
Table F-7. Relative proportion (percentage) of vegetation size classes for
Vegetation Response Units (VRUs).
VRU#
1
2
3-South
3-North
4
5
6
7
8
9
10
17
Non-Forest
(non-stock)
5-10
10-25
5-20
5-20
5-10
5
5-10
1-10
5-20
30-40
10-25
10-25
Seedling/
Sapling
20-30
10-30
5-30
5-30
5-50
10-40
10-30
5-20
5-30
10-30
15-25
15-25
Pole
20-30
30-65
10-20
10-20
10-30
20-60
30-45
10-25
10-20
15-60
20-30
20-30
Medium
Tree
20-30
5-15
20-40
20-40
20-30
5-30
20-40
25-35
30-50
1-10
25-40
20-35
Large Tree
5-15
10-10
20-40
20-40
10-50
3-10
5-20
35-45
20-30
1
15-25
15-40
F-32
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
Non-Forested Vegetation Response Units -Two VRUs within the South Fork Clearwater
River Subbasin are dominated by non-
forest vegetation. Vegetation Response
Units 12 and 16 are located primarily ^p^e
within the low elevation areas of the f J,
subbasin (see image to right). Detailed /JC?
descriptions about these VRUs are '
presented below (USDA 1998).
VRU12: Stream breaklands, bunchgrass,
and shmblands - This VRU is rare on
NPNF lands in the subbasin, but is —
common in the lower canyon on private
lands. Bluebunch wheatgrass and Idaho fescue habitat types are dominant. Shrubland habitat
types are common. Bluebunch wheatgrass and Idaho fescue were historically important.
Shrublands occupied draws or lower slopes. Very frequent (5-25 years), low severity fires
maintained open grasslands and rejuvenated shrublands.
VRU 12: Changes from historic conditions - On all lands, only general trends have been
noted. Disturbed grasslands (annuals and weeds) and pasture have replaced native perennials
over more than 50% of their prior extent. Upland shrublands have increased as much as
100% due to fire suppression and brush invasions of former grasslands. About 2 acres have
burned annually on NPNF lands in the subbasin since fire suppression became effective, a
decline of about 82%.
VRU 16: Plateaus, bunchgrass, and shrubland - This VRU occurs only on non-NPNF
lands. Bluebunch wheatgrass, Idaho fescue, and shrubland habitat types are common.
Bluebunch wheatgrass and Idaho fescue were historically important. Shrublands occupied
draws, lower slopes, and north aspects. Very frequent (5-25 years), low severity fires
maintained open grasslands and rejuvenated shrublands.
VRU 16: Changes from historic conditions - On all lands, only general trends have been
noted. Annual cropland has replaced native perennials on more than 80% of their prior
extent. Hayland and pasture have largely replaced the remaining native prairie. Upland
shrublands have probably also decreased. Fire incidence has certainly declined, but to what
extent is unknown.
F-33 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
Habitat Type Groups
Habitat type grouping is based on similarities in natural disturbance regimes, successional
patterns, and structural characteristics of mature stands. The HTGs are intended to assist
with sub-regional and landscape assessments. Habitat Type Groups were developed for
northern Idaho and western Montana. Classified HTGs within the South Fork Clearwater
River Subbasin were subsequently adapted from the original HTG coverage (Figure F-18).
The HTGs are separated into forest and non-Forest categories. A detailed description for
each category is presented in Appendix H. The HTG information was obtained from the
document, Biophysical Classification - Habitat Groups and Descriptions.
Vegetation Response Units and Habitat Type Groups
Extensive GIS sampling was conducted on both the VRU and HTG coverages in order to
determine the distribution of HTGs for each VRU within a 300-meter buffer surrounding the
South Fork Clearwater River and several major tributaries. Table F-8 presents the measured
distribution for these parameters.
The HTG coverage is at a higher spatial resolution of vegetation land conditions than the
VRU. Accordingly, several HTGs are often observed for each VRU. However, there is a
very close relationship between land cover conditions described within these two data sets.
F-34 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Habitat Type Groups (HTGs)
HTG «0 -Rock
HTG #1 -Warm and diy PP or DF /grass types
HTG #2 - Moderately warm and dry most DF and dry GF typ
HTG #3- Moderately warm and moderately dryDF nithl.lBO ordiyGF
HTG #4 . Moderately warm and moist GF /ginger and clintonia types
HTG #5 - Moderately c ool and moist RC and WM /ginger and clintonia
HTG #6 - Moderately c ool and wet RC/Athyrium, Oplopanax,and Adantium
HTG #7 - Cool and moist AF, MH and E S types
HTG #8 - Cool and wet AF, ES, and Mil types
HTG #9 - Cool and moderately dry AF and LP types
HTG #10 - Cold and moderately dry AF and LPAiasc and Luzula types
HTG #11 Cold high elevation WBP and AF types
HTG #15 G ra ssland steppe
HTG #17 - Grassland steppe, bluebunch wheatgrass predominant
HTG #30 - Shrub land series
HTG #60 - Mountain bottoTnlandsand meadows
HTG #80 - Alpine meadows and scrub
HTG #90 -Water
Figure F-18. Habitat Type Groups Within the South Fork Clearwater River Subbasin
F-35
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
Table F-8. Percent distribution of Habitat Type Groups (HTGs) for each
classified Vegetation Response Units (VRUs) zone within a 300-
meter buffer surrounding the South Fork Clearwater River and
several major tributaries.
Main Stem South Fork Clearwater River
KTG (VRU 3)
0
1
2
3
4
7
15
17
30
50
98
Total
% of Total
1.0%
5.4%
35.6%
14.5%
18.0%
0.2%
0.1%
12.1%
0.0%
1.2%
0.0%
88JO%
HTG(VRU6)
0
2
3
4
Total
% of Total
0.0%
0.2%
4.6%
2.0%
6.8%
HTG(VRU7)
2
3
4
Total
% of Total
0.0%
0.2%
0.3%
04%
KTG (VRU 12)
0
1
2
4
15
17
50
Total
% of Total
0.0%
0.6%
1 .2%
0.0%
0.4%
2.2%
0.0%
4.41
HTG(VRU99)
0
1
2
4
15
17
50
98
Total
% of Total
0.2%
0.0%
0.1%
0.0%
0.0%
0.0%
0.0%
0.0%
04%
Threemile Creek
HTG(VRU3) % of Total
1 0.2%
2 15.1%
3 3.6%
17 17.4%
30 1 .2%
50 1 .4%
Total 39jTJ%
KTG (VRU 12) % of Total
2 4.1%
17 4.5%
30 0.1%
Total 8.7%
HTG(VRU16) % of Total
1 0.2%
2 0.7%
17 30.3%
30 21.1%
50 0.0%
Total 52.3%
Red River
HTG(VRU1)
2
3
7
8
9
Total
% of Total
0.0%
0.1%
1 .2%
0.1%
0.1%
1.5%
HTG(VRU3)
2
3
4
Total
% of Total
1.1%
0.7%
0.3%
2.1%
HTG (VRU 4) | % of Total
0 0.1 %
2 2.7%
3 8.7%
4 0.7%
7 0.3%
60 02%
Total 12.7%
KTG (VRU 6)
0
1
2
3
4
7
8
9
60
Total
% of Total
0.5%
0.0%
2.4%
39.0%
9.9%
6.7%
3.8%
4.3%
17.1%
83.7%
HTG (VRU 99) % of Total
60 0.0%
Total 0.0%
Big Elk Creek
HTG (VRU 1) % of Total
3 00%
7 13%
8 0.8%
9 09%
Tola! 30%
HTG(VRU3) % of Total
4 1.2%
7 0 1 %
Total 1 4%
KTG (VRU 6) % of Total
3 532%
4 16.5%
7 0 1 %
Total 690%
HTG (VRU 7) | % of Total
3 1.1%
4 7.7%
7 2.1%
8 3.2%
Total 140%
HTG (VRU 9) % of Total
3 03%
4 0.0%
8 0.0%
9 0.0%
Total 0 3%
HTG(VRUIO) % of Total
3 0 2%
4 6.5%
7 2 5%
8 2.4%
9 0 0%
Total 115%
HTG (VRU 99)|% of Total
3 a o%
Total 0 0%
F-36
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
Table F-8 (continued). Percent distribution of Habitat Type Groups (HTGs) for
each classified Vegetation Response Units (VRUs) zone within a
300-meter buffer surrounding the South Fork Clearwater River and
several major tributaries.
American River
HTG (VRU 6)
0
2
3
4
7
8
9
60
Total
% of Total
0.4%
0.1%
59.9%
14.3%
0.3%
1.1%
1 .2%
2.3%
79.7%
HTG(VRU7)
3
4
8
Total
% of Total
1 .5%
4.1%
0.4%
6JO%
HTG (VRU 10)
3
4
7
8
Total
% of Total
1.8%
10.0%
2.4%
0.1 %
143%
HTG (VRU 99) % of Total
3 0.1%
Total 0.1%
Little Elk Creek
HTG(VRU6)
0
2
3
4
7
8
9
60
Total
% ofTolal
0.4%
0.1%
59.9%
14.3%
0.3%
1.1%
1 .2%
2.3%
79.7%
HTGfyRU?) % of Total
3 1 .5%
4 4.1%
8 0.4%
Total 6J011
WTG (VRU 10)
3
4
7
8
Total
% of Total
1.8%
10.0%
2.4%
0.1 %
14311.
HTG(VRU99) % of Total
3 0.1%
Total 0.111
Crooked Creek
HTG (VRU 1)|% of Total
0 0.0%
2 1 .2%
3 9.3%
4 0.9%
7 1 .8%
8 4.1%
9 3.0%
Total 204%
HTG (VRU 2)|% of Total
2 0.2%
3 0.6%
4 0.2%
7 0.9%
8 2.4%
9 1.1%
Total 54%
HTG (VRU 3) | % of Total
0 0.4%
1 0.2%
2 7.5%
3 26 7%
4 12.5%
7 1.3%
9 2.2%
Total 50.9%
KTG (VRU 6) hi of Total
2 0.2%
3 8.1%
4 3.6%
7 0.3%
9 1.0%
Total 132%
HTG (VRU 7) % of Total
2 0.1%
3 3.8%
4 5.2%
7 0.7%
9 0.3%
Total 10.1%
Newsome Creek
HTG(VRU1) % of Total
4 0.3%
Total 0.3%
HTG(VRU3)
0
2
3
4
7
8
9
Total
% of Total
00%
32%
21%
10.3%
40%
1.9%
0.3%
21.8%
HTG (VRU 6) | % of Total
3 8.0%
4 13.2%
7 2.7%
8 4.4%
9 0.2%
60 1 4%
Total 29.0%
HTG (VRU 7)
3
4
7
8
60
Total
% of Total
1 1 .2%
29.8%
0.0%
0.0%
0.0%
41.1%
HTG (VRU 10)1% of Total
4 7.1%
Total 7.1%
F-37
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
National Wetlands Inventory
A wetland database has been developed for the South Fork Clearwater River Subbasin
(Harrison and Kellogg 1987). The database, part of the National Wetlands Inventory (NWI),
contains a description of riparian wetland locations throughout the subbasin. Wetlands are
broken into three main categories: 1) herbaceous, 2) forested, and 3) shrub. These are
subdivided into numerous other units based on site-specific information. Classifications
were developed through an analysis of aerial photographs, examining visible vegetation,
hydrology, and geography. Figure F-19 illustrates the spatial distribution of wetland areas
within the South Fork Clearwater River Subbasin.
Figure F-19. National Wetlands Inventory for the South Fork Clearwater River
Subbasin
It was estimated from this work that only 4-6% of the land area within NPNF meets the
Forest Service riparian area definition for a riparian wetland. The purpose of this inventory
was to map out riparian wetland areas so that those areas could be protected, and thus
provide benefits to the public through flood and storm damage control, erosion control, water
quality improvement, and fish and wildlife resource protection.
F-38
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
System Potential Land Cover Condition - "Forest" Vegetation
Mature vegetation height information for species present within the South Fork Clearwater
River Subbasin is listed in Table F-9. Note that the upper end of measured tree heights
within the South Fork Clearwater River Subbasin (illustrated in Figure F-4 and presented in
Table F-2) correspond closely with the values reported below.
Table F-9. Mature vegetation height condition (U.S. Department of Agriculture
Fire Effects Information System [fs.fed.us/database/feis])
Vegetation Type
Grand fir
Engelmann spruce
Douglas fir
Subalpine fir
Ponderosa pine
Lodgepole pine
Western red cedar
Western larch
Rocky mountain maple
Western white pine
Whitebark pine
Sitka alder
Pacific yew
Black cottonwood
Western hemlock
Red osier dogwood
Thimbleberry
Western snowberry
Western serviceberry
Booth willow
Geyer willow
Drummond willow
Carex rostrata
Carex lenticularis
Height (ft)
131 -164
45-130
100-130
60-100
90-130
60-80
70-100
20-30
50-70
10-15
20-40
100-150
3-19
6.6-8.2
2-4
3-26
9-18
up to 20
6.5- 13
1 -4
0.1 -1
Average
Value (ft)
148
88
115
80
110
70
85
164
25
200
60
12
30
100
125
11
7.4
3
15
14
15
10
2.5
0.5
High Elev
(ft)
140
65
130 (upper
SW facing)
110
Mid - Low
Elev (ft)
152
110
170 (lower
NE facing)
140
F-39
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
As mentioned previously, it is unlikely that all sites throughout a watershed will be at a
mature condition due to localize natural disturbances (e.g., fire, flood, landslide, disease,
etc.). causing some fraction of the area to be in a less than "mature" state. Accordingly, the
relative proportion of size classes established for each VRU was used to incorporate age
structure for the estimate of height conditions, which was used to establish system potential
effective shade conditions. That is, the riparian community is represented by various age
classes. Those age classes will be used to calculate respective height conditions for these age
classes. Size class information for each VRU is presented in Table F-7.
The following steps were used to estimate size class distribution for each VRU based on the
reported ranges in Table F-7:
• Step 1 - Allocate maximum value for percent "large tree" class
• Step 2 - Allocate maximum value for percent "non-stock" class
• Step 3 - Allocate maximum, or remaining, value for percent "medium tree" class
• Step 4 - Allocate maximum, or remaining, value for percent "pole" class
• Step 5 - Allocate remaining value for percent "seedling/sapling" class
For example, VRU 4 would be allocated 50% for "large tree" (i.e., maximum value), 10% for
"non-stocked" (i.e., maximum value), 30% for "medium tree" (i.e., maximum or remaining
value), 10% for "pole" (i.e., maximum or remaining value), and 0% for "seedling/sapling"
(i.e., remaining value). As can be seen, this method incorporates an estimate of expected
open areas ("non-stock"), as well as incorporates disturbance through using the expected size
classes.
The following rules were used to estimate height conditions for each of the size classes.
• "Large tree" was assigned the average of mature vegetation height (see Table F-9)
• "Medium tree" and "pole" were assigned a height calculated from species-specific
growth curves developed from data collected within the NPNF (see Table F-3). The
dbh values used in this calculation were assigned the maximum of the range listed for
the size class (see Table F-l)
• "Seedling/sapling" was assigned a value of 20 feet
• "Non-stock" was assigned a height of zero
As noted in Table F-6, numerous vegetation species (categorized into "dominant" and "other
overstory" groups)are shown to be present within each VRU category. Vegetation height
conditions were developed for each species present within the respective VRU, which were
summarized into a weighted average condition using values calculated using the size class
distribution rule set presented above. These values for each species were average within
"dominant," and "other overstory" groups (see Table F-6). A weighting factor of 80% for
dominant and 20% for "other overstory" was used (i.e., (75' * 80% = 60' (dominant)) plus
(90 * 20% = 18 (other overstory)) = 78').
F-40 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
Overhang was assigned a value of 10% of the final vegetation height (i.e., 78 feet * 10% =
7.8 feet). Overhang is the tree branch length from the trunk of the tree.
System Potential Land Cover Condition - "Non-Forest" Vegetation
Vegetation height, used to develop system potential effective shade, for "non-forest" areas,
was calculated as the average of mature vegetation height. The percent of the stream bank
not covered by any vegetation for "non-forest" areas is 10% for both shrub and wetland
areas. This is analogous to the "non-stock" category in forested areas.
Shrub vegetation used to calculate vegetation height was obtained from HTG 30 (shrub
steppe) (Appendix H). Based on shrub species in HTG 30, the average mature height was
8.4 feet. Grass was assigned a height of 1 foot. The distributions of shrub and grass were
assigned 80% and 20%, respectively. Overhang was assigned 50% of height.
Riparian Wetlands
Approximately 4-6% of the land area within the NPNF is comprised of riparian wetlands
(Figure F-20). Specifically, the NWI categorized wetland communities into scrub,
herbaceous, and forest.
Herbaceous Meadow Wetland
A discussion of the best example of potential mature vegetation for a herbaceous meadow
system in the South Fork Clearwater River Subbasin is included in the document, Analysis of
the Riparian Vegetation of Red River Meadows (Brunsfeld 1994). The average of mature
average vegetation heights of listed potential vegetation was 13.75 feet, and the average
sedge height was 1.5 feet. The average of mature average vegetation heights of listed
potential vegetation was used in calculating system potential conditions.
Forest Meadow Wetland
Bureau of Land Management staff provided site data from the East Fork of American River,
(East Fork American River - Site # 3) which is a good example of a mature forest meadow
wetland vegetation community within the South Fork Clearwater River Subbasin (Craig
Johnson, BLM, personal communication). The distribution of vegetation measured at this
site was 18% tree, 22% shrub, and 60% sedge. Tree vegetation at this site was 50% grand
fir, 33% Engelmann spruce, and 17% lodgepole pine. Similar to "herbaceous meadow
wetlands," the average of mature average vegetation heights of listed potential vegetation
was used in calculating system potential conditions.
Scrub Meadow Wetland
Because of a lack of information, system potential land cover conditions used to develop
system potential shade conditions for scrub meadow wetland systems were assigned values
obtained from herbaceous meadow wetlands.
F-41 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
System Potential Effective Shade Calculation
System potential effective shade conditions were calculated using the estimated vegetation
stand information presented above (Figure F-20). The Heat Source 6.5 shade calculator was
used for this analysis (Boyd 1996).
VRU 1 (Convex slopes, subalpine fir)
i 0 or 180 degrees from North
45, 135, 225 or315 degrees from North
• 90 or 270 degrees from North
Near Stream Disturbance Zone (feet)
^ ^ ^ ^ ro
Near Stream Disturbance Zone (meters)
VRU 2 (Glaciated slopes, subalpine fir)
i 0 or 180 degrees from North
45, 135, 225 or 315 degrees from North
t 90 or 270 degrees from North
^—Average
Near Stream Disturbance Zone (Feet)
0%
629.0
Near Stream Disturbance Zone (meters)
Figure F-20. Shade Curves Developed for Vegetation Response Units (VRUs)
F-42
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
VRU 3 (Stream breaklands, grand fir and Douglas-fir)
A 0 or 180 degrees from North
45, 135, 225 or315 degrees from North
• 90 or 270 degrees from North
•—Average
Near Stream Disturbance Zone (Feet)
629.0
Near Stream Disturbance Zone (meters)
VRU 4 (Rolling hills, grand fir)
A 0 or 1 BO degrees from North
45, 135, 225 or315 degrees from North
• 90 or 270 degrees from North
—•Average
Near Stream Disturbance Zone feet)
c
o
o
tf)
1
B29.0
Near Stream Disturbance Zone (meters)
Figure F-20 (continued). Shade Curves Developed for Vegetation Response
Units (VRUs)
F-43
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
VRU 5 (Moraines, subalpine fir and grand fir)
0 or 1 BO degrees from North
45, 135, 225 or315 degrees from North
90 or 270 degrees from North
Near Stream Disturbance Zone (feet)
a
o
C >.
o a
a
1
629.0
Near Stream Disturbance Zone (meters)
VRU 6 (Cold basins, grand fir and subalpine fir)
A 0 or 180 degrees from North
45, 135, 225 or315 degrees from North
• 90 or 270 degrees from North
Near Stream Disturbance Zone (Feet)
100%
90%
80%
O)
c
o
v>
1
629.0
Near Stream Disturbance Zone (meters)
Figure F-20 (continued). Shade Curves Developed for Vegetation Response
Units (VRUs)
F-44
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
VRU 7 (Moist uplands, grand fir and Pacific yew)
A 0 or 180 degrees from North
45, 135, 225 or315 degrees from North
* 90 or 270 degrees from North
^—Average
Near Stream Disturbance Zone (feet)
100%
0%
629.0
Near Stream Disturbance Zone (meters)
VRU 8 (Stream breaklands, cedar and grand fir)
4 0 or 180 degrees from North
45, 135, 225 or 315 degrees from North
• 90 or 270 degrees from North
^—Average
Near Stream Disturbance Zone (feet)
100%
0%
629.0
Near Stream Disturbance Zone (meters)
Figure F-20 (continued). Shade Curves Developed for Vegetation Response
Units (VRUs)
F-45
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
VRU 9 (Glaciated slopes, subalpine fir and whitebark pine)
0 or 1 BO degrees from North
45, 135, 225 or315 degrees from North
90 or 270 degrees from North
Near Stream Disturbance Zone (feet)
a
o
>.
a
-o
1
_
ra
"o
Near Stream Disturbance Zone (meters)
VRU 10 (Uplands, alder, grand fir and subalpine fir habitat types)
4 0 or 180 degrees from North
45, 135, 225 or315 degrees from North
• 90 or 270 degrees from North
^—•Average
Near Stream Disturbance Zone feet)
v>
0%
Near Stream Disturbance Zone (meters)
O)
c
a
o
_
a
"5
v>
1
629.0
Figure F-20 (continued). Shade Curves Developed for Vegetation Response
Units (VRUs)
F-46
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
VRU 12 (Stream breaklands, bunchgrass and shrubland) and
VRU 16 (Plateaus, bunchgrass and shrubland)
i 0 or 1 BO degrees from North
45, 135, 225 or315 degrees from North
• 90 or 270 degrees from North
^—Average
Near Stream Disturbance Zone (Feet)
-^ -^ ro
o CN ro
CD CD 03
CN -^r LO
Near Stream Disturbance Zone (meters)
VRU 17 (Rolling hills, cedar and grand fir)
A 0 or 130 degrees from North
45, 135, 225 or315 degrees from North
• 90 or 270 degrees from North
Near Stream Disturbance Zone (Feet)
•o
a
o
_i
c
o
'
—
o
V)
\
Near Stream Disturbance Zone (meters)
Figure F-20 (continued). Shade Curves Developed for Vegetation Response
Units (VRUs)
F-47
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
Herbaceous/Scrub Wetland
A 0 or 180 degrees from North
45, 135, 225 or315 degrees from North
t 90 or 270 degrees from North
Near Stream Disturbance Zone (Feet)
ro ro CO
D9
_C
•5
a
o
ra
DC
w
o CM en in CD co co ^ CM ^r Ln
Near Stream Disturbance Zone (meters)
Forest Wetland
A 0 or 180 degrees from North
45, 135, 225 or315 degrees from North
• 90 or 270 degrees from North
^—Average
Near Stream Disturbance Zone (Feet)
^ ^ NJ
100%
_C
•5
o
•o
ft
DC
o
V)
0%
629.0
Near Stream Disturbance Zone (meters)
Figure F-20 (continued). Shade Curves Developed for Derived Wetland Areas
F-48
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
Spatial Allocation of Vegetation Land Cover
A determination of the spatial location of vegetation communities throughout the watershed
is necessary to apply system potential effective shade in the South Fork Clearwater River
Subbasin. Accordingly, the following rule set was used to determine this information.
The method utilized three main sources of information: 1) the HTG land cover data set, 2)
the VRU land cover data set, and 3) the NWI land cover data set. The HTGs and VRUs are
available for the entire subbasin and the NWI land cover data set is available for almost the
entire watershed. Figures F-21 and F-22 illustrate the rule set described below.
"Forested" Communities-
Riparian community composition was developed from information provided within the VRU
and HTG land cover data sets, while incorporating site-specific field data. The HTG land
cover data set is at a higher spatial resolution than the VRU. However, the VRUs was
developed specifically for the South Fork Clearwater River Subbasin to describe and develop
an understanding of historic and current conditions and the development of target or desired
landscapes.
Accordingly, vegetation composition used to develop system potential vegetation
composition for "forested" areas was obtained from VRUs. However, the HTG land cover
classification was used to spatially allocate "forested" and "non-forested" locations
throughout the watershed. In addition, the NWI land cover classification was used to
delineate wetlands areas.
"Non-Forested" Communities
Two VRUs are described as "non-forest" conditions (i.e., VRU 12 [Stream breaklands,
bunchgrass and shrublands] and VRU 16 [Plateaus, bunchgrass and shrubland]). These two
VRUs are primarily located within low elevation areas outside of NPNF boundary.
Shrublands are the dominant vegetation within draws and lower slopes in these two VRUs.
Once again, the HTG land cover classification was used to spatially allocate these "non-
forest" locations throughout the watershed. In addition, the NWI was used to delineate
wetlands areas within these coded "non-forested" areas.
F-49 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
Habitat Type Group (HTG) Code
/ \
/
"Forest Type"
HTG Codes
National Wetland
Inventory Code
/ \
Yes / \ No
/ \
Apply Appropriate Apply Appropriate
"Wetland" System "Forested Type"
Potential (SP) Vegetation Response
Shade Curve Unit (VRU) System
Potential (SP) Shade
Curve
\
"Non-Forested Type"
HTG Codes
National Wetland
Inventory Code
/ \
Yes / \ No
/ \
Apply Appropriate Apply Appropriate
"Wetland" System "Non-Forested Type"
Potential (SP) Vegetation Response
Shade Curve Unit (VRU) System
Potential (SP) Shade
Curve
Figure F-21. Vegetation Composition Application Rule Set- South Fork
Clearwater River Main Stem
Habitat Type Group (HTG) Code
/ \
/
"Forest Type"
HTG Codes
National Wetland
Inventory Code
/ \
Yes/ \No
/ \
Apply Appropriate Apply
"Wetland" System Cumulative
Potential (SP) Watershed
Shade Curve Effects (CWE)
Target
\
"Non-Forested Type"
HTG Codes
National Wetland
Inventory Code
/ \
Yes/ \No
/ \
Apply Appropriate Apply Appropriate
"Wetland" System "Non-Forested Type"
Potential (SP) Vegetation Response
Shade Curve Unit (VRU) System
Potential (SP) Shade
Curve
Figure F-22. Vegetation Composition Application Rule Set - Areas Other than
the South Fork Clearwater River Main Stem
F-50
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
Site Specific Calculation of "System Potential Effective Shade"
The rule set illustrated above was applied to the South Fork Clearwater River and other
tributaries throughout the subbasin. Specifically, system potential effective shade conditions
for each 100-foot modeling reach was calculated using the system potential land cover
condition derived using the VRU, HTG, and NWI data sets. In addition, all relevant
landscape features impacting effective shade production were included in model
development for each 100-foot segment (i.e., bankfull width [e.g., NSDZ], aspect, elevation,
topographic shade angle, latitude, and longitude [see Figures F-6 through F-10]).
Using the rule set presented above, system potential effective shade conditions were
calculated and are presented in Figure F-23. Current effective shade conditions, which were
initially presented in Figure F-12, are also plotted on this figure.. System potential effective
shade conditions presented in Figure F-23 utilize the same algorithms and vegetation
community conditions used to develop the shade curves (see Figure F-21).
As can be seen in Figure F-23, observed current effective conditions are often similar to
calculated system potential effective shade conditions; however, there are many areas where
current levels are much below potential conditions. It is important to note that this line
represents a 0.25-mile moving average condition from the 100-foot measurements. This was
done so that general patterns in current and potential shade conditions could become more
apparent in Figure F-23.
100%
90%
40%
30%
System Potential Effective Shade (%) -1/4 Mile Moving Average
— Current Effective Shade - 1/4 Mile Mo vine) Average
0 5 10 15 20 25 30 35 40 45 50 55 60 65
RKrei Mile (South Fork Cleaw.itei Rh/ei»
Figure F-23. Current and System Potential Effective Shade Conditions - South
Fork Clearwater River and Major Tributaries
F-51
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
100% •
90% -
80% •
» 70% •
^ 60% •
5 50% •
'S 40% '
3 30% •
0 20% •
10% •
0% •
C
1/4Mle Moijng A*rage - Currert Effeaile
l/4Mle ruling A*rag= - Syaem Pcterrta
Siegal Creek
Corfluense
!L/x^
4812
Shade (%)
Effective Shads Of-) ©CunBrvt BFW
Ccnfi
I
J
I
16
I
If
\
i
I
I
I
I ,
II
I
•
Creek
j
I
yV
1
.
II 1\ /(
i Vyw 1
20 24 28 32
River Mile (Red Rivei)
5 40% '
15
= 30% •
5 20%-
10% -
0%
,2 - Currert Effective Srade (%)
K • Syaem Paermal FJfects'e Shacfe (%) @Currem BRW
4 6 8 10 12 14
Rivei Mile IThieeMile Creek)
80%
» 70%
_2
"> 60%
1
50%
i 40%
15
3 30%
0 20%
10%
0%
IM Mle Mowig Average - Current Effective Shade fU)
1/4 Mle rutoiing Awrage - Si/Hem Pctartia! Eifectsie Shaj
6 8 10 12
Rr/ei Mile (New wine Cieek}
16 18 20
Figure F-23 (continued). Current and System Potential Effective Shade
Conditions - Red River, Three Mile Creek, and Newsome Creek
F-52
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
100% •
90% •
_ 00%
«f 70%
5 60% -
I
£ 50% •
LU
•a 40%
oi
= 30%
0 20% -
10% -
0%
0
1 fl tulle fufowrfl Aerag? - Qjnent Effects Shade (%)
tttMle Wfaxing Aeragi - System Potential BfeotKe Shade C
1 2
River Mile (Elk Cree 10
100% •
90% -
» 70%
5
«> 60% •
? 50% •
£
u
^ 40% •
1/4 Mile MowigAueag; - Gwent Effects Stade(%)
1/4MileMowigAtfsaga - System Potential Effete Shade (
4567
Rivei Mile (Bill Elk Creek)
Figure F-23 (continued). Current and System Potential Effective Shade
Conditions - Little Elk, Elk, and Big Elk Creeks
100% -
90% -
80% -
70% •
60%
50%
i;4Mile
I /4 Mile
- Cuirem Etfectiu? Shade (^)
- System Potential Effejtiys Shada i
34567
Rivei Mile (Biltchei Cieek)
9 10 11 12
Figure F-23 (continued). Current and System Potential Effective Shade
Conditions - Butcher Creek.
F-53
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
Temperature Impairments
Nine water bodies were identified in Chapter 3 as water quality limited due to temperature
and are included in the Idaho 1998 303(d) List (Table F-10). As part of the TMDL effort for
the South Fork Clearwater River Subbasin, hourly stream temperatures were measured at
various locations throughout the watershed during the past several summers. Stream
temperatures follow a longitudinal (downstream) heating pattern. All streams in the subbasin
that have been monitored have been found to exceed temperature criteria, even though they
are not all currently 303(d) listed. The goal of this effort is to achieve applicable temperature
criteria and restore all of these to "full support of designated beneficial uses" (Idaho Code §
39.3611,3615).
Table F-10. Water bodies included in Idaho 1998 303(d) list for temperature.
Water Body Boundary
SF Clearwater River
SF Clearwater River
SF Clearwater River
SF Clearwater River
SF Clearwater River
Threemile Creek
Butcher Creek
Big Elk Creek
Little Elk Creek
Butcher Creek to mouth
Johns Creek to Butcher Creek
Johns Creek to Butcher Creek
Tenmile Creek to Johns Creek
Crooked River to Johns Creek
Confluence of Red River and American River to Crooked Creek
Source to mouth
Source to mouth
Source to mouth
Water Quality Standard Identification
The five water bodies of the South Fork Clearwater River main stem and Threemile Creek
have designated beneficial uses of cold water aquatic life and salmonid spawning. Little Elk
Creek, Big Elk Creek, and Butcher Creek have existing beneficial uses of cold water aquatic
life and salmonid spawning. All these streams must therefore meet the cold water
temperature criteria and meet the salmonid spawning temperature criteria when spawning
occurs (Table F-l 1).
Table F-11. Applicable temperature criteria.
Beneficial Use
Cold Water Aquatic Life
Salmonid Spawning
Bull Trout
Criteria
19°C(66.2°F)
daily average
9°C (48.2°F)
daily average
22°C(71.6°F)
daily max.
13°C(55.4°F)
daily max.
10°C(50°F)MWMT*
Reference
IDAPA 58.01 .02.250.02.b
IDAPA 58.01 .02.250.02.e.ii
40 CFR Part 131 .33(a)
*maximum weekly maximum temperature
F-54
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
In addition, USEPA has established temperature criteria for bull trout (Figure F-l 1) for a
number of water bodies in the subbasin, including two which are 303(d) listed: Big Elk and
Little Elk Creeks (See Appendix B for a full listing). These creeks must meet the federally-
promulgated bull trout temperature criteria of 10 °C (50 °F) as an average of daily maximum
temperatures over a seven day period (MWMT).
Seasonal Variation - Clean Water Act §303(d)(1)
Stream reaches within the South Fork Clearwater River Subbasin experience prolonged
warming starting in late spring and extending into the fall. Maximum temperatures typically
occur in July and August (see Figure F-l 1). The TMDL focuses the analysis during this
critical period.
Nonpoint Source Component of Loading Capacity
Solar radiation load at system potential vegetation conditions is the loading capacity.
Portions of the loading capacity are typically divided among natural, human, and future
nonpoint pollutant sources. Table F-12 lists load allocations (i.e., distributions of the loading
capacity) according to land use. In the South Fork Clearwater River Subbasin, the loading
capacity of the system is all allocated to natural sources. No assimilative capacity exists for
the other sources. This requires that nonpoint sources reduce temperature inputs to reach
system potential conditions. The means of achieving these conditions is through restoring
and protecting riparian vegetation and narrowing stream channel widths. The remainder of
this section describes how those conditions are assessed.
Table F-12. Temperature allocation summary.
Nonpoint Sources
Source
Natural
Agriculture
Forestry
Urban
Future Sources
Loadinq Allocation
Distribution of Solar Radiation Loading Capacity
100%
0%
0%
0%
0%
Surrogate Measures and Nonpoint Source Load Allocations - 40 CFR § 130.2(i)
The South Fork Clearwater River Subbasin temperature TMDL incorporates measures other
than "daily loads" to fulfill 303(d) requirements. Although a loading capacity for heat energy
can be derived (e.g., Langleys per day), it is of limited value in guiding management
activities needed to solve identified water quality problems. In addition to heat energy loads,
F-55 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
this TMDL allocates "other appropriate measures" (or surrogates measures) as provided
under USEPA regulations (40 CFR
130.2(1)).
The Report of the Federal Advisory Committee on the Total Maximum Daily Load (TMDL)
Program (FACA 1998) offers a discussion on the use of surrogate measures for TMDL
development. The report says:
"When the impairment is tied to a pollutant for which a numeric criterion is
not possible, or where the impairment is identified but cannot be attributed to
a single traditional "pollutant," the state should try to identify another
(surrogate) environmental indicator that can be used to develop a quantified
TMDL, using numeric analytical techniques where they are available, and best
professional judgment (BPJ) where they are not. The criterion must be
designed to meet water quality standards, including the waterbody's
designated uses. The use of BPJ does not imply lack of rigor; it should make
use of the "best" scientific information available, and should be conducted by
"professionals." When BPJ is used, care should be taken to document all
assumptions, and BPJ-based decisions should be clearly explained to the
public at the earliest possible stage.
If they are used, surrogate environmental indicators should be clearly related
to the water quality standard that the TMDL is designed to achieve. Use of a
surrogate environmental parameter should require additional post-
implementation verification that attainment of the surrogate parameter results
in elimination of the impairment. If not, a procedure should be in place to
modify the surrogate parameter or to select a different or additional surrogate
parameter and to impose additional remedial measures to eliminate the
impairment."
The nonpoint source assessment presented above demonstrated that stream temperatures
warm as a result of increased solar radiation loads, due to anthropogenic disturbances to
near-stream vegetation and channel morphology. A loading capacity for radiant heat energy
(i.e., incoming solar radiation) can be used to define a reduction target that forms the basis
for identifying a surrogate. The specific surrogate used is percent effective shade (expressed
as the percent reduction in potential solar radiation load delivered to the water surface).
Factors that affect water temperature are interrelated. The surrogate measures (percent
effective shade and channel width) rely on restoring and protecting riparian vegetation to
increase stream surface shade levels and reducing the NSDZ width by reducing stream bank
erosion and stabilizing channels. This will reduce the surface area of the stream exposed to
radiant energy. Shade is more effective on narrow streams than on wider streams given the
same flow of water at a given point because shadows cast by trees cover a greater percentage
of the stream surface in narrow streams. Effective shade screens the water's surface from
direct rays of the sun. Highly shaded streams often experience cooler stream temperatures
than similar, but less shaded streams, due to reduced solar radiation input (Brown 1969,
F-56 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
Beschta et al. 1987, Holaday 1992, Li et al. 1994). Accordingly, the surrogate measure used
in this portion of the temperature TMDL is "system potential effective shade."
Over the years, the term, "shade," has been used in several contexts, including its
components such as shade angle or shade density. For purposes of this TMDL, shade is
defined as the percent reduction of potential direct beam solar radiation load delivered to the
water surface. Thus, the role of effective shade in this TMDL is to prevent or reduce heating
by solar radiation and serve as a linear translator to the solar loading capacities. Effective
shade is presented in greater detail in Appendix I.
Channel width is only evaluated within this TMDL as a function of stream effective shade
production. It is expected that factors and efforts associated with achieving effective shade
targets will promote channel recovery and improvement. That is, effective shade allocations
associated with this TMDL will achieve, through passive restoration, system potential
channel width conditions. One exception is that areas with serious channel alteration due to
past mining may require active reconfiguration to achieve desired channel conditions. A
specific target is not set for this parameter, but it is expected that these areas will be
identified in the TMDL implementation plan along with appropriate restoration strategies.
Effective Shade Surrogate Measures
The loading allocation is defined in Langleys per day, which is a unit of energy calculated by
the shade calculator (i.e., Heat Source 6.5 [Boyd 1996]). However, a load allocation in terms
of Langleys per day is not very useful in guiding nonpoint source management practices.
Fortunately, percent effective shade is a surrogate measure that can be calculated directly
from the loading capacity (i.e., Langleys per day). Percent effective shade is simple to
quantify in the field or through mathematical calculations. Figure F-20 displayed derived
effective shade curves for the South Fork Clearwater River Subbasin. Specifically, given a
measured or estimated channel width (or NSDZ) and the directional aspect of a stream, the
percent effective shade or the solar radiation loading can be estimated from the data in Figure
F-24. (Effective shade is plotted on the left y-axis, and the associated heat load in Langleys
per day is plotted on the right y-axis on this figure.) Langleys per day presented in this figure
is the load capacity.
Shade curves were applied to site-specific areas using the rule sets illustrated in Figures F-21
and F-22. Figure F-24 illustrates the calculated system potential effective shade presented in
Figure F-23 and the corresponding energy in Langleys per day.
F-57 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
fl Mile Moving Average-System PoieriialEffectise Shade(%)
# Mile Movirg Average-Loadirg Capacity(ly/day)
5 10 15 20 25 30 35 40 45 50 55 60 65
Rivei Mile (South Folk Cleat watei Rrvet)
100% •
90% -
1 80% -
« 70% -
~
« 60% •
UJ —
-. £. 50% •
S 40% -
0
g 30% •
| 20%-
10% -
(
Corfluenw
\
4
— 1 /4 Mile Moving Average - System P otenija Effective Shade (%')
1/4 Mile Moving Average -Loading Capaaty OytJay)
I
.
1
L, III!
j
i
-r
8 12 16
1
I
rii
i
i
ft
20
Corf luerce
s
24 28 3
•629
566
•503 f
•440 2
- X
• 377 i -1
•315 j,s!
•252 ||
•189 ra"1
•126 1
O
•63
•0
2
River Mile (Red River)
100% -I
90% J
£ 80% I
2 70% j
4>
i 60% •
£ 50% - 1
1 40% •
1
0. 30% •
» 20% •
10% •
— 1/4 Mile Moving Average
1/4 MileMoving Average
fl 1 K.L (1 -flfl 1
1
P 1 (
tiff
II
1 1
' 1 1
if
V
1
1 1 f\ ^
|i Y> V"1
y"v
Start cf Csn^cn
1
02468
System Poterrbal Effect ve Shade (%)
Loading C apadiy (lyjUay)
/1A •
i
, /AT —*,
/nf ~~ U
AT\f » U
\f~~-\fi Gran^ville
1
10 12 14 18
0^3
566
c
503 "
0
-440 |
i
377 5
a: ^
315 1 S
252 i~
I
-189 u
f
126 •%
63
18 20
Rivei Mile (TlueeMlle CieeK)
Figure F-24. System Potential Effective Shade and Loading Capacity - South
Fork Clearwater River, Red River and Three Mile Creek
F-58
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
100% -I
90% •
_
£ 80% •
*
| 70% •
.1 60% •
E 50% •
1 40% '
O
£ 30% •
§
§ 20% •
10% •
l//V/V "A
V
\
\
\
rVl
i|
024
—1/4 Mile Moving Average - System Potential Effective Shade (%)
1/4
r\A
Mile Moving Average - Loading Capacity (ly/day)
i
1 Cwfiuencewilh
i feaver Creek
V /
/
6 8 10 12 14
River Mile (Newsome Creeks
629
566
?
503 sg
*
440 g
377 1
a: —
3,511
*? ^
252 |
189 ^
,26 |
63
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1/4 MileMoyrg Average - System Potertial Effective Shade (%)
1/4 Mile Moving Average -Loading Capacity(ly/cfay)
Figure F-24 (continued). System Potential Effective Shade and Loading
Capacity -Newsome Creek, Little Elk Creek, and Elk Creek
F-59
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
Ocbober 2003
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River Nile (Butcher Creek)
Figure F-24 (continued). System Potential Effective Shade and Loading
Capacity -Big Elk Creek and Butcher Creek
Margins of Safety - Clean Water Act §303(d)(1)
The Clean Water Act requires that each TMDL be established with a margin of safety
(MOS). The statutory requirement that TMDLs incorporate an MOS is intended to account
for uncertainty in available data or in the actual effect controls will have on loading
reductions and receiving water quality. An MOS is expressed as unallocated assimilative
capacity or conservative analytical assumptions used in establishing the TMDL (e.g.,
derivation of numeric targets, modeling assumptions, or effectiveness of proposed
management actions).
The MOS may be implicit, as in conservative assumptions used in calculating the loading
capacity, wasteload allocation, and load allocations. The MOS may also be explicitly stated
as an added, separate quantity in the TMDL calculation. In any case, assumptions should be
stated and the basis behind the MOS documented. The MOS is not meant to compensate for
a failure to consider factors that effect water quality.
F-60
Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
A TMDL and associated MOS, which result in an overall allocation, represents the best
estimate of how standards can be achieved. The selection of the MOS should clarify the
implications for monitoring and implementation planning in refining the estimate if
necessary (adaptive management). The TMDL process accommodates the ability to track
and ultimately refine assumptions within the TMDL implementation/planning component
(Table F-13).
Table F-13. Approaches for incorporating a margin of safety into a TMDL.
Type of
Margin
of Safety
Available Approaches
Set numeric targets at more conservative levels than analytical results indicate.
P .. .. Add a safety factor to pollutant loading estimates.
Do not allocate a portion of available loading capacity; reserve for margin of
safety.
Make conservative assumptions in derivation of numeric targets.
. .. .. Make conservative assumptions when developing numeric model applications.
Make conservative assumptions when analyzing prospective feasibility of
practices and restoration activities.
The following factors may be considered in evaluating and deriving an appropriate MOS:
• The analysis and techniques used in evaluating the components of the TMDL process
and deriving an allocation scheme.
• Characterization and estimates of source loading (e.g., confidence regarding data
limitations, analysis limitations, or assumptions).
• Analysis of relationships between the source loading and instream impact.
• Prediction of response of receiving waters under various allocation scenarios (e.g., the
predictive capability of the analysis, simplifications in the selected techniques).
• The implications of the MOS on the overall load reductions identified in terms of
reduction feasibility and implementation time frames.
Calculating a numeric MOS is not easily performed with the methodology presented in this
document. However, the TMDL accounts for uncertainties in the analysis by incorporating
an implicit margin of safety.
By definition, system potential effective shade, developed from system potential vegetation
conditions, is the highest level of shade achievable; and therefore, represents an implicit
MOS.
F-61 Appendix F
-------
South Fork Clearwater River Subbasin Assessment and TMDLs Ocbober 2003
References
Beschta, R.L., R.E. Bilby, G.W. Brown, L.B. Holtby, and T.D. Hofstra. 1987. Stream
temperature and aquatic habitat: Fisheries and forestry interactions. Pages 191-232 in
E.O. Salo and T.W. Cundy, eds. Streamside management: Forestry and fishery
interactions. University of Washington, Institute of Forest Resources, Seattle, WA.
Boyd, M.S. 1996. Heat source: Stream temperature prediction. Master's Thesis. Departments
of Civil and Bioresource Engineering, Oregon State University, Corvallis, OR.
Brown, G.W. 1969. Predicting temperatures of small streams. Water Resource Research
(l):68-75.
Brunsfeld, S. J., 1994. Analysis of the riparian vegetation of Red River Meadows.
Department of Forest Resources, University of Idaho, Moscow, ID.
Garman, S. L., S.A. Acker, J.L. Ohmann, and T.A. Spies. 1995. Asymptotic height-diameter
equations for twenty-four tree species in western Oregon. Research Contribution 10.
Forest Research Laboratory, Oregon State University, Corvallis, OR.
Harrison B. and G. Kellogg, 1987. Mapping riparian/wetland habitats on the Nez Perce
National Forest - A cooperative approach. Nez Perce National Forest.
Holaday, S.A. 1992. Summertime water temperature trends in Steamboat Creek Basin,
Umpqua National Forest. Master's Thesis. Department of Forest Engineering, Oregon
State University, Corvallis, OR.
Li, H.W., G.L. Lamberti, T.N. Pearsons, C.K. Tait, J.L. Li, and J.C. Buckhouse. 1994.
Cumulative effects of riparian disturbance along high desert trout streams of the John
Day Basin, Oregon. American Fisheries Society. 123:627-640.
NPNF 2001. Nez Perce National Forest Codes Legend for Selway, Newsome, and Clea
Creeks. Nez Perce National Forest.
Park, C. 1993. SHADOW: stream temperature management program. User's Manual v. 2.3.
USDA Forest Service. Pacific Northwest Region.
USD A, 1998. South Fork Clearwater River landscape assessment. United States Department
of Agriculture, Nez Perce National Forest.
F-62 Appendix F
-------
Appendix G. The Cumulative Watershed Effects
Temperature Model Applied to the South Fork Clearwater
River Subbasin
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
List of Tables G-i
List of Figures G-ii
The Cumulative Watershed Effects Temperature Model Applied to the South
Fork Clearwater River Subbasin G-1
Background G-1
Methods G-4
CWE Temperature Model Results for SF CWR Subbasin G-5
References G-17
List of Tables
Table G-1. Average daily solar radiation incident on a stream related to
canopy closure G-15
Table G-2. The heat loading capacities for the SF CWR in terms of CWE-
derived percent stream canopy closure by elevation and associated insolation
rates for the 10°C MWMT regulation-defined heat loading capacity G-16
G- i Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Figures
Figure G-1. Current Percent Canopy Closure of the SF CWR Subbasin G-6
Figure G-2. Existing Percent Canopy Closure of Threemile Creek, Butcher
Creek and Surrounding Areas G-6
Figure G-3. Existing Percent Canopy Closure of Little Elk Creek, Big Elk Creek
and Surrounding Areas G-7
Figure G-4. Percent Canopy Closure Predicted by the CWE Temperature
Model as Needed to Protect Stream Temperatures for Salmonid Spawning in
the SF CWR Subbasin G-8
Figure G-5. Percent Canopy Closure Predicted by the CWE Temperature
Model as Needed to Protect Stream Temperatures for Salmonid Spawning in
the Threemile and Butcher Creeks Area G-8
Figure G-6. Percent Canopy Closure Predicted by the CWE Temperature
Model as Needed to Protect Stream Temperatures for Salmonid Spawning in
the Little Elk and Big Elk Creeks Area G-9
Figure G-7. Percent Canopy Closure Targets for the Forested Portions of the
SF CWR Subbasin G-10
Figure G-8. Percent Canopy Closure Targets for the Forested Portions of the
Threemile and Butcher Creeks Area G-10
Figure G-9. Percent Canopy Closure Targets for the Forested Portions of the
Little Elk and Big Elk Creeks Area G-11
Figure G-10. Percent Canopy Closure Increase Needed in the Forested Areas
of the SF CWR Subbasin G-12
Figure G-11. Percent Canopy Closure Increase Needed in the Forested Areas
of Threemile and Butcher Creeks G-12
Figure G-12. Percent Canopy Closure Increase Needed in the Forested Areas
of Little Elk and Big Elk Creeks G-13
G- ii Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
The Cumulative Watershed Effects Temperature Model
Applied to the South Fork Clearwater River Subbasin
Report prepared by:
Tom Dechert, TMDL Project Manager, DEQ
For the South Fork Clearwater River (SF CWR) Subbasin assessment and total maximum
daily load (TMDL), streams were divided into two categories for temperature analysis: 1)
those that still retain a reasonable semblage of the natural forest canopy and are primarily
managed for forestry and/or natural vegetative conditions, and 2) those where the natural
vegetation has been greatly altered by grazing, agriculture, mining, and road building. This
later category includes all of the main stem SF CWR. Those lands primarily managed for
forestry are being analyzed using a method developed under Idaho's Forest Practices Act
(FPA) (IDL 2000), and all the others are being analyzed using a method developed by the
U.S. Environmental Protection Agency (USEPA) based on the system's potential vegetation
(Appendix F). In both cases, vegetative shading is the primary factor being analyzed as the
parameter affecting stream temperature. This appendix describes the FPA Cumulative
Watershed Effects (CWE) temperature model as it was applied for the forested portions of
the SF CWR Subbasin.
Background
The six modes of heat transfer important in stream temperature analyses are (Adams and
Sullivan 1990):
• Solar radiation (short wave)
• Radiation between the stream and the adjacent vegetation and sky (long wave)
• Evaporation from the stream
• Convection between the stream and the air
• Conduction between the stream and the streambed
• Ground water and tributary mass inflow/outflow
There are process-based stream temperature models such as Heat Source (Boyd 1996) or
SSTEMP (Theurer et al. 1984, Bartholow 1997) for analyzing stream temperatures by
quantifying the heat transfer processes. However, these models tend to require extensive
inputs, many of which are not easily available or reliable for remote, mountain streams. The
relative importance of each mode of heat transfer varies according to the specific
environmental conditions present from reach to reach.
Analyses have established that the primary environmental factors affecting stream
temperature are local air temperature, stream depth, ground water inflow, and the extent to
which riparian canopy and topography shade the stream (Sullivan and Adams 1990, Theurer
et al. 1984, Beschta and Weatherred 1984). In forested environments with small first and
second order streams, stream shading and local air temperature are widely recognized as the
major environmental determinants of stream temperature, accounting for up to 90% of stream
G-1 Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
temperature variability (Brown 1971, IDL 2000). Stream shading is also the primary factor
that has been modified by human activities. The Idaho water quality standards for
temperature apply only to characteristics that may vary due to human activities.
The Idaho Forest Practices Act Coordinating Committee (IDL 2000) developed an empirical
model of stream temperatures in forested environments in Idaho north of the Salmon River
based on continuous water temperature measurements, elevation, and percent canopy cover
data. The model is identified as the Cumulative Watershed Effects (CWE) temperature
model and is represented by the following equation:
MWMT = 29.1 - 0.00262 E - 0.0849 C
where MWMT = maximum weekly maximum temperature (° C)
E = stream reach elevation (feet)
C = riparian canopy closure (0/-
Data for this model were collected throughout north Idaho. The model utilizes percent stream
canopy closure and elevation to predict the maximum weekly mean maximum stream
temperature (the MWMT of the hottest week of the year). Elevation and percent canopy
closure are easy to acquire: elevation from topographic maps and percent canopy closure
from aerial photography correlated to percent canopy closure collected using a densiometer.
In mountainous terrain such as the SF CWR Subbasin, increases in elevation result in
reductions in ambient air temperature, thus reducing heat loading in a predictable manner. In
addition, increases in shading decrease heat loading by reducing solar insolation impinging
on the water surface and by lowering the local air temperature under the canopy. The utility
of the CWE temperature model is that it can be solved for percent canopy closure, the major
environmental factor that changes as a result of human activity.
The following is quoted from the Forest Practices Cumulative Watershed Effects Process for
Idaho (IDL 2000) pp C-3 and C-4:
The shade-elevation/temperature relationships used in this section were
developed from data collected throughout Idaho between 1991 and 1998. Two
hundred and forty-six data sets have been analyzed to develop shade-
elevation/temperature relationships for both northern and southern Idaho with
R-square values of 0.58 and 0.71, respectively.
The shade-elevation/temperature relationship has been validated in
Washington State (Sullivan and Adams 1990). In that study, a simple
temperature screen based on elevation and canopy closure over the stream
correctly identified the temperature category according to Washington water
quality criteria 89% of the time. A temperature screen specific to eastern
Washington (CMER, 1993) accurately predicted the necessary level of canopy
cover at 69% of locations, with most errors leading to conservative predictions.
G- 2 Appendix G
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Idaho has the following water temperature standards, reflecting the
needs of different beneficial uses in streams:
1) Cold Water Biota (22°C instantaneous maximum and 19°C
maximum daily average) - Applies to all streams in the state
throughout the year.
2) Salmonid Spawning (13°C instantaneous maximum and 9°C
maximum daily average) - Applies to streams with salmonids
(trout, salmon, char and whitefish) present during the spawning
and incubation period.
3) Bull Trout (12°C daily average during June, July and August and
9°C daily average during September and October) - Applies to
streams where spawning or rearing bull trout occur.
Using different methodologies (instantaneous maximums and maximum
daily averages) to evaluate Idaho stream temperature standards makes this
process confusing and difficult. To simplify this approach, the CWE process
evaluates all temperature standards using one methodology—a rolling 7-day
average of daily maximum temperatures, otherwise known as the maximum
weekly maximum temperature (MWMT). The MWMT is chosen for several
reasons. First, instantaneous maximums can be short in duration and may not
represent the impact stream temperature will have on fish, especially if
significant cooling occurs soon after the peak temperature. Second, the daily
average does not allow evaluation of peak temperatures and can mask large
fluctuations around the mean. Greater fluctuation around the mean can be one
effect of intensive forest canopy management, and can negatively influence fish.
Finally, MWMT is consistent with other temperature criteria that have been
established or recommended to protect bull trout and other fish species (ODEQ
1995; USDA Forest Service 1995; USEPA 1997; Sugden et. al., 1998).
The conversion of Idaho's stream temperature standards to MWMT is show
below. These conversions were accomplished using formulas developed by
Sugden et al. (1998) in their analysis of 220 different stream temperature data
sets collected in Northern Idaho and Western Montana between 1991 and 1997.
Cold Water Biota
22°C instantaneous max = 21.01°C MWMT
19°C daily average = 21.75°C MWMT
Salmonid Spawning
13°C instantaneous maximum = 12.36°C MWMT
9°C daily average = 9.70°C MWMT
Bull Trout
12°C daily average (June, July and August) = 13.31°C MWMT
9°C daily average (September and October) = 9.7°C MWMT
G- 3 Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Methods
Using the conversion factor developed by Sugden et al. (1998) for northern Idaho and
western Montana, a 9°C (48.2°F) daily average temperature is equivalent to a 9.7°C (49.5°F)
MWMT. This means that the federal bull trout temperature standard and Idaho's salmonid
spawning standard are roughly equivalent in terms of MWMT. We assume they are
equivalent and use a 10°C (50°F) MWMT for both standards in our calculations below.
In terms of timing, heat loading in the SF CWR Subbasin is at its greatest during late July
and early August and is reflected in the higher stream temperatures at this time (see
temperature discussion in Chapter 2 and temperature plots in Appendix J). July and August
are the critical months for temperature exceedances. Water temperatures begin to increase
through May and June, but are consistently at their peaks during late July and early August.
Water temperatures decrease rapidly after the first wet cold fronts of late August or early
September. The time periods for which the standards apply are dependent on the salmonid
species spawning and incubation times in the particular water body. The spawning time
periods for the different salmonid species in the SF CWR Subbasin are presented Appendix
D, Attachment D-l. The salmonid species known to be present in the different water bodies
of the SF CWR Subbasin are presented in Appendix D, Tables D-l, D-2 and D-l 1, and
Figures D-9 through D-l7.
The CWE process analyzes heat loading and stream temperature for the critical period of late
July through early August since the data used to develop the model were collected in this
time period. Application of the process assumes that if stream temperatures are in
compliance with the water quality standards during this period, they will be in compliance
throughout the rest of the year.
The stream temperature data in Table J-l (Appendix J) show the stream temperatures for one
location in the water body. These data were usually collected near the mouth of the stream
where temperatures are likely to be the highest. They give some idea of the overall
magnitude of heat loading to the water body, but provide little information about where in the
water body heat is gained. Since water quality standards apply throughout a water body, it is
necessary to understand heat loading throughout a water body.
Solar insolation at some reference elevation over the whole of a water body can be assumed
to be constant at any given moment (i.e., there is no spatial variation in solar insolation at the
scale of a water body). Spatial variation of heat loading to a stream is largely a function of
how solar insolation interacts with a stream and its immediate surroundings. In forested
environments, the major component of this interaction is the amount of shade reducing direct
solar insolation on the water surface and/or other surfaces in the immediate environment of
the stream. The CWE temperature model predicts the spatial distribution of heat loading
throughout a water body based on elevation and the percent canopy closure over the stream.
The CWE temperature analysis method throughout a water body is straightforward. The
majority of the data are gathered using aerial photographs and topographic maps and/or a
G- 4 Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
geographical information system (GIS). All the perennial streams are divided into 200-foot
elevational reaches (i.e., any given analysis reach can have a maximum of 200 feet difference
in elevation between its lower end and upper end). Reaches are also broken at perennial
stream intersections and at points where there is a major change in canopy closure along the
reach. This process resulted in over 3,500 reaches identified for the SF CWR Subbasin.
The stream segments are identified in the GIS such that each stream segment can be located
on a map. For each stream segment, several data types are established: the elevation at the
lower end of the reach, the current percent canopy closure from aerial photo interpretation,
and general orientation of the stream reach. Using maps and information about salmonid
distribution such as those presented in Appendix D and Appendix J, each reach is classified
according to the level of beneficial uses it should support. From these data, the CWE model
is run to predict the percent canopy closure needed to protect stream temperatures for the
desired beneficial use.
Under the FPA-developed CWE process, the target percent canopy closure to protect
beneficial uses is that calculated by the model. Any required percent canopy closure increase
is determined by subtracting the existing percent canopy closure from the CWE model
targeted percent canopy closure, resulting in a CWE target percent canopy closure increase.
If the current canopy is greater than the target canopy, then no canopy closure increase is
required.
However, in the interest of building further stream temperature protection into the TMDL
process, USEPA Region 10 has determined that no percent canopy closure target should be
set at less than the current percent canopy closure (Psyk 2001). In other words, when the
CWE temperature model is used to set targets for a TMDL, the target canopy is to be either
the CWE-modeled percent canopy closure, or the current percent canopy closure, whichever
is greater.
CWE Temperature Model Results for SF CWR Subbasin
The targets by stream segment are presented in graphic form on a map and in an associated
table. The Arc View shapefiles containing the graphics and target allocation data are on the
diskette included with this document.
Using the CWE process, we analyzed the current shade condition of 3,500+ stream reaches in
the 82 watersheds for which TMDLs are being developed. Existing percent canopy closures
as determined by the CWE methods are presented in Figures G-l through G-3. Figure G-l
shows the existing shade for the whole subbasin, except the Cottonwood Creek watershed.
Figures G-2 and G-3 show the existing shade for the Threemile and Butcher Creek areas, and
the area around Little and Big Elk Creeks. We selected these two areas to show at a larger
scale because they are the 303(d) listed areas of interest. Parts of the middle reaches of
Threemile Creek and Butcher Creek were not assessed for lack of aerial photos. The TMDL
for these areas uses the System Potential Vegetation (SPV) methods.
G- 5 Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
CWE Percent Existing Shade
in the South Fork
Clearwater Subbasin
May, 20 D 2
Figure G-1. Current Percent Canopy Closure Over Streams in the SF CWR
Subbasin
Legend
MPT Reservation Boundary
Cotlonwood TMDL Area
Water Body ID watersheds
Threemile Creek
Butcher Creek
Existing % Canopy Closure
o
A/
/\/ 25 - 50
A/ 5°-75
f\/ 75-100
Not assesse
October 2003
\\
Figure G-2. Existing Percent Canopy Closure of Threemile Creek, Butcher
Creek and Surrounding Streams
G-6
Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Legend
SF Clearwater 4th Field HUC
Water Body ID watersheds
303d Temperature Listed WBs
Figure G-3. Existing Percent Canopy Closure of Little Elk Creek, Big Elk Creek
and Surrounding Streams
At the time of interpreting the aerial photos to determine existing percent canopy closure, we
also identified areas that are meadows, hay lands, agricultural lands, or that had been dredge
mined or for some other reason could not be considered related to forest practices. These
areas are being analyzed using the SPY methods and are identified in the subsequent maps as
such.
Figures G-4 through G-6 show the percent canopy closure that the CWE temperature model
predicts is needed to protect stream temperatures. Given that the whole subbasin is being
analyzed for salmonid spawning, the primary variable controlling the predicted percent
canopy closure needed is elevation. The predicted needed percent canopy closure decreases
regularly with elevation. Once again, we show the subbasin as a whole (Figure G-4), then the
two selected areas in more detail (Figures G-5 and G-6). Any area of interest can be printed
in more detail using Arc View and the enclosed Arc View shapefile.
G-7
Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
CWE Temperature Model Predicted
Target Percent Canopy Closure
in the South Fork Clearwater
River Subbasin
J""?\
Figure G-4. Percent Canopy Closure Predicted by the CWE Temperature
Model as Needed to Protect Stream Temperatures for Salmonid
Spawning in the SF CWR Subbasin
CWE % Canopy Closure Target
A/ •-«
25-50
50-75
/\/ 75 - 90
Not Assessed
SPY Analysis
NPT Reservation Boundary
C^> Cottonwood TMDL
<^^> Butcher Creek
C ^) Threemiie Creek
C^> Water Body ID Watershed
October 2003 _J
Figure G-5. Percent Canopy Closure Predicted by the CWE Temperature
Model as Needed to Protect Stream Temperatures for Salmonid
Spawning in the Threemile and Butcher Creeks Area
G-8
Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
CWE Temperature Model
Predicted Target Percent
Canopy Closure
Legend
CWETarget%CC
A/
A/
A/
O
O
0-25
25-50
50-75
75-90
Not Assessed
SPV Analysis
303d Temperature Listed WBs
Water Body ID watersheds
October 2003
Figure G-6. Percent Canopy Closure Predicted by the CWE Temperature
Model as Needed to Protect Stream Temperatures for Salmonid
Spawning in the Little Elk and Big Elk Creeks Area
As noted above, USEPA determined that, as an added measure of protection of stream
temperatures, TMDLs developed using the CWE temperature model should not set stream
shade targets at less than existing percent canopy closure. Thus, in order to set the percent
canopy closure targets for each of the stream segments, the existing percent canopy closure
was compared to the CWE-predicted percent canopy closure, and the greater of the two was
chosen. Figures G-7 through G-9 show the percent canopy closure targets set using the CWE
model modified by the USEPA condition. The regular progression of needed percent canopy
closure is broken in places where existing percent canopy is greater than that predicted as
needed by the CWE temperature model.
G-9
Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
CWE Temperature Model Modified
by USEPA Policy Target Percent
Canopy Closure in the South Fork
Clearwater Subbasin
May, 2002
CWE Modified Target Canopy
A/ •-»
25- 60
/\/ SO- 75
/\/ 75 00
»„««„„,
20 Miles
Figure G-7. Percent Canopy Closure Targets for the Forested Portions of the
SF CWR Subbasin
CWE Temperature Model
Modifed by USEPA PolicyD
Target Percent Canopy
Closure
October2003
Legend
CWE+EPA Target %CC
A/ »•*
25- 50
50-75
A/ 75-90
Not Assessed
SPY Analysis
NPT Reservation Boundary
Butcher Creek
Threemile Creek
Cottonwood TMDL
Cl ^)
Figure G-8. Percent Canopy Closure Targets for the Forested Portions of the
Threemile Creek, Butcher Creek and Adjacent Streams
G-10
Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Target Percent Canopy
Closure Predicted by the
CWE Temperature Model
Modified by USEPA Policy
- '**
© 1
Legend
CWE % Canopy Closure Target
A/ 0-25
25- 50
/V 50-75
/\/ 75 - 80 S
Not Assessed
SPV Analysis
(^^) 303d Temperature Listed WBs
C^^) Water Body ID watersheds
October 2003
Figure G-9. Percent Canopy Closure Targets for the Forested Portions of the
Little Elk and Big Elk Creeks and Adjacent Streams
Finally, in order to show the increase in percent canopy closure needed in the forested areas
to be able to attain the TMDL targets, the existing percent canopy closure is subtracted from
the target percent canopy closure on a stream segment by stream segment basis. The percent
canopy closure increase needed is shown in Figures G-10 through G-12. These data are
included in an Arc View shapefile included on diskette with this document.
G-ll
Appendix G
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
CWE Percent Canopy Closure
Target Increase in the South Fork
Clearwater River Subbasin
18 Miles
Figure G-10. Percent Canopy Closure Increase Needed in the Forested Areas
of the SF CWR Subbasin
CWE-Based Percent
Canopy Closure
Target Increase
Needed
October 2003
Legend
Target %CC Increase
A/ °
1-25
25-50
50-75
/\/ 75-90
Not Assessed
SPV Analysis
^ ^ MPT Reservation Boundary
(^ ^ Butcher Creek
(^ ^) Threemile Creek
CottonwoodTMDL
Water Body ID watersheds
Figure G-11. Percent Canopy Closure Increase Needed in the Forested Areas
of Threemile Creek, Butcher Creek and Adjacent Streams
G-12
Appendix G
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
CWE-Based
Percent Canopy
Closure Targeted
Increase Needed
October 2003
Legend
Target %CC Increase
A/ o
1-25
25 - 50
50-75
75-90
Not Assessed
SPV Analysis
303d Temperature Listed WBs
Water Body I D watersheds
Figure G-12. Percent Canopy Closure Increase Needed in the Forested Areas
of Little Elk and Big Elk Creeks and Adjacent Streams
The heat load reduction allocations presented in terms of the surrogate target, percent canopy
closure, are specific to the 303(d) listed water quality limited streams. In those situations
where the effects of heat loading from non-303(d) listed streams are contributing to water
standard exceedances in a 303(d) listed water body, the assigned load reduction allocation,
defined in terms of the surrogate target, percent canopy closure increase, has been distributed
appropriately throughout the water bodies wherever percent stream canopy closure is
inadequate according to the CWE analytical methods and model, modified by the USEPA
conditions. This resulted in TMDLs being developed for all 82 water bodies in the SF CWR
Subbasin.
Riparian areas along streams do not naturally exhibit 100% or even 90% canopy cover for
the entire length of the streams. Natural events (fires, landslides, wind events) may affect
riparian vegetation along small stream segments or entire streams. In addition, larger streams
(Crooked River, American River, Red River, lower Johns Creek) have larger stream widths
that do not allow for a high canopy closure. Also, colder habitat types typically found at high
elevations or in cold air drainages often do not support 90% canopy cover. An evaluation of
the densiometer field data in conjunction with the aerial photo interpretation results indicates
that 90% canopy closure is approximately the greatest percent canopy closure one should
expect. The surrogate targets have been set, therefore, with 90% canopy closure as the
maximum possible. We have not attempted to sort out the site-specific conditions in relation
G-13
Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
to the CWE predictions where even 90% canopy closure is not possible, but leave that
question for the land managers as they develop their implementation plans.
The heat load targets are the state's water quality temperature standards for salmonid
spawning for the most limiting salmonid species or the federally promulgated temperature
standards for bull trout. The critical time period has been determined to be the months of
July and August; therefore, the targets are set for those months. If the targets are attained
during July and August, when water flows are low and air temperatures are high, it is
relatively certain that water quality temperature standards will be met throughout the rest of
the year.
For federally protected bull trout watersheds, the target shall be 10°C (50°F) MWMT during
the months of July and August. The list of federally protected water bodies (Appendix B)
includes all the water bodies of the SF CWR Subbasin except for the main stem SF CWR,
Threemile Creek, Butcher Creek, Wing Creek, Red Horse Creek, Buffalo Gulch, Maurice
Creek, Sing Lee Creek, Leggett Creek, Fall Creek, Peasley Creek, and Cougar Creek. For
other streams that support cutthroat trout, the target shall be 9°C (48.2°F) mean daily
temperature for the month of July. For water bodies that support only rainbow trout, the
target shall be 9°C (48.2°F) mean daily temperature from July 1 through July 15.
To address the concern regarding conversion of CWE results to heat loading per unit time,
we take an approach of separating the effects of insolation from the other heat flux processes.
The two primary environmental variables that determine stream temperature are air
temperature and stream shading. Air temperature enters into the heat transfer relationships
for many of the heat transfer processes associated with streams (e.g., convection,
evaporation, long wave radiation), and is the primary driver of average water temperature.
The CWE accounts for the variation in air temperature based on elevation. Stream shading
affects the amount of solar radiation impinging on the water surface, and is the primary
driver of the diurnal fluctuations in water temperature. The CWE results are in effect the
change in heat loading associated with changes in stream shading.
In order to quantify heat loading to a stream surface due to insolation, we used SSTEMP
(Bartholow 1997) derived data for August 1 (median hottest day) for insolation rates and
calculated the heat loading for different levels of percent shade. The amounts of solar
radiation incident on the stream and its immediate surroundings at different shadings for two
stream orientations are presented in Table G-l. Fixed conditions used in SSTEMP to
develop the solar radiation numbers are 47 degrees latitude; 5,000 feet elevation; a stream
width of 10 feet; a buffer height of 60 feet; a buffer width of 30 feet; and topographic shade
of 30 degrees. These are generalized standard conditions for streams of the SF CWR
Subbasin. Under these conditions, incident solar radiation decreases regularly by 21 watts
per square meter for every 10% increase in canopy density for north-south oriented streams
and 26 watts per square meter for east-west oriented streams.
G-14 Appendix G
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table G-1. Average daily solar radiation incident on a stream related to
canopy closure.
Canopy Closure
(percent)
0
10
20
30
40
50
60
70
80
90
100
Stream Orientation
North-South
(watts per square meter)
226
205
185
164
143
122
101
80
59
38
17
East-West
(watts per square meter)
274
248
223
197
172
146
120
95
69
43
18
These heat flux amounts do not represent the total heat flux, but just the heat flux directly
from the sun (insolation). This is the portion of heat flux this TMDL addresses because it is
readily increased by human activities that reduce stream shading and can be managed to
decrease stream temperatures. Insolation flux rates decrease linearly with increases in
shading (Table G-2). Considering the CWE model above, the decrease in stream temperature
due to increased percent canopy closure at a given elevation is also linear. Assuming the
CWE model is correct, the linear decrease in temperature implies that the change in heat flux
is constant and directly related to shading. These results indicate that the total heat flux is
linearly related to the insolation rates, such that the percentage heat reduction required by the
TMDL will be the same whether it is calculated from total heat flux or from insolation rates.
In this TMDL, we use the CWE model with percent shade as the dependent variable directly
related to insolation rates.
G-15
Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table G-2. The heat loading capacities for the SF CWR in terms of CWE-
derived percent stream canopy closure by elevation and associated
insolation rates for the 10°C MWMT regulation-defined heat loading
capacity.
Elevation Zones
(feet)
5,400-5,599
5,200-5,399
5,000-5,199
4,800-4,999
4,600-4,799
4,400-4,599
4,200-4,399
4,000-4,199
3,800-3,999
3,600-3,799
3,400-3,599
3,200-3,399
3,000-3,199
2,800-2,999
2,600-2,799
2,400-2,599
2,200-2,399
2,000-2,199
1,800-1,999
1,600-1,799
1,400-1,599
1,200-1,399
1,000-1,199
800-999
Percent Stream
Canopy Closure
(percent)
58
64
71
77
83
89
95
100
100*
100*
100*
100*
100*
100*
100*
100*
100*
100*
100*
100*
100*
100*
100*
100*
Insolation Rate
North-South
Oriented Stream
(watts/meter2)
105
93
78
65
53
40
28
17
**
**
**
**
**
**
**
**
**
**
**
**
**
**
**
**
Insolation Rate
East-West
Oriented Stream
(watts/meter2)
125
110
92
77
61
46
31
18
**
**
**
**
**
**
**
**
**
**
**
**
**
**
**
**
**
Below about 4,000 feet elevation, the CWE model predicts a need for greater than 100% canopy
closure to protect a maximum stream temperature of 10°C MWMT. Since this is not possible, 90%
canopy closure is set as the surrogate heat loading capacity. In some cases, 90% canopy closure may
not be achievable because of the canopy type, in which case it should be noted in the implementation
plan.
SSTEMP predicts insolation rates of 17 or 18 watts per square meter for 100% canopy closure
G-16
Appendix G
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
References
Adams, T.N. and K. Sullivan. 1990. The physics of forest stream heating: 1) A simple
model. Weyerhaeuser Tech. Rep. 044-5002/90/1. Weyerhaeuser Co., Tacoma, WA.
30+ pp.
Bartholow, J. 1997. Stream Segment Temperature Model (SSTEMP), Version 3.9, program
and documentation. Revised September 1997. Temperature Model Technical Note
#2. U.S. Geological Survey River Systems Management Section, Midcontinent
Ecological Science Center, Fort Collins, CO. 14 pp.
Beschta, R.L. and J. Weatherred. 1984. A computer model for predicting stream
temperatures resulting from the management of streamside vegetation. USDA Forest
Service. WSDG-AD-00009. Portland, OR.
Boyd, M.S. 1996. Heat Source: Stream temperature prediction. Master's Thesis,
Department of Civil and Bioresource Engineering, Oregon State University,
Corvallis, OR.
Brown, G.W. 1971. Water temperature in small streams as influenced by environmental
factors and logging. Proceedings: Symposium for Land Uses and Stream
Environment. October 19-21, 1970. Oregon State University, Corvallis, OR. pp.
175-181.
CMER (Cooperative Monitoring Evaluation and Research, Water Quality Steering
CommitteeX 1993. Revision of the water temperature screen; adoption of an eastern
Washington temperature screen. Memorandum dated June 5, 1993. 10 pp.
IDL (Idaho Dept. of Lands). 2000. Forest practices cumulative watershed effects process for
Idaho. Idaho Department of Lands, Boise ID. Chaps A-J + 2 app.
ODEQ (Oregon Department of Environmental Quality). 1995. 1992-1994 water quality
standards review. Final Issue Paper, Standards and Assessment Section. Portland,
OR. 83 pp.
Psyk, C. 2001. Approach for developing temperature total maximum daily loads (TMDL)
for Idaho waterbodies on the 303(d) list. Letter dated Oct. 12, 2001, from Christine
Psyk, Manager, Watershed Restoration Unit, Region 10, USEPA, Seattle, WA, to Mr.
Dave Mabe, Administrator, State Water Quality Programs, DEQ, Boise, ID. 2 pp.
Sugden, G.D., T.W. Hillman, I.E. Cladwell, and R.J. Ryel. 1988. Stream temperature
considerations in the development of Plum Creek's Native Fish Habitat Conservation
Plan. Plum Creek Timber Company, Columbia Falls, MT. 57 + pp.
G-17 Appendix G
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Sullivan, K. and T.N. Adams. 1990. The physics of forest stream heating: 2) An analysis of
temperature patterns in stream environments based on physical principles and field
data. Weyerhaeuser Co., Tacoma, WA. 50 + pp.
Theurer, F.D., K.A. Voos, and WJ. Miller. 1984. Instream water temperature model.
Instream Flow Information Paper No. 16. USDA Fish and Wildlife Service.
FWS/OBS-84/15. Fort Collins, CO. 200pp.
USDA Forest Service. 1995. Inland native fish strategy environmental assessment - FONSI
(Draft). INFISH. Intermountain, Northern, and Pacific Northwest Regions.
USEPA (40 CFR ISl.E.l.i.d (1997))
G-18 Appendix G
-------
Appendix H. U.S. Forest Service Vegetation Response
Unit and Habitat Type Group Descriptions
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
List of Tables H-i
U.S. Forest Service Vegetation Response Unit and Habitat Type Group
Descriptions H-1
Vegetation Response Units H-1
VRU 1: Convex Slopes, Subalpine Fir H-1
VRU 2: Glaciated Slopes, Subalpine Fir H-2
VRU 3: Stream Breaklands, Grand Fir and Douglas Fir H-3
VRU 4: Rolling Hills, Grand Fir H-4
VRU 5: Moraines, Subalpine Fir and Grand Fir H-4
VRU 6: Cold Basins, Grand Fir and Subalpine Fir H-5
VRU 7: Moist Uplands, Grand Fir and Pacific Yew H-6
VRU 8: Stream Breaklands, Cedar and Grand Fir H-7
VRU 9: Glaciated Slopes, Subalpine Fir and Whitebark Pine H-7
VRU 10: Uplands, Alder, Grand Fir and Subalpine Fir Habitat Types
H-8
VRU 12: Stream Breaklands, Bunchgrass and Shrubland H-9
VRU 16: Plateaus, Bunchgrass and Shrubland H-9
VRU 17: Rolling Hills, Cedar and Grand Fir H-10
Habitat Type Groups H-11
Forested Habitat Type Groups and Descriptions H-11
List of Tables
Table H-1. Non-forested Habitat Type Groups (HTGs) (USDA FS 1992) H-14
Table H-2. Summary information for forested Habitat Type Groups within the
South Fork Clearwater River Subbasin H-15
H- i Appendix H
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
U.S. Forest Service Vegetation Response Unit and Habitat
Type Group Descriptions
This appendix presents detailed information for Vegetation Response Units (VRUs) and
Habitat Type Groups (HTGs) for the South Fork Clearwater River Subbasin. The VRU
information was obtained from the South Fork Clearwater River Landscape Assessment
(USFS 1998). The HTG information was obtained from the document Biophysical
Classification - Habitat Groups and Descriptions 5/96.
Vegetation Response Units
The VRUs are broad ecological land units that display unique patterns of habitat type groups
(potential vegetation) and terrain. A VRU classification and delineation was developed for
the South Fork Clearwater River Subbasin. Detailed information for each VRU within the
subbasin is provided below.
VRU 1: Convex Slopes, Subalpine Fir
This VRU is common in the South Fork Clearwater River Subbasin at mid and upper
elevations. Grand fir and subalpine fir habitat types are dominant.
Historic Conditions
Lodgepole pine was historically dominant in many settings in this VRU. Engelmann spruce,
western larch, Douglas fir, and whitebark pine were less common. Wet meadows are
important elements of this landscape. The relative proportion of trees by size class was about
5-10% non-forest (non-stocked), 20-30% seedling/sapling, 20-30% pole, 20-30% medium
tree, and 5-15% large tree at any given time over this VRU in the subbasin. Old growth was
typically limited to moist draw bottoms and north slopes and usually comprised from 10 to
15% of the area.
Large, infrequent (75 to 150 years) severe fires were typical of most settings. Historically,
about 700 acres burned per year in the subbasin. About 60-80% of stands originated from
stand-replacing fires, and 20-40% from mixed severity fires. Moist lower slopes were most
prone to mixed fire. Lodgepole pine, western larch, and Douglas fir sometimes survived one
or more fires to form a scattered overstory. Large blocks (500 to 2,000 acres) of pole and
medium-size fire-killed trees were typically present at any time within any 10,000 acres of
this VRU. Mountain pine beetle activity cycled with fire in lodgepole pine and may have
been important in developing fuel conditions that favored stand-replacing fires.
Changes from Historic Conditions
With advancing forest succession and fire suppression, serai lodgepole pine, western larch,
and whitebark pine have declined, and more shade tolerant grand fir and subalpine fir have
increased. Lodgepole pine forests have decreased by 12% and Engelmann spruce-subalpine
fir forests have increased by 9%. Blister rust has further reduced whitebark pine populations.
H-1 Appendix H
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Today, only about 70 acres of this VRU burn per year in the subbasin; a 90% decrease.
Advancing forest succession has resulted in an 88% reduction in trees in the seedling/sapling
structural stage and a 37% increase in trees in the medium and large tree stages. Fire
suppression has also resulted in increased stand densities, as shade tolerant understories
develop. Harvest has affected about 10% of the area. Recent harvest patterns have replaced
large-scale, infrequent burned areas with frequent, small harvested areas more uniformly
distributed across watersheds than the historical burned areas. The average harvest unit size
is smaller than historic burn patch and there is not as much diversity in frequency of
structural stages within sub watersheds. Each watershed is more like other watersheds in
terms of the representation of structural stages. Due to fire suppression, extensive snag
patches that result from large fires are no longer created.
VRU 2: Glaciated Slopes, Subalpine Fir
This VRU is common in the South Fork Clearwater River Subbasin at upper elevations.
Subalpine fir and whitebark pine habitat types are dominant.
Historic Conditions
Lodgepole pine, Engelmann spruce, and Subalpine fir were historically dominant on side
slopes in this VRU. Whitebark pine was important on ridges. Rock outcrops, lakes and
wetlands, and montane parklands were important elements of this landscape. The relative
proportion of trees by size class was about 10-25% non-forest, 10-30% seedling/sapling,
30-65% pole, and 5-15% medium tree. Old growth was typically limited to moist trough
bottoms and open ridges and usually comprised less than 10% of the area.
Historically about 400 acres burned per year in the subbasin. Midslopes tended to experience
stand-replacing fires at infrequent intervals (75 to 150 years). Open ridges or moist valley
bottoms were more prone to mixed severity fires. Medium blocks (100 to 1,000 acres) of
pole-size fires killed trees were often present at any time within 20,000 acres of this VRU.
Changes from Historic Conditions-
With advancing forest succession and fire suppression, serai whitebark pine has declined.
Blister rust has further reduced whitebark pine by a total of more than 75%. More shade
tolerant Engelmann spruce-subalpine fir forests have increased more than 70%. Today, only
about 18 acres burn each year in the subbasin, a 96% decrease. Advancing forest succession
has resulted in an 84% decline in non-forest openings, a 71% decline in trees in the
seedling/sapling structural stage, a 74% decline in trees in the pole stage, and a 746%
increase in trees in the medium and large tree stages. Fire suppression has also resulted in
increased stand densities in Engelmann spruce-subalpine fir forests, as shade tolerant
understories develop. No recorded harvest has occurred. Due to fire suppression, extensive
snag patches that result from large fires are no longer created.
H- 2 Appendix H
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
VRU 3: Stream Breaklands, Grand Fir and Douglas Fir
This VRU is common at lower to mid elevations in canyons in the South Fork Clearwater
River Subbasin.
Historic Conditions
Small to medium blocks (10 to 200 acres) of pole and medium-size fire-killed trees were
abundant at any time within any 10,000 acres of this VRU. Old growth pine and western
larch, bunchgrass, understories, and rock outcrops are important elements of this landscape.
On the VRU as a whole, the relative proportion of trees by size class was about 5-20% non-
forest or non-stocked, 5-30% seedling/sapling, 10-20% pole, 20-40% medium tree, and
20-40% large tree.
On south aspects, dry Douglas fir habitat types were dominant. Open stands of large Douglas
fir and ponderosa pine were historically common. Low and mixed severity fires occurred at
very frequent intervals (5 to 25 years) on south aspects. Here, 60-90% of the stands survived
through one or more fires. Ponderosa pine old growth occupied about 40 to 60% of these
warm dry sites.
On north aspects, grand fir habitat types were dominant. Grand fir and Douglas fir were
common cover types, with ponderosa pine and western larch and sometimes Engelmann
spruce or lodgepole pine mixed in. Pacific yew grew on lower slopes. Mixed severity fires
were common at frequent intervals (25 to 75 years) on north aspects. About 30-60% of the
stands retained 10 or more trees per acre through at least one fire. Twenty to 30% of the
stands included at least 10 trees per acre older than 150 years. Ponderosa pine, western larch,
Douglas fir, and grand fir formed the old overstory.
Changes from Historic Conditions
With advancing forest succession and fire suppression, ponderosa pine/Douglas fir forests
have declined by 13%. Annual grasslands and weedlands have increased. Timber harvest has
resulted in a 128% increase in non-forest (non-stocked) openings. Forest succession and fire
suppression have resulted in a 33% decline in trees in the seedling/sapling structural stage, an
83% decline in trees in the pole stage, a 36% decrease in trees in the medium tree stage, and
a 6% increase in trees in the large tree stage. However, more of the large trees are in mixed
conifer and less in open pine stands than before. Timber harvest has affected about 11% of
the Forest lands in the subbasin over 50 years. Today, about 255 acres burn annually in the
subbasin, a decline of 70%. Prescribed fire on dry south aspects burns an additional 500 to
1,000 acres annually. The ratio of stand replacement harvest to mixed or low severity
treatments has been about 60% replacement to 34% less severe treatments. This is probably
within the range of natural variability, but harvest has, until recently, favored removal of the
fire tolerant overstory pine and retention of understory Douglas fir and grand fir, the reverse
of fire disturbance effects. This is a higher ratio of stand replacement than would have
occurred under natural disturbance regimes. Total canopy cover appears to have declined.
Whether this is due to increased mortality from insects and disease or harvest is uncertain.
H- 3 Appendix H
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Due to fire suppression, extensive snag patches that result from large fires are no longer
created.
VRU 4: Rolling Hills. Grand Fir
This VRU is common in the South Fork Clearwater River Subbasin at low and mid
elevations. Grand fir habitat types are dominant.
Historic Conditions
Grand fir, Douglas fir, ponderosa pine, and western larch were historically dominant in this
VRU. Lodgepole pine and Engelmann spruce were less common. Old growth pine and
western larch and meadow complexes were important elements of this landscape. The
relative proportion of trees by size class was about 5-10% non-forest, 5-50%
seedling/sapling, 10-30% pole, 20-30% medium tree, and 10-50% large tree.
Mixed and stand-replacing fires occurred at moderate intervals. About 50-60% of stands
originated from stand-replacing fires and 40-50% experienced mixed and low severity fires.
Ponderosa pine, western larch, Douglas fir, and grand fir often survived mixed severity fires
to form a scattered overstory of old large trees. Ten to 25% of the stands included at least 10
trees per acre older than 150 years. Small to large blocks (1,100 to 2,000 acres) of pole-size
trees to large fire-killed trees were common at any time within any 10,000 acres of this VRU.
Changes from Historic Conditions -
With advancing forest succession and fire suppression, ponderosa pine/Douglas fir forests
have declined by 32%. Lodgepole pine forests have decreased by 31%. Grand fir/Douglas fir
forests have increased by 43%. Forest succession and fire suppression have resulted in a 33%
decline in trees in the seedling/sapling structural stage and a 12% decrease in trees in the
large tree stage. The harvest of overstory pines has been most concentrated in this VRU,
affecting about 29% of the Forest acres within the last 50 years. Today, about 5 acres burn
annually in the subbasin, a decline of 99%. The ratio of stand replacement harvest to mixed
or low severity treatments has been about 60% replacement to 40% less severe treatments.
This is slightly more replacement than would have occurred under natural disturbance
regimes. This is probably within the range of natural variability, but harvest has, until
recently, favored removal of the fire tolerant overstory pine and retention of understory
Douglas fir and grand fir, the reverse of fire disturbance effects. Total canopy cover appears
to be about the same. Due to fire suppression, extensive snag patches that result from large
fires are no longer created.
VRU 5: Moraines, Subalpine Fir and Grand Fir
This VRU is rare in the South Fork Clearwater River Subbasin at mid to upper elevations.
Grand fir and subalpine fir habitat types are dominant. Lodgepole pine and Engelmann
spruce are common serai species. Grand fir, Douglas fir, subalpine fir, and western larch are
minor components.
H- 4 Appendix H
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Historic Conditions
In swales, Engelmann spruce-subalpine fir old growth was usually extensive between areas
where rare, large, stand-replacing fires occurred in this VRU. About 10-20% of stands
included at least 10 trees per acre older than 150 years. Wetlands and old growth Engelmann
spruce-subalpine fir forests were important elements of this landscape. The relative
proportion of trees by size class was about 5% non-forest (non-stocked), 10-40%
seedling/sapling, 20-60% pole, 5-30% medium tree, and 3-10% large tree.
Mixed and stand-replacing fires occurred at infrequent intervals. About 35% of the stands
originated from stand-replacing fires and 65% experienced mixed or low severity fires. Small
to large blocks (100 to 2,000 acres) of pole-size to medium-size fire killed trees occurred
occasionally within any 10,000 acres of this VRU.
Changes from Historic Conditions
With advancing forest succession and fire suppression, mixed conifer and Engelmann
spruce-subalpine fir forests have increased. It is uncertain if whitebark pine was ever an
important component in this area, but it is present now in only very small amounts. Forest
succession and fire suppression have resulted in declines in trees in the seedling/sapling and
pole structural stages and increases in trees in the medium and large trees stages. Harvest has
affected about 19% of the Forest acres within the last 50 years. No acres have burned in the
subbasin since fire suppression became effective. The ratio of stand replacement harvest to
mixed or low severity treatments has been about 70% replacement to 30% less severe
treatments. This is probably more replacement than would have occurred under natural
disturbance regimes. Due to fire suppression, extensive snag patches that result from large
fires are no longer created.
VRU 6: Cold Basins, Grand Fir and Subalpine Fir
This VRU is very common in the subbasin at mid elevations. Grand fir and subalpine fir
habitat types are dominant.
Historic Conditions
Lodgepole pine was the dominant serai species in this VRU. Western larch, Douglas fir, and
Engelmann spruce were important. Grand fir was important on mesic sites. Whitebark pine
was found occasionally. Five to 15% of stands included at least 10 trees per acre older than
150 years. Large disturbances and meadow complexes were important elements of this
landscape. The relative proportion of trees by size class was 5-10% non-forest (non-stocked),
10-30% seedling/sapling, 30-45%pole, 20-40% medium tree, and 5-20% large tree.
Medium to large stand-replacing fires occurred at infrequent interval (75 to 150 years).
About 60-90% of the stands originated from stand-replacing fires and 10-40% experienced
mixed severity fires. Moderate to large blocks (500 to 1,000 acres) of pole-size to
medium-size fire-killed trees were common at any time within any 10,000 acres of this VRU.
H- 5 Appendix H
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Changes from Historic Conditions
With advancing forest succession and fire suppression, lodgepole pine has decreased by 23%
and more shade tolerant mixed conifer and Engelmann spruce-subalpine fir forests have
increased by 30%. Whitebark pine has essentially disappeared as even a minor component.
Forest succession and fire suppression have resulted in a 53% decline in trees in the
seedling/sapling stage, a 46% decline in trees in the pole structural stage, a 32% increase in
trees in the medium tree stage, and a 20% increase in trees in the large tree stage. Riparian
meadows appear to have declined either due to forest encroachment or agricultural
conversion. Harvest has affected about 18% of the Forest acres within the last 50 years.
About 13 acres have burned annually in the subbasin since fire suppression became effective,
a decline of about 99%. The ratio of stand replacement harvest to mixed or low severity
treatments has been about 70% replacement to 30% less severe treatments. This is probably
within the range of what would have occurred under natural disturbance regimes. Due to fire
suppression, extensive snag patches that result from large fires are no longer created.
VRU 7: Moist Uplands, Grand Fir and Pacific Yew
This VRU is common in the subbasin at mid elevations, but quite rare elsewhere in northern
Idaho. Mesic grand fir habitat types are dominant and Pacific yew phases are common.
Historic Conditions
Grand fir, Douglas fir, and Pacific yew were the dominant species in this VRU. Western
larch, Engelmann spruce, and lodgepole pine were less common. Old overstory trees (grand
fir, western larch, Douglas fir, Engelmann spruce, and lodgepole pine) were common. About
30-40% of stands had 10 or more trees per acre older than 150 years. Two or more age
classes were common. Pacific yew and mesic old growth were important elements of this
landscape. The relative proportion of trees by size class was about 1 - 10% non-forest (non-
stocked), 5-20% seedling/sapling, 10-25% pole, 25-35% medium tree, and 35-45% large tree.
Small to medium fires of mixed severity occurred at infrequent intervals (75 to 150 years).
Large stand-replacing fires occurred more infrequently. About 60% of the stands experienced
mixed severity fires and about 40% originated from stand-replacing fires. Small and scattered
blocks (5-100 acres) and infrequent large blocks of fire-killed medium and large trees
occurred occasionally within any 10,000 acres of this VRU.
Changes from Historic Conditions
With harvest and planting, Douglas fir/ponderosa pine forests have increased 107%. Upland
and riparian shrublands have declined. Forest succession and fire suppression have resulted
in a 57% decline in trees in the seedling/sapling stage, a 45% decline in trees in the pole
structural stage, and a 22% increase in trees in the large tree stage. Harvest has affected about
28% of the Forest acres within the last 50 years. About 5 acres have burned annually in the
subbasin since fire suppression became effective, a decline of about 99%. The ratio of stand
replacement harvest to mixed or low severity treatments has been about 70% replacement to
H- 6 Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
30% less severe treatments. This relative proportion of stand replacement is higher than
would have occurred under natural disturbance regimes. Due to fire suppression, snag
patches that result from large fires are no longer created.
VRU 8: Stream Breaklands, Cedar and Grand Fir
This VRU is rare in the subbasin, but is common north of the subbasin at low and mid
elevations. Moist grand fir and cedar habitat types are dominant.
Historic Conditions
Grand fir and Douglas fir were the dominant species in this VRU. Western larch, western
redcedar, western white pine, Engelmann spruce, and Pacific yew were less common.
Ponderosa pine and lodgepole pine were minor species. Old overstory trees (Douglas fir,
western larch, grand fir, and occasionally ponderosa pine) were common on ridges and lower
slopes. About 10-15% of stands had 10 or more trees per acre older than 150 years. Coastal
disjunct plant species, early serai tall shrub and hardwood communities, and cedar old
growth along major streams were important elements of this landscape. The relative
proportion of trees by size class was about 5-20% non-forest (non-stocked), 5-30%
seedling/sapling, 10-20% pole, 30-50% medium tree, and 20-30% large tree.
Small to medium fires occurred at moderate intervals (25-75 years) and large stand-replacing
fires occurred at infrequent intervals (75 to 150 years). About 40-50% of stands experienced
mixed severity fires, and 50-60% of stands originated from stand-replacing fires. Small and
scattered blocks (5-100 acres) of fire-killed medium-size and large trees were common at any
time within any 10,000 acres of this VRU, and large blocks (500 to 1,000 acres) occurred
from time to time.
Changes from Historic Conditions
This VRU is poorly represented in the subbasin and only a few trends can be seen. Western
white pine has almost disappeared because of blister rust and forest succession. Shrubs,
hardwoods, trees in the seedling/sapling stage, and trees in the pole structural stage have
probably declined. Trees in the medium and large tree stages have increased. Harvest has
affected 2% of the acres. No acres have burned in the subbasin since fire suppression has
become effective, a decline of 100%. Due to fire suppression, extensive snag patches that
result from large fires are no longer created.
VRU 9: Glaciated Slopes, Subalpine Fir and Whitebark Pine
This VRU is rare in the subbasin, at highest elevations, but is more common to the south and
east of the subbasin. Cold subalpine fir and whitebark pine habitat types are dominant.
H- 7 Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Historic Conditions
This VRU was the major stronghold of whitebark pine. Subalpine fir, Engelmann spruce, and
lodgepole pine were also common. Old whitebark pine or lodgepole pine were common on
rock outcrops and open ridges. About 5-15% of the stands had 10 or more trees per acre older
than 150 years. Whitebark pine and open alpine communities were important elements of this
landscape. The relative proportion of trees by size class was 30-40% non-forest (non-
stocked), 10-30% seedling/sapling, 15-60% pole, 1-10% medium tree, and 1% or less large
tree.
Mixed severity fires occurred at moderate and infrequent intervals (25 to 10 years). About
40-60% of the stands experienced mixed severity fires and 40-60% of the stands originated
from stand-replacing fires. Small to moderate blocks (50-200 acres) of fire-killed trees were
common at any one time in any 10,000 acres of this VRU.
Changes from Historic Conditions
Some conclusions are based on limited data from neighboring watersheds. Anecdotal
information suggests that similar changes have occurred in the subbasin. With advancing
forest succession, fire suppression, and blister rust, whitebark pine has declined by 69%, and
more shade tolerant Engelmann spruce-subalpine fir forests have increased by 190%. Today,
only about 12 acres burn per year in the subbasin, a 90% decrease. Advancing forest
succession has resulted in a 62% reduction in trees in the seedling/sapling structural stage, a
72% decline in trees in the pole stage, and a 4200% increase in trees in the medium tree
stage. No recorded harvest has occurred. Due to fire suppression, snag patches that result
from large fires are no longer created.
VRU 10: Uplands, Alder, Grand Fir and Subalpine Fir Habitat Types
This VRU is common in the South Fork Clearwater River Subbasin, but rare to the south. It
is also called the grand fir mosaic. Mesic grand fir, subalpine fir, and alder habitat types are
dominant.
Historic Conditions
Grand fir, Engelmann spruce, subalpine fir, and Sitka alder were historically important cover
types in this VRU. Douglas fir, western larch, lodgepole pine, and Pacific yew were common
on ridges. About 15-30% of the stands had 10 or more trees per acre older than 150 years.
Open canopied and multi-aged old growth and tall shrub communities were important
elements of this landscape. The relative proportion of trees by size class was 10-25% non-
forest, 15-25% seedling/sapling, 20-30% pole, 25-40% medium tree, and 15-25% large tree.
Small fires occurred frequently, but mixed severity infrequent fires were typical. Stand-
replacing fires were usually confined to ridges. About 40-60% of the stands experienced
mixed severity fires and 40-60% of stands originated from stand-replacing fires. Small
H- 8 Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
blocks (5-50 acres) of fire-killed medium-size and large trees were common at any one time
in any 10,000 acres of this VRU.
Changes from Historic Conditions
With forest succession and fire suppression, shrublands have declined 77%. Other changes in
cover type have been minor. Forest succession and fire suppression have resulted in a 91%
decline in trees in the seedling/sapling stage, a 63% decline in trees in the pole structural
stage, a 25% increase in trees in the medium tree stage, and a 147% increase in trees in the
large tree stage. Harvest has affected about 4% of the Forest acres within the last 50 years.
About 2 acres have burned annually since fire suppression became effective, a decline of
about 99%. The ratio of stand replacement harvest to mixed or low severity treatments has
been about 80% replacement to 20% less severe treatments. This relative proportion of stand
replacement is higher than what would have occurred under natural disturbance regimes. Due
to fire suppression, snag patches that result from large fires are no longer created.
VRU 12: Stream Breaklands, Bunchgrass and Shrubland
This VRU is rare on National Forest lands in the subbasin, but is common in the lower
canyon on private lands. Bluebunch wheatgrass and Idaho fescue habitat types are dominant,
and shrubland habitat types are common.
Historic Conditions
Bluebunch wheatgrass and Idaho fescue were historically important. Shrublands occupied
draws or lower slopes. Very frequent (5-25 years) low severity fires maintained open
grasslands and rejuvenated shrublands.
Changes from Historic Conditions
This VRU is poorly represented on Forest lands. On all lands, only general trends are
indicated. Disturbed grasslands (annuals and weeds) and pasture have replaced native
perennials over more than 50% of their prior extent. Upland shrublands have increased as
much as 100% due to fire suppression and brush invasions of former grasslands. About 2
acres have burned annually on National Forest lands in the subbasin since fire suppression
became effective, a decline of about 82%.
VRU 16: Plateaus, Bunchgrass and Shrubland
This VRU occurs only on non-National Forest lands. Bluebunch wheatgrass, Idaho fescue,
and shrubland habitat types are common.
H- 9 Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Historic Conditions
Bluebunch wheatgrass and Idaho fescue were historically important on this VRU.
Shrublands occupied draws, lower slopes, and north aspects. Very frequent (5-25 years) low
severity fires maintained open grasslands and rejuvenated shrublands.
Changes from Historic Conditions
On all lands, only general trends can been seen. Annual cropland has replaced native
perennials over more than 80% of their prior extent. Hayland and pasture have largely
replaced the remaining native prairie. Upland shrublands have probably also decreased. Fire
incidence has certainly declined, but to what extent is unknown.
VRU 17: Rolling Hills, Cedar and Grand Fir
This VRU is rare in the South Fork Clearwater River Subbasin. Mesic grand fir and western
redcedar habitat types are dominant.
Historic Conditions
Grand fir and Douglas fir were historically important cover types on this VRU. Western
redcedar, western white pine, western larch, Engelmann spruce, and ponderosa pine were less
common. About 20-35% of the stands had 10 or more trees per acre older than 150 years.
Ridge top groves of large old cedar and grand fir old growth and early serai tall shrub
communities were important elements of this landscape. The relative proportion of trees by
size class was 10-25% non-forest, 15-25% seedling/sapling, 20-30% pole, 20-35% medium
tree, and 15-40% large tree.
Small fires occurred frequently, but mixed severity infrequent (75 to 150 years) fires were
typical. About 40-60% of the stands originated from mixed severity fires and 40-60% of the
stands originated from stand-replacing fires. Moderate sized blocks (50-500 acres) of fire-
killed medium-size and large trees were common at any one time in any 10,000 acres of this
VRU.
Changes from Historic Conditions
This VRU is poorly represented in the subbasin and only a few trends can be seen. Western
white pine has virtually disappeared due to blister rust and forest succession. Shrubs,
hardwoods, trees in the seedling/sapling structural stage, and trees in the pole structural stage
have probably declined. Trees in the medium and large tree stages have increased, but
numbers of the largest old trees may have been reduced by harvest. Harvest has affected 11%
of the acres. The ratio of replacement treatment to less severe treatments has been about
100% replacement. This is well above the historic ratio. No acres have burned in the
subbasin since fire suppression has become effective, a decline of 100%. Due to fire
suppression, extensive snag patches that result from large fires are no longer created.
H-10 Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Habitat Type Groups
Habitat type grouping is based on similarities in natural disturbance regimes, successional
patterns, and structural characteristics of mature stands. The HTGs are intended to assist
with subregional and landscape assessments. The HTGs are separated into forest and non-
forest categories. Table H-l presents vegetation conditions expected for non-forest HTGs
and Table H-2 presents vegetation conditions expected for forest HTGs. A detailed
description of HTGs is presented below.
Forested Habitat Type Groups and Descriptions
HTG #1 - Warm and Dry - Pinus ponderosa Types or Pseudotsuga menziesii/Grass
Types
This HTG is characterized in naturally functioning ecosystems by dry and open-grown park-
like stands of Pinus ponderosa or Pseudotsuga menziesii with bunch grass understories.
Most of the sites occur on hot and dry landscapes at low elevations and on west and south
aspects. A natural fire-free interval of 5 to 25 years on these sites maintained these open-
grown park-like stands (Fischer 1987). These fires were low severity, under-burning fires.
Stand replacement fires were probably rare.
HTG # 2 - Moderately Warm and Dry - Most Pseudotsuga menziesii Types and Dry
Abies grandis Types
These habitat types are characterized in naturally functioning ecosystems by open-grown
stands of Pinus ponderosa or Pseudotsuga menziesii with grass and brush understories. Most
of the sites normally occur at lower elevations on many aspects, but are also found at higher
elevation on more southerly and westerly aspects. The natural fire-free interval for under-
burning was historically 5 to 50 years (Fischer 1987). The mostly low- and moderate-
severity fires maintained open, park-like stands dominated by Pinus ponderosa. In some
cases, stand composition was also high in Pseudotsuga menziesii and Larix occidentalis.
Little information is available on stand-replacing fires, but these severe intensity fires
occurred only after a fire-free interval probably exceeding 500 years on dry land types and
50-200 years on moist land types (Smith 1995).
HTG #3 - Moderately Warm and Moderately Dry - Pseudotsuga menziesii with
Linnaea borealis Understory and Most Abies grandis Types
This HTG contains a highly variable group of habitat types. The group is a transition type
between the dry and moist habitat types. It includes types characteristic of each. These
habitat types were characterized in naturally functioning ecosystems by mixed species stands
of Pinus ponderosa, Pseudotsuga menziesii, Larix occidentalis, Pinus contorta, and Abies
grandix. Understories in absence of fire or other disturbance are composed primarily of
dense Pseudotsuga menziesii or Abies grandix thickets, though other tree species may be
present. The natural fire-free interval for under-burning was 15 to 50 years. Mixed
intensities of moderate and severe fires commonly created mosaics of even-aged stands with
H-ll Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
survivor individuals and groups of trees (Smith 1995). Also common in this HTG are open,
park-like stands dominated by Pinus ponder osa, Larix occidentalis, and Pseudotsuga
menziesii.
HTG #4 - Moderately Warm and Moist - Abies grandis Asarum and Clintonia Types
These are warm and moist habitats that occur along the lower slopes and valley bottoms.
The group is highly diverse and nearly all the conifer species in the area can occur in this
HTG. Understory vegetation may be dominated by a wide variety of species. The fire-free
interval is wide, from 50 years for the drier types to over 200 years for the more moist types.
Typical fires are minor ground fires that create a mosaic within the stand. On the other
extreme, with drying, a complete stand replacement fire can occur. Many times this is the
result of a fire burning from an adjacent and drier type. Fire exclusion on these sites has
changed them very little except to reduce the number of acres in early succession types.
HTG #5 - Moderately Cool and Moist - Thuja plicata and Tsuga heterophylla Asarum
and Clintonia Types
These are moderately cool and moist sites. They contain many species, including Thuja
plicata., western Tsuga heterophylla., Pseudotsuga menziesii., Picea engelmannii, Abies
grandix, Pinus contorta, Tsuga mertensiana, Larix occidentalis, and Pinus monticola. Very
high basal areas can be achieved on these types. Fire frequency is low due to the maritime
influence on these sites. Fire severity can be highly variable due the common moist
conditions, but can be severe during periods of drought. Fire-free intervals range from 50 to
greater than 200 years (Fischer 1987). Many species do well on these sites and may thrive
for centuries without disturbance. Thuja plicata is the most notable example.
HTG #6 - Moderately Cool and Wet - Thuja plicata Athyrium, Oplopanax, and
Adiantum Types
These are very wet sites. They are forested riparian areas along streams and are associated
with wetlands. Due to these very wet conditions, the fire-free interval can be very long.
Intervals are probably much longer than the majority of fire group eleven, 50 to greater than
200 years. Centuries may pass without severe, stand-replacing fires (Smith 1995).
HTG #7 - Cool and Moist - Clintonia and Menziesia Types
These types are characterized by cool and moist site conditions. Species diversity can be
high with Larix occidentalis, Pseudotsuga menziesii, Pinus monticola, Picea Engelmannii,
Pinus contorta, Abies lasiocarpa, and Abies grandix. Other sites are dominated by Pinus
contorta after stand-replacing burns. These sites are probably too cool for Tsuga
heterophylla and Thuja plicata. Fire history information is scarce. Fire intervals are
estimated at greater than 120 years for most sites (Fischer 1987).
H-12 Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
HTG #8 - Cool and Wet - Calamagrostis canadensis, Equisetum, Galium, and
Streptopus
These are very wet sites. They are forested riparian areas along streams and associated with
wetlands. Due to these very wet conditions, the fire-free interval can be very long. Intervals
between severe, stand-replacing fires are probably much longer than the majority of fire
group nine (90 to 130 years) and are probably in excess of 150 years.
HTG #9 - Cool and Moderately Dry - Cooler Abies lasiocarpa and Pinus contorta
Types
These are the cooler Abies lasiocarpa habitat types within the area. The fire-free interval of
these types is 50-130 years (Fischer 1987). These periodic fire disturbances and the high
number of moderate- to high-intensity fires favor species such as Pinus contorta,
Pseudotsuga menziesii, and Larix occidentalis. Other species on these sites are commonly
Abies lasiocarpa, Picea, and Pinus albicaulis. Stands dominated by Pinus contorta and over
80 years of age tend to build fuels to become a part of large stand-replacing fire events
encompassing thousands of acres (Fischer 1987). These sites, especially in the Vaccinium
caespitosum and scoparium types, are quite frosty.
HTG #10 - Cold and Moderately Dry - Vaccinium scoparium and Luzula Types
These types are upper elevation, cold, dry sites. Many of these sites are above the cold limits
of conifers such as Pseudotsuga menziesii, Larix occidentalis, and Pinus monticola.
Common species are Pinus albicaulis, Pinus contorta, Tsuga mertensiana, Abies lasiocarpa,
and Larix lyallii. The fire-free interval varies considerably from 35 to over 300 years.
Stand-replacing fires occur after intervals of more than 200 years (Fischer et al. 1987). Most
fires are of low severity because of discontinuous fuels (Arno 1989).
HTG #11 - Cold - High elevation Pinus albicaulis and Abies lasiocarpa Types
These types are cold, high elevation sites. They are near timberline and above the cold limits
of species such as Pseudotsuga menziesii and Larix occidentalis. Common species are Pinus
albicaulis, Tsuga mertensiana, Abies lasiocarpa, and Larix lyallii. The fire-free interval
varies considerably from 35 to over 300 years. Stand replacement fires occur after intervals
of more than 200 years (Fischer et al. 1987).
H-13 Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table H-1. Non-forested Habitat Type Groups (HTGs) (USDA FS 1992).
Habitat Type
Grassland Steppe (HTG 15)
Poasec-Danuni
Agropyron spicatum
Agrspi (lithic)
Festuca idahoensis
Festuca scabrella
Andropogon spp.
Shrubland Steppe (HTG 30)
Artemisia rigida-Poa secunda
Artemesia tridentata
Purshia tridentata
Celtis reticulata
Cercocarpus ledifolius
Cerled-agrspi
Rhus glabra-agropyron spicatum
Symphoricarpos albus
Hardwoods (HTG 50)
Mountain Bottomlands (HTG 60)
Carex spp. (wet complex)
Carex/grass (moist complex)
Deschampsia caespitosa
Tall forb types
Crataegus douglasii
Alnus spp.
Sa/;x spp
Populus tremuloides
Populus trichocarpa
Alpine Meadows and Scrub (HTG 80)
Sedge/grass types
(Includes Carhoo-Fesida, Cargey-
Fesida, Fesvir-Carex)
Forb types
Shrub types
Rock (HTG 0)
Water (HTG 98)
Phase
Code
015
017
018
019
020
030
040
032
035
041
036
044
042
043
050
060
061
065
062
070
071
073
074
078
079
080
081
084
087
0
98
Fire Group Code
0
0
0
0
H-14
Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table H-2. Summary information for forested Habitat Type Groups within the
South Fork Clearwater River Subbasin.
Habitat Types Comprising Habitat Group 1
Habitat Type
Pinus ponderosa/Agropyron
spicatum
Pinus ponderosa/Festuca
idahoensis
Pinus ponderosa/Purshia
tridentata
Pseudotsuga menziesii/
Agropyron spicatum
Pseudotsuga menziesii/Festuca
Idahoensis
Pseudotsuga menziesii/Festuca
scabrella
Pseudotsuga menziesii/
Symphoricarpos albus
Pseudotsuga menziesii/
Calamagrostis rubescens
Phase
Festuca idahoensis
Festuca scabrella
Agropyron spicatum
Festuca idahoensis
Agropyron spicatum
Agropyron spicatum
Code
130
140
141
142
160
161
162
210
220
230
311
321
Fire Group Code
MT
2
2
2
2
2
2
2
4
5
4
4
4
ID
1
1
1
1
1
Habitat Types Comprising Habitat Group 3
Habitat Type
Pseudotsuga menziesii/Linnaea
borealis
Abies grandix/Xerophyllum tenax
Abies grandix/Vaccinium
globulare
Abies grandix/Linnaea borealis
Abies grandix/Clintonia uniflora
Phase
Symphoricarpos albus
Vaccinium globulare
Coptis occidentalis
Vaccinium globulare
Linnaea borealis
Xerophyllum tenax
Xerophyllum tenax
Code
290
291
293
510
511
512
515
590
591
592
523
Fire Group Code
MT
6
6
6
6
11
6
6
11
11
6
11
ID
7
7
7
7
7
7
7
H-15
Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table H-2 (continued). Summary information for forested Habitat Type Groups
within the South Fork Clearwater River Subbasin.
Habitat Types Comprising Habitat Group 2
Habitat Type
Pin us ponderosa/
Symphoricarpos alb us
Pinus ponderosa/Physocarpus
malvaceus
Pseudotsuga menziesii/
Vaccinium caespitosum
Pseudotsuga menziesii/
Physocarpus malvaceus
Pseudotsuga menziesii/
Vaccinium globulare
Pseudotsuga menziesii/Linnaea
borealis
Pseudotsuga menziesii/
Symphoricarpos alb us
Pseudotsuga menziesii/
Calamagrostis rubescens
Pseudotsuga menziesii/Carex
geyeri
Pseudotsuga menziesii/Spiraea
betulifolia
Pseudotsuga menziesii/
Arctostaphylos uva-ursi
Pseudotsuga menziesii/
Juniperus communis
Pseudotsuga menziesii/Arnica
cordifolia
Abies grandis/Spiraea betulifolia
Abies grandis/Physocarpus
malvaceus
Phase
Symphoricarpos albus
Physocarpus malvaceus
Calamagrostis rubescens
Smilacina stellata
Vaccinium globulare
Arctostaphylos uva-ursi
Xerophyllum tenax
Calamagrostis rubescens
Calamagrostic rubescens
Symphoricarpos albus
Arctostaphylos uva-ursi
Calamagrostis rubescens
Pinus ponderosa
Coptis occidentalis
Physocarpus malvaceus
Code
170
171
190
250
260
261
262
263
280
281
282
283
292
310
312
313
320
322
323
324
330
340
350
360
370
505
506
507
508
Fire Group Code
MT
2
2
6/7
6
6
4
6
6
6
6
6
5
6
6
4
4
5
4
4
4
4
ID
1
2
2
2
2
2
2
2
2
2
1
2
2
2
H-16
Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table H-2 (continued). Summary information for forested Habitat Type Groups
within the South Fork Clearwater River Subbasin.
Habitat Types Comprising Habitat Group 4
Habitat Type
Abies grandis/Asarum caudatum
Abies grandis/Clintonia uniflora
Abies grandis/Senecio triangularis
Phase
Asarum caudatum
Menziesia ferruginea
Taxus brevifolia
Clintonia uniflora
Aralia nudicaulis
Physocarpus
malvaceus
Menziesia ferruginea
Taxus brevifolia
Code
516
517
518
519
520
521
522
524
525
526
529
Fire Group Code
MT
11
11
11
11
11
11
7
ID
7
7
7
7
7
7
7
7
H-17
Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table H-2 (continued). Summary information for forested Habitat Type Groups
within the South Fork Clearwater River Subbasin.
Habitat Types Comprising Habitat Group 5
Habitat Type
Thuja plicata/Clintonia uniflora
Thuja plicata/Asarum caudatum
Thuja plicata/Gymnocarpium
dryopteris
Tsuga heterophylla/
Gymnocarpium dryopteris
Tsuga heterophylla/Clintonia
uniflora
Tsuga heterophylla/Asarum
caudatum
Phase
Clintonia uniflora
Aralia nudicaulis
Menziesia ferruginea
Xerophyllum tenax
Taxus brevifolia
Asarum caudatum
Menziesia ferruginea
Taxus brevifolia
Clintonia uniflora
Aralia nudicaulis
Xerophyllum tenax
Menziesia ferruginea
Aralia nudicaulis
Menziesia ferruginea
Asarum caudatum
Code
530
531
532
533
534
535
545
546
547
548
555
565
570
571
572
573
574
575
576
577
578
Fire Group Code
MT
11
11
11
11
11
11
11
11
11
11
11
11
11
11
11
11
11
11
11
11
11
ID
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
H-18
Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table H-2 (continued). Summary information for forested Habitat Type Groups
within the South Fork Clearwater River Subbasin.
Habitat Types Comprising Habitat Group 6
Habitat Type
Thuja plicata/Athyrium filix-femina
Thuja plicata/Oplopanax horridum
Thuja plicata/Adiantum pedatum
Phase
Adiantum pedatum
Athyrium filix-femina
Code
540
541
542
550
560
Fire Group Code
MT
11
ID
9
9
9
9
Habitat Type Groups Comprising Habitat Group 7
Habitat Type
Picea/Clintonia uniflora
Picea/Linnaea borealis
Tsuga heterophylla/Menziesia
ferruginea
Abies lasiocarpa/Clintonia
uniflora
Abies lasiocarpa/Linnaea
borealis
Abies lasiocarpa/Menziesia
ferruginea
Tsuga mertensiana/Menziesia
ferruginea
Phase
Vaccinium caespitosum
Clintonia uniflora
Clintonia uniflora
Aralia nudicaulis
Vaccinium caespitosum
Xerophyllum tenax
Menziesia ferruginea
Linnaea borealis
Xerophyllum tenax
Coptis occidentalis
Luzula hitchcockii
Xerophyllum tenax
Vaccinium scoparium
Luzula hitchcockii
Xerophyllum tenax
Code
420
421
422
470
579
620
621
622
623
624
625
660
661
662
670
671
672
673
674
680
681
682
Fire Group Code
MT
9
9
9
7
9
9
9
9
9
9
9
9
9
9
9
ID
5
5
5
5
5
5
5
5
5
H-19
Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Habitat Type Groups Comprising Habitat Group 7
Habitat Type
Tsuga mertensiana/Clintonia
uniflora
Abies lasiocarpa/Vaccinium
scoparium
Abies lasiocarpa/Alnus sinuata
Abies lasiocarpa/Luzula
hitchcockii
Phase
Menziesia ferruginea
Xerophyllum tenax
Thalictrum occidentale
Menziesia ferruginea
Code
685
686
687
733
740
832
Fire Group Code
MT
10
ID
5
5
Habitat Types Comprising Habitat Group 8
Habitat Type
Picea/Equisetum arvense
Picea/Galium triflorum
Picea/Smilacina stellata
Abies lasiocarpa/Oplopanax
horridum
Abies lasiocarpa/Galium triflorum
Abies lasiocarpa/Streptopus
amplexifolius
Abies lasiocarpa/Calamagrostis
canadensis
Tsuga mertensiana/Streptopus
amplexifolius
Phase
Galium triflorum
Calamagrostis
canadensis
Menziesia ferruginea
Ligusticum canbyi
Calamagrostis
canadensis
Ligusticum canbyi
Galium triflorum
Vaccinium caespitosum
Ledum glandulosum
Luzula hitchockii
Menziesia ferruginea
Code
410
440
480
610
630
631
632
635
636
637
650
651
652
653
654
653
675
676
677
Fire Group Code
MT
9
9
8
9
9
9
9
9
7
ID
5
5
5
5
5
5
5
5
H-20
Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table H-2 (continued). Summary information for forested Habitat Type Groups
within the South Fork Clearwater River Subbasin.
Habitat Types Comprising Habitat Group 9
Habitat Type
PiceaA/accinium caespitosum
Abies lasiocarpaA/accinium
caespitosum
Abies lasiocarpa/Linnaea
borealis
Abies lasiocarpa/Xerophyllum
tenax
Tsuga mertensiana/
Xerophyllum tenax
Abies lasiocarpaA/accinium
globulare
Abies lasiocarpaA/accinium
scoparium
Abies lasiocarpa/
Calamagrostis rubescens
Abies lasiocarpa/Arnica
cordifolia
Pinus contorta/Purshia
tridentate
Pinus contortaA/accinium
caespitosum c.t.
Pinus contorta/Linnaea
borealis c.t.
Pinus contorta/Calamagrostis
rubescens c.t.
Phase
Vaccinium scoparium
Vaccinium globulare
Vaccinium scoparium
Coptis occidentalis
Luzula hitchcockii
Luzula hitchcockii
Xerophyllum tenax
Vaccinium scoparium
Calamagrostis rubescens
Code
450
640
663
690
691
692
693
694
710
711
712
713
720
731
750
780
910
920
930
950
Fire Group Code
MT
7
7
7
8
8
7
8
7
7
7
7
7
ID
3
4
4
4
4
4
4
4
4
4
3
3
3
H-21
Appendix H
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table H-2 (continued). Summary information for forested Habitat Type Groups
within the South Fork Clearwater River Subbasin.
Habitat Types Comprising Habitat Group 10
Habitat Type
Abies lasiocarpaA/accinium
scoparium
Abies lasiocarpa-Pinus albicaulis/
Vaccinium scoparium
Abies lasiocarpa/Luzula
hitchcockii
Tsuga mertensiana/Luzula
hitchcockii
Pin us contorta/Xerophyllum tenax
c.t.
Pinus contorta/Vaccinium
scoparium
Phase
Vaccinium scoparium
Vaccinium scoparium
Vaccinium scoparium
Menziesia ferruginea
Code
730
732
820
830
831
840
841
842
9225
940
Fire Group Code
MT
7
10
10
10
10
10
7
ID
3
6
6
6
3
3
Habitat Types Comprising Habitat Group 11
Habitat Type
Pinus albicaulis-Abies lasiocarpa
h.t.s.
Alpine larch-Abies lasiocarpa
h.t.s.
Pinus albicaulis h.t.s.
Phase
Code
850
860
870
Fire Group Code
MT
10
10
10
ID
6
6
6
c.t. =
h.t.s. = habitat type series
H-22
Appendix H
-------
Appendix I. Overview of Stream Heating Processes
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
List of Tables l-i
List of Figures l-i
Overview of Stream Heating Processes 1-1
Cumulative Effects 1-1
Thermal Role of Riparian Vegetation I-2
Stream Surface Shade - Defined I-2
Microclimate - Surrounding Thermal Environment I-5
Thermal Role of Channel Morphology I-5
Thermal Role of Hydrology I-6
Thermal Role of Ground Water I-7
References I-8
List of Tables
Table 1-1. Factors that influence stream shade I-4
List of Figures
Figure 1-1. Stream Temperature Conceptual Model Flow Chart 1-1
Figure I-2. Definition of Effective Shade I-3
Figure I-3. Parameters that Affect Shade and Geometric Relationships I-4
Figure I-4. Estimated August Mean Monthly Flow Conditions for the South
Fork Clearwater River Subbasin (Lipscomb 1998) I-7
I- i Appendix I
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Appendix I. Overview of Stream Heating Processes
Report prepared by:
Peter Leinenbach, Landscape Ecologist, Region 10, USEPA
At any particular time, a defined stream reach is capable of sustaining a particular water
column temperature. Stream temperature changes that result within a defined reach are
explained rather simply. The temperature of a parcel of water traversing a stream/river reach
enters the reach at a given temperature. If that temperature is greater than the energy balance
of the stream reach is capable of supporting, the temperature will decrease. If that
temperature is less than energy balance is capable of supporting, the temperature will
increase. Stream temperature changes within a defined reach are induced by the difference in
energy balance between the parcel of water and the surrounding environment and transport of
the parcel through the reach. The general relationships between stream parameters,
thermodynamic processes (heat and mass transfer), and stream temperature changes are
outlined in the flow chart below (Figure 1-1.).
Stream Temperature Conceptual Model Flow Chart
Riparian
Vegetation
Channel
Morphology
Hydrology
Rate Change in Stream
Temperature
3 3
0.
So
ro a,
w °
Figure 1-1. Stream Temperature Conceptual Model Flow Chart
Cumulative Effects
It takes time for a water parcel to traverse the longitudinal distance of the defined reach,
during which the energy processes drive stream temperature change. At any particular
instant, water that enters the upstream portion of the reach is never exactly the temperature
that is supported by the defined reach. As the water is transferred downstream, heat energy
and hydraulic processes that are variable with time and space interact with the water parcel
and induce water temperature changes. Further, heat energy is stored within this parcel of
water and its temperature is the result of the heat energy processes upstream. This is
1-1
Appendix I
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
commonly referred to as a cumulative temperature effect, where conditions at a site
contribute to heating of an already heated parcel of stream water. The described scenario is a
simplification; however, understanding the basic processes in which stream temperature
changes occur over the course of a defined reach and period of time is essential.
Thermal Role of Riparian Vegetation
The role of near-stream land cover in maintaining a healthy stream condition and water
quality is well documented and accepted in scientific literature (Beschta et al. 1987).
Riparian vegetation plays an important role in controlling stream temperature changes. The
list of significant impacts that near-stream land cover has upon the stream and the
surrounding environment is long, but warrants listing.
• Near-stream vegetation produces shadows, that when cast across a stream reduce solar
radiant loading. The height, width, and density of the vegetation determine the extent of
this effect..
• Near-stream land cover creates a thermal microclimate that generally maintains cooler air
temperatures, higher relative humidity, and lower wind speeds along stream corridors.
• Near-stream vegetation affects bank stability. Specifically, channel morphology is often
highly influenced by land cover type and condition, as they affect floodplain and instream
roughness by contributing coarse woody debris and influencing sedimentation, stream
substrate composition, and stream bank stability.
The warming of water temperature as a stream travels and drops in elevation (longitudinal
heating) is a natural process. However, rates of heating can be dramatically reduced when
high levels of shade exist and solar radiation loading is minimized. The overriding
justification for attempting to reduce solar radiation loading is to minimize longitudinal
heating. A limiting factor in reducing longitudinal stream heating is that there is a natural
maximum level of shade that a given stream is capable of attaining.
Stream Surface Shade - Defined
Stream surface shade is an important parameter that controls the stream heating derived from
solar radiation. Solar radiation has the potential to be the largest heat transfer mechanism in a
stream system. Human activities can degrade near-stream land cover and/or channel
morphology, and in turn, decrease shade. It follows that human-caused reductions in stream
surface shade have the potential to cause significant increases in heat delivery to a stream
system. Stream shade levels can also serve as indicators of near-stream land cover and
channel morphology condition. For these reasons, stream shade is a focus of this analytical
effort.
Shade is the amount of solar energy that is obscured or reflected by vegetation or topography
above a stream. Shade is expressed in units of energy per unit area per unit time or as a
percent of total possible energy. Canopy cover is the percent of the sky covered by
vegetation or topography. Shade producing features will cast shadows on the water, while
canopy cover may not. In order to assess the ability of riparian land cover to shield a stream
1-2 Appendix I
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
from solar radiation, two basic characteristics of shade must be addressed: shade duration
and shade quality. The length of time that a stream receives shade is referred to as shade
duration. The density of shade that affects the amount of radiation blocked by the shade-
producing features is referred to as shade quality. Effective shade (Figure 1-2) is amount of
potential solar radiation not reaching the stream surface and is a function of shade duration
and shade quality.
Effective Shade Defined
Salary - Potential iJaily direct beam solar ridiatksri load adjusted For
julian day. solar altitude, solar azimuth and site elevatkin.
Shade
[.Solar, - Soter, J
Solar,
Wtere,
Solar.,. Potential Daly Dirwl Beam S&bf Radiation L&ad
Solaf3; Dairy Direct Beam Solar Radiation Load Reeetaed at
Ilie stream Surfaes
Figure 1-2. Definition of Effective Shade
In the northern hemisphere, the earth tilts on its axis toward the sun during summertime
months, allowing longer day length and higher solar altitude, both of which are functions of
solar declination (a measure of the earth's tilt toward the sun) (Figure 1-3). Geographic
position (latitude and longitude) fixes the stream to a position on the globe, while aspect
provides the stream/riparian orientation. Near-stream land cover height, width, and density
describe the physical barriers between the stream and sun that can attenuate and scatter
incoming solar radiation (i.e., produce shade) (Table 1-1). The solar position has a vertical
component (solar altitude) and a horizontal component (solar azimuth) that are both functions
of time/date (solar declination) and the earth's rotation (hour angle measured as 15° per
hour). While the interaction of these shade variables may seem complex, the mathematics
that describes them is relatively straightforward geometry. Using solar tables or mathematical
simulations, the potential daily solar load can be quantified. The measured solar load at the
stream surface can easily be measured with a Solar Pathfinder® or estimated using
mathematical shade simulation computer programs (Boyd 1996, Park 1993).
1- J
Appendix I
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Geometric Relationship that Influence Shads Production
Solar Attitude and Solar Azimuth are two basic measurements of the sun's
position When a stream's orientation, geographic position, riparian condition
and solar position are known, shading characteristics can be simulated
Solar Altitude measures the vertical component of the sun's position
Solar Azimuttt measures ttie horizontal component of the aun's position
Figure 1-3. Parameters that Affect Shade and Geometric Relationships
Table 1-1. Factors that influence stream shade.
Description
Season/Time
Stream Characteristics
Geographic Position
Vegetative Characteristics
Solar Position
Parameter
Date/Time
Aspect, Channel Width
Latitude, Longitude
Near-Stream Land Cover Height, Width,
and Density
Solar Altitude, Solar Azimuth
Bold type - influenced by human activities
1-4
Appendix I
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Microclimate - Surrounding Thermal Environment
A secondary consequence of near-stream vegetation is its affect on the riparian microclimate.
Riparian corridors often produce microclimates that surround the stream where cooler air
temperatures, higher relative humidity, and lower wind speeds are characteristic. Riparian
microclimates tend to moderate daily air temperatures. Relative humidity increases result
from the evapotranspiration that is occurring by riparian plant communities. Wind speed is
reduced simply by the physical blockage produced by riparian vegetation. Dong et al. (1998)
analyzed microclimate data along 20 small streams in western Washington and found that
riparian vegetation removal via timber harvests increased near stream air temperatures by up
to 8 °F. Chen et al. (1995) detected that edge effects (i.e., atmospheric conditions outside of
the near-stream buffer) penetrated to distances greater than 600 feet into a well-vegetated
area. Riparian buffers commonly occur on both side of the stream, compounding the edge
influence of the microclimate.
Brosofske et al. (1997) reported that a minimum stream buffer width of 150 feet was required
to maintain soil temperatures that reflect those of a normal microclimate. Ground
temperatures can be a source of heat energy to the stream. When the ground is warmer than
the stream, heat will transfer from the stream bank to the water column. In fact, ground
surfaces can conduct heat to a stream hundreds of times faster than an air column
surrounding the stream. Solids (ground surfaces) have conductivities on the order of 500 to
3,500 times greater than gases (air) (Halliday and Resnick 1988). Impoverished riparian areas
that allow excessive stream bank warming will introduce heat into the stream faster than
cooler, highly vegetated stream banks. Riparian condition is again implicated as a controlling
factor in stream temperature dynamics, in part because ground/soil temperatures are a
function of shading.
Air affects stream temperatures at a slower rate than the ground. Nevertheless, this should
not be interpreted to mean that air temperatures do not affect stream temperature. Air can
deliver heat to a stream via the convection/conduction pathway, which is the slowest of the
water energy transfer processes (Bowen 1926, Beschta and Weatherred 1984, Boyd 1996,
Chen 1996). However, prolonged exposure to air temperatures warmer than the stream can
induce gradual stream heating. Thus, a cooler microclimate will induce less stream warming.
Thermal Role of Channel Morphology
Changes in channel morphology, mainly channel widening, impact stream temperatures. As a
stream widens, the surface area exposed to radiant sources and the ambient air temperature
increases, resulting in increased energy exchange between the stream and its environment
(Boyd 1996). Further, wide channels are likely to have relatively little shade due to the
distance between the banks and the increased surface area to shade ratio. Conversely, narrow
channels are more likely to receive a lot of shade. An additional benefit inherent of
narrow/deep channels is the higher frequency of pools that contribute to aquatic habitat.
Channel widening is often related to degraded riparian conditions that allow increased stream
bank erosion and sedimentation of the streambed, both of which correlate strongly with
I- 5 Appendix I
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
riparian vegetation type and condition (Rosgen 1994). Riparian vegetation strengthens the
stream bank with its roots (rooting strength) and contributes to floodplain and stream bank
roughness that dissipates erosive energies associated with flowing water. Established or
mature woody riparian vegetation provide the highest level of rooting strength and
floodplain and stream bank roughness. Annual (grassy) riparian vegetation communities
offer less rooting strength and floodplain and stream bank roughness.
Channel morphology is not solely dependent on riparian conditions. Sedimentation can
deposit material in the channel, fill pools, and agrade the streambed, reducing channel depth
and increasing channel width. High flow events play a major role in shaping the stream
channel. Channel modification usually occurs during high flow events. Naturally, land uses
that affect the magnitude and timing of high flow events may negatively impact channel
width and depth. Riparian vegetation conditions will affect the resilience of the stream banks
and floodplain during periods of sediment introduction and high flow. Disturbance processes
may have drastically differing results depending on the ability of riparian vegetation to shape
and protect channels. Riparian vegetation composition and condition affect channel
morphology by:
• Building stream banks: Vegetation traps suspended sediments, encourages deposition of
sediment in the floodplain, and reduces incoming sources of sediment.
• Maintaining stable stream banks: High rooting strength and high stream bank and
floodplain roughness prevent stream bank erosion.
• Reducing flow velocity (erosive kinetic energy): Vegetation supplies large woody
debris to the active channel, creates high pool:riffle ratios, and adds channel complexity
that reduces shear stress exposure to stream bank soil particles.
Thermal Role of Hydrology
Brown (1969) proposed that water temperature change is a proportional function of heat
exchange per unit volume:
AHeat Energy
w (^^
Volume
Therefore, large volume streams are less responsive to temperature change than are low flow
streams. Specifically, stream flow volume will affect the wetted channel dimensions (width
and depth), flow velocity, travel time, and the stream assimilative capacity. Human-related
reductions in flow volume can have a significant influence on stream temperature dynamics,
most likely increasing diurnal variability in stream temperature. Figure 1-4 illustrates the
estimated mean August flow conditions for hydrological subunits within the South Fork
Clearwater River subbasin (Lipscomb 1998). As can be seen in this image, stream flow
conditions are very low throughout the subbasin during the summer, especially within the
subbasin tributaries.
1-6 Appendix I
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
August Mean Monthly Discharge
(Hydrological Boundaries (USGS))
o - s cf s
5-10cfs
10-20cfs
20 - 30 cfs
| | 30 - 50 cfs
^50-100 cfs
| | 100-150 cfs
| | 150-200 cfs
| 1 200 - 250 cfs
I 250 - 300 cfs
Figure I-4. Estimated August Mean Monthly Flow Conditions for the South
Fork Clearwater River Subbasin (Lipscomb 1998)
Thermal Role of Ground Water
Ground water inflow has a cooling effect on summertime stream temperatures. Subsurface
water is insulated from surface heating processes. Ground water temperatures fluctuate little
and are cool (45 °F to 55 °F). Many land use activities that disturb riparian vegetation and
associated floodplain areas may affect the surface water connectivity to ground water
sources. Ground water inflow not only cools summertime stream temperatures, but also
augments summertime flows. Reductions in or elimination of ground water inflow will have
a compounding warming effect. The ability of riparian soils to capture, store and slowly
release ground water is largely a function of floodplain/riparian area health.
The effects of ground water hydrology were not analyzed in this total maximum daily load
(TMDL) effort. However, targets developed as part of this TMDL should passively promote
the protection and creation of ground water areas and the connectivity of these areas with the
stream.
1-7
Appendix I
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
References
Beschta, R.L., R.E. Bilby, G.W. Brown, L.B. Holtby, and T.D. Hofstra. 1987. Stream
temperature and aquatic habitat: Fisheries and forestry interactions. Pages 191-232 in
E.O. Salo and T.W. Cundy, eds. Streamside Management: Forestry and Fishery
Interactions. University of Washington, Institute of Forest Resources, Seattle, WA.
Beschta, R.L. and J. Weatherred. 1984. A computer model for predicting stream temperatures
resulting from the management of streamside vegetation. USDA Forest Service.
WSDG-AD-00009.
Bowen, IS. 1926. The ration of heat loss by convection and evaporation from any water
surface. Physical Review. Series 2, Vol. 27:779-787.
Boyd, M.S. 1996. Heat Source: stream temperature prediction. Master's Thesis.
Departments of Civil and Bioresource Engineering, Oregon State University,
Corvallis, OR.
Brown, G.W. 1969. Predicting temperatures of small streams. Water Resources Research.
5(l):68-75.
Chen, J., J. Franklin, and T. Spies. 1995. Growing season microclimate gradients from edge
into old-growth Douglas fir forest. Ecological Applications. 5:74-86. 75.
Dong, J., J. Chen, K. Brosofske, and J. Naiman. 1998. Modeling air temperature gradients
across managed small streams in western Washington. Journal of Environmental
Management. 53:309-321. 213 pp.
Halliday D. and R. Resnick. 1988. Fundamentals of Physics. 3rd Edition. John Wiley and
Sons, New York. pp. 472-473.
Lipscomb, S.W. 1998. Hydrologic classification and estimation of basin and hydrologic
characteristics of subbasins in central Idaho. U.S. Geological Survey Professional
Paper 1604.
Park, C. 1993. SHADOW: stream temperature management program. User's Manual v. 2.3.
USDA Forest Service. Pacific Northwest Region.
Rosgen, D. 1996. Applied River Morphology. Wildland Hydrology. Pagosa Springs,
Colorado.
I- 8 Appendix I
-------
Appendix J. Stream and River Temperature Data
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
List of Tables J-i
List of Figures J-i
Stream and River Temperature Data J-1
List of Tables
Table J-1. Summary water temperature data for stream and river
monitoring locations in the SF CWR subbasin J-9
List of Figures
Figure J-1. Temperature Data for Little Elk Creek, 50 meters above the
Mouth J-3
Figure J-2. Temperature Data for Little Elk Creek at the USFS Boundary. J-4
Figure J-3. Temperature Data for Big Elk Creek at the Mouth J-5
Figure J-4. Temperature Data for Threemile Creek Below the Wastewater
Treatment Plant J-6
Figure J-5. Temperature Data for Butcher Creek, 1 Mile Above the Mouth ....
J-7
Figure J-6. Temperature Data for the Main Stem South Fork Clearwater
River at the Mt. Idaho Bridge J-8
J-i Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Stream and River Temperature Data
This appendix contains a summary of the stream and river temperature data of the South
Fork Clearwater River (SF CWR) Subbasin. The data summaries are shown in table and
graphical formats below.
Summary data for 142 temperature loggers are shown in Table J-l. These are data
collected by various agencies and are from several years. Some water bodies have
several monitoring stations, others have only one, and many have none.
Each of the temperature logger data sets is evaluated in a computer program developed
by the Idaho Department of Environmental Quality (DEQ) to compare the data to the
state water quality standards (WQS) and the federal bull trout standard. Input to the
program requires the temperature data organized by date and time, elevation, and location
of the temperature logger location. The program also requires the dates of the spawning
periods for the various salmonids using a particular water body. Table J-l shows the
salmonids determined to be present in each of the water bodies. The spawning period for
each of the species was determined by the Fisheries Technical Advisory Group (Fish
TAG) and is shown in Appendix D, Attachment D-l. Results of the stream temperature
evaluation program for selected sites on the 303(d) listed water bodies Little Elk Creek,
Big Elk Creek, Threemile Creek, Butcher Creek, and the main stem SF CWR at Stites are
shown in Figures J-l through J-6, and are discussed below.
For each of the temperature recording locations and for each year of data, a plot is made
of the temperature data, as can be seen below for the selected streams. Different statistics
can be shown on the plot. For example, Little Elk Creek at the mouth shows the daily
maximums, daily averages, and the daily diurnal difference, along with lines showing the
salmonid spawning daily average WQS and the cold water biota daily average WQS;
Little Elk Creek at the Nez Perce National Forest boundary and Big Elk Creek show the
same data except the diurnal differences are not shown; and the other three figures show
the daily maximums, averages, and minimums for their water bodies, along with the
WQS lines.
(In this appendix, we continue to use the antiquated terminology "Cold Water Biota" as
well as the currently approved terminology "Cold Water Aquatic Life" primarily because
the computerized model print out still produces that results as "Cold Water Biota". The
two sets of terms are equivalent.)
In addition to the plots, different data sets are produced summarizing the data in relation
to the different WQS. For bull trout, for example, the data set shows the WQS criteria,
the number of days of exceedance, and the percentage exceedance. These results must be
evaluated in relation to both the dates when the data were collected and the specified
spawning periods. Also, in the case of Idaho salmonid spawning standards evaluation,
the program evaluates separately for spring and fall spawners since different species
J-l Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
spawn at different times. Representative data sets from the 303(d) listed water bodies are
shown on the following pages.
For all of the temperature logger sites and dates, the most important data for exceedance
analyses are presented in Table J-l.
The tables below are auto-generated by the DEQ temperature assessment program and
offer little opportunity for manipulation. For example, they all show assessments for bull
trout water quality standards, even though some water bodies do not support bull trout
and are not federally protected for bull trout. For that reason, a short discussion of the
salient points is presented after each set of tables and figures. The purpose of presenting
all the somewhat confusing data is to show the reader examples of typical temperature
profiles in the SF CWR Subbasin.
J-2 Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
DEQ Summary of Temperature Data
Data Source Name: DEQ-LRO
Water Body Name: Little Elk Creek
Data Collection Site: LittleElk-02, 50 m abv mouth
Data Period: 07/19/2000 - 09/18/2000
MDMT = 23.3, 31 Jul
MWMT = 22.5, 02Aug
MDAT = 20.2, 01 Aug
MWAT= 19.1, 03 Aug
HUC4 Number: 17060305
HUC4Name: South Fork Clearwater
North of the Salmon Clearwater Divide
Idaho Bull Trout Elevation: 1160 M
Waterbody ID Number: 57
Daily Waterbody Temperatures
08/08/2000
Measurement Dates
•High
Average
STATISTICS
Instantaneous Maximum
Instantaneous Mnimum
Q/erall Mean
Mean Daily Maximum
Mean Daily Average
Mean Daily Mnimum
Maximum Daily Average
Maximum 7-Day Maximum
Maximum 7-Day Average
Mnimum 7-Day Mnimum
23.3 °C
8.6 °C
0.0 °C
18.0°C
15.2°C
12.4°C
20.2 °C
22.5 °C
19.1 °C
9.0 °C
EPA Bull Trout
Criteria Exceedance Summary
Criteria
1 0 °C 7-Day Avg of Daily Max
Nmbr of 7-Day Avg;s w/in Dates
Exceedance Counts
Nmbr
56
56
Prcnt
100%
01-Jun 30-Sep
Idaho Cdd Water Biota
Criteria Exceedance Summary
Criteria
22 °C Instantaneous
1 9 °C Average
Days Evaluated & Date Range
Exceedance Counts
Nmbr
6
3
62
Rent
10%
5%
Off22/2000
09/21/2000
Idaho Salmonid Spawning
Criteria Exceedance Summary
Criteria
13 °C Instantaneous Spring
9 °C Average Spring
Spring Days Eval'd Win Dates
13 °C Instantaneous Fall
9 °C Average Fall
Fall Days Eval'd Win Dates
13 °C Instantaneous Total *
9 °C Average Total*
Tot Days Eval'd Win Both Dates *
Exceedance Counts
Nmbr
28
28
28
29
34
34
57
62
62
Rent
100%
100%
01-Jun
85%
100%
16-Aug
92%
100%
15-Aug
30-Sep
q Stall dates overlap double countinq rrav occur.
Figure J-1. Temperature Data for Little Elk Creek, 50 meters above the
Mouth
Comparing the data from Little Elk Creek at the mouth to those for Little Elk Creek at the
USFS boundary (next page) shows the magnitude of the temperature increase across the
unshaded meadows that the creek travels through between these two points. Otherwise
the patterns are relatively the same. This stream is evaluated for salmonid spawning
throughout the summer because of the presence of cutthroat trout and spring chinook
salmon and because of required protection for bull trout.
J-3
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
DEQ Summary of Temperature Data
Data Source Name: DEQ-LRO
Water Body Name: Little Elk Creek
Data Collection Site: LittleElk-01 at USFS Boundajy
Data Period: 07/07/2000 - 09/17/2000
MDMT = 20.7, 01 Aug
MWMT = 19.5, 02Aug
MDAT = 16.8, 01 Aug
MWAT = 15.8, 04 Aug
HUC4 Number: 17060305
HUC4 Name: South Fork Clearwater
North of the Salmon Clearwater Divide
Idaho Bull Trout Elevation: 1280 M
Waterbody ID Number: 57
Daily Waterbody Temperatures
07/27/2000
Measurement Dates
•High
Average
STATISTICS
Instantaneous Maximum
Instantaneous Minimum
Overall Mean
Mean Daily Maximum
Mean Daily Average
Mean Daily Minimum
Maximum Daily Average
Maximum 7-Day Maximum
Maximum 7-Day Average
Minimum 7-Day Minimum
20.7 °C
5.5 °C
0.0 °C
15.2 °C
12.1 °C
9.3 °C
16.8°C
19.5°C
15.8°C
6.2 °C
EPA Bull Trout
Criteria Exceedance Summary
Criteria
10 °C 7-Day Avg of Daily Max
Nmbr of 7-Day Avg's w/in Dates
Exceedance Counts
Nmbr
61
67
Prcnt
91%
01-Jun 30-Sep
Crit jedance Summary
Criteria
22 °C Instantaneous
19 °C Average
Days Evaluated & Date Range
Exceedance Counts
Nhtr
0
0
73
Prcnt
0%
0%
OS'22/2000
09/21/2000
Idaho Salmonid Spawning
Crit £danceSurrmarv
Criteria
13 °C I nstantaneous Spring
9 °C Average Spring
Spring Days Eval'd Win Dates
13 °C Instantaneous Fall
9 °C Average Fall
Fall Days Eval'd Win Dates
13 °C I nstantaneous Total *
9 °C Average Total*
Tot Days Eval'd Win Both Dates *
Exceedance Counts
Nhtr
40
40
40
13
23
33
53
63
73
Prcnt
100%
100%
OUun
39%
70%
16-Aug
73%
86%
15-Aug
3&Sep
*lfsDrina&fall dates a/elaodcubleaxnti no mavocor
Figure J-2. Temperature Data for Little Elk Creek at the USFS Boundary
Even though the water temperature at the USFS boundary was significantly cooler than at
the mouth, water temperatures still exceeded the salmonid spawning WQS during most of
the monitoring period.
J-4
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
DEQ Summary of Temperature Data
Data Source Name: DEQ-LRO
Water Body Name: Big Elk Creek
Data Collection Site: BigElk-01 at mouth
Data Period: 07/19/2000 -10/18/2000
MDMT = 25.0,02Aug
MWMT = 24.2,02Aug
MDAT = 20.7, 01 Aug
MWAT= 19.5, 30 Jul
HUC4 Number: 17060305
HUC4 Name: South Fork Clearwater
North of the Salmon Clearwater Divide
Idaho Bull Trout Elevation: 1160 M
Waterbody ID Number: 58
Daily Waterbody Temperatures
08/08/2000
Measurement Dates
Average
STATISTICS
Instantaneous Maximum
Instantaneous Minimum
Overall Mean
Mean Daily Maximum
Mean Daily Average
Mean Daily Minimum
Maximum Daily Average
Maximum 7-Day Maximum
Maximum 7-Day Average
Minimum 7-Day Minimum
25.0 °C
0.3 °C
0.0 °C
16.0°C
12.6°C
9.3 °C
20.7 °C
24.2 °C
19.5°C
2.2 °C
EPA Bull Trout
Cril edance Summary
Criteria
10 °C 7-Day Avg of Daily Max
Nmbr of 7-Day Avg's w/in Dates
Exceedance Counts
Nmbr
68
68
Prcnt
100%
01-Jun 30-Sep
Idaho Cold Water Biota
Cril ledance Summary
Criteria
22 °C Instantaneous
19 °C Average
Days Evaluated & Date Range
Exceedance Counts
Nmbr
18
5
65
Prcnt
20%
5%
06/22/2000
09/21/2000
Idaho Salmonid Spawning
Criteria Exceedance Summary
Criteria
13 °C Instantaneous Spring
9 °C Average Spring
Spring Days Eval'd w/in Dates
13 °C Instantaneous Fall
9 °C Average Fall
Fall Days Eval'd w/in Dates
13 °C Instantaneous Total *
9 °C Average Total *
Tot Days Eval'd w/in Both Dates *
Exceedance Counts
Nmbr
28
28
28
30
37
46
58
65
74
Prcnt
100%
100%
01-Jun
65%
80%
16-Aug
78%
88%
1 5-Aug
30-Sep
Figure J-3. Temperature Data for Big Elk Creek at the Mouth
The pattern of temperatures of Big Elk Creek at the mouth looks fairly similar to Little
Elk Creek at the mouth, except that Big Elk Creek is even warmer. Salmonid spawning
criteria are exceeded well into September for a high percentage of the days of this record.
J-5
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
DEQ Summary of Temperature Data
Data Source Name: DEQ-LRO
Water Body Name: Threemile Creek
Data Collection Site: Threemile-02, blw Grangeville STP
Data Period: 5/26/00 - 9/18/00
MDMT = 24.8, 11 Aug
MWMT = 23.5, 04Aug
MDAT=21.7, 01 Aug
MWAT = 21.3, 04 Aug
HUC4 Number: 17060305
HUC4 Name: South Fork Clearwater
North of the Salmon Clearwater Divide
Idaho Bull Trout Elevation: 975 M
Waterbody ID Number: 10
Daily Waterbody Temperatures (OOThreemile-02-all, elev 3200 ft)
06/15/2000 07/05/2000
Measurement Dates
High
•Average
STATISTICS
Instantaneous Maximum
Instantaneous Minimum
Overall Mean
Mean Daily Maximum
Mean Daily Average
Mean Daily Minimum
Maximum Daily Average
Maximum 7-Day Maximum
Maximum 7-Day Average
Minimum 7-Day Minimum
31.4°C
7.7 °C
0.0 °C
19.8°C
17.5°C
14.7°C
28.8 °C
24.2 °C
22.0 °C
9.4 °C
EPA Bull Trout
Criteria Exceedance Summary
Criteria
50 °C 7-Day Avg of Daily Max
Nmbr of 7-Day Avg's w/in Dates
Exceedance Counts
Nmbr
0
109
Prcnt
0%
01-Jun 30-Sep
Idaho Cold Water Biota
Criteria Exceedance Summary
Criteria
22 °C Instantaneous
19 °C Average
Days Evaluated & Date Range
Exceedance Counts
Nmbr
31
45
88
Prcnt
27%
39%
06/22/2000
09/21/2000
Idaho Salmonid Spawning
Criteria Exceedance Summary
Criteria
13 °C Instantaneous Spring
9 °C Average Spring
Spring Days Eval'd w/in Dates
13 °C Instantaneous Fall
9 °C Average Fall
Fall Days Eval'd w/in Dates
13 °C Instantaneous Total *
9 °C Average Total *
Tot Days Eval'd w/in Both Dates *
Exceedance Counts
Nmbr
6
7
7
0
0
0
6
7
7
Prcnt
86%
100%
01 -Mar
0%
0%
16-Dec
86%
100%
01-Jun
30-Dec
jccur.
Figure J-4. Temperature Data for Threemile Creek Below the Wastewater
Treatment Plant
Threemile Creek has not been designated for bull trout so is not compared to this
standard. The number of exceedances of the salmonid spawning criteria are small, but
they cover 100% of the record (May 26 through June 1), because the spawning and
incubation period for A-run steelhead ends on June 1. The graph indicates that stream
temperatures are well elevated by the beginning of this record. Cold water biota
standards exceedance numbers are probably the best indicators of the true level of
exceedance at this site, although it should be kept in mind that this site is designated for
salmonid spawning.
J-6
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
DEQ Summary of Temperature Data
Data Source Name: Nez Perce Tribe
Water Body Name: Butcher Creek
Data Collection Site: Butcher-01,1 mile abv mouth
Data Period: 5/18/01 -10/13/01
HUC4 Number: 17060305
HUC4 Name: South Fork Clearwater
North of the Salmon Clearwater Divide
Idaho Bull Trout Elevation: 550 M
Waterbody ID Number: 10
Daily Waterbody Temperatures (01Butcher-01, elev 1800 ft)
06/07/2001 06/27/2001
Measurement Dates
08/06/2001
•High
•Average
STATISTICS
Instantaneous Maximum
Instantaneous Minimum
Overall Mean
Mean Daily Maximum
Mean Daily Average
Mean Daily Minimum
Maximum Daily Average
Maximum 7-Day Maximum
Maximum 7-Day Average
Minimum 7-Day Minimum
25.3 °C
5.3 °C
0.0 °C
18.5°C
15.5°C
12.7°C
20.9 °C
23.9 °C
20.1 °C
6.7 °C
EPA Bull Trout
Criteria Exceedance Summary
Criteria
50 °C 7-Day Avg of Daily Max
Nmbr of 7-Day Avg's w/in Dates
Exceedance Counts
Nmbr
0
122
Prcnt
0%
01-Jun 30-Sep
Idaho Cold Water Biota
Criteria Exceedance Summary
Criteria
22 °C Instantaneous
19 °C Average
Days Evaluated & Date Range
Exceedance Counts
Nmbr
36
27
92
Prcnt
24%
18%
06/22/2001
09/21/2001
Idaho Salmonid Spawning
Cril edance Summary
Criteria
13 °C Instantaneous Spring
9 °C Average Spring
Spring Days Eval'd w/in Dates
13 °C Instantaneous Fall
9 °C Average Fall
Fall Days Eval'd w/in Dates
13 °C Instantaneous Total *
9 °C Average Total *
Tot Days Eval'd w/in Both Dates *
Exceedance Counts
Nmbr
15
15
15
0
0
0
15
15
15
Prcnt
100%
100%
01 -Mar
0%
0%
16-Dec
100%
100%
01-Jun
30-Dec
Dccur.
Figure J-5. Temperature Data for Butcher Creek, 1 Mile Above the Mouth
Butcher Creek has not been designated as protected for bull trout so is not compared to this
standard. The number of days of salmonid spawning criteria exceedances is small, but
represents 100% of the record (May 18 through June 1), because the spawning and
incubation period for A-run steelhead ends on June 1. Cold water biota standards
exceedance numbers are probably better indicators of the true level of exceedance at this site,
although it should be kept in mind that this site is to support salmonid spawning.
J-7
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
May 2003
DEQ Summary of Temperature Data
Data Source Name: Nez Perce Nat'l Forest
Water Body Name: Threemile Creek
Data Collection Site: Threemile-03, at Mt Idaho Bridge
Data Period: 7/3/00 -11/8/00
HUC4 Number: 17060305
HUC4 Name: South Fork Clearwater
North of the Salmon Clearwater Divide
Idaho Bull Trout Elevation: 550 M
Waterbody ID Number: 12
Daily Waterbody Temperatures (OOSFCIearwtr-03, elev 1800 ft)
07/03/2000 07/23/2000 08/12/2000
Measurement Dates
•Average
STATISTICS
Instantaneous Maximum
Instantaneous Minimum
Overall Mean
Mean Daily Maximum
Mean Daily Average
Mean Daily Minimum
Maximum Daily Average
Maximum 7-Day Maximum
Maximum 7-Day Average
Minimum 7-Day Minimum
22.9 °C
1.2°C
0.0 °C
13.9°C
12.8°C
11.8°C
21.9°C
22.3 °C
21.1 °C
2.0 °C
Idaho Cold Water Biota
Criteria Exceedance Summary
Criteria
22 °C Instantaneous
19 °C Average
Days Evaluated & Date Range
Exceedance Counts
Nmbr
26
81
Prcnt
4%
20%
06/22/2000
09/21/2000
Idaho Salmonid Spawning
Criteria Exceedance Summary
Criteria
13 °C Instantaneous Spring
9 °C Average Spring
Spring Days Eval'd w/in Dates
13 °C Instantaneous Fall
9 °C Average Fal
Fall Days Eval'd w/in Dates
13 °C Instantaneous Total *
9 °C Average Total *
Tot Days Eval'd w/in Both Dates * 76
Exceedance Counts
Nmbr
29
41
76
29
41
Prcnt
0%
0%
01-Jan
38%
54%
16-Aug
38%
54%
15-Apr
30-Oct
* If spring & fall dates overlap double counting may occur.
Figure J-6. Temperature Data for the Main Stem South Fork Clearwater River
at the Mt. Idaho Bridge
The main stem SF CWR is not federally protected for bull trout spawning and rearing so the
federal bull trout criteria do not apply. The Fish TAG identified spring chinook as the only
salmonid possibly spawning in the lower main stem SF CWR during the temperature critical
times of year (Appendix D). The main stem exceeds the cold water biota criteria for a
significant period.
J-8
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table J-1. Summary water temperature data for stream and river monitoring locations in the SF CWR subbasin.
WB
1
1
1
1
2
10
10
10
10
10
10
10
Water Body
Name
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
Cottonwood Cr.
Threemile Cr.
Threemile Cr.
Threemile Cr.
Threemile Cr.
Threemile Cr.
Threemile Cr.
Threemile Cr.
Location*
SF Clearwater at Stites
(USGS Gage)
SF Clearwater at Stites
(USGS Gage)
SF Clearwater at Stites
(USGS Gage)
SF Clearwater at Lukes
Gulch
Cottonwood Cr. Above
Mouth
Threemile Cr. at Mouth
Threemile Cr. at Mouth
Threemile Cr. at Mouth
Threemile Cr. Below
Grangeville WWTP
Threemile Cr. Below
Grangeville WWTP
Threemile Cr. Below
Grangeville WWTP
Threemile Cr. Below
Grangeville WWTP
Dates
Monitored
7/9/99-10/30/99
7/4/00-11/8/00
7/11/01-10/2701
6/15/00-10/22/00
6/2/00-10/15/00
4/7/00-8/9/00
5/26/00-1 0/23/00
4/7/00-5/24/00
5/26/00-9/18/00
5/26/00-10/23/00
4/7/00-5/24/00
4/7/00-5/24/00
Salmonids
Present**
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Elev.
(ft)
1,200
1,200
1,200
1,400
1,200
1,200
1,200
1,200
3,200
3,200
3,200
3,200
No. of Days Exceeding***:
Fed.
Bull
Trout
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
Spring
SS
7
12
5
31
44
97
51
44
7
7
32
31
Fall
SS
0
0
0
0
0
0
0
0
0
0
0
0
CWAL
daily
max.
34
49
46
35
91
25
35
1
31
29
1
1
CWAL
daily
ave.
35
45
46
40
83
27
47
1
45
43
1
1
J-9
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
10
10
10
10
10
11
12
12
12
12
12
12
Water Body
Name
Threemile Cr.
Threemile Cr.
Threemile Cr.
Threemile Cr.
Threemile Cr.
Butcher Cr.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
Location*
Threemile Cr. Above
Grangeville WWTP
Threemile Cr. Above
Grangeville WWTP
Threemile Cr. Above
Grangeville WWTP
Threemile Cr. at Spencer
Ranch
Threemile Cr. at Spencer
Ranch
Butcher Cr. 1 mi Above
Mouth
SF Clearwater at Mt.
Idaho Bridge
SF Clearwater at Mt.
Idaho Bridge
SF Clearwater at Mt.
Idaho Bridge
SF Clearwater at Mt.
Idaho Bridge
SF Clearwater Below Mill
Cr.
SF Clearwater Below Mill
Cr.
Dates
Monitored
5/26/00-8/7/00
8/12/00-9/28/00
4/7/00-5/24/00
5/26/00-10/6/00
4/7/00-5/24/00
5/18/01-10/13/01
7/7/98-9/14/98
7/16/99-10/8/99
7/3/00-11/8/00
7/11/01-11/27/01
7/16/99-10/7/99
6/20/00-9/01/00
Salmonids
Present**
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Elev.
(ft)
3,200
3,200
3,200
3,000
3,000
1,800
1,800
1,800
1,800
1,800
2,200
2,200
No. of Days Exceeding***:
Fed.
Bull
Trout
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
NA
Spring
SS
50
0
24
47
14
15
9
0
0
5
0
26
Fall
SS
0
0
0
0
0
0
0
0
41
0
0
0
CWAL
daily
max.
12
2
1
60
1
36
0
0
5
0
0
3
CWAL
daily
ave.
9
1
1
28
1
27
10
7
26
13
0
8
J-10
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
12
12
12
12
12
12
12
12
13
13
13
14
Water Body
Name
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
Mill Cr.
Mill Cr.
Mill Cr.
Johns Cr.
Location*
SF Clearwater Below Mill
Cr.
SF Clearwater at USFS
Boundary
Castle Cr. at Mouth
Earthquake Cr. at Mouth
Green Cr. at Mouth
Lightning Cr. at Mouth
Schwartz Cr. at Mouth
Sears Cr. at Mouth
Mill Cr. at Mouth
Mill Cr. at Mouth
Mill Cr. at Mouth
Johns Cr. at Gage
Dates
Monitored
5/25/01-10/27/01
5/25/01-10/27/01
7/4/01-10/27/01
7/6/01-10/27/01
7/4/01-10/22/01
7/4/01-10/8/01
7/11/01-10/27/01
7/11/01 - 10/22/01
7/14/99-10/7/99
6/17/00-10/4/00
5/25/01 -10/27/01
8/8/99-10/20/99
Salmonids
Present**
Chinook, Rain/Stl
Chinook, Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook.
Rain/Stl, Cut
Elev.
(ft)
2,200
1,800
2,200
2,200
1,600
1,600
1,800
2,200
2,200
2,200
2,200
2,400
No. of Days Exceeding***:
Fed.
Bull
Trout
NA
NA
NA
NA
NA
NA
76
NA
71
95
122
46
Spring
SS
43
44
12
10
43
43
5
5
33
60
68
8
Fall
SS
0
0
1
0
0
0
0
0
40
36
45
41
CWAL
daily
max.
0
0
37
0
0
0
0
0
0
3
0
0
CWAL
daily
ave.
4
16
18
0
0
0
0
0
0
1
0
0
J-ll
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
14
14
22
22
22
22
22
22
22
24
24
25
Water Body
Name
Johns Cr.
Johns Cr.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
Twentymile Cr.
Twentymile Cr.
Tenmile Cr.
Location*
Johns Cr. at Gage
Johns Cr. at Gage
SF Clearwater Below
Twentymile Cr.
SF Clearwater Below
Twentymile Cr.
SF Clearwater Below
Peasley Cr.
SF Clearwater Below
Peasley Cr.
SF Clearwater Below
Peasley Cr.
SF Clearwater Above
Droogs Cr.
SF Clearwater Above
Droogs Cr.
Twentymile Cr. at Mouth
Twentymile Cr. 1 km
Above Road 1 875
Crossing
Tenmile Cr. at Mouth
Dates
Monitored
7/12/00-10/31/00
7/11/01 -10/30/01
6/24/00-11/7/00
7/12/01 -10/9/01
7/16/99-10/6/99
6/20/00-9/1/00
6/19/01 - 10/27/01
6/24/00-11/7/00
7/12/01 -10/9/01
8/7/98-10/31/98
4/4/00 - 9/8/00
7/25/00 - 9/29/00
Salmonids
Present**
Bull, Chinook,
Rain/Stl, Cut
Bull, Chinook,
Rain/Stl, Cut
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Chinook, Rain/Stl
Bull, Rain/Stl, Cut
Bull, Rain/Stl, Cut
Bull, Cut, Chinook,
Rain/Stl
Elev.
(ft)
2,400
2,400
3,000
3,000
2,600
2,600
2,600
3,000
3,000
3,000
4,200
3,400
No. of Days Exceeding***:
Fed.
Bull
Trout
70
76
NA
NA
NA
NA
NA
NA
NA
43
82
47
Spring
SS
35
36
22
4
0
26
27
22
4
9
58
22
Fall
SS
35
45
38
46
41
17
46
38
46
0
0
25
CWAL
daily
max.
0
0
2
1
0
1
0
5
0
0
0
0
CWAL
daily
ave.
0
0
7
3
0
7
0
7
2
0
0
0
J-12
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
30
30
30
30
30
30
31
31
31
31
31
32
Water Body
Name
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
Crooked R.
Crooked R.
Crooked R.
Crooked R.
Crooked R.
Crooked R.
Location*
SF Clearwater Above
Moose Cr.
SF Clearwater Above
Moose Cr.
SF Clearwater Above
Leggett Cr.
SF Clearwater Above
Leggett Cr.
SF Clearwater Above
Tenmile Cr.
SF Clearwater Above
Tenmile Cr.
Crooked R. at Lower
Satellite Intake
Crooked R. at Lower
Satellite Intake
Crooked R. 5 km Above
Mouth
Crooked R. 1 km Above
Mouth
Crooked R. 1 km Above
Mouth
Just Below EF and WF
Confluence
Dates
Monitored
6/23/00- 10/18/00
7/12/01 -10/9/01
6/23/00-11/2/00
7/12/01 -10/9/01
6/23/00-11/7/00
7/12/01 -10/9/01
5/16/98-9/08/98
7/11/00-9/30/00
6/01/00-8/22/00
5/31/00-9/7/00
4/2/00 - 5/30/00
7/29/99-10/15/99
Salmonids
Present**
Chinook, Rain/Stl,
Cut
Chinook, Rain/Stl,
Cut
Chinook, Rain/Stl,
Cut
Chinook, Rain/Stl,
Cut
Chinook, Rain/Stl,
Cut
Chinook, Rain/Stl,
Cut
Bull, Chinook,
Rain/Stl, Brook, Cut
Bull, Chinook,
Rain/Stl, Brook, Cut
Bull, Chinook,
Rain/Stl, Brook, Cut
Bull, Chinook,
Rain/Stl, Brook, Cut
Bull, Chinook,
Rain/Stl, Brook, Cut
Bull, Chinook,
Rain/Stl, Cut
Elev.
(ft)
3,600
3,600
3,600
3,600
3,400
3,400
3,800
3,800
4,000
3,800
3,800
4,600
No. of Days Exceeding***:
Fed.
Bull
Trout
NA
NA
NA
NA
NA
NA
93
55
73
94
0
32
Spring
SS
54
35
54
35
54
35
61
5
66
71
0
16
Fall
SS
38
46
38
46
38
46
24
20
7
23
0
15
CWAL
daily
max.
21
11
14
5
7
2
3
0
8
13
0
0
CWAL
daily
ave.
16
8
12
6
16
6
0
0
0
6
0
0
J-13
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
33
33
34
34
35
35
36
36
36
37
38
39
Water Body
Name
West Fork Crooked
R.
West Fork Crooked
R.
East Fork Crooked
R.
East Fork Crooked
R.
Reliefer.
Reliefer.
South Fork
Clearwater R.
South Fork
Clearwater R.
South Fork
Clearwater R.
RedR.
Little Moose Cr.
Moose Butte Cr.
Location*
WF Crooked R. 1 .6 km
Above Fork
WF Crooked R. 1 .6 km
Above Fork
EF Crooked R.-2.3 km
Above Fork
EF Crooked R. 2.3 km
Above Fork
Reliefer. 0.6 km Above
Mouth
Reliefer. 0.6 km Above
Mouth
SF Clearwater Above Elk
City Mill
SF Clearwater Above Elk
City Mill
SF Clearwater Above
Crooked R. Bridge
Red R. at Mouth Below
Bridge
1 0 m Upstream of USFS
Stream Gage
Upper Moose Butte Cr.
Dates
Monitored
6/1/99- 11/1/99
7/11/00-9/29/00
6/1/99- 11/3/99
7/11/00-9/29/00
5/27/99-10/14/99
7/11/00-9/30/00
6/23/00-11/7/00
7/12/01 -10/9/01
5/15/00-8/29/00
5/5/00 - 9/26/00
5/25/00-9/12/00
8/2/01 -10/31/01
Salmonids
Present**
Bull, Chinook,
Rain/Stl, Cut
Bull, Chinook,
Rain/Stl, Cut
Bull, Chinook, Cut
Bull, Chinook, Cut
Bull, Chinook,
Rain/Stl, Cut
Bull, Chinook,
Rain/Stl, Cut
Rain/Stl
Rain/Stl
Rain/Stl
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook, Cut,
Brook
Elev.
(ft)
4,800
4,800
4,800
4,800
4,200
4,200
3,800
1,800
3,800
3,800
4,200
5,000
No. of Days Exceeding***:
Fed.
Bull
Trout
54
53
29
45
92
63
NA
NA
NA
118
103
34
Spring
SS
25
36
18
36
46
36
23
4
44
75
70
14
Fall
SS
14
19
13
6
18
23
0
0
0
38
19
26
CWAL
daily
max.
0
0
0
0
0
0
18
10
13
13
3
0
CWAL
daily
ave.
0
0
0
0
0
0
14
5
18
16
0
0
J-14
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
41
42
42
42
42
43
43
45
45
45
45
45
Water Body
Name
South Fork Red R.
West Fork Red R.
West Fork Red R.
West Fork Red R.
West Fork Red R.
WF of SF Red R.
WFofSFRedR.
Red R.
Red R.
RedR.
RedR.
RedR.
Location*
SF Red R. Below Road
222 Crossing
WF Red R. 75m Above
Mouth
WF Red R. 75 m Above
Mouth
WF Red R. 20 m Above
Mouth
WF Red R. 20 m Above
Mouth
WF of SF Red R. at
Mouth
Upper WF of SF Red R.
Red R. Above Shissler
Cr.
Red R. Above Shissler
Cr.
Red R. Above Trail Cr.
Red R. Above Trail Cr.
Red R. Above Ditch Cr.
Dates
Monitored
7/26/01 - 10/14/01
5/25/00-9/12/00
5/25/00-9/12/00
5/27/99- 10/31/99
5/25/00-9/12/00
7/26/01 - 10/23/01
7/17/01 -10/15/01
7/18/00-9/29/00
6/27/01 - 10/23/01
7/18/00-9/29/00
6/27/01 - 10/23/01
7/18/00-9/29/00
Salmonids
Present**
Bull, Cut, Rain/Stl,
Brook
Bull, Rain/Stl, Cut,
Brook
Bull, Rain/Stl, Cut,
Brook
Bull, Rain/Stl, Cut,
Brook
Bull, Rain/Stl, Cut,
Brook
Bull, Rain/Stl, Cut
Bull, Rain/Stl, Cut
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Elev.
(ft)
4,600
5,200
5,200
5,200
5,200
5,400
5,800
4,800
4,800
4,600
4,600
4,400
No. of Days Exceeding***:
Fed.
Bull
Trout
29
55
69
55
70
48
55
47
76
65
90
62
Spring
SS
12
29
46
32
47
19
18
29
45
29
50
29
Fall
SS
5
14
8
15
9
0
0
16
24
30
41
30
CWAL
daily
max.
0
0
0
0
0
0
0
0
0
0
0
3
CWAL
daily
ave.
0
0
0
0
0
0
0
0
0
0
0
0
J-15
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
45
45
45
48
48
50
52
52
57
57
58
58
Water Body
Name
RedR.
Red R.
Red R.
Otterson Cr.
Otterson Cr.
Siegel Cr.
American R.
American R.
Little Elk Cr.
Little Elk Cr.
Big Elk Cr.
Big Elk Cr.
Location*
Red R. Above Ditch Cr.
Red R. Above Otterson
Cr.
Red R. Above Otterson
Cr.
Otterson Cr. at Mouth
Otterson Cr. at Mouth
Siegel Cr. at USFS
Boundary
American R. 30 ft
Upstream of Mouth
American R. at River Mile
9.1
Little Elk Cr. at USFS
Boundary
Little Elk Cr. 50 m Above
Mouth
Big Elk Cr. At Mouth
Big Elk Cr. at USFS
Boundary
Dates
Monitored
6/27/01 - 10/23/01
7/18/00- 10/16/00
6/27/01 - 10/31/01
7/18/00- 10/16/00
6/28/01 -10/31/01
7/18/00-9/29/00
5/1 5/00 - 09/26/00
5/1 5/00 - 09/26/00
7/7/00-9/17/00
7/19/00-9/17/00
7/19/00-10/18/00
7/15/00-10/17/00
Salmonids
Present**
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook, Cut,
Brook
Bull, Chinook, Cut,
Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook, Cut,
Rain/Stl, Brook
Bull, Chinook, Cut,
Brook, Rain/Stl
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Elev.
(ft)
4,400
4,800
4,800
4,600
4,600
4,200
3,800
4,000
4,200
3,800
3,800
4,400
No. of Days Exceeding***:
Fed.
Bull
Trout
90
56
90
58
89
65
118
118
61
56
68
54
Spring
SS
50
29
49
29
49
29
74
76
40
28
28
32
Fall
SS
39
23
29
28
37
32
38
37
23
34
37
22
CWAL
daily
max.
0
0
0
0
0
18
23
26
0
6
18
0
CWAL
daily
ave.
0
0
0
0
0
0
12
13
0
3
5
0
J-16
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
62
63
63
65
65
65
65
65
65
68
68
68
68
70
Water Body
Name
Newsome Cr.
BearCr.
BearCr.
NF Beaver Cr.
NF Beaver Cr.
SF Beaver Cr.
SF Beaver Cr.
Beaver Cr.
Beaver Cr.
Newsome Cr.
Newsome Cr.
Newsome Cr.
Newsome Cr.
Baldy Cr.
Location*
Newsome Cr. at Mouth
Bear Cr. at Mouth
Bear Cr. at Mouth
NF Beaver Cr. at Mouth
NF Beaver Cr. at Mouth
SF Beaver Cr. At Mouth
SF Beaver Cr. at Mouth
Beaver Cr. at Mouth
Beaver Cr. at Mouth
Newsome Cr. Below
Radcliff
Newsome Cr. Below
Radcliff
Newsome Cr. Above
Haysfork
Newsome Cr. Above
Haysfork
Baldy Cr. 0.3 km Above
Mouth
Dates
Monitored
6/25/99-10/16/99
6/24/00-10/18/00
6/28/01-10/8/01
7/8/00-10/22/00
6/30/01-10/8/01
6/29/00-10/18/00
6/30/01-10/8/01
6/29/00- 10/18/00
6/28/01-10/8/01
7/9/00-10/16/00
7/25/01-10/17/01
7/9/00-10/24/00
7/27/01-11/6/01
6/1/99-10/30/99
Salmonids
Present**
Bull, Chinook,
Rain/Stl, Cut
Bull Chinook,
Rain/Stl, Cut
Bull Chinook,
Rain/Stl, Cut
Bull, Rain/Stl, Cut
Bull, Rain/Stl, Cut
Rain/Stl, Cut
Rain/Stl, Cut
Bull, Rain/Stl, Cut
Bull, Rain/Stl, Cut
Bull, Rain/Stl, Cut,
Chinook
Bull, Rain/Stl, Cut,
Chinook
Bull, Rain/Stl, Cut,
Chinook
Bull, Rain/Stl, Cut,
Chinook
Bull, Chinook,
Rain/Stl, Cut
Elev.
(ft)
3,600
3,800
3,800
4,400
4,400
4,400
4,400
4,400
3,800
4,000
4,000
4,000
4,000
4,000
No. of Days Exceeding***:
Fed.
Bull
Trout
90
78
77
62
87
58
73
79
89
69
62
73
60
84
Spring
SS
51
53
49
39
45
39
43
48
49
38
22
38
20
47
Fall
SS
41
26
29
0
0
0
0
0
0
27
33
31
39
18
CWAL
daily
max.
0
0
0
0
0
0
0
0
0
0
0
6
0
0
CWAL
daily
ave.
0
0
0
0
0
0
0
0
0
0
0
0
0
0
J-17
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
71
71
71
71
72
72
73
73
75
75
77
77
77
Water Body
Name
Pilot Cr.
Pilot Cr.
Pilot Cr.
Pilot Cr.
Sawmill Cr.
Sawmill Cr.
Sing Lee Cr.
Sing Lee Cr.
Leggett Cr.
Leggett Cr.
Silver Cr.
Silver Cr.
Silver Cr.
Location*
Pilot Cr. 50 m Below
Bridge By Mouth
Pilot Cr. 50 m Below
Bridge By Mouth
Pilot Cr. Above Dredging
Pilot Cr. Above Dredging
Sawmill Cr. at Mouth
Sawmill Cr. at Mouth
Sing Lee Cr. at Mouth
Sing Lee Cr. at Mouth
Leggett Cr. at Mouth
Leggett Cr. at Mouth
Silver Cr. at Mouth
Silver Cr. at Mouth
Silver Cr. at Mouth
Dates
Monitored
6/25/99-10/10/99
7/9/00-9/29/00
7/12/00-8/23/00
6/29/01-10/2/01
6/29/00-10/18/00
6/29/01-10/02/01
7/8/00-10/18/00
6/28/01-10/8/01
8/2/99-10/10/99
6/24/00-10/24/00
7/14/99-10/7/99
6/17/00-10/12/00
6/20/01-10/27/01
Salmonids
Present**
Bull, Chinook,
Rain/Stl, Cut
Bull, Chinook,
Rain/Stl, Cut
Bull, Chinook,
Rain/Stl, Cut
Bull, Chinook,
Rain/Stl, Cut
Bull, Chinook, Cut,
Rain/Stl
Bull, Rain/Stl,
Chinook, Cut
Chinook, Cut,
Rain/Stl
Chinook, Cut,
Rain/Stl
Chinook, Rain/Stl,
Cut
Chinook, Rain/Stl,
Cut
Bull, Rain/Stl, Brook
Bull, Rain/Stl, Brook
Bull, Rain/Stl, Brook
Elev.
(ft)
4,000
4,000
4,000
4,000
4,000
4,000
3,800
3,800
3,600
3,600
2,800
2,800
2,800
No. of Days Exceeding***:
Fed.
Bull
Trout
67
62
37
84
72
78
NA
NA
NA
NA
69
89
97
Spring
SS
38
38
35
48
46
48
39
49
14
53
2
29
26
Fall
SS
17
24
8
31
25
28
25
28
19
29
35
29
41
CWAL
daily
max.
0
0
0
0
0
0
0
0
0
0
0
0
0
CWAL
daily
ave.
0
0
0
0
0
0
0
0
0
0
0
0
0
J-18
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
78
78
78
78
79
79
79
80
80
80
80
80
80
80
80
Water Body
Name
Peasley Cr.
Peasley Cr.
Peasley Cr.
Peasley Cr.
Cougar Cr.
Cougar Cr.
Cougar Cr.
Meadow Cr.
Meadow Cr.
Meadow Cr.
Meadow Cr.
Meadow Cr.
Meadow Cr.
Meadow Cr.
Meadow Cr.
Location*
Peasley Cr. at Mouth
Peasley Cr. at Mouth
Peasley Cr. at Mouth
Peasley Cr. at Mouth
Cougar Cr. at Mouth
Cougar Cr. at Mouth
Cougar Cr. at Mouth
Meadow Cr. at Mouth
Meadow Cr. at Mouth
Meadow Cr. at
Campground
Lower Meadow Cr.
Lower Meadow Cr.
Middle Meadow Cr.
Middle Meadow Cr.
Upper Meadow Cr.
Dates
Monitored
7/17/99-10/7/99
6/30/00-1 0/1 9/00
6/17/00-10/12/00
6/19/01-10/27/01
7/14/99-10/7/99
6/17/00-10/12/00
6/19/01-10/27/01
6/15/00-10/12/00
6/19/01-10/27/01
7/14/99-10/6/99
5/15/99-10/15/99
5/15/00-9/26/00
5/15/99-10/14/99
5/15/00-9/26/00
5/15/99-10/20/99
Salmonids
Present**
Rain/Stl
Rain/Stl
Rain/Stl
Rain/Stl
Cut, Rain/Stl
Cut, Rain/Stl
Cut, Rain/Stl
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Elev.
(ft)
2,600
2,600
2,600
2,600
2,400
2,400
2,400
2,200
2,200
2,200
3,000
3,200
3,200
3,200
3,600
No. of Days Exceeding***:
Fed.
Bull
Trout
NA
NA
NA
NA
NA
NA
NA
99
98
72
112
118
110
118
104
Spring
SS
0
16
29
57
33
60
58
62
58
33
66
72
65
72
57
Fall
SS
0
0
0
0
0
0
0
40
46
42
41
38
41
35
29
CWAL
daily
max.
0
0
0
0
0
0
0
4
1
1
46
44
19
28
0
CWAL
daily
ave.
0
0
0
0
0
0
0
4
3
2
8
20
0
3
0
J-19
Appendix J
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
WB
80
80
80
81
81
Water Body
Name
NF Meadow Cr.
NF Meadow Cr.
Meadow Cr.
Sally Ann Cr.
Sally Ann Cr.
Location*
NF Meadow Cr.
NF Meadow Cr.
Meadow Cr. at McComas
Meadows
Sally Ann Cr. at Mouth
Wall Cr. at Mouth
Dates
Monitored
5/15/99-10/21/99
5/15/00-9/26/00
5/15/00-9/26/00
5/5/01-7/17/01
7/3/01-10/22/01
Salmonids
Present**
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Chinook,
Rain/Stl, Cut, Brook
Bull, Cut
Cut
Elev.
(ft)
3,200
3,200
3,200
1,400
1,600
No. of Days Exceeding***:
Fed.
Bull
Trout
109
116
116
47
NA
Spring
SS
66
72
72
45
44
Fall
SS
36
31
34
0
0
CWAL
daily
max.
0
0
0
8
0
CWAL
daily
ave.
0
0
0
5
0
* USGS = U.S. Geological Survey, WWTP = wastewater treatment plant, USFS = U.S. Forest Service
** Bull = bull trout, Chinook = Chinook salmon, Rain/Stl = rainbow/steelhead trout, Cut = cutthroat trout, Brook = brook trout
*** NA = The bull trout standard is not applicable. Water body has not been designated as protected (Appendix B). SS = salmonid spawning,
CWAL = cold water aquatic life
J-20
Appendix J
-------
Appendix K. Summary of Stream Habitat Data
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
Appendix K. Summary of Stream Habitat Data K-1
Table of Contents K-i
List of Tables K-ii
List of Figures K-ii
Appendix K. Summary of Stream Habitat Data K-1
Summary of DEQ BURP Stream Habitat Data K-1
Width-to-Depth Ratio K-1
Pool Frequency and Quality K-1
Pool-to-Run Ratios K-2
Pools per Mile K-2
Substrate Composition and Percent Fines K-2
Bank Stability K-3
Large Woody Debris K-3
Summary of NPNF Stream Habitat Conditions for the SF CWR
Subbasin K-13
References K-15
K- i Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Tables
Table K-1. Environmental Baseline Habitat Condition (USFS 1999) K-13
List of Figures
Figure K-1. Width-to-Depth Ratios of the SF CWR Subbasin from the BURP
Data Set K-5
Figure K-2. Pool-to-Run Ratios of the SF CWR Subbasin from the BURP
Data Set K-6
Figure K-3. Canopy Cover of the SF CWR Subbasin from the BURP Data
Set K-7
Figure K-4. Large Woody Debris of the SF CWR Subbasin from the BURP Data
Set K-8
Figure K-5. Number of Pools per Meter of the SF CWR Subbasin from the
BURP Data Set K-9
Figure K-6. Bank Stability of the SF CWR Subbasin from the BURP Data
Set K-10
Figure K-7. Average Left/Right Bank Stability of the SF CWR Subbasin
from the BURP Data Set K-11
Figure K-8. Percent Total Fines of the SF CWR Subbasin from the BURP
Data Set K-12
K- ii Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Appendix K. Summary of Stream Habitat Data
Prepared by Ann Storrar, Nez Perce Tribe
and
Karla Baker, DEQ
Summary of DEQ BURP Stream Habitat Data
The graphs following this text summarize in a visual form the Beneficial Use
Reconnaissance Program (BURP) stream habitat data collected by the Department of
Environmental Quality (DEQ) in the South Fork Clearwater River (SF CWR) Subbasin for
the years 1995-2000. The significance of each of the parameters is explained below and a
comparison to regional references is provided. These data refer to one location in a stream,
the BURP site, which is usually near the mouth, and may not necessarily be representative of
the whole stream. The greater value of these data is the overall view one can get of stream
habitat conditions in the SF CWR Subbasin.
Width-to-Depth Ratio
A change in the width-to-depth ratio can be used as an indicator of change in the relative
balance between sediment load and sediment transport capacity. Sediment accumulation in
stream channels reduces stream depth. Large width-to-depth ratios are often a result of
lateral bank erosion due to increased peak flow, increased sediment availability, and eroding
banks due to loss of streamside vegetation (Overton 1995 et al., Beschta and Platts 1986).
The biological community suffers adverse effects from a decrease in channel depth and an
increase in channel width. A decrease in depth may reduce the quantity and quality of pools,
reducing available habitat for fish. The increase in width will lead to increased incidence of
solar radiation and higher water temperatures. The combination of shallower pools and
increased insolation can decrease the suitability of the stream for cold water fish. Width-to-
depth ratios generally vary with channel type.
The SF CWR BURP width-to-depth ratios are suboptimal according to the federal Pacific
Anadromous Fish Strategy (PACFISH) (USFS and BLM 1995) and state of Idaho guidance
(DEQ 1996). The PACFISH objectives specify an optimal ratio of less than 10 for mean
wetted width to mean depth. The DEQ (1996) Waterbody Assessment Guidance specifies an
optimal wetted width-to-depth ratio as less than 7. Only 5 of the 103 sites surveyed had
width-to-depth ratios below 10, indicating most streams are wider and shallower than they
should be according to these references.
Pool Frequency and Quality
Salmonids often require backwater or dammed pools with water moving at a slow velocity to
permit survival of harsh winter conditions. In addition, pools of all shapes, sizes, and quality
are needed to support different age classes (Beschta and Platts 1986). Juvenile fish need
shallow, low quality pools that other fish will not use, until increased growth allows them to
K-1 Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
eventually compete without predation stress in the higher quality pools that have better food
supplies and winter rearing habitat.
The frequency and size of pools is dependent on stream size, gradient, confinement, flow,
sediment load, and amount of large woody debris (Overton et al. 1995). Pools characterized
by low flow velocities (backwater or dammed pools) are particularly susceptible to infilling
with sediment, thus the depth, area, or volume of these pools can serve as indicators of coarse
sediment loading due to land management practices. Overton et al. (1995) found fewer deep
pools in an intensely timber-managed watershed than in a non-timber-managed watershed. A
decrease in the amount of large woody debris may lead to a reduction in the number and size
of pools, and a change in peak flows will alter the ability of a stream to transport sediment,
altering pool measurements (MacDonald et al. 1991). Landslides, debris flows, and other
mass movements typically result in loss of pool area and volume.
Pool-to-Run Ratios
The SF CWR BURP pool-to-run ratios are optimal according to two references. A ratio of 1
to 3 is considered optimal by the Water body Assessment Guidance (DEQ 1996). A ratio of 1
to 1 is considered optimal by other experts (Platts et al. 1983). The majority of BURP sites
had ratios below 1 to 1, and only 8 of the 103 sites exceeded a ratio of 1 to 3.
Pools per Mile
The SF CWR BURP number of pools per mile is well below the optimal level as rated by the
Matrix of Pathways and Indicators for Water shed Condition for Chinook, Steelhead and Bull
Trout (NMFS et al. 1998). This reference is applied locally for biological assessments
required for activities on federal lands.
Substrate Composition and Percent Fines
The particle size of the bed material directly affects the flow resistance in the channel, the
stability of the bed, and the amount of aquatic habitat (Beschta and Platts 1986). In addition,
the size of the bed material controls the amount and type of habitat for small fish and
invertebrates. If the bed is composed only of fine materials, the spaces between particles are
too small for many organisms. The greatest number of species is usually associated with
complex substrates of stone, gravels, and sand. Coarse materials provide a variety of small
niches important for juvenile fish and benthic invertebrates. The mix of coarse particle in
riffles has been shown to provide the richest aquatic insect habitat (Gordon 1992).
Numerous studies have demonstrated reduced invertebrate abundance with fully embedded
streambed particles (Meehan and Murphy 1991). Salmon and trout have evolved and adapted
to the natural size distributions of channel sediments. It is believed that no single particle-
size group will create the ideal environment for all phases of salmonid growth and survival
(Beschta and Platts 1986).
The optimum spawning substrate mix appears to be gravel containing small amounts of fine
sediment and some small rubble to support egg pockets and guard against bed erosion from
floods (Beschta and Platts 1986). High amounts of fine sediments in spawning substrate
K- 2 Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
have been shown to be a major cause of embryo and larval mortality. Survival is high only if
the eggs receive an adequate supply of oxygen, an adequate flow of water through the gravel
to supply this oxygen, and necessary flows to remove metabolic wastes (Beschta and Platts
1986). Percent emergence of swim-up fry has also been shown to be reduced by too much
fine sediment (<6.35 millimeters [mm]) by a number of researchers (Bjornn and Reiser
1991). When particle sizes less than 6.35 mm exceed 20-25% of the total substrate, embryo
survival and emergence of swim-up fry is reduced by 50% (Bjornn and Reiser 1991).
The percent fine sediment at BURP sites is well above optimal levels as rated by DEQ
(1996), fisheries researchers, and the Matrix of Pathways and Indicators for Watershed
Condition for Chinook, Steelhead and Bull Trout (NMFS et al. 1998). Less than 10% fines is
considered optimal by the DEQ Waterbody Assessment Guidance (DEQ 1996). The matrix
of pathways guidance (NMFS et al. 1998) rates high condition habitat as that containing less
than or equal to 10% fines in A and B channel types and less than or equal to 20% for C and
E channel types. Ninety-eight of the 103 BURP sites evaluated exceed 20% fine sediment
and 86 sites exceed 30% fines.
Bank Stability
Eroding stream banks deliver sediment directly to the channel. Steeper banks are subject to
more erosion and failure, and streams with poor banks will often have poor in-stream habitat.
Protection from erosion is provided by plant root systems as well as by boulder, cobble, or
gravel material. Channels with banks and riparian vegetation in good condition handle
flooding with less habitat damage. Channel bank conditions are closely linked to the quality
of fish habitat.
Platts et al. (1983) and PACFISH (USFS and BLM 1995) rate values greater than 80%
stability as excellent and as meeting interim objectives for restoring anadromous fisheries.
Comparing to these standards, the bank stability for the SF CWR subbasin is generally
optimal with only 23 out of the 103 sites evaluated rating less than 80% stability. The Matrix
of Pathways and Indicators for Watershed Condition for Chinook, Steelhead and Bull Trout
criteria for bank stability differs by channel type, with C channel types less than 80%, A and
B channel types less than 90%, and E channel types less than 95% rated as poor condition
(NMFS et al. 1988). The BURP bank stability data generally rate moderate to good
condition as compared to this reference.
Large Woody Debris
Woody debris and root wads create habitat diversity by forming pools and waterfalls,
trapping sediment, and enhancing channel and bank stability. Research has shown a direct
relationship between the amount of woody debris and salmonid production, and woody
debris removal has been shown to reduce fish populations.
The BURP data represent the number of pieces of large woody debris greater than 1 meter in
length and 10 centimeters in diameter within the reach. The PACFISH (USFS and BLM
1995) objectives require more than 20 pieces per mile (1.25 pieces per 100 meters), greater
than 12 inches (30.5 cm) wide and 35 feet long (10.67 meters). This reference is not directly
K- 3 Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
comparable to BURP data because the lengths and widths of pieces are not recorded. Large
woody debris at most sites in the BURP data set exceeded 1.25 pieces per 100 meters with
the exception of the Cotton wood watershed.
K- 4 Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Width to Depth Ratio
0 10 20 30 40 50 60 70 80
Q
•o
0
D
O
z
1
10
BURP Site ID,
1 ' 1 998SLEVW 002 Cottonwood Creek
' "• 1995SL
^^^^^m 1995SL EWA028 Buckhorn Cree
1 1995SLEWAO
A005 Cottonwood Creel
d Creek (U) 3
ick Creek 4
1998SLEWT004 Red Re
Creek 6
! Stockney Creek (L) 6
ley Creek 6
:WA01 0 SF Cottonwood
\004Threemile Creek (I
3reen Creek 12
Sears Creek 12
ISLEWA011 Huddleson
ILEWA010 Wing Creek (
fl.026 Sixmile Creek 29
25 Santiam Creek 30
27 Moose Creek 30
k30
Creek 35
12 Deadwood Creek 37
.EWA047 Moose Butte (
2 MF Red River 42
.EWA037 Ditch Creek 4
!!^ 1996SLEWA003 Lick
1 3 1995SLEWA021 [
3 1996SLEWA004 Kirk;
102 Kirks Fork 53
lint Creek 54
Creek 55
iver 55
Little Elk Creek 57
:003 Big Elk Creek 58
I1996SLEWC004 Buffi
WA053 Whiskey Creek
ISLEWA023 Nugget Cre
8 Beaver Creek 65
lonkey Creek 67
Haysfork Creek 69
ILEWC001 Baldy Creek
ling Lee Creek 73
.EWA009 Leggett Creek
95SLEWA030 Fall Cree
A015 Peasley Creek (L)
1995SLEWA017Couga
995SLEWA013 Meadow
3
ck Creek 5
Creek 8
)10
2000SLEWB008 Three
WA009 Butcher Creek (I
3 Lightning Creek 12
A008 Schwartz Creek 1 :
Creek (L) 22
L)23
LEWA050 Dawson Cre<
5SLEWA046 Moose Bu
> (L) 39
A/A039 Schooner Creek
EWA048SF Red River (
42
F Red River 42
A044 Trapper Creek 44
1995SLEWA049RedR
1995SLEWA036Soda(
SLEWA040 Bridge Cree
49
3 1995SLEWA043Sieg
51
Fork (U) 53
VA002 American River (
o Gulch Cr 59
60
29 Bear Creek 63
eh 64
D24Newsome Creek (U)
3 Creek 67
70
VA031 Pilot Creek (U) T
LEWA032 Pilot Creek (L
EWA034 Leggett Creek
75
76
78
01 6 Cougar Creek (U) 7
Creek (L) 79
Creek (L) 80
\012Meadow Creek (U)
nwood Creek 3
ed Rock Creek 5
LEWA038 Shebang Cn
•nile Creek (U) 10
\iA008 Butcher Creek (U
ohns Creek (L) 14
= 1999SLEWA028Moc
999SLEWA029 Square
007 Huddleson Creek 2
04 Wing Creek (U) 23
6 Crooked River (L) 31
k38
e Cr (U) 39
40
L)40
ver (U) 45
reek 46
47
;l Creek 50
)52
J)55
-VA033 Newsome Creek
71
75
95SLEWA014 Peasley
9
H995SLEWA012Mea
80
VT019 Cottonwood Cres
ek7
1996SLEWA037 Long
11
res Creek 1 9
iM Creek 20
oked River (U) 32
EWC055 Red River (L) 3
1995SLEWA045SF Re
(L)62
SLEWB001 Silver Creel
^reek (U) 78
adow Creek 80
ow Creek (U) 80
k(L)2
998SLEWT006 Red Roc
Haul Creek 9
2000SLEV\
1997;
Red River (Middle) 38
d River (U) 43
77
k Creek (U) 5
B009 Threemile Creek (
LEWC038 Tenmile Cre
k26
Figure K-1. Width-to-Depth Ratios of the SF CWR Subbasin from the BURP
Data Set
K-5
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
c
Stream Name, Water Body ID
masuLtwiuua
1998SLEWT019
• 1995SLE
^^^•1998!
^^^^^=
1997SLEWZ012
1998SLEWT004
1998SLEWT006
HQQ
i 1 995i
1998SLEWT007
•iQQ
: 1 1995SLEV\
3 2000SLEWBOI
3 2000SLEWBOI
MM*
i 1995SLE
= 1996SLEWA
^^ 1996SLEV\
nggg-*
^H 1999SLEW
a 1999SLEWA
HQQQfilFlft
^_^_| 1999SL
^H 1999SLEW
^^M 1999SL
• 1995SLEWA
^^^^^^H
• 1995SLEWAO
^M 1996SLE
1996SLEWA035
^^^ 1995SL
Pool to Run Ratio
23456789 10 11
Cottonwood Cres
Cottonwood Cres
LEWA005 Cottor
A/A006 Cottonwo
LEWA001 Cottor
• 1998SLE
Red Rock Creek
Red Rock Creek
Red Rock Creek
SLEWA001 Stoc
LEWA002 Stockt
Stockney Creek t
SLEWA003 Thre
A004 Threemile C
8 Threemile Cres
9 Threemile Cres
LEWA008 Butchs
1995SLEWAOOE
A/A011 Green Cn
033 Lightning Cre
A034 Sears Cree
LEWA008 Schwc
A009 Johns Cree
028 Moores Cree
999SLEWA029 i
A007 Huddleson
EWA011 Huddle:
A01 OWing Creek
EWB004WingCt
SLEWC038 Tent
D26 Sixmile Creel
^= 1995SLEW
7 Moose Creek 3
1995SLEWA028
A/A036 Crooked 1
Crooked River (L
EWA054 Relief C
^^^^^^^H 1995SLEWC
1995SLEWA050
^=^=^^ 1995SLEWA051
31995SLEWAO
^•1995SLEV\
• 1 995i
• 1995SLEWAO.
1999SLEWA004
• 199
i 1995SL
_- ^^ 1995SLEV\
= ^31995SLEV\
0) H1995SLEWAO
3j •
SSS1 1996SLEWA
.- 1996SL
; . IQQQ.qiFIA
BSa 1996SLEWA
= 1996SLEWA
HQQ*
: 1 1996SLEV\
j 1 1995SLEV\
: HgQRSinA
1 1 995i
^ 1995SLEWA
n*
• 1995SLE
• 1995SL
i 1996SL
• 1995SL
= 1995SLEWA
1995SLEWA01E
ngg
^31995SLEV\
i 1998SL
9 1995SLEWAO
= 1999SLEWB
i 1 995i
SSa 1995SLEWA
SB 1995SLEWA
OBI 1995SLEWA
HH|1995SLEV\
= 1995SLEWA
mmnnnD 1999SLE
i 1 1 qqq.<
^ 1995SLEWA
9 Schooner Cree
A048SFRedRiv
LEWA041 WF R(
2MF Red River-
WF Red River 4;
SLEWA045 SF F
EWA044 Trapper
A038 Baston Cre
A049 Red River (
6 Soda Creek 46
SLEWA043 Sieg
EWA001 Red Hot
005 American Riv
EWA004 Kirks Fc
A002 Kirks ForkE
D02 American Riv
003 Lick CreekSE
LEWC003 Big El
C004 Buffalo Gul
A053 Whiskey Cr
A033 Newsome C
LEWA029 BearC
023 Nugget Creel
95SLEWA018Be
A/A024 Newsome
LEWA020Mule(
EWA021 Donkey
95SLEWA022 Ha
EWC001 BaldyC
EWA031 Pilot Cn
032 Pilot Creek (L
Sing Lee Creek ',
SLEWB003 WF
A034 Leggett Cre
EWA009 Leggett
0 Fall Creek 76
001 Silver Creek
LEWA014 Peasls
015 PeasleyCree
SLEWA016Cou
01 7 Cougar Creel
007 Meadow Cres
A01 2 Meadow Cr
013MeadowCre(
A/A012Meadow(
LEWB002 Meadc
k2
ML) 2
wood Creek 3
d Creek (U) 3
wood Creek 3
A/T005 Red Rock
U)5
eek 22
on Creek (L) 22
(L)23
eek (U) 23
nile Creek 26
29
A025SantiamCr
0
Buckhorn Creek
iver (L) 31
)32
eek 35
D52 Deadwood Ct
D55 Red River (L)
Dawson Creek 3
Red River (Middl
D47 Moose Butte
<40
3r (L) 40
d River 42
2
ed River (U) 43
Creek 44
A037 Ditch Creek
k45
J)45
995SLEWA035 1
B! Creek 50
se Cr (L) 51
996SLEWC002 1
sr (L) 52
k (U) 53
3
sr (U) 55
DOS American Riv
Creek 58
h Cr59
eek 60
reek (L) 62
reek 63
64
aver Creek 65
Creek (U) 66
reek 67
Creek 67
/sfork Creek 69
eek 70
ek (U) 71
71
3
-Jewsome Cr 74
ek75
Creek 75
7
y Creek (U) 78
k (L) 78
ar Creek (U) 79
(L)79
k80
3ek (U) 80
k (L) 80
reek (U) 80
w Creek 80
Creek 4
A038 Shebang C
11
20
ek30
30
eek 37
37
3)38
^r (L) 39
45
rail Creek 49
ed Horse Cr(U)
sr55
98SLEWA002 Co
eek 7
995SLEWA040 E
1
ttonwood Creek 3
EWA046 Moose 1
ridge Creek 47
Creek 48
COOS Flint Creek
utte Cr (U) 39
996SLEWC006 I
995SLEWA010:
ttle Elk Creek 57
F Cottonwood Cr
sek 8
1996SLEWA
37 Long Haul Cr
>ek9
Figure K-2. Pool-to-Run Ratios of the SF CWR Subbasin from the BURP Data
Set
K-6
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
20
40
Canopy Cover
60
100
120
9
S
J8SLEWT008 Cotto wood Creek 2
1998SLEWT019 Cottonwood C
1 1997SLEWZO'
I 1998SLEWT004 Red Rock CrJek 5
1998SLEWT006 Red Rock Cr( sk (U) 5
1998SLE\ IA002 Cottonwood Creek 3
;LEWT005 Red Rock Creek 4
2 Red Rock Creek 5
1998SLEWT007 Stockney Cre * 6
I1996SLEWA038SI (bang Creek 7
^^H 1995SLEWA010 SF Ci
I 1996SLEWA037 Long Haul Ci
3 1995SLEWA002;
ttonwood Creek 8
ek9
95SLEWA003 Thre
2000SLEWB009 Threemile CrJek (L) 10
| | ' 1995SLEWA008 Butcher Ci
] 1995SLEWAOC
1995SLEWA004 Threemile Cr< ek (L) 10
3 1995SLEWA006 Cottonwi
11998SLEWA001 Cottonwi
;LEWA001 Stockney Creek 6
:reek (U) 23
ixmile Creek|29
1 2000SLEWB008 Thres nile Creek (U) 10
WA011 Green Creek 12
' 1996SLEWA033 Lit
WA029 Square Mnt Creek 20
999SLEWA010 Wing Creek (L
95SLEWA039 Schooner Creek
1999SLE\ IA004 WF Red River 42
1995SLEWA03C Fall Creek 76
htning Creek 12
999SLEWA008 Schwartz Creel
9 9SLEWA011 Huddleson Creek
1995SLEWA053 Wniskey Cre
IA023 Nugget Creek 64
95SLEWA015 Peasley Creek (L
.SLEWA016 Cougar Creek (U)
I 1995SLEWA017Coug
EWB<02 Meadow Creek 80
Figure K-3. Canopy Cover of the SF CWR Subbasin from the BURP Data Set
K-7
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
(
Vatcr Body ID
d
I ra
z
g
1
JRP Site? ID, J
CO
Large Woody Debris
D 20 40 60 80 1 00 120 1 40 1 60 1 80
1998SLEWT008CO
1998SLEWT019CO
1995SLEWA005Co
D 1995SLEWA006C
• 1998SLEWA001 C
B1998SLEWA002C
1998SLEWT005Re
1997SLEWZ012 Re
1998SLEWT004Re
1998SLEWT006Re
^= 1995SLEWAOC
^= 1995SLEWAOC
1998SLEWT007Sto
1996SLEWA038Sh
1995SLEWA010SF
1996SLEWA037 Lo
1995SLEWA003Th
I 1 1995SLE
2000SLEWB009 Th
I1995SLEWA009B"
3 1996SLEWA034
I I1995SL
I • 1995S
I H99
' M£
1995SLEWA051 Re
•1E
I I1999SL
tonwood Creek 2
tonwood Creek (L) 2
tonwood Creek 3
ittonwood Creek (U) :
ottonwood Creek 3
ittonwood Creek 3
1 Rock Creek 4
1 Rock Creek 5
1 Rock Creek 5
1 Rock Creek (U) 5
1 Stockney Creek 6
2 Stockney Creek (L)
ckney Creek 6
tbang Creek 7
Cottonwood Creek 8
g Haul Creek 9
eemile Creek 1 0
VA004 Threemile CK
eemile Creek (L) 10
95SLEWA008 Butchf
tcher Creek (L) 11
Sears Creek 12
1999SLEWA011 Hud
WA025 Santiam Cre
.EWA028 Buckhorn (
1SLEWA035 Crookec
95SLEWA052 Deadv
1 River (Middle) 38
^^m 1995SLEWA
95SLEWA049 Red R
EWA002 Kirks Fork £
96SLEWC005 Flint C
D 1 999SLEWA003 American River 55
ek(L)10
EWBOOSThreemileC
r Creek (U) 11
1999SLEWA008Scl
dleson Creek (L) 22
/W\026 Sixmile Creek
k30
>eek 30
036 Crooked River (L
River (U) 32
WA054 Relief Creek
ood Creek 37
3LEWC055 Red Rive
047 Moose Butte Cr (
995SLEWA041 WF F
SLEWA045SFRed
ver (U) 45
1995SLEWA036SO
IA.040 Bridge Creek 4
WC007 Otterson Cre
995SLEWA035 Tra
EWC002 Red Horse
996SLEWA004 Kirk
3
reek 54
NAQQ2 American Rivs
5SLEWA024 Newsot|ne Creek (U) 66
1995SLEWA022 Hayfork Creek 69
{ =1 1995SLE
NAQ3Q Fall Creek 76
SLEWA015 Peasley
ow Creek 80
Badow Creek (L) 80
reek (U) 1 0
reen Creek 12
96SLEWA033 Lightn
wartz Creek 12
999SLEWA009 John
1999SLEWA010Wit
Wing Creek (U) 23
29
995SLEWA027 Moo:
31
35
(L)37
L) 39
ed River 42
River (U) 43
aston Creek 45
a Creek 46
ek48
Creek 49
Siegel Creek 50
> (U) 51
96SLEWA005Amerii
Fork (U) 53
r (U) 55
/ Creek 60
29 Bear Creek 63
\018 Beaver Creek 6
995SLEWA021 Donk
L)71
9 Sing Lee Creek 73
995SLEWA034 Legg
5SLEWA014 Peasle
Creek (L) 78
017 Cougar Creek (L
995SLEWA012Meac
ng Creek 12
Creek (L) 14
Moores Creek 19
07Huddleson Creek
g Creek (L) 23
e Creek 30
A050 Dawson Creek
\039 Schooner Creek
River (L) 40
044 Trapper Creek 4<
AA037 Ditch Creek 4
an River (L) 52
SLEWA003 Lick Cre
-Jugget Creek 64
020 Mule Creek 67
ey Creek 67
1 Baldy Creek 70
1 Pilot Creek (U) 71
3tt Creek 75
Creek (U) 78
3LEWA016CougarC
79
ow Creek (U) 80
1999SLEWA012Mea
2
38
40
6SLEWA001 Red He
k55
BOOS WF Newsome
eek (U) 79
dow Creek (U) 80
997SLEWC038 Tenrr
042 MF Red River 42
se Cr (L) 51
LEWC006 Little Elk C
3 Big Elk Creek 58
1996SLEWC004BU
ewsome Creek (L) 6;
>74
A/A029 Square Mnt C
ile Creek 26
46 Moose Butte Cr (L
1999SLEWAO
eek 57
felo Gulch Cr 59
01 Silver Creek 77
eek 20
)39
04 WF Red River 42
Figure K-4. Large Woody Debris of the SF CWR Subbasin from the BURP Data
Set
K-8
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
0.5
1.5
Number of Pools per 100m
2 2.5 3
4.5
1998SLEWT008 Cottonwood Creek 2
3 1995SLEWAOOE
I
m
1998SLEWAOO;
.EWAOIOSFCotl
laul Creek 9
1995SLEWAOO'
Creek (U) 11
IEWA009 Butcher Ci
9$9SLEWA008Schwar
•eek 1
Cottonwood Creek 3
1995SLEWA006&
Cottonwood Creek 3
1995SLEWA001 Stc
1996SLEWA038Shi
)nwood Creek 8
1995SLEWA003Thi
Threemile Creek (L)
1998SLEWT005
ckney Creek 6
ing Creek 7
mile Creek 10
10
ek(L)11
1995SLEWA011 Grs
1996SLJEWA033 Lightning Ci
1996SL EWA034 Sears Creel
z Creek 12
Creek 12
eek 12
12
3 1999SLJEWA007Huddleson
I1999SL
I 1999SLEWJ
A/X010 Wing Creek (L)
—I nggosiFWRnfi
:reek 22
EWA011 Huddle:
1995SLEWA02!
ISLEWA054 R(
1995SLEWA050Da
^3 1995SL
1995SLEWA047MOJ!
9$5SLEWA039Schoor
EWA046 Moose Butt
ise Butte Cr (L) 39
er Creek 40
1999SLEWA004WF
1995SLEWA04E
^ 1995SLEW
1995SLEWA03f
JSSa 1995SLEW.
Creek 47
•son Creek 48
1995SLEWA041 Wl
1995SLEWA042MF
Red River 42
SF Red River (U) 43
\044 Trapper Creek
1995SLEWA037 Dit
Baston Creek 45
^036 Soda Creek 46
I 1996SLEW
1996SLEWC004Bufal.
1995SLEWA053WT
EWA029 Bear Creek
EWA023 Nugget Cre
Creek 65
,EWA020MuleC
;WA022 Haysfbrk Ci
I1996SLEW
ISLEWA032 Pill
;WA019 Sing Lee Ci
.eggett Creek 75
D14 PeasleyCrs
ISLEWA015 Pe
k (U) 79
1995SLEW.
.EWBO& Wing Creek (U) 23
Santiam Creek 30
1995SLEWA028BU!
:khorn Creek 30
;f Creek 35
1SLEWA052 Deadwi
] 1995SLEW. ^035 Trail Creek 49
1995SLEWA043 Sidgel Creek 50
Red Horse Cr(L "
1SLEWC002 Re(d Horse Cr (U) 51
1996SLEWA004 Kirks Fork (U) 5
•k53
1996SLEWCOO* Flint Creek 54
.EWA002 American River (U) 55
1999SLEWf003 American River
1996SLEWC006 Litt
;003 Big Elk Creek 51
" lo Gulch Cr 59
iskey Creek 60
63
eek 67
'SLEWA021 Donkey
reek 69
;001 Baldy Creek 70
1995SLEWA031 Pile
t Creek (L) 71
• 1999SL
1995SLEWA030 Fal
ek (U) 78
isley Creek (L) 78
^017 Cougar Creek (I
1995SLEW \012 Meadow Creek
1998SLEWT019Co1
:onwood Creek (U) 3
Red Rock Creek 4
Red River 42
Red River 42
EWB003 WF Newsor ne Cr 74
8SLEWA009 Leggett Creek 75
Creek 76
1999SLEWBOC 2 Meadi
:onwood Creek (L) 2
Figure K-5. Number of Pools per Meter of the SF CWR Subbasin from the
BURP Data Set
K-9
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Bank Stability
50
01 9 Cottonw
1995SLEVW
d Creek (L)
005 Cottonwc
1998SLEW1006RedRocl
d Rock Creel
11998SLEWT008 Cottonwood Creek 2
1995SLEWA006 Cottonwood Creek (U) 3
D01 Cottonwood Creek 3
1998SLEWA002 Cottonwood Creek 3
1997SLEWZ012 Red Rock Creek 5
11996SLEWA038 Shebang Creek 7
I 1995! LEWA010 SF Cottonwood Creek 8
1995SLEW4)03 Threemile Creek 10
1995SLEWA004Threemile Creek (L) 10
2000SLEWB008 Threemile Creek (U) 10
Creek 1 2
sek 12
11995SLEWA011 Green Creek 12
1999SLEWA008 Schwartz Creek 12
1999SLEWA009 Johns Creek (L) 14
1999SLEWA028Hoores Creek 19
LEWA029 Square Mnt Creek 20
999SLEWA007 Huddleson Creek 22
1999SLEWA011 Huddleson Creek (L) 22
1999SLEWA010 Wing Creek (L) 23
LEWB004 Wing Creek (U) 23
1997SLEWC038 Tenmile Creek 26
reek 29
1995SLEWA025 Santiam Creek 30
1995SLEWA027 Moose Creek 30
1995SLEW4)28 Buckhorn Creek 30
I36 Crooked Ri
LEWA005 Ar
nerican River
L)52
d Horse Cr (I
LEWC003 Bi
.qqfi_. .......
1996SLEWC
g Elk Creek 5
LEWC004 Bi
006 Little Elk
ffalo Gulch C
LEWA040 Bt
Creek 48
1995SLEWA
Creek 57
59
1995SLEWAI
(L)31
J)32
1995SLEWA054 ReliefCreek 35
1995SLEWA052 Deadwood Creek 37
1995SLEWC055 Red River (L) 37
1995SLEWA050 Dawson Creek 38
1EWA046 Moose Butte Cr (U) 39
1995SLEWA047 Moose Butte Cr (L) 39
1995SLEWA039 Schooner Creek 40
1995SLEWA048 SF Red River (L) 40
1995SLEWA041 WF Red River 42
1995SLEWA042 MF Red River 42
1999SLEWA004 WF Red River 42
1995SLEWA045 SF Red River (U) 43
1995SLEWA044 Trapper Creek 44
1995SLEWA037 Ditch Creek 45
1995SLEWA038 Baston Creek 45
1995SLEWA049 Red River (U) 45
1995SLEWA036 Soda Creek 46
dge Creek 47
SLEWA043 Siegel Creek 50
1001 Red Horse Cr(L) 51
3 1996SLEWA004 Kirks Fork (U) 53
• 1999SLEWA002 Kirks Fork 53
ILEWA003 Lick Creek 55
119 5SLEWA018 Beaver Creek 65
1995SLEWA024 Newsome Creek (U) 66
1995SLEWA020 Mule Creek 67
1995SLEWA021 Donkey Creek 67
119951 LEWA022 Haysfbrk Creek 69
i 1996SLEWC001 Baldy Creek 70
1995SLEWA031 Pilot Creek (U) 71
1 995SLEWA053 Whiskey Creek 60
k (L) 62
1 995SLEWA029 Bear Creek 63
1 995SLEWA023 Nugget Creek 64
ee Creek 73
I 1999|LEWB003 WF Newsome Cr 74
1995SLEWA034 Leggett Creek 75
LEWA009 Leggett Creek 75
1995SLEWA030 Fall Creek 76
1999SLEWB001 Silver Creek 77
LEWA014 Peasley Creek (U) 78
1995SLEWA015 Peasley Creek (L) 78
1995SLEWA016 Cougar Creek (U) 79
1995SLEWA017 Cougar Creek (L) 79
1995SLEWA007 Meadow Creek 80
1995SLEWA012 Meadow Creek (U) 80
1995SLEWA013 Meadow Creek (L) 80
11999SLEWA012 Meadow Creek (U) 80
SLEWB002 Meadow Creek 80
Figure K-6. Bank Stability of the SF CWR Subbasin from the BURP Data Set
K-10
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
P Site ID, Stream Name, Water Body ID
D
m i
Average (L/R) Bank Stablity
D 10 20 30 40 50 60 70 80 90 1C
1998SLEWTC
1998SLEWTC
1 9 Cottonwoo
1995SLEWAC
07 Stockney C
Creek (L) 2
05 Cottonwooc
eek6
1 1996SLEWA005 Am* r can River (L)
Creek 3
LEWA037 Lon
LEWA051 Red
52
1998SLEWTO
LEWA002 Sto
jHaul Creek 9
River (Middle)
1997SLEWZO
06 Red Rock C
kney Creek (L
1995SLEWAC
1995SLEWAC
38
12 Red Rock C
LEWT004 Red
reek (U) 5
6
lOSFCottonw
OSThreemileC
1995SLEWAC
1995SLEWAO
02 Red Horse
I6SLEWC003
Creek (L) 71
reek 5
Rock Creek 5
ood Creek 8
:reek 10
08 Butcher Cr
19 Butcher Cre
tfA034 Sears C
I6SLEWC007
> (U) 51
LEWC005 Flin
I6SLEWC006
iig Elk Creek
LEWC004 Bufi
\TT005 Red Ro
LEWA001 Stoc
i009 Threemile
ek (U) 1 1
;k(L)11
1996SLEWAC
reek 1 2
LEWA035 Cro
Dtterson Creek
Creek 54
.ittle Elk Creek
8
alo Gulch Cr5
LEWA007 Mee
k Creek 4
kney Creek 6
SLEWB008 T
Creek (L) 10
33 Lightning C
LEWA026 Sixn
1995SLEWAC
ked River (U)
35SLEWA040
48
VA002Americs
EWA003 Amer
57
1995SLEWAC
dow Creek 80
EWA01 3 Meac
DO
1998SLEWT008 Cottonwood Creek 2
1995SLEWA006 Cottonwood Creek (U) 3
LEWA001 Cottonwood Creek 3
1998SLEWA002 Cottonwood Creek 3
VA038 Shebang Creek 7
LEWA004 Threemile Creek (L) 1 0
reemile Creek (U) 10
1995SLEWA011 Green Creek 12
eek 12
1999SLEWA008 Schwartz Creek 12
1999SLEWA009 Johns Creek (L) 14
1999SLEWA028Moores Creek 19
LEWA029 Square Mnt Creek 20
999SLEWA007 Huddleson Creek 22
1999SLEWA011 Huddleson Creek (L) 22
1999SLEWA010 Wing Creek (L) 23
99SLEWB004 Wing Creek (U) 23
VCOSSTenmile Creek 26
ile Creek 29
1995SLEWA025 Santiam Creek 30
1995SLEWA027 Moose Creek 30
28Buckhorn Creek 30
LEWA036 Crooked River (L) 31
32
1995SLEWA054 Relief Creek 35
1995SLEWA052 Deadwood Creek 37
1995SLEWC055 Red River (L) 37
1995SLEWA050 Dawson Creek 38
LEWA046 Moose Butte Cr (U) 39
1995SLEWA047 Moose Butte Cr (L) 39
1995SLEWA039 Schooner Creek 40
1995SLEWA048 SF Red River (L) 40
1995SLEWA041 WF Red River 42
1995SLEWA042 MF Red River 42
1999SLEWA004 WF Red River 42
1995SLEWA045 SF Red River (U) 43
1995SLEWA044 Trapper Creek 44
1995SLEWA037 Ditch Creek 45
1995SLEWA038 Baston Creek 45
995SLEWA049 Red River (U) 45
1995SLEWA036 Soda Creek 46
Bridge Creek 47
EWA043 Siegel Creek 50
LEWA001 Red Horse Cr (L) 51
EWA004 Kirks Fork (U) 53
99SLEWA002 Kirks Fork 53
n River (U) 55
96SLEWA003 Lick Creek 55
can River 55
1995SLEWA053 Whiskey Creek 60
VA033 Newsome Creek (L) 62
1995SLEWA029 Bear Creek 63
1995SLEWA023 Nugget Creek 64
5SLEWA01 8 Beaver Creek 65
1995SLEWA024 Newsome Creek (U) 66
1995SLEWA020 Mule Creek 67
1995SLEWA021 Donkey Creek 67
LEWA022 Haysfork Creek 69
996SLEWC001 Baldy Creek 70
1995SLEWA031 Pilot Creek (U) 71
19 Sing Lee Creek 73
LEWB003 WF Newsome Cr 74
1995SLEWA034 Leggett Creek 75
98SLEWA009 Leggett Creek 75
1995SLEWA030 Fall Creek 76
1999SLEWB001 Silver Creek 77
95SLEWA014 Peasley Creek (U) 78
1995SLEWA015 Peasley Creek (L) 78
LEWA016 Cougar Creek (U) 79
1995SLEWA017 Cougar Creek (L) 79
1995SLEWA012 Meadow Creek (U) 80
ow Creek (L) 80
1999SLEWA012 Meadow Creek (U) 80
99SLEWB002 Meadow Creek 80
Figure K-7. Average Left/Right Bank Stability of the SF CWR Subbasin from
the BURP Data Set
K-ll
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
t
10
20
30
Perecent Total Fines
40 50 60
70
90
100
):.LEWI
1995SLEWA033 New^ome Creek (L) 62
995SLEWC055 Rid River (L) 37
MA043 Slegel Creek 50
A025SantlamCreek3
1LEWA007 Huddle son!
998SLEWT007 Stock
Figure K-8. Percent Total Fines of the SF CWR Subbasin from the BURP Data
Set
K-12
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Summary of NPNF Stream Habitat Conditions for the SF CWR Subbasin
Table K-l below illustrates the USFS (1999) rating of the biological condition of 15 major
watersheds in the SF CWR Subbasin for ESA listed species using the Matrix of Pathways
and Indicators of Watershed Condition-Local Adaptation for the Clearwater Basin (NMFS et
al. 1998). The watersheds assessed include Red River, American River, Crooked River,
Newsome Creek, Leggett Creek, Tenmile Creek, Twentymile Creek, Wing Creek, Silver
Creek, Peasley Creek, Cougar Creek, Johns Creek, Meadow Creek, Mill Creek, and the SF
CWR main stem and face drainages. Summarized at a watershed scale, the majority of water
quality and habitat elements rate as "low" condition, while watershed condition (road
parameters), channel conditions, and species take (harassment, redd disturbance, juvenile
harvest) rate as "moderate" condition.
Table K-1. Environmental Baseline Habitat Condition (USFS 1999).
Indicator
High
Moderate
Low
Watershed Condition
Watershed Road Density
Streamside Road Density
Landslide Prone Road Density
Riparian Vegetation Condition
Change in Peak/Base Flow
Water Yield (EGA)
Sediment Yield
X
X
X
X
X
X
X
Channel Conditions and Dynamics
Width/Depth Ratio
Streambank Stability
Floodplain Connectivity
X
X
X
Water Quality
Temperature (Steelhead) Spawning
Temperature (Steelhead) Rearing and Migration
Temperature (Bull Trout)
Turbidity or Suspended Sediment
Chemical Contaminants - Nutrients
X
X
X
X
X
Habitat Access
Physical Barriers - Adults
Physical Barriers - Juvenile
X
X
Habitat Elements
K-l 3
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Indicator
Cobble Embeddedness
Percent Fines (Surface or by Depth)
Large Woody Debris
Pool Frequency
Pool Quality
Off-Channel Habitat
Habitat Refugia
High
Moderate
X
Low
X
X
X
X
X
X
Take
Harassment
Redd Disturbance
Juvenile Harvest
X
X
X
Bull Trout Sub-Population Characteristics
Sub-Population Size
Growth and Survival
Life History Diversity and Isolation
Persistence and Genetic Integrity
Bull Trout Integration of Species and Habitat
X
X
X
X
X
K-14
Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
References
Beschta, R.L. and W.S. Platts. 1986. Morphological features of small streams: significance
and function. American Water Resources Association, Water Resources Bulletin,
Vol. 22(3): 369-379.
Bjornn, T.C. and D.W. Reiser. 1991. Chapter 4: Habitat requirements of salmonids in
streams. In Meehan, W.R Influences of forest and rangeland management on
salmonid fishes and their habitat. American Fisheries Society Special Publication,
Vol. 19: 83-138.
DEQ (Division of Environmental Quality). 1996. Water body assessment guidance. A
stream to standards process. Idaho Division of Environmental Quality, Boise, ID.
109 pp.
Gordon, N.D. 1992. Stream hydrology: an introduction for ecologists. John Wiley & Sons,
New York, NY. 526pp.
MacDonald, L.H., A.W. Smart, and R.C. Wissmar. 1991. Monitoring guidelines to evaluate
the effects of forestry activities on streams in the Pacific and Alaska. EPA/910/9-91-
001. U.S. Environmental Protection Agency and University of Washington, Seattle,
WA. 166 pp.
Meehan, W.R. and M.L. Murphy. 1991. Stream ecosystems: Chapter 2. Influences of
forest and rangeland management on salmonid fishes and their habitats. American
Fisheries Society Special Publication, Vol. 19: 25-46.
NMFS et al. (National Marine Fisheries Service, Cottonwood Bureau of Land Management,
Clearwater National Forest, and Nez Perce National Forest). 1988. Matrix of
pathways and indicators for watershed condition for chinook, steelhead and bull trout,
local adaptation for Clearwater Basin and Lower Salmon. Unpublished guidance. 9
pp.
Overton, C.K., J.D. Mclntyre, R. Armstrong, S. Whitwell, and K.A. Duncan. 1995. User's
guide to fish habitat: natural conditions in the Salmon River Basin, Idaho. USDA
Forest Service Technical Report INT-GTR-322. USDA Forest Service, Intermountain
Research Station, Ogden, UT. 142 pp.
Platts, W.S., W.F. Meehan, and G.W. Minshall. 1983. Methods for evaluating stream,
riparian, and biotic conditions. General Technical Report INT-138. USDA Forest
Service, Intermountain Forest and Range Experimental Station, Ogden, UT. 77 pp.
USFS (USDA Forest Service). 1999. South Fork Clearwater River biological assessment.
Nez Perce National Forest, Grangeville, ID. 603 pp. +app.
K-15 Appendix K
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
USFS and BLM (USDA Forest Service and USDI Bureau of Land Management). 1995.
Environmental assessment for interim strategies for managing anadromous fish-
producing watersheds in eastern Oregon and Washington, Idaho, and portions of
California (PACFISH). U.S. Forest Service, Portland, OR. 72 pp.
K-16 Appendix K
-------
Appendix L. South Fork Clearwater River Subbasin
Sediment Budget
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
List of Tables L-ii
List of Figures L-ii
South Fork Clearwater River Subbasin Sediment Budget L-1
Forest Practices (NEZSED Model) L-2
In-Stream Erosion L-9
State Highway (Highway 14) from Kooskia to Elk City L-10
Mass Failures L-11
County Roads Outside the Federal Boundary (WEPP Roads Model) L-13
Agriculture and Grazing Land Surface Erosion (RUSLE) L-15
Sediment Budget L-18
References L-26
Attachment L-1: South Fork Clearwater Subbasin TMDL Stream Bank
Erosion Inventory Method L-28
L- i Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Tables
Table L-1. Data sources for the SF CWR subbasin sediment budget L-2
Table L-2. NEZSED model sediment estimates for the SF CWR Subbasin.... L-5
Table L-3. In-stream sediment produced in the SF CWR Subbasin L-9
Table L-4. Sediment delivered from State Highway 14 along the SF CWR.. L-10
Table L-5. Sediment from road-related mass failures L-12
Table L-6. Sediment predicted by the WEPP road model for county roads in
the SF CWR Subbasin L-14
Table L-7. RUSLE model sediment predictions from agriculture, grazing and
forestry outside the federal ownership boundary in the SF CWR Subbasin. L-17
Table L-8. Summary sediment budget for all assessed nonpoint sources in the
SF CWR Subbasin L-19
List of Figures
Figure L-1. NEZSED Estimated Human-Caused Sediment Yield per Year 4
Figure L-2. Annual Sediment Production by Water Body in the SF CWR
Subbasin 24
Figure L-3. Annual Sediment Production per Square Mile in the SF CWR
Subbasin 25
L- ii Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Appendix L. South Fork Clearwater River Subbasin
Sediment Budget
This document establishes the record of the sediment budget developed for sources of
sediment in the South Fork Clearwater River (SF CWR) Subbasin Assessment and Total
Maximum Daily Loads (TMDL). The methods used to establish the sediment budget
consisted of identifying the major sources of sediment in the subbasin, identifying methods
of quantifying that sediment on a yearly basis, planning and implementing projects to collect
missing data, organizing all of the data in a geographical information systems (GIS) format
so they could be compared and analyzed, and using the results as the basis for the sediment
loading calculations presented in Chapter 5.
The major sources of sediment identified in the subbasin are forestry, agriculture, grazing,
mining, roads, mass failures, and in-stream erosion.
The SF CWR Subbasin has two distinct areas of management; and therefore, different types
of sets of data about human caused sediment. The eastern two-thirds of the subbasin is
dominantly managed by the Nez Perce National Forest (NPNF) and the Bureau of Land
Management (BLM) and has data sets consistent with federally managed lands. The lower
one-third of the subbasin is largely private land dominated by agriculture and grazing, with
different types of sediment data available. The task was to consider the types of data, figure
out how to fill in the gaps, and make it all fit together in a reasonable manner consistent with
the narrative water quality sediment standard.
In the final analysis, we put together the patchwork of data shown in Table L-l, which
quantifies all the major sources of sediment in the SF CWR Subbasin.
The results of the NPNF Sediment Model (NEZSED) and the Revised Universal Soil Loss
Equation (RUSLE) models were already available at the outset of the project. Significant to
our analysis of the area of federally-managed lands; however, NEZSED does not include
estimates of human activity-induced mass failures, estimates of in-stream erosion, estimates
of road gravel loading from the highway, nor the general effects of mining or grazing.
The NPNF also already had an inventory of mass failures for the upper two-thirds of the
subbasin. We extrapolated those results, along with data from the Cottonwood Creek TMDL
(DEQ, NPT, USEPA 2000) and an aerial photo interpretation, to arrive at an estimate of mass
failures in the non-inventoried part of the basin
We concluded that the sediment producing effects of grazing and mining could largely be
quantified if we inventoried stream bank erosion. With funds made available by U.S.
Environmental Protection Agency (USEPA), we hired an inventory crew that inventoried all
of the significantly eroding stream banks in the subbasin, except for the Cottonwood Creek
watershed. This resulted in a uniform data set across all the lands with respect to in-stream
erosion.
L- 1 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table L-1. Data sources for the SF CWR subbasin sediment budget.
Data Type*
NEZSED Model
NEZSED Model
NEZSED Model
NEZSED Model
NRCS Stream Erosion Inventory
NRCS Stream Erosion Inventory
NPNF/BLM Mass Failure Inventory
Mass Failure Extrapolation
WEPP Roads Model
RUSLE Model
ITD Gravel Estimate
Mining Glory Hole Sediment Estimate
Sediment Source
Fire Erosion
Road Erosion
Logging Erosion
Natural Erosion
Forest and Mining In-Stream Erosion
Agriculture and Grazing In-Stream Erosion
Mass Failures
Agriculture and Grazing Mass Failures
Non-Federal Roads
Agriculture and Grazing Land Erosion
Highway Gravel Use
Eroding Walls
*NEZSED = Nez Perce National Forest Sediment Model, NRCS = Natural Resources Conservation Service,
NPNF = Nez Perce National Forest, BLM = Bureau of Land Management, WEPP = Watershed Erosion
Prediction Project, RUSLE = Revised Universal Soil Loss Equation, ITD = Idaho Transportation Department
Also with funds made available by USEPA, we funded a project through the University of
Idaho to develop a geographic position system (GPS)/GIS interface for the Watershed
Erosion Prediction Project (WEPP) road model. This allowed us to rapidly collect the data to
run the model using GPS, transfer it to the GIS, and load it into the model. This provided the
data set for the non-federal roads, except for the main highway along the river from Kooskia
to Elk City. It had been observed that large portions of the gravel used to maintain safe
driving conditions in the winter were ending up in the river. We got an estimate from the
Idaho Transportation Department (ITD) of the amount of gravel being applied to the road
each year.
Each sediment source, its appropriate data set or model, the calculation results, and the
implications to the sediment loading calculations are discussed below.
Forest Practices (NEZSED Model)
Most of the federally managed land is forested. The main data set from the federally
managed lands was derived from the NEZSED model. The NEZSED model is a
computerized sediment delivery prediction model developed by the NPNF based on
guidelines developed by hydrologists and soil scientists from the U.S. Forest Service (USFS)
Northern and Intermountain Regions (USFS 1981). We used portions of the data set
developed for the South Fork Clearwater Landscape Assessment (USFS 1998). The
sediment yield was modeled for the period 1870 through 2000 and includes the effects of
fire, timber harvest, and roads. It includes natural baseline data and results in a reasonable
estimate of background loads. The model predicts sediment yield recovery to background
L-2
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
rates within five and seven years for burned areas and logged areas, respectively. The model
predicts continuing sediment production from roads so long as they remain on the landscape.
The NEZSED sediment delivery model, along with the whole family of models using the
R1/R4 (USFS 1981) methods, has been subject to considerable scrutiny and has been found
to underpredict more often than it overpredicts. In a fairly intensive research project on the
NPNF, Gloss (1994) found that the model underpredicted actual sediment yield on the order
of 50%. We do not attempt to correct any of the predictions in our use of the NEZSED data;
however, the idea that sediment yield from the upper part of the basin may be greater than
predicted lends weight to our final recommendations that sediment loads from the federally-
managed parts of the subbasin need to be reduced to fully restore the beneficial uses.
Further, since sediment-loading reductions are presented as percentages measured by
NEZSED, any under prediction would be compensated for.
On the other hand, considering the NEZSED model results in relation to the subbasin as a
whole, the magnitude of human activity-caused sediment from agricultural and grazing
practices in the subbasin far outweighs the amount of sediment coming from forestry. If one
is going to be concerned about error levels of the estimates, total human-caused sediment
from forestry is probably less than the error in estimates of eroded sediment from agricultural
and grazing lands in the subbasin.
The NEZSED data were received from the NPNF by sixth order HUC as defined by the
forest. We reallocated those results to the water bodies defined in IDAPA 58.01.02.120.07,
based primarily on the number of miles of roads by area, since the majority of NEZSED
sediment is produced from roads. Table L-2 shows the breakdown of sediment yield for each
of the water bodies in the federally managed portion of the subbasin. Generally, Table L-2
shows total sediment yield, then subtracts out the background sediment, resulting in an
estimate of human-caused sediment.
This human-caused sediment is then routed through the hydrologic network based on the
Roehl (1962) equation, resulting in the final estimate of human-caused sediment in the water
that must be addressed in this TMDL. The Roehl (1962) equation produces a routing
coefficient that is applied to all of the sediment sources identified in the SF CWR Subbasin.
The routing equation simply identifies a relationship between size of the drainage and the
percent of eroded material that moves out of the drainage (Routing Coefficient = drainage
area in square miles raised to the negative 0.18 power [RC = A("ai8)]. The larger the
drainage, the smaller the routing coefficient, indicating that more of the material is being
stored inside the watershed. Figure L-l displays the magnitude of forest practice-caused
sediment from the various water bodies in the subbasin.
L- 3 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
NEZSED Estimated Routed Activity ^.^
Sediment Yield in Tons per
Water Body per Year for the South
Fork Clearwater River Subbasin
Routed Activity Sediment
Routed Activity Sediment (T/WB/yr
0-10
| 10-30
30-50
| 50-70
>70
16 Miles
Figure L-1. NEZSED Estimated Human-Caused Sediment Yield per Year
The interesting results from these data are the totals and the few water bodies that are
delivering 50 tons/year or greater to the system. The major contributors of human-caused
sediment are the main stem water bodies; lower, middle, and upper Red River; lower
American River; East Fork American River; and Meadow Creek. Cougar Creek and Buffalo
Gulch produce slightly less sediment than these other water bodies. Total modeled human-
caused sediment is only about 10% of background.
L-4
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table L-2. NEZSED model sediment estimates for the SF CWR Subbasin.
Water Body
Name
Mid-L. SF
CWR
Mill
L. Johns
Gospel
WF Gospel
Mid Johns
U. Johns
Moores
Sq. Mountain
Hagen
M. SF CWR
Wing
Twentymile
L. Tenmile
M. Tenmile
U. Tenmile
Williams
Sixmile
Water
Body
No.
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
Area
(mi2)
60.98
36.58
41.22
16.92
6.98
15.94
13.55
6.23
3.58
8.65
29.61
8.33
22.88
3.82
11.29
21.28
9.20
8.02
Total
(t/WB/yr)
2,650.54
1,050.29
1,247.94
1,207.07
345.93
510.02
543.73
550.76
316.43
416.83
1,167.08
256.28
476.47
119.74
313.35
998.22
262.21
151.53
Back-
ground
Rate
(t/mi2/yr)
38.22
26.77
29.40
71.68
49.80
31.95
40.16
88.81
88.86
48.47
36.24
30.16
20.04
30.06
26.85
47.09
28.53
16.84
Total
Back-
ground
(t/WB/yr)
2,502.85
971.08
1,211.61
1,207.05
345.59
508.97
543.73
550.64
316.36
416.83
1,072.65
251.20
458.20
114.81
303.10
998.21
262.19
135.04
Human
Caused
Rate
(t/mi2/yr)
2.26
2.18
0.88
0.00
0.05
0.07
0.00
0.02
0.02
0.00
3.19
0.61
0.80
1.29
0.91
0.00
0.00
2.06
Rate
From
Roads
(t/mi/yr)
0.50
0.74
0.47
0.00
0.11
0.11
0.00
0.01
0.05
0.00
1.19
0.36
0.51
2.09
0.58
0.00
0.01
1.06
Total
Human
Caused
(t/WB/yr)
147.69
79.21
36.34
0.03
0.34
1.06
0.00
0.12
0.07
0.00
94.43
5.08
18.27
4.93
10.25
0.01
0.02
16.49
Routing
Coeffic-
ient
0.55
0.52
0.51
0.60
0.70
0.61
0.63
0.72
0.80
0.68
0.54
0.68
0.57
0.79
0.65
0.58
0.67
0.69
Total
Routed
(t/WB/yr)
1,457.80
549.45
638.97
725.44
243.83
309.85
340.11
396.24
251.57
282.67
634.21
175.00
271.24
94.06
202.55
575.71
175.84
104.18
Total
Human
Caused
Routed
(t/WB/yr)
81.23
41.44
18.60
0.02
0.24
0.64
0.00
0.09
0.06
0.00
51.31
3.47
10.40
3.87
6.63
0.01
0.01
11.34
L-5
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water Body
Name
Mid-U. SF
CWR
L. Crooked
U. Crooked
WF Crooked
EF Crooked
Relief
U. SF CWR
L. Red
M. Red
Moose Butte
L. SF Red
M. SF Red
WFRed
U. SF Red
Trapper
U. Red
Soda
Bridge
Water
Body
No.
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
Area
(mi2)
26.82
14.81
22.64
11.87
10.45
11.69
4.21
16.15
25.07
11.07
4.93
4.36
10.01
7.41
11.06
30.08
5.24
3.72
Total
(t/WB/yr)
847.55
417.69
460.01
269.93
286.97
226.15
147.47
375.79
680.29
261.49
111.80
107.84
185.86
135.89
215.15
744.99
115.14
89.97
Back-
ground
Rate
(t/mi2/yr)
28.03
25.07
18.82
22.62
27.08
16.73
25.90
17.41
20.06
17.24
17.93
18.88
17.06
17.10
17.56
19.74
18.11
21.49
Total
Back-
ground
(t/WB/yr)
751.79
370.98
425.24
266.51
280.26
195.80
109.31
281.17
502.62
191.91
88.23
82.13
170.06
124.16
193.15
592.77
94.53
79.93
Human
Caused
Rate
(t/mi2/yr)
3.57
3.16
1.54
0.29
0.65
2.59
9.04
5.86
7.09
6.29
4.79
5.91
1.58
1.62
2.00
5.07
3.95
2.70
Rate
From
Roads
(t/mi/yr)
1.03
1.00
0.75
0.30
0.98
0.70
3.12
1.01
1.37
1.22
1.15
1.37
0.67
0.44
0.65
1.34
1.08
1.38
Total
Human
Caused
(t/WB/yr)
95.77
46.72
34.77
3.42
6.71
30.36
38.15
94.62
177.67
69.58
23.57
25.72
15.79
11.73
21.99
152.23
20.62
10.04
Routing
Coeffic-
ient
0.55
0.62
0.57
0.64
0.66
0.64
0.77
0.61
0.56
0.65
0.75
0.77
0.66
0.70
0.65
0.54
0.74
0.79
Total
Routed
(t/WB/yr)
468.86
257.12
262.36
172.93
188.10
145.27
113.84
227.77
380.95
169.62
83.90
82.73
122.77
94.75
139.60
403.71
85.46
71.03
Total
Human
Caused
Routed
(t/WB/yr)
52.98
28.76
19.83
2.19
4.40
19.50
29.45
57.35
99.49
45.14
17.69
19.73
10.43
8.18
14.27
82.49
15.30
7.93
L-6
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water Body
Name
Otterson
Trail
Siegel
Red Horse
L. American
Kirks Fork
EF American
U. American
Elk
Little Elk
Big Elk
Buffalo
Whiskey
Maurice
L. Newsome
Bear
Nugget
Beaver
M. Newsome
Water
Body
No.
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
Area
(mi2)
3.89
7.13
12.16
9.07
11.27
9.78
17.88
23.87
3.63
7.94
13.78
3.34
2.59
1.71
6.48
5.99
2.27
5.83
1.77
Total
(t/WB/yr)
81.15
160.17
266.48
216.56
281.16
235.13
413.33
621 .65
128.09
190.05
416.10
86.48
62.36
38.92
188.94
143.43
44.24
122.06
51.81
Back-
ground
Rate
(t/mi2/yr)
20.78
19.89
17.74
21.19
17.38
22.95
18.44
23.54
28.96
18.15
24.45
20.70
20.54
19.56
24.24
19.57
16.47
19.18
24.15
Total
Back-
ground
(t/WB/yr)
80.85
141.60
215.88
191.96
195.69
224.70
328.64
559.81
105.13
143.91
337.22
69.15
52.98
33.46
156.82
117.05
37.39
112.01
42.99
Human
Caused
Rate
(t/mi2/yr)
0.08
2.61
4.16
2.72
7.59
1.06
4.75
2.60
6.33
5.82
5.72
5.19
3.63
3.20
4.96
4.41
3.01
1.72
4.95
Rate
From
Roads
(t/mi/yr)
0.10
1.11
1.15
1.13
2.25
0.62
1.60
1.01
2.29
1.72
1.95
1.19
1.05
1.08
1.04
0.81
0.66
0.67
1.12
Total
Human
Caused
(t/WB/yr)
0.30
18.57
50.60
24.61
85.47
10.43
84.68
61.85
22.96
46.14
78.87
17.32
9.38
5.47
32.12
26.38
6.84
10.05
8.82
Routing
Coeffic-
ient
0.78
0.70
0.64
0.67
0.65
0.66
0.60
0.56
0.79
0.69
0.62
0.80
0.84
0.91
0.71
0.72
0.86
0.73
0.90
Total
Routed
(t/WB/yr)
63.55
112.48
169.96
145.61
181.80
155.98
245.96
351.19
101.56
130.89
259.49
69.59
52.53
35.34
134.98
103.93
38.17
88.86
46.73
Total
Human
Caused
Routed
(t/WB/yr)
0.23
13.04
32.27
16.54
55.27
6.92
50.39
34.94
18.20
31.77
49.19
13.94
7.90
4.96
22.95
19.11
5.90
7.32
7.95
L-7
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water Body
Name
Mule
U. Newsome
Haysfork
Baldy
Pilot
Sawmill
Sing Lee
WF
Newsome
Leggett
Fall
Silver
Peasley
Cougar
Meadow
Sally Ann
Rabbit
Water
Body
No.
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
Totals
Area
(mi2)
8.59
9.93
4.96
4.26
6.12
2.76
2.43
5.16
7.80
3.65
25.81
14.21
12.09
37.52
4.09
0.68
857.09
Total
(t/WB/yr)
190.11
223.54
134.79
118.57
163.02
76.91
73.04
151.06
231.19
107.71
638.58
440.00
342.80
1,164.39
128.74
12.90
26,209.85
Back-
ground
Rate
(t/mi2/yr)
17.69
21.13
23.20
25.21
25.87
27.70
27.12
27.77
26.29
26.18
24.18
26.61
23.07
26.75
27.63
17.69
Total
Back-
ground
(t/WB/yr)
151.61
208.98
114.38
106.88
158.09
76.72
65.90
143.29
205.04
95.30
623.03
377.84
278.69
1,003.16
113.56
12.03
23,852.35
Human
Caused
Rate
(t/mi2/yr)
4.49
1.47
4.14
2.76
0.81
0.07
2.94
1.51
3.35
3.41
0.60
4.38
5.31
4.30
3.70
1.28
Rate
From
Roads
(t/mi/yr)
0.87
0.64
0.83
0.59
0.71
0.55
0.69
0.54
0.75
1.02
0.40
0.94
1.25
0.96
0.62
0.21
Total
Human
Caused
(t/WB/yr)
38.50
14.56
20.41
11.69
4.94
0.19
7.14
7.78
26.15
12.41
15.55
62.17
64.12
161.23
15.19
0.87
2,357.51
Routing
Coeffic-
ient
0.68
0.66
0.75
0.77
0.72
0.83
0.85
0.74
0.69
0.79
0.56
0.62
0.64
0.52
0.66
0.67
Total
Routed
(t/WB/yr)
129.09
147.88
101.05
91.36
117.66
64.04
62.25
112.42
159.73
85.33
355.71
272.90
218.88
606.37
85.37
8.64
16,006.74
Total
Human
Caused
Routed
(t/WB/yr)
26.14
9.63
15.30
9.01
3.56
0.15
6.08
5.79
18.07
9.83
8.66
38.56
40.94
83.96
10.07
0.58
1,449.60
L-8
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
In-Stream Erosion
As noted above, the NEZSED model does not account for sediment coming from human-
caused mass failures, impacts from grazing, or impacts from mining. (The background
sedimentation rate in NEZSED does include naturally occurring mass failures.) In order
to account for the impacts of grazing and mining as they affect stream stability, we
collected data on in-stream erosion throughout the whole subbasin, except Cottonwood
Creek. The methods followed in this data collection exercise appear as an attachment at
the end of this appendix (Attachment L-l). Streams sampled and the results are shown in
Table L-3.
Table L-3. In-stream sediment produced in the SF CWR Subbasin.
In-Stream Erosion Data
Water Body No.
10
11
38
39
45
49
50
55
56
57
58
59
62
75
80
81-NonFS*l_and
82-Non FS Land
Water Body Name
Threemile Creek
Butcher Creek
Middle Red River
Moose Butte Creek
Upper Red River
Trail Creek
Siegel Creek
Upper American
River
Elk Creek
Little Elk Creek
Big Elk Creek
Buffalo Gulch
Lower Newsome
Creek
Leggett Creek
Meadow Creek
Sally Ann Creek
Rabbit Creek
Total
Sediment in
Tons per
Stream Mile
(t/mi/yr)
39
23
14
17
5
3
22
3
53
2
11
1
4
1
15
1
1
213
Sediment
in Tons
per Water
Body
(t/WB/yr)
616
211
210
12
62
3
15
39
124
25
63
4
36
1
53
1
1
1,473
Routing
Coeffic-
ient
0.58
0.62
0.56
0.65
0.54
0.70
0.64
0.56
0.79
0.69
0.62
0.80
0.71
0.69
0.52
0.66
0.67
Routed
Sediment
(t/WB/yr)
357
131
118
8
34
2
10
22
98
17
39
3
26
1
27
1
1
891
*Non FS = not federally managed
L-9
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
The largest producers of in-stream sediment are Threemile Creek, Butcher Creek, Middle
Red River, and Elk Creek. We note in the methods that we only sampled streams known
to be actively eroding. These data show that the grand majority of sediment from in-
stream erosion is coming from a few locations. The total routed in-stream erosion
sediment being produced is about 60% of the total routed human-caused sediment being
produced from forest activities on the federal lands. About half of that, however, is
coming from Threemile and Butcher Creeks.
State Highway (Highway 14) from Kooskia to Elk City
Another major source of sediment is the state highway from Kooskia to Elk City. It is
regularly graveled during the winter to improve driving conditions and much of the
gravel ends up in the river.
We estimated the amount of sediment coming from the state highway based on the gravel
crushed by ITD for the Reed's Bar shed. The ITD crushes approximately 10,000 tons of
gravel every four years or so that is used for the portion of the road from the Mt. Idaho
bridge to Elk City, a distance of 50 miles. This results in about 200 tons of gravel per
mile , which over 4 years equals about 50 tons/mile/year. Of course, not all of this
reaches the river, but a significant portion does. Some portion is applied to parts of the
road that have some sort of a buffer to the river. We estimated that about 80% of the
highway is directly adjacent to the river. Given these conditions, we used a 40 tons/mile
rate for the state highway from Harpster to Elk City. We placed these estimates in the
sediment budget before the routing equation was applied, so the estimates are reduced by
the Roehl (1962) routing coefficient. Table L-4 shows the estimates of sediment from
State Highway 14. These estimates of total sediment delivery are the same order of
magnitude as those from NEZSED and the in-stream erosion survey.
Table L-4. Sediment delivered from State Highway 14 along the SF CWR.
Water Body
No.
12
22
30
36
Water Body
Name
Mid-Lower SF
CWR
Middle SF
CWR
Mid-Upper SF
CWR
Upper SF
CWR
Total
Miles of
Road
(miles)
23.7
11.7
11.8
3.7
50.9
Tons of
Sediment
(t/WB/yr)
948
468
472
148
2,036
Routing
Coefficient
0.55
0.54
0.55
0.77
Routed
Sediment
(t/WB/yr)
521
253
260
114
1,148
L-10
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Mass Failures
Another major source of sediment identified from both privately and publicly managed
lands is mass failures that are related to human activities. For the most part, these are
mass failures associated with roads. In general, a few mass failures occur every year, but
the major contributors of sediment are the major episodes of mass failure that occur
during large rain-on-snow events or during other high precipitation events when the soil
mantle becomes supersaturated. The last major mass failure event in the region occurred
during the storms of 1996. The NPNF and BLM conducted an inventory of the mass
failures that occurred during that event.
We acquired the NPNF mass failure database and identified those mass failures
associated with roads. An estimate of percent delivery of sediment to the stream was not
consistently included in the database. As an alternative, we applied the Roehl (1962)
routing coefficient to the total sediment production to arrive at an estimate of percent
delivery. This is consistent with our and NEZSED's application of the routing coefficient
to all the sediment sources in the subbasin, in the absence of a better way to approach the
routing question in a more site-specific or source-specific manner.
The NPNF data set documents mass failures that occurred primarily during the 1996
storms. This sediment production rate cannot be assumed to occur annually. Based on
data from the last century, McClelland et al. (1997) conclude that major rain-on-snow
events of the sort that cause major mass failure episodes occur on a 15 to 20 year interval.
We, therefore, assumed a 15-year interval and divided the total sediment produced by the
mass failures by 15 to arrive at a yearly rate. Table L-5 shows these results.
The NPNF data set only covers lands east of the main federal ownership boundary. We
used three approaches to arrive at an estimate of mass failures that occurred on the non-
federal lands (water bodies 1, 10,11, and 12, those areas downstream from the Mt. Idaho
bridge). We looked at the mass failure rate from the NPNF data set for basalt geologic
and basaltic aquatic landtypes that the NPNF has mapped over the prairie lands. This
resulted in estimates of three to seven mass failures for the non-federal area. In addition,
as we examined aerial photos of the area for evidence of recent mass failures. Three
mass failures were identified that appeared to be about 200 cubic yards in size each. On-
the-ground surveys of Cottonwood Creek (DEQ, NPT, USEPA 2000) identified several
large debris torrents that had occurred in similar terrain. Based on this combination of
information, we chose to ascribe four mass failures in the 200-500 cubic yard size class to
water bodies 1, 10, 11, and 12 as shown in Table L-5. Anecdotal evidence and other
observations confirm that it is likely that at least this much material moved massively
during the 1996 event.
L-ll Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table L-5. Sediment from road-related mass failures.
Mass Failure Data
Water Body No.
1 (Est)
10(Est)
11 (Est)
12-NonFS*l_and (E)
12-FS**l_and
13
14
22
37
55
77
78
79
80
Water Body Name
Lower SF CWR
Threemile Creek
Butcher Creek
Mid-Lower SF CWR
Mid-Lower SF CWR
Mill Creek
Lower Johns Creek
Middle SF CWR
Lower Red River
Upper American R.
Silver Creek
Peasley Creek
Cougar Creek
Meadow Creek
Total
Number
of Mass
Failures
(15yr)
1
2
1
1
28
4
1
4
2
3
2
1
3
2
Total Mass
Failure
Sediment per
Water Body
(t/WB)
320
640
320
320
5,715
2,697
122
340
737
423
170
122
219
180
Mass Failure
Sediment per
Year per
Water Body
(t/WB/yr)
21
43
21
21
381
180
8
23
49
28
11
8
15
12
Routing
Coefficient
0.54
0.53
0.60
0.55
0.55
0.52
0.51
0.54
0.61
0.56
0.56
0.62
0.64
0.52
Routed Mass
Failure Sediment
(t/WB/yr)
12
23
13
12
210
94
4
12
30
16
6
5
9
6
451
*Non FS = not federally managed
**FS = federally managed
L-12
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
The data show that the largest sediment rate from mass failures is in the mid-lower SF
CWR, which is also the largest water body in the subbasin. This is consistent with other
data about the location of rain-on-snow induced mass failures occurring at lower
elevations (McClelland et al. 1997), such as the location of the mid-lower SF CWR. At
higher elevations, the precipitation occurs as snow and thus does not result in over
saturated soil mantle conditions. While the estimated total sediment delivery from mass
failures is less than that for NEZSED/forestry, state and county roads, and in-stream
erosion, it is significant in relation to them and constitutes a major portion of the total
sediment budget for the land above Harpster.
County Roads Outside the Federal Boundary (WEPP Roads Model)
The major sources of sediment from private lands are agriculture, grazing, and roads.
The two other sources of sediment from non-federal lands, gravel from State Highway 14
and mass failures, have been accounted for above. To be able to quantify the sediment
coming from the graveled county roads, we initiated a project, with funding from
USEPA, with the Agricultural and Biological Engineering Department at the University
of Idaho to develop methods to apply the WEPP roads model (Elliot et al. 1995, Flanagan
and Livingston 1995) to unpaved public roads on the non-federal lands. Details of the
results of the project are available at the DEQ Lewiston Regional Office in the final
project report (Boll et al. 2002). A summary of the results is in Table L-6.
The WEPP road model is a process-based model of surface erosion originally developed
for agriculture. A roads module was later added and is being developed by the USFS as a
method of more detailed analysis beyond the NEZSED approach (Elliot et al. 1995). The
model requires detailed input of climate, soils, road surface, local topography, road drain
spacing, road design, road surface condition, and relationship of the road to surface
drainage systems. The amount of detail required is often difficult to attain at the large
scale needed for a subbasin assessment.
We contracted with the University of Idaho to develop a GPS capability to record needed
model inputs and a GIS interface to manipulate the GPS data to provide the inputs for the
WEPP road model. Essentially, the system was set up to run over and over again for
every road segment defined by every high point in a road and every low point and/or
cross drain. The data in Table L-6 show numbers for sediment detachment and sediment
delivery. The model calculates sediment produced (detachment) from the road prism by
precipitation events (a 30-year climate generator was used), then routes the sediment
across the landscape to the surface water system (delivery). If a cross drain or road ditch
empties directly into a surface water system channel, then delivery is 100%. Otherwise,
the sediment carrying water is "buffered" such that percent sediment delivery is reduced
by the landscape conditions before the water reaches a stream channel.
L-13 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table L-6. Sediment predicted by the WEPP road model for county roads in the SF CWR Subbasin.
WEPP Data
Water
Body
No.
1
10
11
12
81
82
Water Body Name
Lower SF CWR
Threemile Creek
Butcher Creek
Mid-Lower SF CWR
Sally Ann Creek
Rabbit Creek
Total
Total
Detached
Sediment
Sampled
(t/WB/yr)
36
79
124
103
57
23
Total
Delivered
Sediment
Sampled
(t/WB/yr)
16
51
59
40
21
12
Weighted
Detached
Sediment
Sampled
(t/mi/yr)
4
6
12
10
8
4
Weighted
Delivered
Sediment
Sampled
(t/mi/yr)
2
4
6
4
3
2
Est. Total
Detached
Sediment
Calculated
(t/WB/yr)
253
393
390
701
177
56
Est. Total
Delivered
Sediment
Calculated
(t/WB/yr)
110
253
185
271
64
29
Routing
Coefficient
Calculated
0.54
0.53
0.60
0.55
0.66
0.67
Est. Total
Routed
Sediment
Calculated
(t/WB/yr)
60
134
111
149
42
20
516
L-14
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
We collected data of a sample of the roads in each of the water bodies to the west of the
federal lands. We calculated a weighted average of sediment per mile of road sampled in
a water body and extrapolated that sediment erosion rate to all the unpaved county roads
in our GIS coverage of the water body. Since WEPP predicts sediment delivery to a
stream channel, once again there is need to route the sediment through the hydrologic
system of the water body. As with all the other sediment data for this sediment budget,
we routed the sediment using the Roehl (1962) routing coefficient.
The estimated sediment produced by county roads is of the same magnitude as estimated
sediment from NEZSED, in-stream erosion, the state highway, and mass failures. Given
the error of the estimates, it would be difficult to argue that any one of these is more or
less important than the other in the overall sediment budget, or that any one of them is not
important to reducing the sediment load in the SF CWR Subbasin
Agriculture and Grazing Land Surface Erosion (RUSLE)
The sediment production situation for the agricultural and grazing lands on the lands to
the west of the NPNF boundary within the SF CWR Subbasin is quite different from the
sources discussed above. The Cottonwood Creek TMDL (DEQ, NPT, USEPA 2000)
identifies a sediment load from Cottonwood Creek alone approximately five times greater
than all the sediment discussed above from the rest of the subbasin. The Threemile Creek
watershed encompasses many of the same land use practices and produces a
proportionate amount of sediment. Since we have to account for all the sediment as it
leaves the subbasin at Kooskia, we have included sediment data from the Cottonwood
Creek TMDL, as well as developed some of our own for comparison purposes.
We were fortunate that at the time when we were starting work on this TMDL, the same
group at the University of Idaho who did the WEPP work for us was completing a
RUSLE model (Renard et al. 1997) of the Clearwater Basin (Boll and Brooks 2002).
They are currently running the model in a GIS mode (Engel 1999), which requires inputs
of digital coverages of the various parameters.
They reran the model in a more detailed manner for our areas of interest, specifically
updating the land use map of Cottonwood Creek, Threemile Creek, Butcher Creek, Sally
Ann Creek, and Rabbit Creek, as well as using the SSURGO soils data set instead of the
STATSGO soils data set. The original land use map had been developed from satellite
imagery and ground-truthed in the Lawyers Creek watershed. We found that in the SF
CWR Subbasin, it showed far too much cropland and too little hay and grassland. We
adjusted these data such that only the Threemile Creek and Cottonwood Creek watershed
show any significant annual cropland, which is consistent with the cropping pattern in the
region.
Table L-7 shows the results of the RUSLE model of sediment production in all the water
bodies to the west of the federal boundary, including the Cottonwood Creek water bodies
(upper and lower Cottonwood Creek, upper and lower Red Rock Creek, Stockney Creek,
Shebang Creek, South Fork Cottonwood Creek, and Long Haul Creek). As with the
L-15 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
NEZSED data, we subtracted out an estimate of background sediment to produce an
estimate of human-caused sediment, then routed it using the routing coefficient. We used
a value of 30 tons/square mile as the estimate of the background sedimentation rate. This
number was derived in part from the range of background sedimentation rates used in
NEZSED for dry forest types on the same landtypes that occur to the west of the NPNF.
We also examined RUSLE results from Washington State University where efforts were
made to determine a minimal erosion rate under grassland conditions (McCool et al.
2000).
In comparison to the estimated sediment production from other sources in the subbasin,
these numbers are an order of magnitude greater. For the croplands, we compared the
estimated sediment numbers to those from Washington State University (McCool et al.
2000) and they are what would be expected for croplands in this region. From the total
routed human-caused sediment, 10,473 tons/year are from the water bodies being
addressed in this TMDL, of which 9,547 tons/year are from the 303(d) listed water
bodies. The differences between the estimates of sediment production for Cottonwood
Creek using the RUSLE model and the sediment loading estimates in the Cottonwood
Creek TMDL are discussed in Appendix M, Sediment Loading Calculations.
L-16 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table L-7. RUSLE model sediment predictions from agriculture, grazing and forestry outside the federal
ownership boundary in the SF CWR Subbasin.
RUSLE Data
Water Body
No.
1
2
3
4
5
6
7
8
9
10
11
12-Non FS*
Land
81 -Non FS Land
82-Non FS Land
Water Body Name
Lower SF CWR
Lower Cottonwood Cr.
Upper Cottonwood Cr.
Lower Red Rock Cr.
Upper Red RockCr.
Stockney Cr.
Shebang Cr.
SF Cottonwood Cr.
Long Haul Cr.
Threemile Cr.
Butcher Cr.
Mid-Lower SF CWR
Sally Ann Cr.
Rabbit Cr.
Total
Sediment in
Tons per
Square Mile
(t/mi2/yr)
86
494
599
567
704
650
423
520
479
347
102
55
87
96
5,209
Sediment in
Tons per
Water Body
(t/WB/yr)
2,638
12,572
19,807
2,633
25,261
19,898
11,691
10,108
6,194
1 1 ,632
1,708
4,817
1,205
784
130,947
Estimated
Background
(t/WB/yr)
925
794
995
139
1,101
937
862
594
413
1,007
503
694
294
270
9,525
Human-
Caused
Sediment
(t/WB/yr)
1,713
11,778
18,812
2,493
24,160
18,962
10,830
9,513
5,781
10,626
1,205
4,123
911
514
121,422
Routing
Coefficient
0.54
0.55
0.53
0.76
0.52
0.54
0.55
0.58
0.62
0.53
0.60
0.55
0.66
0.67
Routed
Human-
Caused
Sediment
(t/WB/yr)
925
6,478
9,970
1,895
12,563
10,239
5,956
5,518
3,584
5,632
723
2,268
601
344
66,698
*Non FS = not federally managed
L- 17
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Sediment Budget
All of the data discussed above are summarized in Table L-8. These summary data are
used in the sediment loading calculations discussed in the sediment TMDLs in Chapter 5
of this document. Of interest for the purposes of a TMDL and loading reductions is the
difference of nearly two magnitudes between sediment loading from forested water
bodies compared to water bodies used primarily for agriculture and grazing. The same
data are presented graphically in Figures L-2 and L-3.
Table L-8 and Figures L-2 and L-3 identify those water bodies that appear to be
contributing significant amounts of sediment to the main stem SF CWR. For the water
bodies above Harpster, the total amount of human-caused sediment being routed through
the water bodies ranges from zero for those water bodies in the wilderness to a high of
3,191 tons/year for the lower-mid SF CWR around Harpster (water body no. 12). The
next two highest sediment producing water bodies are the next two water bodies
upstream from Harpster on the main stem (middle SF CWR (water body no. 22) and the
upper-mid SF CWR (water body no. 30)). Aside from these main stem water bodies, the
following water bodies upstream from Harpster are producing greater than 100 tons of
sediment per year: Mill Creek, middle Red River (which includes Dawson Creek), upper
Red River, lower Elk Creek, and Meadow Creek. Water bodies producing between 50
and 100 tons of sediment per year include: lower Red River, Moose Butte Creek, lower
American River, East Fork American River, upper American River, Big Elk Creek, and
Cougar Creek. Figure L-2 shows the distribution of human-caused sediment by water
body.
To account for the varying sizes of the water bodies, another way of looking at sediment
production is on a per unit area basis. Apart from the main stem water bodies which
produce the most sediment on a per unit area basis, the following water bodies are
producing the most sediment: lower Elk Creek, 32 tons per square mile per year
(t/mi2/yr); middle Red River (which includes Dawson Creek), 98.6 t/mi2/yr; lower
Newsome Creek, 87.5 t/mi2/yr; Big Elk Creek, 6.4 t/mi2/yr; Little Elk Creek, 6.1 t/mi2/yr;
lower Red River, 5.4 t/mi2/yr; and Buffalo Gulch, 5.1 t/mi2/yr. Water bodies in the 3-5
t/mi2/yr range include Mill Creek, Meadow Creek, Cougar Creek, Peasley Creek,
Haysfork Creek, Mule Creek, Bear Creek, middle Newsome Creek, Maurice Creek,
lower and upper American River, Siegel Creek, Moose Butte Creek, lower and middle
South Fork Red River, and upper Red River. The other 303(d) listed water bodies, Sing
Lee Creek, Nugget Creek, and Beaver Creek, are producing in the range of 1 to 3 t/mi2/yr
of human-caused sediment. Figure L-3 shows the distribution of human-caused sediment
per unit area.
L-18 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table L-8. Summary sediment budget for all assessed nonpoint sources in the SF CWR Subbasin.
Water
Body
No.*
1
2
3
4
5
6
7
8
9
10
11
12 NFS
12 FS
13
14
15
16
17
Area
(mi2)
30.8
26.5
33.2
4.6
36.7
31.2
28.7
19.8
13.8
33.6
16.8
27.6
61.0
36.6
41.2
16.9
7.0
15.9
WEPP
and State
Highway
(t/yr/WB)
72.44
205.14
137.24
177.16
948.00
NEZSED
(t/yr/WB)
2,650.54
1,050.29
1,247.94
1,207.07
345.93
510.02
RUSLE
(t/WB/yr)
2,637.89
12,571.52
19,806.96
2,632.50
25,261.17
19,898.12
11,691.41
10,107.69
6,193.82
11,632.46
1,708.16
4,816.93
Mass
Failures
(t/WB/yr)
21.33
42.67
21.33
21.33
381.02
179.82
8.10
In-stream
Erosion
(t/WB/yr)
615.75
211.20
Total
Sediment
(t/WB/yr)
2,731.67
12,571.52
19,806.96
2,632.50
25,261.17
19,898.12
11,691.41
10,107.69
6,193.82
12,496.02
2,077.93
5,015.42
3,979.56
1,230.11
1 ,256.04
1,207.07
345.93
510.02
Background
Sediment
Rate
(t/miA2)
30.00
30.00
30.00
30.00
30.00
30.00
30.00
30.00
30.00
30.00
30.00
30.00
38.22
26.77
29.40
71.68
49.80
31.95
Total
Background
Sediment
(t/WB/yr)
924.60
793.50
994.80
139.20
1,100.70
936.60
861 .60
594.30
413.10
1,006.50
502.80
693.60
2,502.85
971.08
1,211.61
1,207.05
345.59
508.97
Routing
Coefficient
0.54
0.55
0.53
0.76
0.52
0.54
0.55
0.58
0.62
0.53
0.60
0.55
0.55
0.52
0.51
0.60
0.70
0.61
Routed
Human-
Caused
Sediment
(t/WB/yr)
974.97
6,531.78
10,016.73
1,891.57
12,632.50
10,206.73
5,917.66
5,557.88
3,605.64
6,104.73
948.35
2,378.55
812.72
135.51
22.75
0.02
0.24
0.64
L- 19
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body
No.*
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
Area
(mi2)
13.6
6.2
3.6
8.7
29.6
8.3
22.9
3.8
11.3
21.3
9.2
8.0
26.8
14.8
22.6
11.9
10.5
11.7
WEPP
and State
Highway
(t/yr/WB)
468.00
472.00
NEZSED
(t/yr/WB)
543.73
550.76
316.43
416.83
1,167.08
256.28
476.47
119.74
313.35
998.22
262.21
151.53
847.55
417.69
460.01
269.93
286.97
226.15
RUSLE
(t/WB/yr)
Mass
Failures
(t/WB/yr)
22.68
In-stream
Erosion
(t/WB/yr)
Total
Sediment
(t/WB/yr)
543.73
550.76
316.43
416.83
1,657.75
256.28
476.47
119.74
313.35
998.22
262.21
151.53
1,319.55
417.69
460.01
269.93
286.97
226.15
Background
Sediment
Rate
(t/miA2)
40.16
88.81
88.86
48.47
36.24
30.16
20.04
30.06
26.85
47.09
28.53
16.84
28.03
25.07
18.82
22.62
27.08
16.73
Total
Background
Sediment
(t/WB/yr)
543.73
550.64
316.36
416.83
1,072.65
251.20
458.20
114.81
303.10
998.21
262.19
135.04
751.79
370.98
425.24
266.51
280.26
195.80
Routing
Coefficient
0.63
0.72
0.80
0.68
0.54
0.68
0.57
0.79
0.65
0.58
0.67
0.69
0.55
0.62
0.57
0.64
0.66
0.64
Routed
Human-
Caused
Sediment
(t/WB/yr)
0.00
0.09
0.06
0.00
317.96
3.47
10.40
3.87
6.63
0.01
0.01
11.34
314.08
28.76
19.83
2.19
4.40
19.50
L-20
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body
No.*
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
Area
(mi2)
4.2
16.1
25.1
11.1
4.9
4.4
10.0
7.4
11.1
30.1
5.2
3.7
3.9
7.1
12.2
9.1
11.3
9.8
WEPP
and State
Highway
(t/yr/WB)
148.00
NEZSED
(t/yr/WB)
147.47
375.79
680.29
261.49
111.80
107.84
185.86
135.89
215.15
744.99
115.14
89.97
81.15
160.17
266.48
216.56
281.16
235.13
RUSLE
(t/WB/yr)
Mass
Failures
(t/WB/yr)
49.14
In-stream
Erosion
(t/WB/yr)
210.34
12.00
62.26
2.93
15.49
Total
Sediment
(t/WB/yr)
295.47
424.93
890.63
273.49
111.80
107.84
185.86
135.89
215.15
807.25
115.14
89.97
81.15
163.10
281.96
216.56
281.16
235.13
Background
Sediment
Rate
(t/miA2)
25.90
17.41
20.06
17.34
17.93
18.88
17.06
17.10
17.56
19.74
18.11
21.49
20.78
19.89
17.74
21.19
17.38
22.95
Total
Background
Sediment
(t/WB/yr)
109.31
281.17
502.62
191.91
88.23
82.13
170.06
124.16
193.15
592.77
94.53
79.93
80.85
141.60
215.88
191.96
195.69
224.70
Routing
Coefficient
0.77
0.61
0.56
0.65
0.75
0.77
0.66
0.70
0.65
0.54
0.74
0.79
0.78
0.70
0.64
0.67
0.65
0.66
Routed
Human-
Caused
Sediment
(t/WB/yr)
143.71
87.13
217.28
52.92
17.69
19.73
10.43
8.18
14.27
116.23
15.30
7.93
0.23
15.10
42.15
16.54
55.27
6.92
L-21
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body
No.*
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
Area
(mi2)
17.9
23.9
3.6
7.9
13.8
3.3
2.6
1.7
6.5
6.0
2.3
5.8
1.8
8.6
9.9
5.0
4.3
6.1
WEPP
and State
Highway
(t/yr/WB)
NEZSED
(t/yr/WB)
413.33
621.65
128.09
190.05
416.10
86.48
62.36
38.92
188.94
143.43
44.24
122.06
51.81
190.11
223.54
134.79
118.57
163.02
RUSLE
(t/WB/yr)
Mass
Failures
(t/WB/yr)
28.19
In-stream
Erosion
(t/WB/yr)
38.86
123.59
24.53
62.61
3.94
36.04
Total
Sediment
(t/WB/yr)
413.33
688.70
251.68
214.58
478.70
90.41
62.36
38.92
224.97
143.43
44.24
122.06
51.81
190.11
223.54
134.79
118.57
163.02
Background
Sediment
Rate
(t/miA2)
18.44
23.54
28.96
18.15
24.45
20.70
20.54
19.56
24.24
19.57
16.47
19.18
24.15
17.69
21.13
23.20
25.21
25.87
Total
Background
Sediment
(t/WB/yr)
328.64
559.81
105.13
143.91
337.22
69.15
52.98
33.46
156.82
117.05
37.39
112.01
42.99
151.61
208.98
114.38
106.88
158.09
Routing
Coefficient
0.60
0.56
0.79
0.69
0.62
0.80
0.84
0.91
0.71
0.72
0.86
0.73
0.90
0.68
0.66
0.75
0.77
0.72
Routed
Human-
Caused
Sediment
(t/WB/yr)
50.39
72.81
116.20
48.67
88.23
17.11
7.90
4.96
48.69
19.11
5.90
7.32
7.95
26.14
9.63
15.30
9.01
3.56
L-22
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water
Body
No.*
72
73
74
75
76
77
78
79
80
81-NFS
81-FS
82-NFS
82-FS
Totals
Area
(mi2)
2.8
2.4
5.2
7.8
3.6
25.8
14.2
12.1
37.5
9.8
4.1
9.0
0.7
WEPP
and State
Highway
(t/yr/WB)
52.62
27.76
2,708.36
NEZSED
(t/yr/WB)
76.91
73.04
151.06
231.19
107.71
638.58
440.00
342.80
1,164.39
128.74
0.00
12.90
26,209.85
RUSLE
(t/WB/yr)
1,205.09
783.68
130,947.41
Mass
Failures
(t/WB/yr)
11.34
8.10
14.58
11.99
821.63
In-stream
Erosion
(t/WB/yr)
0.20
52.58
0.60
0.30
1,473.20
Total
Sediment
(t/WB/yr)
76.91
73.04
151.06
231.39
107.71
649.92
448.10
357.38
1,228.95
1,258.31
128.74
811.73
12.90
162,160.45
Background
Sediment
Rate
(t/miA2)
27.70
27.12
27.77
26.29
26.18
24.18
26.61
23.07
26.75
30.00
27.63
30.00
17.69
Total
Background
Sediment
(t/WB/yr)
76.72
65.90
143.29
205.04
95.30
623.03
377.84
278.69
1,003.16
294.30
113.56
269.70
12.03
33,377.65
Routing
Coefficient
0.83
0.85
0.74
0.69
0.79
0.56
0.62
0.64
0.52
0.66
0.66
0.67
0.66
Routed
Human-
Caused
Sediment
(t/WB/yr)
0.15
6.08
5.79
18.21
9.83
14.98
43.58
50.25
117.59
639.25
10.07
365.04
0.58
71,168.85
*FS = federally managed lands, NFS = not federally managed lands
L-23
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
__ Legend
^ _ ^ NPT Reservation Boundary
/\/ Major Streams
/\/ Other Streams
/\/ 3D3(d) Listed Streams
Routed Activity Sediment (t/WB/yr)
50-100
100-300
300 - 3500
* 3500
Routed Activity Sediment for the
South Fork Clearwater River Subbasin
in Tons per Water body per Year
Figure L-2. Annual Sediment Production by Water Body in the SF CWR
Subbasin
L-24
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Routed Activity Sediment for the
South Fork Clearwater River Subbasin
in Tons per Square Mile per Year
Legend
(^_J Water Body ID watersheds
NPT Reservation Boundary
/\/ 3D3(d) Listed Streams
/\/ Major Streams
/ \/ OtherStreams
Routed Activity Sediment (t/mi/v2)
O <3
3-5
5-50
50 - 200
October 2003
Figure L-3. Annual Sediment Production per Square Mile in the SF CWR
Subbasin
Generally, one can conclude from these data that human-caused sediment production is
highest in the part of the subbasin where agriculture and grazing dominate (i.e., in the
water bodies below Mill Creek. In the water bodies upstream from Mill Creek, the lands
along the main stem SF CWR are producing the highest levels of human-caused
sediment. Above that, the next level of sediment production comes from the Newsome
Creek, American River, and Red River drainages, and Mill, Cougar, Meadow, and
Peasley Creeks. These areas include all of the 303(d) listed water bodies, even though
the 303(d) listed water bodies themselves are not those producing the highest levels of
sediment.
L-25
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
References
Beechie, TJ. 2001. Empirical predictors of annual bed load travel distance, and
implications for salmonid habitat restoration and protection. Earth Surface
Processes and Landforms 26:1025-1034.
Boll, J., E. Brooks, and D. Traeumer. 2001. Hydrologic and sediment delivery analysis
of agriculturally dominated watersheds in the Clearwater River basin. Report
submitted by the Dept. of Biological and Agricultural Engineering, Univ. of
Idaho, Moscow, ID to the Idaho Soil Conservation Commission. 92 pp.
Boll, J. and E. Brooks. 2002. Sediment data collection and data management for the
South Fork Clearwater River subbasin assessment and TMDL (Contract #C109).
Report submitted to DEQ by the Dept. of Biological and Agricultural
Engineering, University of Idaho, Moscow, ID. 63 pp.
DEQ, NPT, and USEPA (Idaho Dept. of Environmental Quality, Nez Perce Tribe, and
U.S. Environmental Protection Agency). 2000. Cottonwood Creek Total
Maximum Daily Load (TMDL). Chapters 1-5 and Appendices A-J.
Elliot, W.J., R.B. Foltz, and C.H. Luce. 1995. Validation of the Water Erosion
Prediction Project (WEPP) model for low-volume forest roads. Proceedings of
the Sixth International Conference on Low-Volume Roads. Transportation
Research Board, Washington D.C. 178-186 pp.
Engel, B. 1999. Estimating soil erosion using RUSLE (Revised Universal Soil Loss
Equation) using Arc View. Purdue University. Unpublished. 8 pp.
Flanagan, D.C. and SJ Livingston. 1995. WEPP User Summary. NSERL Report No.
11, W. National Soil Erosion Research Laboratory, W. Lafayette, IN. 131 pp.
Gloss, DJ. 1995. Evaluation of the NEZSED sediment yield model using data from
forested watersheds in north-central Idaho. Masters Thesis, University of Idaho,
Moscow, ID. 78 pp.
McClelland D.W., R.B. Foltz, W.D. Wilson, T.W. Cundy, R. Heinemann, J.A.Saurbier,
and R.L. Schuster. 1997. Assessment of the 1995 & 1996 floods and landslides
on the Clearwater National Forest, part 1: landslide assessment. A report to the
Regional Forester, Northern Region, USFS, Missoula, MT. 52 pp.
McCool, O.K., C.D. Pannkuk, K.E. Saxton, P.K. Kalita. 2000. Winter runoff and
erosion on northwestern USA cropland. Internat'l J. of Sediment Res. 15(2): 149-
161.
L-26 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
NRCS (Natural Resources Conservation Service). 1983. Erosion and sediment yield. In:
Proceedings from the Channel Evaluation Workshop: Ventura, California,
November 14-18, 1983.
Renard, K.G., G.R. Foster, G.A. Weesies, O.K. McCool, and D.C. Yoder. 1997.
Predicting soil erosion by water: A guide to conservation planning with the
revised universal soil loss equation (RUSLE). U.S. Dept. of Agriculture,
Agriculture Handbook No. 703. 404 pp.
Roehl, J.W. 1962. Sediment source areas, delivery ratios, and influencing morphological
factors. International. Association of Scientific Hydrology, Commission of Land
Erosion, Publ. 59, pp 202-213.
USFS (USDA Forest Service). 1981. Guide for predicting sediment yields from forested
watersheds. Northern and Intermountain Regions. Missoula, MT. 40 pp + app.
USFS (USDA Forest Service). 1998. South Fork Clearwater River landscape
assessment. Volume 1 -Narrative. NezPerceNational Forest, Grangeville, ID.
210pp.
L-27 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Attachment L-1: South Fork Clearwater River Subbasin TMDL Stream Bank
Erosion Inventory Method
This narrative is intended to document the methodology used to quantify bank erosion in
the South Fork Clearwater River (SF CWR) Subbasin. Stream banks were inventoried to
quantify bank erosion rates and average annual erosion rates per unit length of stream.
These data were used to develop a quantitative sediment budget for the sediment total
maximum daily loads.
This inventory followed methods outlined in proceedings from a Natural Resource
Conservation Service (NRCS) Channel Evaluation Workshop (1983). Using the direct
volume method, sample reaches of selected watersheds within the SF CWR Subbasin
were surveyed to determine the magnitude of chronic bank erosion.
Site Selection
Stream reaches with significant eroding bank problems were identified through
information from the Nez Perce National Forest (NPNF), U.S. Bureau of Land
Management, Idaho County Soil and Water Conservation District, Department of
Environmental Quality, Nez Perce Tribe, and other sources. In general, stream reaches
identified as having problems tended to be response reaches, Rosgen B and C channel
types, with unconsolidated stream bank material. We concluded that, given limited
resources and the fact that we were only interested in stream reaches contributing
significant amounts of sediment in relation to the whole subbasin, there would be very
little value in measuring bank erosion in A type channels. Therefore, we limited our
survey to low gradient reaches with known or expected significant bank erosion
problems.
Low gradient streams with known bank erosion problems or having characteristics
indicating problems were identified using topographic maps, geology maps, NPNF
aquatic landtype maps, and aerial photos. The identified reaches were divided into
"uniform reaches" for sampling based on available data. Normally a uniform reach was
less than 2 miles long. Within each uniform reach, a sample reach of at least 10-20% of
the total length of the uniform reach was selected by the field crew. Exact sample
reaches were often selected based on access and permission by land owners, although the
field crew made every effort to ensure that the sample reach would be representative of
the overall uniform reach. Data collected for the sample reach were assumed to be
representative of the total uniform reach. In some cases, fieldwork revealed that the
uniform reaches were not in fact uniform, and subdivisions were made during the
sampling process. Lumping of uniform reaches after initial layout was not allowed.
Field Methods
The NRCS (1983) document outlines field methods used in this inventory. However,
some modifications to the field methods were made and are documented here. In
L-28 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
addition, we added data types to be collected that could be used to model flow and stream
temperature characteristics, as seen on the field forms attached below.
For each sample reach, two levels of data were collected. A set of data was collected for
the sample reach in general (see the Sample Reach Summary Form at the end of this
document). The whole sample reach, and therefore, the whole uniform reach it
represented, is considered to have the characteristics recorded on the Sample Reach
Summary Form. Most of the data on this form were collected for other characterization
and modeling purposes. The critical measure, recession rate, was determined for the
whole sample reach, rather than at each eroding bank.
The field crew was trained by the NRCS in the use of the methodology. Within the
sample reach, the field crews surveyed both right and left banks for eroding length and
non-eroding length. Within a given sample reach, 100% of both banks were surveyed
and documented on the field forms. One crew member walked along each bank,
measuring the parameters identified on the Stream Erosion Inventory Worksheet. A new
worksheet was started for every new eroding bank encountered. A particular worksheet
shows the intervening length between the previous eroding bank and the length of the
current eroding bank where measurements were taken. One worksheet was completed
for every length of eroding bank, such that for a given sample reach, several (sometimes
numerous) worksheets were completed. As noted above, the length of each sample reach
was 10-20% of length of the uniform reach identified in the office. The worksheet asks
for "Bank Material Classes," so that eroding banks with significantly different particle
size classes over the height of the eroding bank would be recorded separately.
The average annual lateral recession rate is the thickness of soil eroded from a bank
surface (perpendicular to the face) in an average year. Recession rates are measured in
feet per year. Channel erosion often occurs as "chunk" or "blowout" type erosion. A
channel bank may not erode for a period of years when no major runoff events occur.
When a major storm does occur, the bank may be cut back tens of feet for short distances.
It is necessary to assign recession rates to banks with such processes in mind. When a
bank is observed after a flood and ten feet of bank have been eroded, that ten feet must be
averaged with the years when no erosion occurred. This will result in a much lower
average annual lateral recession rate than a recession rate for one storm. We had the
good fortune of surveying the Red River Watershed Management Area where recession
rates have been recorded for years so the field crew was able to calibrate its estimates of
recession rates against real data. The field crew estimated average annual recession rates
by considering evidence of what had happened in the stream over the last 10 years and
projecting what might happen in the stream over the next 10 years based on data and
statistics of long term flows and extreme events.
The recession rate is critical to completing the calculations, but in some cases it is simply
impossible to assess in the field. The indicators used to determine recession rate simply
are not present in some cases. The field crew made the determination whether a
reasonable estimate of the recession rate could be made in the field. Otherwise, the
L-29 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
recession rate was calculated in the office using the correlation methods developed by
NRCS and discussed below.
Bank Erosion Calculations
The direct volume method is a procedure which uses on-the-ground measurement of
eroding bank surface area, coupled with estimates of recession rate and eroding bank
particle size to calculate the total tons of eroding material over a given length of stream.
The direct volume method is summarized in the following equation:
{eroding area)(lateral recession rate)(density}
2000lbs/ton
E = erosion rate in tons/year
The eroding area is in square feet, the lateral recession rate is in feet per year, and density
is in pounds per cubic foot of the identified particle size distribution. The total erosion
rate for the sample reach is extrapolated to the uniform reach it represents, and erosion
rates for all the uniform reaches are summed to develop a total erosion rate for the water
body or watershed of interest. Because we selected all the reaches in the subbasin that
we had reason to believe were contributing significant sediment through stream bank
erosion, we did not attempt to extrapolate our results to the complete stream network in a
water body or watershed. We assume that our set of "uniform reaches" is the complete
set of reaches that are contributing significant sediment to the sediment budget of the
subbasin.
The eroding area is the product of the length of the eroding bank and the eroding bank
height. Eroding bank length and bank height were measured while walking along the
stream channel. The eroding areas for all the eroding banks within a sample reach were
summed and multiplied by the lateral recession rate for the sample reach to get the total
volume of eroding bank material.
As noted above in the field procedures, it is not always possible to determine the lateral
recession rate in the field. The NRCS method uses the correlation between the "total" of
"Rated Factors" one through five (see field sheet below) and lateral recession rates from
field assessments to develop a relationship for predicting the recession rate when it
cannot be determined in the field. We followed this procedure to estimate lateral
recession rates for the approximately 10% of sample reaches where recession rates could
not be estimated in the field.
Total bank erosion is expressed as an annual average. However, the frequency and
magnitude of bank erosion events are a function of stream discharge. Because channel
erosion events typically result from above average flow event, the annual average bank
erosion value should be considered a long term average.
L-30 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
The following conversion rates were used to convert eroded bank material volume to
eroded bank material weight in pounds. When eroding banks had significant differences
in texture from top to bottom and the field crew recorded such, the texture volume-
weights were calculated separately and summed.
Soil Texture
Volume-Weight
(pounds/cubic foot)
Clay
Silt
Sand
Gravel
Loam
Sandy loam
Gravelly loam
Very gravelly sands/loams
Cobbles, boulders, etc.
60-70
75-90
90-110
110-120
80-100
90-110
110-120
120-130
120-130
The question arises in using these data for construction of a sediment budget as to how
much of the eroded bank sediment is actually transported through the system and how
much is simply re-deposited in bars and flood plains further down the channel but still
within the same water body. The degree to which eroded sediment is flushed through a
system is dependent on the flow event causing the erosion, as well as channel
characteristics. For the purposes of calculating the sediment budget, we used the same
routing coefficient (Roehl 1962) for the in-stream erosion data as we used for all the
other sediment source data.
Even then, we realized that the methods being applied resulted in huge estimates of
sediment production from stream banks dominated by cobbles, such as those in
Threemile, Butcher, and lower Newsome Creeks. While it is clear that the recession rates
for these low gradient, cobble-dominated streams is high, as these streams meander
around under high flow events, it is also clear that our estimates of sediment delivery
from one water body to the next using the Roehl (1962) equation was far too high for
cobble-dominated bank systems. Only some small proportion of cobble-sized material
eroded from banks of meandering streams is actually delivered to the adjacent water body
over the 10 to 20 year time frame of this analysis.
For cobble-dominated streams, we applied the concepts discussed in Beechie (2001) and
recognized that only eroded material from reaches near the mouth of a given water body
would likely be delivered to the adjacent downstream water body. Beechie (2001) shows
L-31
Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
that annual travel distance for coarse in-stream material is on the order of twenty times
the bankfull width of a stream. Since we had collected bankfull width for each uniform
reach as part of the data set, we calculated an annual travel distance for each uniform
reach having a significant cobble component, and only delivered cobble from those
uniform reaches that were within the travel distance from the mouth. Finer in-stream
erosion materials were delivered using the Roehl (1962) equation.
L-32 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
STREAM EROSION CONDITION INVENTORY WORKSHEET
Stream Name Reach Number
Left or Right Bank (circle)
Average Bank Height Sample Length
Non-Eroding Length Bank Material Classes (see reverse side)_
RATED FACTORS RATING
1. BANK EROSION EVIDENCE
Does not appear to be eroding. 0
Erosion evident 1
Surface of bank eroding and top of bank has cracking present 2
Slumps and clumps sloughing off into stream (SIZE) 3
2. BANK STABILITY CONDITION (Ability to withstand erosion from streamflows)
Very little unprotected bank, no undercut vegetation, AND/OR bank materials non-erosive 0
Predominantly bare and unprotected, some rills, moderate undercut vegetation 1
Almost completely bare, unprotected bank, rills, severely undercut vegetation, exposed roots 2
Bare, numerous rills/gullies, very severely undercut vegetation, falling trees and/or fences 3
3. BANK COVER/VEGETATION
Predominantly covered with perennials AND/OR stable rodi/bedrock 0
40% or less bare/erodible, AND/OR cover is annual and perennials mixed 1
40% to 70% bare/erodible, AND/OR cover is mostly annual vegetation 2
Predominantly bare and erodible/no cover 3
4. LATERAL CHANNEL STABILITY
No evidence of significant lateral movement of channel 0
Active lateral movement of channel 1
5. CHANNEL BOTTOM STABILITY
Channel in bedrock OR not eroding (Stable) 0
Minor channel bed degradation/downcutting 1
Significant evidence of downcutting, active headcuts 2
6. IN-CHANNEL DEPOSITION
No evidence of recent deposition (includes all sizes of bedload type materials) 0
Mobile material in recent deposition, deposits will probably move down channel in next high flow.. 1
Deposition is stable AND/OR vegetated (more than this growing season) channel is aggrading. -1
TOTAL
Factors contributing to erosion (concentrated flows, animal access-trampling, grazing impacts to
vegetation, fire return flows, roads, bridges, culverts)
Other notes
(Over)
L-33 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Bank Material Classes
(Circle best Choice/s)
Soil Classes
<15% coarse fragments, just use the fine soil class
(15-35%) Gravelly (gr), Cobbley (co), Bouldery (b)
(35-60%) Very gravelly (vgr), very cobbley (vco), very bouldery (vb)
(>60%) Extremely gravelly (exgr) extremely cobbley (exco), extremely bouldery (exbo)
sand - sa
sandy loam - sal
loamy sand - Isa
clayey sand - csa
silt - si
loamy silt - Isi
silt loam - sil
clayey silt - csi
loam -1
clay - c
loamy clay - Ic
sandy clay - sac
silty clay - sic
Notes
L-34 Appendix L
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
SAMPLE REACH SUMMARY FORM
Stream Name
Reach Number
Hydrological Unit
GPS Coordinate: Start_
End.
WBID
Rosgen Channel Type
Slope/Gradient
Bank Full Width
Bank Full Depth
Floodplain Width
Average Wetted Width (ft.)
Average Wetted Depth (ft.)
Average Surface Velocity (ft/sec)_
Sinuosity
Dominant Particle Size_
Adjacent Land Use
Canopy Shade Height (ft.)
Canopy Shade Crown Width (ft.)
Canopy Offset (from waters edge) (ft.)
Canopy Density
Topographic Altitude: Rt. & Lft.
Mannings "n"
Recession Rate (Field Estimate),
Field Crew
Canopy Density Examples
Open Pine 65%
Closed Pine 75% X % Covered
Tight Spruce/Fir 85%
Dense Emergent Vegetation 90%
Bed Particle Size
Clay .001
Silt .004 to .06 .03 median
Sand .06 (Fine) to 2mm
Gravel 4mm (Pea Size) to 64mm (tennis Ball size)
Cobble > 64mm to 250mm (Volleyball size)
Boulder > 250mm
Bedrock
L-35 Appendix L
-------
Appendix M. Total Suspended Solids and Bedload Data
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
List of Tables M-i
List of Figures M-ii
Total Suspended Solids and Bedload Data M-1
List of Tables
Table M-1. Threemile Creek turbidity and total suspended solids (TSS) data... 2
Table M-2. Butcher Creek turbidity and total suspended solids (TSS) data 4
Table M-3. Stites bridge turbidity and total suspended solids (TSS) data 6
Table M-4. Stites bridge bedload data 6
Table M-5. Harpster total suspended solids (TSS) data 8
Table M-6. Harpster bedload data 10
M- i Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
List of Figures
Figure M-1. Threemile Creek Sediment Yield Curves 3
Figure M-2. Butcher Creek Sediment Yield Curves 5
Figure M-3. Stites Bridge Sediment Yield Curves 8
Figure M-4. Harpster Sediment Yield Curves 12
Figure M-5. Excess Sediment Loading for Threemile Creek for the Ten-Year
Analysis Period and Two Critical Years in More Detail 14
Figure M-6. Excess Sediment Loading for Butcher Creek for the Ten-Year
Analysis Period and Two Critical Years in More Detail 15
Figure M-7. Excess Sediment Loading at Stites for the Ten-Year Analysis
Period and Two Critical Years in More Detail 16
M- ii Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Appendix M. Total Suspended Solids and Bedload Data
The sediment loading analyses and target development are driven by the turbidity standard
which says that waters shall not exceed 25 NTU over background for greater than 10 days
and shall not exceed 50 NTU over background at any time. The turbidity measurements used
in the calculations are instantaneous samples. Similarly, the extreme flows which generate
the greatest amount of sediment are in effect instantaneous, or at least do not last for 10 days.
To transform the instantaneous turbidity data to produce continuous sediment loading
numbers, a stochastic flow model of daily average flow for 10 years is developed. The
resulting continuous flow/turbidity/TSS model results are then compared to the 25 NTU over
background criterion to develop daily loading, daily load capacity, daily natural background
loading, and daily excess sediment loading. These results are then annualized to produce the
loading figures presented in this report. Doing all the calculations on a daily, essentially
continuous basis, using the 25 NTU criterion automatically includes all times when the 50
NTU criterion is exceeded. Subsequent discussions of the loading calculations refer to the 25
NTU criterion. It is to be understood that the methods used for the calculations automatically
include the times when the 50 NTU criterion applies.
The total suspended solids (TSS) and bedload data reported herein are the results of several
different efforts on the part of the Department of Environmental Quality (DEQ), the Nez
Perce Tribe (NPT), and the U.S. Environmental Protection Agency (USEPA). The USEPA
provided funding for some of these efforts. DEQ collected instantaneous flow, TSS, and
turbidity data for Threemile Creek as part of its detailed monitoring of that water body. The
NPT collected instantaneous flow, TSS, turbidity, and bedload data for Butcher Creek as part
of its monitoring of that water body. DEQ contracted with Western Watershed Analysts of
Lewiston, Idaho, to provide flow and bedload data for the main stem South Fork Clearwater
River (SF CWR) and Threemile Creek.
Unfortunately, flows in Threemile Creek and Butcher Creek over the sample period were
below the level where significant bedload moved or could be sampled. Therefore, bedload
for these streams was estimated from the sediment budget. Similarly, for the year when the
contractor was to sample bedload in the upper main stem SF CWR, flows did not allow the
bedload to be sampled. The result is that sampled bedload data exist only for the Stites and
Harpster sites.
Other TSS and turbidity data exist for the SF CWR subbasin, but come from such diverse
locations and time periods as to make them difficult to use for a subbasin wide analysis.
DEQ collected turbidity and flow for a number of streams in the SF CWR subbasin (Thomas
1991) and these data provide a comparison for the results of our calculations. The Nez Perce
National Forest (NPNF) collected TSS, turbidity and flow data at the Mt. Idaho bridge from
1988-1992, analyzed these data, and extrapolated them using the data from Thomas (1991).
These results were also used to help validate the results from the 1991-2001 stochastic flow
data used in the sediment loading calculations in Chapter 5.
Sediment yield curves were developed from the TSS and bedload data. The data and
sediment yield curves for the Threemile, Butcher, Stites, and Harpster sites are presented in
M- 1 Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
the tables and figures on the following pages (Tables M-l through M-6 and Figures M-l
through M-4).
Table M-1. Threemile Creek turbidity and total suspended solids (TSS) data.
Date
03/08/2001
03/09/2001
03/10/2001
03/13/2001
02/22/2000
03/07/2000
03/21/2000
04/04/2000
04/18/2000
05/02/2000
05/16/2000
05/30/2000
06/13/2000
06/27/2000
07/11/2000
07/25/2000
08/08/2000
08/22/2000
09/05/2000
09/19/2000
10/03/2000
11/16/2000
12/11/2000
01/17/2001
Discharge
(cfs)*
48
163
73
43
10
9
8
8
7
7
17
10
9
3
2
1
1
2
2
2
4
3
3
4
TSS (mg/L)**
55
153
80
43
56
1
1
1
8
5
5
5
8
1
3
3
5
2
2
1
2
3
1
1
TSS (tons/day)
7.089
67.335
15.727
5.004
1.501
0.025
0.021
0.021
0.152
0.094
0.231
0.136
0.200
0.007
0.018
0.007
0.011
0.008
0.012
0.004
0.021
0.023
0.007
0.011
Turbidity
(NTU)***
107
175
142
82
9
12
10
14
10
8
22
11
13
4
1
3
2
2
4
2
5
nd
nd
nd
* cubic feet per second
** milligrams per liter
*** nephlometric turbidity units
M-2
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Suspended Sediment (mg/L)
Threemile Creek
180
160
140
120
100
80
60
40
/*
/^
^
s' y = 0.9779X
" */^ R2 = 0.9101
^
20 IS.
U i i i i
0 50 100 150 200
Discharge (cfs)
3
^
>,
+j
TJ
!Q
^
3
1-
Threemile Creek
250
200
150
100
50
« j
^
^s^ m
m "
• ^^ y = 1.3182x
B ^S^ R2 = 0.8769
^
U i- i i i
0 50 100 150 200
Discharge (cfs)
Suspended Sediment (mg/L)
Threemile Creek
180
160
140
120
100
80
60
m
^^'
^^
^^^ V = 0.674x
" ^^ " R2 = 0.8225
^^ •
40 ^^~
M L<
u ^-^— — i i
0 50 100 150 200
Turbidity (NTU)
Figure M-1. Threemile Creek Sediment Yield Curves
M-
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table M-2. Butcher Creek turbidity and total suspended solids (TSS) data.
Date
01/07/02
01/16/02
02/27/02
03/27/02
04/30/02
05/01/02
10/31/02
11/26/02
12/12/02
12/19/02
Discharge
(cfs)*
6.1
1.3
12.6
1.6
14.3
25.1
0.8
0.7
0.8
1.0
TSS (mg/L)**
45.3
0.6
16.7
11.5
29.0
75.8
8.1
12.7
8.8
3.3
TSS (tons/day)
0.745
0.002
0.568
0.049
1.120
5.137
0.017
0.024
0.018
0.009
Turbidity
(NTU)***
31.0
4.1
39.0
12.8
43.2
64.4
2.9
1.5
3.2
3.00
* cubic feet per second
** milligrams per liter
*** nephlometric turbidity units
M-4
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Butcher Creek '01
80
1 70
.1 60
lir 50
•a 1 40
1 ~ 30
I 20
£ 10
o
y = 2.381x + 5.8901
R2 = 0.726
10 15 20
Discharge (cfs)
25
30
Butcher Creek '01
80
70
S 60
S, 50
£" 40
5 30
,= 20
10
0
y = 2.6118x + 3.7317
R2 = 0.9467
10 15 20
Discharge (cfs)
25
30
Butcher Creek '01
d 80
I! 70
¥ 60
50
40
30
20
10
fc
CO
•D
y = 0.9056X + 2.6113
R2 = 0.7567
10 20 30 40
Turbidity (NTU)
50
60
70
Figure M-2. Butcher Creek Sediment Yield Curves
M-5
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table M-3. Stites bridge turbidity and total suspended solids (TSS) data.
Date
03/27/2001
04/26/2001
05/01/2001
05/02/2001
05/05/2001
05/14/2001
05/15/2001
05/18/2001
05/21/2001
05/24/2001
Discharge
(cfs)*
1,680
2,960
4,330
3,500
2,710
3,250
4,040
2,920
2,080
2,180
TSS (mg/L)**
18.4
54.7
73.1
70.6
25.6
24.6
46.2
10.4
10.2
9.5
TSS (tons/day)
83
437
855
667
187
216
504
82
57
56
Turbidity
(NTU)***
17.1
19.4
53.4
22.9
6.9
5.5
19.3
5.7
3.9
3.3
* cubic feet per second
** milligrams per liter
*** nephlometric turbidity units
Table M-4. Stites bridge bedload data.
Date*
03/27/2001
03/27/2001
04/26/2001
04/26/2001
05/14/2001
05/14/2001
05/15/2001
05/15/2001
05/18/2001
05/18/2001
05/21/2001
05/24/2001
05/24/2001
Discharge
(cfs)**
1,570
1,550
2,970
2,950
3,330
3,300
4,020
3,980
2,950
2,950
2,060
2,140
2,140
Bedload
(grams)
24.79
53.66
132.22
146.23
253.85
237.67
261.29
740.51
206.07
157.74
24.91
62.48
89.20
Bedload
(tons/day)
1.4
2.9
14.0
15.5
25.0
23.4
27.2
77.0
10.1
7.7
1.2
3.1
4.4
TSS***
(tons/day)
83
83
437
437
216
216
504
504
82
82
57
56
56
Total
Sediment
(tons/day)
84
86
451
452
241
239
531
581
92
90
58
59
60
* duplicate dates indicate two samples from same site on the same day
** cubic feet per second
*** total suspended solids
M-6
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
SF Clearwater
°n
_i yn
D)
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Bed load (T/day)
SF Clearwater at Stites
30 00 -
•
y=3E-12x3-6237
Rz = 0.8401
/
• / '
j^^
v— — f*-~"*"^ "
0 500 1000 1500 2000 2500 3000 3500 4000 4500
Discharge (cfs)
Figure M-3. Stites Bridge Sediment Yield Curves
Table M-5. Harpster total suspended solids (TSS) data.
Date
03/26/01
04/27/01
05/01/01
05/02/01
05/05/01
05/13/01
05/15/01
05/18/01
05/21/01
05/24/01
03/21/88
03/31/88
04/05/88
04/11/88
04/19/88
04/25/88
05/03/88
05/09/88
05/16/88
Discharge
(cfs)*
1,450
2,710
3,250
2,560
2,010
2,350
2,890
2,150
1,580
1,650
498
615
1,010
1,190
4,030
2,740
2,030
2,750
3,140
TSS
(mg/L)**
43.6
51.8
27.8
16.9
11.0
14.2
23.4
10.9
6.8
10.7
9.1
10.7
13.5
24.0
84.0
15.0
6.7
10.8
11.5
TSS
(tons/day)
171
379
244
117
60
90
183
63
29
48
12
18
37
77
914
111
37
80
97
Turbidity
(NTU)***
22
22
11
8
5
5
7
3
2
3
7
8
12
11
13
8
6
10
5
M-8
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Date
05/31/88
06/06/88
06/27/88
03/15/89
03/28/89
04/11/89
04/25/89
05/08/89
05/16/89
05/22/89
06/07/89
06/16/89
07/05/89
04/11/90
04/18/90
04/25/90
05/10/90
05/16/90
05/24/90
06/01/90
06/06/90
06/13/90
07/01/90
07/26/90
04/05/91
04/12/91
04/19/91
05/03/91
05/09/91
05/17/91
05/23/91
05/31/91
06/10/91
06/14/91
Discharge
(cfs)*
2,430
2,456
1,300
1,057
1,610
1,830
3,410
4,810
2,410
2,090
2,410
3,120
722
1,420
1,990
1,830
4,410
2,410
2,190
4,000
2,510
2,160
779
583
1,470
1,240
1,090
1,230
3,620
2,740
3,230
2,850
2,220
1,990
TSS
(mg/L)**
13.0
3.4
3.6
8.5
12.1
10.6
19.3
31.0
15.7
12.6
14.5
39.3
2.6
2.8
15.3
7.9
2.9
9.3
39.0
12.0
24.0
7.0
2.7
13.0
27.0
4.9
6.5
4.1
88.0
13.0
14.0
12.0
7.3
8.3
TSS
(tons/day)
85
23
13
24
53
52
178
403
102
71
94
331
5
11
82
39
35
61
231
130
163
41
6
20
107
16
19
14
860
96
122
92
44
45
Turbidity
(NTU)***
10
4
5
8
10
9
6
9
2
8
3
8
2
3.6
4
3
4
5
nd
nd
nd
nd
nd
nd
10
8
6
5
20
6
7
7
4
2
M-9
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Date
06/19/91
07/02/91
03/17/92
04/10/92
04/24/92
04/30/92
05/29/92
07/09/92
Discharge
(cfs)*
1,630
1,780
1,010
1,230
1,090
1,490
729
799
TSS
(mg/L)**
70.0
6.1
14.2
3.7
5.7
19.6
8.7
34.9
TSS
(tons/day)
308
29
39
12
17
79
17
75
Turbidity
(NTU)***
6
4
10
16
4
7
3
18
* cubic feet per second
** milligrams per liter
*** nephlometric turbidity units
Table M-6. Harpster bedload data.
Date
03/26/01
03/26/01
05/05/01
05/05/01
05/13/01
05/13/01
05/15/01
05/15/01
05/18/01
05/18/01
05/21/01
05/21/01
05/24/01
05/24/01
Discharge
(cfs)*
1,450
1,450
2,010
2,010
2,350
2,350
2,890
2,890
2,150
2,150
1,580
1,580
1,650
1,650
Bedload
(grams)
60
73
185
211
339
207
347
356
118
119
59
71
67
60
Bedload
(tons/day)
2.8
3.4
4.3
5.0
15.9
9.7
16.3
16.8
5.5
5.6
2.8
3.4
3.2
2.9
TSS
(tons/day)
171
171
60
60
90
90
183
183
63
63
29
29
48
48
Total Sediment
(tons/day)
174
174
64
65
106
100
199
200
69
69
32
32
51
51
* cubic feet per second
** total suspended solids
M-10
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
SF CWR near Harpster
100
90
*•' on
C 80
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Bedload Sediment (t/day)
SF CWR near Harpster
1b
14 -
12
8
6 -
4
2 -
_ I
/
/
/ y = 6E-09x2 713
^S R2 = 0.8711
^'
Vtf
U i i i i i
0 500 1000 1500 2000 2500 3000 3500
Discharge (cfs)
Figure M-4. Harpster Sediment Yield Curves
The TSS and bedload yield curves were coupled with daily flow data in the spreadsheet to
predict TSS loads and bedloads on a daily basis. At this point, the estimates of daily flow
were coupled with the sediment yield curves to produce estimates of average daily TSS
sediment load in milligrams per liter (mg/L), which were then converted to tons of sediment
per day and tons of sediment per year. Average daily nephlometric turbidity unit
(NTU) values were calculated from a similarly developed relationship. The NTU to TSS
relationships for the four locations are presented in Figures M-l through M-4 as well.
The TSS sediment load capacity and excess load capacity were then calculated based on the
Idaho water quality standard (WQS) of "turbidity ... shall not exceed background turbidity
by more than fifty NTU instantaneously or more than twenty-five NTU for more than ten
consecutive days" (TDAPA 58.01.02.250.02.d). Plots of the sediment loadings at the
Threemile, Butcher, and Stites sites show that turbidity is elevated for periods considerably
greater than 10 days. Loading calculations are based, therefore, on the 25 NTU above
background WQS. Assuming that as sediment loading reductions are accomplished,
selection of this standard with which to make the calculations results in a large margin of
safety for loading reductions as turbidity begins to be reduced to less than 10 consecutive
days of exceedances.
Background sediment loading was developed from the sediment budget (Appendix L). The
background ratio for each watershed was calculated using an assumed background erosion
rate, multiplied by the routing coefficient, and divided by the total tons of sediment routed
from a watershed. Background erosion rates have been developed for all federally managed
watersheds and range from 16 to 90 tons per square mile per year. After reviewing the range
of background figures from the federally-managed lands, background figures used in other
total maximum daily load reports (TMDLs), erosion studies at Washington State University,
predictions by the RUSLE model, and best professional judgement, a background erosion
rate of 30 tons per square mile per year was assigned for the non-federal lands. The routing
coefficient was that used by the NPNF to route sediment using the NEZSED model (Roehl
M-12
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
1962), and which has been used throughout the sediment budget calculations. The
background ratio developed from the sediment budget for each of the four sites is presented
in the loading calculations in Chapter 5.
Using the background ratio, the amount of daily load that is attributed to background was
calculated by multiplying the daily load by the background ratio. Note that this results in
different background loads depending on flow, as would be expected naturally, as higher
flows naturally result in greater movement of sediment.
The load capacity was calculated by the relationship between turbidity in NTU to the TSS in
milligrams per liter, resulting in a relationship then used to calculate the amount of TSS in
milligrams per liter that the 25 NTU from the state WQS represent. For example, in
Threemile Creek, 25 NTU are equivalent to 17 mg/L TSS. For each day then, the load
capacity is the 17 mg/L plus the percentage of the load that is background. Since the
background load varies with flow, the load capacity varies with flow as well.
Excess loading occurs when current loading is greater than the load capacity. Excess loading
on a daily basis is the current load minus the load capacity. The excess load addressed by the
TMDL for Threemile and Butcher Creeks and the Stites site on the SF CWR is shown in the
following set of paired figures (Figures M-5 through M-7). The first figure for Threemile
Creek shows the distribution and magnitude of excess loads over the 10 years of calculations,
and the subsequent figure for Threemile Creek shows more detail of only two years of those
same data. The point of the figures is to show that excess loading only occurs over short
time frames, the same time frames as high flows, and that the episodes of excess loading are
limited to January through May each year.
The excess load is summed over the 10 years of data, then divided by 10. The result is the
amount of excess loading on a yearly basis. When divided by the average annual TSS yield
per year, this results in the percent reduction needed in TSS sediment for a given water body.
The summaries of these calculations are presented in Tables M-8 through M-l 1. These
calculations indicate that significant load reductions in TSS are needed for Threemile Creek,
Butcher Creek, and for the main stem SF CWR at Stites. The TSS-based sediment TMDLs
for these water bodies are presented in Chapter 5.
The excess load calculations and resulting sediment reduction targets have a large margin of
safety built in them based on the use of the 25 NTU over background over 10 days WQS vs.
the 50 NTU over background instantaneous standard. As water bodies come closer into
being in compliance with the turbidity standards, the periods of exceedance will become less
than 10 days, and the 50 NTU over background standard will be in effect. For example, in
only one event in the last 10 years has the Stites location exceeded the 25 NTU over
background for greater than 10 days. So, one can conclude that the Stites location is close to
the threshold where the 50 NTU over background standard should be in effect. Using the 50
NTU over background standard in the same calculations as above, excess load at Stites is
only 3,578 tons per year, compared to 9,356 tons per year using the 25 NTU standard, and
the percent load reduction required would be 9% compared to 25%. Similar calculations
could be done for Threemile Creek and Butcher Creek. However, the point is that use of the
M-l3 Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
25 NTU over background as the basis for the loading calculations provides a very large
margin of safety in the loading calculations. The use of the 25 NTU in the loading
calculations is justified because that is the standard that should be applied for the current
situation, but as compliance with the TMDL is accomplished, the 50 NTU over background
standard likely will be the appropriate standard at that point.
Threemile Excess Load
_ 400
O)
_c
co
O
in
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Butcher Excess Load
i°n
1 nn
>
TO
5 on
•a
co
Ofin
t/>
« An.
O
X
m 20
X
J ,J .1
L
, i .. iL , LI
X /" /• X X / ./ «/ /"
Butcher Excess Load for Two Years
1 °n
--» 1 nn
>1UU
(Q
^
to an
•a
CQ
ORn
t/>
*" /in
s
X
LJJ on
N^
N\N
^ ^ A . . .u
VxUU
,A
\<£ ^ N.43 & & & &
^ A\* N^ N\NX ^X ^ N^
Figure M-6. Excess Sediment Loading for Butcher Creek for the Ten-Year
Analysis Period and Two Critical Years in More Detail
M-15
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Stites Excess Load
4000
ra 2500
-1 2000
a 1500
£ 1000
Stites Excess Load for Two Years
2000
1000
It I i
Figure M-7. Excess Sediment Loading at Stites for the Ten-Year Analysis
Period and Two Critical Years in More Detail
M-16
Appendix M
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
References
IDAPA 58.01.02. Idaho water quality standards and wastewater treatment requirements.
Roehl, J.W. 1962. Sediment source areas, delivery ratios, and influencing morphological
factors. Int'l. Assoc. Scientific Hydrology, Commission of Land Erosion, Publ. 59,
pp 202-213.
Thomas, D.B. 1991. South Fork Clearwater River turbidity, Idaho County, Idaho, 1988.
Water Quality Status Report no. 96. Idaho Dept. of Health and Welfare, Division of
Environment, Boise, ID. 14 pp + app.
M-17 Appendix M
-------
Appendix N. Reference Watersheds
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
List of Tables N-i
List of Figures N-i
Reference Watersheds N-1
Reference Comparisons for the SF CWR Tributaries N-1
Reference Comparisons of the Main Stem SF CWR N-10
List of Tables
Table N-1. Stream habitat data for Upper Meadow and Bargamin Creek
watersheds and various streams in the SF CWR subbasin N-6
Table N-2. Cobble embeddedness data for the SF CWR N-7
List of Figures
Figure N-1. Locations of Stream Habitat Reference Data for Upper Meadow
Creek, Bargamin Creek, and Various Stream Reaches in the SF CWR
Subbasin N-1
Figure N-2. Comparison of Stream Habitat Data from the SF CWR Subbasin
to Similar Data from Upper Meadow and Bargamin Creeks N-2
Figure N-3. Comparison of Third and Fourth Order Stream Habitat Data
from the SF CWR Subbasin to Similar Data from Upper Meadow and
Bargamin Creeks N-3
Figure N-4. Comparison of First and Second Order Stream Habitat Data
from the SF CWR Subbasin to Similar Data from Upper Meadow and
Bargamin Creeks N-3
Figure N-5. Comparison of Third and Fourth Order Stream Habitat Data
from Newsome Creek to Similar Data from Upper Meadow and Bargamin
Creeks N-4
N- i Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Figure N-6. Comparison of First and Second Order Stream Habitat Data
from Newsome Creek to Similar Data from Upper Meadow and Bargamin
Creeks N-4
Figure N-7. Comparison of Average Bankfull Width of the SF CWR, Lower
Meadow Creek, and the Imnaha River N-10
Figure N-8. Comparison of Average Slopes of the SF CWR, Lower Meadow
Creek, and the Imnaha River N-11
Figure N-9. Comparison of Cobble Embeddedness of the SF CWR and
Lower Meadow Creek N-11
Figure N-10. Residual Pool Volume Comparisons of the SF CWR, Lower
Meadow Creek, and the Imnaha River N-12
Figure N-11. Comparison of Pool Widths of the SF CWR and the Imnaha
River N-12
Figure N-12. Comparison of Pool Lengths of the SF CWR and the Imnaha
River N-13
Figure N-13. Comparison of Bankfull Depths of the SF CWR, Lower
Meadow Creek, and the Imnaha River N-13
Figure N-14. Comparison of Bankfull Widths of the SF CWR, Lower
Meadow Creek, and the Imnaha River N-14
Figure N-15. Comparison of Width-to-Depth Ratios of the SF CWR, Lower
Meadow Creek, and the Imnaha River N-14
Figure N-16. Comparison of Number of Pools per Mile of the SF CWR,
Lower Meadow Creek, and the Imnaha River N-15
Figure N-17. Comparisons of the Main Stem SF CWR with the Imnaha River
and Lower Meadow Creek N-16
N-ii Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Appendix N. Reference Watersheds
One method chosen to assess the seriousness of sedimentation in the upper South Fork
Clearwater River (SF CWR) Subbasin was to compare stream habitat data to that from
watersheds that are generally recognized to be in good condition. With input from the
Watershed Advisory Group, hydrologists, biologists, and other specialists, we selected
Upper Meadow Creek and Bargamin Creeks as reference streams for the tributaries of the
SF CWR. The Imnaha River from across the Snake River in Oregon and the lower, main
stem reach of Meadow Creek were selected as a reference rivers to compare to the main
stem SF CWR.
Reference Comparisons for the SF CWR Tributaries
The Nez Perce National Forest monitors conditions in the Meadow Creek and Bargamin
Creek watersheds because they are relatively undisturbed. Reference and comparison
locations are shown in Figure N-l. Figure N-l also shows that Meadow and Bargamin
Creeks have similar geology to the SF CWR Subbasin. Likewise, Meadow and
Bargamin Creeks have similar rainfall and topography to the upper basin of the SF CWR
Subbasin.
Figure N-1. Locations of Stream Habitat Reference Data for Upper Meadow
Creek, Bargamin Creek, and Various Stream Reaches in the SF
CWR Subbasin
N-l
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
We sorted the data by stream order into two categories, first and second order vs. third
and fourth, so that we would be comparing data from similarly sized streams. We
compared the stratified data from the Upper Meadow and Bargamin Creek watersheds
against stratified stream data from the entire SF CWR Subbasin and against stratified data
from the Newsome Creek watershed only. We selected the Newsome Creek watershed
because it has several 303(d) listed segments and is relatively well sampled. The
comparisons are shown in the following series of figures (Figures N-2 through N-6).
Plots of the data show good trends, but the variability of the data is such that statistical
significance at one standard deviation cannot be shown. In almost all cases, cobble
embeddedness (CE) in the SF CWR Subbasin is significantly higher than in Upper
Meadow and Bargamin Creeks. Similarly, for the pool parameters measured, pool
qualities in Meadow and Bargamin Creeks were better than in the SF CWR Subbasin.
Only a few of the comparisons (average pool tailout depth for small streams from both
Newsome Creek and the whole SF CWR against the reference streams and pool average
maximum depth for large streams between Newsome Creek and the reference streams)
showed statistical significance.
We conclude from these data that sedimentation in the SF CWR Subbasin is increased
over the level in Upper Meadow and Bargamin Creeks watersheds. Cobble
embeddedness is the one parameter where the differences approach statistical
significance in every comparison.
Comparison of Habitat Units of the South Fork Clearwater
Subbasin and Upper Meadow and Bargamin Creeks
Percent Cobble Pool Average Pools per Mile Average Pool Tailout Average Residual Average Residual
Embeddedness Maximum Depth Depth Pool Depth Pool Volume
Category
Figure N-2. Comparison of Stream Habitat Data from the SF CWR Subbasin
to Similar Data from Upper Meadow and Bargamin Creeks
N-2
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Comparison of Habitat Units of Third Order and Greater Streams for the South
Fork Clearwater Subbasin and Upper Meadow and Bargamin Creeks
O South Fork HU - LARGE
Percent Cobble Pool Average Pools per Mile Average Pool Average Residual Average Residual
Embeddedness Maximum Depth Tailout Depth Pool Depth Pool Volume
Category
Figure N-3. Comparison of Third and Fourth Order Stream Habitat Data
from the SF CWR Subbasin to Similar Data from Upper
Meadow and Bargamin Creeks
Comparison of Habitat Units for First and Second Order Streams for the South Fork
Clearwater Subbasin and Upper Meadow and Bargamin Creeks
DSouth ForkHU -SMALL
Percent Cobble Pool Average Pools per Mile Average Pool Average Residual Average Residual
Embeddedness Maximum Depth Tailout Depth Pool Depth Pool Volume
Category
Figure N-4. Comparison of First and Second Order Stream Habitat Data
from the SF CWR Subbasin to Similar Data from Upper Meadow
and Bargamin Creeks
N-3
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Comparison of Habitat Units of Third Order or Greater Streams for
Newsome Creek and Upper Meadow and Bargamin Creeks
[±L
Percent Cobble Pool Average Pools per Mile Average Pool Average Residual Average Residual
Embeddedness Maximum Depth Tailout Depth Pool Depth Pool Volume
Category
Figure N-5. Comparison of Third and Fourth Order Stream Habitat Data
from Newsome Creek to Similar Data from Upper Meadow and
Bargamin Creeks
Comparison of Habitat Units for First and Second Order Streams for the
Newsome Creek and Upper Meadow and Bargamin Creeks
DNewsomeHU - SMALL
Percent Cobble Pool Average Pools per Mile Average Pool Average Residual Average Residual
Embeddedness Maximum Depth Tailout Depth Pool Depth Pool Volume
Category
Figure N-6. Comparison of First and Second Order Stream Habitat Data
from Newsome Creek to Similar Data from Upper Meadow and
Bargamin Creeks
N-4
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table N-l presents the data from which the above graphs were developed and includes
the number of data points and the calculations of standard deviations.
Generally, our conclusions from these data are that bedload in the SF CWR upper basin is
resulting in significant increases in CE throughout the area in addition to some reduction
of pool volume and size.
Analysis of the data, however, shows that while CE is elevated in the SF CWR Subbasin
in comparison to the reference watersheds, the condition is fairly widespread throughout
the basin and not specific to the 303(d) listed water bodies, or even to water bodies that
exhibit high levels of human impact. Table N-2 shows the data set distributed among
water bodies, along with some other conditions of each water body. Shaded water bodies
are those with low road densities; and therefore, little impact from human activities.
Average CE in those water bodies ranges from 12% in the Gospel-Hump Wilderness up
to 72% Silver Creek. Many of the water bodies exhibiting greater than 30% CE have
been assessed using Beneficial Use Reconnaissance Program techniques and evaluated
according to the Department of Environmental Quality's Water Body Assessment
Guidance (Grafe et al. 2002), and show full support of their beneficial uses. The only
303(d) listed streams with CE data are Cougar Creek and Lower Newsome Creek. Lower
Newsome Creek exhibits very good macroinvertebrate index scores (Chapter 2). Cougar
Creek drains a highly weathered granitic watershed, which may account for high CE
here.
From these data, therefore, we cannot conclude that the reference stream data indicate
impairment of beneficial uses of the 303(d) listed streams. Rather, the reference stream
data seem to indicate more of an upper basin-wide issue of elevated sediment levels.
This is consistent with the conclusions of the Fisheries Technical Advisory Group
(Appendix D).
N- 5 Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table N-1. Stream habitat data for Upper Meadow and Bargamin Creek watersheds and various streams in the SF
CWR subbasin.
Habitat Units
Upper Meadow and Bargamin -
LARGE
Upper Meadow and Bargamin -
LARGE
Upper Meadow and Bargamin -
SMALL
Upper Meadow and Bargamin -
SMALL
South Fork Clearwater -
LARGE
South Fork Clearwater -
LARGE
South Fork Clearwater - SMALL
South Fork Clearwater - SMALL
Newsome - LARGE
Newsome - LARGE
Newsome - SMALL
Newsome - SMALL
Statistic
Average
Standard Deviation
Average
Standard Deviation
Average
Standard Deviation
Average
Standard Deviation
Average
Standard Deviation
Average
Standard Deviation
Count
65
65
85
85
69
69
661
661
3
3
45
45
Percent
Cobble
Embedded-
ness
20.25
10.74
26.06
12.70
46.06
20.90
55.01
18.62
56.67
21.13
60.04
14.07
Pool
Average
Maximum
Depth
130.69
39.20
84.51
27.75
94.95
25.75
49.77
19.15
90.67
12.50
48.38
15.56
Pools
per Mile
5.57
5.45
12.43
12.57
7.29
5.11
6.29
6.67
3.00
1.00
5.60
3.65
Average
Pool
Tailout
Depth
45.36
15.23
33.81
13.92
35.88
7.92
15.25
7.57
38.00
5.57
15.72
4.97
Average
Residual
Pool
Depth
85.45
35.67
50.76
19.16
59.24
21.51
34.56
15.52
53.33
10.02
32.85
12.87
Average
Residual
Pool
Volume
221.34
242.18
38.36
34.23
113.45
81.64
14.94
27.83
134.59
85.80
12.82
21.41
N-6
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table N-2. Cobble embeddedness data for the SF CWR.
Water Body
Name
Mill
Lower Johns
Middle Johns
Upper Johns
Moores
Hagen
Lower Crooked
Upper Crooked
Middle Red
Lower SF Red
Middle SF Red
Upper Red
Otterson
Red Horse
Lower
American
Kirks Fork
WBID*
13
14
17
18
19
21
31
32
38
40
41
45
48
51
52
53
CE**
Count
82
45
8
3
2
2
34
50
6
5
5
51
14
25
19
24
CE
Mean
%
45
48
38
29
12
12
52
58
64
43
44
54
40
50
72
54
CE
Max
%
95
84
62
29
12
12
100
95
76
48
58
94
61
60
84
19
CE
Min
%
10
13
14
29
12
12
23
0
45
29
34
29
14
36
64
35
CE***
STD
20
20
19
0
0
0
17
22
10
8
10
16
13
7
8
11
BURP****
(?)
No
Yes
No
No
Yes
No
Yes
Yes
Yes
Yes
No
Yes
Yes
Yes
No
Yes
Road
Density
(mi/mi2)
3.0
1.9
0.6
0.7
1.5
0.4
3.2
2.0
5.2
4.2
4.3
3.8
0.8
2.4
3.4
1.7
Sediment
(t/WB/yr)
145
23
0.64
0
0.09
0
29
20
217
18
20
116
0.23
17
55
7
Dredge
Mined
(?)
No
No
No
No
No
No
Yes
Yes
Yes
No
No
No
No
Yes
No
No
303(d)
Listed
(?)
No
No
No
No
No
No
No
No
No
No
No
No
No
No
No
No
Comments
Bull Trout Spawning
Wilderness & Bull Trout
Spawning
Wilderness & Bull Trout
Spawning
Wilderness & Bull Trout
Spawning
Wlderness
Bull Trout Spawning
Includes Dawson
Creek
Bull Trout Spawning
Bull Trout Spawning
BURP Reference
Side Channels Only
N-7
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water Body
Name
Upper
American
Little Elk
Big Elk
Lower
Newsome
Nugget
Baldy
Pilot
Leggett
Silver
Peasley
Cougar
WBID*
55
57
58
62
64
70
71
75
77
78
79
SF sidewall streams
SF Totals
Upper Meadow
Reference
CE**
Count
31
2
14
3
1
11
15
25
11
21
9
19
545
10
CE
Mean
%
55
86
62
57
48
56
64
59
72
77
94
42
54
49
CE
Max
%
63
86
79
81
48
94
82
86
91
91
97
85
100
68
CE
Min
%
42
86
37
43
48
34
45
39
44
63
92
22
0
39
CE***
STD
5
0
14
21
0
16
13
13
16
9
4
15
19
8
BURP****
(?)
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
Yes
No
Road
Density
(mi/mi2)
2.6
3.4
2.9
4.8
4.6
4.7
1.1
4.4
1.5
4.7
4.3
NA
Sediment
(t/WB/yr)
7.3
49
88
49
6
9
4
18
15
44
50
NA
Dredge
Mined
(?)
Yes
Yes
Yes
(lower)
Yes
Yes
Yes
(lower)
Yes
(lower)
Y
No
No
No
Yes
303(d)
Listed
(?)
No
No
No
Yes
No
No
No
No
No
No
Yes
Yes
Comments
Listed for Temperature
Listed for Temperature
Bull Trout Spawning
Bull Trout Spawning
Mostly Roadless
Granitics
N-8
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Water Body
Name
WBID*
Bargamin
CE**
Count
18
CE
Mean
%
43
CE
Max
%
73
CE
Min
%
19
CE***
STD
14
BURP****
(?)
Road
Density
(mi/mi2)
Sediment
(t/WB/yr)
Dredge
Mined
(?)
303(d)
Listed
(?)
Comments
* Water body identification number
** cobble embeddedness
*** cobble embeddedness standard deviation
**** Beneficial Use Reconnaissance Program (has stream been surveyed by?)
N-9
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Reference Comparisons of the Main Stem SF CWR
For the main stem SF CWR, we compared data from the Imnaha River across the border
in Oregon and from lower Meadow Creek. It was assumed that the Imnaha River and
lower Meadow Creek have similar flow volumes to the SF CWR, although Figure N-7 in
conjunction with the pool volume data to follow indicate that the SF CWR probably is a
somewhat larger river. Lower Meadow Creek is a steeper, more confined system (Figure
N-8). The Imnaha River was chosen particularly as representative of a river system in the
Columbia River basalt plateau. The following sets of figures (Figures N-7 through N-9)
show the comparisons for different river habitat parameters.
180
~-
£ 100
3
<
Comparison of Average Bankfull Width Between Main Stem SFCWR, Imnaha
River, and Lower Meadow Creek
T
H— |
SFCWR L. Meadow Cr. Imnaha River
Figure N-7. Comparison of Average Bankfull Width of the SF CWR, Lower
Meadow Creek, and the Imnaha River
N-10
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
10
Q_
-2 -*
Comparison of Slope Between Main Stem SFCWR, Imnaha River, and Lower
Meadow Creek.
T
1
SFCWR
T I
1 |
L. Meadow Cr. Imnaha River !
Figure N-8. Comparison of Average Slopes of the SF CWR, Lower Meadow
Creek, and the Imnaha River
70 -
'a
J3
a 30
O
Comparison of % Cobble Embeddedness Between Main Stem SFCWR, Imnaha
River, and Lower Meadow Creek.
SFCWR L. Meadow Cr.
Figure N-9. Comparison of Cobble Embeddedness of the SF CWR and
Lower Meadow Creek
Cobble embeddedness data were not available for the Imnaha River. The level of CE in
the main stem SF CWR is elevated by comparison to lower Meadow Creek, but not by as
much as for the smaller streams. There is also some question as to the validity of CE
measurements in larger rivers.
The SF CWR has larger residual pool volume than either lower Meadow Creek or the
Imnaha River (Figure N-10). Figures N-l 1 through N-15 show that the SF CWR also has
N-ll
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
larger pool width, pool length, bank full depth, bank full width, and width-to-depth ratio
than either the Imnaha River or lower Meadow Creek.
rO
|
T3
*
-1000 •
Com
lariso
SFC
n of Residual Pool Volume Between Main Stem SFCWR, Imnaha
River, and Lower Meadow Creek.
T
1
WR L. Meadow Cr. Imnaha River
Figure N-10. Residual Pool Volume Comparisons of the SF CWR, Lower
Meadow Creek, and the Imnaha River
120
B
5
£
1
1 40
Comparison of Average Pool Width Between Main Stem SFCWR, Imnaha River,
and Lower Meadow Creek
T 1
1 I
SFCWR Imnaha River
Figure N-11. Comparison of Pool Widths of the SF CWR and the Imnaha
River
N-12
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
600
JZ
c
iL
1
Comparison of Aver
age Pool Length Between Main Stem SFCWR, Imnaha River,
and Lower Meadow Creek
T
1 i
SFCWR Imnaha River
Figure N-12. Comparison of Pool Lengths of the SF CWR and the Imnaha
River
Comparison of Average Bankfull Depth Between Main Stem SFCWR, Imnaha
River, and Lower Meadow Creek
Figure N-13. Comparison of Bankfull Depths of the SF CWR, Lower
Meadow Creek, and the Imnaha River
N-13
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
180
-
>
1
g,
<
Comparison of Average Bankfull Width Between Main Stem SFCWR, Imnaha
River, and Lower Meadow Creek
T
-+- |
SFCWR L. Meadow Cr. Imnaha River
Figure N-14. Comparison of Bankfull Widths of the SF CWR, Lower
Meadow Creek, and the Imnaha River
45
9
Comparison of Width to Depth Ratio Between Main Stem SFCWR, Imnaha River,
and Lower Meadow Creek
T
SFCWR L. Meadow Cr. Imnaha River
Figure N-15. Comparison of Width-to-Depth Ratios of the SF CWR, Lower
Meadow Creek, and the Imnaha River
The SF CWR has the lowest number of pools per mile of any of the three systems (Figure
N-16). Lower Meadow Creek, with a steeper, more confined channel, may not be a good
comparison for pools per mile. The Imnaha River is more comparable in consideration of
slope, and does have more pools per mile than the SF CWR, but the pools are smaller.
In general, given the variability of these data and the differences between the river
systems, we cannot conclude that habitat in the main stem SF CWR is impaired in
comparison to these other systems. It does appear that CE in the SF CWR is elevated in
comparison to these reference river systems.
N-14
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
12
^
1
Comparison of Pools per Mile Between Main Stem SFCWR, Imnaha River, and
Lower Meadow Creek
1
1
SFCWR
L. Meadow Cr.
Imnaha River
Figure N-16. Comparison of Number of Pools per Mile of the SF CWR,
Lower Meadow Creek, and the Imnaha River
The above data indicate that the sizes of the rivers may be significantly different and this
may be affecting the comparisons. We stratified the reaches by pool size and ran the
comparisons again (Figure N-17). Some small part of the differences among the systems
could be accounted for with this stratification, but the patterns remain the same.
In the end, however, we cannot conclude that the reference rivers indicate any significant
impairment of habitat conditions in the main stem SF CWR.
N-15
Appendix N
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
10000
1000
&
ro
»
en
o
100
10 --
Comparison of Large and Small Pools between Main Stem SFCWR, Imnaha River,
and Lower Meadow Creek.
n SFCWR-Small
n SFCWR-Large
• L. Meadow Cr. -Small
EL. Meadow Cr. -Large
d Imnaha River-Small
D Imnaha River-Large
1
ton
% CE % Slope Bankfull Ave Pool Pool Length Pools per Pool Count Residual Ave Bankfull W/D ratio
Width (ft) Width (ft) (ft) Mile Pool Volume Depth (ft)
(yd*3)
Figure N-17. Comparisons of the Main Stem SF CWR with the Imnaha River and Lower Meadow Creek
N-16
Appendix N
-------
Appendix O. Wastewater Treatment Plant (WWTP) Effluent
Temperature and Heat Loading Analysis
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
Table of Contents O-i
List of Tables O-i
Appendix O. Wastewater Treatment Plant (WWTP) Effluent Temperature and
Heat Loading Analysis O-1
List of Tables
Table O-1. Kooskia WWTP effluent temperature (°C) which would increase
receiving water temperatue by 0.3°C when the receiving water meets the
salmonid spawning temperature criteria 1
Table O-2. Kooskia WWTP heat loading if effluent temperature is capped at
26°C when the receiving water meets the salmonid spawning temperature
criteria 2
Table O-3. Stites WWTP effluent temperature (°C) which would increase
receiving water temperature by 0.3°C when the receiving water meets the
salmonid spawning temperature criteria 3
Table O-4. Stites WWTP heat loading if effluent temperature is capped at 26°C
when the receiving water meets the salmonid spawning temperature criteria. .4
Table O-5. Grangeville WWTP effluent temperature (°C) which would increase
receiving water temperature by 0.3°C when the receiving water meets the
salmonid spawning temperature criteria 5
Table O-6. Elk City WWTP effluent temperature (°C) which would increase
receiving water temperature by 0.3°C when the receiving water meets the
federal bull trout temperature criteria 6
Table O-7. Elk City WWTP heat loading if effluent temperature is capped at
23°C when the receiving water meets the federal bull trout temperature criteria.
7
Table O-8. Red River Ranger Station effluent temperature (°C) which would
increase receiving water temperature by 0.3°C when the receiving water meets
the federal bull trout temperature criteria 8
O- i Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table O-9. Red River Ranger Station WWTP heat loading if effluent
temperature is capped at 23°C when the receiving water meets the federal bull
trout temperature criteria 9
O-ii Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Appendix O. Wastewater Treatment Plant (WWTP) Effluent
Temperature and Heat Loading Analysis
Table O-1. Kooskia WWTP effluent temperature (°C) which would increase
receiving water temperatue by 0.3°C when the receiving water
meets the salmonid spawning temperature criteria.
SF CWR flow
above WWTP
outfall (cfs)
100
200
300
400
500
600
700
WWTP Effluent Discharge (cfs)
0.015
509.3
1009.3
1509.3
2009.3
2509.3
3009.3
3509.3
0.02
384.3
759.3
1134.3
1509.3
1884.3
2259.3
2634.3
0.03
259.3
509.3
759.3
1009.3
1259.3
1509.3
1759.3
0.04
196.8
384.3
571.8
759.3
946.8
1134.3
1321.8
0.05
159.3
309.3
459.3
609.3
759.3
909.3
1059.3
Incremental heat load (million BTU/day) added by effluent, based on effluent
and receiving water temperature in table above.
SFCWR flow
above WWTP
outfall (cfs)
100
200
300
400
500
600
700
WWTP Effluent Discharge (cfs)
0.015
72.83
145.61
218.39
291.18
363.96
436.74
509.53
0.02
72.84
145.62
218.41
291.19
363.98
436.76
509.54
0.03
72.87
145.65
218.44
291.22
364.00
436.79
509.57
0.04
72.90
145.68
218.47
291.25
364.03
436.82
509.60
0.05
72.93
145.71
218.50
291.28
364.06
436.85
509.63
O-l
Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table O-2. Kooskia WWTP heat loading if effluent temperature is capped at
26°C when the receiving water meets the salmonid spawning
temperature criteria.
SF CWR flow
above WWTP
outfall (cfs)
100
200
300
400
500
600
700
WWTP Effluent Discharge (cfs)
0.015
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.02
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.03
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.04
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.05
26.0
26.0
26.0
26.0
26.0
26.0
26.0
Incremental heat load (million BTU/day) added by effluent, based on
capping effluent temperature at 26 C, and receiving water temperature in
table above.
SFCWR flow
above WWTP
outfall (cfs)
100
200
300
400
500
600
700
WWTP Effluent Discharge (cfs)
0.015
2.47
2.47
2.47
2.47
2.47
2.47
2.47
0.02
3.30
3.30
3.30
3.30
3.30
3.30
3.30
0.03
4.95
4.95
4.95
4.95
4.95
4.95
4.95
0.04
6.60
6.60
6.60
6.60
6.60
6.60
6.60
0.05
8.25
8.25
8.25
8.25
8.25
8.25
8.25
O-2
Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table O-3. Stites WWTP effluent temperature (°C) which would increase
receiving water temperature by 0.3°C when the receiving water
meets the salmonid spawning temperature criteria.
SF CWRflow
above WWTP
outfall (cfs)
100
200
300
400
500
600
700
WWTP Effluent Discharge (cfs)
0.01
759.3
1509.3
2259.3
3009.3
3759.3
4509.3
5259.3
0.02
384.3
759.3
1134.3
1509.3
1884.3
2259.3
2634.3
0.03
259.3
509.3
759.3
1009.3
1259.3
1509.3
1759.3
0.04
196.8
384.3
571.8
759.3
946.8
1134.3
1321.8
0.05
159.3
309.3
459.3
609.3
759.3
909.3
1059.3
0.06
134.3
259.3
384.3
509.3
634.3
759.3
884.3
0.07
116.4
223.6
330.7
437.9
545.0
652.2
759.3
0.08
103.1
196.8
290.6
384.3
478.1
571.8
665.6
Incremental heat load (million BTU/day) added by effluent, based on effluent and receiving water temperatue
in table above.
SF CWRflow
above WWTP
outfall (cfs)
100
200
300
400
500
600
700
WWTP Effluent Discharge (cfs)
0.01
72.81
145.60
218.38
291.16
363.95
436.73
509.51
0.02
72.84
145.62
218.41
291.19
363.98
436.76
509.54
0.03
72.87
145.65
218.44
291.22
364.00
436.79
509.57
0.04
72.90
145.68
218.47
291.25
364.03
436.82
509.60
0.05
72.93
145.71
218.50
291.28
364.06
436.85
509.63
0.06
72.96
145.74
218.52
291.31
364.09
436.87
509.66
0.07
72.99
145.77
218.55
291.34
364.12
436.90
509.69
0.08
73.02
145.80
218.58
291.37
364.15
436.93
509.72
o-:
Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table O-4. Stites WWTP heat loading if effluent temperature is capped at 26°C
when the receiving water meets the salmonid spawning
temperature criteria.
SFCWRflow
above VWVTP
outfall (cfs)
100
200
300
400
500
600
700
VWVTP Effluent Discharge (cfs)
0.01
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.02
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.03
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.04
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.05
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.06
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.07
26.0
26.0
26.0
26.0
26.0
26.0
26.0
0.08
26.0
26.0
26.0
26.0
26.0
26.0
26.0
Incremental heat load (million BTU/day) added by effluent, based on capping effluent temperature at 26 C,
and receiving water temperature in table above.
SFCWRflow
above VWVTP
outfall (cfs)
100
200
300
400
500
600
700
VWVTP Effluent Discharge (cfs)
0.01
1.65
1.65
1.65
1.65
1.65
1.65
1.65
0.02
3.30
3.30
3.30
3.30
3.30
3.30
3.30
0.03
4.95
4.95
4.95
4.95
4.95
4.95
4.95
0.04
6.60
6.60
6.60
6.60
6.60
6.60
6.60
0.05 0.06
8.25
8.25
8.25
8.25
8.25
8.25
8.25
9.90
9.90
9.90
9.90
9.90
9.90
9.90
0.07
11.55
11.55
11.55
11.55
11.55
11.55
11.55
0.08
13.20
13.20
13.20
13.20
13.20
13.20
13.20
O-4
Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table O-5. Grangeville WWTP effluent temperature (°C) which would increase
receiving water temperature by 0.3°C when the receiving water
meets the salmonid spawning temperature criteria.
Threemile Creek
flow above
WWTP outfall
(cfs)
0.1
1
3
5
7
9
10
WWTP Effluent Discharge (cfs)
0.4
9.3
9.5
9.9
10.2
10.6
11.0
11.2
1
9.3
9.4
9.5
9.7
9.8
10.0
10.1
1.5
9.3
9.4
9.5
9.6
9.7
9.8
9.8
2
9.3
9.3
9.4
9.5
9.6
9.6
9.7
2.5
9.3
9.3
9.4
9.5
9.5
9.6
9.6
Incremental heat load (million BTU/day) added by effluent, based on effluent
and receiving water temperature in table above.
Threemile Creek
flow above
WWTP outfall
(cfs)
0.1
1
3
5
7
9
10
WWTP Effluent Discharge (cfs)
0.4
1.24
1.89
3.35
4.80
6.26
7.72
8.44
1
2.98
3.64
5.09
6.55
8.01
9.46
10.19
1.5
4.44
5.09
6.55
8.01
9.46
10.92
11.65
2
5.90
6.55
8.01
9.46
10.92
12.37
13.10
2.5
7.35
8.01
9.46
10.92
12.37
13.83
14.56
O-5
Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table O-6. Elk City WWTP effluent temperature (°C) which would increase
receiving water temperature by 0.3°C when the receiving water
meets the federal bull trout temperature criteria.
Bk Creek flow
above VWVTP
outfall (cfs)
3
5
10
15
20
25
30
35
VWVTP Effluent Discharge (cfs)
0.01
31.8
46.8
84.3
121.8
159.3
196.8
234.3
271.8
0.02
20.6
28.1
46.8
65.6
84.3
103.1
121.8
140.6
0.03
16.8
21.8
34.3
46.8
59.3
71.8
84.3
96.8
0.04
14.9
18.7
28.1
37.4
46.8
56.2
65.6
74.9
0.05
13.8
16.8
24.3
31.8
39.3
46.8
54.3
61.8
0.1
11.6
13.1
16.8
20.6
24.3
28.1
31.8
35.6
0.15
10.8
11.8
14.3
16.8
19.3
21.8
24.3
26.8
0.2
10.4
11.2
13.1
14.9
16.8
18.7
20.6
22.4
Incremental heat load (million BTU/day) added by effluent, based on effluent and receiving water
temperature in table above.
Bk Creek flow
above VwVTP
outfall (cfs)
3
5
10
15
20
25
30
35
VWVTP Effluent Discharge (cfs)
0.01
2.21
3.67
7.31
10.95
14.59
18.22
21.86
25.50
002
2.24
3.70
7.34
10.98
14.61
18.25
21.89
25.53
0.03
2.27
3.73
7.37
11.00
14.64
18.28
21.92
25.56
0.04
2.30
3.76
7.39
11.03
14.67
18.31
21.95
25.59
0.05
2.33
3.78
7.42
11.06
14.70
18.34
21.98
25.62
0.1
2.47
3.93
7.57
11.21
14.85
18.49
2213
25.77
0.15
2.62
4.08
7.72
11.35
14.99
18.63
2227
25.91
0.2
2.77
4.22
7.86
11.50
15.14
18.78
22.42
26.06
O-6
Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table O-7. Elk City WWTP heat loading if effluent temperature is capped at
23°C when the receiving water meets the federal bull trout
temperature criteria.
Elk Creek flow
above VWVTP
mitfall lrf*\
3
5
10
15
20
25
30
35
VWVTP Effluent Discharge (cfs)
0.01
23.0
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.02
20.6
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.03
16.8
21.8
23.0
23.0
23.0
23.0
23.0
23.0
0.04
14.9
18.7
23.0
23.0
23.0
23.0
23.0
23.0
0.05
13.8
16.8
23.0
23.0
23.0
23.0
23.0
23.0
0.1
11.6
13.1
16.8
20.6
23.0
23.0
23.0
23.0
0.15
10.8
11.8
14.3
16.8
19.3
21.8
23.0
23.0
0.2
10.4
11.2
13.1
14.9
16.8
18.7
20.6
22.4
Incremental heat load (million BTU/day) added by effluent, based on capping effluent temperature at 23 C,
and receiving water temperature in table above.
Elk Creek flow
above VWVTP
outfall (cfs)
3
5
10
15
20
25
30
35
VWVTP Effluent Discharge (cfs)
0.01
1.36
1.36
1.36
1.36
1.36
1.36
1.36
1.36
0.02
2.24
2.72
2.72
2.72
2.72
2.72
2.72
2.72
0.03
2.27
3.73
4.08
4.08
4.08
4.08
4.08
4.08
0.04
2.30
3.76
5.43
5.43
5.43
5.43
5.43
5.43
0.05
2.33
3.78
6.79
6.79
6.79
6.79
6.79
6.79
0.1
2.47
3.93
7.57
11.21
13.59
13.59
13.59
13.59
0.15
2.62
4.08
7.72
11.35
14.99
18.63
20.38
20.38
0.2
2.77
4.22
7.86
11.50
15.14
18.78
22.42
26.06
O-7
Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table O-8. Red River Ranger Station effluent temperature (°C) which would
increase receiving water temperature by 0.3°C when the receiving
water meets the federal bull trout temperature criteria.
SF Red River flow
above WWTP
outfall (cfs)
5
10
20
30
40
50
60
WWTP Effluent Discharge (cfs)
0.002
196.8
384.3
759.3
1134.3
1509.3
1884.3
2259.3
0.004
103.1
196.8
384.3
571.8
759.3
946.8
1134.3
0.006
71.8
134.3
259.3
384.3
509.3
634.3
759.3
0.008
56.2
103.1
196.8
290.6
384.3
478.1
571.8
0.01
46.8
84.3
159.3
234.3
309.3
384.3
459.3
0.02
28.1
46.8
84.3
121.8
159.3
196.8
234.3
Incremental heat load (million BTU/day) added by effluent, based on effluent and
receiving water temperature in table above.
SF Red River flow
above WWTP
outfall (cfs)
5
10
20
30
40
50
60
WWTP Effluent Discharge (cfs)
0.002
3.64
7.28
14.56
21.84
29.12
36.40
43.68
0.004
3.65
7.29
14.57
21.85
29.12
36.40
43.68
0.006
3.66
7.30
14.57
21.85
29.13
36.41
43.69
0.008
3.66
7.30
14.58
21.86
29.14
36.41
43.69
0.01
3.67
7.31
14.59
21.86
29.14
36.42
43.70
0.02
3.70
7.34
14.61
21.89
29.17
36.45
43.73
O-8
Appendix O
-------
South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table O-9. Red River Ranger Station WWTP heat loading if effluent
temperature is capped at 23°C when the receiving water meets the
federal bull trout temperature criteria.
SF Red River flow
above WWTP
outfall (cfs)
5
10
20
30
40
50
60
WWTP Effluent Discharge (cfs)
0.002
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.004
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.006
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.008
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.01
23.0
23.0
23.0
23.0
23.0
23.0
23.0
0.02
23.0
23.0
23.0
23.0
23.0
23.0
23.0
Incremental heat load (million BTU/day) added by effluent, based on effluent and
receiving water temperature in table above.
SF Red River flow
above WWTP
outfall (cfs)
5
10
20
30
40
50
60
WWTP Effluent Discharge (cfs)
0.002
0.27
0.27
0.27
0.27
0.27
0.27
0.27
0.004
0.54
0.54
0.54
0.54
0.54
0.54
0.54
0.006
0.82
0.82
0.82
0.82
0.82
0.82
0.82
0.008
1.09
1.09
1.09
1.09
1.09
1.09
1.09
0.01
1.36
1.36
1.36
1.36
1.36
1.36
1.36
0.02
2.72
2.72
2.72
2.72
2.72
2.72
2.72
O-9
Appendix O
-------
Appendix P. Lucas Lake, Beneficial Use Assessment and
Reconnaissance Metals Monitoring
-------
Water Quality Summary Report 33
Lucas Lake, Beneficial Use Assessment and
Reconnaissance Metals Monitoring
August 2, 2002
-------
Water Quality Summary Report 33
Lucas Lake, Beneficial Use Assessment and
Reconnaissance Metals Monitoring
Idaho County, Idaho
August 2, 2002
Prepared by:
Robert Steed
Office of Technical Services
Idaho Department of Environmental Quality
1410 N.Hilton
Boise, ID 83706
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
Table of Contents
Table of Contents P-i
List of Tables P-ii
List of Figures P-ii
List of Appendices P-ii
Introduction P-1
Objectives P-1
Methods P-2
Preliminary Site Visit P-2
Metals Monitoring Objectives P-2
Monitoring P-3
Description of Samples Collected During Initial Visit P-3
Field Parameters P-4
Sediment Monitoring During Follow-Up Visit P-4
Analysis Results P-4
Discussion P-5
Metals P-5
Sediment P-6
Conclusions P-6
P-i Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
List of Tables
Table 1. Metals Water Quality Report Data P-4
Table 2. Sediment Water Quality Report Data P-4
Table 3. Metals Calculator Input and Outputs P-5
Table 4. Lucal Lake Results Copmared to Criteria P-5
List of Figures
Figure 1. Lucas Lake and surrounding area P-1
Figure 2. Location of Lucas Lake within Idaho P-1
Figure 3. Aerial photo of Lucas Lake and watershed P-2
Figure 4. Using auger to drill through ice P-3
Figure 5. Measuring field parameters with multi-meter P-4
List of Appendices
Appendix A. State Of Idaho Laboratory Water Quality Report P-7
Appendix B. University of Idaho Analytical Sciences Laboratory
Certificate of Analysis P-9
P-ii Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
"Dredge
.Tailings"
,•
Figure 1. Lucas Lake and
surrounding area
Introduction
Lucas Lake, which is a small (less than one acre)
locally-named waterbody, is in Idaho county, Idaho
(45° 49' 17"N and 115° 28' 04" W). Lucas Lake
outflow discharges into the American River between
the town of Elk City and the South Fork Clearwater
River. Lucas Lake's location is indicated on Figures
1 and 2.
Although it is not classified in Idaho's Water Quality
Standards, Lucas Lake is currently listed on Idaho's
1998 §303(d) list1 with sediment as its pollutant.
Lucas Lake was originally put in Idaho's §303(d)
program because of its 1988 305(b)2 status, which
was suggested by the Bureau of Land Management
(BLM). The pollutants on the 1988 §305(b) report were identified only as "sediment and
toxic substances." These §305(b) listings were the basis for listing Lucas Lake on Idaho's
1994 §303(d) list. Based on recent observations and anecdotal information, Lucas Lake's
existing beneficial uses include Cold Water Aquatic Life and Primary Contact Recreation.
The only available previous assessment of Lucas Lake was
performed by the BLM in 1981. This assessment, by Craig
Johnson on August 21, 1981, is comprised of half a page of field
notes and five captioned photographs. Craig states that the
"Lake has suspended/sediment (colloidal?)."
Objectives
The Objectives of this study are to:
• Analyze appropriate metals and sediment samples, and
collect water quality information to determine Lucas Lake's
support status, and
• Determine if Lucas Lake should remain on Idaho's §303(d)
list and have a TMDL developed.
Figure 2. Location of
Lucas Lake in Idaho
1 The 303(d) list is a federally required, public reviewed, list of waterbodies whose status is "not fully
supporting" one or more beneficial uses.
2 The 305(b) report is a report to congress listing waterbody beneficial use status and/or monitoring status, and
may include causes and sources of pollution for impaired waterbodies.
P-l
Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
Methods
Preliminary Site Visit
Daniel Stewart and Robert Steed visited Lucas Lake on November 13, 2001. Lucas Lake is a
short walk south from neighboring dredge tailings. There is no surface water connection
with these dredge tailings contrary to what is shown on the United States Geological Service
(USGS) 1:24K map (see Figure 1). The outlet does function and discharges to the American
River.
Lucas Lake is a sink or depression, whose genesis is unknown to the author. Daniel Stewart
has hypothesized that it may be an old "glory hole" (a large open pit ore is extracted from).
It is also possible that it is a natural erosional feature. Lucas Lake has steep underwater
banks (steeper than 45°), and appears to maintain full pool conditions throughout the year.
Lucas Lake is surrounded by a very small, steep, contributing watershed, which is conifer
covered and made up of small grained (l-10mm) sedimentary outcrops and clay. (In Figure
3, the outcrops are light, almost-white areas, not quite as light and white as the lake surface.)
Many raw outcroppings of this
erosive sedimentary parent material
are visible. Lucas Lake has healthy
riparian vegetation that filters
sediment around approximately 95%
of its perimeter. With no non-
natural sediment sources identified,
it is anticipated that Lucas Lake
sedimentation rates reflect natural
conditions. There is a distinct blue-
green color to the water, probably
colloidal in nature, which may have
been mistaken for toxic substances
in past assessments. Abundant
waterboatman (Hemiptera
Corixidae) or backswimmer
(Hemiptera Notonectidae) insects
were observed, but past observations
of fish were not verified. Lucas
Lake has characteristics of both a
lake and a wetland.
Figure 3. Aerial photo of Lucas Lake and watershed
Metals Monitoring Objectives
This investigation is to evaluate Lucas Lake for two existing uses: Cold Water Aquatic Life
and Primary Contact Recreation. The bases for declaring these existing beneficial uses are
direct observation (Cold Water Aquatic Life) and Anecdotal reference (Primary Contact
Recreation).
To assess Cold Water Aquatic Life as an existing beneficial use, Lucas lake was monitored
for toxic substances (metals), and compared to Aquatic Life Criteria for Toxic Substances
P-2
Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
(Equivalent to 40 CFR 131.36(b)(l), Columns Bl, B2 and D23). Based on the neighboring
lode and typical mining practices in the area, the following list of potential toxics was
developed: cadmium, zinc, arsenic, mercury, copper, and iron. Iron is not identified in
Aquatic Life Criteria for Toxic Substances and should be compared to a value of 5000jig/l as
an asphyxiate (Bruce Schuld, personal communication).
For the other beneficial use, Primary Contact Recreation,
Lucas Lake is to be monitored for pathogens, and
compared to Idaho Water Quality Standards, E. coli
Criteria.
Monitoring
On December 18, 2001, at 11:48 am, Robert Steed and
Daniel Stewart collected water quality samples from
Lucas Lake. The lake was frozen over with a slight snow
cover. A hole was drilled through approximately 6 inches
of ice and snow, with a steel auger (see Figure 4.). Three
500-ml samples of Lucas Lake water were taken, using
new, 3-foot long disposable bailers, at a depth of 0 to 2.5
feet below lake surface. Samples were collected and
transported in decontaminated or new sterilized
equipment. Samples were then chilled and transported to
State of Idaho Bureau of Laboratories. These samples
were submitted at 8:43 am the following day (December
19, 2001) for immediate analysis.
Figure 4. Using auger to drill
through ice
Description of Samples Collected During Initial Visit
Samples were taken and labeled as follows:
Sample container 1 was
• not filtered
• analyzed for hardness
• not preserved.
Sample container 2 was
• not filtered
• analyzed for total iron
• preserved with 3 ml nitric acid.
Sample container 3 was
• filtered with a 0.45 jim filter using syringes and disposable filter cartridges
• analyzed for dissolved: cadmium, zinc, arsenic, mercury, and copper; these analyses
supplied at least 50 - 60 ml/analyte
• preserved with 3 ml nitric acid.
3 Code of Federal Regulations, Title 40, Part 131, Section 6.
P-3
Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
Field Parameters
The following field parameters were measured immediately after samples were taken (see
Figure 5):
• Water Temperature - 3.6°C
• pH-7.46
• Dissolved Oxygen - 8.98 mg/1
• Conductivity -31.6 u S/cm.
Sediment Monitoring During Follow-Up Visit
One June 12, 2002, Daniel Stewart performed a follow-up
monitoring visit to Lucas Lake. During this visit he
measured turbidity at 0.80 NTU,4 and also collected a
sample to be analyzed for Total Suspended Sediment (TSS).
This sample was transported to University of Idaho's
Analytical Sciences Laboratory (lab) for analysis. Both 0.80
NTU and 1 mg/1 TSS (see lab results in Table 1) indicate
low sediment.
Figure 5. Measuring field
parameters with a multi-meter
Analysis Results
Analysis results from the initial visit were received from the lab on January 18, 2002, and are
presented in Table 1. A copy of the lab bench sheet is included as Appendix A.
Table 1. Metals Water Quality Report Data
STORET" Test Performed Results Completed
01000
01025
01040
00900
01046
01045
71890
00530
01090
Arsenic, Dissolved
Cadmium, Dissolved
Copper, Dissolved
Hardness (as CaCOs)
Iron, Dissolved
Iron, Total
Mercury, Dissolved
Total Suspended Solids (TSS) (105 C)
Zinc, Dissolved
6 (ug/1)
< i (ns/i)
< 10 (ug/1)
6 (mg/1)
90 (ug/1)
150 (ug/1)
< 0.5 (ug/1)
1 (mg/1)
20 (ug/1)
01/14/02
01/04/02
12/20/01
01/08/02
12/20/01
12/21/01
12/27/01
12/20/01
12/20/01
a. Reference identification for test performed, from EPA Water Quality database
Analysis results from the follow-up visit were received from the lab on June 28, 2002, and
are presented in Table 2. A copy of the Certificate of Analysis is included as Appendix B.
Table 2. Sediment Water Quality Report Data
Test No. Test Performed Results
EPA 160.2 I Non-Filterable Residue/TSS b I BDL
MDLa
4 mg/1
a. method detection limit
b. total suspended solids
c. below detection limit
1 Nephelometric Turbidity Units
P-4
Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
Discussion
Metals
Hardness-dependent metals criteria are calculated by formula. Originally, formulas were
based on total recoverable metals values, but the Environmental Protection Agency later
recommended metals criteria be based on the more bioavailable dissolved form, and
developed conversion factors to estimate the dissolved fraction of the metals values. Idaho
has subsequently adopted either the conversion factors values or the Code of Federal
Regulations (CFR) formula values as acceptable criteria. The criteria in Table 3 were
developed using an inhouse metals calculator spreadsheet. This spreadsheet calculates both
the conversion factors and resulting criteria values for a given hardness value. The lowest
hardness that is to be used in calculating metals criteria, according to CFR, is 25 mg/1. Lucas
Lake's hardness was much lower, at 6 mg/1.
Table 3. Metals Calculator Input and Outputs.
Metal Hardness CMC" (ug/1) CCCb (ug/1)
Arsenic (III)
Cadmium
Copper
Mercury
Zinc
25
25
25
25
25
360
0.8227
4.6090
2.0400
35.3574
190
0.3369
3.4719
0.0120
32.1519
a. Criterion Maximum Concentration, from 40 CFR 131.36(b)(l), Column Bl
b. Criterion Continuous Concentration, from40 CFR 131.36(b)(l), ColumnB2
Table 4. Lucas Lake Results Compared to Criteria.
Status Test Performed Results CMC" (ug/1) CCCb (ug/1) HHc(ug/l)
Pass
BDL
Pass
Pass
BDL
Pass
Arsenic, Dissolved
Cadmium, Dissolved
Copper, Dissolved
Iron, Total
Mercury, Dissolved
Zinc, Dissolved
6 (ug/1)
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
Sediment
Based on observation of the site, it appears that there are minimal anthropogenic sources of
sediment, limited to recreation on the North shore near the trail. The underwater banks of
Lucas Lake are steep, nearly matching above water banks, which demonstrates minimal
sediment deposition, or recent genesis. Most banks are well vegetated with sedges and
bushes, which also demonstrates bank stability and indicates that over-surface flow-filtering
mechanisms are functional.
Field and laboratory results show minimal water column sediment. Idaho Water Standards
criteria for turbidity for Cold Water Aquatic Life (IDAPA 58.01.02.250.02.d) states:
"Turbidity, below any applicable mixing zone set by the Department, shall not exceed
background turbidity by more than fifty (50) NTU instantaneously or more than twenty-five
(25) NTU for more than ten (10) consecutive days." Turbidity measured on June 12, 2002
was 60 times less than the instantaneous criteria.
Total Suspended Solids (TSS) concentrations are below the 4 mg/1 detection limit. It is
unlikely that sediment is impairing beneficial uses.
Conclusions
• Water quality metals criteria have been not been exceeded as far as we know.
• From visual observation, sediment does not appear to be impairing existing beneficial
uses.
• Lucas Lake should be removed from the §303(d) list, and should not be a candidate for
TMDL development.
• The potential exists for cadmium and mercury concentrations in Lucas Lake to be above
Water Quality criteria. However, given the low metals values (some BDL), and the
morphology of the lake, and the BDL results, DEQ concludes that Lucas Lake does not
have problems with toxic substances.
P-6 Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
Appendix A. State Of Idaho Laboratory Water Quality
Report
State of Idaho, Department of Health and Welfare
Bureau of Laboratories - Boise Laboratory
2220 Old Penitentiary Road, Boise, Idaho 83712
WATER QUALITY REPORT - CHEMICAL REPORT
LAB: BOISE, Phone: (208) 334-2235
Section Manager, Inorganic Chemistry: Barry Pharaoh
IDEQ-BSO
ROBERT STEED
1410 N. HILTON
BOISE, ID 83706
Tracking Number: 41201-0281/
(Please Refer to this Tracking Number on any communications)
RECEIVED
JAN 11 2002
OEPT. OF ENVIRONMENTAL QUALITY
TECHNICAL SERVICES OFFICE
Grant/Project:
Survey Name:
Storet:
NPDES No.:
Sample Location;
Submitted by:
Purpose:
Taken From:
Type of Sample:
Composite:
Preservation:
8206
Watersheds
DEEP PART OF LAKE
ROBERT STEED
Other-
Lake - L
Grab
No
HN03, Cooled 4° C
Dace Collected: 12/18/01
Time Collected: 11:00
Date Received in Lab: 12/19/01
STORET TEST PERFORMED
0 1 0 0 0
01025
01040
00900
01046
01045
71890
00530
01090
Arsenic, Dissolved
Cadmium, Dissolved
Copper, Dissolved
Hardness (as CaCO3)
Iron, Dissolved
Iron, Total
Mercury, Dissolved
Total Suspended Solids
Zinc, Dissolved
(105 C)
RESULTS
6 (mg/1)
90 (ug/1)
150 (ug/1!
cO.5 lug/1}
1 (mg/1)
20 tug/1)
COMPLETED ANST
01/14/02
01/04/02
12/20/01
01/08/02
12/20/01
12/21/01
12/27/01
12/20/01
12/20/01
JS
JS
HH
BO
HH
HH
JS
LB
HH
Page 1
ID00018
P-7
Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
Appendix B. University of Idaho Analytical Sciences
Laboratory Certificate of Analysis.
University of Idaho
Holm Research Center
Moscow, Idaho 83844-2203
Phone: (208)885-7081 Fax: (208)885-8937
CERTIFICATE OF ANALYSIS
Submitted by:
Daniel Stewart UIASL Case #: WJUN02-14
Submitter Case #: Grangeville
Dept. of Environmental Quality Group: WATER
300WMAinStRm203 Date Received: 06/12/2002
Grangeville ID 83530 Report Status: Final
Laboratory Comments:
1st Level QC: ^ pate:
2nd Level QC: JfcH*^Lj- Date:
P-8 Appendix P
-------
Lucas Lake, Beneficial Use Assessment and Reconnaissance Metals Monitoring August 2002
ANALYTICAL SCIENCES LABORATORY ^
CERTIFICATE OF ANALYSIS ^ E C E f V E D
Owner: Project Name:
Submitter ID: Lucas Lake
DIASL #: W0201459
Samp. Type: Wafer - Surface
Test: EPA Iti0.2-Non-Filterable Eesidue/T.S.S.
Ref: 06/13/2002 03:33:49 PM
JUN 282082
EPA 160.2
Non-Filterable Res.
Results
BDL
MDL
4
Units
mglL
Samples will be discarded one month after d«(e of final report, unless otherwise requested.
All lamples classified as hazardous waste will be returned to the submitter after analysis.
U'-
P-9
Appendix P
-------
Appendix Q. Unit Conversion Chart
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South Fork Clearwater River Subbasin Assessment and TMDLs
October 2003
Table Q-1. Metric - English unit conversions.
Distance
Length
Area
Volume
Flow Rate
Concentration
Weight
Temperature
English Units
Miles (mi)
Inches (in)
Feet (ft)
Acres (ac)
Square Feet (ft2)
Square Miles (mi2)
Gallons (g)
Cubic Feet (ft3)
Cubic Feet per
Second (ft3/sec)1
Parts per Million
(ppm)
Pounds (Ibs)
Fahrenheit (°F)
Metric Units
Kilometers (km)
Centimeters (cm)
Meters (m)
Hectares (ha)
Square Meters (m2)
Square Kilometers
(km2)
Liters (L)
Cubic Meters (m3)
Cubic Meters per
Second (m3/sec)
Milligrams per Liter
(mg/L)
Kilograms (kg)
Celsius (°C)
To Convert
1 mi = 1.61 km
1 km = 0.62 mi
1 in = 2.54 cm
1 cm = 0.39 in
1 ft = 0.30m
1 m = 3.28 ft
1 ac = 0.40 ha
1 ha = 2.47 ac
1 ft2 = 0.09 m2
1 m2 = 10.76 ft2
1 mi2 = 2.59 km2
1 km2 = 0.39 mi2
1 g = 3.78 I
1 I = 0.26 g
1 ft3 = 0.03 m3
1 m3 = 35.32 ft3
1 ft3/sec = 0.03 m3/sec
1 m3/sec = ft3/sec
1 ppm = 1 mg/L2
1 Ib = 0.45 kg
1 kg = 2.20 Ibs
°C = 0.55 (F - 32)
°F = (C x 1 .8) + 32
Example
3 mi = 4.83 km
3 km = 1 .86 mi
3 in = 7.62 cm
3 cm = 1.18 in
3ft = 0.91 m
3 m = 9.84 ft
3 ac= 1.20 ha
3 ha = 7.41 ac
3 ft2 = 0.28 m2
3 m2 = 32.29 ft2
3 mi2 = 7.77 km2
3 km2 = 1.16 mi2
3g = 11.35l
3 1 = 0.79 g
3 ft3 = 0.09 m3
3m3= 105.94ft3
3 ft3/sec = 0.09 m3/sec
3m3/sec= 105.94 ft3/sec
3 ppm = 3 mg/L
3 Ib = 1 .36 kg
3 kg = 6.61 kg
3°F = -15.95°C
3 ° C = 37.4 °F
1 ft /sec = 0.65 million gallons per day; 1 million gallons per day is equal to 1.55 ft /sec.
2The ratio of 1 ppm = 1 mg/L is approximate and is only accurate for water
Q-i
Appendix Q
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Appendix R. Public Comment Distribution List
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
South Fork Clearwater River Subbasin Assessment and TMDLs
Public Comment Version
Distribution List
Department of Environmental Quality, State Office
1410 N. Hilton, Boise, ID 83706
Department of Environmental Quality Lewiston Regional Office
1118 F Street, Lewiston, ID, 83501
Department of Environmental Quality, Grangeville Office
300 W. Main Street, Grangeville, ID 93530
US Environmental Protection Agency, Region 10
1435 N. Orchard, Boise, ID 83706
Nez Perce Tribe
120 Bever Grade, Lapwai, ID 83540
Ken Gortsema, City of Grangeville
225 W. North Street, Grangeville, ID 83530
Grangeville Public Library
225 West North Street, Grangeville, ID 83530
Kooskia Public Library
P.O. Box 447, Kooskia, ID 83539
Idaho County Library
P.O. Box 419, Elk City, Idaho 83525
Kamiah Community Library
P.O. Box 846, Kamiah, ID 83536
Nick Gerhardt, Nez Perce National Forest
Rt. 2, Box 475, Grangeville, ID 83530
Craig Johnson, Bureau of Land Management
Rt. 3, Box 181, Cottonwood, ID 83522
Palouse Clearwater Environmental Institute
P.O. Box 8596, Moscow, ID 83843
R-l Apprendix R
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
University of Idaho Library, Government Documents
University of Idaho, Moscow, ID 83843
Lewis & Clark State College Library
500 8th Ave., Lewiston, ID 83501
Eileen Rowan, Soil Conservation Commission
2200 Michigan Avenue, Orofmo, ID 83544
Todd Bates, Idaho Department of Lands
P.O. Box 190, Kamiah, ID 83536
Susan Burch, U.S. Fish & Wildlife Service
1387 S. Vinnell Way, Room 368, Boise, ID 83709
Dale Brege, NOAA Fisheries
102 North College, Grangeville, ID 83530
Clearwater Basin Advisory Group Members
South Fork Clearwater River Watershed Advisory Group Members
R-2 Apprendix R
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Appendix S. Responses to Public Comments
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Table of Contents
Appendix S. Responses to Public Comments 1
Table of Contents i
Appendix S. Responses to Public Comments 1
Process -General 2
Process - Public Participation 3
Process - Economic Analysis 5
Process - Effects on Grangeville 8
Process - Combining TMDL and IDWR WAGs 8
Process - Address Aesthetics 9
Water Quality Standards - Temperature 9
Beneficial Uses - General 11
Beneficial Uses - Endangered Species 11
Beneficial Uses - Threemile Creek 12
Pollutant Sources - CAFOs 14
Nonpoint Sediment Sources - Roads 14
Nonpoint Sediment Sources - Suction Dredge Mining 15
Nonpoint Temperature Sources - Roads 16
Missing Data 16
Delisting Proposal - Sediment 16
TMDLs - Grangeville WWTP 20
TMDLs - Grangeville WWTP and Temperature 200
TMDLs - Kooskia WWTP and Temperature 22
TMDLs - Grangeville WWTP and Nutrients 22
TMDLs - Nutrients/DO 23
TMDLs - Bacteria 23
TMDLs -Sediment 24
TMDLs -Temperature 25
Implementation - General 26
Implementation - Negative Effects 27
Implementation - Grangeville WWTP 288
S- i Appendix S
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Appendix S. Responses to Public Comments
A draft of the South Fork Clearwater River Subbasin Assessment and TMDLs was available
for public comment from June 1, 2003 through July 15, 2003. The draft was distributed for
comment to those individuals and entities listed in Appendix R. In addition, the draft was
available for review and comment on the DEQ, USEPA and NPT web sites.
Comments received are identified by number of the comment letter as assigned below:
No. 1 - Letter from Dick Wilhite, chair of the SF Clearwater WAG:
"The South Fork Clearwater WAG submits the following public comments on the
South Fork Clearwater Sub-basin Assessment and the draft TMDL. These comments
were either expressed at the July 1, 2003 WAG meeting or have been submitted by
WAG representatives. A list of those in attendance is attached at the end of this
letter."
No. 2 - Letter from Phil Jahn, WAG member representing federal land managers:
"This is my response to the South Fork Clearwater River Watershed Advisory Group
letter to the Clearwater Basin Advisory Group. The version of the letter we had for
review was current as of July 8, 2003. The letter seems to include the individual
views of several WAG members and I was unable to provide my comments in time
for the July 10 BAG meeting. This represents my input as the WAG representative
for the federal land management agencies."
No. 3 - Letter from Kevin Gardes on behalf of the City of Grangeville:
"I am writing to comment on the Draft SF Clearwater River Subbasin Assessment
and TMDLs. My comments are on behalf of the City of Grangeville."
No. 4 - Letter from Jane Kissinger, Grangeville City Councilwoman:
"I write this letter to you from the perspective of a citizen in a small community and
as a member of the Grangeville City Council. I have served on the Council for 14
years. In that period of time, I have witnessed the closure of the last of our five
sawmills, the closure of the Camas Prairie Railroad and the severe deterioration of
our economy."
No. 5 - Letter from Jonathan Oppenheimer on behalf of Idaho Conservation League:
"Thank you for allowing us to comment on the water quality assessment and Total
Maximum Daily Loads standards (TMDLs) in the South Fork Clearwater River (SF
CWR) Subbasin Assessment and TMDLs. The Idaho Conservation League has a
long history of involvement with resource management issues. As Idaho's largest
state-based conservation organization we represent over 3,000 members, many of
whom have a deep personal interest in protecting our water, wildlands, and wildlife
from the harmful effects of pollution and watershed degradation."
No. 6 - Email from Bonnie Schonefeld, WAG member representing environmentalists:
"I would like to respond to the public comment draft of the TMDL, and to the letter
written to the Clearwater Basin Advisory Group (BAG) by the South Fork Clearwater
Watershed Advisory Group (WAG). I was unable to attend the meeting at which that
letter was drafted, but would like to add my comments as the environmental
representative of the WAG."
S- 1 Appendix S
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
No. 7 - Email from Borg Hendrickson, WAG member representing recreation:
"The SF Clearwater WAG's July of '03 letter to the BAG was written without my
input, as I was unable to attend the meeting at which it was composed. I would not
have concurred and do not concur with some of its contents."
No. 8 - Email from Linwood Laughy, WAG member representing outfitters/guides:
"As a member of the South Fork Clearwater Watershed Advisory Group, I wish to
make some remarks regarding the SF TMDL Public Draft."
Comments have been grouped by topic. Comments were copied into the topical area from
the letters received. They were copied for the most part on a whole paragraph by whole
paragraph basis. Where a part of a paragraph has been extracted to a separate topical area, it
is set off by (...) notation.
Process -- General
No. 1
What is the advantage of doing the TMDLs under the MOU? The state should be capable of
doing the TMDLs themselves. The state is better able to dialog with the local residents.
Local residents would prefer to work with DEQ. The NPT only has jurisdiction within the
reservation boundary over a very few miles at the lower end of the SF Clearwater watershed,
yet has exerted an inordinate influence over this TMDL. The TMDL itself is probably far
more complicated and less likely to be implemented than if DEQ had done it alone.
(Response: This TMDL is written under an MOA with the NPT, USEPA and DEQ
because portions of the SF CWR Subbasin are contained within the Nez Perce Tribe
Reservation boundary, and the Tribe has ceded territory treaty rights in other areas
of the watershed. An agreement was reached whereby the TMDLs would be written
cooperatively by the three agencies using the state's processes and water quality
standards in order to set aside jurisdictional differences, focus on restoring water
quality, and promote support and cooperation among citizens, businesses, and
governments.)
One of my main concerns is that if any question of detriment water quality exists, even if it is
totally off the wall, the EPA and NPT say it must be fixed. There is data within the tables of
this draft that is inaccurate. How much data that we are not familiar with is incorrect? We
need more than one or two years of data to help set the TMDLs.
Two sets of the TMDLs in this document are being written without clear evidence of
impairment to beneficial uses. This reflects the tribal and federal mind set that if any
question exists about water quality, then the TMDL must be written, as opposed to a local
perspective that TMDLs should not be written unless there is clear evidence of impairment.
No matter what people say, TMDLs will result in some level of restriction to private and
industrial use of the land, which is not warranted without clear evidence. Especially in an
economically depressed area like Idaho County, governmental restrictions simply so
bureaucrats can justify their jobs is out of order.
S- 2 Appendix S
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
TMDLs need to be set at realistic and attainable levels, so that they can be met without
harming the local economy but also help with the water quality. They need to be set so they
are easily attainable and then after they have been met and water quality still needs
improvement, then reset and try to attain them again, with the least amount of impact to all.
Response: The three parties preparing this subbasin assessment and TMDLs are
well aware of the general process issues raised above. We are legally obligated to
write the documents in a particular time frame. In the case of the South Fork
Clearwater River Subbasin Assessment and TMDLs, we asked for and received a
rare extension of time to complete the process. We have collected far more data,
and completed far more analyses than time or resources allow for most TMDLs in
the state of Idaho. The courts have made it clear that lack of data is not an excuse
for not completing TMDLs. TMDLS must be written with the available data, under
the assumption that if and when more data become available, they can be modified.
Existing data are used to determine whether impairments exist, using the state water
quality standards as the measure.
Some interpretation of narrative water quality standards is necessary, and it is clear
from the comments that some of the TMDLs are not supported by all the WAG
members. However, the TMDLs were based on the best available data and followed
the state of Idaho's process for meeting CWA requirements. We are aware of the
specifics of the concerns expressed above, have examined them carefully, and
conclude that the decisions to write the TMDLs in question are reasonable and
justified.
Process -- Public Participation
No. 1
Generally speaking, the South Fork Clearwater WAG does not support this TMDL.
Generally speaking, this is a dismal failure in the bureaucratic process of using local input on
a mandated project to address the water quality of Idaho. As a group, we want to have
quality and quantity water. We do not want to see water quality and quantity come before
the livelihood of our county.
I have been a member of the South Fork Water Advisory Group (WAG) for nearly two years,
attending one meeting each month. I have listened to agency people informing us on
temperature, sediment, nutrients, etc. I understood that the group was to make
recommendations and have a say in the final decision. Although we as a group have made
decisions on several important issues, the agency people have not acted upon those
proposals. In fact, when the temperature was found unreasonable to attain, it was lowered
another 5 degrees instead of being raised. Even though we have been told that this will be
changed when the final document is written, it still appears in the draft. I, again, state that
these temperatures are unreasonable and can never be reached.
The WAG has largely bought off, or been worn down, on the need for temperature TMDLs
basin-wide even though the Draft TMDL data, both WBAG 1996 and WBAG 2000, show
S- 3 Appendix S
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
that all listed water bodies except Three Mile and Butcher Ck. are fully supporting their
beneficial uses. The WAG agrees with the need for sediment TMDLs for the lower part of
the basin. It is the opinion of the WAG that addressing these areas will likely return all
streams in the basin to the full beneficial use support status. Let's deal with the major
problems first, the ones people can agree on, and see where we are after that. For plans that
are supposedly going to be voluntary in their implementation, it does no good to include
issues that are not agreed upon by those who will have to do the implementation.
No. 5
A key element to the success of this proposal is public cooperation and participation. We
feel that the success of this TMDL assessment and subsequent implementation would be
improved by increased public participation. This concept was given little priority in the draft
assessment. The role of the Watershed Advisory Group (WAG) was not clearly defined in
the assessment or TMDL. Aside from the WAG, formulating a strategy that involves the
greater public would improve the efficacy of the TMDLs through establishing a basis of
education, trust, and collaboration.
No. 7
I would have welcomed more active participation by Nez Perce Tribe representatives.
According to the Nez Perces' 1855 treaty with the United States, all of the SF Clearwater
watershed falls within reservation boundaries. This fact, combined with the fact of the Nez
Perces' cultural longevity in the area and the development of their fisheries program in recent
years, make Nez Perce involvement in the WAG process pertinent and valuable.
I would like here to add some general comments regarding the WAG process. I think almost
everyone WAG members and agency personnel would agree that in some ways, the SF
Clearwater WAG process has been, as the WAG letter states, a "dismal failure" in that it
became a painful saga of tremendous contention and, at times, even of chaos. I'd like to
suggest what I feel would be a better process for future WAGs: I suggest that initial WAG
formation and ongoing WAG meetings be conducted by a neutral facilitator who has a strong
character and training in group dynamics and methods of mediation. No meetings conducted
primarily by agency folks; no WAG member chair; no dominating tactics by vocal WAG
members; no side-winding surprises by agency representatives vying for supremacy. But a
skilled neutral facilitator. Please.
No. 8
First, I unfortunately find myself in agreement with that portion of the letter from the SF
WAG of July 7, and probably only that portion, that referred to the process as a "dismal
failure." However, my reasoning is much different than expressed in that letter. I had
assumed that the WAG process would present community members with the opportunity for
meaningful dialogue regarding the future of the SFCR and with the opportunity to search for
creative solutions to problems facing the river, always with the possibility of reaching some
consensus in this regard. In these respects, the WAG was indeed a dismal failure.
S- 4 Appendix S
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
The draft I have seen of the letter apparently crafted at the July 1, 2003 WAG meeting, which
I was unable to attend, does not represent my perspective at all. As stated in that letter, the
unchanging position of several WAG members can be summarized as follows:
1. Water quality and quantity are of secondary concern after the economic well-being of the
region.
2. The WAG does not want to see any added restrictions on the free use of any part of the
entire SF drainage, particularly if such restrictions might cause problems with position #1
above.
3. State and federal water quality standards are too high, can't be met, and therefore are not
worthy of pursuit, particularly of course if such pursuit would bump up against position #1
above.
In other words, the basic position of the WAG as stated in the July 7 letter addressing the SF
TMDL was not much different than that of the miners who dredged the drainage in the early
1900s.
These three general beliefs were blended with frequently confusing models, sometimes
limited data sets, interagency disagreements, masses of confusing information, and behind-
the-scenes maneuvering. The failure in the process was not only dismal, it was depressing.
And just in case you missed this point: I do not agree with positions 1, 2 and 3 above!
I would finally like to express my appreciation to the many agency folks who tried to
accomplish their task of meeting the requirements of state and federal law under what was
clearly a difficult situation. While the process was flawed and they didn't always do a
commendable job, the challenge was immense and I found them to be sincere in their efforts.
Response: The watershed advisory group (WAG) was established to solicit input
from the wide range of local interests in the South Fork Clearwater River Subbasin.
It is unfortunate, but not surprising given the wide range of views represented, that
many of those interests are not fully satisfied with the results of the subbasin
assessment and TMDLs. We have taken the global mandates of the federal Clean
Water Act, coupled them with sometimes ambiguous state water quality standards,
considered the WAG's input, and have crafted a plan to restore water quality in
South Fork Clearwater River Subbasin. The plan may be imperfect, but we do think
it is a reasonable synthesis of all available data and opinions, and a good
compromise among the federal, state, local and tribal viewpoints that will meet state
WQS. We will recommend to management that a neutral facilitator be considered
for future WAGs involving the 3 parties and diverse local interests.
Process - Economic Analysis
No. 1
Several members of the WAG have asked for economic analyses of the impacts that the
TMDLs will have, especially for the changes that will be required of the WWTP. There is a
real issue here that should be addressed. Regulations such as those being emplaced by this
S- 5 Appendix S
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
TMDL are an economic cost to our community. There is a real fear that our communities are
dying economically. Especially if Endangered Species considerations are going to drive
decisions within the TMDL, then economic analyses should be required. But even within the
CWA process itself, much more attention needs to be given to the economic impacts.
Economic impacts on the public, business and industry should be considered in writing the
TMDLs. Without an economy water quality doesn't matter.
No. 4
Grangeville has always been a progressive city and the Council wants to see our city do its
part in preserving our environment and protecting our streams. However, it is unfortunate
that many of the government environmental regulations placed upon small communities
carry a huge price tag and thus place a great financial strain on tight budgets.
No. 7
While the WAG letter states that "As a group, we do not want to see water quality and
quantity come before the livelihood of our county," the letter is expressing the opinion only
of a majority of our 16-person group. I do not accept "poor economic conditions" as an
excuse for pollution. Indeed, I feel that economic "poorness" may be ameliorated by the
"richness" of one's environmental surroundings. In other words, I do not agree that Idaho
County residents have, under any economic circumstances, the right to pollute, or damage in
any other way, the SF Clearwater watershed. Nor do I believe they have the right to ignore
needed improvements.
However, if we wish to talk of economics, I'd like to remind the reader that according to an
economic survey done in 2000 for the Kooskia Chamber of Commerce, the Idaho
Department of Commerce economic figures for recent years show that, second only to
timber, tourism is a powerful engine in central Idaho's economy. Removing federal dollars
from the picture, agriculture sits third in the list of mainstays in the area's economy. Tourism
flourishes here primarily because of the quality and beauty of our natural environment. In
light of the already existing lucrativeness of tourism in our area, the exceptional potential for
growth in tourism, and the already heavy use of the South Fork by local recreationists, I find
it extremely narrow-sighted for some WAG members to have stated at meetings that asking
even one cattleman to go to the expense of putting up a fence to limit his cows' access to the
stream is asking too much. The spirit of this statement apparent in the WAG letter is
inappropriate.
According to recently published figures, Kooskia alone reaped $3 million in economic
benefit from one (2001) salmon-steelhead fishing season. If we wish to put economics first,
these figures point directly to the importance of maintaining high water quality in order to
support fish survival. We have, according to a fisheries study presented to the WAG, seven
sensitive, threatened and endangered fish living part of their life cycles in the SF Clearwater
watershed, the one watershed in Idaho pointed to as the habitat with the greatest potential for
supporting species recoveries. I favor any restrictions on any sector of the SF Clearwater
drainage that does support that survival and any TMDL targets that do support that survival.
S- 6 Appendix S
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
I find no standards or targets in the TMDL, excepting where they may be more stringent, that
will negatively and/or drastically impact the socio-economic situation in Idaho County. Nor
do I feel that we need to conduct an economic impact study. We know what we need to
know: streams in the watershed are impaired and it's up to us to improve them. An economic
impact study would be irrelevant to the focal issues: impairment/improvement.
No. 8
I would be remiss if I did not challenge the frequently expressed belief at WAG meetings that
Idaho County's economic lifeblood is logging and agriculture, since this position appears to
underlie a significant part of the objections to the TMDL. Contrary to the statement
expressed by the WAG's tourism representative that "you can't make any money cleaning
toilets," travel and tourism play a significant and growing role in the economy of the state, of
north central Idaho, and of Idaho County. For example, in some recent years total sales in
the travel and tourism sector have exceeded the sales of all agricultural products on both a
county and regional basis. To ignore the economic advantages to the county and region of
clean and plentiful water in our rivers and streams is a grave mistake. Even beyond the
major economic impact of travel and tourism, many people in today's world of
telecommunications select the area in which they choose to live and work based upon the
quality of the nearby environment, with particular emphasis on clean air and water. Many of
these potential newcomers can bring with them small businesses, retirement income, and the
strong probability of an expanded tax base.
On a related note, I recall in the early 1970s during the implementation of the Wild and
Scenic Rivers Act in Idaho County that a common local opinion was that the land along the
Middle Fork of the Clearwater River would become worthless because of government
regulations on land use. Today the highest priced land in the county is that within the scenic
easement boundaries.
Response: We agree with the general concept that economic impacts should be
factored into decisions on how to address environmental problems. In theory, the
subbasin assessment and TMDL development should concern itself primarily with
the technical question of whether waters are polluted and how much the pollutants
need to be reduced for the waters to meet water quality standards. The economic
questions should come during implementation when decisions are made of how to
reduce the pollutant loading. In reality, however, the development of the subbasin
assessment and TMDLs is not a purely technical problem and requires numerous
decisions that take into consideration political, social and economic interests. We
think we have been sensitive to these interests, through interactions with the WAG
and others, and have attempted to structure the TMDLs so they do not limit options
available for reducing the pollutants.
We are obligated to write subbasin assessments and TMDLs within the framework of
state and federal regulations. None of the rules or regulations under which these
TMDLs were developed includes any consideration of economic factors or analyses
as a component of the TMDL process. In the current climate of limited government
finances and a court-ordered time frame for completing the TMDLs, the option of
S- 7 Appendix S
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
economic analysis was not available, nor is it clear that the results could influence
TMDL targets.
Process - Effects on Grangeville
No. 4
I would like to see some tolerance extended to small communities. It stands to reason that
costly solutions to environmental problems require an increase in taxes and water and sewer
rates. Our citizens must bear the brunt of these expenses at a time when Grangeville and all
of Idaho County are experiencing economic depression and high unemployment.
I feel some slack should be give to small towns in meeting environmental quality standards.
If not, we may end up protecting water quality and fish habitat while destroying the quality
of life for human beings.
The Grangeville city Council has been forced to authorize the expenditure of thousands of
dollars for water and fish studies on Three-Mile Creek to try to protect our rights - thousands
of dollars our city budget can ill afford. Therefore, I hope you will:
1. Carefully consider the points made by Kevin Gardes, P.E., of Kimball
Engineering - the engineer conducting our water study.
2. Grant consideration to Grangeville and other small communities who are
facing additional financial stress from government imposed environmental
regulations.
Response: This subbasin assessment and TMDLs have identified temperature and
nutrient problems with the city of Grangeville WWTP, and as a permitted point
source, the city is underpressure to deal with the problems. The possible solutions
to the problems and the time frames for implementing those solutions do appear
limiting in light of the technical complexity and economics of the situation. USEPA,
DEQ, and the NPT have let it be known that they understand the need for time to
develop and implement possible solutions. We are committed to working with the
city and their engineers to craft a viable strategy for addressing the problems, and
have adjusted wasteload allocations for nutrients based on comments from Kevin
Gardes, Kimball Engineering. We commend the city in their efforts to work with us in
the development of the TMDLs and look forward to continued constructive
engagement between the city and agencies as we look for viable means to bring
Threemile Creek up to state standards.
Process - Combining TMDL and IDWR WAGs
No. 1
It has not been easy to keep the IDWR water planning process separate from the TMDL
water quality process with respect to the understanding of the WAG members. While it may
seem like an efficiency of effort to have the same WAG for both processes, many of the
WAG members see them as the same water planning process, implying that they probably
should be combined in some way.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Response: The TMDL process took longer than expected, thus overlapping the
timeframe set up for the WAG to work with the IDWR water planning process. The
resultant effort to work on both processes at the same time was confusing because
they do raise many of the same issues. The WAG's recommendation of combining
the two processes will be forwarded to program staff of DEQ and IDWR for
consideration.
Process - Address Aesthetics
No. 7
... Also, I recommend that a means be found to address watershed "aesthetics" in the TMDL
process.
Response: We appreciate the concern about watershed aesthetics, but the TMDL
process by law can only address loading of pollutants to surface water. It is our
expectation that when streamside vegetation is reestablished to a state somewhat
resembling its natural condition as a result of implementing the sediment and
temperature TMDLs, aesthetics will be improved.
Water Quality Standards - Temperature
No. 1
Since November 2001, the WAG has heard presentations by the agencies, and the WAG has
repeatedly informed the agencies of unrealistic water quality standards. The natural water
temperature exceeds the WQS. Streamside shade restoration will not make the impact
necessary to lower the temperature. We have heard offish populations, in streams like Three
Mile Creek, where there was never factual data to support such classifications. The list of
unattainable water quality standards does not end here. The agencies need to work more with
the community to reach attainable standards, those that will not be negatively and drastically
impacting the socio-economic impacts of Idaho County.
The Water quality standards are unrealistic for the South Fork Clearwater drainage. The
'natural' temperature presently exceeds the WQS. The agencies have acknowledged that
fact, and have commented the human cause components will be the targets.
... In fact, when the temperature was found unreasonable to attain, it was lowered another 5
degrees instead of being raised. Even though we have been told that this will be changed
when the final document is written, it still appears in the draft. I, again, state that these
temperatures are unreasonable and can never be reached.
The state's water temperature standards are almost too bizarre for words. We have numeric
temperature standards which everyone agrees are unrealistic and largely unattainable. So, in
order to address this problem, the state inserts language in the code that we only have to deal
with the human caused part of heat loading in the TMDL. But the point sources such as the
WWTPs still have to deal with the unrealistic numeric standards. We clearly need some
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
temperature standards that relate directly to natural conditions and the needs of the fish in the
waters being considered.
No. 7
First, I have throughout the WAG process understood that implementation of proposed
improvements involves "moving towards" targets, making genuine attempts towards
improving water quality. Therefore, I have no objection to temperature targets that some
people consider unachievable.
Response: The agencies recognize that there are in fact problems with existing
temperature criteria. Much time and effort has been spent over the last few years
trying to develop temperature criteria that work better. USEPA has issued new
guidance for temperature standards for Washington, Oregon, and Idaho. The
temperature standards issues have been a major stumbling block in the
development of these TMDLs, partly because they changed in the middle of the
process, but also partly because the numeric criteria are probably cooler than
stream temperatures would be naturally in lower elevation streams in the absence of
man's influence.
In the end, however, the nonpoint source temperature TMDLs are written based on
the simple premise of returning stream and river shading to its natural level. It is
assumed that human disturbance of natural stream shading is a major source of
increased heat loading that is human caused and is the most easily remedied.
Stream widening also increases heat loading and may be due to human activities,
but making channel modifications is typically more difficult and expensive. The
targets of all of the nonpoint temperature TMDLs are set in an attempt to return
stream shading to its natural level. These targets are reasonable and attainable.
They are expected to restore full beneficial use conditions of the streams, even
though the stream temperature under those more natural conditions is not currently
known.
The discrepancy between the target base for nonpoint vs. point sources in this
TMDL is real, as noted by the commentor. The Grangeville WWTP is the only point
source with a significant heat load problem. We were unable to develop an
acceptable estimate of natural stream temperatures for Threemile Creek. In the
absence of reliable site-specific temperature data, the wasteload allocation is based
on the numeric temperature criteria, with the provision that Grangeville can increase
stream temperature by 0.3°C above these criteria. This approach is consistent with
the most recent guidance for establishing point source allocations, but we realize
that if natural background temperatures are somewhat higher than the current
criteria, this results in a very conservative estimate of the needed heat load
reductions by the Grangeville WWTP.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Beneficial Uses - General
No. 1
The WAG has largely bought off, or been worn down, on the need for temperature TMDLs
basin-wide even though the Draft TMDL data, both WBAG 1996 and WBAG 2000, show
that all listed water bodies except Three Mile and Butcher Ck. are fully supporting their
beneficial uses.
Response: An issue throughout the assessment of sediment and nutrients in this
document has been the question of what constitutes impairment of beneficial uses,
particularly impairment of the salmonid spawning beneficial use. The Idaho water
quality standards leave considerable room for interpretation. DEQ utilizes the
WBAG methodology to provide such interpretations. However, the three parties
were not able to reach agreement in all cases on the interpretation of WBAG results.
TMDLs were only written for waterbodies for which all three parties could agree.
Beneficial Uses - Endangered Species
No. 1
Endangered species considerations have greatly influenced the actions of the government
agencies involved with this TMDL, yet there evidently is no authority for them to be doing
so under the Clean Water Act. Salmonid spawning is occurring throughout the upper basin
above Harpster, by general consensus of the Fisheries Technical Advisory Group and
reported in this TMDL. There should be no question of full-support status for all streams
above Harpster given the fish populations that exist up there. The fact that they are not
adequate for some tribal needs, or some vague plan by NMFS, should not be construed as
evidence that water quality, as envisioned under the Clean Water Act, is not being attained.
No. 2
The fish species currently listed under the Endangered Species Act were discussed during the
TMDL process. They must be considered in the context of the South Fork Clearwater River
subbasin. However, there is no evidence to suggest that ESA-listed species greatly affected
the draft TMDL, as indicated in the WAG letter.
No. 6
The WAG letter draft that I saw indicated that ESA listed species greatly affected the draft
TMDL. The WAG and agencies did discuss species listed under the ESA. The ESA is the
law and must be considered in this basin. However, at no time did I feel that the species listed
under the ESA was the driving force behind the draft TMDL, nor do I feel it had any great
impact on the draft. In fact, my concern is that not enough significance was given to listed
species nor to the fact the SF CWR has the greatest habitat potential in the state for species
recovery. The DEQ should be striving to attain the highest possible water quality and habitat
in this basin, not the lowest quality capable of sustaining minimum numbers of the species.
Response: The issue of habitat for endangered species, especially spring Chinook
and steelhead, has been a major consideration throughout the deliberations for this
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
document. The targets of the most relevant TMDLs, sediment and temperature,
were derived from existing Idaho water quality standards. These standards are
established to fully support cold water aquatic life and salmonid spawning. Some of
the salmonid species intended to be protected by these standards are threatened or
endangered species under the ESA. While it is expected that these TMDLs will be
an important step in improving water quality conditions for these species, the targets
and goals within the TMDLs reflect what is needed to achieve Idaho's WQS, and
have not been further modified simply because some of the salmonid species in the
sub basin are listed under the ESA.
We have reached compromise agreements among the agencies for this sub basin
assessment process to move forward. As with any compromise, there are parties on
both sides of the issue, as shown in the comments. We have given full and fair
consideration to endangered species within the requirements of the CWA and
Idaho's water quality standards.
Beneficial Uses -- Threemile Creek
No. 1
... We have heard offish populations, in streams like Three Mile Creek, where there was
never factual data to support such classifications...
Three Mile Creek (Grangeville Wastewater Treatment Plant) is a terribly big issue. We
loudly disagree with the draft on this issue. We as a group voted to take the salmonid
spawning issue off the creek above the falls. An ironic situation is involved with this creek.
If the WWTP puts their water on the land in the summer, the creek will be dry below the
plant and there will be no water to test! Where is the thinking here? Do you want water or
do you want NO water?
Motion on November 20, 2002: That we change the beneficial use status of Three Mile
Creek, above the falls at sk 9.5, from salmonid spawning to cold water biota.
Vote: In favor (14) Opposed (0)
No. 3
Page 29, subsection entitled Threemile Creek: The third sentence states "Adult steelhead
have been observed during the past in the segment of the creek flowing through Grangeville
(BLM 1999)."
It is our understanding that this sentence comes from Craig Johnson (BLM) and is based on
anecdotal evidence. The statement about steelhead evidently comes from a conversation that
Daniel Stewart (IDEQ) had with a former USFS-Moose Cr. ranger district fire type, Mark
Woods (currently Fire Warden, Southern Idaho Timber Protective Association, McCall, ID,
208-634-2268), that was cited by Mr. Johnson. Mr. Stewart recently tracked down Mr.
Woods to verify the account. The person who caught the fish was Bruce Fulton and it was in
the early 60's. The fish was purported to be 18" in length. The fish was found in the Creek
after high water went down. This fish likely was washed out of someone's pond along the
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
creek. The fish was not identified as a steelhead. In previous studies on the Creek, other
rainbow trout in this size range (this size being the upper end) have been found in Threemile
Creek. It is our understanding that there is no way that a fish in the 18" size range could be
conclusively called a steelhead without further evidence, which to our knowledge does not
exist. We request that any reference to finding steelhead in the upper portion of Threemile
Creek (above the migration barrier - chute/falls) be removed from the TMDL.
The City of Grangeville is actively pursuing reclassification of the upper portion of
Threemile Creek from salmonid spawning to year-round cold water biota. The City hired
EcoAnalysts of Moscow to perform fish survey work, including characterization of a
potential migration barrier on Threemile Creek. This work is being done in consultation with
IDEQ-Lewiston. A full migration barrier has been identified. Previously, portions of the
fish survey and barrier characterization report have been sent to Tom Dechert in draft form.
A full report will be submitted in the near future to IDEQ. Recent electrofishing activities on
Threemile Creek revealed some adult rainbow trout, but no young of year trout (none were
found that would have shown spawning activity in the last 2 years). In other words a viable
(reproducing) population is not present in the upper portion of Threemile Creek. This
ongoing work should be identified in the TMDL, to give a link back to the TMDL in the
future when reclassification is completed.
The City of Grangeville recently completed a survey of local landowners in the Grangeville
area (upstream of the WWTP) that have ponds in the near vicinity to Threemile Creek, and
that have been stocked with fish in the past. I am attaching an e-mail from Ken Gortsema,
Public Works Director in Grangeville that indicates the results of the City's survey. (The
email is not copied into this TMDL document because it contains personal information of
landowners. It is available for review at the DEQ office in Lewiston.) As you can see, there
are a number of ponds that have been stocked with rainbow trout that overflow into
Threemile Creek. The occasional rainbow trout that turns up in previous electrofishing
activities is almost certainly a result of escapees from one of the ponds identified.
Response: Salmonid spawning is one of the designated beneficial uses in the
Idaho administrative rules for Threemile Creek (IDAPA 58.01.02.120.07). The point
of these comments is that salmonid spawning in not a beneficial use of Threemile
Creek; that in fact its highest beneficial use is cold water aquatic life. The conclusion
is that the salmonid spawning designation in the administrative rules is incorrect and
needs to be changed.
It is beyond the scope of the subbasin assessment to change a designated
beneficial use, especially if that change is to downgrade the use designation, as
changing the beneficial use from salmonid spawning to cold water aquatic life would
be. The only tool available for downgrading a beneficial use designation is the Use
Attainability Analysis (UAA). A UAA pulls together all the information to justify the
use change, which will then be moved forward through the administrative rule
making process, approval by the state legislature, and final approval by USEPA.
Some of the comment provided comes from the UAA process that has been set in
motion to try to change the beneficial use designation for Threemile Creek.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
It is unknown at this time whether the UAA and subsequent steps will result in an
eventual USEPA approved change to the Idaho administrative rule designation for
Threemile Creek. In the meantime, the subbasin assessment and TMDL loading
analyses have been developed based on the current designation. We have no
authority to do otherwise, except to defer the development of the TMDL altogether,
which is strongly discouraged under current guidance for TMDL development in
Idaho. At whatever time it is known that the UAA/rule change has been successful,
the waste load allocation for the WWTP will be adjusted accordingly. In the
meantime, the City of Grangeville is encouraged to begin considering options to
reduce heat loading to Threemile Creek. This TMDL does not stipulate or advocate
any particular solution for the WWTP, including land application; only that the City of
Grangeville begin looking for ways to deal with the problems their WWTP effluent is
causing in Threemile Creek.
It seems prudent to develop the temperature TMDLs based on the salmonid
spawning beneficial use as an indicator to the city of Grangeville and landowners
along Threemile Creek of the magnitude of water quality degradation from both
nutrients and temperature. Planning needs to take place to come up with measures
to correct the problems. There are both point source and non-point source
contributions to the problems, and the solutions may be complex and a long time in
coming. From the water quality point of view, there is no reason to delay identifying
the problem in general terms, and encouraging the development of solutions.
Pollutant Sources - CAFOs
No. 1
This document states that Confined Animal Feeding Operations (CAFOs) are a point source
and also a non-point source. There are no outright CAFOs (as per CAFO definition) in this
sub-basin, but there are small animal feeding operations.
On page 212 the TMDL states that CAFOs are common in neighboring areas. This is
untrue!! Most of the last paragraph should be taken out!!
Response: We appreciate these inconsistencies being brought to our attention and
have made the corrections.
Nonpoint Sediment Sources - Roads
No. 1
The major contribution of sediment in the drainage is from the roads. At this time, the road
district will have to explore options on how to make a reduction in the impact. At this time,
there are limited alternatives.
If there is a reduction in sediment loading from the roads, ultimately the temperature will also
decrease. At this time, the road district will have to explore options on how to make a
reduction in the impact. Again, there are limited alternatives.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
No. 7
The major contributor to sediment in the watershed is not roads, as the WAG letter states,
but, as I understand the information presented to us, agricultural run-off. Further, to address
the sediment issue, as the letter does, by complaining "there are limited alternatives," reflects
an attitude that can only negatively impact the watershed. I am glad that the TMDL has been
written, that it has, in effect, pushed through at least some of the wall that such an attitude
erects.
Response: Roads probably are the major source of sediment in the forested part of
the subbasin, while agriculture is the major source in the non-forested part. For
roads that fall under the jurisdiction of the Forest Practices Act, a large number of
BMPs have been developed to address sediment. The federal management
agencies have developed additional BMPs for roads on their land. For county roads,
especially those running through agricultural lands, economically viable sediment
reduction BMPs are much harder to come by. We look forward to working with the
road districts as they begin examining their alternatives.
Nonpoint Sediment Sources - Suction Dredge Mining
No. 1
Suction dredge mining: Current federal regulations from the Idaho Water Rights Board
address suction dredge (recreational) mining. There is not a significant impact on sediment
with current operations, as being federally regulated. Therefore, the South Fork Clearwater
WAG is in agreement with the comments on pages 99 and 100 (3.1- Sources of Pollutants of
Concern/Suction Dredge Mining).
No. 2
The Idaho Water Resources Board does not set federal regulations for suction dredge mining,
as stated in the WAG letter (no. 1). They have oversight responsibility for the Idaho Stream
Alteration Act that does affect suction dredge mining. There are separate federal mining
regulations that apply to suction dredging on federal lands.
No. 6
On Page 100 of the draft TMDL state that "...dredging is only allowed from July 15 through
August 15 each year, in order to avoid periods when chinook, cutthroat, and steelhead are
spawning and eggs are incubating." It also mentions that the USFS has received three
applications to operate suction dredges for larger scale operations who propose to operate
dredges larger than 5 inches. One application is for year round dredging in Red River,
another is for operation July-October on the SF CWR. Issuing permits for these time frames
would be inconsistent with the need to avoid spawning and incubating time periods.
Response: We understand and appreciate that these comments are supportive of
the TMDL as it addresses suction dredging. The comments identify regulatory
agencies that need to be aware of controls established by Idaho's water quality
standards.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Nonpoint Temperature Sources -- Roads
No. 1
If there is a reduction in sediment loading from the roads, ultimately the temperature will also
decrease. At this time, the road district will have to explore options on how to make a
reduction in the impact. Again, there are limited alternatives.
Response: We certainly agree most of the BMPs as we know them that would
reduce sediment from roads will also result in reducing temperatures.
Missing Data
No. 8
A second concern relates to the need for additional data in several areas with which to make
wise, scientifically-based decisions. The lack of adequate data was a problem throughout the
WAG process. The TMDL mentions the need for additional data, but treats this topic very
lightly.
Response: We agree that filling data gaps is an important consideration. Additional
discussion of data gaps and the need to fill them has been included in Section 5.5
Implementation Strategies. It is expected that more detailed plans and commitments
to collect this data will be included in the Implementation Plan, and we encourage
stakeholder participation in its development.
Delisting Proposal - Sediment
No. 1
As a group, we voted to take sediment off the list of problems above the Mt. Idaho Bridge.
The agencies came back and told us that that was done. ONLY now sediment is listed for all
the tributaries into the main South Fork, so what did we actually accomplish? The SFC
WAG voted no on sediment TMDL above the Mt. Idaho Bridge.
Motion on November 20, 2002: That with the additional data received today that the WAG
move to remove all streams (from the 303-d list) above Harpster Bridge, with the exception
of Beaver Creek in the upper reaches, that would have been listed for sediment on the 1998
WBAG
Vote: In favor (11) Opposed (3)
Motion on May 21, 2003, to clarify the November 20 motion:
That the tributaries as well as the main stem of the South Fork of the Clearwater be removed
from the sediment TMDL, above Harpster Bridge, with the exception of Beaver Creek.
Vote: In favor (8) Opposed (2) Abstain from the vote (2)
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No. 5
We understand the need to assess this watershed and set TMDLs based on state regulations
and the best available data. We feel, though, that insufficient discussion and evidence was
given to support the decision to delist the eight streams for sediment. Habitat for fish and
macroinvetebrates have been degraded for decades by human activities and should not be
further compromised through more lenient restrictions on development.
There was insufficient discussion in the SB A concerning the delisting of the many tributaries
in the upper main stem of the SF CWR. The statements and comments that were in the
report regarding the delisted streams were not clear and were not well organized and
documented. A more complete and succinct summary of the rationale for delisting the
tributaries of the upper SF CWR should be provided to the public and also be made available
for comment in a supplementary document.
Response: This TMDL is not the official proposal to delist these tributaries, which
will occur during the 2004 Integrated Report process, in which the 303(d) list is
established. We appreciate the comments we received on this issue, but encourage
you to submit your comments on these issues during the 2004 listing process.
Sediment as represented by total suspended solids, cobble embeddedness, pool frequency,
pool volume, and turbidity all have an effect on the ability offish and macroinvertebrate
species to survive, spawn, migrate, and seek habitat. A high amount of fine sediment
decreases interstitial space on the stream bed and thereby decreases the dissolved oxygen
concentrations along and in the stream bed. Habitat for smaller fish and other species
becomes filled with fine sediment, thus decreasing species diversity and abundance.
Of the streams on the 303(d) list for sediment, only three are proposed for TMDLs for
sediment. All of the streams that are being delisted for sediment pollution are also classified
for salmonid spawning and secondary contact recreation, both of which depend largely on the
levels of sediment in the water and along the beds of these streams. Sediment loads should
not be defined based solely on turbidity, but as a combination of turbidity and cobble
embeddedness, especially in the portion of the SF CWR subbasin above Harpster. The Water
Body Assessment Guidance does not restrict the assessment of impairment for sediment to a
limited amount or type of data. Inclusion of additional data in assessing the streams
proposed for sediment delisting may convey that they are impaired, do not meet beneficial
use of salmonid spawning, and should be provided for public comment.
Discussion concerning the degree of cobble embeddedness needs to be included in the SBA
and deserves to be included among the criteria for sediment TMDL development. Cobble
embeddedness is used throughout much of the Pacific NW as an indicator of management-
related sediment impacts in streams, with high cobble embeddedness levels associated with
declines in salmonid spawning activity. There needs to be a discussion of the importance of
the cobble embeddedness and percent fine sediment data and how it can affect the vitality of
fish and macroinvertebrate species. The assessment and TMDL gives poor indication that
the tributaries to be delisted are not free from impairments and pollution from sediment.
Rather, in the assessment the main rationale seems to be based on assumptions that all of the
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
SF CWR sediment problems would be resolved by reductions in lower parts of the subbasin.
Also, the assessment and TMDL do not indicate that the beneficial uses are being entirely
met. Salmon once flourished in the SF CWR and tributaries. Due to habitat degradation and
the effect of dams and pollution, and other developments their populations have decreased
drastically. Now they exist in these streams in smaller populations and with less vigor
because the habitat is not optimal for their existence. A basic first step to improving salmon
habitat would be to set stricter TMDLs for sediment in order that pool frequencies increase
and cobble embeddedness decrease.
In the TMDL section for Total Suspended Solids and Bedload Data, it was indicated that
some of the data, due to spatial and temporal diversity, were difficult to use for subbasin
analysis. More data needs to be collected while other parameters and indicators (percent fine
sediment, pool frequency, pool volume, and cobble embeddedness, total dissolved solids,
Wolman pebble count) need to be given a more complete analysis, especially in streams
above Harpster. In order that a more thorough description of the subbasin be developed, we
recommend that assessments be based on data sets that were developed over multiple
sessions of sampling throughout various times of the year at a diversity of sites. In addition,
consultations with the US Fish and Wildlife Service and the Idaho Department of Fish and
Game would increase the value and usefulness of your assessment and inventory offish
species and habitats.
We suggest that TMDLs for sediment be set for the streams and main stem of the SF CWR
and subbasin above Harpster. Cobble embeddedness surrogate targets below 20-30% should
be set in salmon rearing habitat depending on channel type. Targets should be set on
reference conditions for cobble embeddedness, percent fines by depth, and pool volume.
Surface fine sediment should be less than or equal to 20% in spawning areas. There should
also be an objective set for an increasing trend in residual pool volume. The current proposal
is not only ignoring the full scope of sediment problems in the subbasin, it is also
inconsistent with the management objectives of the Nez Perce National Forest, the National
Oceanic and Atmospheric Administration - Fisheries consultation for the Endangered
Species Act, and designation by the state as a Special Resource Water.
No. 6
I strongly object to delisting any of the tributaries or upper main stem of the SF CWR for
sediment. While the lower SF CWR has greater sediment from ag lands, the upper SF CWR
does have significant sources of sediment that could be addressed in the implementation plan.
Also, the upper SF CWR has the highest percentage of critical habitat for spawning
spring/summer chinook and steelhead which should carry greater weight in the equation. All
of the listed streams had high cobble embeddedness numbers that support listing.
Much discussion was given to various testing numbers and the validity of one scientific
method of measuring or another. I have been kayaking the SF CWR, all of it above Harpster,
for over 20 years and I don't need a test to tell me that there is a problem with sediment. I
can see it with my own eyes every time I boat this river.
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No. 7
I do not concur with some WAG members' contention that we ought to have delisted any
303d listed streams in the watershed. Indeed, I feel we ought to have added some.
I would like to have seen greater, consistent attention given to studying cobble embeddedness
and stream flow and recommend that thorough, consistent data be built in these two areas for
future use. Also, I recommend that a means be found to address watershed "aesthetics" in the
TMDL process.
No. 8
In terms of the TMDL itself, I have concerns about the proposed delisting for sediment of 7
SF tributaries. If the SF mainstem has sediment problems throughout much of its length, at
least some of this sediment must be coming from its tributaries. Further, all of these same
streams exceed water quality standards for temperature, and temperature is negatively
impacted by sediment. It thus seems unwise to leave unaddressed the issue of sediment in
these 7 streams. Cobble embeddedness as it relates to salmonid spawning adds to my
concerns in this area.
Response: The final document has been changed such that delisting of tributary
streams above Harpster is not being recommended as a conclusion. It has been
concluded that the delisting recommendations are properly a function of the
integrated listing process within which the 303(d) list is created, the next cycle for
revision occurring in 2004.
Consistent with the state of Idaho guidance for pollutant assessment related to the
development of TMDLs, we have collected and analyzed all of the available and
pertinent data. We solicited a wide range of professional opinion. We drew our
conclusions based on the totality of the data and professional opinion. The volume
of available information is huge, much of which is presented in the subbasin
assessment. Idaho's narrative standard for sediment requires the use of best
professional judgement, based on all the information.
As the public comments reflect, there is not any broad agreement on 1) the definition
of beneficial use impairment, 2) how to measure whether sediment is impairing
beneficial uses, and 3) how to weigh different measures against each other within
the state water quality guidance. In the South Fork Clearwater River Subbasin,
these questions are confounded by impacts on beneficial uses of elevated stream
temperatures. The BURP/WBAG information, the Fish TAG information, the
sediment budget information, the reference watershed information, local users
information, and technical literature information all address these issues in different
ways. In the final analysis, the three parties weighed all of the available data,
information and input from the WAG and resource professionals in relation to the
state water quality standards. The parties could not agree on the need to write
sediment TMDLs in the upper tributaries, but did agree to write sediment TMDLs for
the mainstem South Fork Clearwater River, as presented in the final TMDL.
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TMDLs - Grangeville WWTP
No. 1
The Grangeville wastewater treatment plant's requirements to land apply their waster water
will greatly reduce and sometimes totally eliminate the flow of Three Mile Creek. What sort
of impact on water quality is that? That is not considered. Also, what economic impact is it
on the City of Grangeville?
Response: There is no requirement in the TMDL for the Grangeville WWTP to land
apply their waste water. That possibility has been under discussion, was overstated
in the public comment draft of the TMDL, and has been corrected in the final version.
... An ironic situation is involved with this creek. If the WWTP puts their water on the land
in the summer, the creek will be dry below the plant and there will be no water to test!
Where is the thinking here? Do you want water or do you want NO water?
No. 3
Page 145, subsection entitled Target Selection: The second sentence states " Grangeville is
considering land application of its wastewater during the critical time period for excessive
growth (July thru mid-September)."
Page 147, subsection entitled Load and Wasteload Allocations: Third paragraph, first
sentence, states "The WLA for the Grangeville WWTP was established as 0 for both TP and
TN, as the city has agreed to land apply effluent during the critical time period (July through
mi d- S eptemb er)."
The sentence on Page 145 is correct, the one on Page 147 is not. (Response: Page 147
has been corrected.) After the TMDL is finalized the City of Grangeville will complete a
wastewater facility plan to determine their options and select a preferred alternative to meet
the requirements outlined in their next NPDES permit and the requirements of the TMDL as
incorporated into the permit. While land application is certainly an alternative that will be
considered, it has not been selected as the preferred alternative. Options (e.g. treatment) that
continue the wastewater treatment plant's year-round discharge to Threemile Creek will also
be evaluated.
Response: There is no intent in the TMDLs to limit the city of Grangeville's options
for meeting the state water quality standards. The water quantity issue is one the
city and community will have to grapple with as they evaluate options to improve
water quality.
TMDLs - Grangeville WWTP and Temperature
No. 3
Page xiii, states "Sub-basin-wide temperature analyses were conducted in light of an
extensive database indicating that no stream in the SF CWR Subbasin, not even ones in
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
relatively pristine condition, meets the Idaho numeric temperature criteria for salmonid
spawning."
and
Section 5.3 Temperature TMDLs
On pages 178 and 179, Tables 45 and 46 list the daily maximum effluent temperatures for the
Grangeville wastewater treatment plant. They appear to be based on 9°C (Table 45) and
19°C (Table 46). These values are the daily average criteria for Salmonid Spawning and
Cold Water Biota, respectively. It would seem more appropriate to either change the Table
from "Maximum" to "Average", or recalculate the Table utilizing the daily maximum criteria
from the WO standards.
Response: Tables 45 and 46 are intended to insure compliance with the daily
average criteria for salmonid spawning. While the wasteload allocation is expressed
as a "maximum daily" value, "daily discharge" is defined in 40 CFR 122.2 as "... the
average measurement of the pollutant over the day...". Consequently, daily average
effluent values may be used for compliance determinations, which is consistent with
the use of a daily average temperature criteria.
Per IDAPA 58.01.02.401.03.a.v, "If temperature criteria for the designated aquatic life use
exceeded in the receiving waters upstream of the discharge due to natural background
conditions, then Sub sections 401.03.a.iii. and 401.03.a.iv. do not apply and instead
wastewater must not raise the receiving water temperatures by more than three tenths (0.3)
degrees C."
However, it appears that for Tables 45 and 46 the WQ standard criteria is utilized as the
stating point and no consideration is given if the stream naturally exceeds the WQ criteria.
For instance, if the water temperature above the WWTP outfall is naturally 10°C (daily
average) for a given day in May, and the effluent discharge is 1.0 cfs, and the Creek flow is 7
cfs, the Table lists 9.8°C as the daily maximum. In this example, it does not seem that the
intent of the natural conditions provision is incorporated into the Tables. It would be more
appropriate to utilize a target temperature that is 0.3°C higher than the upstream (of
discharge) water temperature, measured on a daily basis, except for periods when the Creek
is meeting WO standards.
When the draft SF Clearwater TMDL was presented to the Clearwater BAG in Clarkston on
July 10, 2003, the impression left from the DEQ presentation was that the State is moving
away from a numeric target with respect to temperature to a narrative target (percent canopy
or shading) due to the recognized problem of streams naturally exceeding the temperature
standard. However, this same line of reasoning is not applied to point sources, such as
wastewater treatment plant discharges. There is a good deal of cover over Threemile Creek
as it moves from the base of the forested mountain area through the City to the wastewater
treatment plant outfall. It therefore, seems reasonable to assume that the temperature in
Threemile Creek just above the outfall pipe represents the natural temperature condition, and
the wastewater treatment plant discharge target should be 0.3°C above this reading, measured
on a daily basis.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
Response: Several options for determining the natural temperature of Threemile
Creek were considered in drafting the TMDL, including using temperatures
measured immediately upstream of the outfall, as suggested by the commentor. In
reviewing land use information for the watershed upstream of the outfall, it was
determined that road construction and timber harvest had occurred in the uppermost
watershed, including encroachment within the riparian zone. Between the forested
upper watershed and Grangeville, land use changes to a mix of residential and
pasture (grazing) with at least two road crossings. While riparian vegetation
(primarily hawthorne and low grass) occurs in the pasture area, grazing appears to
have impacted vegetation and streambanks in this reach, which would affect stream
shading and stream temperature. Threemile Creek flows through the city of
Grangeville below this point, where there are numerous stream crossings and a
severely altered stream channel. Given the extent of human activities within the
watershed upstream of the WWTP, particularly factors within the riparian area which
would affect stream temperature, the watershed and hence temperature conditions
could not be considered to represent "natural conditions" for purposes of
establishing a wasteload allocation for temperature for the Grangeville WWTP.
TMDLs - Kooskia WWTP and Temperature
No. 1
The City of Kooskia will be asking for a motion by the SFC WAG to support the City of
Kooskia, as to have the Regulatory Agencies to use waste load allocations for effluent
temperature, based on mass balance calculations and provisions as set in Idaho Water Quality
Standards and not using their best guess scenario to establish a daily maximum temperature.
Where as Stites has received funding to transport their wastewater to Kooskia beginning this
winter, and where as Elk City has the capacity to store their wastewater in the summer, those
two communities will not be included in this motion.
Response: The wasteload temperature allocations for Kooskia have been revised
in the final TMDL to reflect recent temperature data provided by the city, which
indicates that effluent temperatures reach a maximum of26°C.
TMDLs - Grangeville WWTP and Nutrients
No. 3
.. ._We request that a TP target of 0.1 mg/1, converted to mass loading (Ib/day), as identified
in the TMDL be used to calculate a wasteload allocation for the wastewater treatment plant,
not 0 mg/1 as identified in the draft TMDL^
(Response: Thank you. We have corrected this in the final document.)
Page 145, subsection entitled Target Selection: The fifth paragraph addresses a TN target of
0.3 mg/1.
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
With a TP target of 0.1 mg/1, phosphorus would become the limiting nutrient, and there
would not be a need for a nitrogen limit. Use of a limiting nutrient has been standard
practice on other TMDLs (e.g. Paradise Creek). EPA has previously accepted that
phosphorus is normally limiting in freshwater systems. At this point in time, there are
treatment technologies that may reduce TP to levels in the 0.1 mg/1 range, however we do not
know of any to treat TN to 0.3 mg/1 levels. We request that all mention of a TN target be
removed from the TMDL.
Response: Thank you for the comment. We have revised the nutrient TMDLs to
eliminate the TMDL for nitrogen, and focused the TMDL on phosphorus as the
limiting nutrient. The expectation is that phorphorus will be reduced to a level that
will limit nuisance algal growth.
TMDLs - Nutrients/DO
No. 1
... And nutrient/DO TMDLs are written for Three Mile Creek, where no impairment is
shown. In addition, in the case of Three Mile Creek, there is no evidence that the nutrient
load reductions being required of the WWTP will result in improved water quality. In fact if
the city decided to land apply, water quanity during the summer will be reduced and water
quality during that time period may decline.
Response: Both phosphorus and nitrogen concentrations in the creek below the
WWTP are more than 100 times the USE PA guidance concentrations. While no
direct link could be shown to the beneficial uses, such high levels are a very strong
indication that beneficial uses are being impaired, and in and of themselves warrant
development of the nutrient TMDL. In addition, IDEQ is currently collecting 24-hour
DO data to document the relation of nutrients to numeric DO concentrations in
Threemile Creek. Phosphorus targets and the seasonality of their application may
require adjustments in the future as additional data is collected.
TMDLs - Bacteria
No. 1
The document also states that animal feeding operations can be significant contributions to
water quality detriment. However the Lower Boise River coliform bacteria DNA testing
showed that through the lower reaches of the Boise River, which flows through a
predominantly agricultural area, agriculture only had 9-14% of the sources of coliform
bacteria. And that wildlife, especially water fowl and avian (34.9%), and deer and elk
(15.4%) were the significant contributors. Why isn't some of this type of data used to help
write TMDLs?
Response: We appreciate this comment about the possible sources of bacteria in
Threemile Creek. We do not truly know the source of the bacteria, and do not have
the resources to conduct the sort of research as was conducted in the Lower Boise
River. The bottom line for the TMDL, however, is that bacteria levels in Threemile
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
need to be reduced In order to meet water quality standards. The effects of livestock
on the water quality of Threemile Creek need to be addressed for the sediment and
temperature TMDLs as well as the bacteria TMDL
TMDLs - Sediment
No. 1
As a group, we voted to take sediment off the list of problems above the Mt. Idaho Bridge.
The agencies came back and told us that that was done. ONLY now sediment is listed for all
the tributaries into the main South Fork, so what did we actually accomplish? The SFC
WAG voted no on sediment TMDL above the Mt. Idaho Bridge.
Motion on November 20, 2002: That with the additional data received today that the WAG
move to remove all streams (from the 303-d list) above Harpster Bridge, with the exception
of Beaver Creek in the upper reaches, that would have been listed for sediment on the 1998
WBAG
Vote: In favor (11) Opposed (3)
Motion on May 21, 2003, to clarify the November 20 motion:
That the tributaries as well as the main stem of the South Fork of the Clearwater be removed
from the sediment TMDL, above Harpster Bridge, with the exception of Beaver Creek.
Vote: In favor (8) Opposed (2) Abstain from the vote (2)
Specifically, TMDLs are written for sediment in the main stem above Harpster where no
impairment of beneficial uses is shown....
No. 5
We suggest that TMDLs for sediment be set for the streams and main stem of the SF CWR
and subbasin above Harpster. Cobble embeddedness surrogate targets below 20-30% should
be set in salmon rearing habitat depending on channel type. Targets should be set on
reference conditions for cobble embeddedness, percent fines by depth, and pool volume.
Surface fine sediment should be less than or equal to 20% in spawning areas. There should
also be an objective set for an increasing trend in residual pool volume. The current proposal
is not only ignoring the full scope of sediment problems in the subbasin, it is also
inconsistent with the management objectives of the Nez Perce National Forest, the National
Oceanic and Atmospheric Administration - Fisheries consultation for the Endangered
Species Act, and designation by the state as a Special Resource Water.
Response: These two comments bracket opinions that range from believing that no
sediment TMDLs are warranted above Harpster to believing that all streams above
Harpster not in pristine condition deserve sediment TMDLs (also see comments on
the proposed sediment dellstlngs above). To the best of the three agencles's (DEQ,
NPT, USEPA) abilities to Interpret the Intent of the Clean Water Act and Idaho's
water quality standards, there is agreement that that sediment from many tributaries
above Harpster is accumulating in the main stem and impairing beneficial uses in
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
the main stem. One must keep in mind that "impairment" is a legally defined
condition and does not equal degradation or other general terms for the effects of
sediment. Likewise, the opinions of the WAG are advisory; it is the legal
responsibility of the agencies to identify when and where impairment occurs.
Similarly, management objectives of other agencies, while perhaps providing some
level of understanding of impairment, do not constitute legal definitions of
impairment.
Sediment impairment in the state narrative water quality standard is defined in terms
of beneficial uses. In the case of the streams above Harpster, the beneficial use in
question is salmonid spawning. The sediment TMDLs for the main stem above
Harpster extend the numeric 25% sediment reduction target for Stites throughout the
system. Reference watershed and research data in the subbasin assessment
indicate that one of the effects of sediment being added to the main stem is
degraded in-stream habitat. The effects of the targeted reduction in sediment on in-
stream habitat are not quantifiable, yet we agree with commentors that stream
habitat needs to be improved. In the final draft of this document, we have set a
surrogate target of an improving trend in river habitat. The improving trend
surrogate target is set to insure that BMPs applied to the landscape actually result in
improved stream habitat.
We think that the 25% sediment reduction target is conservative, and when coupled
with the improving river habitat trend, will insure that the river will be returned to full
support of its beneficial uses, as relates to sediment. One must remember as well
that temperature TMDLs have been written for the basin as a whole, the
implementation of which should result in streamside vegetative restoration
throughout the basin. Such vegetative restoration will almost automatically result in
a significant reduction of sediment loading to streams.
TMDLs - Temperature
No. 1
With respect to the temperature TMDLs, from the forest industry perspective, we see no need
for the caveat added by EPA to the CWE temperature model. The shade targets in this
TMDL pretty clearly indicate that the CWE temperature model targets by themselves are
more protective than the EPA-promulgated System Potential Vegetation (SPY) targets. The
forest industry developed the CWE model based on local data, which EPA apparently turned
down without much data at all. The SPV data used in this TMDL is much less specific than
the CWE data, and results in lower, much less well-defined targets. It's simply another case
of the feds riding rough-shod over locally developed and accepted methods.
No. 5
We appreciate efforts to assess our streams and rivers, assuring citizens that our water and
wildlife are not being neglected. We also appreciate efforts to restore our streams and
supporting tributaries. This has impacts not only on the quality of human use and recreation,
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
but also on wildlife habitat. It has not gone unnoticed that temperature TMDLs were
developed for all 74 water bodies in the subbasin. We commend you for that effort.
No. 7
First, I have throughout the WAG process understood that implementation of proposed
improvements involves "moving towards" targets, making genuine attempts towards
improving water quality. Therefore, I have no objection to temperature targets that some
people consider unachievable.
Response: Generally, the targets for the temperature TMDLs throughout this
document have been set for the level of shade attainable under natural conditions,
which incorporates impacts from natural disturbance processes such as fire and
mass wasting. These shade targets do not represent maximum tree heights or
maximum riparian vegetation density, but are intended to represent shade levels
which could realistically be expected to occur given a natural disturbance process
and minimal human disturbance. The modification to the OWE methodology helps
insure that this level of shade will be maintained in forested zones, even though the
OWE model may not indicate it. This is consistent with our goal of restoring
streamside vegetation and shade throughout the subbasin to enhance both the
temperature and sediment effects on water quality. The complete streamside shade
restoration goal is justified by identifying shade as the most important component of
stream heating that is human caused and can be managed. By focusing on the
human-caused and manageable component of stream heating, and setting targets to
largely eliminate those effects, this TMDL has side-stepped many of the
controversial issues associated with interpreting the numeric water temperature
criteria. We think this is justified given the recent change in the Idaho water quality
standards allowing such an approach, and will result in significant improvements to
stream temperatures throughout the subbasin.
Implementation -- General
No. 2
The federal land management agencies have reviewed the draft South Fork Clearwater River
Subbasin Assessment and TMDL and we feel that the provisions are generally
implementable, with specific measures to be worked out within the implementation plan. We
look forward to working with the IDEQ, EPA, NPT and WAG on development of the
implementation plan.
No. 5
For some of the TMDLs, adequate plans and strategies for implementing and monitoring the
TMDLs were developed. Plans to implement and monitor the TMDLs for sediment and
temperature were developed. The strategy for temperature is deserving of merit. However,
the sediment TMDL lacks a timeframe and provides few actual basic steps required for the
implementation and monitoring of the TMDLs and reductions. Additionally, there were no
indicators of progress or interim measures of success established in the assessment. These
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
are important in determining if implementation is effective and if reductions are being
fulfilled. The TMDLs for E. Coli and Nutrients for Threemile Creek did not include
monitoring or implementation plans. If strategies for the sediment and temperature TMDLs
were developed, the same should be completed for the bacteria and nutrient TMDLs.
No. 7
I feel that perhaps the weakest aspect of upcoming TMDL implementation is provision for
monitoring of progress and of support for such monitoring. Monitoring should be
vigorously, consistently conducted for years to come.
No. 8
Finally, the TMDL could be improved with greater attention paid to a plan for future
monitoring of stream and river conditions.
Response: Thank you for these comments. For the final document, we have
completely revised the discussion of implementation planning into one section that
addresses all the TMDLs in a more-or-less integrated fashion. Considerable
monitoring has been identified as a needed component of implementation.
Implementation - Negative Effects
No. 1
The South Fork Clearwater WAG does not want to see the TMDL be utilized to apply added
restrictions on any sector of the drainage.
Economic consideration: LOGGING and AGRICULTURE are the lifeblood of this county.
In any decision made, these must be considered. In the South Fork drainage, these
occupations must be recovered and preserved for our county to survive. It's WAY past time
for the NezPerce Forest to manage this drainage and clear the dead and dying trees. The
whole area at the head of this drainage will burn one of these summers and the sediment will
flow thick from the blackened forest. The water temperature will soar then. We should
address this issue. It must be cleaned up now but I fear it's too late.
Recreation is important to tourists as well as to those of us who live and play here. Many
roads and trails are used by recreation. Road obliteration in most cases is not necessary.
Each time a road is gated and a road is obliterated, recreationists are closer to being locked
out of the area. Hunting, swimming, tubing, fishing, etc. are all important to our economics.
As for the roads on federal lands, one option is to decommission the roads. Many on the SF
WAG do not view this alternative as favorable. Many of the listed roads to be de-
commissioned are used for recreation by many Idaho County residents and visitors to the
county. Also, some of the roads are completely overgrown, and are not contributing
sediment to the drainage. Therefore, why disturb what has naturally grown back?
.. .No matter what people say, TMDLs will result in some level of restriction to private and
industrial use of the land, which is not warranted without clear evidence. Especially in an
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
economically depressed area like Idaho County, governmental restrictions simply so
bureaucrats can justify their jobs is out of order.
No. 2
The WAG letter (no. 1) refers to a list of roads to be decommissioned. There is not such a
list for federal lands in the South Fork Clearwater subbasin. The South Fork Clearwater
Landscape Assessment, completed by the Nez Perce National Forest in 1998, included maps
showing the results of a preliminary assessment of roads that may not be needed for long
term access. Before any of these roads could decommissioned, they would go through an
appropriate level of NEPA analysis, including public involvement.
No. 6
At no time was a list of roads for decommissioning discussed with or given to the WAG.
Road decommissioning was discussed as one of many possibilities of measures that could be
taken under the implementation plan. Closing roads to motorized use either permenently or
seasonally is a management tool that has and should be used when necessary for wildlife,
water quality, sediment, and road bed issues. I would like to point out that NONE of these
closures or decommissions lock anyone out of the forest. These areas are open 24/7 to all
other uses except motorized. I frequently use, and have never had a problem using, areas
behind closed roads.
No. 7
I would like to note that no list of roads for decommissioning was ever presented at a WAG
meeting that I attended, and no focus whatever was given during the WAG process to the
notion of decommissioning roads.
Response: Generally, the TMDLs for nonpoint sources of pollutants will result in an
implementation plan that identifies possible BMPs to address the loading targets.
For nonpoint sources of pollutants, actual implementation of those BMPs is voluntary
on the part of the land owner/manager. Certainly, the system provides some
incentives of various kinds to ecourage implementation of the BMPs. Any possible
negative effects of implementing the BMPs, however, should be weighed during the
period of decision to implement. All the situations brought up in the comments
above should be addressed during the implementation planning and decision to
implement phases. The TMDLs themselves in this document do not prescribe any
specific action.
Implementation - Grangeville WWTP
No. 3
One potential solution for the City of Grangeville will be land application of it's WWTP
effluent during part of the summer period. This will mean removal of the flow from
Threemile Creek during the period of time the Creek normally has it's lowest flow levels.
There is a good chance sections of the Creek will go dry depending on the time of year
and/or whether the yearly precipitation levels are above or below normal. Since Grangeville
gets its municipal water from groundwater wells, the flow it provides to Threemile Creek,
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South Fork Clearwater River Subbasin Assessment and TMDLs October 2003
through the WWTP outfall, is fairly recent from a historical perspective. Obviously, in a
situation like this, there is a benefit to leaving the flow in the stream, however from an
economic stand point, land application may be less expensive in the long run than treatment
of temperature, phosphorus and nitrogen (if left in the TMDL). Therefore, the TMDL was
remiss in not considering these impacts and investigating what incremental or phased
improvements the treatment plant could make that would not be as much of an economic
burden to the City and would provide the benefit of flow year-round in the stream. In other
words, flexibility was not built into the draft TMDL that would enable a more holistic
solution to be explored.
Response: Similar to the response above for nonpoint source pollutants, the TMDL
itself does not prescribe any particular action, only the level of load reductions that
are needed. However, we are also aware that in the case of point source pollutants,
the TMDL leads directly to action within the NPDES permitting system. And we are
aware that the NPDES permitting system has some time frames associated with it.
Having said that, we think that the NPDES permitting system, including input from
DEQ, has the capability to allow for incremental and/or phased improvements to the
treatment plant, for example through the establishment of a compliance schedule.
We encourage you to discuss this with permitting officials from USEPA and staff
engineers from DEQ.
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DEQ-646, TM79, 22058, 10/03
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