Water-Resources Investigations Report 03–4076

Prepared in cooperation with

Idaho Department of Environmental Quality

U.S. Department of the Interior

U.S. Geological Survey

Aquatic Assemblages and Their Relation to Temperature

Variables of Least-Disturbed Streams in the Salmon

River Basin, Central Idaho, 2001
COVER: Center, Middle Fork Salmon River; left, collecting benthic invertebrates; right, bull trout
Aquatic Assemblages and Their Relation to 

Temperature Variables of Least-Disturbed Streams 

in the Salmon River Basin, Central Idaho, 2001

By Douglas S. Ott and Terry R. Maret

Water-Resources Investigations Report 03–4076

Prepared in cooperation with 

Idaho Department of Environmental Quality

Boise, Idaho

2003
U.S. DEPARTMENT OF THE INTERIOR

Gale A. Norton, Secretary

U.S. GEOLOGICAL SURVEY

Charles G. Groat, Director

Any use of firm, trade, and brand names in this report is for identification purposes

only and does not constitute endorsement by the U.S. Government.

Additional information can be 

obtained from:

District Chief

U.S. Geological Survey

230 Collins Road

Boise, ID 83702-4520

http://idaho.usgs.gov

Copies of this report can be 

purchased from:

U.S. Geological Survey

Information Services

Box 25286

Federal Center

Denver, CO 80225

e-mail: infoservices@usgs.gov

Copies of this report also are 

available in PDF format, which can 

be viewed using Adobe Acrobat 

Reader, at URL:

http://idaho.usgs.gov/public/reports.html 
Contents iii

CONTENTS

Contents

Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Purpose and scope. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Description of study area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Data collection methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Site selection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Environmental variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Stream temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Onsite water quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Physical habitat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Benthic invertebrate collection and processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Fish collection and processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Analytical methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

General approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Environmental variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Stream temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Water quality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Benthic invertebrate assemblages and metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Fish assemblages and metrics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Results of temperature data and metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Stream temperature metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Comparison of stream temperature metrics with life-stage stream temperature criteria . . . . . . . . . . . . . . . . 13

Results of water-quality data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Results of benthic invertebrate taxa and metrics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Comparison of benthic invertebrate assemblages at multiple-reach sites. . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Coldwater taxa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Stream Macroinvertebrate Index scores and metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Results of fish taxa and metrics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Comparison of fish assemblages at multiple-reach sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Stream Fish Index scores and metrics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Correlations between stream temperature and environmental variables. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Correlations between stream temperature and benthic invertebrate variables . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Correlations between stream temperature and fish variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

References cited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Supplemental information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Table A. Habitat characteristics for selected sample sites in the Salmon River Basin, central Idaho, 

2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Table B. Microhabitat characteristics for all sample sites in the Salmon River Basin, central Idaho, 

2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Table C. Water-quality and nutrient data for all sample sites in the Salmon River Basin, central 

Idaho, 2001. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
iv Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

FIGURES

1. Location of sample sites in the Salmon River Basin, central Idaho . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2–6. Graphs showing:

2. Percent coldwater benthic invertebrate taxa in relation to maximum daily-maximum stream 

temperature at all sample sites in the Salmon River Basin, central Idaho, July through 

September 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

3. Elevation in relation to seasonal degree-days (July through August, above 0 degrees Celsius) 

for selected sample sites in the Salmon River Basin, central Idaho, 2001 . . . . . . . . . . . . . . . . . . . . . . 24

4. Range of maximum weekly-maximum stream temperatures (based on date of sample collection 

and 6 days prior) at which fish and tailed frogs were collected in the Salmon River Basin, 

central Idaho, 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

5. Bull trout densities in relation to maximum daily-maximum stream temperature at selected

sample sites in the Salmon River Basin, central Idaho, 2001. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

6. Model-predicted probabilities of occurrence of juvenile bull trout in relation to maximum dailymaximum stream temperature, based on regional and Salmon River Basin datasets. . . . . . . . . . . . . . 32

TABLES

1. Basin and site characteristics for all sample sites in the Salmon River Basin, central Idaho, 2001 . . . . . . 7

2. Definition of stream temperature metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

3. Stream temperature metrics for selected sample sites in the Salmon River Basin, central Idaho, 

July through September 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

4. Relations between stream temperature metrics and life-stage stream temperature criteria for 

selected sample sites in the Salmon River Basin, central Idaho, July through September 2001 . . . . . . . . 16

5. Spearman rank correlation coefficients for relative abundance of coldwater benthic invertebrate 

taxa and selected stream temperature metrics for selected sample sites in the Salmon River Basin, 

central Idaho, July through September 2001. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

6. Relations between benthic invertebrate metrics and Stream Macroinvertebrate Index scores for 

selected sample sites in the Salmon River Basin, central Idaho, 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

7. Relations between fish metrics and Stream Fish Index scores for selected sample sites in the 

Salmon River Basin, central Idaho, 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

8. Spearman rank correlation coefficients for selected habitat variables and selected stream 

temperature metrics for selected sample sites in the Salmon River Basin, central Idaho, July 

through September 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

9. Spearman rank correlation coefficients for relative abundance of benthic invertebrate taxa and 

selected stream temperature metrics for selected sample sites in the Salmon River Basin, central 

Idaho, July through September 2001. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

10. Spearman rank correlation coefficients for relative abundance of fish species and selected stream 

temperature metrics for selected sample sites in the Salmon River Basin, central Idaho, July 

through September 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

11. Spearman rank correlation coefficients for selected fish and stream temperature metrics for 

selected sample sites in the Salmon River Basin, central Idaho, July through September 2001 . . . . . . . . 30
Contents v

CONVERSION FACTORS AND VERTICAL DATUM

Multiply By To obtain

centimeter (cm) 0.3937 inch (in.)

cubic meter per second (m3/s) 35.31 cubic foot per second (ft3/s)

kilometer (km) 0.6214 mile (mi)

meter (m) 3.281 foot (ft)

millimeter (mm) 0.03937 inch (in.)

square kilometer (km2) 0.3861 square mile (mi2)

square meter (m2) 10.76 square foot (ft2)

Temperature in degrees Celsius (oC) can be converted to degrees Fahrenheit (oF) as follows:

oF=(1.8)(oC) + 32

Other abbreviated units:

μm micrometer

μS/cm microsiemens per centimeter

mg/L milligram per liter

Sea Level: In this report “sea level” refers to the National Geodetic Vertical Datum of 1929 (NGVD of 1929)—a geodetic 

datum derived from a general adjustment of the first-order level nets of the United States and Canada, formerly called Sea 

Level Datum of 1929.

290

Outlier

Number of sites where

 species were collected

3rd Quartile plus 1.5

 times the IQR

3rd Quartile

Median

1st Quartile

Outlier

Interquartile

Range (IQR)

1st Quartile minus 1.5

 times the IQR

EXPLANATION

for boxplots shown

in figures 4 and 6
Abstract 1

Aquatic Assemblages and Their Relation to Temperature 

Variables of Least-Disturbed Streams in the Salmon River 

Basin, Central Idaho, 2001

By Douglas S. Ott and Terry R. Maret

 Abstract

Abstract. 

In the late 1990s, Idaho’s established stream 

temperature criteria for the protection of coldwater 

biota and salmonid spawning were considered 

inadequate because the criteria did not agree with 

observed biological conditions in many instances 

and did not allow for variability in environmental 

condition or species diversity across a broad area 

such as the entire State of Idaho.

In 2001, benthic invertebrate and fish assemblages in 34 least-disturbed streams in the Salmon 

River Basin, central Idaho, were evaluated in relation to stream temperature and other environmental variables. The Salmon River Basin retains 

watersheds that are minimally affected by human 

activities. These “natural” stream conditions provide a basis for deriving attainable stream temperatures that can be used to set new, and revise existing, water-quality criteria for stream habitats 

affected by human activities.

During July through September 2001, data 

were collected to document the thermal regime of 

least-disturbed streams, characterize the distribution of aquatic biota at streams representing a gradient of temperature, and describe the relations 

between environmental variables and benthic 

invertebrate and fish assemblages. Nine stream 

temperature metrics were compared with the U.S. 

Environmental Protection Agency’s criterion of 

10°C (degrees Celsius) for bull trout spawning and 

juvenile rearing. The maximum weekly-maximum 

temperature at all 33 sites where temperature data 

were available exceeded this criterion. The maximum daily-maximum temperature (MDMT) at 30 

of the sites exceeded the Idaho Department of 

Environmental Quality (IDEQ) criterion of 13.0°C

for the protection of salmonid spawning; and the 

maximum daily-average temperature at all 33 sites 

exceeded the 9.0°C criterion for the protection of 

salmonid spawning. The thermal regime at most 

sites did not exceed the IDEQ criteria for the protection of coldwater biota. Nine environmental 

variables—water-surface gradient, discharge, 

wetted channel width, width:depth ratio, aspect, 

total seasonal thermal input, open canopy, riparian 

canopy density, and elevation were selected for 

correlation with the nine stream temperature metrics. Elevation showed the strongest inverse correlation with the stream temperature metrics.

Two hundred and one benthic invertebrate 

taxa from the 34 sampling sites were identified. 

The most abundant taxa were Baetis tricaudatus, 

Oligochaeta, Tvetenia bavarica gr., Acari, 

Rhithrogena, Cinygmula, Heterlimnius, 

Micropsectra, Eukiefferiella devonica gr., 

Drunella doddsi, and Cricotopus. Of the 201 

benthic invertebrate taxa collected during this 

study, 57 taxa (present at a minimum of 5 sampling sites) were significantly correlated with one 

or more of the stream temperature metrics. Among 

the invertebrate taxa collected, 32 were identified 

as coldwater taxa. Of the coldwater taxa collected, 

Zapada oregonensis gr. showed the strongest 

inverse correlation with the stream temperature 

metrics and was collected at sites where maximum 

weekly-maximum temperature (based on date of 

sample and 6 days prior) ranged from 11.3° to 

18.5°C.

Ten species of fish in the families Salmonidae, Cottidae, and Cyprinidae were collected. 

Two species (bull trout and chinook salmon) listed 

as threatened under the U.S. Fish and Wildlife Service Endangered Species Act were collected. 

Among all species, bull trout showed the strongest 

inverse correlation between relative fish abundance and stream temperature. Bull trout and juvenile bull trout densities were inversely correlated 
2 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

with stream temperature. The probability of occurrence of juvenile bull trout was significantly correlated with MDMT on the basis of results from a 

logistic regression model developed during this 

study. However, this model differed from a similar 

model developed by the U.S. Forest Service on the 

basis of regional data collected in the Pacific 

Northwest. The regression model based on data 

collected during this study showed higher probabilities of occurrence of bull trout at colder stream 

temperatures (10° to 15°C) and lower probabilities 

of occurrence at warmer stream temperatures (16°

to 21°C) than did the model based on regional 

data. The model comparisons suggest that regional 

or local differences need to be considered when 

deriving stream temperature criteria. 

INTRODUCTION

Introduction. 

Throughout the United States, watersheds have 

been altered by various forms of human disturbance. 

As a result, the distribution and structure of aquatic 

assemblages in rivers and streams within these watersheds have changed. Many endemic fish species of the 

Western United States are endangered, threatened, or 

of special concern as a result of human activities 

(Warren and Burr, 1994). Documenting these spatial 

and temporal changes in aquatic assemblages among 

streams can provide important information on waterresource quality and the biotic integrity of freshwater 

systems (Karr, 1991). However, before the effects of 

human alteration of streams can be evaluated, biological information is required from least-disturbed or “reference” streams, or by using suitable historical data 

(Hughes and others, 1986). 

Unlike many areas of the United States, Idaho still 

retains watersheds that are minimally affected by 

human disturbance. It is assumed that these wilderness 

and roadless watersheds are without human sources of 

pollution and, thus, represent a priori natural background conditions (Grafe and others, 2002). Because 

the habitat structure and associated aquatic assemblages of a stream are determined by climate, geology, 

vegetation, and other features of the surrounding 

watershed (Frissell and others, 1986), streams within 

these watersheds are assumed to approximate historical 

conditions. The assessment of aquatic assemblages and 

environmental variables in relation to least-disturbed 

landscape characteristics is important for documenting 

resource potential (Hughes and others, 1986; Maret 

and others, 1997). In addition, this type of information 

provides the basis for deriving attainable conditions 

that can be used to set new and revise existing criteria 

within water-quality standards for stream habitats 

affected by human activities. 

According to Karr (1991), criteria are those 

conditions that are presumed to support or protect the 

designated uses. In Idaho, the Idaho Department of 

Environmental Quality (IDEQ) is responsible for 

establishing and enforcing water-quality standards as 

mandated by Section 303 of the Clean Water Act. 

Idaho water-quality standard IDAP 58.01.02 (see 

http://www2.state.id.us/deq/rules/waterrul.htm) defines 

the goal of a water body by designating the use or uses 

of the water, setting criteria to protect those uses, and 

preventing degradation of water quality (Grafe and 

others, 2002). 

Idaho water-quality standards WQS 3.35 and 

100.01 to 100.05 designate four beneficial uses which 

all water bodies must meet: (1) aquatic life support— 

coldwater biota, seasonal coldwater biota, warm-water 

biota, and salmonid spawning; (2) contact 

recreation—primary (swimming) and secondary 

(boating); (3) water supply—domestic, agricultural, 

and industrial; and (4) wildlife habitat and esthetics.

In the early 1990s, Idaho WQS adopted the criteria of a 22.0°C maximum daily-maximum temperature 

(MDMT) and a 19.0°C maximum daily-average temperature (MDAT) for the protection of coldwater biota, 

and a 13.0°C MDMT and a 9.0°C MDAT for the protection of salmonid spawning, within the aquatic life 

support beneficial use (Grafe and others, 2002). 

In addition to the Idaho WQS stream temperature 

criteria, the U.S. Environmental Protection Agency 

(USEPA) imposed a site-specific rule on those water 

bodies where bull trout (Salvelinus confluentus) are 

present (40 CFR 131.E.1.i.d, 1997). This rule set a 

10.0°C maximum weekly-maximum temperature 

(MWMT) during June through September for the protection of bull trout spawning and juvenile rearing in 

natal streams. 

At the time the criteria were adopted, little was 

known about the thermal regime of most Idaho streams. 

This lack of information led to the acceptance of 

stream temperature criteria that, in part, were established on the basis of laboratory studies of temperature 

tolerances of various species of aquatic life (Beitinger 

and others, 2000; Selong and others, 2001). While use-
Introduction 3

ful, laboratory studies of this type have limitations 

when applied to actual environmental conditions 

because laboratory studies don’t take into account the 

ecologically diverse conditions in natural environments. By 1998, IDEQ had concluded that the established temperature criteria for Idaho streams were not 

adequate because they did not agree with observed biological conditions in many instances and did not allow 

for variability in environmental condition or species 

diversity (Essig, 1998). 

Significant study of Idaho stream temperatures 

and their relation to established criteria had not been 

undertaken until recently, when exceedances were 

found to be common. During the summer of 2000, 

Donato (2002) studied the temperature regime of 183 

minimally disturbed streams in the Salmon and Clearwater River Basins. Her results showed that temperatures in 100 percent (183 of 183) of the streams failed 

to meet the IDEQ 9.0°C MDAT and the 13.0°C 

MDMT criteria for the protection of salmonid spawning. Her results also showed that temperature in 35 percent (64 of 183) of the streams exceeded the IDEQ 

19.0°C MDAT criterion, and temperatures in 40 percent (73 of 183) exceeded the 22.0°C MDMT criterion 

for the protection of coldwater biota. Results from this 

study underscore the fact that exceedances of temperature criteria are likely in many or most Idaho streams. 

In fact, Maret and others (2001), who studied sites 

across Idaho as part of the Idaho statewide surfacewater quality monitoring program during 1996–98, 

identified 62 percent (25 of 40) of their sites where 

temperatures exceeded the Idaho WQS criterion of 

22.0°C MDMT for protection of coldwater biota.

Within Idaho, most rivers and streams are presumed or explicitly designated such that their water 

quality supports coldwater biota (Grafe, 2002). Essig 

(1998) and Hillman and Essig (1998), on the basis of 

their reviews of several studies within Idaho, concluded that, although temperatures in many streams 

exceed criteria, these same streams are supporting populations of coldwater indicator species. Bugosh (1999), 

who looked at temperature regimes of streams and rivers draining wilderness or minimally disturbed watersheds in the Lochsa River Basin, concluded that, 

although summer stream temperatures naturally exceed 

the current criteria, the streams continue to support 

their beneficial uses.

Results of studies such as these support the fact 

that a single stream temperature standard is difficult to 

apply across a broad area such as the entire State of 

Idaho because streams differ in environmental complexity and biological diversity. 

In 2001, the U.S. Geological Survey (USGS), in 

cooperation with IDEQ, began a study of 34 least-disturbed streams in the Salmon River Basin to document 

the environmental complexity and biological diversity 

of sites that are minimally affected by human activities. 

Objectives of the study were to provide a basis for 

defining attainable thermal conditions for stream habitats affected by human activities and to provide waterquality managers, policymakers, and the public with an 

improved scientific basis which would aid in establishing new, and revising current, life-stage temperature 

criteria for streams throughout Idaho. 

Purpose and Scope

This report characterizes selected environmental 

variables, with a focus on stream temperature, and 

benthic invertebrate and fish assemblages for 34 wadeable (primarily second- through fourth-order), leastdisturbed stream sites in the Salmon River Basin. Environmental and aquatic biota data were collected during 

the summer of 2001. Purposes of this report are to 

(1) document the thermal regime of least-disturbed 

streams; (2) characterize the distribution of aquatic 

biota in streams that represent a gradient of temperature; and (3) describe relations between environmental 

variables and benthic invertebrate and fish assemblages. Study results will assist resource managers in 

the development of applicable criteria that will protect 

coldwater biota and salmonid spawning and take into 

account natural environmental diversity.

Description of Study Area

The Salmon River Basin (fig. 1) is located in central Idaho and extends 684 km from its headwaters on 

the east side of the Sawtooth Range to the confluence 

with the Snake River, draining an area of approximately 36,324 km2 (Lipscomb, 1998). The basin contains large areas that have been designated as wilderness, several national forests, and a national recreation 

area. Certain reaches of the Salmon River and its tributaries are designated as wild and scenic rivers. These 

features make the basin a popular destination for hiking, whitewater rafting, and other outdoor activities. 

Elevation above sea level ranges from 3,852 m at 

Borah Peak, the highest point in Idaho, to 310 m at the 
4 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

Salmon

River

Salmon

River

Salmon River

Little

South Fork Salmon

River

East Fork

South Fork

Salmon River

Salmon

River

Middle

Fork

Salmon

River

North Fork

Lemhi

River

Pahsimeroi

River

East

Fork

Salmon

River

VALLEY

LEMHI

CUSTER

IDAHO

White

Bird

Riggins

Salmon

Challis

Stanley

Lemhi

1

2

3

4 5 6

7

8

9

10

11

12

13

16

15

17

14

20

19

21

18

23

24

22

25

28

27

29

26

30

32

31

33

34

EXPLANATION

Sampling site and number

28

0

0

10

10

20

20

30 MILES

30 KILOMETERS

Base from U.S. Geological Surveydigital data, 1:100,000, 1980Albers Equal-Area projectionStandard parallels 43° 30', 47° 30'

and -114° 00', 41° 45'

No false easting or false northing

Figure 1. Location of sample sites in the Salmon River Basin, central Idaho. (Site names and characteristics shown in table 1)

116° 115°

114°

114°

115°

116°

46° 46°

45° 45°

44° 44°
Data Collection Methods 5

confluence of the Salmon and Snake Rivers. Mean elevation of the basin is 2,014 m. Climate in most of the 

basin is semiarid and annual precipitation ranges from 

less than 10 to 50 cm; at higher elevations in the southwestern part of the basin, annual precipitation can average more than 50 cm (Lipscomb, 1998). Precipitation 

is primarily snow, and peak flows in streams generally 

result from spring snowmelt.

The Salmon River Basin is located in the Blue 

Mountains, Idaho Batholith, and Middle Rockies 

ecoregions (McGrath and others, 2001), which consist 

primarily of coniferous forests in upper elevations and 

sagebrush and grasslands in the valleys. Pine and fir 

predominate, covering 67 percent of the basin; rangeland and agricultural land cover 30 and 3 percent, 

respectively. 

Geologically, the basin consists primarily of metamorphic and sedimentary rocks, granite, volcanic 

rocks, and alluvium (King and Beikman, 1974). The 

most noticeable geological feature within the basin is 

the Mesozoic Idaho batholith, which makes up the central mountains. Much of the basin is characterized by 

stream channels deeply incised in bedrock and bordered by steep terrain. Two major exceptions are the 

Lemhi and Pahsimeroi River Basins in the eastern part 

of the basin. Both of these basins have broad, alluvial 

valleys bounded by steep mountains (Lipscomb, 1998).

Mean annual streamflow of the Salmon River at 

the USGS streamflow gaging station near White Bird, 

Idaho, is 316 m3/s for the period of record. The drainage area of the basin upstream from this gaging station 

is 35,095 km2, or 97 percent of the entire basin area. 

Streamflow conditions for the study period were below 

the long-term average. The mean streamflow for 2001 

was 55 percent of the mean annual streamflow for the 

Salmon River near White Bird (O’Dell and others, 

2002).

Streams in the upper parts of watersheds in the 

basin typically have high water clarity, coarse-grained 

substrates (cobble and boulders), high stream gradients 

(>0.5 percent), well-defined riffles and pools, and very 

sparse macrophyte growth. Streams in these areas 

show few signs of human activities. Where present, 

most noticeable are the effects from historical logging, 

mining, and cattle grazing activities.

In contrast, streams in the lower parts of watersheds typically have lower water clarity, more finegrained sediments, lower stream gradients, abundant 

run habitat, and generally denser macrophyte growth. 

These lower parts frequently are subjected to channelization, loss of riparian habitat by cattle grazing, and 

diversion of water for irrigation.

Invertebrates and fish in the Salmon River and its 

tributaries consist primarily of coldwater species. The 

most common benthic invertebrate orders are 

Ephemeroptera (mayflies), Plecoptera (stoneflies), Trichoptera (caddisflies), and Diptera (true flies); the most 

common fish families are Salmonidae (trout), Cottidae 

(sculpins), Cyprinidae (minnows), and Catostomidae 

(suckers). 

Acknowledgments

Numerous individuals assisted in collecting and 

processing data during the course of this study, including Mike A. Beckwith, Ross G. Dickinson, Mary M. 

Donato, Dorene E. MacCoy, Marcia Medford, William 

H. Mullins, and Kenneth D. Skinner, all from the 

USGS. Several individuals from IDEQ also contributed significantly to the study: Don W. Zaroban, who 

assisted with data collection and logistics; Christopher 

A. Mebane and Don A. Essig, who contributed to the 

study design and facilitated its support; and Nick Gerhardt, who assisted with site selection. Craig Johnson, 

Bureau of Land Management, also assisted with site 

selection. Jason B. Dunham, U.S. Forest Service 

(USFS), Intermountain Research Station, provided 

regional data and assistance with the logistic regression 

model. Les Bechtal of Canyons, Inc., provided professional guide service to access tributary sites along the 

Middle Fork Salmon River. Funding for this study was 

provided by the USGS and IDEQ.

DATA COLLECTION METHODS

Data Collection Methods. 

Site Selection

Sampling sites in the Salmon River Basin were 

selected to represent least-disturbed conditions with an 

emphasis on sites minimally affected by prior logging 

or mining activities within their watersheds. Criteria 

outlined by Hughes and others (1986) guided the selection of sample sites representing minimal human disturbance. These criteria included determining the level 

of human disturbance, quantifying stream size, characterizing stream channels, locating refuges, and determining migration barriers. 

Other methods used to select least-disturbed sites 

included examination of existing data, review of previ-
6 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

ous qualifications of levels of disturbance of Idaho 

streams reported by Overton and others (1995), and 

consultation with local land management agencies 

familiar with streams in the area. Sites also were 

selected to represent a gradient of temperature as indicated by a previous study of least-disturbed streams in 

the basin (Donato, 2002). Final selection of sampling 

sites was made only after a thorough field reconnaissance of candidate sites to verify their lack of human 

disturbance.

In all, 34 sites were selected (table 1, fig. 1). Each 

site consisted of a representative reach generally containing repeating geomorphic channel units (riffles, 

runs, and pools). The length of a reach was determined 

as a function of stream width (Fitzpatrick and others, 

1998). Reach lengths sampled during this study ranged 

from 130 to 280 m and usually exceeded 20 times the 

wetted channel width. The stream sites represented 

second- through fifth-order streams (Strahler, 1957), 

and all were wadeable. At two sites, Valley Creek (site 

4) and Big Creek (site 30), three spatially disjunct 

stream reaches were sampled to evaluate spatial variability in the invertebrate and fish assemblages along a 

stream segment.

Environmental Variables

Several environmental variables, including 

basin and reach characteristics (table 1), physical 

habitat characteristics (tables A and B, back of report), 

and water physicochemistry (table C, back of report), 

were evaluated for each site. Several sources were used 

to construct geographic data layers. Basin characteristics, including basin size, stream elevation, stream 

order, and land cover, were determined using Arc 

Macro Language programs written for ArcInfo 

(Environmental Systems Research Institute, Inc., 

1999). Basin boundaries were determined from 

the National Elevation Dataset (NED), which is 

based on a 30-m-resolution digital elevation dataset 

(http://gisdata.usgs.gov/ned). Hydrologic derivatives of 

the NED, including stream elevation and order, were 

developed using procedures similar to those in Stage 1 

processing, using a custom projection for Idaho 

(http://edcnts12.cr.usgs.gov/ned-h/about/Stage1.html). Percent land cover (agricultural, barren, forest/upland, 

herbaceous upland, and range/shrub land) also was 

determined for each basin by using the National Land 

Cover Dataset (Vogelmann and others, 1998). Hydrologic unit code was determined from the Hydrologic 

Unit Map of Idaho (U.S. Geological Survey, 1975). 

Stream type was determined onsite following guidelines outlined by Rosgen (1994). Stream latitude and 

longitude were determined onsite by handheld Global 

Positioning System receivers. 

STREAM TEMPERATURE 

Temperature data collection and data logger deployment followed procedures outlined by Stevens and 

others (1975) and Zaroban (2000). The two digital data 

loggers used in this study (StowAway TidbiT and Optic 

StowAway; Onset Computer Corporation, Pocasset, 

Mass.) measure temperature to within ±0.4°C and 

record temperature within a range of – 0.5° to 37°C.

Prior to deployment of the data loggers, a calibration audit was conducted using an ice water and ambient temperature bath. Results of the audit showed that 

all data loggers recorded temperature to within ±0.4°C 

of the audit temperatures as determined by a thermometer calibrated by the American Society of Testing and 

Materials.

Data loggers were deployed in mid-June 2001 at 

most sites and programmed to record stream temperature hourly. Sites 16 through 22, located on tributaries 

to the Middle Fork Salmon River in the Frank Church 

River of No Return Wilderness Area, have limited 

access; an extensive, multiday trip by whitewater raft 

was required to reach these sampling sites. Data loggers were deployed at these sites in September 2000 

during a raft trip conducted by IDEQ. Data loggers at 

these sampling sites varied in their collection intervals 

and recording time ranged from 30 to 72 minutes. 

With the exception of sites 16 through 22, two 

data loggers were deployed at each site. Upon selection 

of a representative stream reach, data loggers were 

installed near both the upper and lower reach boundaries. At each boundary, cross-sectional measurements 

of stream temperature and specific conductance were 

made to verify stream mixing and lack of ground-water 

influence. Once a location near a reach boundary was 

determined to be well mixed, a data logger (wrapped in 

aluminum foil to reduce the effects of solar radiation) 

was attached to a steel rod that was driven into the

streambed in the thalweg. Data loggers were placed at 

mid-depth and out of direct sunlight when possible. In 

addition, physical measurements of stream depth, 

stream aspect, percent open canopy, and riparian canopy density were made.
Data Collection Methods 7

Table 1. Basin and site characteristics for all sample sites in the Salmon River Basin, central Idaho, 2001[Site locations shown in figure 1; No., number; latitude and longitude in degrees, minutes, and seconds; HUC, hydrologic unit code; km2, square kilome

Site 

No. Site name Latitude Longitude HUC

Rosgen 

(1994) 

stream 

type

Stream 

order

Basin 

area 

(km2)

Elevation

(meters

above

sea 

level)

 Percen

Forest/

upland

Range/

shrubland

Herbaceous

upland

1 Alpine Creek . . . . . . . . . . . . . 435351 1145439 17060201 C 3 24.8 2,146 39.5 3.1 3.0 

2 Fourth of July Creek . . . . . . . 440148 1144802 17060201 B 3 44.6 2,182 69.8 5.1 5.9 3 Huckleberry Creek. . . . . . . . . 440452 1145214 17060201 C 2 20.2 2,030 79.6 6.7 4.3 4 Valley Creek. . . . . . . . . . . . . . 441823 1150312 17060201 C 3 115 2,036 76.9 5.2 7.2 

5 Basin Creek . . . . . . . . . . . . . . 441609 1144944 17060201 B 3 129 1,865 74.6 6.0 9.8 6 Warm Springs Creek . . . . . . . 441436 1144046 17060201 B 3 208 1,829 68.6 7.0 8.3 7 Germania Creek. . . . . . . . . . . 440219 1142745 17060201 B 3 130 1,950 60.5 8.1 8.1 8 Big Creek, South Fork . . . . . . 442629 1133558 17060202 B 2 67.0 2,006 62.8 17.0 11.2 

9 Morse Creek . . . . . . . . . . . . . 443756 1134717 17060202 B 3 33.5 1,908 44.1 25.7 22.6 

10 Hayden Creek, East Fork. . . . 444345 1134017 17060204 C 2 20.4 2,286 63.5 12.3 12.8 11 Sheep Creek. . . . . . . . . . . . . . 452955 1135528 17060203 B 3 87.5 1,341 78.6 9.8 10.6 12 Owl Creek . . . . . . . . . . . . . . . 451916 1142660 17060203 B 3 139 975 60.4 15.8 22.8 

13 Cape Horn Creek . . . . . . . . . . 442322 1151030 17060205 C 3 64.1 1,996 71.4 7.1 4.5 

14 Sulphur Creek . . . . . . . . . . . . 443227 1151844 17060205 C 4 132.7 1,731 70.3 9.9 7.8 

15 Vanity Creek . . . . . . . . . . . . . 443247 1150344 17060205 B 3 46 1,853 70.0 5.7 4.8 

16 Indian Creek . . . . . . . . . . . . . 444609 1150533 17060205 B 3 215.3 1,450 69.2 10.5 8.9 

17 Marble Creek . . . . . . . . . . . . . 444440 1150102 17060205 B 4 338 1,355 68.6 11.5 12.1 18 Loon Creek . . . . . . . . . . . . . . 444755 1144819 17060205 B 5 887 1,225 65.9 9.0 14.1 19 Camas Creek . . . . . . . . . . . . . 445331 1144313 17060206 B 4 1,029 1,160 76.7 7.5 9.0 
8 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001 20 Wilson Creek. . . . . . . . . . . . . 450201 1144326 17060206 B 3 97.8 1,116 58.6 10.5 12.2 

21 Papoose Creek. . . . . . . . . . . . 451027 1144319 17060206 A 3 76.2 1,040 61.7 12.3 9.5 22 Ship Island Creek . . . . . . . . . 451035 1144312 17060206 A 2 31.8 975 64.2 10.0 5.1 23 Big Mallard Creek . . . . . . . . 453446 1151833 17060207 B 3 100.8 1,561 97.2 .9 .9 

24 Blackmare Creek. . . . . . . . . . 444920 1154218 17060208 B 3 45.8 1,332 72.8 12.3 11.5 

25 Fourmile Creek . . . . . . . . . . . 445147 1154124 17060208 A 3 39.1 1,276 91.3 3.1 3.6 26 Fitsum Creek. . . . . . . . . . . . . 450003 1154323 17060208 A 3 80.6 1,188 74.0 11.0 12.4 27 Tamarack Creek . . . . . . . . . . 445735 1152322 17060208 B 3 47.5 1,700 68.6 8.1 6.0 28 Profile Creek . . . . . . . . . . . . . 445729 1152544 17060208 B 3 50.4 1,615 76.4 4.4 3.8 29 Riordan Creek . . . . . . . . . . . . 445424 1152907 17060208 B 3 58.2 1,494 90.1 3.0 1.7 30 Big Creek . . . . . . . . . . . . . . . 453509 1153128 17060207 C 3 42.1 1,859 96.5 1.0 1.0 31 French Creek. . . . . . . . . . . . . 452523 1160138 17060209 A 3 194 624 81.3 8.2 8.0 

32 Hazard Creek . . . . . . . . . . . . 451058 1161657 17060210 A 3 109 719 74.7 12.0 9.8 33 Skookumchuck Creek . . . . . . 454207 1161553 17060209 C 3 77.5 451 65.6 20.4 10.3 

34 Rice Creek. . . . . . . . . . . . . . . 455226 1162412 17060209 B 3 93 419 33.8 45.0 14.5 

Site No. Site name Latitude Longitude HUC Rosgen (1994) stream type Stream order Basin area (km2

)

Elevation

(meters

above

sea 

level)

 Percen

Forest/

upland

Range/

shrubland

Herbaceous

upland

Table 1. Basin and site characteristics for all sample sites in the Salmon River Basin, central Idaho, 2001—Continued
Data Collection Methods 9

ONSITE WATER QUALITY

Water-quality samples were collected at each site 

by using methods described by Wilde and others 

(1999) for analysis of selected nutrients. A portion of 

each sample was filtered through a 0.45-μm filter; 

analytes in this portion hereafter are referred to as 

dissolved. Samples were shipped on ice to the USGS 

National Water Quality Laboratory in Arvada, Colorado, for analysis (Fishman, 1993). Onsite measurements of water temperature, dissolved oxygen, pH, and 

specific conductance also were recorded (Wilde and 

Radtke, 1998).

Onsite quality assurance (QA) consisted of waterquality blank samples and replicates. Laboratory QA 

consisted of routine blank analyses and replicates for 

water samples (Fishman, 1993). All analysis results for 

QA laboratory samples were within acceptable USGS 

method standards.

PHYSICAL HABITAT

Physical habitat measurements followed procedures as outlined in Fitzpatrick and others (1998). The 

reach length, lengths of geomorphic channel units 

(riffle, run, and pool) within the reach, and the watersurface gradient were measured. Six habitat transects 

were placed perpendicular to streamflow, equidistant 

throughout the reach. At each transect, wetted channel 

width, bankfull width, percent open canopy, percent 

riparian canopy density, and stream aspect were measured. In addition, along each transect at the thalweg 

and two intermediate locations, depth, velocity, bottom 

substrate size, percent substrate embeddedness, and 

instream habitat cover types were measured. Velocities 

were measured at 0.6 of the stream depth. Bottom substrate size, percent substrate embeddedness, instream 

habitat cover, and bank features were categorized 

visually. 

Instream habitat cover was determined visually 

within a 1-m strip along each transect at the three 

instream locations and the left and right banks. 

Instream habitat cover is expressed as percent woody 

debris, overhanging vegetation, undercut banks, boulders, aquatic macrophytes, and artificial structures 

(such as tires and riprap). For data analysis, a mean 

value for each habitat variable was calculated to represent a reach. 

Flow, channel, and bank conditions were characterized using combinations of easily measurable, but 

representative, descriptors. Discharge was calculated 

on the basis of width, depth, and velocity measured at 

the time of sampling. Width:depth ratio was determined as a relative measure of channel cross-sectional 

shape. Three measures of habitat complexity were calculated: the coefficients of variation (CV) for width, 

depth, and velocity (Gorman and Karr, 1978; Rahel 

and Hubert, 1991). A flow stability index was calculated as the ratio between low flow depth and estimated 

bankfull depth (Rosgen, 1994; Lammert and Allan, 

1999). A flow stability index approaching 1.0 represents minimal flow fluctuation between low and bankfull flow and, therefore, higher stability. A bank stability index also was calculated on the basis of measures 

of bank angle, height, substrate type, and vegetative 

cover (Fitzpatrick and others, 1998). Scores were 

assigned to each measure and summed for a total bank 

stability score. The mean of all bank scores was used to 

represent the bank stability index score for the reach. 

Scores of 4 to 7 represent stable banks; 8 to 10 represent banks at risk of erosion; and 16 to 22 represent 

unstable banks. 

Total seasonal thermal input for the months of 

June through September was determined using a Solar 

Pathfinder. This measure of the amount of incident 

solar radiation striking the surface of the water was 

determined at mid-channel at the upper, lower, and 

middle transects of each stream reach following procedures outlined by Platts and others (1987).

At each riffle location where invertebrates where 

sampled, microhabitat data were collected following 

procedures outlined by Cuffney and others (1993). 

Depth, velocity, percent substrate fines (<2 mm), bottom substrate size, percent substrate embeddedness, 

and percent open canopy were measured. Bottom substrate particle size was measured quantitatively across 

each riffle following procedures outlined by Wolman 

(1954). As stated previously, for the purpose of data 

analysis, a mean value for each habitat variable was 

calculated to characterize a riffle sample location.

Benthic Invertebrate Collection and Processing

Benthic invertebrates were collected once at all 

sites during low streamflow conditions from July 

through September 2001. Three riffle areas within the 

reach were selected and then sampled using a Slack 

rectangular kick net sampler equipped with a 425-μm 

mesh net (Cuffney and others, 1993). At each riffle, 
10 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

large gravel and cobbles within a 0.25-m2 sample area 

in front of the net were brushed to dislodge organisms, 

after which the sample area was disturbed by kicking 

the loose gravel for 30 seconds. 

Onsite processing consisted of elutriation of each 

sample by repeated washing with a 424-μm mesh 

sieve. After processing, the three riffle samples were 

composited (total sample area of 0.75 m2) in a 1-L 

plastic jar, fixed with 10 percent buffered formalin, and 

shipped to EcoAnalysts in Moscow, Idaho, for taxonomic processing. At EcoAnalysts, samples were 

sorted and organisms were identified and counted to 

the lowest practical taxonomic level (genus or species 

for most taxa). Voucher specimens from this study 

were deposited in the Orma J. Smith Museum of Natural History, Albertson College of Idaho, Caldwell, 

Idaho.

Fish Collection and Processing

All sites but one were sampled during low streamflow conditions from July through September 2001. 

Fish were collected once at all sites except at Marble 

Creek (site 17). This site was not sampled because of 

high flow conditions and extreme turbidity. A scientific collection permit was obtained from the Idaho 

Department of Fish and Game (IDFG), and species 

data were provided to them as a provision of the permit. Fish sampling consisted of single-pass electrofishing. Single-pass electrofishing has been shown to be an 

effective method of sampling fish species richness, 

abundance, and assemblage structure in small streams 

(Simonson and Lyons, 1995; Kruse and others, 1998). 

Fish were collected using a backpack electrofisher 

(Smith-Root model 12) emitting pulsed direct current. 

Sampling was done in an upstream direction and 

included all available habitats within the reach. Sampling effort was measured as the total time that power 

was applied to the electrode, typically from 500 to 

2,000 seconds.

Fish were anesthetized with a dilute solution of 

clove oil and ethanol, identified to species, measured 

for total length and weight, and examined for external 

anomalies following methods described by Meador 

and others (1993). After examination, the fish were 

returned to the stream. Specimens of selected species 

were retained for reference and verification of field 

identifications. Age class determinations for salmonids 

and cottids were based on length-frequency distributions and descriptions by Scott and Crossman (1973) 

and Wydoski and Whitney (1979). 

In addition to fish, tailed frogs (Ascaphus truei) 

and salamanders, which have been shown to be effective indicators of stream conditions (Bennett and 

Fisher, 1989; Corkran and Thoms, 1996), also were 

identified and counted. A voucher collection from this 

study is located in the Orma J. Smith Museum of Natural History, Albertson College of Idaho, Caldwell, 

Idaho. 

ANALYTICAL METHODS

Analytical Methods. 

General Approach

A variety of analytical methods were used to describe and evaluate aquatic communities and environmental variables. Initially, analysis focused on identifying general patterns and relations by data tabulation 

and graphical displays. Metrics then were calculated to 

quantify thermal regimes and to describe benthic invertebrate and fish assemblages. A metric is a biological 

or physical attribute which helps evaluate a stream’s 

water-quality condition, or biotic integrity. According 

to Karr and others (1986), a metric is an enumeration 

representing an assemblage characteristic or combination of characteristics that change in a predictable way 

with disturbance. A metric score can be used as a single numeric index, such as MDMT, or combined into a 

comparative rating of multiple metrics, such as the 

Stream Fish Index (SFI) (Mebane, 2002) described in 

the section “Fish Assemblages and Metrics” later in 

this report. Once metrics were calculated, Spearman 

rank correlation matrices were developed to examine 

all possible combinations of responses and explanatory 

variables. As guided by the rank correlations, selected 

metrics were examined further using boxplots, scatterplots, and bar graphs. The latter analyses helped evaluate specific relations between fish and benthic invertebrate metrics and environmental variables and provided a visual description of variability among sample 

sites. All statistical analyses were performed using 

SYSTAT, version 9.0 (Wilkinson, 1999).

To evaluate spatial variability, community data 

collected among multiple reaches at a single sampling 

site were compared by calculating Jaccard’s coefficient 

of community similarity (JC) index. The JC index is 

calculated for each site pair as the proportion of species 

out of the total list of species common to both sites: 

JC = C/ (A+B+C), where C is the number of species 
Analytical Methods 11

common to both sites, and A and B are the number of 

species unique to each of the two sites. 

Finally, logistic regression (Hosmer and Lemeshow, 1989) was used to develop an algorithm that 

predicts the probability of occurrence of juvenile 

(<150 mm) bull trout as a function of maximum dailymaximum stream temperature. In logistic regression, 

the dependent variable (for this study, juvenile bull 

trout) is a binary variable. Unlike linear regression, 

logistic regression does not require normally distributed data. Model results were compared with a regional 

bull trout dataset compiled by the USFS (Dunham and 

others, 2001).

Environmental Variables

STREAM TEMPERATURE

Stream temperature data were inspected for obvious errors such as data logger malfunction and exposure to air temperature. Data collected prior to deployment and after retrieval were removed from the dataset. 

Time-series plots and other forms of graphical displays 

were used to visually inspect the data and to compare 

datasets. Quantitative summaries of the thermal regime, or metrics, were calculated for all sites and are 

described in table 2. Because most sites were equipped 

with two data loggers, the paired datasets were compared to evaluate spatial variability.

WATER QUALITY

Because the water-quality data in this study were 

collected to establish a baseline, extensive data analysis was not conducted. Primarily, data were collected 

to provide a more comprehensive understanding of 

environmental conditions during this study, to document water-quality conditions of least-disturbed 

streams, and to publish data for comparison with 

data from future studies. 

Benthic Invertebrate Assemblages and Metrics

Benthic invertebrate assemblages were analyzed 

without accounting for ambiguous taxonomic groups. 

Ambiguities in the benthic invertebrate dataset arise 

when some specimens in a sample lack the characterisTable 2. Definition of stream temperature metrics

Stream 

temperature 

metric Definition

MDMT Maximum daily-maximum temperature, in degrees Celsius

MDAT Maximum daily-average temperature, in degrees Celsius

MWMT

Maximum weekly-maximum temperature. Derived from 7-day moving average of daily maximum temperatures, in 

degrees Celsius

MWAT

Maximum weekly-average temperature. Derived from 7-day moving average of daily average temperatures, in degrees 

Celsius

MWMTS

Maximum weekly-maximum temperature for date of sample collection. Derived from 7-day moving average of daily maximum temperatures on sample date and 6 days prior, in degrees Celsius

MWATS

Maximum weekly-average temperature for date of sample collection. Derived from 7-day moving average of daily average 

temperatures on sample date and 6 days prior, in degrees Celsius

MAX∆T

Maximum of the maximum daily temperature minus minimum daily temperature (diurnal fluctuation) for deployment 

period, in degrees Celsius

BIG∆T

Maximum daily-maximum temperature minus minimum daily-minimum temperature for deployment period, in degrees 

Celsius

DEGDAY

Seasonal degree-days. Derived as sum of differences between daily average temperature and base temperature of 0 degrees 

Celsius for period July 1 through August 31, 2001
12 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

tics that allow identification to the targeted level of taxonomic resolution. Slight variations in the results of the 

benthic invertebrate data can occur if ambiguous taxonomic groups are accounted for prior to analysis. 

Benthic invertebrate assemblages were analyzed 

using relative abundance data, density data, and the 

Stream Macroinvertebrate Index (SMI) (Jessup and 

Gerritsen, 2002). The SMI is a multimetric index that 

uses a bioregional scheme based on a grouping of 

ecoregions. These bioregions include the Northern 

Mountains, Central and Southern Mountains, and 

Basins. All sample sites in this study were located in 

the Central and Southern Mountains bioregion. Six 

metric categories—richness, composition, pollution 

tolerance, diversity, feeding group, and habitat—were 

used to identify assemblage attributes. The richness 

category consists of metrics for total number of taxa 

and total number of Ephemeroptera (mayflies), Plecoptera (stoneflies), and Trichoptera (caddisflies) (EPT) 

taxa. The composition category consists of the metric 

percent Plecoptera, or percent of sample that includes 

stonefly nymphs. The pollution tolerance category 

derives a metric using the Hilsenhoff Biotic Index 

(HBI) that determines the abundance-weighted average 

tolerance of organisms to pollution (Hilsenhoff, 1987). 

According to Hilsenhoff (1987), an HBI value between 

0 and 3.50 indicates “excellent” water quality with no 

apparent organic pollution. An HBI value between 

3.51 and 4.50 indicates “very good” water quality with 

slight organic pollution. An HBI value between 4.51 

and 5.50 indicates “good” water quality with some 

organic pollution. An HBI value above 5.51 indicates 

“fair” to “very poor” water quality with varying 

degrees of organic pollution from fairly significant to 

severe. The diversity category consists of the metric 

percent five dominant taxa, or percent of sample 

including the five most abundant taxa. The feeding 

group category consists of one metric, scraper taxa, or 

number of taxa that scrape periphyton from substrates. 

The final category, habitat, consists of the metric 

clinger taxa. This metric is the number of taxa that 

have fixed retreats or adaptations that allow them to 

attach to substrate in flowing water.

The multimetric index value (SMI score) for a 

sample site is the sum of the individual metric scores. 

Once an SMI score for a sample site is determined, 

comparisons are made with conditions at least-disturbed sites within the same bioregion. This comparison allows assignments of a narrative rating for the 

sample site ranging from “very good” to “very poor.” 

According to Jessup and Gerritsen (2002), SMI scores 

between 79 and 100 are considered “very good,” scores 

between 58 and 78 are considered “good,” scores 

between 39 and 57 are considered “fair,” and scores 

below 38 are considered “poor” to “very poor.”

Fish Assemblages and Metrics

Fish assemblages were analyzed using relative 

abundance data, density data, and the SFI (Mebane, 

2002). Like the SMI just described, the SFI is a multimetric index. The SFI was developed for use on two 

separate site classes, montane-forested and desert 

basin-rangeland, on the basis of a grouping of ecoregions. All sites in this study were located in the Northern Rockies ecoregion, which is one of four ecoregions 

that make up the montane-forested classification 

grouping. Hence, the montane-forested classification 

was used for all sites in this study. Three metric categories—species richness and composition, reproductive 

function, and abundance—were used to identify fish 

assemblage attributes. The richness and composition 

category consists of the metrics number of coldwater 

native species, percent coldwater individuals, and percent sensitive native individuals. The reproductive 

function category consists of the metrics number of 

cottid age classes and number of salmonid age classes. 

The abundance category consists of one metric, catch 

per unit effort (CPUE, fish caught per minute of electrofishing). The presence of amphibians also was 

included as part of the SFI as a qualitative presence 

metric only. Supplemental points are added to the 

final index scores when amphibians are present. 

Absence of amphibians, however, is not considered 

a negative factor. 

As with the SMI, the SFI score for a sample site 

is the sum of the individual metric scores. The higher 

the SFI score, the more closely a sample site represents 

least-disturbed conditions within its ecoregion. According to Mebane (2002), scores above 81 would place a 

sample site above the median of reference condition. A 

narrative rating of “very good” could be inferred for 

scores above 81, and a rating of “good” to “very poor” 

could be inferred for scores less than 81 to 0. 

RESULTS OF TEMPERATURE DATA AND METRICS

Results of Temperature Data and Metrics. 

Temperature data loggers were retrieved from 

all sites during late September and early October 
Results of Temperature Data and Metrics 13

2001. The raw temperature data can be accessed at 

http://idaho.usgs.gov/public/studies.html. Of the 68 data 

loggers deployed, 64 were retrieved. Both data loggers 

at Skookumchuck Creek (site 33) and French Creek 

(site 31) were missing. Of the 64 retrieved, three data 

loggers either were damaged or malfunctioned, and no 

stream temperature record was obtained. These 

included one of two data loggers at both Valley Creek 

(site 4) and Fourth of July Creek (site 2) and the only 

data logger at Marble Creek (site 17). 

After the data loggers were downloaded, July 1 

through September 30 (92 days) was selected as the 

period used to calculate the stream temperature metrics 

for most sites. Stream temperature records for Skookumchuck Creek and French Creek were available for 

2000 from Donato’s (2002) work in the basin and were 

used for calculations of the metrics at both sites. However, the deployment period in 2000 did not span the 

entire 92-day period as in 2001. The stream temperature record at Skookumchuck Creek in 2000 comprised 

a 76-day period from July 11 through September 24. 

The stream temperature record at French Creek in 2000 

comprised a 77-day period from July 13 through September 27. No alternate stream temperature record was 

available for Marble Creek. 

Other inconsistencies in the stream temperature 

records for sites 16 and 18 through 22 were evident. 

Data loggers were removed from these sites, which 

were located on tributaries to the Middle Fork Salmon 

River, on the day the sampling crew visited the site. 

Ending dates for the temperature record at these sites 

ranged from September 13 to September 20. 

Because two data loggers were deployed at most 

sites, the variability between these paired data loggers 

was determined. Analysis of the stream temperature 

record of 24 paired data loggers indicated that the maximum difference in temperatures between any paired 

data logger was 1.4°C, and 96 percent of all temperatures recorded by paired data loggers were within 

1.0°C. 

Stream Temperature Metrics

Comparison of the nine stream temperature metrics for the 33 sites where data were available (table 3) 

indicated that water temperature varied substantially 

among sites within the basin, and that the range of 

observed temperatures varied over a broad gradient. 

Spearman rank correlations among the nine stream 

temperature metrics indicated that all were significantly correlated (all p-values <0.01); correlation coefficients ranged from 0.70 to 0.99. MDMT ranged from 

12.0°C at Morse Creek (site 9) to 23.6°C at Indian 

Creek and Skookumchuck Creek (sites 16 and 33, 

respectively). MDAT ranged from 10.2°C at Morse 

Creek to 21.1°C at Skookumchuck Creek. MWMT 

ranged from 11.5°C at Morse Creek to 23.2°C at Skookumchuck Creek. The maximum weekly-average temperature (MWAT) ranged from 9.7°C at Morse Creek 

and East Fork Hayden Creek (site 10) to 20.7°C at 

Skookumchuck Creek. Maximum weekly-maximum 

temperature for date of sample (MWMTS) ranged 

from 11.3°C at Morse Creek to 22.9°C at Skookumchuck Creek. Maximum weekly-average temperature 

for date of sample (MWATS) ranged from 9.4°C at 

East Fork Hayden Creek to 20.4°C at Skookumchuck 

Creek. The maximum diurnal fluctuation (MAX∆T) 

ranged from 3.0°C at Ship Island Creek (site 22) to 

12.2°C at Valley Creek (site 4). The maximum fluctuation for period of deployment (BIG∆T) ranged from 

7.0°C at Morse Creek to 18.6°C at Basin Creek (site 5). 

The number of seasonal degree-days (DEGDAY) 

ranged from 550 at East Fork Hayden Creek to 1,070 

at Rice Creek (site 34).

Comparison of Stream Temperature Metrics with 

Life-Stage Stream Temperature Criteria

Stream temperatures exceeded criteria for bull 

trout and chinook salmon spawning at all sites. A comparison of stream temperatures with life-stage stream 

temperature criteria is presented in table 4. Criteria 

established by USEPA (40 CFR 131.E.1.i.d, 1997) for 

the protection of bull trout spawning and juvenile rearing in natal streams are applicable during the months of 

June through September. Criteria established by IDEQ 

(Grafe and others, 2002) for the protection of salmonid 

spawning are specific to species and their spawning/

egg incubation period. These criteria are intended to be 

applicable only during the period when a species is 

present and actually spawning. 

During this study, the stream temperature record 

overlapped the core period for spring/summer run 

chinook salmon (Oncorhynchus tshawytscha) spawning and egg incubation, which extends from August 15 

to June 1 (Grafe and others, 2002). Consequently, the 

criteria were applicable for this species during this 

period of time. To determine exceedances, the salmo-
14 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

Table 3. Stream temperature metrics for selected sample sites in the Salmon River Basin, central Idaho, July through 

September 2001

[Site locations shown in figure 1; site names and characteristics shown in table 1; description of temperature metrics shown in table 2; No., 

number; med, median; min, minimum; max, maximum; —, data unavailable; no temperature record available for site 17 because of missing 

data logger]

Site 

No. MDMT MDAT MWMT MWAT MWMTS MWATS MAX∆T BIG∆T DEGDAY

1 15.6 12.4 14.4 11.5 13.9 10.6 7.2 11.4 649

2 15.0 11.2 13.9 10.4 13.2 9.6 8.2 13.6 580

3 18.4 13.5 16.7 12.4 16.4 11.1 10.8 15.5 677

4 22.1 16.1 20.1 15.0 18.6 13.9 12.2 18.3 838

5 21.7 16.5 20.2 15.5 18.4 14.1 12.1 18.6 863

6 16.2 13.0 15.2 12.3 14.1 10.9 7.0 11.8 688

7 16.3 12.3 15.5 11.6 15.3 11.0 8.7 13.9 660

8 15.0 11.9 14.0 11.2 13.5 11.0 7.5 10.9 627

9 12.0 10.2 11.5 9.7 11.3 9.6 4.2 7.0 556

10 13.9 10.3 13.2 9.7 12.7 9.4 7.5 13.4 550

11 13.3 10.8 12.5 10.3 12.4 10.2 4.8 8.3 595

12 20.1 17.9 18.9 16.8 18.5 16.5 5.5 11.5 980

13 19.9 14.0 18.7 12.9 18.5 12.1 12.1 16.9 732

14 21.0 16.8 19.9 16.0 18.8 14.9 9.2 14.9 923

15 13.8 11.4 13.2 10.7 12.6 9.7 5.9 10.1 604

16 23.6 17.3 22.1 16.5 16.3 11.7 11.7 17.3 956

18 21.6 18.4 20.3 18.0 16.3 14.4 5.7 12.8 1,045

19 20.3 17.7 19.1 17.1 14.9 13.6 5.5 12.1 1,001

20 17.6 15.4 16.8 15.0 13.8 12.7 4.9 9.2 —

21 18.2 16.0 17.3 15.6 14.2 13.1 4.4 8.8 908

22 16.0 15.0 15.5 14.5 12.4 11.8 3.0 7.2 840

23 19.6 16.5 18.7 15.7 18.7 15.7 6.8 13.9 850

24 16.3 14.4 15.4 13.5 14.6 12.7 5.0 11.1 766

25 16.3 14.7 15.4 14.1 14.9 13.4 3.9 10.6 795

26 19.5 16.2 18.1 15.3 18.0 15.3 6.9 13.2 875

27 17.6 12.5 16.8 12.2 14.9 11.5 8.9 12.7 703
Results of Temperature Data and Metrics 15

nid spawning criteria were applied from August 15 to 

the end of the stream temperature record (September 

30, in most cases). Criteria established by IDEQ for the 

protection of coldwater biota apply year round, but the 

warmest period (July through August) was the time of 

focus. To determine exceedances, the coldwater biota 

criteria were applied from July 1 to the end of the 

stream temperature record (September 30, in most 

cases).

Comparison of the stream temperature metrics 

with the stream temperature criterion showed that temperatures at all 33 sites exceeded USEPA’s 10.0°C 

MWMT criterion for bull trout spawning and juvenile 

rearing. The percentage of total days that the temperatures exceeded the criterion ranged from 58 to 100. 

Temperatures at 20 of 33 (58 percent) sites exceeded 

the criterion 100 percent of the time. Although this criterion is applicable only to those streams where bull 

trout are present, and bull trout were collected at only 

19 of the 33 sites, it is notable that temperatures at none 

of these least-disturbed sites met this criterion during 

this study.

Temperatures at 91 percent (30 of 33) of the sites 

exceeded the IDEQ 13.0°C MDMT criterion for the 

protection of salmonid spawning; temperatures at all 

sites exceeded the 9.0°C MDAT criterion. The percentage of total hours that temperatures exceeded the 

13.0°C MDMT criterion ranged from 0.4 to 91. Those 

sites where temperatures did not exceed the 13.0°C 

MDMT criterion were Morse Creek, Sheep Creek, and 

Vanity Creek (sites 9, 11, and 15, respectively). Temperatures at all 15 sites where chinook salmon were 

collected exceeded IDEQ criteria for the protection of 

salmonid spawning. The percentage of total hours that 

temperatures at these sites exceeded the 13.0°C 

MDMT criterion ranged from 5.9 to 87. The MDAT 

ranged from 9.8° to 19.2°C.

Thermal regime at most sites did not exceed the 

IDEQ criteria for the protection of coldwater biota. 

Thermal regime exceeded the criteria at Valley Creek, 

Indian Creek, and Skookumchuck Creek (sites 4, 16, 

and 33, respectively), where temperatures exceeded the 

22.0°C MDMT criterion; and French Creek (site 31), 

Skookumchuck Creek, and Rice Creek (site 34), where 

temperatures exceeded the 19.0°C MDAT criterion. 

The percentage of total hours that temperatures exceeded the 22.0°C MDMT criterion ranged from 1.4 to 

4.8. The MDAT ranged from 10.2° to 21.1°C.

28 15.5 12.2 14.8 11.8 13.5 11.3 6.2 10.6 674

29 17.4 15.4 16.6 14.5 16.2 14.3 6.1 12.0 806

30 19.4 13.8 18.3 12.9 18.3 12.9 11.1 17.0 703

31 21.5 19.7 20.9 19.1 20.0 18.1 4.0 15.3 —

32 20.5 17.6 19.9 17.2 19.9 17.1 6.3 13.0 963

33 23.6 21.1 23.2 20.7 22.9 20.4 6.1 14.4 —

34 21.9 19.4 21.1 19.0 20.9 18.8 5.4 12.8 1,070

Med 18.2 15.0 16.8 14.5 15.3 12.7 6.3 12.8 781

Mean 18.2 14.9 17.2 14.2 16.0 13.1 7.1 12.7 783

Max 23.6 21.1 23.2 20.7 22.9 20.4 12.2 18.6 1,070

Min 12.0 10.2 11.5 9.7 11.3 9.4 3.0 7.0 550

Site 

No. MDMT MDAT MWMT MWAT MWMTS MWATS MAX∆T BIG∆T DEGDAY

Table 3. Stream temperature metrics for selected sample sites in the Salmon River Basin, central Idaho, July through 

September 2001—Continued
16 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

Table 4. Relations between stream temperature metrics and life-stage stream temperature criteria for selected sample sites in the Salmon

River Basin, central Idaho, July through September 2001

[Idaho Department of Environmental Quality salmonid spawning criteria exceedances based on summer chinook salmon spawning period 

beginning August 15 to end of temperature record (September 30, most cases); site locations shown in figure 1; site names and characteristics shown in table 1; °C, degrees Celsius; MWMT, maximum weekly-maximum temperature; MDMT, maximum daily-maximum temperature; MDAT, maximum daily-average temperature; No., number; no temperature record available for site 17 because of missing data logger]

U.S. Environmental Protection Agency

bull trout spawning

and juvenile rearing criterion

of 10.0°C MWMT

June 1 through September 30 (most 

cases) 

Idaho Department of Environmental Quality

Salmonid spawning criteria

of 13.0°C MDMT and 9.0°C MDAT

August 15 through September 30 (most cases)

Coldwater biota criteria

of 22.0°C MDMT and 19.0°C MDAT

July 1 through September 30 (most cases)

MWMT MDMT 13.0°C

MDAT 

9.0°C MDMT 22.0°C

MDAT 

19.0°C

Site

No.

No. 

days 

above 

10.0°C1

Percent 

days

above 

10.0°C

Consecutive 

days

above 10.0°C

No. 

hours 

above 

13.0°C2

Percent 

hours

above 

13.0°C

Consecutive 

hours

above 13.0°C MDAT2

No. 

hours 

above 

22.0°C1

Percent 

hours

above 

22.0°C

Consecutive 

hours

above 22.0°C MDAT1

1 71 77 71 17 1.5 6 11.2 0 0 0 12.4

2 70 76 70 16 1.4 3 9.9 0 0 0 11.2

3 92 100 92 141 13 8 11.2 0 0 0 13.5

4 92 100 92 306 27 13 14.0 2 0 2 16.1

5 92 100 92 302 27 16 14.4 0 0 0 16.5

6 91 99 91 75 6.6 7 11.6 0 0 0 13.0

7 90 98 90 99 8.8 8 11.3 0 0 0 12.3

8 75 82 64 18 1.6 5 11.2 0 0 0 11.9

9 53 58 45 0 0 0 9.8 0 0 0 10.2

10 69 75 69 5 .4 2 9.8 0 0 0 10.3

11 71 77 62 0 0 0 10.4 0 0 0 10.8

12 92 100 92 696 62 530 16.6 0 0 0 17.9

13 92 100 92 206 18 10 12.1 0 0 0 14.0

14 92 100 92 416 37 18 15.6 0 0 0 16.8

15 68 74 68 0 0 0 10.2 0 0 0 11.4

16 375 100 75 4326 54 17 416.3 321 1.4 4 317.3

18 578 100 78 6572 87 444 617.7 500 0 518.4

19 779 100 79 8541 80 199 816.7 700 0 717.7

20 972 100 72 10492 59 125 1014.8 900 0 915.4

21 1182 100 82 12519 70 440 1215.3 1100 0 1116.0
Results of Water-Quality Data 17

RESULTS OF WATER-QUALITY DATA

Results of Water-Quality Data. 

The analytical results (table C) indicate that water 

quality at sites sampled during this study is representative of least-disturbed conditions. Although samples 

from most sites did contain some form of a nutrient 

(nitrogen or phosphorus), many nutrient concentrations 

were at or near the method detection limit (MDL). 

Under ideal sample and analytical conditions, a few 

of the nutrient compounds in table C were positively 

identified at or below the determined MDL. However, 

concentrations reported below the MDL are considered 

qualitative. Nutrient concentrations were highest at 

sites in areas of recent forest fires. It is assumed that 

these high nutrient concentrations are a result of these 

fires. Dissolved oxygen concentrations ranged from 

7.3 mg/L at Marble Creek (site 17) to 10.0 mg/L at 

Ship Island Creek (site 22). pH values at most sampling sites were near neutral and ranged from 6.9 at 

Morse Creek (site 9) to 8.4 at several sites. Specific 

1 days, n=92; hours, n=2,208 5 days, n=78; hours, n=1,560 9 days, n=72; hours, n=1,728 13 days, n=77; hours, n=1,848 2 days, n=47; hours, n=1,128 6 days, n=33; hours, n=660 10 days, n=35; hours, n=840 14 days, n=44; hours, n=1,056 3 days, n=75; hours, n=1,500 7 days, n=79; hours, n=1,580 11 days, n=82; hours, n=1,640 15 days, n=76; hours, n=1,824 4 days, n=30; hours, n=600 8 days, n=34; hours, n=680 12 days, n=37; hours, n=740 16 days, n=41; hours, n=984

22 1182 100 82 12245 33 25 1213.8 1100 0 1115.0

23 92 100 92 341 30 20 15.3 0 0 0 16.5

24 78 85 71 67 5.9 15 13.9 0 0 0 14.4

25 81 88 72 127 11 30 14.4 0 0 0 14.7

26 92 100 92 275 24 25 15.5 0 0 0 16.2

27 92 100 92 162 14 9 12.2 0 0 0 12.5

28 91 99 91 66 5.9 7 11.9 0 0 0 12.2

29 85 92 85 110 9.8 16 14.0 0 0 0 15.4

30 92 100 92 165 15 11 12.7 0 0 0 13.8

31 13 77 100 77 14594 56 161 1416.3 1300 0 1319.7

32 92 100 92 610 54 126 17.1 0 0 0 17.6

33 1576 100 76 16898 91 461 1618.3 1588 4.8 8 1521.1

34 92 100 92 946 84 285 19.2 0 0 0 19.4

U.S. Environmental Protection Agency

bull trout spawning

and juvenile rearing criterion

of 10.0°C MWMT

June 1 through September 30 (most 

cases) 

Idaho Department of Environmental Quality

Salmonid spawning criteria

of 13.0°C MDMT and 9.0°C MDAT

August 15 through September 30 (most cases)

Coldwater biota criteria

of 22.0°C MDMT and 19.0°C MDAT

July 1 through September 30 (most cases)

MWMT MDMT 13.0°C

MDAT 

9.0°C MDMT 22.0°C

MDAT 

19.0°C

Site

No.

No. 

days 

above 

10.0°C1

Percent 

days

above 

10.0°C

Consecutive 

days

above 10.0°C

No. 

hours 

above 

13.0°C2

Percent 

hours

above 

13.0°C

Consecutive 

hours

above 13.0°C MDAT2

No. 

hours 

above 

22.0°C1

Percent 

hours

above 

22.0°C

Consecutive 

hours

above 22.0°C MDAT1

Table 4. Relations between stream temperature metrics and life-stage stream temperature criteria for selected sample sites in the Salmon

River Basin, central Idaho, July through September 2001—Continued
18 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

conductance values ranged from 27 μS/cm at Big 

Creek (site 30) to 162 μS/cm at Fourth of July Creek 

(site 2). Dissolved nitrogen concentrations ranged from 

less than detection to 0.018 mg/L as N at Marble 

Creek. Total nitrogen concentrations ranged from less 

than detection to 0.647 mg/L as N at Marble Creek. 

Dissolved nitrite plus nitrate concentrations ranged 

from less than detection at Sulphur Creek (site 14) to 

0.225 mg/L as N at Rice Creek (site 34). Total phosphorus concentrations ranged from less than detection 

at several sites to 0.2470 mg/L as P at Marble Creek 

(site 17). Orthophosphorus concentrations ranged from 

less than detection at several sites to 0.073 mg/L as P at 

Rice Creek. 

RESULTS OF BENTHIC INVERTEBRATE TAXA AND 

METRICS

Results of Benthic Invertebrate Taxa and Metrics. 

Two hundred and one benthic invertebrate 

taxa from the 34 sampling sites were identified. 

The raw invertebrate data can be accessed at 

http://idaho.usgs.gov/public/studies.html. The most abundant taxa (greater than 1 percent of total abundance and 

identified in 75 percent or more of the samples) were 

Baetis tricaudatus, Oligochaeta, Tvetenia bavarica gr., 

Acari, Rhithrogena, Cinygmula, Heterlimnius, 

Micropsectra, Eukiefferiella devonica gr., Drunella

doddsi, and Cricotopus. Fifty-eight rare taxa (composing less than 0.005 percent total abundance and identified in less than 5 percent of the samples) were collected. 

Total abundance (density expressed as individuals/m2) varied greatly and ranged from 1,331 to 27,040 

individuals/m2 at Alpine Creek (site 1) and Basin 

Creek (site 5), respectively. The high abundance at site 

5 resulted from large numbers of Simulium (blackflies) 

and Cricotopus (midges). 

Comparison of Benthic Invertebrate Assemblages 

at Multiple-Reach Sites 

The JC index was used to compare spatial variability in the benthic invertebrate assemblages at multiple-reach sites (Valley Creek and Big Creek). Differences among reaches in similarity of community structure (taxonomic composition), as determined by the JC 

index, provide an indication of how well a single sampling reach represents the biological conditions within 

that stream segment. Values for this index range from 0 

(no species in common) to 1 (species composition is 

identical). Gauch (1982) suggested that, because biological community samples can be highly variable, JC 

values for replicate samples from a community often 

are less than 1 and typically range from 0.60 to 0.90. 

During this study, JC values ranged from 0.54 to 

0.63 at Valley Creek (site 4), and from 0.54 to 0.66 at 

Big Creek (site 30). JC values in the lower end of the 

typical range, such as these, indicate a greater degree 

of spatial variability in taxa occurrence between the 

multiple reaches. 

Coldwater Taxa

According to Grafe and others (2002), coldwater 

obligates are taxa which have less than a 10-percent 

chance of occurrence in streams where the temperature 

exceeds 19.0°C. To determine obligate coldwater taxa 

in streams throughout Idaho, the IDEQ analyzed 

stream temperature and macroinvertebrate community 

data from more than 1,000 sampling locations (Grafe 

and others, 2002). From this information, a list of 64 

coldwater obligate taxa was empirically derived. 

Of the designated 64 coldwater obligates, 32 taxa 

(present at a minimum of 5 sampling sites) were collected during this study (table 5). Coldwater taxa represented 16 percent (32 of 201) of all taxa collected. The 

most frequently collected coldwater taxon was the 

mayfly Drunella doddsi, which was collected at 28 

sampling sites. The most abundant coldwater taxon 

was Oligophlebodes, a caddisfly typically associated 

with mountain streams in the West. The number of 

individual coldwater taxa collected ranged from 4 at 

Skookumchuck Creek (site 33) to 29 at Big Creek (site 

30). The percentage of coldwater taxa collected ranged 

from 1 at Camas Creek, Skookumchuck Creek, and 

Rice Creek (sites 19, 33, and 34, respectively) to 74 at 

East Fork Hayden Creek (site 10) (fig. 2).

 Coldwater taxa were collected at all five sites 

(sites 4, 16, 31, 33, 34) where temperatures exceeded 

the IDEQ criteria for the protection of coldwater biota. 

The number of taxa at these sites ranged from 2 at 

Skookumchuck Creek (site 33) to 12 at Valley Creek 

(site 4). 

Nine additional taxa, not classified by Grafe and 

others (2002) as coldwater obligates, were significantly 

(p<0.05) inversely correlated with one or more of the 

stream temperature metrics (table 5). Of these taxa, 

Rhithrogena, a mayfly typically associated with high 

velocity streams, was the most frequently collected at 

30 sampling sites. 
Results of Benthic Invertebrate Taxa and Metrics 19

Stream Macroinvertebrate Index Scores and 

Metrics

In general, invertebrate metrics describe expected 

conditions for least-disturbed sites with SMI scores 

ranging from 69 (Marble Creek, site 17) to 100 (table 

6). SMI scores for 85 percent (29 of 34) of the sample 

sites were above 79, which places these sites in the 

“very good” category when compared with other sites 

in the same bioregion. 

Within the richness category (number of species), 

the total number of taxa ranged from 38 at Hazard 

Creek (site 32) to 68 at Fitsum Creek (site 26). Hazard 

Creek is a high-gradient stream with large boulder substrate and plunge-pool habitat conditions that may limit 

the diversity of taxa at this location. The total number 

of EPT taxa ranged from 17 at Marble Creek, Camas 

Creek, and Skookumchuck Creek (sites 17, 19, and 33, 

respectively) to 39 at Fourmile Creek (site 25). 

The low diversity of EPT taxa at some locations 

may have been the result of severe forest fires in the 

summer of 2000 in parts of many drainages in the Middle Fork of the Salmon River Basin, including Marble 

Creek and Camas Creek. These fires caused large 

amounts of silt and sediment to be transported to the 

streams by overland runoff during localized rainstorms. According to Minshall and others (2001), 

“blowouts” in the headwaters of Marble Creek continue to send large amounts of silt and sediment into 

this creek following local rainstorms. The effect of 

continued high sediment transport is the destruction of 

the benthic habitat by sediment deposition (Minshall 

and others, 2001). On the day of sampling, Marble 

Creek and Camas Creek both were transporting large 

amounts of silt and sediment as a result of a recent 

rainstorm. In addition, high flow conditions made sampling these two sites extremely difficult. Either of these 

conditions may help to explain the low diversity of 

EPT taxa at these locations. 

Within the composition category, percent Plecoptera ranged from 0.4 to 25.2. The HBI scores within the 

pollution tolerance category ranged from 1.91 to 4.97. 

HBI scores for 82 percent (28 of 34) of the sample sites 

were below 4.50, which indicates “very good” water 

80

70

60

50

40

30

20

10

0

25

20

15

10

10 1 15 25 27 8 24 9 28 6 11 7 2 22 30 3 21 20 23 29 13 26 4 18 14 12 32 5 16 17 31 19 33 34

Figure 2. Percent coldwater benthic invertebrate taxa in relation to maximum daily-maximum stream temperature at all sample

sites in the Salmon River Basin, central Idaho, July through September 2001. (Site locations shown in figure 1; site names and

characteristics shown in table 1)

Maximum daily-maximum

stream temperature at site

PERCENT COLDWATER BENTHIC

INVERTEBRATE TAXA

MAXIMUM DAILY-MAXIMUM STREAM

TEMPERATURE, IN DEGREES CELSIUS

SITE NUMBER
20 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

Table 5. Spearman rank correlation coefficients for relative abundance of coldwater benthic invertebrate taxa and selected stream 

temperature metrics for selected sample sites in the Salmon River Basin, central Idaho, July through September 2001

[Number of sites sampled, 33; taxa shown were collected at five or more sample sites; bold denotes significance (p<0.05); see table 2 for 

description of stream temperature metrics; No., number]

Taxon

No. of 

sites 

where 

collected MDMT MDAT MWMT MWAT MWMTS MWATS DEGDAY1

Coldwater taxa2

Baetis bicaudatus 8 -0.34 -0.38 -0.30 -0.35 -0.30 -0.27 -0.32

Cinygmula sp. 26 -.49 -.43 -.47 -.41 -.54 -.53 -.39

Drunella coloradensis/flavilinea 14 -.52 -.61 -.55 -.61 -.42 -.53 -.59

Drunella doddsi 28 -.72 -.68 -.71 -.67 -.61 -.60 -.65

Drunella spinifera 10 -.38 -.39 -.38 -.38 -.23 -.23 -.38

Epeorus deceptivus 12 -.61 -.61 -.64 -.61 -.52 -.65 -.63

Epeorus grandis 14 -.59 -.61 -.56 -.61 -.44 -.48 -.60

Epeorus sp. 22 0 -.06 .01 -.08 .05 -.01 -.04

Ephemerellidae 7 -.35 -.39 -.33 -.40 -.33 -.40 -.39

Cultus sp. 5 .48 .37 .46 .35 .25 .25 .36

Leuctridae 18 -.59 -.68 -.59 -.70 -.55 -.68 -.67

Megarcys sp. 15 -.67 -.74 -.67 -.74 -.56 -.68 -.71

Perlidae 7 .06 .15 .04 .11 .19 .23 .11

Sweltsa sp. 25 -.29 -.44 -.33 -.45 -.21 -.43 -.48

Taeniopterygidae 8 -.54 -.42 -.51 -.39 -.61 -.40 -.36

Visoka cataractae 5 -.33 -.25 -.29 -.25 -.32 -.24 -.25

Yoroperla sp. 5 -.23 -.22 -.23 -.20 -.09 -.06 -.23

Zapada columbiana 17 -.66 -.57 -.62 -.53 -.62 -.41 -.48

Zapada oregonensis gr. 13 -.70 -.76 -.70 -.77 -.59 -.76 -.75

Heterlimnius sp. 26 -.10 -.29 -.18 -.33 .07 -.19 -.36

Lara sp. 7 .02 .15 .02 .17 -.08 .22 .20

Narpus sp. 5 .33 .47 .36 .48 .35 .47 .46

Apatania sp. 10 -.20 -.35 -.25 -.38 -.09 -.22 -.38

Oligophlebodes sp. 10 -.34 -.11 -.35 -.14 -.29 .01 -.10
Results of Fish Taxa and Metrics 21

quality with slight organic pollution. The highest HBI 

score (5.20), was for Riordan Creek (site 29). Within 

the diversity category, the percent five dominant taxa 

ranged from 38.9 to 76.4. The number of scraper taxa 

in the feeding group category ranged from 4 to 12, and 

the number of clinger taxa in the habitat category 

ranged from 19 to 35. 

RESULTS OF FISH TAXA AND METRICS

Results of Fish Taxa and Metrics. 

Ten species of fish in the families 

Salmonidae, Cottidae, and Cyprinidae were 

collected. The raw fish data can be accessed at 

http://idaho.usgs.gov/public/studies.html. A total of 4,199 

fish were collected from the 33 sites sampled during 

1Sites 20, 31, and 33 not included (n=30).

2Coldwater taxa from Grafe and others (2002).

3Taxa significantly correlated with one or more temperature metrics. 

Parapsyche elsis 13 -0.69 -0.62 -0.68 -0.61 -0.65 -0.60 -0.61

Rhyacophila betteni gr. 16 -.74 -.68 -.70 -.66 -.63 -.61 -.66

Rhyacophila brunnea gr. 19 -.30 -.39 -.34 -.42 -.24 -.35 -.43

Rhyacophila hyalinata gr. 12 -.29 -.27 -.29 -.23 -.16 -.15 -.25

Rhyacophila narvae 14 -.45 -.45 -.50 -.47 -.30 -.39 -.51

Rhyacophila pellisa/valuma 6 -.38 -.40 -.41 -.41 -.31 -.44 -.42

Rhyacophila vagrita gr. 5 -.25 -.28 -.25 -.28 -.18 -.28 -.26

Glutops sp. 5 -.10 -.17 -.13 -.16 .02 -.13 -.17

Other taxa3

Rhithrogena sp. 30 -.49 -.45 -.47 -.45 -.45 -.41 -.44

Serratella tibialis 18 -.23 -.45 -.27 -.46 -.08 -.30 -.45

Chloroperlidae 9 -.38 -.36 -.33 -.39 -.29 -.32 -.40

Perlodidae 18 -.20 -.37 -.26 -.37 -.12 -.25 -.36

Glossosoma sp. 20 -.33 -.32 -.31 -.31 -.56 -.48 -.30

Pericoma sp. 5 -.38 -.39 -.37 -.39 -.32 -.37 -.40

Parametriocnemus sp. 12 -.34 -.38 -.28 -.38 -.28 -.34 -.34

Ostracoda 19 -.49 -.43 -.46 -.39 -.54 -.37 -.36

Polycelis sp. 21 -.52 -.69 -.57 -.69 -.47 -.66 -.69

Taxon

No. of 

sites 

where 

collected MDMT MDAT MWMT MWAT MWMTS MWATS DEGDAY1

Coldwater taxa2

Table 5. Spearman rank correlation coefficients for relative abundance of coldwater benthic invertebrate taxa and selected stream 

temperature metrics for selected sample sites in the Salmon River Basin, central Idaho, July through September 2001—Continued
22 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

Table 6. Relations between benthic invertebrate metrics and Stream Macroinvertebrate Index scores for selected sample sites in the Salmon 

River Basin, central Idaho, 2001

[Total SMI scores were calculated from the metric values reported by Jessup and Gerritsen (2002); site locations shown in figure 1; site 

names and characteristics shown in table 1; No., number, SMI, Stream Macroinvertebrate Index]

Site 

No.

No. 

species

No.

Ephemeroptera 

taxa

No. 

Plecoptera 

taxa

No. 

Trichoptera 

taxa

Percent

Plecoptera

Hilsenhoff 

Biotic

Index

Percent

five 

dominant

taxa

No. 

scraper 

taxa

No. 

clinger 

taxa

Total

SMI 

score

1 56 17 7 10 13.0 2.87 46.5 11 23 100

2 53 11 7 17 9.5 2.67 50.4 10 27 100

3 49 14 6 10 5.9 4.35 58.2 6 21 91

14 61 14 6 10 4.9 4.02 41.6 8 27 95

5 48 14 5 9 .9 4.97 68.8 7 25 86

6 48 11 8 12 4.6 1.91 59.0 10 25 100

7 60 15 11 8 11.1 3.35 41.7 10 27 100

8 57 10 11 14 15.2 2.62 49.4 10 30 100

9 51 14 9 10 13.5 3.21 44.9 10 24 100

10 42 9 10 7 25.2 2.71 63.3 9 19 98

11 60 13 11 11 7.8 3.08 55.3 12 31 100

12 48 10 3 9 1.3 4.64 67.2 7 26 81

13 55 16 6 7 7.0 3.84 53.0 8 25 99

14 53 10 7 9 5.6 4.33 38.9 4 25 92

15 53 11 10 11 13.1 3.32 49.0 7 25 100

16 44 8 4 10 1.9 4.65 68.0 7 23 78

17 41 6 5 6 3.4 3.69 74.0 6 20 69

18 51 10 6 9 3.8 3.79 59.9 11 30 98

19 43 7 2 8 .9 3.73 66.0 8 21 73

20 43 8 7 6 13.6 3.98 53.9 8 23 88

21 43 7 7 6 10.7 4.51 57.3 6 26 83

22 51 8 9 11 15.1 4.42 50.0 8 30 100

23 53 12 9 8 8.8 3.66 42.0 7 29 100

24 49 13 5 14 2.4 2.32 64.7 9 26 100

25 59 13 11 15 7.8 2.42 53.6 7 32 100
Results of Fish Taxa and Metrics 23

this study. Fish collected at all sites appeared in good 

health with few external anomalies. The number of 

species collected at a site ranged from 1 at East Fork 

Hayden Creek (site 10) to 8 at Indian Creek (site 16). 

Six salmonid species, composing 54 percent of the 

total number of fish collected, were collected during 

the study. Two species listed as threatened under the 

U.S. Fish and Wildlife Service Endangered Species 

Act (ESA) were collected—bull trout and chinook 

salmon—at 58 and 45 percent of the sampling sites, 

respectively. Rainbow trout (Oncorhynchus mykiss), 

which are considered native in the Salmon River Basin 

(Simpson and Wallace, 1982), were collected at 82 

percent of the sampling sites, composing 33 percent of 

the total number of fish collected. According to the 

IDFG, rainbow trout are stocked in streams and rivers 

in the Salmon River Basin. However, less than 1 percent (6 of 1,381) of the rainbow trout collected showed 

signs such as eroded fins, deformities, and scars typically associated with hatchery fish. Cutthroat trout 

(Oncorhynchus clarki) were collected at 55 percent of 

the sampling sites; however, they composed only 2.6 

percent of the total number of fish collected. Mountain 

whitefish (Prosopium williamsoni) were collected at 

21 percent of the sampling sites. One introduced species, brook trout (Salvelinus fontinalis), was collected 

at 21 percent of the sampling sites.

Two cottid species were collected during the 

study. Shorthead sculpin (Cottus confusus) were collected at 85 percent of the sampling sites and was the 

most abundant species, composing 43 percent of the 

total number of fish collected. Torrent sculpin (Cottus 

rhotheus) were collected at 12 percent of the sampling 

sites.

Although common to the basin, suckers (Catostomus sp.) were not collected at any of the sampling 

sites. In addition to fish, tailed frogs and salamanders 

were collected at 48 percent and 18 percent of the sampling sites, respectively.

Comparison of Fish Assemblages at MultipleReach Sites

The JC index was used to compare spatial variability in the benthic invertebrate assemblages at multiple-reach sites (Valley Creek and Big Creek). The 

lower range of JC values for the multiple reaches sampled at Valley Creek (site 4) ranged from 0.29 to 0.57, 

1 Average of three multiple reaches.

26 68 17 9 12 7.4 4.15 45.5 11 35 100

27 59 15 8 7 8.9 3.08 39.4 9 23 100

28 59 13 8 13 5.0 4.20 46.2 9 32 100

29 53 9 3 11 .8 5.20 39.6 7 24 88

130 54 12 8 10 11.4 4.08 42.1 6 27 99

31 44 6 4 13 2.5 4.02 76.4 11 27 87

32 38 10 2 7 .4 4.18 57.5 7 22 74

33 45 7 3 7 5.2 4.95 42.2 5 23 76

34 47 6 5 8 14.9 4.28 52.4 5 22 82

Site 

No.

No. 

species

No.

Ephemeroptera 

taxa

No. 

Plecoptera 

taxa

No. 

Trichoptera 

taxa

Percent

Plecoptera

Hilsenhoff 

Biotic

Index

Percent

five 

dominant

taxa

No. 

scraper 

taxa

No. 

clinger 

taxa

Total

SMI 

score

Table 6. Relations between benthic invertebrate metrics and Stream Macroinvertebrate Index scores for selected sample sites in the Salmon

River Basin, central Idaho, 2001—Continued
24 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

indicating that the fish species were taxonomically dissimilar among multiple reaches. In other words, species composition varied substantially among the individual reaches. This variability is not easily explained. 

Typically, low JC values can be explained by low capture efficiency when sampling large rivers or streams 

with complex habitat. Valley Creek is neither large nor 

complex. This third-order, meandering, meadow 

stream can be sampled easily and contains little habitat 

variability. 

The JC values for the multiple reaches sampled at 

Big Creek (site 30) ranged from 0.50 to 1.0 and were 

more typical of values for a small, wadeable stream. 

This range indicates that fish species were generally 

taxonomically similar and that fish collected at a single 

reach at this site are representative of the fish community assemblage.

Stream Fish Index Scores and Metrics

Similar to invertebrate metrics, the fish metrics 

describe expected conditions for least-disturbed sites; 

SFI scores ranged from 74 (Big Mallard Creek, site 23) 

to 100 at several sites (table 7). SFI scores for 91 percent (30 of 33) of the sample sites were above 81, 

which places these sites above the median of reference 

conditions for their ecoregion. 

Within the richness and composition categories, 

the number of coldwater native species ranged from 1 

at East Fork Hayden Creek (site 10) to 7 at Indian 

Creek and Camas Creek (sites 16 and 19, respectively); 

percent coldwater individuals ranged from 76 at Hazard Creek (site 32) to 100; and percent sensitive native 

individuals ranged from 25 at Big Mallard Creek (site 

23) to 100. Within the reproductive function category, 

the number of cottid age classes ranged from 0 to 5. 

The number of salmonid age classes ranged from 2 to 

5. Within the abundance category, CPUE ranged from 

2.3 at Fourth of July Creek (site 2) to 21.9 at Skookumchuck Creek (site 33).

CORRELATIONS BETWEEN STREAM 

TEMPERATURE AND ENVIRONMENTAL 

VARIABLES

Correlations Between Stream Temperature and Environmental Variables. 

Representative environmental variables consisting 

of basin, site, and habitat characteristics (tables 1, A, 

and B) were analyzed in relation to the stream temperature metrics by using Spearman rank correlation analysis. Nine environmental variables—water-surface 

gradient, discharge, wetted channel width, width:depth 

ratio, aspect, total seasonal thermal input, open canopy, 

riparian canopy density, and elevation were selected 

for correlation with the nine stream temperature 

metrics. 

Analysis of Spearman rank correlation coefficients for pairwise comparisons between the selected 

variables (table 8) determined that elevation showed 

the strongest inverse correlation with the stream temperature metrics, especially those metrics associated 

with mean temperature. Seasonal degree-days for July 

through August exhibited the strongest inverse correlation with elevation (r=-0.71) (fig. 3). Donato (2002) 

also reported that elevation showed a strong negative 

correlation with stream temperature in the Salmon 

River Basin. Riparian canopy density showed a strong 

inverse correlation with stream temperature metrics 

associated with maximum temperature. Wetted channel width and width:depth ratio were positively correlated with all stream temperature metrics. Donato 

(2002) also reported that these two variables showed a 

significant positive correlation with temperature in the 

Salmon River Basin. Discharge was positively corre34

18

19

12

32 16

14

26

21

22 23

29 4

5

24

25

27

28 6

30

7

3

11 15

2

8

1

13

9 10

R= -0.71

(p<0.01)

1,100

1,000

900

800

700

600

500

0 500 1,500 2,500 1,000 2,000 3,000

SEASONAL DEGREE-DAYS

ELEVATION, IN METERS ABOVE SEA LEVEL

Figure 3. Elevation in relation to seasonal degree-days (July through

August, above 0 degrees Celsius) for selected sample sites in the

Salmon River Basin, central Idaho, 2001. [Trend line based on

LOWESS smoothing technique (Helsel and Hirsch, 2002); site

locations shown in figure 1; site names and characteristics shown

in table 1]
Correlations Between Stream Temperature and Environmental Variables 25

Table 7. Relations between fish metrics and Stream Fish Index scores for selected sample sites in the Salmon River Basin, central Idaho, 2001

[Site locations shown in figure 1; site names and characteristics shown in table 1; No., number; CPUE, catch per unit effort; electrofishing not conduct

Site 

No.

No. 

coldwater 

native 

species

Percent 

coldwater 

individuals

Percent 

sensitive 

native 

individuals

No.

cottid

age 

classes

No. 

salmonid 

age

classes

CPUE

(No.

coldwater 

individuals

per

minute 

electrofishing)

Stream

Fish

Index 

(forest)

Site 

No.

No. 

coldwater 

native 

species

Percent 

coldwater 

individuals

Percent 

sensitive 

native 

individuals

No. 

cottid 

age 

classes

N

salm

a

clas

1 3 100 75 4 5 4.3 95 19 7 100 52 4 2 4 100 96 5 2 2.3 80 20 2 99 99 5 3 2 100 80 3 2 10.1 87 21 5 100 100 5 4 3 100 84 4 3 10.9 97 22 2 100 100 0 5 4 99 99 4 2 9.1 90 23 2 100 25 0 6 5 100 96 5 4 2.6 89 24 5 99 99 4 7 4 100 91 5 5 6.9 99 25 3 100 100 0 8 4 100 100 5 3 4.5 96 26 3 97 97 4 9 3 100 100 5 4 4.6 97 27 3 100 100 5 

10 1 100 100 0 5 5.4 75 28 4 100 98 5 11 3 100 100 5 3 8.5 98 29 4 100 100 5 12 5 98 72 5 3 9.2 98 30 2 100 100 0 13 4 100 90 4 2 10.4 100 31 5 94 93 5 14 3 100 99 4 2 5.0 90 32 4 76 76 4 15 3 100 98 4 3 4.2 100 33 2 93 93 4 16 7 100 94 4 5 7.7 100 34 2 97 97 3 18 6 96 68 3 3 3.0
26 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

lated with all stream temperature metrics except those 

associated with the date of sample and 6 days prior 

(MWMTS and MWATS). Total seasonal thermal input 

was positively correlated (p<0.05) with all stream temperature metrics except MWATS. Open canopy was 

positively correlated with MDMT and MWMT. Neither water-surface gradient nor aspect was correlated 

with the stream temperature metrics.

CORRELATIONS BETWEEN STREAM 

TEMPERATURE AND BENTHIC INVERTEBRATE 

VARIABLES

Correlations Between Stream Temperature and Benthic Invertebrate Vari- ables. . . Correlations Between Stream Temperature and Benthic Invertebrate Variables. 

Of the 201 benthic invertebrate taxa collected during this study, 57 taxa (present at a minimum of 5 sampling sites) were significantly correlated with one or 

more of the stream temperature metrics. Spearman 

rank correlation coefficients for pairwise comparisons 

of relative benthic invertebrate abundance and stream 

temperature metrics are shown in tables 5 and 9. 

Of the 32 coldwater taxa collected, only 20 taxa 

showed a significant inverse correlation with one or 

more of the stream temperature metrics at the <0.05 

probability level (table 5). Two of the designated coldwater obligates, Cultus and Narpus, showed a significant positive correlation with one or more of the stream 

temperature metrics. Of the coldwater taxa collected, 

Zapada oregonensis gr. showed the strongest inverse 

correlation with the stream temperature metrics and 

was collected at sites where MWMTS ranged from 

11.3° to 18.5°C. Of the nine additional taxa not classified by Grafe and others (2002) as coldwater obligates, 

Polycelis showed the strongest inverse correlation with 

all stream temperature metrics and was collected at 

sites where MWMTS ranged from 11.3° to 18.6°C.

As expected, the percentage of coldwater taxa 

showed a strong inverse correlation (-0.73 to -0.87) 

with all stream temperature metrics. Figure 2 illustrates 

this correlation and indicates that, as MDMT increases, 

percent coldwater taxa decreases. 

In contrast to coldwater taxa, 26 invertebrate taxa 

(present at a minimum of 5 sampling sites) showed a 

significant (p<0.05) positive correlation with one or 

more of the stream temperature metrics (table 9). These 

results suggest that these taxa may be tolerant of 

warmer water temperatures. These taxa represented 13 

percent (26 of 201) of the total number of invertebrate 

taxa collected. Of the 26, the most frequently collected 

Table 8. Spearman rank correlation coefficients for selected habitat variables and selected stream temperature metrics for selected sample 

sites in the Salmon River Basin, central Idaho, July through September 2001

[Number of sample sites, 33; bold denotes significance (p<0.05); see table 2 for description of stream temperature metrics; m3/s, cubic 

meters per second; m, meters; BTUs/m2/d, British thermal units per square meter per day]

1 Sites 20, 31, and 33 not included (n = 30).

Habitat parameter MDMT MDAT MWMT MWAT MWMTS MWATS DEGDAY1

Water-surface gradient (percent) . . . . . . . -0.25 -0.01 -0.21 0.04 -0.26 0.11 0.10

Discharge (m3/s). . . . . . . . . . . . . . . . . . . . .37 .40 .40 .43 .20 .24 .46

Wetted channel width (m) . . . . . . . . . . . . .58 .64 .62 .66 .46 .49 .66

Wetted stream width:depth ratio. . . . . . . . .52 .48 .54 .49 .51 .44 .47

Stream aspect . . . . . . . . . . . . . . . . . . . . . . .01 -.14 -.05 -.15 .20 -.13 -.18

Total seasonal thermal input, June through 

September 2001 (BTUs/m2/d) . . . . . . . .60 .41 .60 .40 .45 .29 .43

Open canopy (percent) . . . . . . . . . . . . . . . .48 .22 .46 .19 .36 .10 .24

Riparian canopy density (percent) . . . . . . -.59 -.30 -.57 -.27 -.52 -.19 -.29

Elevation (m above sea level). . . . . . . . . . -.29 -.62 -.35 -.66 -.13 -.60 -.71
Correlations Between Stream Temperature and Benthic Invertebrate Variables 27

Table 9. Spearman rank correlation coefficients for relative abundance of benthic invertebrate taxa and selected stream temperature metrics 

for selected sample sites in the Salmon River Basin, central Idaho, July through September 2001

[Number of sample sites, 33; taxa shown were collected at five or more sample sites; No., number; bold denotes significance (p<0.05); see 

table 2 for description of stream temperature metrics] 

1 Sites 20, 31, and 33 not included (n=30).

Taxon

No. of sites 

where 

collected MDMT MDAT MWMT MWAT MWMTS MWATS DEGDAY1

Acentrella turbida. . . . . . . . . . . 10 0.58 0.51 0.57 0.50 0.57 0.54 0.50

Baetis tricaudatus. . . . . . . . . . . 33 .30 .49 .30 .48 .40 .56 .49

Diphetor hageni . . . . . . . . . . . . 14 .53 .38 .54 .38 .52 .37 .39

Hesperoperla pacifica . . . . . . . 14 .46 .34 .45 .33 .50 .32 .31

Pteronarcys californica . . . . . . 7 .46 .57 .49 .57 .44 .51 .55

Pteronarcys sp. . . . . . . . . . . . . . 6 .54 .55 .54 .54 .40 .44 .54

Skwala sp.. . . . . . . . . . . . . . . . . 6 .44 .40 .45 .44 .29 .37 .42

Cleptelmis addenda . . . . . . . . . 12 .40 .28 .39 .30 .52 .40 .24

Optioservus sp.. . . . . . . . . . . . . 17 .57 .74 .61 .74 .40 .61 .73

Zaitzevia sp. . . . . . . . . . . . . . . . 16 .29 .48 .35 .49 .14 .37 .51

Brachycentrus americanus. . . . 19 .47 .30 .41 .27 .41 .24 .24

Hydropsyche sp. . . . . . . . . . . . . 19 .67 .81 .69 .82 .50 .66 .81

Lepidostoma sp. . . . . . . . . . . . . 12 .53 .53 .53 .51 .31 .31 .51

Micrasema sp. . . . . . . . . . . . . . 13 .41 .36 .38 .37 .61 .51 .31

Neophylax rickeri . . . . . . . . . . . 5 .38 .30 .34 .27 .33 .31 .26

Antocha sp. . . . . . . . . . . . . . . . . 20 .62 .74 .65 .78 .41 .65 .80

Atherix sp.. . . . . . . . . . . . . . . . . 8 .53 .45 .51 .45 .47 .40 .44

Cricotopus 

(Nostococladius) sp.. . . . . . . 17 .39 .25 .38 .24 .36 .28 .22

Cricotopus sp.. . . . . . . . . . . . . . 26 .50 .50 .49 .52 .42 .49 .52

Orthocladius Complex . . . . . . . 22 .36 .25 .32 .22 .46 .40 .20

Orthocladius sp. . . . . . . . . . . . . 24 .44 .47 .49 .50 .26 .44 .53

Polypedilum sp. . . . . . . . . . . . . 6 .34 .29 .34 .28 .47 .43 .23

Rheotanytarsus sp. . . . . . . . . . . 21 .55 .47 .55 .44 .59 .54 .43

Sublettea sp. . . . . . . . . . . . . . . . 5 .48 .43 .51 .45 .39 .32 .42

Thienemanniella sp. . . . . . . . . . 8 .33 .28 .33 .30 .41 .39 .30

Acari (=Acarina) . . . . . . . . . . . 32 .59 .62 .61 .63 .47 .59 .66
28 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

was Baetis tricaudatus, which was collected at 33 of 

the 34 sampling sites. The caddisfly Hydropsyche

showed the strongest positive correlation with the 

stream temperature metrics. 

CORRELATIONS BETWEEN STREAM 

TEMPERATURE AND FISH VARIABLES

Correlations Between Stream Temperature and Fish Variables. 

Spearman rank correlation coefficients for pairwise comparisons of relative fish abundance and 

stream temperature metrics are shown in table 10. 

Results of this comparison indicate that bull trout 

showed the strongest inverse correlation with stream 

temperature. According to Selong and others (2001), of 

salmonids in North America, bull trout are regarded as 

having one of the lowest thermal tolerances and typically do not live where maximum temperatures exceed 

15°C. In this study, bull trout were collected at sites 

where MWMTS ranged from 11.3° to 20.0°C (fig. 4). 

In contrast, rainbow trout were positively correlated with all stream temperature metrics except 

MDMT and MWMTS. Chinook salmon also showed a 

weak positive correlation with all stream temperature 

metrics except MWAT and MWATS. These two species were collected at sites where MWMTS ranged 

from 12.4° to 22.9°C and 14.2° to 20.0°C, respectively 

(fig. 4). 

Two additional species were positively correlated 

with the stream temperature metrics. Longnose dace 

(Rhinichthys cataractae) showed a strong positive correlation with stream temperature, and torrent sculpin, 

although less pronounced, also showed a positive correlation with all stream temperature metrics except 

MWAT, MWMTS, and MWATS. The correlation 

between brook trout, cutthroat trout, speckled dace 

(Rhinichthys osculus), shorthead sculpin, mountain 

whitefish, or tailed frogs and the stream temperature 

metrics was not significant (p>0.05).

Correlations between SFI metrics, selected fish 

densities, and the stream temperature metrics are presented in table 11. As expected, percent coldwater individuals showed a strong inverse correlation with 

stream temperature. Percent sensitive native individuTable 10. Spearman rank correlation coefficients for relative abundance of fish species and selected stream temperature metrics for 

selected sample sites in the Salmon River Basin, central Idaho, July through September 2001

[Number of sample sites, 33; No., number; bold denotes significance (p<0.05); see table 2 for description of stream temperature metrics] 

1 Sites 20, 31, and 33 not included (n=30).

Fish species

No. of sites 

where 

collected MDMT MDAT MWMT MWAT MWMTS MWATS DEGDAY1

Brook trout . . . . . . . . . . . . . . . . 7 -0.01 -0.16 -0.07 -0.19 0.11 -0.16 -0.25

Bull trout . . . . . . . . . . . . . . . . . 19 -.64 -.54 -.63 -.51 -.63 -.53 -.52

Chinook salmon . . . . . . . . . . . . 15 .45 .37 .40 .34 .38 .32 .41

Cutthroat trout . . . . . . . . . . . . . 18 -.21 -.20 -.23 -.20 -.29 -.25 -.11

Longnose dace . . . . . . . . . . . . . 11 .64 .66 .65 .66 .53 .61 .55

Rainbow trout. . . . . . . . . . . . . . 27 .36 .53 .44 .56 .30 .54 .55

Speckled dace. . . . . . . . . . . . . . 2 .22 .36 .26 .34 .30 .35 .25

Shorthead sculpin . . . . . . . . . . . 27 -.06 -.31 -.10 -.33 -.07 -.32 -.31

Torrent sculpin . . . . . . . . . . . . . 4 .45 .37 .42 .35 .12 .13 .44

Mountain whitefish. . . . . . . . . . 11 .30 .32 .30 .31 .16 .14 .35

Tailed frog . . . . . . . . . . . . . . . . 14 -.05 -.08 -.02 -.04 -.02 .04 .07
Correlations Between Stream Temperature and Fish Variables 29

25

21

17

13

9

Bull trout

Cutthroat trout

Tailed frog

Shorthead sculpin

Rainbow trout

Mountain whitefish

Torrent sculpin

Brook trout

Chinook salmon

Longnose dace

Speckled dace

19

18

14

28 27

11

11

2

7

15

4

TEMPERATURE, IN DEGREES CELSIUS

AQUATIC VERTEBRATE SPECIES

Figure 4. Range of maximum weekly-maximum stream temperatures (based on date of sample collection and 6 days prior) at which

fish and tailed frogs were collected in the Salmon River Basin, central Idaho, 2001. [Species are ranked by median water temperatures at all sites where collected; site locations shown in figure 1; site names and characteristics shown in table 1]

als showed a weak inverse correlation with all stream 

temperature metrics except MWATS. Catch per unit 

effort showed a weak positive correlation with stream 

temperature metrics associated with maximum temperatures (MDMT, MWMT, MWMTS); all other stream 

temperature metrics were not correlated with this fish 

metric. No significant (p>0.05) correlation was evident 

between any of the stream temperature metrics and 

number of coldwater native species, number of sculpin 

and salmonid age classes, or percent sculpins. 

Results of the fish density and stream temperature 

metric comparison were similar to the comparisons of 

relative fish abundance and stream temperature metrics; bull trout and juvenile bull trout (<150 mm) density showed strong inverse correlations with stream 

temperature (table 11 and fig. 5). Bull trout densities 

ranged from 0.001 fish/m2 at Hazard Creek (site 32) to 

0.094 fish/m2 at Morse Creek (site 9). Juvenile bull 

trout densities ranged from 0 to 0.049 fish/m2 at the 19 

sites where bull trout were collected. Morse Creek and 

East Fork Hayden Creek (site 10) contained exceptionally high densities of bull trout relative to densities at 

other sites (fig. 5). MDMT at these sites was 12.0° and 

13.9°C, respectively. Neither salmonid nor sculpin 

density was correlated with the stream temperature 

metrics.

Because bull trout are listed as threatened under 

the ESA and are believed to be among the most thermally sensitive species in coldwater habitats (Selong 

and others, 2001), regional models have been developed to predict their occurrence at various stream

temperatures. These predictive tools also have been 

used to develop stream temperature water-quality 

criteria to protect bull trout. Dunham and others (2001) 

developed a univariate logistic regression model predicting the probability of occurrence of juvenile bull 

trout using MDMT as the predictor variable for 643 

stream sites throughout the Western United States 

(fig. 6). They selected MDMT because it was significantly correlated with other stream temperature metrics 
30 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

and is an easily understood metric with strong biological implications for acute exposure. Juvenile fish were 

used because they represent resident (nonmigratory) 

individuals that are present for at least an entire annual 

thermal regime within the stream. Model predictions 

for the regional data set showed that the probability 

of occurrence is relatively low (<0.50) until MDMT 

declines to approximately 14° to 16°C, and the probability of occurrence is not high (>0.75) until MDMT 

declines to approximately 11° to 12°C. 

To determine the probability of occurrence of bull 

trout in Salmon River Basin streams, a univariate logistic regression model was developed using MDMT 

from 33 sites in this study. The model developed during this study describes a significant (p<0.001) correlation between the probability of occurrence of juvenile 

bull trout and MDMT. However, this model differed 

from the regional model developed by Dunham and 

others (2001) in that the range of observed stream temperatures for the Salmon River Basin dataset is narrower than for the regional dataset. Perhaps this is 

because sites in the Salmon River Basin represent only 

minimally disturbed reference sites and constitute a 

much smaller sample size. 

The regression model for this study showed 

higher probabilities of occurrence of bull trout at 

colder stream temperatures (10° to 15°C) and lower 

probabilities of occurrence at warmer stream temperatures (16° to 21°C) than the regional model showed. 

Most importantly, the regional model likely would 

overpredict the probability of bull trout occurrence at 

warmer stream temperatures if applied to streams in 

the Salmon River Basin. The boxplots comparing the 

predicted probabilities for both datasets (fig. 6) show 

that, for sites where no bull trout were present, the 

regional model predicts a median probability of occurrence of about 40 percent, whereas the model developed during this study predicts the median probability 

Table 11. Spearman rank correlation coefficients for selected fish and stream temperature metrics for selected sample sites in the Salmon 

River Basin, central Idaho, July through September 2001

[Number of sample sites, 33; No., number; bold denotes significance (p<0.05); see table 2 for description of stream temperature metrics; m2, 

square meters; <, less than; mm, millimeters] 

1 Sites 20, 31, and 33 not included (n=30).

Metric MDMT MDAT MWMT MWAT MWMTS MWATS DEGDAY1

Stream Fish Index

(forested)

No. of coldwater native species . . . . . . . . . . . 0.22 0.27 0.22 0.27 0.05 0.11 0.33

Percent coldwater individuals . . . . . . . . . . . . -.52 -.64 -.55 -.63 -.42 -.58 -.63

Percent sensitive native individuals . . . . . . . . -.48 -.46 -.45 -.43 -.48 -.31 -.39

No. of cottid age classes. . . . . . . . . . . . . . . . . -.32 -.31 -.32 -.30 -.33 -.29 -.27

No. of salmonid age classes . . . . . . . . . . . . . . -.22 -.18 -.20 -.18 -.35 -.34 -.15

Catch per unit effort (No. of coldwater individuals per minute electrofishing) . . . . . . . . . .41 .28 .36 .26 .44 .31 .25

Density

(No. fish/m2)

Salmonid. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .06 .15 .05 .15 .11 .24 .14

Bull trout . . . . . . . . . . . . . . . . . . . . . . . . . . . . -.61 -.52 -.60 -.49 -.58 -.51 -.51

Juvenile bull trout (<150 mm in length). . . . . -.66 -.62 -.67 -.61 -.52 -.54 -.63

Sculpin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .19 -.04 .14 -.08 .16 -.09 -.08
Summary 31

0.10

0.09

0.08

0.07

0.06

0.05

0.04

0.03

0.02

0.01

0

25

20

15

10

9 10 28 1 15 8 2 23 27 25 29 21 22 16 24 19 6 31 32

BULL TROUT, PER SQUARE METER

MAXIMUM DAILY STREAM TEMPERATURE,

IN DEGREES CELSIUS

SITE NUMBER

Bull trout longer than 150 mm

Bull trout shorter than 150 mm

Maximum daily-maximum

 stream temperature at site

Figure 5. Bull trout densities in relation to maximum daily-maximum stream temperature at selected sample sites in the Salmon

River Basin, central Idaho, 2001. [mm, millimeter; site locations shown in figure 1; site names and characteristics shown in table 1]

of bull trout occurrence at about 10 percent. A MannWhitney test for both datasets shows a significant 

(p<0.001) difference in predicted probability between 

cases where bull trout are absent and cases where they 

are present. Regression model results using all bull 

trout and MDMT did not perform as well as the model 

using juveniles only; the significance level was 

p=0.01. McFadden’s rho, a measure of model performance (goodness of fit), was 0.40 and 0.15 for the 

model using juvenile bull trout and all bull trout, 

respectively. Values between 0.2 and 0.4 suggest a 

good fit to the model (Hosmer and Lemeshow, 1989). 

As suggested in the preceding discussion, the 

model developed in this study probably would be a 

better predictor of bull trout occurrence for Salmon 

River Basin streams than would a model based on 

regional data for the entire Pacific Northwest, possibly 

because of other limiting factors that may not be 

present at least-disturbed sites sampled in this study. 

Additionally, the regional dataset was composed of 

a wide variety of data sources and varying collection 

methods that may have influenced model results, 

whereas during the Salmon River Basin study, consistent electrofishing effort was applied at each study site 

to standardize fish capture efficiency. The model comparisons suggest that regional or local differences need 

to be considered when deriving stream temperature criteria. These comparisons should be viewed with caution because of sample size differences—the regional 

dataset contained an order-of-magnitude more observations than those modeled in this study.

SUMMARY

Summary. 

Environmental variables, with a focus on stream 

temperature, and benthic invertebrate and fish assemblages were evaluated for 34 least-disturbed, wadeable, 

second- through fifth-order streams in the Salmon 

River Basin, Idaho. Data were collected to document 

the thermal regime of least-disturbed streams, characterize the distribution of aquatic biota in streams representing a gradient of temperature, and describe relations between environmental variables and benthic 

invertebrate and fish assemblages.

The Salmon River Basin is located within the 

Blue Mountains, Idaho Batholith, and Middle Rockies 
32 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

0 5 10 15 20 25 30

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

Absent Present

1.0

0.9

0.8

0.7

0.6

0.5

0.4

0.3

0.2

0.1

0

Absent Present

PREDICTED PROBABILITY OF OCCURRENCE (P)

MAXIMUM DAILY-MAXIMUM TEMPERATURE (MDMT), IN DEGREES CELSIUS

PREDICTED PROBABILITY OF OCCURRENCE (P)

JUVENILE BULL TROUT, SHORTER THAN 150 MILLIMETERS

USFS regional data

Mann-Whitney U test, p<0.001

USGS, Salmon River Basin data

Mann-Whitney U test, p<0.001

USFS—Regional data

USGS—Salmon River Basin

[11.91 + (-0.71)(MDMT)] e

[11.91 + (-0.71)(MDMT)] 1 + e P =

[4.81 + (-0.29)(MDMT)] e

[4.81 + (-0.29)(MDMT)] 1 + e P =

290

21

353

12

Figure 6. Model-predicted probabilities of occurrence of juvenile bull trout in relation to maximum daily-maximum stream temperature, based on regional and Salmon River Basin datasets. [Boxplots show predicted probabilities of occurrence for both models;

regional data from U.S. Forest Service (Dunham and others, 2001); Salmon River Basin data from U.S. Geological Survey (this study);

USFS, U.S. Forest Service; USGS, U.S. Geological Survey]
Summary 33

ecoregions, which consist primarily of coniferous forests. Land use in the basin comprises 67 percent forest, 

30 percent rangeland, and 3 percent agricultural land. 

Large areas of the basin are designated as wilderness, 

and parts of the Salmon River and its tributaries are 

designated as wild and scenic rivers. 

Sampling sites were selected to represent leastdisturbed conditions with an emphasis on sites minimally affected by historical logging or mining activities within their watersheds. Several environmental 

variables, including basin and reach characteristics, 

physical habitat characteristics, and water physicochemistry, were examined and relations with benthic 

invertebrate and fish assemblages were evaluated.

Nine different stream temperature metrics were 

calculated for the 33 sites where stream temperature 

data were available. Stream temperature metrics indicated that water temperature varied substantially 

among sites within the basin and that the range of 

observed temperatures varied over a broad gradient. A 

comparison of stream temperature metrics with current 

stream temperature criteria showed that temperatures at 

all 33 sites where data were available exceeded the 

U.S. Environmental Protection Agency 10.0°C maximum weekly-maximum temperature criterion for bull 

trout spawning and juvenile rearing. Temperatures 

exceeded the Idaho Department of Environmental 

Quality 13.0°C maximum daily-maximum temperature 

criterion for the protection of salmonid spawning at 30 

sites and exceeded the 9.0°C maximum daily-average 

temperature criterion for the protection of salmonid 

spawning at all 33 sites. Thermal regimes at most sites 

did not exceed the Idaho Department of Environmental 

Quality criteria for the protection of coldwater biota.

Nine environmental variables—water-surface 

gradient, discharge, wetted channel width, width:depth 

ratio, aspect, total seasonal thermal input, open canopy, 

riparian canopy density, and elevation were selected 

for correlation with the nine stream temperature metrics. Results of this analysis indicated that seasonal 

degree-days for July through August exhibited the 

strongest inverse correlation with elevation.

Two hundred and one benthic invertebrate taxa 

from the 34 sampling sites were identified. The most 

abundant taxa were Baetis tricaudatus, Oligochaeta, 

Tvetenia bavarica gr., Acari, Rhithrogena, Cinygmula, 

Heterlimnius, Micropsectra, Eukiefferiella devonica

gr., Drunella doddsi, and Cricotopus. Thirty-two coldwater taxa, representing 16 percent of the total number 

of invertebrate taxa collected, were collected during 

this study. Coldwater taxa were collected at all sites 

where temperatures exceeded the Idaho Department of 

Environmental Quality criteria for the protection of 

coldwater biota. Stream Macroinvertebrate Index 

scores ranged from 69 to 100 and, in general, describe 

expected conditions for least-disturbed sites. Of the 

201 benthic invertebrate taxa collected during this 

study, 57 taxa were significantly correlated with one or 

more of the stream temperature metrics. Of the 32 

coldwater taxa collected, only 20 taxa showed a significant inverse correlation with one or more of the stream 

temperature metrics. In contrast to coldwater taxa, 26 

invertebrate taxa showed a significant positive correlation with one or more of the stream temperature metrics.

A total of 4,199 fish were collected from the 33 

sites sampled during this study. Ten species of fish in 

the families Salmonidae, Cottidae, and Cyprinidae 

were collected. Bull trout and chinook salmon, two 

species listed as threatened under the U.S. Fish and 

Wildlife Service Endangered Species Act, were collected. In addition to fish, tailed frogs and salamanders 

also were collected. Stream Fish Index scores ranged 

from 74 to 100 and, in general, describe expected conditions for least-disturbed sites. 

Correlation between relative fish abundance and 

the stream temperature metrics indicated that bull trout 

showed the strongest inverse correlation with stream 

temperature and were collected at sites where the maximum weekly-maximum temperature (based on date of 

sample and 6 days prior) ranged from 11.3° to 20.0°C. 

Correlations between the Stream Fish Index metrics, 

selected fish densities, and the stream temperature metrics indicated that percent coldwater individuals 

showed the strongest inverse correlation with stream 

temperature metrics. Results of the fish density and 

stream temperature metric comparison were similar to 

the comparisons of relative fish abundance and stream 

temperature metrics. Bull trout and juvenile bull trout 

density showed strong inverse correlations with stream 

temperature. 

A univariate logistic regression model developed 

during this study predicts the probability of occurrence 

of juvenile bull trout on the basis of the maximum 

daily-maximum temperature. Compared with a 

regional model, the regression model for the Salmon 

River Basin predicted higher probabilities of occurrence of bull trout at colder stream temperatures (10° to 

15°C) and lower probabilities of occurrence at warmer 

stream temperatures (16° to 21°C). The model devel-
34 Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001

oped in this study appeared to be more effective at predicting the probability of bull trout for Salmon River 

Basin streams than did the regional model. The model 

comparison suggests that regional or local differences 

need to be considered when deriving stream temperature criteria. 

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SUPPLEMENTAL INFORMATION
tics for selected sample sites in the Salmon River Basin, central Idaho, 2001

; site names and characteristics shown in table 1; No., number; m, meter; m/s, meters per second; mm, millimeters; m3/s, cubic meters per second; CV, coefficient of vari

mal units per square meter per day; no data available for site 17]

e

a

ent)

Run

area 

(percent)

Pool

area

(percent)

Watersurface 

gradient

(percent)

Wetted 

channel 

width1

(m)

Bankfull

width1

(m)

Open 

canopy1

percent)

Riparian 

canopy

(percent)

Stream 

aspect1

Stream

depth1

(m)

Thalweg

depth1

(m)

Bankfull

thalweg

depth1

9 29 32 1.0 7.3 9.3 27 71 92 0.28 0.35 0.677 28 15 3.8 4.3 4.9 3 93 220 .25 .31 .717 60 13 1.0 4.3 4.9 21 59 360 .19 .30 .55

6 59 7 1.0 5.6 6.9 86 6 148 .20 .28 .720 27 13 2.1 7.4 10.6 32 39 120 .27 .36 1.009 31 0 3.5 11.5 13.4 32 43 360 .39 .51 .943 27 0 2.7 7.8 8.5 27 57 159 .28 .39 .685 6 9 1.8 4.5 6.2 16 80 275 .21 .24 .777 13 10 3.5 3.7 5.4 26 78 253 .15 .17 .65

0 57 23 1.0 4.1 6.0 36 45 360 .27 .35 .555 13 2 2.2 5.4 7.0 16 87 275 .25 .31 .707 10 13 3.4 6.8 8.3 14 88 140 .27 .34 .750 40 0 1.0 10.0 11.0 61 25 360 .23 .36 .792 38 0 1.8 12.0 14.1 34 33 117 .27 .32 .817 20 3 2.4 7.9 8.7 20 61 360 .25 .36 .614 37 9 1.9 12.1 15.9 43 11 127 .30 .4 .89

0 0 0 1.0 23.2 26.7 48 12 276 .42 .50 1.120 0 0 1.8 15.1 21.7 52 237 316 0.60 0.69 1.37

5 3 22 3.5 8.0 9.7 14 90 262 .30 .41 .82

Table A. 
6 3 31 14.0 7.5 9.2 26 84 98 0.35 0.50 1.43 4 0 26 21.5 6.2 10.7 13 90 268 .23 .33 1.19 0 57 23 1.7 8.8 11.3 18 63 195 .29 .41 .97 2 0 8 3.1 6.5 7.9 31 60 30 .28 .37 .68 8 19 23 5.7 5.8 6.3 16 92 296 .23 .35 .65 2 29 9 5.9 8.7 10.9 24 69 51 .27 .38 .92 8 2 70 4.5 7.3 10.2 38 37 234 .34 .40 1.14 0 37 3 4.5 7.8 9.1 24 77 238 .24 .32 .77 2 18 0 6.3 6.3 7.6 25 58 314 .29 .37 .90

7 38 6 1.7 6.5 7.5 46 28 226 .22 .30 .640 0 20 4.5 11.8 16.8 22 89 233 .35 .54 1.520 0 20 5.9 14.6 16.8 24 69 235 .29 .45 1.093 14 53 4.5 2.5 8.9 0 100 360 .20 .25 1.01

e

a

ent)

Run

area 

(percent)

Pool

area

(percent)

Watersurface 

gradient

(percent)

Wetted 

channel 

width1

(m)

Bankfull

width1

(m)

Open 

canopy1

percent)

Riparian 

canopy

(percent)

Stream 

aspect1

Stream

depth1

(m)

Thalweg

depth1

(m)

Bankfull

thalweg

depth1

tics for selected sites in the Salmon River Basin, 2001—Continued
m

te

Percent 

substrate 

embeddedness1

Percent 

instream 

habitat

cover

Percent 

large 

woody

debris

Discharge

(m3/s)

Wetted

width/depth

ratio

Width

CV

(percent)

Stream

depth

CV

(percent)

Velocity

CV

(percent)

Bank

stability

index

Flow

stability

index

Total

seasonal

thermal

input

(BTUs/m2/d)

80 18.8 9.4 0.18 26 72 68 81 10 0.52 31,501

0 17.8 1.7 .32 17 27 39 71 8 .44 8,077

37 6.1 0.6 .29 23 27 75 46 10 .55 19,760

26 6.5 .2 .23 29 22 53 58 10 .39 95,62719 8.9 1.6 .64 27 20 52 69 8 .36 42,44819 20.0 5.0 2.25 29 28 30 43 8 .54 57,97938 8.9 3.3 1.25 28 21 38 51 11 .57 22,506

0 10.0 4.4 .40 22 16 24 43 8 .31 17,564

18 8.8 2.7 .15 25 16 28 63 7 .26 19,70286 12.0 5.0 .13 15 36 67 78 10 .64 35,63215 6.1 3.3 .60 22 24 32 51 10 .44 8,83618 20.0 5.0 .48 25 10 35 72 9 .45 17,08427 7.7 0 1.03 43 17 57 45 10 .46 78,38438 6.0 1.6 .78 44 29 34 43 7 .40 67,79828 20.0 4.0 1.07 32 12 42 47 10 .59 44,00819 5.6 1.1 1.11 40 21 42 55 9 .45 79,59219 6.7 0 3.76 55 8 27 26 10 .45 85,718

0 17.0 0 3.68 25 16 29 41 10 .50 76,403

tics for selected sites in the Salmon River Basin, 2001—Continued
n at six transects. 

 measurements taken at 18 transects. 

16 13.3 1.7 1.16 27 22 41 53 8 0.50 30,297 

7 12.0 2.2 .91 22 45 48 92 12 .35 39,645 4 19.4 3.3 .24 27 52 50 97 10 .28 10,088 

79 18.9 6.1 .55 30 26 61 50 10 .42 17,058 11 13.8 2.7 .70 23 30 43 75 8 .54 40,498 22 12.7 2.7 .20 25 29 48 73 8 .54 8,739 32 12.0 1.7 .77 32 16 37 62 8 .41 33,989 17 18.9 4.4 .90 21 22 26 38 9 .35 60,065 14 16.1 1.7 .74 32 13 42 54 8 .42 40,234 22 17.0 1.6 .68 22 20 37 62 9 .41 59,389 

47 17.4 1.7 .36 29 24 39 47 10 .47 64,131 

0 12.7 0 2.39 34 26 51 61 10 .36 26,835 0 18.3 0 1.03 50 16 56 55 10 .41 47,872 0 8.3 1.1 .04 12 38 104 67 10 .25 29,453 

m 

te 

Percent substrate embeddedness1 Percent instream habitat cover Percent large woody debris Discharge (m3/s) Wetted width/depth ratio Width CV (percent) Stream depth CV (percent) Velocity CV (percent) Bank stability index Flow stability index Total seasonal thermal input (BTUs/m2/d) 

tics for selected sites in the Salmon River Basin, 2001—Continued
Table B 43

Table B. Microhabitat characteristics for all sample sites in the Salmon River Basin, central Idaho, 2001

[Values represent average of measurements taken at riffle collection sites within each reach; site locations shown in figure 1; site 

names and characteristics shown in table 1; No., number; m, meters; m/s, meters per second; <, less than; mm, millimeters; —, data 

unavailable]

Site 

No.

Stream

depth

(m)

Stream

velocity

(m/s)

Percent

substrate

fines

(<2mm)

Bottom

substrate

size

(mm)

Substrate

embeddedness

(percent)

Wolman

bottom

substrate

size

(mm)

Wolman

fines,

<6mm

(percent)

Open

canopy

(percent)

1 0.13 0.65 18 64 23 31 33 13

2 .19 .67 0 96 15 31 13 26

3 .10 .59 5 48 23 48 23 24

4 .22 .44 5 64 7 64 11 80

5 .19 .47 0 96 15 96 11 23

6 .17 .57 5 96 15 96 12 27

7 .12 .71 3 64 38 96 20 34

8 .15 .52 0 96 12 96 13 25

9 .28 .35 3 96 15 96 15 29

10 .09 .79 20 23 100 23 42 37

11 .23 .61 0 128 8 96 16 19

12 .17 .76 3 256 8 384 22 18

13 .17 .48 0 64 38 96 18 68

14 .20 .38 7 192 15 192 31 30

15 .15 .45 13 96 23 48 20 20

16 .25 .49 7 96 38 96 14 44

17 .30 .65 10 64 46 192 13 43

18 .20 .61 3 64 15 — — 25

19 .31 .41 3 256 15 — — 49

20 .20 .48 3 64 23 192 17 18

21 .22 .53 3 192 8 192 2 23

22 .18 .39 3 96 15 1,536 8 6

23 .13 .59 3 64 23 48 32 12

24 .25 .51 13 96 23 96 22 24

25 .14 .29 10 192 23 192 28 10

26 .11 .32 0 192 30 192 19 19

27 .23 .49 0 96 15 96 9 50

28 .19 .62 0 192 15 192 5 25

29 .13 .52 0 192 46 192 11 46

30 .12 .45 5 75 28 64 24 46

31 .25 .59 0 768 15 384 9 28

32 .22 .13 0 768 23 384 4 16

33 .19 .19 0 192 5 — — 31

34 .14 .23 0 192 38 96 3 0

Table B. 
utrient data for all sample sites in the Salmon River Basin, central Idaho, 2001

1; site names and characteristics shown in table 1; No., number; sample date, month/day/year; sample time, 24-hour; °C, degrees Celsius; 

μS/cm, microsiemens per centimeter; N, nitrogen; P, phosphorus; —, data unavailable; <, less than; E, estimated value reported by laboratory]

le 

e

Water 

temperature 

°C

Dissolved 

oxygen 

(mg/L)

Dissolved 

oxygen 

saturation 

(percent)

pH 

(standard 

units)

Specific 

conductance

(μS/cm)

Nitrogen, 

ammonia, 

dissolved 

(mg/L as N)

Nitrogen, 

ammonia + 

organic, 

total

(mg/L as N)

Nitrite + 

nitrate, 

dissolved 

(mg/L as N)

Phosphorus 

total

(mg/L as P)

Orthophosphorus, 

dissolved

(mg/L as P)

0 8.0 8.7 97 7.8 55 <0.002 <0.080 0.011 <0.0040 <0.007

0 12.2 7.9 — 8.1 162 .014 E.054 .010 .0096 E.0040 6.8 9.5 100 8.1 37 .002 E.049 .013 E.0025 <.0070 18.3 7.6 102 8.4 95 <.002 E.052 .009 E.0032 <.0070 9.0 9.1 99 7.9 97 <.002 E.058 .008 .0046 <.0070 9.5 9.6 105 8.4 148 <.002 E.068 .016 .0041 <.0070 6.5 9.7 100 8.2 155 <.002 E.054 .006 .0278 <.0070 8.6 9.5 — 7.6 77 .006 E.077 .029 .0329 .0230 7.9 8.9 — 6.9 33 .006 E.064 .049 .0192 .0120 5.9 9.1 96 8.0 60 .005 E.076 .037 .0175 .0090 10.9 8.7 92 7.9 64 <.002 E.051 .015 .0160 .0070 14.3 8.8 98 8.0 81 .004 E.067 .007 .0098 <.0070 8.5 9.2 101 8.2 67 <.002 E.042 .006 .0039 <.0070 12.8 8.3 — 8.0 82 <.002 <.080 <.005 .0040 <.0070 6.4 9.7 99 8.2 108 <.002 E.059 .007 E.0028 <.0070 17.9 8.0 — 7.8 118 .002 .376 .009 .1506 .0140 15.8 7.3 — 8.0 98 .018 .647 .087 .2470 E.0050 13.8 8.6 — 8.1 126 .003 .128 .009 .0133 <.0070 13.5 8.7 — 8.0 129 .005 .453 .010 .1844 <.007
5 12.3 9.2 — 7.7 84 0.006 0.084 0.024 0.0048 <0.0070 12.0 9.8 — 7.8 78 .005 .087 .020 .0104 <.0070 10.1 10.0 — 7.0 50 <.002 .080 .113 .0110 <.0070 13.8 8.7 102 7.9 32 <.002 .098 .005 .0179 .0110 11.9 9.0 — 7.4 45 <.002 <.080 .009 .0061 <.0070 13.1 8.7 98 8.0 47 .002 E.044 .032 .0244 .0140 10.7 9.7 103 7.8 43 <.002 E.069 .005 .0045 <.0070 10.7 8.5 94 8.3 111 <.002 .130 .006 E.0029 <.0070 9.2 9.3 99 8.4 113 .005 <.080 .007 <.0040 <.0070 9.6 9.3 99 8.1 73 <.002 E.075 .006 .0047 <.0070 8.5 9.0 97 7.5 27 .009 .097 .006 .0093 E.0040 17.0 8.8 — 7.7 82 .007 .108 .011 .0069 <.0070 16.5 8.6 — 7.6 50 .009 .089 .014 .0099 E.0050 15.8 9.0 — 7.7 72 .003 .162 .030 .0609 .0440 17.3 8.6 — 7.9 118 .010 .195 .225 .0854 .073

le 

e

Water 

temperature 

°C

Dissolved 

oxygen 

(mg/L)

Dissolved 

oxygen 

saturation 

(percent)

pH 

(standard 

units)

Specific 

conductance

(μS/cm)

Nitrogen, 

ammonia, 

dissolved 

(mg/L as N)

Nitrogen, 

ammonia + 

organic, 

total

(mg/L as N)

Nitrite + 

nitrate, 

dissolved 

(mg/L as N)

Phosphorus 

total

(mg/L as P)

Orthophosphorus, 

dissolved

(mg/L as P)

utrient data for all sites in the Salmon River Basin, central Idaho, 2001—Continued
Ott and Maret—Aquatic Assemblages and Relation to Temperature Variables, Least-Disturbed Streams, Salmon River Basin, Idaho, 2001—U.S. Geological Survey Water-Resources Investigations Report 03 –4076

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