Prepared in cooperation with the Bureau of Reclamation

Instream Flow Characterization of Upper Salmon River Basin 

Streams, Central Idaho, 2003

U.S. Department of the Interior

U.S. Geological Survey

Scientific Investigations Report 2004 – 5173

Version 1.2

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Page 115, Valley Creek section - Temperature in degrees Fahrenheit information 

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Instream Flow Characterization of Upper 

Salmon River Basin Streams, Central Idaho, 

2003

By Terry R. Maret, Jon E. Hortness, and Douglas S. Ott

Prepared in cooperation with the Bureau of Reclamation

Scientific Investigations Report 2004–5173

U.S. Department of the Interior

U.S. Geological Survey

Version 1.2
Instream Flow Characterization of Upper 

Salmon River Basin Streams, Central Idaho, 

2003

By Terry R. Maret, Jon E. Hortness, and Douglas S. Ott

Prepared in cooperation with the Bureau of Reclamation

Scientific Investigations Report 2004–5173

U.S. Department of the Interior

U.S. Geological Survey

Version 1.2
iv Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2004

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

World Wide Web: http://www.usgs.gov/

Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Maret, T.R., Hortness, J.E., and Ott, D.S., 2004, Instream Flow Characterization of Upper Salmon River Basin Streams, 

Central Idaho, 2003: Reston, VA., U.S. Geological Survey Scientific Investigations Report 2004–5173, 158 p.

URLs in the printed version of this report are not complete. Refer to the

Web version of this report at http://id.water.usgs.gov/public/reports.html

for complete URLs (which are indicated in blue).
Contents v

Contents

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

Introduction ............. ............................................................................................................................... 1

Purpose and Scope ....................................................................................................................... 3

Previous Studies ............................................................................................................................ 3

Description of Study Area ............................................................................................................ 5

Acknowledgments ......................................................................................................................... 6

Data Collection Methods ....................................................................................................................... 6

Site Selection................................................................................................................................. 6

Environmental Variables ............................................................................................................... 7

Physical Habitat .................................................................................................................... 7

Stream Temperature ............................................................................................................. 8

Analytical Methods for Instream Flow Characterization ................................................................. 8

Physical Habitat Simulation Model ............................................................................................. 8

Hydraulic Modeling and Calibration .................................................................................. 8

Habitat Modeling .................................................................................................................. 9

Selection of Target Species and Suitability Criteria .............................................. 9

Passage Criteria ........................................................................................................... 9

Stream Temperature ...................................................................................................................... 10

Guidelines for Using Study Results ............................................................................................. 10

Climatic and Hydrologic Conditions During 2003 ............................................................................... 11

Climatic Conditions ........................................................................................................................ 12

Hydrologic Conditions ................................................................................................................... 12

Results of Study Site Investigations During 2003 .............................................................................. 14

Pole Creek Section ........................................................................................................................ 21

Pole Creek ....... ............................................................................................................................... 22

Hydrology During 2003 ......................................................................................................... 22

Habitat Modeling and Passage Results ............................................................................ 24

Stream Temperature Results .............................................................................................. 25

Pole Creek Appendix Abbreviations .................................................................................. 26

Fourth of July Creek Section ........................................................................................................ 40

Fourth of July Creek ...................................................................................................................... 41

Hydrology During 2003 ......................................................................................................... 41

Habitat Modeling and Passage Results ............................................................................ 42

Stream Temperature Results .............................................................................................. 44

Fourth of July Creek Appendix Abbreviations ................................................................. 46

Elk Creek Section ........................................................................................................................... 90

Elk Creek ......... ............................................................................................................................... 91

Hydrology During 2003 ......................................................................................................... 91

Habitat Modeling and Passage Results ............................................................................ 93

Stream Temperature Results .............................................................................................. 94

Elk Creek Appendix Abbreviations ..................................................................................... 95

Valley Creek Section ..................................................................................................................... 110

Valley Creek .... ............................................................................................................................... 111

Hydrology During 2003 ......................................................................................................... 111

Habitat Modeling and Passage Results ............................................................................ 113

Stream Temperature Results .............................................................................................. 114

Valley Creek Appendix Abbreviations ............................................................................... 116

Summary .................. ............................................................................................................................... 14

References Cited .... ............................................................................................................................... 17
vi Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

Figures

1. Location of upper Salmon River Basin, Idaho ..................................................................... 4

2. Hierarchical mesohabitat classification .............................................................................. 7

3. Mean daily air temperature for period June through September 2003 in relation 

to long-term (1971 through 2000) mean daily temperature measured at Stanley 

Ranger Station, upper Salmon River Basin, Idaho ............................................................. 12

4. Pole Creek study site, diversion, and gaging station location, upper Salmon River 

Basin, Idaho, 2003 .................................................................................................................... 21

5. Daily mean discharge at upper Pole Creek below Pole Creek Ranger Station

near Obsidian (13292380), upper Salmon River Basin, Idaho, June 1 through

September 30, 2003 ................................................................................................................. 22

6. Daily mean discharge for water year 2003, estimated long-term daily mean 

discharge, and estimated 80-, 50-, and 20-percent exceedance statistics for 

upper Pole Creek below Pole Creek Ranger Station near Obsidian (13292380), 

upper Salmon River Basin, Idaho, July 1 through September 30 .................................... 23

7. Maximum daily water temperature for period June 25 through September 28, 2003,

at Pole Creek, upper Salmon River Basin, Idaho ............................................................... 26

8. Fourth of July Creek study sites, diversions, and gaging station locations, upper 

Salmon River Basin, Idaho, 2003 ........................................................................................... 40

9. Daily mean discharge at Fourth of July Creek upstream from diversions near 

Obsidian (13293350), upper Salmon River Basin, Idaho, June 1 through 

September 30, 2003 ................................................................................................................. 41

10. Daily mean discharge for water year 2003, estimated long-term daily mean 

discharge, and estimated 80-, 50-, and 20-percent exceedance statistics for 

Fourth of July Creek upstream from diversions near Obsidian (13293350), upper 

Salmon River Basin, Idaho, July 1 through September 30 ................................................ 42

11. Maximum daily water temperature for period June 25 through September 28,

2003, at Fourth of July Creek, upper Salmon River Basin, Idaho ..................................... 45

12. Elk Creek and Valley Creek study sites, diversions, and gaging station locations, 

upper Salmon River Basin, Idaho, 2003...................................................................90 and 110

13. Daily mean discharge at lower Elk Creek upstream from diversions near Stanley 

(13294640), upper Salmon River Basin, Idaho, June 1 through September 30, 2003 .... 91

14. Daily mean discharge for water year 2003, estimated long-term daily mean 

discharge, and estimated 80-, 50-, and 20-percent exceedance statistics for Elk 

Creek upstream from diversions near Stanley (13294640), upper Salmon River 

Basin, Idaho, July 1 through September 30 ........................................................................ 92

15. Maximum daily water temperature for period June 19 through September 29, 2003, 

at Elk Creek, upper Salmon River Basin, Idaho .................................................................. 94

16. Daily mean discharge at Valley Creek upstream from diversions near Stanley 

(13294600), upper Salmon River Basin, Idaho, May 1 through September 30, 2003 ..... 111

17. Daily mean discharge for water year 2003, estimated long-term daily mean 

discharge, and estimated 80-, 50-, and 20-percent exceedance statistics for 

Valley Creek upstream from diversions near Stanley (13294600), upper Salmon 

River Basin, Idaho, July 1 through September 30 .............................................................. 112

 18. Maximum daily water temperature for period June 19 through September 29, 

2003, at Valley Creek, upper Salmon River Basin, Idaho (site VC1 period 

July 15 through September 29, 2003) .................................................................................... 115
Contents vii

Tables

1. Basin and site characteristics for gaging stations, diversions, and study sites in 

the upper Salmon River Basin, Idaho, 2003 ......................................................................... 13

2. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance 

discharge values for Pole Creek below Pole Creek Ranger Station near Obsidian 

(13292380), upper Salmon River Basin, Idaho, 2003 ........................................................... 23

3. Miscellaneous discharge measurements collected on Pole Creek, upper Salmon 

River Basin, Idaho, 2003 ......................................................................................................... 24

4. Habitat and discharge measurements for upper Pole Creek (PC2), upper Salmon 

River Basin, Idaho, 2003 ......................................................................................................... 25

5. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance 

discharge values for Fourth of July Creek upstream from diversions near 

Obsidian (13293350), upper Salmon River Basin, Idaho, 2003 .......................................... 43

6. Miscellaneous discharge measurements collected on Fourth of July Creek, 

upper Salmon River Basin, Idaho, 2002 – 03 ........................................................................ 43

7. Habitat and discharge measurements for upper (JC3), middle (JC2), and lower 

(JC1) Fourth of July Creek, upper Salmon River Basin, Idaho, 2003 ............................... 44

8. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance 

discharge values for Elk Creek upstream from diversions near Stanley (13294640), 

upper Salmon River Basin, Idaho, 2003 ............................................................................... 92

9. Miscellaneous discharge measurements collected on Elk Creek, upper Salmon 

River Basin, Idaho, 2003 ......................................................................................................... 93

10. Habitat and discharge measurements for lower Elk Creek (EC1), upper Salmon 

River Basin, Idaho, 2003 ......................................................................................................... 93

11. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance discharge 

values for Valley Creek upstream from diversions near Stanley (13294600), upper 

Salmon River Basin, Idaho, 2003 ........................................................................................... 112

12. Miscellaneous discharge measurements collected on Valley Creek, upper 

Salmon River Basin, Idaho, 2003 ........................................................................................... 113

13. Habitat and discharge measurements for upper (VC3), middle (VC2), and lower 

(VC1) Valley Creek, upper Salmon River Basin, Idaho, 2003 ............................................. 114
viii Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F = 1.8 °C + 32

Sea level: In this report, “sea level” refers to the National Geodetic Vertical Datum 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.

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD83)

Water Year: In U.S. Geological Survey reports dealing with surface-water supply, a water year 

is the 12-month period, October 1 through September 30. The water year is designated by the 

calendar year in which it ends; thus, the year ending September 30, 2003, is called the “2003 

water year.”

Conversion Factors and Datum

 Multiply By To obtain

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

foot (ft) 0.3048 meter (m)

foot per second (ft/s) 0.3048 meter per second (m/s)

inch (in.) 25.4 millimeter (mm)

mile (mi) 1.609 kilometer (km)

square mile (mi2) 2.590 square kilometer (km2)
Contents ix

Abbreviations

ASTM American Society of Testing and Materials

AVDEPTH/AVPERM Hydraulic parameter option in PHABSIM for Windows

BIA Bureau of Indian Affairs

CI Composite index

ESA Endangered Species Act

HABTAE Habitat program option in PHABSIM for Windows

IDEQ Idaho Department of Environmental Quality

IDFG Idaho Department of Fish and Game

IFIM Instream Flow Incremental Methodology

MAD Mean annual discharge

MANSQ Manning’s equation

MDAT Maximum daily-average temperature

MDMT Maximum daily-maximum temperature

MWMT Maximum weekly-maximum temperature

MWAT Maximum weekly-average temperature

NOAA National Oceanic and Atmospheric Administration

PHABSIM Physical Habitat Simulation Model

Q.20 Daily mean discharge exceeded 20 percent of the time during a 

specified month 

Q.50 Daily mean discharge exceeded 50 percent of the time during a

specified month (same as median discharge)

Q.80 Daily mean discharge exceeded 80 percent of the time during a

specified month

SI Suitability index

SNRA Sawtooth National Recreation Area

SRA Snake River Adjudication

SSTEMP Stream Segment Temperature Model

STGQ Stage-discharge relation

USEPA U.S. Environmental Protection Agency

USFS U.S. Forest Service

USFWS U.S. Fish and Wildlife Service

USGS U.S. Geological Survey

WSP Water surface profile

WUA Weighted usable area

WY03 Water year 2003
Abstract

Anadromous fish populations in the Columbia River Basin have plummeted in the last 100 years. 

This severe decline led to Federal listing of chinook 

salmon (Oncorhynchus tshawytscha) and steelhead trout 

(Oncorhynchus mykiss) stocks as endangered or threatened 

under the Endangered Species Act (ESA) in the 1990s. 

Historically, the upper Salmon River Basin (upstream from 

the confluence with the Pahsimeroi River) in Idaho provided 

migration corridors and significant habitat for these ESA-listed 

species, in addition to the federally listed bull trout (Salvelinus 

confluentus). Human development has modified the original 

streamflow conditions in many streams in the upper Salmon 

River Basin. Summer streamflow modifications, as a result 

of irrigation practices, have directly affected the quantity and 

quality of fish habitat and also have affected migration and 

(or) access to suitable spawning and rearing habitat for these 

fish.

As a result of these ESA listings and Action 149 of the 

Federal Columbia River Power System Biological Opinion 

of 2000, the Bureau of Reclamation was tasked to conduct 

streamflow characterization studies in the upper Salmon River 

Basin to clearly define habitat requirements for effective 

species management and habitat restoration. These studies 

include the collection of habitat and streamflow information 

for the Physical Habitat Simulation (PHABSIM) model, a 

widely applied method to determine relations between habitat 

and discharge requirements for various fish species and life 

stages. Model results can be used by resource managers to 

guide habitat restoration efforts in the evaluation of potential fish habitat and passage improvements by increasing 

streamflow.

Instream flow characterization studies were completed 

on Pole, Fourth of July, Elk, and Valley Creeks during 2003. 

Continuous streamflow data were collected upstream from 

all diversions on each stream. In addition, natural summer 

streamflows were estimated for each study site using regression equations.

PHABSIM results are presented for bull trout, chinook salmon, and steelhead trout over a range of summer 

streamflows. Habitat/discharge relations are summarized 

for juvenile, adult, and spawning life stages at each study 

site. Adult fish passage and discharge relations are evaluated 

at specific transects identified as a potential low-streamflow 

passage barrier at each study site. Continuous summer water 

temperature data for selected study sites also are summarized 

and compared with Idaho Water Quality Standards and various 

temperature requirements of targeted fish species.

Results of these habitat studies can be used to prioritize 

and direct cost-effective actions to improve fish habitat for 

ESA-listed anadromous and native fish species in the basin. 

These actions may include acquiring water during critical 

low-flow periods by leasing or modifying irrigation delivery 

systems to minimize out-of-stream diversions.

Introduction

Rivers, streams, and lakes in the upper Salmon River 

Basin (defined as the area upstream from the confluence 

with the Pahsimeroi River) historically provided migration 

corridors and significant spawning and rearing habitat for 

anadromous Snake River spring/summer chinook salmon 

(Oncorhynchus tshawytscha), sockeye salmon (Oncorhynchus 

nerka), and steelhead trout (Oncorhynchus mykiss). Wild 

salmon and steelhead in the basin migrate nearly 900 mi 

between the mountain streams at elevations of 7,000 ft or 

more where they spawn, hatch, and rear, and the Pacific Ocean 

where they mature to adulthood. High-elevation spawning 

and rearing and extensive migration represent a life-history 

strategy unique among Columbia River chinook salmon and 

steelhead and may be very important for the long-term survival of these species.

However, anadromous fish populations in the Columbia 

River Basin have plummeted in the last 100 years (Chapman, 

1986; Thurow, 2000; Thurow and others, 2000). This severe 

decline led to Federal listing of these salmon and steelhead 

stocks as endangered or threatened under the Endangered 

Species Act (ESA) in the 1990s. Most remaining populations 

are severely depressed; fewer than 2 percent of the watersheds 

in the Columbia River Basin are classified as supporting 

strong, wild populations of steelhead trout or chinook salmon 

(Thurow and others, 2000). In addition, at least 214 stocks of 

Instream Flow Characterization of Upper Salmon River 

Basin Streams, Central Idaho, 2003

By Terry R. Maret, Jon E. Hortness, and Douglas S. Ott
2 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

anadromous salmonids are on the decline or at risk of extinction in the Pacific Northwest and California (Nehlsen and 

others, 1991).

Wild salmon and steelhead continue to migrate into the 

upper Salmon River Basin and depend on available spawning and rearing habitat. Resident bull trout (Salvelinus 

confluentus) also inhabit many of the rivers and streams. 

However, human development has modified the original 

streamflow conditions in many streams in the basin. Summer streamflow modifications (July through September) have 

directly affected the quantity and quality of fish habitat and 

also have affected migration and (or) access to suitable spawning and rearing habitat for these fish (Munther, 1974; Scott 

and others, 1981).

Reduced streamflows resulting from diversions also may 

contribute to increased water temperatures that may be unsuitable for native salmonids in the Sawtooth National Recreation Area (SNRA; M. Moulton, U.S. Forest Service, oral 

commun., 2003). Stream temperatures vary both spatially, 

throughout a stream, and temporally, over time. Many factors, 

both natural and human, can affect stream temperature. Water 

temperatures are controlled naturally by interactions between 

solar radiation, ambient air temperature, streamflow, channel 

geomorphology, and riparian vegetation. There is a natural 

tendency for stream temperature to increase as water travels 

downstream. Human activities such as the removal of riparian 

shading and the alteration of streamflow can accentuate this 

increase in water temperature.

In general, high water temperatures coincide with high 

ambient air temperatures and usually occur during the months 

of July and August. It also is at this time that diversions of 

streamflow for agricultural purposes are at their highest and 

streamflows are generally at their lowest. This reduction in 

streamflow, coupled with high ambient air temperatures, can 

have severe negative effects on the distribution, health, and 

survival of coldwater fish species.

Most Pacific Northwest fish are ectothermic (coldblooded), and their survival depends on water temperatures 

that are within their optimal range. When water temperature exceeds an organism’s optimal range, the organism can 

experience adverse health effects such as reduced growth or 

increased susceptibility to disease (Countant, 1976; Beitinger 

and others, 2000; McCullough and others, 2001; Sauter and 

others, 2001; Selong and others, 2001). Different species have 

unique temperature requirements, and an individual species 

may have a unique temperature requirement for each of its life 

stages. For example, salmonids require varying temperatures 

to initiate and carry out spawning, incubation, juvenile growth, 

and adult migration activities (Poole and others, 2001). For 

chinook salmon, optimal water temperatures range between 

10.0 o and 17.0 oC. Adult spawning activities are triggered at 

water temperatures between 7.0 o and 14.0 oC. Water temperatures above 21.0 oC can create thermal barriers that can block 

adult migration to spawning grounds. These thermal barriers 

can be created by diverting streamflow for irrigation during 

the summer when air temperatures are at their highest.

Exposure to water temperatures greater than 21.0 oC for 

more than 1 week is usually fatal to adult chinook salmon, 

whereas constant temperatures above 16.0 oC have been shown 

to be intolerable for bull trout (Poole and others, 2001). Ott 

and Maret (2003) predicted a higher probability of bull trout 

occurrence in streams in the Salmon River Basin where daily 

maximum temperatures are 10.0 o to 15.0 oC. Passage of bull 

trout into tributary streams to spawn in late summer may be 

decreased when temperatures exceed 13.0 oC and may be 

potentially blocked when water temperatures exceed 18.0 oC 

(J. Dunham, U.S. Forest Service, written commun., 2004).

The Bureau of Reclamation (Reclamation) was tasked 

through Reasonable and Prudent Alternative Action 149 of 

the Federal Columbia River Power System Biological Opinion of 2000 to address streamflow deficiencies in 16 priority 

subbasins in the Columbia River Basin (National Oceanic and 

Atmospheric Administration, 2000). Flow characteristic studies were undertaken to evaluate streamflow requirements of 

ESA-listed fish. Results of these studies will be used to prioritize and direct cost-effective actions to improve fish habitat for 

ESA-listed anadromous and native fish species in the basin. 

These actions may include acquiring water during critical 

low-flow periods by leasing or modifying irrigation delivery 

systems to minimize out-of-stream diversions. Reclamation 

considers flow characterization studies an integral part of the 

information needed to correct flow deficiencies within the 10-

year timeframe allotted for work in each subbasin (Spinazola, 

2002).

Many landowners; Federal, State, and Tribal governments; and other local and private parties have completed 

or are completing projects to maintain, improve, and restore 

riparian habitat, water quality, fish passage, and other environmental conditions important to protect and restore ESA-listed 

anadromous and native fish species in the basin (Spinazola, 

2002). In addition, the Idaho Department of Fish and Game 

(IDFG) has completed annual redd counts and fish population assessments on the upper Salmon River and many of its 

major tributaries (P. Murphy, Idaho Department of Fish and 

Game, oral commun., 2003). The livelihoods of many of the 

people who inhabit the basin also depend on streamflows that 

are used for agricultural, domestic, commercial, municipal, 

recreational, and other purposes. Formulating an approach to 

meet the needs of both people and fish rests on understanding how much streamflow is needed by each. The amount of 

water necessary for different human uses frequently can be 

determined from readily available information; however, the 

amount of streamflow necessary to conserve habitat for ESAlisted fish is more difficult to identify because the relevant 

information for fish is rarely available.

Numerous methods can be used to determine streamflow 

needs for fish and wildlife (Instream Flow Council, 2002), but 

one of the most widely used is the Instream Flow Incremental Methodology (IFIM), developed in the 1970s by physical 

and biological scientists in the U.S. Fish and Wildlife Service 

(USFWS). IFIM integrates concepts of water-supply planning, analytical hydraulic engineering models, and empirically 
Introduction 3

derived habitat/discharge relations to address water-use and 

instream-flow issues, questions concerning life-stage-specific 

effects on selected species, and the general well-being of 

aquatic biological populations. Accepted by many resource 

managers as an excellent process for establishing habitat/discharge relations, it is the most widely used method in the 

United States (Instream Flow Council, 2002).

A major component of IFIM is a collection of computer 

algorithms called the Physical Habitat Simulation Model 

(PHABSIM). This model incorporates hydrology, stream 

morphology, and microhabitat preferences to create relations 

between streamflow and habitat availability (Bovee and others, 

1998). Habitat availability is measured by an index called 

the weighted usable area (WUA), which is the wetted area of 

a stream weighted by its suitability for use by an organism 

(expressed as the number of square feet of usable habitat per 

1,000 feet of stream). PHABSIM simulates habitat/discharge 

relations for various species and life stages and allows quantitative habitat comparisons at different discharges of interest.

Streamflow restoration projects developed and completed 

in the headwaters of the upper Salmon River will provide 

immediate localized benefits by restoring quality, quantity, 

and access to important spawning and rearing habitats. As 

more studies are completed in order of biological priority 

and more restoration projects are implemented on the basis 

of streamflow study results, streamflows needed for migration, spawning, and rearing for all fish will be systematically 

improved. Furthermore, the restored streamflows have the 

potential for improving spawning and rearing habitat within 

downstream reaches of the main stem of the Salmon River. 

Additionally, if the streamflows obtained from these projects 

are protected from downstream diversion, these benefits are 

increased by improved conditions for survival throughout the 

Salmon River migration corridor, thereby improving long-term 

productivity of the stocks.

Purpose and Scope

This report summarizes instream flow characterization 

results for Pole, Fourth of July, Elk, and Valley Creeks in the 

upper Salmon River Basin of Idaho. Natural streamflows were 

characterized using continuous summer streamflow data collected upstream from diversions. Comparisons between these 

data and monthly discharge exceedance estimates, based on 

regional regression analyses, were reported.

Purposes of this report are to (1) compile, review, and 

analyze hydrologic and biological data for selected streams; 

(2) assemble habitat suitability curves for the targeted species 

and life stages that are needed to perform PHABSIM modeling and analysis; (3) provide instream flow characterization 

results for selected streams to identify streamflow needs during July through September for fish passage and various life 

stages of chinook salmon, steelhead trout, and bull trout; and 

(4) evaluate the effects of water diversions on water temperature for the selected streams.

Ultimately, the goal of these studies is to provide 

streamflow and fish habitat information to water-resource 

managers so informed decisions can be made to enhance 

instream habitat needs of ESA-listed fish species. A Web page 

maintained by the U.S. Geological Survey (USGS) that provides supporting data and modeling results can be accessed at

http://id.water.usgs.gov/projects/salmon_streamflow/

Previous Studies

Previous instream flow studies conducted in the upper 

Salmon River Basin consist of investigations for the Snake 

River Adjudication (SRA) process, which were funded by 

the Bureau of Indian Affairs (BIA) and U.S. Forest Service 

(USFS). The BIA funded a number of fishery studies in 

the Salmon River Basin that focused on the development 

of instream flow recommendations for the preservation of 

important fishery resources. Between 1989 and 1992, the 

BIA contracted with EA Engineering, Science, and Technology to develop instream flow recommendations for important 

fishery resources and prepared suitability criteria, conducted 

instream flow studies, made recommendations, and filed water 

right claims as part of the SRA (EA Engineering Science and 

Technology Incorporated, 1989, 1991a, b, 1992a, b, c). The 

BIA also funded the USGS to classify Salmon River subbasins 

on the basis of basin and hydrologic characteristics to assist in 

the filing of water right claims (Lipscomb, 1998).

Investigations by the USFS also were conducted by 

Hardy and others (1992) to file water right claims for protection of fishery resources on public lands. More recent (1997–

98) instream flow studies also were completed by the USFS on 

selected streams in the upper Salmon River Basin (M. Combs, 

Utah State University, oral commun., 2003). These data also 

were collected for the SRA to evaluate minimum and maintenance streamflows for the protection of important fishery 

resources; however, these data were never published.

A variety of methods have been developed to estimate 

streamflow needs for fish. Tennant (1976) offered one of the 

first methodologies for determining instream flows to protect 

aquatic resources. This simple approach recommends minimum stream discharges based on a percentage of mean annual 

discharge (MAD) that varies with the level of resource protection from poor to outstanding. Hatfield and Bruce (2000) 

developed equations for predicting optimum (maximum) 

discharge for selected salmonid life stages in western North 

America streams by using results from 127 PHABSIM studies. 

They concluded that MAD was the best predictor of optimum 

discharge. However, the 95-percent error estimates around the 

optimum predicted discharge can be substantial. The National 

Oceanic and Atmospheric Administration (NOAA) has draft 

protocols to estimate tributary streamflows to protect salmon 

listed under the ESA (D. Arthaud, National Oceanic and 

Atmospheric Administration, written commun., 2001). These 

protocols offer specific guidelines based on percentages of 

mean monthly streamflow and PHABSIM optimum estimates.
SAWTOOTH

NATIONAL

RECREATION AREA

BOUNDARY

Yankee

Fork

Valley

Creek

Elk

Fourth Creek of July

Pole

Creek

Creek

Smiley

Creek

Salmon

Salmon

East

Fork

River

River

River

Salmon

Salmon

River

Redfish

Lake

Alturas

Lake

Challis

Obsidian

Stanley

Ellis

SAWTOOTH RANGE

Sawtooth Valley

White Cloud

Peaks

Vienna

Mine

Castle

Peak

Mill Creek

Summit

Galena

Summit

Banner

Summit 13296500

13295000

44° 20'

44° 00'

44° 40' 44° 40'

44° 20'

44° 00'

114° 00'

114° 00'

114° 20'

114° 20'

114° 40'

114° 40'

115° 00'

115° 00'

0

0

4

4

8

8

12

12

16 MILES

16 KILOMETERS

Base from U.S. Geological Survey digital data; 1998; 1:40,000,

Transverse Mercator projection; Factor at central meridian: 0.99960;

Longitude of central meridian: -114° 00'; Latitude of origin: 42° 00' False easting (meters): 500,000; False northing (meters): 100,000

Hydrography from U.S. Geological Survey; 1999; 1:24,000

EXPLANATION

U.S. Geological Survey gaging

 station and identification

Salmon River below Yankee Fork

Valley Creek at Stanley

13296500

13295000

4 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003

I DAHO

Upper Salmon

River Basin

Study area

River

Pahsimeroi River

Salmon

Figure 1. Location of upper Salmon River Basin, Idaho.
Introduction 5

Hydrologic studies by the USGS have provided information on streamflow statistics and geomorphology for streams 

in the Salmon River Basin. Hortness and Berenbrock (2001) 

developed regional regression equations that may be used to 

relate monthly and annual streamflow statistics to various 

basin characteristics (for example, basin area, basin elevation, 

percentage of forest cover in the basin, mean annual precipitation, and average basin slope). These equations are useful for 

predicting streamflow statistics in ungaged basins. Emmett 

(1975) evaluated hydrology, geomorphology, and water-quality characteristics of selected streams in the Salmon River 

Basin.

Habitat suitability curves for depth, velocity, and substrate are available for most native fish species of the Salmon 

River Basin. Rubin and others (1991) empirically determined 

suitability curves for juvenile chinook salmon and steelhead 

trout for small tributary streams in the Salmon River Basin. 

Cochnauer and Elms-Cockrum (1986) developed suitability 

curves for a number of Idaho salmonid species and their life 

stages by using guidelines provided by Bovee and Cochnauer 

(1977). EA Engineering Science and Technology Incorporated (1991b) developed a complete set of habitat suitability 

curves for depth, velocity, and substrate for most of the native 

fish species in the Salmon River Basin for the BIA as part 

of the SRA. These curves were developed following guidelines presented by Crance (1985) which consisted of a Delphi 

approach. This approach involves formal meetings among 

fishery experts to reach a consensus on suitability curves for 

various species and life stages.

Until recently, a significant study of stream temperature 

in the Salmon River Basin had not been undertaken. Starting 

in 2000, the USGS, in cooperation with the Idaho Department 

of Environmental Quality (IDEQ), initiated studies to document the natural spatial and temporal variability of stream 

temperature and to examine relations among stream temperature, environmental variables, and aquatic biota in streams 

minimally disturbed by human activities in the Salmon River 

Basin. Results showed that temperatures in these minimally 

disturbed streams commonly exceeded current State and Federal stream temperature standards.

During the summer of 2000, Donato (2002) studied the 

temperature regime of 183 minimally disturbed streams in the 

Salmon and Clearwater River Basins to develop a predictive 

stream temperature model. A major finding of this study was 

that temperatures in 100 percent (119 of 119) of the streams 

in the Salmon River Basin failed to meet the IDEQ 9.0 oC 

maximum daily-average temperature (MDAT) and the 13.0 oC 

maximum daily-maximum temperature (MDMT) criteria for 

the protection of salmonid spawning. Results also showed that 

stream temperatures in 33 percent (39 of 119) of the streams 

exceeded the IDEQ 19.0 oC MDAT criterion, and temperatures 

in 39 percent (47 of 119) of the streams exceeded the 22.0 oC 

MDMT criterion for the protection of coldwater biota.

In 2001, Ott and Maret (2003) studied 34 minimally 

disturbed streams in the Salmon River Basin to document the 

temperature regime, characterize the distribution of aquatic 

biota in streams representing a gradient of temperature, and 

describe the relations between environmental variables and 

benthic invertebrate and fish assemblages. Results of this 

study showed that the maximum weekly-maximum temperature (MWMT) in 100 percent (33 of 33) of the streams for 

which temperature data were available exceeded the U.S. 

Environmental Protection Agency (USEPA) criterion of 10 oC 

for bull trout spawning and juvenile rearing. The MDMT 

in 91 percent (30 of 33) of the streams exceeded the IDEQ 

criterion of 13.0°C for the protection of salmonid spawning; 

and the MDAT in all 33 streams exceeded the 9.0°C criterion 

for the protection of salmonid spawning. Results also showed 

that stream temperatures in 9 percent (3 of 33) of the streams 

exceeded the IDEQ 19.0°C MDAT and the 22.0 °C MDMT 

criteria for the protection of coldwater biota.

Even though temperatures in all streams exceeded at least 

one temperature criterion, Ott and Maret (2003) concluded 

that these same streams support populations of coldwater 

indicator species. They also concluded that a single stream 

temperature standard is difficult to apply across such a broad 

area as the entire State of Idaho because streams differ in environmental complexity and biological diversity.

Description of Study Area

The upper Salmon River Basin (figure 1) is located in 

central Idaho and extends 121 mi from the headwaters on the 

east side of the Sawtooth Range to the confluence with the 

Pahsimeroi River near the town of Ellis, Idaho, draining an 

area of approximately 2,428 mi2. The basin contains large 

areas that have been designated as wilderness, several national 

forests, and the SNRA. These features make the basin a 

popular destination for fishing, hiking, whitewater rafting, and 

other outdoor activities.

Elevation above sea level ranges from 11,815 ft at 

Castle Peak to 4,640 ft at the confluence of the Salmon and 

Pahsimeroi Rivers. Mean elevation of the basin is 7,570 ft. 

Climate in most of the basin is semiarid and annual precipitation averages 24 in. per year. Precipitation is primarily 

snow, and peak flows in streams generally result from spring 

snowmelt.

The upper Salmon River Basin is located in the 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 44 percent of the basin; 

rangeland covers the remaining 56 percent.

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

alluvium (King and Beikman, 1974). Much of the basin is 

characterized by stream channels deeply incised in bedrock 

and bordered by steep terrain.

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-
6 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

defined riffles and pools, and very sparse macrophyte growth. 

In contrast, streams in the lower part of the basin typically 

have lower water clarity, more fine-grained sediments, lower 

stream gradients, and generally denser macrophyte growth. 

These streams frequently are subjected to channelization, loss 

of riparian habitat by cattle grazing, and diversion of water for 

irrigation.

Designated aquatic life beneficial uses of the study 

streams include coldwater biota and salmonid spawning (Idaho 

Department of Environmental Quality, 2003). Limited waterquality sampling on small tributaries of the upper Salmon 

River Basin has indicated few signs of human activities (Ott 

and Maret, 2003). On the basis of IDEQ’s total maximum 

daily load assessments, study streams were not water-quality 

limited and all beneficial uses were fully supporting (Idaho 

Department of Environmental Quality, 2003). In a few areas 

in the upper part of the basin, the effects of historical logging, 

mining, and cattle-grazing activities are noticeable. 

According to SNRA biologists, the greatest impacts on 

anadromous fish and their habitat in the upper Salmon River 

Basin are the effects of water diversions and related instream 

flow problems (Scott and others, 1981). Of about 497 diversions in the basin, about 189 are within the SNRA boundary 

(M. Moulton, U.S. Forest Service, written commun., 2004). 

However, the actual amount of water diverted is unknown. 

The impacts of dewatering these streams include direct loss 

of valuable spawning and rearing habitats; blocking of access 

to historical spawning and rearing habitat; and disruption of 

the aquatic ecosystem brought about by annual recurrence of 

unnaturally low streamflows. Most diversions in the study 

area are screened to prevent loss of fish into irrigation diversions. Generally, water for irrigation in the basin is diverted 

from July through September and, because of the high elevation (> 7,000 ft), the resulting growing season is only about 80 

days.

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). The most common fish 

species in the upper Salmon River Basin include bull trout, 

chinook salmon, resident rainbow (Oncorhynchus mykiss) and 

steelhead trout, brook trout (Salvelinus fontinalis), cutthroat 

trout (Oncorhynchus clarki), mountain whitefish (Prosopium 

williamsoni), longnose dace (Rhinichthys cataractae), and 

shorthead sculpin (Cottus confusus). Little historical information exists prior to irrigation on the use of upper Salmon 

River tributary streams by anadromous fish for spawning 

and rearing. According to IDFG, most tributary streams of 

the upper Salmon River offer coldwater refugia for juvenile 

salmonid rearing when the Salmon River water temperatures 

are not suitable (P. Murphy, Idaho Department of Fish and 

Game, oral commun., 2004). The endangered sockeye salmon 

once was found in five lakes within the upper Salmon River 

Basin; however, it now returns only to Redfish Lake, where 

active recovery efforts are in operation (National Oceanic and 

Atmospheric Administration, 2002).

Acknowledgments

Numerous individuals assisted in collecting and processing data during the course of this study. Joseph Bunt, Ross 

Dickinson, Jack Doyle, Alvin Sablan, Kenneth Skinner, and 

Christopher Mebane, USGS, assisted with data collection. Jim 

Henriksen and Terry Waddle, USGS, provided training and 

technical guidance for PHABSIM modeling. Paul Devries 

of R2 Consultants provided useful background information 

on previous PHABSIM work they completed for the BIA. 

Matt Combs of Utah State University provided data sets from 

previous instream flow studies completed in the Salmon River 

Basin. Several individuals from the USFS also contributed 

to the study: Mark Moulton provided useful information 

about previous studies in the SNRA and gave valuable advice 

regarding stream characteristics and study design, Ruth Wooding assisted with obtaining landowner permission to access 

private land, and Tim Page provided information on previous studies conducted for the SRA process. Joe Spinazola, 

Ronald Sutton, and Al Simpson, Reclamation, contributed to 

planning and study design. A number of representatives of 

the Interagency Technical Workgroup organized by Reclamation also provided guidance: Cynthia Robertson and Thomas 

Curet (IDFG), Jim Morrow and Donald Anderson (NOAA), 

and Janna Brimmer (USFWS). Jacque Coles of the USGS 

provided assistance in building the Web site that accompanies 

this report. The authors wish to thank the colleague reviewers 

for improving the quality of this report. Funding for this study 

was provided by Reclamation and USGS.

Data Collection Methods

Site Selection 

Once a list of priority streams based on input from the 

Interagency Technical Workgroup (see “Acknowledgments” 

for a list of members) was provided by Reclamation, the 

USGS conducted a reconnaissance on each stream to locate 

diversions and select potential study sites. Reclamation and 

USFS assisted in identifying private landowners and obtaining 

permission to access their land. PHABSIM study sites in the 

upper Salmon River Basin were selected following guidelines 

described by Bovee (1997). According to these guidelines, 

a geographical hierarchy is used to represent a study area in 

PHABSIM. The first-order subdivision of the study area is the 

stream segment. Stream segments are typically long sections 

of stream with a uniform flow regime and consistent geomorphology. Within the stream segment, there can be several 

habitat-related subdivisions, including representative reaches, 

mesohabitats, and microhabitats.
 Data Collection Methods 7

The representative reaches and mesohabitat types 

describe the stream segment and make up the second-order 

division of the study area. A representative reach is approximately 10 to 15 channel widths in length and typically contains many or all of the mesohabitat types present in the entire 

segment. The proportions of the mesohabitat types in the 

reach also are assumed to be the same as their proportions in 

the segment. Mesohabitats are short sections of stream, usually with a length of about the same magnitude as the width, 

and have unique characteristics that distinguish them from 

other mesohabitat types. Mesohabitat types are identified 

through a process known as mesohabitat typing, which is an 

inventory of the proportions of each mesohabitat in a segment. 

Mesohabitat types commonly are delineated by localized 

slope, channel shape, and structure and generally are described 

as runs, riffles, or pools. Collectively, all the mesohabitat 

types represent the stream segment.

Typically, either the representative reach or mesohabitat 

typing is used to describe the stream segment. In this study, 

mesohabitat typing, using a cumulative-lengths approach, 

was used to describe the stream segment. In the cumulativelengths approach, the length of each mesohabitat type is measured during the inventory, and the proportion of a particular 

mesohabitat type in a segment is calculated as the cumulative 

length of all similar mesohabitat types divided by the total 

length of the segment that was surveyed.

Although a mesohabitat type often is described simply as 

a run, riffle, or pool, it can be stratified into finer subdivisions 

to describe the stream segment more accurately. Often, these 

finer subdivisions take into account varying degrees of slope, 

width, velocity, and depth. Eight mesohabitat categories were 

used in this study and represent backwater (pools) and varying 

degrees of slopes (riffles and runs) in both narrow and wide 

channels (figure 2). Specifically, these mesohabitats included 

shallow and deep pools representing backwater with a hydraulic control. Slopes were designated as low, moderate, or high 

on the basis of the amount of surface turbulence, velocity, 

and substrate size. Because of the large variation in stream 

types encountered, mesohabitat typing was based on relative 

changes within each stream. The overall goal of this approach 

was to categorize major habitat types present in each segment 

and represent them in the PHABSIM modeling by weighting 

their relative importance.

PHABSIM study sites, the third-order division of a study 

area, describe either the representative reaches or the mesohabitat types. The study sites are divided longitudinally by 

stream cells and transects. When mesohabitat types are used 

to describe the stream segment, transects are established at the 

study site to represent the mesohabitat type and are weighted 

according to the proportion of the mesohabitat type in the 

segment. The segment is represented by all transects from all 

mesohabitat types. Generally, mesohabitats making up less 

than 10 percent of the stream segment were not included in the 

assessment.

Transects, the fourth-order division of a study area, are 

subdivided by lateral stream cells and verticals along which 

measures of microhabitat are made. Microhabitats are usually shorter than one channel width and represent a relatively 

homogeneous area utilized by an individual fish (Bovee, 

1997). Examples of microhabitat include undercut banks, 

velocity shelters behind boulders, and woody debris.

Stream sites were established downstream from all diversions on each stream to evaluate the cumulative impact of 

multiple diversions. Additional study sites on the same stream 

were selected downstream from other upstream diversions if 

significant amounts of water (>10 percent of the streamflow) 

were being diverted and (or) there were marked changes in 

stream geomorphology.

Shallow riffle habitats that potentially could create a 

bottleneck to passage were evaluated at each study site. One 

or more transects were placed across these areas at each study 

site to evaluate discharge relations and stream depth across the 

entire stream width.

Environmental Variables

Physical Habitat

Data were collected at verticals along transects to represent hydraulic and geomorphologic conditions in each cell in 

a mesohabitat type. Water-surface elevations were determined 

at each transect for at least two measured discharges. One 

additional stage-discharge pair was collected at some transects 

when cross-sectional data were collected at the verticals in the 

transect.

The data were collected at about 30 to 40 verticals to 

better define the habitat features of each transect. At each 

vertical in a transect, depth and mean velocity were measured, 

and cover and substrate types were determined. Cell width 

was determined from the spacing of the verticals. Channel 

structure and hydraulic variables were collected using standard 

USGS procedures described by Benson and Dalrymple (1967) 

and Rantz (1982). Transect and reference mark locations were 

georeferenced (±1 ft).

Hydrologic information for each study site was expressed 

using the Q.80, Q.50, and Q.20 exceedance discharge statisMesohabitat type

Pools

(backwater

with

hydraulic

control)

Slopes

(no backwater,

riffles and

runs)

Deep – thalweg not wadable

Shallow – thalweg wadable

Wide channel

Narrow channel

Moderate

Moderate

Low

High

Low

High

Figure 2. Hierarchical mesohabitat classification (Mesohabitats are equivalent to gemorphic channel units such as 

riffles, pools, and runs)
8 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

tics. The exceedance discharge Qxx indicates the discharge 

(Q) that is equaled or exceeded xx percent for a specified time, 

such as annual or specific month.

Substrate types were identified by visual observation and 

were classified as silt, sand, gravel, cobble, or boulder. When 

more than one substrate type was observed at the vertical, such 

as gravel and cobble, the dominant substrate was determined.

Instream cover that provided velocity shelter and (or) 

protection from predators for fish was determined across each 

transect. Types of cover included woody debris, undercut 

banks, large substrate (for example, boulder or large cobble), 

aquatic vegetation, and overhanging vegetation (see Raleigh 

and others, 1986). To characterize stream shading, percent 

canopy opening was estimated at each transect with a clinometer following procedures described Fitzpatrick and others 

(1998).

Stream Temperature 

Data loggers were used to record stream temperature 

throughout the study area. Data logger deployment and data 

collection followed procedures outlined by Stevens and others 

(1975) and Zaroban (2000). The digital data loggers used in 

this study (StowAway TidbiT; Onset Computer Corporation, 

Pocasset, Mass.) measure temperature to within ± 0.4 oC and 

record temperature within a range of − 0.5o to 37oC. 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 ± 0.4oC of the audit temperatures as 

determined by a thermometer calibrated in accordance with 

American Society of Testing and Materials (ASTM) standards.

To capture the natural thermal regime and to assess the 

effects of diversions on stream temperature, the data loggers 

were deployed spatially throughout each stream. Generally, a data logger was placed far enough upstream from all 

diversions to avoid possible effects of diversions, at study site 

locations, and near the stream’s mouth. Deployment consisted 

of selecting a well-mixed location in the stream, usually in the 

thalweg below a riffle, and attaching the data logger to a steel 

rod that was driven into the streambed. Data loggers were 

placed at mid-depth out of direct sunlight when possible and 

were programmed to record stream temperature hourly.

Analytical Methods for Instream Flow 

Characterization

Physical Habitat Simulation Model

Hydraulic and habitat simulation models contained 

in PHABSIM were used to characterize instream physical 

attributes (depth, velocity, substrate, and cover) over a range 

of expected summer (July through September) discharges. 

A recently updated version of PHABSIM for Windows was 

used to analyze data for each study site (Waddle, 2001). To 

estimate the amount of fish habitat available over a range of 

discharges, hydrologic and habitat data were collected at a few 

targeted discharges representing the range of discharges for 

the period of interest at each study site. These data were used 

to calibrate a hydraulic model, which then was used to predict 

the stream hydraulic attributes (depth and velocity) over the 

range of discharges of interest. The biological importance 

of the stream hydraulic attributes then was assessed with the 

suitability criteria for each species and life stage to produce a 

relation between habitat availability and discharge. The final 

output was expressed as WUA for a representative stream 

segment. To facilitate interpretation, the WUA results were 

normalized to a percentage of maximum for the range of discharges simulated.

Hydraulic Modeling and Calibration

The hydraulics portion of the PHABSIM model includes 

calculation of water-surface elevations and velocity distributions. The following data collected in the field are required 

in this portion of the model: channel geometry, Manning’s 

roughness (n) values, water-surface elevations, specific cell 

velocities, and stream discharges. Water-surface elevations 

can be calculated using one or any combination of the following methods: (1) stage-discharge relation or rating curve 

(STGQ), (2) Manning’s equation (MANSQ), or (3) step-backwater water-surface profile (WSP) (Waddle, 2001). In most 

cases, the stage-discharge relation method is used only when 

three or more discharges and corresponding water-surface 

elevations are available. In both the stage-discharge relation 

and Manning’s equation methods, the individual transects are 

independent of each other. In the WSP method, the individual 

transects are hydraulically connected.

The hydraulic portion of the PHABSIM model is calibrated in two separate steps. First, attempts are made to match 

the simulated water-surface elevations with the measured elevations. Calibration is performed by adjusting the n-values or 

related roughness variables within a realistic range as observed 

in the field until the simulated water-surface elevations match 

or nearly match the measured elevations. Typically, a difference of 0.02 ft or less between the simulated and measured 

values is desirable (Waddle, 2001). Second, attempts are 

made to match the simulated velocities at each transect with 

the measured velocities for the measured discharges. This 

calibration is performed by adjusting local n-values in specific 

cells until the simulated velocities match or nearly match the 

measured velocities. A difference of 0.02 ft/s between the 

simulated and measured values is desirable (Waddle, 2001). 

It may be unrealistic to exactly simulate a measured velocity 

distribution. However, in relatively smooth, uniform channels, 

it may be possible to be close. On the contrary, velocity distributions for fairly rough, nonuniform channels are much more 

difficult to simulate, and the final calibration values are based 

on the user’s selection of the simulation that best represents 
Analytical Methods for Instream Flow Characterization 9

the measured values (J. Henriksen, Biological Resources Division, oral commun., 2004).

Habitat Modeling

Selection of Target Species and Suitability Criteria

Use of PHABSIM requires selection of target species, life 

stages present during the period of stream use (periodicity), 

and suitability criteria. This information was derived from 

previous SRA work by the BIA and USFS in the Salmon River 

Basin (EA Engineering Science and Technology Incorporated, 

1991a, b). Upon review of this information, the Interagency 

Technical Workgroup directed the USGS to target the ESAlisted species bull trout, chinook salmon, and steelhead trout 

for juvenile, adult, and spawning life stages. The fry life 

stage (<50 mm, or about 2 in.) was not modeled because of 

the inability to accurately measure microhabitat parameters at 

a scale that would be meaningful. The endangered sockeye 

salmon was not selected as a target species because its habitat 

in the upper Salmon River Basin generally is not directly 

affected by diversions. Because water is diverted for irrigation predominantly in summer (July through September), the 

Interagency Technical Workgroup recommended targeting this 

period for study. High streamflows for channel maintenance 

generally have not been as great an issue in the upper Salmon 

River Basin (M. Moulton, U.S. Forest Service, oral commun.,

Suitability criteria represent the quantification of the relative importance of depth, velocity, and channel index (substrate) for specific life stages of each species. Suitability index 

(SI) values for depth, velocity, and channel index range from 0 

(no suitability) to 1.0 (maximum suitability). The Interagency 

Technical Workgroup recommended using suitability criteria 

previously developed for the SRA process (EA Engineering 

Science and Technology Incorporated, 1991a). The suitability 

curves selected for use in this study were developed within 

the Pacific Northwest and Idaho, making them applicable to 

upper Salmon River Basin streams. The suitability criteria and 

periodicity (period of stream use) for the various fish species 

and life stages targeted in this study can be accessed at http:// 

id.water.usgs.gov/projects/salmon_streamflow/habitat_curves

The habitat program HABTAE within PHABSIM was 

used to estimate WUA for the simulated discharges of interest. 

A number of specific settings were used in this habitat simulation program. The geometric mean calculation was used to 

derive the composite index (CI) score for each cell. The CI 

was calculated as the geometric mean of the input variable:

CI =(SI1 x SI2 x . . . x SIn)

1/n,

where SIn is the suitability index value for variable n, and n is 

the number of input variables. Calculating the CI on the basis 

of the geometric mean allows for more compensatory relations 

among variables than an arithmetic mean does (J. Henriksen,

Biological Resources Division, oral commun., 2003). For 

example, if two of three individual composite suitabilities 

are within the maximum range and the third is very low, the 

third individual composite suitability has a reduced effect on 

computation of the CI. The resulting CI value, combined with 

the surface area measured for various discharge scenarios, represents the weighted suitability, where a value of 1.0 indicates 

maximum habitat for the target species and life stage. The 

WUA is the sum of the products of CI values and surface area 

for all transect cells representing the study area.

Nose velocity settings were used for adult and juvenile 

bull trout as recommended by EA Engineering Science and 

Technology Incorporated (1991b). Specific settings for nose 

velocity consisted of estimates of Manning’s n, which ranged 

from 0.04 to 0.06 for the study sites, depth of 0.2 ft from 

the stream bottom, and use of a power law to calculate nose 

velocity from mean column velocity (Waddle, 2001). Default 

settings and mean column velocities were used to compute SI 

scores for all other species and life stages.

Because instream cover is important to juvenile 

salmonids for velocity shelters and protection from predators 

(Hillman and others, 1987; Spangler and Scarnecchia, 2001), 

and because all substrates are considered suitable for juvenile 

life stages, cover was substituted for substrate as a component 

of channel index in PHABSIM. Model results are reported 

separately for total WUA cover in relation to incremental 

changes in discharge for each site.

Passage Criteria

The passage criterion recommended by Thompson (1972) 

for stream depth over width was used to evaluate individual 

transects at each study site. For adult passage, the minimum 

depth criterion to be applied must be present over 25 percent 

of the total stream width and contiguous over at least 10 percent of the stream width at a representative transect. This criterion represents a minimum depth over relatively short stream 

distances, generally less than 20 ft (Arthaud and others, 2001). 

The minimum depth criterion recommended by Thompson 

(1972) is 0.8 ft for chinook salmon. According to SNRA 

biologists, this criterion is too high for marginally acceptable 

anadromous adult fish passage in the upper Salmon River 

Basin (Scott and others, 1981). Therefore, a depth criterion 

of 0.6 ft (Scott and others, 1981) was used in this study to 

assess anadromous fish passage. Shallower water depths can 

allow passage. On August 15, 2002, adult chinook were 

observed in Valley Creek moving through a shallow riffle that 

was 0.2 ft deep. Depths that would provide marginal adult 

chinook passage also would meet the requirements of passage 

for other adult and juvenile fish.

A hydraulic parameter option within PHABSIM called 

AVDEPTH/AVPERM was used to characterize the hydraulic 

properties of each passage transect (Waddle, 2001). Stream 

depth criteria between 0.4 and 0.8 ft were used to evaluate the 

amount of stream width available for passage at the simulated 

discharges for each transect. Results are displayed graphically 

2003).1

1This sentence was revised January 13, 2005.
10 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

to show the relation between discharge and the specified depth 

criteria over stream width.

Stream Temperature

Stream temperature data were inspected for obvious 

errors such as data logger malfunction and exposure to air 

temperatures. Data collected prior to deployment and after 

retrieval were removed from the data set. Time-series plots 

and other forms of graphical displays were used to inspect the 

data and to compare data sets. Temperature metrics, which 

characterize the thermal regime of stream temperatures, were 

calculated for all data sets and consisted of MDMT, MDAT, 

MWMT, and maximum-weekly (7-day) average temperature 

(MWAT). Maximum 7-day metrics were derived from the 7-

day moving average of daily (maximum or average) temperatures.

To ensure that stream temperatures stay within the 

optimal range, State and Federal regulatory agencies have 

established stream temperature standards. IDEQ is tasked 

with establishing and enforcing water-quality standards, 

which include stream temperature criteria. In the early 1990s, 

the IDEQ established stream temperature criteria of 22.0 ̊ C 

MDMT and 19.0 ̊ C MDAT for the protection of coldwater 

biota, and 13.0 ̊ C MDMT and 9.0 ̊ C MDAT for the protection 

of salmonid spawning (Grafe and others, 2002). In addition to 

the Idaho water-quality standard stream temperature criteria, 

the USEPA imposed a site-specific rule on those water bodies 

where bull trout are present (40 CFR 131.E.1.i.d, 1997). This 

rule set a criterion of 10.0 ̊ C MWMT during June through 

September for the protection of bull trout spawning and juvenile rearing in natal streams.

Although these stream temperature criteria have been 

established, it is recognized that a single stream temperature 

criterion for all streams may not accommodate the natural 

temperature variation within and among streams or the existence of naturally warm water. Consequently, temperatures 

in Idaho streams commonly exceed the criteria (Essig, 1998; 

Maret and others, 2001; Donato, 2002; Ott and Maret, 2003).

A Stream Segment Temperature (SSTEMP) model (Bartholow, 2002), developed to assist resource managers predict 

the consequences of stream and watershed manipulation on 

water temperatures, was explored for use in determining the 

effects of diversions on water temperature in streams in the 

upper Salmon River Basin. SSTEMP is a mechanistic, onedimensional, heat-transport model that predicts daily mean and 

maximum water temperatures as a function of stream distance 

and environmental heat flux. The model calculates net heat 

flux as the sum of heat to or from a stream by using longwave atmospheric radiation, direct short-wave solar radiation, 

convection, conduction, evaporation, shading, streambed 

fluid friction, and the water’s back radiation. The model also 

incorporates ground-water influx. SSTEMP is based on the 

dynamic temperature steady-flow equation and assumes that 

all input data, including meteorological and hydrological 

variables, can be represented by daily averages. SSTEMP can 

be used to predict natural stream temperatures at a location 

that then can be compared with measured water temperatures affected by dewatering of the stream by diversions. 

Ultimately, this model can be used to identify streamflows 

required to minimize temperature effects on the targeted fish 

species.

Guidelines for Using Study Results

The results presented in this report summarize the hydrology, habitat, and temperature characteristics of each stream 

in the study area. PHABSIM, the primary analysis tool used, 

provides output of WUA in relation to discharge for target 

species and life stages. WUA is thought to be proportional 

to habitat availability (Bovee and others, 1998). This output 

can be illustrated with a series of graphs showing curves for 

each life stage for the fish species of interest. The highest 

point on each curve represents the discharge at which WUA is 

maximized for adult, spawning, or juvenile life stages. These 

maximum values rarely coincide among life stages for any one 

species or for several species. Furthermore, the habitat/discharge relation does not address water availability; even the 

unregulated flow may commonly be less than the discharge 

at which the maximum WUA is available. The amount of 

WUA lost or gained can be determined by comparison with 

a reference, or unregulated, streamflow condition. Typically, 

the maximum, percentiles, or inflections are chosen from these 

curves at the level of protection desired or at points above 

which greater amounts of flow provide only minor gains in 

usable habitat. In streams with more than one species of 

interest, it would be appropriate to review the results to ensure 

that the recommended flows are beneficial to all species and 

harmful to none.

Discharge/depth relations for adult fish passage were 

evaluated at each study site at selected transects across wide, 

shallow areas. These areas were identified during the stream 

mesohabitat typing phase of the assessment and represent 

potential passage barriers or “bottlenecks.” If available, results 

from multiple passage transects can be averaged to best represent the overall passage conditions and streamflow needs for a 

particular stream segment. The relative percentage of mesohabitat types representing selected passage transects can be 

used to approximate the amount of potential passage habitat in 

various stream segments. This information may help identify 

those streams that have a relatively large amount of wide, shallow habitat that may restrict adult fish passage.

The mechanisms by which the various components are 

integrated and the relative importance they are assigned within 

the water-management decision process is a matter of professional judgment and beyond the scope of this study. Failure 

to provide adult fish passage connecting to the Salmon River 

would preclude success of improved conditions for spawning; 

therefore, ensuring enough water for adult fish passage would 

be foremost in management priorities. Water depth for adult 
Climatic and Hydrologic Conditions During 2003 11

passage is an additional consideration for the adult life stage. 

If possible, the choice of target flows should not reduce the 

water depth below that required for adult fish passage.

Discharge estimates providing maximum WUA for juvenile salmonid life stages are usually less than summer base 

flows, indicating a disconnect between the PHABSIM model 

results and actual juvenile salmonid needs. PHABSIM studies 

on streams in Washington demonstrated that streamflows estimated to produce maximum WUA for juvenile coho salmon 

(Oncorhynchus kisutch) were less than streamflows determined to actually increase juvenile recruitment (H. Beecher, 

Washington Department of Fish and Wildlife, oral commun., 

2004). When estimated flow for maximum juvenile WUA is 

less than estimated unimpaired summer base flow, the unimpaired summer base flow would be considered optimum until 

stream-reach-specific fish population and streamflow relations 

can be obtained (J. Morrow, National Oceanic and Atmospheric Administration, written commun., 2004).

Reasons for the apparent disparity between juvenile 

WUA curves and actual fish population and flow relations 

may include: inability to accurately measure and (or) quantify 

habitat parameters such as velocity, cover, and substrate at a 

scale that is meaningful for small fish; inability to accurately 

quantify side channels, bank indentations, riparian wetlands, 

or other lateral habitat that is important for rearing juvenile 

salmonids; inability to adequately incorporate temperature 

or other water-quality parameters into the model; and use of 

habitat suitability criteria that do not consider importance of 

high-velocity water in adjacent cells. Hampton (1988) determined that water velocity is the critical hydraulic parameter 

that determines microhabitat selection for juvenile chinook 

salmon and steelhead trout. For example, juvenile chinook 

salmon are strongly associated with pool habitat with little or 

no velocities (Hillman and others, 1987; Roper and others, 

1994). However, stream salmonids have been observed to 

reside in, and forage from, microhabitat locations that were 

shielded from the current but adjacent to high-velocity water 

(Everest and Chapman, 1972). Likewise, foraging models 

that address improved foraging conditions associated with 

high-velocity flow near cover are correlated with growth and 

survival of juvenile Atlantic salmon (Salmo salar) (Nislow and 

others, 2004). Accurately modeling WUA for juvenile stream 

salmonids may require use of habitat suitability criteria developed using foraging models (Baker and Coon, 1997) and (or) 

more comprehensive modeling of habitat parameters.

To focus the integration of the various modeling results 

and relevant species and life stages, it is suggested that a priority species and life stage ranking approach be developed for 

each stream and period of concern. For example, the USFS 

prioritized federally listed anadromous species with the highest ranking, followed by Species of Special Concern, in 

their adjudication of water right claims for selected streams in 

central Idaho (Hardy, 1997). Prioritizing life stages present 

for the month or period of concern would benefit the selection 

of a target flow using the assumption that the priority life stage 

would require higher streamflows than other life stages would. 

Generally, for small tributary streams of the upper Salmon 

River Basin, this priority ranking would be (from high to low): 

passage > spawning > adult > juvenile. The ranking approach 

should involve discussions among resource-management 

agency representatives familiar with the streams of interest. 

Once the priority species and life stage are ranked, then each 

study site should be examined to determine streamflow and 

passage conditions for the period of interest. The results from 

PHABSIM provide a science-based linkage between biology 

and river hydraulics; however, there is no one single answer 

from this approach. PHABSIM results, along with other 

hydrologic and biological information, are intended to be used 

in negotiations or mediated settlements.

Habitat results are presented for each target species and 

life stage over an incremental range of discharges, allowing 

flexibility in interpretation. Because the streams studied are 

relatively small tributaries (basin size < 80 mi) to the Salmon 

River, a greater proportion of discharge is required to provide 

suitable water depths for fish habitat and connectivity for passage (Hatfield and Bruce, 2000). Once an adequate number 

of sites have been characterized using PHABSIM, it may be 

feasible to develop habitat / discharge relations for streams 

with similar basin characteristics within specific geographic 

locations. This could provide a regional planning tool that 

could eliminate intensive, site-specific studies.

The natural hydrograph also needs to be considered when 

developing flow targets. In drought years, summer flows 

that provide maximum possible habitat may not be attainable because of the hydrologic limits on the stream. Also, 

PHABSIM does not estimate flow or habitat needs of downstream juvenile migrants or spring runoff conditions necessary 

for maintenance of channel morphology or riparian zone functions. Arthaud and others (2001) have shown that downstream 

juvenile migrant survival can increase significantly with 

discharge. Thus, high spring flows that mimic the natural 

hydrograph can be a consideration in managing streamflows 

outside PHABSIM analysis.

Climatic and Hydrologic Conditions 

During 2003

Climatic and hydrologic conditions in the upper Salmon 

River Basin were near normal (30-year record, 1971–2000) 

during water year 2003 (WY03). Monthly snowpack levels 

were slightly below normal between January 1 and 

June 1, 2003. The average temperature during the 12 months 

of WY03 was slightly higher than the 30-year record average, 

whereas the average monthly temperatures were both above 

and below average. Annual mean streamflows in the basin

were slightly below the long-term means, whereas monthly 

mean streamflows were both above and below the long-term 

means.
12 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

Climatic Conditions

Average monthly snowpack levels for the Salmon River 

Basin upstream from Salmon, Idaho, ranged from 83 to 105 

percent of normal during the period January 1 to June 1. The 

average snowpack value for this area on April 1, 2003, was 

96 percent of normal (Natural Resources Conservation Service, 2004b). The April 1 value is the most commonly used 

indicator of snowpack conditions since, in most years, it is 

the final value calculated before snowmelt begins. Observation sites located within or near the upper Salmon River Basin 

are Banner Summit (near the headwaters of Valley Creek), 

Galena Summit (at the headwaters of the Salmon River), Mill 

Creek Summit (at the headwaters of Yankee Fork), and Vienna 

Mine (at the headwaters of Smiley Creek). Specific snowpack 

levels at these sites on April 1, 2003, were as follows: Banner 

Summit, 93 percent of normal; Galena Summit, 96 percent of 

normal; Mill Creek Summit, 78 percent of normal; and Vienna 

Mine, 86 percent of normal (Natural Resources Conservation 

Service, 2004a).

The mean temperature at Stanley, Idaho, during WY03 

was about 2.44o C (36.4o F), slightly higher than the 30-year 

(1971–2000) mean of 1.83o C (35.3o F). Mean daily temperatures were slightly higher during June through September 

2003 than during the long-term (1971–2000) record 

(figure 3). Mean monthly temperatures during the period 

when snowpack generally accumulates (October through 

April) were somewhat variable. Mean temperatures during October, November, and February were below the mean, 

whereas those during December, January, and March were 

above the mean. The mean April temperature was equal to the 

30-year mean (Western Regional Climate Center, 2004).

Hydrologic Conditions

Annual mean streamflows at the long-term USGS gaging stations on Valley Creek at Stanley (13295000; 63 years 

of record) and on the Salmon River below Yankee Fork 

(13296500; 73 years of record) were approximately 7.5 and 

9.7 percent below the long-term means, respectively. The 

annual mean streamflow at Valley Creek at Stanley was 

185 ft3 / s compared with the long-term mean of 200 ft3 / s, 

and the annual mean streamflow at the Salmon River below 

Yankee Fork was 883 ft3 / s compared with the long-term mean 

of 978 ft3 / s. Monthly mean streamflows at Valley Creek at 

Stanley were generally slightly below the long-term means, 

with the exception of those for February, March, April, and 

June, which were slightly above the long-term means. Similarly, monthly mean streamflows at the Salmon River below 

Figure 3. Mean daily air temperature for period June through September 2003 in relation to long-term (1971 through 2000) 

mean daily temperature measured at Stanley Ranger Station, upper Salmon River Basin, Idaho MEAN DAILY AIR TEMPERATURE, IN DEGREES CELSIUS

MONTH

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2003

1971–2000
Table 1. Basin and site characteristics for gaging stations, diversions, and study sites in the upper Salmon River Basin, Idaho, 2003 [Site locations shown in figures 1, 4, 8, and 12; No., number; USGS, U.S. Geological Survey; C, continuous streamflow recorded at this site; M, instantaneous streamflow measured aSimulation (PHABSIM) study site; T, continuous water temperature recorded at this site; latitude and longitude in degrees, minutes, and seconds; mi2, square miles; in., inches; —, no 

Site No. Site name Site type Latitude Longitude Basin area (mi2) Basin slope (percent) Mean elevation (feet above sea level) Percent forest Mean annual precipi- tation (in.) S

PCG Pole Creek at USGS gage C, M, T 435436 1144524 18.4 38 8487 74 30 — PCD1 Pole Creek diversion M 435435 1144526 — — — — — — PC2 Upper Pole Creek M, P, T 435431 1144531 18.6 38 8477 74 30 Private prope

PCD11 JCG Fourth of July Creek at USGS gage C, M, T 440226 1144520 15.8 40 8934 72 33 — JCD3 Upper Fourth of July Creek diversion M 440228 1144523 — — — — — — JC3 Upper Fourth of July Creek M, P, T 440213 1144655 17.0 39 8862 71 33 JCD2 upstrea

JCD2 Middle Fourth of July Creek diversion M 440146 1144803 — — — — — — JC2 Middle Fourth of July Creek M, P, T 440138 1144908 17.8 38 8763 68 32 JCD1 upstreaJCD1 Lower Fourth of July Creek diversion M 440145 1144942 — — — — — — JC1 Lower Fourth of July Creek M, P, T 440155 1145011 18.1 37 8731 67 31 Mouth upstreECG Elk Creek at USGS gage C, M, T 441712 1150416 18.1 31 7559 65 27 — ECD2 Upper Elk Creek diversion M 441720 1150343 — — — — — — ECD1 Lower Elk Creek diversion M 441726 1150142 — — — — — — EC1 Lower Elk Creek M, P, T 441734 1150129 20.4 28 7471 67 26 Mouth upstreVCGU Valley Creek at upper USGS gage C, M, T 441857 1150401 29.4 30 7695 80 27 — VCD4 Upper Valley Creek diversion M 441837 1150321 — — — — — — VC3 Upper Valley Creek M, P, T 441835 1150320 27 29 7681 79 27 Private prope

to VCD3 VCD3 Upper/middle Valley Creek diversion M 441729 1150107 — — — — — — VC2 Middle Valley Creek M, P, T 441739 1150130 41.9 25 7490 77 26 Confluence wpublic acc

VCD2 Middle Valley Creek diversion M 441724 1150056 — — — — — — VCD1 Lower Valley Creek diversion M 441623 1150030 — — — — — — VC1 Lower Valley Creek M, P, T 441601 1150023 76 25 7396 72 25 Public acces

fluence wi

VCGL Valley Creek at lower USGS gage C, M, T 441321 1145549 148 26 7320 63 24 — 1 Access to private land restricted stream segment length.
14 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

Yankee Fork were slightly below the long-term means, with 

the exception of those for February, March, and June, which 

were slightly above the long-term means.

Results of Study Site Investigations During 2003

Investigations were performed on four separate tributaries 

to the Salmon River during the summer and fall of 2003. Data 

were collected at eight study sites (table 1): one site on upper 

Pole Creek (PC2), three sites on Fourth of July Creek (JC3, 

JC2, and JC1), one site on lower Elk Creek (EC1), and three 

sites on Valley Creek (VC3, VC2, and VC1). A plan view of 

each PHABSIM study site showing the locations of specific 

transects can be found in the appendices, figure 1A, figure 

10A, figure 19A, figure 28A, figure 39A, figure 48A, figure 

57A, and figure 66A.

In addition to the data collected at these study sites, continuous streamflow was recorded at four locations upstream 

from all diversions on Pole Creek (PCG), Fourth of July Creek 

(JCG), Elk Creek (ECG), and Valley Creek (VCGU). Longterm streamflow information, especially for basins smaller 

than 20 to 30 mi 2, in the upper Salmon River Basin is lacking. 

Additional streamflow data collected in these smaller basins 

not only would provide much needed information in these 

areas, but also could improve the accuracy of the regression 

equations used to estimate streamflows at ungaged sites.

Instream cover plays an important role in habitat selection for juveniles (Hampton, 1988). However, modeling fish 

cover presence for juvenile life stages proved to be problematic because of model limitations. Because all substrate 

types receive a suitability score of 1.0 for juvenile life stages, 

an attempt was made to substitute fish cover presence in the 

PHABSIM model by running this as a component of channel 

index. Because the composite suitability score equals zero 

when cover is absent in a cell, the resulting output produced 

WUA results only for cells with cover. Refinements of suitability criteria to score fish cover types by means of a discrete 

score rather than a binary score (that is, present or absent) 

may provide an opportunity to use cover more effectively in 

PHABSIM. Currently, this type of discrete scoring criteria for 

cover does not exist.

Juvenile instream cover WUA results were tabulated over 

the range of discharges modeled (see appendices, table 1A, 

table 3A, table 5A, table 7A, table 10A, table 12A, table 14A, 

and table 16A); however, final WUA graphs for each study 

site in the appendices do not include a cover component. Plots 

of cover WUA and discharge were evaluated for each study 

site, but these plots did not provide additional information that 

would enhance the determination of maximum habitat/discharge relations using PHABSIM (the maximum discharge 

range was essentially the same with and without the cover 

component). During their analysis of Snake River Adjudication data collected in Idaho, EA Engineering and Science 

Technology, Incorporated, also determined that PHABSIM 

was not effective in modeling instream cover (P. Devries, R2 

Consultants, oral commun., 2003).

Pole Creek (click here for study site investigation, figures 

1A– 9A , and tables 1A– 2A)

Fourth of July Creek (click here for study site investigation,

figures 10A– 38A, and tables 3A– 9A)

Elk Creek (click here for study site investigation, figures 

39A– 47A, and tables 10A– 11A)

Valley Creek (click here for study site investigation, figures 

48A– 74A and tables 12A– 17A)

Summary

Rivers, streams, and lakes in the upper Salmon River 

Basin historically provided migration corridors and significant 

habitat for anadromous chinook salmon, sockeye salmon, 

and steelhead trout. Wild salmon and steelhead in the basin 

migrate nearly 900 miles between the mountain streams and 

the Pacific Ocean. Resident bull trout also inhabit many of the 

rivers and streams in the basin. High-elevation spawning and 

rearing and extensive migrations may be very important for 

the long-term survival of these species.

Anadromous fish populations in the Columbia River 

Basin have plummeted in the last 100 years; this severe 

decline led to Federal listing of chinook salmon and steelhead 

stocks as endangered or threatened under the Endangered Species Act (ESA) in the 1990s. Human development has modified the original flow conditions in many streams in the upper 

Salmon River Basin. Summer streamflow modifications, as a 

result of irrigation practices, have directly affected the quantity 

and quality of fish habitat and also have affected migration and 

(or) access to suitable spawning and rearing habitat for these 

fish. Reduced streamflows resulting from diversions may contribute to increased water temperatures that may be unsuitable 

for native salmonids.

As a result of these ESA listings and Action 149 of the 

Federal Columbia River Power System Biological Opinion of 

2000, the Bureau of Reclamation (Reclamation) was tasked 

to conduct streamflow characterization studies in the upper 

Salmon River Basin to clearly define habitat requirements for 

effective species management and habitat restoration. These 

studies were undertaken to evaluate potential fish habitat 

improvements by increasing streamflows as called for by the 

Federal Columbia River Power System Biological Opinion of 
Summary 15

2000. Results of these studies will be used to prioritize and 

direct cost-effective actions to improve fish habitat for ESAlisted anadromous and native fish species in the basin.

Numerous methods can be used to determine streamflow 

needs for fish and wildlife, but one of the most widely used 

is the Instream Flow Incremental Methodology, developed in 

the 1970s by physical and biological scientists in the U.S. Fish 

and Wildlife Service. A major component of Instream Flow 

Incremental Methodology is a collection of computer models 

called the Physical Habitat Simulation Model (PHABSIM). 

This model incorporates hydrology, stream morphology, 

and microhabitat preferences to create relations between 

streamflow and habitat availability. Habitat availability is 

measured by an index called the weighted usable area, which 

is the wetted area of a stream weighted by its suitability for 

use by an organism. PHABSIM simulates habitat/discharge 

relations for various species and life stages and allows quantitative habitat comparisons at different streamflows of interest.

Once a list of priority streams based on input from the 

Interagency Technical Workgroup was provided by Reclamation, the U.S. Geological Survey (USGS) conducted a 

reconnaissance on each stream to locate diversions and select 

potential study site locations. Mesohabitat typing, using a 

cumulative-lengths approach was used to describe the stream 

segment. In the cumulative-lengths approach, the length of 

each mesohabitat type is measured directly during the inventory, and the proportion of a particular mesohabitat type in 

a segment is calculated as the cumulative length of all like 

mesohabitat types divided by the total length of the segment 

that was surveyed. Because of the large variation in stream 

types encountered, mesohabitat typing was based on relative 

changes within each stream. Data were collected at verticals 

along transects to represent hydraulic and geomorphologic 

conditions in each cell in a mesohabitat type. At each vertical 

in a transect, depth and mean velocity were measured, and a 

cover and substrate type were determined.

Shallow riffle habitats that potentially could create a 

bottleneck to passage were evaluated at each study site. One 

or more transects were placed across these areas at each study 

site to evaluate discharge relations and stream depth across the 

entire stream width.

To capture the natural thermal regime and to assess the 

effects of diversions on stream temperature, data loggers were 

deployed spatially throughout each stream. Generally, a data 

logger was placed well upstream from all diversions, at study 

site locations, and near the stream’s mouth.

Hydraulic and habitat simulation models contained in 

PHABSIM were used to characterize the instream physical 

attributes (depth, velocity, substrate, and cover) over a range of 

expected summer (July through September) discharges. The 

final output is expressed as weighted usable area (WUA) for a 

representative stream segment.

Climatic and hydrologic conditions in the upper Salmon 

River Basin were near normal during water year 2003 

(WY03). Monthly snowpack levels were slightly below normal between January 1 and June 1, 2003. The average temperature during the 12 months of WY03 was slightly higher 

than the 30-year (1971 – 2000) average, whereas the average 

monthly temperatures were both above and below average. 

Annual mean streamflows in the basin were slightly below the 

long-term means, whereas monthly mean streamflows were 

both above and below the long-term means. Average monthly 

snowpack levels for the Salmon River Basin upstream from 

Salmon, Idaho, ranged from 83 to 105 percent of normal during the period January 1 to June 1.

The mean temperature at Stanley, Idaho, during 

WY03 was about 2.44 ̊C, slightly higher than the 30-year 

(1971 – 2000) mean of 1.83 ̊C. Mean daily temperatures were 

slightly higher during June through September 2003 than during the long-term (1971 – 2000) record.

Annual mean streamflows at the long-term USGS gaging stations on Valley Creek at Stanley (13295000; 63 years 

of record) and on the Salmon River below Yankee Fork 

(13296500; 73 years of record) were approximately 7.5 and 

9.7 percent below the long-term means, respectively.

The results of PHABSIM provide a science-based linkage 

between biology and river hydraulics; however, there is no one 

single answer from this approach. Habitat results are presented for each target species and life stage over an incremental range of discharges, allowing flexibility in interpretation. 

Because the streams studied are relatively small tributaries 

(basin size <80 square miles) to the Salmon River, a greater 

proportion of discharge is required to provide suitable water 

depths for fish habitat and connectivity for passage.

Once an adequate number of sites have been characterized using PHABSIM, it may be feasible to develop habitat/

discharge relations for streams with similar basin characteristics within specific geographic locations. This could provide a 

regional planning tool that could eliminate intensive, site-specific studies.

Modeling fish cover presence for juvenile life stages 

proved to be problematic because of model limitations. 

Refinements of suitability criteria to score fish cover types by 

means of a discrete score rather than a binary score (that is, 

present or absent) may provide an opportunity to use cover 

more effectively in PHABSIM. Plots of cover, WUA, and 

discharge were evaluated for each study site, but these plots 

did not provide additional information that would enhance the 

determination of maximum habitat/discharge relations.

Caution is needed when interpreting juvenile WUA 

results because the streamflows necessary for maximum 

habitat for juvenile rearing may be underestimated using 

PHABSIM results. In fact, for streams that are being managed 

specifically for juvenile rearing, PHABSIM-derived WUA 

maximum discharges could be unrealistically low, resulting in 

flow regimes that are not protective of the fishery resource.

Investigations were performed on four separate tributaries 

to the Salmon River during the summer and fall of 2003. Data 

were collected at a total of eight study sites: one site on upper 

Pole Creek, three sites on Fourth of July Creek, one site on 

lower Elk Creek, and three sites on Valley Creek.
16 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2003 

Continuous streamflow was recorded at four locations 

upstream from all diversions on Pole Creek, Fourth of July 

Creek, Elk Creek, and Valley Creek. Long-term streamflow 

information, especially for basins smaller than 20 to 30 square 

miles, in the upper Salmon River Basin is lacking. Additional 

streamflow data collected in these smaller basins not only 

will provide much needed information in these areas, but also 

could improve the accuracy of the regression equations used to 

estimate streamflows at ungaged sites.

Analyses were completed to relate streamflows in Pole 

Creek during WY03 to long-term mean streamflows. Comparisons of July, August, and September monthly mean discharge 

during WY03 with long-term monthly mean discharge for the 

Valley Creek at Stanley gaging station (13295000) showed 

that WY03 monthly means were 25.3, 20.9, and 18.1 percent 

below the long-term monthly means, respectively.

Pole Creek is considered the highest quality fishery habitat within the Sawtooth National Recreation Area (SNRA) and 

has great potential to accommodate spawning of anadromous 

fish. However, this potential may be realized only if additional 

summer flows are provided to allow passage into spawning 

areas. Upper Pole Creek discharges required for maximum 

WUA ranged 7 to 17 cubic feet per second (ft3/s), 7 to 29 ft3/s, 

and 9 to 29 ft3/s for bull trout, chinook salmon, and steelhead 

trout life stages, respectively. Discharges required for passage 

over shallow riffle habitat ranged from 25 to 5 ft3/s for the 

depth criterion of 0.6 foot over 25 percent of the total channel 

width and over 10 percent of the contiguous channel width, 

respectively.

Median discharge estimates for the months of July, 

August, and September for upper Pole Creek were 45.0, 17.3, 

and 13.7 ft3/s, respectively. The mean annual discharge estimate was 43.6 ft3

/s.

Analysis of the stream temperature metrics for upper Pole 

Creek indicated a slight warming trend in a downstream direction. Results of the individual metric calculations showed that 

the maximum daily-maximum temperature (MDMT) was well 

below the MDMT of 21.0 ̊C that can create a thermal barrier 

that would block adult chinook salmon from migrating to their 

spawning grounds. Also, the MDMT in upper Pole Creek 

never exceeded the 18.0 ̊C threshold that may decrease bull 

trout migration.

Analyses were completed to relate streamflows in Fourth 

of July Creek during WY03 to long-term mean streamflows. 

The same techniques used to estimate long-term streamflows 

for Pole Creek also were used for Fourth of July Creek, Elk 

Creek, and Valley Creek study sites.

Upper Fourth of July Creek discharges required for 

maximum WUA ranged from 9 to 51 ft3/s, 9 to 39 ft3/s, and 9 

to 39 ft3/s for bull trout, chinook salmon, and steelhead trout 

life stages, respectively. Discharges required for passage over 

shallow riffle habitat were both 15 ft3/s for the depth criterion 

of 0.6 foot over 25 percent of the total channel width and over 

10 percent of the contiguous channel width.

Median discharge estimates for upper Fourth of July 

Creek for the months of July, August, and September were 

59.8, 20.7, and 15.3 ft3/s, respectively. The mean annual discharge estimate was 51.4 ft3

/s.

Middle Fourth of July Creek discharges required for 

maximum WUA ranged from 12 to 18 ft3/s, 9 to 27 ft3/s, and 

9 to 27 ft3/s for bull trout, chinook salmon, and steelhead trout 

life stages, respectively. Discharges required for passage over 

shallow riffle habitat ranged from 11 to 9 ft3/s for the depth 

criterion of 0.6 foot over 25 percent of the total channel width 

and over 10 percent of the contiguous channel width, respectively.

Median discharge estimates for middle Fourth of July 

Creek for the months of July, August, and September were 

59.9, 20.8, and 15.6 ft3/s, respectively. The mean annual discharge estimate was 52.8 ft3

/s.

Lower Fourth of July Creek discharges required for maximum WUA ranged from 12 to 18 ft3

/s, 7 to 30 ft3/s, and 12 to 

30 ft3/s for bull trout, chinook salmon, and steelhead trout life 

stages, respectively. Discharges required for passage over two 

shallow riffle habitats near the mouth of the stream ranged 

from 18 to 5 ft3/s and 27 to 12 ft3/s for the depth criterion of 

0.6 foot over 25 percent of the total channel width and over 10 

percent of the contiguous channel width, respectively.

Median discharge estimates for lower Fourth of July 

Creek for the months of July, August, and September were 8, 

20.2, and 15.4 ft3/s, respectively. The mean annual discharge 

estimate was 51.9 ft3/s.

Analysis of the stream temperature metrics for Fourth of 

July Creek showed that temperatures were variable, but a gradual downstream warming trend was apparent. Large increases 

in water temperature in the lower end of Fourth of July Creek 

are not uncommon. In 2001, the U.S. Forest Service measured stream temperature increases of about 10 ̊C between the 

U.S. Forest Service boundary and the mouth of Fourth of July 

Creek. The MDMT at all sites was below the 21.0 ̊C threshold that can create a thermal barrier that would block adult 

chinook salmon from migrating to their spawning grounds. 

The MDMT exceeded 18.0 ̊C in July and August at the lower 

site, indicating there may be decreased bull trout passage into 

Fourth of July Creek from the Salmon River as a result of high 

temperatures.

Lower Elk Creek discharges required for maximum WUA 

ranged from 34 to 59 ft3/s, 18 to 62 ft3/s, and 18 to 62 ft3/s 

for bull trout, chinook salmon, and steelhead trout life stages, 

respectively. Discharges required for passage over shallow 

riffle habitat ranged from 34 to 12 ft3/s for the depth criterion 

of 0.6 foot over 25 percent of the total channel width and 

over 10 percent of the contiguous channel width, respectively. 

Maximum WUA estimates determined by Utah State University at this same study site in 1999 were compared with maximum WUA estimates in this study. The University’s WUA 

estimates ranged from 13 to 36 ft3/s, 13 to 64 ft3/s, and 18 to 

64 ft3/s for bull trout, chinook salmon, and steelhead trout, 

respectively, for the same three life stages. These maximum 

WUA estimates for bull trout were much lower than estimates 

in this study, whereas WUA estimates from both studies for 

chinook salmon and steelhead trout were similar.
References Cited 17

Median discharge estimates for lower Elk Creek for the 

months of July, August, and September were 34.3, 14.1, and 

12.4 ft3/s, respectively. The mean annual discharge estimate 

was 39.2 ft3/s.

The MDMT measured on Elk Creek was below the 

21.0 ̊C threshold that can create a thermal barrier that would 

block adult chinook salmon from migrating to their spawning 

grounds. The MDMT exceeded 18.0 ̊C in July and August at 

Elk Creek sites, indicating there may be decreased bull trout 

habitat and passage in Elk Creek as a result of high temperatures.

Valley Creek is one of the SNRA’s most heavily utilized 

spawning streams for chinook salmon and steelhead trout. 

Upper Valley Creek discharges required for maximum WUA 

ranged from 13 to 29 ft3/s, 9 to 40 ft3/s, and 15 to 37 ft3/s for 

bull trout, chinook salmon, and steelhead trout life stages, 

respectively. Discharges required for passage over shallow 

riffle habitat ranged from 15 to 8 ft3/s for the depth criterion of 

0.6 foot over 25 percent of the total channel width and over 10 

percent of the contiguous channel width, respectively.

Median discharge estimates for upper Valley Creek for 

the months of July, August, and September were 19.0, 11.5, 

and 11.2 ft3/s, respectively. The mean annual discharge estimate was 29.7 ft3

/s.

Middle Valley Creek discharges required for maximum 

WUA ranged from 36 to 84 ft3/s, 24 to 84 ft3/s, and 36 to 84 

ft3/s for bull trout, chinook salmon, and steelhead trout life 

stages, respectively. Discharges required for passage over 

shallow riffle habitat were both 15 ft3/s for the depth criterion 

of 0.6 foot over 25 percent of the total channel width and over 

10 percent of the contiguous channel width. Maximum WUA 

estimates determined by Utah State University at this same 

study site in 1999 were compared with maximum WUA estimates in this study. The University’s WUA ranged from 9 to 

44 ft3/s, 11 to 70 ft3/s, and 21 to 70 ft3/s for bull trout, chinook 

salmon, and steelhead trout, respectively, for the same three 

life stages. Generally, these maximum WUA estimates were 

lower than those in this study.

Median discharge estimates for middle Valley Creek for 

the months of July, August, and September were 32.9, 17.9, 

and 17.9 ft3/s, respectively. The mean annual discharge estimate was 48.2 ft3

/s.

Lower Valley Creek discharges required for maximum 

WUA ranged from 23 to 75 ft3/s, 20 to 69 ft3/s, and 23 to 69 

ft3/s for bull trout, chinook salmon, and steelhead trout life 

stages, respectively. Discharges required for passage over 

shallow riffle habitat ranged from 50 to 16 ft3/s for the depth 

criterion of 0.6 foot over 25 percent of the total channel width 

and over 10 percent of the contiguous channel width.

Median discharge estimates for lower Valley Creek for 

the months of July, August, and September were 60.6, 31.5, 

and 31.0 ft3/s, respectively. The mean annual discharge estimate was 84.9 ft3

/s.

Lower Valley Creek was the only study site where side 

channel habitat made up a significant portion (>10 percent) 

of the stream segment assessed. Analysis of the inlet and 

outlet portions of the side channel revealed that a discharge of 

approximately 150 ft3/s would be required to allow for a minimum passage depth of 0.4 foot for adult chinook. Because it 

is highly unlikely that natural discharges at this site during the 

months of July, August, and September would exceed 150 

ft3/s, this side channel likely does not contain suitable fish habitat during those months. In addition, no fish were observed 

during the initial site visit in July.

Analysis of the stream temperature metrics for Valley 

Creek indicated that, most of the time, there was a gradual 

warming trend downstream from upper to lower study sites. 

The MDMT at all sites was below the 21.0 ̊C threshold that 

can create a thermal barrier that would block adult chinook 

salmon from migrating to their spawning grounds. The 

MDMT exceeded 18.0 ̊C in July and August at all Valley 

Creek sites, indicating that there may be limited bull trout 

habitat and passage as a result of high water temperature.

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Manuscript approved for publication, July 7, 2004.

Manuscript released on World Wide Web, December 2004,

 at URL: http://id.water.usgs.gov/public/reports.html

Prepared by U.S. Geological Survey Publishing staff, Idaho 

District, Boise, Idaho:

Launa H. Allen

Linda K. Channel

Linda Buckmaster

Richard L. Helton

For more information concerning the research in this report, 

contact:

Idaho District Chief

U.S. Geological Survey

230 Collins Road

Boise, Idaho 83702-4520

http://id.water.usgs.gov
Maret, T.R., Hortness, J.E., and Ott, D.S.—Instream Flow, Upper Salmon River Basin Streams, Central Idaho, 2003—Scientific Investigations Report 2004 – 5173