&EPA
c
United States
Environmental Protection
Agency
Office of Research and
Development
Washington, D.C. 20460
EPA/600/R-00/011
January 2000
Northeastern Nevada
Landscape and Aquatic
Resource Characterization
on Federal Lands -
Research Plan
GAP Vegetation Map
40
Miles
0 40
80
Humboldt River Basin
GAP Vegetation (30m grid)
r~"l Aspen
Subalpine Pine, Juniper
^M Mtn Mahogany, Pinyon, PJ
^M Subalpine Fir
BH Greasewood, Mtn. Shrub
I I Sagebrush
i i Sagebrush, Per. Grass
I I Salt Desert Scrub
I I Alpine & Dry Meadow
I I Grassland
i i Agriculture
I I Barren
i i Riparian
I I Playa
i i Sand Dune
i iSnow
Urban
^m Water
I I Wetland
IZZI No Data
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EPA/600/R-00/011
January 2000
Northeastern Nevada Landscape and
Aquatic Resource Characterization on
Federal Lands - Research Plan
Participants and Agencies
Robert K. Hall
U.S. Environmental Protection Agency
Region IX
75 Hawthorne Street, WTR2
San Francisco, CA 94105
(415)744-1936
hall.robertk@epamail.epa
Daniel Heggem
U.S. Environmental Protection Agency
National Exposure Research Laboratory
Las Vegas, NV89119
(702) 798-2278
hegaem.daniel@epa.aov
John Hillenbrand
U.S. Environmental Protection Agency
Region IX
75 Hawthorne Street, WTR7
San Francisco, CA 94105
(415)744-1912
hillenbrand.iohn@epa.epa
Thomas Porta
Bureau Chief
Bureau of Water Quality Planning
Nevada Division of Environmental Protection
333 West Nye Lane
Carson City, NV 89706-0851
(775) 687-4670, ext. 3098
Peter Tuttle
U.S. Fish and Wildlife Service
1340 Financial Blvd.
Reno, NV
(775)861-6325
Pete Tuttle@fws.gov
Peter Husby
U.S. Environmental Protection Agency
Regional Laboratory
Richmond, CA
(510)412-2331
husbv.peter@epa.gov
Lee Roberts
Shoshone-Paiute Tribe
P.O. Box 219
Owyhee, NV 89832
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Table of Contents
Proposal Summary IV
Section I Background 1
Section II Project Design 3
Objectives 3
Section III Sampling Design 5
Section IV Methods 6
Landscape 6
Watershed Land Use, Land Cover, and Development Indicators 7
Forest Indicators 8
Remotely-sensed Vegetation Indicators 8
Chemical Loadings 9
Riparian Indicators 9
Description of Selected Landscape Indicators (Jones et al., 1997) 10
Human Use Index 10
Road Density 10
Landscape Units 11
Forest and Agriculture Land Cover Along Streams 11
Roads Along Streams 11
Impoundment Density 11
Crop Land and Agriculture Land on Steep Slopes 11
Potential Nitrogen and Phosphorus Loadings to Streams 12
Soil Loss Potential 12
Forest Land Cover 12
Forest Fragmentation 12
Forest Edge Habitat 12
Forest Interior Habitat 13
Departure of the Largest Forest Patch Size 13
Calculation of NDVI and its Change 13
NDVI Change within Watersheds 13
NDVI Loss on Steep Slopes 14
Reconnaissance - Office and Field 14
Office Reconnaissance Methods 15
Field Reconnaissance Methods 18
Determining Stream Site Status 19
Nontarget 19
Target 19
Inaccessible 19
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Flow Models 20
Aquatic Biota 21
Fish 22
Species Assemblage Assessment 22
Assessment of Fish Condition and General Health 22
Assessment of Teratogenic Effects 23
Organosomatic Assays Analyses 23
Toxicity 24
Laboratory Procedures 24
Quality Assurance/Quality Control 24
Aquatic Reference Condition 24
Biotic Indices 25
Physical Habitat 26
Stream Sample Reach 27
Habitat Sampling 28
Thalweg 29
Subbank 29
Fish Cover 30
Large Woody Debris 30
Canopy Cover - Densiometer 31
Riparian Structure and Human Influence 31
Stream Discharge 32
Periphyton 32
Sediment Metabolism 33
Chemical Analyses 33
Water Chemistry 34
Sediment Chemistry 35
Benthic Invertebrates 36
Fish 36
Data Analysis 37
Section V Data Management 38
Data Sharing with EPA, USGS, NDEP, and NDOW 38
Section VI Justification 39
Section VII References Cited 41
Figures 47
-in-
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Proposal Summary
The basin and range province of northeastern Nevada is dominated by mining and agriculture land
use. Impacts on surface water quality and aquatic resources from these land use practices are poorly
known, especially in the areas of ore processing, valley fill waste rock drainage, and inactive or
abandoned mines. This proposal seeks to define the Nonpoint Source (NFS) loadings to streams and
examine their effect on aquatic resources. The State of Nevada 305(b) and 303(d) report states Total
Maximum Daily Loads (TMDL) development for Total Phosphorus (TP) and Total Suspended Solids
(TSS) for reaches of the Humboldt River is a high priority. This project will address Nevada Division of
Environmental Protection (NDEP) and Nevada tribal concerns in the areas of grazing and mining
activities on lands under federal management.
This proposal is a multiagency effort between the U.S. Environmental Protection Agency (USEPA)
Region IX, the USEPA Office of Research and Development (USEPA ORD), the U.S. Fish and Wildlife
Service (USFWS), the Duck Valley Indian Reservation, the Fort McDermitt Indian Reservation, and the
South Fork of the Humboldt River Indian Reservation. Partnerships with the U.S. Forest Service
(USFS), the U.S. Bureau of Land Management (BLM), and the NDEP will be forth coming. The study
area of interest is land managed by federal agencies USFS and the BLM in the Humboldt River and
Snake River watersheds, located in northeastern Nevada. This proposed project will be an addition to the
already existing EPA Region IX Humboldt River Watershed Regional Environmental Monitoring and
Assessment Program (R-EMAP), which is a regional subset of the EPA's Office of Research and
Development (ORD) national Environmental Monitoring and Assessment Program (EMAP). The EPA
Region IX R-EMAP Surface Water study concentrates on the aquatic resources of an arid environment
dominated by mining activities within the Humboldt River Watershed. Objectives of this proposed study
are to characterize the habitat and aquatic macroinvertebrates within the Humboldt River and Snake
River watersheds, define reference sites and conditions, and develop TMDLs for NFS runoff. This study
will be divided into two phases: 1) high elevation, high gradient USFS lands with low grazing impacts
and 2) lower elevation, low gradient USFS and BLM lands with mining and grazing impacts. Each phase
can be implemented in sequence or concurrently depending on funding and stakeholder participation.
This proposed federal land bioassessment study will be a 2 to 4 year project dependent on funding. If
funding requirements are met, the study area will be expanded to include federal land holdings in other
parts of the state and EPA Region DC. Future research areas will coincide with the State of Nevada
TMDL priority watersheds.
The Humboldt River and Snake River drainage is an area of ecological concern because of the
potential impacts of current and proposed anthropogenic activities including extensive mining, ,
agriculture, livestock grazing, land development, water use, and timber harvest. This area has seen some
of the most intense mining in Nevada history. It is also experiencing accelerated ground-water
dewatering in addition to acid mine drainage from older abandoned mines. Surface and ground water
interacting with rocks exposed during mining activity results in the discharge of acidic metal-laden
waters. Nonacidic drainage and runoff from mine sites may also contain elevated concentrations of
inorganic contaminants, such as arsenic, selenium, and sulfate. Because of the periodic nature of
drainage and runoff in this arid region, characterization of mine drainage quality is difficult. Aquatic
-IV-
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bioassessment and landscape characterization are cost-effective tools to enable characterization of water
quality and condition of terrestrial and aquatic biological resources.
The northern Great Basin ecoregion in Nevada covers an extensive area, yet very little is known of
the water quality and associated aquatic invertebrate communities there. The proposed study will
provide a data set that can serve as a basis for evaluating anthropogenic change, and it can substantially
increase our knowledge of aquatic invertebrate communities in the basin and range ecoregion from data
collected from approximately 80 sites over a period of 2 years. The proposed aquatic bioassessment in
the Humboldt River drainage will also provide much needed information on the condition of aquatic
resources in the Humboldt River drainage, an area of ecological concern, and will establish biocriteria for
monitoring perennial streams throughout the state. Additional information on the ecology of aquatic
invertebrates in the basin and range ecoregion will also be obtained, with insight into how aquatic
macroinvertebrate and fish community structure is affected by various physical and chemical parameters.
The large scale investigation will also provide information on the biodiversity of aquatic
macroinvertebrates in the northern Great Basin ecoregion of Nevada.
-v-
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Section I
Background
The basin and range province of northeastern Nevada is dominated by mining and agriculture land
use. Impacts on surface water quality and aquatic resources from these land use practices are poorly
known, especially in areas of ore processing, valley fill waste rock drainage, and inactive or abandoned
mines. Surface and ground water interacting with rocks exposed during mining activity results in the
discharge of acidic metal-laden waters. Nonacidic drainage and runoff from mine sites may also contain
elevated concentrations of inorganic contaminants, such as arsenic, selenium, and sulfate. Because of the
periodic nature of drainage and runoff in this arid region, characterization of mine drainage quality is
difficult. Aquatic bioassessment and landscape characterization are cost-effective tools to enable
characterization of water quality and condition of terrestrial and aquatic biological resources.
This proposal seeks to define the Nonpoint Source (NFS) loadings to streams and examine their
effect on aquatic resources in arid environments. The State of Nevada 305(b) and 303(d) report states
Total Maximum Daily Loads (TMDL) development for Total Phosphorus (TP) and Total Suspended
Solids (TSS) for reaches of the Humboldt River is a high priority. Water quality monitoring programs by
the Nevada Division of Environmental Protection (NDEP) and the U.S. Geological Survey (USGS), and
observations made as part of the U.S. Environmental Protection Agency (USEPA) Region IX Humboldt
River Watershed REMAP project indicate, grazing and mining have the most prevalent environmental
impact within the basin and range and Snake River High Desert ecoregions. These studies indicate
nutrients and metals contamination are the primary causes of beneficial use impairments. This project
will address NDEP and Nevada tribal concerns in the areas downstream of grazing and mining activities
on lands under federal management of northeastern Nevada (Figure 1). The Duck Valley Indian
Reservation on the Owyhee River, the Fort McDermitt Indian Reservation on the Quinn River, and the
South Fork Indian Reservation on the South Fork of the Humboldt are potentially impacted by these
problems.
The Humboldt River and Snake River drainage is an area of ecological concern because of the
potential impacts of current and proposed anthropogenic activities, including extensive mining,
agriculture, livestock grazing, land development, water use, and timber harvest. Within the next few
years, further open pit mining will commence within the Humboldt river drainage area using heap leach
technology. These activities may adversely affect unique aquatic biota, including four threatened or
endangered fishes and one amphibian candidate for listing as endangered or threatened. The Humboldt
River drainage supports most of the remaining fluvial populations of endemic Lahontan cutthroat trout
(Sigler and Sigler, 1987). The area examined in the proposed investigation includes two of the three
distinct population segments of Lahontan cutthroat trout. In addition, little information is available on the
types of aquatic macroinvertebrates found in the streams and rivers within the Humboldt River and Snake
River drainage.
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The study area is located in northeastern Nevada and covers an area approximately 17,000 mi2. The
region is located in the northern basin and range physiographic province with north-south trending
fault-bounded horst and graben geomorphology. The mountains are steep and deeply incised with
alluvial/colluvial deposits in the canyons with fine sediments becoming the dominant substrate in the
broad valleys. The main stem of the Humboldt River is the longest river in the Great Basin. The main
tributaries to the Humboldt are the Reese, Marys, South Fork Humboldt, and North and South Forks of
the Little Humboldt rivers. Water flow from the Quinn, North Fork Humboldt, and East Fork Humboldt
rivers rarely reaches the main stem Humboldt River (Sigler and Sigler, 1987). The main stem of the
Humboldt River is very sinuous (Sigler and Sigler, 1987) and has an extent of 300 miles, 1,000
meandering miles, from the headwaters to its terminus within the Humboldt Sink south of Lovelock. The
Owyhee river flows north into the Snake River.
As a result of the dramatic topographical relief, a considerable change in aquatic habitat occurs along
the stream continuum. Mountain streams are categorized as cold, high gradient with a substrate
dominated by boulder, cobble, and gravel. Valley streams and rivers are categorized as warm, low
gradient streams dominated by sand and silt.
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Section II
Project Design
This proposed project will be an addition to the already existing EPA Region DC Humboldt River
Watershed Regional Environmental Monitoring and Assessment Program (R-EMAP), which is a regional
subset of the EPA's Office of Research and Development (ORD) national Environmental Monitoring and
Assessment Program (EMAP). The EPA Region DC R-EMAP Surface Water study concentrates on the
aquatic resources of an arid environment dominated by mining activities within the Humboldt River
Watershed.
The study area of interest is land managed by federal agencies U.S. Department of Agriculture Forest
Service (USFS) and the Department of the Interior Bureau of Land Management (BLM) in the Humboldt
River and Snake River watersheds, located in northeastern Nevada (Figure 1). This study will focus on
tributaries of the Humboldt River upstream of Winnemucca and tributaries of the Snake River that drain
northward from Nevada into Snake River Basin. The study area will be a 2 by 4 degree quadrant of
northeastern Nevada bounded by the coordinates of 40° and 42° north latitude, 114° and 118° west
longitude.
This study will be divided into two phases: 1) high elevation, high gradient USFS lands with low
grazing impacts; and 2) lower elevation, low gradient USFS and BLM lands with mining and grazing
impacts. Each phase will consist of four major tasks (Figure 2). Task 1 will identify and evaluate
landscape indicators to conduct a comparative landscape assessment and determine any ecological
changes occurring from human influence. As seen in the conceptual model in Figure 2, Task 2 will
review and identify flow models, which utilize the most appropriate statistical methods for the analysis of
water and sediment chemistry parameters using aquatic biota and landscape indicators. Task 3 will be to
determine baseline conditions, aquatic resources, and identify reference sites within the study area. Task
4 will develop a management tool for implementing Best Management Practices (BMP) based on cost
benefits, which will include parameters from Tasks 1 to 3 and the determination of load allocation within
a watershed or sub watersheds and/or particular stream reach(es). Each phase can be implemented in
sequence or concurrently depending on funding and stakeholder participation.
Objectives
This proposed federal land bioassessment study will be a 2 to 4 year project dependent on funding. If
funding requirements are met, the study area will be expanded to include federal land holdings in other
parts of the state. Future research areas will coincide with the State of Nevada TMDL priority
watersheds. The proposed study will initiate a 2-year biological assessment of lands under federal
management in the Humboldt River and Snake River drainage in northeastern Nevada. The objectives of
this study are:
1. Assess the condition of aquatic resources (macroinvertebrates and fish) within the study area.
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2. Identify landscape indicators that represent natural and human factors which have an effect on
water quality.
3. Establish baseline values for water and sediment chemistry parameters and toxicity, determine
trend relationships for individual chemical parameters, and estimate loading rates related to time
(kilogram per year [kg/yr]) and unit area (kilogram per hectare [kg/ha]) for each subwatershed.
4. Define aquatic reference conditions for perennial streams and rivers.
5. Quantify nutrient and metal nonpoint source loads from the various land use categories identified
in objective 2.
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Section III
Sampling Design
Background landscape and aquatic conditions in the area are poorly known due to inadequate
concentration of water quality and biological sampling away from the main stem of the Humboldt River.
This study will identify baseline conditions and reference sites in higher and lower elevation streams
(Gerritsen and Leppo, 1998) on USFS and BLM lands using the EMAP random sampling design. An
Index of Biological Indicators (IBI) for fish and invertebrates will be created for high
gradient/elevation/cold water streams affected predominantly by mining and logging activities, and for
low gradient/elevation/warm water areas where impacts have been documented by several sources.
Northeastern Nevada has seen some of the most intense mining in Nevada history. It is also experiencing
accelerated ground-water dewatering in addition to acid mine drainage from older abandoned mines.
A random sampling design will be employed to determine site locations within the watershed. A total
of 40 sites per year will be allocated between first and third order streams on a stream mile basis, with
the greatest sampling effort occurring at the order with the largest number of stream miles. The number
of sites at a given stream order and location of those sites will be determined upon consultation with EPA
statisticians. Field crews will collect biological, physical habitat, and chemical data during the index
period of July and August.
Sampling sites are selected using a random tessellation stratified design (Stevens and Olsen, 1999;
Stevens, 1997). The tessellation stratified design confines the sample site selection to ensure the target
population represents the spatial coverage of the study area. For this study, the target population is
streams (Strahler Order 1-4) within USFS and tribal lands of northeastern Nevada. USEPA's River Reach
File 3 (RF3), 1:100,000 Digital Line Graph (DLG), data is used as the sampling frame for identifying
target population streams (Horn and Grayman, 1993). To achieve an approximately equal expected
sample size across stream order and across basins, the sample design is weighted by stream order
categories to ensure sampling will occur in the higher order streams (Hall et al., 1998).
Acid rock drainage (ARD) is characterized by high frequency variations and seasonal effects
(Robertson, 1990). Concentrations of ARD in streams are influenced by precipitation and runoff.
During the spring snow melt and in heavy precipitation, events will add more ARD into streams, with
low concentrations occurring in dry periods, frozen conditions, and light precipitation. To determine the
frequency and range of ARD concentrations in streams, and the acute or chronic effects on the aquatic
community, a continuous water quality monitoring program will be implemented. Long term fixed
station water quality monitoring sites will be selected to represent mining and grazing impacted streams.
These sampling sites will be identified from the data collected from the randomly selected sites and/or by
the stakeholders.
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Section IV
Methods
Characterization of the watershed habitat and aquatic macroinvertebrates within the Humboldt River
and Snake River watersheds will be the primary focus of the proposed study. Watershed habitat
assessment will provide information on stream condition such that trends from natural (i.e., storm events,
flow, etc.) and human influenced stfessors (i.e., impoundments, channelization, land use, etc.). These
data can be determined spatially and temporally. Aquatic macroinvertebrate diversity and population
structure will be determined in Ist-nth order streams found within the watershed.
Basin and range streams generally have a low diversity of native fish species, with only eight native
species of known fish from the Humboldt River drainage. Numerous exotic fish have been introduced
into the Humboldt River with 17 exotic species found in the main stem Humboldt River from Battle
Mountain to Rye Patch Reservoir (U.S. Department of the Interior, BLM, 1995). Because of the low
species diversity of native fishes, negative effects of introduced species on native species, and the
haphazard introductions of exotic fish throughout the Humboldt River drainage (Moyle, 1976; Sigler and
Sigler, 1987), the stability of communities in the Humboldt River drainage is uncertain and may not be a
reliable indicator of stream condition. However, the proposed investigation will determine if measures of
fish community structure correlate with water and habitat variables. The relationship between water and
habitat variables and the general condition and health of fish will also be examined.
Landscape
Understanding watershed characteristics will help in the identification and interpretation of
biogeographical patterns in biological communities (Fitzpatrick et al., 1998). To characterize a watershed
or a stream, it is necessary to identify the geologic, geomorphologic, hydrologic, land cover vegetation
and distribution, and land use (Figure 2). The first step is to identify a set of landscape indicators with
which to conduct a comparative landscape assessment on the sub-regional study areas. The landscape
monitoring and assessment approach involves the analysis of spatially explicit patterns of, and
associations between, ecological characteristics such as soils, topography, climate, vegetation, land use,
and drainage pathways, and interprets the resulting information relative to ecological conditions on areas
ranging in size from small watersheds (a few hundred hectares) to entire basins (several million hectares)
(Foreman, 1990; O'Neill et al., 1994; Kepner et al., 1995; Jones et al., 1997).
Five characteristics distinguish a landscape monitoring and assessment approach from most
traditional field- or site-based monitoring programs:
1) it involves analysis of spatially explicit patterns of ecological characteristics (e.g., forests near
streams) to interpret ecological conditions;
2) it applies the concept from the field of landscape ecology that changes in landscape patterns
result in changes in fundamental ecological processes, including fluxes in energy, biota,
materials and nutrients, and water;
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3) it applies the concept of ecological hierarchy theory in analyzing the consequences of
landscape change on ecological resources and processes at multiple scales;
4) it utilizes digital maps or coverages of biophysical (e.g., soils, vegetation, topography, and
climate) and human use (e.g., land use, population change) characteristics to analyze and
interpret spatially explicit landscape patterns relative to ecological condition; and
5) it includes rather than excludes humans as part of the environment.
The fundamental basis for this type of approach is that spatially explicit changes in a landscape
pattern result in changes to ecological processes from which important ecological goods and services are
derived and sustained (Turner, 1989; Foreman, 1990, Figure 1). For example, losses of forested riparian
habitats in a watershed reduce that watershed's ability to filter sediment from overland surface flows -
(Karr and Schlosser, 1978; Lowrance et al., 1984, 1985; Peterjohn and Correll, 1984). This results in
reduced water quality in the streams of that watershed. Similarly, clear-cutting of forests on areas with
steep slopes results in soil losses which in turn can decrease the likelihood of sustaining harvestable
forests on those areas and increase sediment loadings to streams (Lee, 1989; Franklin, 1992).
Following is a list of landscape indicators being evaluated for use in the EMAP Western Pilot (Jones
et al., 1997). For this study, these indicators will be assessed to meet the needs of the project objectives.
Watershed Land Use, Land Cover, and Development Indicators
UINDEX
NINDEX
RDDENS
MPERV
RIPFOR
RIPAG
STRD
DAMS
CROPSL
AGSL
PSOIL
Human use index (proportion of watershed area with agriculture or urban land
cover)
Natural land cover diversity (heterogeneity of watershed area relative to land
covers which are not agriculture or urban)
Road density (average number of kilometers [km] of roads per square
kilometer of watershed area)
Amount impervious surfaces (roads, parking lots, urban factors)
Proportion of total streamlength with adjacent forest land cover
Proportion of total streamlength with adjacent agriculture land cover
Proportion of total streamlength that has roads within 30 meters (m)
Number of impoundments per 1,000 km of stream length
Proportion of a watershed with crop land cover on slopes that are greater than
3 percent
Proportion of a watershed with agriculture land cover on slopes that are greater
than 3 percent
Proportion of a watershed with potential soil loss greater than 1 ton per acre
per year
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Watershed Land Use, Land Cover, and Development Indicators, Continued
Surface mine impacts Indicator describing how the mine density and distribution in a watershed, and
their proximity to streams, affect water quality. The indicator will be stratified
by mine type.
Point source (NPDES) Density and diversity of pollution discharges in a watershed (or subregion)
index (stratified by types of contaminants and media of release + modeled T&F)
WATSTOR Amount of surface water storage capacity for a watershed (total area of lakes,
rivers, and wetlands areas)
*
Feedlots Index of feedlot locations and densities (CAFO program)
Ownership Land ownership (GAP, RLM ALMRS, ICBEMP)
T & E species metrics Distribution of biodiversity relative to conservation lands (similar to GAP
mission), vulnerability of T&E species to disturbance
Rangeland disturbance Terrestrial indicator distinguishing between natural and disturbed
grasslands/rangelands
Drought index Not defined
Weather patterns Not defined
Forest Indicators May be modified to accommodate rangelands and other arid land covers in the
West.
FOR% Percent of a watershed area that has forest land cover
FORFRAG Forest fragmentation index
EDGEx Proportion of a watershed area with a suitable forest edge habitat (where x is
scale)
INTx Proportion of a watershed area with a suitable interior forest habitat (where x
is scale)
INTALL Proportion of a watershed area with a suitable interior forest habitat at three
scales
FORDIF Departure of the largest forest patch size from the maximum possible for a
given amount of anthropogenic land cover
Remotely-sensed Vegetation Indicators
NDVIDEC Decrease in a normalized difference vegetation index from 1975 to 1990
NDVnNC Increase in a normalized difference vegetation index from 1975 to 1990
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Remotely-sensed Vegetation Indicators, Continued
NDVITOT
1STDEC
1STINC
1STTOT
NDVB%
NDVIDIV
Surface roughness
Total change in a normalized difference vegetation index from 1975 to 1990
Difference between observed and expected decreases in a normalized
difference vegetation index from 1975 to 1990 in first order stream regions
(stream order criteria may be different in the West)
Difference between observed and expected increases in a normalized
difference vegetation index from 1975 to 1990 in first order stream regions
(stream order criteria may be different in the West)
Difference between observed and expected total change in a normalized
difference vegetation index from 1975 to 1990 in first order stream regions
(stream order criteria may be different in the West)
Proportion of a watershed with normalized difference vegetation index
decreases from 1975 to 1990 on slopes greater than 3 percent (slope criteria
may be different in the West)
Spatial and temporal diversity in the NDVI signal across landscapes. A
developmental indicator of land cover classes (C3 v. C4 vegetation) and their
response to stress (drought or grazing).
An indicator of the presence of vegetation - not well defined
Chemical Loadings
STNL
STPL
Potential nitrogen loadings to streams
Potential phosphorus loadings to streams
Riparian Indicators
Riparian patchiness
Shading
Indicators of riparian
"reference" conditions
Hydrologic
connectivity
Linked landscape/WQ
indicators
Greenness patch dynamics to identify stream bank stability at subpixel scale
(could be an indicator of grazing impacts of stream riparian)
Amount of stream shading (and subsequent temperature regulation)
attributable to topography and riparian vegetation
Not well defined
Index of "lateral plumbing" along streams as indicator of vulnerability (phase
3 or 4, i.e., applied at large areas)
A nested indicator linking remote sensing-based analysis with EMAP Surface
Water analysis
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Riparian Indicators, Continued
Channel Multiresolution identification of channel geomorphology and changes in
geomorphology geometry
Runoff characteristics Flooding characteristics, stream flow regime (or surrogates)
Cow grazing intensity Impacts on riparian vegetation, erosion, bank stability; derived from
indicator agriculture and land use data
Description of Selected Landscape Indicators (Jones et al., 1997)
Human Use Index (UINDEX)
Two different methods will be used to create the two maps of the human use index. The surface map
for the mid-Atlantic region will be produced by using a spatial filter. The window size will be about 65
ha and contain 729 pixels in a 27x27 pixel window. The window will be moved one pixel at a time across
the land cover map. At each step, the number of pixels that had agriculture or urban land cover will be
counted. Dividing this sum by the number of pixels in the window (729) yielded the index value which
will then be mapped at the location corresponding to the center of the window. A second spatial filter
will then be applied to "smooth" the surface map. The smoothing filter will find the median index value
in 9x9 pixel windows (about 7 ha). The final map will be shown at 7-ha resolution. The watershed map
will be produced by using a cookie-cutter procedure to extract the land cover information for each
watershed separately. The number of pixels with agriculture or urban land cover will then be counted in
each watershed, and the total will be divided by the total number of pixels for a given watershed to yield
the per-watershed index value.
Road Density (RDDENS)
The U.S. Geological Survey (USGS) road maps are very detailed maps which are available as digital
line drawings. To create the surface map of relative road density, the line drawings will be first converted
to raster images (or bitmaps) with a resolution of 90 m. That is, each 90-m by 90-m square in the region
that contained at least one road segment will be coded as containing a road. Then, a spatial filter will be
applied to this 90-m resolution map. The window size will be approximately 1 km2 and contain 121
pixels in a 11x11 pixel window. The window will be moved one pixel at a time across the land cover
map. At each step, the number of pixels that are coded as containing at least one road segment will be
counted. The road density score will be obtained by dividing this sum by the number of pixels in the
window (121), and this score will then be mapped at the location corresponding to the center of the
window. This procedure tends to emphasize the importance of the first occurrence of a road in a given
location and to give less weight to subsequent occurrences.
To create the watershed map of road density, a different procedure will be used. The line drawings
representing all roads will be clipped using the watershed boundaries, so that a per-watershed value could
be calculated. The total length of roads in each watershed will be divided by the total area of the
watershed. The resulting value represents road density as road length (kilometers) per unit area (square
kilometers).
10
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Landscape Units
The land cover map will be analyzed using the spatial filtering technique. The window size will be
about 590 ha and contain 6,561 pixels. The window will be moved one pixel at a time across the land
cover map. At each step, counts will be made of the number of pixels that were forest, agriculture, and
urban in the window. Then, a landscape unit type will be assigned to the location at the center of the
window by using rules which are described in the text. To simplify the resulting map, a majority-rule
spatial filter will be applied and the resolution will be reduced to about 7 ha. The majority-rule filter will
examine all landscape pattern types within 7-ha windows and assign the most common type to the whole
window.
Forest and Agriculture Land Cover Along Streams (RIPFOR, RIPAG)
Maps of forest and agriculture land cover along streams will be created by using the overlay
technique. The map of streams will be converted to a raster format with 30-pixels. This version of the
streams will be overlaid on the land cover map to determine the stream length that flowed through forest
and agriculture land cover. The length of streams flowing through forest and agriculture land cover,
respectively, will be divided by the total length of streams in each watershed to arrive at the index value.
A 30-m pixel size will be used because it is consistent with the pixel size of the land cover map. The
proportions will change with different stream pixel sizes, depending on the amount of forest and
agriculture land cover in the riparian zone defined by the pixel size.
Roads Along Streams (STRD)
The procedure will be similar to that used for the preceding indicators. Road and stream maps will be
converted to a raster format with 30-m pixels and then overlaid. The number of pixels where both a road
and a stream occurred will be divided by the total number of stream pixels in the watershed.
Impoundment Density (DAMS)
The USGS defines large dams as those that are able to store at least 5,000 acre-feet of water. The
source data will be converted into a map of point locations and overlaid on the watershed map. The
number of dams in each watershed will be then divided by the total stream length for the watershed to
estimate the density of impoundments. The density estimate is expressed as the number of dams per
1,000 km of streams.
Crop Land and Agriculture Land on Steep Slopes (CROPSL, AGSL)
Agriculture on steep slopes was mapped by overlaying the slope map and the land cover map.
Percent slope is calculated from the USGS digital elevation model (DEM) as the vertical rise in elevation
per horizontal distance traveled. After overlaying the two maps, the proportion of watershed area that is
crop, or agriculture, on slopes greater than 3 percent was found by using the cookie-cutting technique.
The 3 percent threshold value will be taken from U.S. Department of Agriculture studies that classified
slopes into six categories. Based on this classification, slopes greater than or equal to 3 percent have a
greater risk of soil erosion.
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Potential Nitrogen and Phosphorus Loadings to Streams (STNL, STPL)
A literature survey of North American nutrient export studies (Young and others, 1996, in the
Journal of Environmental Management) provided coefficients for estimated export (kilogram per hectare
per year) for nitrogen and phosphorus under different types of land uses. To estimate total nutrient export
potential pn a per-watershed basis, the reported median coefficients for comparable agricultural uses
were multiplied by the amount of land cover in the agriculture land cover classes. The coefficient-times-
land use model was developed in 1980 for the U.S. EPA by Rechow and others (U.S. EPA 440/5-80-011,
Washington, DC). The coefficients reported for nitrogen varied from 2.6 to 6.2 kg/ha/yr, with a median
value of 3.9 kg/ha/yr. The values reported for phosphorous ranged from 0.3 to 1.5 kg/ha/yr, with a
median value of 0.7 kg/ha/yr.
Soil Loss Potential (PSOIL)
The Universal Soil Loss Equation (USLE) estimates soil erosion from agricultural lands as a function
of rainfall, soil type, slope, and land cover characteristics. The basic equation is: A = R * K * LS * C * P,
where A is long-term average annual soil loss (tons per acre per year), R is the long-term erosive
potential of rainfall, K is the soil erodibility factor, LS is the length-slope factor, C is cover and
management factor, and P is the support management factor (e.g., strip cropping, buffer-strip cropping,
grazing, etc.). Representative values for the basin and range province will be created for each parameter
in the model (rainfall erosive potential, soil erodibility, length-slope, cover, and support management) on
a pixel-by-pixel basis. R factor values will be taken from USDA Agricultural Handbook 537, soil
erodibility was taken from USDA and Soil Conservation Service digital soil maps, and length-slope
values will be taken from USGS DEM data. The area of each watershed with the potential for soil losses
greater than 1 ton per acre per year will then be found by summing the number of pixels in each
watershed that exceeded this threshold value. The indicator is the proportion of the watersheds above that
threshold value.
Forest Land Cover (FOR%)
The cookie-cutter procedure to extract the land cover information will be applied to each watershed
separately. The number of pixels with forest land cover will then be counted in each watershed, and the
total will be divided by the total number of pixels for a given watershed to yield the per-watershed index
value.
Forest Fragmentation (FORFRAG)
Forest fragmentation will be assessed at a resolution of about one-tenth ha by using a version of the
land cover map which had only two lumped categories, forest and nonforest. The fragmentation statistic
measures the probability that a randomly selected forested spot in a watershed is not adjacent to another
forested spot. Higher values indicate higher fragmentation. The statistic will be calculated separately for
the forest cover within each watershed in the region, rather than using a sliding window technique.
Forest Edge Habitat (EDGE7, EDGE65, EDGE600)
Forest edge habitat differences among watersheds will be assessed by the sliding window technique.
The fragmentation indicator described above is used but calculated in a small window that will be placed
within a watershed. If the calculated indicator value exceeded one-half the maximum value for that
amount of forest, then the center of the window will be marked as suitable edge habitat. After moving the
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calculation window throughout the watershed, the proportion of the watershed that will be labeled
suitable will be calculated and used as the indicator value. The exact window sizes used will be 7.29 ha,
65.61 ha, and 590.49 ha.
Forest Interior Habitat (INT7, INT65, INT600, INTALL)
The sliding window technique will be used to assess an interior forest habitat. The proportion of
forest cover will be calculated within a window that will be placed within a watershed. If the proportion
of forest exceeded a threshold value of 90 percent, then that place in the watershed will be considered to
be a suitable interior habitat. After placing the calculation window everywhere in a watershed, the
proportion of the watershed that is a suitable habitat will be determined. These proportions will then be
used to rank the watersheds. The proportion of watershed area supporting three scales of the interior
forest habitat will be calculated as the proportion of pixels in a watershed that exceeded the threshold
value for all three window sizes (7.29 ha, 65.61 ha, and 590.49 ha).
Departure of the Largest Forest Patch Size from the Maximum Possible for a Given Amount of
Anthropogenic Cover (FORDIF)
Each forest patch will be determined with a routine that finds all adjacent pixels of the same cover
type and then each one is assigned a unique value and also retains the original land cover value. There
are as many unique values as there are patches in the watershed. From these data, we will create a file of
forest patches and sort it to find the largest forest patch. A proportion will be calculated using the
watershed area as the denominator. The proportion was then subtracted from 1.0 minus the U-index to
derive the indicator value.
Calculation ofNDVI and its Change (NDVIDEC, NDVIINC, NDVITOT)
NDVI is calculated from the satellite spectral reflectance data in the red and infrared wavelengths,
using the equation: NDVI = (infrared - red) / (infrared + red). The reason that NDVI in particular, and all
vegetation indices in general, is able to distinguish plants from all other surface features is that vegetation
reflectance jumps dramatically in the infrared region of light and is strongly absorbing (not reflective) in
the red region. For vegetation, typical infrared and red values might be 0.8 and 0.1 respectively, giving an
NDVI value of 0.78. For other earth surface features, the infrared and red reflectance values are more
similar. Because of this, the numerator tends to be close to zero (or even slightly negative), while the
denominator tends to double. NDVI values for barren surfaces are typically close to or less than zero.
Once the NDVI maps are made for each date, differences are calculated simply by subtraction. The
resulting differences range negative to positive, centered on zero (0). Values close to zero indicate that
there has not been a change in land cover. Calculating the difference of temporal satellite images usually
yields an approximately normal distribution. For a normal distribution, about 70 percent of the values are
within one standard deviation of the mean, which is zero in this case. Previous research (Heggem et al.,
1999) has shown that one standard deviation is an accurate threshold to distinguish change from no
change. We chose one standard deviation as our change/no change threshold.
NDVI Change within Watersheds (1STDEC, 1STINC, 1STTOT)
Observed values for the three aspects of vegetation change come simply from the change that
occurred in the first order stream region. Expected values come from the product of the change over the
whole watershed multiplied by the proportion of the watershed in the first order stream region. It will be
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necessary to choose a threshold to decide if a calculated difference between observed and expected is
significant.
NDVI Loss on Steep Slopes (NDVI3%)
Vegetation loss on slopes greater than 3 percent was created using the overlay technique. The NDVI
change data will be overlaid upon the USGS DEM data which will be reclassified into percent slope.
Proportional values were calculated by dividing the amount NDVI loss, gain, or total change by total
watershed area.
Reconnaissance - Office and Field
The main objectives of reconnaissance are to:
1. Locate the sample site before the actual sampling begins.
2. Obtain permission to access the site from landowners (including state and federal resource
agencies).
3. Estimate the difficulty of sampling a particular reach (i.e., length of a hike into the reach;
amount of large woody debris).
4. Determine if any restrictions to sampling might are applicable (i.e., wilderness area).
Stream sample sites were chosen from the blue lines stream network represented on 1:100,000 scale
USGS maps following a systematic randomized design developed for EMAP stream sampling (Stevens
and Olsen, 1999; Stevens, 1997). Sample sites were then marked with an X on finer-reduction 1:24,000
scale USGS maps. This spot is referred to as the X-site. Reconnaissance for this study will be done in a
two-step process. Step 1 - office evaluation, and Step 2 - field evaluation of the selected sites. Sample
sites are selected from an RF3 sample frame (Stevens, 1994) and mapped onto transparent overheads at
1:62,500 map scale, which is equivalent to a 7.5 minute (min) USGS quadrangle map sheet. Each
overhead shows the random sampling site location, latitude, longitude, county, and 7.5 min USGS
topographical map name. Each overhead is overlain onto the appropriate map sheet to determine the
altitude and directions to the site.
Sites are discarded if they reside in steep and inaccessible terrain (Hall et al., 1998). The remaining
sites are selected for further field reconnaissance to verify the presence or absence of water, wadeability,
accessibility, safety, or if ownership could be determined (Hall et al., 1998). A major portion of the sites
being field visited could be viewed without prior landowner permission (Hall et al., 1998). Upon
reaching a site, it is determined whether the site will be sampleable or nonsampleable during the
designated index period. The site is considered nonsampleable if it is:
wider than 30 m
potentially dangerous
dry
no longer existed
difficult access, or no visible access point
If the site was determined to be sampleable, then the approximate width, depth, directions, possible
site contacts, and any additional comments are noted.
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Office Reconnaissance Methods
The methods used for evaluating a stream habitat at the various scales combine existing information
from sources such as Geographic Information System (GIS) data bases and maps with field-controlled
data on instream and riparian features. These methods provide a basis for national consistency yet allow
flexibility in habitat assessment at all scales of the hierarchy (Fitzpatrick et al., 1998).
The term "basin" denotes the area drained by all surface waters located upstream of a selected site.
The development of a stream habitat is influenced by spatial factors, which include physiographic
province, geology, climate, etc. (Fitzpatrick et al., 1998). The "basin unit" is useful for characterizing the
environmental setting of selected sites (Fitzpatrick et al., 1998). Evaluation of basin-wide natural and
human factors will enhance comparative analysis of biogeographic patterns in relationship to biological
communities (Fitzpatrick et al., 1998; Karr and Chu, 1999).
The GIS data bases are a primary component of basin characterization. For the aggregation of data
among study units, data related to basin-level variables must be gathered. For analysis of data at the
study-unit level, local coverage maps and aerial photographs generally provide better resolution per data
base (Hall et al., 1998). Also, nondigital coverages may provide valuable information for individual study
units. Thus, two levels of data base coverage are required for basin characterization to ensure the use of
the most complete basin-level information at the greatest resolution for individual study units, as well as
to allow comparisons of basin characterizations among study units (reference, Meador et al., 1993).
A basin characterization is conducted at fixed and synoptic sites using the basic instructions outlined
below as adapted from Meador et al. (1993).
1. Study unit: Use the watershed name or study ID.
2. Date: Record the date as month, day, year.
3. Station name: List the EMAP station name, or create one (i.e., river name, unnamed ditch, etc.).
4. Station identification number: List the EMAP station identification number for the site.
5. Investigator(s): Self-explanatory.
6. Location of site: Briefly describe the direction to the site location. Record any USGS (i.e.,
bench marks, etc.) or thematic information from the topographic sheets (i.e., latitude and
longitude, USFS or BLM land, etc.).
7. Drainage area: Delineate drainage basin boundaries on a l:24,000-scale 7.5-min quad map and
calculate the drainage area of the basin upstream of the sample site. For items 7 through 13, if
the information cannot be obtained realistically from a GIS data base (e.g., OEMs) or 7.5-min
quad sheets, then collect the data at l:250,000-scale resolution or any other small quad sheet.
8. Drainage density: Measure the cumulative length of all perennial streams and canals in the
basin upstream of the reference location using RF3 or as noted on a 7.5-min quad sheet. Then
divide the cumulative length by the drainage area to calculate drainage density.
9. Drainage texture: Drainage texture is an expression of the closeness of spacing of stream
channels in the basin upstream of the reference location and is calculated by determining the
basin contour with the most crenations as noted by visual inspection of a 7.5-min map.
Following that contour, determine the number of channel crossings. Divide the number of
stream channel crossings by the length of the perimeter of the basin (Meador et al., 1993).
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10. Drainage shape: To determine drainage shape, measure the basin length, square it, and divide it
by the drainage area using a 7.5-min map.
11. Stream length: Measure the length of the stream from the headwaters to the reference location
as noted on a 7.5-min quad sheet.
12. Basin relief: Determine the highest elevation in the basin minus the elevation of the reference
location as noted on a 7.5-min quad sheet.
13. Storage: Determine the cumulative area of the drainage that is composed of stored water,
including reservoirs, lakes, ponds, swamps, and wetlands, using a 7.5-min quad sheet.
14. Ecoregion: Record up to three of the spatially dominant ecoregions for the basin upstream of
the reference location and the percentage of the basin that each occupies (Omernik, 1987).
Omernik (1987) identified relatively homogeneous ecological regions of the United States based
on regional patterns of spatially variable combinations of land use, mineral availability (soils
and geology), potential natural vegetation, and physiography. Ecoregions have been compiled at
two map scales, a national map at l:7,500,000-scale resolution and regional maps at
l:2,500,000-scale resolution. State maps may also be available. Record the local coverage scale
of the highest resolution (i.e., largest map scale) available.
15. Physiographic province: Coverage of a national map of physiographic provinces is available as
a GIS data base and is derived from 25 physiographic provinces representing distinct areas that
have common topography, rock types and structures, and geologic and geomorphic history.
Record up to three of the spatially dominant physiographic provinces for the basin, upstream of
the reference location, and the percentage of the drainage area that each province occupies.
Record the local coverage scale of the highest resolution.
16. Land use: Use the Geographic Information Retrieval and Analysis System (GIRAS) data base
to record land use. GIRAS data are based on the Anderson classification system (Anderson and
others, 1976), which uses four-letter codes to describe a two-stage hierarchy of land use. For
example:
Level I
UR Urban or Built-up Land
Level III
Re Residential
Co Commercial and services
In Industrial
Ic Industrial and commercial complexes
Tr Transportation, communications, and utilities
AG Agricultural
Ci Cropland-irrigated
Cn Cropland-nonirrigated
Pa Pasture
Or Orchards, groves, vineyards or nurseries
Fe Confined feeding operations
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RA Rangeland
He Herbaceous
Sh Shrub and brush
FO Forest Land
De Deciduous
Ev Evergreen
WE Wetland
Fo Forested
Nf Non-forested
BA Barren Land
Ds Dry salt flats
Sa Sandy areas
Ex Bare exposed rock
Sm Strip mines, quarries, and gravel pits
Tr Transitional areas
Using the abbreviations listed above, record up to three of the spatially dominant Level n land uses
and the percentage of the basin upstream of the sample site occupied by each. The national coverage
scale is 1:250,000). Record the local coverage scale of the highest resolution available.
17. Geologic type: A national map of bedrock geology at 1:2,500,000-scale resolution is available
from GIS data bases (note: some states may have high resolution data, e.g., Nevada). Identify up
to three of the spatially dominant geologic rock units (units are based on age and kind; King and
Beikman, 1974) within the basin and report the percentage of the basin upstream of the sample
site occupied by each (Meador et al., 1993). The national coverage scale is 1:2,500,000. Record
the local coverage scale of the highest resolution available.
18. Soil type: Two soil-type data bases are available through the Natural Resources Conservation
Service (NRCS) (formerly known as Soil Conservation Service): the National Soil Geographic
Data Base (NATSGO) and the State Soil Geographic Data Base (STATSGO). Each represents
a different map resolution. Each data base is linked to soil interpretations, which provide
information on the extent and properties of the soils. Attributes include:
1. particle-size distribution,
2. bulk density,
3. available water capacity,
4. soil reaction,
5. salinity,
6. percentage of organic matter.
The NATSGO data base provides a general description of soils based on major land-resource area
boundaries developed from state general soil maps. The NATSGO map is available in ARC/INFO format
at l:7,500,000-scale resolution. The STATSGO data base is derived from soil survey maps. Where soil
surveys are unavailable, geology, topography, vegetation, and climate data are used with satellite imagery
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to classify soils. These data are compiled by state at l:250,000-scale resolution. Identify up to three of
the spatially dominant soil types within the basin upstream of the sample site and report the percentage of
the drainage area occupied by each (Meador et al, 1993). The national coverage scale is 1:7,500,000, and
the local coverage scale is 1:250,000 for STATSGO provided data.
19. Potential natural vegetation: Potential natural vegetation is defined as vegetation that would
exist today if man were removed from the scene (Kuchler, 1970). Characterizing potential
natural vegetation provides important baseline information for evaluating the influence of
human activities on vegetation within a basin (Meador et al., 1993). National coverage data on
potential natural vegetation is available from GIS data bases at l:3,200,00-scale resolution.
Record up to three of the spatially dominant types of potential natural vegetation for the basin
upstream of the sample site and the percentage of the drainage area that each occupies. The
national coverage scale is 1:3,100,000; record the local coverage scale of the highest resolution
available.
20. Wetlands: The U.S. Fish and Wildlife Service's (USFWS) National Wetlands Inventory is
designed to determine the status of and trends in wetlands throughout the United States (Meador
et al., 1993). Wetlands are defined on the basis of plant types, soils, and frequency of flooding.
The map is structured using a hierarchical classification, with the highest levels described as
Marine, Estuarine, Riverine, Lacustrine, or Palustrine (Meador et al., 1993). Approximately 70
percent of wetlands in the United States have been mapped at l:24,000-scale resolution.
Approximately 20 percent of compiled l:24,000-scale resolution maps have been digitized and
are available in the Map Overlay Statistical System (MOSS) format (Meador et al., 1993).
Identify up to three of the spatially dominant wetland types within the basin upstream of the
sample site and report the percentage of the drainage area occupied by each (Meador et al.,
1993). The national coverage scale is 1:24,000. Record the local coverage scale of the highest
resolution available.
21. Mean annual precipitation: Use National Weather Service information to record mean annual
precipitation for the basin. Methods for calculating mean annual precipitation can vary among
sites. Therefore, record how mean annual precipitation was calculated for the basin.
Field Reconnaissance Methods
Crews should use all available means to ensure that they are at the correct site as marked on the map
including: 1:24,000 USGS map orienting, topographic landmarks, county road maps, and Global
Positioning System (GPS) confirmation of site latitude and longitude using the reconnaissance
information conducted in the office. Upon finding the X-site, fill out the R-EMAP Location Data Input
Form (Lazorchak and Klemm, 1997). The latitude/longitude of the site will be listed on the stream
information sheet that will be available to the crews for each sample site.
Record the latitude/longitude as displayed on the GPS for the X-site on the form. Also record the
pertinent GPS data on the strength of the signal (2-D or 3-D fix) in the appropriate box on the field form.
If possible, wait for the GPS to get a 3-D fix. This might require moving the GPS to a more open area
near the X-site (GPS works on line of sight to orbiting satellites). If the given latitude/longitude and the
GPS latitude/longitude differ by more than 10 seconds, double check that you are at the correct site. Give
a detailed description of the directions to the stream site in the comment section of the form and use
additional pages, if necessary. It is hoped that R-EMAP, or other programs, will be able to revisit the
exact same sites at some point in the future.
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Determining Stream Site Status
Not all chosen sites will turn out to be streams. On the basis of previous synoptic surveys, the maps
used in the office reconnaissance are far from perfect representations of the stream network. A significant
part of EMAP is the estimation of the actual extent of streams in the area. Once the crews have reached
the marked sample point, evaluate the X-site and place it into one of the following categories. The
primary distinction is that the nontarget categories have no stream channel or are too deep to wade, while
the target categories have a definable stream channel. This information will be recorded on the
Reconnaissance form.
Nontarqet
1. No stream Channel (map error) - Examination of the X-site showed no water body or channel.
2. Impounded stream - Stream is submerged under a lake or pond due to man-made or natural (e.g.,
a beaver dam) impoundments. If the impounded stream, however, is still wadable, record the
stream as Altered and sample the stream.
3. Marsh/Wetland - Standing water but no defineable stream channel. In cases of wetlands
surrounding a stream channel, define the site as target but restrict sampling to the stream
channel.
4. Unwadable Stream - A stream too deep to be safely sampled by wading following our current
protocols. If over half of the reach is unwadable, classify the reach as unwadable and do not
sample it. If more than half of the survey reach is wadable (e.g., only a couple of deep pools)
classify the reach as target and sample what can be safely sampled. Before making this.
determination, evaluate whether you expect the flow to drop between now and sampling time.
NOTE: In all cases, evaluate the site at the X-site; don't "find" another spot to sample.
1. Regular Stream - Sampleable stream with our current protocols.
2. Intermittent Stream - Flow of water is not continual at the site, but the channel is wet.
3. Dry Channel - No water in the channel during the index period.
4. Altered Channel - Stream channel does not appear the way # is marked on the map. However,
there is a stream in the field that appears to be the stream marked with the X-site on the map. An
example would be a channel rerouting following a flood event that can cut off a loop of a
stream. Position a new X-site at the same relative position in the altered channel and make
careful notes and sketches of the changes on the Reconnaissance form.
Inaccessible
1. Physical Barriers - If you are physically unable to reach the X-site because of heavy wetlands,
steep gorge, or another barrier that prohibits safe entry, check off "NO" on the stream sampled
box on the site verification form and explain why in the explanations field.
2. No Permission - If you are denied access to the site by the landowner, check off "NO" on the
stream sampled box on the site verification form and explain in detail in the explanations field.
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Record the site class and pertinent site verification information on the R-EMAP Location Data Input
Form (Lazorchak and Klemm, 1997). If the site is in one of the target classes, schedule it for sampling. If
the site is nontarget or inaccessible, the site visit is complete and does not require further sampling.
Each visit to a possible site is informative. If time permitting, crews will fill out an RBP Habitat
sheet for the site. If access to the stream is inaccessible without landowner permission, obtaining the
primary components (Plafkin, et al., 1989) of the RBP habitat will be difficult. Record as much
information as possible so it can be correlated to the landscape and habitat characterization done in the
office reconnaissance.
Flow Models
The U.S. EPA has promoted watershed assessment and integrated analysis of point and nonpoint
sources. As part of a watershed assessment, the state samples the river systems to identify the types and
concentrations of pollutants. In most cases, the limiting factor for a water monitoring program is funding
resources. As such, the state may only maintain a sampling program along the main stems of the rivers
and in a few lower stream order systems. The lower order streams are usually sampled just a few miles
above the confluence of the larger system. The EPA allows states to consider a wide range of pollutants,
including toxins, nutrients, metals, temperature, and flow. The states determine what level of pollution in
a body of water is acceptable in relationship to established water quality standards. If the system does not
meet the established water quality standards, it is placed on the CWA section 303(d) list. When a system
is placed on the 303(d) list, the state is required to create a Total Maximum Daily Load (TMDL) for that
river system.
To calculate a load background, concentrations and pollution from point sources (i.e., factories,
wastewater treatment facilities) are determined. The remaining pollution load is attributed to nonpoint
sources. There are several flow models in the public domain (e.g., ModFlow, HEC, QUAL2E, MMS,
SPARROW, SWWM, etc.). The EPA-supported program for creating TMDL is Better Assessment
Science Integrating Point and Nonpoint Sources (BASINS) an integrated system, which incorporates
GIS, national watershed data, and modeling tools. TMDL experiences in Oregon and southern California
shows that water bodies require site-specific programs for data collection and analysis. For this study, it
is important to adopt a flow model that is capable of dealing with landscape indicators at the scale of the
land use and land cover data. The model must also have the ability to input response indicators such as
physical habitat, invertebrate, and fish data. This project will review the various flow models and develop
an index of which models will work with a set of predefined indicators.
The most effective measure of the integrity of a water body is determining the status of its aquatic
organisms. Water quality standards are driven primarily by the monitoring of toxicological and chemical
indicators. A focus on chemical and toxicology ignores other human impacts on aquatic biota, such as
altered physical habitat or flow patterns. Biological monitoring provides information and a response
mechanism to the overall health of the watershed and any chronic impairments from chemical and
physical alterations resulting from human activities (Karr and Chu, 1999). Karr and Chu (1999) describe
how the success of a biological monitoring program is dependent on "identifying biological attributes
that provide reliable signals about resource condition" in relationship to "human actions on biological
systems." Human influenced stressors can be manifested as loss of riparian, habitat fragmentation,
increase of alien species, excessive water withdrawals as a result of agriculture and urbanization, mining,
and logging practices. Modeling of a watershed should simulate the effects of overland flow (i.e., surface
runoff), stream flow, water depth, temperature, dissolved oxygen (DO), and the fate and transport of
potential stressors (i.e., sediments, metals, nutrients, etc.) to the aquatic community (Goldstein, 1998).
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For example, surface runoff may erode soil (depending on landscape use and cover) and carry sediment
and absorbed constieunts (i.e., metals from ARD, phosphate from soils, etc.) to the stream. Kaufmann et
al. (1999) state that the alteration of a watershed can result in excessive transport of sediments into
streams, which reduces leads to unstable substrate and a reduction in habitat condition.
Aquatic Biota
For high-gradient streams, a comparative analysis for reach indentification will be done between
EMAP and RBP protocols. Macroinvertebrates will be sampled using an adapted version of the EMAP
protocols (Klemm et al., 1997) by targeting the more productive riffle habitats. At each sampling site, a
five-pool/five-riffle reach will be established by moving upstream from the initial GIS site location
provided by the EPA until a suitable reach is identified. This reach identification will be compared with
the 40 X wetted width reach length of the EMAP protocols. The X-site of the reach location is then
recorded with a GPS. Riffles, the habitat supporting the richest community of aquatic
macroinvertebrates, and pools will be the primary areas sampled. The aquatic macroinvertebrate
communities within pools will be sampled because of their apparent sensitivity to sediment input.
The physical habitat of third and fourth order low-gradient streams change considerably from first
and second order streams with the substrate in the prior habitat being composed mainly of silt and sand
and the latter being dominated by gravel and cobble. In addition, the physical structure of the river
channel changes considerably; thus, establishing a five-pool, five-riffle reach may not be possible at third
order or larger rivers. If the habitat is found to be relatively homogeneous within higher order rivers with
no really defined riffle/pool habitat components, the reach will be established as 40 times the stream
width. Sampling sites will correspond to the GIS location determined by the EMAP random design. A
number of different sampling techniques may be employed for these conditions with possible sampling
devices, including the Hess, Stovepipe, Eckman, or Ponar samplers. If aquatic macrophytes are found
throughout the river length, they may also be used as a sampling substrate. The most appropriate
sampling technique and the corresponding protocols will be determined following a preliminary
investigation of the aquatic fauna and the physical habitat within third and fourth or larger order streams
and rivers.
RPB Riffles - Three riffles, within a reach, will be sampled at three locations with a total of nine
riffle samples per reach. Locations of the sampling points within each riffle will be determined by first
randomly selecting three transects across a riffle. One location along each transect will be determined
randomly and a sample corresponding to that location will be taken and preserved individually (three
samples per riffle, nine samples per reach). Macroinvertebrate sampling in first and second order stream
riffles will be conducted using a Hess invertebrate sampler with a 500-yum mesh net. The Hess sampler
will be placed on the substrate in the randomly established location. Cobble and large gravel within the
sample area will be rubbed by hand within the sampling device to ensure clinging invertebrates are
removed. The cleaned large cobble and rocks are then removed from the sampling device. The remaining
substrate pebbles are dislodged and enter the net. To reduce variability in sampling effort, each riffle
sample will be a timed collection over a 2-minute period. Following collection, the sample will be placed
into a #35 standard sieve (500-^m mesh) and rinsed to remove fine particulates smaller than 500 um. The
remaining sample contents will be grossly cleaned in the field by removing large gravel and other
inorganic material. The samples then will be transferred to ajar and 70 percent ethanol will be added to
preserve the samples.
RBP Pool - Macroinvertebrate samples in pools will be obtained by either using a Hess invertebrate,
an Eckman dredge sample., or a core sampler. The sampling device used will be determined following
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preliminary investigations of the dominant substrates in the pool habitats of first and second order
streams in the Humboldt River drainage. Three of the five pools in the sample reach will be selected
randomly for sampling. Within a pool, three randomly assigned transects will be established and one
location along each transect then will be determined randomly and a sample corresponding to that
location will be taken and preserved individually (three samples per pool, nine samples per reach).
Sample collection methods will vary depending on the method employed. Samples will be preserved with
70 percent ethanol.
Fish
The objective of the fish assemblage portion of the protocol is to collect a representative sample of
the fish assemblage by methods designed to: 1) collect all except rare species in the assemblage, 2)
provide a measure of the relative abundance of species in the assemblage, and 3) document the
amphibians collected during electrofishing. A major constraint is to do this sampling within a 4-hour
limit. Data will be summarized, analyzed for correlations among biotic and physical-chemical data, and
tested for site differences.
Species Assemblage Assessment
Environmental stress and habitat quality can affect aquatic community structure. An Index of
Biological Integrity (IBI) methodologies were developed to provide a reproducible method for assessing
stream fish community condition (Miller et al., 1988; Plafkin et al., 1989). These methodologies may be
used to compare relative stream fish community condition on a geographic scale and to assess change
over time. IBI uses up to 12 metrics related to fish community taxonomic and trophic structure, fish
abundance, and general health to assess the relative condition of stream fish communities. The
application of metrics may be modified for specific geographic regions. It is anticipated IBI
methodologies developed for the Sacramento/San Joaquin drainage will be applied in this investigation.
Representative reaches of the North Fork Humboldt River and the reference stream will be isolated
and systematically electroshocked to collect fish using the EMAP protocols (McCormik and Hughes,
1997). Methods presented in Kolz et al. (1995) will be followed during electrofishing. During
collection, captured fish will be placed temporarily in a 5-gallon bucket during collection and then
transferred to a live car in the stream. All fish will be identified to species level and counted. To assess
population size distribution, up to 50 fish of each species will be weighed and measured (discussed
below).
Assessment of Fish Condition and General Health
Environmental stress can affect growth rate and general condition of fish. Condition factors, such as
Fulton's condition factor, provide a relative measure of nutritional state or "well being" of individual fish
and populations (Anderson and Gutreuter, 1983). Such factors may also be used to compare relative
condition of populations and to monitor environmental change over time (Ney, 1993). Additionally,
degraded environmental conditions and a variety of environmental contaminants have been associated
with effects to fish health. Such effects may include increased susceptibility to disease, increased
parasitism, and teratogenic deformities.
To assess the fish health and general condition, up to 50 fish of each species from each site will be
measured, weighed, and assessed for indicators of disease, parasites, and external anomalies. Fish to be
assessed will be selected at random. Length and weight data will be used to calculate Fulton's condition
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factor for each fish and the species for each stream. Methods described in Anderson and Gutreuter
(1983) will be used. Examination of external condition of fish will be adapted from procedures provided
in Meyers and Barclay (1990) and methods of external fish condition assessment provided in Foott
(1990) and Goede and Barton (1987). Fish species, length, weight, and any abnormalities will be
recorded on a separate form for each site. All fish, with the exception trout collected for chemical
analyses, will be released back to the stream from which they were collected.
Assessment of Teratogenic Effects
The incidence of teratogenesis may provide a reliable indicator of population-level impacts of
selenium. Elevated selenium concentrations have been identified in drainage from some mines in
northeastern Nevada. Lemly (1997) provided an index which uses information on the incidence of
teratogenic deformity and selenium concentrations in whole-body fish to predict effects of selenium on
reproductive success and impacts on a fish population. This methodology will be applied to fish species
captured in during this investigation.
Up to 50 individuals of each fish species from each stream will be examined for teratogenic
deformities using methods described in Lemly (1997). Each individual will be examined for: 1) lordosis,
2) scoliosis, 3) kyphosis, 4) missing or deformed fins, 5) missing or deformed gills or gill covers, 6)
abnormally shaped heads, 7) missing or deformed eyes, and 8) a deformed mouth. Additionally, each
individual will be inspected for bulging of abdomens, bulging or protrusion of eyes, and cataracts, an
indication of exposure to elevated selenium. Fish species, length, weight, and any abnormalities will be
recorded on a separate form for each site. All fish, with the exception trout collected for chemical
analyses, will be released back to the stream from which they were collected.
Organosomatic Assays Analyses (Optional)
Up to 10 trout from each stream will be evaluated by an organosomatic assay developed by Goede
and Barton (1987) as modified by Foott (1990). Lahontan cutthroat trout will be collected during
electrofishing described above. The initial 10 fish of appropriate size (150-250 mm) collected from each
stream will be assessed. An organosomatic assay is a method for the ordered observation of gross
morphological features of general appearance, morphology of selected organs, hematological parameters,
and size criteria and presents a general indication of organism health. For each observational endpoint, a
ranking of the severity of impact is established and assigned a numerical value. Each fish is evaluated in
terms of the predetermined ranking criteria and the scores are recorded. Blood samples will be collected
into lithium-heparinized vacutainer and microhematocrit sample tubes. The blood samples will be
centrifuged at 10,000 RPM for 10 minutes for measurement of hematocrit, leucocrit, and collection of
blood plasma. Differential leukocyte counts will be performed on "diff-quick" stained blood smears
(Stoskopf, 1993 as cited in Rice and Schlenk, 1995). Blood plasma will be frozen on dry ice and stored
at -80 °C. Two microbiological assay media (TSA and TYES) will be inoculated with a swab from
either the kidney or spleen and incubated at room temperature for 3 days. Isolated colonies will be
identified by standard biochemical methods. Kidney or spleen tissue will be prepared for standard
virological assays and inoculated (1:20 and 1:100 dilution) onto EPC and CHSE-214 cell lines and held
at 15 °C for up to 15 days (J.S. Foott, written communication). Liver, gonad, gill, and kidney samples
will be collected soon after death, fixed in Davidson's fixative (Humason 1979), transferred to 70 percent
ethanol, processed for 5-jum paraffin sections, and stained with hematoxylin and eosin. Prior to
preservation, the maturation stage of ovaries and testes will be visually classified into the six phases
described by Hovarth (1986). Samples of liver, gonad, and muscle tissue will be retained for metal and
trace element residue analyses. Tissue abnormalities and parasite infections will be analyzed by light
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microscopy for evaluation of histological effects which may be associated with exposure to
environmental contaminants. If tissue damage is observed in hepatopancreas, an aliquot of blood plasma
will be tested for the presence of the hepatic injury enzymes alanine aminotransferase (ALT) and
asparate aminotransferase (AST). A sample of midbody muscle tissue will be excised from the
remaining carcass and frozen for muscle-lipid content analysis to provide an indication of organism
energy reserves (Brown et al., 1993). Organosomatic assays will be performed by Dr. J. Scott Foott in
the field. Histological, bacteriological, virological, parasitological, blood chemistry, and enzymological
assessments will be performed at the California-Nevada Fish Health Center in Anderson, California
under the direction of Dr. Foott.
Toxicity
Sediment provides a habitat for many aquatic organisms and is a major repository for many of the
chemicals that are introduced into surface waters. Determination of bulk sediment concentrations does
not always correlate well to bioavailability, and many factors affect the partitioning and availability of
chemicals found in the sediment. Contaminated sediments may be directly toxic to aquatic life or can be
a source of contaminants for bioaccumulation in the food chain. The object of a sediment toxicity test is
to determine whether contaminants in a sediment are harmful to benthic organisms. Surrogate organisms
are exposed to sediments under controlled conditions in the laboratory. Sediment toxicity tests provide
direct, quantifiable evidence of biological consequences of sediment contamination that can only be
inferred from chemical or benthic community analyses.
Laboratory Procedures
In the laboratory, samples will be placed in a #35 standard sieve and rinsed under tap water for 3
minutes. Large debris is removed after inspecting for invertebrates to aid in the sorting process. Each
sample will be distributed evenly over a subdivided tray and covered with 70 percent ethanol. Grids
within the tray are then randomly selected for sorting order. Using a dissecting microscope, aquatic
macroinvertebrates will be removed from each grid in a systematic pattern (left to right movement
through the material with the microscope at low power) until 300 organisms are obtained or until the
remainder of organisms within the grid are removed. The unsorted portion of the sample will be returned
to the jar and will be saved for future use. Aquatic macroinvertebrates will be identified to the lowest
possible taxonomic level and placed in a separate vial.
Quality Assurance/Quality Control
To ensure that samples are representative and that data are reliable, accurate, complete, and
comparable, a quality assurance/quality control (QA/QC) program will be implemented according EMAP
QA/QC guidance documents for surface waters (in review) and landscape ecology (in review). QA/QC
procedures will be established for field collections, laboratory processing of samples, and data analysis
after a preliminary investigation determines the natural variability within the biological systems in the
Humboldt River drainage. All samples and data will be collected by trained personnel following the
established EMAP protocols.
Aquatic Reference Condition
To assess the condition of aquatic resources within the Humboldt River drainage, reference
conditions need to be established for first through fourth or larger order streams. Following biological,
physical, and chemical assessments of reference sites, it will be possible to make comparisons between
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reference sites (nonimpaired) and other sites by using calculated indices. The following criteria will be
used when determining which streams and rivers will be appropriate for establishing reference
conditions:
I. Extent of disturbance
- flow regulation
- road construction
- water use including ground-water pumping
- bank damage
- land development
n. Representativeness of streams and rivers in the region sampled
HI. Ownership of land and long term status of ownership
IV. Access limitations
A consensus must be reached between biologists and researchers conducting work in the Humboldt
River drainage or among those who have previous experience and/or knowledge with reference stream
conditions before a reference site is established. Preliminary investigations will also be conducted at
potential reference stream sites meeting the above criteria to ensure that appropriate reference sites are
chosen.
Reference stream samples will be collected using the same protocols outlined above for collecting
site samples. One to three reference streams will be established for each first, second, and third order
stream category for a total of 3-9 reference streams. Reference streams will be sampled annually for 2
years.
As a result of large scale disturbance and modification of larger order streams in the Humboldt River
drainage and the Great Basin in general, it may be difficult to establish reference conditions for third and
fourth or larger order streams. If no reference streams or conditions can be identified, a biological
baseline will be established by sampling numerous locations along a stream or river using the obtained
information as a baseline. It is likely that no reference stream condition exists for the mainstem
Humboldt River. Therefore, 10 sites along the mainstem Humboldt River will be sampled annually
between the cities of Wells and Lovelock to establish a biological baseline.
Biotic Indices
The following indices will be used to determine the biological condition of aquatic macroinvertebrate
communities in perennial streams and rivers in the Humboldt River drainage.
A) EPT/EPT + Chironomid
B) EFT
C) Percent change in total taxa richness
D) Total taxa richness
E) Hisenhoff Biotic Index
F) Shannon - Weaver Diversity Index
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G) Percent Dominant Taxa
H) Percent Shredders
I) Percent Filterers
J) Percent Scrapers
K) Percent Scrapers/Percent Scrapers + Filterers
L) Percent Crustacean + Mollusks
Depending on results offish assemblage assessment, indices of biological integrity methodologies
may be applied. Metrics and scoring criteria are anticipated to generally follow methods developed for
the Sacramento/San Joaquin drainage (Miller et al., 1988). The following parameters will be determined
at each site where fish are found:
A) Percent Native Fishes (by number)
B) Percent Native Species
C) Total Fish Abundance
D) Total Fish Species
E) Number of Salmonid Species
F) Juvenile Salmonid Abundance
G) Catchable Trout (150 mm TL)
H) Sculpin Abundance
I) Percent of Individuals with Disease, Tumors, Fin Damage, or Skeletal Abnormalities
Potential physical and chemical perturbations within the Humboldt River drainage that may impair
the biological system include livestock grazing, agriculture, road construction, timber harvest, and
mining activities. The biological condition of sampled sites, as measured by the biotic indices, will be
compared to the reference stream conditions using EPA Protocol HI methods described by Plafkin et al.
(1989). The overall assessment of the biological condition will be achieved by summing the metric scores
and comparing on a percentage basis the difference between the reference conditions and sampled sites.
The biological condition categories are unimpaired, slightly impaired, moderately impaired, and severely
impaired. Once the level of impairment has been established, it is possible to determine whether the
physical and chemical conditions of a site reflect that level of impairment observed for the metrics.
Attempts will be made to devise additional metrics following a preliminary analysis of the first year of
data. Devised metrics will be tested using the first and second year of data to ensure repeatability of
results.
Physical Habitat
Physical habitat data will be collected at each site according to the EMAP Surface Water protocols
(Lazorchak and Klemm, 1997). Summary metrics of the habitat data will be generated according to
Kaufmann et al. (1999, submitted). Collected data will help determine the physical and chemical
condition of the streams sampled. Kaufmann (1993) identified seven general physical habitat attributes
important in influencing stream ecology. These include Channel Dimensions, Channel Gradient, Channel
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Substrate Size and Type, Habitat Complexity and Cover, Riparian Vegetation Cover and Structure,
Anthropogenic Alterations, and Channel-Riparian Interaction. Anthropogenic influences can adversely
affect the physical habitat of streams in many ways (Rankin, 1995). Because of the dry arid climate of
northeastern Nevada, there is a heavy reliance upon surface and ground water. This results in
considerable water diversions and extensive ground-water pumping throughout the drainage. Water
diversions can impact a stream biota in many ways including loss of surface flow, increased water
temperatures, unnatural flow regimes, and loss of a riparian habitat. Influences of mining, agriculture,
livestock grazing, and timber harvest can include alteration of channel morphology, loss of riparian
vegetation, elevated water temperatures, high sediment loads, embedded substrate, stream bank
instability, and loss of instream and terrestrial cover. A rating scale, for the physical habitat conditions,
will be modeled after Kaufmann et al. (1999, submitted). The following parameters will be measured and
compared to reference conditions in order to characterize the physical habitat structure and detect
possible impairment of sampled streams (data collected will be qualitative unless noted otherwise):
A) Instream cover
B) Embeddedness
C) Channel alteration
D) Sediment deposition (quantitative)
E) Riffle frequency/pool frequency
F) Channel flow (quantitative)
G) Depth, width, residual pool volume (quantitative)
H) Bank Vegetation
- Characterization
- Overhead canopy (quantitative-densiometer)
- Substrate Composition
I) Bank Stability
J) Riparian Zone Width and extent of Coverage
K) Stream Discharge (quantitative)
Analysis of physical habitat data and corresponding aquatic biota data at a given stream site will
enable the investigator to determine the relationships between habitat condition and biological integrity
of the streams. In addition, relationships between various aquatic and terrestrial habitat features and
aquatic invertebrate taxa will provide further insight into the determinants of aquatic invertebrate
community structure.
Stream Sample Reach
Biological and habitat structure measures require sampling a certain distance of stream to get an
accurate picture of the ecological community and morphologic characteristics. EMAP protocol requires a
reach length of 40 times the wetted channel width. The reach 40 channel widths along around our X-site
to characterize the community and habitat of our chosen sample point. Upon reaching the site, survey the
site according to the following protocol described in Lazorchak and Klemm, 1997. Determine channel
width at the X-site by measuring the wetted width across the channel with a surveyor's rod or tape
measure at three places considered to be of "typical" width. Scout the sample reach up and downstream
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to check the condition of the sample reach. The objective of the scouting is to determine if the reach is
clear of obstacles. NOTE: For streams less than 4 m wide, use 150 m as a minimum sample reach length
(Kaufmann and Robison, 1997). Conditions may require "sliding" the reach - if a confluence is reached,
note the distance and flag the confluence as the reach end. Make up for the loss of reach length by
moving ("sliding") the other end of the reach an equivalent distance away from the X-site. Similarly, if
the reach runs into a lake, resevoir, or pond. Flag the lake/stream confluence at the reach end, and make
up for the loss of reach length by moving the other end of the reach an equivalent distance from the
X-site. NOTE: Do not slide the reach to avoid man-made obstacles such as bridges, culverts, rip-rap, or
channelization. Starting back at the X-site, measure a distance of 20 channel widths downstream along
the side of the stream using a tape measure (be careful not to "cut corners"). At the 20 widths point, find
the closest habitat break and flag the location as the start point (transect A). Using the tape measure,
measure one-tenth (4 channel widths in big streams or 15 m in small streams) of the required stream
length upstream from transect A. Flag the next cross-section or transect (transect B). Proceed upstream
with the tape measure and lay out the nine additional transects at one-tenth of the reach length intervals
(transects C-K). Draw a rough map of the stream. Include any interesting features and note any
landmarks/directions to be used to find the X-site for future visits.
Habitat Sampling
The physical habitat measurements described in the EMAP-SW field manual (Kaufmann and
Robison, 1997) are intended to evaluate the physical properties in wadable streams. The protocol is most
efficiently applied during low flow conditions. It is designed for monitoring applications where robust,
quantitative descriptions of a reach-scale habitat are desired in a short amount of time. The protocol
employs a randomized, systematic spatial sampling that minimizes bias in the placement and positioning
of measurements (Hayslip, 1993). Measures are taken over defined channel areas and these sampling
areas or points are placed systematically at spacings that are proportional to baseflow channel width
(Kaufmann and Robison, 1997). This systematic sampling design scales the sampling reach length and
resolution in proportion to stream size. This allows statistical and series analyses of the data (Kauffman
et al., 1999).
The Physical Habitat Protocol consists of six different components:
1. Thalweg - longitudinal survey of depth, wetted-width, habitat class, pool-forming code, bars,
side-channels, presence/absence of soft/fine sediments at 100-150 equally spaced points along
the sample stream reach, slope, and bearing;
2. Subbank - channel morphology class for the entire reach, which includes bankfull widths and
depths, incision height, detailed channel and riparian cross-sections, measures of channel
cross-sectional wetted width and depth, substrate, percent surface fines;
3. Fish Cover areal cover class of filamentous algae, aquatic macrophytes, large woody debris,
brush/small woody debris, overhanging vegetation, undercut banks, rock ledge, and boulder
cover and artificial structure;
4. Large Woody Debris - continuous tally of large woody debris along the reach;
5. Densiometer Lemmon model densiometer canopy measurements;
6. Measurement of instantaneous discharge, measurements, and/or visual estimates of riparian
vegetation structure, human disturbance.
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Thalweg
The "thalweg" refers to the flow path of the deepest water in a stream channel. The thalweg profile is
a longitudinal survey of maximum depth and several other selected characteristics at 100 or 150 equally
spaced points of the stream between the two ends of the stream reach (Kaufmann and Robison, 1997).
Data from the thalweg profile allows calculation of indices of residual pool volume, stream size, channel
complexity, and the relative proportions of habitat types such as riffles and pools. The EMAP habitat
assessment modifies traditional methods by proceeding upstream in the middle of the channels, rather
than along the thalweg (Kaufmann and Robison, 1997). Each thalweg depth measurement is taken at the
deepest point at each incremental position. The thalweg profile measurements are spaced evenly over the
entire reach length and are sufficiently close together so any deep areas and habitat units are not missed
(Kaufmann and Robison, 1997). Follow these specifications for choosing the interval between thalweg
profile measurements:
Channel Width < 2.5 m Intervals = 1.0 m
Channel Width 2.5-3.5 m Intervals = 1.5 m
Channel Width > 3.5 m Intervals = 0.01 (reach length)
Thalweg profile increments at cross-section stations and midway between them, the wetted width is
measured. As the thalweg is being measured, the presence/absence of soft fine sediments is recorded.
Soft fine sediments are defined as fine gravel, sand, silt, clay, or muck readily apparent by feeling the
stream bed with the fiberglass stadia rod used for measuring the water depth. Mid-channel bars, islands,
and side-channels are noted to reflect their presence within the reach.
Slope and bearing are measured by backsiting with a clinometer, or bubble level, and a compass
downstream among the cross-section stations (i.e., B and A, C and B, etc.). The overall stream gradient
gives an estimate of potential water velocities and stream power. These are important factors for the
control on aquatic habitat and sediment transport (Kaufmann et al., 1999). The water surface slope will
be used to calculate the residual pool depths and volumes from the multiple width and depth taken during
the thalweg measurements (Kaufmann et al., 1999 submitted). The compass bearing backsites, between
cross-sectional stations, will be used to determine the channel sinuosity.
Stream morphologic features are visually classified over the entire reach (Kaufmann and Robison,
1997). At the channel reach level, distinct morphologies may be identified based on sediment transport
characteristics and channel roughness configurations. There are six different alluvial channel types
defined by Montgomery and Buffington (1993): Cascade (c); Step-pool (SP); Pool-Riffle (PR); Plane-bed
(PB); Regime (R); and Braided channel (BC). These six categories are applied to the entire reach.
Subbank
Substrate and channel dimension measurements contribute directly to assessments of habitat volume,
channel and stream bed stability, and habitat quality for aquatic resources (Kaufmann et al., 1999
submitted). According to Kaufmann and Robison (1997), substrate size and embeddedness are evaluated
at each of the 11 detailed cross-sections. Substrate size is the most important determinant of habitat
character for fish and macroinvertebrates in streams. The substrate influences the hydraulic roughness
and consequently the range of water velocities in the channel. It also influences the size range of
interstices that provide living space and cover for macroinvertebrates. Sediment characteristics are often
sensitive indicators of the effects of human activities on streams (Karr and Chu, 1999). Decreases in the
mean sediment size and increases in the percentage of fine sediments will destabilize channels, and it
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also indicates changes in the rates of sediment supply and erosion. In this protocol, substrate size will be
evaluated at each of the 11 detailed cross-sections (Kaufmann and Robison, 1997). The basis of the
procedure is a systematic selection of 5 substrate particles from each of the 11 channel cross-sections
(Kaufmann et al., 1999 submitted).
At each channel cross-section, measurements of the wetted width of the channel and the water depths
at each sediment sample point will be taken. If the wetted channel is split by a midchannel bar, the five
substrate points will be centered between the wetted width boundaries regardless of the bar in between
(Kaufmann and Robison, 1997). For dry channels, cross-section measurements will be made across the
unvegetated portion of the channel (Kaufmann and Robison, 1997).
Bank morphology measurements contribute to an assessment of channels stability during high flows.
These measurements also help make assessments of long-term channel down-cutting and fish
concealment features such as undercut banks (Kaufmann et al., 1999 submitted). Bank angle and
undercut distances are measured on the left and right banks (looking downstream) at each of the 11 cross-
sections. The field crews will also measure the wetted width of the channel, the width of exposed
midchannel gravel or sand bars, estimate incision height (depth), and estimate height (depth) and width
of the channel at a bankfull stage (Kaufmann and Robison, 1997).
Fish Cover
This portion of the EMAP physical habitat protocol is a visual estimation to evaluate,
semi-quantitatively, the type and amount of cover for fish and macroinvertebrates. According to
Kaufmann et al. (1999), metrics are developed to assess habitat complexity, fish cover, and channel
disturbance. Observations to assess fish cover and several other in-channel features apply to the channel
area upstream 5 m and downstream 5 m from each of the 11 cross-section stations (Kaufmann and
Robison, 1997). The five entry choices for areal cover of fish concealment and other features are "0"
(absent-zerocover), "1" (sparse: < 10percent), "2" (moderate: 10-40percent), "3" (heavy: 40-75
percent), and "4" (very heavy: > 75 percent). The ranges of percentage areal cover corresponding to each
of these codes are the same as for riparian vegetation (Kaufmann and Robison, 1997). Field crews will
estimate the areal cover of all of the fish cover and other listed features that are in the water and on the
banks 5 m upstream and downstream of the cross-section.
Filamentous algae pertain to long streaming algae that often occur in slow moving water. Aquatic
macrophytes refer plants with stems or roots in the stream that could provide cover for fish or
macroin vertebrates. If the stream channel contains live wetland grasses, these are included as
macrophytes. Woody debris is referred to as the larger pieces of wood that can provide cover and
influence stream morphology. Brush/woody debris pertains to the smaller wood that primarily affects
cover but not morphology (Kaufmann and Robison, 1997). The tree or brush within 1 m of the surface is
the amount of brush, twigs, small debris etc., that is not in the water but is close to the stream and
provides cover (Kaufmann and Robison, 1997). Boulders are typically basketball to car sized particles
(Kaufmann and Robison, 1997). Many streams have artificial structures in them designed for a fish
habitat. Streams may also have in channel structures for diversions, impoundment, and other purposes
(Kaufmann and Robison, 1997). These structures are accounted for as part of the protocol.
Large Woody Debris
The Large Woody Debris (LWD) component of the EMAP physical habitat protocol allows
quantitative estimates of the number, size total volume, and distribution of wood within the stream reach.
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LWD is defined as woody material with a large diameter of at least 10 centimeters (cm) (4 in) and length
of at least 1.5 m (5 ft). All pieces of LWD will be counted if they are at least partially in the baseflow
channel, the "active channel" (a flood channel up to a bankful stage), or spanning above the active
channel. Wood at least partially within those zones is not tallied. LWD in the active channel is tallied
over the entire length of the reach, including the area between channel cross sections (Kaufmann and
Robison, 1997). Each LWD piece is visually estimated for its length and its large and small end
diameters in order to place it in one of the diameter and length categories. The diameter classes are 0.1 m
to < 0.3 m, 0.3 m to < 0.6 m, 0.6 m to < 0.8 m, and > 0.8 m. The length classes are 1.5 m to < 5.0 m, 5 m
to < 15 m, and >15 m (Kaufmann and Robison, 1997). Sometimes LWD is not cylindrical, so it has no
clear "diameter." In these cases, visually estimate what the diameter would be for a piece of wood with a
circular cross section that would have the same volume.
Canopy Cover - Densiometer
Riparian canopy cover over a stream is important not only in its role in moderating stream
temperatures through shading but also as an indicator of conditions controlling bank stability. Organic
inputs from riparian vegetation become food for stream organisms. Canopy densiometer measurements
are a precise way of quantifying vegetation cover. Vegetative cover over the stream is measured at each
of the 11 detailed cross-section stations (Kaufmann and Robison, 1997). This measurement employs the
Convex Spherical Densiometer, model B (Lemmon, 1957). The densiometer is taped to limit the number
of square grid intersections to 17 (Kaufmann and Robison, 1997). To take a canopy cover density
measurement, the observer looks down on the densiometer held 6 inches above the water's surface
concentrating on these 17 points of intersection. If the reflection of a tree or high branch or leaf overlies
any of the intersection points, that particular intersection is counted as having cover (Kaufmann and
Robison, 1997). The measure to be recorded on the form is the count (from 0 to 17) of all the
intersections with vegetation covering them. A greater number indicates increasing canopy extent and
density.
For each of the 11 stations, densiometer measures are taken separately in four directions standing at
the center of the stream (Kaufmann and Robison, 1997). These 44 measures will be used to estimate
canopy cover over the channel (Kaufmann et al., 1999 submitted). Canopy measurements are also taken
at the left and right side of the stream facing the bank at each of the 11 cross-sections. These 22 bank
densiometer readings complement the visual estimates of vegetation structure and cover within the
riparian zone (Kaufmann et al., 1999 submitted). These measures are particularly important in wide
streams, where a riparian canopy may not be recorded by the densiometer standing midstream
(Kaufmann et al., 1999 submitted).
Riparian Structure and Human Influence
Riparian vegetation and human influence visual estimation procedures are applied as a
semiquantitative evaluation of these parameters. This assessment is used to evaluate the condition and
level of disturbance of the stream corridor and the surrounding area (Kaufmann et al., 1999 submitted).
It also indicates the present and future potential for various types of organic inputs and shading
(Kaufmann and Robison, 1997). Observations to assess riparian vegetation apply to the riparian area
upstream 5 m and downstream 5 m from each of the 11 cross-section stations (Kaufmann and Robison,
1997). They include the visible area from the stream back a distance of 10 m (30 ft) shoreward from both
the left and right banks, a 10x10 m riparian on each side of the stream (Kaufmann and Robison, 1997). If
the wetted channel is split by a midbar, the bank and riparian measurements will be for each side of the
channel, not the bar (Kaufmann and Robison, 1997).
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The riparian vegetation falls into three layers: a CANOPY LAYER (> 5 m/15 ft high), an
UNDERSTORY (0.5 m/1.5 ft to 5 m/15 ft high), and a GROUND COVER layer (< 0.5 m/1.5 ft high).
Note that several vegetation types (e.g., grasses or woody shrubs) can potentially occur in more than one
LAYER (Kaufmann and Robison, 1997). Similarly note that some things other than vegetation are
possible entries for the "GROUND COVER" layer (e.g., barren ground). The areal coverage of the
vegetation layers is estimated and the type of vegetation (deciduous, coniferous, mixed, or none) in each
of the two taller layers (canopy and understory) is determined (Kaufmann and Robison, 1997). "Mixed"
layer is considered to be more than 10 percent of the areal coverage if it is made up of the alternate
vegetation type (Kaufmann and Robison, 1997).
Areal cover is estimated separately in each of the three vegetation layers. Note: the areal cover can be
thought of as the amount of shadow caste by a particular layer (Kaufmann et al., 1999 submitted). The
maximum cover in each layer is 100 percent so the sum of the areal covers for the combined three layers
could add up to 300 percent (Kaufmann and Robison, 1997). The five entry choices for areal cover
within each of the three vegetation layers are "0" (absent: zero cover), "1" (sparse: < 10 percent). "2"
(moderate: 10-40 percent), "3" (heavy: 40-75 percent), and "4" (very heavy: > 75 percent) (Kaufmann
and Robison, 1997).
The presence and proximity of various types of human land use activities, in the stream riparian area,
are used in combination with mapped watershed land use information to assess the potential degree of
disturbance. At each of the 11 cross-sections includes the presence/absence and the proximity of 11
categories of human influences: walls/dikes/revetments of buildings, pavement, roads/railroads, pipes,
landfills/trash, parks/lawns, row crops, pasture/range/hay fields, logging operations, and mining activities
(Kaufmann et al., 1999 submitted). These categories and their proximity to the stream channel are
evaluated by the following for the left and right banks:
B for any and all the items you observe on the STREAM BANK
C for any and all the items that you observe within 10m from the stream bank ("CLOSE")
P for those items that are PRESENT but farther than 10 m from the bank
O for those NOT PRESENT
Stream Discharge
Discharge measurements are done at a chosen optimal cross section near the X-site after benthos
samples have been collected. Discharge can be measured either before or after electrofishing. In medium
and large streams, the water depth and velocity (60 percent of water depth measured from the surface) are
measured at 15 equally spaced intervals across one carefully chosen channel cross-section. If using an
electromagnetic current meter, it should be equilibrated to the average stream velocity for 20 seconds.
Periphyton
Periphyton are organic matter associated with channel substrates and are excellent indicators of
environmental condition (Lazorchak and Klemm, 1997). Periphyton samples will be collected according
to the protocols described in the EMAP Streams protocol (Hill, 1997). Periphyton are algae, fungi,
bacteria, protozoa, and associated organic matter associated with channel substrates (Hill, 1997).
Periphyton are useful indicators of environmental condition because they respond rapidly and are
sensitive to a number of anthropogenic disturbances, including habitat destruction, contamination by
nutrients, metals, herbicides, hydrocarbons, and acids (Hill, 1997). Periphyton samples will be collected
from the near-shore shallows near the point of collection for the macroinvertebrate kick sample (see
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macroinvertebrate protocols). The substrate selected for sampling should be collected from a depth no
deeper than can be reached by submerging your arm to midbicep depth (Hill, 1997). Periphyton are
collected, using the appropriate method, from flowing (riffles) and slack water (pools) habitats (Hill,
1997). Rock and wood samples, which are small enough (< 15 cm diameter) and can be easily removed
from the stream, are collected by placing the substrate in a funnel which drains into a sample bottle. A
defined area of a substrate surface (12 cm2) is enclosed, and attached periphyton is dislodged with 30
seconds of brushing with a stiff-bristled toothbrush. Care must be taken to ensure that the upper surface
of the rock is the surface that is being scraped (Hill, 1997). Loosened periphyton is then washed, using
stream water from a wash bottle, from the substrate into the 500 milliliter (mL) sample bottle (Hill,
1997). Soft-sediments are collected by vacuuming the upper 0.5 cm of sediments confined within the 12
cm2 sampling ring into a 60-mL syringe (Hill, 1997). All samples, regardless of substrate type, are
composited by habitat (riffle or pool) and mixed thoroughly (Hill, 1997). Four subsamples will be taken
from each composite sample. These are:
a. Identification/Enumeration
b. Chlorophyll a
c. Ash Free Dry Mass (AFDM)
d. Alkaline/Acid Phosphatase
Sediment Metabolism
Ecosystems are complex units defined by flow rates and physical processes. Functional indicators
measure energy flow and material transformation within an ecosystem (Hill, 1997). Community
respiration is one of the most commonly measured functional attributes of ecosystems and is a sensitive
indicator of ecosystem stress (Matthews et al., 1982; Bott et al., 1985; Hill and Gardner, 1987). Niemi et
al. (1993) analyzed the ability of several measures of chemical and biological structure and function to
detect impact and recovery in stream ecosystems. They found that gross primary productivity (GPP) and
respiration (R) were more sensitive to perturbations than most structural measures (Hill et al., 1997; Hill
et al., 1998; Hill et al., 1999 submitted). Sediment community metabolisms will be collected according to
the protocols described in the EMAP Streams protocol (Hill, 1997).
Samples will be collected from the top 2 cm of find-grained depositional habitats within cross-
sections B-J of the stream reach. The sample will be mixed throughly and subsampled into 5 mL screw-
top centrifuge tubes (Hill, 1997). Each tube will contain 10 mL of the fine-grained sediment composite
and be filled to the top with no head space with stream water (Hill, 1997). The tubes are placed into a
half-filled ice chest with stream water, or into a dark "goody bag" placed in the stream, for a 2-hour
incubation period (Hill, 1997). One additional tube is added to the incubation chamber to serve as a
blank. The DO and temperature are measured at the beginning of the experiment. At the end of the
incubation period, DO and temperature are measured in each tube, including the blank. The water is
decanted off from the tubes (Hill, 1997). The tubes are tightly sealed and frozen as soon as possible for
laboratory analysis (Hill, 1997).
Chemical Analyses (Water, Sediment, Benthic Invertebrates and Fish)
Note: Some samples, such as filtered water and invertebrates, may be deleted to reduce costs. It is
recommended to retain unfiltered water, sediment, and five fish samples per site.
Water and sediment chemistry analysis will be performed primarily in the field with metal analysis of
water, sediment, invertebrate, and fish samples being conducted in the laboratory. Water quality and
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chemistry differences between sites may be attributed to geological differences between watersheds, but
it can also result from land use practices. Agriculture (input of fertilizers and pesticides), livestock
grazing (nitrogen enrichment), and mining (elevated metal concentrations in addition to low pH) all can
profoundly affect the water quality and chemistry of streams. Analysis of water quality and chemistry
data on a drainage basis can provide valuable insight into the effects of differing water quality and
chemical conditions on the stream biota and can also provide valuable information on the condition of
watersheds within the Humboldt River drainage. The following parameters will be analyzed for all
sampled sites.
A) Temperature
B) Dissolved Oxygen
C) pH
D) Conductivity
E) Turbidity
F) Total Suspended Solids
G) Alkalinity
H) Total Hardness
I) Nitrate-Nitrite
J) Total Phosphorous
K) Total Persulfate Nitrogen
L) Ammonia as Nitrogen
M) Sulfate (important in mining an impacted watershed)
N) Metals and Trace Elements
Cl
Hg
Zn
Al
Cu
Fe
Mn
Ag
Cr
Pb
As
Se
Ca
Mg
Na
K
manganese, arsenic, and selenium are
concerns in the area; silver, chromium,
and lead may be toxic and may be concerns
in some mining districts; aluminum
(inorganic monomeric).
Past monitoring has demonstrated that several major and trace constituents of concern are elevated in
some streams in northeastern Nevada. Due to the diverse behavior of some of these contaminants in the
environment and in biological systems, several sample matrices are required to assess the potential for
impacts to the aquatic organisms and habitats. The suite of analytes included under EPA methods 130.2,
160.1, and 300.0 for water and the Contract Laboratory Program (CLP) Analytical Services metals
methods encompass constituents of concern. The precision, accuracy, and detection limit criteria
specified in the Client Request Forms for CLP analytes have been determined to be adequate for the
purposes of this investigation.
Water Chemistry
Water will be collected to assess the mobilization and transport of contaminants and the exposure of
aquatic organisms. Because it is assumed that stream water is well mixed, grab samples will be collected
to reduce the possibility of sample contamination. Water samples should include filtered water samples
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for analysis of major ions, which would enable an evaluation of water chemistry and environmental
factors affecting water quality. Filtered and unfiltered water samples would also be collected for analysis
of dissolved and total trace elements, respectively. This sampling scenario would provide for the
evaluation of the chemical form of various contaminants and an assessment of potential exposure
pathways of aquatic organisms. Additionally, aquatic life water quality standards for several metals are
currently based on dissolved concentrations. Analysis of dissolved and total trace elements in water
coupled with chemical residue data in other sample matrices would also enable an evaluation of potential
relationships among residue concentrations in various sample matrices.
Unfiltered water samples will be collected from midstream from midwater column depth while facing
in an upstream direction. Samples will be collected by immersing a closed certified cleaned polyethylene
bottle of appropriate volume and then opening under water. Each sample bottle will be rinsed three times
using the above collection technique prior to collection of the sample. Rinsate will be disposed of
downstream of the sample collection site. Water samples for a trace element (metal) analysis will be
collected in 500 mL polypropylene bottles. Filtered samples will be filtered through a 0.45 jum acetate
filter into 500 mL polypropylene bottles. These bottles will be rinsed at least twice with filtered water.
For filtered and unfiltered samples designated as laboratory QC samples, a sample volume of 1 L will be
collected. Water samples for major ion analysis will be collected in 250 mL bottles. All water samples
will be immediately chilled and shipped chilled to the designated analytical laboratory within 24 hours of
collection. To minimize the potential for inadvertent contamination of the sample, samples for metal
analyses will be acidified upon receipt by the receiving laboratory.
Water processing equipment (filter apparatus) will be washed with a brush and phosphate-free
detergent, rinsed with a dilute nitric acid solution, and triple rinsed with deionized water before and after
each use. One field blank and one filtration blank, each consisting of deionized water exposed to sample
collection and processing conditions, will be collected. These blanks will be treated as individual
samples and submitted for metal and trace element analysis. Additionally, one duplicate water sample
and one double volume sample (lab QA/QC) will be collected.
At the fixed station sites, continuous monitoring equipment will be used (e.g., Hydrolab) to measure
pH, temperature, DO, etc. An automatic sampler will be used to collect water at timed intervals. At the
synoptic sites, water chemistry samples will be collected of stream water to ship to the analytical
laboratory and in situ measurements of specific conductance, dissolved oxygen, pH, and temperature.
These samples will be stored in a cooler packed with Ziploc bags filled with ice and shipped to the
analytical laboratory within 7 days of collection (Lazorchak and Klemm, 1997). Streamside
measurements will be made using field meters. The primary function of the stream water samples and the
streamside chemistry measurements are to determine: trophic condition (nutrient status); chemical
stressors; and classification of water chemistry type (Lazorchak and Klemm, 1997). Specific
conductance, or conductivity, is a measure of the ability of the water to pass an electrical current, which
is related to the ionic strength of a solution. DO is a measure of the amount of oxygen dissolved in
solution. Measures of DO and temperature are used to assess water quality and the potential for healthy
aerobic organism populations (Hayslip, 1993).
Sediment Chemistry
Sediment will be collected to assess deposition and exposure of benthic organisms to contaminants.
Composite samples will be collected to increase the chances of obtaining representative samples of
stream sediment. Collection of samples from these sites would enable an evaluation of relationships
between trace element concentrations in sediment and concentrations in aquatic invertebrates and fish.
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Sediment samples will be collected from areas of fine sediment deposition in pool areas. Sediment
samples will include surficial materials (i.e., top 3 cm of sediment) collected with a Wildco model
number 2422 H12 core sampler. Each sample will consist of a minimum of five subsamples collected
within a 10-m reach of a stream. Subsamples will be composited in a stainless steel bowl and mixed with
a stainless steel spoon. A minimum of 75 grams (g) of each composited material will be placed in
certified clean 125 mL glass jars with Teflon-lined closures. Sediment samples will be stored on ice in
the field and transferred to a freezer each evening. Samples will remain frozen before and during
shipment to the specified analytical laboratory.
Between each sampling site, all collecting equipment will be washed with a brush and mild
detergent, rinsed with a dilute nitric acid solution, triple rinsed with deionized water, and submerged in
site water for at least 1 minute prior to use. During use at the site, an equipment blank will be collected
by rinsing deionized water over the equipment after decontamination. The rinsate will be collected and
submitted as a water sample for analysis of metals and trace elements. Additionally, one duplicate
sediment sample and one laboratory QC sediment sample will be collected from areas of possible
contamination.
Benthic Invertebrates
Benthic invertebrates will be collected to determine their accumulation of metals and trace elements
and the potential for food chain transfer of contaminants. Invertebrate samples will be collected from the
general areas from which sediment samples are collected using procedures described in Cuffney et al.
(1993). It is anticipated that a Surber sampler will be used to collect invertebrates from riffle and run
habitats within the stream. If possible, a single invertebrate family ubiquous to both study streams will
be used for residue analysis. The target invertebrate family will be chosen following a survey of each
stream. Target invertebrates will be sorted from unwanted debris and placed in certified clean 60 mL-
jars with Teflon-lined closures in the field. Each sample for trace element residue analysis will consist of
a minimum of 5 g of whole invertebrates. If possible, samples will consist of 10-15 g of whole
invertebrates. Invertebrate samples will be stored on ice in the field and transferred to a freezer each
evening. Samples will remain frozen before and during shipment to the specified analytical laboratory.
Between each sampling site, all collecting equipment will be washed with a brush and mild
detergent, triple rinsed with deionized water, and submerged in site water for at least 1 minute prior to
use.
Fish
Inorganic contaminant accumulation in fish reflects environmental exposure. Tissue residues may be
used to evaluate the potential for specific metals or trace elements to adversely affect individual
organisms and populations. To evaluate metal and trace element accumulation in fish, five whole fish
will be collected from each sampling site. Individual fish will be submitted for analysis of metals and
trace elements. If possible, all samples will consist of a single family (i.e., Salmonidae). Trout will be
collected by electroshocking (discussed above). Whole fish of appropriate size (150-200 mm) will be
placed in plastic bags. Samples will be stored on ice in the field and transferred to a freezer each
evening. Samples will remain frozen before and during shipment to the specified analytical laboratory.
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Data Analysis
Trace element concentrations will be transformed to common logarithms to improve homogeneity of
variance, while geometric means were calculated when a trace element was detected in at least 50 percent
of the samples within a given stream and year. A value equal to one-half of the detection limit was
assigned to samples for which a specific trace element was not detected. Significance in all statistical
tests was assigned at p < 0.05.
Two-way analysis of variance (ANOVA) and Tukey's multiple comparison tests will be used to
examine relationships among sampling sites for water quality parameters and constituent concentrations
in water, sediment, invertebrates, and fish. These tests will also be used to examine relationships among
sites for invertebrate and fish community metrics and measures offish condition and health. Pearson's
chi-square test will be used to examine relationships between trace element concentrations in unfiltered
water, sediment, invertebrates, and fish.
Concentrations of major and trace constituents in water generated during this investigation will be
compared to applicable state water quality standards and federal criteria for the variety of contaminants
evaluated in this investigation. Additionally, concentrations of contaminants in water found at this site
will be compared to aquatic life effect concentrations from published literature (i.e., LC50).
Concentrations of metals and other trace elements in sediment and tissues will be compared to
concentrations associated with adverse effects to aquatic life identified in published literature.
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Section V
Data Management
After the data has been released by the principal investigators, it will be permanently stored on the
EMAP Surface Water data base at the U.S. EPA ORD Laboratory in Corvallis, Oregon.
Data Sharing with EPA, USGS, NDEP, and NDOW
Available data on the water chemistry / water quality, physical habitat and aquatic biota of the
Humboldt River drainage will be obtained prior to field sampling from various agencies, including the
U.S. Environmental Protection Agency (EPA), the U.S. Geological Survey (USGS), the U.S. Fish and
Wildlife Service (USFWS), the Nevada Division of Environmental Protection (NDEP), and the Nevada
Division of Wildlife (NDOW). Existing fish community data collected by Tom Meier and Pat Coffin of
NDOW will be used to supplement the presence or absence of fish species data in the Humboldt River
drainage. The USGS has numerous gauging stations within the Humboldt River drainage, in addition to
extensive data on the geological formations found within Nevada. These data will be useful in relating
observed chemical conditions with geological formations in watersheds within the Humboldt River
drainage. NDEP has been conducting a water quality monitoring program within 14 hydrographic regions
throughout the state. Existing water quality data will be compared with computed biotic indices, and
physical habitat data, in order to make a comprehensive assessment of the condition of the aquatic
system.
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Section VI
Justification
The northern Great Basin ecoregion in Nevada covers an extensive area, yet very little is known of
the water quality and associated aquatic invertebrate communities there. Changes in landscape patterns
associated with human activities are thought to be the greatest threat to sustaining ecological goods and
services derived from our natural environment (Houghton, 1994; Ojima et al., 1994). This proposed study
will provide a data set that can serve as a basis for evaluating anthropogenic change and increase basic
knowledge of aquatic invertebrate communities in the basin and range ecoregion. The expansion of the
R-EMAP aquatic bioassessment project in the Humboldt River drainage to encompass the federal lands
of northeastern Nevada will provide further information on the condition of aquatic resources in these
areas. The proposed study in conjunction with the overall Nevada R-EMAP project will further assist the
State of Nevada in developing and potentially establishing biocriteria throughout the state. Additional
information on the ecology of aquatic invertebrates in the basin and range ecoregion will also be
obtained, with insight into how aquatic macroinvertebrate and fish community structure is affected by
various physical and chemical parameters. The large scale investigation will also provide information on
the biodiversity of aquatic macroinvertebrates in the northern Great Basin ecoregion of Nevada.
Analysis of status and trends in landscape indicators should significantly enhance the value of "site-
level" ecological monitoring activities, such as those being proposed by EMAP and the CENR. Data,
such as those derived from satellites, are now or will soon become available for entire regions of the
United States at scales relevant to ecological processes (20-80 m resolution). Costs of these data are low
when compared to similar spatial coverages acquired from finer-scale monitoring studies. Additionally,
spatial data lend themselves to analysis in a GIS (Ball, 1994). Also, because certain data, such as those
derived from satellites, can be composited (in a mosaic) for a large area, landscape analysis can be
performed on different spatial units, including natural units such as watersheds and ecoregions and
political units such as states, parks, and land-care units. This makes it possible to report landscape
statistics at a number of scales for many different types of units and to determine cross-scale
relationships between landscape composition and pattern, fundamental ecological processes, and
environmental values. Finally, because they can be generated from data that cover an entire region at
scales as fine as 30 m (as opposed to a sample that covers only a small portion of the total area in a
region), landscape indicators can provide information not only on the magnitude of problems, but where
the problems exist as well. As a result, this information can be used to develop multiscale plans to
reduce vulnerability or risk and prioritize the restoration of ecological function, condition, and
sustainability.
Clearly, not all environmental changes relevant to local communities and environmental managers
can be detected through changes in landscape features from satellite imagery (O'Neill et al., 1997).
Many pollutants or the replacement of native wildlife with introduced species may cause little or no
change in landscape composition or pattern. To achieve a complete assessment across many scales
within a region, landscape indicators must be integrated with monitoring at the "site" and "community"
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levels (Jones and Riddle, 1996). This is one of the primary challenges of federal agencies conducting
multiscale environmental monitoring and assessment.
An analysis of spatially explicit landscape change over the past 30 years would assist us in
identifying those areas of the country where water resources are most vulnerable to landscape changes. It
would also help us target specific areas where restoration or protection would yield the greatest reduction
in risk. However, we currently lack a comprehensive approach to conduct an assessment of this nature
and magnitude.
Such an approach requires the development of landscape indicators that capture ecological and
hydrological important aspects of landscape change and that can be generated from digital maps of
biophysical characteristics. It also requires development of spatially distributed models to interpret how
landscape changes influence risks to sustainable water resources. Although considerable progress has
been made in developing landscape indicators and models (Jones et al., 1997), the current state of science
in landscape indicators and models prevents implementation of such an approach nationally.
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Section VII
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Figures
Figure 1. Location map of the study area in northeastern Nevada.
Figure 2. Flow model for development of TMDLs and estimating the cost effectiveness.
Figure 3. General conceptual model of landscape change and sustainability environmental attributes
values by society.
47
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Northeastern Nevada
Federal & Tribal Lands
Mining & Exploration
LEGEND
BIA (Tribal)
BLM
BOR
DOD
FS
FWS
IZZI Private Land
Study Area
Highway
Road
- Major Stream
Mine/Exploration
o 10 a> ».
NEVADA
T«*i C . *»»i Con. F«tai»y t*M.
F*MLMM.*o«U&.
Figure 1. Location map of the study area in northeastern Nevada.
-------
Landscape Characterization
DEM
RF3
Slope
Aspect
Geology
Hydrology
Land Use
Urban
Agriculture
Mining
Grazing
etc.
Land Cover
Cropland
Rangeland
Industrial
Forest
Residential, etc.
ModFlow
HEC
BASINS
Flow Modeling
QUAL2E
HEC-RAS
WARMF
SPARROW
MMS
etc.
Stream Assessment
Multimetric Multivariate
Estimated Total Maximum Daily Loads (TMDL)
Environmental Economic Modeling
Best Management Practices (BMP)
Figure 2. Flow model for development of TMDLs and estimating the cost effectiveness.
49
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Changes in Uses of Land
Modification of
Landscape Pattern
Landscape
Indicators
X
I
I
I
I
Y
Socio-Economic
Indicators
\
\
\
\
\
Changes in
Human Behavior
Changes in Ecological and
Hydrological Processes
Changes in Human
Benefits Derived from
the Environment
Figure 3. General conceptual model of landscape change and sustainability environmental attributes values by society.
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