United States
Environmental Protection
Ecological Risk
Assessment for the
Middle Snake River, Idaho
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EPA/600/R-01/017
February 2002
ECOLOGICAL RISK ASSESSMENT FOR THE MIDDLE SNAKE RIVER, IDAHO
U.S. Environmental Protection Agency
National Center for Environmental Assessment-Washington Office
Office of Research and Development
Washington, DC
Office of Environmental Assessment
Region 10
Seattle, Washington
/T~V Recycled/Recyclable
V/Ly. Printed with vegetable-based ink on
~ paper that contains a minimum of
50% post-consumer fiber content
processed chlorine free.
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DISCLAIMER
This document has been reviewed in accordance with U.S. Environmental Protection
Agency policy and approved for publication. Mention of trade names or commercial products
does not constitute endorsement or recommendation for use.
ABSTRACT
An ecological risk assessment was completed for the Middle Snake River, Idaho. In this
assessment, mathematical simulations and field observations were used to analyze exposure and
ecological effects and to estimate risk.
The Middle Snake River which refers to a 100 km stretch (Milner Dam to King Hill) of
the 1,667 km long Snake River lies in the Snake River Plain of southern Idaho. The contributing
watershed includes 22,326 square km of land below the Milner Dam and adjacent to the study
reach. The demands on the water resources have transformed this once free-flowing river
segment to one with multiple impoundments, flow diversions, significant alterations to river
habitat, loss of native macroinvertebrate species, extirpation of native fish species, expansion of
pollution-tolerant organisms, and excessive growth of macrophytes and algae.
The environmental management goals for this assessment are: "attainment of water
quality standards, establishment of total maximum daily loads for major pollutants, water for
hydropower, recreation, and irrigation, recovery of endangered species, and sustained economic
•well being." The diversity, reproduction, growth, and survival of representative species from
three major trophic levels (fish, invertebrates, and plants) were chosen as assessment endpoints
in order to complete an ecosystem level analysis.
Simulation of habitat conditions (temperature, water velocity, and water depth) and
review of field studies show that most spawning, rearing, and adult habitats available to native
fish species and in the Middle Snake River are undesirable. In addition to high water
temperatures, our analysis showed that low flows and sedimentation are main stressors affecting
these fish species. These same factors are thought to be responsible for the decline of native
snail populations. Risks of eutrophication were estimated by changes in the plant biomass. The
simulation of macrophyte growth, under existing conditions in the study reach, indicates the river
is eutrophic based on aquatic plant biomass exceeding 200 g/m2. The lines of evidence drawn
from the model simulation suggest that nutrients, temperature, flow, and water depth are the
major factors controlling macrophyte growth.
Preferred citation:
U.S. Environmental Protection Agency (EPA). (2002) Ecological risk assessment for the Middle Snake River,
Idaho. National Center for Environmental Assessment, Washington, DC; EPA/600/R-01/017. Available from:
National Technical Information Service, Springfield, VA; PB2002-104231, .
ii
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CONTENTS
List of Tables vii
List of Figures ix
Foreword ...:.. xi
Preface xii
Authors, Contributors, and Reviewers xiii
Acknowledgments , •'. xv
1. EXECUTIVE SUMMARY 1-1
1.1. INTRODUCTION 1-1
1.2. PLANNING > 1-3
1.3. PROBLEM FORMULATION : 1-3
1.4. ANALYSIS 1-4
1.5. RISK CHARACTERIZATION 1-5
2. INTRODUCTION 2-1
3. PLANNING . ..... 3-1
4. PROBLEM FORMULATION 4-1
4.1. METEOROLOGY ' !.... 4-1
4.2. GEOLOGY 4-1
4.3. HYDROLOGY 4-8
4.4. DEMOGRAPHICS AND LAND USE 4-10
4.5. FISH POPULATIONS 4-12
4.6. BENTHIC MACROINVERTEBRATES 4-13
4.7. AQUATIC PLANT COMMUNITIES 4-14
4.8. ASSESSMENT ENDPOINTS 4-15
4.9. DECISION PATHWAY 4-16
4.10. CONCEPTUAL MODEL 4-17
4.11. LAND-USE ACTIVITIES THAT ALTER ECOSYSTEMS 4-18
4.11.1. TwinFalls Sewage Treatment Plant 4-19
4.11.2. Confined Animal Feeding Operations 4-19
4.11,3. Aquaculture 4-19
4.11.4. Irrigated Agriculture and Cattle Grazing 4-20
4.11.5. Nutrient and Sediment Loading 4-22
4.11.6. Impoundments 4-22
4.11.7, Other Nonpoint Sources 4-24
4.12. ECOSYSTEM DYNAMICS 4-24
4.12.1. Water Column Dynamics 4-25
4.12.2. Sediment Dynamics 4-29
4.12.3. Dynamics of the Benthic Plant Community 4-31
5. SIMULATION OF ECOLOGICAL RISK ... 5-1
111
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CONTENTS (continued)
5.1. QUANTITATIVE MEASURES OF EFFECT 5-1
5.1.1. Water Quality Standards 5-1
5.1.2. Habitat Suitability Indices 5-3
5.2. RISKESTIMATES 5-6
5.2.1. Exceedance of Water Quality Standards 5-6
5.2.2. Habitat Suitability Indices 5-9
6. ANALYSIS OF EXPOSURE AND EFFECTS FOR THREE FISH POPULATIONS ... 6-1
6.1. RAINBOW TROUT (Oncorhynchus mylriss) 6-1
6.1.1. Spawning Habitat 6-2
6.1.2. Rearing Habitat 6-2
6.1.3. Adult Habitat 6-3
6.1.4. Overwintering Habitat 6-4
6.1.5. Discussion 6-4
6.2. MOUNTAIN WHITEFISH (Prosopium williamsonf) 6-5
6.2.1. Loss and Alteration of Lotic Habitat 6-6
6.2.2. Effects on Movement 6-7
6.2.3. Effects on Spawning Activities 6-8
6.2.4. Loss and Alteration of Rearing Areas 6-9
6.2.5. Effects Due To an Altered Food Source and Prey Base 6-10
6.2.6. Discussion 6-13
6.3. WHITE STURGEON (Acipenser trammontanus) 6-14
6.3.1. Loss and Alteration of Lotic Habitat 6-15
6.3.2. Effects on Movement 6-16
6.3.3. Effects on Spawning Activities 6-17
6.3.4. Predation on Eggs and Larvae 6-20
6.3.5. Loss and Alteration of Rearing Areas 6-21
. 6.3.6. Effects Due to an Altered Food Source and Prey Base 6-22
6.3.7. Loss of Genetic Diversity 6-24
6.3.8. Discussion 6-25
7. ANALYSIS OF EXPOSURE AND EFFECTS FOR MACROINVERTEBRATES 7-1
7.1. OVERVIEW 7-1
7.2. SAMPLING BY IDAHO STATE UNIVERSITY 1992-1994 7-1
7.3. STATUS OF THREATENED AND ENDANGERED
MOLLUSCS.IN THE MIDDLE SNAKE RIVER 7-7
7.3.1. Bliss Rapids Snail (Taylorcho'ncha serpenticold) 7-7
7.3.2. Idaho Springsnail (Pyrgulopsis idahoensis) 7-8
7.3.3. Snake River Physa (Physa natricind) 7-9
7.3.4. Utah Valvata (Valvata utahensis) 7-10
7.3.5. Banbury Springs Lanx (Lanx sp.) 7-11
IV
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CONTENTS (continued)
8. ANALYSIS OF EXPOSURE AND EFFECTS FOR AQUATIC PLANTS .. 8-1
8.1. HISTORIC TRENDS 8-1
8.1.1. Phytoplankton 8-2
8.1.2. Vascular Macrophytes 8-2
8.2. DENSITIES OF PLANT COMMUNITIES IN THE MIDDLE SNAKE RIVER ... 8-4
8.3. FACTORS CONTROLLING PLANT GROWTH, BIOMASS,
AND DIVERSITY 8-7
8.4. EFFECTS OF EXCESS GROWTH ON THE MIDDLE SNAKE SYSTEM
INCLUDING EUTROPHICATION 8-10
9. RISK CHARACTERIZATION 9-1
9.1 SUMMARY OF RISKS TO THE ASSESSMENT ENDPOINTS 9-1
9.1.1. Reproduction and Survival of Rainbow Trout 9-1
9.1.2. Reproduction and Survival of the Mountain Whitefish 9-3
9.1.3. Reproduction and Survival of the White Sturgeon 9-8
9.1.4. Reproduction, Survival, and Diversity of Macroinvertebrates 9-9
9.1.5. Growth and Diversity of Phytoplankton, Macrophytes, and Epiphytes ... 9-13
9.2. SOURCES OF UNCERTAINTY 9-17
9.2.1. Variability in Driving Forces and Stresses : 9-18
9.2.2. Sources of Mass and Energy 9-18
9.2.3. Model Error ; 9-19
9.2.4. Parameter Estimation ; 9-21
9.2.5. Measurements 9-21
9.2.6. Quantitative Measures of Effect 9-22
9.2.7. Lack of Knowledge 9-23
9.3. CONCLUSIONS , 9-23
10. MANAGEMENT IMPLICATIONS OF THE MIDDLE SNAKE RIVER
RISK ANALYSIS ! 10-1
11. REFERENCES 11-1
APPENDIX A.; PARTICIPANTS IN THE PROTECTION OF THE MIDDLE SNAKE
RIVER A-l
APPENDIX B. ECOLOGICAL COMPONENTS OF THE MIDDLE SNAKE RIVER
ECOSYSTEM ...... B-l
APPENDIX C. LIFE HISTORIES OF THE DOMINANT MACROPHYTE SPECIES IN THE
MIDDLE SNAKE RIVER C-l
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CONTENTS (continued)
APPENDIX D. ANALYSIS OF ECOLOGICAL RISK IN THE MID-SNAKE RIVER USING
SIMULATION METHODS '. D-l
VI
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LIST OF TABLES
4-1. Hydrologic, geomorphologic, and cultural features of segments of
the Middle Snake River between Milner Dam and King Hill 4-3
4-2. Primary land-use activities in the Middle Snake River between
Milner Dam and King Hill, Idaho (from Bowler et al., 1993) 1 . 4-12
4-3. Estimated nutrient and sediment loadings for point, nonpoint, and
background sources 4-22
4-4. Retention times for the five reservoirs in the Middle Snake River for
low and average annual river flows ' 4-23
4-5. Average concentrations of nitrogen and phosphorus in the Middle
Snake River (from Brockway and Robison, 1992) •. 4-26
4-6. Mean values for selected water chemistry variables from 1992 to 1994 in the Middle
Snake River (see Royer et al., 1995, for full description) 4-26
4-7. Water column variables simulated by the mathematical model for
characterizing ecological risk 4-29
5-1. Variables simulated by the dynamic model and their associated measures
of effect (State of Idaho water quality standards and habitat suitability
factors) and assessment endpoints , 5-2
5-2. Maximum biomass of macrophytes in water bodies with water
quality problems 5-3
5-3. Time of the year for which habitat factors are applied to various life stages
of cold-water fish native to the Snake River (from Anglin et al., 1992) 5-5
5-4. Frequency with which simulated values of water temperature and dissolved oxygen (DO)
are outside the envelope of the State of Idaho's water quality standards for cold-water
biota, spawning rainbow trout and mountain whitefish , 5-7
6-1. Summary of studies on the diet of the mountain whitefish, 1936 to 1981 6-12
6-2. Total lengths and mean growth rates for white sturgeon in the Middle
Snake, main-stem Columbia River in the United States, and
Fraser River, Canada 6-23
7-1.. Mean (SD) relative abundance (%) of the ten most common invertebrate taxa in the
Middle Snake River on each of the sampling dates. Values for each date calculated from
all nine sampling stations (from Royer et al., 1995) 7-5
8-1. Riverwide mean plant biomass and percent of the total biomass,
Crystal Springs, Idaho, 1994 (from Falter and Burris, 1996) 8-3
9-1. Factors limiting reproduction, growth, and survival of the rainbow trout
population in the Middle Snake River 9-2
9-2. Factors limiting reproduction, growth, and survival of the mountain
whitefish population in the Middle Snake River 9-4
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LIST OF TABLES (continued)
9-3. Factors limiting reproduction, growth, and survival of the white sturgeon
population in the Middle Snake River 9-6
9-4. Factors limiting the reproduction, growth, and survival of macroinvertebrates
in the Middle Snake River 9-11
9-5. Factors limiting the reproduction, growth, and survival of aquatic molluscs
in the Middle Snake River 9-12
9-6. Factors limiting reproduction, growth, and survival of aquatic plant communities
in the Middle Snake River 9-15
vni
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LIST OF FIGURES
1-1. Framework for ecological risk assessment. .' 1-2
4-1. Snake River Basin 4-2
4-2. Hydrologic unit for the Middle Snake River 4-6
4-3. Schematic of the Middle Snake River from Milner Dam to King Hill
showing major tributaries, springs, dams, and point sources 4-7
4-4. Shoshone Falls during low-flow conditions * 4-8
4-5. Flow (cfs) in the Middle Snake River at Rkm 893 (RM555). 4-9
4-6. Generalized land cover for the Middle Snake River Basin 4-11
4-7. Decision pathway for analysis of ecological risk using simulation methods 4-16
4-8. Conceptual model for the Middle Snake River Risk Assessment 4-18
4-9. Frequency of N:P ratios in the Snake River at Rkm 965.4 (RM 600) 4-27
4-10. Simulated water temperatures (°.C) in the Middle Snake River
atRkm893 (RM555) 4-28
4-11. Flow of energy and materials for aquatic plant growth in the
Middle Snake River 4-32
5-1. Cumulative distribution function for total phosphorus, Rock Creek
to Crystal Springs 5-10
5-2. Cumulative distribution for total phosphorus, Bliss Dam to King Hill 5-10
5-3. Cumulative distribution function for simulated rnacrophyte biomass in the
Snake River at RJon 965.4 (RM 600) 5-11
5-4. Probability of life stage impairment for rainbow trout in the Middle Snake River ... 5-12
5-5. ., Probability of life stage impairment for mountain whitefish in the
Middle Snake River. 5^-14
5-6. Probability of life stage impairment for white sturgeon in the Middle Snake River .. 5-15
6-1. Water temperature and flow during the white sturgeon spawning season at
Snake River Rkm 893 (RM555) 6-19
7-1. Mean density of aquatic macro invertebrates in the Middle Snake River at
locations sampled by Idaho State University 7-3
7-2. Mean taxa richness of aquatic macroinvertebrates in the Middle Snake River
at locations sampled by Idaho State University 7-4
7-3. Mean relative abundance of the exotic snail, Potamopyrgus antipodarum,
at two locations sampled by Idaho State University 7-6
8-1. Snake River at Crystal Springs, July 1992 8-3
8-2. Blue Heart Springs with Box Canyon in the background,
Middle Snake River, August 1993 8-7
IX
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LIST OF FIGURES (continued)
9-1. Factors controlling molluscs survival in the Middle Snake River 9-10
9-2. Factors controlling aquatic plants in the Middle Snake River 9-16
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FOREWORD
Risk assessment is playing an increasingly important role in determining environmental
policies and decisions at the U.S. Environmental Protection Agency (EPA). EPA's first Agency-
wide guidelines for ecological risk assessment, published in May 1998, provided a broad
framework applicable to a range of environmental problems associated with chemical, physical,
and biological stressors. As ecological risk assessment evolves, it is moving beyond a focus on
single species toward addressing multiple species and their interactions, and from assessing
effects of simple chemical toxicity to the cumulative impacts of multiple interacting chemical,
physical, and biological stressors on species, populations, communities, and ecosystems in
watersheds, regions, or other "places."
To further develop and demonstrate the use of the ecological risk assessment paradigm in
addressing such environmental problems, the EPA sponsored and is completing four watershed
assessments, including this one on the Middle Snake River. Ecological risk assessments, when
applied to watersheds, must be adaptable to a lack of complete knowledge about complex
ecosystem dynamics and the need to reach consensus in watershed groups. Thus, watershed
ecological risk assessments may not characterize every structural and functional element of the
ecosystem and may be limited by management constraints. The strengths of applying ecological
risk assessment and adaptations that need to be made to implement the approach in watersheds
are discussed in other EPA reports and in scientific journal articles and conference proceedings
(see wwwrepa.gov/ncea).. The other three assessments are also presented elsewhere.
The Middle Snake River was selected as one of these watershed assessments because of
its unique species which are threatened or endangered, the multiple stressors, and the related
concerns of interested citizens, government institutions, and private industry. This assessment is
intended to address such concerns by analyzing the Middle Snake River's stressors and resulting
ecological effects and to stimulate broader public awareness and participation in decision making
for reducing ecological risks. This watershed assessment report serves as an example of how
ecological risk assessment principles can be applied at the watershed scale to improve the use of
science in decision making.
Michael Slimak
Associate Director of Ecology
EPA, National Center for Environmental Assessment
XI
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PREFACE
The National Center for Environmental Assessment-Washington Office (NCEA-W)
provided document production, printing, and distribution support for this document. Funding
was provided by EPA's Office of Water, Region 10, and the State of Idaho Department of
Environmental Quality (IDEQ).
This document presents the ecological assessment of several years of monitoring data as
well as a simulation of present and future conditions of the river. The idea for this assessment
began with EPA Region 10 managers working closely with managers from IDEQ. They had a
vision for a comprehensive assessment of the Middle Snake River. Their goal was a restoration
of this system for the people who live in the area as well as the aquatic organisms that inhabit the
river.
The initial work for this study began in 1987, with river monitoring work done by the
IDEQ. The EPA was invited to participate in the design of this data collection and ultimately
the risk assessment by the Middle Snake River County Planning Group. Thus, genesis of the
ecological risk assessment began before EPA had completed its Guidelines for Ecological Risk
Assessment in 1998. Additionally, as discussed in the Foreword, ecological risk assessments
implemented in watersheds need to be flexible due to data limitations and client needs. Although
there may be a few inconsistencies, the process for completing the final assessment and this
report were based on the EPA guidelines and advice and support from NCEA-W.
This risk assessment provided decision makers and interested citizens with factual
information.for their deliberations. They are able to draw on components of the analysis as well
as the conclusions of the assessment for their actions on the river. The results of the. assessment
were used by the IDEQ in developing their Nutrient Management Plan and Total Maximum
Daily Loads (TMDL) for pollutant discharge permits on the river.
This final document reflects a consideration of all comments received during internal and
external peer review provided by a number of experts between 1996-2001.
xn
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AUTHORS, CONTRIBUTORS, AND REVIEWERS
Authors
Patricia A. Cirone
Duane W. Kama
John R. Yearsley
U.S. Environmental Protection Agency
Office of Environmental Assessment
Region 10
Seattle, WA
C. Michael Falter
University of Idaho
Moxcow, ID
Todd V. Royer
University of Illinois
Urbana, IL
Contributors
Dr. Gerald Filbin
U.S. Environmental Protection Agency
Washington, DC
Dr. Suzanne Marcy
U.S. Environmental Protection Agency
NCEA
Anchorage, AK
Victor Serveiss
U.S. Environmental Protection Agency
NCEA-W
Washington, DC
Dr. Michael Watson
U.S. Environmental Protection Agency
Region 10
Seattle, WA
Xlll
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AUTHORS, CONTRIBUTORS, AND REVIEWERS (continued)
Reviewers
Jim Andreason
U.S. Environmental Protection Agency
NCEA-W
Washington, DC
Peter Bowler
University of California, Irvine
Irvine, CA
Kellie Kubena
U.S. Environmental Protection Agency
Region 10
Seattle, WA
Wayne Minshall
Idaho State University
Pocatello, ID
Geoffrey Poole
U.S. Environmental Protection Agency
Region 10
Seattle, WA .
xiv
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ACKNOWLEDGMENTS
, This assessment is one of four prototype assessments supported by EPA's National
Center for Environmental Assessment—Washington Office (NCEA-W) to demonstrate the use of
the ecological risk assessment paradigm in watershed or large-scale river segments. NCEA—W
provided document production, printing, and distribution support, and funding was provided by
EPA's Office of Water, Region 10, and the State of Idaho Department of Environmental Quality
(IDEQ). ,
The authors would like to acknowledge the support of the following individuals:
• Vic Serveiss ensured compliance with the Guidelines for Ecological Risk Assessment
and consistency with other watershed ecological risk assessments.
• Dr. Michael Watson, Dr. Suzanne Marcy, Dr. Gerald Filbin, Lorraine Edmond, John
Olson, Warren McFall, Dr. Bernard Patton, Paul Dey, Zimri Moore, and Joan Meitl in the
problem formulation phase of the assessment.
• The Middle Snake River County Planning group for the impetus to begin this
assessment and their valuable insights during the initial discussions about the problems in
the Middle Snake River.
• Carla Fromm and Nickie Arnold provided information on pollution discharge permits.
• Dr. Peter Bowler and Dr. Wayne Minshall provided advice in designing this study,
valuable information throughout the process, and excellent review comments.
Our library research support was outstanding, particularly the efforts of Joanne Meyer.
and Althea Burton. We would also like to acknowledge the staff of The CDM Group, Inc., for
editorial, graphic, and word-processing support.
We would like to dedicate this report to Dr. Tim Litke, IDEQ, who was the inspiration for
many of us. He brought a diverse group of people together and established a common goal. We
hope that the restoration of this ecosystem will be the memorial to his special contribution.
xv
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1. EXECUTIVE SUMMARY
1.1. INTRODUCTION
This report presents the results of an ecological risk assessment for the Middle Snake
River, Idaho. Ecological risk assessment is a process for analyzing and presenting information
on the risks of exposures of organisms, populations, communities, or ecosystems to stressors and
disturbances. The assessment process (Figure 1-1) begins with planning and problem
formulation, proceeds through analysis of exposure and effects, and ends with risk
characterization. During the planning phase the management goals are established for the
watershed. In problem formulation, the watershed is described, ecologically relevant assessment
endpoints are defined, and a conceptual model is developed. In this assessment, mathematical
simulations and observations are used to analyze exposure and ecological effects and to estimate
risk. Finally, in risk characterization, all the elements of the assessment are brought together to
reach a conclusion. These elements include an uncertainty analysis, lines of evidence supporting
the risk estimate(s), and the likelihood of recovery.
The Snake River is the tenth longest river in the United States, extending 1,667 km from
its origins in western Wyoming to its union with the Columbia River at Pasco, Washington.
The river reach of concern (Milner Dam to King Hill), hereafter referred to as the Middle
Snake River, spans roughly 150 km and lies hi the Snake River Plain of southern Idaho. The
contributing watershed includes 22,326 square km of land below the Milner Dam and adjacent to
the study reach.
The demands on the water resources have transformed this once free-flowing river
segment to one with multiple impoundments, flow diversions, and increased chemical and
microbiological pollutant loadings. The Snake River has long been valued as a resource of water
for irrigation for hydropower. Physical changes include significant alterations to rapids and pool
areas of the river. Prior to impoundment of the river, chinook salmon were able to migrate as far
as Shoshone Falls, a natural barrier. Resulting biological changes include loss of native
macroinvertebrate species, invasion and dominance by exotic species, extirpation of native fish
species, expansion of pollution-tolerant organisms, and excessive growth of aquatic plants and
algae. The increasing demand for energy, irrigation resources, springs, and dairy feedlots
projected for this region will place additional burdens on an ecosystem that human activity has
already substantially changed.
The U.S. Environmental Protection Agency sponsored five watershed ecological risk
assessment case studies projects across the country. The purpose is to learn how to develop ways
to analyze, characterize, and communicate the severity of ecological risk to valued
1-1
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Ecological Risk Assessment
Planning
(Risk
Assessor/
Risk Manager/
Interested
Parties
Dialogue)
Characterization
of
Ecological
Effects
Characterization
of
Exposure
RISK CHARACTERIZATION
Communicating Results
to the Risk Manager
Risk Management arid ,V
- Communicating pResults to -
Figure 1-1. Framework for ecological risk assessment.
1-2
_
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environmental resources. The Middle Snake River was selected as one of the five watershed
case studies because of its unique species that are threatened or endangered, the multiple
stressors, and the concerns of interested citizens, government institutions, and industry
individuals. This ecological risk assessment was undertaken to address such concerns by
analyzing the Middle Snake River's stressors and resulting ecological effects, and to stimulate
broader public awareness and participation hi decision making for reducing ecological risks.
1.2. PLANNING
During the planning phase of this assessment a number of Federal, State, and county
organizations, along with private organizations, academic researchers, and interested citizens,
participated in workshops and meetings to discuss long-term goals for the river. The
management goals that were identified in this process were:
attainment of-water quality standards, establishment of total maximum daily loads
for major pollutants, -water for hydropower, recreation, and irrigation; recovery
of endangered species, and sustained economic-well being.
1.3. PROBLEM FORMULATION
Representative species from three major trophic levels (fish, invertebrates, and plants)
were chosen as assessment endpoints to complete an ecosystem-level analysis that would provide
information for the public and decision makers. Each group is an important link hi the structure
and function of this riverine ecosystem. It was determined that analysis of the factors controlling
the species' functions (reproduction, growth, and survival) should provide evidence for the
primary causes of the ecosystem changes.
This risk analysis began with the identification of the ecosystem driving forces
(hydrology, hydraulics, meteorology, and land-use activities) that define the structure and
function of this ecosystem. The land-use activities were superimposed on the natural system.
Irrigated agriculture, aquaculture, cattle feeding lots, sewage treatment, and impoundments were
found to be the major land use activities in the watershed. The hypothesis for this analysis is that
materials (nutrients, sediments, thermal energy, and ammonia) released from these activities, as
well as the habitat alterations resulting from impoundments, can produce stressful conditions that
are harmful to the native aquatic biota. Stressful conditions result from altered water velocity
and depth, decreased dissolved oxygen, increased water temperature, disrupted sedimentation,
excessive nutrient loading, and increased eutrophication.
1-3
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1.4. ANALYSIS
A mathematical model was developed for the river reach of concern for the period
January 1990 to December 1994. Ecosystem driving forces and land-use activities were
combined in the model to describe the ecosystem dynamics. The dynamics of the ecosystem
were simulated with variables including meteorological conditions, hydrological and hydraulic
conditions, carbonaceous biological oxygen demand, dissolved oxygen, phytoplankton biomass,
organic nitrogen, ammonia nitrogen, nitrite and nitrate nitrogen, organic phosphorus,
orthophosphorus, temperature, coliform bacteria, water depth, water velocity, rooted aquatic
plants, epiphytes, and periphyton. Stressor characteristics are defined hi terms of probability
models for point-source loadings and nonpoint-source loadings.
Risks for fish and macroinvertebrates were estimated by determining the likelihood of
being above or below cold-water biota tolerance limits. Tolerance limits are generally the natural
levels to which most native species have adapted. Excursions above and below these boundaries
or tolerance levels can be stressful.. The tolerance limits for fish and macroinvertebrates were
based on the State of Idaho Water Quality Standards for temperature, dissolved oxygen, total
phosphorus, and ammonia. In addition to comparison with water quality standards, the risks to
fish species were estimated by determming the likelihood of the river supporting suitable habitats
for their reproduction and survival. These habitat limits are based on Habitat Suitability Indices
developed by the U.S. Fish and Wildlife Service. The indices used in this risk assessment were
based on temperature, water depth, and water velocity preferences for fish species of interest.
Risks of eutrophication, were estimated by changes in plant biomass. The State of Idaho
defines "nuisance" as unacceptable for plant biomass. For the purposes of this analysis,
"nuisance" was defined as exceeding a biomass level (200 g/m2) found in eutrophic systems.
Finally, a qualitative analysis of data from field surveys in the Middle Snake River,
literature reviews of other studies, and best professional judgment were discussed as additional
lines of evidence for factors controlling the fish, macroinvertebrate, and aquatic plant
populations.
The quantitative measures of effect included water quality standards and habitat
suitability indices. The water quality standards that were used to define the level of concern for
temperature, dissolved oxygen, ammonia, and rhacrophytes were limited in the breadth of
applicability. The standards were expressed as discrete numbers rather than distributions. As
discrete numbers they did not necessarily reflect the specific requirements of individual species.
The habitat suitability indices are based primarily on water depth and water velocity; thus the
effects of biological interactions or substrate morphology are not taken into account. These other
factors could have significant effects on fish populations.
1-4
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1.5. RISK CHARACTERIZATION
The results of mathematical simulations of a 67-year record for daily average and
maximum levels of dissolved oxygen and temperature at 13 distinct river locations were
compared to the water quality criteria for cold-water biota, spawning whitefish, and spawning
rainbow trout. The cold-water biota limits were seldom exceeded (less than 1% of the time).
However, the frequency of not attaining dissolved oxygen limits in certain locations for spawning
mountain whitefish or rainbow trout ranged from 1% to 57% depending on the location and
timing of spawning. Further, water temperatures needed for spawning and incubation are
essentially absent for these fish. Ammonia did not appear to be a major stressor in this
ecosystem. The likelihood of exceeding chronic or acute ammonia tolerance limits was less than
5% and 1%, respectively.
Our simulation of habitat conditions (temperature, water velocity, and water depth) and
review of field studies also show that most spawning, rearing, and adult habitats available to
rainbow trout, mountain whitefish, and white sturgeon in the Middle Snake River are
undesirable. In addition to high water temperatures, our analysis showed that low flows and
sedimentation are main stressors affecting these fish species. These adverse conditions can be
improved if a spring freshet is reestablished with flows large enough for successful spawning,
and with post-spawning water temperatures low enough to allow for healthy embryonic
development other than during a narrow window of tune.
Analysis of ecological effects for macroinvertebrates was made primarily by inference.
Water quality standards for cold-water biota were assumed to represent conditions favorable to
invertebrate growth and survival. In most cases, the likelihood of falling below these limits was
low throughout the river. This result implies that the temperature and dissolved oxygen levels
did not exceed tolerance limits for macroinvertebrates. The evidence from field surveys conflicts
with the standards set for cold-water biota. The decline of native snails in this reach suggests
that the temperature, dissolved oxygen, and physical habitat changes are hi fact detrimental to the
survival, reproduction, and diversity of the snails. Their life history information indicates that
they prefer colder temperatures, more swiftly flowing water, and higher dissolved oxygen than
are allowed for in the standards.
The simulation of macrophyte growth under existing conditions hi the study reach
indicates the river is eutrophic because aquatic plant biomass exceeds 200 g/m2. The lines of
evidence drawn from the model simulation suggest that nutrients, temperature, flow, and water
depth are the major factors controlling macrophyte growth. The evidence for phosphorus as a
limiting factor is derived from model simulations. There is a 23% to 25% likelihood that
phosphorus will be equal to or less than the State of Idaho's limit of 0.075 mg/L hi the upper
reaches of the river. The inflow of large volumes of spring water with low levels of phosphorus
1-5
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decreases the likelihood to 7% to 18%. There is only a 1% chance the macrophyte biomass will
be less than 200 g/m2.
However, this evidence does not in and of itself define all the factors controlling the
excess growth of aquatic plants. In fact, it is the field surveys that provide the additional
evidence to describe control of plant growth. Water chemistry data show that nitrogen as well as
phosphorus can be limiting, depending on the volume and quality of inflow to the river. Thus,
the nutrient limits will shift from nitrogen to phosphorus during seasons and years. In addition,
the physical characteristics of the water column and bottom substrate are critical factors in
limiting growth. On the basis of field observations, the combination of deep, fine, nutrient-rich
sediments downstream of those areas in the Middle Snake River receiving organic and nutrient
loading favors aquatic plant growth. Once beds develop in these regions, internal water
velocities slow, resulting in further sediment deposition. These reduced velocities and relatively
clear waters provide optimum conditions for increased plant growth. These sediments provide an
anchor for rooted vascular plants, which in turn provide the habitat for nonrooted plants. In
addition to a substrate for growth, the sediments store nutrients vital to the growth of rooted
aquatic plants. This cycle is borne out in numerous areas throughout the river. The evidence is
strengthened by the high flow season in 1997. With the rush of water, the sediments were
flushed and the macrophytes did not develop to levels seen in previous years when flows were
much lower.
Uncertainty in this assessment includes variability in ecosystem driving forces and
stressors, sources of mass and energy, model error, parameter estimation error, measurement
error, errors in measures of effect, and lack of knowledge. Variability in estimates of stressors
(loading from land-use activities) was expressed as cumulative distributions with error bars.
Variability in the ecosystem driving forces (hydrology and meteorology) was based on the actual
and adjusted 67-year record, respectively.
Bias in the model was examined by comparing, the simulated results with field data
collected from the Middle Snake River. The best correlation was found between temperature and
nitrate-nitrite nitrogen. The correlation of simulated and observed dissolved oxygen levels was
only partially good, implying that the model may not accurately predict primary productivity.
Correlation of simulated and observed total phosphorus and total ammonia nitrogen was low.
The model predicted higher values of ammonia and underpredicted total phosphorus. The high
levels of ammonia may be due to poor loading estimates for the sewage treatment plant or other
biological interactions. The underprediction of phosphorus also may be due to poor loading
estimates or loss of phosphorus through sediment and plant sequestration.
Uncertainty due to lack of knowledge will result in errors of judgment as well as model
errors. In particular, the lack of species-specific information for the snails endemic to the Middle
1-6
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Snake River makes it difficult to confirm a definitive cause for ecological effects on these
organisms. However, the evidence for rainbow trout, mountain whitefish, sturgeon, and other
cold-water biota can be used by inference to bolster the argument for snails.
The processes of eutrophication and habitat.alteration in the Middle Snake River are
driven by a series of changes. It is clear that these cannot be attributed to any one factor. It is
therefore difficult to define management options that would foster an easy recovery. The .
influence of increased water flows on system recovery was clearly demonstrated in 1997; the
movement of sediments, nutrients, and macrophytes was dramatic. However, the
macroinvertebrate and fish populations are not going to recover after 1 year of high flows. Flow
and sedimentation processes must return to a more natural regime before the aquatic populations
will rebound.
1-7
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2. INTRODUCTION
Ecological risk assessment is a method for estimating which stressors or disturbances
cause adverse effects on the integrity of ecosystems. The assessment process begins with
planning and problem formulation, proceeds through analysis of exposure and effects, and ends
with risk characterization.
Planning is the process of identifying interested individuals, management goals, and
resource constraints for completing an assessment. Problem formulation includes a description
of the ecosystem and its resources, driving forces, and stressors. Assessment endpoints based on
the ecological and management goals are selected. These are woven together in a conceptual
model that outlines the elements of the analysis phase. This is followed by quantitative and
qualitative analyses of simulated and observed measures of exposure and effect. The uncertainty
and variability of all elements of the analysis are explained. In risk characterization, the lines of
evidence, type and severity of effect, and likelihood of recovery are discussed. Conclusions and
recommendations for further analysis are drawn from a comparison of the uncertainty in the risk
estimates and the evidence supporting the likelihood of ecological effect from exposure to the
stressor(s).
This assessment is an analysis of environmental problems in the Middle Snake River,
Idaho. The planning and problem formulation elements for this assessment were completed in
1996 (U.S. EPA, 1996). A synopsis of these elements is given in this report.
2-1
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3. PLANNING
As a result of human activities spanning the past century, water quality and biological
resource problems have developed in the Middle Snake River and its tributaries. The demands
on the water resources have transformed this once free-flowing river segment to one with
multiple impoundments, flow diversions, and increased physical, chemical, and microbiological
pollutant loadings. Physical changes include significant alterations to rapids and pool areas.
Biological changes include loss of native macroinvertebrate species, invasion and dominance of
exotic species, an expansion of pollution-tolerant organisms, and excessive growth of
macrophytes and algae.
The rapid rate of human population growth projected for the south Idaho region, as well
as an increasing demand for energy and irrigation resources, commercialization of springs, and a
burgeoning of dairy feedlots, will place additional burdens on an ecosystem that already has been
substantially changed by human activity during this century. This ecological risk assessment
was undertaken to address such concerns by analyzing the Middle Snake River's stressors and
resulting ecological effects, and to stimulate broader public awareness and participation hi
decision making for reducing ecological risks. The ecological changes in this watershed have
been observed by local, State, and Federal agencies; academic researchers; private organizations
and businesses; recreational users; and individuals concerned about the loss of a species-rich
ecosystem and cold-water fishery and degradation of water quality. The perspective with which
local, State, and Federal planning agencies; scientists; and the general public view this watershed
is changing as the community becomes more aware of how activities in the watershed impact the
ecology of the river.
The development of a comprehensive watershed management plan involves close
coordination of government, public, and private interests. Several working groups were formed
to address both regulatory and nonregulatory issues. The agencies and organizations that have
been identified as active in decision-making and management activities for the Middle Snake
River include Federal, State, county, and private organizations; academic researchers; and
interested citizens.
During the preliminary development of this analysis a variety of activities were
undertaken to identify those interested in the area. A number of planning efforts were initiated
by county officials (Mid-Snake River Planning Group) and the State of Idaho, Department of
Environmental Quality Watershed Steering and Technical Committees. Most of the planning
efforts were directed toward restoration of the cold-water biota and reduction of aquatic plant
biomass in the Middle Snake River. A detailed list of the interested groups from 1987 to 1995 is
3-1
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presented in Appendix A. These original working groups have evolved into a Middle Snake
River Watershed Council.
Since 1969, several programs have been implemented to improve water quality in the
Snake River Basin. The activities have included the advancement of best available technology at
the municipal sewage treatment plant, regulation of waste handling at cattle feedlots, the
initiation of best management practices on agricultural land through both State and Federal
programs, permits for the aquaculture industry, and total maximum daily load limits for
phosphorus.
The management goals for this watershed are associated with, and largely driven by, the
specific requirements of State and Federal environmental legislation and the development of
comprehensive land-use plans at the county level. These goals are:
• Attainment of State water quality standards;
• Establishment of total maximum daily loadings for water-quality-limited segments of
the river;
• Sustained economic activity in the region;
• Water for hydropower and irrigation;
• Recovery of endangered species; and
• Recreational uses.
The goals for the risk analysis are determined by the state of our knowledge of the
ecosystem and our ability to develop simulation models for the flow of energy, materials, and
information between ecosystem compartments.
The goals of this risk analysis are to:
• Provide scientific information to address management goals;
• Develop an ecosystem perspective for environmental planning that can be used in
other river basins throughout the region;
• Increase the knowledge of the structure and function of the Middle Snake River
ecosystem; and,
• Expand the scope of simulation methods to include more complex compartments in
the ecosystem.
In addition to advancing the science of risk analysis, this assessment is also undertaken to
ensure that the public and special-interest users, government agencies, and scientists understand
the ecological damage and that they develop a sense of partnership in reaching solutions for the
recovery and protection of the Middle Snake River ecosystem. Too often, when such groups act
in isolation, problems remain unresolved and each group becomes entrenched in its own rhetoric
and territoriality. A consensus-building method of reaching shared solutions is inherently slow
3-2
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but fundamentally democratic. Recognizing deadlines, limited resources, and the continued
decline of the habitat, it is important that progress be apparent.
The approach used to understand the interaction of sources, stressors, and resources on
the Middle Snake River includes: (1) field studies and experiments to increase our understanding
of the Middle Snake River ecosystem, (2) characterization of ecological risk using mathematical
modeling methods, and (3) qualitative evaluation of biological changes. Ultimately, this risk
analysis will be used to develop comprehensive management plans through the cooperative
efforts of local, State, and Federal agencies; academic researchers; and an informed public. The
analysis must reflect the interests of the interested parties. These measures alone cannot return
the Middle Snake River to its original state, but they can provide a better environment for the
natural heritage resources that have survived. Furthermore, if this approach is successful, the
Snake River can provide an example for environmental stewardship in other river basins.
3-3
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4. PROBLEM FORMULATION
In problem formulation the available information on stressors, ecological resources
potentially at risk, and ecological effects is used to (1) identify the ecological resources
(assessment endpoints) that will be the focus of the risk assessment, (2) develop conceptual
models of how these resources may be affected by stressors, and (3) develop a plan for the
analysis. In this report, a brief overview of the physical, chemical, and social forces that affect
the natural ecosystem of the Middle Snake River is followed by the conceptual model and
description of analytical methods. The results of the analysis are presented in Sections 6,7, 8,
and 9.
4.1. METEOROLOGY
The climate of the region is semiarid, characterized by low annual rainfall (e.g., 26.4
cm/yr at Twin Falls), with moderately hot summers and cold winters.
Precipitation is fairly evenly distributed throughout the year. November through January
are the wettest months; July and August the driest. Precipitation during 1988-1993 was low,
followed by a dramatic rise in 1996. The magnitude of precipitation is important because snow
melt is a primary source of water in the Middle Snake watershed.
The average temperature from 1928 to 1989 was 10°C. The variation in temperature is
also reflected in water temperatures.
Air temperature, relative humidity or dewpoint, cloud cover, wind speed, and atmospheric
pressure are required inputs to the model for estimating the heat budget and the amount of solar
energy available for heat transfer for primary productivity. For the purposes of this assessment,
the Middle Snake River was divided into two meteorological provinces: one from Milner Dam to
Upper Salmon Falls Dam, the other from Upper Salmon Falls Dam to King Hill.
4.2. GEOLOGY
The Snake River is the tenth longest river in the United States, extending 1,667 km from
its origins in western Wyoming to its union with the Columbia River at Pasco, Washington.
Along the way, it undergoes an elevation drop of about 2,895 meters. Its watershed (Figure 4-1)
encompasses an area of approximately 267,000 km2 in the States of Idaho, Oregon, Wyoming,
Nevada, Utah, and Washington.
For the risk analysis, it was useful to characterize the length scales for the river in terms of
geomorphologic, hydrologic, and cultural features. These segments are described in Table 4-1.
4-1
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SNAKE RIVER BASIN
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4-2
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4-3
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4-4
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The Snake River Plain comprises approximately 41,000 km2 of the Snake River Basin in
southern Idaho. The basin is subdivided into two geographic units: the eastern plain and the
western plain. The boundary between eastern and western plains is near King Hill, Idaho.
The river reach of concern, hereafter referred to as the Middle Snake River, lies entirely
within the eastern unit of the Snake River Plain. The study reach extends from Milner Dam
(river kilometer [Rkm] 1,028; river mile [RM] 640) to King Hill (Rkm 877.6; RM 546.4).
The contributing watershed includes 22,326 km2 (Figure ,4-2) of land below the Milner
Dam and adjacent to the study reach. Figure 4-3 shows a schematic diagram of the Middle Snake
River, including the locations of all dams, tributaries, irrigation returns, and water withdrawals.
Land surface elevation ranges from 1,260.3 meters mean sea level (MSL) at Milner Dam
to 762 meters MSL at King Hill. The predominant feature of the western part of the Snake River
Basin, through which the Middle Snake River flows, is the relatively flat Snake River Plain, a.
structural downwarp filled with quaternary basaltic lava flows and bounded by interbedded
sedimentary deposits (Clark, 1994). The geologic units include Pleistocene and older basaltic
lava flows, pillow lavas (formed by lava flowing into water), alluvial deposits, and lake deposits
from ancient lakes. The eastern plain is underlain by a thick sequence of volcanic rocks that
store and yield large volumes of water, comprising the largest and most productive aquifer .
(Snake River Plain Aquifer) in the Northwest. The Snake River incises the aquifer just upstream
of Twin Falls, near Kimberly. More than 80% of the groundwater emerges in the Thousand
Springs area, breaking through hundreds of fissures or cracks in the basalt layers of the canyon
walls (Travis and Waite, 1964).
The Snake River Canyon was scoured by overflow from the ancient Lake Bonneville ,
during the Pleistocene, approximately 13,500 to 15,000 years ago. The flood waters deposited
sandbars and gravel with boulders more than 3 meters in diameter. Many rapids and waterfalls
are formed by these boulders. Below Milner Dam, the Snake River enters a deep (20-90 m)
canyon cut through basalt and overlying sedimentary deposits and continues for 150 kilometers
to King Hill. The river is incised in a steep-sided basalt canyon of about 91 to 122 meters depth
through the reach.
Four major waterfalls over basalt ledges occur in the Middle Snake reach: (1) Star Falls
at 8 meters, (2) Twin Falls at 34 meters, (3) Shoshone Falls at 65 meters (Figure 4-4), and (4)
Auger Falls, a cascade that drops 12 meters. Average stream gradient is 3.4 meters/ km (0.33%)
from Milner Dam to King Hill. Downstream of Twin Falls, Idaho, the Snake River canyon
widens into small areas of bottomland and terraces. The largest of these areas is the Hagerman
Valley, approximately 10 km long and 2 to 6 km wide.
4-5
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State of Idaho
U.S. Forest Service
U. S. Bureau of Land Management
U. S. Bureau of Reclamation
|/\/l HUG 17040212 boundary
County boundaries
[ /r\J/ | Streams
ID 20
80
Blonwtete
yt-JH
10 15 a 25 30 35 40 'sSf/
•I-
OFtmMnKrtaaiWT b nnr«.-f=icpnncHr:H HDCKM ID
Figure 4-2. Hydrologic unit for the Middle Snake River.
4-6
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North
••-• ••*.
Milner Dam
Star Falls
Twin Falls Dam
Shoshone Falls Dam
Blue Lakes Spring
Auger Falls
Crystal Springs
crystal springs Keacn
Rkrn 96i.8-yb/.0
Box Canyon Springs
Box Canyon Reach
Rkm 936.4-960.6
Riley Creek
Billingsley Creek
Twin Falls SewageTreatment Plant
Rock Creek
Cedar Draw
"~ Niagara Springs
Mud Creek
Deep Creek
Banbury Spring
Blue Heart-Spring
Nature Conservancy Springs
Salmon Falls Creek
Thousand Springs
Malad River
Dam
Not Drawn to Scale
Upper Salmon Falls
Lower Salmon Falls
Bliss Bridge
Bliss Dam
Bancroft Springs
KING HILL
Figure 4-3. Schematic of the Middle Snake River from Milner Dam to King Hill, showing
major tributaries, springs, dams, and point sources.
4-7
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Figure 4-4. Shoshone Falls during low-flow conditions.
4.3. HYDROLOGY
The alteration of the natural hydrologic regime in the Middle and Upper Snake River
began with the construction of the Swan Falls Dam in 1901 and continued with the construction
of Milner Dam (1905), Minidoka Dam (1906), Lower Salmon Falls Dam (1910), Jackson Lake
Dam (Wyoming - 1911), American Falls Dam (1927), Upper Salmon Falls Dam (1937), and
finally Bliss Dam in 1949. Because of the management of this system as well as the geology, the
hydrology of this segment of the Snake River is complex. Water sources are snow melt and
groundwater recharge via springs. The Snake River above Milner Dam has an average annual
flow of about 6 x 109 nrVyear (212 x 109 cfs/yr). Until recently the entire river was diverted at
Milner Dam for irrigation during low-flow years from April to October. In 1992, an operating
license issued by the Federal Energy Regulatory Commission to the Idaho Power Co. required
that Milner Reservoir be kept full and a target flow of 6 m3/s be released, if available. Mean
annual water flow at Milner Dam is 92.3 m3/s (3,259 cfs) (1910-1990 record). Average flow at
Milner Dam disguises the fact that low flows (hi the mid- and late irrigation season) may
approach zero as a result of water diversion from the channel. Over the 1980-89 period, flows
from Milner Dam were less than 2.8 m3/s (99 cfs) 10% of the time (Clark, 1994), usually during
the summer irrigation months. An inspection of the U.S. Geological Survey (USGS) historical
streamflow daily graphs from 1970 to 1997 shows that the annual low flow for the King Hill
station (Figure 4-5) may occur in any month except November and December. However, low
flows usually occur from July to September. In low- to average-flow years, flows decline
. 4-8
-------
o
u.
40000 .,
35000 -
30000 -
25000 -
20000 -
15000 -
10000 -
5000 -
• 0 .
*'.»"* * x f ~- . *
\ — ^"°v_ 'L r~
in o 4-
CO CM
O
CD
CM
^" I I III 1^
CM OO CM I*- •»- tt> -T-
T- -r- CM CM
Date
Figure 4-5. Flow (cfs) in the Middle Snake River at Rkm 893 (RM555), mean + or - 2 SD.
Icfs = 0.02832 cms.
through the winter to early summer unless a higher flow year such as 1993 causes spill from
Milner (Myers et al., 1995). With low precipitation during 1988-1993, the flows were extremely
low. However, in 1996 there was a dramatic rise in precipitation and concomitant snow melt
with nearly 1,670 m3/s (58,968 cfs) flowing over Shoshone. Falls at the height of runoff.
Downstream from Milner Dam, flows increase substantially (average flow is 3 x 109
nrVyear or 106 cfs) because of tributaries, groundwater discharge, and irrigation returns. There
are eight major tributaries to the Middle Snake River (Figure 4-2): East Perrine Coulee, Rock
Creek, Cedar Draw Creek, Mud Creek, Deep Creek, Salmon Falls Creek, Billingsley Creek, and
the Malad River. The total contribution of these tributaries averages 48 mVs (1,695 cfs), with
the major contribution from the Malad River.
In his water budget analysis for the entire Snake River Plain during 1980, Kjelstrom
(1992) found that groundwater contributed 146 mVsec (5,155 cfs) of flow to the Middle Snake
River segment. This represents-more than 50% of the average annual flow at Lower Salmon
Falls. Kjelstrom (1992) reports, however, that groundwater discharge to the Snake River has
varied as recharge conditions have changed. From 1902 to the early 1950s, groundwater
discharge to the Middle Snake River segment increased because of recharge from flood irrigation
on the north side of the Snake River. In the 1950s, the estimated average annual groundwater
4-9
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flow to the Middle Snake exceeded an estimated 190 m3/s (6,709 cfs). Since that time, flows
declined until 1992 because of drought conditions in the basin and increases in groundwater
pumpage from the Snake Plain aquifer, with an accompanying shift from flood to sprinkler
irrigation (Kjelstrom, 1992). In 1996, the increased precipitation should have increased the
groundwater flow as well as the surface water flows.
Mundorff et al. (1964) found that the total gain from the aquifer to the Snake River
between Milner Dam and King Hill is equal to about two-thirds of the discharge measured at the
USGS gauge at King Hill. The major springs are Devil's Washbowl, Devil's Corral, Warm
Creek, Crystal Springs, Niagara Springs, Clear Springs, Briggs Springs, Box Canyon Springs,
Sand Springs, Thousand Springs, Riley Creek, and Malad Springs.
North-side springs to the river from about Rkm 957.5 (RM 595) upstream are supplied
primarily from local surface water recharge in agricultural areas between Minidoka and Twin
Falls, whereas springs below Rkm 957.5 (RM 595) are derived primarily from regional
groundwater, mainly intermontane basin stream recharge (Clark, 1997a). Clark and Ott (1996)
estimated that the upstream springs received more than 90% of their flow from irrigation
recharge, whereas the downstream springs received less than 20% of their flow from irrigation
recharge. When most of the river is diverted during the irrigation season, the springs are the
primary source of river flow.
4.4. DEMOGRAPHICS AND LAND USE
The political boundary of the study area includes six Idaho counties (Twin Falls, Jerome,
Gooding, Lincoln, Blaine, Camas) and portions of Minidoka, Cassia, Owyhee, and Elmore. This
area is commonly referred to as the Magic Valley. About 136,831 people (11% of the population
of the State of Idaho) live along the Snake River. The five largest municipalities in the Middle
Snake study area are Twin Falls (27,951), Burley (8,984), Jerome (6,529), Rupert (5,455), and
Hailey (3,687) (Figure 4-2). The remaining population lives in unincorporated areas.
About 26% of the land is privately owned, 70% is Federal land, and the remaining 4% is
State land. The primary land use by surface area is irrigated agriculture (23%) and grazing
(56.4%) (Figure 4-6). Forest and urban land make up less than 7% of the total land use.
Most of the land adjacent to the Middle Snake River is used for agriculture, roads, golf
courses, small cattle operations, private homes, boat docking facilities, and fish hatcheries.
Recreation activities include fishing, boating, and swimming in some limited areas.
Key industries in the area are agriculture, livestock production, and aquaculture. The
primary crops are potatoes, sugar beets, and barley. Most of the livestock production is dairy
cows. Seventy-six percent of the trout produced in the Nation come from Idaho.
4-10
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Conifer & Aspen Forests
Shrub/scrub
Grasslands & Meadows
Wetland & Riparian
^m^f^srss^Hv^^-^-i"'^-^'--.^,^'' ••-,-• - ,.-',. .••: *<&&*£•••;•&*
f«3L P^U'^/^--.-.'.,^..:..-.,if..^.L.....;,_,_i'5e "4^i^fev^*Tf^5*^'ft--i'-:5r'^?'V^
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Remote Sensing/GIS Lai), 1998
) 10 20 30
w:i^%^rt;^
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^:^:;^:^
ici:.r::;-;v:..^
^
70
10
Klomstfiis
15 20 &
30
Mies
Figure 4-6. Generalized land cover for the Middle Snake River Basin.
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Table 4-2. Primary land-use activities in the Middle Snake River between
Milner Dam and King Hill, Idaho (from Bowler et al., 1993)
Point sources
Combined animal
feeding operations
Aquaculture
Publicly owned
treatment works
Nonpoint sources
Irrigated agriculture
and cattle grazing
Impoundments.,
diversions, and
hydroelectric facilities
Quantities
600 dairies and feedlots
80 facilities
Twin Falls
Quantities
227,000 hectares irrigated
from the Snake River;
150,000 hectares irrigated
from the Snake River aquifer;
Return flow from 13 streams
and >50 surface drains
5 existing on mainstem; 7
proposed on mainstem; many
on tributaries
For the purposes of this analysis, land-use activities (Table 4-2) have been divided into
three categories: (1) point sources of pollutants, (2) nonpoint sources of pollutants, and (3)
structural alterations.
Sources upstream of Milner Dam are not included as individual releases in this
assessment. The total load from Milner Reservoir is included as a single discharge point in the
analysis.
4.5. FISH POPULATIONS
Before 1900, the Snake River was the most important drainage in the Columbia River
system for the production of anadromous fishes. Prior to the development of hydropower on the
Snake River, the Middle Snake sustained a variety of anadromous fish species that migrated as
far upstream as Shoshone Falls. This included fall and summer chinook salmon (O.
tshawytschd), steelhead trout (O. myMss), and Pacific lamprey (Lampetra tridentata). The
anadromous salmonids were first severely impacted by the construction of Swan Falls Dam in
1901 without adequate fish passage facilities. The final major hydroelectric events resulting in
4-12
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the termination of migrant fish stocks were the sequential closures of the Bliss Dam (1949), C. J.
Strike Dam (1952), and ultimately Brownlee Dam (1960). All these darns form impassable
barriers to the upstream movement of any anadromous species and sturgeon because they were
constructed without any fish passage facilities.
The completion of these facilities terminated lamprey, salmon, and steelhead migration
into the Middle Snake area (Smith, 1978; Bowler, 1992). The remaining downstream Snake
River stocks of fall and spring/summer chinook salmon have been listed as threatened or
endangered (USFWS, 1995). Although a number of impoundments presently block the
migration of anadromous salmonids, a number of resident cold-water species, including trout and
sturgeon, have survived in the river and tributaries.
Currently, there are approximately 24 native fish species below Shoshone Falls in the
subbasin and 14 above the falls (Appendix B). White sturgeon (Acipenser transmontanus),
rainbow and steelhead trout (Oncorhynchus mykiss), and mountain whitefish (Prosopium
-williamsoni) are Dative to the Middle Snake River.
The majority of the remaining fish in the Middle Snake are eutrophic-tolerant species,
such as some catostomids (suckers), northern pike minnow (Ptychocheilus oregonensis), the non-
native European carp, and various other cyprinids.
4.6. BENTHIC MACROINVERTEBRATES
The historic diversity of native molluscs in the river was high at 42 species, including 27
species of snails in 7 families and 15 species of clams in 3 families (Frest and Bowler, 1993). In
the past, the river supported a diverse cold-water macroinvertebrate fauna (in addition to the
molluscs and Crustacea), including numerous Ephemeroptera, Plecoptera, and Trichoptera.
Currently the benthic community (see Appendix B) is dominated by a few taxa indicative of
degraded conditions (Dey and Minshall, 1992). These taxa include Potamopyrgus antipodarum
(Gray, 1843), Chironomidae, Oligochaeta, and Hyallela. The exotic New Zealand mudsnail (P.
antipodarum) is now the dominant mollusc as well as the dominant benthic macroinvertebrate.
The hydrobiid P. antipodarum is native to New Zealand. It was first recorded in the
Middle Snake River by Taylor (1987). It has been observed attached to algae, macrophytes, arid
rocky boulder habitats (Bowler, 1991). By 1989, P. antipodarum dominated the benthic
macroinvertebrate habitats in the Middle Snake River (Bowler, 1991). P. antipodarum
dominates the preferred habitat of other hydrobiid snails and physically covers their egg-laying
sites. The species also crowds out other species as the density of its population increases to
600,000 individuals/m2 (Bowler and Frest, 1992).
The large freshwater clam Margaritiferafalcata, once a food staple for Native
Americans along the river, is now Virtually eliminated from the Middle Snake. The decline may
4-13 .
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be due to sedimentation, loss of rapids (Vannote and Minshall, 1982), or a significant reduction
in the juvenile salmonid population, which serves as a host for tihe parasitic larval stage of this
organism. Although M. falcata is common in the Blackfoot River and elsewhere in the Upper
Snake, the species has been replaced by the smaller pelecypod Gonidea angulata (Bowler and
Frest, 1992) in the Middle Snake River. .
The following eight species are listed under the Endangered Species Preservation Act as
threatened, endangered, or species of concern:
Threatened:
(1) the Bliss Rapids snail, Taylorconcha serpenticola (Hershler et al., 1994)
Endangered:
(2) the Utah valvata snail, Valvata utahensis (Call, 1884)
(3) the Snake River physid snail, Physa natricina (Taylor, 1988)
(4) the Idaho springsnail, Pyrgulopsis idahoensis (Pilsbry, 1933) (also known as the
Homedale Creek springsnail)
(5) the Banbury Springs limpet.(undescribed Lanx sp.)
Species of concern:
(6) the California floater, Anodonta californiensis
(7) the giant Columbia River limpet, Fisherola nuttalli (Haldeman, 1841)
(8) the Columbia River spire snail, Fluminicola columbiana auct.
The Banbury Springs limpet, Snake River Physa, the Bliss Rapids snail, and the Idaho
springsnail are found nowhere else outside of the Middle Snake River. They are endemic to the
ancient Lake Idaho, which once covered most of the area during the Pliocene.
4.7. AQUATIC PLANT COMMUNITIES
Aquatic plant composition and densities, as well as patterns of mixed vascular, epiphyte,
and periphyton interactions, are highly variable through a rapidly changing series of habitats of
the Middle Snake River.
Aquatic vascular plants through this reach are generally dominated by Ceratophyllum
demersum, Potamogetonpectinatus, and P. crispus in reaches of significant attached plant
growth (Falter and Carlson, 1994). Ceratophyllum demersum and P. pectinatus are generally
associated with well-buffered, nutrient-rich waters (Filbin and Barko, 1985; Best and Mantai,
1978). Subdominants are P.foliosus, Elodea nuttallii, and E. canadensis. Ceratophyllum and
Elodea, although vasculars, lack true roots and obtain most needed nutrients from the water
column. They are therefore considered functional epiphytes along with filamentous algae. Other
primary components of this epiphyton community are the filamentous green algae, Cladophora
sp., Hydrodictyon sp., and Enteromorpha. There are many locations in the Middle Snake where
4-14
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epiphytal is the principal component of the total summer-fall macrophyte biomass (Falter and
Carlson, 1994; Falter et al., 1995, Falter and Burris, 1996).
Blooms of planktonic (Microcystis, Cydotella, Ceratium), periphytic, and epiphytic algae
(Cladophora, Hydrodyctiori) occur continuously during the spring and summer in specific
reaches of the Middle Snake. The total epiphytic algae and vascular macrophyte biomass
may exceed 2,000 g/m2 dry weight, with Cladophora averaging 50% of the plant biomass in
summer months (Falter et al., 1995).
A detailed life history of the dominant attached aquatic plants is given in Appendix C.
4.8. ASSESSMENT ENDPOINTS
Assessment endpoints are explicit expressions of the actual ecological values that are to
be protected (U.S. EPA, 1998). These endpoints form a basis for linkage to risk management
activities in the watershed. The endpoints for this analysis were selected in 1996 (U.S. EPA
Problem Formulation, 1996). They are:
• The reproduction and survival of three fish species:
.' White sturgeon (Acipenser transmontanus), mountain whitefish, (Prosopium
williamsonf), and rainbow trout (Oncorhynchus mykiss).
• The reproduction, survival, and diversity of macroinyertebrates:
Bliss Rapids snail (Taylorconcha serponticold), Utah valvata (Valvata utahensis),
Snake River physa (Physa natricind), Idaho springsnail (Pyrgulopsis idahoensis),
and Banbury Springs lanx (undescribed Lanx sp.).
• The growth of periphyton, macrophytes, and epiphytes:
Potamogeton pectinatus, P. crispus, Ceratophyllum demersum, Elodea canadensis,
Hydrodictyon, Cladophora, Spirogyra, and Enteromorpha.
The growth of periphyton, macrophytes, and epiphytes was selected as an assessment
endpoint because their presence at an appropriate level is ecologically important for protecting
cold-water fish and macroinvertebrates. Had this assessment started after publication of the.
Guidelines for Ecological Risk Assessment (U.S. EPA, 1998) growth of periphyton, ,
macrophytes, and epiphytes may have served as a measure of effect for the other two assessment
endpoints. . ,
Representative species from three major trophic levels were chosen as endpoints in order
to complete an ecosystem-level analysis. Each of these groups (fish, invertebrates, and plants) is
an important link in the structure and function of this riverine ecosystem. Analysis of the factors
controlling their functions (growth, reproduction, and survival) should provide evidence for the
primary causes of the ecosystem changes.
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In addition to being indicators of ecosystem structure, fish and macroinvertebrates were
selected as assessment endpoints because they exhibit marked sensitivity to stressors, and changes
in populations of these assemblages can be linked quantitatively to several environmental
parameters (e.g., numeric criteria) to document the stressor and ecological response relationships.
Target fish species for this study were rainbow trout (Oncorhynchus mykiss), mountain
whitefish (Prosopium williamsoni), and white sturgeon (Acipenser transmontanus); all are cold-
water species of recreational importance in the Snake River. An assessment of the life stage
requirements for these species will provide an overview of most freshwater habitats used by
native fish species in the Middle Snake River. The macroinvertebrates were also selected because
the populations are either threatened or endangered. The decline of native species indicates that
they are sensitive to the changes that have occurred in the Middle Snake River. An analysis of the
factors contributing to their decline is necessary in order to preserve the remaining numbers as
well as promote recovery for the populations.
The high aquatic plant densities are indicators of ecological conditions (eutrophication)
that are not conducive to the growth and survival of cold-water biota. The reduction of aquatic
plant biomass is an essential step to the restoration of cold-water biota.
4.9. DECISION PATHWAY
The decision pathway (Figure 4-7) for this risk analysis begins with the description of the
land-use activities that may result in harm to the riverine ecosystem. For those properties that are
Figure 4-7. Decision pathway for analysis of ecological risk
using simulation methods.
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quantitative measures of stressors and ecological effects, simulation with mathematical models
can be used to make quantitative estimates of ecological risk. Stressor characteristics are defined
in terms of probability models for point source loadings, nonpoint source loadings, and
meteorologic and hydrologic conditions. These characteristics are used as forcing functions for a
mathematical model of the river ecosystem and to develop cumulative distribution functions for
environmental factors such as dissolved oxygen, temperature, and macronutrients. The
mathematical model developed by Yearsley (1991, modified in 1996) uses standard kinetics to
simulate temperature, dissolved oxygen, nitrogen, phosphorus, and primary productivity for time
scales of hours to decades, vertical length scales of meters, and horizontal length scales of
meters to kilometers. Limitations in our understanding of ecosystem processes in the Middle
Snake River are such that the model does not simulate all the variables that characterize the
primary stressors described hi the introduction. In particular, the model does not include those
variables necessary to characterize sediment loading and habitat alteration associated with
changes in the substrate.
The quantitative risk is estimated by comparing simulated measures of temperature,
dissolved oxygen, phosphorus, and macrophyte biomass with quantitative measures of effect.
Measures of effect are quantitative estimates of the state of the ecosystem that can be
related in some way to the values expressed by the assessment endpoints. For this analysis, the
Idaho water quality standards and U.S. Fish and Wildlife habitat suitability indices are
considered to be quantitative measures of effect.
Finally, the quantitative risk estimates are analyzed qualitatively using best professional
judgment and field observations.
A detailed description of the simulation methods, results, and uncertainty analysis is
presented in Appendix D of this report.
4.10. CONCEPTUAL MODEL
The conceptual model (Figure 4-8) for this assessment illustrates the land-use activities,
stressors, ecological processes affected, and biological consequences of these process changes.
The hypothesis for this analysis is that flow and temperature alteration, sediment
deposition and scouring, ammonia toxicity, decrease in dissolved oxygen, and nutrient loading
are the principal stressors in this ecosystem. These stressors interact with the biota, causing a
decline in native cold-water biota as a result of individual or synergistic influences.
The parameters identified as stressors (flow, temperature, ammonia, dissolved oxygen,
sediments, and nutrients) are driving forces in natural ecosystems. They are the physical and
chemical characteristics that define the structure and function of ecosystems. It is only when
these parameters exceed biological tolerance limits that they become stressful or harmful to
4-17
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Ecological
effects
Ecological
Processes
Increase
in Plant&
Algal
Populations
Decline
in Native
Coldwater
Snail
Populations
Eutrophication
Habitat Alteration
^
Flow
Modification
1 11
Sediment
Scourino
&
Deposition
*
Temperature
Modification
w A ^fc
Sediment
Loading
^Jf ^
Stressors
Land use
Figure 4-8. Conceptual model for the Middle Snake River Risk
Assessment.
aquatic life. The tolerance limits are generally equal to the natural levels that have defined the
ecological boundaries for which most native species have adapted. Excursions above and below
these boundaries or tolerance levels can be stressful. These tolerance levels depend on life stage
and vulnerability of the organisms at risk as well as the likelihood of exposure or contact with the
stressful environment. • .
4.11. LAND-USE ACTIVITIES THAT ALTER ECOSYSTEMS
Land-use activities can affect ecosystem structure and function through point and
nonpoint source release of pollutants (thermal, chemical, physical) and physical disturbance.
Sources of ecological stressors identified in the conceptual model as point sources include the
Twin Falls Sewage Treatment Plant, confined animal feeding operations, and aquaculture
facilities. These facilities release nutrients and sediments through discharge canals and pipes
directly into the river. The nonpoint sources include irrigated agriculture and cattle grazing.
These activities result in releases to groundwater and surface water through leaching and runoff.
Finally, impoundments cause physical changes to the river ecosystem that can be harmful to
native biota.
4-18
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4.11.1. Twin Falls Sewage Treatment Plant
There is only one sewage treatment plant in the study area. The Twin Falls Sewage
Treatment Plant discharges sewage after secondary treatment. The plant uses an activated sludge
system designed to treat 7.8 million gallons per day (mgd) of wastewater. The facility consists of
the following unit operations: bar screens, grit removal, primary clarification, activated biofilter
tower, intermediate clarification, activated sludge, secondary clarification, and ultraviolet
disinfection. A city-owned anaerobic digester was recently added between Lamb-Weston
(formerly Universal Frozen Foods) and the treatment plant to digest potato solids before they
reach the plant. The Twin Falls facility discharges nutrients, ammonia, settleable solids, total
suspended solids, and organic matter.
4.11.2. Confined Animal Feeding Operations
Confined feeding operations are required to contain all wastewater and are allowed to
discharge only during extreme rain events (once in 25-year 24-hour storms). Unfortunately, such
events do occur, and during these events or because of accidental or illegal discharges, nutrients,
pathogens, and sediments reach the river through surface runoff and via groundwater
contamination. The Middle Snake River area is very popular for dairy operations because of the
climate and close proximity to cheese factories. Dairies and feedlots dispose of their liquid and
solid wastes through land application, primarily on cropland. There are more cattle in the Magic
Valley than in the entire rest of the State.
4.11.3. Aquaculture
There are 80 private and State-owned aquaculture facilities that have been operating for
more than 30 years in the Middle Snake River. They are required to obtain Federal National
Pollutant Discharge Elimination System (NPDES) permits. More than 20 additional facilities
have applied for permits to discharge.
These facilities operate earth and concrete raceways in series or in parallel on a
continuous or batch basis. These include both cold-water facilities, which raise trout, steelhead,
salmon, and sturgeon; and warm-water facilities, which raise catfish, tilapia, and carp. The
annual production of these facilities ranges from 9,072 kilograms to more than 453,600
kilograms. They supply approximately 80% of the trout consumed in restaurants in the United
States.
Discharges from aquaculture operations typically contain organic and inorganic solids,
chemicals used in prevention and treatment of disease, and nutrients. Discharges could impact
water quality in the receiving stream by adding ammonia, bacteria, dead fish, feces, residual
4-19
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disinfectants and disease-control drags, settleable solids, thermal energy, and total suspended
solids.
Several aquaculture facilities have associated fish processing facilities that butcher fish
for market onsite. Production ranges from hundreds to tens of thousands of trout, catfish, or
tilapia per day. Pollutant discharges from the fish processors consist of rinse and washdown
water and entrained blood and gut remnants, measured in terms of biochemical oxygen demand,
total suspended solids, settleable solid residues, nutrients, disinfectants, and pH.
Pollution reduction by Idaho's aquaculture industry began with the construction of
settling ponds in the mid- to late 1970s. Effluent from raceways and rearing ponds would pass
through these ponds slowly, allowing solids to settle before the facility discharge point
(Aquaculture Watershed Reduction Plan for the Middle Snake River, 1997; e.g., Brown et al.,
1974; Kendra, 1991; Westers, 1989). By 1984, a number of aquaculture facilities were
experimenting with the use of screens to keep resident fish from congregating within 3 to 6
meters of the effluent weir in each raceway (JRB, 1984). These areas of the raceways became
known by industry as quiescent zones. They were effective at settling solids in the raceway,
allowing industry to meet the 5.0 mg/L total suspended solids limit on raceway discharges.
Settled solids were removed either by mechanical or siphon vacuuming or by draining through
opened stand pipes in the quiescent zone. Facilities were also experimenting with the
effectiveness of solids removal using standpipe siphon hydraulics. Vacuumed or siphoned solids
would be sent to off-line settling ponds for further treatment. Improved feed conversions, lower
phosphorus feeds, and improvements hi availability of phosphorus in feeds are believed to have
reduced phosphorus discharges by the industry during the 1990s (Aquaculture Watershed
Reduction Plan for the Middle Snake River, 1997).
A study of six fish farms discharging to Deep Creek, a tributary of the Middle Snake
River, was completed in 1993 by the University of Idaho (Deep Creek Fish Farm Effluent Study,
Collins and Brannon, 1994). Because of the quality of the source water (Deep Creek), these fish
farms had a negative net contribution of suspended solids and nitrite-nitrate levels, but they had a
positive net contribution of ammonia and phosphorus in their effluent. The study found that
solids and dissolved nutrients can be reduced in settling areas below rearing ponds, at least in the
low-fish-density ponds of this study. It is much more difficult to achieve settling in high-fish-
density, high-flow raceways. '
4.11.4. Irrigated Agriculture and Cattle Grazing
Agriculture is made possible by water withdrawal from the Snake River. Early settlers
used water from the Snake River tributaries for irrigation. In the.summer of 1903, the Twin Falls
South Side Land and Water Company tract was opened to farmers (IDEQ, 1995) for irrigation of
4-20
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their crops. The Twin Falls North Side Land and Water Company was granted permission to
construct canal systems and withdraw water from Milner Reservoir under the provisions of the
Federal Carey Act in 1907.
Poor agricultural practices from crop production can result in increased sediment loading.
The Soil Conservation Service's River Basin Reports of 1976,1979, and 1981 identified
substantial areas of serious erosion on surface-irrigated lands in the Upper Snake River basin.
Gooding and Jerome Counties each had more than 20,000 hectares with erosion rates exceeding
1.8 metric tons/hectare/year, while Twin Falls County had between 2,000 and 20,000 hectares
exceeding 1.8 metric tons/hectare/year.
Sediment loads increase dramatically with increased runoff flow rates from cropland
(Carter, 1976). Greater rates of flow off the land into irrigation-return canals increase the amount
of the sediment inputs into the streams and river. Irrigation return flows carry pesticides,
fertilizers, and sediment loads to the river. Runoff from individual fields, especially those using
furrow irrigation, carries sediment into drainage canals, which eventually reaches the river.
Different crops yield different levels of sediment, e.g., sediment loss from alfalfa fields is fairly
low whereas that from dry-bean production is fairly high.
Most of the smaller canals that flow over the precipitous canyon wall percolate through
talus debris piles formed from rock falling off the canyon wall. Accumulated sediment and rock
debris tend to remove some of the other pollutants associated with irrigation wastewaters in a
fashion similar to.wastewater treatment by land treatment systems. During heavy rains or after
snow melt, the overflow into the river occurs with little or no percolation through debris piles.
Most larger irrigation return flows are much more damaging to the river. Irrigation return flows
at the Perrine Coulee hydroelectric facility (NPDES Draft Permit, 1998) are conveyed through a
penstock to a hydroelectric turbine. Thus, the water bypasses the talus slope and is discharged
directly to the river, creating a sediment-laden pollutant plume.
Although some farmers have incorporated low-till and other best management practices
as part of their cultural practices, implementation of best management practices is not widespread
in the region.
Agricultural practices also result in the release of nutrients into the groundwater and into
surface waters of the watershed. Carter et al. (1971) estimated that 2,737 metric tons of nitrate
were transported from the Twin Falls irrigation system into the Snake River. Sediment from
Twin Falls was estimated at 2,377 metric tons/year (Brown et al., 1974).
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4.11.5. Nutrient and Sediment Loading
The total industry loading estimates are presented in Table 4-3 (from IDEQ's Nutrient
Management Plan, 1995). From this table, it is obvious that agriculture is the primary source of
sediments and that springs are the primary source of nitrogen. The nitrogen load from springs is
a result of leaching of wastes from agricultural, cattle grazing, and cattle feedlots.
Water chemistry data collected by the University of Idaho Agricultural Research Station,
the Idaho Division of Environmental Quality (IDEQ), Clear Springs Food Inc., and the City of
Twin Falls were used to estimate daily mass loadings for point sources in the study.
4.11.6. Impoundments
Impoundments that store and divert water for hydropower and irrigation result in flow
modifications in the mainstream and tributaries. Summer-fall flows into this reach are controlled
by several large upstream storage reservoirs (American Falls, Island Park, Palisades, and Ririe
Reservoirs). There are five existing impoundments within the study area downstream from
Table 4-3. Estimated nutrient and sediment loadings for point, nonpoint, and background
sources. This table is an excerpt from the State of Idaho Department of Environmental
Quality Nutrient Management Plan for the Middle Snake River (from IDEQ, 1995). These
estimates are based on weighted mean net discharge levels reported by the industry, which
were averaged with estimates of net contributions estimated by Brockway and Robinson
(1992). The result is an industrywide net contribution. These loads are based oh an
assumption of industrywide water usage of 85 m3/s (IDEQ, 1995).
Sources
Upstream
Springs
Aquaculture
Twin Falls
POTW
Irrigated
agriculture
Other
Sediments (TSS)a
(kg/day)
0.3 (251)
0
13,497
733
157,873
42,876
Total phosphorus
(kg/day)
16 (282.5 )
359 (304)
733
467
276
228
Total nitrogen
'(kg/day)
118(282.6)
27,713 (22,150.6)
5,794
7,097
2,336
References
Brockway and Robison, 1992
Brockway (unpublished),
MacMillan, 1992; Clark, 1994
1991 DMRsb; Brockway
(unpublished)
1991 and 1992 DMRs
Brockway and Robison, 1992
Brockway and Robison, 1992
"Total suspended solids.
""Discharge monitoring reports from NPDES permits.
4-22
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Milner Dam: Twin Falls, Shoshone Falls, Upper Salmon Falls, Lower Salmon Falls, and Bliss
Dams (Figure 4-3). All five facilities are operated under licenses with the Federal Energy
Regulatory Commission. In the Middle Snake River, there has been a 37% loss of free-flowing
habitat (Cochnauer, 1983), a direct result of operating dams for hydroelectric power, flood
control, and agricultural purposes. The fluctuations of water levels in impoundments, reservoirs,
and tailwaters are both seasonal and diurnal in nature. Of these, the greatest change in water
level in the Middle Snake River occurs during diurnal fluctuations hi the tailwaters of a dam
(Irving and Cuplin, 1956).
The change from a riverine system to a reservoir system is driven by the time water
remains hi one location. The longer the retention tune, the more likely the system will function
like a lake rather than a swiftly flowing stream. Retention times of the five reservoirs, at low
river flow and average annual flow, are given in Table 4-4.
Low river flow for Twin Falls and Shoshone Falls are 5.66 cms (200 cfs) and 78.25 cms
(2,763 cfs), respectively. Corresponding low flows for Upper and Lower Salmon Falls are 156
cms (5,510 cfs) and 254 cms (8,978 cfs) for Bliss. For the Middle Snake River assessment, Twin
Falls and Shoshone Falls reservoirs were treated as reservoirs with the potential for vertical
stratification, on the basis of data collected by the Idaho Power Company (Myers arid Pierce,
1996).
Construction of impoundments destroys the natural geomorphological structure of the
channel and mobilizes sediments. Stream flow regulation at hydroelectric dams can alter the
upstream and downstream sediment distribution and thermal regime. Water released from dams
results in increased erosion of the riverbed and banks below dams, particularly in the littoral
areas. These habitats are most often altered in ways that are not-compatible with the survival of
Table 4-4. Retention times for the five reservoirs in the Middle Snake River for low
and average annual river flows
Hydroelectric
project
Twin Falls
Shoshone Falls .
Upper Salmon Falls
Lower Salmon Falls
Bliss
Retention time
at low river flow
(days)
2.56
4.57.
0.26
0.83
0.30
Retention time
at average annual river flow
(days)
0.18
0.33
0.22
0.51
0.18
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diverse native benthic communities. Downstream of the dams, the higher velocity discharges
erode banks and the river bottom and carry suspended sediment to the backwaters of the next
impoundment. The net result is deposition of suspended material upstream of a dam and
scouring of the river bottom and shoreline areas downstream of the dam. Sediment transport
capacities are lower upstream of impoundments because the velocity and turbulence of river
currents is dissipated hi the slowly moving backwaters of impoundments. Sediment scouring and
deposition eliminate niches for species that prefer boulders or gravel and clear water (some
invertebrates and fish species) and create niches for species that require sediment substrate for
growth (rooted macrophytes).
The backwater upstream of these dams is slowed, warmed, and often stratified under
relatively stagnant flow conditions. Falls or rapids in these areas are drowned by the elevated
water surface upstream of the dam, and aeration capacity of the falls is lost.
Dams fragment a river system, isolating resident fish in tailwater reaches between them.
Fish may be stranded and die in tailwater reaches, or they may be unable to reproduce because of
inadequate habitats. The much longer hydraulic residence times permit development of
planktonic algae and accumulation of soft bottom sediments, two conditions normally not
associated with swift-flowing streams. Increased suspended sediments may also smother species
or alter their behavior.
The annual range of water temperatures tends to fluctuate more because of the presence
of the impoundments. The increase in surface area exposes more water to solar radiation, which
tends to raise summer surface water temperatures. The combination of slower velocities and
higher temperatures that results from dam operation creates an optimal environment for the
growth of plankton and macrophytes.
4.11.7. Other Nonpoint So.urces
Stream bank erosion (exacerbated by cattle grazing) and urban runoff also contribute
sediments and nutrients to the river. There is minimal information on these sources in the
Middle Snake drainage.
4.12. ECOSYSTEM DYNAMICS
To implement the dynamic model of mass and energy, the^ Middle Snake River has been
divided into two major ecosystem components. One describes the chemical, physical, and
biological characteristics of the moving water column, and the other describes the benthic plant
community attached to or associated with the river bottom.
. 4-24
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4.12.1. Water Column Dynamics
River water quality is high during most of the year, but may decline significantly at low
flows in mid- and late summer. It is these extreme low-flow conditions that set bounds for
aquatic species. In the fall with increasing water flows, water quality generally improves as less
water is removed from the river channel and overland and subsurface irrigation return flows
increase, especially below Niagara Springs. Most in-stream water quality parameters (with the
exception of NO3") decline in concentration through the fall (Myers et al., 1995).
The water quality of the river is strongly influenced by the natural springs. Alcove
springs (springs discharging from the lower canyon walls along the Snake River banks) are
common along the Middle Snake River below Twin Falls. These springs discharge exceptionally
clear (Secchi disk transparency > 10 m) and cool water that influences the water quality of the
river channel.
However, these springs are not always removed from pollution. Clark and Ott (1996)
estimated that the springs upstream of Twin Falls received more than 90% of their flow from
irrigation recharge whereas the downstream springs receive less than 20% of their flow from
irrigation recharge. As a result, conductivity and NO3" increase down through Rkm 957.4 (RM
595) and decrease from dilution below that point.
Nitrogen contributions to the Middle Snake River include nitrates in spring flows and
limited instances of nitrogen fixation by blue-green algae. The State of Idaho completed a survey
of groundwater of the Middle Snake River in 1991 (IDWR, 1992) and found that approximately
95% of the 129 sites monitored exhibited elevated levels of nitrate nitrogen. The springs'
constant water temperatures, along with high conductivity and NO3-abundant shallow depths,
high alkalinity, high transparency, and hard-water conditions (Clark, 1997a), are all conducive to
sustained high plant and invertebrate productivity in the springs proper; these inflows
significantly influence water quality of the main river channel.
The range of nitrate nitrogen in the mainstem (Table. 4-5) decreases in a downstream
direction. At Rkm 985.7 (RM 612.6), the range is from less than 0.5 mg/L to more than 2.5
mg/L, while at Rkm 784.4 (RM 487.5) it is from about 1 to 2 mg/L. As in the case of
temperature, this change can be attributed to the moderating effect of the springs on both flow
and concentration. Natural levels of nitrogen were reported (Allen, 1995) as 0.12 mg/L dissolved
inorganic nitrogen. Average phosphorus levels in the mainstem ranged from 0.06 to 0.17 mg/L
for total phosphorus and 0.02 to 0.1 mg/L for ortho phosphate (Table 4-5).
In conjunction with the sampling of the invertebrates, several water chemistry variables
were assessed at monthly intervals during the summer and autumn (Table 4-6).
4-25
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Table 4-5. Average concentrations of nitrogen and
Middle Snake River (from Brockway and Robison,
phosphorus in the
1992)
Rkm(RM)
995 (619)
• 993.2 (617.3)
988.9 (614.6)
982.3 (610,'S)
977.6 (607.6)
956.7 (594.6)
938 (583.0)
932.6 (579.6)
922 (573.0)
902.8 (559.9)
NH4-N
mg/L
0.07
0.08
0.07
0.07
0.28
0.11
0.11
0.10
0.10
0.09
NO2+NO3-N
' mg/L
1.76
1.70
1.73
1.67
1.79
2.01
1.46
1.46
1.38
1.36
Total P
mg/L
0.09
0.08
0.08
0.09
0.17
0.13
0.09
0.09
0.08
0.08
PO4-P
mg/L
0.08
0.07
0.06
0.06
0.14
0.12
0.08
0.03
0.08
0.07
Table 4-6. Mean values for selected water chemistry variables from 1992 to 1994
in the Middle Snake River (see Royer et aL, 1995, for full description)
Year
1992
1993
1994
Alkalinity,
mg CaCO3/L
195
186
188
Hardness,
mg CaCO3/L
243
212
218
NO2+NO3
ppm
1.90
1.28
1.54
Total P,
ppm
0.119
0.172
0.151
Specific
conductance, •
(iS/cm
535
490
449
Natural phosphorus levels in streams throughout the United States have been reported at
0.01 mg/L PO4 (Allen, 1995). Concentrations of phosphorus exceeding 0.03 mg/L are generally
indicative of eutrophication (Wetzel, 1983).
The ratio of nitrogen to phosphorus (Redfield, 1958) is 16:1 hi plant tissue. In systems
where the ratio falls below 16 it is assumed that nitrogen may be limiting. In the Middle Snake,
the ratio ranges from >19 to 5 at Rkm 965.4 (RM 600) (Figure 4-9). Thus, the system at tunes
may be both nitrogen and phosphorus limited. However, for most fresh waters phosphorus is
assumed to be the driver for plant growth (Allen, 1995).
The abundant growth of aquatic macrophytes and filamentous algae, together with the
high mean concentrations of nitrogen and phosphorus, indicate that the Middle Snake River was
a highly eutrophic system during the years 1992-94. The eutrophic condition also was reflected
4-26
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in the extremely fast rate at which organic material in the river decomposed (Royer and Minshall,
1996).
Higher and later spring flows in 1993-94 were the cause of cooler temperatures those
years. Optimal growth temperatures in the model were set at 25°C for both rooted and nonrooted
forms. It is possible that nonrooted optimal growth temperature should be set lower to project
greater growth at cooler temperatures. In the Box Canyon reach, where water temperatures were
much cooler because of unpolluted springs influence, the modeled nonrooted growth was also
much less than the observed growth.
An important characteristic of the water temperature in the Middle Snake River, as
reflected in both the simulated and observed values, is the change in temperature range from
upstream to downstream. At me location farthest upstream (TRJon 984.5, RM 612), water
temperature varies from near 0°C to approximately 22°C. At the downstream locations the water
temperature ranges from approximately 7°C to 20°C. The difference in water temperature range
is due to the moderating effects of the spring flow on river temperatures in the lower reaches.
Water temperature varies seasonally in the river, depending on meteorological conditions and
groundwater flow. Average daily water temperatures at Rkm 893 (RM 555) vary seasonally
from 5°C in winter to a maximum of approximately 21°C in summer (Figure 4-10). Average
o
0>
3
U1
0)
N:P Ratio
Figure 4-9. Frequency of N:P ratios in the Snake River at Rkm 965.4
(RM600).
4-27
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temperature for the springs was about 15°C; for the tributaries 12°C to 14.5°C. In 1994,
monitoring of water temperature in the Middle Snake River near the Magic Valley Fish Hatchery
(approximately Rkm 944, RM 590) revealed 40 days during July and August hi which the mean
daily water temperature exceeded 20°C.
The mathematical description of mass and energy flow in the water column described in
this report is based on the mathematical model RBM10 (Yearsley, 1991). RBM10 has been used
as a decision support tool in a number of river basins in the Pacific Northwest, including the
Snake River above Milner Dam (Yearsley, 1976) and the Spokane River (Yearsley and Duncan,
1988). RBM10 makes use of concepts that have been used in other modeling efforts (e.g.,
Thomann et al., 1975; Patten et al., 1975; DiToro et al., 1975; Chen and Orlob, 1975; Scavia,
1980) and is conceptually similar to these models. Variables in the water column simulated by
this model are given in Table 4-7.
The sediments with which the benthic plants are associated in the Middle Snake River are
segmented into well-mixed compartments organized longitudinally only. In general (e.g.,
Ambrose et al., 1993), many of the physical, chemical, and biological processes in the sediments
are similar conceptually to those in the water column. However, in this application of simulation
methods to risk analysis, the analysis includes sediments only to the extent they provide substrate
for benthic plants including vascular macrophytes, epiphytes, and periphyton. Sedimentation
rates for phosphorus reported by Falter and Burns (1996) proved to be important to simulating
changes in concentrations in the vicinity of maximum macrophyte density.
o
s
I
f
25
20
15
10
5
l
I
Date
Figure 4-10. Simulated water temperatures (°C) in the Middle Snake River at Rkm 893
(RM555); maximum, mean, and minimum.
4-28
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The flow of mass and energy within the sediments is generally not included in this
analysis. However, the flow of mass and energy within the water column as it affects uptake by
the roots of vascular macrophytes is included hi the analysis. Where flow of mass or energy from
the sediments are part of the analysis, as in the case of nutrient flow to the roots of vascular
macrophytes, it is assumed to be unlimited by plant uptake. Similarly, the flow of solids to and
from the sediments is assumed to be at steady state. That is, there is neither gain nor loss of
substrate due to deposition and scouring.
Chemical oxygen demand from point and nonpoint discharges does not appear to be a
major source of oxygen demand in the Middle Snake River. Limited testing of the model
showed that the dissolved oxygen in the river was not sensitive to changes in this parameter
within the ranges typical of this system (Bowie et al., 1985).
4.12.2. Sediment Dynamics
Sediment dynamics in rivers and streams are driven by system hydrology and properties
of sediment sources. In natural streams and rivers, a broad spectrum of both flows and sediment
sources (Hill et al., 1991) shapes the character of the material that is transported hi the river as
suspended load or bed load, as well as shaping the character of the river channel form and
bottom. When flow and sediment sources are the result of a broad spectrum of natural processes,
river channels are characterized by a diverse ensemble of sediment types. Higher gradient river
segments are typically ones with gravel, cobble, or boulder sediments. Smaller particle sizes
ranging from sands to silts are associated with low-gradient segments or deep holes. The
character of the substrate for the lower gradient segments is generally more transient as a result
Table 4-7. Water column variables simulated by the mathematical model for
characterizing ecological risk
Carbonaceous biological Organic
oxygen demand (CBOD) nitrogen
Dissolved oxygen
Phytoplankton biomass
Ammonia
nitrogen
Nitrite + nitrate
nitrogen
Organic
phosphorus
Coliform bacteria
Orthophosphorus Water depth
Temperature Water velocity
4-29
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of high-flow events. Higher flow events are more likely to occur in a natural hydrologic regime,
and such events are more likely to alter the river sediments in segments with smaller particle
sizes.
In highly regulated systems, such as the Snake River, the spectrum of flows is modified
considerably. As a result, the likelihood of high flows or rapid changes in flows is much less
than that of the natural river. The construction and operation of hydroelectric facilities and the
diversion of water for irrigation impose additional constraints on river hydraulics (Richter 1996).
These constraints in turn can result hi significant changes to both the channel geomorphology and
substrate composition.
In the Middle Snake River, significant changes in the sources of sediments have also had
a major impact on sediment dynamics. Field studies by Brockway and Robison (1992) found
that the cumulative input of solids to the study reach from upstream sources during the period
June 1990 to July 1991 near Milner Dam was approximately 3,400 tons, while the cumulative
output from the study reach at King Hill was approximately 70,000 tons. During this same
period, the input of solids to the segment between Rock Creek (Rkm 971.2) and the Gridley
Bridge (Rkm 938.0) was 14,800 tons from the Snake River, 14,400 tons from irrigation canals,
44,500 tons from tributaries draining irrigated agriculture, and 4,100 tons from the major
aquaculture facilities. Approximately 48,700 tons of solids was output from the study reach at
the Gridley Bridge, leaving an excess of approximately 29,100 tons of fine-grained solids that
were presumably deposited in the study reach during this period.
High deposition rates of fine-grained solids in the Middle Snake River during this period
were confirmed hi the results of field studies reported by Platts (1991). Platts (1991) separated
substrate types hi the reach from Rkm 967.0 to Rkm 951.7 into nine categories: silt, silt and sand,
sand, sand and gravel, gravel, cobble, boulder, boulder and bedrock, and bedrock. Platts (1991)
found that silts made up 56.7% of the area surveyed. Studies of sediment chemistry by Falter and
Burns (1996) in this same segment found that organic matter in the surficial sediments varied
between 2.6% and 4% and that average phosphorus concentrations varied between 1,073 and
1,577 mg/g. These sediments provided an ideal substrate for the luxuriant growths of
macrophytes and epiphytes observed in this segment of the Middle Snake River.
The period during which high deposition rates of fine-grained, nutrient-rich sediments
were observed in the study reach was a period of extremely low flows. In 1997, flows in the
study reach were extremely high. Two studies of sediments and sediment transport conducted
during the summer of 1997 (Clark, 1997a; McLaren, 1998) provided insight into how channel
morphology and deposition rates in the regulated river respond to high flow conditions.
McLaren (1998) found that deposition during this period was occurring only in Shoshone Falls
Reservoir, the most upstream reservoir included in this study. Downstream from Shoshone Falls,
4-30
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percentage of fine particles increased in a downstream direction. McLaren (1998) concluded that
most of the suspended sediments transported by the river were derived principally from the river
bed itself and. that the increase in fine-grained sediments in the downstream direction was a result
of the natural progression of size sorting in the direction of sediment transport. Because of the
manner in which sediments had been scoured from the study reach, McLaren (1998) likened the
river to a "chute contained hi bedrock." These conclusions were supported by the work of Clark
(1997), who found that in some areas of the river, the bed sediment material was hard-packed
sand, essentially impervious to penetration. Clark (1997) also found that the only segment of the
system that had fine-grained clay-sized sediments was near Bliss Dam at Rkm 901.5, supporting
McLaren's (1998) hypothesis that fine-grained sediments had moved downstream.
The picture of sediment dynamics in the Middle Snake River that emerges from these
studies is one in which the ends of the spectrum of sediment processes are represented, but there
is no continuum. That is, the processes that might lead to a more natural system have been
impaired by changes in the river hydrology and sediment inputs. This results hi a system with
predominantly high-organic, nutrient-rich, fine sediments during periods of low flows. Most of
these sediments come from land-use practices related to irrigated agriculture and aquaculture.
When river flows are high enough to scour the fine-grained particles, which McLaren (1998)
suggests is at about 283 cms (10,000 cfs), the sediments are transported downstream. Some of
these sediments are deposited in the downstream reservoirs, as evidenced by the organic
sediments found by Clark (1997) at Bliss Dam. In river segments outside of the reservoirs, a
scoured channel composed of hard-packed sands and bedrock may occur because there is a lack
of connection with upstream, natural sources of sediment. This condition can be made worse
during periods of high river flows.
4.12.3. Dynamics of the Benthic Plant Community
The benthic plant community variables included in the analysis for the sediments are
macrophytes with roots, macrophytes with limited roots, epiphytes, and periphyton. The flow of
energy, mass, and information for the benthic plant community is shown in Figure 4-11.
The concept for kinetics of vascular macrophytes is based on the terrestrial ecosystem energy
model developed by O'Neill et al. (1972) for a closed-canopy, homogeneous forest ecosystem in
the eastern deciduous biome. Bloomfield et al. (1973) adapted the concept to simulate aquatic
macrophytes in Lake George, New York. The analysis for aquatic macrophytes in the Middle
Snake River is similar to the Lake George model. Important features of this concept are:
• The organic matter associated with vascular macrophytes can be idealized by three
compartments for organic carbon, including roots, leaves/shoots, and carbon
storage.
4-31
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e The accumulation of carbon in carbon storage is by photosynthesis. Carbon flows
to roots and leaves/shoots from storage.
Other features of the analysis for vascular macrophytes are based on previous research and
observations of macrophytes in the Middle Snake River (Falter and Carlson, 1994; Falter et al.,
1995; Falter and Burris, 1996). These features are characterized by several assumptions:
• Michaelis-Menten formulations are appropriate for light, nutrient, and habitat
limitations (e.g., Barber, 1991; Porcella et al., 1983).
• Nutrient uptake rates are low at low river velocities because of poor rates of
exchange, but increase with river velocity up to a certain optimal velocity (Horner
et al., 1983). As river velocity increases beyond a. certain point, physical stresses
begin to occur in the plants. These stresses lead to mortality of the plants and
increase the rate of sloughing (Chambers et al., 1991a,b).
• Vascular macrophytes with extensive root systems, such as Potamogeton, take a
Dissolved &
Particuiate
Nutrients
Stored Carbon from
Photosynthesis
SEDIMENT
Figure 4-11. Flow of energy and materials for aquatic plant growth in the Middle
Snake River.
4-32
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large percentage of their nutrients from the sediments (Howard-Williams and
Allanson, 1981). Macrophytes with limited root systems, such as Ceratophyllum,
derive the majority of their nutrients from the water column.
The analysis for epiphytes is a population model with Michaelis-Menten formulations for
light, nutrient, and habitat limitations. This analysis was modified to include the assumption
that, in the Middle Snake River, epiphytes such as Cladophora are generally associated with a
macrophyte substrate on which they attach themselves and grow. Furthermore, the epiphytes
intercept solar radiation in the top 10% of the water column, rather than over the entire water
column. This assumption was based on observations made during the 1992-1994 studies of
macrophytes (Falter and Carlson, 1994; Falter et al., 1995; Falter and Bums, 1996).
Rates of phytoplankton growth, respiration, nutrient, light, and temperature limitations
and stoichiometry were initially based on values typical of those used in other phytoplankton
model studies (Bowie et al., 1985). Sensitivity analysis showed the dynamics of phytoplankton
in the Middle Snake River to be more responsive to hydrology and to initial conditions from
upstream sources.
Rooted aquatic macrophytes in the Middle Snake appear to be most responsive to water
depth and sediment composition. These two factors are controlled by sediment loading
(primarily from agricultural drains and fish hatcheries) and localized hydrology. Once physical
structure is prdvided, nonrooted macrophtyes can develop, given sufficient structure and nutrient
supply from the water column.
' In addition to the parameters characterizing mass and energy transfer, a benthic habitat
factor was introduced. The benthic habitat factor was an estimate of the fraction of the bottom '
area available for macrophyte growth in each river segment. Downstream of Auger Falls this
factor was estimated from the macrophyte studies conducted by Hill (1992). Above Auger Falls
the habitat factor for macrophytes was assumed to be zero, primarily because of lack of data.
Initial estimates for the parameters characterizing growth rates, rates of senescence, and
nutrient uptake were varied by trial and error using mass and energy loading as described by
1990-1994 water chemistry and hydrology data given above and 1992-1994 macrophyte data
reported by Falter and Carlson (1994).
4-33
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5. SIMULATION OF ECOLOGICAL RISK
The following chapters (5, 6, 7, and 8) present the results of the analysis of exposure and
effects on the assessment endpoints described in Chapters 3 and 4. The analysis begins with the
results of the simulation of ecological events (Chapter 5) in the basin. This is followed by a
qualitative analysis of the factors affecting fish (Chapter 6), invertebrates (Chapter 7), and plants
(Chapters).
The methods and results for the simulation of ecological risk are provided hi Appendix D
of this report. A summary of the quantitative measures of effect and risk estimates is presented
in this chapter.
5.1. QUANTITATIVE MEASURES OF EFFECT
5.1.1. Water Quality Standards
A logical source for measures of effect is the State of Idaho's water quality standards
(Table 5-1). The standards for dissolved oxygen, temperature, and ammonia are numerical
thresholds based on reviews of the literature. The standards for nutrients and macrophytes are
narrative. In order to estimate risks quantitatively, these narrative standards must be converted to
numeric limits.
The State of Idaho's Department of Environmental Quality (IDEQ) derived a numeric
criterion for phosphorus for the purposes of establishing a total maximum daily load (TMDL).
The TMDL requires that total phosphorus be 0.075 mg/L when the river flow is equal to the 1-in-
10-year 7-day average low flow (7Q10), as measured at the Gridley Bridge. The TMDL limits
total phosphorus in the Middle Snake River at the Gridley Bridge to 1,088.6 kg/day. This
corresponds to a concentration of 0.075 mg/L total phosphorus for a flow of approximately 167
m3/s (5,900 cfs) in the Snake River. This criterion is less than that suggested by U.S. EPA
(1976) for flowing waters (0.10 mg/L), but greater than that suggested by U.S. EPA (1976) for
flowing waters that enter lakes or reservoirs (0.05 mg/L). The criterion for total phosphorus
developed by IDEQ has not been specifically related to the levels of macrophyte growth in the
river that would exceed the State of Idaho's narrative water quality standard for nutrients.
In an effort to define a quantitative measure for nuisance levels of aquatic macrophytes, a
literature survey was conducted (Appendix D). Only those papers that made reference to water
quality impacts and had quantitative data for macrophyte biomass were used to develop the
measurement endpoint. Types of water quality impacts included general water quality
5-1
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Table 5-1. Variables simulated by the dynamic model and their associated measures of
effect (State of Idaho water quality standards and habitat suitability factors) and
assessment endpoints
Variable
Dissolved oxygen
Water temperature
Dissolved oxygen
and water temperature
Total phosphorus
Water depth
Water velocity
Nutrients
Un-ionized ammonia
Measures of effect
State of Idaho Water Quality Standards:
6 mg/L except in: (1) bottom 20% of
lakes or reservoirs with water depths <
35 m, (2) bottom 7 meters with water
depths > 35 m, and (3) hypolimnion of
stratified lakes or reservoirs
State of Idaho Water Quality Standards:
equal to or < 22°C, maximum daily
average equal to or < 19°C. Habitat
suitability factors
1-day minimum DO is not < 90%
saturation. Water temperatures equal to
or < 13°C and maximum daily average
<9°C
State of Idaho phosphorus TMDL
target of 0.075 mg/L
Habitat suitability factors
Habitat suitability factors
Macrophyte biomass < 200 g/m2
State of Idaho Water Quality Standards
Assessment endpoint
Reproduction and survival of cold-water
biota
Reproduction and survival of cold-water
biota
Salmonid spawning and incubation .
periods:
Rainbow trout: Jan 15 to July 15
Mountain whitefish: Oct 15 to Mar 15
Growth of vascular macrophytes and
algae
Reproduction and survival of cold-water
biota
Reproduction and survival of cold-water
biota
Surface water of the State shall be free
from excess nutrients that can cause
visible slime growth or other nuisance
aquatic growths impairing designated
beneficial uses
Reproduction and survival of cold-water
biota
degradation, aquatic environment alteration, and eutrophication.' The results of this survey
(Table 5-2) suggest that an average maximum biomass of 200 g/m2 as ash-free dry matter
(AFDM) is a reasonable lower bound for nuisance levels of aquatic macrophytes. •
For the Middle Snake River, there are site-specific measures of effect that can be .
integrated into the analysis plan to provide additional lines of evidence. Among these are indices
the U.S. Fish and Wildlife Service (USFWS) developed to characterize habitat suitability for
certain cold-water species.
5-2
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Table 5-2. Maximum biomass of macrophytes in water bodies with water quality problems
Species
Heterantherea dubia
Myriophyllum spicatum
Potamogeton sp.
Myriophyllum spicatum
Potamogeton crispus
Elodea canadensis
Hydrilla verticillata
Ceratophyllum demersum
Ceratophyllum demersum
Potamogeton pectinatus
Ceratophyllum demersum
Myriophyllum spicatum
Potamogeton sp.
Chora vularis
Cladaphorafracta
Utricularia vulgaris
'Myriophyllum spicatum •
Ceratophyllum demersum
Potamogeton pectinatus
Lyngbya birgei
Scapania undulata
Marsupelld aquatica
Fontinalis dalicarlica
F. antipyretica
Bulbochaetae sp.
Microspora sp.
Mougeotia sp.
Zygnema sp.
Biomass
150to275g/m2
Standing crop
, 350to900g/m2
200 to 800 g/m2
ODWa
-200 to 800 g/m2
300 g/m2
ODW
250 g/m2
AFDMb
300 to 600 g/m2
AFDM
120 to 1,300 g/m2
ODW
140 to 670 g/m2
Dry weight
Impact
Water quality degradation
Eutrophic lake
Altered aquatic
environment
Eutrophic lake
Eutrophic lake
Eutrophic lake
Mesotrophic slow
flowing
Major nuisance growth
Regulated stream with
reduced river amenity
Reference
Barber, 1991
Nichols and Shaw, 1986
Bowes etal., 1979.
Westlake, 1963
Filbin and Barko, 1985
Hough et al., 1989
Falter etal., 1991
Beer etal., 1986
Rorslett and Johansen,
1995
is oven dry weight.
bAFDM is ash-free dry matter.
5.1.2. Habitat Suitability Indices
Although the water quality standards do provide measures of exposure and effect, they
typically relate to a fairly broad range of aquatic species and environments. For example, the
water quality standards define certain criteria for the protection of cold-water species without
5-3
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specifically defining the set of cold-water species. These criteria may be protective of aquatic
organisms within the group characterized as cold-water species, but there well may be some
organisms or certain life stages of organisms in this group that are more vulnerable. Because of
this, it is desirable to develop site-specific lines of evidence if they are available. The USFWS
uses habitat suitability indices to assess the impacts of flow modification on aquatic habitat
resources of rivers and streams. An important objective of this method, called the Instream Flow
Incremental Method (IFIM), is to make quantitative comparisons of habitat conditions at
differing regimes of river flow.
The USFWS, in support of the IFIM, has developed habitat curves for many aquatic
organisms. In a cooperative study conducted with the Idaho Power Company, Anglin et al.
(1992) describe habitat suitability curves for cold-water fishes. The periods of the year to which
these suitability indices apply are shown in Table 5-3.
In applications of IFIM, the habitat suitability curves are used to develop flow-weighted
measures of habitat suitability. In this ecological risk assessment, the simulation results from the
ecological model were compared with the IFIM habitat suitability curves. The frequency.with
which the simulated results were less than a reasonable value of the habitat suitability curve was
used to assess whether the system would support a particular life stage of the target organism.
The reasonable level for habitat suitability was defined as 0.6. That is, values of the habitat
index greater than 0.6 were assumed to be representative of conditions supporting the particular
life stage of the target organism, whereas values of the index less than 0.6 were assumed to be
representative of conditions that would not support that life stage. The criterion of 0.6 was
chosen simply because it is slightly greater than 0.5. Although this was somewhat arbitrary^ the
estimates of ecological risks are not particularly sensitive to the criterion, given the shapes of the
habitat suitability curves. Most of the uncertainty in the estimates of ecological risks using these
habitat suitability curves is in the shapes of the curves.
Quantitative comparisons are accomplished in the IFIM by calculating habitat suitability
for various regimes of river flow. Integral components of this calculation are the habitat
suitability curves. These curves define suitability indices for different life stages of target
aquatic species selected for a particular study. The suitability indices are functions of ecosystem
variables such as water depth, water velocity, water temperature, and substrate or cover type.
Because the indices measure suitability of habitat as a function of the condition of the
ecosystem, they can also be used as measures of effect. However, the target species for which
suitability is quantified must be relevant in terms of the assessment endpoints. In the case of the
5-4
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Middle Snake River, this means they must be cold-water species that are native to the region. On
the basis of the work of Anglin et al. (1992), three cold-water fishes found in the Middle Snake
River, the mountain whitefish, rainbow trout, and white sturgeon, have been selected as target
species to be used with the habitat suitability indices. Anglin et al. (1992) developed habitat
suitability indices for these species for the Snake River from CJ. Strike Dam downstream to the
upper end of Brownlee Pool. Because habitat suitability indices appropriate for large river
systems were lacking for these species, Anglin et al. (1992) used criteria from smaller river
systems. Extension of the criteria from smaller river systems to the Snake River was done
subjectively and based on the judgment of regional biologists. For the purposes of the ecological
risk analysis, we have assumed the process adequately represents the habitat requirements for the
target species in the Middle Snake River.
For cold-water biota, the ecological variables, measures of effect, and assessment
endpoints used in this simulation are shown in Table 5-1.
5.2. RISK ESTIMATES
5.2.1. Exceedance of Water Quality Standards
Ecological integrity of an aquatic ecosystem depends on the characteristics of the water
temperature and dissolved oxygen regimes. To characterize stress associated with temperature
and dissolved oxygen, the simulated 67-year record of variables is compared with the water
quality criteria in each of the representative segments. The comparison is made for the general
category of cold-water species and for spawning of two species, the mountain whitefish and the
rainbow trout. .
Stress occurs when the temperature-dissolved oxygen envelope experienced by the target
organism is larger than the envelope associated with its physiological requirements.
Superimposing the envelope for water temperature and dissolved oxygen given in the water
quality standards for each of these groups on the simulated temperature-DO diagram is a way of
assessing stress associated with the temperature-DO regime in a particular segment. The
frequencies with which the simulated values fail to fall within the envelope for temperature and .
DO defined by the State of Idaho's water quality standards are given in Table 5-4.
5.2.1.1. Dissolved Oxygen
For cold-water biota, the frequencies with which the simulated daily-averaged DO falls
outside the envelope defined by the water quality standards is less than 0.01 in all of the
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Table 5-4. Frequency with which simulated values of water temperature and dissolved
oxygen (DO) are outside the envelope of the State of Idaho's water quality standards for
cold-water biota, spawning rainbow trout and mountain whitefish
Study reach
segment
Milner Dam to
Twin Falls
Twin Falls to
Shoshone Falls
Shoshone Falls
to RM 609
RM 609 to
Rock Creek
Rock Creek to
Crystal Springs
Crystal Springs
to Boulder
Rapids
Boulder Rapids
to Kanaka
Rapids
Kanaka Rapids
to Gridley
Bridge
Gridley1 Bridge
to Upper Salmon
Falls •
Upper Salmon
Falls to Lower
Salmon Falls
Lower Salmon
Falls to Bliss
Bridge
Bliss Bridge to
Bliss Darn
Bliss Dam to
King Hill
Cold-water biota
Temp.,
daily
avg.
0.19
0.20
0.17
0.15
0.17
0.13
0.13
0.04
0.01
0.03
0.05
0.07
0.11
Temp.,
max.
0.13
0.11
0.02
0.01
0.14
0.01
0.01
0.01
0.01
0.01
0.01
0.01
0.01
DO,
daily
avg.
0.01
0.01
0.01
0.01
0.01
0.01
0.01
0.01
. 0.01
0.01
0.01
o.or
0.01
Rainbow trout
Temp.,
daily
avg.
0.58
0.60
0.63
0.64
0.62
0.66
0.67
0.74
0.80
0.78
0.69
0.69
0.68
Temp.,
max.
0.48
0.47
0.49
0.50
0.53
0.52
0.50
0.53
0.54
0.52
0.48,
0.48
0.48
DO,
daily
avg.
0.57
0.58
0.56
0.55
0.54
0.37
0.26
0.54
0.19
0.26
0.42
0.44
0.33
Mountain whitefish
Temp.,
daily
avg.
0.05
0.06
0.07
0.08
0.07
0.10
0.10
0.17
0.22
0.20
0.11 .
0.11
0.10
Temp.,
max.
0.02 .
0.01
0.02
0.03
0.03
0.03
0.02
0.03
0.04
0.03
0.01
0.01
0.01
DO,
daily
avg.
0.06
0.05
0.03
0.03
0.02
0.01
0.01
0.11
0.01
0.01
0.01
0.01
0.01
segments. Frequencies for spawning mountain whitefish are less than 0.06 throughout the
Middle Snake River, except in the segment from Kanaka Rapids to Gridley Bridge, where the
frequency is 0.11. The frequencies for spawning rainbow trout range from 0.26 to 0.57
between Milner Dam and the Gridley Bridge, and 0.19 to 0.45 between the Gridley Bridge and
King Hill. The higher frequencies associated with spawning rainbow trout are due to the fact
that applicable water quality standards include some summer months, whereas the water
quality standards for spawning mountain whitefish apply to fall and winter months when
saturation levels of DO are higher.
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5.2.1.2. Temperature
The frequency with which the daily-average simulated water temperature falls outside
the envelope for cold-water biota ranges between 0.13 and 0.20 for the segments between
Milner Dam and Kanaka Rapids. The frequency decreases to less than 0.05 from Kanaka
Rapids to the Bliss Bridge because of the large volume of cooler water supplied by the spring
flow. Between the Bliss Bridge and King Hill, the frequency increases slightly as the spring
flow decreases and the transfer of thermal energy across the air-water interface becomes more
important.
The pattern for the frequencies with which the simulated maximum water temperatures
fall outside the envelope for cold-water biota is similar to that of the simulated daily-averaged
water temperature. The decrease in frequency occurs hi the Crystal Springs to Boulder Rapids
segment, slightly upstream from the Boulder Rapids to Kanaka Rapids segment, in which the
frequency of daily-averaged water temperatures decreases. In addition, the magnitude of the
frequencies for which the maximum temperatures fall outside the envelope for cold-water biota
is less than for the daily-averaged temperatures. The frequencies for maximum simulated
water temperatures varied between 0.01 and 0.13 from Milner Dam to Boulder Rapids and
were less than 0.01 between Boulder Rapids and King Hill.
The frequencies with which simulated daily-average water temperatures fall outside the
envelope for spawning rainbow trout is greater than 0.58 throughout the Middle Snake River
and greater than 0.48 for simulated maximum daily water temperatures. As in the case of DO,
the high frequency of excursions above the criterion is due to the fact that the water quality
standards for spawning rainbow trout include some summer months.
Frequencies of daily-averaged temperatures falling outside the envelope for spawning
mountain whitefish are lowest in the upstream segments between Milner Dam and Kanaka
Rapids and highest in the segments between Kanaka Rapids and Bliss Dam. Frequencies for
daily-averaged simulated water temperatures vary between 0.05 and 0.10 in the upstream
segments and between 0.10 and 0.22 in the downstream segments. The relatively low
frequency of excursions above the criterion is due to the fact that water quality standards for
spawning mountain whitefish apply to fall and winter periods when water temperatures are
low.
5.2.1.3. Phosphorus
The simulation results from the dynamic model were used to obtain an empirical
cumulative distribution function for total phosphorus at locations representing the segments
given in Table 1. The empirical cumulative distribution function gives the probability that the
5-8
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simulated total phosphorus is equal to or less than some specified value. These functions
represent stressor characteristics for existing levels of management.
In the segments of the Middle Snake River upstream from major point source and
nonpoint source inputs, the estimated probability that total phosphorus will be equal to or less
than 0.075 mg/L is between 0.23 and 0.25. In the segments between Rock Creek and Crystal
Springs, total phosphorus loads from the City of Twin Falls STP, fish hatcheries, and irrigation
return flows reduce the probability that total phosphorus will be equal to or less than 0.075 to
between 0.01 and 0.04 (Figure 5-1). Between Bliss Dam and King Hill, the large volume of
spring inflow with low levels of total phosphorus increases the estimated probability to 0.2-
0.6 (Figure 5-2). All the cumulative frequency distributions are included in Appendix D.
5.2.1.4. Macrophyte Biomass
The cumulative distribution function for total macrophyte and epiphyte biomass was
estimated for the Crystal Springs to Boulder Rapids segment. This segment was chosen
because it has had among the highest levels of macrophyte growth measured during field
studies by the University of Idaho (Falter et al., 1995; Falter and Bums, 1996). The
probability that the simulated values of macrophyte biomass, measured as the sum of rooted
macrophytes, nonrooted macrophytes, and epiphytes, would be less than 200 g C AFDM/m2
was estimated to be less than 0.01 for the 67-year period of record (Figure 5-3).
Simulated levels of un-ionized ammonia were compared with the chronic and acute
criteria of the State of Idaho's water quality standards. The frequency with which the
simulated levels exceeded the criteria was computed as the ratio of the number of values that
exceeded a criterion divided by the number of simulated values. The estimated frequency with
which the simulated values of un-ionized ammonia were below the chronic and acute criteria
was estimated to be less than 0.05 and 0.01, respectively, throughout the Middle Snake River.
5.2.2. Habitat Suitability Indices
Measures of stress to the target cold-water species—mountain whitefish, rainbow trout,
and white sturgeon—attributable to water temperature and hydrologic effects were obtained
from habitat suitability indices developed by the USFWS (Anglin et al., 1992). The measures
of habitat suitability associated with water temperature, water depth, and velocity were
obtained for each life stage of the target organism and determined in the following way.
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0.0
0.2 0.3
Total Phosphorus - mg/1
0.4
0.5
Figure 5-1. Cumulative distribution function for total phosphorus, Rock
Creek to Crystal Springs. Results are for: (1) mean of simulated values, (2)
mean minus one standard deviation, and (3) mean plus one standard
deviation.
1.0
0.9
0.8
0.7
•S 0.6
fc. 0.5
-------
1.0
0.9
0.8
0.7
>g 0.6
v
1. 0.5
1
°- 0.4
0.3
0.2
0.1
0.0
_
o
a.
•a
m
100 200 300 400 500 600 700 800 900 1000
Macrophyte Biomass, M - gm AFDM/sq. meter
Figure 5-3. Cumulative distribution function for simulated macrophyte biomass in the
Snake River at Rkm 965.4 (RM 600). Results are for (1) mean of simulated values, (2)
mean minus one standard deviation, and (3) mean plus one standard deviation.
The index of impairment for each life stage was computed as the ratio of the number of
simulated days in which impairment of habitat occurred (when the habitat index fell below 0.6)
to the total number of days for which the life stage was vulnerable (Table 5-3). Four
categories of impairment were defined based on the index of impairment:
1. less than or equal to 0.1, lowest impairment;
2. greater than 0.1 and less than or equal to 0.5;
3. greater than 0.5 and less than or equal to 0.9;
4. greater than 0.9 and less than or equal to 1, greatest impairment.
. The index of impairment was generally high (Figure 5-4) throughout the Middle Snake
River for all life stages of rainbow trout. Estimated levels of impairment for adults were
estimated to be moderate to low in some portions of the segments from Rock Creek to Crystal
5-11
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Straight Line Representation of Impairment and River Miles
SKI Stt S 572 J73 fl» JS4 .58 JK JHC W »< «5 812 JS KO £2 .823
Each color along a line characterizes
tht probability of Impairment for the
Ufa stage as a function of river mile.
•i v Values less than or equal to 0.1
/V ™ (lowest Impairment)
'A/ Values greater than 0.1 and
/,y ~ loss than or equal to 05
* m Valuiis greater than OS and
- loss than or equal to 0.9
'Kjf _ Values greater than 03 and
less than or equal to 1.0
(greatest Impairment)
Life stages (bottom to upper line): Spawning, Fry,
Juvenile and Adult
Fisheries
Springs
Irrigation Returns
Tributaries
Major Dams
Figure 5-4. Probability of life stage impairment for rainbow trout in the Middle Snake River.
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Springs, from Boulder Rapids to Kanaka Rapids, and in the upper portion of Upper Salmon
Falls reservoir.- Estimated levels of impairment for spawning were low to moderate in some
portions of the segment from Boulder Rapids to Kanaka Rapids, as were estimated levels of
impairment for rainbow trout fry.
Estimated values of the index of impairment for spawning, fry, and juvenile mountain
whitefish were high throughout the Middle Snake River (Figure 5-5). For adult mountain
whitefish, the values of the index of impairment were estimated to be moderate to high
throughout the Middle Snake River. Most favorable conditions for adult mountain whitefish
(moderate impairment) were found hi Upper Salmon Falls and Lower Salmon Falls Reservoirs.
These somewhat favorable conditions were primarily a result of high-quality, cooler water
entering the Middle Snake River from springs.
Above Lower Salmon Falls Dam, estimated values of the index of impairment for
white sturgeon were generally high for all life stages (Figure 5-6). Exceptions were found hi
the pool below Auger Falls and in Upper Salmon Falls Reservoir, where the index of
impairment for adult white sturgeon was estimated to be low and the index of impairment for
juveniles was to estimated to be moderate. Portions of the Wiley reach (Lower Salmon Falls
Dam to the Bliss Bridge) had low to moderate values of the index of impairment for spawning
and larval stages. The most favorable conditions for all life stages of white sturgeon were
estimated to occur in the Middle Snake River below Bliss Dam.
5-13
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Straight Line Representation of Impairment and River Miles
f« 552 Sit ;« 5W p« fa at f». < 5M Sft , ?« , t». f» , O» . «S _ 812 516 ^ ^0. JM ( J!3
fill I 1 t T
Each color along a line charactertees
the probability of impairment for the
lir« stag* as a function of river mile.
r7v"7, _ Values loss than or equal to 0.1
»'"- ™ (lowest Impalnnonl)
TO" _ Values greater than 0.1 and less
ttJCJ than or equal tB 0^
„,_, ^ Values gtsalar
-------
Straight Line Representation of Impairment and River Miles
CM
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6. ANALYSIS OF EXPOSURE AND EFFECTS FOR THREE FISH POPULATIONS
The objective of this assessment is to provide a forecast for the long-term natural
reproductive survival of rainbow trout (Oncorhynchus mykiss), mountain whitefish (Prosopium
williamsoni), and white sturgeon (Acipenser transmontanus) in the Middle Snake River. The
assessment will focus on rainbow trout and mountain whitefish from King Hill to Milner Dam
and white sturgeon between C. J. Strike and Bliss Dams (the Bliss reach), between Bliss and
Lower Salmon Falls Dams (the Lower Salmon Falls reach), and between Upper Salmon Falls
Dam and Shoshone Falls (the Shoshone Falls reach). Loss and alteration of lotic habitats,
increased water temperatures, and other stressors such as sedimentation that can directly and
indirectly adversely affect these fish populations are discussed.
6.1. RAINBOW TROUT (Oncorhynchus mykiss)
The rainbow trout is the most important game fish in the Middle Snake River (Dey and
Minshall, 1992). As the numbers of wild rainbow trout are at low levels (Cochnauer, 1980a,
1981; Lukens, 1982), hatchery fish have been stocked throughout this reach for many decades.
Steelhead, the anadromous form of this species, originally inhabited this area, but dam
construction for irrigation and power generation has reduced its range to that portion of the
Snake River below Hells Canyon Dam (Simpson and Wallace, 1982).
In determining the viability of a rainbow trout population, an assessment is needed of the
quantity and quality of four types of habitat: spawning, rearing, adult, and overwintering
habitats. Deficiencies in any one of the four habitat types will limit a trout population (Behnke,
1992). Trout populations may also be limited by food availability (Filbert and Hawkins, 1995).
Identifying habitat bottlenecks and the viability of trout populations, however, is difficult without
an abundance of hydrologic-, habitat-, and population-related data (Stalnaker et al., 1995).
Optimum riverine habitat for rainbow trout is characterized by: (1) clear, cold water; (2) a
silt-free rocky substrate in riffle-run areas; (3) an approximate 1:1 pool-to-riffle ratio that
includes slow, deep water; (4) abundant in-stream and stable stream-bank cover; and (5)
relatively stable water flows and temperatures (Raleigh et al., 1984). Some information is
available for rainbow trout habitat in the Middle Snake River and closely associated tributaries,
but it is insufficient to clearly identify the main factors limiting the wild rainbow trout
population. In absence of this information, measures of stress to rainbow trout were obtained
from habitat suitability indices developed by the U.S. Fish and Wildlife Service (Anglin et al.,
1992). Our habitat suitability analysis (i.e., index of impairment) found that the degree of
impairment was generally high for all life stages of rainbow trout in the Middle Snake River.
6-1
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6.1.1. Spawning Habitat
Rainbow trout, stimulated by rising water temperatures, spawn almost exclusively in
streams, normally during the period from January to July (Raleigh et al., 1984). Spawning
usually occurs when daily maximum temperatures range from 10°C to 15.5°C (Scott and
Grossman, 1973), and female rainbow trout are most productive in waters where temperatures do
not exceed 13 °C for 6 months prior to spawning (Leitritz and Lewis, 1980).
Spawning habitat for rainbow trout in the mainstem of the Middle Snake River has been
adversely affected by sedimentation and high temperatures (Hill, 1991c). Our estimates of the
quality of the spawning habitat, developed from habitat suitability indices, show that impairment
is moderate to high throughout the Middle Snake River except for small river segments just
upstream of Kanaka Rapids, where impairment was low (Figure 5-4).
The only known spawning habitat for rainbow trout hi the Middle Snake River is located
in tributaries off the main channel. For example, spawning occurs in the lower reach of'the
Malad River, the Thousand Springs Complex, and other short-run springs (Partridge and Corsi,
1993; Lukas et al., 1995). Habitat availability studies by Lukas et al. (1995) found that an
estimated 8.5% of the Thousand Springs outfall channels were suitable for spawning. This level
exceeds the 5% mioimum needed to sustain trout populations (Raleigh et al., 1984). However,
because the outflow channels enter the Snake River (the Upper Salmon Falls Reservoir) where
no spawning habitat is known to exist, this spawning is not likely enough to sustain populations
in both water bodies. Spawning habitat studies are not available for the lower Malad River, but it
is likely that fish produced in this area also migrate to the Snake River.
The spawning habitat in the tributaries has also been adversely affected by land and water
use decisions. Bell (1980) sampled several springs between Twin Falls and King Hill and found
good to excellent populations of wild rainbow trout, which was evidence of natural production in
these small tributaries. Subsequently, two of these springs (Lower White and Briggs Springs)
were developed for fish culture operations and all rainbow trout habitat was lost (F. Partridge,
personal communication, January 6, 1999). It is unknown if similar land use decisions are
adversely affecting the remaining springs.
6.1.2. Rearing Habitat
During the first months after hatching, trout need rearing habitat with protective cover
and shallow water with low velocity. Cover in the form of aquatic vegetation, debris piles, and
interstices between rocks is critical (Raleigh et al., 1984). Some streams may have too much
spawning and rearing habitat, resulting in excessive recruitment to populations (Behnke, 1992).
However, this does not appear to be the case in the Middle Snake River, where the only
6-2
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identified spawning and rearing habitat occurs in spring seeps, side channels, and small
tributaries. ,
A stable stream flow appears to be important for successful rearing conditions. Year-
class strength hi a native population of rainbow trout hi the Spokane River was positively
correlated with spring water flows. A high, relatively constant flow between April 1 and June 25
produced a strong year class, whereas a fluctuating low flow during this tune produced a weak
year class (Underwood and Bennett, 1992). However, excessively high flows during this time
can adversely affect recruitment for trout populations (Bums and Eiserman, 1979).
From 1978 to 1998, the Idaho Department of Fish and Game planted just over 1:5 million
fingerling rainbow trout between Glenns Ferry and Milner Dam (records provided by S. Clark,
personal communication, January 7,1999). Most (77%) of these fish were planted between
Lower Salmon Falls Dam and Shoshone Falls. According to the Idaho Department of Fish and
Game (F. Partridge, personal communication, February 23, .1999), the survival rate for the
fingerlings is believed to be dependent on flow. The highest survival was believed to occur
during low-flow years, but field studies were not conducted to quantify or qualify the rearing
habitat available to these fish.
Lukas et al. (1995) estimated fry and juvenile habitat at 3.5% and 9.1% of the outflow
channels, respectively, in the Thousand Springs Complex, but believed there was additional
unsurveyed rearing habitat in adjacent small seep springs. Similar studies are not available for
the lower Malad,River, which also may be an important rearing area for rainbow trout, or for the
main stem of the Snake River. We have shown, using habitat suitability indices, that the quality
of the rearing habitat for fry and juvenile rainbow trout hi the Middle Snake River is highly
impaired (Figure 5-4).
6.1.3. Adult Habitat
Adult rainbow trout inhabiting lotic environments typically live at water depths of 0.3 m
or greater in areas where slow (0-0.1 m/sec) water for resting is juxtaposed with faster water
carrying food and where protective cover is provided by boulders, logs, overhanging vegetation,
and undercut banks (Behnke, 1992). In the Middle Snake River, cover for adult fish is limited as
streamside vegetation, overhanging banks, and woody debris are not commonly found in this
area. In absence of these features, adult rainbow trout use deep pools for cover during the day
(Hill, 1991c).
Raleigh et al. (1984) found a definite relationship between the annual flow regime and the
quality of trout habitat. The most critical period is usually from late summer to winter, when the
lowest flows occur. A stable base flow during this tune that is at least 50% of the average annual
6-3
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daily flow is considered excellent for maintaining quality trout habitat, a flow of 25% to 50% is
considered fair, and a flow of < 25% is poor. An inspection of the USGS historical streamflow
daily graphs from 1970 to 1997 shows that the annual low flow for the King Hill station (No.
13154500) may occur in any month except November or December. However, low flows
usually occur from July to September. Information is not available to determine how these low
flows compare against the average annual daily flows used by Raleigh et al. (1984).
Adult habitat usually limits the biomass for resident trout in most streams (Behrike,
1992). A determination that adult habitat limits rainbow trout in the Middle Snake River is,
loosely supported by the fact that rainbow are present in low numbers. Warm-water species,
particularly catastomid suckers, are the most common fish species and make up more than
90% of the fish biomass in the Middle Snake River (Lukens, 1982; Dey and Minshall, 1992;
Maret, 1997). Our estimates of the quality of the habitat for adult rainbow trout in this reach
indicate that it is highly impaired, except for small river segments with low impairment between
Rock Creek and Upper Salmon Falls Dam and below Bliss Dam (Figure 5-4).
Lukas et al. (1995) found that a large proportion (68.5%) of the Thousand Springs outfall
channels, an area with stable year-round flows, was suitable adult rainbow trout habitat;
however, few large fish were present. This was attributed to recreational fishing harvest and
migration of adult fish into Upper Salmon Falls Reservoir. Similar surveys are unavailable for
the lower Malad River or for the Middle Snake River.
6.1.4. Overwintering Habitat
Overwintering habitat is very important to fish whose survival is related to the amount of
deep water with low current and protective cover, such as that occurring in deep pools with large
boulders and large woody debris or other types of cover (Bjornn, 1971).
The amount and quality of overwintering habitat for rainbow trout in the Middle Snake
River is unknown.
6.1.5. Discussion
Introducing hatchery-reared rainbow trout into the Middle Snake River may have varied
effects on the wild rainbow in this area. Vincent (1987) found that stocking catchable-sized
hatchery rainbow trout depressed the abundance of wild rainbow and brown trout (Salmo truttd)
in the Madison River, Montana. Native trout biomass increased after stocking ceased, and the
relative degrees of recovery indicated the wild rainbow trout were more negatively affected than
wild brown trout. In the Middle Snake River, because wild fish are at low levels, these negative
6-4
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effects may not occur or may be minimal. In the adjacent short-run springs outlets and channels
and small tributaries, however, these adverse effects may occur.
Hybridization of native fish is another area of concern when stocking hatchery fish.
Whenever hatchery rainbow trout are stocked outside their native range, they almost always
hybridize with native fish (Behnke, 1992). Since 1978, at least eight different stocks of rainbow
and one rainbow x cutthroat cross have been planted in the Snake River between Glenns Ferry
and Milner Dam (S. Clark, personal communication, January 7,1999.). Given this history, the
wild rainbow trout residing in the Middle Snake River likely has a mixed genotype and probably
a low potential for survival in the conditions found in this reach. Even in a similar system
(Spokane River) that supports native, wild rainbow trout, annual mortality can approach 75% of
the population (Underwood and Bennett, 1992).
6.2. MOUNTAIN WHITEFISH (Prosopiumwilliamsoni)
The mountain whitefish is native to cold-water rivers and lakes hi western North
America, both east and west of the Continental Divide (Scott and Grossman, 1973; Sigler and
Sigler, 1987), and is widely distributed throughout all of Idaho (Simpson and Wallace, 1982).
Unlike more popular game fish, their geographic distribution has changed little over the past
century (Rogers et al., 1996). Mountain whitefish are found at elevations ranging from 1,370 to
2,225 m in Utah's Logan River (Sigler, 1951), and above approximately 1,370 m in other parts
of its range in Utah, Nevada, and California, apparently because of high water temperatures at
lower elevations (McAfee, 1966). As a rule, however, they are not found hi small mountain
tributaries (Brown, 1952), where Gard and Flittner (1974) believe their upstream distribution is
limited by an increased stream gradient and change of substrate from silt-gravel to rubble-gravel.
In Western Canada, P. williamsoni usually dominates fish communities hi mountain lakes at
elevations of about 1,400 to 1,950 m when the lake has a large outlet, i.e., stream orders 4-5
(Donald, 1987).
On the basis offish surveys conducted since 1980, the mountain whitefish population hi
the Middle Snake River is at a low level. Estimates of the size of the pre-impoundment
population of the mountain whitefish in this reach are not available, but as late as 1953-54 "a
substantial run" of mountain whitefish used the fishway at Lower Salmon Falls Dam (Irving and
Cuplin, 1956). Since 1980, small numbers of fish have been observed in the Bliss reach
(Cochnauer, 1981; Maret, 1997), in the Lower Salmon Falls reach (Cochnauer, 1980b), at several
locations hi the river between Lower Salmon Falls Dam and Shoshone Falls (Dey and Minshall,
1992; Partridge and Warren, 1994), and in the following tributaries to the Middle Snake River:
6-5
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Malad and Big Wood Rivers (Partridge and Corsi, 1993), Little Wood River (Maret, 1997),
Thousand Springs outfall channels (Lukas et al., 1995), and Crystal Springs (Hill, 1991a).
Growth rates for the mountain whitefish vary considerably, and fish are smaller for any
given age with increasing altitude (McHugh, 1942). Maximum growth rates occur over the first
two growing seasons (Pettit and Wallace, 1975) and this fish usually becomes sexually mature
from age 2 to 4 years (Brown, 1952; Thompson and Davies, 1976). Female whitefish mature
later than the males in a lake environment (Hagen, 1956). The average lifespan of this species is
7 or 8 years (Sigler and Sigler, 1987), although it can live at least 18 years (McAfee, 1966).
Seven-year old fish range in length and weight from 307 to 387 mm and from 475 to 890 g,
respectively, while the ranges for 8-year-old fish are 330 to 410 mm and 501 to 944 g (Scott,
1960; Pettit and Wallace, 1975; Thompson and Davies, 1976). The largest mountain whitefish
on record, which weighed 2,665 g and was 57 cm long, was caught in Island Park Reservoir,
Idaho (F. Partridge, personal communication, December 28, 1998). The density of stream
populations of mountain whitefish varies greatly by site and season, but may reach a maximum
of about 3,400 fish/ha (Wydoski and Helm, 1980).
6.2.1. Loss and Alteration of Lotic Habitat
Dam construction and operation affect riverine environments by reducing the amount of
lotic habitat and causing the fluctuation of water levels above and below the dam. There has
been a 37% loss of the free-flowing habitat hi the Middle Snake River (Cochnauer, 1983). The
fluctuation of water levels of impoundments, reservoirs, and tailwaters are both seasonal and
diurnal in nature. Of these, the greatest change in water level in the Middle Snake River occurs
during diurnal fluctuations in the. tailwaters of a dam (Irving and Cuplin, 1956).
The loss of lotic habitat may seriously affect spawning, rearing, and overwintering habitat
used by the mountain whitefish (Northcote and Ennis, 1994). Fleming and Smith (1988, in their
Figures 10-13) document the reduction hi abundance of native cold-water fishes, including the
mountain whitefish, and the increase of "coarse" fish (e.g., catostomids and cyprinids) in
reservoirs 2 to 42 years after construction in the Upper Columbia River (British Columbia). In
contrast, Nelson (1965) observed no decreased growth and little change in distribution of
mountain whitefish populations residing in a complex of four reservoirs on the Kananaskis River
(Alberta) over 25 years (1936-61) in conjunction with hydroelectric development. Since 1936,
however, no appreciable change hi water temperature has occurred in three of the four reservoirs.
The low water temperatures hi the Kananaskis River likely contributed to the stability of the
mountain whitefish populations following reservoir development.
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6.2.2. Effects on Movement
Upon emergence, the mountain whitefish fry, having a weak swimming ability, drift
passively downstream until suitable holding water is encountered. They inhabit shallow areas 5
to 20 cm deep from June to August (Pettit and Wallace, 1975; Davies and Thompson, 1976).
Whitefish fry show strong positive phototaxis (Liebelt, 1970), which probably accounts for their
selection of shallow backwaters and stream margins. After reaching about 5.5 cm in length, they
inhabit low-velocity areas of the river margin having gravel, sand, or mud substrates. Schooling
of juvenile mountain whitefish occurs at age 7 months in river and reservoir populations in the
Kananaskis River (Alberta) (Nelson, 1965). Yearlings also undergo seasonal migrations between
feeding and overwintering habitats, but these probably do not exceed a few kilometers
(Northcote and Ennis, 1994).
Movement by adults appears to be complex and includes both nonmigratory and
migratory behavior, and some fish exhibit a homing behavior when displaced (Erickson, 1966;
Liebelt, 1970). For example, there is a nonmigratory population in the Sheep River watershed in
Alberta (Canada), but the majority have annual movement patterns including spawning
migrations of > 60 km (Davies and Thompson, 1976, Northcote and Ennis, 1994). Other
mountain whitefish populations inhabiting rivers in Utah (Sigler, 1951; Wydoski and Helm,
1980), Montana (Brown, 1952), and in the southern part of their range in North America
(McAfee, 1966) did not appear to travel long distances to spawn. Pettit and Wallace (1975)
found that mountain whitefish movement usually slows and apparently ceases during the
summer, but they did observe movements of > 80 km by, some adults from late May to July hi
the watershed of the North Fork Clearwater River in Idaho. Erickson (1966) observed some
trophic movements by whitefish out of the Snake River (Wyoming) into tributary streams during
the spring and summer.
Of the three dams located in the Middle Snake River, the Bliss Dam is a barrier to
upstream movement by mountain whitefish because it lacks a fish ladder. The other two dams at
Lower and Upper Salmon Falls have fishways, but they generally are not hi operation (F.
Partridge, personal communication, December 28,1998). Irving and Cuplin (1956) observed a
substantial run of mountain whitefish using the fishway over Lower Salmon Falls dam; however,
fewer fish used the fishway over the Upper Salmon Falls Dam, owing hi part to the poor location
of its lower entrance. Irving and Cuplin believed that the dams hi the Middle Snake River, with
or without fishways, did not present much of an obstacle to the downstream movement offish.
They noted that nearly 50% (197 fish) of the tagged rainbow (Oncorhynchus mykiss) planted
above the Lower Salmon Falls Dam were recovered below the dam. The mortality of rainbow,
or mountain whitefish, passing through hydroelectric installations was not determined.
6-7
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Unrestricted seasonal movements by mountain whitefish to feeding and overwintering
habitats and to spawning areas by adults is no longer possible in the Middle Snake River. The
extent of the adverse effects on these movement caused by the construction and operation of
dams in this reach, however, has not been determined.
6.23. Effects on Spawning Activities
Mountain whitefish usually spawn from October to December (McAfee, 1966; Sigler and
Sigler, 1987), but may spawn earlier or later depending on the latitude and water temperature. In
the northern part of their range or at higher elevations, whitefish spawn from September to
October (Thompson and Davis, 1976), and lake populations may spawn from September to
February (Hagen, 1956; McPhail and Lindsey, 1970). These fish spawn in riffle areas of streams
where sediment particle size may range from fine gravel to coarse rubble (Brown, 1952). These
fish do not construct redds, and spawning typically occurs nocturnally when a small number of
fish move into tributary streams from a large river, or onto the margin of a lake. In riverine
environments, the fish concentrate in shallow water with depths ranging from 13 to 122 cm and
currents ranging from 63 to 155 cm/sec (Brown, 1952; Thompson and Davies, 1976). In Phelps
Lake (Wyoming), mountain whitefish spawned at water depths ranging from 6 to 12 m in areas
with fine or coarse rubble substrate (Hagen, 1956). The eggs are adhesive when released and
stick to the bottom substrate (Sigler and Sigler, 1987).
The thermal requirements for gonadal development of mountain whitefish are unknown,
but Ihnat (1981) believes exposure to unnaturally high water temperatures for an extended time
during the fall could be detrimental to gamete maturation. Mountain whitefish spawn at water
temperatures ranging from 0°C to 9°C, but usually in the 3°C to 5°C range (Northcote and Ennis,
1994). Brown (1952) noted that they do not spawn until the water temperature decreases below
5.5°C and that peak spawning activity at high elevations in the Madison River (Montana)
occurred with temperatures just over 2°C.
The upper optimum water temperature for successful egg development is 6°C. Some
hatching occurs at water temperatures ranging from 9°C to 11°C, but there are high levels of
alevin mortality and abnormality. In a laboratory study, egg mortality was 98% to 100% at -
11°C, and at 12°C, all embryos died within 2 weeks (Rajugopal, 1979). In a hatchery,
Thompson and Davies (1976) noted that 61 days were required to hatch 95% of fertilized eggs at
a temperature of 7.5°C. The last eggs hatched 71 days after fertilization. At 7.2°C, Stalnaker
and Gresswell (1974) found that the incubation period for mountain whitefish eggs raised in a
laboratory ranged from 52 to 76 days. Optimum temperatures for growth of whitefish fry ranges
from 9°C to 12°C (Stalnaker and Gresswell, 1974; Rajugopal, 1979). Juveniles and adults of this
6-8
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species have been collected in the summer in areas with water temperatures of 11°C to 20°C
(Ihnat and Bulkley, 1984).
Simulations of water temperatures at two locations (Rkm 896; RM 556.4 and Rkm 956;
RM 593.7) in the main stem of the Middle Snake River were evaluated from 1970 to 1994 to
determine if they were favorable for mountain whitefish spawning and incubation. These
locations were chosen because they are below and above the Thousand Springs complex, which
affects the water temperature in the main stem of the Snake River. Favorable spawning
conditions were identified as 75 days with a water temperature of <7°C during a possible
spawning-incubation window extending from September to February. Modeling results for Rkm
896 (RM 556.4; 5 km below Bliss Dam) indicate that favorable spawning and incubation did not
occur in the Bliss reach from 1970 to 1994. In this reach, the number of consecutive days during
the potential spawning-incubation window with water temperatures <7°C ranged from 5 (1977)
to 45 (1985). Modeling results for Rkm 956 (RM 593.7; near Empire Rapids) also found that a
75-day spawning-incubation window did not occur in this reach from 1970 to 1994. However,
water temperatures in this reach were somewhat lower than those in the Bliss reach. In 13 of 25
years, water temperatures <7°C occurred from 45 to 55 consecutive days from September to
February.
Impairment of spawning habitat for the mountain whitefish was also estimated in this
assessment with habitat suitability indices developed by the U.S. Fish and Wildlife Service
(Anglin et aL, 1992). This analysis showed that the spawning habitat available to this species is
highly impaired in the Middle Snake River (Figure 5-5).
6.2.4. Loss and Alteration of Rearing Areas
Fry and yearling mountain whitefish are found along the shore in water depths of only 5
to 20 cm in small, well-protected pockets created by rubble or boulders arid in backwater areas
connected to the main stream (Brown, 1952). In tailwaters below dams, the water levels
fluctuate diurnally and disrupt rearing by mountain whitefish by pushing them into deeper water
where they are more susceptible to predation. Stranding of small fish when the water level drops
rapidly is also a concern. Depending on the season, water levels varied from 1.5 to 2 m in the
tailwaters of the Lower Salmon Falls Dam, and from 1 to 1.5 m at 22 km and from 0.5 to 1 m at
56 km below Bliss Dam (Irving and Cuplin, 1956). These fluctuations exposed shallow water
areas to drying and, during the whiter, freezing temperatures. The average surface area of the
zone of fluctuation in four typical sections of the tailwaters below these dams was 18% of the
surface area as measured during high diurnal flows (Irving and Cuplin, 1956).
6-9
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The early life stages of the mountain whitefish appear to be able to withstand a reduction
in dissolved oxygen. Siefert et al. (1974) found that a reduction in dissolved oxygen
concentration to 50% saturation at 4°C and 7°C did not affect the survival of young mountain
whitefish, but did delay hatching and early larval growth. However, Siefert believed a dissolved
oxygen reduction to 35% saturation would be harmful to survival and a drop to 25% would be
lethal to most early stages of the whitefish.
Impairment of rearing habitat for mountain whitefish fry and juveniles was also estimated
in this assessment with habitat suitability indices developed by the U.S. Fish and Wildlife
Service (Anglin et al., 1992). This analysis showed that the impairment of this habitat was
moderate to high hi the Middle Snake River (Figure-5-5). . .
In studying the microhabitat of the mountain whitefish in the Fisher River (Montana),
DosSantos (1985, Table 7) observed that as this species increases in size, it occupies deeper,
slower waters. The habitats for these fish as described by average facing velocity, Q.6 depth
velocity, and water depths were 3.44 cm/s, 16.06 cm/s, and 0.695 m for small fish (10 to 19.9 cm
in total length, TL); 1.86 cm/s, 13.47 cm/s, and 0.988 m for medium fish (20 to 27.7 cm TL); and
1.13 cm/s, 9.48 cm/s, and 1.25 m for large fish (>27.7 cm TL), respectively. During the season
of least flow hi the Logan River (Utah), adults could be found in pools at least 4.8 m wide and
having 0.9 to 1.2 m of water depth (Siglef, 1951).
Similar to the evaluation of spawning habitat, rearing habitat for mountain whitefish in
the Middle Snake River was moderately to highly impaired under the previously mentioned
habitat suitability indices (Figure 5-5).
6.2.5. Effects Due To an Altered Food Source and Prey Base
Mountain whitefish feed primarily on immature forms of bottom-dwelling aquatic insects
such as Diptera (true flies and midges), Trichoptera (caddisflies), Ephemeroptera (mayflies), and
Plecoptera (stoneflies) (Wydoski and Whitney, 1979). The general morphology of the mountain
whitefish with its subterminal mouth suggests it is adapted to feeding on or near the bottom
(Pontius and Parker, 1973). Underwater observations of bottom feeding by DosSantos (1985)
confirm that this fish actively forages by overturning rocks and plowing through substrates of
small particle sizes. In other underwater observations, Thompson and Davies (1976) noted
feeding on drift organisms within about 2 to 10 cm of the bottom. Large mountain whitefish can
be more generalized feeders and utilize a greater range of prey than do smaller fish. For
example, gastropods, small crayfish, leeches, dragonfly nymphs, the amphipod Gammarus,
young fish, whitefish eggs, and eggs of other species are sometimes eaten by adults (McHugh,
1940; Sigler, 1951; McAfee, 1.966; DosSantos, 1985). When bottom fauna are scarce, this fish
6-10
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will eat midwater plankton and surface insects, but under these conditions, the fish is usually less
abundant (Godfrey, 1955).
The larvae of midges and caddisflies and the nymphs of mayflies and stoneflies represent
very important food items for juvenile and adult mountain whitefish (Pontius and Parker, 1973;
Thompson and Davies, 1976; Sigler and Sigler, 1987). A summary of the diet of mountain
whitefish from field and laboratory studies conducted from 1936 to 1981 can be found in Table
6-1. With some exceptions, adult fish eat the same aquatic insects in about the same proportion
in Montana (Yellowstone, Gallatin, and Kootenai Rivers), Wyoming (Upper Snake River),
Alberta (Sheep River), and likely throughout the range of this species. The exceptions occur
when whitefish feed heavily on a large emergence of a particular invertebrate or on terrestrial
organisms when their aquatic food base is at a low level (Table 6-1). For example, freshwater
opossum shrimp, Mysis relicta, were the most common food item found in the stomachs of
mountain whitefish during a January 1991 study in Kootenay Lake and Brilliant Reservoir (an
impoundment on the Kootenay River), and in two areas on the Columbia River in British
Columbia (Boyle etal., 1992).
Generally, dipterans and caddisflies are more commonly eaten by mountain whitefish,
but mayflies and stoneflies are important food sources at some locations arid during some
seasons. Overall, chironomids appear to be the most important food item for both juvenile and
adult fish; at times they make up nearly 100% of the diet of small fish (Pontius and Parker, 1973;
Stalnaker and Gresswell, 1974).
Stream flow regulation at hydroelectric dams can alter the downstream thermal regime
and the amount of drifting particulate organic matter. Hauer and Stanford (1982) observed these
phenomena and the resultant change in caddisfly community structure in the Flathead River
below Hungry Horse Dam. In describing the distribution and abundance of macroinvertebrates
in the vicinity of Kanaka, Empire, and Boulder Rapids hi the Middle Snake River, Hill (1991b)
found that the quality and quantity of the food base for trout were limited. The majority of
aquatic insects present were tolerant of organic enrichment, indicative of deteriorated water
quality conditions (increased nutrients and sedimentation and depressed dissolved oxygen). As
whitefish and trout eat the same macroinvertebrates (McHugh, 1940; Laakso, 1951; Godfrey,
1955; Ellison, 1980; DosSantos, 1985), the prey base for the mountain whitefish is also probably
being adversely affected by the deteriorated water quality conditions hi the Middle Snake River.
Irving and Cuplin (1956) also found that production of aquatic invertebrates, the primary
source of food for whitefish, was adversely affected by diurnal fluctuation of water levels in the
tailwaters of the Lower Salmon Falls and Bliss Dams. They found that food production for cold-
water game fish was virtually absent within the zone of fluctuation in the tailwaters of these
6-11
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dams. The loss was attributed to the diurnal drying or freezing of this shallow zone of fluctuation, which
made up about 20% of the food production area.
During an April-May 1997 macroinvertebrate survey hi the 42-km (26 mile) free-flowing reach
of the Snake River below C. J. Strike Dam, Cazier (1997b) found the number of species and relative
densities were not significantly different between the fluctuation (shoreline area < 2 m deep) zone and
the main river.
6.2.6. Discussion
High water temperatures limit the mountain whitefish to elevations above 1,370 m throughout
much of its range (McAfee, 1966; Sigler, 1951). Even though the elevation of the Middle Snake River
extends from approximately 762 m at King Hill to 1,260 m at Milner Dam, this species appears to have
been able to live and reproduce in the Middle Snake River and its nearby tributaries prior to the
impoundment of the Snake River. With the increased water temperatures caused by flow depletion for
power generation and agricultural irrigation, the river has become an undesirable environment for this
cold-water species. This is borne out by our modeling, which shows that water temperatures needed for
spawning and incubation are essentially absent; and that water temperatures from mid-April to
November on average exceed the maximum optimum temperature, 12°C (Rajagopal, 1979), for growth
of mountain whitefish fry each year. Our estimates of habitat impairment using habitat suitability
indices also show that most spawning, rearing, and adult habitats available to this species in the Middle
Snake River are undesirable.
Competition with other salmonid species for any available habitat left in the Middle Snake River
does not appear to be a factor limiting mountain whitefish populations. Across their range in North
America, mountain whitefish coexist and may compete with several other fish species. This competition
does not appear to have adversely affected mountain whitefish populations, as this fish has evolved with
sympatric fishes and appears to occupy a slightly different niche from its competitors. DosSantos (1985)
found that the habitats and food sources of small (<20 cm TL) mountain whitefish and rainbow trout
were quite similar. However, in comparing the habitat of adult fish (>27.8 cm TL), DosSantos observed
rainbow trout in shallower areas with greater velocities and with substrates with double the boulder
composition than where adult mountain whitefish were found.
In comparing the food habits of the mountain whitefish with those of cutthroat trout
(Oncorhynchus clarki) in the Snake River over 2 years, Erickson (1966) showed that only
37% of the total volume of food utilized by cutthroat was also used by the whitefish. The dominant food
(>48% of the total volume) for the cutthroat trout was fish. Ellison (1980) found the diets of mountain
whitefish and brook trout (Salvelinus fontinalis) to be significantly different. Brook trout fed mainly on
6-13
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drifting terrestrial and aquatic insects, whereas whitefish stomachs contained mostly immature aquatic
insects, suggesting a bottom-feeding habit Within its range, the mountain whitefish typically
outnumbers sympatric salmonids (McAfee, 1966; DosSantos, 1985)..
Others (e.g., Sigler, 1951; McAfee, 1966) believe the mountain whitefish is an important
competitor for food and space with more recreationally valuable trout. Mountain whitefish are also
reported to compete with the following nonsalmonids for food: peamouth (Mylocheilus caurinus),
northern pilceminnow (Ptychocheilus oregonensis), yellow perch (Percaflavescens), and various suckers
(Catostomus sp.) (Daily, 1971). None of these investigations, however, demonstrated that either the
mountain whitefish or a sympatric fish species was detrimentally affected by competition for food or
space.
6.3. WHITE STURGEON (Acipenser transmontanus)
White sturgeon are presently depressed in abundance throughout their native range in Idaho, and
the now landlocked sturgeon in the Snake River is classified as a State of Idaho Species of Special
Concern (Idaho Department of Fish and Game, 1994). These fish have evolved life history
characteristics that have allowed them to thrive for centuries in large, dynamic river systems containing
diverse habitats with multiple food sources. These characteristics include opportunistic food habits,
delayed maturation, longevity, high fecundity, and mobility (Beamesderfer and Farr, 1997). White
sturgeon appear to have an innate hypometabolic response to hypoxia by reducing spontaneous
swrniming activity (Crocker and Cech, 1997), which may increase their survival during prolonged
hypoxic conditions.
Unfortunately, many of the adaptations by white sturgeon for living in large rivers are now
working against maintaining viable populations in riverine environments altered by dam construction.
Between its confluence with the Columbia River and Shoshone Falls, 12 hydroelectric projects on the
main stem of the Snake River have changed the river into separate, smaller, and less diverse habitats. In
the Middle Snake River, there has been a 37% loss of free-flowing habitat (Cochnauer, 1983), which is a
direct result of operating dams for hydroelectric power, flood control, and agricultural purposes.
Important white sturgeon spawning, rearing, and feeding areas have been changed and, in some cases,
lost as a result. These changes, along with past overharvesting, have resulted in significant decline of
white sturgeon populations in the Middle Snake River.
Little historical information is available for Idaho white sturgeon populations, but past harvest
and abundance trends are believed to be similar to those in the Columbia River. Unregulated
commercial harvest in the late 1800s significantly reduced white sturgeon populations throughout the
6-14
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Columbia River basin. Sturgeon populations recovered during the early to mid-1900s, only to be
reduced again by a resurgence of fishing activities and the loss of habitat. The main cause of habitat
destruction in the Middle Snake River is directly related to the construction and operation of
hydroelectric and irrigation dams. The loss of diversified riverine habitats required by the white
sturgeon began with the construction of the Swan Falls Dam in 1901 and continued with Lower Salmon
Falls Dam in 1910, Upper Salmon Falls Dam in 1937, and Bliss Dam in 1949.
It is not possible to quantify the actual decline that occurred in the white sturgeon population
after the Middle Snake River was dammed because only anecdotal information is available on the size of
the population prior to dam construction. For example, hi discussing the size of the historic population
in this reach, Cochnauer (1983) was only able to determine that this area "was known to contain large
numbers of sturgeon," some weighing as much as 307 kg (677 Ibs). Presently, the largest number of
white sturgeon in the Middle Snake River occurs in CJ. Strike Reservoir; a 1991-93 field study in this
area estimated the population offish > 80 cm and > 160 cm fork length (FL) at 2,554 and 268 sturgeon,
respectively (Lepla and Chandler, 1995a). Smaller numbers of sturgeon occur in a free-flowing section
of the river below Bliss Dam, Rkm 888 to 898 (RM 552 to 558); between Bliss and Lower Salmon Falls
Dams; and between Upper Salmon Falls Dam and Shoshone Falls (Lukens, 1981; Lepla and Chandler,
1995a,b). This remnant population is only a fraction of a larger population that occurred in the
preimpounded Middle Snake River.
Patterson et al. (1992) provide detailed records of planting 3,583 white sturgeon from Rkm 844
to 989 in the Snake River hi 1989-90. Since 1989, however, roughly 5,200 juvenile sturgeon (mostly
age 1 fish) were planted by the Idaho Department of Fish and Game between CJ. Strike Dam and
Shoshone Falls (T. Patterson, personal communication, September 9,1997). Of this total, approximately
960 juvenile sturgeon were planted in the upper reach above Upper Salmon Falls Dam after 1989 (Platts
and Pratt, 1992; S. Clark, personal communication, May 9, 1996). Some of these fish have survived and
may reproduce in this area, particularly if food supplies and rearing areas are not limited. However, the
overall success of the planting operation is unknown.
6.3.1. Loss and Alteration of Lotic Habitat
The loss and alteration of unrestricted flows in the Middle Snake River have caused widespread
change and reduction in spawning activities, rearing areas, prey species, and feeding areas for white
sturgeon. These adverse effects are discussed using available published studies and the results of
simulations of habitat, water quality, and ecological processes (Chapter 6 and Appendix D).
6-15
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63.2. Effects on Movement
Historically, white sturgeon could move freely between the Snake and Columbia Rivers
(Cochnauer et al., 1985) and up the Snake River as far as Shoshone Falls (Coon, 1978). The mobility of
this fish gave it historic access to diverse spawning, rearing, and feeding habitats in the Snake River.
This access was effectively reduced or halted by the construction and operation of irrigation and
hydroelectric dams. Of the dams in the Middle Snake River, only the complex of dams and barriers at
Lower and Upper Salmon Falls have fishways (Irving and Cuplin, 1956), but these are not adequate for
the passage of sturgeon (Cochnauer et al., 1985). The Bliss and CJ. Strike Dams form impassable
barriers to at least the upstream movement of sturgeon because they were constructed without any fish
passage facilities.
White sturgeon are capable of moving long distances over a short period of time. Galbreath
(1985) reported apparently random movement for 1,141 previously tagged white sturgeon in the Lower
Columbia River (below Bpnneville Dam) from 1976 through 1983; the fastest fish traveled 37 km in 3
days. While studying 29 radio-transmitter-tagged juvenile and adult white sturgeon, TL 83 to 218 cm,
in a free-flowing reach hi the mid-Columbia River, Haynes et al. (1978) observed movement of 3 to 12
km/week upstream and >15 km/week downstream. The average distance traveled for fish that moved at
least 0.8 km from the point of release was 40.2 km (25 miles). Haynes and Gray (1981) continued
tracking some of these fish and 19 additional sturgeon (98 to 236 cm TL) that were similarly tagged and
observed that long-distance travel appeared to be initiated when water temperature reached 13°C.
The movement of white sturgeon in the free-flowing Hells Canyon reach of the Snake River
appears to be more restricted than for Columbia River fish. During a 4-year study in the unimpounded
222 km (138 mi) reach between Hells Canyon and Lower Granite Dams, Coon (1978) observed that
22% (39 of 175 fish) of the small sturgeon (45 to 91.5 cm TL) moved downstream an average of 8.6 km
(range 1 to 39 km) from their release site over 1.2 years. The remaining 78% of the small sturgeon and
fish larger than 92 cm TL (total of 164 fish) remained within about 15 km of their release sites.
White sturgeon in reservoir systems are also capable of moving considerable distances. After
capture and release, sturgeon moved a maximum of 152 km (94 miles) but averaged 8.1 km (5 miles) in
the three lowest reservoirs hi the Lower Columbia River; the tune of travel was not given (North et al.,
1993). Fish size did not appear to affect the distance or direction traveled, and 49.9% moved upstream
and 50.1% moved downstream. Four percent of the tagged sturgeon moved past a dam (26 fish moved
downstream and 1 upstream).
Movement and survival of hatchery-stocked and wild white sturgeon downstream through or
over Bliss and CJ. Strike Dams was observed by Lepla and Chandler (1995a, 1997). Observations in
the impounded part of the Lower Columbia River (North et al., 1993; Beamesderfer et al., 1995) indicate
6-16
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that white sturgeon rarely use fish passage facilities designed for the passage of salmonids. Avenues for
passage more frequently used by this fish are navigation locks, which are not present in the Middle
Snake River or downstream, through turbines, or perhaps over spillways.
Access to white sturgeon spawning habitat appears to be limiting recruitment in the Middle
Snake River. Spawning habitat for sturgeon populations isolated by dams is limited to that occurring
within the reach where the fish live. Because white sturgeon can only move downstream through or
over dams, potential spawning areas located upstream of the dams in the Middle Snake River may be
underutilized on a long-term basis. This appears to be the case for the white sturgeon hi the reaches
between Bliss and Upper Salmon Falls Dams and below C.J. Strike Dam. These fish cannot move
upstream into known spawning sites or potential spawning sites like Kanaka, Empire, and Boulder
Rapids.
Sturgeon living in the Bliss reach have a somewhat different problem reaching spawning habitat.
During periods of low flow, the larger sturgeon population in CJ. Strike Reservoir does not appear to be
attracted to the numerous spawning sites located upstream between King Hill and Bliss Dam. In 1992-
93, fish in this area moved about 6.5 km upstream of the reservoir and spawned hi the Grass Hole, but
none were observed moving further upstream. The 37 km free-flowing section between Grass Hole and
King Hill flows through relatively flat terrain characterized by slow-moving runs with shallow riffles
and few deep holes (Lepla and Chandler, 1995a). During low-flow (e.g., < 255 m3/s; 9,000 cfs)
conditions, this reach may restrict the upstream movement of white sturgeon to spawning areas above
King Hill.
6.3.3. Effects on Spawning Activities
Spawning by white sturgeon in the impounded Middle Snake River is limited by low numbers of
adult spawners in the reaches above Bliss Dam, loss of access to historic spawning areas, loss of high
flows, and poor water quality during the spawning season.
In the Columbia River basin, white sturgeon usually spawn in areas of high current velocity over
large rocky substrates from February to June (Platts and Pratt, 1992; Parsley et al., 1993). A high
discharge rate (flow) appears to stimulate spawning activity. A high flow appeared to cue white
sturgeon spawning activity in the tailrace of The Dalles Dam. Water temperature, however, was not an
acute spawning cue, unlike higher river discharge, discharge coefficient of variability, and water column
velocity (Anders and Beckman, 1995). Mean water column velocities near white sturgeon spawning
sites in the Lower Columbia River were 0.8 to 2.8 m/sec, and velocities near the substrate were 0.5 to
2.4 m/sec (Parsley etal, 1993). ,
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The amount of white sturgeon spawning habitat available in the tailraces of four dams on the
Lower Columbia River is controlled by the discharge rate arid water temperature. The amount (area) of
spawning habitat in these tailraces increased as discharge increased, and the spawning period was
defined by a range of water temperatures acceptable for spawning (Parsley and Beckman, 1994). White
sturgeon in the Columbia River spawn in water temperatures of 10°C to 18°C, with most spawning
occurring at 14°C (Parsley et al., 1993). Successful egg incubation is possible within a temperature
range of 10°C to 18°C, but best results occur at 14°C to 16°C. Temperatures 18°C to 20°C may cause
substantial mortalities during sensitive embryonic stages, and temperatures above 20°C.are clearly lethal
to white sturgeon embryos (Wang et al., 1985,1987). In-laboratory growth of white sturgeon weighing
<1 g increased significantly from 15°C to 20°C, but was not significantly different from 20°C to 25°C
(Cechetal., 1984).
Since at least 1980, recruitment of white sturgeon hi the Middle Snake River appears to have
been limited by the lack of or low numbers of spawning fish. Lukens (1981) captured only seven fish
(ages 4 to 9 years) in the Lower Salmon Falls reach, none between Lower and Upper Salmon Falls
Dams, and nine fish (ages 4 to 27 years) in the Shoshone Falls reach in 1980-81. According to
Cochnauer et al. (1985), a female white sturgeon may not mature until at least 11 years of age and
probably does not spawn but every 3 to 11 years. Eleven-year-old white sturgeon in the Middle Snake
River are approximately 125 cm in length. Cochnauer et al. (1985) found only two fish older than 11
years and six fish greater than 125 cm hi length between Bliss Dam and Shoshone Falls. A 1993 field
survey (Lepla and Chandler, 1995b) in the Lower Salmon Falls reach captured only 3.8 sturgeon, none
greater than 115 cm in length. Lepla and Chandler (1995a) believed that a small number of gravid
females, along with poor water quality conditions during the time of egg incubation, were factors
limiting recruitment in the Bliss reach in 1991 -93.
In areas where adequate numbers of spawning fish exist, the loss of high flows during the
spawning season and high water temperatures during embryonic development appear to represent the
most important factors limiting successful recruitment of white sturgeon in the Middle Snake River
(Lepla and Chandler, 1995a). To evaluate these potential limiting factors, 30 years of flow and water
quality conditions were simulated (Chapter 6 and Appendix D). The flow data were developed from
actual data; the temperature data are simulated.
Spawning conditions hi the upper Bliss reach were assessed using model output developed for
the river at Rkm 893 (RM 555). This site is 1.3 km below the known white sturgeon spawning area hi
Porterfield Hole and is believed to fairly represent conditions in the upper Bliss reach. Spawning
problems caused by low flows and high water temperatures at this location are probably indicative of the
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entire free-flowing area below Bliss Dam. The site at Rkm 893 (RM 555) was modeled because the
channel morphology was known at that location.
Potential spawning times for white sturgeon can be identified by evaluating the annual flows and
water temperatures for the site at Rkm 893 (RM 555). As discussed above, an increasing water flow
appears to cue sturgeon to spawn, and the time frame for spawning can be further defined by a 10°C to
18°C range in water temperature. To assist in identifying potential spawning periods, flows and water
temperatures for the site at Rkm 893 (RM 555) are plotted together from March through July, which
includes the observed spawning season for this area.
The potential spawning period begins near the end of March, when, the water temperature
increases above 10°C, and continues for about 3 months until the high flows drop off and water
temperatures rise above 18°C (Figure 6-1). Given that 19.5 days are required at 17°C for embryonic
40000
Lethal temperature far white sturgeon embryos
Upper temperature of successful
Lower temperature of successful spawning range
——•—•—**
Date
1 cfs ac 0.02832 cms
Figure 6-1. Water temperature and flow during the white sturgeon spawning season at
Snake River Rkm 893 (RM555).
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development to be completed (complete absorption of the yolk) (Wang et al., 1985), the effective
spawning period extends from April through the first week of June. Favorable spawning conditions
exist when high flows occur during this period. White sturgeon may spawn in the absence of high flow
(e.g., see Lepla and Chandler, 1995a, Figures 32 and 33), but these are less than optimum conditions.
Optimum spawning conditions are believed to occur when high flows, as represented by the maximum
flow in Figure 5, coincide with water temperatures ranging from 10°C to 18°C. Under these conditions,
not only is there a longer time period of increasing flows to attract sturgeon for spawning, but the water
temperature conditions after spawning are more favorable for the survival of sturgeon eggs and embryos.
Simulations of conditions (described in Chapter 6) favorable for white sturgeon spawning and
incubation were evaluated. Favorable spawning and incubation conditions were identified because the
optimum conditions are unknown. Using just two variables, flow and water temperature, favorable
white sturgeon spawning and incubation periods were identified from 1970 to 1994 by modeling flows
>425 mVsec (15,000 cfs) with water temperatures ranging from 10°C to 18°C (for spawning) followed
by water temperatures <8°C for 20 days (for incubation). The tune period modeled each year was from
March to July. The modeling results show that during the 25-year period (1970-94) favorable spawning
conditions followed by favorable incubation conditions occurred 52% of the time. These conditions
occurred in 1970-72,1974-76,1978,1980, and 1982-86. Unfavorable conditions occurred during all
other years, including the eight consecutive years from 1987 to 1994. These results may be an
underestimate of favorable conditions, as the 425 mVsec (15,000 cfs) flow modeled is believed to be too
low for favorable spawning conditions. Spawning years 1995-96 were not modeled, but the USGS daily
streamflow reports for the King Hill station (No. 13154500) show that flows were more favorable for
spawning in both years. •
The low level of successful spawning in recent years is further indicated by the predominance of
hatchery fish in some areas. For example, 87% (33 fish) captured in 1993 in the Lower Salmon Falls
reach and 50% to 87%, depending on capture technique, offish <80 cm FL in the Bliss reach from 1991
to 1993 were of hatchery origin (Lepla and Chandler, 1995a,b). Fish <80 cm FL would be about 7 to 8
years of age or younger (Cochnauer, 1983).
63 A. Predation on Eggs and Larvae
Another factor that may limit white sturgeon recruitment is the loss of eggs and larvae to
predators during low-flow conditions. Miller and Beckman (1996) believed that white sturgeon reduce
the opportunity for predation from sympatric fishes by broadcasting their eggs in extremely fast-flowing
water, which may limit predator access to the spawning and incubation areas. They found white
sturgeon eggs in the guts of northern pikeminnow (Ptychocheilus oregonensis), largescale sucker
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(Catostomus macrochettus ), carp (Cyprinus carpid), and the prickly sculpin (Cottus asper). All except
the sculpin can be found in the Middle Snake River, and the largescale sucker may be the most abundant
fish in this area (Cochnauer, 1980a,b, 1981; Simpson and Wallace, 1982). The higher velocities (>1
m/sec) used for spawning appear to exclude these predators. Faler et al. (1988) found that northern
pikeminnow in the McNary tailrace avoided areas with surface velocities greater than 70 cm/sec. Adult
largescale suckers maintain position in water with velocities only up to 1.1 m/sec in laboratory
exposures (Dauble, 1986). Carp generally avoid swift current and prefer quiet water in areas with dense
vegetation (Wydoski and Whitney, 1979).
Furthermore, the risk of predation should be reduced with increased water flows because at high
flows predators must search a greater volume of water for white sturgeon eggs and larvae. Turbid water
associated with high flows may also provide protection from visual predators. McCabe and Tracy
(1994) theorized that wide dispersal of eggs also allows utilization of more feeding areas and rearing
habitats by larval and postlarval white sturgeon and minimizes competition for resources. Poor dispersal
during low flows may result in greater loss of developing eggs to fungal and other diseases because
clumping of the adhesive eggs would be more likely to occur.
6.3.5. Loss and Alteration of Rearing Areas
The protection and restoration of rearing habitats for white sturgeon do not appear to be as
critical as for spawning habitats (Beamesderfer and Farr, 1997). Parsley et al. (1993) captured juvenile
white sturgeon in the Lower Columbia River in areas with water depths of 2 to 58 m, mean water
column velocities of 1.2 m/sec or less, and substrates of hard clay, mud and silt, sand, gravel, cobble,
boulder, and bedrock. Young-of-the-year were found in similar areas. The habitats where these fish
were captured indicate a tolerance of, but not necessarily a preference for, a wide range of environmental
conditions. In the Lower Columbia River, young-of-the-year and juvenile white sturgeon appeared to
have a preference for the thalweg, as that is where Parsley et al. (1993) most often captured them;
samples adjacent to the thalweg in shallow water rarely contained sturgeon. The absence of white
sturgeon from shallow areas suggests the photonegative behavior observed in the larval stage also occurs
in more advanced life stages (Brannon et al., 1985).
Shallow-water areas, however, may represent important rearing habitat for white sturgeon. In the
Middle Columbia River, Haynes and Gray (1981) observed diel movements by white sturgeon 98 to 236
cm TL into shallow water nearshore and slough areas in late afternoon and evening and a return to deep
water the following morning. These movements were into areas where benthic organisms and smaller
fish were more abundant. In the Lower Columbia River, McCabe et al. (1993) believed that juvenile
white sturgeon 144 to 724 mm FL fed in water 1 to 6 m deep where a favorite prey item, a tube-dwelling
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amphipod, reached densities more than 10 times greater than deeper water areas. In the Bliss reach,
juvenile sturgeon <129 cm TL used areas with water depths a| shallow as 3 m (Lepla and Chandler,
1995a).
Rearing habitat for young-of-the-year and juvenile white sturgeon in the Middle Snake River has
not been documented as well as that hi the Lower Columbia River, where rearing habitat appears not to
be limited (Parsley and Beckman, 1994). Although the Snake River white sturgeon show a tolerance for
a wide range of environmental conditions, the riverine-reservoir system in the Middle Snake River has
poorer water quality and much lower flows than the Lower Columbia River. These factors may limit the
amount of acceptable rearing habitat available to the white sturgeon in the Middle Snake River.
6.3.6. Effects Due to an Altered Food Source and Prey Base
Prior to impoundment of the Snake River, white sturgeon could take advantage of scattered and
seasonal food sources by moving between different riverine habitats. They are opportunistic feeders
with a wide range of food items including zooplankton, molluscs, amphipods, aquatic larvae, benthic,
invertebrates, and fish (McCabe et al., 1993; Lepla and Chandler, 1995a). White sturgeon are more
predaceous than any other North American sturgeon (Semakula and Larkin, 1968) and can capture and
consume large prey (Beamesderfer and Farr, 1997). Seasonal migrations occur hi the Lower Columbia
River where sturgeon move to feed on eulachon, northern anchovy, American shad, moribund
salmonids, amphipods, and other invertebrates (DeVore et al., 1995), This species is also capable of
subsisting for long periods when food is not available (Beamesderfer and Farr, 1997).
In the Middle Snake region, use of historic food sources and feeding areas by white sturgeon was
greatly unpaired by the construction of dams and by the loss of an unrestricted lotic environment.
Anadromous fish runs that occurred at different times of the year likely provided very important food
sources for the sturgeon. Anadromous species previously entering this area were Summer and fall
Chinook salmon (Oncorhynchus tshawytschd), steelhead (O. mykiss), and lamprey (Lampetra tridentatd);
some historical evidence indicates that coho salmon (O. kisutch) may have also inhabited this area (Dey
and Minshall, 1992). This prey base was temporarily stopped from reaching the Middle Snake River
about 1901 when Swan Falls Dam was constructed and a fish ladder was not added until about a decade
later. This fish passage facility, however, only operates intermittently during high water conditions
(Irving and Cuplin, 1956). The anadromous prey base was eliminated entirely in 1952 when CJ. Strike
Dam was constructed without any fish passage facilities. Unfortunately, at that time, the only remaining
anadromous fish returning to this part of the river was a small run of steelhead (Irving and Cuplin,
1956).
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Platts and Pratt (1992) discussed two other historical food sources no longer available to the
white sturgeon in the Middle Snake River. Unrestricted river flows transported organic debris in the
form of dead fish and incoming terrestrial organisms from upstream locations. The continuous input of
organic debris along with incoming gravels and rubble also provided habitat for large mussel and
crayfish populations. Both the mcoming organic debris and the abundant mussel and crayfish
populations were important food sources.
It is ironic that the largest population of white sturgeon at this time in the Middle Snake River
resides in C. J. Strike Reservoir, which was created by a dam. Food sources for white sturgeon in the
C.J. Strike Reservoir are apparently adequate for maintaining this population. As shown in Table 6-2,
the growth rate of sturgeon in this area compares favorably with the unimpounded sections of the Lower
Columbia River and the Fraser River in British Columbia. The growth rates of white sturgeon in C.J.
Strike Reservoir are a testament to their ability to shift their prey base in a changing environment.
. The growth rate of white sturgeon in the Hells Canyon reach of the Snake River was similar to
that in C.J. Strike Reservoir. In studying 650 sturgeon (ages estimated to range from 2 to 56 years) in
this area, Coon (1978, his Figure 12) found that the growth rate was generally quite rapid up to about 4
years of age (up to 60 cm TL), averaged about 2 cm/yr from ages 4 to 15 years (up to 85 cm TL),
increased to about 8 cm/yr from ages 15 to 30 years (up to 210 cm TL), and then decreased to 2 cm/yr
from ages 30 to 45 years (up to 240 cm TL). Coon noted that sturgeon growth decreased after the
construction of the three dams hi Hells Canyon, located upstream of his study area. It appears the
existing prey base, which is reduced from historical levels, may not be an important factor limiting
growth in the present-day sturgeon population in the Middle Snake River. A return of the anadromous
prey base would likely improve the production of white sturgeon, but the return of these fish species
Table 6-2. Total lengths and mean growth rates for white sturgeon in the Middle Snake,
main-stem Columbia River in the United States, and Fraser River, Canada
Water body
C.J. Strike
Reservoir
Lower Columbia
River
Fraser River2
Total length (cm)
12yrs 20yrs
125
122
97
180
183
142
Mean growth
rate (cm/yr)
7.2 from
5 to 25 yrs
6.6 from
1 to 21 yrs
5.1 from
5 to 25 yrs
References
Cochnauer et al, 1985
Galbreath, 1985
Scott and Grossman, 1973
"All were female sturgeon and with fork lengths converted to total lengths (TL = FL x 1.110).
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is a much larger issue than just providing for adequate passage at the main-stem dams. An .assessment
of the long-term reproductive survival of each of these anadromous species similar to that being
conducted for white sturgeon would be required. Their life histories and environmental requirements are
more complex than those of the sturgeon and would require significant repair not only on main-stem
Snake River habitats, but on important tributaries as well.
6.3.7. Loss of Genetic Diversity
Genetic diversity is required for the maintenance of long-term health and robustness of any
biological community. In reviewing the evolution of animals, Brown (1985) noted that mitochondrial
DNA (mtDNA) has been widely used as a genetic marker in population studies because of its higher
mutation rate relative to nuclear DNA, generally maternal inheritance, and lack of sexual recombination.
Brown et al. (1992) studied mtDNA variation in A. transmontanus populations in the Fraser and
Columbia Rivers. With regard to Idaho white sturgeon populations, genetic analysis of Kootenai River
fish by Setter and Brannon (1990) indicates they are a unique stock and constitute a distinct
interbreeding population. These fish have been isolated from the Columbia River for about 10,000 years
(Northcote, 1973). An analysis of the genetic diversity of the white sturgeon populations in the Middle
Snake River has not been performed.
The three-year study by Brown et al. (1992) suggests that overexploitation of the white sturgeon
in the Columbia River during the late 1800s and early 1900s and the subsequent habitat destruction
caused by the construction of hydroelectric dams caused a "genetic bottleneck" that reduced mtDNA or
genetic diversity in Columbia River white sturgeon. Brown et al. (1'992) found a steep reduction in the
mtDNA diversity in the landlocked sturgeon populations hi the Columbia River. Of six observed
genotypes in the river, the upriver population above McNary Dam shares only one genotype with fish
found below Bonneville Dam.
At present, information is not available to determine if there is a reduction in genetic diversity in
the Snake River white sturgeon populations. However, because this population has experienced very
similar overexploitation and habitat destruction due to the construction and operation of dams, and
appears to be even more isolated than any of the mainstem Columbia River fish, it is likely that a
reduction in mtDNA diversity is occurring.
As discussed by Brown et al. (1992), any reduction in the genetic diversity hi sturgeon
populations should be of special concern in the conservation of this species, given its long generation
time and advanced age at reproductive maturity.
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6.3.8. Discussion
The populations of all eight species of sturgeon in North America are presently depleted,
threatened, or extinct (Smith, 1990; Birstein, 1993). Recovery efforts for white sturgeon and other
sturgeon species in North America have tended to focus on flow augmentation during spawning periods
and supplementation of populations through hatchery rearing programs (Hildebrand et al., 1999). These
two efforts have been used with some success in the Kootenai River in northern Idaho (Duke et al.,
1999), and are planned for the Upper Columbia River in British Columbia (Hildebrand et al., 1999).
Beamesderfer and Farr (1997), hi a survey of sturgeon and paddlefish in North America, identified
protecting and restoring critical habitat, especially for spawning, restoring the natural hydrography and
improving passage at dams as being the most important for benefiting the conservation, productivity,
and diversity of these fish.
Over the past century, white sturgeon in the Middle Snake River have experienced a reduction of
thek diverse riverine environment and an alteration of the dynamic hydrologic cycle to which they are
historically adapted. In some cases, for example in the C.J. Strike Reservoir and in the free-flowing
reach from King Hill to Bliss Dam, the white sturgeon has survived. But overall, judging by their
reduced and declining population numbers, the white sturgeon is not adapting well to the habitat
alteration, unfavorable spawning and rearing conditions, and isolation caused by the dams. These
unfavorable environmental conditions are worsened during periods of drought.
Witibi one exception, the habitat suitability analysis showed that unfavorable living conditions
(i.e., the highest impairment) for all life stages of the white sturgeon generally occurred above Lower
Salmon Falls Dam (Figure 5-6). The exception was that the juvenile and adult stages had the lowest
impairment in the reach from Box Canyon downstream to Upper Salmon Falls Dam. In the reaches
downstream from Lower Salmon Falls Dam, living conditions were shown to improve, except for the
Bliss Reservoir, which had unfavorable living conditions for all life stages (Figure 5-6).
Even though significant restoration of lost habitat for the white sturgeon will not occur without
dam removal, it is possible to improve conditions by altering the way the dams are operated in the
Middle and Upper Snake River. Past studies have shown that spawning and early embryonic
development have been unsuccessful in large part because of poor water quality (Lepla and Chandler,
1995a), which has resulted hi depressed natural recruitment. These adverse conditions can be improved
if a spring freshet is reestablished with flows large enough to stimulate spawning, and with post-
spawning water temperatures low enough (<18°C) to allow for healthy embryonic development other
than during a narrow window of time.
Improved recruitment to the white sturgeon population may also be achieved by reducing or
avoiding block loading (or load shaping) at the dams during the spawning season. During these loading
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events there is a sudden increase followed by a sudden decrease in water flows each day. Observations
in the Snake River (Chandler and Lepla, 1997) and in the Columbia River (Hildebrand et al., 1999) show
that this type of flow management at dams my influence the intensity of spawning and the survival of
spawned eggs.
Anglin et al. (1992) used Instream Flow Incremental Methodology (IFIM) to develop habitat vs.
flow relationships for white sturgeon in the 241-km section of the Snake River from CJ. Strike Dam. to
Brownlee Reservoir. Habitat time series analysis (Anglin et al., 1992) shows that a 339.8 m3/s (12,000
cfs) flow scenario provided the best habitat for adults, juveniles, spawning, and incubation. In general,
habitat for these white sturgeon life stages continued to increase with flows up to at least 425-566 m3/s
(15,000 to 20,000 cfs). However, the flows for the scenarios identifying critical habitat for white
sturgeon life stages may be low, at least for spawning and incubation. Marcuson et al. (1995) and
Paragamian et al. (1997) recommended minimum flows of 991-1,132 m3/s (35,000 to 40,000 cfs) hi
their investigations of flows necessary to produce conditions favorable for recruitment of white sturgeon
in the Kootenai River.
The freshets would also scour the annual buildup of sediment from deep holes that provide
rearing habitat for white sturgeon. Without annual freshets, the bedload transport may gradually fill
some of these deep holes, particularly in areas with low gradients. During a 1979-81 study, Lukens
(1982) described the lower part of the Bliss reach below King Hill as "relatively flat (0.32 m/km) with
few distinguishable shallow riffles, long runs, and thirteen traditional sturgeon fishing holes." Just over
10 years later, Lepla and Chandler (1995a) found few sturgeon (4% of the Bliss reach population or 24
fish) inhabiting this reach. Rearing habitat for sturgeon appears to have been reduced hi this area.
Anecdotal information from "older local fishermen" indicates that sediment has filled sturgeon holes in
the reach below CJ. Strike Dam (Lukens, 1982). Poor water quality during the summer may also have
attributed to the low number offish captured during the 1991-93 surveys hi the low-gradient area of the
Bliss reach.
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7. ANALYSIS OF EXPOSURE AND EFFECTS FOR MACROINVERTEBRATES
7.1. OVERVIEW
Aquatic macroinvertebrates are the primary tool for bioassessment of freshwater
ecosystems (Rosenberg and Resh, 1993). A quantitative analysis of macroinvertebrate
communities provides a comprehensive assessment of the overall ecological integrity of a
system, particularly when combined with information on water chemistry and in-stream habitat
conditions (Minshall, 1993). Fish assemblages have been used with noted success as a
bioassessment tool in streams and rivers in the midwesiern United States (e.g., Karr et al., 1986).
In the western United States, however, the use offish assemblages as a bioassessment tool is
constrained by the natural paucity of species, stocking of game fish, and the anadromous life
history of many native species (Fore et al., 1996). The sessile nature of macroinvertebrates
(relative to fish) makes the macroinvertebrate community of a river a natural integrator of
physical and chemical conditions within that system. The bioassessment of freshwater
ecosystems in the western United States should focus on macroinvertebrates, although the
assessment offish assemblages still can provide useful information, particularly when focused on
fisheries concerns or toxicological endpoints (see Maret et al., 1997; Clark et al., 1998; and
Maret, 1999, for examples from the Snake River).
This chapter is presented in two sections. The first section describes the
macroinvertebrate community of the Middle Snake River at several locations between Twin Falls
and Hagerman, ID. This sampling was conducted by Idaho State University from 1992 through
1994. The second section reviews the status of several of the threatened or endangered molluscs
found in the Middle Snake River.
7.2. SAMPLING BY IDAHO STATE UNIVERSITY 1992-1994
During the time of this sampling effort, the riverbed of the Middle Snake River was
composed predominantly of soft sediments with occasional large boulders. Only the sampling
location immediately downstream of Pillar Falls (Rkm 980.8, RM 613) contained abundant
gravel and small cobble-sized substrate (Todd V. Royer, personal observation).
Because of the reduced water velocity, favorable substrate, and elevated concentrations of
dissolved nutrients, the Middle Snake River at that time supported dense populations of aquatic
macrophytes, primarily Ceratophyllum demersum, Potamogetonpectinatus, and P. crispus
(Falter et al., 1995). These macrophytes provided substrate for filamentous green algae, mostly
Cladophora and Hydrodictyon (Falter et al., 1995), which formed thick mats on the surface of
the river during the summer months. .
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The abundant growth of aquatic macrophytes and filamentous algae, together with the
high mean concentrations of nitrogen and phosphorus (Table 4-6), indicate that the Middle Snake
River was a highly eutrophic system during the years 1992-94. The eutrophic condition also was
reflected in the extremely fast rate at which organic material in the river decomposed (Royer and
Minshall, 1997). In addition to the eutrophic condition of the river, reduced water velocity due to
impoundment allowed greater solar heating of the water. In 1994 (a high-flow year), monitoring
of water temperature in the Middle Snake River near the Magic Valley Fish Hatchery
(approximately Rkm 944; RM 590) revealed 40 days during July-August in which the mean daily
water temperature exceeded 20°C. Furthermore, 35 of the 40 days were consecutive, essentially
precluding the existence of cold-water biota from the Middle Snake River.
Mean density of aquatic macroinvertebrates in the Middle Snake River often exceeded
75,000 and occasionally approached 200,000 individuals per m2 (Figure 7-1). The exception to
this occurred hi April 1994 when density at all stations was less than 50,000 individuals/m2.
These values of density are high relative to other rivers in southern Idaho. Density of
macroinvertebrates in the Owhyee River in 1995 was approximately 12,300 individuals per m2
(Royer and Minshall, 1996), or about 25% of that in the Middle Snake River. Despite the high
density of macroinvertebrates, taxa richness was low, never exceeding a mean value of 15 taxa at
any sampling location (Figure 7-2). The greatest values for richness usually were observed
between Rkm 931.6 and Rkm 952.5 (RM 579 and RM 592), the most downstream stations
examined in the study. In 1993 and 1994, the most upstream location (Rkm 986.3, RM 613) also
displayed relatively high taxa richness, although the absolute values always were less than-12
taxa. The lowest values of richness occurred around Rkm 957.4 (RM 595), with mean richness
values of 3 to 7 taxa over the duration of the study.
The taxonomic resolution of the study was typically to genus, although some of the most
abundant groups (e.g., Chironomidae, Oligochaeta, and Turbellaria) were left at a more coarse
resolution. Taxonomic resolution notwithstanding, the macroinvertebrate community of the
Middle Snake River during 1992-94 displayed a paucity of taxa. For example, quantitative
sampling of the Owhyee River in southern Idaho, using a similar level of taxonomic resolution,
revealed 24 taxa in 1995 (Royer and Minshall, 1996), whereas no location sampled in the Middle
Snake River exceeded 15 taxa on any date.
In addition to the low diversity of taxa in the Middle Snake River, the macroinvertebrate
community was composed primarily of pollution-tolerant and sediment-dwelling taxa (Table
7-1). Typically, the 3 to 4 most common taxa made up 80% to 95% of the benthic
macroinvertebrate community. Throughout the Middle Snake River from 1992 to 1994,
Oligochaeta, Hyalella azteca, Chironomidae, Turbellaria, and Potamopyrgus antipodarum were
7-2
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o
z;
aj
Q
250
200
150
100
50
0
June 1992
580 585 590 595 600
River Mile
605
610
615
Figure 7-1. Mean density of aquatic macro invertebrates in the Middle Snake River at
locations sampled by Idaho State University. Error bars equal +/- SD, n=9.'
7-3
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-------
Table 7-1. Mean (SD) relative abundance (%) of the ten most common invertebrate taxa in
the Middle Snake River on each of the sampling dates. Values for each date calculated
from all nine sampling stations (from Royer et al., 1995)
Potamopyrgus
antipodarum
Oligochaeta
Hya.le.lla azteca
Chironomidae
Turbellaria
Caeciodotea
Pisidium
Vorticifex
Ferrissia
Piscicola
Total
Jun 1992
38.0 (21.4)
44.5 (16.9)
2.9 (6.3)
7.4 (6.2)
1.0- (0.9)
0.6 (0.7)
2.1 (1.8)
0.7 (1.0)
NP
0.1 (0.1)
97:3
Sept 1992
51.1 (27.7)
29.6 (22.6) .
2.9 (3.8)
3.4 (4.5)
4.7 (3.4)
1.6 (2.2)
1.8 (2.1)
1.1 (1.1)
' NP
1.0 (2.3)
97.2
Sept 1993
63.7 (27.1)
21.0(17.6)
5.7 (13.2)
4.5 (8.3)
1.5 (1.7)
0.1 (0.1)
0.4 (0.5)
0.2 (0.4)
1.1 (3.0)
NP
98.1
Apr 1994
31.2(14.5)
58.1 (13.1)
1.4(3.0)
6.2(11.1)
0.3 (0.7)
0.4 (0.8)
0.6 (0.5)
0.5 (0.9)
<0.1 (0.1)
NP
98.9
Oct 1994
70.0 (19.4)
17.5 (6.5)
4.6 (10.6)
1.7 (3.2)
2.0 (1.3)
0.4 (0.3)
0.6 (0.6)
0.3 (0.3)
1.0 (2.8)
NP
98.0
NP, not present. .
the most abundant taxa, and all are considered tolerant to organic pollution (Clark and Maret,
1993). Aquatic insects other than Chironomidae were rare in the Middle Snake River.
Particularly scarce were those groups adversely affected by organic pollution, elevated water
temperatures, and sedimentation, such as Ephemeroptera and Plecoptera (e.g., Clark and Maret,
1993; Merrit and Cummins, 1996). Indeed, during the course of the ISU sampling, no Plecoptera
(stoneflies) were found at any Middle Snake River station. However, 8 to 10 species of
Plecoptera were collected from 1981 to 1988 at various locations in Rock Creek (Maret, 1989), a
tributary to the Middle Snake River.
The New Zealand mud snail, Potamopyrgus antipodarum (Gray) (=P. jenkinsi [Smith]),
was first discovered in the Middle Snake River in 1987 and has spread rapidly since that time
(Bowler, 1991). Sampling from 1992 to 1994 revealed P. antipodarum to be the most common
invertebrate in the Middle Snake River. The relative abundance of P. antipodarum during the
study at two representative stations (Rkm 986.3 and Rkm 932.4, RM 613.0 and RM 579.5) is
shown in Figure 7-3. At Rkm 986.3 (RM 579.5), P. antipodarum represented as much as 80% of
the individuals of the macro-invertebrate community. At Rkm 986.3, however, its abundance was
lower, accounting for only 2% to 20% of the individuals in the community from 1992 to 1994.
7-5
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River Mile 613.0
River Mile 579.5
I
•a
Figure 7-3. Mean relative abundance of the exotic snail, Potamopyrgus
antipodarum, at two locations sampled by Idaho State University. Error bars
equal +/- 1SD, n=9.
P. antipodarum is known to do well in eutrophic systems (Dorgelo, 1988); therefore, it is not
surprising that it has been successful in the Middle Snake River.
In addition to the sampling conducted from 1992 to 1994, the macroinvertebrate
community in the Middle Snake River at King Hill was sampled in August 1995 as part of a
separate research project (Royer and Minshall, 1996). Sampling was limited to areas of the river
approximately 1.3 m or less in depth and thus does not include deep-water habitats. At mat time,
the community at King Hill consisted primarily of Chironomidae, Oligochaeta, and Hydropsyche
(a filter-feeding Trichopteran). Other benthic insects that occurred in the Middle Snake River at
King Hill included Baetis (Ephemeroptera), Tricorythodes (Ephemeroptera), and Hydroptila
(Trichoptera), all of which are moderately or very tolerant of habitat degradation. The sampling
at King Hill revealed Potamopyrgus antipodarum to be a relatively minor component of the
fauna, representing 6% of the sampled community.
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7.3. STATUS OF THREATENED AND ENDANGERED MOLLUSCS IN THE MIDDLE
SNAKE RIVER
Presently, cold-water natives survive only in limited, spring-fed areas in the Middle Snake
River. The preferred habitat for cold-water biota has temperatures less than 17°C with minimal
sediment in free-flowing water. Cold-water molluscs are most likely to be found adjacent to
rapids, near spring-influenced sites, or near the mouths of major tributaries.
7.3.1. Bliss Rapids Snail (Taylorchoncha serpenticold)
The Bliss Rapids snail is moderately negatively phototaxic and generally resides under
rocks during the day (Bowler, 1991). The Bliss Rapids snail grazes during the night on small
algae and diatoms living on rock surfaces (USFWS, 1994). Egg laying takes place in December
through March in the main stem and from January to late June hi the large spring colonies. Eggs
are laid singly in very small capsules attached to the lateral and undersides of rocks, which also
are inhabited by adults. Eggs hatch roughly 1 month after oviposition. Juveniles are
predominant in river colonies by early June and as early as April in large springs. There appears
to be an annual turnover of most adult populations (Frest and Johannes, 1992).
T. serpenticola occurred historically in the main stem of the Snake River and associated
springs from Indian Cove Bridge (Rkm 845.9, RM 525.3) to Twin Falls (Hershler et al., 1994;
USFWS, 1995). The USFWS reports (1995) that colonies are concentrated in the Hagerman
reach, unpolluted springs (Thousand, Box Creek, and Niagara Springs), and the tailwaters of the
Bliss and Lower Salmon Falls Dams. Pentec (1991) reported finding this snail in springs above
American Falls Reservoir, but Hershler et al. (1994) believe this requires verification, which has
not occurred.
As of 1995, the distribution of known populations of this species was believed to be
discontinuous in areas either in or influenced by springs, on the edge of rapids, and near
shorelines (USFWS, 1995). In more recent work, Cazier and Myers (1996) and Cazier (1997a)
observed a more or less continuous population in edgewater, runs, eddies, and deep-water
habitats (5.5 to 6:7 m) from Lower Salmon Falls Dam to Bancroft Springs. However, the Bliss
Rapids snail is not found in pools or reservoirs.
In aggregate, Frest and Johannes (1992) estimated the total number of Bliss Rapids snails in
the Nature Conservancy's preserve in Thousand Springs to number in the low millions. At that
time, it was the largest known concentration of this species. Cazier and Myers (1996) estimated
relative densities of Bliss Rapids snail colonies at 3.4 to 8.2 snails/0.5 m2 at Rkm 917 (RM
569.5) in the Snake River. In studying Bliss Rapids snail colonies during 1996, Cazier (1997a)
estimated relative densities at 0.24 to 23.2 snails/0.5 m2 in the Snake River and 49.6 to 98.6
snails/0.5 m2 in Thousand Springs.
7-7
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The Bliss Rapids snail occurs in flowing waters on exposed lateral and undersides of stable
cobble-boulder substratum (Frest and Johannes, 1992). This snail does not burrow into the
sediment and normally avoids surfaces with attached plants (Taylor, 1982a; Hershler et al.,
1994). Taylor (1982a) found it locally quite abundant on smooth rock surfaces with encrusting
algae. Cazier (1997a) found that the Bliss Rapids snail inhabits most environments available in
springs and in the main river below Lower Salmon Falls Dam, but the snail is rarely found on
fine sediments. Pentec (1991) reported finding 56 live specimens in 4 sites (near Rkms 941 and
1207, RM 584.4 and 749.6) with water depths of 10 to 33 cm and water currents of 6 to 100
cm/sec (facing velocity) and 43 to 122 cm/sec (0.6 depth velocity). The 56 snails were found on
rock substrate 1 to 41 cm in diameter at a distance of 2.4 to 4.6 m offshore.
During 1995, dissolved oxygen ranged from 7.8 to 9.8 mg/L, temperature 7.6 °C to
19.8 °C, total hardness 172 to 195 mg/L, specific conductance 472 to 496 umho/cm, and pH 8.3
to 8.6 in the Bliss Rapids snail colony at Rkm 917 (RM 569.5) (Cazier and Myers, 1996). These
parameters were also measured at this location during 1996 (Cazier, 1997a). Dissolved oxygen
ranged from 7.8 mg/L in July to 11.2 mg/L in February, temperature ranged from 4.6°C in
December to 19.3°C in July, total hardness 140 to 212 mg CaCO3/L, specific conductance 354 to
514 umho/cm, and pH 8.2 to 8.8. Pentec (1991) measured dissolved oxygen at 6.9 to 8.6 mg/L
in the four upriver snail beds they reported finding. Water quality conditions required to
maintain reproduction and recruitment for the Bliss Rapids snail currently are unknown.
7.3.2. Idaho Springsnail (Pyrgulopsis idahoensis)
Information is not available on the life history of this species. The historical distribution of
the Idaho springsnail was in permanently flowing waters of the mainstem Snake River from
Homedale (Rkm 670, RM 416) to Bancroft Springs. It was not found in tributaries to the Middle
Snake River or in marginal cold-water springs (Taylor, 1982b; USFWS, 1995). Taylor (1982b)
collected this species from Bancroft Springs to Indian Cove Bridge, a distance of about 45 km.
The consistent occurrence of this snail hi Taylor's samples led him to believe its distribution was
nearly continuous along this reach of the Snake River.
As of 1995, Idaho springsnail populations were believed to occur in approximately 20% of
their historical range and were discontinuous in the reach from the headwaters of C.J. Strike
Reservoir (Rkm 834, RM 517.9) to Bancroft Springs (USFWS, 1995). More recent
investigations by Cazier and Myers (1996) and Cazier (1997a,b) have found the Idaho springsnail
in a 34-km reach below CJ. Strike Dam, within the C.J. Strike Reservoir, and in the 5-km reach
above Bancroft Springs. These investigations expanded the range of the Idaho springsnail, which
now appears to extend from Rkm 761 (RM 472.6) to Rkm 895 (RM 555.8).
7-8
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Taylor (1982b) believed the upriver limit for the Idaho springsnail populations was the fast
water in a narrow canyon section of the Snake River above Bancroft Springs and the downstream
limiting factors were unknown. Cazier and Myers (1996) estimated relative densities of Idaho
springsnail at 0.63 to 1.5 snails/0.5 m2 at Rkm 895 (RM 555.8) in the main river. Cazier (1997a)
estimated densities from 10 to 60 snails/0.5 m2 in Idaho springsnail colonies in the C.J. Strike
Reservoir and in the 34-km reach below the dam.
The Idaho springsnail is found in mud or sand among cobbles and boulders and its probable
habitat includes the entire width of the Snake River, except in strictly coarse-grained sediments
(Taylor, 1982b). After observing this snail living at water depths of 15 cm to 7 m on cobble,
gravel with or without vegetation, on mud or sand between cobble, and on gravel covered with
algae, Cazier (1997a) believes this snail is an ecological opportunist. Further, Cazier (1997b)
found P. idahoensis occurring in the fluctuation zone (area <2 m deep affected by block loading)
in the Snake River below CJ. Strike Dam.
During 1995, dissolved oxygen ranged from 7.8 to 9.8 mg/L, temperature 7.6 °C to
19.8 °C, total hardness 172 to 195 mg/L, specific conductance 472 to 496 umho/cm, and pH 8.3
to 8.6 in an Idaho springsnail colony in the main river (Cazier and Myers, 1996). Cazier (1997a)
reported finding Idaho springsnail colonies in C. J. Strike Reservoir in an area with summer
water temperatures of more than 22°C. Water quality conditions required to maintain
reproduction and recruitment for the Idaho springsnail are currently unknown.
7.3.3. Snake River Physa (Physa natricina)
Although little is known of the general life history of the Snake River Physa, longevity
probably averages 2 years (USFWS, 1994). The distribution of this species is based on the
collection of only a few live specimens and empty shells. The historical distribution of the Snake
River Physa was believed to extend from Grandview (Rkm 783.4, RM 486.5) upstream through
the Hagerman Reach (Rkm 917, RM 569.5) (USFWS, 1995). The range of this snail may extend
further upriver than reported by the USFWS as Pentec (1991) reported finding two live snails at
two new sites (Rkm 1191 and 1205, RM 739.6 and RM 748). This appears to be a very rare snail
with less than fifty specimens collected. Population densities are not available. At present, two
colonies are believed to remain in the Hagerman and King Hill reaches, and a possible third
colony may be located immediately downstream of Minidoka Dam (USFWS, 1995).
The Snake River Physa lives primarily in deep, swift water. Taylor (1982c) found live
snails on boulders in the deepest accessible part of the Snake River at the margins of rapids.
Pentec (1991) reported finding two snails on substrate 0.7 and 5 cm in diameter at locations 7
and 30m offshore during low-water conditions. The water at these locations was 5 and 46 cm in
depth, and the water currents were 30 and 46 cm/sec (facing velocity) and 46 and 52 cm/sec (0.6
7-9
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depth velocity). The Snake River Physa requires cold, clean, well-oxygenated, swiftly flowing
water with low turbidity (USFWS, 1995). Pentec (1991) measured dissolved oxygen at 7.7 and 8
mg/L at the two locations where Snake River Physa were found. Water quality conditions
required to maintain reproduction and recruitment for this species are currently unknown.
7.3.4. Utah Valvata (Valvata utahensis)
V. utahensis is primarily a detritivore, grazing on diatoms and other periphyton (USFWS,
1995). Little is known of its life history, but it is believed to have a maximum longevity of 2
years (USFWS, 1994). The "modern" historical range of Utah valvata extended from Grandview
upstream to American Falls (USFWS, 1995). The present distribution of this snail includes
springs and the main-stem Snake River in about a 6-km reach of the Hagerman Valley, a 724on
reach of Lake Walcott, and a site below American Falls Dam (Taylor, 1982d; USFWS 1995;
Bureau of Reclamation, 1998).
The Bureau of Reclamation (1998) found that Lake Walcott serves as a refuge for a large
Utah valvata population. In 1996 surveys, Ralston and Associates (1997) reported average
population densities of 0.5 to.4 snails/m2 (range 0.09 to 15.1 snails/m2) for live Utah valvata
colonies in Lake Walcott. The highest density was near Eagle Rock and the lowest density was
recorded between Jackson Bridge and Minidoka Dam. Overall, the Lake Walcott reservoir
average density was 1.8 snails/m2, whereas density averaged 0.5 snails/m2 in the reservoir/spring
sites.
Surveys by Frest and Johannes (1992) in the Nature Conservancy's Thousand Springs
Preserve found average population densities of about 0.25 snails/m2 in two colonies with totals of
about 6,000 snails per colony. Frest and Johannes (1992) believe these colonies were in decline.
Taylor (1985) concluded that sediments deposited in a natural pool in lower Box Canyon from
the construction of an earthen diversion dam upstream in 1973 increased the habitat for Utah
valvata but severely degraded the habitat for the Bliss Rapids snail.
According to Taylor (1982d), this species inhabits large streams and lakes, where it occurs
on mud, fine sand, and silt bottoms. Taylor (1982d) found Utah valvata living on fine silt among
beds of submerged aquatic plants (Potamogeton, Ceratophyllum, Myriophyllum, and sedges) in
the Hagerman Valley. USFWS (1995) reports Utah valvata inhabits pools adjacent to rapids in
the main river or in perennial flowing waters associated with large spring complexes, but avoids
areas of high water velocity and rapids. The snail prefers well-oxygenated areas of limestone
mud or mud-sand substrate among beds of submerged vegetation (USFWS, 1995). Cazier
(1997a) found that this snail burrows into mud/sand substrate and suggested the snail is a
generalist, not a specialist, in terms of habitat requirements. In Lake Walcott during 1997, the
USGS found Utah valvata in 80 of 195 (41%) sites; the snails were present in water depths
7-10
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ranging from 0.8 to 13.8 m. Seventy-five percent (60 of 80) of the sites were at depths greater
than about 3 m (Bureau of Reclamation, 1998).
During 1996-97 field sampling in the Snake River just below Minidoka Dam and in Lake
Walcott, the Bureau of Reclamation (1998) measured six water quality parameters at sites with
Utah valvata. Their observations found this snail living in Lake Walcott under the following
ranges of water quality conditions: water temperatures from 4.5°C (in November) to 18.2°C (in
June); dissolved oxygen from 8.3 mg/L (in June) to 16.1 mg/L (in November); pH from 7.5 (in
November) to 9.0 (in October); specific conductance 334 umho/cm (in June) to 897 umho/cm (in
November); total alkalinity 123 mg CaCO3/L (in June) to 155 mg CaCO3/L (in November); and
total hardness 129 mg CaCO3/L (in June) to 345 mg CaCO3/L (in November). The colony of
snails living in the river below Minidoka Dam was found in similar water quality conditions,
except they were exposed to higher temperatures (19.2°C in August) and lower dissolved oxygen
(6.8 mg/L in August). Water quality conditions required to maintain reproduction and
recruitment for the Utah valvata currently are unknown. However, it appears that this snail is
capable of living in lake or reservoir conditions and does not require cooler, riverine conditions. .
7.3.5. Banbury Springs Lanx {Lanx sp.) .
This mollusc, as with other lancids, appears to feed exclusively on aufwuchs. It occurs
primarily on the lateral and undersides of rocks, but not in contact with the sediment (Frest and
Johannes, 1992). For most of the population, a 1-year life span is typical and adults experience
mortality during the late winter or early spring following reproduction (Frest and Johannes, 1992;
USFWS, 1994). As with other lancids, oviposition likely occurs 1 month after copulation, which
has been observed only in the spring. Eggs of Lanx sp. are laid only on rocks and have been seen
from April through June. The egg capsules are small (no more than 1.5 mm in diameter) with ho
more than 6 eggs per capsule. Juveniles have been observed from May through July and growth
is most rapid between July and October.
The Bliss Rapids snail commonly occurs in association with the Banbury Springs lanx
(Frest and Johannes, 1992). After being first discovered hi Banbury Springs at Rkm 949 (RM
589) in 1988, this lanx (or limpet) was found in two other alcove spring complexes: Box Canyon
Springs near Rkm 946 (RM 588) and hi Thousand Springs near Rkm 941 (RM 584.4) (Pentec
1991; USFWS, 1995). With one possible exception, this species is known to occur only hi these
large, undisturbed springs. With regard to the possible exception, Beak (1987) reported finding
20 individuals of Lanx sp. in the main stem of the Snake River at Rkm 889.5 (RM 552.3).
Subsequent references on the distribution of the Banbury Springs lanx, however, have not
recognized this finding.
7-11
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In a June-July 1991 survey in the Nature Conservancy's Thousand Spring Preserve, Frest
and Johannes (1992) found a small Banbury Springs lanx colony in an area covering roughly 14
m2. The limpets were very sporadically distributed in the area; average densities ranged from 16
to 48 individuals/m2. The total number of adults in the colony was estimated to be between 600
and 1,200 individuals. Descriptions of the colonies hi Box Canyon and Thousand Springs are
not available.
The Banbury Springs lanx is found only in spring-run habitats and avoids areas with large,
attached plants or areas with fluctuating water levels. This species is typically found in water
depths of 15 cm, but it did occur in water as shallow as 5 cm deep. All sites had relatively swift
water currents with mostly smooth basalt boulders having a maximum dimension of at least 7
cm. The Banbury Springs lanx avoids granites and rocks with vesicular textures (all from Frest
and Johannes, 1992). During March 1991 in Thousand Springs, Pentec (1991) reported finding
five live individuals of Lanx sp. on rock substrate estimated to be 25 to 40 cm in diameter at a
location 6 m offshore. This site had a water depth of 40 cm and water currents of 33.5 cm/sec
(facing velocity) and 51.8 cm/sec (0.6 depth velocity).
This lanx is a member of the family Lancidae, a small group of pulmonates that respire
solely through a highly vascularized mantle. As specialized respiratory organs are lacking, the
lancids are particularly susceptible to fluctuations in dissolved oxygen (Baker, 1925; from Frest
and Johannes, 1992). The three sites in Banbury Springs where Frest and Johannes (1992)
collected this species had well-oxygenated, clear, cold (15 °C to 16°C) water. However, Pentec
(1991) measured dissolved oxygen at 6.9 mg/L at the site surveyed in the Thousand Springs.
7-12
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8. ANALYSIS OF EXPOSURE AND EFFECTS FOR AQUATIC PLANTS
8.1. HISTORIC TRENDS
Early works addressing biotic conditions in the Middle Snake River generally ignored
aquatic macrophytes, focusing instead on game fish, chemical water quality, and eventually,
attached benthic algae and benthic macroinvertebrates (Gebhards, 1969; U.S. EPA, 1974; Falter
et al., 1976). These reports made no, or only passing, mention of aquatic macrophytes in tibis
reach. Known high macrophyte density areas in the mid-1970s were hi the shallow upper
reaches of Milner Pool, Box Canyon, and the upstream reach of Upper Salmon Falls Reservoir.
The 8-year extreme low-flow period of 1986-93 undoubtedly exacerbated the long-term trend of
riverbed shallowing and subsequent development of high density macrophyte beds where they
had been little noticed in earlier studies. Idaho Power (1995) assessed macrophytes in the three
reservoir reaches from 1987 aerial photography and found that approximately 20% of Upper
Salmon Falls Reservoir was covered with submerged or floating plant beds. Macrophyte
densities declined downstream hi Lower Salmon Falls and Bliss Pools. Idaho Power described
15 species of macrophytes (including all of the species found by Falter and Carlson, 1994; Falter
et al., 1995; and Falter and Burris, 1996), but did not address epiphytes.
The Federal Energy Regulatory Commission (1990) stated that "...overall, however, plant
production in the study reach (Milner-Star Falls) is very high, especially during the low-flow,
summer irrigation season, when warm water, high nutrients, low flow, and high light provide
ideal conditions for the plants." The Federal Energy Regulatory Commission (1990) commented
that submerged macrophytes occupied 23.4% of Lower Salmon Falls Reservoir, but only 2.1% of
the more turbid Wiley reach. Idaho Power (1990) noted that shallow, low-velocity areas of Bliss,
Lower Salmon Falls, and Upper Salmon Falls Reservoirs supported dense macrophyte
populations, but related their occurrence more to areas "...where spring water enters the main
stem." Idaho Power thought that "aquatic macrophytes hi Upper Salmon Falls and Lower
Salmon Falls reservoirs are more prevalent than would be expected hi a free-flowing system, and
the aquatic plants may affect water quality and recreational value of the reservoirs." Hill (1991c)
delineated macrophyte beds in the Middle Snake River by using aerial photographs and GIS
maps. He found 20% aerial coverage of the river between Crystal Springs and Banbury Springs.
Ceratophyllum and Potamogeton spp. were the dominant taxa. Falter and Carlson (1994), Falter
et al. (1995), and Falter and Burris (1996) described composition, biomass, and sediment
characteristics of the reach from on-ground studies.
8-1
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8.1.1. Phytoplankton
Summer chlorophyll a concentrations in the main river are in the mesotrophic to
eutrophic range, mostly 2 to 20 mg/m3 (2 to 10 mg/m3 for mesotrophy and >10 mg/m3 for
eutrophy as defined for lakes by U.S. EPA, 1990). Using chlorophyll a level for lakes is
reasonable in the Middle Snake because the decreased flows cause the river ecosystem to
resemble lentic dynamics with nutrients being readily available. Mean chlorophyll a
concentrations hi the Crystal Springs reach (3.7 to 12.1 mg/m3) showed little variation with the
exception of the above-the-plant bed site in July. Concentrations were comparable to those in the
Box Canyon reach (1.8 to 19.3 mg/m3). Mean chlorophyll a concentrations in the Box Canyon
reach were hi the mesotropbie range.
Model sensitivity analysis showed the dynamics of phytoplankton hi the Middle Snake
River to be more responsive to hydrology and to initial conditions from upstream sources. There
was little or no correlation between chlorophyll a concentrations and physical or chemical water
quality variables hi the Middle Snake River, with the exception of total Kjehldahl nitrogen
(TKN). Regression analysis showed a positive relationship between TKN concentrations in the
water column and chlorophyll a in both the Crystal Springs and Box Canyon reaches.
The mean chlorophyll a levels hi the river transects below the springs were markedly
lower than hi the main river. Chlorophyll a concentrations ranged from 0.5 to 1.6 mg/m3 for all
below-springs transects. The lowest concentrations were measured along the Box Canyon Spring
transect hi June and August (0.5 mg/m3 for both months). Banbury Springs and the Nature
Conservancy Springs' transects both showed a decrease hi mean chlorophyll a concentrations
from June to August. Concentrations along the Banbury Spring transect dropped from 1.5 to 1.3
mg/m3, and the concentrations along the Nature Conservancy Spring transect dropped from 1.3 to
0.7 mg/m3 from June to August.
8.1.2. Vascular Macrophytes
The most detailed treatment of aquatic macrophytes in the Middle Snake River has been
provided by the studies of Falter and Carlson (1994), Falter et al. (1995), and Falter and Bums
(1996). These studies, however, only addressed the reach from Twin Falls downstream to Upper
Salmon Falls Dam, with most coverage from Crystal Springs reach and Box Canyon reach. The
following information is taken from those studies. These described reaches are believed to
represent the most dense occurrences, but composition and habitat descriptions as well as
macrophyte controlling factors are thought to be representative of the entire Middle Snake reach.
Plant material at all sites during summer in the Crystal Springs reach was dominated by • .
epiphyton (Figure 8-1). Epiphytes made up <1% of the plant community (Table 8-1) early in the
8-2
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Figure 8-1. Snake River at Crystal Springs, July 1992.
Table 8-1. Riverwide mean plant biomass and percent of the total biomass, Crystal
Springs, Idaho, 1994 (from Falter and Burns, 1996)
Apr
May
Jun
Jul
Aug
Oct
Epiphytes,
mean
g/m2
0.1
1.3
231.5
163.4
173.8
214.4
Non-
rooted,
mean
g/m2
34.0
3.6
78.5
25.6
248.9
138.3
Rooted,
mean
g/m2
30.6
230.8 .
239.2
137.1
81.8
104.1
52.9
Total,
g/m2
64.7
235.7
549.2
326.1
504.4
456.7
162.8
Epiphytes,
% of total
0.2%
0.6%
42.2%
50.2%
34.5%
46.9%
38.9%
Nonrooted,
% of total
52.5%
1.5% .
14.3%
7.8%
• 49.3%
30.3%
28.6%
Rooted,
% of total
47.3%
: 97.9%
43.5%
42.0%
16.2%
22.8%
32.5%
All types,
total
100.0%
100.0%
100.0%
100.0%
100.0%
100.0%
100.0%
8-3
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season, but shifted to approximately 50% dominance by midsummer to late fall. Rooted
macrophytes dominated the plant community early in the year, accounting for up to 98% of total
composition in May, before gradually declining as a percent of total composition later in the year.
In August, rooted macrophytes were only 16% of total macrophyte biomass. The epiphyton
component gradually decreased at all sites through the summer.
In the Box Canyon reach, Potamogeton crispus was dominant at above-plant bed and
open-channel sites, ranging from 19% to 47% of total biomass. Epiphyton was virtually absent
from both the open-channel and the above-plant bed sites, but was a dominant component in the
plant bed sites. The exceptions were in the open-channel site in August when P.foliosus was
dominant and at the above-plant bed site hi July when no plants were collected.
In the Thousand Springs reach, macrophyte diversity was higher than in Crystal Springs
and not as dominated by epiphyton. The dominant macrophyte in the littoral plant bed area was
E. nuttallii in July (20%) and C. demersum in August (32%).
Mean percent composition of the aquatic plant community in the springs and in localized
areas of the river channel where water quality is dominated by springs was strikingly different
from that in the main river. Composition of aquatic plant communities hi the alcove springs
along the Middle Snake River is more diverse and balanced than the communities in the main
channel of the Middle Snake River. Epiphyton was still a component of total biomass, albeit a
minor component and not nearly as dominating as in the river, especially in upstream reaches.
There was a much wider variety and evenly distributed array of species represented in the
springs. Myriophyllum spicatum var. exalbescens was present in three of the springs and was
found nowhere else hi the main river. The moss Drepanodacladius sp. (requiring clear, cold
water rich in CO2) and Ranunculus sp. along with M. spicatum var. exalbescens all were found
only in the unique environment of the springs.
Box Canyon Spring had the most diverse macrophyte composition. There were five
species making up 8% or more of the aquatic plant biomass present in June. The plant
community hi the Nature Conservancy Spring also consisted of a broader range of species
compared with the main river reaches.
8.2. DENSITIES OF PLANT COMMUNITIES IN THE MIDDLE SNAKE RIVER
In the early 1990s, plant beds hi the Middle Snake River would develop very high
biomass levels (up to 3,000 g/m2), greater than those considered "nuisance levels" on the Pend
Oreille River, WA (Coots and Willms, 1991; Falter et al., 1991). The results of our survey
(Table 5-2) suggest that 200 g/m2 average maximum biomass as ash-free dry matter (AFDM) is a
reasonable lower bound for nuisance levels of aquatic macrophytes.
8-4
-------
Heavy plant beds in the Middle Snake River are found downstream of agricultural return
flows and/or aquaculture discharges, with the heaviest growths downstream of the combination
of both discharges. In the immediate vicinity of irrigation drain discharges to the river,
sediments are predominantly fine sands and silts. High sediment deposition rates and increased
turbidity hi the first several hundred yards below discharge points preclude aquatic macrophyte
development. After a space of low growth, plant beds increase in size and density. Similarly, the
first 90 to 200 meters downstream of aquaculture effluent discharge points are a sediment
deposit area of fine sands and silts, but with a higher organic content. This immediate area is
generally devoid of plant growth except for about a 0.2-m-thick bed of Cladophora sp. growing
on the sediments. In these latter instances, the anaerobic, reducing nature of the organic-rich
sediments apparently impedes rooted plant growth even though sediment nutrient concentrations
are high. Further downstream, about 90 to 200 meters, very high plant aquatic plant densities
begin to occur. Unless indicated otherwise, the following mean biomass values from summer to
fall 1992 are derived from three to eight replicate samples per area or transect.
Summary plant biomass values in the Crystal Springs reach show the following summer-
long downstream trend of site means:
Above-plant bed (upstream end of reach) - 348 g/m2 *
Left channel (mid-reach, in plant beds) - 784 g/m2
Right channel (mid-reach, in plant beds) , - 772 g/m2
Top-of-plant bed (downstream end of reach) - 1,551 g/m2
Bottom-pf-plant bed (downstream end of reach) - 1,141 g/m2
* Only littoral (<2.0 m depth) samples were included in all means in this data set.
Summer mean plant biomass increased fourfold downstream through the 2.9-km
(1.8-mile) Crystal Springs reach. The highest mid- and downstream densities were below a
series of aquaculture effluent discharges. No other effluents came into this (2.9-km) 1.8-mile
reach during the sampling years. Means were also significantly different between the top and the
bottom of the plant bed.
Table 8-1 summarizes 1994 aquatic macrophyte mean dry biomass over all transects and
months (Falter and Burris, 1996) for the Crystal Springs reach. The dry weights in g/m2 are
overall river means, separated into three functional groupings: epiphytic algae, nonrooted
vascular macrophytes, and rooted vascular macrophytes. Epiphytic algae and nonrooted vascular
macrophytes may be considered functionally grouped, as they absorb their nutrients from the
water column rather than from sediments. The following overall river means are true average
concentrations over the entire river, plant-covered and plant-free areas alike, and are more
appropriate for use in a river ecological model that considers the entire river bottom.
8-5
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Biomass of all plant types combined (i.e., mean total aquatic macrophyte biomass) in
Crystal Springs reach increased from 65 g/m2 in April to an average of 459 g/m2 in the summer-
fall months of June, July, August, and October. Biomass fell to 163 g/m2 in November. High-
biomass months were June and August with 549 and 504 g/m2 mean biomass, respectively.
Epiphytes followed a similar trend, increasing from <1 g/m2 in April to a summer-fall mean of
196 g/m2 (June to October). High epiphyte months were June and October, with 232 and 214
g/m2 mean biomass, respectively. Nonrooted vascular macrophytes developed later in the
season, averaging only 35 g/m2 April through July to an annual peak mean of 249 g/m2 in
August. True rooted macrophytes developed first, attaining an average of 231 g/m2 by May
before steadily declining to 53 g/m2 in November.
Mean aquatic plant biomass hi the Box Canyon reach, a slightly deeper site than Crystal
Springs, followed a different pattern., Mean biomass in the Box Canyon reach above-plant beds
site was near zero for June and July. Mean biomass at the above-plant beds site increased to 14
g/m2 in August, a time when water transparency had increased to 2.0 m. Mean aquatic plant
biomass hi the open channel decreased gradually through the summer from 31 g/m2 to 20 g/m2.
Plant biomass in these two sites would be expected to be less than in Crystal Springs because of
greater mean depths in Box Canyon. Mean aquatic macrophyte biomass in the plant bed in June
was about 225 g/m2 and increased to 337 g/m2 in July. Aquatic plant biomass hi the plant bed
decreased sharply in August to a mean of 68 g/m2.
Aquatic plant biomass in the shallower Thousand Springs reach was higher than in Box
Canyon. Mean biomass hi the littoral plant bed area hi July was 314 g/m2, increasing to 483 g/m2
hi August.
Mean aquatic plant biomass hi the river transects at the springs showed wide cross-
channel biomass variation as water quality gradients changed in very short distances across the
river. Lowest biomass measurements were from Blue Heart Spring transect for both June and
August (13 and 102 g/m2 Respectively). Highest biomass measurements from spring transects
were hi June (345 g/m2) and August (876 g/m2). The remaining two transects, Banbury and
Nature Conservancy Springs (immediately upstream, and contiguous to Box Canyon and
Thousand Springs reaches, respectively), had August biomass means (612 and 478 g/m2,
respectively) that were as high or higher than those in the Box Canyon and Thousand Springs
reaches (337 and 483 g/m2, respectively).
Blue Heart Spring (Figure 8-2) transect had mean plant biomass values of 56 g/m2 in
June and 97 g/m2 hi August. Box Canyon Spring transect had plant biomass values of 1,376 g/m2
hi June and 961 g/m2 hi August. Banbury Spring transect had plant biomass values of 79 g/m2 in
June and 1,885 g/m2 hi August. The Nature Conservancy Springs transect had plant biomass
values of 776 g/m2 hi June and 777 g/m2 hi August.
8-6
-------
Figure 8-2. Blue Heart Springs with Box Canyon in the
background, Middle Snake River, August 1993.
Mean plant densities in the mid-1990s studies were generally lower in springs than in the
river, even with the very clear water (Falter and Carlson, 1994; Falter et al., 1995; and Falter and
Burris, 1996). Cross-river transects at the springs showed that Blue Heart, Box Canyon,
Banbury, and Nature Conservancy Springs in the Middle Snake River were all high water quality,
cold-water habitats of significantly lower mean water column and sediment nutrient
concentrations than the main channel of the Middle Snake River.
8.3. FACTORS CONTROLLING PLANT GROWTH, BIOMASS, AND DIVERSITY
There are many environmental variables that both shape plant communities in the Middle
Snake River and are shaped by the plant communities.
Correlation of total aquatic macrophyte biomass with the physical variables of depth,
temperature, and velocity did not show significant relationships. By including Ceratophyttum
demersum with the epiphyte component, a strong relationship was identified between the
epiphytic portion of total aquatic macrophyte biomass and water velocity. This grouping was
'based on the fact that Ceratophyttum demersum does not have a well-developed root structure
and obtains its nutrients in a fashion similar to filamentous epiphytic algae, i.e., from the water
column (Kennedy and Gunkel, 1987).
8-7
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Plant biomass values were significantly related to soluble reactive phosphorus (SRP) only
in the Crystal Springs reach. The correlation was observed in both linear and second degree
polynomial models (Falter and Bums, 1996). The second-degree polynomial demonstrated a
significant correlation (negative) between plant biomass and SRP (r2 = 0.51, F = 31.39, n = 64) hi
the Crystal Springs reach.
In the Middle Snake River, as in most aquatic macrophyte situations, there is generally
poor correlation of dissolved nutrients to aquatic plant biomass. Notable exceptions are soluble
reactive phosphorus in the Crystal Springs reach and nitrite/nitrate in the Thousand Springs
reach. The reason for this poor correlation is the inherent complexity of aquatic systems. A
rooted macrophyte may well draw the majority of its nutrient needs from the sediments most of
the time, but when other aspects of the system are also considered, it is apparent that high-water-
column nutrients eventually result in higher macrophyte coverage, both in terms of growth rates
and aerial coverage. There are several major considerations:
• Rooted macrophytes do not exist hi a vacuum, but in a complex community of many
plants with different nutritive strategies.
• Epiphyte cover on the rooted plant (both unicellular and filamentous) absorbs
nutrients from the water column and builds sediments upon the plant's senescence.
• Epiphytes can pass nutrients to foliar surfaces of their supporting plants.
• Nonrooted vascular macrophytes absorb nutrients from the water column, build
biomass, and contribute to building nutrient-rich sediments supportive of rooted
macrophytes. .
• A matrix of aquatic macrophytes, whatever mix of rooted, nonrooted, or epiphytes,
filters planktonic algae and nutrient-rich detritus from the water column, building
sediments for further nutrition of rooted macrophytes.
True rooted macrophytes developed earlier in the year (May) than nonrooted and
epiphytic macrophytes hi the Middle Snake River. It is likely that the nutrient and energy
reserves of the perennial root masses permit earlier, faster plant development than in epiphytes
and rootless plants. Epiphytic algae cannot reach high biomass levels until June, when epiphytes
can obtain three required conditions: (1) high enough temperatures (Millner et al., 1982), (2)
sufficient nutrients from the water column, and (3) adequate physical support provided by rooted
plants high enough in the water column to obtain their required high light nearer the water
surface. By midsummer, the combined community of epiphytes and nonrooted macrophytes
apparently outcompetes rooted forms. The faster rates of nutrient uptake by the entire nonrobted
plant and the light-favored position higher in the water column permit epiphytes to avoid light
8-8
-------
limitation and ensure their success. Considering their absence of nutrient-absorbing roots, the
epiphytes and nonrooted forms, which are dominant hi late summer and fall, can only attain high
biomass levels with high-water-column nutrients. Howard-Williams (1981) found that
fertilization with N and P sharply increased the development of epiphytes (Cladophora) on P.
pectinatus communities, but did not increase the rooted plant biomass.
Low nutrient thresholds of sediment TKN, sediment phosphorus, and water column SRP
probably dictate low nutrient limitation for controlling plant biomass; high nutrient thresholds of
sediment TKN are related to other direct controllers of plant biomass, i.e., anaerobic sediments,
high sediment levels of ammonia, hydrogen sulfide, and carbon dioxide (Falter and Carlson
1994, Falter and Burris 1996). This would explain the near absence of most macrophytes
(except for Cladophora spp) in areas of the Middle Snake River accumulating organic sediments
from aquaculture facilities. Barko (1983) similarly found that high-level accumulations of
organic matter in sediments inhibited milfoil growth. He concluded that the low redox
potentials, accumulations of organic acids, low pH, increased metal availability, and evolution of
growth-inhibiting gases in highly organic sediments overshadowed the high fertility provided by
a high-organic-matter and high-nutrient environment.
The distribution of vascular macrophytes in the Middle Snake River is controlled
primarily by available light, which in turn is controlled by water clarity and depth, sediment
particle size, sediment nutrient concentrations, and water velocity. Also, the plant beds
themselves have a major feedback role in creating desirable water velocity and sediment
conditions. Water column nutrient concentrations contribute to this process via the mechanisms
described above. Plant beds occur in the Middle Snake River only where water depth is < 6 m.
Heaviest plant densities were hi the 0.5 to 2.0 m depth range over flat to very gently sloping
bottom. Water velocities in the 0 to 1.0 meters per second (mps) range were ideal for plant
development. At deeper depths, light availability is apparently the limiting factor to occurrence
of significant plant beds. Where depth is not limiting, water transparency > 0.7 m is required for
significant development of plant beds. Moderate to high turbidity levels in the main river often
limit high plant production in the channel. In waters of < 6 m, ideal sediment conditions for
plant development are where sediments are in the fine sand-silt-clay range of particle size.
Given the above conditions; true rooted vascular macrophytes may start as an island of
rooted stems, even in high water velocity as with Potamogeton pectinatus. As the plant bed
develops in size and stem density, intrabed conditions are increasingly shaped by the plant
community as described above. In the protected "nursery" environment within a bed, low-
velocity-preferring forms such as Elodea and Ceratophyllum (nonrooted plants) can then
develop. Floating epiphytes seem to do best at intermediate water velocities in the Middle Snake
River. In the heavier plant beds, water velocity drops to near zero compared with 0.5 to 1.0 mps
8-9
-------
in open channels only several decimeters away. Near-bottom velocities are especially low,
permitting further settling of fine particles.
In 1993 and 1994, Falter et al. (1995) and Falter and Burris (1996) found sediment total
phosphorus in the Middle Snake River to be strongly related to plant biomass. Maximal plant
biomass occurred at a total phosphorus level of approximately 1,100 mg/g dry weight. This trend
was seen throughout areas in the Middle Snake River where sediment composition was studied.
With the higher sediment phosphorus levels hi downstream transects (up to and beyond 1,000
mg/g), plant biomass increased to peak levels observed. Biomass tended to decline at sediment
phosphorus >1,100 mg/g. There were well-defined upper limits of sediment organic matter
(4.0%) and sediment nitrogen (0.35%) above which macrophyte densities declined. High
concentrations of nutrients are not likely to directly cause plant biomass decline. The direct
limiting factors are likely other parameters associated with extremely high sediment nutrients and
organic matter, i.e., low sediment oxygen, redox potential, and pH; and higher ammonia,
hydrogen sulfide, hydrogen (i.e., reduced organic matter), organic acids, and carbon dioxide
levels.
8.4. EFFECTS OF EXCESS GROWTH ON THE MIDDLE SNAKE SYSTEM
INCLUDING EUTROPfflCATION
Diel oxygen levels may fall below 6.0 mg/L with pH sometimes >9.0 in heavy plant beds,
but oxygen stress has not been documented in these dense Middle Snake plant communities.
Plant densities may be high enough so that significant nutrient depletion may be seen from
upstream to downstream within some of the heavier plant beds, such as Crystal Springs and Box
Canyon (Falter and Carlson, 1994; Falter and Burris, 1996).
In the Crystal Springs reach of the Middle Snake River, total phosphorus (TP) declined at
a rate of 0.22 mg/L/kilometer from upstream to downstream through a dense, mixed-species
plant bed in August, which was the month of maximum standing crop (Falter et al., 1995). At
that tune, SRP declined at a rate of 0.04 mg/L/km through the same plant bed. SRP increased
downstream through macrophyte beds in response to reach loading in June and November,
months of low plant density, but sharply decreased downstream through plant beds in July,
August, and October, months of high density. These observations show that Middle Snake River
plant beds were clearly removing TP and SRP from the water column at times of high plant
densities. The nutrients do not leave the river, but are stored in the plant material. During
senescence, leaching nutrients contribute to the cycle of excessive growth.
Mean aquatic plant biomass (oven dry weight) was highest in the Crystal Springs reach,
with mean values for some sites in excess of 2,000 g/m2 (Falter and Carlson, 1994; Falter et al.,
1995). No sites in any of the other reaches approached this level. The next highest biomass
8-10
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measurements were from Box Canyon Springs proper. The distribution of macrophytes within
the reaches was uneven and limited to waters < 4.0 m deep. There were some exceptions with
macrophytes growing in waters > 4.0 m depth. These exceptions included the Box Canyon and
Thousand Springs sites where sparse growths of Potamogeton crispus occurred in waters up to
6.0 m deep.
Mean sediment TKN and TP were highest in the Crystal Springs reach. Aquatic plant
biomass was up to eight times greater in the Crystal Springs reach than in any other site. Very
high sediment nutrient concentrations (TKN and TP) are also found in the Snake River proper at
the head of Upper Salmon Falls Pool (Falter and Carlson, 1994; Falter et al., 1995). Sediment
nutrient and TOC (total organic carbon) levels in the pools were lower than in the adjacent
shallower reaches. This reflected sediment trapping by macrophytes hi the upstream shallow
plant bed reaches.
The combination of deep, fine, and nutrient-rich sediments downstream of those areas in
the Middle Snake River receiving organic and nutrient loading favors macrophytic plant growth.
Once beds develop in these regions, internal water velocities are slowed, resulting in further
sediment deposition. The end result is that sediments beneath plant beds in the Middle Snake
River are fine (<6 mm), nutrient-rich, organic-rich, and oxygen-stressed. The percentage of very
fine (<75 p,m) sediment particles in the plant beds is even greater than in the deeper pool areas.
Probing of sediments beneath plant beds in the Crystal Springs found up to 3 m of fine sediments
overlying a cobble stream bed (Falter and Carlson, 1994; Falter and Burris, 1996);
Initial deposition of sediments is key to the high levels of macrophytes observed in the
early- and mid-1990s. Deposits of fine, largely inorganic sediments, mostly from irrigation
return flows, cause shallowing of extensive reaches until water depths approach approximately
2 m. At that point, sufficient light reaches the bottom to support macrophyte growth. These
macrophyte growths, as dense plant beds, trap sediments and detritus from the water column,
enriching sediments with organic matter and nutrients. By midsummer, very thick epiphytic
algae mats develop on the vascular macrophytes, taking advantage of water column nutrients in
the enriched river to further build plant biomass. This epiphyte biomass is later incorporated into
sediments, supplementing nutrient levels at a time when rooted plant uptake has started to
deplete sediment nutrients from the root zone. Through this late-summer high-growth period,
however, sediment nitrogen and phosphorus concentrations decline slightly, apparently a result of
plant uptake. During this period, hi the bottom areas devoid of plants, nitrogen and phosphorus
concentrations continue to build through the fall (Falter and Burris, 1996). The fall senescence of
some plants (such as the early-fading P. crispus) enhances the environment for continued plant
bed succession.
8-11
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An important result of these plant beds in the Middle Snake River is the overall slowing
of organic carbon turnover rates. Thomas et al. (1995) found that despite very high rates of
respiration in the Middle Snake River, which are 1 to 2 orders of magnitude higher than the
Kootenai River, the river was turning over its organic carbon pool very slowly, in fact at about
10% of the rates measured in the Kootenai River. This indicates that intense carbon utilization
occurred, as might be expected in a system receiving allochthonous loadings. Turnover time for
carbon is the time required for the average carbon molecule to pass from being fixed in
photosynthesis to being released via oxidative decomposition. This indicates intense trapping of
detritus, energy, and nutrients in the Middle Snake River, a process facilitated by the sediment
deposits and abundant, dense plant beds. The classic downstream nutrient spiral from water
column into biota and back to the water column is thereby shortened in the Middle Snake River,
with intense cycling within plant beds and less flow of nutrients or organic carbon downstream.
8-12
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9. RISK CHARACTERIZATION
Risk characterization is the final phase of the ecological risk assessment. At this point,
the lines of evidence and likelihood of recovery for each assessment endpoint are summarized.
The sources of uncertainty and the likelihood of recovery for each assessment endpoint are
described. Finally, conclusions are drawn for the entire ecosystem including all assessment
endpoints.
9.1. SUMMARY OF RISKS TO THE ASSESSMENT ENDPOINTS
This section reviews the risks to the assessment endpoints by summarizing the lines of
evidence and evaluating the likelihood of recovery.
9.1.1. Reproduction and Survival of Rainbow Trout
9.1.1.1. Lines of Evidence
The most critical factors limiting rainbow trout growth and survival include elevated
water temperatures, irregular flows, and excessive sedimentation (Table 9-1). Lines of evidence
supporting this conclusion include the frequency of exceeding standards for dissolved oxygen
and temperature (Table 5-4), estimates of areas meeting habitat suitability indices (Figure 5-4),
and field studies in the Middle Snake River and in other areas.
The frequency with which simulated dissolved oxygen falls below the standard for
spawning for rainbow trout (Table 5-4) ranged from 0.19 to 0.58, i.e., from 19% to 58% of the
time during the January 15 to July 15 spawning period. The frequency of exceeding the
temperature standard for spawning was somewhat higher, ranging from 0.58 to 0.80, mainly
because of a spawning season that extends into the summer months.
The risks to all life stages of rainbow trout from unacceptable habitat conditions were
high throughout much of the Middle Snake River. These estimates of risk are based on habitat
indices derived from water velocity, depth, and temperature and substrate type (Figure 5-4).
Some areas with improved habitat are located just below the mouth of Rock Creek, in the reach
between Kanaka Rapids and Crystal Springs, near Box Canyon, and below Bliss Dam.
Field work by Hill (1991c) demonstrated that spawning habitat for rainbow trout in some
segments of the Middle Snake River has been adversely affected by sedimentation and high
temperatures. Sedimentation clogs spawning gravels and reduces dissolved oxygen needed by
developing embryos. A comparison to similar conditions in the Spokane River indicated that
year-class strength in a native population of rainbow trout in the Spokane River was positively
correlated with spring water flows.
9-1
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9-2
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Other factprs that may affect native trout survival include competition from and
hybridization with planted hatchery-reared rainbow trout.
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9.1.1.2. Likelihood of Recovery
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Without substantial changes in the management of flows in the Middle Snake River, the
outlook for wild native rainbow trout appears bleak. Considering the habitat requirements
discussed by Behnke (1992) and our estimation of the impairment of spawning, rearing, and adult
habitat, the Middle Snake River cannot support a viable rainbow trout population. It is widely
known that flow and water temperature have the most environmental influence on trout
populations (Behnke, 1992), but management of the river to improve these conditions for these
s
species has not occurred. Incremental improvement of rainbow trout habitat may be possible if
potential spawning and rearing habitats hi the river are identified, protected, and enhanced by
water and land usp management. The underlying question, however, is how many adult fish this
system can support. In smaller rivers, native trout have returned and displaced warm-water
species after their! habitat was improved. Other studies (Partridge and Corsi, 1993; Lukas et al.,
1995) found some suitable habitats in and near springs. However, these areas may not provide
spawning and rearing habitat at levels that would sustain a population of native rainbow trout hi
the Middle Snakd River.
9.1.2. Reproduction and Survival of the Mountain Whitefish
9.1.2.1. Lines of Evidence
The most important factors limiting the recovery of the mountain whitefish population hi
the Middle Snake! River appear to be high water temperatures, loss of lotic habitat, fluctuating
water flows, and sedimentation (Table 9-2). The evidence for these effects is demonstrated by
evaluating favorable spawning conditions (<7°C during a 75-day spawrting-incubation window)
at two locations in the river from 1970 to 1994 (see p. 8-6, Effects on Spawning Activities),
comparison with habitat suitability indices (Figure 5-5), and review of the literature.
The evaluation of water temperatures during the spawning season at two locations, above
and below the Thousand Springs Complex, showed that favorable spawning conditions did not
occur from 1970 to 1994, whereas the frequency with which simulated temperature exceeded the
standard (no greater than 9°C) for spawning for mountain whitefish (Table 5-4) ranged from 0.05
to 0.22 (5% to 22% of the tune) during the spawning season. The implication here is that water
quality standards may not be adequate to protect the optimum spawning requirements for this
fish.
9-3
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9-4
-------
The evaluation of the frequency with which simulated dissolved oxygen exceeded water
quality standards (>90% saturation) during the spawning season for this fish ranged only from 0.01
to 0.11 (Table 5-4}. Low dissolved oxygen is not an issue because these fish spawn during the
winter when saturation levels for dissolved oxygen are high.
The risk estimates for mountain whitefish based on habitat suitability factors (water
velocity, depth, and temperature and substrate type) show high impairment for all life stages
(Figure 5-5). The [least impairment occurred for the adult stage in the reach from Thousand
Springs to Lower Salmon Falls. This may be due to variation in the sources of water to the river,
where intrusions of cool, clear water alleviate the adverse effect of low flow and increased
sedimentation.
i
Other factors such as competition with other sahnonid species for any available habitat left
in the Middle Snake River do not appear to limit mountain whitefish populations. Across their
range in North America, mountain whitefish coexist and may compete with several other fish
species. i ,
9.1.2.2. Likelihood of Recovery
Similar to the native rainbow trout, the recovery potential for mountain whitefish in the
f
Middle Snake River is low. Mountain whitefish hi this area face serious habitat deficiencies,
including poor spawning and rearing conditions, reduction and alteration of food sources, and loss
of free movement jto feeding and overwintering areas. The loss of lotic habitat, fluctuating water
levels, poor water'quality/quantity, and restriction offish movement are associated with dam
construction and operation. Some of these impacts may be lessened by changing the way the dams
are operated, but there appears to have been a net loss of habitats for all life stages of the mountain
whitefish that cannot be mitigated.
Some spawning and rearing habitat in adjacent tributaries has also been altered or destroyed
by land and waterj use operations and activities. These tributaries provide valuable refuge for
mountain whitefish and need to be protected to maintain existing populations and for any possible
recovery. '
Other factors, in combination with previously discussed impacts, may also contribute to the
low numbers of mountain whitefish in the study reach. For example, this reach is below the
elevation range (l',370 to 2,225 m) where this fish is usually found in other parts of its range in the
western United States. •
9-5
-------
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9-7
-------
9.1.3. Reproduction and Survival of the White Sturgeon
9.1.3.1. Lines of Evidence
Factors limiting the growth and survival of the white sturgeon population in the Middle
Snake River are characterized in Table 9-3. The main factors affecting white sturgeon appear to
be unfavorable spawning and incubation conditions due to high water temperatures and/or low
flows, the loss of spawning and rearing habitat, and low recruitment owing to a.low number of
spawning fish in some reaches. It is also possible there is increased egg-larval stage mortality
due to predation and disease. The evidence linking these factors to white sturgeon growth and
survival are the habitat suitability indices (Figure 5-6), frequency of exceeding temperature
standards (Table 5-4), and field and laboratory studies reported in the literature.
Risk estimates based on habitat suitability indices showed the lowest survival for life
stages from spawning through larval development in the reach above Lower Salmon Falls Dam
(Figure 5-6). In comparison, juvenile and adult habitat has the lowest impairment from the Box
Canyon reach downstream to King Hill. An analysis of habitat suitability indices was not
completed for the reach from King Hill to C. J. Strike, where the main white sturgeon population
resides.
The frequency that simulated values of water temperature exceeded Idaho's water quality
standards (for cold-water biota, Table 5-4) ranged from 0.01 to 0.20 (i.e., up to 20% of the time
during the year). The river areas having greater exceedances were from Milner Dam to Kanaka
Rapids and below Bliss Dam (Table 5-4). It is important to note that the water quality standard
used in this analysis, a maximum daily average of no greater than 19°C, falls in the range (18°C-
20°C) where substantial mortality occurs to the embryonic stages of the white sturgeon (Wang et
al., 1985,1987). Therefore, the risk of adverse effects to the developing stages of white
sturgeon is likely to occur much more than 20% of the time. Similar to whitefish, the water
quality standard applied in the Middle Snake River does not appear to be adequate to protect the
spawning requirements of the white sturgeon.
Other factors listed in Table 9-3, with more information, may prove to be more important
than presently considered. For example, Chandler and Lepla (1997) believed that spawning
activity immediately below CJ. Strike Dam was potentially adversely affected by daily block
loading at the dam. Block loading at C. J. Strike Darn occurs when the dam is operated to follow
peak power loads. This generally results in a sudden increase followed by a sudden decrease in
water flows in the morning and evening each day. The change in water flow associated with
block loading effectively reduces spawning habitat for the white sturgeon. It is not known
whether block loading at Bliss Dam has any adverse effects on white sturgeon spawning habitat
in the King Hill reach.
9-8
-------
It is unknown how many, of the approximately 5,200 white sturgeon planted in the Middle
Snake River between C. J. Strike Dam and Shoshone Falls will survive and reproduce. The
overall success of these fish plants has not been determined. Observations by Lepla and
Chandler (1995a,b) showed that hatchery fish stocked below Lower Salmon Falls Dam were
entrained through Bliss Dam, but with unknown turbine mortality. It also appears that hatchery
fish may not be adjusting to the conditions in the Middle Snake River, as noted by their
significantly lower condition factors when compared with similarly sized wild fish in the Bliss
reach (Lepla and Chandler, 1995a).
Factors other than those discussed above may also be affecting the growth and survival of
the white sturgeon1 population in the Middle Snake River. These factors include mortality of
juvenile sturgeon passing over or through the turbines at dams, disease, and exposure to
riverborne contaminants.
!
9.1.3.2. Likelihood of Recovery
If the white sturgeon populations in the Middle Snake River are to be restored to levels
capable of sustaining some level of recreational harvest, habitat and flow restoration will be
required. White sturgeon evolved to depend on unrestricted spring freshets on an annual basis as
spawning cues. Recovery would require difficult choices regarding restoration of flows for long-
term spawning and rearing success. Flow management is possible, as the water temperatures and
flows needed for successful spawning are generally known. Maintaining these conditions will
require further information on the survival of year classes reared under different or poorer
conditions. For example, some spawning activity was observed in 1993 in the Bliss reach at
flows less than 283 m3/s (10,000 cfs), but it was followed by an incubation window with water
temperatures unfavorable for larvae survival. Further, potential and existing rearing areas for
white sturgeon need to be identified in each reach. If recovery is to be successful, the rearing
areas need to be enhanced by restoration of spring freshets/ These areas also need to be protected
by land and water use planning on a long-term basis.
9.1.4. Reproduction, Survival, and Diversity of Macroinvertebrates
9.1.4.1. Lines of Evidence
The lotic invertebrate fauna of the Middle Snake River have been affected by dam -
development for hydroelectric power and irrigation, flow reduction, water quality deterioration,
and the presence of the New Zealand mudsnail (Potamopyrgus antipodarum), an exotic species.
In general,! the endemic mollusc populations in the Middle Snake River appear to have
declined from historical abundances and have become more localized in distribution. It is clear
that no single river habitat favors the existence of all the species. For example, the Snake River
• : 9-9
-------
Physa requires deep, swiftly flowing water whereas the Utah valvata inhabits pools and
macrophyte beds with sediments of sand and silt (Figure 9-1). Declines in mollusc populations
are likely due to loss of much of the original habitat heterogeneity in the Middle Snake River
following multiple impoundments of the Snake River. Historically, this heterogeneity facilitated
the co-occurrence of molluscs with very disparate habitat requirements. Once-common river
habitat features in the Middle Snake River, such as large rapids and cascades, are now rare
habitat "islands" often separated by nearly lentic environments.
The probability of exceeding limits of temperature (<22°C, or maximum daily average of
19°C) for cold-water biota (Table 5-4) is an indication of the areas in the Snake River that are not
likely to support the growth and survival of native cold-water macroinvertebrates. The current
state of the macroinvertebrate community itself is evidence that the temperature needs of native
macroinvertebrate communities are not being met.
9.1.4.2. Likelihood of Recovery
Improvement of the macroinvertebrate community (e.g., greater taxa richness, the
presence of pollution-intolerant taxa, and sustainable populations of endemic molluscs) is
unlikely to occur without substantial improvement of in-stream habitat conditions. Such
improvements include reduced water temperature, reduced sediment loads, and increased water
velocities (Tables 9-4 and 9-5).
Zone of increased
aeration and
sediment flushing,
and decreased
temperature
\j\jater
—-
Pool RAPIDS
macrophytes
^^^ '
Gravel Gravel
_.._ils
Sediment
Pool
macrophytes
Sediment
Figure 9-1. Factors controlling molluscs survival in the Middle
Snake River.
9-10
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9-12
-------
It appears that several tributaries to the Middle Snake, as well as some downstream
locations, contain bpecies of aquatic insects not currently found in the Middle Snake River.
Should in-stream conditions improve within the Middle Snake River, these outside populations
would likely serve as a source of colonists for the Middle Snake River. Thus, given
improvement in the water quality and benthic habitat of the Middle Snake, the potential for
recovery of aquatic insects is high.
The recovery of mollusc populations also is dependent upon improved habitat conditions
in the Middle Snake River. However, the recovery potential for these organisms is not as great
i
as that for aquatic insects because:
• dispersal, particularly in an upstream direction, is limited;
i, ...
• source populations for molluscs are not as large or widespread as those for
aquatic insects; and
• genetic diversity within the source populations may have been reduced.
9.1.5. Growth and Diversity of Phytoplankton, Macrophytes, and Epiphytes
9.1.5.1. Lines of Evidence
9.1.5.1.1. Phytoplankton. Plankton chlorophyll a values Would classify the Middle Snake River
as eutrophic when| rooted plants are low and meso-eutrophic when rooted plants are dense.
Sediment nutrients, dissolved nutrient levels, and aquatic plant biomass all indicate that the river
is more eutrophic than indicated by the phytoplankton chlorophyll a levels.
9.1.5.1.2. Macrophytes and epiphytes. The risk that total macrophyte and epiphyte biomass will
exceed 200 g/m2, established as the standard for this study, is high at the Crystal Springs to
Boulder Rapids reach on the basis of the simulation. A review of the literature supports this risk
r
estimate. Densities measured in the Crystal Springs, Box Canyon, and Thousand Springs reaches
all compared with| or exceeded, levels measured hi other systems classified as eutrophic (Nichols
and Shaw, 1986; Kennedy and Gunkel, 1987; Anderson and Kalff, 1988; van Wijk, 1988; Falter
et al., 1991; Urbanc-Bercic and Glejec, 1993). The evidence that nutrients are high is also
substantiated by simulations that show that the likelihood of exceeding a phosphorus limit of
0.075 mg/L is extremely high between Rock Creek and Crystal Springs because of the total
phosphorus load from the City of Twin Falls STP, fish hatcheries, and irrigation returns (Figure
5-1). Again, as with other water quality parameters, the nutrient concentrations decrease below
Bliss Dam because bf spring inflows (Figure 5-2).
These exceptional growths were possible because of sedimentation and shallowing of the
water depth along
with concomitant nutrient enrichment of sediments and the water column.
Once that physical/chemical set of precursor conditions was in place, a low-flow year such as
9-13
-------
1992 resulted in very high levels of aquatic plant development, in particular heavy growths of
epiphytes. Slightly higher summer flows in 1993 and 1994 altered macrophyte development,
especially by reducing early-season epiphyte development.
As in most water bodies, the dominant controlling factors of the attached plant
community in the Middle Snake River are water depth and clarity (both controlling available
light), substrate composition, substrate nutrient content, and water velocity. Ideal combinations
of these dominant controlling factors are shallow, clear, slow waters over fine, nutrient-rich
sediments (Table 9-6). Given ideal conditions of these factors, nutrient concentrations of
overlying water may further enhance plant communities, especially nonrooted forms.
The majority of plant biomass hi the Middle Snake River is found in water less than 2 m
in depth. Except for the higher velocity rapids and narrow intra-plant-bed open channels, water .
velocities in the Middle Snake River are generally less than 1 m/sec, within the optimal velocity
range for submerged aquatic macrophytes (Haslam, 1978; Biggs, 1996). Alcove springs (springs
discharging from the lower canyon walls along the Snake River banks) are common along the
Middle Snake River below Twin Falls. These springs discharge about 170 mVs (6,000 cfs) year-
round to the river. Exceptionally clear waters (Secchi disk transparency > 10 m) and cool water
of the springs influence the river channel for a distance downstream of the springs. This
combination of a constant water environment and the increased transparency of the water
downstream of the springs/river confluences provides optimal conditions for attached plant
growth.
The process of macrophyte development begins in sediments that are predominantly fine
sands and silts. These sediments cause shallowing of extensive reaches until water depths
approach approximately 2 m. At that point, sufficient light reaches the bottom to support
macrophyte growth (Figure 9-2). If the sediment organic load is too high, macrophyte growth
will be inhibited: As the density of the plant bed increases, more sediments are trapped along
with nutrients.
Epiphyte biomass is later incorporated into sediments, supplementing nutrient levels at a
time when rooted plant uptake has started to deplete sediment nutrients from 'the root zone.
Epiphytic algae cannot reach high biomass levels until three required conditions are met: (l)bigh
enough temperatures (Millner et al., 1982), (2) sufficient nutrients from the water column, and
(3) adequate physical support provided by rooted plants high enough in the water column to
obtain their required high light nearer the water surface. By midsummer, the combined
community of epiphytes and nonrooted macrophytes apparently outcpmpetes rooted forms.
9-14
-------
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Nutrients
sediment
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Sediment
deposition
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Figure 9-2. Factors controlling aquatic plants in the Middle
Snake River.
By including Ceratophyllum demersum with the epiphyte component, a strong
relationship was identified between the epiphytic portion of total aquatic macrophyte biomass
and water velocity. This grouping was based on the fact that Ceratophyllum demersum does not
have a well-developed root structure and obtains its nutrients in a similar fashion to filamentous
epiphytic algae, i.e., from the water column (Kennedy and Gunkel, 1987).
9.1.5.2. Likelihood of Recovery
Growth of macrophytes as simulated by the model (Figure 5-3) is predicted to exceed
"nuisance" levels, characterized by a maximum biomass greater than 200 mg/m2 (ash-free dry
matter). Such growth is highly probable, especially in low-flow years, as long as current
management practices continue.
The likelihood of recovery is dependent upon the availability of clear, cold water, with
high flows capable of scouring out long-deposited sediments. Spring water is one source of
clear, cold water. The composition of aquatic plant communities in the alcove springs along the
Middle Snake River is more diverse and balanced than in the communities in the main channel of
the Middle Snake River. This is an indication of the type of plant community that the river
would support if the excess levels of nutrients and sediments were diminished and flow patterns
followed the natural hydrograph.
9-16
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As to the eyentual outcome of continued enrichment, Moss (1976) concurred with the
general observations of sewage and fish pond managers that continued nutrient enrichment to
hypereutfophic ranges of limiting nutrients will.push the community through rooted macrophyte
dominance and epiphyte dominance, attaining phytoplankton dominance with eventual complete
suppression of the' macrophyte community.
. i '
9.2. SOURCES OF UNCERTAINTY
One of the [goals of ecological risk assessment is to describe all sources of uncertainty.
Sources of uncertainty in this assessment stem from the simulation model and qualitative analysis
. f
of .effects due primarily to the lack of knowledge about the specific life histories of species in the
[
Middle Snake River. For the qualitative analysis, there is limited information on the native
macroinvertebrateispecies. Without site-specific data, the analysis is based on similar species,
I
genera, or even members of the. mollusc family. This information is evaluated by scientists with
expertise in the field of macrqinvertebrate ecology. Their judgment is biased according to their
experience and education. In addition, their analyses often include a review of field studies
where measurement error can bias the results.
A mathematical model was used to simulate ecosystem dynamics in the Middle Snake
River from RJkm 1,028 to Rkm 877.6 (RM 640 to 545.5) for the period from January 1, 1990, to
December 31, 1994. As part of the uncertainty analysis, surface water quality results were
compared with water quality collected at various locations in the river by the University of
Idaho's Agricultural Research Station, Idaho State University, and Clear Springs Foods, Inc. The
macrophyte biomass estimates generated by the model were compared to observations made by
the University of Idaho (Falter and Carlso, 1994; Falter et al., 1995; Falter and Bums, 1996).
The sourcqs of uncertainty in the simulation model are presented in the following
categories: ;
• ecosysiem driving forces and stresses,
• uncertainty in sources of mass and energy,
• model error,
• parameter estimation error,
• measurement error,
• quantitative measures of exposure and effect, and
• lack of knowledge,
A detailed discussion of the uncertainties in the simulation is provided in Appendix D of this.
report. The follo-Wng is a brief summary of that discussion.
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9.2.1. Variability in Driving Forces and Stresses
Principal environmental factors for the study reach are hydrology and meteorology. The
conceptual model accounts for variability and uncertainty of these environmental factors by
assuming that the 67-year data record from 1928 to 1994 for river flow and air temperature for
Twin Falls and Glenns Ferry is a representative sample for hydrology and meteorology.
The models for variability in both hydrology and meteorology are based on the actual 67-
year record in the case of the meteorology and the adjusted 67-year record for the hydrology.
Although using the actual record captures some of the variability in a simple and straightforward
manner, it represents only a sample of the actual population. As such, it may not include events
that have a low probability of occurrence. Such events would likely be associated with long-term
changes in regional and global weather patterns.
Because of changes in the hydrologic regime, the existing record of actual flows cannot
be used directly to characterize risk associated with present management of the system
hydrology. However, the Idaho Department of Water Resources (IDWR) has developed a model
that estimates the historical monthly average flow and reach gain in the Snake River given
present-day operating rules for the system. There is uncertainty in the way in which the monthly
flows estimated by the IDWR hydrologic model were disaggregated into daily values. The
results of applying the model to the period 1928-1994, reported as IDWR Study 150 (Robert
Suter, IDWR, personal communication), are used to characterize hydrologic variability for the
risk analysis in the study reach.
9.2.2. Sources of Mass and Energy
Correlation of modeled results with observed values for water quality was generally high
with a few exceptions. The correlation between simulated and observed values of total ammonia
nitrogen and total phosphorus was generally low. The total ammonia nitrogen results showed
significant positive bias (the model predicted higher values, on the average, than were observed)
downstream from the City of Twin Falls Sewage Treatment Plant (STP) and Auger Falls and in
the area of dense macrophyte beds. The bias in the total ammonia nitrogen at the station
downstream from Auger Falls and from the City of Twin Falls STP could be due to error in the
loading from the City of Twin Falls STP. It could also be due to incorrectly characterizing the
sources and sinks for total ammonia in the Auger Falls segment of the study reach.
With the limited data available, it was difficult to account for or separate uncertainty in
the sources of mass and energy. The longest record available for developing models for the
sources of mass and energy was 5 years (1990 to 1994). In addition, sampling periods for these
sources were generally biweekly or greater. In the case of the springs, which play an extremely
important role in the study reach, data gaps were much larger. The relatively low variability of
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both the quantity ajnd quality of the spring flows mitigates the impact of these data gaps to a
degree. For sources with important high-frequency components such as irrigation return flows,
the data gaps are likely to be significant. In general, the limited data imply a high degree of
uncertainty for both high-frequency and low-frequency components of the sources of mass and
energy. i
i
1. ' ,
9.2.3. Model Error
Errors in trie simulation model for ecological risk analysis contribute to uncertainty in the
estimate of ecological risk in a number of ways. Errors in structure are generally the major
sources of uncertainty in ecological models. Structural errors result from omitting important
i . •
variables or flow paths between variables.
Spatial and temporal aggregation of variables in the simulation model also contribute to
model uncertainty. The equations of mass and energy balance for this model assume the
variables describing the water body vary only vertically or longitudinally, depending on the
nature of the water body. In addition, the simulated variables represent volume-averages for
i
river segments 0.5' to 5 km (0.3 to 3.3 miles) in length and reservoir segments 1.5 meters
(5 ft) thick. Variables are also averaged over a 3-hour period.
The model! structure may not include all the processes required to accurately simulate
primary productivity in the study reach. For instance, correlation between simulated and
observed concentrations of dissolved oxygen is generally good, with the exception of the first
' part of 1992, when supersaturated levels of dissolved oxygen were observed (Minshall et al.,
1993) but were nojt simulated by the model.
The conceptual model for the macrophytes includes the assumption that nutrient flow
from the sediments to the roots of macrophytes is unlimited by plant uptake. This assumption
plays a significant role in the development of management strategies for reducing macrophytes in
the study reach. Given an essentially infinite supply of nutrients, reduction in the discharge of
dissolved nutrients is unlikely to result in a decrease in macrophyte biomass. Although results of
macrophyte studies from 1990 to 1994 in the study reach (Falter and Carlson, 1994; Falter et al.,
1995; Falter and Burris, 1996) suggest that the assumption may not be met in the densest plant
beds in late summer (i.e., some phosphorus depletion from sediments was observed), it is a
reasonable first approximation for extended periods of low flow when sediment deposition rates
are high. However, under conditions of high flow, when sediments are being removed by
scouring, it is likely to result in unreasonably high rates of nutrient flow to rooted macrophytes.
Structural errors in the model also may be an important source of bias and poor
correlation between simulated and observed total ammonia nitrogen in the vicinity of the
macrophyte beds at Crystal Springs and Boulder Rapids. This segment of the study reach is one
' • 9-19
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of high biological productivity. Uptake and release of ammonia by macrophytes is an important
part of the nutrient dynamics in the model. Additional field and/or laboratory studies would be
required to adequately test the hypotheses that control ammonia uptake and release in the model.
The model predictions for macrophytes and epiphyte growth in the Crystal Spring reach
and Box Canyon reach were generally correct. There were some exceptions. In 1992, the
predicted rooted and nonrooted macrophyte densities in Crystal Springs reach were about 3 to 4
tunes greater than observed values. Also, the observed epiphyte demise preceded the predicted
timing. A low-flow year such as 1992 resulted in very high levels of aquatic plant development,
in particular, heavy growths of epiphytes. It is likely that the warm, low flows of 1992 favored
early epiphyte development which suppressed rooted and nonrooted macrophytes by blanketing,
light suppression, and nutrient competition through the first half of the summer. Slightly higher
summer flows of 1993 and 1994 altered macrophyte development, especially by reducing early-
season epiphyte development. In 1993, predicted rooted macrophytes closely modeled observed,
both in magnitude and tuning. Predicted nonrooted macrophytes were slightly lower and about a
month later than observed. These biological interactions were not incorporated into the model.
The model was also quite sensitive to the magnitude of the habitat factors. The habitat
factors, in principle, should be derived from knowledge of sedimentation processes. However, in
this case, lack of knowledge of these processes made it necessary to use the limited data that
were available (Hill, 1992) regarding macrophyte habitat. Although these data provided
information about conditions existing during 1990 for certain segments of the study reach, they
were not sufficient for predicting habitat conditions under various river flow regimes. Recent
data (McLaren, 1998) show that habitat factors for macrophytes change dramatically as a result
of scouring of sediment deposits and associated macrophytes during periods of high flows in the
Snake River. On the basis of his study of sediment transport during July and October 1997,
McLaren (1998) concluded habitat factors change when the flow in the study reach exceeds
approximately 283 m3/s (10,000 cfs). Such conditions have occurred during the past, but are not
reproduced in the cumulative distribution function generated by the model. Incorporating a
predictive model for macrophyte habitat would require more study of the sedimentation
processes in the study reach.
The simulation results for macrophytes were also sensitive to the parameters used to
characterize the physical stress placed on plants by high water velocities. This component of the
model had much greater impact on macrophyte density than did changes in the concentration of
total phosphorus in the water column. The initial estimates of the parameters used to
characterize physical stress from high water velocity were estimated from the work of Chambers
et al. (1991a,b). The magnitude of parameters relating macrophyte growth to water velocity was
modified to account for the results obtained by McLaren (1998). However, this change was not
9-20
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able to account for the dramatic changes in macrophyte growth observed in 1997, which were
likely due to the fact that these parameter changes affected only the plant physiology and were
not related to the physical processes associated with sediment transport.
As is the qase for most ecological models, the structure for the ecological model used in
this analysis of ri$k is a hypothesis derived from previous ecological model construction and field
studies in rivers, lakes, and reservoirs, including field studies done in the study reach. There are,
at this point, no widely accepted protocols for testing hypotheses regarding state-space models of
the type used in this analysis. Oreskes et al. (1994) suggest a qualitative comparison of model
simulations with observed values of the variables as a way of establishing the credibility of earth
science models. :
9.2.4. Parameter Estimation
i
Formal solutions of the parameter estimation problem are difficult to obtain. The
difficulty arises from the nonlinear nature of the mass and energy balance equations, limited data,
and the large number of parameters. Because of this, parameter estimation was done by trial and
error for selected parameters only. The trial-and-error process included initial selection from the
literature, followed by adjusting parameters until simulated values agreed reasonably well with
observations. j .
i
Those parameters included in the trial-and-error process were ones that determine the-
sedimentation rates of phosphorus: loss, uptake, and release of ammonia nitrogen; growth and
death rates of macrophytes and epiphytes; and habitat factors for macrophytes. Model response
was particularly sensitive to the parameters for growth and mortality rates of macrophytes,
i
epiphytes, and habitat factors for macrophytes. Of particular importance for parameters
i
characterizing growth rates and mortality rates of macrophytes and epiphytes was the role of the
sediments and sedimentation processes hi the study reach.
9.2.5. Measurements
Field measurements of variables are needed for testing model hypotheses and ultimately
for evaluating the reliability of the simulation methods. However, there are several sources of
uncertainty in field measurements. There is generally some error associated with the instrument
or laboratory technique and with the manner in which samples are taken and handled. In general,
the largest variability is usually due to spatial or temporal variability of the variable being
measured. This is particularly true for the biological variables. For example, Falter et al. (1995)
and Falter and Bums (1996) observed high spatial variability of macrophyte density at Boulder
Rapids with a high number of replicates. Dissolved oxygen is a variable that can also have high
temporal variability during periods of high primary productivity. There will be uncertainty in
i 9-21
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characterizing the average state of dissolved oxygen in the system when only one grab sample is
taken every 2 weeks.
There is also uncertainty in comparing field observations with simulated results because
the field observations are point measurements whereas the simulated values are space- and time-
averaged. The magnitude of the uncertainty depends, of course, on each variable's spatial and
temporal characteristics.-
9.2.6. Quantitative Measures of Effect
Uncertainty in the quantitative measures of effect can also make significant contributions
to variance in the estimates of ecological risk. For this risk assessment, the measures are based
on the water quality criteria established by the State of Idaho and on habitat suitability indices
developed by the U.S. Fish and Wildlife Service. The quantitative water quality criteria have
been developed from a wide range of field and laboratory tests and assays. Such tests often show
considerable variability in results. Furthermore, they may not always be appropriate for local
conditions because of variability in environmental factors and in the response of the target
organisms. .
In many cases, the exposure period used in the tests or assays used to develop criteria may
not be commensurate with exposure periods experienced in the real system. For example, many
of the water quality criteria are based on results from bioassays conducted over a period of 48
hours. The results of the bioassays are interpreted in terms of acute or chronic impacts on test
organisms. The acute and chronic values are converted to criteria stated in terms of
instantaneous or 4-day averages, respectively, in the water body. Interpreting the results of tests
and assays in this way is meant to be protective of the ecosystem, but it does introduce
uncertainty.
There is even more uncertainty associated with the quantitative interpretation of narrative
standards. The narrative criterion for rhacrophytes is "nuisance" levels. There is no qualitative
or quantitative definition of "nuisance." There is general agreement that the levels observed
during the period 1990 to 1994 were unacceptable. However, there is as yet no agreement on
what quantitative measures of macrophyte growth constitute a violation of these standards. The
analysis of macrophyte literature used in this study is limited in scope and may not necessarily
reflect local conditions in the study reach. The nuisance criterion should undoubtedly be
adjusted for the type of plant community. For example, densities of P. pectinatus at a level of
200 g/m2 might not hinder beneficial uses. Densities of Cladophora of this magnitude, because
of their surface-floating habit, could severely hinder beneficial uses and therefore be considered a
nuisance. Until further discussion and analysis is devoted to this issue, the measurement
endpoint for macrophyte biomass should be considered provisional.
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9.2.7. Lack of Knowledge
The habitat suitability indices, based on the IFIM procedure used by the U.S. Fish and
Wildlife Service (Anglin et al., 1992) in the Swan Falls reach of the Snake River, are valuable as
t •
measurement endppints because they were derived for target organisms found in the study reach.
i
They provide measures of ecological impacts on target organisms attributable primarily to
physical stressors. i The uncertainty in these indices is due primarily to lack of specific knowledge
regarding impacts bf the stressors on the target organisms. Some of these habitat suitability
indices, for example, are based on surveys of the best professional judgment of regional fisheries
biologists. The results of the surveys were converted to indices as part of the IFIM (Anglin et al.,
1992) without quantifying the uncertainty in the responses. Even though the results of IFIM
modeling are somewhat subjective, they effectively reveal temporal habitat trends.
Because the focus of IFIM is on instream flows, the habitat suitability indices give
i
considerable weight to the physical parameters, i.e., depth and velocity. Some researchers (e.g.,
Mathur et al., 1985) have reported there is little evidence showing correlation between these
>
habitat indices and fish biomass. Proponents of the methodology (e.g., Armour and Taylor,
1991) acknowledge the lack of post-project monitoring to document the value of IFIM, while
noting that IFIM has become widely accepted as a tool for investigating the impacts of flow
regulation on aquatic resources. The rationale for adapting the IFIM methodology for ecological
risk assessment in the study reach was based primarily on this acceptance. However, given the
manner hi which the indices were developed and the lack of documented support for the method,
the results reported here are likely to have a high degree of uncertainty.
E . -
9.3. CONCLUSIONS
The Middle Snake River is clearly altered from the natural lotic ecosystem that existed
i
prior to construction of impoundments and water withdrawal. It is now a series of reservoirs
with few remaining rapids. The result is a system dominated by low-flow dynamics. In addition,
the springs that should provide cool, clear, low-nutrient water are being preempted for
aquaculture facilities. ,
i
Loading of nutrients, sediments, and thermal energy into this ecosystem has caused the
natural cold-water [populations to decline and eutrophication to accelerate. Natural events (high
flows) can alleviate this trend. High flows during 1996-1998 scoured much of the deposited
sediments and proyided higher flows and cooler temperatures for aquatic growth and survival.
However, the cycl£ of eutrophication and loss of diverse habitats will be repeated when the flows
are reduced. The only way to sustain a viable cold-water population is to reduce all
anthropogenic loadings to negligible levels unless the .natural hydrograph can be reinstated.
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Sediment dynamics are as important as water column dynamics in providing the
necessary habitat for growth and survival of native biota of the river. Sediment deposition alters
habitat by providing substrate for the growth of macrophytes and by smothering gravel beds that
are normally niches for fish and invertebrates.
The physical removal of both the nutrient-laden substrate and the macrophytes by
transport processes was the primary factor leading to reduction of macrophyte biomass in the
study reach (Clark, 1997b). The methods described here did not include an analysis of the
physical processes characterizing sediment deposition and scouring. Additional studies are
necessary to describe these processes and their effects on macrophyte and epiphyte mortality.
" Eutrophication leads to several ecological changes in the structure and function of
freshwater ecosystems. Such changes include increased plant (macrophyte) production and shifts
in species composition, decreased water transparency, and shifts in the consumer community
towards undesirable species. The results of eutrophication are manifested in a macroinvertebrate
community comprised predominantly of pollution-tolerant taxa. The restriction of the
community to pollution-tolerant taxa resulted in the increased abundance of the species present,
particularly in the early 1990s. Additionally, the habitat conditions of the Middle Snake River in
the early 1990s favored the distributional expansion and increased abundance of the exotic snail
Potamopyrgus antipoddrum.
The impoundment and subsequent alteration of hydrologic regimes is the most disruptive
of all common anthropogenic forces acting on rivers (Ligon et al., 1995; Sedell et al, 1990). In
•the Middle Snake River, impoundment has altered the hydrologic regime, created lentic
environments, and reduced water velocities in many of the remaining lotic reaches. These
changes have resulted in warmer water temperatures, increased deposition of fine sediments,
increased residence tunes for dissolved nutrients, and the proliferation of aquatic macrophytes
(Royer et al., 1995; Thomas et al., 1995; Falter and Carlson, 1994). The aquatic
macroinvertebrate community of the Middle Snake River now reflects the altered riverine
conditions. The above changes in the river have created a habitat favoring warm-water,
sediment-dwelling, and generally pollution-tolerant taxa.
Salmon and steelhead trout once spawned in the Snake River as far upstream as Auger
Falls, indicating that the Middle Snake River was a clear, cobble/gravel-bottomed, cold-water
river (Evermann, 1896). Indeed, Evermann (1896) stated, "The spawning grounds of chinook
salmon in [the] Snake River between Huntington and Auger Falls have been ... the most
important in Idaho." Although anecdotal, descriptions such as Evermann's suggest the Middle
Snake River once displayed characteristics typical of rivers productive for anadromous salmon.
A return of a part of this habitat is needed to sustain cold-water resources in this area:
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10. MANAGEMENT IMPLICATIONS OF THE MIDDLE SNAKE RIVER
RISK ANALYSIS
The assessment process, in particular the problem formulation, furthered a better
understanding of environmental problems. Developing the conceptual model provided
participants with an improved understanding of the interrelationships between various
components of the ecosystem and how human activities contribute to environmental problems
within the watershed. Assessment endpoint selection helped ensure data that was collected and
analyzed would be relevant to decision-making needs. The risk assessment helped lend further
credence to what many professional resource manages had long conjectured about problems
within the watershed, thereby providing more scientific support for actions to address problems.
For example, there is now a better understanding of the contribution of sediment to the changes,
f
in ecosystem, including eutrophication and decline offish species. This information is useful to
managers as they begin to regulate the sediment sources.
The conceptual model and analysis plan were helpful to the State of Idaho Department of
Environmental Quality (IDEQ) in designing monitoring plans for the river. The simulation
techniques as described in appendix D, were the IDEQ to prepare its Nutrient Management Plan
(1995) for phosphorus in the river. The mathematical models predicted phosphorus levels in the
river and these were compared with macrophyte growth rates to develop the phosphorus Total
Maximum Daily Load (TMDL) concentration. The qualitative analysis of literature and field
surveys of the survival threshold limits of freshwater biota was used by EPA in its review of the
TMDL for sediment, which was completed by the IDEQ in 1999. The qualitative analysis also
provided information for the U.S. Fish and Wildlife Service for its Snail Recovery Plan (1995).
Assessment findings provided information for the National Pollution Discharge Elimination
System (NPDES); (1999) permits for aquaculture facilities on the Middle Snake River.
i
In 1992, the simulation techniques developed as part of the risk analysis as well as the ,
conceptual mpdel were used by EPA in their determination of the impacts from a proposed new
hydroelectric facility (Auger Falls) on the Middle Snake River. The Federal Energy Regulatory
i
Commission (FERC) was convinced by EPA's risk analysis that cumulative impacts should be
addressed when reviewing new or continued licensing for hydroelectric facilities. The EPA risk
analysis also proyided the community groups with a more robust analysis of the possible impacts
of impoundments on the river.
i •
In 1995, a Watershed Advisory Group was formed from the State of Idaho Nutrient
Management Plan committee. The state legislation established such groups to provide guidance
to the state on pollution control efforts that would lead to full support of designated uses for
10-1
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high-priority water bodies as defined in the state water quality standards. The legislation
specified that members of the watershed advisory groups should include representatives of local
governments and agencies. The comprehensive analysis of the Middle Snake watershed and the
compilation of information from literature and field surveys will be useful to the Watershed
Advisory Group as it begins comprehensive strategic planning for watershed protection.
The simulation methods developed in this watershed can be used to test management
scenarios. For instance, how does changing river flow, sediment input, or point and nonpoint
sediment dynamics impact different macrophyte biomass levels or fish populations. This allows
all those interested in land-use activities, as well as resource protection, to explore such
alternative management options for the river and to make more informed decisions. The
simulation techniques developed through this risk analysis can also be applied to other
watersheds and similar conditions. It is currently being used on the main stern of the Columbia
and Snake rivers for examining alternative impoundment options to protect salmonid habitat.
The biggest benefit from performing this watershed ecological risk assessment is that a
number of federal, state, and local environmental agencies and academics, interested citizens,
and industrial groups came together to share data, explore, and develop solutions and undertake
actions within the watershed.
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11. REFERENCES
! ,
Allen, JD. (1995) Stream ecology structure and function of running waters. London: Chapman and Hall.
Ambrose, RB; Wool, TA; Martin, JL. (1993) The water quality analysis simulation program, WASPS. Athens,
GA: Environmental Research Laboratory, U.S. Environmental Protection Agency.
! • < •
Anders, PJ; Beckmanj LG. (1995) White sturgeon spawning cues in an impounded reach of the Columbia River.
In: Status and habitat requirements of the white sturgeon populations in the Columbia River downstream of
McNary Dam. Final report of research volume II - supplemental papers and data documentation, July 1986 -
September (1992), Portland, OR: Bonneville Power Administration, Project No. 86-50, Contract No. DE-AI79-
86BP63584; Beamesderfer, RC; Nigro, AA, eds., pp. 123-140.
Anderson, MR; Kalff; J. (1988) Submerged aquatic macrophyte bipmass in relation to sediment characteristics in
ten temperate lakes. Freshwater Biol 19:115-121.
Anglin, DR; Cummings, TR; Ecklund, AE. (1992) Swan Falls instream flow study. Report No. AFF1-FRO-92-14.
Vancouver, WA: U.Sl Department of Interior, Fish and Wildlife Service, Lower Columbia River Fishery Resource
Office. i • .'
Armour, CL; Taylor, JG. (1991) Evaluation of the instream flow incremental methodology by U.S. Fish and
Wildlife Service users. Fisheries 16:36-43.
Baker, HB. (1925) Anatomy of lanx, a limpet-like lynaeid mollusk. Proc Cal Acad Sci 14:143-169.
Barber, ME. (1991) Modeling water quality and biota in the Colorado River below Austin, Texas. Ph.D. Thesis,
University of Texas, Austin, TX.
Barko, JW. (1983) The growth of Myriophyllum spicatum in relation to selected characteristics of sediment and
solution. AquatBot 15:91-103.
Beak Consultants, Inc. (1987) Unpublished mollusc survey in the Snake River during the fall of 1987. Submitted
by February 18, 1991, letter to the U.S. Fish and Wildlife Service.
Beamesderfer, RCP; Fair, RA. (1997) Alternatives for the protection and restoration of sturgeons and their habitat.
Environ Biol Fishes 48:407-417. •
Beamesderfer, RCP; Rien, TA; Nigro, AA. (1995) Differences in the dynamics and potential production of
impounded and unimpounded white sturgeon populations in the Lower Columbia River. Trans Am Fish Soc
124(6):857-872.
Beer, S; Spencer, W; Bowes, G. (1986) Photosynthesis and growth of filamentous blue-green alga Lyngbya birgei
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i
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I ' •• - • .
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| •
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11-14
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APPENDIX A. PARTICIPANTS IN THE PROTECTION
OF THE MIDDLE SNAKE RIVER
i
Federal
L
U.S. Environmental Protection Agency (U.S. EPA)
• • Department of the Interior
i U.S. Fish and Wildlife Service (USFWS)
I
Bureau of Land Management/Minerals Management Service
I National Biological Survey
: Department of Energy
Federal Electric Regulatory Commission
! Department of Agriculture
; National Park Service
i U.S. Geologic Survey
I Northwest Power Planning Council
i
I State
I
' Idaho Department of Health and Welfare
\ Division of Environmental Quality
Idaho Department of Water Resources
i
| - Idaho Department of Fish and Game
! Idaho Fish and Game Commission
; Idaho Water Board
' Idaho Department of Parks and Recreation
L
County/Local
Mid Snake River Planning Group
Private Organizations
Idaho Power Company
North Side Canal Company
A-l
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The Nature Conservancy
Natural Heritage Program
The Research Community
The University of Idaho
Idaho State University
University of California at Irvine
A-2
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APPENDIX B. ECOLOGICAL COMPONENTS
OF THE MIDDLE SNAKE RIVER ECOSYSTEM
Wetland and shoreline plants found in the Snake River (from Stanford, 1942; Dey and
i
Minshall, 1992). Dey and Minshall species are marked with an asterisk. The names are in
accordance with Hitchcock and Cronquist (1981).
Scientific Name I
Salix lasiandra
Populus trichocarpa
Nepeta cataria
Solanum triflorum
Veronica americana
Solidago missouriehsis
Rumex persicarioides
Vicia americana •
Glycyrrhiza lepidota
Apocynum cdnnabinum
Verbena hastata
Mentha arvensis lanta
Helenium autumnale
Xanthiumpensylvanicum
Bidens cernua
Artemisia sp.
Sarcobatus^ sp.
Phragmites communis
Paspalum distichum
Polypogon monspeliensis
Cyperus strigosus
Eleocharispalustris
Scirpus validus
Typha latifplia
Polygonum natans
Common Name
Willow
Cottonwood
Catnip
Nightshade
American brooklime
Goldenrod
Dock
Vetch
Licorice
Dogbane
Verbena
Mint
Sneezeweed
Cocklebar
Beggar-ticks
Mugwort
Greasewood
Reed
Knotgrass
Beard-grass
Flatsedge
Spike-rush
Soft-stem bulrush
Cat-tail
Doorweed
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Scientific Name
Polygonum lapathifoliwn
Sagittaria sp.
Potamogeton epihydrus
Potamegeton pectinatus ,
Ceratophyllum demersum
Rorippa nasturtium
Lemna minor
Azolla sp.
Toxicodendron diversiloba
Potamogeton crispus*
Potamogeton foliosus *
Elodea nuttallii*
Elodea canadensis*
Ranunculus spp. *
Myriophyllum spicatum*
Common Name
Doorweed
Arrowhead
Pondweed
Pondweed
Hornwort
Cress
Duckweed
Water-fern
Sumac
Pondweed
Pondweed
Waterweed
Waterweed
Buttercup
Water-milfoil
Fish species found in Middle Snake River between King Hill and Milner Darn (personal
communication with Idaho Department of Fish and Game, 1993; Idaho Division of
Environmental Quality, 1995; Maret, 1995).
Scientific Name
Common Name
Family: Acipenseridae - Sturgeons
Acipenser transmontanus Ii2>3'4
Family: Salmonidae -Trouts
Oncorhynchus clarkil
Oncorhynchus mykiss 1>4 .
Oncorhynchus mykiss gairdneri5
Prosopium -williamsoniM
Salmo trutta 4-6
White sturgeon
Cutthroat trout
Rainbow trout
Redband trout
Mountain whitefish
Brown trout
B-2
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Family: Cyprinidae - Carps and Minnows
Cyprinus carpio 4'6
Ptychocheilus oregonensis.4
Mylocheilus caurinus 4
Acrocheilus alutaceus 4
Richardsonius balteatus4
Rhinichthys osculus4
Gila atraria6
Rhinichthys cataractae4
Rhinichthys falcatus 4
Family: Catostomidae - Suckers
Catostomus columbianus4
Catostomus macrocheilus 4
Catostomus platyrhynchus 4
Catostomus ardens 7
Family: Ictaluridae - Bullhead catfish
Ictalurus punctatus li2'4'6
Ameiurus nebulosus 4-6
Ameiurus. melas 4'6
Family: Centrarchidae - Sunfishes
Micropterus dolomieu l'2'4-6
Micropterus salmoides 1>4>6
Lepomis gibbosus 4>6
Pomoxis higromaculatus 4>6
Lepomis macrochirus4-6
Family: Percidae t- Perches
Percaflavescens 1>4>6,
Stizostedion yitreum 4>6
Family: Cottidae - Sculpins
i
Cottus bairdi4
Coitus greenei3>4
Cottus beldingi4
Common carp
Northern pikeminnow
Peamouth
Chiselmouth
Redside shiner
Speckled dace
Utah chub
Longnose dace
Leopard dace
Bridgelip sucker
Largescale sucker
Mountain sucker
Utah sucker
Channel catfish
Brown bullhead
Black bullhead
Smallmouth bass
Largemouth bass
Pumpkinseed
Black crappie
Bluegill
Yellow perch
Walleye
Mottled sculpin
Shoshone sculpin
Paiute sculpin
B-3
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Cottus confusus 4
Coitus rhotheus 4
Family: Sciaenidae - Drums
Aplodinotus grunniens 4>6
Shorthead sculpin
Torrent sculpin
Freshwater drum
Native fish species extirpated from the Middle Snake River
Onchorhynchus tshawytscha
O. kisutch
O. mykiss
Lampetra tridentata
Chinook salmon
Coho salmon (possible inhabitant)
Steelhead trout
Pacific lamprey
Notes for fish species:
1 Game fish in the Middle Snake River (IDEQ, 1995).
2 Spawning fish (IDEQ, 1995).
3 Considered a Species of Special Concern by the State of Idaho.
4 Fish fauna of the Snake River drainage below Shoshone Falls (Bowler et al., 1992;
Bowler, personal communication, 1992).
5 The only pure surviving population of redband trout is believed to be in King Hill
Creek; hybrids are found in other tributaries.
6 Non-native species. Five additional non-native species likely present are:
Tilapia mossambica
T. zelli
T. nilotica
Lepomis cyanellus
L. microlophus
Mozambique tilapia
Redbelly tilapia
Nile tilapia
Green sunfish
Redear sunfish
7 Federal Energy Regulatory Commission (1990).
B-4
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Some Molluscans found in the Middle Snake River (from Frest and Bowler, 1992; Dey and
Minshall, 1992). i
Scientific Name ;
Class Gastrioida (Snails)
Ancylidae
Ferrissia parallelus
Ferrissia riyularis
Hydrobiidae
Fluminicola columbiana'
Fluminicola hindsi
i
Potamopyrgus antipodarum
Pyrgulopisis idahoensis 2
Taylorchoncha serpenticola3
Potamopyrgus antipodarum 4
Lancidae |
Fisherola nuttalli'
Lanx sp.2 !
Fossaria bulimoides
Fossaria dqlli
Fossaria exigua
Fossaria modicella
Fossaria parva
Fossaria obrussa
Stagnicolacaperata
Stagnicola catascopium
i
Stagnicolaihinkleyi
Radix auricularia 4
Physidae i
Physa natrfcina 2
Physa mexicana
Physella gyrina
Physella Integra
Common Name
Columbia River spire snail
Idaho springsnail
Bliss Rapids snail
New Zealand mudsnail
Giant Columbia River limpet
Banbury Springs lanx (undescribed)
Snake River physa
B-5
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Scientific Name
Planorbidae
Gyraulus parvus
Planorbella subcrenatum
Promenetus exacuous
Vorticifex effusus
Valvatidae
Valvata utahensis 2
Valvata humeralis
Common Name
Utah valvata snail
Class Pelecypoda
Corbiculidae
Corbiculafluminea 4
Margaritiferidae
Margaritiferafalcata 5
Sphaeriidae
Musculium lacustre
Musculium securis
Pisidium compression
Pisidium caesertanum
Pisidium insigne
Pisidium nitidum
Pisidium pauperculum
Pisidium punctatum
Pisipium variabile
Sphaerium nitidum
Sphaerium patella
Sphaerium striatinum
Unionidae
Anodonta californiensis
Gonidea angulata
Asian clam
California floater
B-6
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Notes for molhiscan species:
1 Species of concern. Conclusive data not currently available for listing under the
Endangered Species Act.
2 Listed as an endangered species under the Endangered Species Act.
3 Listed as a threatened species under the Endangered Species Act.
4 Non-native species.
5 Extirpated from the Middle Snake River.
B-7
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REFERENCES
Bowler, PA. (1992) Personal communication, December 10,1992, letter to Paul Dey and
Wayne Minshall, Idaho State University.
Bowler, PA; Watson, CM; Yearsley, JR; et al. (1992) Assessment of ecosystem quality and its
impact on resource allocation in the Middle Snake River sub-basin. Desert Fishes Council
24:42-51. ' ~
Dey, PD; Minshall, GW. (1992) Middle Snake River biotic resources: a summary of literature in
the Snake River water quality assessment bibliographic databases. Final report. Pocatello, ID:
Department of Biological Sciences, Idaho State University.
Federal Energy Regulatory Commission. (1990) Final environmental impact statement, the
Milner (FERC No. 2899), Twin Falls (FERC No. 18), Auger Falls (FERC No. 4797), and Star
Falls (FERC No. 5797) hydroelectric projects on the mainstem of the Snake River, Idaho.
FERC/EIS-0048F.
Frest, TJ; Bowler, PA. (1992) A preliminary checklist of the aquatic and terrestrial mollusks of
the Middle Snake River sub-basin. Proc Desert Fishes Council 24:53-58.
Hitchcock, CL; Cronquist, A. (1981) Flora of the Pacific Northwest. Seattle and London:
University of Washington Press.
Idaho Division of Environmental Quality. (1995) The Middle Snake River nutrient management
plan. South Central Regional Office.
Maret, TR. (1995) Water-quality assessment of the Upper Snake River basin, Idaho and western
Wyoming — summary of aquatic biological data for surface water through 1992. Boise, ID:
U.S. Geological Survey, Water-Resources Investigations Report 95-4006.
Stanford, LM. (1942) Preliminary studies in the biology of the Snake River. Ph.D. Thesis,
University of Washington.
B-8
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APPENDIX C. LIFE HISTORIES OF DOMINANT MACROPHYTE
SPECIES IN THE MIDDLE SNAKE RIVER
Potamogeton pectinatus
P. pectinatus is a leathery-stemmed, perennial angiosperm. Stems may be up to 2 m long
with 3- to 15-cm leaves about 1 mm wide. All stems and leaves are submerged and tough and
leathery. P. pectinatus does well in high-velocity waters, well over 1 m/sec. The fruit, 3 to 4
mm long and short-beaked, is prime waterfowl food, especially for dabbling ducks. Perennial
rhizomes are much-branched and tipped by fleshy tubers. P. pectinatus prefers eutropbic
(Grasmuck et al., 1995), alkaline waters, and hence is probably the most common rooted
macrophyte across waters of the arid and irrigated Western United States (Falter et al., 1974).
Biomass levels of 500 to 1,000 g/m2 are not rare in irrigation drain waters. In the inland
Northwest, by the first week of May, shoots began to emerge from perennial rhizomes when the
water temperature ^exceeds 4°C to 5°C. Stem growth develops slowly until mid-June, when
water temperatures and light eriergy increase towards summer maxima. While growth of foliage
slows in July, flowering begins then with fruit starting to form by mid-July. The fruits mature by
early August and begin to fall to the sediments. In early September new growth occurs in the leaf
axils of the shoot.: These growths develop into leaflike branches or axillary tubers which are well
developed by October. Much of the foliage dies back by mid-October.
Reproduction in P. pectinatus is either by sexual or vegetative means. The monoecious
(single-sex) flowers are fertilized with help of movement of pollen along the surface of water to
the stigmas. This results in the formation of a new plant embryo or seed/fruit. Vegetative
propagation occurs by stolons branching out at the base of the main shoot. At each node on the
stolon a new set of roots and shoot may develop, potentially creating a new plant.
Potamogeton crispus
P. crispus was introduced into North America in the mid-nineteenth century from
Eurasian waters and can now be found in all 48 contiguous States. It is a submerged aquatic
vascular plant that perennates by detaching a fleshy winter bud. Vegetative reproduction is very
important to this species because sexual reproduction has not yet been observed. Flowering
occurs in the early spring but formation of seeds is little understood. P. crispus is a cool-water
strategist that can overwinter as the entire green plant under ice or via winter buds. The thick,
f
crinkled, crisp leaves grow very quickly in spring as temperature and light intensity increase.
C-l
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This allows P. crispus to establish itself early in the growing season. P. crispus has three
vegetative forms: (1) the previously mentioned winter bud, which can survive low-light
conditions under ice; (2) the spring form stimulated by warming water, which is the plant form
one sees from mid-spring to June and early July; and (3) the dormant apices (viable bud tips, a
vegetative reproduction mechanism). The dormant apices detach before germinating in autumn,
then begin to grow into a flat, narrow-leaved winter form. Spring germination of dormant apices
is controlled by temperature (Nichols and Shaw, 1986; Stuckey et al., 1978). The magnitude of
vegetative propagation can be phenomenal, especially in warmer waters. Despite being a cool-
water strategist in the winter, this plant's optimal temperature for photosynthesis is about 30°C.
Yeo (1966) planted a single dormant apex of P. crispus in a 6 m2 container and counted 23,250
dormant apices produced by the end of the growing season. Dormant apex densities of 23 to
1,650/m2 have been found in natural P. crispus populations (Kunii, 1982).
P. crispus prefers moderately to very alkaline waters and does very well in eutrophic and
even saline waters. Like E. canadensis, the plant is considered an indicator of eutrophic
conditions (Hellquist, 1980; Nichols and Shaw, 1986). It similarly has a high tolerance for
pollution. Under these borderline conditions for most native species, P. crispus may often
dominate a plant community, at least early and mid-growing season. Its habit for summer die-
back exacerbates late-summer planktonic algae blooms by sudden release of nutrients pumped
from sediments earlier in the season. Another reason for the plant's explosive growth potential is
undoubtedly its ability to absorb nutrients either from sediments via roots or from the water
column via shoots and leaves (Carignan and Kalff, 1980; Nicholls and Shaw, 1986). Like milfoil
and E. canadensis, P. crispus may also experience catastrophic die-off where it may nearly
disappear from a habitat where it previously dominated. All three species, however, are
remarkably disease-free.
Several researchers have demonstrated the ability of P. crispus to thrive hi highly turbid
waters or deep in the water column at low light intensity. It is considered a deepwater species,
one that typically develops at depths where light intensity is <, 15% of full sunlight (Nicholls and
Shaw, 1986).
Ceratophyllum demersus
C. demersus is a submerged, free-floating, rootless aquatic vascular. This species usually
overwinters by surviving in densely crowded, dormant stem apices and sometimes as an intact
vegetative plant body, especially in deeper water covered by ice (Stuckey et al., 1978). C.
C-2
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demersus reproduces sexually and by fragmentation (Tarver et al., 1979). In sexual reproduction
the pollen is most often released from monoecious flowers. Pollen is released from the stamen at
some time in the niiddle of summer and sinks through the water until caught on a stigma. This
results in the formation of fruit, which needs warmer temperatures to mature. The fruit is a
persistent, hooked nutlet. The seed germinates at the bottom of an enclosing water body. When
plantlets reach about 7.5 cm (3 inches) in length, they can rise to the surface to float. These
young shoots form in the spring. C. demersus is more sensitive to colder temperatures than are
i
other aquatic plants (Arber, 1920; Mason, 1969). The plant seems to prefer slow-moving
streams, quiet ponds, and protected bays on lakes (Tarver et al., 1979).
C. demersus is clearly favored by polluted, enriched waters. Kurimo (1970) found the
plant to prefer locations below industrial and urban waste inputs, so long as the water was not too
acid. In Japanese waters impacted by irrigation, Kunii (1991) used canonical analyses to place
macrophytes on environmental gradients. C. demersus occurrence was associated with higher
pH, conductivity, alkalinity, Ca, Mg, and Na. . .
Elodea canadensis .
E. canadehsis is a submerged, branching, leafy, perennial but poorly rooted aquatic
vascular. Native to North America from Quebec to the Gulf Coast States and west to the Pacific
(although notably absent from the higher Rockies), it often behaves as an exotic in its rapid
1 ;.
spread and dense, (luxuriant growths. It reproduces almost entirely vegetatively, but will rarely
reproduce sexually. The sexual fecundity of this species is low and depends on the dioecious
form of the plant.' The staminate plants are rather rare compared to their pistillate counterparts
i • . _
(Arber, 1920). Vegetative reproduction is therefore important to E. canadensis as seed formation
is rare. Rapid propagation can result when a branch containing one or more nodes is broken off
and continues to grow. Such stem fragmentation is the most common method of E. canadensis
reproduction. E. canadensis can withstand cold temperatures in the winter by living in dense
colonies. It has commonly been observed that the foliage can remain green throughout the
winter under ice. This species is a cold-water strategist and thus has an edge in the spring when
temperatures and light intensities increase and its foliage is already in place and ready to grow.
Unlike P. crispus,1 the growing season for E. canadensis extends throughout early spring to late
fall. :
i
E. canadehsis may obtain nutrients either from soil or water. A number of studies have
shown both occurring, depending upon relative nutrient concentration of the water or sediments.
C-3
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Opportunism seems to be the rule (Nicholls and Shaw, 1986; Stuckey et al., 1978). Its depth
preference is broad, possibly dominating communities from 1 to 12 m depth.
Hydrodictyon
Hydrodictyon (water net) is a filamentous green alga in the class Chlorophyceae. This
alga is colonial, forming large cylindrical nets up to 60 cm long. Individual cells are also
cylindrical and can themselves be up to 1 cm long. At each end, they are attached to three other
cells, the result producing a reticulate net of pentagonal or hexagonal shapes. Colonies resemble
a nylon mesh stocking in the current. In the Middle Snake River, these tubes are aligned parallel
to the current with the tubal opening facing the current. The tubes are very efficient detrital
traps, eventually settling to the stream bottom where they add to the sediment store of organic
matter^ energy, and nutrients. Water net occurs worldwide in slowly flowing or nearly still
freshwaters, where it can form large growths, particularly in nutrient-rich waters. This species
prefers eutrophic waters. In the Middle Snake River, Hydrodictyon grow in the top half of the
water column in dense rooted macrophyte beds where there is just enough current to fill out the
nets. This genus has the distinction of being one of the earliest known alga mentioned in
literature, being referenced in one ancient Chinese poem, Bible of Poems.
Reproduction is quite complex. Asexual reproduction occurs through the formation of
autocolonies in which the cytoplasm is forced to the outer surfaces of the cell wall by a large
vacuole. The cytoplasm then divides to many protoplasts, small flagellated zoids. Eventually,
there may be up to 20,000 flagellated cells linked together in the form of a haplontic (adult cells
are IN) netlike colony. Asexual reproduction continues when these same zoospores may
disperse to form individual water nets. A net with 10,000 cells could theoretically produce
10,000 nets in the water. Such efficient reproduction explains why in a very short time,
Hydrodictyon may form thick and tangled mats in streams and irrigation canals. Judging from
the appearance of detritus-laden Hydrodictyon nets in the Mid-Snake River, the colonies
apparently trap and remove drifting sestonic nutrients and organic matter from the water column.
Given its rapid reproductive rate and net structure, Hydrodictyon undoubtedly has a significant
role in nutrient and organic matter removal from water flows through the aquatic macrophyte
beds.
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Cladophora \
Cladophora, another filamentous branched green alga, is sometimes called "blanket
weed." Its life form is macrophytic, branched filaments that initially develop attached to rocks
via a holdfast or rhizoidal outgrowths or even as epiphytic growths on vascular macrophytes. In
streams, attached streamers may attain lengths of 10 m. Older colonies often leave the substrate
and become self-supporting in the water column. If not crowded, the growth form may develop
as bushy tufts waying in the current. In streams, the clusters may form streaming hanks of algae
tissue. The plant may take advantage of vascular macrophyte growths on the sediments and a
rich water column! environment by forming blanketing mats on the vasculars. Light restriction to
underlying macrophyte communities may be extreme and responsible for vascular macrophyte
declines (Phillips et al, 1978; MacMillan, 1992).
Cladophora may be marine or freshwater, but does best in areas of some water
movement, such as streams or tidal flows. The genus is one of the better plant indicators of
organic loading and nutrient enrichment. Pitcairn and Hawkes (1973) found high correlation
between Cladophora growth and soluble inorganic phosphorus concentration up to about 2,000
|j,g/L. It is a very common form below sewage outfalls, aquaculture facilities, and food
processing facilities, and in sublittoral zones of bathing beaches. Its presence nearly always
indicates enhanced concentrations of soluble organics in the water. Cladophora is known for its
very high biomass levels, sometimes exceeding 1,000 g/m2 dry weight.
Most reproduction is by asexual cell fission, resulting hi filaments several decimeters
long. In the freshvyater species, there is a cytological alteration of generations, the plantlike
phase being the sporopyte. In the winter months the sporophytes produce diploid planogonidia
or aplanogonidia depending on the species. During the spring the sporophyte forms sporangia
where meiosis occurs. This results in the formation of haploid nuclei representing the spores.
The spores germinate within the sporangia. This leads to the production of biciliate gametes,
which are then released to join via syngamy. Following syngamy, a 2N zygote is formed and the
zygote attaches to; some substrate growing into a new sporophyte, which grows into a vegetative
filament. ',
\
Spirogyra
Spirogyra-is a genus of filamentous green algae sometimes referred to as water silk.
Filaments can be several decimeters long, are unbranched, and do not require attachment to,
substrate. Spirogyras prefer a range of living conditions that is rather wide, from deep, cold
C-5
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springs to shallow, warm ponds, or from very hard water areas to waters with large amounts of
organic acids. Cooler conditions are preferred because they are especially common in spring and
early summer. They are ubiquitous in habitat selection and therefore, are not good biotic
indicators of any particular range of water productivity. Generation time of a colony is variable,
but 2 months is a common time period from zygote germination to filament senescence.
Vegetative growth peaks at from 2 to 6 weeks, followed by sexual reproduction as well as
formation of and burial of zygotes (fertilized 2N embryos) in the substrate. These zygotes are
quite resistant to anaerobic conditions in decomposing muds over fall and winter.
Most growth is vegetative through intercalary cell division splitting at the cross walls.
Sexual reproduction is common and complex. Starting with a Spirogyra zygote, which can be
thought of as the sporophyte, meiosis will occur when conditions are favorable. The zygote is a
very resistant cell able to withstand extreme cold or desiccation. It is able to do this by being
released after conjugation and settling into the mud, covered with slime. So, when meiosis
occurs in the diploid zygote, four haploid nuclei are produced and only one nucleus will remain
after the other three break down and disappear. When the remaining haploid cell begins to
divide, it will form a young gametophyte. The young gametophyte is either a female or male
filament These are the IN filaments commonly seen. Spirogyra is therefore haplontic, where
2N exists only in the zygote and "adult" filaments, either male or female. Each gametophyte cell
contains one haploid gamete. Conjugation, the mode of sexual reproduction, occurs when the
male and female filaments lie appressed and the male gamete passes into the female
gametangium by a conjugation tube. The male and female gametes fuse by.syngamy, which
results in a new diploid zygote. The gametophyte filaments can also reproduce by vegetative
means when a segment breaks off.
Enteromorpha
Entermorpha spp. is a filamentous green alga genus that grows as hollow, intestinal-
shaped rubes up to 15 cm or more in length. The genus may be freshwater or marine; freshwater
forms are considered halophytic, doing well in brackish water. It is a common alga around the
world in tropical tidal pools. Freshwater species do best in alkaline waters (about 300 to 500
mg/L total alkalinity) and in high phosphorus concentrations, and can tolerate high ammonia.
The entrail-shaped sporophyte is usually attached to some type of substrate. Species of this
genus have a typical algal alteration-of-generations life cycle. The 2N sporophyte produces
sporangia where meiosis occurs resulting in haploid (N) motile spore formation. The spores are
C-6
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released through an opening in the outer cell wall of the sporophyte cells to the surrounding
water. The spores move away, eventually germinating and attaching to some substrate. A
gametophyte phase then develops where the gametophyte is tubular and filamentous, resembling
the sporophyte. There are male and female gametophytes which produce and release male and
female haploid, motile gametes. A male and female gamete fuse by syngamy and produce a
diploid zygote, which germinates and forms a new sporophyte.
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REFERENCES
Arber, A. (1920) Water plants, a study of aquatic angiosperms. Cambridge: Cambridge
University Press.
Carignan, R; Kalff, J. (1980) Phosphorus sources for aquatic weeds: water or sediments?
Science 207:987-989.
Falter, CM; Naskali, R; Leonard, J; et al. (1974) Aquatic macrophytes of the Columbia and
Snake River drainages. Final report submitted to the U.S. Army Corps of Engineers, Walla
Walla, WA.
Grasmuck, N; Haury, J; Leglize, L; et al. (1995) Assessment of bio-indicator capacity of aquatic
macrophytes using multivariate analysis. Hydrobiologia 300/301:115-122.
Hellquist, CB. (1980) Correlation of alkalinity and the distribution of Potamogeton in New
England. Rhodora 82:331-344.
Kunii, H. (1982) Life cycle and growth of Potamogeton crispus L. in shallow pond Ojage-ike.
Botan Mag Tokyo 95:109-124.
Kunii, H. (1991) Aquatic macrophyte composition in relation to environmental factors of
irrigation ponds around Lake Shinji, Shimane, Japan. Vegetation 97:137-148.
Kurimo, U. (1970) Effect of pollution on the aquatic macroflora of the Varkaus area, Finnish
Lake District. Ann Bot Fennici 7:213-254.
MacMillan, R. (1992) Aquatic plant growth Mid-Snake River from Shoshone Falls to below
Box Canyon. Buhl, ID: Clear Springs Foods, Inc.
Mason, HL. (1969) A flora of the marshes of California. University of California, Berkeley.
Nichols, SA; Shaw, BH. (1986) Ecological life histories of the three aquatic nuisance plants,
Myriophyllum spicatum, Potamogeton crispus and Elodea canadensis. Hydrobiologia 131:3-21.
C-8
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Phillips, GL; Eminson, D; Moss, B. (1978) A mechanism to account for macrophyte decline in
progressively eutrophicated freshwaters, AquatBot 4:103-106.
Pitcairn, CER; Hawkes, HA. (1973) The role of phosphorus in the growth of Cladophora.
Water Res 7:159-171.
..i
Stuckey, RL; Wehfmeister, JR; Bartolotta, RJ. (1978) Submersed aquatic vascular plants in ice-
covered ponds of central Ohio. Rhodora 80:575-580.
Tarver, DP; Rodgers, JA; Mahler, MJ; et al. (1979) Aquatic and wetland plants of Florida,
second edition. Bureau of Aquatic Plant Research and Control, Florida Department of Natural
Resources.
Yeo, RR. (1965) Life history of Sago pondweed. Weeds 13:314-321.
C-9
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APPENDIXD
Analysis of Ecological Risk in the
Mid-Snake River Using Simulation Methods
March 10, 2000
John R. Yearsley
U.S. Environmental Protection Agency
Reagion 10
Seattle, WA
C. Michael Falter
University of Idaho
Moscow, ID
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APPENDIX D. ANALYSIS OF ECOLOGICAL RISK IN THE
MID-SNAKE RIVER USING SIMULATION METHODS
i -
D.I. INTRODUCTION
Mathematical models of mass and energy flow in an aquatic ecosystem are used in the
assessment of the Study Reach, the Middle Snake River from Milner Dam (river mile [RM]
640.0) to King Hill (RM 545.3) (Figure D-l), to obtain quantitative estimates of ecological risk.
The mathematical1 models simulate physical, chemical, and biological state variables that
characterize important features of the aquatic ecosystem. The probabilistic measures developed
i •
from the simulations will be compared with the relevant measurement endpoints to estimate
exposure and effect in the Snake River. The probabilistic aspects of the analysis arise from the
uncertainty and variability hi environmental factors such as hydrology and meteorology and in
the loadings, both anthropogenic and natural, of nutrients, toxic substances, and thermal energy.
The mathematical model is based on a set of hypotheses regarding physical, chemical,
and biological processes in the aquatic ecosystem. These hypotheses are derived from
laboratory and field experiments and from conservation laws for mass, energy, and momentum.
State variables simulated by the mathematical model are compared with field observations from
i
the Study Reach to estimate model parameters and to characterize the uncertainty of the
simulated results. | The mathematical model is then used to make quantitative estimates of
ecological risk for certain components of the aquatic ecosystem.
D.2. MODEL DEVELOPMENT
The process of model development includes (1) stating of hypotheses that form the basis
for the model; (2) ;estimating the parameters that control the flow of mass and energy in the
model using laboratory and field studies and other available research; and (3) characterizing the
uncertainty of simulated results from the mathematical model. The hypotheses forming the basis
for the mathematipal model of the Study Reach are:
i ,
• Major features of the Study Reach can be described in terms of compartments between
which there can be flows of energy, material, and information.
• The flows !of energy, mass, and information between ecosystem compartments can be
described mathematically on the basis of the results of existing ecosystem theory.
• Probabilistic models can be developed for describing the uncertainty and variability of
environmental driving forces including meteorology and hydrology.
D-l
-------
• Probabilistic models can be developed for describing the uncertainty and variability of
loadings of nutrients, toxic substances, and thermal energy from both anthropogenic and
natural sources.
it
• Measurement endpoints for the risk analysis can be derived from the State of Idaho's
water quality standards and from habitat suitability measures developed from biological
research.
D.2.1. Dynamic Model of Mass and Energy Balances
In Figure D-2, ecosystem driving forces, characterized by variability found in the Study
Reach, are input to a dynamic model of mass and energy balance. The simulated state variables
output from the model will have variability derived from the input driving forces. The model
output can be used to characterize stressors and exposure where simulated state variables
correspond to measures of ecosystem effects. To implement the dynamic model of mass and
energy, the Study Reach has been divided into two major ecosystem components: one that
describes the chemical, physical, and biological characteristics of the moving water column and
one that describes the benthic plant community attached to or associated with the river bottom.
The flow of energy, mass and information for these components is shown in Figures D-3 and
D-4.
D.2.1.1. Water Column
For purposes of capturing spatial variation, the water column is segmented as well-mixed
compartments organized either longitudinally as in Figure D-5 or vertically as in Figure D-6.
The longitudinal organization is used to describe freely flowing segments or run-of-the-river
reservoir segments. The vertical organization is used to describe segments where vertical
stratification of water quality constituents may be important. Within each of the well-mixed
compartments., the flow of energy and material is the .same as shown in Figure D-3.
The mathematical description of mass and energy flow in the water column described in
this report is based on the mathematical model RBM10 (Yearsley, 1991). RBM10 has been used
as a decision support tool in a number of river basins in the Pacific Northwest, including the
Snake River above Milner Dam (Yearsley, 1976) and the Spokane River (Yearsley and Duncan,
1988). RBM10 makes use of concepts that have been used in other modeling efforts (e.g.,
Thomann et al., 1975; Patten et al., 1975; DiTorb et al., 1975; Chen and Orlob, 1975; Scavia,
1980) and is conceptually similar to these models. State variables in the water column simulated
by this model are given in Table D-l.
The general assumptions associated with the mathematical development of the model for
water column state variables are:
D-2
-------
• State variables of the ecosystem can be characterized by volume-averages over a
given computational element (Figure D-5 for free-flowing rivers or run-of-the-river
reservoirs and Figure D-6 for stratified reservoirs) and a finite time interval.
• Horizontal and vertical advection and vertical eddy diffusion are the primary physical
processes for water and mass transport.
i
• The vertical coefficient of eddy diffusivity is the same for all state variables.
•. Rate constants for the various reactions do not change over a given length segment.
i ' .
• The river system can be divided into a finite number of segments within which cross-
sectionally averaged hydrodynamic characteristics are constant.
• Hydrodynamic characteristics of free-flowing river segments and run-of-the-river
reservoirs can be expressed as a simple function of the flow in any segment.
• The river flow varies gradually such that hydraulic characteristics can be estimated
using the standard methods for calculating steady, gradually varied flow in natural or
man-made channels.
• Hydrodynamic characteristics of stratified reservoir segments are a function of the
density structure of the reservoir. The density structure in freshwater systems is a
function of water temperature and the concentration of suspended material.
s
• The tune required for flow in a reach to adjust to changes in elevation is small
compared with the travel time of some constituent.
Given these assumptions for a state variable, C, representing a water column constituent
that is spatially averaged over a computational element, the general conservation equation in the
1th free-flowing riyer or run-of-the-river reservoir segment can be described by the mass balance
equation: \
(D-la)
D-3
-------
Similarly, for the j* stratified reservoir segment, the general conservation equation is
= A(QC)X + A(QC)z + A(KAC)
n=l
(D-lb)
where
Vj — the volume of the j* water column computational element, where j refers to
the segment number;
Cj = the length- and time-averaged value of the 1th water column state variable
over the j* computational element;
A(QC)X = the advective transfer in the longitudinal (x-) direction;
A(QC)Z = the advective transfer in the vertical (z-) direction;
A(QC) n = the transfer of flows from the computational element due to inputs or outputs
such as point source discharges, nonpoint source return flows, and
withdrawals for drinking water or irrigation;
A(KAC) =• the eddy diffusion in the vertical (z-) direction;
A y = the surface area of the ij* element;
.$3 = the source term for the state variable, Q, in the j* element; and
TJJ = the sink term for the state variable, Q, in the j element.
For all state variables, gains and losses due to the physical processes of advection and
eddy diffusion are treated in the same manner. The source, &ijt and sink, rij5 for each of the state
variables are determined from existing knowledge of physical, chemical, and biological
processes.
The rates at which mass and thermal energy are transported, or advected, A(QC)X and
A(QC)Z, are determined by the hydrodynamics of the river system. This implementation of the
D-4
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model assumes the river flow varies gradually and that the hydraulic characteristics can be
estimated using the methods for calculating steady, gradually varied flow developed by the U.S.
Army Corps of Engineers' Hydrologic Engineering Center (HEC). The model used for the
hydraulic analysis was HEC-RAS (HEC, 1995). This model cannot be used to analyze the
effects of storm events or high-frequency flow fluctuations associated with load-following at
hydroelectric facilities. However, the model is relatively easy to implement and provides
sufficient flexibility to evaluate the effect of seasonal and long-term changes in river flow.
The hydraulic characteristics of the river system are specified in the ecosystem model hi
terms of simple relationships between depth and flow and depth and velocity. That is,
D
=, Ad QBd
(D-2)
where
D = the average depth of the river segment, feet;
Q = the river flow, cfs;
Ad = a coefficient determined from hydraulic data;
Bd = a coefficient determined from hydraulic data;
and
(D-3)
where
B
=r a coefficient determined from hydraulic data; and
I
= a coefficient determined from hydraulic data.
The coefficients Ad, Bd, Au, and Bu are determined using the steady, gradually varied
flow, or step-backwater model, HEC-RAS (HEC, 1995). Given data describing cross-sectional
elevation profiles, riverbed elevation, and friction factors as a function of distance along the
i
river, HEC-RAS provides estimates of river surface profiles at various flows. These estimates
are obtained by balancing the energy associated with friction losses, changes hi riverbed
elevation, and changes in river velocity. The output from the models includes estimates of river
depth and river velocity at these flows. Regression analysis is performed on this output to
estimate the coefficients in Equations D-2 and D-3.
D-5
-------
Diffusion-like processes, A(KAC)Z, characterize the vertical transport of mass and
thermal energy by random motions, or turbulence, in the reservoir segments of the river. The
coefficient of eddy diffusivity, K.,, can be estimated from available data. For example, methods
for estimating the coefficient of eddy diffusivity for water temperature are described by Water
Resources Engineers (1968). Generally, it is assumed the coefficient of eddy diffusivity, K^, is
the same for all state variables. When sufficient data are not available for estimating the
coefficient of eddy diffusivity, as is the case for the reservoirs in the Snake River, turbulence
closure methods such as those described by Bowie et al. (1985) must be used.
An additional assumption is that horizontal transport of mass and thermal energy by
random motions, or turbulence, in the river segments is negligible compared to advection
, processes.
The kinetics of mass and energy flow for the water column state variables simulated by
the model (Table D-l) are similar to the kinetics described in other modeling efforts. Bowie et
al. (1985) give a comprehensive discussion of the kinetics of models of this type. Process
diagrams and the kinetic formulations for mass and energy flow of water column state variables
are described in detail in Appendix A.
D.2.1.2. Sediments
The sediments associated with the benthic plants in the Study Reach are segmented into
well-mixed compartments organized longitudinally. In general (e.g., Ambrose et al., 1993),
many of the physical, chemical, and biological processes in the sediments are similar
conceptually to those in the water column. However, in this application of simulation methods
to risk analysis, the model hypothesis includes sediments only to the extent they provide
substrate for benthic plants, including vascular macrophytes, epiphytes, and periphyton.
The flow of mass and energy within the sediments is generally not included in this
model. However, the flow of mass and energy within the water column, as it affects uptake by
the roots of vascular macrophytes, is included in the conceptual model. Where flow of mass or
energy from the sediments are part of the conceptual model, as in the case of nutrient flow to the
roots of vascular macrophytes, it is assumed to be unlimited by plant uptake. Similarly, the flow
of solids to and from the sediments is assumed to be at steady state. That is, there is neither gain
nor loss of substrate due to deposition and scouring.
For benthic component state variables, Bi5 the model hypothesis for the flow of mass and
energy is:
dt
D-6
-------
where
B; = the length- and tune-averaged value of the Ith benthic component state
variable over the jth computational element;
Vj = the volume of the j* water-column computational element, where j refers to
the segment number;
(fry = the source term for the state variable, Bi5 in the j* element; and
i • .
Fij =' the sink term for the state variable, Bi, in the j* element.
The benthic plant community state variables included in the model for the sediments are
given in Table D-2.
D.2.1.3. Vascular Macrophytes
The hypothesis for the kinetics of vascular macrophytes is based on the terrestrial
ecosystem energy model developed by O'Neill et al. (1972) for a closed-canopy, homogeneous
forest ecosystem in the eastern deciduous biome. Bloomfield et al. (1973) adapted the concept
to simulate aquatic macrophytes in Lake George, New York. The model for aquatic
macrophytes in the Study Reach is similar to the Lake George model. Important features of this
hypothesis are: \
• The organic matter associated with vascular macrophytes can be idealized by three
compartments for organic carbon: roots, leaves/shoots, and carbon storage.
• The accumulation of carbon in carbon storage is by photosynthesis. Carbon flows to
roots and leaves/shoots from storage.
Other features of the model for vascular macrophytes are based on previous research and
observations of macrophytes in the Middle Snake River (Falter and Carlson, 1994; Falter et al.,
1995; Falter and Burris, 1996). These features are characterized by the following assumptions:
• Michaelis-Menten formulations are appropriate for light, nutrient, and habitat
limitations (e.g., Barber, 1991; Porcella et al., 1983).
D-7
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• Nutrient uptake rates are low at low river velocities because of poor rates of
exchange, but increase with river velocity up to a certain optimum (Horner et al.,
1983). As river velocity increase beyond a certain point, physical stresses begin to
occur in the plants. These stresses lead to mortality of the plants and increase the rate
• of sloughing due to physical processes (Chambers et al., 1991 a,b).
• Vascular macrophytes with extensive root systems, such as Potamogeton, take a large
percentage of their nutrients from the sediments (Howard-Williams and Allanson,
1981). Macrophytes with limited root systems, such as Ceratophyllum, derive the
majority of their nutrients from the water column.
D.2.1.4. Epiphytes
The hypothesis forming the basis for the model of epiphytes is a population model with
Michaelis-Menten formulations for light, nutrient, and habitat limitations. This model was
modified to include the assumption that in the Middle Snake River epiphytes such as
Cladophora are generally associated with a macrophyte substrate on which they attach
themselves and grow. Furthermore, the epiphytes intercept solar radiation in the top 10% of the
water column, rather than over the entire water column. This assumption was based on
observations made during the 1992-1994 studies of macrophytes (Falter and Carlson, 1994;
Falter et al., 1995; Falter and Burns, 1996).
D.2.1.5. Periphyton
The hypothesis forming the basis for the model of periphyton is a population model with
Michaelis-Menten formulations for light, nutrient, and habitat limitations. It is similar to those
of Porcella et al. (1983) and Runke et al. (1981).
The mass balance equations for vascular macrophytes, epiphytes, and periphyton are
given in Appendix B.
D.2.2. Variability and Uncertainty in Environmental Factors
Principal environmental factors for the Study Reach are hydrology and meteorology.
The model accounts for variability and uncertainty of these environmental factors by assuming
that the 67-year data record from 1928 to 1994 for river flow and air temperature for Twin Falls
and Glenns Ferry is a representative sample for hydrology and meteorology. Use of the actual
data record obviates the need for a complex time-series model, which would account for serial
correlation between flows at various locations and times, serial correlation between air
temperatures at various locations and times, and serial correlation between flows and
meteorological conditions.
D-8
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D.2.2.1. Meteorology
Meteorology data required for the analysis include air temperature, cloud cover, some
measure of water yapor in the air such as dewpoint or relative humidity, and wind speed. Air
temperature data for Glenns Ferry were used to characterize weather for segments of the Study
Reach from SnakeiRiver Mile 547.0 to Snake River Mile 579.6. Air temperature data for Twin
Falls were used to characterize water for the segments of the Study Reach from Snake River
Mile 579.6 to Snake River Mile 640.0.
Estimates of daily values of dewpoint, cloud cover, and wind speed were made using a
statistical analysis jof data from the closest station with a long-term record for these variables.
Daily values of these variables for each of the eight 3-hour periods in a day were assumed to be
equal to the monthly averages for the eight 3-hour periods in a day for Burley, Idaho, as reported
by the Pacific Northwest River Basin Commission (PNRBC) (1968).
! ' ' •
D.2.2.2. Hydrology
The U.S. Geological Survey (USGS) maintains gaging stations at several locations in the
i
Study Reach, including the beginning (USGS 13088000, Snake River at Milner) and ending
(USGS 13154500,; Snake River at King Hill) segments. In addition, it maintains gages at
important surface inflows and springs. The records from these stations are very good and have
I
been used to develop water budgets for the Snake River Plain in Idaho and Eastern Oregon
(Kjelstrom, 1992). However, during the period in which flows have been recorded in the Snake
River there have been numerous changes to the system. Major changes include the construction
of dams for irrigation and power generation. Furthermore, the pattern of diversion for irrigation .
purposes has changed during this period. These changes have resulted in alterations of the
hydrologic regime|of the Snake River, in terms of both the magnitude and timing of flow
(Richter, 1996). |
Because of these changes in the hydrologic regime, the existing record of actual flows
cannot be used directly to characterize risk associated with present management of the system
hydrology. However, the Idaho Department of Water Resources (IDWR) has developed a model
that estimates the historical monthly average flow and reach gain in the Snake River given
present-day operating rules for" the system. The results of applying the model to the period 1928-
1994, reported as IDWR Study 150 (Robert Suter, IDWR, personal communication), are used to
characterize hydrologic variability for the risk analysis in the Study Reach.
D.2.3. State Variables as Measurement Endpoints
In the framework for ecological risk, the focus in risk characterization is provided by
assessment endpoints. The assessment endpoints represent the specific environmental goals to
be addressed in the risk assessment. Measurement endpoints are quantitative estimates of the
: D-9
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state of the ecosystem, which can be related in some way to the values expressed by the
assessment endpoints. The assessment endpoints and their associated measurement endpoints
are those shown in Table D-3. A logical source for measurement endpoints is the State of
Idaho's water quality standards. These standards were developed in accordance with the Clean
Water Act, in which the stated goal is "to restore and maintain the chemical, physical, and
biological integrity of the Nation's waters." Those water quality standards that provide numeric
criteria, or ones for which numeric criteria can be developed from narrative standards, are
included in the analysis plan as measures of effect.
' Although the water quality standards do provide measures of effect, they are typically
measures that relate to a fairly broad range of aquatic species and environments. For example,
the water quality standards-define certain criteria for the protection of cold-water species without
specifically describing which ones are the target organisms. These criteria may be protective of
aquatic organisms within the group characterized as cold-water species, but there may be some
organisms or certain life stages of organisms in this group that are not protected. Because of this
it is desirable to develop site-specific lines of evidence if they are available.
For the Study Reach, there are site-specific measures of effect that can be integrated into
the analysis plan to provide additional lines of evidence. Among these are indices the USFWS
developed to characterize habitat suitability for certain cold-water fishes. The USFWS uses
habitat suitability indices for assessing the impacts of flow modification on aquatic habitat
resources of rivers and streams. An important objective of this method, called the Instream Flow
incremental Method (IFIM), is to make quantitative comparisons of habitat conditions at
differing regimes of river flow.
Quantitative comparisons are accomplished in the IFIM by calculating habitat suitability
for various regimes of river flow. Integral components of this calculation are the habitat
suitability curves. These curves define suitability indices for different life stages of target
aquatic species selected for a particular study.. The suitability indices are functions of ecosystem.
state variables such as water depth, water velocity, water temperature, and substrate or cover
type.
Because the indices measure suitability of habitat as a function of ecosystem state, they
can also be used as measurement endpoints. However, the target species for which suitability is
quantified must be relevant in terms of the assessment endpoints. For the Study Reach, this
means they must be cold-water species that are native to the region. On the basis of the work of
Anglin et al. (1992), three cold-water fishes found in the Study Reach, the mountain whitefish,
rainbow trout, and white sturgeon, have been selected as target species to be used with the
habitat suitability indices. Anglin et al. (1992) developed habitat suitability indices for these
species for the Snake River from C.J. Strike Dam downstream to the upper end of Brownlee
Pool. Because habitat suitability indices appropriate for large river systems were lacking for
D-10
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these species, Anglin et'al. (1992) used criteria from smaller river systems. Extension of the
criteria from smaller river systems to the Snake River was done subjectively based on the
judgment of regional biologists. For the purposes of the ecological risk analysis, we have
i
assumed the process adequately represents the habitat requirements for the target species in the
Study Reach.
Performing ecological risk using simulation methods requires that measurement
endpoints selected from the water quality standards and from the habitat suitability indices are
also state variables simulated by the dynamic model (Tables D-l and D-2). Those measurement
endpoints for which state variables are simulated by the model and for which there are numeric
water quality criteria and habitat suitability indices are given in Table D-4. The environmental
values, or assessment endpoints, to which these quantitative measures are linked are also given
in Table D-4. ;
The analysis of ecological risk using simulation methods addresses only a subset of the
issues associated with ecological risk in the Study Reach. The hierarchy of interactions, from
stressor source to stressor-to-stressor characteristics to endpoint for each of the assessment
endpoints, as conceptualized in the Problem Formulation, is shown in Figure D-7. Those
elements for which the simulation methods do not apply are shown as shaded and are primarily
those affecting sediments and sediment transport. ,
D.2.4. System Boundaries, Length and Time Scales
D.2.4.1. System Boundaries
As defined previously, the Study Reach includes the segment of the Snake River from
Milner Dam (RM ,640.0) to King Hill (RM 545.3). The ecological risk analysis applies only to
the main stem of the Snake River, but includes inputs of mass and energy from tributaries,
irrigation returns, municipal waste discharge facilities, springs, and groundwater. The Study
Reach was divided into two meteorological provinces, one from Milner Dam (RM 640.0) to
Upper Salmon Falls Dam (RM 579.6), the other from Upper Salmon Falls Dam to King Hill
(RM 545.3). The risk analysis also assumes that management rules for controllable input, both
explicit and implicit, are based on existing conditions.
i
D.2.4.2. Length Scales
To obtain optimal spatial resolution with the mathematical model, the river was divided
into several segments of the type shown in Figure D-5 (longitudinal orientation) for run-of-the-
river reservoirs and freely flowing river segments and segments, of the type shown in Figure D-6
(vertical orientation) for those reservoirs exhibiting vertical stratification. Twin Falls and
Shoshone Falls Reservoirs were treated as reservoirs with the potential for vertical stratification,
on the basis of data collected by the Idaho Power Company (Myers and Pierce, 1996). For the
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run-of-the-river reservoirs and freely flowing river reaches, short segment lengths (0.1-0.3 miles)
characterized the rapids, whereas the deeper, slower-moving sections between rapids were
characterized by longer segment lengths (0.5-3.3 miles). Segments in the stratified reservoirs
were chosen such that concentration gradients over vertical distances of 5.0 feet or more could
be resolved.
For the risk analysis, it was useful to characterize the length scales for the river in terms
of geomorphologic, hydrologic, and cultural features as shown in Table D-5. the rationale for
these length scales is based on the work of Brockway and Robison (1992) and Covington and
Weaver (1989,1990a-c, 1991).
D.2.4.3. Time Scales
Time scales associated with the analysis are a function of the computational scheme used
to solve the equations, the rates of response of ecological processes included in the model, and
the time scales of the system inputs or driving forces. For purposes of obtaining an accurate
solution in the mathematical sense, it is necessary to satisfy certain stability criteria required by
the numerical methods used. These criteria are a function of the river flow, the rates of turbulent
diffusion, and the volume of the river as described previously. The Study Reach is generally
dominated by advection. For pure advection, the criterion for stability of the computational
scheme is given by:
where
Atc = the time increment for the numerical solution technique, seconds;
V = the net volume associated with the computational element, cubic feet; and
Q = flow into the computational element, cfs.
This time interval, Atc, is basically the time it takes a molecule of water to traverse a
given segment. The numerical method that simulates the time history of mass and thermal
energy computes the critical time increment necessary to satisfy this stability criterion.
Therefore, the smallest tune interval (highest frequency) for which state variables are simulated
is a function of the river velocity and the segment length. For the Study Reach, this
computationally driven time interval is smallest in the short, high-velocity segments (rapids) and
can be as small as 100-200 seconds for some segments of the Snake River. In certain reservoir
D.-12
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segments under low-flow conditions, this time interval can be on the order of days. For obtaining
an accurate, stable: solution to the set of difference equations, the integration time step must be
equal to or less than the stability criterion given above.
The ecosystem processes included in the mathematical model (Equations A-1 to A-16
and B-l to B-4) determine the time scales associated with ecosystem response. In this model,^
the ecosystem processes with the highest frequencies (shortest time scales) are those affected by
diurnal variations in solar radiation. Ecosystem processes affected by diurnal variations in solar
radiation are photosynthesis and the thermal energy budget. Therefore, the shortest time scales
of ecological significance in the simulation results are those associated with the diurnal
variations in solar radiation.
Other important time scales of simulated ecosystems processes are those associated with
(1) rates of transfer of dissolved oxygen (deoxygenation and reaeration), (2) rates of transfer of
i
the various forms of nitrogen and phosphorus (nitrification, mineralization, uptake by growth of
\
aquatic plants), and (3) growth, respiration, and mortality rates of aquatic plants. The tune scales
for these processes are determined by the various rates of transfer. The tune scales can vary
from the order of hours to the order of months. The time scales of these rates are discussed in
Section D.3. (Parameter Estimation).
The time scales of the system inputs or driving forces include, in addition to the diurnal
variations in solar lenergy, annual variations in thermal energy budget and hydrology. Time
scales associated with hydrology affect constituent loadings, as these loadings are also generally
a function of hydrology. Available meteorology, hydrology, and constituent concentration data
were used to characterize these time scales as described in Section D.3 (Parameter Estimation).
i , . -
D.3. PARAMETER ESTIMATION
For analysis of ecological risk through simulation, it is necessary to estimate the
parameters in the mathematical model as well as those that characterize the measures of
ecological effects. The parameters in the mathematical model are those quantifying the rates at
which mass and energy flow between state variables (Equations A-l to A-16 and B-l to B-4) and
those quantifying the input or driving forces. Available data from the Study Reach and results of
scientific studies in other river and lake systems provided the basis for estimating the parameters
in the mathematical model. The State of Idaho's water quality standards and habitat suitability
studies by the USFWS provided the basis for estimating the parameters used to characterize
measures of ecological effects.
D-13
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D.3.1. Ecosystem Driving Forces and Stressors
D.3.1.1. Meteorology
Air temperature, relative humidity or dewpoint, cloud cover, wind speed, and
atmospheric pressure are required inputs to the model for estimating the heat budget and the
amount of solar energy available for primary productivity. For the upstream segment (Milner
Dam to Upper Salmon Falls Dam), meteorology was characterized by daily maximum and
minimum air temperatures for Twin Falls using the data from Twin Falls Weather Service Office
and monthly averaged wind speed, cloud cover and dewpoint for Gooding (PNRBC, 1968). For
the downstream segment (Upper Salmon Falls Dam to King Hill), the meteorology was
characterized by daily maximum and minimum air temperatures for Glens Ferry (National
Weather Service's Local Climatological Summaries) and monthly averaged wind speed., cloud
cover, and dewpoint for Gooding (PNRBC, 1968). Diurnal variations in air temperature were
estimated from the maximum and minimum temperatures by assuming the temperature varied
sinusoidally with a period of 24 hours. Incident solar radiation at the water surface was
computed every 3 hours using air temperature, cloud cover, and solar altitude by the method
described in WRE (1968).
D.3.1.2. Hydrology
The hydrology of this segment of the Snake River is complex. According to the USGS
(1992), the springflow/groundwater contribution to the Snake River between Milner Dam and
King Hill, Idaho, was approximately 4,000 cfs in 1980. In addition, there are major tributaries
such as Rock Creek, Mud Creek, Deep Creek, and Salmon Falls Creek, as well as numerous
irrigation return flows.
The water budget was derived from USGS daily flow data at Milner Dam (USGS
13088000), Kimberly (USGS 13090000), Buhl (USGS 13094000), King Hill (USGS 13154500);
estimates of surface return flow given in Brockway and Robison (1992) and the State of Idaho's
Division of Environmental Quality (DEQ) (1995); and estimates of the spring flows (Covington
and Weaver; 1989,1990a-c, 1991). The study area from Milner to King Hill was divided into
four sections, the endpoints of each section being determined by the location of a USGS gaging
station. For each section, estimates of the total surface return flows and spring flows were
compared to the reach gain between gages as reported by the USGS. Differences between the
total surface gains and the reach gain estimated from the gaging station were assigned to
"groundwater" return flow. In addition, it was assumed that the groundwater flow between
USGS gages, computed in this way, was distributed uniformly along the length of the river
between the gages.
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D.3.1.3. Hydraulic Characteristics
The coefficients needed to define the hydraulic properties with relationships of the type
i
described by Equations D-2 and D-3 were obtained from a regression analysis of surface water
profiles simulated tHEC-RAS (HEC, 1995). Cross-sectional characteristics of the river between
Milner Dam and King Hill were obtained from a number of sources, including the U.S. Army
Corps of Engineers, the Idaho Power Company, and local consulting firms (Gebhardt, 1992).
Surface water profile analyses obtained using HEC-2 (HEC, 1991) by Brockway and Ralston
(1992) were used for river segments between RM 610 and RM 607.0, whereas U.S. Army Corps
of Engineers data were used for RM 607.0 to RM 588. Soundings of reservoir depth reported by
Idaho Power Company were used to develop relationships for volume and area as a function of
reservoir elevations for Twin Falls and Shoshone Falls reservoirs. Results of surface water
profile analyses done for the Idaho Power Company were used to describe the hydraulic
properties of the river segment between the Gridley Bridge and Bliss Dam.
An example of the calculation of the coefficients for velocity as a function of flow
(Equation D-3) is given in Figure D-8. The example is taken from the Study Reach at RM
599.0. HEC-RAS; was used to estimate average river velocities and water depths at flows of
1,500, 3,000, 5,000, 7,500, and 10,000 cfs. In the example shown in Figure D-8, a least-squares
analysis of the log-transformed velocity and flow output from the HEC-RAS model provided
estimates of the parameters, Au and Bu.' Using this method, coefficients for the relationship
between velocity and flow and depth and flow were estimated for the other segments of the
Study Reach. Hydraulic coefficients for Study Reach, estimated in this manner, are given in
Table D-6. ! .
D.3.2. Sources of Mass and Energy
There are a number of sources of energy and mass in the Study Reach. The sources
included in the model are given in Table D-7. Water chemistry data collected by the University
of Idaho Agricultural Research Station, Idaho DEQ, Clear Springs Food Inc., and the City of
Twin Falls were used to estimate daily mass loadings from these point sources. The frequency at
which the data were collected by each of these entities varied considerably from source to
source. Much of the water quality and quantity data were collected from tributaries, irrigation
,!
returns, and fish hatcheries on a biweekly schedule during the period April through October and
less frequently during the remaining months. The sampling frequency for the City of Twin Falls
varied from daily for state variables such as flow, temperature, and pH to weekly for major
nutrients. With the exception of the river flows measured at USGS gaging stations, very few
measurements of water quality or quantity were made on a daily basis.
The numerical method that performs the simulations requires data at each computational
time step. To accommodate this requirement, it was necessary to fill in missing data. In general,
i .. D-15
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the method of filling in data was no more complex than linear interpolation between the times at
which observations were made.
D.3.2.1. Hatcheries
Long-term averages of water chemistry, from the U of I/ARS data set, collected during
1990-91, were used to characterize the mass loading from hatcheries. The average
concentrations of flow and water chemistry for the hatcheries, as used in the analysis, are given
in Table D-8. Daily estimates of mass loading, for input to the model, were estimated as being
equal to the long-term values.
D.3.2.2. Major Tributaries
East Perrine Coulee, Rock Creek, Cedar Draw Creek, Mud Creek, Deep Creek, Salmon
Falls Creek, Billingsley Creek, and the Malad River were treated as major tributaries to the study
section. Water chemistry used to characterize mass loading for these sources was obtained from
various sources. Data source and period of record for each of these tributaries are shown in
Table D-9. To obtain daily values for input to the model, missing data were filled in by linear
interpolation when the data gap was less than 30 days. For data gaps greater than 30 days, the
daily values were set equal to the monthly average, as computed from the rest of the record.
D.3.2.3. Minor Tributaries and Irrigation Return Flows
Monthly averages of water chemistry, from the U of I/ARS data set (Brockway and
Robison, 1992), were used for minor tributaries and irrigation return flows. Monthly averages of
flow and water chemistry for the minor irrigation return flows are given in Table D-10. Daily
values for input to the model were set equal to the average values for the appropriate month.
D.3.2.4. City of Twin Falls Sewage Treatment Plant
Water quality and quantity data for Twin Falls sewage treatment plant were provided by
the City of Twin Falls for the period 5/27/92 to 12/31/94. In addition, some measurements of
quality and quantity were reported in the study conducted by Clear Springs Food, Inc.
(MacMillan, 1992). For estimating model parameters, the entire available record was used, with
linear interpolation between those days for which there were measurements filling in missing
data.
For the ecological risk analysis, only that segment of data from the period 2/23/93-
12/31/94 was used. The City of Twin Falls upgraded its treatment facility in late 1991 -early
1992 (Nikki Arnold, EPA Region 10 Idaho Operations Office, personal communication) to
increase the efficiency of solids removal. According to data provided by the City of Twin Falls
(Figure D-9), an increase in ammonia removal efficiency did not occur, until early 1993 (see
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arrow in Figure D-9). The ammonia data from the beginning of February 1993 were therefore
assumed to be representative of present operation of the sewage treatment facility. Means and
standard deviations for various water quality and quantity of the sewage treatment plant effluent
are given in Table P-11. These statistics were used to generate time series of effluent quality
using the random walk model
where
X(t)
N(0,o2) =
X(t) + N(0,a2)
(D-4)
the value of some constituent, or its log transform, at the time, t; and
a normal random deviation of mean, 0, and variance, a2.
Constituents with means and standard deviations of the log-transformed measurements in
Table D-l 1 were modeled as the log transform then converted. Effluent temperature was
modeled with the seasonal model
where
T(t) = the daily effluent temperature, °C;
— the annual average effluent temperature, °C;
AT =, the annual temperature variation from the average, °C;
= the time, days; and
=H the phase shift in the temperature, days.
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D.3.2.5. Spring Flows and Groundwater
Water chemistry data collected by the USGS (USGS 13095500, Clark and Ott, 1996) and
the University of Idaho Agricultural Research Station at Kimberly were used to estimate mass
loadings from spring flows and groundwater. Springs included in the model are shown in Table
D-12, as are the sources of water chemistry. The daily values of water chemistry input to the
model were set equal to the long-term averages for the stations as shown in Table D-13. Daily
values of water temperature were estimated from an equation of the form:
T(t) = T + ATsin
365
(D-5)
where
T(t) = the daily spring temperature, °C;
T = the annual average spring temperature, °C;
AT = the annual temperature variation from the average, °C;
t = the tune, days; and
t0 = the phase shift in the temperature, days.
Parameters for Equation D-5 were estimated with nonlinear regression methods and are
shown in Table D-14.
Water chemistry of the groundwater return flow, estimated as the difference between
accumulated spring and surface return flow and actual flows measured at the USGS gaging
stations, was assumed to be equal to the water chemistry of certain springs. The correspondence
between water quality of the groundwater return flow and measured water quality of spring flow
for each of the gaged segments is shown in Table D-15.
D.3.3. Dynamic Model of Mass and Energy Flow
In principle, the parameters for the equations (A-l to A-16 and B-l to B-4) of mass and
energy flows can be inferred from properly designed field studies or observations. A properly
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designed field study is one in which all driving forces and environmental conditions are
specified and there are enough measurements of state variables to formulate the problem
properly. Because the parameter estimation process depends on the availability of data
describing driving forces and the response of the river ecosystem to these forces, a
comprehensive sampling program was designed jointly by the State of Idaho's DEQ and EPA
Region 10. The sampling program included collection of water chemistry data hi the Study
Reach, tributaries,; and point sources, as well as observations of biomass in the macrophyte,
phytoplankton, and benthic invertebrate communities. The major data collection effort occurred
during the period 1990-1994 and the results are reported in Brockway and Robison (1992,1993),
Falter and Carlson (1994), Falter et al. (1995), Falter and Bums (1996), Minshall et al. (1993),
Minshall and Robinson (1994), and Royer et al. (1995). Data collected by Idaho Power •
Company (Ralph Myers, Shaun Parkinson, personal communication), Clear Springs Food
(Macmillan, 1992), the City of Twin Falls (personal communication), and DEQ (Don Essig,
personal communication) have also been used in the process.
When the problem is well defined, formal techniques (Menke, 1984) can be used to
obtain estimates of parameters. Solving the parameter estimation problem generally involves
minimizing some aspect of the difference between simulated and observed values. For example,
the sum of the squared difference or, in some cases, the sum of the weighted squared difference
between each simulated and observed value is commonly used. An estimate of the parameters is
then obtained formally by solving the Equations A-l to A-16 and B-l to B-4 with the parameters
as unknowns and the measured state variables as known. The solution, which minimizes the cost
function, provides an estimate of the parameters. This process becomes extremely difficult as the
number of parameters increases and as the nonlinearity of the governing equations increases.
The number of parameters is large in the Study Reach, the degree of nonlinearity is high,
the number of measured state variables is limited, and the measurements are not without error.
This makes it difficult to perform parameter estimation with formal methods. Because of the
difficulty of applying formal techniques to solving the inverse problem, initial estimates of the
parameters defining kinetics of mass and energy transfer for the water column were selected to
be within the range of values used in similar models of surface water quality (Bowie et al.,
1985). Selected parameters were then adjusted by trial and error to improve agreement between
simulated and observed state variable estimates.
D.3.4. Rates of Mass and Energy Transfer
D.3.4.1. Carbonaceous Biological Oxygen Demand (CBOD)/Dissolved Oxygen (DO)
No data were available in the Study Reach to estimate the deoxygenation rate, K,.
Therefore, a value;of K! = 0.1 days"1 (Equation A-l) was chosen for the entire river. CBOD from
point and nonpoint discharges does not appear to be a major source of oxygen demand in the
D-19
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Study Reach. Limited testing of the model showed that DO in the river was not sensitive to
changes in this parameter within the ranges typical of this system (Bowie et al., 1985).
The reaeration rate, K2 (Equation A-2), was estimated in a number of different ways,
depending on the hydraulic properties of each reach. For the two reservoirs, Twin Falls and
Shoshone Falls, the formulation for reaeration coefficients in lakes developed by Smith (1978)
was used. In run-of-the-river segments where the water was moving relatively slowly, the
O'Connor-Dobbins (1958) formulation was applied. In run-of-the-river segments where the
water velocities were higher, such as Auger Falls, Boulder Rapids, Empire Rapids, and Kanaka
Rapids, the Churchill et al. (1962) formulation was applied.
D.3.4.2. Phytoplankton Biomass
Rates of phytoplankton growth, respiration, nutrient, light and temperature limitations,
and stoichiometry were initially based on values typical of those used in other phytoplankton
model studies (Bowie et al., 1985). Sensitivity analysis showed the dynamics of phytoplankton
in the Study Reach to be more responsive to hydrology and to initial conditions from upstream
sources.
D.3.4.3. Nitrogen
Rates of flow of nitrogen between the species, organic N, NH4-N, and
NO2+NO3-N were initially estimated as being in the range found in other studies (Bowie et al.,
1985). In the Auger Falls segment below the City of Twin Falls STP, the nitrification rate, K55,
was increased from the initial estimate of 0.25 days"1 to 2.25 days'1 to achieve better agreement
between simulated and observed values.
D.3.4.4. Phosphorus
The rate of mineralization for organic phosphorus was estimated from the literature
(Bowie et al., 1985) as 0.005 days'1 throughout the entire Study Reach. This corresponds to a
time constant of approximately 200 days. The residence time of a water parcel in the Study
Reach is much less than this. The simulation results are, therefore, not sensitive to changes in
this parameter.
Initial simulations resulted in a consistent overestimate of total phosphorus at all
locations hi the Study Reach. Unbiased simulations of phosphorus were obtained by
incorporating a loss rate for organic and inorganic phosphorus into the mass balance equations
(Equations A-13 and A-15). The rates were estimated to be 0.5 days'1 and 0.05 days'1 for
organic and inorganic phosphorus, respectively. Sediment trap data reported by Falter and
Bums (1996) provided the basis for these estimates.
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D.3.4.5. Vascular Macrophytes and Epiphytes
The mathematical model for vascular macrophytes and epiphytes (Equations B-l to B-4)
is a hypothesis based on previous work in lakes (Bloomfield et al., 1973) and the eastern
deciduous forest biome (O'Neill et al., 1972). The model is highly nonlinear and contains many
parameters. Extensive field studies of aquatic macrophytes were conducted in the Study Reach
(Falter and Carlson, 1994; Falter et al., 1995; Falter and Burris, 1996). However, given the
complexity of the model, it was necessary to estimate many of the parameters from the literature
and then to adjust the most sensitive parameters until there was reasonable agreement between
simulated and observed state estimates.
The extensive macrophyte literature provided a basis for the initial parameter estimation
process. MacMillan (1992) has a comprehensive discussion of macrophyte and epiphyte kinetics
by Barber (1991), and Krousel (1991) reported values for growth rates, respiration rates,
Michaelis-Menten half-saturation constants for nitrogen and phosphorus, and mortality rates hi
three species of vascular macrophytes and epiphytes, van Wijk (1989) measured Michaelis-
Menten half-saturation levels for phosphorus and nitrogen in Potamogeton pectinatus.
Chambers et al. (1991a,b) measured the response of macrophytes to river velocity and to nutrient
concentrations in the sediments and the water column. Horner et al. (1983) developed a
mechanism-based ;model of periphyton growth based on river velocity and nutrient enrichment.
Initial estimates of parameters describing macrophyte and epiphyte kinetics were derived
from these studies. Many of the initial estimates came from the work of Barber (1991), given
the similarities between Barber's model and the one used in this analysis.
In addition to the parameters characterizing mass and energy transfer, a benthic habitat
I .
factor was introduped. The benthic habitat factor was an estimate of the fraction of the bottom
area available for macrophyte growth in each river segment. Downstream of Auger Falls (RM
606.6) this factor was estimated from the macrophyte studies conducted by Hill (1992). Above
Auger Falls the habitat factor for macrophytes was assumed to be zero, primarily because of a
lack of data. The habitat factors used for each segment are given in Table D-16.
Initial estimates for the parameters characterizing growth rates, rates of senescence, and
nutrient uptake were varied by trial and error using mass and energy loading as described, 1990-
1994 water chemistry and hydrology data described above, and 1992-1994 macrophyte data
reported by Falter and Carlson (1994).
Parameters in the surface water and benthic systems equations were varied until the
outcomes appeared as shown in Figures D-10 to D-16. Parameters for the model of surface
water quality are given in Table D-17 and for the model of benthic plants are given in Tables D-
18-D-20. Because the parameter set for the system of equations is so large and the database
limited, the resulting parameter set (Tables D-17 to D-20) may not be unique. That is, there may
be other parameter sets that lead to results similar to those obtained in this initial test.
D-21
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D.3.5. Results
The mathematical model described above was used to simulate state variables (Tables 1
and 2) in the Snake River between RM 640.0 and RM 545.5 for the period January 1,1990, to
December 31,1994. The simulated surface water quality results are compared with water
quality data collected by the University of Idaho's Agricultural Research Station, Idaho State
University, and Clear Springs Foods, Inc., at various locations in the Snake River (Table D-21)
in Figures D-10 to D-16. Means and standard deviations of the differences between simulated
and observed values at these locations are shown hi Table D-22.
Comparison of simulated and observed results for those days on which measurements of
macrophytes and epiphytes were made by the University of Idaho (Falter and Carlson, 1994;
Falter et al., 1995; Falter and Bums, 1996) are shown in Figures D-17-D-19. Simulated results
are for laterally averaged values of the two macrophyte types (Potamogeton and Ceratophyllum)
and the epiphyte (Cladophord).
D.3.6. Discussion
D.3.6.1. Dissolved Oxygen
Differences in simulated and observed DO are biased in the direction of underprediction
(simulated values less than observed, on average) at the upstream stations (S04, SI3, S21, and
S31) and biased in the direction of overprediction at the downstream stations (S40, S49, and
S72). The differences are generally independent of the magnitude, although the model
consistently underpredicts the maxima at Stations SI3, S21, S31, S40, and S49. These maxima
appear to be related to periods of high primary productivity. Some of this difference may
therefore be due to the simulated results being estimated as daily-averaged values whereas the
observations are point measurements at a particular instant in time.
D.3.6.2. Water Temperature
Differences in simulated and observed water temperatures are biased in the direction of
underprediction at all stations except S40 (Table D-22). The average difference between
simulated and observed water temperature at S49 is not significantly different from 0.0. With
the exception of the two upstream stations (S04 and S13), the difference between simulated and
observed is negative at water temperature below about 12 °C and positive above (Figures D-20b
to D-26b). This bias is most likely due to incomplete knowledge of the inflow temperature from
nonpoint sources, particularly springs.
An important characteristic of the water temperature hi the Study Reach, as reflected in
both the simulated and observed values, is the change in temperature range from upstream to
downstream. At the location farthest upstream (RM 612), water temperature varies from near 0
°C to approximately 22 °C. At the downstream locations the water temperature ranges from
D-22
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approximately 7 °G to 20 °C. The difference in water temperature range is due to the moderating
effects of the spring flow on river temperatures.,
D.3.6.3. Ammonia Nitrogen
Bias in the differences between simulated and observed values of ammonia nitrogen
shows no consistent pattern (Table D-22). Bias is highest at station S13, which is just below the
Auger Falls reach of the Snake River. However, the degree of correlation between model and
observed is low at stations S40, S49, and S72. This implies that the kinetics of the model may
not properly represent important processes found in the Study Reach (Figures D-24c to D-26c),
particularly in those areas for which primary productivity is high.
D.3.6.4. Nitrate Nitrogen
Differences between simulated and observed values of nitrate nitrogen are biased in the
I
direction of underprediction at the upstream stations (S04, SI3, and S21) and in the direction of
overprediction at the downstream stations (S31, S40, S49, and S72) (Table D-22). The variance
of the difference decreases in a downstream direction. The range of nitrate nitrogen also
decreases in a downstream direction. At S04 the range is from less than 0.5 mg/L to more than
2.5 mg/L, whereas at S72 it is from about 1 mg/L to 2 mg/L. As in the case of temperature, this
change can be attributed to the moderating effect of the springs on both flow and concentration.
D.3.6.5. Total Phosphorus
Initial simulations of total phosphorus gave results that were biased in the direction of
overprediction at the upstream locations and in the vicinity of the maximum macrophyte density
(Stations S04, S13;, S21, and S31). That is, the simulated levels of total phosphorus were
generally higher than the observed levels of total phosphorus. The model appears to be either
underpredicting phosphorus uptake by aquatic macrophytes or failing to account for deposition
of phosphorus associated with sediments or particulate matter. Using sedimentation rates for
phosphorus reported by Falter and Bums (1996) gave results that were nearly unbiased, as
shown in Figures D-20e to D-23e and Table D-21. Model simulations at the downstream
stations (Stations S40, S49, and S72) are biased only slightly hi the direction of overprediction
(Figures D-24e to D-26e). The standard deviation of the model error is highest above Snake
River Mile 581 (Upper Salmon Falls Dam), where primary productivity is also high.
D.3.6.6. Vascular Macrophytes and Epiphytes
Simulated and observed macrophyte biomass values are plotted for calendar years 1990-
94 at two locations in the MSR, RM 600 and 589 (Crystal Springs and Box Canyon,
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respectively) (Figures D-17 to D-19). Separate plots of macrpphyte density (g C oven-dry
weight/m2) are given for rooted macrophytes, nonrooted macrophytes, and epiphytes.
D.3.6.7. Crystal Springs (RM 600)
In 1992, predicted rooted and nonrooted macrophytes were three to four times greater
than observed values. Predicted epiphytes closely matched observed, but predicted levels of
epiphyte demise lagged observed by about 1 month. The answer could well lie in the very early
development of epiphytes in 1992. By early June, epiphytes were at annual peak levels, 4 to 6
weeks ahead of 1993 and 1994 peaks (Falter et al. 1994). The high temperatures and very low
flows of early 1992 are a likely reason for the early epiphyte development in those years, as
water temperatures were 22 °C-24 °C by mid-June. In 1993 and 1994, however, mid-June water
temperatures were 4 °C-5 °C cooler than in 1992. Higher and later spring flows in 1993-94 were
the cause of cooler temperatures those years. It is likely that the warm, low flows of 1992
favored early epiphyte development, which suppressed rooted and nonrooted macrophytes by
blanketing, light suppression, and nutrient competition through the first half of the summer.
These biological interactions were not captured by the model. The likely cause for epiphyte
demise earlier than predicted is not apparent.
In 1993, predicted rooted macrophytes closely modeled observed, both in magnitude and
timing. Predicted nonrooted macrophytes were slightly lower and about a month later than
observed. In 1993, water flows were much different than in 1992. Flows had a May flood pulse
of 14,000 cfs and a midsummer pulse of about 2,100 cfs, compared with 1992 midsummer flows
of 350 cfs. These higher flows were 4 °C-5 °C cooler than in 1992 and could have favored both
rooted and nonrooted macrophytes. Observed values of these forms were several-fold greater
than 1992 values. Optimal growth temperatures in the model were set at 25 °C for both rooted
and nonrooted forms. It is possible that nonrooted optimal growth temperature should be set
lower to project greater growth at cooler temperatures. (It should be noted that modeled
nonrooted growth in Box Canyon reach, where water temperatures were much cooler because of
springs influence, was also much less than observed growth.) Early growth of observed
epiphytes was suppressed in 1993 and did not peak more than a few months after 1992 observed
epiphyte peaks. The model correctly predicted epiphyte levels, but predicted levels declined in
the fall about 2 months before the observed epiphyte decline (Figure A-l 8).
In 1994, there was no spring flood pulse, but flows through the summer and fall held at
high summer flows -60 mVs (compared with 10 mVs in 1992 and 10 m3/s with an early summer
pulse in 1993). Early summer temperatures were about 6 °C-7 °C cooler than in 1992. The onset
and peaks of rooted macrophytes were correctly predicted; the prediction missed, however, the
observed midsummer decline and low rooted levels through the fall. Nonrooted predictions
more closely matched observed, both in levels and tuning (Figure D-17). Predicted epiphyte
D-24
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peaks and timing matched observed but declined about a month and a half sooner in the fall than
observed. '
i
D.3.6.8. Box Canyon (RM 589)
Predicted and observed macrophyte comparisons are available only for 1992. As in
Crystal Springs, rcjoted growth was overpredicted, but only by -50%. Nonrooted growth was
underpredicted by about the same amount. In both cases, predicted peaks lagged observed by
about 2 months. This lag was also observed in Crystal Springs in 1992. Epiphyte biomass peaks
and timing were reasonably predicted at Box Canyon in 1992.
D.3.6.9. Measurement Endpoints
The relationships among state variables, measurement endpoints, and assessment
endpoints are shown in Table 4. The parameters characterizing the measurement endpoints are
derived from the State of Idaho water quality standards and from habitat suitability curves
developed for certain cold-water fishes native to the Snake River. As discussed in Chapter 3
(Conceptual Model), the target organisms chosen for the Study Reach are the rainbow trout,
mountain whitefish, and white sturgeon. Therefore, where the measurement endpoints are in
terms of specific organisms, the target organism was selected from this group of three.
D.3.7. State of Idaho Water Quality Standards
For cold-water biota, the water quality standards of the State of Idaho require the waters
of the Study Reach to have the following characteristics.
D.3.7.1. Dissolved Oxygen
Dissolved oxygen concentrations must exceed 6 mg/L at all times, with the following
exceptions: \
• The bottom 20% of water depth in natural lakes and reservoirs where depths are 35
meters or less.
• The bottom 7 meters of water depth in natural lakes and reservoirs where depths are
greater than 35 meters.
• Those waters of the hypolimnion that are in stratified lakes and reservoirs.
For salmonid spawning, the State of Idaho water quality standards require the one-day
minimum dissolved oxygen be not less than the greater of 6.0 mg/L or 90% of saturation during
I
' D-25
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the spawning period and incubation period for the particular species inhabiting the waters. Tune
periods for spawning and incubation of species native to the waters of Idaho are given in Table
D-23.
D.3.7.2. Water Temperature
For cold-water biota, the water quality standards of the State of Idaho require the waters
of the Study Reach to have water temperatures of 22 °C or less with a maximum daily average of
no greater than 19 °C. For salmonid spawning, water temperatures must be equal to or less than
13 °C, with a maximum daily average no greater than 9 °C during the spawning period and
incubation for the particular species inhabiting the waters of the Study Reach.
D.3.7.3. Ammonia
Criteria for toxicity of un-ionized ammonia to coldwater species hi the Study Reach are
shown in Tables III and IV of the State of Idaho's water quality standards. Criteria are given as a
function of pH and water temperature for both chronic and acute toxicity.
D.3.7.4. Excess Nutrients
The State of Idaho's water quality criteria for nutrients are in a narrative form:
"Surface waters of the state shall be free from excess nutrients that can cause visible
slime growths or other nuisance aquatic growths impairing designated beneficial uses."
For purposes of establishing a Total Maximum Daily Load (TMDL) for total phosphorus
in the Study Reach, the State of Idaho's DEQ (1995) interpreted these narrative water quality
criteria in the Study Reach hi terms of a numeric criterion. The TMDL requires that total
phosphorus be 0.075 mg/L when the river flow is equal to the 1-in-lOryear 7-day average low
flow (7Q,0), as measured at the Gridley Bridge (Snake RM 583.0). This criterion is less than that
suggested in U.S. EPA (1976) for flowing waters (0.10 mg/L), but greater than that suggested by
U.S. EPA (1976) for flowing waters that enter lakes or reservoirs (0.05 mg/L). The criterion for
total phosphorus developed by Idaho DEQ has not been specifically related to the levels of
vascular macrophyte growth hi the river that would exceed the State of Idaho's narrative water
quality standard for nutrients. The State of Idaho's DEQ (1995) identified aquatic macrophyte
growth as being present at high or nuisance levels. In an effort to define a measurement endpoint
for nuisance levels of aquatic macrophyte, a literature survey was conducted. Only those papers
that made reference to water quality impacts and that had quantitative data for macrophyte
biomass were used to develop the measurement endpoint. Types of water quality impacts
included general water quality degradation, alteration of the aquatic environment, and eutrophic
D-26
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conditions. The results of this survey (Table D-24) suggest that 200 g/m2, average maximum
biomass as AFDM, is a reasonable lower bound for nuisance levels of aquatic macrophytes.
D.3.8. Habitat Suitability Curves
The U.S. Fish and Wildlife Service, in support of the IFIM, has developed habitat curves
for many aquatic organisms. In a cooperative study conducted with the Idaho Power Company,
Anglin et al. (1992) described habitat suitability curves for the three cold-water fishes identified
as target organisms for the Study Reach. The suitability indices used in this study for spawning,
incubation, fry/larvae, juvenile, and adult stages of the mountain whitefish, rainbow trout, and
white sturgeon are shown in Figures D-27 to D-38. The periods of the year to which these
suitability indices apply are shown in Table D-25.
In applications of IFIM, the habitat suitability curves are used to develop flow-weighted
measures of habitat suitability. In this ecological risk assessment, the simulation results from the
ecological model were compared to the IFIM habitat suitability curves. The frequency with
which the simulated results were less than a reasonable value of the habitat suitability curve was
used to assess whether or not the system would support a particular life stage of the target
organism. The reasonable level for habitat suitability was defined as 0.6. That is, values of the
habitat index greater than 0.6 in Figures D-27 to D-38 were assumed to represent conditions
supporting the particular life stage of the target organism, and values of the index less than 0.6
were assumed to represent conditions that would not support that life stage. The criterion of 0.6
was chosen simply because it is slightly greater than 0.5. Although this choice was somewhat
arbitrary, the estimates of ecological risks are not particularly sensitive to the criterion, given the
shapes of the habitat suitability curves (Figures D-27 to D-38). Most of the uncertainty in
estimates of ecological risks using these habitat suitability curves is in the shapes of the curves.
i ...
D.4. EXPOSURE ANALYSIS
I
The objective of this analysis is to characterize elements of exposure by simulating the
space/time distribution of state variables that are also measures of effects to the ecosystem. The
simulations are performed with the dynamic model of mass and energy balance. Environmental
driving forces are input to the model with measures of variability and uncertainty developed
from the historical record. The simulated state variables will have uncertainty and variability
that is representative of the Study Reach, assuming the models for driving forces and for mass
and energy balance are representative of the processes in the Study Reach.
Limitations in our understanding of ecosystem processes in the Study Reach are such that
the model does not simulate all the state variables that characterize the primary stressors
described in the Problem Formulation. In particular, the model does not include those state
variables necessary to characterize sediment loading and habitat alteration associated with
D-27
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. changes in the substrate. The state variables simulated by the model that are primary stressors
and can be used to measure effects of exposure are listed in Table D-4. The quantitative analysis
of ecological risk, within the framework of the simulation methods described in this study,
addresses only those stressors shown in Figure D-3.
D.4.1. Stressor Characterization
The stresses to the Study Reach ecosystem are a result of hydrologic modification and
the input of nutrients from point and nonpoint sources. The stressors for this analysis have been
characterized in terms of the existing conditions. Existing conditions for the analysis are
described in Table D-26.
D.4.2. Temperature-Dissolved Oxygen
Ecological integrity of an aquatic ecosystem is dependent on the characteristics of the
water temperature and dissolved oxygen regimes. The State of Idaho water quality standards for
the Study Reach protect beneficial uses associated with cold-water species and spawning of
cold-water fishes. For characterizing stress associated with temperature and dissolved oxygen,
the simulated 67-year record of state variables is compared to the water quality criteria in each of
the representative segments. The comparison is made for the general category of cold-water
species and for spawning of two species, the mountain whitefish and the rainbow trout. The
temperature-dissolved oxygen state-space diagram, which plots the temperature as a function of
dissolved oxygen, provides a compact format for making the comparison.
Stress occurs when the temperature-dissolved oxygen .envelope experienced by a target
organism is larger than the envelope associated with its physiological requirements.
Superimposing the envelope for water temperature and dissolved oxygen given in the water
quality standards for each of these groups on the simulated temperature-DO state-space diagram
is a way of assessing stress associated with the temperature-DO regime in a particular segment
(Figures D-39 to D-51). The frequencies with which the simulated values fail to fall within the
envelope for temperature and DO defined by the State of Idaho's water quality standards are
given in Table D-27.
For cold-water biota the frequency with which the simulated daily-average DO falls
outside the envelope defined by the water quality standards is less than 0.01 in all of the
segments. Frequencies for spawning mountain whitefish are less than 0.06 throughout the Study
Reach, except in the segment from Kanaka Rapids to Gridley Bridge, where the frequency is
0.11. The frequencies for spawning rainbow trout range from 0.26 to 0.57 between Milner Dam
and the Gridley Bridge, and 0.19 to 0.45 between the Gridley Bridge and King Hill. The higher
frequencies associated with spawning rainbow trout are due to the fact that applicable water
quality standards include some summer months, whereas the water quality standards for
D-28
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spawning mountain whitefish apply to fall and winter months when saturation levels of DO are
higher. ; . .
The frequency with which the daily-average simulated water temperature falls outside the
envelope for cold-water biota ranges between 0.13 and 0.20 for the segments between Milner
Dam and Kanaka Rapids. The frequency decreases to less than 0.05 from Kanaka Rapids to the
Bliss Bridge because of the large volume of cooler water supplied by the spring flow. Between
the Bliss Bridge and King Hill the frequency increases slightly as the spring flow decreases and
the transfer of thermal energy across the air-water interface becomes more important.
The pattern for the frequency with which the simulated maximum water temperature falls
outside the envelope for cold-water biota is similar to that of the simulated daily-average water
temperature. The decrease in frequency occurs in the Crystal Springs to Boulder Rapids
segment slightly upstream from Boulder Rapids to Kanaka Rapids, the segment in which the
I
frequency of daily ^average water temperatures decreases. In addition, the magnitude of the
frequencies for which the maximum temperatures fall outside the envelope for cold-water biota
is less than for the |daily-average temperatures. The frequencies for maximum simulated water
temperatures varied between 0.01 and 0.13 from Milner Dam to Boulder Rapids and were less
than 0.01 between Boulder Rapids and King Hill.
The frequencies with which simulated daily-average water temperatures fall outside the
envelope for spawning rainbow trout is greater than 0.58 throughout the Study Reach and greater
than 0.48 for simulated maximum daily water temperatures. The high frequency with which DO
falls outside the envelope is due to the fact the water quality standards for spawning rainbow
trout include some summer months.
For water quality standards applicable to the spawning of mountain whitefish, the
frequency with which water temperature falls outside of the envelope is reversed compared to
cold-water biota. Frequencies with which daily-average and maximum water temperatures fall
outside the envelope are lowest in the upstream segments between Milner Dam and Kanaka
Rapids and highest in the segments between Kanaka Rapids. Frequencies for daily-average
simulated water temperatures vary between 0.05 and 0.10 in the upstream segments and between
0.10 and 0.22 in the downstream segments. The reversal in the pattern and the relatively low
frequency of exceedances is due to the fact that water quality standards for spawning mountain
whitefish apply to fall and winter periods when water temperatures are low.
D.4.3. Total Phosphorus/Macrophytes
Phosphorus in sufficiently high concentrations is a stressor inasmuch as it promotes the
growth of undesirable aquatic plants and large blooms of phytoplankton. Vascular macrophytes
in segments of the. Study Reach have caused the loss of beneficial water uses. An environmental
goal of watershed management, and an assessment endpoint in the Study Reach is to reduce the
! D-29
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density of macrophytes and levels of phytoplankton. A major element in this goal is the
reduction of phosphorus from both point and nonpoint source discharges.
The State of Idaho's DEQ has developed a TMDL for total phosphorus in the Study
Reach as part of the management plan to reduce macrophyte density. The TMDL limits total
phosphorus in the Study Reach at the Gridley Bridge (RM 583.0) to 2,400 Ib/day. This
corresponds to a concentration of 0.075 mg/L total phosphorus for a flow of approximately 5,900
cfs in the Snake River.
The simulation results from the dynamic model were used to obtain an empirical
cumulative distribution function (CDF) for total phosphorus at a location representing the
segments given in Table D-5, The CDFs for total phosphorus are shown in Figures D-52 to D-
64. Uncertainty bands for the CDFs in Figures D-52 to D-64 reflect the standard deviations for
the differences between simulated and observed total phosphorus as shown in Table D-26. The
empirical CDF gives the probability that the simulated total phosphorus is equal to or less than
some specified value. These empirical CDFs represent stressor characteristics for existing levels
of management and do not incorporate the limits specified in the TMDL.
In the segments of the Study Reach upstream from major point source and nonpoint
source inputs, the estimated probability that total phosphorus will be equal to or less than 0.075
mg/L is between 0.23 and 0.25. Total phosphorus loads from the City of Twin Falls STP, fish
hatcheries, and irrigation return flows reduce the probability that total phosphorus will be equal
to or less than 0.075 to between 0.01 and 0.04 in the segments between Shoshone Falls and
Gridley Bridge. The large volume of spring inflow with low levels of total phosphorus to the
Study Reach increases the estimated probability to 0.07-0.18 between Gridley Bridge and King
Hill.
The cumulative distribution function for total macrophyte and epiphyte biomass was
estimated for the Crystal Springs to Boulder Rapids segment. This segment was chosen because
it has had among the highest levels of macrophyte growth measured during field studies by the
University of Idaho (Falter et al., 1995; Falter and Bums, 1996). The probability that the
simulated values of macrophyte biomass, measured as the sum of rooted macrophytes, nonrooted
macrophytes, and epiphytes, would be less than 200 gm C AFDM/m2 was estimated to be less
than 0.01 for the 67-year period of record (Figure D-65).
D.4.4. Un-Ionized Ammonia
Simulated levels of un-ionized ammonia were compared to the chronic and acute criteria
in Tables III and IV of the State of Idaho's water quality standards. The frequency with, which
the simulated levels exceeded the criteria was computed as the ratio of the number of values that
exceeded a criterion divided by the number of simulated values.
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The estimated frequency with which the simulated values of un-ionized ammonia are
below the chronic and acute criteria was estimated to be less than 0.05 and 0.01, respectively,
throughout the Study Reach.
D.4.5. Habitat Suitability Curves
Measures of stress to the target cold-water species, mountain whitefish, rainbow trout,
and white sturgeon, due to water temperature and hydrologic effects were obtained from habitat
suitability indices developed by the USFWS (Anglin et al., 1992). The measures of habitat
suitability associated with water temperature, water depth, and velocity were obtained for each
life stage of the target organism and determined in the following way. Initially, a value of 0.6
was chosen as a limiting value that would apply to both upper and lower limits of habitat
suitability for all habitat factors (water depth, water velocity, and water temperature), all life
stages, and all species. For each of the suitability curves (Figures D-27 to D-38), when the
simulated value of the habitat factor resulted in an index value less than 0.6, the condition of the
water in the simulated segment was characterized as impaired for that factor, life stage, and
target organism. For simulated values of the habitat factor resulting in an index value greater
than 0.6, the condition of the habitat was characterized as unimpaired, or impaired if the value
was less than 0.6. \
The index of impairment for each life stage was computed as the ratio of the number of
simulated days in which impairment of habitat occurred to the total number of days for which
the life stage was vulnerable (Table D-23). Four categories of impairment were defined on the
basis of the index of impairment. The results are shown in Figures D-66 to D-6S for the various
life stages of the target organisms: rainbow trout, mountain whitefish, and white sturgeon.
The index pf impairment was generally high throughout the Study Reach for all life
stages of rainbow trout. Estimated levels of impairment for adults were estimated to be
moderate to low in some portions of the segments from Rock Creek to Crystal Springs, from
Boulder Rapids to Kanaka Rapids, and hi the upper portion of Upper Salmon Falls reservoir.
Estimated levels of impairment for spawning were low to moderate in some portions of the
segment from Boulder Rapids to Kanaka Rapids, as were estimated levels of impairment for
rainbow trout fry. I
Estimated values of the index of impairment for spawning, fry, and juvenile mountain
whitefish were high throughout the Study Reach. For adult mountain whitefish, the values of
the index of impairment were estimated to be moderate to high throughout the Study Reach. The
most favorable conditions for adult mountain whitefish (moderate impairment) were found in
Upper Salmon Falls and Lower Salmon Falls reservoirs. These somewhat favorable conditions
were primarily a result of high-quality cooler water entering the Study Reach from springs.
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Above Lower Salmon Falls Dam, estimated values of the index of impairment for white
sturgeon were generally high for all life stages. Exceptions were found in the pool below Auger
Falls and in Upper Salmon Falls reservoir, where the index of impairment for adult white
sturgeon was estimated to be low and the index of impairment for juveniles was estimated to be
moderate. Portions of the Wiley reach (Lower Salmon Falls Dam to the Bliss Bridge) had low to
moderate values of the index of impairment for spawning and larval stages. The most favorable
conditions for all life stages of white sturgeon were estimated to occur in the Study Reach below
Bliss Dam.
D.4.6. Uncertainty and Variability
Ecological risk is the likelihood that adverse ecological effects may occur as a result of
exposure to one or more stressors (U.S. EPA, 1992) The primary goal of ecological risk
assessment is to identify and reduce variance in characterizing the response of ecosystems to
stressors. This variance arises from variability and uncertainty. The taxonomy of variability and
uncertainty in risk assessment has been discussed by a number of authors. Suter (1990), for
example, identified the following three sources of uncertainty and variability: the inherent
randomness of the world (stochasticity), imperfect or incomplete knowledge of things that could
be known (ignorance), and mistakes in execution of assessment activities (error). For this risk
assessment, using simulation methods, sources of uncertainty arid variability include
« variability and uncertainty in ecosystem driving forces and stresses,
° variability and uncertainty in sources of mass and energy,
• model error,
° parameter estimation error,
• state variable measurement error, and
• variability and uncertainty in measurement endpoints.
D.4.6.1. Ecosystem Driving Forces
The models for characterizing the variability of the ecosystem driving forces, hydrology
and meteorology are described in Section 4.1. The models for variability in both hydrology and
meteorology are based on the actual 67-year record of the meteorology and the adjusted 67-year
D-32
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record of the hydrology. Even though using the actual record captures some of the variability in
a simple and straightforward manner, the record represents only a sample of the actual
population. As.such, it may not include events that have a low probability of occurrence. Such
events would likely be associated with long-term changes in regional and global weather
j
patterns. |
In addition to the variability in the ecosystem driving forces, there is uncertainty in the
models for these forces. In the case of hydrology, there is uncertainty in the model IDWR uses
to account for water management in the Snake River basin. There is also uncertainty in the way
in which the monthly flows estimated by the IDWR hydrologic model were disaggregated to the
daily values. For the meteorology, there is uncertainly in the spatial variability of weather
despite the fact that an effort was made to account for some of this by using two weather
stations. The meteorologic variables most likely to be affected by the uncertainty in spatial
variability are wind speed and air temperature. Although the energy budget of the Snake River
in the Study Reach is dominated by advection, the ecological risk analysis would benefit from a
reduction of uncertainty in wind speed and air temperature.
i
[ •
D.4.6.2. Sources of Mass and Energy
With the limited data available, it was difficult to account for or separate uncertainty and
variability in the sources of mass energy. The longest record available for developing models
for the sources of mass and energy was 5 years (1990-1994). In addition, sampling periods for
these sources were generally biweekly or greater. The data gaps were much larger for the
springs, which play an extremely important role in the Study Reach. The relatively low
variability of both |the quantity and quality of the spring flows mitigates the impact of these data
gaps to a degree. For sources with important high-frequency components such as irrigation
return flows, the data gaps are likely to be significant. In general, the limited data imply a high
degree of uncertainty for both high-frequency and low-frequency components of the sources of
mass and energy., j .
D.4.6.3. Model Error
\
Errors in the simulation model for ecological risk analysis (Appendices A and B)
contribute to uncertainty in the estimate of ecological risk in a number of ways. Errors hi
structure are generally the major sources of model uncertainty in ecological models, and result
from omitting important state variables or flow paths between state variables.
Spatial and temporal aggregation of state variables hi the simulation model also
contribute to model uncertainty. The equations of mass and energy balance for this model
assume the state variables describing the water body vary only vertically or longitudinally,
depending on the nature of the water body. In addition, the simulated state variables represent
! ' - D-33
-------
volume averages for river segments 0.3 to 3.3 miles in length and reservoir segments 5.0 feet
thick. State variables are also averaged over a 3-hour period. There will therefore be
uncertainty regarding the system state at spatial scales smaller than the segment size and at time
scales less than 3 hours.
Aggregation of state variables in space and time can result in errors generated by the
method used to solve the finite difference equations (Appendices A and B). These errors are
largest where there are strong spatial gradients in state variables and where the time increment
for the numerical solution technique, Atc, is not equal to time required for a molecule of water to
traverse a given segment.
All of these errors in model structure can give rise to uncertainty in the ecological risk
analysis. As is the case for most ecological models, the structure for the ecological model used
in this analysis of risk is a hypothesis derived from previous ecological model construction and
field studies in rivers, lakes, and reservoirs, including the field studies done in the Study Reach.
There are at this point no widely accepted protocols for testing hypotheses regarding state-space
models of the type used in this analysis. Oreskes et al. (1994) suggest a qualitative comparison
of model simulations with observed values of the state variables as a way of establishing the
credibility of earth science models.
Simulated results for DO, water temperature, total ammonia nitrogen, nitrite-nitrate
nitrogen, and total phosphorus are plotted against observed values of these same state variables
in Figures D-20 to D-26. These plots show that the best correlation between simulated and
observed state variables occurs for water temperature and for nitrite-nitrate nitrogen. Correlation
between simulated and observed values for DO is generally good, with the exception of the first
part of 1992, when supersaturated levels of DO were observed (Minshall et al., 1993) but were
not simulated by the model. This implies the model structure may not include all the processes
required to accurately simulate primary productivity in the Study Reach.
Correlation between simulated and observed values of total ammonia nitrogen and total
phosphorus was generally low. The total ammonia nitrogen results showed significant positive
bias (the model predicted higher values, on the average, than were observed) downstream from
the City of Twin Falls STP and Auger Falls (Station S13) and in the area of dense macrophyte
beds (Stations S21 and S31). The bias in the total ammonia nitrogen at the station downstream
from Auger Falls and from the City of Twin Falls STP could be due to error in the loading from
the City of Twin Falls STP. It could also be due to incorrectly characterizing the sources and
sinks for total ammonia in the Auger Falls segment of the Study Reach.
Structural errors in the model also may be an important source of bias and poor
correlation between simulated and observed total ammonia nitrogen in the vicinity of the
macrophyte beds (Stations S21 and S31). This segment of the Study Reach is one of high
biological productivity. Uptake and release of ammonia by macrophytes is an important part of
D-34
-------
the nutrient dynamics in the model. This is evident from the high-frequency components in the
simulated values of total ammonia nitrogen (Figures D-12c and D-13c). Additional field and/or
laboratory studies would be required to adequately test the hypotheses that control ammonia
uptake and releaselin the model.
D.4.6.4. Parameter Estimation
As discussed in Chapter 4, formal solutions of the parameter estimation problem are
difficult to obtain. | The difficulty in this ecological risk assessment arises from the nonlinear
nature of the mass 'and energy balance equations, limited data, and a large number of parameters.
Because of this, parameter estimation was done by trial and error for selected parameters only.
The trial-and-errori process included initial selection from the literature, followed by adjustment r
of parameters until simulated values agreed reasonably well with observations. Those
parameters estimated by trial and error are listed in Tables D-18 to D-20.
Those parameters included in the trial-and-error process were ones that determine the
sedimentation rates of phosphorus; loss, uptake, and release of ammonia nitrogen; growth and
death rates of macrophytes and epiphytes; and habitat factors for macrophytes. Model response
was particularly sensitive to the parameters for growth and mortality rates of macrophytes and
epiphytes and habitat factors for macrophytes. Of particular importance for parameters
characterizing growth rates and mortality rates of macrophytes and epiphytes was the role of
sediments and sedimentation processes in the Study Reach.
The conceptual model for the macrophytes includes the assumption that nutrient flow
from the sediments to the roots of macrophytes is unlknited by plant uptake. This assumption
i * _
plays a significant !role in the development of management strategies for reducing macrophytes
in the Study Reach. Given an essentially infinite supply of nutrients, reduction in the discharge
of dissolved nutrients is unlikely to result in a decrease in aggregate macrophyte biomass.
Although results of macrophyte studies in the Study Reach during 1992 and 1993 (Falter and
Carlson, 1994; Falter et al., 1995) suggest that the assumption may not be met in the densest
plant beds in late summer, it is a reasonable first approximation for extended periods of low flow
when sediment deposition rates are high. However, under conditions of high flow, when
sediments are being removed by scouring, this assumption is likely to result in unreasonably
high rates of nutrient flow to rooted macrophytes.
The model; was also quite sensitive to the magnitude of the habitat factors
(Table D-16). The habitat factors, in principle, should be derived from knowledge of
sedimentation processes. However, in this case lack of knowledge of these processes made it
necessary to use the limited data that were available (Hill, 1992) regarding macrophyte habitat.
Although these data provided information about conditions existing during 1990 for certain
segments of the Study Reach, they were not sufficient for predicting habitat conditions under
! D-35
-------
various river flow regimes. Recent data (McLaren, 1998) show that habitat factors for
macrophytes change dramatically as a result of scouring of sediment deposits and associated
macrophytes during periods of high flows in the Snake River. On the basis of his study of
sediment transport during July and October 1997, McLaren (1998) concluded these changes
occur when the flow in the Study Reach exceeds approximately 10,000 cfs. Such conditions
have occurred in the past, but are not reproduced in the cumulative distribution function
generated by the model (Figure D-65). Incorporating a predictive model for macrophyte habitat
would require more study of the sedimentation processes hi the Study Reach.
The simulation results for macrophytes were also sensitive to the parameters used to
characterize the physical stress placed on plants by high water velocities. This component of the
model had much greater impact on macrophyte density than did changes in the concentration of
total phosphorus in the water column. The initial estimates of the parameters used to
characterize physical stress from high water velocity were estimated from the work of Chambers
et al. (1991a,b). The magnitude of parameters relating macrophyte growth to water velocity was
modified to account for the results obtained by McLaren (1998). However, this change was not
able to account for the dramatic changes in macrophyte growth observed in 1997. It is likely this
is due to the fact that these parameter changes affected only the plant physiology and were not
related to the physical processes associated with sediment transport. The physical removal of
both the nutrient-laden substrate and the macrophytes through transport processes was the
primary factor leading to reduction of macrophyte biomass in the Study Reach (Clark, 1997).
The methods described here did not include an analysis of the physical processes characterizing
sediment deposition and scouring. Additional studies are necessary to describe these processes
and their effects on macrophyte and epiphyte mortality.
D.4.6.5. State Variable Measurement Variability and Uncertainty
Field measurements of state variables are needed for testing model hypotheses and,
ultimately, evaluating the reliability of the simulation methods. However, there are several
sources of variation and uncertainty in field measurements. There is generally some error
associated with the instrument or laboratory technique and with the manner in which samples are
taken and handled. In general, the largest variability is usually due to spatial or temporal
variability of the state variable being measured. This is particularly true for the biological state
variables. For example, Falter et al. (1995) and Falter and Bums (1996) observed high spatial
variability of macrophyte density at Snake River Mile 600.0 with a high number of replicates.
DO is a state variable that can also have high temporal variability during periods of high primary
productivity. There will be uncertainty in characterizing the average state of the system's DO
when only one grab sample is taken every 2 weeks.
D-36
-------
There is also uncertainty in comparing field observations with simulated results because
the field observations are point measurements whereas the simulated values are space and time-
averaged. The magnitude of the uncertainty depends, of course, on each state variable's spatial
and temporal characteristics.
D.4.6.6. Measurement Endpoints
Uncertainty and variability in the measurement endpoints can also make significant
contributions to variance in the estimates of ecological risk. For this risk assessment, the
measurement endpoints are based on the water quality criteria established by the State of Idaho
and on habitat suitability indices developed by the USFWS. The quantitative water quality
criteria have been developed from a wide range of field and laboratory tests and assays. Such
tests often show considerable variability in results. Furthermore, they may not always be
appropriate for local conditions because of variability in environmental factors and the response
of the target organisms.
In many cases, the exposure period used in the tests or assays used to develop criteria
may not be commensurate with exposure periods experienced in the real system. For example,
many of the water quality criteria are based on results from bioassays conducted over a period of
48 hours. The results of the bioassays are interpreted in terms of acute or chronic impacts on test
organisms. The acute and chronic values are converted to instantaneous or 4-day averages,
respectively, in the water body. Interpreting the results of tests and assays in this way is meant
to be protective of the ecosystem, but it does introduce uncertainty into the assessment of
ecological risk. ;
There is even more uncertainty associated with the quantitative interpretation of narrative
standards. In the Study Reach, the major impact of nutrient and sediment loads is abundant ,
macrophyte growth. There is general agreement that the levels observed during the period 1990-
1994 were unacceptable in terms of the narrative standards set by the State of Idaho. However,
there is as yet no agreement at the local level on what quantitative measures of macrophyte
growth constitute a violation of these standards. Table D-24 represents an effort to develop a
measurement endpoint for characterizing nuisance levels of macrophyte biomass. However, the
analysis of macrophyte literature is limited in scope and may not necessarily reflect local
conditions in the Study Reach. The nuisance criterion should undoubtedly be adjusted for the
type of plant community. For example, densities off. pectinatus at a level of 200 g/m2 might
not hinder beneficial uses. Densities ofCladophora of this magnitude, because of their surface-
floating habit, could severely hinder beneficial uses and therefore be considered a nuisance.
Until further discussion and analysis are devoted to this issue, the measurement endpoint for
macrophyte biomass should be considered provisional.
D-37
-------
The habitat suitability indices, based on the IFIM procedure used by the USFWS (Anglin
et al., 1992) in the Swan Falls reach of the Snake River, are valuable as measurement endpoints
because they were derived for target organisms found in the Study Reach. They provide
measures of ecological impacts on target organisms that are due primarily to physical stressors.
These measures have been developed for various life stages of the target organisms and can be
used to evaluate the time history of impacts to these life stages. There is uncertainty in the
values of these indices, however. The uncertainty is due mostly to lack of specific knowledge
regarding impacts of the stressors on the target organisms. Some of these habitat suitability
indices, for example, are based on surveys of the best professional judgment of regional: fisheries
biologists. The results of the surveys were converted to indices as part of the IFIM (Anglin et
al., 1992) without quantifying the variability and uncertainty in the responses.
Because the focus of IFIM is on instream flows, the habitat suitability indices give
considerable weight to the physical parameters, depth and velocity. Some researchers (e.g.,
Mathur et al., 1985) have reported there is little evidence showing correlation between the
habitat suitability indices and fish biomass. Proponents of the methodology (e.g., Armour and
Taylor, 1991) acknowledge the lack of post-project monitoring to document the value of IFIM,
while noting that IFIM has become widely accepted as a tool for investigating the impacts of
flow regulation on aquatic resources. The rationale for adapting the IFIM methodology for
ecological risk assessment in the Study Reach was based primarily on this acceptance. However,
given the manner hi which the indices were developed and the lack of documented support for
the method, the results reported here are likely to have a high degree of uncertainty.
D-38
-------
APPENDIX D-l
Equations of Mass and Energy Conservation
for Surface Waters
-------
-------
Appendix D-l. EQUATIONS OF MASS AND ENERGY CONSERVATION FOR
SURFACE WATERS
The general equation (Equation D2-1) contains terms for advection, turbulent diffusion,
and source/sink terms for physical, chemical, and biological processes. The advection and
turbulent diffusion processes are the same for all constituents and are described in Section 2.1.1.
This appendix contains the conceptual models and the equations for the source/sink terms in the
equations of conservation of mass and energy in surface waters.
D.I.I. Carbonaceous Biological Oxygen Demand (CBOD), Cl
When microorganisms metabolize organic matter in rivers, lakes, and streams, they use
dissolved oxygen as they reduce the organic carbon to carbon dioxide. The available demand for
dissolved oxygen associated with organic carbon is characterized as carbonaceous biological
oxygen demand (CBOD) (Figure Dl-1). The rate at which dissolved oxygen is consumed is
assumed to be a linear function of the mass of available CBOD and that one unit of CBOD is
metabolized for each unit of dissolved oxygen.
The source/sink terms in the conservation equations for CBOD can be written as:
r =K,c,vi.
u ' ' i j
(Dl-1)
where
20
20
K!
01T
.6lT •
=ithe deoxygenenation rate at 20° C, days"1; and
=-the temperature correction factor for deoxygenation.
Figure Dl-1. Conceptual model for sources and sinks of carbonaceous biological oxygen
demand (CBOD)i
D-l-1
-------
D.1.2. Dissolved Oxygen (DO), C2
The major source and sink terms for dissolved oxygen (DO) (Figure Dl-2) include the
following:
• oxygen used by microorganisms to metabolize organic matter (CBOD),
• oxygen used by nitrifying microorganisms to convert ammonium to nitrate
(nitrogenous biological oxygen demand, NBOD),
• respiration of phytoplankton, and
• photosynthesis by phytoplankton.
The mass balance is
-------
where
K2
20
K
92T
CSat
«oc
the reaeration rate, days" ;
20
~K
= the reaeration rate at 20°C (C9-20.0);
=; 1.024;
i
- saturation level of dissolved oxygen, mg/L;
= the stoichiometric relationships between oxygen and carbon in photosynthesis
and respiration, mg O2/mg C;
= the stoichiometric relationships between oxygen and nitrogen for
the oxidation of ammonia to nitrate, mg O2/mg NH4-N;
K56 = the nitrification rate for converting ammonia to nitrate, days"!-
= K™ 05T (C9-20.0);
6_« _ 1.084; .
Bphoto
Bresp
= dissolved oxygen produced by photosynthesis in benthic
plants, mg O2/day; and
= dissolved oxygen converted to CO2 during respiration in
; benthic plants, mg O2/day.
D.1.3. Phytoplankton Biomass, C3
The major elements characterizing the dynamics of phytoplankton biomass (Figure Dl-3)
are:
growth driven by energy from sunlight in the presence of the macronutrients
nitrogen and phosphorus,
respiration of organic carbon stores, and
settling of plankton due to gravitational influences.
D-l-3
-------
Figure Dl-3. Conceptual model for sources and sinks of phytoplankton biomass as carbon.
Mathematical formulation of the mass balance for these processes is given by
*3y-GjrC3Vj. (D1_4)
(Dl-5)
where
Gmax
fT(C9)
' Gmax ft(C9) fl(I)
= the maximum growth rate for phytoplankton biomass, days'1;
= the function describing the temperature-dependency of the phytoplankton
growth rate '
[-2.3
-
•opt
T -T
opt •"• bw
whenC9
-------
fid)
tp
Y
10
Is
fN
KN
C5
C6
Fp
[-2.3C
T - C
-"•opt ^-9 2
P
•opt" 1high
when C9 > Topt
= e
; = the function describing the dependency of the growth rate on solar
i radiation;
i I - z I - z
! 2.718 fp , TTeY2 -T^ l
p
.e
-e
= the photo period, fraction of days;
= the extinction coefficient, meters" 1 '
= net solar radiation at the water surface, kcal/meter^/second;
= the optimal radiation for phytoplankton growth, kcal/meters^/second;
= depth below surface of top of the jtn element, meters;
= depth below surface of bottom of the jth element, meters; and
= growth limiting factor for nitrogen.
= the half-saturation constant for nitrogen, mg/L N;
= the concentration of ammonia nitrogen, mg/L N;
C+C •
= the concentration of nitrate nitrogen, mg/L N; and
= growth limiting factor for phosphorus.
D-l-5
-------
Kp = the half-saturation constant for phosphorus, mg/L P;
Cg — the concentration of orthophosphate, mg/L P;
R = RmaxfT(C9);
Rmax ' *= the maximum phytoplankton respiration rate, days~l; and
Wg = the sinking rate of phytoplankton, meters/day.
D.1.4. Organic Nitrogen, €4
The major sources and sinks for organic nitrogen (Figure Dl-4) are:
* waste products from respiration of phytoplankton, and
• mineralization to ammonia nitrogen attributable to bacterial action.
NH4-N
Organic
N
Figure Dl-4. Conceptual model for the kinetics of organic nitrogen.
D-l-6.
-------
The corresponding equation for mass balance is
where
K44 = the mineralization rate of organic nitrogen, days"
K
e_
20
'44
20
= £44647.
= the mineralization rate at 20° C;
= 1.084 (C9-20.0); and
aNC = th'e nitrogen/carbon ratio in phytoplankton.
D.1.5. Ammonia Nitrogen,
The major source and sink terms for ammonia nitrogen (Figure Dl-5) are:
i
• mineralization of organic nitrogen to ammonia,
• nitrification of ammonia to nitrate, and
• uptake of ammonia by phytoplankton growth.
The mass balance equation is written
(Dl-6)
(Dl-7)
(Dl-8)
(Dl-9)
D-l-7
-------
Figure Dl-5. Conceptual model for sources and sinks of ammonia nitrogen.
where
^NH = algal preference factor for ammonia uptake.
3
D.1.6. Nitrate Nitrogen, C6
The major sources and sinks for nitrate nitrogen (Figure Dl-6) are:
• uptake of nitrate nitrogen by phytoplankton growth, and
• nitrification of ammonia to nitrate.
The mass balance equation is
C3V.
(Dl-10)
(Dl-11)
D-l-8
-------
Figure Dl-6. Conceptual model for sources and sinks of nitrate nitrogen.
I
D.1.7. Organic Phosphorus, Cy
The major sources and sinks for organic phosphorus (Figure Dl-7) are:
• waste products due to respiration of algae, and
• mineralization to dissolved inorganic phosphorus due to bacterial action.
The mass balance equation is
7j =apc R C3V.
r = K c v
1 7j **• 77 *- 7 v j
(Dl-12)
(Dl-13)
Figure Dl-7. Conceptual model for sources and sinks of organic phosphorus.
D-l-9
-------
where
ape
K?7,
the phosphorus/carbon ratio in algae; and
the mineralization rate of organic phosphorus, days'l.
D.1.8. Orthophosphate, Cg
The major sources and sinks for Orthophosphate are:
• mineralization of organic phosphorus, and
» uptake of Orthophosphate by phytoplankton growth.
The mass balance equation is
8j
rgj
77
V
7 V j
G
(Dl-14)
(Dl-15)
D.1.9. Temperature, Cp
The heat budget method is used to simulate changes in water temperature in the river basin.
The elements of the heat budget (Figure Dl-8) include:
• net short-wave radiation,
• net atmospheric (long-wave) radiation, qat;
• water surface (long-wave) radiation, q'w;
• evaporative heat flux, qe; and
• convective heat flux, qc.
The mass balance equation is
(Dl-16)
D-l-10
-------
§
a
.1
.S3
1
"I
M
Water Temperature
Figure Dl-S. Conceptual model for sources and sinks of water temperature.
where
qnet
= the water density,
= the specific heat capacity of .water, kcal/kg/°C;
i
= qsn + qat -qw - qe +qc
= the net heat flux across the air-water interface, kcal/m^/second; and
= the surface area of the computational element, m-^.
D-l-ll
-------
-------
APPENDIX D-2
Formulation of the Mathematical Model
for Benthic Plants
-------
APPENDIX D-2. FORMULATION OF THE MATHEMATICAL MODEL IFOR
BENTHIC PLANTS
• The equations describing the rates of changes of benthic plant biomass due to internal
sources and sinks are developed below.
D.2.1. Macrophyte Root Biomass
The growth of root biomass is controlled by a basic growth rate, which is a function of
the ambient temperature, the quantity of labile carbon stores, and the level of habitat affected by
crowding. Endogenous respiration is controlled by temperature only. The model assumes no
grazing by herbivores or mortality due to scouring.
dM,
-
(D2-1)
where
MR = macrophyte root biomass, gm/m2;
UR
Mc-MCo
Mr,
)ffCD. days-1;
f Rl (T) = e
T > T
opt
T < T
opt
D-2-2
-------
M
= minimum carbohydrate stores for root or shoot/leaf growth, gm/m2,
M R = maximum concentration of macrophyte root mass, gm/meter2,
level of carbohydrate store for which growth levels are Vz maximum, gm/m2.
D.2.2. Macrophyte Shoot/Leaf Biomass
The growth of shoot/leaf biomass is also controlled by a basic growth rate, which is a
function of the ambient temperature, the quantity of labile carbon stores, and the level of habitat
affected by crowdmg. Endogenous respiration is controlled by temperature only. The model
accounts for mortality due to high river velocities, but assumes there is no grazing by herbivores.
dt
ML-DL-GL
ML = macrophyte leaf/shoot biomass, gm/m2,
= u, MAX(
(D2-2)
-M
KMc + Mc-MCr
-,ox
ML.
ML +V M,
Lmnx 4—t *-
) f£ (T) f £ (L) ..days'1
(L)~ Biomass limitation for leaf/shoot growth, dimensionless,
D-2-3
-------
2/ T-T°Pt
__ _ ^Tmax Topt J
T>X
opt
23|
T_
l I
n T . — T
__ V. ^itlin ^o
T240 and water temperature, T < 15.0 C,
= 1 otherwise.
f£(T) = 1 - f £ (T), dimensionless,
D-2-4
-------
PL = maximum mortality rate for leaf/shoots from river velocity, days'1,
1 • •
D.2.3. Macrophyte Carbohydrate Pool
In this model, as net organic carbon is produced during photosynthesis it is stored as
labile carbon. Carbon from this pool is used for roots and shoot/leaf biomass. Carbon stores are
also lost during respiration.
dM
c _,
dt
Mc = carbohydrate pool, gm/m2,
(D2-3)
LCmax = maximum photosynthetic rate, days"1,
I0 = photosynthetically active solar radiation, kcal/m2/second,
Kn
I = limiting, photosynthetically active solar radiation,
kcal/m2/second,
k = light extinction coefficient, meters"1,
z = water depth, meters,
D-2-5
-------
T>T
opt
T<
•opt
ZSRP
K SRP + SRP
UN = the sum of dissolved inorganic forms of nitrogen, mg/L,
ESRP = the sum of dissolved inorganic forms of phosphorus, mg/L,
KN = the Michaelis-Menten constant for inorganic nitrogen, mg/L,
KSRP = the Michaelis-Menten constant for inorganic phosphorus, mg/L,
= efficiency of converting from labile stores to roots and leaf/shoot, dimensionless.
D.2.4. Epiphyte Biomass
The growth rate of epiphytic algae is a function of the available depth-averaged light, the
ambient temperature, the concentration of inorganic phosphorus and nitrogen, and the velocity.
At low velocities, the growth rate is reduced to account for limited nutrient supply. At high
velocities the growth is reduced as the epiphytes are physically stressed. Respiration rates are a
function of ambient temperature. The model assumes there is no mortality due to grazing.
dM-
--=
(D2-4)
D-2-6
-------
ME = the biomass of epiphytes, gm/m2,
MEma = the maximum growth for epiphytes, days-1,
f*(I0,z,k)=-
-In
max opt
T > T t , dimensionless,
-2.31 ^
T T
T To
min * opt
T
-------
= the total biomass of macrophyte leaves, gm/m2,
K. L = leaf biomass for which optimal epiphyte growth rate i
1/2 the maximum, gm/m2,
is
fEP(T),days-i,
= the maximum ephiphyte respiration rate, days-1,
)P (^-20)
~E1° , dimensionless.
D.2.5. Periphyton Biomass
The growth rate of periphyton is a function of the available depth-averaged light., the
ambient temperature, the concentration of inorganic phosphorus and nitrogen, and the velocity.
At low velocities the growth rate is reduced to account for limited nutrient supply. At high
velocities the growth is reduced as the periphyton are physically stressed. Respiration rates are a
function of ambient temperature. The model assumes there is no mortality due to grazing.
at
(D2-5)
Mp = the biomass of periphyton, gm/m2,
= the maximum growth for periphyton, days'1,
i D-2-8
-------
f,-d..z.K)-
K(Z^-ZI)
^ Topt 9 dimensionless,
T < T
opt
ZSRP
, dimensionless,
V
^ dimensionless,
PP=PP
, days -i,
_ ^g jnaxunimn periphyton respiration rate, days'1,
, dimensionless
D-2-9
-------
-------
APPENDIX D, D-l, AND D-2 REFERENCES
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j -
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\ ' ' -
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D-Ref-1
-------
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D-Ref-6
-------
TABLE D-1. Water column state variables simulated by the mathematical model for
characterizing ecological risk.
Carbonaceous biological oxygen demand (CBOD)
1 Dissolved oxygen
; Phytoplankton biomass
Organic nitrogen
Ammonia nitrogen
Nitrite + nitrate nitrogen
Organic phosphorus
Orthophosphorus
Water temperature
Coliform bacteria
.; Water depth
| Water velocity
-------
TABLE D-2. Benthic plant state variables simulated
by the mathematical model for characterizing
ecological risk.
Macrophytes with roots
Macrophytes with limited roots
Epiphytes
Periphyton
-------
TABLE D-3. Assessment and measurement endpoints for the ecological risk
analysis of the Middle Snake River.
Assessment Endpoint #1
the reproduction and survival of coldwater biota including trout, sturgeon and
benthic macrbinvertebrates
Measurement Endooints
• Numeric water quality criteria for
dissolved oxygen
: - temperature
[ - ammonia
I - phosphorus
i - nitrogen
; - suspended sediment
• Physical measures of habitat structure and suitability
channel morphology
• Presence, absence and abundance of cold water fish species
• Benthic community diversity metrics
- macroinvertebrates populations
: - periphyton populations
Assessment Endpoint #2
The growth of vascular macrophytes and green and bluegreen algae
Measurement Endpoints
• Numeric water quality criteria for
i - dissolved oxygen
- temperature
ammonia
phosphorus
- nitrogen
- suspended sediment
• Metrics of vascular macrophyte community
1 - vascular macrophyte populations, abundance, biomass,
composition
- epiphytic communities-bibmass and composition
• Metrics of plankton and periphyton communities
; - phytoplankton abundance, composition
, - periphyton abundance, composition
- zooplankton abundance
Physical measures of habitat structure and suitability
i - • channel morphology
- sediment volume
- flow (volume, seasonal timing and duration)
;- substratum characteristics
-------
TABLE D-4. State variables simulated by the dynamic model and their associated
measurement and assessment endpoints.
State Variable
Measurement Endpoint
Assessment
Endpoint
Dissolved Oxygen
Water Temperature
State of Idaho Water
Qualjty^Standardls
State of Idaho Water
Quality Standards
Habitat Suitability
Factors
fotal Phosphorus
Water Depth
State of Idaho Water
Quality Standards
Habitat Suitability
Factors
Water Velocity
Habitat Suitability
Factors
Un-ionized Ammonia
State of Idaho Water
Quality Standards
Reproduction and survival of
coldwater biota
Reproduction and survival of
coldwater biota
Growth of vascular macropfiytes
and algae
Reproduction and survival of
coldwater biota
Reproduction and survival of
coldwater biota
Reproduction and survival of
coldwater biota
-------
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TABLE D-6. Segmentation scheme for the Snake River between R.M. 640.0 and 545.3
and coefficients for characterizing the hydraulic properties of depth and velocity.
Reach #
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
31
32
33
34
35
36
37
Starting
River Mile
640.0
619.0
. 617.5
614.7
610.4
609.9
609.2
608.6
608.3
608.1
607.9
607.7
607.5
607.2
606.8
606.6
606.3
604.6
602.6
601.6
600.6
599.7
599.3
598.8
598.2
597.8
597.3
597.1
596.8
596.0
595.2
594.5
594.2
594.0
593.7
593.2
592.7
Ending
River Mile
619.0
617.5
614.7
610.4
609.9
609.2
608.6
608.3
608.1
607.9
607.7
607.5
607.2
606.8
606.6
606.3
604.6
602.6
601.6
600.6
599.7
599.3
598.8
598.2
597.8
597.3
597.1
596.8
596.0
595.2
594.5
594.2
594.0
593.7
593.2
592.7
. 592.0
AU
0.2
21.081
0.248
0.0404
0.0404
0.0377
0.0833
0.7459
0.0613
0.0464
0.0213
3.5614
16.5635
6.3206
0.0027
0.0020
0.0434
0.0077
0.0020
0.1031
0.0246
0.0282
0.2480
0.0094
0.0036
2.0493
0.00074
74.650
0.0029
0.03191
0.0459
0.9450
0.1518
6.1186
0.0746
0.1497
0.0254
Bu
0.4
0.0666
0.0686
0.3361
0.3361
0.3431
0.2990
0.2220
0.3375
0.3969
0.5070
-0.1057
-0.2306
-0.0688
0.8725
0.7871
0.4095
0.5829'
0.7129
0.2652
0.4079
0.3975
0.1922
0.5425
0.6474
0.1585
0.8330
-0.3298
0.7214
0.4638
0.4090
0.261 1
0.3266
-0.0261
0.3966
0.3345
0.6813
.Ad
1.0
76.953
4.644
0.4281
0.4281
0.4375
1.6885
1.6177
2.5896
2.2613
2.4991
0.5392
0.3741
0.4891
15.6674
23.360
0.4565
0.4504
6.1860
0.0605
0.1340
0.1423
0.5495
0.3798
0.5802
0.1318
16.335
0.0036
5.1412
0.1973
0.6522
0.0251
3.5621
2.7256
0.1790
0.0618
0.7227
Bd
0.2
0.121
0.0667
0.4651
0.4651
0.4659
0.3058
0.2797
0.2631
0.2649
0.2395
0.4150
0.4849
0.4250
0.0582
0.0000
0.1697
0.3727
0.0933
0.5372
0.4693
0.4583
0.0479
0.3524
0.3230
0.3164
0.0731
0.8373
0.1250
0.3818
0.2585
0.5339
0.1129
0.0949
0.4525
00.5585
0.2453
-------
TABLE D-6. Segmentation scheme for the Snake River between R.M. 640.0 and 545.3
and coefficients for characterizing the hydraulic properties of depth and velocity.
(continued)
Reach #
38
39
40
41
42
43
44
45
46
47
48
49
50
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
Starting
I River Mile
592.0
; 591.7
; 586.7
586.0
! 585.0
584.0
583.0
! 582.6
582.1
581.8
581.6
581 .4
579.6
i 578.2
577.5
576.5
; 575.2
574.1
573.8
573.5
; 573.0
572.6
572.3
571 .9
571.5
: 570.5
569.9
565.1
564.3
: 563.2
: 562.3
561.9
561,7
! 561.2
560.0
558.5
'. 557.5
Ending
River Mile
591.7
586.7
586.0
585.0
584.0
583.0
582.6
582.1
581.8
581.6
581.4
579.6
578.9
577.5
576.5
575.2
574.1
573.8
573.5
573.0
572.6
572.3
571.9
571.5
570.5
569.9
565.1
564.3
563.2
562.3
561.9
561.7
561.2
560.0
558.5
557.5
556.5
Au
0.5658
0.0011
3.068e-4
2.692e-4
1.891e-4
1.555e-4
2.300e-4
1.4006-4
1.600e-4
5.8006-5
1.700e-4
1.555e-4
1.4006-4
1.2006-4
8.4006-5
8.4006-5
7.400e-5
5.9006-5
7.6006-5
5.3006-5
0.003
0.139
0.058
0.227
0.304
0.106
0.01
0.003
2.6006-4
1.0006-4
5.9006-5
4.4006-5
7.1006-5
6.5006-5
0.6389
0.0941
0.0735
Bu
0.2369
0.7864
1.0
1.0
1.0
1.0
0.980
0.980
0.989
1.020
1.000
1.0
1.0
0.972
0.982
0.982
0.979
0.994
1.0
1.02
0.708
0.388
0.469
0.349
0.341
0.422
0.621
0.751
0.989
0.988
0.973
1.023
1.000
0.970
0.2332
0.4905
0.4266
Ad
0.0125
7.8080
7.5
6.9
9.9
13.2
32.7
32.7
18.5
58.1
18.6
13.2
18.6
21.4
23.6
32.8
42.5
45.0
50.8
39.5
9.3
0.149
0.618
1.120
2.510
0.832
1.816
3.440
31.1
51.2
65.5
67.1
67.2
57.7
3.9523
10.972
0.2085
Bd
0.7342
0.1431
0.0
0.0
0.0
0.0
0.005
0.005
0.003
0.001
0.000
0.000
0.000
0.012
0.007
0.003
0.001
- 0.001
4.7006-4
0.0
0.131
0.443
0.363
0.299
0.212
0.316
0.248
0.15
0.004
4.5006-4
2.2006-4
2.500e-4
2.2006-4
0.0
0.1454
0.0309
0.4207
-------
TABLE D-6. Segmentation scheme for the Snake River between R.M. 640.0 and 545.3 and
Reach #
76
77
78
79
80
81
82
•83
Starting
River Mile
556.5
555.5
554.5
553.5
552.0
550.0
548.0
546.0
Ending
River Mile
555.5
554.5
553.5
552.0
550.0
548.0
546.0
545.0
AU
1.9189
0.1249
0.3469
8.1198
0.3307
0.5578
0.1974
0.1377
Bu
0.1446
0.4679
0.2377
-0.0332
0.2858
0.2296
0.3168
0.3598
Ad
0.0111
0.5656
0.1723
1.4801
0.1924
0.1388
0.2459
0.3007
Bd
0.6823
0.3042
0.4074
0.1570
0.4267
0.4615
0.4314
0.3893
-------
TABLE D-7. Listing of point sources and major springs discharging to the Snake River
between R.M. 640.0 and R.M. 545.3. Includes Snake River Mile of confluence, station
identification code used by Brockway and Robison (1992) and a description of the
source. i
River
Mile
627.6
619.5
619.0
618.0
617.8
617.7
616.7
612.9
611.0
610.0
609.9
609.1
608.5
608.3
608.1
606.4
605.3
603.6
602.2
601.4
600.9
600.5
600.0
600.0
599.1
599.0
598.7
598.0
595.1
593.5
592.2
592.0
591.5
591.5
590.3
589.5
j Station
Code
!
IR02N
IR03S
I IR04N
IR07S
TS06N
.SPR01
SPR02
IR11S
IR12S
FH14N
; FH15N
' IR16S
ST01S
IR17S
SPR07
TS19S
; IR20S
; IR21S
IR22S
: IR23N
, IR24S
' FH25N
SPR09
i FH26S
•; TS27S
SPR10
! FH28N
.; IR29S
IR30N
; TS32N
; TS33S
' TS34S
IR35S
FH35S
i SPR12
IR36N
Point Source Description
Northside A Drain
Southside A10 Drain
Northside C55 Drain
Southside Twin Falls Coulee
Vineyard Lake
Devil's Washbowl
Devil's Corral
Southside East Perrine Coulee
Southside Main Perrine Coulee
Blue Lakes Trout Farm Fish Processing
Blue Lakes Trout Farm Hatchery
Southside West Perrine Coulee
Twin Falls STP
Southside 43 Drainage
Warm Creek
Rock Creek
Southside 30 Drain
LQ and LS Drain
Southside LS2/39A Drain
Northside N42 Drain on Canyon Rim
Southside 39 Drain
Crystal Springs Hatchery
Crystal Springs
Magic Valley Fish Hatchery
Southside Cedar Draw Creek
Niagara Springs
Rim View Hatchery
Southside I Drain
, Northside J8 Drain
Clear Lakes Outlet
, Southside Mud Creek
Southside Deep Creek
Plant
Southside N Drain prior to Idaho Fish Breeders
Idaho Fish Breeders
Briggs Creek
Northside S29 Drain
-------
Table D-7. Listing of point sources and major springs discharging to the Snake River
between R.M. 640.0 and R.M. 545.3. Includes Snake River Mile of confluence, station
identification code used by Brockway and Robison (1992) and a description of the
source, (continued)
River
Mile
588.4
588.4
588.4
588.4
586.7
586.5
584.3
584.2
583.1
573.6
571.4
Station
Code
SPR16
TS40N
IR39N
FH38S
TS41S
SPR18
IR42N
SPR19
SPR20
TS49N
TS50N
Point Source Description
Box Canyon Springs
Blind Canyon Creek
Northside S19/S Drains
. Box Canyon Fish Hatchery
Salmon Falls Creek
Sand Springs
Northside W26 Drain
Thousand Springs
Riley Creek
Billingsley Creek
Malad River
-------
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-------
TABLE D-12. Springs included specifically in the analysis and the sources
of water quality and quantity data. C&W signifies Covington and Weaver
(see bibliography). Data from Clark and Ott (1996) were used to estimate
concentrations of NO2+NO3-N in all springs.
Spring
Name
Devil's Washbowl
Devil's Corral
Warm Creek
Crystal Springs
Niagara Springs
Clear Springs
Briggs Springs
3ox Canyon Springs
Sand Springs
"housand Springs
3iley Creek
Malad Springs
Spring
ID
SPR01
SPR02
SPR07
SPR09
SPR10
TS32N
SPR12
' SPR16
SPR18
SPR19
SPR20
TS50N
Data Sources
Water Quality
Uof I/ARS -
GW02S
U of I/ARS -
GW02S
U of I/ARS -TS18N
U of I/ARS - GW07
U of I/ARS -
GW08.5
U of I/ARS - TS32N
U of I/ARS - GW1 1
USGS 13095500
Uof I/ARS-GW13
Uofl/ARS-GW13
Uof I/ARS-GW13
U of I/ARS - TS50N
Water Quantity
C&W (Map 2)
C&W (Map 2)
C&W (Map 2)
C&W (Map 3)
C&W (Map 3)
C&W (Map 3)
C&W (Map 3)
C&W (Map 3)
C&W (Map 3)
C&W (Map 3)
C&W (Map 4)
C&W (Map 4)
-------
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-------
TABLE D-14.; Estimates of parameters for the spring temperature model (Eq 3 3)
Spring identification code is from Table D-12.
Spring ID
SPR01
\
SPR02
SPR07
SPR09
SPR10
SPR12
SPR16
SPR18
SPR19
SPR20
T
14.6
14,6
14.6
14.6
14.8
14.8
15.1
14.5
14.5
14.5
AT
1.11
1.11
1.11
0.65
0.43
1.40
1.17
0.95
0.95
0.95
TO
-71.6
-71.6
-71.6
-72.2
-49.6
-74.8
-43.3
-82.5
-82.5
-82.5
-------
TABLE D-15. Segmentation scheme for characterizing return flow to the Study
Reach and measured springs used to characterize return flow water quality.
Correspondence between spring ID #'s and data sources are given in Table D-12.
Return Flow
ID
NPRF1
NPRF2
NPRF3
. NPRF4
Spring
ID
SPR01
SPR09
SPR19
SPR19
Beginning Snake
River Mile
639.7
617.5
596.8
572.2
Ending ,
Snake River Mile
617.5
596.8
572.2
545.2
-------
TABLE D-16. Estimated fraction of segment available
Ifor the growth of macrophytes in the Snake River
between R.M. 640.0 and R.M. 545.0.
Segment
: • #
[ 1
1 2
3
4
5
6
7
'. 8
i 9
10
11
12
13
5 14
15
; is
17
18
i 19
20
• • 21
22
i 23
24
25
26
! 27
28
29
30
31
32
33
34
35
36
37
38
Beginning
River Mile
640.0
617.5
614.7
610.4
609.9
609.2
608.6
608.3
608.1
607.9
607.7
607.5
607.2
606.8
606.6
606.3
604.6
602.6
601.6
600.6
599.7
599.3
598.8
598.2
597.8
597.3
597.1
596.8
596.0
595.2
594.5
594.2
594.0
593.7
593.2
592.7
592.0
591.7
Ending
River Mile
617.5
614.7
610.4
609.9
609.2
608.6
608.3
608.1
607.9
607.7
607.5
607.2
606.8
606.6
606.3
604.6
602.6
601.6
600.6
599.7
, 599.3
598.8
598.2
597.8
597.3
597.1
596.8
596.0
595.2
594.5
594.2
594.0
593.7
593.2
592.7
592.0
591.7
586.7
Habitat
Factor
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.090
0.061
0.255
0.682
0.519
0.519
0.378
0.356
0.356
0.476
0.089
0.050
0.175
0.226
0.464
0.500
0.500
0.159
0.159
0.132
0.010
0.040
0.583
-------
TABLE D-16. Estimated fraction of segment available
for the growth of macrophytes in the Snake River
between R.M. 640.0 and R.M. 545.0. (continued)
Segment
#
39
40
41
42
43-83
Beginning
River Mile
586.7
586.0
585.0
584.0
581.0
Ending
River Mile
586.0
585.0
584.0
581.0
545.0
Habitat
Factor
0.583
0.446
0.439
0.550
0.0
-------
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Parameter estimates
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TABLE D-18. Rate constants used to characterize the growth dynamics of
Potamogeton in the middle Snake River, Idaho developed with data
collected by the University of Idaho during 1992.
M_
j HR
. TtC
; PL
; PR
ML
•Hmax
MR
•••"max
I Kl
KN
KSRP
Vmax
MCO
i
KMC
T0pt
Tmin
Tmax
QR10
^NH4
fSED
X
:8L
Maximum leaf
growth rate
Maximum root
growth rate
Maximum
photosynthetic rate
Maximum leaf respiration
rate
Maximum root respiration
rate
Maximum leaf density
Maximum
root density
Limiting
light intensity^
Half-saturation
constant for nitrogen
Half-saturation
constant for phosphorus
River velocity limitation
Minimum carbohydrate
storage
Half-saturation for
carbohydrate storage
Optimal growth
temperature
Minimum growth
temperature
Maximum growth
temperature
Temperature rate
coefficient
Preference for uptake of
ammonia
Preference for uptake of
sediment nutrients
Light extinction coefficient
Maximum mortality rate for
leaf/shoots
1.2
0.12
1.20
0.006
0.002
900.0
400.0
.0.006
0.50
0.015
1.0
10.0
20.0
25.0
0.0
30.0
1.024
0.50
0.90
0.040
0.20
days'"!
days'1
days"1
days"1
days'1
gm/meter2
gm/meter2
kcal/sec/meter2
mg/l
mg/l
meters/second
gm/meter2
gm/meter2
oc
°C
QC
dimensionless
dimensionless
dimensionless
meters"1
days"1
-------
TABLE D-19. Rate constants used to characterize the growth dynamics of
Ceratophyllum in the middle Snake River, Idaho developed with data
collected by the University of Idaho during 1992.
M_
P-R
TIC
PL
PR
Mr
•L>max
max
K|
KN
KSRP
Vrnax
MCo
&MC
Topt
Tmin
Tmax
QR10
fNH4
^SED
A.
SL
Maximum leaf
qrowth rate
Maximum root
growth rate
Maximum
photosyrtthetic rate
Maximum leaf respiration
rate
Maximum root respiration
rate
Maximum leaf density
Maximum
root density
Limiting
light intensity
Half-saturation
constant for nitrogen
Half-saturation
constant for phosphorus
River velocity limitation
Minimum carbohydrate
storaae
Half-saturation for
carbohydrate storage
Optimal growth
temperature
Minimum growth
temperature
Maximum growth
temperature
Temperature rate
coefficient
Preference for uptake of
ammonia
Preference for uptake of
sediment nutrients
Light extinction coefficient
Maximum mortality rate for
leaf/shoots
1.50
0.08
1.20
0.006
0.002
900.0
50.0
0.006
0.50
0.030
1.0
10.0
20.0
25.0
0.0
30.0
1.024
0.50
0.10
0.040
0.20
days"1
days"1
days"1
days"1
days"1
gm/meter2
gm/meter2
kcal/sec/meter2
mg/l
mg/l
meters/second
gm/meter2
gm/meter2
°C
°C
°C
dimensionless
dimensionless
dimensionless
meters"1
days"1
-------
TABLE D-20. Rate constants used to characterize the growth dynamics of
Cladophora in the middle Snake River, Idaho developed with data
collected by the University of Idaho during 1992.
.w.
;PL
!K|
KN
KSRP
KL
KME
Vmax
fNH4
Topt
Tmin
Tmax
QRIO
( X
Maximum growth rate
Maximum respiration rate
Limiting light intensity
Half-saturation constant
for nitrogen
Half-saturation constant
for phosphorus
Optimal substrate density
Optimal epiphyte density
River current limitation
Preference for uptake of
ammonia
Optimal growth
temperature
Minimum growth
temperature
Maximum growth
temperature
Temperature rate
coefficient
Light extinction coefficient
1.70
0.02
0.001
0.50
0.002
300.0
500.0
2.0
0.50
25.0
0.0
30.0
1.024
0.015
davs~1
days"1
kcal/sec/meter2
mg/l
mg/l
gm/meter2
gm/meter2
meters/second
dimensionless
OG
°c
QC
dimensionless
meters"1
-------
TABLE D-21. Snake River Miles and identification code for stations used to compare
simulated and observed values. ID codes for simulations correspond to the reach
numbers in TABLE D- 6. ID numbers for data collected by the University of
Idaho/Agricultural Research Station (Uofl/ARS), Idaho State University (ISU) and Clear
Springs Foods Inc (CSF) correspond to the codes used by each of those organizations.
Simulation
R.M. ID
612.6
607.6
600.2
594.8
586.3
580.5
567.5.
S04
S13
S21
S31
S40
S49
S72
Uofl/ARS
R.M. ID
610.6
607.6
—
594.6
583.0
579.6
560.0
IS13S
IS19S
—
IS31S
IS44M
IS45S
IS51N
ISU CSFI
R.M. ID R.M. ID
611.0
607.6
600.5
594.6
586.6
581.3
— -
S-1 615.0
S-2
S-3 600.0
S-5 593.7
S-7 586.3
S-9
»««»
S-1
—
S-3
S-5
S-8
—
-------
TABLE D-22. Mean and standard deviation of difference between selected simulated
and observed state variables in the Study Reach.
River Mile
612
607
600
595 ;
586
581
561
DO
-0.41
1.86
-0.20
1.03
-0.35
1.07
-0.11
1.24
0.17
1.20
-0.04
1.22
0.32
0.80
Temp
-0.64
1.50
-0.24
1.24
-0.43
1.23
-0.41
1.03
-0.22
1.07
-0.04
1.03
-0.98
1.10
NH4-N
0.02
0.05
0.11
0.14
0.06
0.05
0.08
0.04
0.02
0.07
0.03
0.04
-0.02
0.08
NOs-N
-0.39
0.41
-0.34
0-42
-0.20
0.30
-0.21
0.28
0.01
0.22
-0.02
0.20
-0.10
0.18
Total P
0.01
0.05
0.04
0.07
0.01
0.04
0.00
0;05
0.01
0.04
-0.01
0.05
0.01
0.02
-------
TABLE D-23. Time periods for spawning and incubation of various salmonid species
native to Idaho.
Fish Species
Chinook salmon (spring)
Chinook salmon (summer)
Chinook salmon (fall)
.Sockeye salmon
Steelhead trout
Redband trout
Cutthroat trout
Sunapee trout
Bull trout
Golden trout
Kokanee
Rainbow trout
Mountain whitefish
Brown trout
Brook trout
Lake trout
Arctic grayling
Time Period (annually)
Aug 1 - Apr 1
Aug 15-June 15
Sept 15-Apr 15
Oct 1 - June 1
Feb1 -July 15
Marl -July 15
Apr 1 - Aug 1
Sept 15-June 10
Sept 1 - Apr 1
June 15-Aug 15
Aug 1 - June 1
Jan 15-July 15*
Oct 15-Mar 15*
Oct 1 - Apr 1
Oct 1 - June 1
Oct 1 - Apr 1
Apr 1 -July 1
: Target species for this risk analysis
-------
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TABLE D-26. Stressor characteristics in the Study Reach for existing conditions.
Stressor
Hydrology
Meteorology
Characterization
IDWR Base Flow Study
Twin Falls & Glenns Ferry meteorology data
for 1967-1995
~\sh Hatcheries
Brockwayand Robison (1992) Study
Irrigation Return Flows
Brockway and Robison (1992) Study
fributary Flows
Brockwayand Robison (1992) Study, Idaho
DEQ(1995)
City of Twin Falls
Discharge Monitoring Data (1993-1994)
-------
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State of Idaho
U.S. Forest Service
U. S. Bureau of Land Management
U. S. Bureau of Reclamation
HUC17040212 boundary
I /\XI County boundaries
Streams
10 15 20 25 30 35 40
Figure D-1. Hydrologic unit for the Middle Snake River.
-------
Point Sources
Water quality
Standards
Habitat Suitability
Relationships
Driving Forces and
Stressors
Management
Ecosystem
Model
Measurements.
Exposure and Effects
Analysis
Figure D-2. Conceptual model for analysis of ecological risk using simulation methods.
-------
ATMOSPHERIC
DO
Figure D-3. Energy and nutrient flow in water column for the Snake River a'quatic'ecosvstoms"
model. • *
-------
Dissolved
Particulate
Nutrients
Stored cartxin due
to phytosynthesis
Figure D-4. Conceptual model for macrophyte growth in the Middle Snake River.
-------
Reach
Computational
Element
Figure D-5. Segmentation scheme for river or river-run reservoir showing typical reach
and typical computational element.
-------
Computational
Element'^^
Reach
Figure D-6. Segmentation scheme for stratified reservoir showing typical reach and
typical computational element.
-------
Decline
in
Fish Populations
Increase
in
Plant & Algal Populations
Decline
in
Native ColdwaterSnailPopulatioris
Sediment
Scouring
Temperature
Modification
Impoundments
Irrigated
Agriculture &
Feedlots
Aquacutture
Sewage
Treatment
Plant
Figure D-7. Conceptual model for interactions of stressors and their effects on the ecosystem
structure and function.
-------
1.6
15-
1.4
1.3
1.1 -
1.0-
0.9
U = 0.2480 *Q°-1S22
• HEC-RAS analysis
Leastsquares analysis
0 2,000 4,000 6,000 8,000 10,000 12,000
Flow - cf s
Figure D-8. Sample regression analysis for relating flow and
velocity using HEC-RAS
-------
ou -
40-
S
£
• 30 -
CC
c
E
< 20 -
i :
10-
0 -
1990
-
}
1
1
1991
—
I
i
1992
In
•
n
_!-•
_
1
~i
_
\
/
^~
^
if
1993
/
-H
— i —
1994
_T
LT_
I
1995
Time - years
Figure D-9. Concentrations of total ammonia nitrogen in the effluent of the
City of Twin Falls STP.
-------
1990
1991
1992 1993
Time - years
1994
1995
Figure D-10a. Simulated and observed dissolved oxygen in the the
Snake River near RM 612.
O
1990
1991
1992 1993
Time - years
1994
1995
Simulated
, O Observed - Uofl/ARS
O Observed - CSFI
A Observed-ISU
Figure D-10b. Simulated and observed water temperature in the
Snake River near RM 612.
-------
0.0
1990
1991
1992
1993
1994
1995
Time - years
Figure D-10c. Simulated and observed NH4-nitrogen in the Snake
River near RM 612.
OJ
E
O
O
3 -
2 -
1990
1991
1992 1993
Time -years
1994
1995
Simulated
O Observed -Uofl/ARS
o Observed -CSFI
A Observed - ISU
Figure D-10d. Simulated and observed NO2 + NO3- nitrogen in the
Snake River near RM 612.
-------
1.0
D)
E
(0
Q.
(0
O
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2 E-
0.1
0.0
1990
1991
1992
1993
1994
—- Simulated
O Observed - Uofl/ARS
n Observed - CSFI
A Observed - ISU
Time - years
1995
Figure D-10e. Simulated and observed total phosphorus in the Snake River near RM 612.
-------
0)
en
>.
x
o
T3
I
O
01
m
16
15
14
13
12
11
10
9
8
7
6
5
4
1990
A
—' —' -«- • ' ' r LJL
1991
1992
1993
1994
1995
Time - years
Figure D-11a. Simulated and observed dissolved oxygen in the Snake River
near RM 607.
1990
1991
1992 1993
Time - years
1994
1995
O
A
Simulated
Observed - Uofl/ARS
Observed -ISU
Figure D-11b. Simulated and observed water temperature in the Snake
River RM 607.
-------
D>
E
0.4
0.3
0.0
1990
1995
Time - years
Figure D-11c. Simulated and observed NH4-nitrogen in the Snake
River near RM 607.
1990 ,
1991
1992
1993
1994
1995
—;— Simulated
Q Observed - Uofl/ARS
A Col 51 vs Col 58
Time - years
Figure D-11d. Simulated and observed NO2 + NO3- nitrogen in the
Snake River near RM 607.
-------
1991
1992
1993
1994
1995
O
A
Simulated
Observed - Uofl/ARS
Observed - ISU
Time - years
Figure D-11e. Simulated and observed total phosphorus in the Snake River near RM 607.
-------
1990
1991
1992 1993
Time - years
1994
1995
Figure D-12a. Simulated and observed dissolved oxygen in the Snake River near
R.M.600.
O
1990
1991
Simulated
9 Observed - CSFI
A Observed - ISU
1992 1993
Time - years
1994
1995
Figure D-12b. Simulated and observed water temperature in the Snake River near
R.M.600.
-------
O)
E
a-.
2
1990
1991
1992 1993
Time - years
1994
1995
Figure D-12c. Simulated and observed NH4-nitrogen in the Snake
River near RM 600.
1990
1991
D
A
Simulated
Observed - CSFI
Observed - ISU
1992 1993
Time - years
1994
1995
Figure D-12d. Simulated and observed NO2 + NO3-nitrogen in the
Snake Rriver near RM 600.
-------
0.0
1990
1991
Simulated
O Observed - CSFI
A Observed -ISU
1992 1993
Time - years
1994
1995
Figure D-12e. Simulated and observed total phosphorus in the Snake River near
RM 600.
-------
D>
E
o
2
X
O
oj
1990
1991
1992 1993
Time - years
1994
1995
Figure D-13a. Simulated and observed dissolved oxygen in the
Snake River near RM 595.
o
1990
1991
1992 1993
Time - years
1994
1995
O
n
Simulated
Observed-UoWARS
Observed-CSF!
Observed-ISU
Figure D-13b. Simulated and observed water temperature in the
Snake River near RM 595.
-------
0.4
0,0
1990
1991
1992 1993
Time - years
1994
1995
Figure D-13c. Simulated and observed NH4-nitrogen in the Snake
River near RM 595.
E 3
Z
CO
O 2
1990
A-
1991
1992
1993
1994
1995
Time - years
Simulated
;o Observed - Uofl/ARS
D Observed - CSFI
A Observed-ISU
[Figure D-13d. Simulated and observed NO2 + NO3-nitrogen in the
Snake River near RM 595.
-------
O)
I
CL
CO
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
O
1990
1991
Simulated
1992
1993
O Observed-Uofi/ARS
n Observed-CSFl
A Observed-ISU
Time - years
A
1994
1995
Figure D-13e. Simulated and observed total phosphorus in the Snake River near RM 595.
-------
0.4
0.0
1990
1991
1992 • 1993
Time - years
1994
1995
Figure D-14a. Simulated and observed dissolved oxygen in the
Snake River near RM 586.
CD
E
O
2
1 •
1990
D
n
1991
n
A
• Simulated
Observed-CSFI
Observed-lSU
1992 1993
Time - years
1994
1995
Figure D-14b. Simulated and observed water temperature in the
Snake River near RM 586.
-------
16
14 -
TO 12
0 10 H
TJ
' 0)
I »
W
CO
n 6
1990
1991
1992 1993
Time - years
1994
1995
Figure D-14c. Simulated and observed NH4-nitrogen in the Snake
River near RM 586.
1990
1991
a
^
Simulated
Observed-CSFI
Observed-ISU
1992 1993
Time - years
1994
1995
Figure D-14d. Simulated and observed NO2+NO3-nitrogen in the
Snake River RM 596.
-------
0.0
1990
1991
Simulated
n Observed - CSFI
A Observed - ISU
1992 1993
Time - years
1994
1995
Figure D-14e. Simulated and observed total phosphorus in the Snake River near RM 586.
-------
— 12
0)
E
c
0)
en
>.
X
O
1
O
(0
03
11 -
10 -
9 -
8 -
7 -
6 -
1990
1991
1992 1993
Time - years
1994
1995
Figure D-15a. Simulated and observed dissolved oxygen in the
Snake River near RM 580.
o
O>
0)
£
••*
a
03
Q.
E
.2
1990
1991
Simulated
O Observed-Uofl/ARS
1992 1993
Time - years
1994
1995
Figure D-15b. Simulated and observed water temperature in the
Snake River near RM 580.
-------
0.4
a; 0.3
D)
E
O.o
1990
i i i , , , P,
1991
1992 1993
Time - years
1994
1995
Figure 15c. Simulated and observed NH4-nitrogen in the Snake
River near RM 580.
1990
1991
1992 1993
Time - years
1994
1995
Simulated
O Observed - Uofl/ARS
Figure D-15d. Simulated and observed NO2 + NO3-nitrogen in the
Snake River near RM 580.
-------
I
i
tn
i
i
0.
I
1.0
0.9
0.8
0.7
0.6
0.4
0.3
0.2
0.1
0.0
1990
1991
Simulated
Observed - ISU
1992 1993
Time - years
1994
1995
Figure D-15e. Simulated and observed total phosphorus in the Snake River near RM 580.
-------
D)
i
0)
8)
•o
2
8
(0
12
11 -
10 -
9 -
8 -
7 -
6 -
5-
1990
1991
1992 1993
Time - years
1994
1995
Figure D-16a. Simulated and observed dissolved oxygen in the Snake River near
R.M. 567.
O
1990
1991
1992 1993
Time-years
1994
1995
Simulated
O Observed - Uof l/ARS
Figure D-16b. Simulated and observed water temperature in the Snake River near
R.M.567.
-------
0.4
5: o.s
D>
E
Z 0.2
i
«
X
0.0
1990
1991
1992 1993
Time - years
1994
1995
Figure D-16c. Simulated and observed NH4-nitrogen in the Snake
River near RM 567.
oo
E
O
I1
1990
1991
1992 1993
Time - years
Simulated
O Observed - Uofl/ARS
1994
1995
Figure D-16d. Simulated and observed NO2 + NO3-nitrogen in the
Snake River near RM 567.
-------
1)
in
a.
I
OL
"co
I
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
1990
1991
Simulated
1992 1993
Time - years
1994
1995
O Observed - Uof I/ARS
Figure D-16e. Simulated and observed total phosphorus in the Snake River near RM 567.
-------
1990
1991
1992 1993
Time - years
1994
1995
Figure D-17. Simulated and observed biomass of rooted
macrophytes in the Snake River near RM 600.
Simulated
Observed'- Uofl
1992 1993
Time - years
1994
1995
Figure D-18. Simulated and observed biomass of nonrooted
macrophytes in the Snake River near RM 600.
-------
200
<
180-
160 -
jw" 140
O
E 120
0)
CO
0)
Q
f.
100 -
80 -
60 -
.3-
Q.
HI
,2- 40 -
20 -
1990
1991
Simulated
Observed - Uof I
1992 1993
Time - years
1994
1995
Figure D-19. Simulated and observed epiphyte biomass in the Snake River near RM 600.
-------
(a) Dluolved Oxygen
• • W 11 12 » U 15
Simulated
(b) Water Totnparatura
g »
JQ
O w
6- > At •
10 «
Slmulattad
(c) Total Ammonia - Nitrogen
I
6JS O.10 Q.1S O3O 62 OJO 8J3 CU9 0.« OSO
Simulated
(d) Nitrite + Nitrate - Nitrogen
Simulated
(a) Total Phosphorus
aas we CUB OM 0^5
Simulated
Figure D-20. Comparison of simulated and observed state variables at
Station S04 in the Study Reach. Station locations are given in Table 21.
-------
(a) DUmolVcd Oxygon
6 a 7 • e
U U 14 IS
Elmufttid
(b) Water Temperature
Simulated
(c) Total Ammonia - Nitrogen
/>*.
-------
(a) Dissolved Oxygen
(b) Water Temperature
S
A
o
fl 10 1 1 12 1 3 1 4 IS
Simulated
(c) Total Ammonia - Nitrogen
(d) Nitrite + Nitrate - Nitrogen
OBJ (US 0.10 0.15 O20 O2S O30 (US C.W O«S OSO
Simulated
Simulated
(e) Total Phosphorus
(MO
ass
030
TJ
-------
(a) Dissolved Oxygen
(b) Water Temperature
& 10 1 I 12 t 3 1 4 16
Simulated
Simulated
(e) Total Ammonia - Nitrogen
(d) Nltrtte + Nitrate - Nitrogen
(XOO Ate 0.10 0.18
-------
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(b) Water Tttmparaturo
s :
s „
« I
Slmulittd
(c) Tata I Amman fa - Nltragon
(d) Nitrite + Nltr.to -Nltrogan
s
§
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S
S
a
a
tun ua B.19 0.11 QJO frz
Elmulttod
Rgure Dr24. Comparison of simulated and observed state variables at Station S40 in
the Study Reach. Station locations are given in Table 21.
-------
(a) Dissolved Oxygen
(b) Water Temperature
Simulated
-------
(a) Dissolved Oxygen
Simulated
i ;:
i
O
(b) Water Temperature
S 1Q is
Simulated
(c) Total Ammonia - Nitrogen "
eja etfs 030 oas
Simulated
CUtO
0.6S •
(a) Total Phosphorus
(d) Nitrite + Nitrate . Nitrogen
Simulated
0.10 0.1S OiO (U5 BJO OJS 0.40
Simulated
Figure D-26. Comparison of simulated and observed state variables at Station S72
in the Study Reach. Station locations are given in Table 21.
-------
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0.8
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0.5
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0.8
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(0
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0.9
0.8
0.7
0.6
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0.4
0.3
0.2 -
0.1 t-
0.0
Tern perature - deg C
Figure D-27. Habitat suitability curves for rainbow trout spawning (Bovee, 1978).
-------
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w
1.0
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1.0
0.9
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0.6
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0.4
0.3
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Depth - feet
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