Instream Flow Characterization of Upper Salmon River 

Basin Streams, Central Idaho, 2005

Scientific Investigations Report 2006–5230

Prepared in cooperation with the Bureau of Reclamation 

U.S. Department of the Interior

U.S. Geological Survey

Yankee

Fork

Valley

Creek

Elk

Fourth Creek of July

Pole

Creek

Creek

Smiley

Creek

Creek

Squaw

Creek

Thompson

Champion Creek

Beaver

Creek

Iron Creek

Salmon

Salmon

East

Fork

River

River

River

Salmon

Salmon

River

Redfish

Lake

Alturas

Lake

Challis

Obsidian

Stanley

Ellis

Instream Flow Characterization of 

Upper Salmon River Basin Streams, 

Central Idaho, 2005

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

Prepared in cooperation with the Bureau of Reclamation

Scientific Investigations Report 2006–5230

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK A. KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2006

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Suggested citation:

Maret, T.R., Hortness, J.E., and Ott, D.S., 2006, Instream flow characterization of upper Salmon River Basin streams, 

central Idaho, 2005: U.S. Geological Survey Scientific Investigations Report 2006-5230, 110 p.
iii

Contents

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

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

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

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

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

Data Collection Methods..............................................................................................................................7

Site Selection ........................................................................................................................................7

Environmental Variables......................................................................................................................8

Physical Habitat ...........................................................................................................................8

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

Analytical Methods for Instream Flow Characterization ........................................................................9

Physical Habitat Simulation Model....................................................................................................9

Hydraulic Modeling and Calibration.........................................................................................9

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

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

Passage Criteria................................................................................................................10

Stream Temperature...........................................................................................................................11

Guidelines for Using Study Results..................................................................................................11

Climatic and Hydrologic Conditions During 2005....................................................................................12

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

Hydrologic Conditions........................................................................................................................13

Results of Study Site Investigations .........................................................................................................14

Big Boulder Creek...............................................................................................................................14

Hydrology ....................................................................................................................................14

Habitat Modeling and Passage Criteria.................................................................................14

Stream Temperature..................................................................................................................18

Challis Creek and Major Tributaries ................................................................................................19

Hydrology ....................................................................................................................................21

Habitat Modeling and Passage Criteria.................................................................................21

Stream Temperature..................................................................................................................24

Morgan Creek......................................................................................................................................28

Hydrology ....................................................................................................................................28

Habitat Modeling and Passage Criteria.................................................................................28

Stream Temperature..................................................................................................................28

Summary........................................................................................................................................................33

Acknowledgments.......................................................................................................................................35

References Cited..........................................................................................................................................35

Appendixes A-H. Plan views, weighted useable areas, and passage criteria

assessments for bull trout, Chinook salmon, steelhead trout, and invertebrates

for study sites in the upper Salmon River Basin, Idaho, 2005.................................................39
iv

Figures

Figure 1. Map showing location of selected streamflow-gaging stations in the upper 

Salmon River Basin, Idaho.................................................................. 6

Figure 2. Diagram showing hierarchical habitat classification used in this study. ............ 7

Figure 3. Graph showing relation between mean daily air temperatures measured at 

Stanley Ranger Station, June through September 2005, and long-term values 

(1971 through 2000), upper Salmon River Basin, Idaho ................................. 13

Figure 4. Map showing location of study sites on lower Big Boulder Creek, diversions, 

streamflow-gaging stations, temperature monitoring locations, and Physical 

Habitat Simulation (PHABSIM) study site, upper Salmon River Basin, 

Idaho, 2005.................................................................................... 16

Figure 5. Graph showing daily mean discharge at Big Boulder Creek near 

Clayton (13297500), upper Salmon River Basin, Idaho, April 1 through 

September 30, 2005 ........................................................................ 17

Figure 6. Graph showing daily mean discharge for water year 2005 and 80-, 50-, and 

20-percent exceedance statistics for the period of record (1926–29, 2005) at 

Big Boulder Creek near Clayton (13297500), upper Salmon River Basin, Idaho, 

July 1 through September 30............................................................... 17

Figure 7. Graph showing maximum daily water temperature at Big Boulder Creek, upper 

Salmon River Basin, Idaho, June 12 through September 12, 2005 ..................... 19

Figure 8. Map showing location of study sites on Challis, Bear, and Mill Creeks, 

diversions, streamflow-gaging stations, temperature monitoring locations, and 

Physical Habitat Simulation (PHABSIM) study sites, upper Salmon River Basin, 

Idaho, 2005.................................................................................... 20

Figure 9. Graph showing maximum daily water temperature at Challis Creek, upper 

Salmon River Basin, Idaho, June 12 through September 12, 2005 ..................... 25

Figure 10. Graph showing maximum daily water temperature at Bear Creek (BE1), upper 

Salmon River Basin, Idaho, June 12 through September 12, 2005 ..................... 26

Figure 11. Graph showing maximum daily water temperature at Mill Creek (ML1), upper 

Salmon River Basin, Idaho, June 12 through September 12, 2005 ..................... 27

Figure 12. Map showing location of study sites on Morgan Creek, diversions, streamflowgaging stations, temperature monitoring locations, and Physical Habitat 

Simulation (PHABSIM) study sites, upper Salmon River Basin, Idaho, 2005 ......... 29

Figure 13. Graph showing daily mean discharge at Morgan Creek above West Fork 

Morgan Creek, near Challis (13299255), upper Salmon River Basin, Idaho, 

March 30 through September 30, 2005 ................................................... 30

Figure 14. Graph showing daily mean discharge for water year 2005, estimated long-term 

daily mean discharge, and estimated 80-, 50-, and 20-percent exceedance 

statistics at Morgan Creek above West Fork Morgan Creek, near Challis 

(13299255), upper Salmon River Basin, Idaho, July 1 through September 30......... 30

Figure 15. Graph showing maximum daily water temperature at Morgan Creek, upper 

Salmon River Basin, Idaho, June 12 through September 12, 2005 ..................... 32
Tables

Table 1. Basin and site characteristics for streamflow-gaging stations, diversions, and 

study sites, in the upper Salmon River Basin, Idaho, 2005.............................. 15

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

discharge values for Big Boulder Creek near Clayton (13297500), upper 

Salmon River Basin, Idaho.................................................................. 18

Table 3. Summary of habitat and hydrologic measurements for lower Big Boulder Creek 

(BB1), upper Salmon River Basin, Idaho, 2005 .......................................... 18

Table 4. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance 

discharge values for Challis Creek near Challis (13299000), upper 

Salmon River Basin, Idaho.................................................................. 21

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

discharge values for Challis Creek below Jeffs Creek, near Challis (13299200), 

upper Salmon River Basin, Idaho ......................................................... 22

Table 6. Summary of instantaneous discharge measurements for the Challis Creek Basin, 

upper Salmon River Basin, Idaho, water year 2005 .................................... 22

Table 7. Summary of habitat and hydrologic measurements for Challis Creek and major 

tributaries including upper Challis Creek (CH4), lower Bear Creek (BE1), upper 

middle Challis Creek (CH3), lower Mill Creeks (ML1), lower middle Challis Creek 

(CH2), and lower Challis Creek (CH1), upper Salmon River Basin, Idaho, 2005 ...... 23

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

discharge values for Morgan Creek above West Fork Morgan Creek near 

Challis (13299255), upper Salmon River Basin, Idaho.................................... 31

Table 9. Summary of habitat and hydrologic measurements for lower Morgan 

Creek (MC1), upper Salmon River Basin, Idaho, 2005 ................................. 31

Conversion Factors, Datum, and Acronyms

Conversion Factors

Multiply By To obtain

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

foot (ft) 0.3048 meter

inch (in.) 2.54 centimeter 

inch per year per foot [(in/yr)/ft] 83.33 millimeter per year per meter

mile (mi) 1.609 kilometer 

square foot (ft2) 0.09290 square meter

square mile (mi2) 2.590 square kilometer 

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

°F = (1.8×°C)+32

Datum

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.
vi

Acronyms

AVDEPTH/AVPERM Hydraulic parameter option in PHABSIM for Windows

BIA Bureau of Indian Affairs

BiOp Biological Opinion

CI Composite index

EPT Ephemeroptera, Plecoptera, and Trichoptera

ESA Endangered Species Act

FCRPS Federal Columbia River Power System

HABTAE Habitat program option in PHABSIM for Windows

HSC Habitat suitability criteria

IDEQ Idaho Department of Environmental Quality

IDFG Idaho Department of Fish and Game

IFIM Instream Flow Incremental Methodology

ITWG Interagency Technical Workgroup

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 System 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

WY05 Water year 2005
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 of the 

confluence with the Pahsimeroi River) in Idaho provided 

migration corridors and significant habitat for these ESA-listed 

species, in addition to the ESA-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 resulting from 

irrigation practices, have directly affected 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 collection of habitat and streamflow information for 

the Physical Habitat Simulation System (PHABSIM) model, a 

widely applied method to determine relations between habitat 

and discharge requirements for various fish species and life 

stages. Model simulation results can be used by resource 

managers to guide habitat restoration efforts by evaluating 

potential fish habitat and passage improvements by increasing 

or decreasing streamflow.

In 2005, instream flow characterization studies were 

completed on Big Boulder, Challis, Bear, Mill, and Morgan 

Creeks. Continuous streamflow data were recorded upstream 

of all diversions on Big Boulder. Instantaneous measurements 

of discharge were also made at selected sites. In addition, 

natural summer streamflows were estimated for each study site 

using regional regression equations. 

This report describes PHABSIM modeling results for 

bull trout, Chinook salmon, and steelhead trout during summer 

streamflows. Habitat/discharge relations were summarized 

for adult and spawning life stages at each study site. In 

addition, streamflow needs for riffle dwelling invertebrate taxa 

(Ephemeroptera, Plecoptera, and Trichoptera) are presented. 

Adult fish passage and discharge relations were evaluated 

at specific transects that were identified as potential lowstreamflow passage barriers at each study site. 

Continuous summer water temperature data for selected 

study sites were summarized and compared with Idaho Water 

Quality Standards and various water 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 of 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 trout in the basin migrate nearly 900 mi between 

the mountain streams at altitudes 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 trout 

and may be important for 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 listing these salmon and steelhead trout stocks 

as endangered or threatened under the Federal Endangered 

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

are severely depressed; fewer than 2 percent of drainage basins 

in the Columbia River Basin are classified as supporting 

Instream Flow Characterization of Upper Salmon River 

Basin Streams, Central Idaho, 2005

By Terry R. Maret, Jon E. Hortness, and Douglas S. Ott
strong, wild populations of steelhead trout or Chinook salmon 

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

of 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 trout 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 rivers and streams in the 

Salmon River Basin. 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 summer 

streamflows may decrease juvenile rearing space, resulting in 

poor growth and survival (Quinn, 2005). 

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. Stream 

temperatures are controlled naturally by interactions between 

solar radiation, ambient air temperature, streamflow, channel 

geomorphology, and riparian vegetation. Stream temperature 

tends to increase as water travels downstream. Human 

activities such as removal of riparian shading and alteration of 

streamflow can accentuate this increased water temperature. 

High water temperatures generally coincide with high 

ambient air temperatures and usually occur during July and 

August. Diversions of streamflow for agricultural purposes are 

at their highest and streamflows generally are at their lowest 

during July and August. 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 (cold 

blooded), 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 (Coutant, 1976; Beitinger 

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

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

unique water temperature requirements, and an individual 

species may have a unique water temperature requirement 

for each of its life stages. For example, salmonids require 

varying water 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 from 10.0o to 17.0oC. Adult spawning 

activities are triggered at water temperatures from 7.0o to 

14.0oC. Water temperatures greater than 21.0oC, can create 

thermal barriers that can block adult migration to spawning 

grounds (Poole and others, 2001). These thermal barriers 

can be created by diverting streamflow for irrigation during 

summer when air temperatures are highest. Exposure to 

water temperatures greater than 21.0oC for more than 1 week 

usually is fatal to adult Chinook salmon, whereas constant 

temperatures greater than 16.0oC 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 water temperatures range from 10.0o to 15.0oC. Bull 

trout passing into tributary streams to spawn in late summer 

may decrease when water temperatures exceed 13.0oC and 

may be blocked when water temperatures exceed 18.0oC. 

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

The Bureau of Reclamation was tasked through 

Reasonable and Prudent Alternative Action 149 of the 

National Oceanic and Atmospheric Administration (NOAA) 

Fisheries Biological Opinion (BiOp) of 2000 on the operation 

of the Federal Columbia River Power System (FCRPS) to 

address streamflow deficiencies in 16 priority subbasins in the 

Columbia River Basin (National Oceanic and Atmospheric 

Administration, 2000). Flow characteristic studies were 

done 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. Bureau of Reclamation 

considers flow characterization studies an integral part of 

information needed to correct flow deficiencies in the 10-year 

timeframe allotted for studies in each subbasin (Spinazola, 

2002). 

On November 30, 2004, NOAA Fisheries issued a new 

BiOp for the FCRPS in response to a court order in June 2003. 

Action 149 objectives are restated in specific metric goals in 

selected subbasins for entrainment (screens), streamflow, and 

channel morphology (passage and complexity) in the 2004 

BiOp.

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 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 

people inhabiting the basin also depend on streamflows used 

for agricultural, domestic, commercial, municipal, industrial, 

recreational, and other purposes. Developing an approach to 

meet the needs of both people and fish rests on understanding 

how much streamflow is needed by each. Water quantities 

   Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
needed for human uses frequently can be determined from 

available information; however, streamflow quantities needed 

for ESA-listed fish habitat conservation are difficult to identify 

because relevant information is rarely available.

Numerous methods can be used to determine streamflow 

needs for fish and wildlife (Instream Flow Council, 2004), but 

one of the most widely used is the Instream Flow Incremental 

Methodology (IFIM), developed in the 1970s by the U.S. Fish 

and Wildlife Service (USFWS). IFIM integrates water-supply 

planning concepts, analytical hydraulic engineering models, 

and empirically 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, IFIM is the most 

widely used method to determine streamflow needs for fish 

and wildlife in the United States (Instream Flow Council, 

2004). 

A major component of IFIM is a collection of computer 

algorithms called the Physical Habitat Simulation System 

(PHABSIM) model. 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 the 

weighted usable area (WUA) index, 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 ft of stream). PHABSIM simulates habitat/discharge 

relations for various species and life stages and allows 

quantitative habitat comparisons at different discharges. 

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 based on streamflow 

study results, streamflows needed for migration, spawning, 

and rearing for all fish will be systematically improved. 

Furthermore, restored streamflows could potentially improve 

spawning and rearing habitat in downstream reaches of the 

mainstem of the Salmon River. Additionally, if streamflows 

obtained from these projects are protected from downstream 

diversion, these benefits can be increased by improved 

conditions for survival throughout the Salmon River migration 

corridor, thereby improving long-term fish productivity. 

Purpose and Scope

This report summarizes instream flow characterization 

results for selected streams in the upper Salmon River 

Basin, Idaho. Natural streamflows were characterized using 

continuous summer streamflow data collected upstream 

of diversions at selected sites. Comparisons were reported 

between these data and monthly discharge exceedance 

estimates, based on regional regression analyses.

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

analyze hydrologic and biologic data for selected streams; (2) 

assemble habitat suitability curves for targeted species and life 

stages needed to complete PHABSIM modeling and analysis; 

(3) provide instream flow characterization results for selected 

streams to identify streamflow needs from July to September 

to provide fish passage and support various life stages of bull 

trout, Chinook salmon, and steelhead trout; and (4) evaluate 

effects of diversions on water temperature for the selected 

streams.

The ultimate goal 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 in the upper Salmon 

River Basin consisted 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 development of instream 

flow recommendations for preservation of important fishery 

resources. Between 1989 and 1992, BIA contracted with 

EA Engineering, Science, and Technology, Inc., 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, Inc., 1989, 1991a, 1991b, 1992a, 1992b, 1992c). 

In cooperation with the BIA, the USGS classified Salmon 

River subbasins based on basin and hydrologic characteristics 

to assist in filing water right claims (Lipscomb, 1998). R2 

Resource Consultants (2004) recently published a report 

about the SRA process describing methods, results, and flow 

recommendations for about 1,100 drainages primarily in the 

Salmon and Clearwater River Basins, Idaho. 

Investigations by the USFS also were done by Hardy 

and others (1992) 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 not published. The USGS completed instream flow 

studies on upper Salmon River Basin tributaries in 2003 and 

2004 (Maret and others, 2004; 2005). In addition, instream 

flow studies were completed on Big Timber, Big Eightmile, 

Bohannon, and Hayden Creeks in the Lemhi Basin (Sutton 

and Morris 2004; 2005) .

Introduction 
Various 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 proposes 

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 

could be substantial. NOAA Fisheries has draft protocols 

to estimate tributary streamflows to protect ESA-listed 

salmon (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 predictions.

Hydrologic studies by the USGS have provided 

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 can be 

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 Salmon River tributary streams. 

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, Inc. 

(1991a) developed a complete set of habitat suitability curves 

for depth, velocity, and substrate for most 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 involved formal meetings among fishery experts to 

reach a consensus on suitability curves for various species and 

life stages. 

In 2000, the USGS, in cooperation with the Idaho 

Department of Environmental Quality (IDEQ), initiated 

studies in the Salmon River Basin to document the natural 

spatial and temporal variability of stream water temperature 

and to examine relations among stream water temperature, 

environmental variables, and aquatic biota in streams 

minimally disturbed by human activities. Results showed that 

temperatures in these minimally disturbed streams commonly 

exceeded current State and Federal stream water temperature 

standards. 

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

water temperature regime of 183 minimally disturbed streams 

in the Salmon and Clearwater River Basins to develop a 

predictive stream water temperature model. A major finding of 

this study was that water temperatures in 100 percent (119 of 

119) of the streams in the Salmon River Basin failed to meet 

the IDEQ 9.0oC maximum daily-average temperature (MDAT) 

and the 13.0oC 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 in the upper Salmon River Basin 

exceeded the IDEQ 19.0oC MDAT criterion, and temperatures 

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

MDMT criterion for the protection of cold water biota. 

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

disturbed streams in the Salmon River Basin to document 

the temperature regime, characterize the aquatic biota 

distribution in streams representing a gradient of temperature, 

and describe the relations between environmental variables 

and benthic invertebrate and fish assemblages. Study results 

showed that the maximum weekly maximum temperature 

(MWMT) in 100 percent (33 of 33) of the streams for which 

water temperature data were available exceeded the U.S. 

Environmental Protection Agency (USEPA) criterion of 10oC 

for bull trout spawning and juvenile rearing. The MDMT 

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

criterion of 13.0oC for the protection of salmonid spawning; 

and the MDAT in all 33 streams exceeded the 9.0oC criterion 

for the protection of salmonid spawning. Results also showed 

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

exceeded the IDEQ 19.0oC MDAT and the 22.0oC MDMT 

criteria for the protection of coldwater biota.

Even though temperatures in all streams exceeded at 

least one water 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 a 

broad area such as the State of Idaho because streams differ in 

environmental complexity and biological diversity.

Continuous summer water temperature data recorded in 

2003 and streamflow relations were evaluated for Fourth of 

July Creek using a Stream Segment Temperature model that 

simulates mean and maximum daily water temperatures with 

changes in streamflow. Model simulation results from lower 

Fourth of July Creek predicted a slight increase in mean daily 

water temperature of 1.0oC because of the upstream diversions 

removing 72 percent of the streamflow (Maret and others, 

2005). 

 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Description of Study Area

The upper Salmon River Basin (fig. 1) is 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 about 

2,428 mi2. The basin contains large areas 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/yr. Precipitation primarily is 

snow, and peak flows in streams generally result from spring 

snowmelt.

The upper Salmon River Basin is 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 upper Salmon River Basin geology 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 drainage basins in the 

Salmon River Basin typically have high water clarity, 

coarse-grained substrates (cobble and boulders), high stream 

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

very sparse macrophyte growth. Designated beneficial uses 

for aquatic life of these study streams include cold water biota 

and salmonid spawning (Idaho Department of Environmental 

Quality, 2003). Limited water-quality sampling on small 

tributaries of the upper Salmon River Basin has indicated 

few signs of human activities (Ott and Maret, 2003). Based 

on IDEQ’s total maximum daily load assessments, higher 

elevation streams were not water-quality limited and all 

beneficial uses were fully supported (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. In contrast, lower 

elevation streams 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 diversions for irrigation. 

Ground water’s effect on streams in the area, especially 

smaller tributary streams, is important to the overall hydrology 

and biology. As is typical with streams in mountainous 

terrains, streamflow between precipitation and snowmelt 

periods generally is sustained by discharge from the local 

ground-water system. This is important because the area 

typically receives little precipitation during the late summer 

and early autumn months, which results in streamflows 

(baseflows) that can be directly related to local ground-water 

conditions. In addition, the discharge of relatively cold ground 

water into streams during baseflow conditions can have a 

significant effect on the overall water temperature of the 

stream. 

According to SNRA biologists, the greatest effects 

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 effects of dewatering these streams include 

losing valuable spawning and rearing habitats; blocking access 

to historical spawning and rearing habitat; and disrupting the 

aquatic ecosystem brought about by annual recurrence of 

unnaturally low streamflows. Most irrigation diversions in 

the study area are screened to prevent loss of fish. Water for 

irrigation in the basin generally 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 cold water 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 upper 

Salmon River tributary streams used by anadromous fish for 

spawning and rearing. According to IDFG, most tributary 

streams of the upper Salmon River offer cold water 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). In the past, the 

endangered sockeye salmon was found in five lakes in 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).

Introduction   
ID19-0028-SalmonRiver2005_fig01

SAWTOOTH

NATIONAL

RECREATION AREA

BOUNDARY

Yankee

Fork

Valley

Creek

Elk

Pole

Creek

Creek

Smiley

Creek

Squaw

Creek

Beaver

Creek

Iron Creek

Fourth of July Creek

Champion Creek

Thompson Creek

Creek

Morgan

West Fork

Creek

Bear

Creek Challis

Creek

Mill

Big Boulder 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

13294600

13295000

13299255

13299000

13299200

13292280

13297500

13296500

114°20’ 114°

44°

44°

20’

115° 114°40’

44°

40’

0

0

5

5

10 15 20 25 30 MILES

10 15 20 25 30 35 40 45 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; 1:500,000

I DAHO

Upper Salmon

River Basin

study area

Pahsimeroi River

Salmon

River

EXPLANATION

Valley Creek at upper USGS gage

Salmon River at USGS gage

U.S. GEOLOGICAL SURVEY

 STREAMFLOW-GAGING STATION

13292280

13294600

13295000 Valley Creek at lower USGS gage

13297500 Big Boulder Creek at USGS gage

13299000

13299200

13299255

Challis Creek at upper

 historical USGS gage

Challis Creek at lower

 historical USGS gage

Morgan Creek above

 West Fork Morgan Creek

13296500 Salmon River below Yankee Fork

Figure 1. Location of selected streamflow-gaging stations in the upper Salmon River Basin, Idaho.

 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Data Collection Methods

Site Selection 

A list of priority streams based on input from the 

Interagency Technical Workgroup was provided by the 

Bureau of Reclamation. USGS conducted a reconnaissance 

on each stream to locate diversions and select potential study 

sites. The Bureau of 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 geographic 

hierarchy is used to represent a study area in PHABSIM. The 

first-order subdivision of the study area is the stream segment. 

Stream segments typically are long sections of stream with 

a uniform flow regime and consistent geomorphology. Each 

stream segment, can have several habitat-related subdivisions, 

including representative reaches, mesohabitats, and 

microhabitats. 

Representative reaches and mesohabitat types describe 

the stream segment and make up the second-order division 

of the study area. A representative reach is about 10 to 15 

channel widths in length and typically contains many or 

all of the mesohabitat types present in the entire segment. 

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 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 

each mesohabitat proportion 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.

Either the representative reach or mesohabitat typing 

typically is used to describe the stream segment. In 2005, due 

to difficulty gaining access to private lands to walk streams for 

measuring mesohabitats, representative reaches were selected 

based on field reconnaissance from nearby public access areas 

and the use of topographical maps. When possible, a stream 

length exceeding 40 times the wetted channel width was 

walked to select a representative reach to assess. The various 

mesohabitats were measured in each reach and transects were 

weighted in the PHABSIM model according to their relative 

lengths in the reach. 

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 (fig. 2). Specifically, these mesohabitats included 

shallow and deep pools representing backwater with a 

hydraulic control. Slopes, designated as low, moderate, or high 

were measured qualitatively based on professional judgment 

and are not transferable between streams (for example, high 

slopes on one stream may or may not compare to high slopes 

on another). Because of the large variation in stream types, 

mesohabitat typing was based on relative changes in 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. 

Mesohabitat Type

Deep

 (thalweg not wadeable)

Shallow

 (thalweg wadeable)

Narrow channel

Wide channel

Pools

 (backwater

 with hydraulic

 control)

Slopes

 (riffles and runs;

 no backwater)

High

Moderate

Low

High

Moderate

Low

Figure 2. Hierarchical habitat classification used in this study. Mesohabitats are equivalent 

to geomorphic channel units such as riffles, pools, and runs.

Data Collection Methods 
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. Transects typically represent the 

most common habitats and hydraulic controls in each reach. 

Generally, one to two transects were selected to represent 

each major mesohabitat in each reach. Cell boundaries 

are defined by transects and verticals perpendicular to 

streamflow. 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 representative 

reach. Mesohabitats making up less than 10 percent of the 

representative reach generally were not included in the 

assessment.

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

subdivided by lateral stream cells with longitudinal boundaries 

and verticals along which measures of microhabitat are made. 

Microhabitats usually are shorter than one channel width and 

represent a relatively homogeneous area used by an individual 

fish (Bovee, 1997). Examples of microhabitat include undercut 

banks, velocity shelters behind boulders, and woody debris. 

Stream sites were established downstream of all 

diversions on each stream to evaluate the cumulative effect of 

multiple diversions. Additional study sites on the same stream 

were selected downstream of other upstream diversions if 

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

being diverted. 

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 

verticals in the transect.

Data were collected at about 30 to 40 verticals to 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. Velocity calibration 

sets were collected during two periods to represent a range 

of summer streamflows. 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). 

Hydrologic information for each study site was expressed 

using the estimated monthly 80-, 50-, and 20-percent 

exceedance discharge statistics. These statistics were estimated 

for each site using regional regression equations from Hortness 

and Berenbrock (2001). The regional regression equations use 

basin characteristics such as drainage area, precipitation, and 

basin slope to estimate streamflow statistics at ungaged sites. 

Exceedance discharges indicate the discharge that is expected 

to be equaled or exceeded a specific percentage of the time 

for a specific month or other time period. Estimates generated 

by these regional regression equations represent natural or 

unregulated streamflows.

Substrate and cover were also recorded. Substrate types 

were identified by visual observation and were classified as 

organic detritus, silt, sand, small gravel, coarse gravel, cobble, 

boulder, bedrock, and aquatic vegetation. 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 large gravel, boulder, or large cobble), 

aquatic vegetation, and overhanging vegetation (Raleigh and 

others, 1986). To characterize stream shading, percentage 

of canopy opening was estimated at each transect with a 

clinometer following procedures described by Fitzpatrick and 

others (1998).

Stream Temperature

Onset TidbiTTM data loggers were used to record 

stream temperature at several locations throughout the study 

area. Data logger deployment and data collection followed 

procedures outlined by Stevens and others (1975) and Zaroban 

(2000). 

To capture the natural thermal regime and to assess the 

effects of diversions on stream temperature, data loggers were 

deployed spatially throughout a stream. Where permission to 

access private land was granted, a data logger was placed far 

enough upstream of all diversions to avoid possible effects 

of diversions. Data loggers also were deployed 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.

 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Analytical Methods for Instream Flow 

Characterization

Physical Habitat Simulation Model

Hydraulic and habitat simulation models contained in 

PHABSIM (Waddle, 2001) were used to characterize instream 

physical attributes (depth, velocity, and substrate) during 

expected summer (July through September) streamflow. 

Estimates of fish cover also were recorded, but were not used 

in the model. To estimate 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 

the water-surface elevations and velocity distributions. Data 

required in this part of the model and collected in the field 

are: channel geometry, Manning’s roughness (n) values, 

water-surface elevations, water velocities, and stream 

discharges. Water-surface elevations can be calculated using 

one or any combination of the following methods: (1) stagedischarge relation or rating curve (STGQ), (2) Manning’s 

equation (MANSQ), or (3) step-backwater water-surface 

profile (WSP) (Waddle, 2001). In most cases, the stagedischarge 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 steps. First, attempts are made to match 

simulated water-surface elevations with measured elevations 

for the calibration discharges. Calibration is done by adjusting 

the n values or related roughness variables within a realistic 

range as observed in the field until simulated water-surface 

elevations match or nearly match measured elevations. 

A difference of 0.02 ft or less between the simulated and 

measured values typically is desirable (Waddle, 2001). 

Second, attempts are made to match simulated velocities at 

each transect with measured velocities for the calibration 

discharges. This calibration is done by adjusting local n

values in specific cells until simulated velocities match or 

nearly match measured velocities. It may be unrealistic to 

exactly simulate a measured velocity distribution. However, 

in relatively smooth, uniform channels, it may be possible to 

closely simulate a measured velocity. Velocity distributions 

for fairly rough, nonuniform channels are more difficult to 

simulate, and the final calibration values are based on the 

user’s selection of the simulation that best represents the 

measured values (J. Henriksen, U.S. Geological Survey, oral 

commun., 2004). Velocity adjustment factors that generally 

increase with increasing discharge (Waddle, 2001) also were 

used to evaluate model performance. Calibration data sets 

for each study site are available in IFG4 data files at http://

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

Habitat Modeling

Selection of Target Species and Habitat Suitability Criteria

PHABSIM use requires target species selection, life 

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

and habitat suitability criteria (HSC). This information 

was derived from previous SRA studies by the BIA 

and USFS in the Salmon River Basin (EA Engineering, 

Science, and Technology, Inc., 1991a, 1991b; R2 Resource 

Consultants, 2004; Rubin and others, 1991). Upon review 

of this information, the Interagency Technical Workgroup 

(ITWG) (see “Acknowledgments” for list of members) 

directed the USGS to target the ESA-listed species bull trout, 

Chinook salmon, and steelhead trout for juvenile, adult, and 

spawning life stages (J. Spinazola, Bureau of Reclamation, 

written commun., 2005). 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. The ITWG also directed the USGS to not include 

the fry life stage (<50 mm, or about 2 in.) because of the 

inability to accurately measure microhabitat parameters at a 

meaningful scale. 

Species-specific HSC that accurately reflect habitat 

requirements during the life stage of interest are essential 

to developing meaningful and defensible instream flow 

recommendations. Suitability criteria quantify the relative 

importance of depth, velocity, and channel index (substrate) 

for specific life stages of each species. HSC are interpreted 

using a suitability index (SI) on a scale of 0 to 1, with zero 

being unsuitable and one being most used or preferred. The 

best approach is to develop site-specific HSCs for each 

species and life stage of interest. Alternatively, HSCs can be 

developed from existing literature. 

Analytical Methods for Instream Flow Characterization 
Because time and budget constraints precluded 

developing stream-specific HSC, ITWG also directed the 

USGS to use existing HSC developed SRA processes. The 

fish species HSCs selected for this study were developed in 

the Pacific Northwest and Idaho. In addition, invertebrate 

HSCs published by Gore and others (2001) were used to 

simulate streamflow and habitat suitability for riffle dwelling 

Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa. These 

three orders of insects make up the predominant invertebrate 

fauna of riffle habitat and provide a major food source for 

stream dwelling trout and salmon (Gore and others 2001; 

Maret and others, 2001). Evaluating desirable streamflow 

needs for riffle habitat and associated invertebrates is 

particularly important because these are the first habitats to 

become dry when streamflows are reduced below baseflow. 

According to Jowett (2003) instream flow requirements for 

fish should also consider habitat for benthic invertebrates, 

particularly where food availability may limit fish numbers 

and (or) growth. The HSC 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.

Maximum juvenile WUAs and median (Q.50) summer 

(July and August) streamflow data collected by Maret and 

others (2004) from Fourth of July, Pole, Elk, and Valley 

Creeks revealed that maximum preferred juvenile salmonid 

habitat predicted by the model often was less than summer 

median streamflow. For example, a summer streamflow 

comparison from streams in the upper Salmon Basin 

established on average that maximum WUA for juvenile 

Chinook salmon were only 33 and 63 percent of the July 

and August Q.50, respectively. Similar relations between 

streamflow and maximum WUA also were determined for 

juvenile steelhead and bull trout. Reasons for this likely result 

from HSCs that were developed during drought conditions 

(Rubin and others, 1991) and the potential inability to measure 

accurately microhabitat parameters at a scale that would be 

meaningful using PHABSIM. Therefore, modeling results for 

the juvenile life stage are not presented. 

ITWG recommended a July through September study 

period because water is diverted for irrigation mostly during 

summer. High streamflows for channel maintenance generally 

have not been a problem in the upper Salmon River Basin 

(Bohn and King, 2000; M. Moulton, U.S. Forest Service, oral 

commun., 2003). 

The habitat program HABTAE in PHABSIM was used 

to estimate WUA for the simulated discharges of interest. 

HABTAE uses the SI values derived from each cell in a 

transect for depth, velocity, and substrate. The geometric 

mean calculation was used to derive the composite index (CI) 

score for each cell at a transect. The CI was calculated as the 

geometric mean of the input variable: 

CI = (SIdepth × SIvelocity × SIsubstrate ×...SIn)

l/n,

where

SIn is the suitability index value for variable n, and

n is the number of input variables (Waddle, 2001). Calculating the CI based on the geometric mean allows 

for more compensatory relations among variables than an 

arithmetic mean (J. Henriksen, U.S. Geological Survey, oral 

commun., 2003). For example, if two of three individual 

composite suitabilities are high (close to 1.0) and the third is 

low, the third individual composite suitability has a reduced 

effect on CI computation. 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.

Mean column velocities (0.6 ft of the depth) and default 

settings were used to compute SI scores for all species and 

life stages, except bull trout. Nose velocity settings were used 

for adult bull trout as recommended by EA Engineering, 

Science, and Technology, Inc. (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, 0.2-ft depth from 

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

velocity from mean column velocity (Waddle, 2001). 

Passage Criteria

For adult passage, the minimum depth criterion must 

be present greater than 25 percent of the total stream width 

and contiguous greater than at least 10 percent of the stream 

width at a representative transect (Thompson, 1972). 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 

0.6-ft depth criterion (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 

salmon were observed moving through a shallow riffle that 

was 0.2-ft deep on Valley Creek. Depths that would provide 

marginal adult Chinook passage also would meet the passage 

requirements for other adult and juvenile fish.

A hydraulic parameter option in 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 

stream width available for passage at the simulated discharges 

for each transect. Simulated discharge results graphically 

display the relation between discharge and the specified depth 

criteria over stream width.

10 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
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 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 MDAT, MDMT, MWMT, 

and maximum weekly-average (7-day) 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 22.0oC 

MDMT and 19.0oC MDAT for the protection of coldwater 

biota, and 13.0oC MDMT and 9.0oC 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 water bodies where 

they considered bull trout likely are present (40 CFR 131.

E.1.i.d, 1997). This rule set a criterion of 10.0oC MWMT 

during June through September for protection of bull trout 

spawning and juvenile rearing in natal streams. 

Although these stream temperature criteria have been 

established, a single stream temperature criterion for all 

streams may not accommodate the natural temperature 

variation in 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; Maret and others, 

2004, 2005). 

Guidelines for Using Study Results

The study 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 WUA output 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 or spawning 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 natural unregulated 

flow may not provide the discharge approaching the maximum 

WUA or water depth sufficient for adult passage. Also, 

WUA-discharge curves can be used to estimate how much 

habitat is gained or lost with incremental streamflow changes. 

In some cases, small streamflow changes can result in major 

habitat changes. WUA is an instantaneous representation of 

how much water it takes to create a certain amount of habitat. 

Seasonal, monthly, or daily streamflow regimes have to be 

applied to the instantaneous WUA curves to estimate how 

much habitat is actually present. The amount of WUA lost or 

gained can be determined by comparison with a reference, or 

unregulated, streamflow condition. Maximum, percentiles, 

or inflections typically are selected from these curves at the 

protection level desired or at points above which greater flow 

amounts provide only minor gains in usable habitat. In streams 

with more than one species of interest, study results should be 

reviewed to ensure that 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 and represent potential passage 

barriers or “bottlenecks.” If available, results from multiple 

passage transects can be averaged to represent overall 

passage conditions and streamflow needs for a particular 

stream segment. 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. Passage transects 

not representative of mesohabitats and (or) not perpendicular 

to the streamflow were not included in PHABSIM habitat 

modeling. 

The mechanisms by which the various components are 

integrated and the relative importance they are assigned in the 

water-management decision process is a matter of professional 

judgment and beyond the scope of this study. Failure to 

provide adult fish passages 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 

passage is an additional consideration for the adult life stage. 

If possible, target flows should not reduce the water depth less 

than that required for adult fish passage. In addition, providing 

streamflow for optimum protection of riffle habitat will ensure 

healthy invertebrate communities, which are a major food 

source for fish.

Discharge estimates providing maximum WUA for 

juvenile salmonid life stages are usually less than summer 

base flows, indicating a disconnect between the PHABSIM 

model simulation results and actual juvenile salmonid 

needs (Maret and others, 2004). 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 

Analytical Methods for Instream Flow Characterization 11
WUA is less than estimated unimpaired summer base flow, the 

unimpaired summer base flow should 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 (including escape 

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 

essential 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, 

shielded microhabitat locations, 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 using habitat suitability criteria 

developed from foraging models (Baker and Coon, 1997) and 

(or) more comprehensive habitat parameter modeling.

To focus integration of the various modeling results 

and relevant species and life stages, a priority species and 

life stage ranking approach should be developed for each 

stream and period of concern. For example, the USFS 

prioritized ESA-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 target 

flow selection using the assumption that the priority life 

stage would require higher streamflows than other life stages. 

This priority ranking generally would be (from high to 

low) for small tributary streams of the upper Salmon River 

Basin: passage > spawning > adult > juvenile. The ranking 

approach should involve discussions among resourcemanagement agency representatives familiar with the streams 

of interest (J. Spinazola, Bureau of Reclamation, written 

commun., 2005). Once the priority species and life stage 

are ranked, each study site should be examined to determine 

streamflow and passage conditions for the period of interest. 

Results from PHABSIM provide a science-based linkage 

between biology and river hydraulics; however, no one single 

answer can be determined 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 mi2 ) to the Salmon 

River, a greater discharge proportion is required to provide 

suitable water depths for fish habitat and connectivity for 

passage than larger streams (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 in 

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. In addition, 

PHABSIM does not estimate flow or downstream migrants’ 

habitat needs or spring runoff conditions necessary for channel 

morphology maintenance or riparian zone functions. Arthaud 

and others (2001) have shown that downstream migrant 

survival can increase significantly with discharge; therefore, 

high spring flows that mimic the natural hydrograph should 

be considered in managing streamflows outside PHABSIM 

analysis. 

Climatic and Hydrologic Conditions 

During 2005

Climatic and hydrologic conditions in the upper Salmon 

River Basin generally were below normal (30-year record, 

1971–2000 for climatic conditions; long-term means for 

hydrologic conditions) during water year 2005 (WY05). 

Monthly snowpack levels were significantly below normal 

between January 1 and June 1, 2005. The average air 

temperature during WY05 was slightly higher than the 30-year 

average, whereas the average monthly air temperatures were 

both above and below average. Annual mean streamflows in 

the basin were significantly below the long-term means, as 

were monthly mean streamflows.

Climatic Conditions

Average monthly snowpack levels for the Salmon 

River Basin upstream of Salmon, Idaho, ranged from 34 to 

79 percent of normal from January 1 to June 1, 2005. Average 

12 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
snowpack value for this area on April 1, 2005, was 61 percent 

of normal (Natural Resources Conservation Service, 2006b). 

The most commonly used snowpack condition indicator is 

the April 1 value because in most years it is the final value 

calculated before snowmelt begins.

Measurement sites in the general vicinity of the study 

sites include Galena Summit (at the headwaters of the Salmon 

River), Mill Creek Summit (at the headwaters of Yankee 

Fork), and Morgan Creek (at the headwaters of Morgan 

Creek). Specific snowpack levels at these sites on April 1, 

2005, were: Galena Summit, 79 percent of normal; Mill Creek 

Summit, 59 percent of normal; and Morgan Creek, 51 percent 

of normal (Natural Resources Conservation Service, 2006a).

Mean air temperature at Stanley, Idaho, during WY05 

was about 1.94oC (35.5oF), slightly higher than the 30-year 

(1971-2000) mean of 1.78oC (35.2oF). Mean daily air 

temperatures generally were higher during July and lower 

during June, August, and September 2005, than during the 

long-term (1971–2000) record (fig. 3). Mean monthly air 

temperatures during the period when snowpack generally 

accumulates (October through April) were somewhat 

variable. Mean air temperatures during October, November, 

and February were below the 30-year mean; those during 

December, January, March, and April were above the 30-year 

mean (Western Regional Climate Center, 2006).

Hydrologic Conditions

Annual mean streamflows at the long-term USGS 

streamflow-gaging stations on Valley Creek at Stanley 

(13295000; 65 years of record) and on the Salmon River 

below Yankee Fork (13296500; 75 years of record) for WY05 

were both about 30 percent below the long-term means. 

Annual mean streamflow at Valley Creek at Stanley was 139 

ft3/s compared to the long-term mean of 198 ft3/s; and, the 

annual mean streamflow at the Salmon River below Yankee 

Fork was 683 ft3/s, compared to the long-term mean of 970 ft3/

s. All monthly mean streamflows for Valley Creek at Stanley 

were less than the long-term means. Similarly, all monthly 

mean streamflows at Salmon River below Yankee Fork also 

were less than the long-term means.

MEAN DAILY AIR TEMPERATURE, IN DEGREES CELSIUS

DATE

June July August September

24

22

20

18

16

14

12

8

6

4

2

0

10

2005

1971–2000

Figure 3. Relation between mean daily air temperatures measured at Stanley Ranger Station, June through 

September 2005, and long-term values (1971 through 2000), upper Salmon River Basin, Idaho.

Climatic and Hydrologic Conditions During 2005 13
Results of Study Site Investigations

PHABSIM investigations were done on six Salmon 

River tributaries during summer 2005. Data were collected 

at eight study sites (table 1): one site on lower Big Boulder 

Creek (BB1), four sites on Challis Creek (CH1, CH2, CH3, 

and CH4) and two of its perennial tributaries, lower Bear 

Creek (BE1) and lower Mill Creek (ML1), and one site on 

lower Morgan Creek (MC1). A plan view of each PHABSIM 

study site showing locations of specific transects are shown 

in the appendixes, figs. A1, B1, C1, D1, E1, F1, G1, and 

H1. Fishery information from Murphy and Yankey (2003a, 

2003b) were used to help with selection of study sites on 

Challis and Morgan Creeks. PHABSIM WUA results are 

presented for adult and spawning bull trout, Chinook salmon, 

and steelhead trout for each study site. In addition, WUA 

results are presented for riffle dwelling invertebrate taxa 

(Ephemeroptera, Plecoptera, and Trichoptera) for each site. 

Because of the concerns about PHABSIM modeling results 

for juveniles, they are not presented in this report. Mulitple 

passage transects also were evaluated for various depth 

criteria at each study site.

In addition to instantaneous streamflow data collected 

at these study sites, continuous streamflow was recorded at 

USGS streamflow-gaging stations upstream of all diversions 

on the Salmon River (SRG), Valley Creek (VCGU), Big 

Boulder Creek (BBG) and Morgan Creek above West Fork 

Morgan Creek (MCabvWFMC). Long-term streamflow 

information is lacking in the upper Salmon River Basin, 

especially for basins smaller than 20 to 30 mi2. Additional 

streamflow data collected in these smaller basins not only 

would provide much needed information, but also could 

improve the accuracy of regression equations used to estimate 

streamflows at ungaged sites.

Continuous summer water temperatures were recorded 

at BBG, BB1, CH4, BE1, CH3, ML1, CH2, CH1, Morgan 

Creek above Alder Creek (MCabvAC), MCabvWFMC, 

and MC1. Permission to access private property precluded 

installation of data loggers above diversions on Bear and 

Mill Creeks.

Big Boulder Creek

Big Boulder Creek is an easterly flowing stream in the 

central part of the upper Salmon River Basin. Big Boulder 

Creek is a tributary to the East Fork Salmon River and its 

headwaters originate in the White Cloud Peaks (fig. 1). The 

Big Boulder Creek basin covers 26.9 mi2, of which about 41 

percent is forest. Mean elevation in the basin is about 8,810 ft 

above sea level and the basin receives an average of 29.1 in/yr 

of precipitation.

Hydrology

A short-term streamflow-gaging station (Big Boulder 

Creek near Clayton; 13297500; BBG) was installed on Big 

Boulder Creek about 0.75 mi upstream of the confluence 

with the East Fork Salmon River and operated from April 1 

through October 3, 2005. The USGS also operated a long-term 

streamflow-gaging station at this location from May 1926 

through January 1930. This gaging station is upstream of the 

two active diversions on Big Boulder Creek (fig. 4). A plot of 

the continuous daily mean discharge at BBG during WY05 is 

presented in figure 5, along with markers indicating when field 

data were collected at study site BB1, between the mouth and 

the first upstream diversion.

Additional analyses were completed to relate streamflows 

in Big Boulder Creek during WY05 to long-term streamflows. 

The July, August, and September daily mean discharge 

hydrograph at BBG for WY05 and the 80-, 50-, and 20-

percent monthly exceedance statistics for the period of record 

(1926-29 and 2005) are presented in figure 6. The plot shows 

that WY05 streamflows in Big Boulder Creek generally were 

near or slightly below the long-term median (50-percent 

exceedance) during the months shown. Analyses of WY05 

and long-term monthly exceedance discharge data for Big 

Boulder Creek are presented in table 2. The July, August, 

and September 80-percent exceedances for WY05 were 

slightly above the long-term values, although the 20-percent 

exceedances were all below the long-term values. Table 2

also shows the 80-, 50-, and 20-percent monthly exceedance 

discharge estimates and confidence limits based on regional 

regression equations (Hortness and Berenbrock, 2001). 

Comparison between long-term statistic values and values 

calculated on the basis of the regression equations can provide 

some insight as to the applicability of the regression equations 

for Big Boulder Creek. In this case, the regression estimates 

tend to be lower than the long-term values, indicating that the 

equations, to some degree, could underestimate streamflow 

conditions in Big Boulder Creek.

Habitat Modeling and Passage Criteria

The lower Big Boulder Creek (BB1) discharges required 

for maximum WUA ranged from 24 to 39 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout 

(table 3). Discharge required for maximum WUA was 24 ft3/s 

for EPT taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged from 

18 to 27 ft3/s for the depth criterion of 0.6 ft greater than 25 

percent of the total channel width and 15 to 27 ft3/s greater 

than 10 percent of the contiguous channel width, respectively 

(see transects 1, 4, and 6 photographs at http://id.water.usgs.

gov/projects/salmon_streamflow). Appendix A provides more 

information summarizing these study results. 

14  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table 1. Basin and site characteristics for streamflow-gaging stations, diversions, and study sites, in the upper Salmon River Basin, 

Idaho, 2005.

[Site locations shown in figure 1. Site type: C, continuous streamflow recorded; M, instantaneous streamflow measured; P, Physical Habitat Simulation (PHABSIM) study site; T, continuous water temperature recorded; W, surface-water pump withdrawal. Latitude and longitude, in degrees, minutes, and seconds. 

Abbreviations: USGS, U.S. Geological Survey; USFS, U.S. Forest Service; mi2, square mile; in., inch; –, no data]

Site No. Site name Site 

type

Latitude Longitude

Basin 

area 

(mi2)

Basin slope 

(percentage)

Mean 

elevation 

(feet above 

sea level)

Percent 

forest

Mean 

annual 

precipitation

(in.)

Study site

SRG 

13292280

Salmon River at 

USGS gaging 

station

C, M 435407 1144724 27.5 35 8,300 65 36 –

VCGU 

13294600

Valley Creek at upper 

USGS gaging 

station

C, M 441857 1150401 29.4 30 7,695 80 27 –

VCGL 

13295000

Valley Creek at lower 

USGS gaging station at Stanley

C, M 441321 1145549 148 26 7,320 63 24 –

BBG 

13297500

Big Boulder Creek at 

USGS gaging station near Clayton

C, M, T 440653 1142624 26.9 37.1 8,810 41.3 29.1 –

BB1 Lower Big Boulder 

Creek

M, P, T 440658 1142605 27 37.1 8,810 41.2 29.1 Mouth upstream to 

diversion

CH4 Upper Challis Creek M, P, T 443408 1142146 32.4 35.9 7,920 73.5 27.4 From confluence with 

Bear Creek upstream to Lodgepole 

Creek 

BE1 Lower Bear Creek M, P, T 443411 1142150 14.1 38.6 8,170 69 27.1 Mouth upstream to 

diversion

CHHGU 

13299000

Challis Creek at 

upper historical 

USGS gaging 

station

C 443420 1141820 85 37.2 7,790 62.4 25.6

CH3 Upper Middle Challis 

Creek

M, P, T 443414 1141812 84.9 37.2 7,780 62.2 25.6 From Highline Ditch 

Canal upstream to 

Bear Creek 

CHHGL

13299200

Challis Creek at 

lower historical 

USGS gaging 

station

C 443341 1141642 91.2 36.6 7,700 58.5 24.9

ML1 Lower Mill Creek M, P, T 443336 1141631 28.3 36.2 7,650 51 24 Mouth upstream diversion

CH2 Lower Middle Challis 

Creek

M, P, T 443344 1141448 123 36.1 7,620 55.1 24.1 Mouth upstream to 

Highline Ditch 

Canal

CH1 Lower Challis Creek M, P. T 443411 1141120 148 34.9 7,450 48.9 23.1 Mouth upstream to 

Highline Ditch 

Canal

MCabvAC Morgan Creek above 

Alder Creek

M, T 444831 1141540 3.4 33.7 7,470 77.5 24.8 –

MCabvWFMC 

13299255

Morgan Creek above 

West Fork Morgan 

Creek

C, M, T 444102 1141447 60.2 34.9 7,320 48.2 21.9 –

MC1 Lower Morgan Creek M, P, T 443705 1141054 107 35.7 7,140 443.1 20.1 Mouth upstream to 

Mud Spring Gulch

Results of Study Site Investigations 15
ID19-0028-SalmonRiver2005_fig04

100 200 300 400 500 600 METERS

0 500

0

1000 1500 2000 FEET

EXPLANATION

Privately owned land

Streamflow, PHABSIM, and temperature site

Streamflow and temperature site

Diversion

Big

Boulder

Creek

East

Fork

Salmon

Rive

BB1 r

BBG

114°26'20" 114°26'10" 114°26' 114°25'50"

44°

06'

50"

44°

07'

44°

07'

10"

Big Boulder Creek Road

East Fork Road

Upper Salmon

River Basin

Figure location

Figure 4. Location of study sites on lower Big Boulder Creek, diversions, streamflow-gaging stations, 

temperature monitoring locations, and Physical Habitat Simulation (PHABSIM) study site, upper Salmon River 

Basin, Idaho, 2005. Diversion locations were determined by U.S. Geological Survey.

16  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
ID19-0028-SalmonRiver2005_fig05

0

10

20

30

40

50

60

70

80

APRIL MAY

DISCHARGE, IN CUBIC FEET PER SECOND

JUNE JULY AUGUST SEPTEMBER

DATE

Study site visit:

Big Boulder Creek #1 (BB1)

June 21, 2005

Study site visit:

Big Boulder Creek #1 (BB1)

April 27, 2005

Figure 5. Daily mean discharge at Big Boulder Creek near Clayton (13297500), upper Salmon River Basin, Idaho, 

April 1 through September 30, 2005.

Daily mean discharge-WY05

80-percent exceedance

50-percent exceedance (median)

20-percent exceedance; 1926-29, 2005

0

20

10

60

70

50

40

30

DISCHARGE, IN CUBIC FEET PER SECOND

JULY AUGUST

DATE

SEPTEMBER

Figure 6. Daily mean discharge for water year 2005 and 80-, 50-, and 20-percent exceedance statistics for the period 

of record (1926–29, 2005) at Big Boulder Creek near Clayton (13297500), upper Salmon River Basin, Idaho, July 1 

through September 30.

Results of Study Site Investigations 17
Summer (July through September) discharges for BB1 

were estimated on the basis of regression equations and are 

listed in table 3. Median discharge (Q.50) estimates were 

32.1 ft3/s for July, 15.1 ft3/s for August, and 10.7 ft3/s for 

September. The mean annual discharge estimate was 15.2 ft3/s. 

Stream Temperature

Temperature recording data loggers were deployed at 

BBG and BB1 in early June 2005 (fig. 7). Data loggers were 

retrieved in mid-September 2005. After downloading and 

reviewing the data, June 12 through September 12 (93 days) 

was selected as the period of record for calculating stream 

temperature metrics.

Analysis of the stream temperature records for Big 

Boulder Creek indicated a slight warming trend downstream of 

BBG to BB1 (fig. 7). However, the difference in temperature 

between BBG and BB1 was only slightly greater than the 

measurement error associated with the temperature recording 

data logger (± 0.4). The difference in MDMT between BBG 

and BB1 on any given day was less than 0.5oC, 97 percent (3 

of 93 days) of the time.

Individual metric calculation results showed the MDMT 

was 16.2oC at BBG and 16.6oC at BB1, well below the 

MDMT threshold of 21.0oC that, according to Poole and 

others (2001), can create a thermal barrier that would block 

adult Chinook salmon from migrating to their spawning 

grounds. The MDMT at both sites also was below the 18.0oC 

threshold that may block bull trout migration (J. Dunham, U.S. 

Forest Service, written commun., 2004).

Table 2. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance discharge values for Big Boulder Creek near Clayton 

(13297500), upper Salmon River Basin, Idaho.

[Values presented in cubic feet per second. Long term: Based on data for water years 1926–29 and 2005]

July August September

Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Q.80 Q.50 Q.20

Water year 2005 25.7 38.2 54.1 15.1 17.8 22.9 10.3 11.5 12.4

Long term 24.7 43.6 65.4 14.7 22.1 28.0 8.00 12.5 16.0

Regional regression equations

Upper confidence limit 40.4 58.6 81.1 21.4 32.7 36.9 15.4 22.2 23.2

Estimate 18.2 32.0 51.8 10.2 15.0 23.1 7.56 10.6 15.0

Lower confidence limit 8.21 17.5 33.1 4.85 6.88 14.4 3.71 5.06 9.69

Table 3. Summary of habitat and hydrologic measurements for lower Big Boulder Creek (BB1), upper Salmon River Basin, Idaho, 2005.

[Values presented in cubic feet per second. Discharge passage criteria: Passage criteria taken from Thompson (1972) and Scott and others (1981); both width 

criteria must be met to ensure passage. Channel width: Represents measurements at three transects. Discharge estimates: Based on regional regression 

equations using basin and climatic characteristics (Hortness and Berenbrock, 2001); Q.xx, daily discharge exceeded xx percent of the time during the specified month; Qa, mean annual discharge. Abbreviations: WUA; weighted usable area; WUA optimum discharge estimates were based on PHABSIM (Physical 

Habitat Simulation) model output; EPT, Ephemeroptera, Plecoptera, and Trichoptera taxa; ND, not determined]

Lifestage

Discharge required for 

maximum WUA

Discharge required for 

adult salmonid passage 

0.6-foot depth criterion Discharge estimates

Channel width

Bull trout Chinook 

salmon

Steelhead 

trout

EPT 

invertebrates

Greater than

25 percent 

(total)

Greater than

10 percent

(contiguous)

July August September

Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Qa

Adult 24 39 39 ND 27, 18, 21 27, 15, 15 18.2 32.1 52.0 10.2 15.1 23.2 7.6 10.7 15.1 15.2

Spawning 33 39 39 ND ND ND

Immature ND ND ND 24 ND ND

18  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
ID19-0028-SalmonRiver2005_fig07

DATE

DAILY WATER TEMPERATURE, IN DEGREES CELSIUS

JUNE JULY AUGUST SEPTEMBER

6

8

10

12

14

16

18

Big Boulder Creek (BB1)

Big Boulder Creek at U.S. Geological Survey 

gaging station (BBG)

Figure 7. Maximum daily water temperature at Big Boulder Creek, upper Salmon River Basin, Idaho, June 12 through 

September 12, 2005.

The MDAT was 13.5oC at BBG and 14.0oC at BB1, well 

below the 17.8oC MDAT upper temperature threshold that 

according to McHugh and others (2004) can decrease the 

survival rate of summer Chinook salmon juveniles in natal 

streams.

Comparing the temperature regime at the two sites on 

Big Boulder Creek to the IDEQ criteria for protection of 

coldwater biota (applicable from June 22 through September 

21) indicates the temperature regime at BBG and BB1 was 

below the 19.0oC MDAT and 22.0oC MDMT criteria. A 

summary of individual temperature metrics for all study sites 

can be accessed at http://id.water.usgs.gov/projects/salmon_

streamflow.

Challis Creek and Major Tributaries

Challis Creek is an easterly flowing tributary to the 

Salmon River with its mouth just north of Challis, Idaho. 

The Challis Creek headwaters are along the northern-most 

boundary of the upper Salmon River Basin (fig. 1). The 

Challis Creek Basin covers about 148 mi2, of which about 

49 percent is forested. Mean elevation in the basin is about 

7,450 ft above sea level and the basin receives an average of 

23.1 in/yr of precipitation. Six study sites were in the Challis 

Creek Basin. Four of those sites were on the main stem of 

Challis Creek (CH1, CH2, CH3, and CH4) and the other two 

sites were on Bear Creek (BE1) and Mill Creek (ML1), both 

major tributaries of Challis Creek (fig. 8).

Results of Study Site Investigations 19
ID19-0028-SalmonRiver2005_fig08

Creek

Lodgepole

Salmon River

Salm

o

n

River

Salm

o

n

River

114°28' 114°24' 114°20' 114°16' 114°12'

44°

34'

44°

30'

44°

32'

Challis

CHHGU

CH1

CH2

ML1

CH3 CH4

BE1

US

93

CHHGL

CH4

CHHGU

EXPLANATION

Privately owned land

Streamflow, PHABSIM, and temperature site

Historical USGS gaging station

Diversion

Darling

Mill

Creek

Creek

Creek

Challis

Highline Canal

Mill

Creek

Creek

Creek

Challis

Bear

Creek

Challis

Darling

Creek

White Valley Cr

Eddy

Cr

0 .5 1

.5

2 3 4 5 MILES

Upper Salmon 0 1 2 3 4 5 6 7 KILOMETERS

River Basin

Figure location

Figure 8. Location of study sites on Challis, Bear, and Mill Creeks, diversions, streamflow-gaging stations, temperature 

monitoring locations, and Physical Habitat Simulation (PHABSIM) study sites, upper Salmon River Basin, Idaho, 2005. Diversion 

locations were taken from Montgomery and others (2002).

20 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Hydrology

No continuous record streamflow data were collected 

on Challis Creek during WY05. Historical continuous record 

streamflow data are available for locations on Challis Creek 

about 6.9 (Challis Creek near Challis; 13299000) and 4.9 mi 

(Challis Creek below Jeffs Creek, near Challis; 13299200) 

upstream of the mouth for water years 1944-63 and 1963-70, 

respectively. The 80-, 50-, and 20-percent monthly exceedance 

discharge values for those gaging stations for the periods of 

record along with exceedance estimates derived from regional 

regression equations (Hortness and Berenbrock, 2001) are 

presented in tables 4 and 5. These values indicate that the 

regression equations generally may tend to underestimate 

monthly streamflow statistics in the Challis Creek Basin. 

In addition to historical data, instantaneous discharge 

measurements were made at all study sites during water WY05 

and are presented in table 6. Because of their proximity, the 

similarities in size, and other basin characteristics of the 

Challis and Morgan Creek basins, it also may be possible to 

make some inferences as to the characteristics of streamflow 

in Challis Creek based on information from Morgan Creek.

Habitat Modeling and Passage Criteria

Upper Challis Creek (CH4) discharges required for 

maximum WUA ranged from 22 to 37 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout 

(table 7). Discharge required for maximum WUA was 16 ft3/s 

for EPT taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged from 

16 to 22 ft3/s for the depth criterion of 0.6 ft greater than 25 

percent of the total channel width and 10 to 19 ft3/s greater 

than 10 percent of the contiguous channel width, respectively 

(see transects 3, 4, and 5 photographs at http://id.water.usgs.

gov/projects/salmon_streamflow). Appendix B provides more 

information summarizing these study results. 

Summer (July through September) discharges for CH4 

were estimated on the basis of regression equations and are 

listed in table 7. Median discharge (Q.50) estimates were 17.3 

ft3/s for July, 8.7 ft3/s for August, and 6.9 ft3/s for September. 

The mean annual discharge estimate was 17.4 ft3/s. 

Lower Bear Creek (BE1) discharges required for 

maximum WUA ranged from 8 to 26 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout 

(table 7). Discharge required for maximum WUA was 11 ft3/s 

Table 4. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance discharge values for Challis Creek near Challis 

(13299000), upper Salmon River Basin, Idaho.

[Values presented in cubic feet per second. Long term: Based on data for water years 1944–63]

July August September

Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Q.80 Q.50 Q.20

Long term 48.1 60.7 82.8 29.6 38.5 48.4 21.2 25.7 32.0

Regional regression equations

Upper confidence limit 61.4 88.2 129 34.5 52.6 57.4 29.5 41.7 42.7

Estimate 27.7 48.4 82.4 16.4 24.1 35.9 14.5 19.9 27.6

Lower confidence limit 12.5 26.2 52.6 7.80 11.1 22.5 7.10 9.50 17.8

Results of Study Site Investigations 21
July August September

Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Q.80 Q.50 Q.20

Long term 47.0 67.6 102 37.1 46.0 54.7 22.4 27.1 38.2

Regional regression equations

Upper confidence limit 59.4 85.6 127 33.6 51.2 56.8 29.1 41.3 42.9

Estimate 26.8 46.7 81.1 16.0 23.5 35.5 14.3 19.7 27.7

Lower confidence limit 12.1 25.5 51.8 7.60 10.8 22.2 7.00 9.40 17.9

Table 6. Summary of instantaneous discharge measurements for 

the Challis Creek Basin, upper Salmon River Basin, Idaho, water 

year 2005.

[Site locations shown in figure 8. Discharge: Values presented in cubic feet 

per second. Abbreviations: –, no data available]

Date

Discharge

CH4 BE1 CH3 ML1 CH2 CH1

04-20-05 – – – – – 2.89

04-21-05 – – – – 6.18 –

04-22-05 – – 10.99 3.24 – –

04-25-05 6.97 – – – – –

04-26-05 – 3.72 – – – –

05-22-05 – 32.6 – 27.4 – –

05-23-05 49.0 – – – – –

05-24-05 – – 102 – 85.5 74.4

06-06-05 – – – – 57.9 46.8

06-07-05 35.1 27.4 78.1 24.4 – –

07-15-05 13.4 14.4 35.9 6.07 – 2.52

08-12-05 17.3 7.22 29.7 3.28 4.59 .73

09-13-05 13.2 4.84 21.2 2.89 .68 .41

Table 5. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance discharge values for Challis Creek below Jeffs Creek, 

near Challis (13299200), upper Salmon River Basin, Idaho.

[Values presented in cubic feet per second. Long term: Based on data for water years 1963–70]

for EPT taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged 

from 5 to 14 ft3/s for the depth criterion of 0.6 ft greater than 

25 percent of the total channel width and 4 to 14 ft3/s greater 

than 10 percent of the contiguous channel width, respectively 

(see transects 3, 5, and 6 photographs at http://id.water.usgs.

gov/projects/salmon_streamflow). Appendix C provides more 

information summarizing these study results. 

Summer (July through September) discharges for BE1 

were estimated on the basis of regression equations and are 

listed in table 7. Median discharge (Q.50) estimates were 10.1 

ft3/s for July, 5.1 ft3/s for August, and 3.8 ft3/s for September. 

The mean annual discharge estimate was 8.9 ft3/s. 

Upper middle Challis Creek (CH3) discharges required 

for maximum WUA ranged from 19 to 67 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout 

(table 7). Discharge required for maximum WUA was 27 ft3/s 

for EPT taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged from 

<11 to 23 ft3/s for the depth criterion of 0.6 ft greater than 25 

percent of the total channel width and <11 to 11 ft3/s greater 

than 10 percent of the contiguous channel width, respectively 

(see transects 1, 5, and 6 photographs at http://id.water.usgs.

gov/projects/salmon_streamflow). In some cases, the passage 

criteria were less than the lower limit of the model conditions. 

In those cases graphs for a given transect may be useful to 

estimate the discharge required for passage. Appendix D

provides more information summarizing these study results. 

22 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table 7. Summary of habitat and hydrologic measurements for Challis Creek and major tributaries including upper Challis Creek (CH4), 

lower Bear Creek (BE1), upper middle Challis Creek (CH3), lower Mill Creeks (ML1), lower middle Challis Creek (CH2), and lower Challis 

Creek (CH1), upper Salmon River Basin, Idaho, 2005.

[Values presented in cubic feet per second. Discharge passage criteria: Passage criteria taken from Thompson (1972) and Scott and others (1981); both width 

criteria must be met to ensure passage. Channel width: Represents measurements at three transects. Discharge estimates: Based on regional regression 

equations using basin and climatic characteristics (Hortness and Berenbrock, 2001); Q.xx, daily discharge exceeded xx percent of the time during the specified month; Qa, mean annual discharge. Abbreviations: WUA; weighted usable area; WUA optimum discharge estimates were based on PHABSIM (Physical 

Habitat Simulation) model output; EPT, Ephemeroptera, Plecoptera, and Trichoptera taxa; ND, not determined; <, less than]

Lifestage

Discharge required for 

maximum WUA 

Discharge required for adult 

salmonid passage 0.6-foot 

depth criterion Discharge estimates

Channel width

Bull 

trout

Chinook 

salmon

Steelhead 

trout

EPT 

invertebrates

Greater than

25 percent 

(total)

Greater than

10 percent

(contiguous)

July August September

Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Qa

Upper Challis Creek (CH4)

Adult 25 34 34 ND 22, 16, 19 19, 10, 13 9.9 17.3 31.0 6.0 8.7 14.0 5.0 6.9 10.3 17.4

Spawning 22 37 37 ND ND ND

Immature ND ND ND 16 ND ND

Lower Bear Creek (BE1)

Adult 8 20 20 ND 14, 11, 5 14, 8, 4 6.0 10.1 17.8 3.6 5.1 8.1 2.8 3.8 5.6 8.9

Spawning 26 26 26 ND ND ND

Immature ND ND ND 11 ND ND

Upper Middle Challis Creek (CH3)

Adult 19 67 67 ND 23, <11, <11 11, <11, 

<11

27.6 47.8 82.0 16.3 24.0 35.7 14.4 19.9 27.5 46.6

Spawning 35 67 67 ND ND ND

Immature ND ND ND 27 ND ND

Lower Mill Creek (ML1)

Adult 9 18 18 ND 9,12, 6 3, 9, 3 6.8 11.7 21.8 4.2 6.0 9.9 3.7 4.9 7.5 15.4

Spawning 15 18 18 ND ND ND

Immature ND ND ND 9 ND ND

Lower Middle Challis Creek (CH2)

Adult 26 50 50 ND <6, 14, 18 <6, 6, 14 33.9 59.6 103.0 20.3 29.9 45.0 18.5 25.5 35.9 64.5

Spawning 26 50 50 ND ND ND

Immature ND ND ND 22 ND ND

Lower Challis Creek (CH1)

Adult 15 55 55 ND 15, 19, 15 7, 11, 11 33.1 59.2 105.0 20.2 29.8 45.9 19.0 26.1 37.7 74.1

Spawning 47 55 55 ND ND ND

Immature ND ND ND 35 ND ND

Results of Study Site Investigations 23
Summer (July through September) discharges for CH3 

were estimated on the basis of regression equations and are 

listed in table 7. Median discharge (Q.50) estimates were 

47.8 ft3/s for July, 24.0 ft3/s for August, and 19.9 ft3/s for 

September. The mean annual discharge estimate was 46.6 ft3/s.

Lower Mill Creek (ML1) discharges required for 

maximum WUA ranged from 9 to 18 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout 

(table 7). Discharge required for maximum WUA was 9 ft3/s 

for EPT taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged 

from 6 to 9 ft3/s for the depth criterion of 0.6 ft greater than 

25 percent of the total channel width and 3 to 9 ft3/s greater 

than 10 percent of the contiguous channel width, respectively 

(see transects 3, 5, and 6 photographs at http://id.water.usgs.

gov/projects/salmon_streamflow). Appendix E provides more 

information summarizing these study results. 

Summer (July through September) discharges for ML1 

were estimated on the basis of regression equations and are 

listed in table 7. Median discharge (Q.50) estimates were 11.7 

ft3/s for July, 6.0 ft3/s for August, and 4.9 ft3/s for September. 

The mean annual discharge estimate was 15.4 ft3/s.

Lower middle Challis Creek (CH2) discharges required 

for maximum WUA ranged from 26 to 50 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout 

(table 7). Discharge required for maximum WUA was 22 ft3/s 

for EPT taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged from 

<6 to 18 ft3/s for the depth criterion of 0.6 ft greater than 25 

percent of the total channel width and <6 to 14 ft3/s greater 

than 10 percent of the contiguous channel width, respectively 

(see transects 1, 6, and 7 photographs at http://id.water.usgs.

gov/projects/salmon_streamflow). In some cases, the passage 

criteria were less than the lower limit of the model conditions. 

In those cases, graphs for a given transect may be useful 

to estimate the discharge required for passage. Appendix F

provides more information summarizing these study results. 

Summer (July through September) discharges for CH2 

were estimated on the basis of regression equations and are 

listed in table 7. Median discharge (Q.50) estimates were 

59.6 ft3/s for July, 29.9 ft3/s for August, and 25.5 ft3/s for 

September. The mean annual discharge estimate was 64.5 ft3/s.

Lower Challis Creek (CH1) discharges required for 

maximum WUA ranged from 15 to 55 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout 

(table 7). Discharge required for maximum WUA was 35 ft3/s 

for EPT taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged from 

15 to 19 ft3/s for the depth criterion of 0.6 ft greater than 25 

percent of the total channel width and 7 to 11 ft3/s greater 

than 10 percent of the contiguous channel width, respectively 

(see transects 5, 6, and 7 photographs at http://id.water.usgs.

gov/projects/salmon_streamflow). Appendix G provides more 

information summarizing these study results. 

Summer (July through September) discharges for CH1 

were estimated on the basis of regression equations and are 

listed in table 7. Median discharge (Q.50) estimates were 

59.2 ft3/s for July, 29.8 ft3/s for August, and 26.1 ft3/s for 

September. The mean annual discharge estimate was 74.1 ft3/s.

Stream Temperature

Temperature recording data loggers were deployed at 

four locations in Challis Creek (CH4, CH3, CH2, and CH1), 

and two major tributaries Bear Creek (BE1) and Mill Creek 

(ML1) in 2005 (fig. 8). All data loggers were deployed in June 

2005. All data loggers were retrieved in mid-September 2005. 

After downloading and reviewing the data, June 12 through 

September 12 (93 days) was selected as the period of record 

for calculating stream temperature metrics.

Analysis of the stream temperature records for Challis 

Creek indicated a slight cooling trend downstream of CH4 to 

CH2 and then a pronounced warming trend downstream of 

CH2 to CH1 (fig. 9). This warming trend appears to strengthen 

over time and most likely is due to increasing air temperatures 

and the diversion of streamflow for irrigation over the course 

of the summer. 

Individual metric calculation results showed the MDAT 

was 16.2oC at CH4, 15.3oC at CH3, 16.6oC at CH2, and 

19.5oC at CH1. The MDAT at CH4, CH3, and CH2 was below 

the 17.8oC MDAT upper temperature threshold that according 

to McHugh and others (2004) can decrease the survival rate of 

summer Chinook salmon juveniles in natal streams; however, 

the MDAT at CH1 was above the 17.8oC MDAT upper 

temperature threshold.

24  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
ID19-0028-SalmonRiver2005_fig09

DATE

DAILY WATER TEMPERATURE, IN DEGREES CELSIUS

JUNE JULY AUGUST SEPTEMBER

16

18

20

22

24

26

8

10

12

44

28

Challis Creek (CH4)

Challis Creek (CH3)

Challis Creek (CH2)

Challis Creek (CH1)

Figure 9. Maximum daily water temperature for period June 12 through September 12, 2005, at Challis Creek,

upper Salmon River Basin, Idaho

Figure 9. Maximum daily water temperature at Challis Creek, upper Salmon River Basin, Idaho, June 12 through 

September 12, 2005.

Results of Study Site Investigations 25
Figure 10. Maximum daily water temperature for period June 12 through September 12, 2005, at Bear Creek, upper

Salmon River Basin, Idaho

DATE

DAILY WATER TEMPERATURE, IN DEGREES CELSIUS

JUNE JULY AUGUST SEPTEMBER

6

8

10

12

14

16

Figure 10. Maximum daily water temperature at Bear Creek (BE1), upper Salmon River Basin, Idaho, June 12 through 

September 12, 2005.

The MDMT was 21.0oC at CH4, 20.2oC at CH3, 20.8oC 

at CH2 and 26.3oC at CH1. The MDMT at all sites was very 

near or above the MDMT threshold of 21.0oC that, according 

to Poole and others (2001), can create a thermal barrier 

that would block adult Chinook salmon from migrating to 

their spawning grounds. The MDMT at all sites exceeded 

the 18.0oC threshold that may block bull trout migration (J. 

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

The temperature regime at all sites except CH1 was 

below the 19.0oC MDAT and below the 22.0oC MDMT IDEQ 

criteria, for protection of coldwater biota (applicable from 

June 22 through September 21). A summary of individual 

temperature metrics for all study sites can be accessed at 

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

A temperature recording data logger was deployed at 

BE1 downstream of the diversions in early June 2004 (fig. 10). 

The data logger was retrieved in late September 2004. 

After downloading and reviewing the data, June 12 through 

September 12 (93 days) was selected as the period of record 

for calculating stream temperature metrics. 

Individual metric calculation results showed that the 

MDAT was 11.4oC at BE1, well below the 17.8oC MDAT 

upper temperature threshold that according to McHugh 

and others (2004) can decrease the survival rate of summer 

Chinook salmon juveniles in natal streams. 

The MDMT was 14.4oC at BE1, well below the 18.0oC 

threshold that may limit bull trout habitat and block passage 

because of high water temperatures (J. Dunham, U.S. Forest 

Service, written commun., 2004). The MDMT also was below 

the 21.0oC threshold that, according to Poole and others 

(2001), can create a thermal barrier that can possibly block 

adult Chinook salmon from migrating to their spawning 

grounds. 

26  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
The temperature regime at BE1 also was below the 

19.0oC MDAT and 22.0oC MDMT IDEQ criteria for the 

protection of coldwater biota (applicable June 22 through 

September 21). A summary of individual temperature metrics 

for all study sites can be accessed at http://id.water.usgs.gov/

projects/salmon_streamflow.

A temperature recording data logger was deployed at 

ML1 downstream of all diversions in early June 2004 (fig. 11). 

The data logger was retrieved in late September 2004. 

After downloading and reviewing the data, June 12 through 

September 12 (93 days) was selected as the period of record 

for calculating stream temperature metrics. 

Individual metric calculation results showed that the 

MDAT was 18.1oC at ML1, slightly above the 17.8oC MDAT 

upper temperature threshold that according to McHugh 

and others (2004) can decrease the survival rate of summer 

Chinook salmon juveniles in natal streams.

The MDMT was 22.0oC at ML1, above the 18.0oC 

threshold that may limit bull trout habitat and block passage 

because of high water temperatures (J. Dunham, U.S. Forest 

Service, written commun., 2004). The MDMT at ML1 also 

was above the 21.0oC threshold that according to Poole and 

others (2001) can create a thermal barrier that can possibly 

block adult Chinook salmon from migrating to their spawning 

grounds. 

Comparison of the temperature regime at ML1 to the 

IDEQ criteria of 19.0oC MDAT and 22.0oC MDMT for the 

protection of coldwater biota (applicable from June 22 through 

September 21), indicates that the MDAT was below the 19.0oC 

criterion, although the MDMT was at the 22.0oC MDMT 

criterion. A summary of individual temperature metrics for all 

study sites can be accessed at http://id.water.usgs.gov/projects/

salmon_streamflow.

DAILY WATER TEMPERATURE, IN DEGREES CELSIUS

JUNE JULY AUGUST SEPTEMBER

DATE

17

19

21

23

9

11

13

15

Figure 11. Maximum daily water temperature at Mill Creek (ML1), upper Salmon River Basin, Idaho, June 12 through 

September 12, 2005.

Results of Study Site Investigations 27
Morgan Creek

Morgan Creek is an easterly flowing tributary to the 

Salmon River with its mouth just north of Challis, Idaho. 

The Morgan Creek headwaters are along the northern-most 

boundary of the upper Salmon River Basin (fig. 1). The 

Morgan Creek Basin covers about 107 mi2, of which about 36 

percent is forested. Mean elevation of the basin is about 7,140 

ft above sea level and the basin receives an average of 20.1 

in/yr of precipitation. One study site (MC1) was on Morgan 

Creek about 0.5 mi upstream of the mouth (fig. 12).

Hydrology

The USGS began operating a continuous-record 

streamflow-gaging station on Morgan Creek (Morgan Creek 

above West Fork Morgan Creek; 13299255; MCabvWFMC) 

on March 30, 2005, for the U.S. Forest Service. This gaging 

station is on the main stem of Morgan Creek just upstream 

of West Fork Morgan Creek and about 6 mi upstream of 

the mouth. Active streamflow diversions are upstream and 

downstream of the gaging station and do affect the streamflow 

at the gaging station. A plot of the continuous daily mean 

discharge in Morgan Creek for WY05 is presented in 

figure 13, along with markers indicating the times when field 

data were collected at the study site (MC1).

Additional analyses were completed that compared 

streamflows in Morgan Creek to estimates of long-term 

streamflow statistics. The July, August, and September daily 

mean discharge hydrograph for MCabvWFMC for WY05 

along with the estimated 80-, 50-, and 20-percent monthly 

exceedances based on regression equations developed by 

Hortness and Berenbrock (2001) are presented in figure 14. 

Monthly exceedance statistics for July, August, and September 

streamflows at MCabvWFMC during WY05 along with the 

estimated monthly exceedances and their confidence limits 

(Hortness and Berenbrock, 2001) are presented in table 8. 

Daily mean discharges for MCabvWFMC are affected by 

upstream diversions; however, monthly exceedance estimates 

are indicators of natural streamflow conditions unaffected 

by diversions. The effects of diversions on streamflow at 

MCabvWFMC are quite apparent in figure 14, when compared 

to estimates of long-term monthly statistics.

Habitat Modeling and Passage Criteria

The lower Morgan Creek (MC1) discharges required 

for maximum WUA ranged from 15 to 42 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout 

(table 9). The very low WUA for bull trout spawning shown 

in appendix figure H2 is attributed to the lack of suitable 

substrate. Discharge required for maximum WUA was 30 ft3/s 

for EPT taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged from 

<11 to 15 ft3/s for the depth criterion of 0.6 ft greater than 

25 percent of the total channel width and <11 ft3/s greater 

than 10 percent of the contiguous channel width, respectively 

(see transects 2, 3, and 4 photographs at http://id.water.usgs.

gov/projects/salmon_streamflow). In some cases, the passage 

criteria were less than the lower limit of the model conditions. 

In those cases, graphs for a given transect may be useful to 

estimate the discharge required for passage. Appendix H

provides more information summarizing these study results. 

Summer (July through September) discharges for 

MC1 were estimated on the basis of regression equations 

and are listed in table 9. Median discharge (Q.50) estimates 

were 31.2 ft3/s for July, 16.4 ft3/s for August, and 14.9 ft3/s 

for September. The mean annual discharge estimate was 

55.5 ft3/ s. 

Stream Temperature

Temperature recording data loggers were deployed at 

three locations in Morgan Creek in 2005 (fig. 15). These 

locations included MCabvAC, MCabvWFMC, and MC1. All 

data loggers were deployed in June 2005. All data loggers 

were retrieved in mid-September 2005. After downloading and 

reviewing the data, June 12 through September 12 (93 days) 

was selected as the period of record for calculating stream 

temperature metrics.

Analysis of the stream temperature records for Morgan 

Creek indicated a pronounced warming trend downstream of 

MCabvAC to MC1 (fig. 15). This warming trend appears to 

strengthen over time and most likely is due to increasing air 

temperatures and the diversion of streamflow for irrigation 

over the course of the summer. 

28  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
ID19-0028-SalmonRiver2005_fig12

Figure 12. Location of study sites on Morgan Creek, streamflow-gaging, and temperature monitoring 

locations, upper Salmon River Basin, Idaho, 2005. Diversion locations were determined by 

U.S. Geological Survey.

Upper Salmon

River Basin

Figure location

River

Salmon

Eddy

Creek

Mudspring

Gulch

Alder

Creek

Morgan

Creek

River

Salmon

Eddy

Creek

West

Fork Morgan

Creek

West

Fork Morgan

Creek

Mudspring

Gulch

Alder

Creek

Morgan

Creek

0 1 2 3 4 5 6 MILES

0 1 2 3 4 5 6 7 8 KILOMETERS

114°25’ 114°20’ 114°15’ 114°10’ 114°5’

44°47’30”

44°45’

44°42’30”

44°40’

44°37’30”

EXPLANATION

Privately owned land

Streamflow, PHABSIM, and temperature site

Streamflow and temperature site

Diversion

MC1

MCabvAC

MCabvWFMC

MC1

MCabvAC

Figure 12. Location of study sites on Morgan Creek, diversions, streamflow-gaging stations, temperature monitoring 

locations, and Physical Habitat Simulation (PHABSIM) study sites, upper Salmon River Basin, Idaho, 2005. Diversion 

locations were determined by U.S. Geological Survey.

Results of Study Site Investigations 29
ID19-0028-SalmonRiver2005_fig13

Study site visit:

Morgan Creek #1 (MC1)

June 6, 2005

0

10

20

30

40

50

60

Study site visit:

Morgan Creek #1 (MC1)

April 19, 2005

APRIL MAY

DISCHARGE, IN CUBIC FEET PER SECOND

JUNE JULY AUGUST SEPTEMBER

DATE

Figure 13. Daily mean discharge at Morgan Creek above West Fork Morgan Creek, near Challis (13299255), upper 

Salmon River Basin, Idaho, March 30 through September 30, 2005.

0

5

10

15

20

25

30

35

40

DISCHARGE, IN CUBIC FEET PER SECOND

JULY AUGUST

DATE

SEPTEMBER

Daily mean discharge-WY05

80-percent exceedance

50-percent exceedance (median)

20-percent exceedance

Figure 14. Daily mean discharge for water year 2005, estimated long-term daily mean discharge, and estimated 80-, 50-

, and 20-percent exceedance statistics at Morgan Creek above West Fork Morgan Creek, near Challis (13299255), upper 

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

30 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table 8. Calculated and estimated 80-, 50-, and 20-percent monthly exceedance discharge values for Morgan Creek above West Fork 

Morgan Creek near Challis (13299255), upper Salmon River Basin, Idaho.

[Values presented in cubic feet per second]

July August September

Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Q.80 Q.50 Q.20

Water year 2005 1.43 5.08 10.7 0.33 0.55 0.98 3.47 5.08 5.62

Regional regression equations

Upper confidence limit 23.5 34.5 55.8 14.2 21.3 25.6 13.0 17.9 20.3

Estimate 10.6 18.8 35.6 6.77 9.76 16.0 6.36 8.52 13.1

Lower confidence limit 4.80 10.3 22.7 3.20 4.50 10.0 3.10 4.10 8.50

Table 9. Summary of habitat and hydrologic measurements for lower Morgan Creek (MC1), upper Salmon River Basin, Idaho, 2005.

[Values presented in cubic feet per second. Discharge passage criteria: Passage criteria taken from Thompson (1972) and Scott and others (1981); both width 

criteria must be met to ensure passage. Channel width: Represents measurements at three transects. Discharge estimates: Based on regional regression 

equations using basin and climatic characteristics (Hortness and Berenbrock, 2001); Q.xx, daily discharge exceeded xx percent of the time during the specified month; Qa, mean annual discharge. Abbreviations: WUA; weighted usable area; WUA optimum discharge estimates were based on PHABSIM (Physical 

Habitat Simulation) model output; EPT, Ephemeroptera, Plecoptera, and Trichoptera taxa; ND, not determined; <, less than]

Lifestage

Discharge required for 

maximum WUA 

Discharge required for adult 

salmonid passage 0.6-foot 

depth criterion Discharge estimates

Channel width

Bull 

trout

Chinook 

salmon

Steelhead 

trout

EPT 

invertebrates

Greater than

25 percent 

(total)

Greater than

10 percent

(contiguous)

July August September

Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Q.80 Q.50 Q.20 Qa

Adult 15 42 42 ND 15, <11, 15 <11, <11, <11 17.9 31.2 58.2 11.3 16.4 25.6 11.1 14.9 21.9 55.5

Spawning 24 42 42 ND ND ND 

Immature ND ND ND 30 ND ND

Individual metric calculation results showed the MDAT 

was 14.8oC at MCabvAC, 18.6oC at MCabvWFMC, and 

19.0oC at MC1. The MDAT at MCabvAC was below, while 

the MDAT at MCabvWFMC and MC1 was above the 17.8oC 

MDAT upper temperature threshold that according to McHugh 

and others (2004) can decrease the survival rate of summer 

Chinook salmon juveniles in natal streams.

The MDMT was 19.0oC at MCabvAC, 22.2oC at 

MCabvWFMC, and 24.1oC at MC1. The MDMT at MCabvAC 

was below, while the MDMT at MCabvWFMC and MC1 was 

above the MDMT threshold of 21.0oC that according to Poole 

and others (2001) can create a thermal barrier that would 

block adult Chinook salmon from migrating to their spawning 

grounds. The MDMT at all sites exceeded the 18.0oC 

threshold that may block bull trout migration (J. Dunham, U.S. 

Forest Service, written commun., 2004). 

The temperature regime at MCabvAC was below the 

19.0oC MDAT and the 22.0oC MDMT IDEQ criteria, for 

protection of coldwater biota (applicable from June 22 through 

September 21). The temperature regime at MCabvWFMC 

was below the 19.0oC MDAT, but above the 22.0oC MDMT 

criteria. The temperature regime at MC1 was above the 

19.0oC MDAT and the 22.0oC MDMT criteria. A summary 

of individual temperature metrics for all study sites can 

be accessed at http://id.water.usgs.gov/projects/salmon_

streamflow.

Results of Study Site Investigations  31
ID19-0028-SalmonRiver2005_fig15

7

9

11

13

15

17

19

21

23

25

Morgan Creek (MC1)

Morgan Creek above West Fork Morgan Creek (MCabvWFMC)

Morgan Creek above Alder Creek (MCabvAC)

DATE

JUNE JULY AUGUST SEPTEMBER

DAILY WATER TEMPERATURE, IN DEGREES CELSIUS

Figure 15. Maximum daily water temperature at Morgan Creek, upper Salmon River Basin, Idaho, June 12 through 

September 12, 2005.

32 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
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-altitude 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 listing Chinook salmon and steelhead trout stocks 

as endangered or threatened under the Federal Endangered 

Species Act (ESA) in the 1990s. Human development has 

modified the original flow conditions in many streams of 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 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 done to evaluate potential fish habitat improvements by 

increasing streamflows as called for by the National Oceanic 

and Atmospheric Administration Fisheries Biological Opinion 

of 2000. These study results will be used to prioritize and 

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

Hydraulic and habitat simulation models contained in 

Physical Habitat Simulation System model 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. 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. 

Climatic and hydrologic conditions in the upper Salmon 

River Basin generally were below normal (30-year record, 

1971–2000 for climatic conditions; long-term means for 

hydrologic conditions) during water year 2005 (WY05). 

Monthly snowpack levels were significantly below normal 

between January 1 and June 1, 2005. Average air temperature 

during WY05 was slightly higher than the 30-year average, 

whereas the average monthly air temperatures were both 

above and below average. Annual mean streamflows in the 

basin were significantly below the long-term means, as were 

monthly mean streamflows.

Mean air temperature at Stanley, Idaho, during WY05 

was about 1.94 degrees Celsius (oC) (35.5 degrees Fahrenheit 

[oF]), slightly higher than the 30-year (1971-2000) mean of 

1.78oC (35.2oF). Annual mean streamflows at the long-term 

U.S. Geological Survey streamflow-gaging stations on Valley 

Creek at Stanley (13295000; 65 years of record) and on the 

Salmon River below Yankee Fork (13296500; 75 years of 

record) for WY05 were about 30 percent below the long-term 

means.

The lower Big Boulder Creek discharges required for 

maximum WUA ranged from 24 to 39 cubic feet per second 

(ft3/s) for adult and spawning bull trout, Chinook salmon, 

and steelhead trout. Discharge required for maximum WUA 

was 24 ft3/s for Ephemeroptim, Plecoptera, and Trichoptera 

(EPT) taxa in riffle habitat. Discharges required for adult 

passage over three shallow riffle habitat transects ranged from 

18 to 27 ft3/s for the depth criterion of 0.6 ft greater than 25 

percent of the total channel width and 15 to 27 ft3/s greater 

than 10 percent of the contiguous channel width, respectively. 

Median discharge estimates were 32.1 ft3/s for July, 15.1 ft3/s 

for August, and 10.7 ft3/s for September. The mean annual 

discharge estimate was 15.2 ft3/ s. 

Analysis of the stream temperature records for the two 

sites on Big Boulder Creek indicated a slight warming trend 

downstream. Individual metric calculation results showed 

the maximum daily-maximum temperature (MDMT) was 

well below the MDMT threshold of 21.0oC that would block 

adult Chinook salmon from migrating to their spawning 

grounds. The MDMT at the two sites on Big Boulder Creek 

also was below the 18.0oC threshold that may block bull trout 

migration. Temperature regimes at both sites were below 

Idaho Department of Environmental Quality’s (IDEQ) criteria 

of 19.0oC maximum daily-average temperature (MDAT) and 

22.0oC MDMT.

Upper Challis Creek discharges required for maximum 

WUA ranged from 22 to 37 ft3/s for adult and spawning bull 

trout, Chinook salmon, and steelhead trout. Discharge required 

for maximum WUA was 16 ft3/s for EPT taxa in riffle habitat. 

Discharges required for adult passage over three shallow 

riffle habitat transects ranged from 16 to 22 ft3/s for the depth 

criterion of 0.6 feet (ft) greater than 25 percent of the total 

channel width and 10 to 19 ft3/s greater than 10 percent of 

the contiguous channel width, respectively. Median discharge 

(Q.50) estimates were 17.3 ft3/s for July, 8.7 ft3/s for August, 

and 6.9 ft3/s for September. The mean annual discharge 

estimate was 17.4 ft3/s. 

Lower Bear Creek discharges required for maximum 

WUA ranged from 8 to 26 ft3/s for adult and spawning 

bull trout, Chinook salmon, and steelhead trout. Discharge 

required for maximum WUA was 11 ft3/s for EPT taxa in 

riffle habitat. Discharges required for adult passage over three 

shallow riffle habitat transects ranged from 5 to 14 ft3/s for 

Summary  33
the depth criterion of 0.6 ft greater than 25 percent of the total 

channel width and 4 to 14 ft3/s greater than 10 percent of the 

contiguous channel width, respectively. Median discharge 

(Q.50) estimates were 10.1 ft3/s for July, 5.1 ft3/s for August, 

and 3.8 ft3/s for September. The mean annual discharge 

estimate was 8.9 ft3/s. 

Upper middle Challis Creek discharges required for 

maximum WUA ranged from 19 to 67 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout. 

Discharge required for maximum WUA was 27 ft3/s for EPT 

taxa in riffle habitat. Discharges required for adult passage 

over three shallow riffle habitat transects ranged from less 

than 11 to 23 ft3/s for the depth criterion of 0.6 ft greater than 

25 percent of the total channel width and less than 11 to 11 

ft3/s greater than 10 percent of the contiguous channel width, 

respectively. Median discharge (Q.50) estimates were 47.8 ft3/s 

for July, 24.0 ft3/s for August, and 19.9 ft3/s for September. 

The mean annual discharge estimate was 46.6 ft3/s.

Lower Mill Creek discharges required for maximum 

WUA ranged from 9 to 18 ft3/s for adult and spawning bull 

trout, Chinook salmon, and steelhead trout. Discharge required 

for maximum WUA was 9 ft3/s for EPT taxa in riffle habitat. 

Discharges required for adult passage over three shallow riffle 

habitat transects ranged from 6 to 9 ft3/s for the depth criterion 

of 0.6 ft greater than 25 percent of the total channel width and 

3 to 9 ft3/s greater than 10 percent of the contiguous channel 

width, respectively. Median discharge (Q.50) estimates 

were 11.7 ft3/s for July, 6.0 ft3/s for August, and 4.9 ft3/s for 

September. The mean annual discharge estimate was 15.4 ft3/s.

Lower middle Challis Creek discharges required for 

maximum WUA ranged from 26 to 50 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout. 

Discharge required for maximum WUA was 22 ft3/s for EPT 

taxa in riffle habitat. Discharges required for adult passage 

over three shallow riffle habitat transects ranged from less 

than 6 to 18 ft3/s for the depth criterion of 0.6 ft greater than 

25 percent of the total channel width and less than 6 to 14 

ft3/s greater than 10 percent of the contiguous channel width, 

respectively. Median discharge (Q.50) estimates were 59.6 ft3/s 

for July, 29.9 ft3/s for August, and 25.5 ft3/s for September. 

The mean annual discharge estimate was 64.5 ft3/s.

Lower Challis Creek discharges required for maximum 

WUA ranged from 15 to 55 ft3/s for adult and spawning 

bull trout, Chinook salmon, and steelhead trout. Discharge 

required for maximum WUA was 35 ft3/s for EPT taxa in 

riffle habitat. Discharges required for adult passage over three 

shallow riffle habitat transects ranged from 15 to 19 ft3/s for 

the depth criterion of 0.6 ft greater than 25 percent of the total 

channel width and 7 to 11 ft3/s greater than 10 percent of the 

contiguous channel width, respectively. Median discharge 

(Q.50) estimates were 59.2 ft3/s for July, 29.8 ft3/s for August, 

and 26.1 ft3/s for September. The mean annual discharge 

estimate was 74.1 ft3/s.

Analysis of the stream temperature records for Challis 

Creek indicated a slight cooling trend downstream of upper 

Challis Creek to lower middle Challis Creek and then a 

pronounced warming trend downstream of lower middle 

Challis Creek to lower Challis Creek. This warming trend 

appears to strengthen over time and most likely is due to 

increasing air temperatures and the diversion of streamflow for 

irrigation over the course of the summer. The MDAT at upper 

Challis, upper middle Challis, and lower middle Challis Creek 

sites was below, although the MDAT at lower Challis Creek 

was above, the 17.8oC MDAT upper temperature threshold 

that can decrease the survival rate of summer Chinook salmon 

juveniles in natal streams. The MDMT at all sites was very 

near or above the MDMT threshold of 21.0oC that can create 

a thermal barrier that would block adult Chinook salmon 

from migrating to their spawning grounds. The MDMT at all 

sites exceeded the 18.0oC threshold that may block bull trout 

migration. The temperature regime at all sites except lower 

Challis Creek was below the 19.0oC MDAT and below the 

22.0oC MDMT IDEQ criteria, for protection of coldwater 

biota. 

Individual metric calculation results showed that the 

MDAT was 11.4oC at lower Bear Creek, well below the 17.8oC 

MDAT upper temperature threshold that can decrease the 

survival rate of summer Chinook salmon juveniles in natal 

streams. The MDMT was 14.4oC at lower Bear Creek, well 

below the 18.0oC threshold that may limit bull trout habitat 

and block passage as a result of high water temperatures. The 

MDMT also was below the 21.0oC threshold that can create a 

thermal barrier that can possibly block adult Chinook salmon 

from migrating to their spawning grounds. The temperature 

regime at lower Bear Creek also was below the 19.0oC 

MDAT and 22.0oC MDMT IDEQ criteria for the protection of 

coldwater biota.

Individual metric calculation results showed that the 

MDAT was 18.1oC at lower Mill Creek, slightly above the 

17.8oC MDAT upper temperature threshold that can decrease 

the survival rate of summer Chinook salmon juveniles in natal 

streams. The MDMT was 22.0oC at lower Mill Creek, above 

the 18.0oC threshold that may limit bull trout habitat and block 

passage as a result of high water temperatures. The MDMT 

at lower Mill Creek also was above the 21.0oC threshold that 

can create a thermal barrier that can possibly block adult 

Chinook salmon from migrating to their spawning grounds. 

Comparison of the temperature regime at lower Mill Creek 

with the IDEQ criteria of 19.0oC MDAT and 22.0oC MDMT 

for the protection of coldwater biota indicates that the MDAT 

was below the 19.0oC criterion while the MDMT was at the 

22.0oC MDMT criterion. 

The lower Morgan Creek discharges required for 

maximum WUA ranged from 15 to 42 ft3/s for adult and 

spawning bull trout, Chinook salmon, and steelhead trout. 

Discharge required for maximum WUA was 30 ft3/s for EPT 

taxa in riffle habitat. Discharges required for adult passage 

over three shallow riffle habitat transects ranged from less than 

11 to 15 ft3/s for the depth criterion of 0.6 ft greater than 25 

percent of the total channel width and less than 11 ft3/s greater 

than 10 percent of the contiguous channel width, respectively. 

Median discharge (Q.50) estimates were 31.2 ft3/s for July, 

34  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
16.4 ft3

/s for August, and 14.9 ft3/s for September. The mean 

annual discharge estimate was 55.5 ft3/s. 

Analysis of the stream temperature records for Morgan 

Creek indicated a pronounced warming trend downstream of 

Morgan Creek above Alder Creek to lower Morgan Creek. 

This warming trend appears to strengthen over time and most 

likely is due to increasing air temperatures and the diversion 

of streamflow for irrigation over the course of the summer. 

Individual metric calculation results showed the MDAT 

was 14.8oC at Morgan Creek above Alder Creek, 18.6oC at 

Morgan Creek above West Fork Morgan Creek, and 19.0oC 

at lower Morgan Creek. The MDAT at Morgan Creek above 

Alder Creek was below, while the MDAT at Morgan Creek 

above West Fork Morgan Creek and lower Morgan Creek was 

above, the 17.8oC MDAT upper temperature threshold that 

can decrease the survival rate of summer Chinook salmon 

juveniles in natal streams. The MDMT at Morgan Creek above 

Alder Creek was below while the MDMT at Morgan Creek 

above West Fork Morgan Creek and lower Morgan Creek 

was above the MDMT threshold of 21.0oC that can create 

a thermal barrier that would block adult Chinook salmon 

from migrating to their spawning grounds. The MDMT at all 

sites exceeded the 18.0oC threshold that may block bull trout 

migration. 

The temperature regime at Morgan Creek above Alder 

Creek was below the 19.0oC MDAT and below the 22.0oC 

MDMT IDEQ criteria, for protection of coldwater biota. The 

temperature regime at Morgan Creek above West Fork Morgan 

Creek was below the 19.0oC MDAT but above the 22.0oC 

MDMT criteria. The temperature regime at lower Morgan 

Creek was above the 19.0oC MDAT and above the 22.0oC 

MDMT criteria. 

Acknowledgments

Numerous individuals assisted in collecting and 

processing data during 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, Bureau of 

Reclamation, contributed to planning and study design. 

A number of representatives of the Interagency Technical 

Workgroup organized by Bureau of Reclamation also provided 

guidance: Cynthia Robertson and Thomas Curet (IDFG), Jim 

Morrow and Donald Anderson (NOAA), and Janna Brimmer 

(USFWS). Traci Hoff of the USGS provided assistance in 

building the Web site that accompanies this report. Colleague 

reviews by Ronald Sutton and Christopher Mebane improved 

the quality of the report.

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Natural Resources Conservation Service, 2006b, State basin 

outlook reports, water year 2005: accessed March 2006, at 

http://www.wcc.nrcs.usda.gov/cgibin/bor.pl.

Nehlsen, W., Williams, J.E., and Lichatowich, J.A., 1991, 

Pacific salmon at the crossroads: stocks at risk from California, Oregon, Idaho, and Washington: Fisheries, v. 16, no. 2, 

p. 4-21.

Nislow, K.H., Sepulveda, A.J., and Folt, C.L., 2004, Mechanistic linkage of hydrologic regime to summer growth of 

age-0 Atlantic salmon: Transactions of the American Fisheries Society, v. 133, p. 79-88.

Ott, D.S., and Maret, T.R., 2003, Aquatic assemblages and 

their relation to temperature variables of least-disturbed 

streams in the Salmon River Basin, central Idaho, 2001: 

U.S. Geological Survey Water-Resources Investigations 

Report 03-4076., 45 p.

References Cited  37
Poole, G., Dunham, J., Hicks, M., Keenan, D., Lockwood, 

J., Materna, E., McCullough, D., Mebane, C., Risley, J., 

Sauter, S., Spalding, S., and Sturdevant, D., 2001, Scientific 

issues relating to temperature criteria for salmon, trout, and 

char native to the Pacific Northwest−Technical Synthesis of 

the Water Temperature Criteria Technical Workgroup: U.S. 

Environmental Protection Agency, Region 10, 21 p.

Quinn, T.P., 2005, The behavior and ecology of Pacific salmon 

and trout: Seattle University of Washington Press, Chap. 11, 

Juvenile salmonids in streams, p. 185-208.

Raleigh, R.F., Miller, W.J., and Nelson, P.C., 1986, Habitat suitability index model and instream flow suitability 

curves−Chinook salmon: U.S. Fish and Wildlife Service 

Biological Report 82 (10.122), 64 p.

Rantz, S.E., 1982, Measurement and computation of 

streamflow−Volume 1. Measurement of stage and discharge: U.S. Geological Survey Water-Supply Paper 2175, 

284 p.

Roper, B.B., Scarnecchia, D.L., and LaMarr, T.J., 1994, Summer distribution of and habitat use by Chinook salmon and 

steelhead within a major basin of the south Umpqua River, 

Oregon: Transactions of the American Fisheries Society, v. 

123, p. 298-308.

Rubin, S.P., Bjornn, T.C., and Dennis, B., 1991, Habitat suitability curves for juvenile Chinook salmon and steelhead 

developed using a habitat-oriented sampling approach: Rivers, v. 2, no. 1, p. 12-29.

R2 Resource Consultants, 2004, Instream flow claims for the 

Snake River Basin Adjudication, Idaho: Redmond, Wash., 

Prepared for Bureau of Indian Affairs, v. 1, part 1 – main 

report, variously paged.

Sauter, S.T., McMillan, J., and Dunham, J., 2001, Salmonid 

behavior and water temperature, issue paper 1: U.S. Environmental Protection Agency, EPA-910-D-01-001, 36 p.

Scott, M., Contreras, G., Forsgren, H., Reynoldson, K., and 

McDevitt, G., 1981, Anadromous fish instream flow needs 

and conflicts within the Sawtooth National Recreation Area: 

U.S. Forest Service, 46 p.

Selong, J.H., McMahon, T.E., Zale, A.V., and Barrows, F.T., 

2001, Effect of temperature on growth and survival of bull 

trout, with application of an improved method for determining thermal tolerance in fishes: Transactions of the American Fisheries Society, v. 130, p. 1026–1037.

Spinazola, J.M., 2002, Upper Salmon River Basin flow characterization studies: Boise, Idaho, Bureau of Reclamation, 

4 p.

Stevens, H.H., Jr., Ficke, J.F., and Smoot, G.F., 1975, Water 

temperature−influential factors, field measurement, and 

data presentation: U.S. Geological Survey Techniques of 

Water-Resources Investigations, book 1, chap. D1, 65 p.

Sutton, R. and Morris, C., 2004, Instream flow assessment Big 

Timber Idaho: Bureau of Reclamation, Technical Services 

Center, Denver, 119 p., accessed April 2004 at http://www.

usbr.gov/pn/programs/fcrps/pdf/instreamflow-june2004.pdf.

Sutton, R. and Morris, C., 2005, Instream flow assessment 

Big Eightmile Creek, Bohannon Creek, and Hayden Creek, 

Idaho: Bureau of Reclamation, Technical Services Center, 

Denver, 183 p., accessed April 2005 at http://www.usbr.

gov/pn/programs/fcrps/pdf/instreamflow-june2005.pdf.

Tennant, D.L., 1976, Instream flow regimens for fish, wildlife, 

recreation, and related environmental resources, in Osborne, 

J., and Allman, C., eds., Instream flow needs, volume 2: 

Bethesda, Md., American Fisheries Society, Western Division, p. 359-373.

Thompson, K.E., 1972, Determining stream flows for fish life: 

Proceedings of the Instream Flow Requirement Workshop, 

March 15-16, 1972, Portland, Oreg.: Pacific Northwest 

River Basins Commission, p. 31-50.

Thurow, R.F., 2000, Dynamics of Chinook salmon populations 

within Idaho’s Frank Church Wilderness−implications for 

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the wilderness science in a time of change conference, 

Missoula, Montana, May 23-27, 1999, U.S. Forest Service 

RMRS-P-15-VOL-3, p. 143-151.

Thurow, R.F., Lee, D.C., and Rieman, B.E., 2000, Status and 

distribution of Chinook salmon and steelhead in the Interior 

Columbia River Basin and portions of the Klamath River 

Basin, in Knudsen, E.E., Steward, C.R., MacDonald, D.D., 

Williams, J.E., and Reiser, D.W., eds., Sustainable fisheries management−Pacific salmon: Boca Raton, Fla., Lewis 

Publishers, p. 133-160.

Waddle, T.J., 2001, PHABSIM for Windows—user’s manual 

and exercises: U.S. Geological Survey Open-File Report 

01-340, 288 p.

Western Regional Climate Center, 2006, Desert Research 

Institute, Idaho climate summaries: accessed January 2005, 

at http://www.wrcc.dri.edu/summary/climsmid.html.

Zaroban, D.W., 2000, Protocol for placement and retrieval of 

temperature data loggers in Idaho streams: Idaho Department of Environmental Quality, Water Quality Monitoring 

Protocols, Report no. 10, 34 p.

38  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
IDSalmon

AppFigA01.ai

EASTING, IN FEET

N

ORTHIN

G, IN FEET

Transect

Local reference mark

For reference only; stream schematic not to scale.

Point Latitude Longitude

LH1 44° 6' 57.48" N 114° 26' 4.92" W

RH1 44° 6' 58.35" N 114° 26' 3.99" W

LH2 44° 6' 58.14" N 114° 26' 5.14" W

RH2 44° 6' 58.41" N 114° 26' 4.45" W

LH3 44° 6' 58.14" N 114° 26' 5.14" W

RH3 44° 6' 58.61" N 114° 26' 4.89" W

LH4 44° 6' 58.06" N 114° 26' 5.83" W

RH4 44° 6' 58.35" N 114° 26' 6.21" W

LH5 44° 6' 57.7" N 114° 26' 6.32" W

RH5 44° 6' 57.97" N 114° 26' 6.65" W

LH6 44° 6' 57.59" N 114° 26' 7.14" W

RH6 44° 6' 58.02" N 114° 26' 7.45" W

LH7 44° 6' 57.37" N 114° 26' 8.24" W

RH7 44° 6' 57.66" N 114° 26' 8.35" W

Transect Endpoint Coordinates (NAD 83)

Point Latitude Longitude

Transect Endpoint Coordinates (NAD 83)

RM1

RM3

RM2

4750

4800

4850

4900

4950

5000

5050

5100

4750 4800 4850 4900 4950 5000 5050 5100 5150

T3

T7

T5

T6

T4

T2 T1

Appendix A. Plan view, weighted usable areas, and passage criteria assessments for bull trout, Chinook salmon, 

steelhead trout, and invertebrates for lower Big Boulder Creek (BB1), upper Salmon River Basin, Idaho, 2005.

Figure A1. Plan view of lower Big Boulder Creek (BB1), upper Salmon River Basin, Idaho, 2005.

Appendix A  39
IDSalmon_AppFigA02.ai

WEIGHTED USABLE AREA (WUA), IN FEET SQUARE PER 1,000 FEET

PERCENTAGE OF MAXIMUM HABITAT

DISCHARGE, IN CUBIC FEET PER SECOND

Bull Trout WUA Normalized

Steelhead Trout WUA

DISCHARGE, IN CUBIC FEET PER SECOND

Invertebrate WUA Invertebrate WUA

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0 10 20 30 40 50 60

Invertebrates

Steelhead Trout WUA Normalized

Bull Trout WUA

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

Spawning

Adult

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

Chinook Salmon WUA Normalized

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60

Chinook Salmon WUA

Figure A2. Weighted usable area and percentage of maximum habitat for bull trout, Chinook salmon, steelhead trout, and 

invertebrates, site BB1, lower Big Boulder Creek, upper Salmon River Basin, Idaho, 2005.

40 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table A1. Weighted usable area for bull trout, Chinook salmon, steelhead trout life stages, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) 

invertebrates, site BB1, lower Big Boulder Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 4. Abbreviations: WUA, weighted usable area; ft3/s, cubic foot per second; ft2, square foot; ft2/l,000 ft, square foot per 1,000 feet]

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Bull trout

9.240 21,037 5,279 1,558 72.5 38.9

12 21,913 5,976 2,069 82.1 51.7

15 22,509 6,796 2,552 93.4 63.8

18 23,059 7,070 2,926 97.2 73.1

21 23,564 7,225 3,330 99.3 83.2

24 24,048 7,277 3,612 100.0 90.3

27 24,474 7,209 3,744 99.1 93.6

30 24,931 7,266 3,920 99.8 98.0

33 25,405 7,214 4,001 99.1 100.0

36 26,393 6,861 3,934 94.3 98.3

39 27,200 7,061 3,864 97.0 96.6

42 27,506 7,023 3,701 96.5 92.5

45 27,794 6,944 3,526 95.4 88.1

48 28,071 6,921 3,527 95.1 88.1

49.900 28,245 7,258 3,505 99.7 87.6

Chinook salmon

9.2 21,037 8,163 3,777 63.2 50.4

12 21,913 9,240 4,424 71.5 59.0

15 22,509 10,088 5,021 78.1 66.9

18 23,059 10,794 5,738 83.5 76.5

21 23,564 11,282 6,196 87.3 82.6

24 24,048 11,854 6,577 91.7 87.7

27 24,474 12,228 6,790 94.6 90.5

30 24,931 12,604 7,025 97.5 93.7

33 25,405 12,871 7,229 99.6 96.4

36 26,393 12,902 7,337 99.8 97.8

39 27,200 12,923 7,501 100.0 100.0

42 27,506 12,850 7,492 99.4 99.9

45 27,794 12,757 7,292 98.7 97.2

48 28,071 12,700 6,971 98.3 92.9

49.900 28,245 12,645 6,906 97.9 92.1

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Steelhead trout

9.2 21,037 8,163 3,777 63.2 50.4

12 21,913 9,240 4,424 71.5 59.0

15 22,509 10,088 5,021 78.1 66.9

18 23,059 10,794 5,738 83.5 76.5

21 23,564 11,282 6,196 87.3 82.6

24 24,048 11,854 6,577 91.7 87.7

27 24,474 12,228 6,790 94.6 90.5

30 24,931 12,604 7,025 97.5 93.7

33 25,405 12,871 7,229 99.6 96.4

36 26,393 12,902 7,337 99.8 97.8

39 27,200 12,923 7,501 100.0 100.0

42 27,506 12,850 7,492 99.4 99.9

45 27,794 12,757 7,292 98.7 97.2

48 28,071 12,700 6,971 98.3 92.9

49.900 28,245 12,645 6,906 97.9 92.1

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

EPT Invertebrates

9.240 21,037 9,709 77.6

12 21,913 10,797 86.3

15 22,509 11,536 92.2

18 23,059 12,019 96.1

21 23,564 12,410 99.2

24 24,048 12,508 100.0

27 24,474 12,506 100.0

30 24,931 12,437 99.4

33 25,405 11,908 95.2

36 26,393 11,250 89.9

39 27,200 10,912 87.2

42 27,506 10,606 84.8

45 27,794 10,237 81.8

48 28,071 9,730 77.8

49.900 28,245 9,654 77.2

Appendix A  41
IDSalmon_AppFigA03.ai

DISCHARGE, IN CUBIC FEET PER SECOND

Passage Transect 1

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

Passage Transect 1

(wide moderate slope)

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

0

10

20

30

40

50

60

70

80

0 10 20 30 40 50 60

0

10

20

30

40

50

60

70

80

CRITERIA LINE

0

10

20

30

40

50

60

70

80

0

10

20

30

40

50

60

70

80

Figure A3. Percentages of contiguous and total stream width for passage transect 1, lower Big 

Boulder Creek (BB1), upper Salmon River Basin, Idaho, 2005.

42 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table A2. Passage criteria assessment for transect 1 (wide moderate slope), site BB!, lower Big Boulder Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 4. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

9.2 54.3 10.7 19.7 5.9 10.9

12 58.1 19.2 33.1 9.0 15.5

15 61.9 25.1 40.6 11.1 17.9

18 65.4 30.6 46.8 21.1 32.3

21 68.4 35.6 52.0 22.9 33.5

24 71.3 40.3 56.6 24.7 34.6

27 72.5 45.0 62.1 39.1 53.9

30 73.2 47.0 64.2 39.6 54.1

33 73.8 48.8 66.1 40.1 54.3

36 74.4 50.5 67.9 40.5 54.5

39 75.6 52.4 69.3 41.0 54.3

42 76.7 54.1 70.6 41.4 54.1

45 77.7 55.8 71.8 41.9 53.9

48 78.7 57.4 72.9 42.3 53.8

49.9 79.3 58.5 73.7 42.7 53.8

Stream widths greater than 0.6-ft depth

9.2 54.3 0.0 0.0 0.0 0.0

12 58.1 0.2 0.3 0.2 0.3

15 61.9 0.8 1.2 0.8 1.2

18 65.4 6.9 10.5 5.0 7.7

21 68.4 10.0 14.6 5.8 8.4

24 71.3 13.0 18.2 6.5 9.1

27 72.5 19.8 27.3 9.2 12.7

30 73.2 23.2 31.7 10.4 14.2

33 73.8 26.4 35.8 11.5 15.6

36 74.4 29.6 39.8 20.7 27.9

39 75.6 33.1 43.8 22.0 29.1

42 76.7 36.3 47.4 23.2 30.3

45 77.7 39.5 50.8 24.4 31.4

48 78.7 44.0 56.0 38.9 49.4

49.9 79.3 45.0 56.8 39.1 49.3

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

9.2 54.3 0.0 0.0 0.0 0.0

12 58.1 0.0 0.0 0.0 0.0

15 61.9 0.0 0.0 0.0 0.0

18 65.4 0.0 0.0 0.0 0.0

21 68.4 0.0 0.0 0.0 0.0

24 71.3 0.0 0.0 0.0 0.0

27 72.5 0.2 0.3 0.2 0.3

30 73.2 0.6 0.8 0.6 0.8

33 73.8 0.9 1.2 0.9 1.2

36 74.4 6.2 8.4 4.9 6.5

39 75.6 8.4 11.2 5.4 7.1

42 76.7 10.5 13.7 5.9 7.7

45 77.7 12.5 16.0 6.4 8.2

48 78.7 18.1 22.9 8.6 10.9

49.9 79.3 19.8 25.0 9.2 11.6

Appendix A  43
IDSalmon_AppFigA04.ai

PERCENTAGE OF TOTAL STREA

M

WIDTH PERCENTAGE OF CONTIGUOUS STREAM WIDTH

STREA

M

WIDTH, IN FEET

DISCHARGE, IN CUBIC FEET PER SECOND

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 4

(wide moderate slope)

Passage Transect 4

(wide moderate slope)

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60

0

5

10

15

20

25

30

CRITERIA LINE

Figure A4. Percentages of contiguous and total stream width for passage transect 4, lower Big 

Boulder Creek (BB1), upper Salmon River Basin, Idaho, 2005.

44  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table A3. Passage criteria assessment for transect 4 (wide moderate slope), site BB1, lower Big Boulder Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 4. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

9.2 22.8 7.7 34.0 6.1 26.8

12 23.8 9.1 38.1 7.0 29.4

15 24.1 11.6 48.0 7.5 31.3

18 24.4 13.9 56.9 8.0 32.9

21 24.6 14.8 60.0 12.3 50.0

24 24.8 15.6 62.8 13.0 52.3

27 25.0 17.1 68.1 13.6 54.2

30 25.3 19.0 75.4 14.1 56.0

33 25.5 21.1 82.6 14.7 57.7

36 25.7 22.2 86.2 22.2 86.2

39 25.9 22.8 88.1 22.8 88.1

42 26.1 23.5 89.8 23.5 89.8

45 26.3 23.9 90.7 23.9 90.7

48 26.5 24.0 90.6 24.0 90.6

49.900 26.6 24.1 90.6 24.1 90.6

Stream widths greater than 0.6-ft depth

9.2 22.8 0.0 0.0 0.0 0.0

12 23.8 1.3 5.5 1.0 4.3

15 24.1 4.1 16.9 2.8 11.8

18 24.4 6.6 27.2 5.2 21.4

21 24.6 7.5 30.7 5.9 24.2

24 24.8 8.4 33.9 6.6 26.8

27 25.0 9.8 39.0 7.2 28.6

30 25.3 11.5 45.7 7.5 29.8

33 25.5 13.3 52.3 7.9 31.0

36 25.7 14.4 55.8 12.0 46.6

39 25.9 15.0 57.9 12.5 48.3

42 26.1 15.6 59.9 13.0 49.8

45 26.3 16.7 63.6 13.5 51.2

48 26.5 18.4 69.4 14.0 52.6

49.900 26.6 19.4 72.9 14.2 53.5

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

9.2 22.8 0.0 0.0 0.0 0.0

12 23.8 0.0 0.0 0.0 0.0

15 24.1 0.0 0.0 0.0 0.0

18 24.4 0.0 0.0 0.0 0.0

21 24.6 0.0 0.0 0.0 0.0

24 24.8 0.0 0.0 0.0 0.0

27 25.0 2.1 8.3 1.1 4.3

30 25.3 4.0 16.0 2.8 11.2

33 25.5 6.0 23.7 4.7 18.3

36 25.7 7.1 27.8 5.6 21.9

39 25.9 7.8 30.2 6.2 23.8

42 26.1 8.5 32.4 6.7 25.6

45 26.3 9.5 36.1 7.1 27.0

48 26.5 11.0 41.4 7.4 27.9

49.900 26.6 11.9 44.5 7.6 28.5

Appendix A  45
IDSalmon_AppFigA05.ai

PERCENTAGE OF TOTAL STREA

M

WIDTH PERCENTAGE OF CONTIGUOUS STREAM WIDTH

STREA

M

WIDTH, IN FEET

DISCHARGE, IN CUBIC FEET PER SECOND

Passage Transect 6

(wide moderate slope)

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 6

(wide moderate slope)

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60

0

5

10

15

20

25

30

CRITERIA LINE

Figure A5. Percentages of contiguous and total stream width for passage transect 6, lower Big 

Boulder Creek (BB1), upper Salmon River Basin, Idaho, 2005.

46  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table A4. Passage criteria assessment for transect 6 (wide moderate slope), site BB1, lower Big Boulder Creek, upper Salmon River Basin, Idaho, 2005

[Site location shown in figure 4. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

9.2 22.8 8.4 32.2 4.1 15.7

12 23.8 10.8 39.6 4.8 17.4

15 24.1 13.0 46.8 5.3 19.3

18 24.4 22.7 81.0 16.8 60.1

21 24.6 23.5 83.3 17.2 61.0

24 24.8 24.3 85.3 24.3 85.3

27 25.0 24.6 85.9 24.6 85.9

30 25.3 25.0 86.5 25.0 86.5

33 25.5 25.4 87.1 25.4 87.1

36 25.7 25.7 87.6 25.7 87.6

39 25.9 26.0 88.1 26.0 88.1

42 26.1 26.3 88.6 26.3 88.6

45 26.3 27.4 91.9 27.4 91.9

48 26.5 27.5 92.2 27.5 92.2

49.900 26.6 27.6 92.3 27.6 92.3

Stream widths greater than 0.6-ft depth

9.2 22.8 0.0 0.0 0.0 0.0

12 23.8 3.0 11.0 2.4 8.9

15 24.1 4.7 16.9 3.0 10.9

18 24.4 6.4 22.8 3.5 12.6

21 24.6 8.1 28.8 4.0 14.2

24 24.8 9.8 34.4 4.5 15.7

27 25.0 11.4 39.6 4.9 17.1

30 25.3 12.9 44.6 5.3 18.4

33 25.5 22.4 76.8 16.7 57.3

36 25.7 23.0 78.6 17.0 57.9

39 25.9 23.6 80.2 17.3 58.5

42 26.1 24.2 81.6 17.5 59.1

45 26.3 24.5 82.3 24.5 82.3

48 26.5 24.8 83.0 24.8 83.0

49.900 26.6 25.0 83.4 25.0 83.4

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

9.2 22.8 0.0 0.0 0.0 0.0

12 23.8 0.0 0.0 0.0 0.0

15 24.1 0.0 0.0 0.0 0.0

18 24.4 0.0 0.0 0.0 0.0

21 24.6 0.0 0.0 0.0 0.0

24 24.8 2.2 7.8 2.1 7.5

27 25.0 3.4 11.9 2.6 8.9

30 25.3 4.6 15.9 3.0 10.3

33 25.5 5.7 19.7 3.4 11.5

36 25.7 7.1 24.4 3.7 12.8

39 25.9 8.4 28.6 4.1 13.9

42 26.1 9.6 32.4 4.4 14.9

45 26.3 10.8 36.3 4.8 16.0

48 26.5 11.9 40.0 5.1 16.9

49.900 26.6 12.6 42.2 5.2 17.5

Appendix A  47
Appendix B. Plan view, weighted usable areas, and passage criteria assessments for bull trout, Chinook salmon, 

steelhead trout, and invertebrates for upper Challis Creek (CH4), upper Salmon River Basin, Idaho, 2005.

Figure B1. Plan view of upper Challis Creek (CH4), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigB01.ai

Transect

Local reference mark

For reference only; stream schematic not to scale.

Point Latitude Longitude

RH1 44° 34' 8.57" N 114° 21' 46.74" W

LH1 44° 34' 8.17" N 114° 21' 46.22" W

RH2 44° 34' 8.24" N 114° 21' 46.99" W

LH2 44° 34' 8.02" N 114° 21' 46.63" W

RH3 44° 34' 7.98" N 114° 21' 47.21" W

LH3 44° 34' 7.76" N 114° 21' 46.82" W

RH4 44° 34' 7.27" N 114° 21' 47.84" W

LH4 44° 34' 6.95" N 114° 21' 47.43" W

RH5 44° 34' 6.96" N 114° 21' 48.55" W

LH5 44° 34' 6.66" N 114° 21' 48.17" W

RH6 44° 34' 6.78" N 114° 21' 48.91" W

LH6 44° 34' 6.48" N 114° 21' 48.47" W

Transect Endpoint Coordinates (NAD 83)

Point Latitude Longitude

Transect Endpoint Coordinates (NAD 83)

RM1

RM2

RM3

4930

4980

5030

5080

5130

5180

5230

5280

4840 4890 4940 4990 5040 5090 5140 5190

EASTING, IN FEET

N

ORTHIN

G, IN FEET

T3

T5

T6

T4

T2

T1

48  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure B2. Weighted usable area and percentage of maximum habitat for bull trout, Chinook salmon, steelhead trout, and 

invertebrates, upper Challis Creek (CH4), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigB02.ai

WEIGHTED USABLE AREA (WUA), IN FEET SQUARE PER 1,000 FEET

PERCENTAGE OF MAXIMUM HABITAT

DISCHARGE, IN CUBIC FEET PER SECOND

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50

Chinook Salmon WUA

Bull Trout WUA Normalized

Steelhead Trout WUA

DISCHARGE, IN CUBIC FEET PER SECOND

Invertebrates

Spawning

Adult

Bull Trout WUA

Chinook Salmon WUA Normalized

Steelhead Trout WUA Normalized

Invertebrate WUA Invertebrate WUA

0

2,000

4,000

6,000

8,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

0

10

20

30

40

50

60

70

80

90

100

4,000

6,000

8,000

10,000

12,000

0 10 20 30 40 50

Appendix B  49
Table B1. Weighted usable area for bull trout, Chinook salmon, steelhead trout life stages, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) 

invertebrates, site CH4, upper Challis Creek, upper Salmon River Basin, Idaho, 2005. 

[Site location shown in figure 8. Abbreviations: WUA, weighted usable area; ft3/s, cubic foot per second; ft2, square foot; ft2/l,000 ft, square foot per 

1,000 feet]

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Bull trout

7.0 15,075 1,231 1,274 71.0 87.8

10 15,611 1,333 1,118 76.8 77.0

13 16,033 1,460 1,245 84.1 85.8

16 16,399 1,419 1,295 81.8 89.3

19 16,720 1,595 1,370 91.9 94.4

22 17,015 1,692 1,451 97.5 100.0

25 17,284 1,735 1,409 100.0 97.2

28 17,503 1,680 1,306 96.9 90.0

31 17,720 1,516 1,160 87.4 79.9

34 18,117 1,404 1,163 80.9 80.2

37 18,602 1,439 1,182 82.9 81.5

40 19,501 1,424 1,123 82.1 77.4

43 19,661 1,399 1,133 80.6 78.1

46 19,805 1,416 1,105 81.6 76.2

49.100 19,947 1,373 1,124 79.2 77.5

Chinook salmon

7.0 15,075 5,208 4,490 73.7 70.6

10 15,611 5,970 5,088 84.5 80.0

13 16,033 6,539 5,542 92.6 87.1

16 16,399 6,868 5,885 97.2 92.5

19 16,720 6,997 6,128 99.0 96.3

22 17,015 6,968 6,220 98.6 97.7

25 17,284 6,868 6,227 97.2 97.9

28 17,503 7,002 6,236 99.1 98.0

31 17,720 6,997 6,217 99.0 97.7

34 18,117 7,065 6,338 100.0 99.6

37 18,602 7,029 6,363 99.5 100.0

40 19,501 6,931 6,350 98.1 99.8

43 19,661 6,738 6,233 95.4 97.9

46 19,805 6,555 6,054 92.8 95.1

49.100 19,947 6,288 5,779 89.0 90.8

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Steelhead trout

7.0 15,075 5,208 4,490 73.7 70.6

10 15,611 5,970 5,088 84.5 80.0

13 16,033 6,539 5,542 92.6 87.1

16 16,399 6,868 5,885 97.2 92.5

19 16,720 6,997 6,128 99.0 96.3

22 17,015 6,968 6,220 98.6 97.7

25 17,284 6,868 6,227 97.2 97.9

28 17,503 7,002 6,236 99.1 98.0

31 17,720 6,997 6,217 99.0 97.7

34 18,117 7,065 6,338 100.0 99.6

37 18,602 7,029 6,363 99.5 100.0

40 19,501 6,931 6,350 98.1 99.8

43 19,661 6,738 6,233 95.4 97.9

46 19,805 6,555 6,054 92.8 95.1

49.100 19,947 6,288 5,779 89.0 90.8

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

EPT Invertebrates

6.970 15,075 8,873 86.9

10 15,611 9,729 95.3

13 16,033 9,941 97.4

16 16,399 10,207 100.0

19 16,720 10,062 98.6

22 17,015 9,737 95.4

25 17,284 9,270 90.8

28 17,503 8,631 84.6

31 17,720 7,774 76.2

34 18,117 7,460 73.1

37 18,602 7,380 72.3

40 19,501 6,812 66.7

43 19,661 6,503 63.7

46 19,805 6,108 59.8

49.100 19,947 5,679 55.6

50 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure B3. Percentages of contiguous and total stream width for passage transect 3, upper Challis 

Creek (CH4), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigB03.ai

DISCHARGE, IN CUBIC FEET PER SECOND

Passage Transect 3

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

Passage Transect 3

(wide moderate slope)

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50

0

5

10

15

20

25

30

CRITERIA LINE

Appendix B 51
Table B2. Passage criteria assessment for transect 3 (wide moderate slope), site CH4, upper Challis Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

7.0 15.9 5.9 36.9 3.2 20.2

10 16.2 10.8 66.7 10.8 66.7

13 16.4 12.1 73.9 12.1 73.9

16 16.6 13.3 80.2 13.3 80.2

19 16.7 13.8 82.5 13.8 82.5

22 16.8 14.1 83.8 14.1 83.8

25 16.9 14.4 85.0 14.4 85.0

28 17.1 14.7 86.1 14.7 86.1

31 17.2 14.9 87.0 14.9 87.0

34 17.2 15.2 88.0 15.2 88.0

37 17.3 15.4 88.8 15.4 88.8

40 17.4 15.6 89.5 15.6 89.5

43 17.5 15.7 89.8 15.7 89.8

46 17.6 15.8 90.1 15.8 90.1

49.1 17.7 16.0 90.4 16.0 90.4

Stream widths greater than 0.6-ft depth

7.0 15.9 0.0 0.0 0.0 0.0

10 16.2 0.0 0.0 0.0 0.0

13 16.4 0.0 0.0 0.0 0.0

16 16.6 0.0 0.0 0.0 0.0

19 16.7 4.0 23.9 2.6 15.5

22 16.8 6.5 38.7 3.4 20.3

25 16.9 8.9 52.5 4.2 24.8

28 17.1 11.1 64.9 11.1 64.9

31 17.2 11.8 68.6 11.8 68.6

34 17.2 12.5 72.3 12.5 72.3

37 17.3 13.1 75.8 13.1 75.8

40 17.4 13.6 78.0 13.6 78.0

43 17.5 13.8 78.8 13.8 78.8

46 17.6 14.0 79.6 14.0 79.6

49.1 17.7 14.2 80.4 14.2 80.4

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

7.0 15.9 0.0 0.0 0.0 0.0

10 16.2 0.0 0.0 0.0 0.0

13 16.4 0.0 0.0 0.0 0.0

16 16.6 0.0 0.0 0.0 0.0

19 16.7 0.0 0.0 0.0 0.0

22 16.8 0.0 0.0 0.0 0.0

25 16.9 0.0 0.0 0.0 0.0

28 17.1 0.0 0.0 0.0 0.0

31 17.2 0.0 0.0 0.0 0.0

34 17.2 0.0 0.0 0.0 0.0

37 17.3 0.0 0.0 0.0 0.0

40 17.4 2.6 15.1 2.1 12.3

43 17.5 4.2 23.9 2.7 15.1

46 17.6 5.7 32.7 3.2 18.0

49.1 17.7 7.4 41.9 3.7 21.0

52 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure B4. Percentages of contiguous and total stream width for passage transect 4, upper Challis 

Creek (CH4), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigB04.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 4

(wide moderate slope)

Passage Transect 4

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50

0

5

10

15

20

25

30

Appendix B 53
Table B3. Passage criteria assessment for transect 4 (wide moderate slope), site CH4, upper Challis Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

7.0 17.8 7.3 41.0 6.6 37.1

10 18.2 12.0 65.7 9.9 54.5

13 18.5 14.3 77.1 11.1 59.9

16 18.8 15.3 81.6 15.3 81.6

19 19.1 15.9 83.5 15.9 83.5

22 19.3 16.7 86.3 16.7 86.3

25 19.6 17.4 89.1 17.4 89.1

28 19.7 17.8 90.2 17.8 90.2

31 19.8 18.0 90.8 18.0 90.8

34 19.9 18.2 91.3 18.2 91.3

37 20.0 18.3 91.8 18.3 91.8

40 20.1 18.5 92.3 18.5 92.3

43 20.1 18.7 92.8 18.7 92.8

46 20.2 18.9 93.3 18.9 93.3

49.1 20.3 19.0 93.7 19.0 93.7

Stream widths greater than 0.6-ft depth

7.0 17.8 0.0 0.0 0.0 0.0

10 18.2 1.9 10.5 1.9 10.5

13 18.5 3.5 18.8 3.5 18.8

16 18.8 7.3 39.0 6.6 35.2

19 19.1 9.9 51.8 8.2 43.1

22 19.3 12.9 66.6 10.4 53.7

25 19.6 14.5 74.3 11.2 57.3

28 19.7 15.3 77.5 15.3 77.5

31 19.8 15.7 79.3 15.7 79.3

34 19.9 16.2 81.2 16.2 81.2

37 20.0 16.7 83.9 16.7 83.9

40 20.1 17.3 86.3 17.3 86.3

43 20.1 17.7 87.8 17.7 87.8

46 20.2 17.8 88.3 17.8 88.3

49.1 20.3 18.0 88.7 18.0 88.7

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

7.0 17.8 0.0 0.0 0.0 0.0

10 18.2 0.0 0.0 0.0 0.0

13 18.5 0.0 0.0 0.0 0.0

16 18.8 0.0 0.0 0.0 0.0

19 19.1 0.0 0.0 0.0 0.0

22 19.3 2.5 13.1 2.5 13.1

25 19.6 3.7 18.7 3.7 18.7

28 19.7 7.0 35.3 6.4 32.4

31 19.8 8.8 44.6 7.6 38.2

34 19.9 11.7 58.8 9.8 49.1

37 20.0 13.0 65.1 10.4 52.3

40 20.1 14.2 70.9 11.1 55.1

43 20.1 15.1 74.8 15.1 74.8

46 20.2 15.4 76.3 15.4 76.3

49.1 20.3 15.8 77.8 15.8 77.8

54  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure B5. Percentages of contiguous and total stream width for passage transect 5, upper Challis 

Creek (CH4), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigB05.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 5

(narrow high slope)

Passage Transect 5

(narrow high slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50

0

5

10

15

20

25

30

Appendix B 55
Table B4. Passage criteria assessment for transect 5 (narrow high slope), site CH4, upper Challis Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

7.0 15.3 4.8 31.7 4.2 27.3

10 15.5 8.6 55.4 5.6 36.0

13 15.6 12.7 81.0 12.7 81.0

16 15.8 13.1 82.9 13.1 82.9

19 16.0 13.6 85.0 13.6 85.0

22 16.1 14.0 87.0 14.0 87.0

25 16.2 14.4 88.8 14.4 88.8

28 16.3 14.8 90.4 14.8 90.4

31 16.5 15.1 92.0 15.1 92.0

34 18.3 15.4 84.0 15.4 84.0

37 21.0 15.5 74.1 15.5 74.1

40 27.4 15.8 57.8 15.8 57.8

43 27.5 15.9 57.8 15.9 57.8

46 27.6 16.0 57.9 16.0 57.9

49.1 27.6 16.0 58.0 16.0 58.0

Stream widths greater than 0.6-ft depth

7.0 15.3 0.0 0.0 0.0 0.0

10 15.5 0.0 0.0 0.0 0.0

13 15.6 2.7 17.5 2.7 17.5

16 15.8 3.7 23.2 3.7 23.2

19 16.0 6.0 37.4 4.6 28.7

22 16.1 8.3 51.5 5.5 34.0

25 16.2 12.5 76.9 12.5 76.9

28 16.3 12.8 78.2 12.8 78.2

31 16.5 13.1 79.6 13.1 79.6

34 18.3 13.7 74.8 13.7 74.8

37 21.0 14.3 68.2 14.3 68.2

40 27.4 15.2 55.5 15.2 55.5

43 27.5 15.3 55.5 15.3 55.5

46 27.6 15.3 55.6 15.3 55.6

49.1 27.6 15.4 55.7 15.4 55.7

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

7.0 15.3 0.0 0.0 0.0 0.0

10 15.5 0.0 0.0 0.0 0.0

13 15.6 0.0 0.0 0.0 0.0

16 15.8 0.0 0.0 0.0 0.0

19 16.0 0.0 0.0 0.0 0.0

22 16.1 0.0 0.0 0.0 0.0

25 16.2 2.3 14.3 2.3 14.3

28 16.3 3.0 18.2 3.0 18.2

31 16.5 3.6 22.0 3.6 22.0

34 18.3 6.5 35.7 4.8 26.2

37 21.0 12.4 59.0 12.4 59.0

40 27.4 13.1 48.0 13.1 48.0

43 27.5 13.4 48.6 13.4 48.6

46 27.6 13.6 49.2 13.6 49.2

49.1 27.6 13.8 49.8 13.8 49.8

56  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Appendix C. Plan view, weighted usable areas, and passage criteria assessments for bull trout, Chinook salmon, 

steelhead trout, and invertebrates for lower Bear Creek, upper Salmon River Basin, Idaho, 2005.

Figure C1. Plan view of lower Bear Creek (BE1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigC01.ai

Transect

Local reference mark

For reference only; stream schematic not to scale.

Point Latitude Longitude

RH1 44° 34' 11.08" N 114° 21' 49.32" W

LH1 44° 34' 10.89" N 114° 21' 49.46" W

RH2 44° 34' 11.31" N 114° 21' 49.76" W

LH2 44° 34' 11.2" N 114° 21' 49.98" W

RH3 44° 34' 11.59" N 114° 21' 50.2" W

LH3 44° 34' 11.37" N 114° 21' 50.39" W

RH4 44° 34' 11.81" N 114° 21' 51.22" W

LH4 44° 34' 11.72" N 114° 21' 51.47" W

RH5 44° 34' 12.3" N 114° 21' 51.74" W

LH5 44° 34' 12.1" N 114° 21' 51.8" W

RH6 44° 34' 12.29" N 114° 21' 52.37" W

LH6 44° 34' 12" N 114° 21' 52.29" W

Transect Endpoint Coordinates (NAD 83)

Point Latitude Longitude

Transect Endpoint Coordinates (NAD 83)

RM1

RM3

RM2

4820

4870

4920

4970

5020

5070

5120

5170

4930 4980 5030 5080 5130 5180 5230 5280

EASTING, IN FEET

N

ORTHIN

G, IN FEET

T1

T2

T4 T3

T5

T6

Appendix C 57
Figure C2. Weighted usable area and percentage of maximum habitat for bull trout, Chinook salmon, steelhead trout, and invertebrates, 

lower Bear Creek (BE1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigC02.ai

Steelhead Trout WUA Normalized

Bull Trout WUA

Chinook Salmon WUA Normalized

Chinook Salmon WUA

Steelhead Trout WUA

Invertebrate WUA Invertebrate WUA

Bull Trout WUA Normalized

Invertebrates

Spawning

Adult

WEIGHTED USABLE AREA (WUA), IN FEET SQUARE PER 1,000 FEET

PERCENTAGE OF MAXIMUM HABITAT

DISCHARGE, IN CUBIC FEET PER SECOND DISCHARGE, IN CUBIC FEET PER SECOND

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

8,000

9,000

10,000

0

10

20

30

40

50

60

70

80

90

100

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

8,000

9,000

10,000

0

10

20

30

40

50

60

70

80

90

100

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

8,000

9,000

10,000

0

10

20

30

40

50

60

70

80

90

100

0

1,000

2,000

3,000

4,000

5,000

6,000

7,000

8,000

9,000

10,000

0 10 20 30 40

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40

58  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table C1. Weighted usable area for bull trout, Chinook salmon, steelhead trout life stages, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) 

invertebrates, site BE1, lower Bear Creek, upper Salmon River Basin, Idaho, 2005. 

[Site location shown in figure 8. Abbreviations: WUA, weighted usable area; ft3/s, cubic foot per second; ft2, square foot; ft2/l,000 ft, square foot per 

1,000 feet]

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Bull trout

3.8 12,567 2,557 461 83.0 24.4

5 12,916 2,802 629 90.9 33.3

8 13,542 3,081 983 100.0 52.0

11 13,917 3,026 1,302 98.2 68.9

14 14,225 3,039 1,547 98.6 81.9

17 14,486 2,850 1,715 92.5 90.8

20 14,697 2,457 1,818 79.7 96.2

23 14,873 2,081 1,878 67.5 99.4

26 15,035 1,695 1,890 55.0 100.0

29 15,182 1,568 1,850 50.9 97.9

32 15,328 1,638 1,750 53.2 92.6

32.600 15,364 1,627 1,719 52.8 91.0

35 15,490 1,672 1,700 54.3 89.9

Chinook salmon

3.8 12,567 4,850 2,357 70.5 45.5

5 12,916 5,325 2,839 77.4 54.8

8 13,542 6,116 3,776 88.9 73.0

11 13,917 6,528 4,450 94.9 86.0

14 14,225 6,716 4,730 97.6 91.4

17 14,486 6,767 4,843 98.3 93.6

20 14,697 6,881 5,054 100.0 97.6

23 14,873 6,882 5,125 100.0 99.0

26 15,035 6,800 5,176 98.8 100.0

29 15,182 6,661 5,105 96.8 98.6

32 15,328 6,509 5,036 94.6 97.3

32.600 15,364 6,482 5,041 94.2 97.4

35 15,490 6,523 5,083 94.8 98.2

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Steelhead trout

3.8 12,567 4,850 2,357 70.5 45.5

5 12,916 5,325 2,839 77.4 54.8

8 13,542 6,116 3,776 88.9 73.0

11 13,917 6,528 4,450 94.9 86.0

14 14,225 6,716 4,730 97.6 91.4

17 14,486 6,767 4,843 98.3 93.6

20 14,697 6,881 5,054 100.0 97.6

23 14,873 6,882 5,125 100.0 99.0

26 15,035 6,800 5,176 98.8 100.0

29 15,182 6,661 5,105 96.8 98.6

32 15,328 6,509 5,036 94.6 97.3

32.600 15,364 6,482 5,041 94.2 97.4

35 15,490 6,523 5,083 94.8 98.2

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

EPT Invertebrates

5 12,916 7,567 82.8

8 13,542 8,451 92.5

11 13,917 9,140 100.0

14 14,225 9,059 99.1

17 14,486 8,792 96.2

20 14,697 8,810 96.4

23 14,873 8,262 90.4

26 15,035 7,416 81.1

29 15,182 7,010 76.7

32 15,328 6,432 70.4

32.600 15,364 6,351 69.5

35 15,490 6,114 66.9

Appendix C 59
Figure C3. Percentages of contiguous and total stream width for passage transect 3, lower Bear 

Creek (BE1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigC03.ai

Passage Transect 3

(wide high slope)

Passage Transect 3

(wide high slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

CRITERIA LINE

0

20

40

60

80

100

120

0

5

10

15

20

0

20

40

60

80

100

120

0 10 20 30 40

0

5

10

15

20

60 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table C2. Passage criteria assessment for transect 3 (wide high slope), site BE1, lower Bear Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

3.8 15.8 1.8 11.6 1.1 7.0

5 16.3 3.6 22.1 1.6 9.6

8 17.0 8.7 51.5 3.2 18.6

11 17.2 14.3 83.3 8.1 47.1

14 17.3 15.1 87.2 8.5 48.9

17 17.4 15.8 90.5 8.8 50.4

20 17.6 16.4 93.1 9.0 51.2

23 17.7 16.7 94.7 9.2 52.1

26 17.8 17.0 95.8 17.0 95.8

29 17.9 17.1 95.8 17.1 95.8

32 18.0 17.2 95.8 17.2 95.8

33 18.0 17.3 95.8 17.3 95.8

35 18.1 17.3 95.8 17.3 95.8

Stream widths greater than 0.6-ft depth

3.8 15.8 0.0 0.0 0.0 0.0

5 16.3 0.0 0.0 0.0 0.0

8 17.0 0.8 4.6 0.8 4.6

11 17.2 3.4 19.7 1.5 8.8

14 17.3 6.9 39.7 2.6 14.8

17 17.4 13.8 78.9 7.8 44.9

20 17.6 14.4 82.2 8.2 46.4

23 17.7 15.1 85.3 8.5 47.9

26 17.8 15.7 88.0 8.7 49.1

29 17.9 16.2 90.2 8.9 49.8

32 18.0 16.5 91.9 9.1 50.5

33 18.0 16.6 92.2 9.1 50.7

35 18.1 16.9 93.1 9.3 51.2

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

3.8 15.8 0.0 0.0 0.0 0.0

5 16.3 0.0 0.0 0.0 0.0

8 17.0 0.0 0.0 0.0 0.0

11 17.2 0.0 0.0 0.0 0.0

14 17.3 0.5 2.7 0.5 2.7

17 17.4 1.7 9.8 1.1 6.1

20 17.6 3.8 21.9 1.6 9.2

23 17.7 6.9 38.7 2.6 14.5

26 17.8 13.6 76.5 7.8 43.6

29 17.9 14.2 79.3 8.0 44.9

32 18.0 14.7 81.9 8.3 46.1

33 18.0 14.8 82.4 8.3 46.3

35 18.1 15.3 84.4 8.6 47.3

Appendix C  61
Figure C4. Percentages of contiguous and total stream width for passage transect 5, lower Bear 

Creek (BE1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigC04.ai

Passage Transect 5

(wide moderate slope)

Passage Transect 5

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

CRITERIA LINE

0

5

10

15

20

25

30

35

40

45

50

0

5

10

15

20

0

10

20

30

40

50

60

70

80

90

0 10 20 30 40

0

5

10

15

20

62 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table C3. Passage criteria assessment for transect 5 (wide moderate slope), site BE1, lower Bear Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

3.8 15.4 6.1 39.7 2.6 16.8

5 15.7 8.1 51.3 4.0 25.7

8 16.3 9.4 57.9 4.5 27.5

11 16.7 10.3 61.7 7.6 45.9

14 17.0 10.9 64.1 7.7 45.3

17 17.3 11.4 66.2 7.7 44.9

20 17.5 12.9 73.8 7.8 44.5

23 17.7 13.2 74.5 7.8 44.2

26 17.9 13.5 75.2 7.9 43.9

29 18.1 13.7 75.8 7.9 43.6

32 18.2 13.9 76.3 7.9 43.4

33 18.3 14.0 76.4 7.9 43.4

35 18.4 14.1 76.9 7.9 43.2

Stream widths greater than 0.6-ft depth

3.8 15.4 0.0 0.0 0.0 0.0

5 15.7 2 12.4 1.5 9.3

8 16.3 3 19.3 1.8 10.9

11 16.7 4 24.9 2.0 12.1

14 17.0 5 29.6 2.2 12.9

17 17.3 6 33.5 2.5 14.3

20 17.5 8 43.4 3.9 22.2

23 17.7 8 45.8 4.1 22.9

26 17.9 9 48.1 4.2 23.5

29 18.1 9 50.1 4.4 24.1

32 18.2 9 51.8 4.5 24.6

33 18.3 10 52.3 4.5 24.7

35 18.4 10 53.6 7.6 41.4

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

3.8 15.4 0.0 0.0 0.0 0.0

5 15.7 0.0 0.0 0.0 0.0

8 16.3 0.0 0.0 0.0 0.0

11 16.7 0.0 0.0 0.0 0.0

14 17.0 0.0 0.0 0.0 0.0

17 17.3 0.0 0.0 0.0 0.0

20 17.5 1.5 8.8 1.4 7.8

23 17.7 2.0 11.2 1.5 8.4

26 17.9 2.4 13.5 1.6 8.9

29 18.1 2.8 15.5 1.7 9.4

32 18.2 3.2 17.3 1.8 9.8

33 18.3 3.2 17.8 1.8 9.9

35 18.4 3.6 19.3 1.9 10.2

Appendix C  63
Figure C5. Percentages of contiguous and total stream width for passage transect 6, lower Bear 

Creek (BE1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigC05.ai

Passage Transect 6

(wide moderate slope)

Passage Transect 6

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

0

5

10

15

20

0

10

20

30

40

50

60

70

80

90

0 5 10 15 20 25 30 35 40

0

5

10

15

20

64  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table C4. Passage criteria assessment for transect 6 (wide moderate slope), site BE1, lower Bear Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

3.8 14.8 9.2 61.9 9.2 61.9

5 15.1 9.9 65.6 9.5 63.1

8 15.8 13.3 84.2 13.3 84.2

11 16.4 13.7 83.6 13.7 83.6

14 16.8 14.0 83.1 14.0 83.1

17 17.2 14.2 82.8 14.2 82.8

20 17.5 14.4 82.7 14.4 82.7

23 17.6 14.6 83.1 14.6 83.1

26 17.7 14.8 83.3 14.8 83.3

29 17.9 15.0 83.6 15.0 83.6

32 18.1 15.2 83.9 15.2 83.9

33 18.1 15.2 84.0 15.2 84.0

35 18.3 15.4 84.3 15.4 84.3

Stream widths greater than 0.6-ft depth

3.8 14.8 3.5 23.4 3.5 23.4

5 15.1 6 36.5 5.5 36.5

8 15.8 9 54.4 8.6 54.4

11 16.4 9 55.8 9.1 55.8

14 16.8 10 59.8 9.6 57.0

17 17.2 11 64.3 10.0 57.9

20 17.5 13 76.5 13.4 76.5

23 17.6 14 76.9 13.5 76.9

26 17.7 14 77.2 13.7 77.2

29 17.9 14 77.4 13.8 77.4

32 18.1 14 77.4 14.0 77.4

33 18.1 14 77.4 14.0 77.4

35 18.3 14 77.4 14.1 77.4

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

3.8 14.8 1.4 9.7 1.4 9.7

5 15.1 1.8 12.2 1.8 12.2

8 15.8 2.7 16.9 2.7 16.9

11 16.4 3.4 21.0 3.4 21.0

14 16.8 5.7 33.8 5.7 33.8

17 17.2 6.9 40.1 6.9 40.1

20 17.5 8.6 49.4 8.6 49.4

23 17.6 8.9 50.6 8.9 50.6

26 17.7 9.2 51.6 9.2 51.6

29 17.9 9.5 53.0 9.4 52.4

32 18.1 10.1 55.8 9.6 53.1

33 18.1 10.2 56.4 9.6 53.2

35 18.3 10.7 58.4 9.8 53.7

Appendix C  65
Appendix D. Plan view, weighted usable areas, and passage criteria assessments for bull trout, Chinook salmon, 

steelhead trout, and invertebrates for upper middle Challis Creek (CH3), upper Salmon River Basin, Idaho, 2005.

Figure D1. Plan view of upper middle Challis Creek (CH3), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigD01.ai

Transect

Local reference mark

For reference only; stream schematic not to scale.

Point Latitude Longitude

RH1 44° 34' 14.69" N 114° 18' 11.52" W

LH1 44° 34' 14.33" N 114° 18' 12.23" W

RH2 44° 34' 15.09" N 114° 18' 11.96" W

LH2 44° 34' 15.12" N 114° 18' 12.43" W

RH3 44° 34' 15.29" N 114° 18' 11.9" W

LH3 44° 34' 15.45" N 114° 18' 12.23" W

LH4 44° 34' 16.02" N 114° 18' 12.01" W

RH5 44° 34' 16.54" N 114° 18' 12.67" W

LH5 44° 34' 16.26" N 114° 18' 13.11" W

RH6 44° 34' 16.64" N 114° 18' 12.78" W

LH6 44° 34' 16.46" N 114° 18' 13.3" W

RH7 44° 34' 16.9" N 114° 18' 12.86" W

Transect Endpoint Coordinates (NAD 83)

Point Latitude Longitude

Transect Endpoint Coordinates (NAD 83)

RM1

RM2

RM3

4660

4710

4760

4810

4860

4910

4960

5010

5060

5110

4920 4970 5020 5070 5120 5170 5220 5270 5320 5370

EASTING, IN FEET

N

ORTHIN

G, IN FEET

T3

T7

T5

T6

T4

T2

T1

RH4 44° 34' 16.31" N 114° 18' 11.82" W LH7 44° 34' 17.09" N 114° 18' 13.41" W

66  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure D2. Weighted usable area and percentage of maximum habitat for bull trout, Chinook salmon, steelhead trout, and 

invertebrates, upper middle Challis Creek (CH3), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigD02.ai

Steelhead Trout WUA Normalized

Bull Trout WUA

C Chinook Salmon WUA Normalized hinook Salmon WUA

Steelhead Trout WUA

Invertebrate WUA Invertebrate WUA

Bull Trout WUA Normalized

Invertebrates

Spawning

Adult

WEIGHTED USABLE AREA (WUA), IN FEET SQUARE PER 1,000 FEET

PERCENTAGE OF MAXIMUM HABITAT

DISCHARGE, IN CUBIC FEET PER SECOND DISCHARGE, IN CUBIC FEET PER SECOND

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0 10 20 30 40 50 60 70 80 90 100 110

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90 100 110

Appendix D  67
Table D1. Weighted usable area for bull trout, Chinook salmon, steelhead trout life stages, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) 

invertebrates, site CH3, upper middle Challis Creek, upper Salmon River Basin, Idaho, 2005. 

[Site location shown in figure 8. Abbreviations: WUA, weighted usable area; ft3/s, cubic foot per second; ft2, square foot; ft2/l,000 ft, square foot per 

1,000 feet]

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Bull trout

10.9 20,178 6,544 2,236 91.8 64.0

15 20,724 6,938 2,509 97.3 71.9

19 21,146 7,128 2,881 100.0 82.5

23 21,528 6,786 3,115 95.2 89.2

27 21,880 6,735 3,323 94.5 95.1

31 22,212 6,542 3,435 91.8 98.4

35 22,513 6,326 3,492 88.8 100.0

39 22,797 6,056 3,463 85.0 99.2

43 23,093 5,821 3,451 81.7 98.8

47 23,555 5,741 3,419 80.5 97.9

51 23,999 5,555 3,379 77.9 96.8

55 24,295 5,327 3,393 74.7 97.2

59 24,624 5,132 3,402 72.0 97.4

63 24,937 5,021 3,446 70.4 98.7

67 25,221 4,988 3,451 70.0 98.8

71 25,529 4,891 3,420 68.6 98.0

75 25,897 4,724 3,352 66.3 96.0

79 26,260 4,816 3,225 67.6 92.4

83 26,531 4,900 3,213 68.7 92.0

87 26,818 4,796 3,100 67.3 88.8

91 27,084 4,917 3,097 69.0 88.7

95 27,360 4,973 3,068 69.8 87.9

99 27,642 4,931 2,993 69.2 85.7

102 27,849 5,030 2,949 70.6 84.4

Chinook salmon

10.9 20,178 9,322 6,657 69.1 58.4

15 20,724 10,254 7,478 76.0 65.7

19 21,146 11,042 8,353 81.9 73.3

23 21,528 11,567 8,958 85.8 78.6

27 21,880 11,916 9,361 88.3 82.2

31 22,212 12,246 9,725 90.8 85.4

35 22,513 12,493 10,089 92.6 88.6

39 22,797 12,677 10,294 94.0 90.4

43 23,093 12,858 10,521 95.3 92.4

47 23,555 13,110 10,752 97.2 94.4

51 23,999 13,243 10,887 98.2 95.6

55 24,295 13,308 10,942 98.7 96.1

59 24,624 13,301 10,924 98.6 95.9

63 24,937 13,401 11,111 99.4 97.6

67 25,221 13,489 11,390 100.0 100.0

71 25,529 13,337 11,314 98.9 99.3

75 25,897 13,104 11,160 97.1 98.0

79 26,260 13,027 11,094 96.6 97.4

83 26,531 13,117 11,150 97.2 97.9

87 26,818 13,042 11,051 96.7 97.0

91 27,084 12,937 11,013 95.9 96.7

95 27,360 12,828 10,879 95.1 95.5

99 27,642 12,620 10,589 93.6 93.0

102 27,849 12,513 10,401 92.8 91.3

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Steelhead trout

10.9 20,178 9,322 6,657 69.1 58.4

15 20,724 10,254 7,478 76.0 65.7

19 21,146 11,042 8,353 81.9 73.3

23 21,528 11,567 8,958 85.8 78.6

27 21,880 11,916 9,361 88.3 82.2

31 22,212 12,246 9,725 90.8 85.4

35 22,513 12,493 10,089 92.6 88.6

39 22,797 12,677 10,294 94.0 90.4

43 23,093 12,858 10,521 95.3 92.4

47 23,555 13,110 10,752 97.2 94.4

51 23,999 13,243 10,887 98.2 95.6

55 24,295 13,308 10,942 98.7 96.1

59 24,624 13,301 10,924 98.6 95.9

63 24,937 13,401 11,111 99.4 97.6

67 25,221 13,489 11,390 100.0 100.0

71 25,529 13,337 11,314 98.9 99.3

75 25,897 13,104 11,160 97.1 98.0

79 26,260 13,027 11,094 96.6 97.4

83 26,531 13,117 11,150 97.2 97.9

87 26,818 13,042 11,051 96.7 97.0

91 27,084 12,937 11,013 95.9 96.7

95 27,360 12,828 10,879 95.1 95.5

99 27,642 12,620 10,589 93.6 93.0

102 27,849 12,513 10,401 92.8 91.3

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

EPT Invertebrates

10.9 20,178 10,366 82.8

15 20,724 11,185 89.3

19 21,146 11,873 94.8

23 21,528 12,292 98.2

27 21,880 12,519 100.0

31 22,212 12,517 100.0

35 22,513 12,496 99.8

39 22,797 12,375 98.8

43 23,093 12,226 97.7

47 23,555 11,378 90.9

51 23,999 11,157 89.1

55 24,295 10,880 86.9

59 24,624 10,691 85.4

63 24,937 10,187 81.4

67 25,221 9,910 79.2

71 25,529 9,528 76.1

75 25,897 8,986 71.8

79 26,260 8,598 68.7

83 26,531 8,211 65.6

87 26,818 7,863 62.8

91 27,084 7,503 59.9

95 27,360 6,937 55.4

99 27,642 6,828 54.5

102 27,849 6,722 53.7

68  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure D3. Percentages of contiguous and total stream width for passage transect 1, upper middle 

Challis Creek (CH3), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigD03.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 1

(wide moderate slope)

Passage Transect 1

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

35

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90 100 110

0

5

10

15

20

25

30

35

Appendix D  69
Table D2. Passage criteria assessment for transect 1 (wide moderate slope), site CH3, upper middle Challis Creek, upper Salmon River Basin, Idaho, 

2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

10.9 23.5 10.1 42.9 8.5 36.0

15 24.0 17.0 70.7 9.8 41.0

19 24.4 20.7 85.0 20.7 85.0

23 24.7 21.2 85.9 21.2 85.9

27 25.0 21.7 86.5 21.7 86.5

31 25.4 22.1 87.1 22.1 87.1

35 25.6 22.5 87.6 22.5 87.6

39 25.9 22.8 88.1 22.8 88.1

43 26.2 23.2 88.5 23.2 88.5

47 26.4 23.5 88.7 23.5 88.7

51 26.7 23.7 88.8 23.7 88.8

55 26.9 23.9 88.8 23.9 88.8

59 27.1 24.1 88.8 24.1 88.8

63 27.3 24.2 89.0 24.2 89.0

67 27.4 24.4 89.1 24.4 89.1

71 27.5 24.6 89.2 24.6 89.2

75 27.7 24.7 89.4 24.7 89.4

79 27.8 24.9 89.6 24.9 89.6

83 27.9 25.1 89.8 25.1 89.8

87 28.0 25.2 90.0 25.2 90.0

91 28.2 25.4 90.2 25.4 90.2

95 28.3 25.5 90.3 25.5 90.3

99 28.4 25.7 90.5 25.7 90.5

102 28.5 25.8 90.7 25.8 90.7

Stream widths greater than 0.6-ft depth

10.9 23.5 2.9 12.2 2.9 12.2

15 24.0 3.5 14.5 3.5 14.5

19 24.4 5.4 22.2 4.2 17.2

23 24.7 7.6 30.7 4.9 19.8

27 25.0 11.4 45.6 8.7 34.8

31 25.4 15.7 61.9 9.6 37.8

35 25.6 20.4 79.6 20.4 79.6

39 25.9 20.8 80.2 20.8 80.2

43 26.2 21.1 80.6 21.1 80.6

47 26.4 21.4 81.1 21.4 81.1

51 26.7 21.7 81.5 21.7 81.5

55 26.9 22.0 81.9 22.0 81.9

59 27.1 22.3 82.3 22.3 82.3

63 27.3 22.6 82.8 22.6 82.8

67 27.4 22.8 83.3 22.8 83.3

71 27.5 23.1 83.8 23.1 83.8

75 27.7 23.3 84.2 23.3 84.2

79 27.8 23.5 84.5 23.5 84.5

83 27.9 23.6 84.7 23.6 84.7

87 28.0 23.8 84.8 23.8 84.8

91 28.2 23.9 85.0 23.9 85.0

95 28.3 24.1 85.2 24.1 85.2

99 28.4 24.2 85.3 24.2 85.3

102 28.5 24.3 85.4 24.3 85.4

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

10.9 23.5 1.1 4.6 1.1 4.6

15 24.0 1.7 7.0 1.7 7.0

19 24.4 2.2 8.9 2.2 8.9

23 24.7 2.6 10.6 2.6 10.6

27 25.0 3.0 12.0 3.0 12.0

31 25.4 3.4 13.3 3.4 13.3

35 25.6 4.1 16.0 3.8 14.7

39 25.9 5.7 22.0 4.3 16.5

43 26.2 7.2 27.3 4.8 18.2

47 26.4 9.1 34.5 8.3 31.3

51 26.7 12.2 45.9 8.9 33.3

55 26.9 15.1 56.2 9.5 35.2

59 27.1 17.8 65.6 10.0 36.9

63 27.3 20.5 75.3 20.5 75.3

67 27.4 20.8 75.8 20.8 75.8

71 27.5 21.0 76.3 21.0 76.3

75 27.7 21.2 76.8 21.2 76.8

79 27.8 21.5 77.3 21.5 77.3

83 27.9 21.7 77.7 21.7 77.7

87 28.0 21.9 78.1 21.9 78.1

91 28.2 22.1 78.6 22.1 78.6

95 28.3 22.3 78.9 22.3 78.9

99 28.4 22.5 79.3 22.5 79.3

102 28.5 22.7 79.6 22.7 79.6

70 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure D4. Percentages of contiguous and total stream width for passage transect 5, upper middle 

Challis Creek (CH3), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigD04.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 5

(wide moderate slope)

Passage Transect 5

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

35

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90 100 110

0

5

10

15

20

25

30

35

Appendix D  71
Table D3. Passage criteria assessment for transect 5 (wide moderate slope), site CH3, upper middle Challis Creek, upper Salmon River Basin, Idaho, 

2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

10.9 28.0 12.6 44.9 12.6 44.9

15 28.5 15.0 52.5 14.6 51.1

19 29.0 18.5 63.7 16.7 57.5

23 29.4 25.0 85.1 25.0 85.1

27 29.7 25.5 86.0 25.5 86.0

31 30.0 26.1 86.8 26.1 86.8

35 30.3 26.5 87.6 26.5 87.6

39 30.6 27.0 88.3 27.0 88.3

43 30.8 27.4 88.9 27.4 88.9

47 31.0 27.7 89.2 27.7 89.2

51 31.3 27.9 89.3 27.9 89.3

55 31.5 28.2 89.5 28.2 89.5

59 31.7 28.4 89.6 28.4 89.6

63 31.9 28.6 89.7 28.6 89.7

67 32.0 28.8 89.8 28.8 89.8

71 32.2 29.0 89.9 29.0 89.9

75 32.3 29.1 90.1 29.1 90.1

79 32.5 29.3 90.2 29.3 90.2

83 32.6 29.5 90.3 29.5 90.3

87 32.8 29.6 90.4 29.6 90.4

91 32.9 29.8 90.5 29.8 90.5

95 33.0 29.9 90.6 29.9 90.6

99 33.2 30.0 90.6 30.0 90.6

102 33.2 30.2 90.7 30.2 90.7

Stream widths greater than 0.6-ft depth

10.9 28.0 8.2 29.1 8.2 29.1

15 28.5 9.4 33.1 9.4 33.1

19 29.0 10.4 36.1 10.4 36.1

23 29.4 11.5 39.1 11.5 39.1

27 29.7 12.7 42.6 12.7 42.6

31 30.0 13.8 45.9 13.8 45.9

35 30.3 15.8 52.2 15.1 49.8

39 30.6 18.0 58.9 16.4 53.6

43 30.8 20.0 64.9 17.6 57.0

47 31.0 25.0 80.7 25.0 80.7

51 31.3 25.4 81.3 25.4 81.3

55 31.5 25.8 81.9 25.8 81.9

59 31.7 26.1 82.4 26.1 82.4

63 31.9 26.4 83.0 26.4 83.0

67 32.0 26.7 83.5 26.7 83.5

71 32.2 27.0 84.0 27.0 84.0

75 32.3 27.3 84.5 27.3 84.5

79 32.5 27.6 84.9 27.6 84.9

83 32.6 27.8 85.1 27.8 85.1

87 32.8 27.9 85.2 27.9 85.2

91 32.9 28.1 85.4 28.1 85.4

95 33.0 28.2 85.5 28.2 85.5

99 33.2 28.4 85.7 28.4 85.7

102 33.2 28.5 85.7 28.5 85.7

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

10.9 28.0 1.5 5.4 1.5 5.4

15 28.5 5.3 18.6 5.3 18.6

19 29.0 6.4 22.2 6.4 22.2

23 29.4 7.4 25.2 7.4 25.2

27 29.7 8.2 27.7 8.2 27.7

31 30.0 9.0 29.9 9.0 29.9

35 30.3 9.7 31.9 9.7 31.9

39 30.6 10.3 33.7 10.3 33.7

43 30.8 10.9 35.3 10.9 35.3

47 31.0 11.6 37.4 11.6 37.4

51 31.3 12.4 39.7 12.4 39.7

55 31.5 13.2 41.8 13.2 41.8

59 31.7 13.9 43.8 13.9 43.8

63 31.9 15.3 48.0 14.8 46.4

67 32.0 16.9 52.6 15.7 49.0

71 32.2 18.3 56.9 16.6 51.5

75 32.3 19.7 60.9 17.4 53.8

79 32.5 24.9 76.5 24.9 76.5

83 32.6 25.1 77.0 25.1 77.0

87 32.8 25.4 77.5 25.4 77.5

91 32.9 25.7 78.0 25.7 78.0

95 33.0 25.9 78.4 25.9 78.4

99 33.2 26.1 78.8 26.1 78.8

102 33.2 26.3 79.1 26.3 79.1

72 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure D5. Percentages of contiguous and total stream width for passage transect 6, upper middle 

Challis Creek (CH3), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigD05.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 6

(wide moderate slope)

Passage Transect 6

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90 100 110

Appendix D  73
Table D4. Passage criteria assessment for transect 6 (wide moderate slope), site CH3, upper middle Challis Creek, upper Salmon River Basin, Idaho, 

2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

10.9 24.0 16.3 67.9 16.3 67.9

15 24.3 16.9 69.5 16.9 69.5

19 24.6 17.4 70.7 17.4 70.7

23 24.9 17.8 71.8 17.8 71.8

27 25.1 19.1 76.1 18.2 72.7

31 25.3 20.3 80.3 18.6 73.6

35 25.5 21.4 83.9 19.0 74.3

39 25.7 22.4 87.2 19.3 75.0

43 25.8 23.3 90.2 19.6 75.6

47 26.0 23.9 91.8 23.9 91.8

51 26.2 24.0 91.8 24.0 91.8

55 26.3 24.2 91.9 24.2 91.9

59 26.4 24.3 91.9 24.3 91.9

63 26.6 24.4 92.0 24.4 92.0

67 26.7 24.6 92.0 24.6 92.0

71 26.8 24.7 92.0 24.7 92.0

75 26.9 24.8 92.1 24.8 92.1

79 27.0 24.9 92.2 24.9 92.2

83 27.1 25.0 92.3 25.0 92.3

87 27.2 25.1 92.5 25.1 92.5

91 27.3 25.2 92.6 25.2 92.6

95 27.3 25.3 92.7 25.3 92.7

99 27.4 25.4 92.8 25.4 92.8

102 27.6 25.7 93.2 25.7 93.2

Stream widths greater than 0.6-ft depth

10.9 24.0 8.7 36.2 5.8 24.1

15 24.3 11.8 48.4 6.8 28.0

19 24.6 15.0 61.1 15.0 61.1

23 24.9 16.0 64.3 16.0 64.3

27 25.1 16.4 65.3 16.4 65.3

31 25.3 16.8 66.3 16.8 66.3

35 25.5 17.1 67.1 17.1 67.1

39 25.7 17.4 67.8 17.4 67.8

43 25.8 17.7 68.5 17.7 68.5

47 26.0 18.3 70.2 18.0 69.1

51 26.2 19.1 73.1 18.2 69.7

55 26.3 19.9 75.8 18.5 70.3

59 26.4 20.7 78.2 18.7 70.8

63 26.6 21.4 80.6 19.0 71.3

67 26.7 22.1 82.9 19.2 71.8

71 26.8 22.8 85.1 19.4 72.3

75 26.9 23.4 87.0 19.6 72.7

79 27.0 23.8 88.2 23.8 88.2

83 27.1 24.0 88.4 24.0 88.4

87 27.2 24.1 88.5 24.1 88.5

91 27.3 24.2 88.7 24.2 88.7

95 27.3 24.3 88.8 24.3 88.8

99 27.4 24.4 89.0 24.4 89.0

102 27.6 24.7 89.4 24.7 89.4

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

10.9 24.0 0.8 3.3 0.8 3.3

15 24.3 2.5 10.4 2.5 10.4

19 24.6 4.0 16.3 4.0 16.3

23 24.9 5.3 21.2 5.3 21.2

27 25.1 9.2 36.8 6.0 23.7

31 25.3 11.1 43.9 6.6 26.0

35 25.5 14.4 56.4 14.4 56.4

39 25.7 15.1 58.6 15.1 58.6

43 25.8 15.7 60.7 15.7 60.7

47 26.0 16.1 62.0 16.1 62.0

51 26.2 16.4 62.7 16.4 62.7

55 26.3 16.6 63.3 16.6 63.3

59 26.4 16.9 63.8 16.9 63.8

63 26.6 17.1 64.4 17.1 64.4

67 26.7 17.3 64.9 17.3 64.9

71 26.8 17.5 65.4 17.5 65.4

75 26.9 17.7 65.9 17.7 65.9

79 27.0 18.1 67.0 17.9 66.3

83 27.1 18.7 69.1 18.1 66.9

87 27.2 19.3 71.1 18.3 67.4

91 27.3 19.9 73.0 18.5 67.8

95 27.3 20.4 74.8 18.7 68.3

99 27.4 21.0 76.6 18.8 68.7

102 27.6 22.6 82.0 19.3 70.1

74  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Appendix E. Plan view, weighted usable areas, and passage criteria assessments for bull trout, Chinook salmon, 

steelhead trout, and invertebrates for lower Mill Creek (ML1), upper Salmon River Basin, Idaho, 2005.

Figure E1. Plan view of upper lower Mill Creek (ML1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigE01.ai

Transect

Local reference mark

For reference only; stream schematic not to scale.

Point Latitude Longitude

RH1 44° 33' 36.5" N 114° 16' 30.86" W

LH1 44° 33' 36.46" N 114° 16' 30.58" W

RH2 44° 33' 36.2" N 114° 16' 31.05" W

LH2 44° 33' 36.02" N 114° 16' 30.8" W

RH3 44° 33' 35.81" N 114° 16' 31.46" W

LH3 44° 33' 35.72" N 114° 16' 31.21" W

LH4 44° 33' 35.39" N 114° 16' 31.46" W

RH5 44° 33' 34.91" N 114° 16' 31.87" W

LH5 44° 33' 34.85" N 114° 16' 31.6" W

RH6 44° 33' 34.51" N 114° 16' 32.23" W

LH6 44° 33' 34.4" N 114° 16' 32.01" W

Transect Endpoint Coordinates (NAD 83)

Point Latitude Longitude

Transect Endpoint Coordinates (NAD 83)

RM3

RM2

RM1

4830

4880

4930

4980

5030

5080

5130

5180

4950 5000 5050 5100 5150 5200 5250 5300

EASTING, IN FEET

N

ORTHIN

G, IN FEET

T3

T5

T6

T4

T2

T1

Appendix E  75
Figure E2. Weighted usable area and percentage of maximum habitat for bull trout, Chinook salmon, steelhead trout, and invertebrates, 

lower Mill Creek (ML1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigE02.ai

Steelhead Trout WUA Normalized

Bull Trout WUA

Chinook Salmon WUA Normalized

Chinook Salmon WUA

Steelhead Trout WUA

Invertebrate WUA Invertebrate WUA

Bull Trout WUA Normalized

Invertebrates

Spawning

Adult

WEIGHTED USABLE AREA (WUA), IN FEET SQUARE PER 1,000 FEET

PERCENTAGE OF MAXIMUM HABITAT

DISCHARGE, IN CUBIC FEET PER SECOND DISCHARGE, IN CUBIC FEET PER SECOND

0

2,000

4,000

6,000

8,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

0 10 20 30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30

76  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table E1. Weighted usable area for bull trout, Chinook salmon, steelhead trout life stages, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) 

invertebrates, site ML1, lower Mill Creek, upper Salmon River Basin, Idaho, 2005. 

[Site location shown in figure 8. Abbreviations: WUA, weighted usable area; ft3/s, cubic foot per second; ft2, square foot; ft2/l,000 ft, square foot per 

1,000 feet]

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Bull trout

3.3 11,523 2,725 924 86.6 49.5

6 11,902 3,020 1,435 96.0 76.9

9 12,149 3,147 1,756 100.0 94.0

12 12,328 2,926 1,857 93.0 99.4

15 12,479 2,559 1,867 81.3 100.0

18 12,613 2,181 1,780 69.3 95.3

21 12,732 1,901 1,661 60.4 89.0

24 12,839 1,799 1,519 57.2 81.3

27 12,937 1,696 1,293 53.9 69.3

27.400 12,951 1,683 1,268 53.5 67.9

Chinook salmon

3.3 11,523 4,159 1,886 65.4 51.4

6 11,902 5,178 2,617 81.4 71.4

9 12,149 5,814 3,079 91.4 83.9

12 12,328 6,110 3,402 96.0 92.8

15 12,479 6,284 3,589 98.8 97.9

18 12,613 6,362 3,667 100.0 100.0

21 12,732 6,247 3,606 98.2 98.3

24 12,839 6,077 3,562 95.5 97.1

27 12,937 5,692 3,459 89.5 94.3

27.400 12,951 5,657 3,437 88.9 93.7

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Steelhead trout

3.3 11,523 4,159 1,886 65.4 51.4

6 11,902 5,178 2,617 81.4 71.4

9 12,149 5,814 3,079 91.4 83.9

12 12,328 6,110 3,402 96.0 92.8

15 12,479 6,284 3,589 98.8 97.9

18 12,613 6,362 3,667 100.0 100.0

21 12,732 6,247 3,606 98.2 98.3

24 12,839 6,077 3,562 95.5 97.1

27 12,937 5,692 3,459 89.5 94.3

27.400 12,951 5,657 3,437 88.9 93.7

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

EPT Invertebrates

3.25 11,523 5,753 72.9

6 11,902 7,123 90.3

9 12,149 7,890 100.0

12 12,328 7,883 99.9

15 12,479 7,865 99.7

18 12,613 7,565 95.9

21 12,732 6,706 85.0

24 12,839 5,927 75.1

27 12,937 5,266 66.7

27.400 12,951 5,198 65.9

Appendix E  77
Figure E3. Percentages of contiguous and total stream width for passage transect 3, lower Mill 

Creek (ML1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigE03.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 3

(wide moderate slope)

Passage Transect 3

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30

0

5

10

15

20

78  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table E2. Passage criteria assessment for transect 3 (wide moderate slope), site ML1, lower Mill Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

3.3 11.3 4.9 43.2 3.1 27.2

6 11.5 6.1 52.9 3.7 32.4

9 11.6 7.7 66.6 4.4 37.7

12 11.7 9.2 78.9 9.2 78.9

15 11.8 10.5 88.8 10.5 88.8

18 11.9 10.9 91.8 10.9 91.8

21 11.9 11.3 94.5 11.3 94.5

24 12.0 11.4 94.8 11.4 94.8

27 12.1 11.4 94.8 11.4 94.8

27 12.1 11.4 94.8 11.4 94.8

Stream widths greater than 0.6-ft depth

3.3 11.3 1.8 15.9 1.8 15.9

6 11.5 2.4 21.2 2.4 21.2

9 11.6 4.4 37.7 3.0 25.4

12 11.7 5.4 46.3 3.4 28.8

15 11.8 6.1 51.7 3.7 31.6

18 11.9 7.1 60.0 4.1 34.9

21 11.9 8.1 67.6 4.5 37.8

24 12.0 9.2 76.6 9.2 76.6

27 12.1 9.4 78.1 9.4 78.1

27 12.1 9.4 78.3 9.4 78.3

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

3.3 11.3 0.0 0.0 0.0 0.0

6 11.5 0.0 0.0 0.0 0.0

9 11.6 1.4 12.3 1.4 12.3

12 11.7 2.1 17.8 2.1 17.8

15 11.8 2.5 20.9 2.4 20.7

18 11.9 3.7 30.9 2.8 23.3

21 11.9 4.8 40.0 3.1 25.6

24 12.0 5.3 44.4 3.3 27.7

27 12.1 5.8 48.0 3.6 29.6

27 12.1 5.8 48.4 3.6 29.8

Appendix E  79
Figure E4. Percentages of contiguous and total stream width for passage transect 5, lower Mill 

Creek (ML1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigE04.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 5

(wide low slope)

Passage Transect 5

(wide low slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30

0

5

10

15

20

80 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table E3. Passage criteria assessment for transect 5 (wide low slope), site ML1 lower Mill Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

3.3 13.7 4.4 32.0 2.4 17.4

6 14.0 7.6 54.1 5.5 38.9

9 14.3 10.8 75.2 6.0 41.8

12 14.5 12.2 84.1 6.3 43.7

15 14.7 12.9 87.7 6.7 45.2

18 14.9 13.4 90.0 13.4 90.0

21 15.1 13.5 90.0 13.5 90.0

24 15.2 13.7 90.0 13.7 90.0

27 15.3 13.8 90.0 13.8 90.0

27 15.3 13.8 90.0 13.8 90.0

Stream widths greater than 0.6-ft depth

3.3 13.7 0.0 0.0 0.0 0.0

6 14.0 0.0 0.0 0.0 0.0

9 14.3 3.2 22.4 2.0 14.0

12 14.5 5.0 34.6 4.6 31.7

15 14.7 6.8 46.1 5.2 35.2

18 14.9 9.2 61.7 5.7 38.0

21 15.1 10.4 68.9 5.9 39.2

24 15.2 11.5 75.6 6.1 40.4

27 15.3 12.2 79.7 6.3 41.4

27 15.3 12.3 80.0 6.4 41.5

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

3.3 13.7 0.0 0.0 0.0 0.0

6 14.0 0.0 0.0 0.0 0.0

9 14.3 0.0 0.0 0.0 0.0

12 14.5 0.0 0.0 0.0 0.0

15 14.7 0.0 0.0 0.0 0.0

18 14.9 1.7 11.4 1.5 10.1

21 15.1 2.8 18.8 1.9 12.5

24 15.2 3.9 25.8 2.2 14.7

27 15.3 5.0 32.4 4.6 29.9

27 15.3 5.1 33.3 4.6 30.2

Appendix E  81
Figure E5. Percentages of contiguous and total stream width for passage transect 6, lower Mill Creek 

(ML1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigE05.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 6

(wide moderate slope)

Passage Transect 6

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30

0

5

10

15

20

82 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table E4. Passage criteria assessment for transect 6 (wide moderate slope), site ML1 lower Mill Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

3.3 9.9 6.6 66.7 5.0 50.5

6 10.3 9.0 87.4 9.0 87.4

9 10.6 9.4 88.4 9.4 88.4

12 10.9 9.7 89.1 9.7 89.1

15 11.2 10.0 89.6 10.0 89.6

18 11.4 10.2 89.8 10.2 89.8

21 11.5 10.4 89.9 10.4 89.9

24 11.7 10.5 90.1 10.5 90.1

27 11.9 10.7 90.2 10.7 90.2

27 11.9 10.7 90.2 10.7 90.2

Stream widths greater than 0.6-ft depth

3.3 9.9 1.5 14.7 1.5 14.6

6 10.3 4.7 45.2 4.7 45.2

9 10.6 7.3 68.4 5.3 49.9

12 10.9 9.0 82.8 9.0 82.8

15 11.2 9.3 83.6 9.3 83.6

18 11.4 9.6 84.2 9.6 84.2

21 11.5 9.8 84.7 9.8 84.7

24 11.7 10.0 85.1 10.0 85.1

27 11.9 10.1 85.3 10.1 85.3

27 11.9 10.1 85.3 10.1 85.3

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

3.3 9.9 0.0 0.0 0.0 0.0

6 10.3 .6 5.6 .6 5.6

9 10.6 3.0 28.6 1.9 17.5

12 10.9 4.7 43.0 4.7 43.0

15 11.2 6.9 62.3 5.2 46.3

18 11.4 7.8 69.0 5.6 49.0

21 11.5 9.1 78.8 9.1 78.8

24 11.7 9.3 79.3 9.3 79.3

27 11.9 9.5 79.9 9.5 79.9

27 11.9 9.5 79.9 9.5 79.9

Appendix E  83
Appendix F. Plan view, weighted usable areas, and passage criteria assessments for bull trout, Chinook salmon, 

steelhead trout, and invertebrates for lower middle Challis Creek (CH2), upper Salmon River Basin, Idaho, 2005.

Figure F1. Plan view of upper lower middle Challis Creek (CH2), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigE01.ai

Transect

Local reference mark

For reference only; stream schematic not to scale.

Point Latitude Longitude

RH1 44° 33' 36.5" N 114° 16' 30.86" W

LH1 44° 33' 36.46" N 114° 16' 30.58" W

RH2 44° 33' 36.2" N 114° 16' 31.05" W

LH2 44° 33' 36.02" N 114° 16' 30.8" W

RH3 44° 33' 35.81" N 114° 16' 31.46" W

LH3 44° 33' 35.72" N 114° 16' 31.21" W

LH4 44° 33' 35.39" N 114° 16' 31.46" W

RH5 44° 33' 34.91" N 114° 16' 31.87" W

LH5 44° 33' 34.85" N 114° 16' 31.6" W

RH6 44° 33' 34.51" N 114° 16' 32.23" W

LH6 44° 33' 34.4" N 114° 16' 32.01" W

Transect Endpoint Coordinates (NAD 83)

Point Latitude Longitude

Transect Endpoint Coordinates (NAD 83)

RM3

RM2

RM1

4830

4880

4930

4980

5030

5080

5130

5180

4950 5000 5050 5100 5150 5200 5250 5300

EASTING, IN FEET

N

ORTHIN

G, IN FEET

T3

T5

T6

T4

T2

T1

84  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure F2. Weighted usable area and percentage of maximum habitat for bull trout, Chinook salmon, steelhead trout, and invertebrates, 

lower middle Challis Creek (CH2), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigF02.ai

Steelhead Trout WUA Normalized

Bull Trout WUA

Chinook Salmon WUA Normalized

Chinook Salmon WUA

Steelhead Trout WUA

Invertebrate WUA Invertebrate WUA

Bull Trout WUA Normalized

Invertebrates

Spawning

Adult

WEIGHTED USABLE AREA (WUA), IN FEET SQUARE PER 1,000 FEET

PERCENTAGE OF MAXIMUM HABITAT

DISCHARGE, IN CUBIC FEET PER SECOND DISCHARGE, IN CUBIC FEET PER SECOND

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0 10 20 30 40 50 60 70 80 90

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90

Appendix F  85
Table F1. Weighted usable area for bull trout, Chinook salmon, steelhead trout life stages, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) 

invertebrates, site CH2, lower middle Challis Creek, upper Salmon River Basin, Idaho, 2005. 

[Site location shown in figure 8. Abbreviations: WUA, weighted usable area; ft3/s, cubic foot per second; ft2, square foot; ft2/l,000 ft, square foot per 

1,000 feet]

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Bull trout

6.2 22,307 4,947 1,744 77.3 74.0

10 23,494 5,706 2,033 89.2 86.2

14 24,052 5,886 2,210 92.0 93.7

18 24,516 6,140 2,260 96.0 95.9

22 24,920 6,258 2,318 97.8 98.3

26 25,286 6,399 2,358 100.0 100.0

30 26,497 6,348 2,349 99.2 99.6

35 26,839 6,055 2,231 94.6 94.6

38 27,157 5,910 2,140 92.4 90.8

42 27,448 5,399 2,156 84.4 91.4

46 27,717 5,102 2,105 79.7 89.3

50 28,306 5,017 1,938 78.4 82.2

54 28,924 4,958 1,849 77.5 78.4

58 29,616 4,912 1,760 76.8 74.6

62 31,557 4,824 1,580 75.4 67.0

66 33,641 4,953 1,473 77.4 62.5

70 34,339 4,996 1,398 78.1 59.3

74 34,613 4,941 1,312 77.2 55.6

78 34,871 4,813 1,221 75.2 51.8

82 35,127 4,693 1,109 73.3 47.0

85.5 35,363 4,638 1,066 72.5 45.2

Chinook salmon

6.2 22,307 7,925 4,064 56.6 42.8

10 23,494 9,561 5,752 68.3 60.7

14 24,052 10,816 6,811 77.3 71.8

18 24,516 11,681 7,548 83.5 79.6

22 24,920 12,164 8,015 86.9 84.5

26 25,286 12,487 8,325 89.2 87.8

30 26,497 12,850 8,571 91.8 90.4

35 26,839 13,190 8,747 94.3 92.2

38 27,157 13,493 8,823 96.4 93.0

42 27,448 13,709 9,141 98.0 96.4

46 27,717 13,765 9,318 98.4 98.2

50 28,306 13,995 9,484 100.0 100.0

54 28,924 13,951 9,416 99.7 99.3

58 29,616 13,798 9,207 98.6 97.1

62 31,557 13,735 9,100 98.1 95.9

66 33,641 13,623 8,862 97.3 93.4

70 34,339 13,429 8,512 96.0 89.7

74 34,613 13,175 8,105 94.1 85.5

78 34,871 12,750 7,511 91.1 79.2

82 35,127 12,361 7,128 88.3 75.2

85.5 35,363 11,962 6,659 85.5 70.2

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Steelhead trout

6.2 22,307 7,925 4,064 56.6 42.8

10 23,494 9,561 5,752 68.3 60.7

14 24,052 10,816 6,811 77.3 71.8

18 24,516 11,681 7,548 83.5 79.6

22 24,920 12,164 8,015 86.9 84.5

26 25,286 12,487 8,325 89.2 87.8

30 26,497 12,850 8,571 91.8 90.4

35 26,839 13,190 8,747 94.3 92.2

38 27,157 13,493 8,823 96.4 93.0

42 27,448 13,709 9,141 98.0 96.4

46 27,717 13,765 9,318 98.4 98.2

50 28,306 13,995 9,484 100.0 100.0

54 28,924 13,951 9,416 99.7 99.3

58 29,616 13,798 9,207 98.6 97.1

62 31,557 13,735 9,100 98.1 95.9

66 33,641 13,623 8,862 97.3 93.4

70 34,339 13,429 8,512 96.0 89.7

74 34,613 13,175 8,105 94.1 85.5

78 34,871 12,750 7,511 91.1 79.2

82 35,127 12,361 7,128 88.3 75.2

85.5 35,363 11,962 6,659 85.5 70.2

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

EPT Invertebrates

6.180 22,307 9,886 68.5

10 23,494 11,769 81.5

14 24,052 12,998 90.1

18 24,516 13,940 96.6

22 24,920 14,433 100.0

26 25,286 14,386 99.7

30 26,497 14,195 98.4

35 26,839 13,798 95.6

38 27,157 13,615 94.3

42 27,448 13,382 92.7

46 27,717 12,761 88.4

50 28,306 12,252 84.9

54 28,924 11,538 79.9

58 29,616 11,068 76.7

62 31,557 10,704 74.2

66 33,641 10,354 71.7

70 34,339 9,631 66.7

74 34,613 9,226 63.9

78 34,871 9,009 62.4

82 35,127 8,679 60.1

85.5 35,363 8,126 56.3

86  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure F3. Percentages of contiguous and total stream width for passage transect 1, lower middle 

Challis Creek (CH2), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigF03.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 1

(wide high slope)

Passage Transect 1

(wide high slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

35

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90

0

5

10

15

20

25

30

35

Appendix F  87
Table F2. Passage criteria assessment for transect 1 (wide high slope), site CH2, lower middle Challis Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

6.2 27.0 17.9 66.4 9.5 35.2

10 29.2 23.9 81.7 12.8 43.8

14 29.6 24.6 83.0 20.7 69.8

18 29.9 25.2 84.2 20.9 69.8

22 30.1 25.7 85.3 21.0 69.8

26 30.3 26.1 86.2 21.2 69.9

30 30.5 26.5 87.0 21.3 69.9

35 30.7 27.0 87.9 21.4 69.9

38 30.8 28.3 92.1 21.5 70.0

42 30.9 28.7 92.9 21.6 70.0

46 31.0 29.0 93.5 21.7 70.0

50 31.1 29.3 94.0 29.3 94.0

54 31.2 29.4 94.2 29.4 94.2

58 31.3 29.6 94.3 29.6 94.3

62 31.4 29.7 94.5 29.7 94.5

66 31.5 29.8 94.6 29.8 94.6

70 31.7 29.9 94.4 29.9 94.4

74 31.8 30.0 94.3 30.0 94.3

78 32.0 30.1 94.1 30.1 94.1

82 32.1 30.2 94.0 30.2 94.0

85.5 32.2 30.2 93.9 30.2 93.9

Stream widths greater than 0.6-ft depth

6.2 27.0 8.5 31.4 5.2 19.2

10 29.2 10.2 35.0 6.1 20.9

14 29.6 16.5 55.6 8.8 29.6

18 29.9 20.6 68.8 11.5 38.3

22 30.1 22.7 75.5 12.3 40.9

26 30.3 24.1 79.4 20.5 67.7

30 30.5 24.5 80.3 20.6 67.7

35 30.7 24.9 81.2 20.8 67.8

38 30.8 25.2 81.8 20.9 67.8

42 30.9 25.5 82.4 21.0 67.9

46 31.0 25.8 83.0 21.1 67.9

50 31.1 26.0 83.6 21.1 67.9

54 31.2 26.3 84.2 21.2 68.0

58 31.3 26.5 84.7 21.3 68.0

62 31.4 26.8 85.2 21.4 68.0

66 31.5 28.1 89.1 21.5 68.1

70 31.7 28.4 89.5 21.5 68.0

74 31.8 28.6 89.8 21.6 67.9

78 32.0 28.8 90.1 21.7 67.8

82 32.1 29.0 90.5 21.7 67.7

85.5 32.2 29.2 90.7 29.2 90.7

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

6.2 27.0 2.6 9.8 2.6 9.8

10 29.2 6.7 22.9 4.3 14.6

14 29.6 7.9 26.7 4.9 16.5

18 29.9 8.9 29.8 5.4 18.1

22 30.1 9.8 32.4 5.9 19.5

26 30.3 14.0 46.3 7.5 24.9

30 30.5 15.9 52.1 8.5 27.7

35 30.7 17.8 58.2 9.5 30.8

38 30.8 20.5 66.5 11.4 37.1

42 30.9 21.8 70.6 12.0 38.7

46 31.0 23.1 74.3 12.5 40.2

50 31.1 24.0 77.0 20.5 65.8

54 31.2 24.2 77.6 20.6 65.8

58 31.3 24.5 78.1 20.6 65.9

62 31.4 24.7 78.6 20.7 65.9

66 31.5 24.9 79.1 20.8 66.0

70 31.7 25.2 79.4 20.9 65.9

74 31.8 25.4 79.8 20.9 65.8

78 32.0 25.6 80.0 21.0 65.7

82 32.1 25.8 80.3 21.1 65.6

85.5 32.2 26.0 80.6 21.1 65.6

88  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure F4. Percentages of contiguous and total stream width for passage transect 6, lower middle 

Challis Creek (CH2), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigF04.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 6

(wide moderate slope)

Passage Transect 6

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

-5

5

15

25

35

45

55

0

10

20

30

40

50

60

70

80

90

0 10 20 30 40 50 60 70 80 90

-5

5

15

25

35

45

55

Appendix F  89
Table F3. Passage criteria assessment for transect 6 (wide moderate slope), site CH2, lower middle Challis Creek, upper Salmon River Basin, Idaho, 

2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

6.2 23.4 8.7 37.3 5.3 22.7

10 24.9 9.8 39.4 5.9 23.8

14 26.0 11.5 44.2 6.4 24.7

18 26.9 14.4 53.6 7.9 29.4

22 27.7 16.4 59.3 8.3 29.8

26 28.5 18.9 66.4 16.6 58.4

30 29.1 19.7 67.9 17.1 58.9

35 29.9 23.1 77.5 20.1 67.4

38 30.3 23.6 77.9 20.4 67.2

42 30.9 24.2 78.4 20.7 66.9

46 31.4 24.7 78.8 20.9 66.7

50 33.1 25.3 76.6 25.2 76.1

54 35.0 26.0 74.2 25.7 73.3

58 37.1 26.5 71.5 26.1 70.3

62 44.0 27.6 62.6 26.8 61.0

66 51.5 28.4 55.2 27.5 53.4

70 52.1 28.7 55.1 27.7 53.2

74 52.6 29.0 55.1 27.9 53.0

78 53.2 29.3 55.0 28.1 52.8

82 53.7 29.5 55.0 28.3 52.7

85.5 54.2 29.8 54.9 29.8 54.9

Stream widths greater than 0.6-ft depth

6.2 23.4 3.4 14.5 3.0 12.8

10 24.9 5.8 23.4 3.7 15.0

14 26.0 7.6 29.4 4.7 18.2

18 26.9 8.8 32.7 5.4 19.9

22 27.7 9.4 34.0 5.7 20.7

26 28.5 10.3 36.1 6.1 21.3

30 29.1 11.2 38.7 6.3 21.8

35 29.9 13.6 45.6 7.8 26.0

38 30.3 14.7 48.5 8.0 26.3

42 30.9 16.0 51.9 8.2 26.5

46 31.4 17.2 54.9 8.4 26.8

50 33.1 19.1 57.8 16.8 50.6

54 35.0 19.9 57.0 17.3 49.3

58 37.1 23.1 62.2 20.1 54.2

62 44.0 24.2 55.0 20.7 47.0

66 51.5 25.1 48.8 25.0 48.7

70 52.1 25.4 48.8 25.3 48.5

74 52.6 25.7 48.8 25.5 48.4

78 53.2 26.0 48.8 25.7 48.3

82 53.7 26.2 48.8 25.9 48.1

85.5 54.2 26.5 48.8 26.0 48.0

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

6.2 23.4 0.0 0.0 0.0 0.0

10 24.9 0.1 0.3 0.0 0.1

14 26.0 2.0 7.5 1.0 3.8

18 26.9 3.6 13.3 3.0 11.3

22 27.7 5.0 18.2 3.5 12.6

26 28.5 6.3 22.2 4.0 14.1

30 29.1 7.4 25.4 4.6 15.7

35 29.9 8.5 28.6 5.2 17.5

38 30.3 8.9 29.3 5.4 17.8

42 30.9 9.3 30.1 5.6 18.3

46 31.4 9.7 30.8 5.9 18.7

50 33.1 10.5 31.9 6.1 18.5

54 35.0 11.5 32.8 6.4 18.3

58 37.1 13.6 36.5 7.8 20.9

62 44.0 16.1 36.5 8.2 18.6

66 51.5 18.8 36.6 16.6 32.2

70 52.1 19.2 36.9 16.8 32.3

74 52.6 19.6 37.2 17.1 32.4

78 53.2 20.0 37.5 17.3 32.5

82 53.7 20.3 37.8 17.5 32.5

85.5 54.2 20.6 38.0 17.7 32.6

90 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure F5. Percentages of contiguous and total stream width for passage transect 7, lower middle 

Challis Creek (CH2), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigF05.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 7

(wide moderate slope)

Passage Transect 7

(wide moderate slope) PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80 90

0

5

10

15

20

25

30

Appendix F  91
Table F4. Passage criteria assessment for transect 7 (wide moderate slope), site CH2, lower middle Challis Creek, upper Salmon River Basin, Idaho, 

2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

6.2 25.2 6.1 24.3 5.4 21.4

10 25.7 9.5 37.1 6.0 23.6

14 26.0 17.3 66.4 8.4 32.3

18 26.3 20.1 76.4 9.2 34.9

22 26.6 22.2 83.5 11.4 42.9

26 26.9 23.8 88.5 12.0 44.8

30 27.1 25.1 92.6 25.1 92.6

35 27.4 25.4 92.9 25.4 92.9

38 27.5 25.6 93.0 25.6 93.0

42 27.7 25.8 93.1 25.8 93.1

46 27.9 26.0 93.1 26.0 93.1

50 28.1 26.2 93.2 26.2 93.2

54 28.3 26.4 93.2 26.4 93.2

58 28.4 26.5 93.2 26.5 93.2

62 28.6 26.7 93.3 26.7 93.3

66 28.8 26.8 93.3 26.8 93.3

70 28.9 27.0 93.4 27.0 93.4

74 29.1 27.1 93.4 27.1 93.4

78 29.2 27.3 93.4 27.3 93.4

82 29.4 27.4 93.4 27.4 93.4

85.5 29.5 27.6 93.3 27.6 93.3

Stream widths greater than 0.6-ft depth

6.2 25.2 0.0 0.0 0.0 0.0

10 25.7 0.7 2.6 0.7 2.6

14 26.0 5.2 20.0 5.1 19.5

18 26.3 6.7 25.3 5.6 21.1

22 26.6 9.4 35.2 6.0 22.6

26 26.9 11.3 42.1 6.4 23.9

30 27.1 18.4 67.9 8.7 32.2

35 27.4 20.9 76.4 9.4 34.3

38 27.5 22.0 79.9 11.3 41.1

42 27.7 23.2 83.7 11.8 42.6

46 27.9 24.9 89.3 24.9 89.3

50 28.1 25.2 89.5 25.2 89.5

54 28.3 25.4 89.7 25.4 89.7

58 28.4 25.6 89.9 25.6 89.9

62 28.6 25.7 89.9 25.7 89.9

66 28.8 25.9 90.0 25.9 90.0

70 28.9 26.0 90.0 26.0 90.0

74 29.1 26.2 90.1 26.2 90.1

78 29.2 26.3 90.1 26.3 90.1

82 29.4 26.5 90.2 26.5 90.2

85.5 29.5 26.6 90.0 26.6 90.0

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

6.2 25.2 0.0 0.0 0.0 0.0

10 25.7 0.0 0.0 0.0 0.0

14 26.0 0.0 0.0 0.0 0.0

18 26.3 0.0 0.0 0.0 0.0

22 26.6 0.6 2.2 0.6 2.2

26 26.9 1.6 6.0 1.6 6.0

30 27.1 5.8 21.3 5.3 19.4

35 27.4 7.1 25.8 5.7 20.8

38 27.5 9.1 33.1 6.0 21.6

42 27.7 10.6 38.3 6.3 22.7

46 27.9 17.0 61.0 8.3 29.9

50 28.1 18.8 66.8 8.8 31.4

54 28.3 20.4 72.1 9.2 32.7

58 28.4 21.7 76.4 11.2 39.4

62 28.6 22.7 79.4 11.6 40.6

66 28.8 23.7 82.2 12.0 41.7

70 28.9 25.0 86.4 25.0 86.4

74 29.1 25.2 86.6 25.2 86.6

78 29.2 25.3 86.7 25.3 86.7

82 29.4 25.5 86.9 25.5 86.9

85.5 29.5 25.6 86.8 25.6 86.8

92 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Appendix G. Plan view, weighted usable areas, and passage criteria assessments for bull trout, Chinook salmon, 

steelhead trout, and invertebrates for lower Challis Creek (CH1), upper Salmon River Basin, Idaho, 2005.

Figure G1. Plan view of lower Challis Creek (CH1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigG01.ai

Transect

Local reference mark

For reference only; stream schematic not to scale.

Point Latitude Longitude

RH1 44° 34' 10.97" N 114° 11' 19.61" W

LH1 44° 34' 10.6" N 114° 11' 19.61" W

RH2 44° 34' 10.72" N 114° 11' 21.78" W

LH2 44° 34' 10.41" N 114° 11' 21.51" W

RH3 44° 34' 9.85" N 114° 11' 23.82" W

LH3 44° 34' 9.68" N 114° 11' 23.43" W

RH4 44° 34' 9.97" N 114° 11' 25.13" W

LH4 44° 34' 9.76" N 114° 11' 25.49" W

RH5 44° 34' 10.32" N 114° 11' 25.99" W

LH5 44° 34' 9.91" N 114° 11' 26.01" W

RH6 44° 34' 10.63" N 114° 11' 29.31" W

LH6 44° 34' 10.28" N 114° 11' 29.39" W

RH7 44° 34' 10.71" N 114° 11' 30.3" W

LH7 44° 34' 10.3" N 114° 11' 30.38" W

Transect Endpoint Coordinates (NAD 83)

Point Latitude Longitude

Transect Endpoint Coordinates (NAD 83)

RM2

RM1

4650

4750

4850

4950

5050

5150

5250

5350

5450

4460 4560 4660 4760 4860 4960 5060 5160 5260 5360

EASTING, IN FEET

N

ORTHIN

G, IN FEET

T3

T7

T5

T6

T4

T2

T1

Appendix G  93
Figure G2. Weighted usable area and percentage of maximum habitat for bull trout, Chinook salmon, steelhead trout, and 

invertebrates, lower Challis Creek (CH1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigG02.ai

Steelhead Trout WUA Normalized

Bull Trout WUA

Chinook Salmon WUA Normalized Chinook Salmon WUA

Steelhead Trout WUA

Invertebrate WUA Invertebrate WUA

Bull Trout WUA Normalized

Invertebrates

Spawning

Adult

WEIGHTED USABLE AREA (WUA), IN FEET SQUARE PER 1,000 FEET

PERCENTAGE OF MAXIMUM HABITAT

DISCHARGE, IN CUBIC FEET PER SECOND DISCHARGE, IN CUBIC FEET PER SECOND

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0 10 20 30 40 50 60 70 80

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80

94  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table G1. Weighted usable area for bull trout, Chinook salmon, steelhead trout life stages, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) 

invertebrates, site CH1, lower Challis Creek, upper Salmon River Basin, Idaho, 2005. 

[Site location shown in figure 8. Abbreviations: WUA, weighted usable area; ft3/s, cubic foot per second; ft2, square foot; ft2/l,000 ft, square foot per 

1,000 feet]

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Bull trout

2.9 17,831 5,573 508 57.8 14.0

7 20,368 8,356 1,094 86.6 30.2

11 21,829 9,037 1,710 93.7 47.2

15 23,491 9,648 2,166 100.0 59.8

19 24,529 9,566 2,419 99.2 66.8

23 25,366 9,223 2,690 95.6 74.2

27 26,832 8,801 2,946 91.2 81.3

31 27,280 8,496 3,126 88.1 86.3

35 27,964 8,035 3,252 83.3 89.8

39 28,436 7,575 3,485 78.5 96.2

43 28,795 7,243 3,582 75.1 98.8

47 29,126 7,125 3,624 73.9 100.0

51 29,580 6,926 3,587 71.8 99.0

55 29,771 6,602 3,531 68.4 97.4

59 29,947 6,515 3,450 67.5 95.2

63 30,119 6,376 3,382 66.1 93.3

67 30,292 6,397 3,345 66.3 92.3

71 30,461 6,310 3,269 65.4 90.2

74.400 30,596 6,186 3,195 64.1 88.2

Chinook salmon

2.9 17,831 6,798 1,359 42.7 13.6

7 20,368 9,101 3,512 57.2 35.1

11 21,829 10,589 5,225 66.5 52.3

15 23,491 11,653 6,535 73.2 65.4

19 24,529 12,340 7,254 77.5 72.6

23 25,366 12,966 7,945 81.4 79.5

27 26,832 13,851 8,577 87.0 85.8

31 27,280 14,432 8,938 90.6 89.4

35 27,964 15,014 9,193 94.3 92.0

39 28,436 15,447 9,554 97.0 95.6

43 28,795 15,659 9,736 98.3 97.4

47 29,126 15,774 9,869 99.1 98.7

51 29,580 15,898 9,963 99.8 99.7

55 29,771 15,925 9,996 100.0 100.0

59 29,947 15,806 9,934 99.3 99.4

63 30,119 15,615 9,817 98.1 98.2

67 30,292 15,431 9,578 96.9 95.8

71 30,461 15,154 9,247 95.2 92.5

74.400 30,596 14,928 8,976 93.7 89.8

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Steelhead trout

2.9 17,831 6,798 1,359 42.7 13.6

7 20,368 9,101 3,512 57.2 35.1

11 21,829 10,589 5,225 66.5 52.3

15 23,491 11,653 6,535 73.2 65.4

19 24,529 12,340 7,254 77.5 72.6

23 25,366 12,966 7,945 81.4 79.5

27 26,832 13,851 8,577 87.0 85.8

31 27,280 14,432 8,938 90.6 89.4

35 27,964 15,014 9,193 94.3 92.0

39 28,436 15,447 9,554 97.0 95.6

43 28,795 15,659 9,736 98.3 97.4

47 29,126 15,774 9,869 99.1 98.7

51 29,580 15,898 9,963 99.8 99.7

55 29,771 15,925 9,996 100.0 100.0

59 29,947 15,806 9,934 99.3 99.4

63 30,119 15,615 9,817 98.1 98.2

67 30,292 15,431 9,578 96.9 95.8

71 30,461 15,154 9,247 95.2 92.5

74.400 30,596 14,928 8,976 93.7 89.8

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

EPT Invertebrates

2.880 17,831 5,982 43

7 20,368 7,996 58

11 21,829 9,447 68

15 23,491 11,074 80

19 24,529 12,040 87

23 25,366 12,576 91

27 26,832 13,315 96

31 27,280 13,699 99

35 27,964 13,835 100

39 28,436 13,836 100

43 28,795 13,715 99

47 29,126 13,328 96

51 29,580 12,877 93

55 29,771 12,183 88

59 29,947 11,505 83

63 30,119 10,523 76

67 30,292 9,389 68

71 30,461 8,574 62

74.400 30,596 8,155 59

Appendix G  95
Figure G3. Percentages of contiguous and total stream width for passage transect 5, lower Challis 

Creek (CH1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigG03.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 5

(wide moderate slope)

Passage Transect 5

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

35

40

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80

0

5

10

15

20

25

30

35

40

96  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table G2. Passage criteria assessment for transect 5 (wide moderate slope), site CH1, lower Challis Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

2.9 27.7 5.7 20.6 5.7 20.6

7 29.1 14.8 50.9 8.8 30.3

11 30.0 25.3 84.3 23.4 77.9

15 30.7 27.2 88.4 27.2 88.4

19 31.3 27.8 88.9 27.8 88.9

23 31.9 28.4 89.2 28.4 89.2

27 32.4 28.9 89.4 28.9 89.4

31 32.8 29.4 89.5 29.4 89.5

35 33.2 29.8 89.6 29.8 89.6

39 33.5 30.2 89.9 30.2 89.9

43 33.7 30.5 90.5 30.5 90.5

47 33.9 30.9 91.0 30.9 91.0

51 34.1 31.2 91.5 31.2 91.5

55 34.2 31.5 92.0 31.5 92.0

59 34.4 31.8 92.4 31.8 92.4

63 34.5 32.0 92.9 32.0 92.9

67 34.6 32.3 93.3 32.3 93.3

71 34.8 32.6 93.7 32.6 93.7

74.4 34.9 32.8 94.0 32.8 94.0

Stream widths greater than 0.6-ft depth

2.9 27.7 0.8 2.9 0.8 2.9

7 29.1 4.1 14.2 4.1 14.2

11 30.0 6.4 21.3 6.4 21.3

15 30.7 13.8 44.9 8.5 27.6

19 31.3 24.1 76.8 23.1 73.6

23 31.9 26.5 83.2 26.5 83.2

27 32.4 27.1 83.7 27.1 83.7

31 32.8 27.6 84.0 27.6 84.0

35 33.2 28.0 84.4 28.0 84.4

39 33.5 28.5 84.8 28.5 84.8

43 33.7 28.8 85.4 28.8 85.4

47 33.9 29.1 86.0 29.1 86.0

51 34.1 29.5 86.5 29.5 86.5

55 34.2 29.8 87.0 29.8 87.0

59 34.4 30.0 87.4 30.0 87.4

63 34.5 30.3 87.9 30.3 87.9

67 34.6 30.6 88.3 30.6 88.3

71 34.8 30.9 88.7 30.9 88.7

74.4 34.9 31.1 89.1 31.1 89.1

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

2.9 27.7 0.0 0.0 0.0 0.0

7 29.1 0.0 0.0 0.0 0.0

11 30.0 1.9 6.4 1.9 6.4

15 30.7 4.0 13.0 4.0 13.0

19 31.3 5.8 18.6 5.8 18.6

23 31.9 8.7 27.3 6.8 21.3

27 32.4 13.1 40.5 8.2 25.5

31 32.8 23.3 71.1 22.9 69.7

35 33.2 24.6 74.1 23.2 69.8

39 33.5 26.5 79.1 26.5 79.1

43 33.7 26.9 79.9 26.9 79.9

47 33.9 27.3 80.6 27.3 80.6

51 34.1 27.7 81.2 27.7 81.2

55 34.2 28.0 81.9 28.0 81.9

59 34.4 28.3 82.4 28.3 82.4

63 34.5 28.6 82.9 28.6 82.9

67 34.6 28.9 83.4 28.9 83.4

71 34.8 29.1 83.8 29.1 83.8

74.4 34.9 29.4 84.1 29.4 84.1

Appendix G  97
Figure G4. Percentages of contiguous and total stream width for passage transect 6, lower Challis 

Creek (CH1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigG04.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 6

(wide moderate slope)

Passage Transect 6

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

35

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80

0

5

10

15

20

25

30

35

98  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table G3. Passage criteria assessment for transect 6 (wide moderate slope), site CH1, lower Challis Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

2.9 26.1 3.9 14.8 3.1 11.7

7 28.4 8.3 29.2 6.6 23.3

11 29.3 22.6 77.4 17.7 60.7

15 29.5 24.8 84.1 24.8 84.1

19 29.8 25.4 85.2 25.4 85.2

23 30.0 25.8 86.0 25.8 86.0

27 30.2 26.1 86.5 26.1 86.5

31 30.4 26.4 86.9 26.4 86.9

35 30.6 27.0 88.4 27.0 88.4

39 30.7 27.8 90.6 27.8 90.6

43 30.8 28.5 92.5 28.5 92.5

47 31.0 29.0 93.8 29.0 93.8

51 31.1 29.2 93.8 29.2 93.8

55 31.2 29.3 93.8 29.3 93.8

59 31.3 29.4 93.8 29.4 93.8

63 31.5 29.5 93.9 29.5 93.9

67 31.6 29.6 93.9 29.6 93.9

71 31.7 29.7 93.9 29.7 93.9

74.4 31.8 29.8 93.9 29.8 93.9

Stream widths greater than 0.6-ft depth

2.9 26.1 0.0 0.0 0.0 0.0

7 28.4 1.0 3.6 1.0 3.6

11 29.3 4.0 13.7 3.1 10.7

15 29.5 5.9 20.0 5.6 19.0

19 29.8 7.9 26.4 6.4 21.6

23 30.0 20.6 68.8 17.2 57.4

27 30.2 22.4 74.2 17.7 58.6

31 30.4 24.1 79.3 18.1 59.7

35 30.6 24.9 81.6 24.9 81.6

39 30.7 25.3 82.2 25.3 82.2

43 30.8 25.6 82.9 25.6 82.9

47 31.0 25.8 83.3 25.8 83.3

51 31.1 26.0 83.6 26.0 83.6

55 31.2 26.2 83.9 26.2 83.9

59 31.3 26.4 84.2 26.4 84.2

63 31.5 26.7 84.9 26.7 84.9

67 31.6 27.3 86.4 27.3 86.4

71 31.7 27.8 87.8 27.8 87.8

74.4 31.8 28.3 89.0 28.3 89.0

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

2.9 26.1 0.0 0.0 0.0 0.0

7 28.4 0.0 0.0 0.0 0.0

11 29.3 0.0 0.0 0.0 0.0

15 29.5 0.2 0.6 0.2 0.6

19 29.8 0.9 2.9 0.9 2.9

23 30.0 2.6 8.8 2.5 8.3

27 30.2 3.9 12.8 3.1 10.1

31 30.4 5.0 16.4 3.6 11.9

35 30.6 6.2 20.3 5.7 18.8

39 30.7 7.4 24.1 6.2 20.3

43 30.8 8.5 27.6 6.7 21.7

47 31.0 20.6 66.5 17.2 55.6

51 31.1 21.8 70.2 17.5 56.4

55 31.2 23.0 73.6 17.8 57.1

59 31.3 24.0 76.7 18.1 57.8

63 31.5 24.8 78.8 24.8 78.8

67 31.6 25.0 79.3 25.0 79.3

71 31.7 25.3 79.7 25.3 79.7

74.4 31.8 25.4 80.1 25.4 80.1

Appendix G  99
Figure G5. Percentages of contiguous and total stream width for passage transect 7, lower Challis 

Creek (CH1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigG05.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 7

(wide moderate slope)

Passage Transect 7

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

35

40

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50 60 70 80

0

5

10

15

20

25

30

35

40

100 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Table G4. Passage criteria assessment for transect 7 (wide moderate slope), site CH1, lower Challis Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 8. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

2.9 23.6 4.8 20.3 2.1 9.1

7 28.1 14.1 50.2 7.8 27.9

11 29.5 17.2 58.5 8.9 30.3

15 30.5 18.8 61.6 9.6 31.4

19 31.4 21.2 67.7 14.4 45.9

23 31.9 22.3 70.0 14.9 46.7

27 32.4 23.3 72.0 15.3 47.4

31 32.8 24.5 74.7 16.3 49.6

35 33.2 25.7 77.3 17.2 51.9

39 33.6 26.8 79.9 18.2 54.2

43 33.9 27.7 81.6 27.7 81.6

47 34.2 28.1 82.1 28.1 82.1

51 34.5 28.5 82.6 28.5 82.6

55 34.8 29.0 83.2 29.0 83.2

59 35.1 29.3 83.6 29.3 83.6

63 35.2 29.7 84.4 29.7 84.4

67 35.3 30.1 85.1 30.1 85.1

71 35.4 30.4 85.8 30.4 85.8

74.4 35.5 30.6 86.3 30.6 86.3

Stream widths greater than 0.6-ft depth

2.9 23.6 0.0 0.0 0.0 0.0

7 28.1 2.2 7.7 1.4 4.8

11 29.5 7.1 24.1 6.3 21.4

15 30.5 9.3 30.5 7.0 22.9

19 31.4 13.3 42.5 7.6 24.2

23 31.9 15.0 47.2 8.2 25.6

27 32.4 16.6 51.4 8.7 26.9

31 32.8 17.7 54.0 9.1 27.8

35 33.2 18.5 55.8 9.5 28.5

39 33.6 19.3 57.5 9.8 29.2

43 33.9 21.1 62.2 14.3 42.3

47 34.2 21.8 63.6 14.6 42.8

51 34.5 22.4 64.9 14.9 43.2

55 34.8 23.0 66.1 15.2 43.7

59 35.1 23.6 67.2 15.5 44.1

63 35.2 24.4 69.2 16.1 45.8

67 35.3 25.1 71.0 16.7 47.4

71 35.4 25.8 72.8 17.3 48.9

74.4 35.5 26.3 74.1 17.8 50.1

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

2.9 23.6 0.0 0.0 0.0 0.0

7 28.1 0.0 0.0 0.0 0.0

11 29.5 0.0 0.0 0.0 0.0

15 30.5 0.0 0.0 0.0 0.0

19 31.4 1.5 4.8 1.1 3.7

23 31.9 3.0 9.4 1.6 5.0

27 32.4 4.4 13.6 2.0 6.3

31 32.8 7.8 23.7 6.5 19.9

35 33.2 8.9 26.8 6.9 20.7

39 33.6 10.0 29.8 7.2 21.4

43 33.9 13.1 38.7 7.5 22.2

47 34.2 14.2 41.4 7.9 23.0

51 34.5 15.2 44.0 8.2 23.8

55 34.8 16.2 46.5 8.6 24.6

59 35.1 17.1 48.6 8.8 25.2

63 35.2 17.6 50.0 9.1 25.8

67 35.3 18.1 51.3 9.3 26.3

71 35.4 18.6 52.5 9.5 26.8

74.4 35.5 19.0 53.4 9.7 27.2

Appendix G 101
Appendix H. Plan view, weighted usable areas, and passage criteria assessments for bull trout, Chinook salmon, 

steelhead trout, and invertebrates for lower Morgan Creek (MC1), upper Salmon River Basin, Idaho, 2005.

Figure H1. Plan view of lower Morgan Creek (MC1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigH01.ai

Transect

Local reference mark

For reference only; stream schematic not to scale.

Point Latitude Longitude

RH1 44° 34' 4.73" N 114° 10' 53.22" W

LH1 44° 34' 4.73" N 114° 10' 53.77" W

RH2 44° 34' 5.86" N 114° 10' 52.94" W

LH2 44° 34' 5.95" N 114° 10' 53.58" W

RH3 44° 34' 6.85" N 114° 10' 52.75" W

LH3 44° 34' 6.98" N 114° 10' 53.33" W

RH4 44° 34' 7.49" N 114° 10' 52.45" W

LH4 44° 34' 7.67" N 114° 10' 52.86" W

RH5 44° 34' 8.88" N 114° 10' 52.01" W

LH5 44° 34' 8.62" N 114° 10' 52.45" W

RH6 44° 34' 9.03" N 114° 10' 52.53 W

LH6 44° 34' 8.87" N 114° 10' 52.81" W

Transect Endpoint Coordinates (NAD 83)

Point Latitude Longitude

Transect Endpoint Coordinates (NAD 83)

RM1

RM3

RM2

4550

4650

4750

4850

4950

5050

5150

4850 4950 5050 5150 5250 5350

EASTING, IN FEET

N

ORTHIN

G, IN FEET

T3

T5

T6

T4

T2

T1

102 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure H2. Weighted usable area and percentage of maximum habitat for bull trout, Chinook salmon, steelhead trout, and 

invertebrates, lower Morgan Creek (MC1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigH02.ai

Steelhead Trout WUA Normalized

Bull Trout WUA

Chinook Salmon WUA Normalized Chinook Salmon WUA

Steelhead Trout WUA

Invertebrate WUA Invertebrate WUA

Bull Trout WUA Normalized

Invertebrates

Spawning

Adult

WEIGHTED USABLE AREA (WUA), IN FEET SQUARE PER 1,000 FEET

PERCENTAGE OF MAXIMUM HABITAT

DISCHARGE, IN CUBIC FEET PER SECOND DISCHARGE, IN CUBIC FEET PER SECOND

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0

10

20

30

40

50

60

70

80

90

100

0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

0

10

20

30

40

50

60

70

80

90

100

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

0 10 20 30 40 50

Appendix H 103
Table H1. Weighted usable area for bull trout, Chinook salmon, steelhead trout life stages, and Ephemeroptera, Plecoptera, and Trichoptera (EPT) 

invertebrates, site MC1, lower Morgan Creek, upper Salmon River Basin, Idaho, 2005. 

[Site location shown in figure 12. Abbreviations: WUA, weighted usable area; ft3/s, cubic foot per second; ft2, square foot; ft2/l,000 ft, square foot per 

1,000 feet]

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Bull trout

11.2 22,018 8,724 200 98.6 63.8

15 22,462 8,851 248 100.0 79.0

18 22,762 8,835 279 99.8 88.9

21 23,024 8,727 301 98.6 95.8

24 23,261 8,527 314 96.3 100.0

27 23,478 8,164 314 92.2 100.0

30 23,680 7,638 311 86.3 99.0

33 23,865 7,115 305 80.4 97.1

36 24,039 6,373 288 72.0 91.7

39 24,195 6,034 267 68.2 85.1

42 24,314 5,683 244 64.2 77.6

45 24,429 5,483 220 61.9 70.1

46.100 24,471 5,412 213 61.1 67.8

Chinook salmon

11.2 22,018 10,984 4,170 79.5 62.2

15 22,462 11,740 4,895 84.9 73.1

18 22,762 12,317 5,367 89.1 80.1

21 23,024 12,770 5,789 92.4 86.4

24 23,261 13,079 6,044 94.6 90.2

27 23,478 13,306 6,225 96.3 92.9

30 23,680 13,479 6,363 97.5 95.0

33 23,865 13,635 6,470 98.6 96.6

36 24,039 13,706 6,554 99.2 97.8

39 24,195 13,802 6,650 99.9 99.3

42 24,314 13,821 6,700 100.0 100.0

45 24,429 13,754 6,674 99.5 99.6

46.100 24,471 13,705 6,628 99.2 98.9

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

Adult Spawning Adult Spawning

Steelhead trout

11.2 22,018 10,984 4,170 79.5 62.2

15 22,462 11,740 4,895 84.9 73.1

18 22,762 12,317 5,367 89.1 80.1

21 23,024 12,770 5,789 92.4 86.4

24 23,261 13,079 6,044 94.6 90.2

27 23,478 13,306 6,225 96.3 92.9

30 23,680 13,479 6,363 97.5 95.0

33 23,865 13,635 6,470 98.6 96.6

36 24,039 13,706 6,554 99.2 97.8

39 24,195 13,802 6,650 99.9 99.3

42 24,314 13,821 6,700 100.0 100.0

45 24,429 13,754 6,674 99.5 99.6

46.100 24,471 13,705 6,628 99.2 98.9

Discharge 

(ft3/s)

Total 

area

(ft2)

Summary of WUA

 (ft2/1,000 ft)

Percentage of 

maximum habitat

EPT Invertebrates

11.2 22,018 11,220 87.6

15 22,462 11,894 92.9

18 22,762 12,313 96.2

21 23,024 12,482 97.5

24 23,261 12,586 98.3

27 23,478 12,768 99.7

30 23,680 12,802 100.0

33 23,865 12,775 99.8

36 24,039 12,723 99.4

39 24,195 12,506 97.7

42 24,314 11,846 92.5

45 24,429 11,370 88.8

46.100 24,471 11,209 87.6

104  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure H3. Percentages of contiguous and total stream width for passage transect 2, lower Morgan 

Creek (MC1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigH03.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 2

(wide moderate slope)

Passage Transect 2

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50

0

5

10

15

20

25

30

Appendix H 105
Table H2. Passage criteria assessment for transect 2 (wide moderate slope), site MC1, lower Morgan Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 12. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

11.2 28.4 21.7 76.4 21.7 76.4

15 28.5 22.7 79.5 22.7 79.5

18 28.6 23.4 81.6 23.4 81.6

21 28.7 24.2 84.1 24.2 84.1

24 28.8 24.9 86.3 24.9 86.3

27 28.9 25.5 88.4 25.5 88.4

30 29.0 25.8 89.1 25.8 89.1

33 29.1 26.1 89.7 26.1 89.7

36 29.1 26.3 90.3 26.3 90.3

39 29.2 26.6 91.1 26.5 90.9

42 29.2 27.0 92.4 26.7 91.4

45 29.3 27.5 93.7 26.9 92.0

46 29.3 27.6 94.2 27.0 92.1

Stream widths greater than 0.6-ft depth

11.2 28.4 6.1 21.5 6.1 21.5

15 28.5 12.9 45.3 8.4 29.4

18 28.6 17.6 61.5 10.0 34.8

21 28.7 20.6 71.7 20.6 71.7

24 28.8 21.2 73.4 21.2 73.4

27 28.9 21.7 75.0 21.7 75.0

30 29.0 22.2 76.6 22.2 76.6

33 29.1 22.6 77.9 22.6 77.9

36 29.1 23.1 79.3 23.1 79.3

39 29.2 23.5 80.6 23.5 80.6

42 29.2 24.0 82.2 24.0 82.2

45 29.3 24.5 83.7 24.5 83.7

46 29.3 24.7 84.2 24.7 84.2

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

11.2 28.4 0.0 0.0 0.0 0.0

15 28.5 0.0 0.0 0.0 0.0

18 28.6 0.0 0.0 0.0 0.0

21 28.7 0.0 0.0 0.0 0.0

24 28.8 0.0 0.0 0.0 0.0

27 28.9 0.0 0.0 0.0 0.0

30 29.0 9.5 32.8 7.2 25.0

33 29.1 12.5 43.0 8.2 28.4

36 29.1 15.6 53.5 9.3 31.9

39 29.2 20.1 68.8 20.1 68.8

42 29.2 20.5 70.1 20.5 70.1

45 29.3 20.9 71.3 20.9 71.3

46 29.3 21.0 71.7 21.0 71.7

106  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure H4. Percentages of contiguous and total stream width for passage transect 3, lower Morgan 

Creek (MC1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigH04.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 3

(wide moderate slope)

Passage Transect 3

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50

0

5

10

15

20

25

30

Appendix H 107
Table H3. Passage criteria assessment for transect 3 (wide moderate slope), site MC1, lower Morgan Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 12. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

11.2 24.8 18.7 75.5 18.7 75.5

15 25.6 20.1 78.5 20.1 78.5

18 26.0 21.1 81.1 21.1 81.1

21 26.4 21.8 82.4 21.8 82.4

24 26.8 22.2 83.0 22.2 83.0

27 27.1 22.6 83.5 22.6 83.5

30 27.4 23.0 83.9 23.0 83.9

33 27.7 23.4 84.3 23.4 84.3

36 28.0 23.7 84.7 23.7 84.7

39 28.2 24.0 85.1 24.0 85.1

42 28.4 24.3 85.7 24.3 85.7

45 28.5 24.6 86.3 24.6 86.3

46 28.6 24.7 86.5 24.7 86.5

Stream widths greater than 0.6-ft depth

11.2 24.8 10.3 41.3 5.3 21.3

15 25.6 14.0 54.6 12.8 50.2

18 26.0 16.6 63.8 14.1 54.1

21 26.4 18.0 68.0 18.0 68.0

24 26.8 18.6 69.3 18.6 69.3

27 27.1 19.1 70.4 19.1 70.4

30 27.4 19.8 72.0 19.8 72.0

33 27.7 20.4 73.7 20.4 73.7

36 28.0 21.0 75.1 21.0 75.1

39 28.2 21.6 76.4 21.6 76.4

42 28.4 21.9 77.0 21.9 77.0

45 28.5 22.1 77.6 22.1 77.6

46 28.6 22.2 77.8 22.2 77.8

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

11.2 24.8 0.0 0.0 0.0 0.0

15 25.6 3.7 14.3 2.6 10.3

18 26.0 5.8 22.4 3.6 13.6

21 26.4 7.8 29.6 4.4 16.5

24 26.8 9.6 36.0 5.1 18.9

27 27.1 11.4 42.0 5.7 21.2

30 27.4 13.2 48.0 12.5 45.4

33 27.7 14.9 53.6 13.3 47.8

36 28.0 16.4 58.7 14.0 50.0

39 28.2 17.7 62.7 17.7 62.7

42 28.4 18.1 63.7 18.1 63.7

45 28.5 18.5 64.7 18.5 64.7

46 28.6 18.6 65.0 18.6 65.0

108  Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Figure H5. Percentages of contiguous and total stream width for passage transect 4, lower Morgan 

Creek (MC1), upper Salmon River Basin, Idaho, 2005.

IDSalmon_AppFigH05.ai

0.4 ft

0.6 ft

0.8 ft

STREAM WIDTH

STREAM DEPTH

Passage Transect 4

(wide moderate slope)

Passage Transect 4

(wide moderate slope)

PERCENTAGE OF TOTAL STREA

M

WIDTH

STREA

M

WIDTH, IN FEET

PERCENTAGE OF CONTIGUOUS STREAM WIDTH

DISCHARGE, IN CUBIC FEET PER SECOND

CRITERIA LINE

0

10

20

30

40

50

60

70

80

90

100

0

5

10

15

20

25

30

0

10

20

30

40

50

60

70

80

90

100

0 10 20 30 40 50

0

5

10

15

20

25

30

Appendix H 109
Table H4. Passage criteria assessment for transect 4 (wide moderate slope), site MC1, lower Morgan Creek, upper Salmon River Basin, Idaho, 2005.

[Site location shown in figure 12. Abbreviations: ft, foot; ft3/s, cubic foot per second]

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.4-ft depth

11.2 24.9 19.6 78.4 14.7 58.9

15 25.3 21.7 85.8 21.7 85.8

18 25.5 22.1 86.6 22.1 86.6

21 25.7 22.4 87.2 22.4 87.2

24 25.8 22.7 87.8 22.7 87.8

27 26.0 22.9 88.2 22.9 88.2

30 26.1 23.1 88.6 23.1 88.6

33 26.2 23.3 89.0 23.3 89.0

36 26.3 23.5 89.3 23.5 89.3

39 26.5 23.7 89.7 23.7 89.7

42 26.6 23.9 90.0 23.9 90.0

45 26.7 24.1 90.3 24.1 90.3

46 26.7 24.1 90.4 24.1 90.4

Stream widths greater than 0.6-ft depth

11.2 24.9 5.4 21.6 5.4 21.6

15 25.3 7.0 27.5 6.0 23.7

18 25.5 8.8 34.7 6.4 25.2

21 25.7 10.5 41.0 6.8 26.5

24 25.8 16.2 62.9 13.5 52.1

27 26.0 18.0 69.1 14.1 54.3

30 26.1 19.6 74.9 14.7 56.2

33 26.2 21.1 80.3 15.2 58.1

36 26.3 21.7 82.2 21.7 82.2

39 26.5 21.9 82.6 21.9 82.6

42 26.6 22.1 83.0 22.1 83.0

45 26.7 22.2 83.4 22.2 83.4

46 26.7 22.3 83.5 22.3 83.5

Discharge 

(ft3/s)

Stream 

width

(ft)

Passage criteria assessment

Total Percentage Contiguous Percentage 

contiguous

Stream widths greater than 0.8-ft depth

11.2 24.9 0.0 0.0 0.0 0.0

15 25.3 0.6 2.4 0.6 2.4

18 25.5 1.5 5.9 1.5 5.9

21 25.7 2.3 9.1 2.3 9.1

24 25.8 4.8 18.5 4.8 18.5

27 26.0 5.1 19.6 5.1 19.6

30 26.1 5.4 20.6 5.4 20.6

33 26.2 5.7 21.6 5.7 21.6

36 26.3 6.5 24.8 5.9 22.4

39 26.5 7.6 28.9 6.2 23.3

42 26.6 8.7 32.6 6.4 24.0

45 26.7 9.6 36.0 6.6 24.7

46 26.7 9.9 37.2 6.7 25.0

110 Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005
Manuscript approved for publication, September 14, 2006

Prepared by the USGS Publishing Network, 

Publishing Service Center, Tacoma, Washington

Bill Gibbs 

Bob Crist

Debra Grillo

Bobbie Jo Richey

For more information concerning the research in this report, contact the 

Director, Idaho Water Science Center 

U.S. Geological Survey, 230 Collins Road

Boise, Idaho 83702

http://id.water.usgs.gov/
Maret and others Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, 2005 SIR 2006–5230