Fish Communities and Related Environmental 

Conditions of the Lower Boise River, 

Southwestern Idaho, 1974-2004

Scientific Investigations Report 2006–5111

Prepared in cooperation with the Idaho Department of Environmental Quality

U.S. Department of the Interior

U.S. Geological Survey
Cover: Photograph of shorthead sculpin (Cottus confusus) from lower Boise River in Barber Dam Reach, 

southwestern Idaho. (Photograph taken by Dorene MacCoy, U.S. Geological Survey, 2006.)
Fish Communities and Related 

Environmental Conditions of the 

Lower Boise River, Southwestern Idaho, 

1974–2004

By Dorene E. MacCoy

Prepared in cooperation with the 

Idaho Department of Environmental Quality

Scientific Investigations Report 2006-5111

U.S. Department of the Interior

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

Dirk A. Kempthorne, Secretary

U.S. Geological Survey

P. Patrick Leahy, Acting Director

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

For sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

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endorsement by the U.S. Government.

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

reproduce any copyrighted materials contained within this report.

Suggested citation:

MacCoy, D.E., 2006, Fish communities and related environmental conditions of the lower Boise River, southwestern 

Idaho, 1974–2004: U.S. Geological Survey Scientific Investigations Report 2006-5111, 36 p. 
iii

Contents

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

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

Purpose and Scope ................................................................................. 1

Description of Lower Boise River Basin ......................................................... 3

Historical Changes in the Fishery ............................................................... 3

Previous Fishery Investigations .................................................................. 5

Idaho Department of Fish and Game, 1974-75 ............................................. 6

U.S. Geological Survey, 1988 ............................................................... 6

Idaho Department of Fish and Game, 1992 and 1993-94 ................................. 6

U.S. Geological Survey, 1995–96 ............................................................ 7

U.S. Geological Survey, 1996–97 ............................................................ 7

U.S. Geological Survey, 2001 and 2004...................................................... 7

U.S. Geological Survey and City of Boise, 2003 .......................................... 7

Data Compilation and Analysis ........................................................................ 7

Subbasins, Sampling Reaches, and Water-Quality Sampling Locations ..................... 7

Data-Collection Methods........................................................................... 8

Habitat, Hydrology, and Water Quality...................................................... 8

Fish Community .............................................................................. 8

Analytical Methods ................................................................................. 9

Fish Communities and Related Environmental Conditions .......................................... 10

Habitat................................................................................................ 10

Hydrology .......................................................................................... 12

Water Quality ....................................................................................... 15

Occurrence and Status of Fish in the Lower Boise River .................................... 16

Occurrence .................................................................................... 16

Status .......................................................................................... 20

Fish Communities Upstream and Downstream of Wastewater-Treatment 

Facilities .......................................................................................... 23

Analysis of Mountain Whitefish Condition ...................................................... 23

Data Limitations and Potential Future Investigations ................................................ 25

Summary ................................................................................................... 26

Acknowledgments ....................................................................................... 27

References Cited.......................................................................................... 27

Appendix A. Relative percentage of abundance of fish species in the lower

Boise River, Idaho .................................................................................... 32
iv

Figures

Figure 1. Map showing location of study area in the lower Boise River Basin, 

southwestern Idaho ........................................................................ 2

Figure 2. Graphs showing mean annual and mean monthly discharge rates for the

Boise River recorded at the U.S. Geological Survey Glenwood Bridge near

Boise, Idaho (13206000) and near Parma, Idaho (13213000) gaging stations ......... 13

Figure 3. Schematic diagram showing diversions, drains, and tributaries along the

Boise River from Lucky Peak Lake to the Snake River, southwestern Idaho......... 14

Figure 4. Graphs showing mean monthly discharge for December and August

recorded during pre- (1895–1916) and post-dam (1957–2002) periods at the

U.S. Geological Survey Boise River near Boise gaging station (13202000),

southwestern Idaho ........................................................................ 15

Figure 5. Photograph showing mountain whitefish (Prosopium williamsoni) .................. 16

Figure 6. Photograph showing brown trout (Salmo trutta) ....................................... 16

Figure 7. Photograph showing rainbow trout (Oncorhynchus mykiss)........................... 16

Figure 8. Photograph showing shorthead sculpin (Cottus confusus) and mottled

sculpin (Cottus bairdi) ..................................................................... 19

Figure 9. Photograph showing largescale sucker (Catostomus macrocheilus) ............... 19

Figure 10. Photograph showing bridgelip sucker (Catostomus columbianus) .................. 19

Figure 11. Photograph showing northern pikeminnow (Ptychocheilus oregonensis) ......... 19

Figure 12. Photograph showing smallmouth bass (Micropterus dolomieu) ..................... 19

Figure 13. Graphs showing fish index of biological integrity scores by year calculated

for low-flow sampling events (November to April) in seven reaches of the

lower Boise River, 1988–2003............................................................... 22

Figure 14. Graph showing percentages of invertivores and piscivores versus

percentages of omnivores and herbivores derived from 1996 fish collections

in the lower Boise River, southwestern Idaho .......................................... 22

Figure 15. Graph showing changes in the occurrence of sculpin upstream and

downstream of Lander Wastewater Treatment Facility, lower Boise River,

southwestern Idaho, 1988–2003............................................................ 23

Figure 16. Graph showing comparison of relative weight equations calculated for

mountain whitefish collected from the lower Boise River with the North

American standard weight equation for mountain whitefish and

measurements from least-disturbed rivers in southern Idaho ........................ 24

Figure 17. Graph showing mountain whitefish length and weight relations for the lower

Boise River and least-disturbed sites in southern Idaho, 1988–2004.................. 25
Tables

Table 1. Summary of U.S. Geological Survey and Idaho Department of Fish and Game

sampling of fish communities in the lower Boise River, southwestern Idaho,

1974 to 2004 ................................................................................. 5

Table 2. Fish sampling reach locations, lower Boise River, southwestern Idaho, 

1988–2004 .................................................................................... 6

Table 3. Habitat features measured for each subbasin of the historic (1867–1868) and

recent (1994­–2002), lower Boise River, southwestern Idaho ........................ 11

Table 4. Median, minimum, and maximum values of instantaneous water-quality

measurements and select constituent concentrations from sites on the

lower Boise River, southwestern Idaho, 1994–2002 .................................... 15

Table 5. Occurrence of fish species in the lower Boise River, southwestern Idaho,

1988–2004 .................................................................................... 17

Table 6. Selected metrics and Index of Biological Integrity scores calculated for fish

samples collected during low-flow periods (November to April) from the

lower Boise River and least disturbed sites in southwestern Idaho .................. 21

Table 7. Subbasin areas, selected land-use metrics, and fish Index of Biotic Integrity

scores for selected sampling events on the lower Boise River, southwestern

Idaho, 2000–03 .............................................................................. 22

Conversion Factors, Datums, and Abbreviations

Inch/Pound to SI

Multiply By To obtain

cubic foot (ft3) 0.02832 cubic meter (m3) 

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

foot (ft) 0.3048 meter (m)

foot per mile (ft/mi) 0.189394 meter per km (m/km)

inch (in.) 2.54 centimeter (cm)

mile (mi) 1.609 kilometer (km)

square mile (mi2) 2.590 square kilometer (km2) 

SI to Inch/Pound

gram (g) 0.03527 ounce, avoirdupois (oz)

meter (m) 1.094 yard (yd) 

millimeter (mm) 0.03937 inch (in.)

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

°F=(1.8×°C)+32.

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 

25°C).

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) 

or micrograms per liter (μg/L).

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Altitude, as used in this report, refers to distance above the vertical datum.
vi

Conversion Factors, Datums, and Abbreviations—Continued

Abbreviations

Abbreviation Definition

BLM Bureau of Land Managment

BMP best management practice

BOR Bureau of Reclamation

Corps U.S. Army Corps or Engineers

CPUE catch per unit effort

DEM digital elevation model

DRG digital raster graphic

EMAP Environmental Monitoring and Assessment Program (EPA)

EPA U.S. Environmental Protection Agency

GIS Geographic Information System

IBI Index of Biotic Integrity

IDEQ Idaho Department of Environmental Quality

IDFG Idaho Department of Fish and Game

IDWR Idaho Department of Water Resources

IHA Indicators of Hydrologic Alteration

IPC Idaho Power Company

NAWQA National Water Quality Assessment (USGS)

NMFS National Marine Fisheries Service

NPDES non-point discharges and elimination system

NWIS National Water Information System (USGS)

TMDL total daily maximum load

USGS U.S. Geological Survey

WTF wastewater-treatment facility
Abstract

Within the last century, the lower Boise River has been 

transformed from a meandering, braided, gravel-bed river that 

supported large runs of salmon to a channelized, regulated, 

urban river that provides flood control and irrigation water 

to more than 1,200 square miles of land. An understanding 

of the current status of the river’s fish communities and 

related environmental conditions is important to support the 

ongoing management of the Boise River. Therefore, fish 

community data from the U.S. Geological Survey and the 

Idaho Department of Fish and Game collected since 1974 

were analyzed to describe the status of fish communities in the 

lower Boise River. Each set of data was collected to address 

different study objectives, but is combined here to provide an 

overall distribution of fish in the lower Boise River over the 

last 30 years. Twenty-two species of fish in 7 families have 

been identified in the lower Boise River—3 salmonidae, trout 

and whitefish; 2 cottidae, sculpins; 3 catostomidae, suckers; 

7 cyprinidae, minnows; 4 centrarchidae, sunfish; 2 ictaluridae, 

catfish; and 1 cobitidae, loach.

Analysis of fish community data using an Index of 

Biotic Integrity (IBI) for Northwest rivers shows a decrease 

in the biotic integrity in a downstream direction, with the 

lowest IBI near the mouth of the Boise River. The number of 

tolerant and introduced fish were greater in the lower reaches 

of the river. Changes in land use, habitat, and water quality, 

as well as regulated streamflow have affected the lower Boise 

River fish community. IBI scores were negatively correlated 

with maximum instantaneous water temperature, specific 

conductance, and suspended sediment; as well as the basin 

land-use metrics, area of developed land, impervious surface 

area, and the number of major diversions upstream of a site. 

Fish communities in the upstream reaches were dominated 

by piscivorous fish, whereas the downstream reaches were 

dominated by tolerant, omnivorous fish. The percentage of 

sculpin in the river decreased in a downstream direction, 

and sculpin disappear completely at sites downstream 

of Glenwood Bridge. The sculpin population increased 

downstream of the Lander wastewater-treatment facility 

within the last decade, possibly as a result of improved 

wastewater treatment. The condition of the mountain whitefish 

(Prosopium williamsoni) throughout the lower Boise River 

was good and was similar both to the condition of mountain 

whitefish from least-disturbed rivers in southern Idaho and to 

the North American standard weight for mountain whitefish. 

Introduction 

Purpose and Scope

Fish community sampling has been included in some 

water-quality studies in the lower Boise River from 1974 

to 2004. These sampling events have not been summerized 

in one report until now. These studies differed somewhat 

in objectives, sampling protocols, and findings. The data, 

however, can be compiled and summarized for selected 

reaches of the lower Boise River to further the understanding 

of the fish community and associated environmental 

conditions. The purposes of this report are to describe the 

occurrence and distribution of fish species of the lower Boise 

River using data collected by IDFG and USGS from 1974 to 

2003 to describe temporal trends in fish-community structure 

and fish condition, and to identify environmental factors 

affecting occurrence, distribution, and community trends. 

Historic land and channel features from the late 1800s were 

used to compare fish habitat prior to and following hydrologic 

modification of the lower Boise River Basin.

Fish Communities and Related Environmental 

Conditions of the Lower Boise River, 

Southwestern Idaho, 1974-2004

By Dorene E. MacCoy
Area diverted to neighboring basin

Area diverted to neighboring basin

Figure 1. Location of study area in the lower Boise River Basin, southwestern Idaho.

   Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004 84 84 84 20 26 44 116°00’ 115°52’30”

43°15’

43°30’

43°45’

43°52’30”

117°00’

116°45’

116°30’

116°15’

00 5

5

10 KILOMETERS

10 MILES

ELMORE

BO ISE

ADA

CANYON

GEM

PAYETTE

Dixie

Drain

Willow

Creek

Mill

Slough

Mason

Slough

Fivemile

Creek

Tenmile

Creek

Thurman

Drain

Eagle

Drain

Mason

Creek

New

York

Canal

New

York

Canal

Creek

Fifteenmile

Creek

Wilson

Drain Lake

Lowell

Boise

River

Boise

River

Snake River

LoggersCreek

Indian

South Lucky Peak

Lake

I

D

A

H

O

Western Snake

River Plain

Study Area

Snake

River

Boise

Parma

Notus

Caldwell

Middleton

Star

Nampa

Kuna

Meridian

Eagle

Garden

City

Select one of the sub-basins listed below to view that sub-basin on the study area 

Upstream of Eagle IslandUpstream of Eagle Road

(south channel)

Upstream of MiddletonUpstream of the Mouth 13213000

13202000

13203510

13206000

13210050

13212500

9

2

3

4

5

6

7

8

1

West Boise

Wastewater 

Treatment

Facility

Lander

Wastewater 

Treatment

Facility

Glenwood

Bridge

Barber

Diversion

Dam

Dam

Conway

Gulch

West

Hartley

Gulch

East

Hartley

Gulch

BOISE MOUNTAINS

LuckyPeakDam

Eagle Island

Base from U.S. Geological Survey digital data, 1:100,000, 1980Albers Equal-Area projectionStandard parallels 43 30', 47 30',and -114 00', 41 45'No false easting or false northing

EXPLANATION

Water-quality and/or discharge sampling site  with USGS gage numberReach where fish were sampled—See table 2Hydrologic Unit Code (HUC) 17050114 boundary

Clear all selections

6

13210050
Description of Lower Boise River Basin

The 1,290 mi2 lower Boise River Basin is located in Ada 

and Canyon Counties in southwestern Idaho between Lucky 

Peak Dam (river mile 64) and the confluence of the Boise and 

Snake Rivers (river mile 395) (fig. 1). The basin contains the 

most industrialized and urbanized areas in Idaho. In 2000, the 

population in Ada and Canyon Counties was about 432,300 

(U.S. Census Bureau, 2002), which is 33 percent of Idaho’s 

population. Population in 2000 increased more than 46 percent 

over the 1990 population in these two counties. 

The lower Boise River Basin is in the northern part 

of the western Snake River Plain (fig. 1), and it lies in a 

broad, alluvium-filled basin with several step-like terraces, 

or benches, which are more pronounced and continuous 

on the south side of the river. The upper basin, upstream of

Lucky Peak Dam, is mountainous and sparsely populated. 

Downstream of Lucky Peak Dam, the basin floor slopes 

northwestward at a gradient of about 10 ft/mi. The altitude 

of the basin near Lucky Peak Dam is about 2,800 ft above 

sea level; the altitude near the river mouth is about 2,200 ft 

(Thomas and Dion, 1974). In addition to the lower Boise 

River, several tributaries are interconnected by a complex 

irrigation system of canals, laterals, and drains. Climate in the 

lower Boise River Basin is characterized as semiarid; winters 

are cool and wet, and summers are warm and dry. Some years 

considered to have normal to high amounts of precipitation are 

1995 to 1998, and 2000; and some years categorized as severe 

drought are 1999, 2001, and 2002. Thomas and Dion (1974), 

Mullins (1998), and the lower Boise subbasin assessment 

conducted by the Idaho Department of Environmental Quality 

(1999) provide more information on the geography, geology, 

and climate of the lower Boise River Basin.

Flow in the lower Boise River between Lucky Peak Dam 

and the mouth is controlled primarily by reservoir regulation, 

irrigation withdrawals and return flows, and seepage of 

shallow ground water (Thomas and Dion, 1974). The three 

reservoirs upstream in the upper Boise River Basin have a 

combined storage capacity of about 1 million acre-ft. These 

reservoirs are managed primarily for irrigation and flood 

control, and secondarily for recreation and power generation 

(Mullins, 1998). Some storage is assigned to salmonid flow 

augmentation in Lucky Peak Lake as required by the National 

Marine Fisheries Service (NMFS) 1995 Biological Opinion 

for the Snake River Basin (Bureau of Reclamation, accessed 

March 2002, at http://www.usbr.gov/dataweb/html/boise.

html). 

Land use and land cover in 1994 within the lower 

Boise River Basin included urban activities (4 percent); 

irrigated agriculture, pasture, and other agriculture-related 

activities (47 percent); and rangeland, water, and unclassified 

land (49 percent) (Kramer and others, 1994). Crops in the 

basin consist of alfalfa hay and seed, corn and corn seed, 

wheat, potatoes, onions, sugar beets, barley, spearmint and 

peppermint, and dry edible beans (Koberg and Griswold, 

2001). This land use contrasts with that in the upper Boise 

River Basin, which consists primarily of logging and 

recreation. Parts of the upper basin were heavily mined 

for gold during the late 1800s and early 1900s (Love and 

Benedict, 1940; Chandler and Chapman, 2001).

 Land use in the lower Boise River Basin has undergone 

major changes since 1994; particularly conversions of large 

tracts of farmland to residential subdivisions and commercial 

facilities, and conversions of many residential areas in and 

near cities to businesses, shopping centers, and parking 

lots. These land-use changes typically cause a reduction 

in agricultural non-point runoff, and may increase urban 

stormwater runoff to the lower Boise River and its tributaries, 

depending on the development practices implemented. Under 

the Clean Water Act, numerous public and private entities in 

the lower Boise River Basin are required to seek non-point 

discharge and elimination system (NPDES) stormwater 

discharge permits. These permits require these entities to 

implement best management practices that reduce pollutant 

loads to the “maximum extent practicable” (Johanna Bell, 

City of Boise, written commun., April 17, 2006). U.S. 

Environmental Protection Agency (EPA) regulation guidance 

and requirements are available online at http://yosemite.epa.

gov/r10/WATER.NSF/webpage/Storm+Water?OpenDocument

(accessed June 15, 2006). State of Idaho guidance is available 

online at http://www.deq.state.id.us/water/permits_forms/

permitting/catalog_bmps.cfm (accessed June 16, 2006). 

Boise municipal regulations and guidance are available 

online at the Partners for Clean Water web site at http://www.

partnersforcleanwater.org (accessed June 16, 2006). The City 

of Boise stormwater program is implementing a plan to reduce 

the stormwater load of sediment (p. 61 of Lower Boise River 

total daily maximum load [TMDL] at http://www.lbrwqp.

boise.id.us/tmdl/tmdl_4.pdf; accessed June 15, 2006) and 

total phosphorus. The stormwater sediment load reduction 

is a result of the development of a sediment TMDL (Idaho 

Department of Environmental Quality, 1999). Development of 

a total phosphorus TMDL and a temperature assessment are 

currently being done for the lower Boise River (Robbin Finch, 

City of Boise, written commun., November 2005). 

Historical Changes in the Fishery

The fishery of the lower Boise has changed over time 

partly in response to multiple human impacts caused by 

development of the study area. Settlers began to divert water 

from the lower Boise for irrigation in the late 1800s and early 

1900s; irrigation return flows were an early source of waterquality and stream habitat degradation. Also at that time, 

extensive mining began in the upper basin, and numerous 

lumber mills were operated east of Boise to supply timber for 

development (Stacy, 1993; Simonds, 1997). Temporal changes 

due to natural factors (climate change) in the lower Boise are 

unknown.

Introduction 
Soon after development began, farmers recognized the 

need for flood control and storage of irrigation water, which 

led to the 1902 “Boise Project,” one of the earliest projects by 

the Bureau of Reclamation (Stacy, 1993; Simonds, 1997). By 

1906, the New York Canal and several small irrigation projects 

had been built as part of the Boise Project. One of the Bureau 

of Reclamation’s (BOR) “big dams,” Arrowrock, was built in 

1915 on the mainstem Boise River, about 17 mi upstream of 

the City of Boise. The U.S. Army Corps of Engineers (Corps) 

built Anderson Ranch Dam on the South Fork of the Boise 

River (the world’s highest earthfill dam at the time of its 

completion in 1950). Anderson Ranch Dam is the uppermost 

storage facility on the Boise system located 42 mi upstream of

Arrowrock Dam. Anderson Ranch Dam and Powerplant is a 

multiple-purpose structure that provides benefits in irrigation, 

power, and flood and silt control (accessed April 17, 2006, 

at: http://www.usbr.gov/power/data/sites/anderson/anderson.

html). In 1957, the Corps built the third and final large dam, 

Lucky Peak, less than 10 mi upstream of the City of Boise, in 

response to concerns about potential flooding and to the need 

for additional irrigation water (Stacy, 1993). The construction 

of these dams affected the lower Boise fishery by blocking 

fish passage, changing the thermal regime and flow patterns of 

the river, modifying sediment transport and substrate size, and 

altering water quality and channel shape. 

Progressive urbanization around the City of Boise 

increased the need to treat wastewater prior to discharge 

to the lower Boise River. The construction of wastewatertreatment facilities (WTFs) downstream of Boise in the early 

1950s helped to disinfect wastewater entering the river, but 

introduced toxic concentrations of chlorine that resulted in 

frequent fish kills (Stacy, 1993). In the late 1950s, the lower 

Boise River was identified as one of the three most polluted 

waters in Idaho (Casey and Webb, 1996; Chandler and 

Chapman, 2001). In 1976, a second outlet was proposed for 

installation in Lucky Peak Dam to implement a minimum 

flow of about 150 ft3/s during winter, which helped to dilute 

effluent. According to the IDEQ, minimum flow varied as a 

result of water allocations downstream (Idaho Department 

of Environmental Quality, 1999). Continuing cleanup efforts 

in the lower Boise River Basin include upgrading WTFs and 

implementing best management practices (BMPs) for urban 

and agricultural runoff.

Prior to construction of dams, levees, and extensive 

irrigation in the lower Boise River Basin, a large (as wide as 

0.75 mi) hyporheic zone (an area beneath the main channel 

where surface water interacts with ground water) existed. 

The river’s interaction with the hyporheic zone allowed the 

river to develop side channels and other habitat for refuge 

and areas ideal for salmon spawning and rearing (David 

Blew, Idaho Department of Water Resources, oral commun., 

2002). Operation of the three Boise River dams for irrigation 

and flood control created a flow regime with higher than 

natural flows during the peak irrigation season (April 

through September) and lower than natural flows during the 

nonirrigation season (October through March). The change 

in hydraulic regime and the construction of levees has caused 

the lower reaches of the lower Boise River to incise to the 

point that depositional areas, backwater sloughs, and wetlands 

associated with the hyporheic zone have diminished (David 

Blew, Idaho Department of Water Resources, oral commun. 

2002; MacCoy and Blew, 2005). For further information on 

the effect of dams on alluvial rivers please refer to Williams 

and Wolman (1984), Collier and others (1996), and the World 

Commission on Dams (2000).

The lower Boise fishery was described in the early 

1800s as the “most renowned fishing place in the country,” 

because of the large numbers of salmon caught there (Pratt 

and others, 2001). The lower reaches of the Snake and its 

adjoining tributaries, which include the lower Boise River, 

were highly productive fisheries in the early 1800s for the 

Shoshone-Bannock Tribes (accessed March 2005, at http://

www.shoshonebannocktribes.com/fhbc.html). The historical 

distributions of Chinook salmon (Onchorhynchus tshawytscha)

and steelhead (Oncorhynchus mykiss) were evaluated by Idaho 

Power Company (IPC) as part of an ongoing hydroelectric 

project relicensing effort for the Hells Canyon Complex on 

the Snake River. The Complex includes the lower Boise River 

as an important tributary. Chandler and Chapman (2001) 

documented evidence of Chinook salmon spawning in the 

lower reaches of the lower Boise River until the early 1860s, 

coincident with the time when mining and irrigation projects 

began. They also reported steelhead runs in the lower Boise 

River, as well as the presence of Pacific lamprey (Lampetra 

tridentatus) in the river near Caldwell. 

Within the last century, the lower reaches of the 

lower Boise River changed from a thriving, cold water fish 

community with significant numbers of salmon and trout 

to a cool- and warm-water fish community. Nonindigenous 

warm-water fishes, including common carp (Cyprinus carpio), 

largemouth bass (Micropterus salmoides), smallmouth 

bass (M. dolomieu), bluegill (Lepomis macrochirus), 

channel catfish (Ictalurus punctatus), tadpole madtom 

(Noturus gyrinus), and oriental weatherfish (Misgurnus 

anguillicaudatus) have been introduced into the lower Boise 

River since the turn of the 20th century (Mullins, 1999a; 

Chandler and Chapman, 2001). Some of these nonindigenous 

fish species are known to be detrimental to salmonid 

populations (Li and others, 1987; Fuller and others, 1999). The 

Hells Canyon Complex of dams (Brownlee, Oxbow, and Hells 

Canyon), built between 1959 and 1967, prevented salmonids 

from entering the lower Boise River (Chandler and Chapman, 

2001). Chandler and Chapman (2001) concluded, following 

   Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Table 1. Summary of U.S. Geological Survey and Idaho Department of Fish and Game sampling of fish communities in the lower Boise River, 

southwestern Idaho, 1974 to 2004.

[Abbreviations: IDFG, Idaho Department of Fish and Game; USGS, U.S. Geological Survey; WAG, Lower Boise Watershed Advisory Group; WRI, Water 

Resources Investigation; WTF, wastewater-treatment facility]

Date Project

Lead 

collection 

agency

Study objectives Reference

March 1974 to 

February 1975

Snake River 

Fisheries 

Investigations

IDFG Identify fish population, and habitat 

and water-quality characteristics

Idaho Department of Fish and Game, 1975

January 1988 to 

March 31, 1988

Regional Fishery 

Management 

Investigation

IDFG Fish community assessment upstream 

and downstream of WTF

Frenzel and Hansen, 1988; Idaho 

Department of Fish and Game, 1988; 

Frenzel, 1990

March to 

April 1992

Regional Fishery 

Management 

Investigation

IDFG Fish community assessment upstream 

and downstream of WTF

Idaho Department of Fish and Game, 2000

December 1993 to 

March 1994

Regional Fishery 

Management 

Investigation

IDFG Characterize trout1 and whitefish2

population

Idaho Department of Fish and Game, 2000

February and March 

1995, and 

October 1996

USGS WRI USGS Fish community assessment upstream 

and downstream of WTF

Mullins, 1998

December 1996 to 

August 1997

USGS WRI USGS Examine biological integrity of fish 

population as related to water 

quality

Mullins, 1999

December 2001 USGS Idaho 

Statewide Water 

Quality Network

USGS Examine biological integrity of fish 

population as part of a long-term 

trend statewide water-quality study

MacCoy, 2004

November 2003 USGS WRI USGS Fish community assessment upstream 

and downstream of WTF

Data available on USGS web site at http://

id.water.usgs.gov/projects/fish/index.html

December 2004 USGS Idaho 

Statewide Water 

Quality Network

USGS Examine biological integrity of fish 

population as part of a long-term 

trend statewide water-quality study

Data available on USGS web site at http://

id.water.usgs.gov/projects/fish/index.html

1Brown trout (Salmo trutta); rainbow trout (Oncorhynchus mykiss).

2Mountain whitefish (Prosopium williamsoni).

the 2001 study, that the lower Boise River was no longer 

suitable to support salmonid spawning because of high water 

temperatures (greater than 20oC) in the late summer. 

Benke (1992) designated all native rainbow trout 

(Oncorhynchus mykiss) in the Columbia River Basin east of 

the Cascade Mountains, which includes the lower Boise River 

Basin, as redband trout. The Idaho Department of Fish and 

Game (IDFG) has not verified that the wild rainbow trout 

in the lower Boise River are a genetically distinct species 

(Jeff Dillon, oral commun., November 2005). The American 

Fisheries Society has grouped redband trout and rainbow 

trout into one group but does recognize that with additional 

genetic data this could be revised (Nelson and others, 2004). 

The IDFG manages the lower Boise River as a “put and take” 

fishery through the City of Boise (Idaho Department of Fish 

and Game, 2000). IDFG has created a very popular urban 

fishery by stocking the river with hatchery-reared rainbow 

trout of catchable size (greater than 6 in. total length). For 

example, more than 56,000 rainbow trout were stocked in the 

lower Boise River in 2004 (accessed June 15, 2006, at http://

fishandgame.idaho.gov/apps/stocking/year.cfm?region=3). In 

addition, IDFG has stocked Chinook salmon and steelhead in 

the lower Boise River.

Previous Fishery Investigations

The impairment of water quality and biological integrity 

in the lower Boise River and several of its tributaries has been 

evaluated as part of Federal and State monitoring programs, 

but only a few of those programs included an examination 

of fish communities (MacCoy, 2004). A summary of U.S. 

Geological Survey (USGS) and IDFG fish sampling in the 

lower Boise River since 1974 is shown in table 1, and the 

location of sampling reaches is shown in table 2. 

Introduction 
Table 2. Fish sampling reach locations, lower Boise River, southwestern Idaho, 1988–2004.

[Reach locations are shown in figure 1. Reach lengths varied according to project sampling protocol; upstream and downstream latitude and longitude given is 

for the maximum reach sampled using North American Datum of 1983 (NAD 83). Abbreviations: WTF, wastewater-treatment plant]

Reach

No. Reach name Subbasin location Upstream latitude/longitude Downstream latitude/longitude

1 Barber Dam Upstream of Eagle Island 116o08’03”W/43o34’07”N 116o09’34”W/43o34’58”N

2 Upstream of Lander WTF Upstream of Eagle Island 116o13’53”W/43o37’02”N 116o14’05”W/43o37’23”N

3 Downstream of Lander WTF Upstream of Eagle Island 116o15’02”W/43o38’30”N 116o16’46”W/43o39’38”N

4 Upstream of West Boise WTF Upstream of Eagle Road 116o18’09”W/43o40’10”N 116o19’22”W/43o40’16”N

5 Downstream of WTF Upstream of Eagle Road 116o20’23”W/43o40’30”N 116o21’15”W/43o40’29”N

6 Star Upstream of Middleton 116o27’01”W/43o40’47”N 116o28”13”W/43o41’02”N

7 Middleton Upstream of Middleton 116o33’34”W/43o40’55”N 116o34’17”W/43o41’03”N

8 Caldwell Upstream of Mouth 116o41’19”W/43o40’45”N 116o41’40”W/43o40’40”N

9 Upstream of Mouth Upstream of Mouth 116o27’03”W/43o67’41”N 116o58’16”W/43o46’41”N

Idaho Department of Fish and Game, 1974-75

The IDFG conducted a survey of fish populations and 

water quality in the lower Boise from its mouth upstream 

to Barber Dam during 1974 and 1975 (Idaho Department 

of Fish and Game, 1975). The 1974 sampling of 10 reaches 

(1 through 9 and a reach near Notus, fig. 1) of the lower Boise 

River was part of the Snake River Fisheries Investigation (a 

survey of the physical and biological information of the Snake 

River upstream of Brownlee Reservoir; Idaho Department of 

Fish and Game, 1975). The lower Boise River was included 

in the investigation because of its importance to the Snake 

River drainage. This study was the first extensive assessment 

of the fish community in the lower Boise River. The IDFG 

found abundant mountain whitefish populations in the Barber 

Dam to Star reach. The report concluded that these fish were 

competing with juvenile and adult trout, and it recommended 

cropping the population. The IDFG also recommended 

that this reach be managed as a cold water fishery. The 

Star to mouth reach was dominated by warm water species 

(mainly in the sloughs), and the IDFG recommended that 

the reach be managed as a warm water fishery. They also 

stated that minimum and maximum flow requirements 

should be established for the well being of aquatic life (Idaho 

Department of Fish and Game, 1975).

U.S. Geological Survey, 1988

In 1988, the USGS evaluated the effect of multiple 

wastewater discharges on water quality and aquatic 

communities in the lower Boise River (Frenzel, 1988; 1990). 

The study was designed primarily to assess trace-element 

effects on aquatic communities. Artificial substrates were used 

to assess macroinvertebrate communities, and IDFG assisted 

in the assessment of the fish community by electrofishing 

reaches 2 through 5 (fig. 1) upstream and downstream of

the Lander and West Boise WTFs (reaches 2, 3, 4, and 5; 

fig. 1). Frenzel (1988) found no evidence of adverse affects 

of the effluent from these facilities on the macroinvertebrate 

and fish communities. Asbridge and Bjornn (1988) included 

information from the USGS study and additional data in a 

survey of potential and available salmonid habitat in the lower 

Boise River. They concluded that the lower Boise River was 

not ideally suited to trout due to high velocities in the upper 

reaches and high temperature in the lower reaches. Winter 

cover also was mentioned as affecting trout abundance.

Idaho Department of Fish and Game, 1992 and 

1993-94

Population estimates of trout and mountain whitefish 

were conducted by IDFG during the spring of 1992 and the 

winter of 1993–94 at reach locations similar to those in 1988 

through the City of Boise (Frenzel, 1988). Idaho Department 

of Fish and Game (2000) noted that sportfish populations 

continued to decrease, with the most likely cause being the 

low winter flows.

 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
U.S. Geological Survey, 1995–96

As a follow-up study to the 1988 and 1992 studies, the 

USGS, in cooperation with the City of Boise, sampled fish 

communities upstream and downstream of the Lander and 

West Boise WTFs during the spring of 1995 and the autumn 

of 1996 (reaches 2 through 5, fig. 1). An IBI was calculated 

using percentages of sculpin, salmonids, pollution-tolerant 

species, invertivores, juvenile trout (assumed to be those 

less than 100 mm total length), juvenile mountain whitefish 

(assumed to be those less than 210 mm total length), and 

percentage of individuals with one or more anomalies 

(Mullins, 1999b). High flows in autumn of 1996 in the lower 

Boise River affected sampling efforts. Therefore, accurate 

species abundance estimates could not be made, and this 

data are not included in this report. The IBI scores were 

similar among the four sampling reaches, although Mullins 

(1999b) noted variability between riffles sampled within a 

reach. He suggested that more frequent sampling would help 

to determine any statistical differences between reaches. 

Sculpins were only found upstream of the Lander WTF, with 

shorthead sculpin (Cottus confusus) being the most abundant 

species (appendix A). Mullins (1996a) also noted the absence 

of juvenile trout at all locations, which may have been an 

indication of poor natural recruitment. 

U.S. Geological Survey, 1996–97

The USGS conducted fish-community surveys at five 

locations (reaches 1, 3, 7, 8 and 9; fig. 1) during December 

1996 and August 1997, as part of an ongoing water-quality 

and biological integrity study done in cooperation with IDEQ 

and the Lower Boise River Water Quality Plan (Mullins, 

1999a). Representative reaches at each location were sampled 

with both boat and backpack electrofishing equipment. IBI 

for each reach using five metrics (percentages of sculpin, 

salmonids, pollution-tolerant species, invertivores, and 

individual anomalies) were summarized only for the data 

collected in 1996 (Mullins, 1999a). The 1997 data were 

of poor quality due to problems associated with high-flow 

sampling, and those data were not used in the assessment 

of biotic integrity. The IBI scores calculated for reaches 3, 

7, and 9 (fig. 1) in 1996 indicated a longitudinal decrease in 

biological integrity, with the lowest score from reach 9 near 

the mouth (fig. 1). At reach 9, the fish community consisted 

of a high percentage of pollution-tolerant species, a reduced 

number of salmonids and invertivores, and a relatively high 

occurrence of anomalies. Mullins (1999a) concluded that 

the lower Boise River was moderately impaired in the upper 

reaches, and that river water quality decreased gradually 

downstream. He described a lack of well-developed pools, 

riffles, and fish cover, and he also noted extended low winter 

flow and high summer water temperatures in the lower 

reaches. Mullins (1999a) recommended monitoring the fish 

community and habitat in the lower Boise River on a 3- to 

5-year cycle.

U.S. Geological Survey, 2001 and 2004

The USGS sampled the fish community at reach 3 (fig. 1) 

in 2001 and 2004, as part of the Idaho Statewide Water Quality 

Network. Data from 2001 were summarized in MacCoy 

(2004), but the data collected in 2004 have not been previously 

published. The IBI score calculated for reach 3 in 2001 (68) 

was higher than the score calculated for the 1996 data (57), 

indicating a possible improvement to the fish community. 

U.S. Geological Survey and City of Boise, 2003

In November 2003, the USGS, in cooperation with the 

City of Boise, conducted another follow-up study of the fish 

community upstream and downstream of the WTFs. This 

evaluation included reaches 1 through 5 (fig. 1), and the 

sampling reaches were extended to 40 times the channel width 

(about 1 mi long) to capture the maximum fish diversity in 

each reach as described by Maret and Ott (2003). The 2003 

data have not been previously published. 

Data Compilation and Analysis

Subbasins, Sampling Reaches, and 

Water-Quality Sampling Locations

The lower Boise River Basin was divided into four 

subbasins to assess associations in land use, habitat, and 

fish community. The divisions were selected using both 

geomorphic channel features and water-quality aspects of 

the river. These divisions are described in more detail in 

MacCoy and Blew (2005). These subbasins include: upstream 

of Eagle Island to Lucky Peak Dam (upstream of Eagle 

Island); upstream of the south channel of the Boise River 

at Eagle Island downstream of West Boise WTF at Eagle 

Road (upstream of Eagle Road); upstream of Middleton 

(Middleton); and upstream of mouth (Mouth) (fig. 1). Each 

subbasin consists of one to three fish sampling reaches 

and one to two water-quality sampling locations (table 2). 

Beginning in 1994, the USGS sampled water quality at four 

lower Boise River sites: Boise River below Diversion Dam 

13203510 (Diversion), Boise River above Glenwood Bridge 

1320600 (Glenwood), Boise River near Middleton 13210050 

(Middleton), and Boise River near Parma 13213000 (Parma) 

(fig. 1). Diversion and Glenwood are in the upstream of Eagle 

Island subbasin, Middleton is in the Middleton subbasin, and 

Parma is in the upstream of Mouth subbasin. 

Data Compilation and Analysis   
Data-Collection Methods

Habitat, Hydrology, and Water Quality

Data pertaining to recent land and channel features were 

obtained primarily from biological surveys done between 1994 

and 2002 by the USGS (Mullins, 1999a). With the exception 

of measurements of channel width, most of the data collected 

were qualitative. Recent measurements of bankfull width 

were obtained from cross sections of the lower Boise River 

surveyed in 1997 and 1998 (Hortness and Werner, 1999) and 

from surveys at biological sampling sites (Mullins, 1999a). 

Historic geomorphic data (1867 and 1868) are used 

to compare fish habitat prior to and following hydrologic 

modification in the lower Boise River Basin. Land-cover 

data from cadastral survey notes obtained from the Bureau of 

Land Management (BLM) for the lower Boise Valley were 

used to re-create the “historical” lower Boise River. These 

data were summarized by the Idaho Department of Water 

Resources (David Blew, written commun., 2003) and in the 

methods published by MacCoy and Blew (2005). In their 

notes, surveyors documented slough and meander widths 

and azimuths, which typically were measured at the mean 

high-water mark. Therefore, these measurements were used 

to indicate bankfull width of the river and tributaries. The 

surveyors also noted land features such as gravel or sand bars.

Flow records were obtained from the National Water 

Information System web site (NWIS). Historic and recent 

flow conditions were compared by analyzing discharge 

data from the USGS gaging station “Boise River at Boise,” 

(13202000), which has the longest record on the lower Boise 

River from 1895 to 2002 (U.S. Geological Survey National 

Water Information System web site, accessed October 1, 

2005, at http://nwis.waterdata.usgs.gov/id/nwis/qwdata). The 

Indicators of Hydrologic Alteration (IHA) program was used 

to evaluate the magnitude of change in the natural flow regime 

following dam construction (The Nature Conservancy, 2001). 

The magnitude and variation of mean monthly discharges and 

the average monthly discharges for December and August 

were summarized for the Boise River at the Boise streamflow 

gaging station. 

Water-quality collection methods and data on the lower 

Boise River from 1994 to 2002 presented in this report 

are published in MacCoy (2004). Temperature, dissolved 

oxygen, pH, and specific conductance data were based on 

instantaneous readings. Data on suspended sediment and 

nutrients were based on depth- and width-integrated water 

samples.

Fish Community

Fish-community data were compiled from studies 

conducted by the USGS and IDFG between 1974 and 2004 

(table 1). U.S. Geological Survey fish sampling reaches were 

usually located near water-quality sampling locations in the 

lower Boise River (MacCoy, 2004). Fish communities were 

assessed by electrofishing a representative reach of river 

using protocols developed by the USGS National Water 

Quality Assessment (NAWQA) Program (Meador and others, 

1993). Shallow riffle areas were sampled using backpack 

electrofishing equipment (Smith-Root models 12 and 12A), 

and deep-water areas were sampled using a drift boat or 

a pontoon boat carrying a Smith-Root model VI-A and a 

5,000-watt, 240-volt generator with either multiple handheld 

or two bow-mounted electrodes. Netting crews consisted of 

four to six people and included personnel from IDFG, USGS, 

and the City of Boise. Usually two electrofishing passes 

were made through each reach, and an effort was made to 

sample all representative habitat types. Captured fish were 

held in livewells until they were processed and released. Fish 

were identified, counted, measured, weighed, and examined 

for types and numbers of anomalies. Fish were identified 

onsite by Dorene MacCoy and Terry Maret, USGS; Don 

Zoroban, IDEQ; and Dale Allen, IDFG using taxonomic 

names described in Nelson and others (2004). Voucher 

samples were taken of selected species, and those samples 

are in the collection of the Orma J. Smith Museum of Natural 

History, Albertson College, Caldwell, Idaho. The taxonomy 

of sculpin (Cottus sp.) and dace (Rhinichthys sp.) was verified 

by Dr. Carl E. Bond and Dr. Douglas F. Markel, Oregon 

State University, Corvallis, Oregon, and by Dr. Gordon Haas, 

University of British Columbia, Vancouver, Canada. 

Sampling techniques in November 2003 and August 2004 

changed slightly with the use of a raft-mounted electrofisher 

and techniques described in the U.S. Environmental Protection 

Agency’s Environmental Monitoring and Assessment Program 

(EMAP) fish sampling protocols (Peck and others, 2002). 

Each sampling reach was 40 times the mean channel width, or 

about 1 mi. A raft-mounted electrofisher was used to collect 

fish from near-shore habitats while floating downstream 

through the entire sampling reach. In addition, 100 m of riffle 

within each reach were sampled using a backpack electrofisher 

to capture small benthic species often missed by boat 

electrofishing. Sample data for these studies are summarized 

on the USGS Web site, accessed June 15, 2006, at http://

id.water.usgs.gov/projects/fish/index.html. Increasing the 

reach length provided a larger sample of the population but the 

percentage of composition of each species would be similar.

 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
General locations of IDFG sampling areas were 

predetermined by either the senior IDFG fishery research 

biologist or cooperators such as the USGS and the City 

of Boise. The IDFG used boat-mounted or shore-based 

electrofishing equipment for all fish community sampling. For 

the 1974 sampling, boats were powered upstream against the 

current while electrofishing (Idaho Department of Fish and 

Game, 1975). Boat-mounted electrofishing equipment using 

a variable voltage pulsator (0-600 watts DC) was powered by 

a 2,000 watt portable generator. This equipment was mounted 

on either an aluminum jet boat or on a smaller boat where 

maneuverability was limited. All species were counted, game 

fish were weighed and measured, and a summary of findings 

was produced (Idaho Department of Fish and Game, 1975). 

In 1988, the City of Boise and the USGS worked 

with the IDFG to choose sampling locations in reaches 2 

through 5 (fig. 1; table 2). A three-pass population depletion 

electrofishing technique (Zippin, 1958) was used at six 200-m 

reaches from Diversion Dam to Star. Crews in two drift 

electrofishing boats sampled from upstream to downstream in 

each reach using Coffelt model VVP 2-E electrofishers with 

direct current (600 volt) on a pulse frequency of 120 and a 

pulse width of 5 (Idaho Department of Fish and Game, 1988). 

Both game and nongame species were placed in livewells and 

counted separately. The game fish were weighed and measured 

for their total length. Nongame fish were counted, and all fish 

were returned to the river following the third pass. Attempts 

were made to use block nets at the upstream and downstream 

ends of each reach, but organic debris and higher streamflows 

made it difficult to keep the nets in place (Idaho Department of 

Fish and Game, 1988).

In 1992 and 1994, estimation techniques similar to the 

1988 sampling were used (J. Dillon, Idaho Department of Fish 

and Game, written commun., 2004). In 1994, electrofishing 

efficiency was improved with new equipment. A new Coffelt 

VVP-15 electrofisher with a 5,000-watt, shore-based generator 

and five anodes was used (Idaho Department of Fish and 

Game, 2000). In 1994, the focus of the sampling was to better 

characterize the trout and mountain whitefish populations in 

the river. No nongame species were identified. The 1994 data 

are mentioned, but not used in statistical summaries in this 

report due to the lack of nongame species. 

Analytical Methods

As a result of the Clean Water Act’s objective to “restore 

and maintain the physical, chemical, and biological integrity 

of the Nation’s waters,” there has been a growing focus on the 

development of biocriteria in State water-quality standards. 

Increasingly, biological monitoring programs and biocriteria 

development have expanded to include large rivers. In the 

United States, the IBI is used by the EPA and many State 

agencies to assess fish assemblage structure because it serves 

as an indicator of the history and current health or condition 

of a stream system (Karr, 1991). The IDEQ has recently 

published monitoring protocols and an IBI to evaluate large 

rivers of Idaho using aquatic organisms and habitat measures 

(Grafe, 2002; Mebane and others, 2003). Zaroban and 

others (1999) classified Northwest fish species into various 

attributes to facilitate the evaluation of surface-water resource 

conditions.

The fish community was evaluated using an IBI 

(Mebane and others, 2003) that consists of: (1) number of 

cold water native species; (2) percentage of abundance of 

sculpin; (3) percentage of cold water species; (4) percentage 

of sensitive native individuals; (5) percentage of tolerant 

individuals; (6) number of nonindigenous species; (7) catch 

per unit effort (CPUE) of cold water fish; (8) percentage 

of fish with anomalies (deformities, eroded fins, lesions, 

or tumors); (9) number of trout age classes (determined by 

length distribution); and (10) percentage of individual species 

of common carp. Hatchery fish were not included in the IBI 

calculations. Each of these 10 metrics was standardized and 

weighted to produce a score ranging from 0 to 100. Within 

this range, three classifications of biotic integrity can be 

identified. According to Mebane and others (2003), sites 

with scores between 75 and 100 exhibit high biotic integrity 

with minimal disturbance, and they possess an abundant and 

diverse community of native cold water species (classification 

= high biotic integrity). Sites with scores between 50 and 74 

are of somewhat lower quality. Nonindigenous species occur 

more frequently, and the community is dominated by cold 

water, native species (classification = intermediate biotic 

integrity). Finally, sites with scores less than 50 have poor 

biotic integrity. In these sites, cold water and sensitive species 

are rare or absent, and tolerant fish predominate (classification 

= poor biotic integrity). The relative abundance of each species 

by site and year, origin (native or introduced), tolerance to 

pollutants (tolerant, intermediate, or sensitive), and trophic 

guilds (percentage of invertivores and piscivores, and 

percentage of omnivores and herbivores) also are summarized. 

Selected metrics and IBI scores were summarized for fish 

community data collected during low-flow periods (November 

through March) only. The sample effort was similar for each 

study: two or more netters using at least a 2,000 watt generator 

to sample at least 0.16 mi of the river (about six times the 

channel width). Maret and Ott (2003) found that a sample size 

of greater than 100 represented 85 percent of the species in 

Data Compilation and Analysis   
a reach; therefore, IBI scores were calculated for samples of 

at least 120 individuals. Individual fish community metrics 

and IBI scores were compared spatially and temporally in the 

lower Boise River. They were then compared to one upstream 

site near Twin Springs (13185000) assumed to be unaffected 

by urban and agricultural activities, as well as to three leastdisturbed sampling sites in southern Idaho (Maret and others, 

2001; Terry Maret, U.S. Geological Survey, oral commun., 

April 2005). The least-disturbed sites were the Henry’s Fork 

River near St. Anthony (13050500), South Fork Snake River 

near Heise (13037500), and South Fork Payette River near 

Lowman (13235000). These sites were sampled as part of the 

Statewide Water Quality Network. For more information on 

this network, see the web page at http://id.water.usgs.gov/

public/wq/index.html. Land-use and water-quality parameters 

for these sites have been published in Clark (1994), Maret 

(1997), and Maret and others (2001). The least-disturbed 

sites were sampled during normal flow years but not always 

during the same years as the lower Boise River (mean monthly 

flows and long-term flows for the least-disturbed sites can be 

accessed at http://waterdata.usgs.gov/id/nwis/rt). These sites 

provide a comparison of the best available data from leastdisturbed streams in Idaho. 

Land-use derived metrics that include area of developed 

land, area of impervious surface, and number of major 

diversions calculated for each subbasin were compared 

with IBI scores. Subbasins were delineated upstream of 

the downstream end of a fish-sampling reach, and land-use 

metrics were derived from Geographic Information System 

(GIS) spatial datasets of the basin. Subbasin boundaries 

were delineated from 10-m digital elevation model (DEM) 

spatial data (accessed June 15, 2006, at http://ned.usgs.

gov/) and visually compared with digital raster graphic 

(DRG) datasets to detect any delineation errors. Points of 

diversions within each subbasin were obtained from the 

Idaho Department of Water Resources (IDWR) web site, 

accessed June 16, 2006, at http://www.idwr.idaho.gov/gisdata/

new%20data%20download/water_rights.htm), and impervious 

surface data were obtained from the NOAA-NESDIS National 

Geophysical Data Center’s web site, accessed June 15, 

2006, at http://dmsp.ngdc.noaa.gov/. Habitat features were 

summarized from both historic (1867 to 1868) and recent 

(1994 to 2002) qualitative and quantitative measurements. 

Spearman rank correlation coefficients (Zar, 1974) were used 

to determine significant correlation between land use and 

select water-quality parameters and IBI scores. A Spearman 

Rank coefficient is considered significant if it is greater than 

0.5.

Condition indices were used to determine the ‘health’ or 

‘robustness’ of individual fish by comparing length to weight. 

Mountain whitefish, a native, and the most abundant salmonid 

in the lower Boise River, was used to compare relative 

condition of this species to the North American standard 

weight equation (Rogers and others, 1996) and measurements 

of mountain whitefish from least-disturbed sites in southern 

Idaho. Because only a few mountain whitefish were sampled 

in the downstream reaches of the lower Boise River, mountain 

whitefish at sites upstream of Eagle Road of a length between 

150 and 350 mm were used for comparison. To determine 

a linear relation between fish length and weight, data were 

log10 transformed prior to regression analysis. Exponential 

equations for the length and weight relation used the following 

equation described in Armour and others (1983):

W aLb = , (1)

where

W is weight, and

L is length.

The equation is a transformation of the log-linear 

equations where “a” is the antilog of the Y-intercept and “b” is 

the slope of the regression line.

Fish Communities and Related 

Environmental Conditions

Habitat

Human actions and their impacts on streams are welldocumented by numerous authors (Heede and Rinne, 1990; 

Bayley, 1991; Gilvear and Winterbottom, 1992; Gilvear, 

1993; Baker, 1994; Brookes, 1996; Stanford and others, 

1996; Bravard and others, 1999; Schick and others, 1999; 

and McDowell, 2000). River alterations include the acute 

impacts of dams, channelization, water pollution, and longterm hydrologic and sediment modifications that result from 

these activities. The natural disturbance regimes that maintain 

habitats and biological communities are lost (Stanford and 

others, 1996). These changes can dramatically affect many 

aspects of aquatic ecosystems, including the habitat structure 

and the water quality necessary to maintain a viable fish 

population. To fully comprehend and appreciate changes to 

aquatic ecosystems, and to develop appropriate restoration 

plans, the condition of a river must be viewed as the result of a 

complex history of alterations and not just the result of current 

watershed conditions. 

10 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Table 3. Habitat features measured for each subbasin of the historic (1867–1868) and recent (1994­–2002), lower Boise River, southwestern Idaho.

[Subbasin and reach locations are shown in figure 1. Derived from MacCoy and Blew (2005). Abbreviations: ft, foot; oC, degrees Celsius; –, no data]

Habitat features 

Subbasins

Upstream of 

Eagle Island

Upstream of 

Eagle Road Middleton Mouth

Fish sampling reach numbers

1, 2, and 3 4 and 5 7 9

Embeddedness Historic – – – –

Recent 50 percent 75 percent 75 percent 50 percent

Dominant substrate Historic – – – –

Recent Cobble Cobble Gravel

Average bankfull 

width

Historic 900 ft North channel 790 ft

South channel 390 ft

520 ft 620 ft

Recent 140 ft North Channel 400 ft

South channel 150 ft

280 ft 250 ft

Channel forms, 

parafluvial surfaces

Historic Mid-channel Islands, 

gravel bars

Gravel and sand bars Some islands, sand bars Some islands, sand bars, 

split channel at the 

mouth

Recent Run, riffle, pool Run, stabilized. Run, exposed islands. Deep run, few islands, 

no sand bars, single 

channel at the mouth

Sloughs Historic Few sloughs Some development of 

sloughs

Abundant Abundant

Recent None Sloughs filled or 

converted to irrigation 

or drain ditches

Sloughs filled or 

converted to 

irrigation or drain 

ditches

Few natural sloughs, 

sloughs converted 

to irrigation or drain 

ditches

Vegetation Historic Willow and wildrose 

scattering of 

cottonwood

Willows and cottonwood Cottonwood, some 

willow

Cottonwood, some willow

Recent Some stands of native 

cottonwood.

Alien species dominate – –

Mean temperature Historic – – – –

Recent1 16oC – 19oC 21oC

Recent2 17oC – 19oC 21oC

1Mean temperature for July and August 1996 at U.S. Geological Survey water-quality sites at Glenwood, Middleton, and Parma (MacCoy, 2004).

2Mean daily average temperature for July and August 2004 at U.S. Geological Survey water-quality sites at Glenwood, Middleton, and Parma (City of Boise 

written commun., June 2005).

The habitat of the lower Boise River has changed 

dramatically over the past century, as indicated by comparison 

of recent (1994–2002) and historic (1867 and 1868) habitat 

features (MacCoy and Blew, 2005, table 3). Qualitative 

measures of embeddedness and substrate size collected by the 

USGS from 1994 to 2002, summarized in table 3, indicate 

an “armoring” of substrate throughout the lower Boise River.

In its investigation of the availability of habitat for salmonid 

spawning in the lower Boise River, the IDFG also noted 

armoring of the bottom substrate and a lack of spawning-sized 

gravels (Asbridge and Bjornn, 1988). When gravels were 

suitable, the IDFG reported embeddedness from 25 to 49 

percent (Asbridge and Bjornn, 1988). U.S. Geological Survey 

embeddeddness measures increased in a downstream direction 

with the highest embeddedness (75 percent) measured in 

reach 7, upstream of Middleton (Mullins, 1999a). Both 

historic and recent data were available for average bankfull 

width, channel forms, and number of sloughs in the basin 

Fish Communities and Related Environmental Conditions 11
(table 3). The average bankfull widths measured in most 

reaches in recent years have decreased to less than one-half of 

the historic width. For example, the historic average bankfull 

width of 900 ft upstream of Eagle Island has decreased 

to 140 ft (table 3). Historic channel forms and parafluvial 

surfaces (coarse sediments within the active channel and 

outside the wetted stream) have almost disappeared from 

all reaches of the lower Boise River. Gravel and sand bars 

were dominant downstream of Eagle Island, but these habitat 

features either have been stabilized or have been exposed 

(table 3). Historically, sloughs were abundant in the lower 

Boise River downstream of Eagle Island. Recently, the sloughs 

either have been filled in or have been converted to irrigation 

drains (table 3). 

Cottonwood stands are considered to be major 

components to large gravel-bed alluvial systems (Merigliano. 

1996; Poff and others, 1997) and are native to the lower Boise 

River. Historically, the lower Boise River’s riparian vegetation 

was dominated by willows and cottonwoods, owing to the 

dynamic flows and spring flooding that occurred. In 2002, 

cottonwood stands were confined to a narrow corridor at the 

river margins (table 3). Rood and Mahoney (1993) list several 

impacts on riparian cottonwood forests on dammed rivers 

in North America, including the lack of extreme flows that 

reduce forest abundance and seedling production. Today’s 

(2002) absence of parafluvial surfaces and the limited 

recruitment of new cottonwood or willow trees are largely due 

to the lack of extreme flows to recruit and move instream and 

riparian substrate. The extent to which the lower Boise River’s 

riparian vegetation has been affected by alteration in the 

natural flow regime is still unknown.

Hydrology

Higher than normal flows on the lower Boise River, 

resulting from flood-control releases and springtime irrigation 

returns, can last from January through June and persist all the 

way to the Snake River. The highest instantaneous discharge 

recorded between 1994 and 2002 was greater than 8,000 ft3/s 

measured at Glenwood in the spring of 1998. In years of 

severe and (or) consecutive drought, late winter and spring 

discharge remains low. Irrigation releases typically begin 

in mid-April (or following flood releases from Lucky Peak 

Dam during high-flow years) and continue through midOctober. Recent annual and mean monthly discharges for 

the lower Boise River at Glenwood and Parma illustrate the 

wide variation between water years and the regulated monthly 

discharge in the river (fig. 2). Water is diverted from the 

lower Boise River at several locations, and 12 major irrigation 

tributary/drains discharge to the lower Boise River between 

Lucky Peak Lake and the mouth (fig. 3). 

Recent annual mean flow in the lower Boise at Diversion 

is less than one-half of the calculated unregulated flow. 

Regression equations were used to estimate unregulated flow 

calculated from basin characteristics at Diversion (Hortness 

and Berenbrock, 2001; USGS Streamstats online report, 

accessed June 16, 2006, at http://streamstats.usgs.gov/html/

idaho.html). The estimated annual mean flow for Diversion 

based on unregulated flow was about 1,870 ft3/s (average 

standard error of 33 percent; Hortness and Berenbrock, 2001), 

and the regulated annual mean flow for the period of record 

(1987–1993) was about 830 ft3/s (U.S. Geological Survey 

National Water Information System Web site, accessed August 

30, 2005, at http://nwis.waterdata.usgs.gov/id/nwis/qwdata). 

Examination of the long-term flow record from the Boise 

River near Boise gaging station (USGS station 13202000) 

just downstream of Lucky Peak Dam shows a change in the 

magnitude and variability of seasonal flow following dam 

construction (fig. 4). Median mean monthly discharge for 

December and August prior to 1915 were about 1,090 and 

1,200 ft3/s, respectively, with standard deviations near 

460 ft3/s. In comparison, median discharge after dam 

construction (post-1957) for December and August were 350 

and 4,020 ft3/s, respectively, with standard deviations of 350 

and 640 ft3/s, respectively (U.S. Geological Survey National 

Water Information System Web site, accessed August 30, 

2005, at http://nwis.waterdata.usgs.gov/id/nwis/qwdata). In 

fact, the flow regime in 2002 is opposite of pre-dam flows in 

December and August (fig. 4). The mean December postdam flows are significantly lower than those in pre-dam years 

(P<0.001, Wilcoxon rank sum test with α=0.05); and the mean 

August post-dam flows are significantly higher (P<0.001, 

Wilcoxon rank sum test with α=0.05) than those recorded 

during pre-dam years. 

Little information is available on the effect of flow 

alteration on the lower Boise River fishery, although most of 

the lower Boise River fish investigations have indicated that 

low winter flows were the reason for the decrease in the fish 

community (Idaho Department of Fish and Game, 1975; 1988; 

2000; Mullins, 1999a). Altering the flow regime affects not 

only the fish community, but the entire aquatic environment. 

Several studies have shown that altering the natural river flow 

regime affects fish community biodiversity, food availability, 

habitat complexity, life history patterns, and connectivity 

(the ability of an organism to move freely through the stream 

hierarchy) (Ward and Stanford, 1983; Collier and others, 1996; 

Poff and others, 1997; Bunn and Arthington, 2002; Postel and 

Richter, 2003). 

12 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Figure 2. Mean annual and mean monthly discharge rates for the Boise River recorded at the U.S. Geological Survey Glenwood Bridge near 

Boise, Idaho (13206000) and near Parma, Idaho (13213000) gaging stations.

id3093_figure02

4,000

3,000

2,000

1,000

0

1982 1984 1986 1988 1990 1994 1996 1998 2000 2001

4,000

3,000

2,000

1,000

0

OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEPT

1972 1974 1976 1978 1980 1982 1984 1986 1988 1990 1992 1994 1996 1997

4,000

3,000

2,000

1,000

0

4,000

3,000

2,000

1,000

0

1992

MONTH

DISCHARGE, IN CUBIC FEET PER SECOND

Mean annual discharge for recent period of record 

Mean annual discharge for period of record 

(Discharge data for water years 1998-2001

 from Idaho Power, 2002)

MEAN MONTHLY DISCHARGE, Boise River near Parma Water years 1994-2001

MEAN ANNUAL DISCHARGE, Boise River at Glenwood Bridge Recent period of record 1982-2001

MEAN ANNUAL DISCHARGE, Boise River near Parma Period of record 1972-1997

MEAN MONTHLY DISCHARGE, Boise River at Glenwood Bridge Water years 1994-2001

WATER YEARS

Fish Communities and Related Environmental Conditions 13
id3093_figure03

EXPLANATION

Inflow

Outflow

USGS gaging station with 

 number and name

RM 58.8 River mile

RM 63.6

RM 58.8

RM 58.3

RM 52.0

RM 51.0 RM 50.4

RM 47.5

RM 38.0

RM 32.9

RM 32.4

RM 29.1

RM 27.7

RM 26.3

RM 24.7

RM 23.2

RM 22.6

RM 22.4

RM 21.9

RM 21.1

RM 19.7

RM 17.9

RM 17.6

RM 16.0

RM 13.8

RM 3.8

RM 0.0

Lucky

Peak

Lake

Snake River

13202000

Boise River near Boise

13203510 Boise River below Diversion Dam

13206000

Boise River at Glenwood Bridge

13210050

Boise River near Middleton

13212500

Boise River at Notus

13213000

Boise River near Parma

Penitentiary Canal Boise Project Main (New York) Canal

Barber Dam

Ridenbaugh Canal

Boise City Canal

Settlers Canal

Bubb, Meeves, #1 & #2, Rossi Mill

Drainage District #3

Davis Ditch Farmers Union and Boise Valley Canals

Lander Wastewater Treatment Facility

Eagle

Island

9 Eagle

Island

Canals

New Dry Creek and New Union Canals

Ballentine Canal

Eagle Drain

Little Pioneer Canal

Middleton Canal

West Boise Wastewater Treatment Facility

Thurman Drain

Eureka #1 and Phyllis Canals

Caldwell Wastewater Treatment Facility

Bowman and Swisher Canal

Caldwell Highline Canal Canyon Canal

Riverside and Pioneer Dixie Canals

Mill Slough below Grade Ditch

Fifteenmile Creek Fivemile Creek

Tenmile Creek

Willow Creek

Mason Slough; Mason Creek

Hartley Drain and Gulch

Indian Creek

Sebree, Campbell, and Siebenburg Canals

Conway Gulch

Baxter and Boone Canals

Caldwell Bridge

McManus and Teater Canals

Eureka #2 Canal

Upper Center Point Canal

Lower Center Point Canal

Andrews Ditch

Mammon Pumps

Parma Canal

Dixie Drain

Haas Canal

Island Highland Canal

McConnel Island Canal

Figure 3. Diversions, drains, and tributaries along the Boise River from Lucky Peak Lake to the Snake River, southwestern Idaho.

(Modified from Warnick and Brockway, 1974).

14 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
id3093_figure04

1890 1900 1920 1940 1960 1980 2000 2010

0

1,000

2,000

3,000

4,000

5,000

YEAR

1895 1916 1957 2002

Pre-Impact Period Post-Impact Period

August

MEAN MONTHLY DISCHARGE, IN CUBIC FEET PER SECOND

0

500

1,000

1,500

2,000

2,500

December

75th percentile

median

25th percentile

Figure 4. Mean monthly discharge for December and 

August recorded during pre- (1895–1916) and post-dam 

(1957–2002) periods at the U.S. Geological Survey Boise 

River near Boise gaging station (13202000), southwestern 

Idaho.

Water Quality

Recent water-quality data revealed longitudinal 

increases in constituent concentrations in the lower Boise 

(Mullins, 1998; MacCoy, 2004). Nitrogen, phosphorus, 

and suspended-sediment concentrations increased between 

Diversion and Parma (table 4). Increased agricultural activity 

in the lower basin appears to increase nutrient and sediment 

concentrations and is directly correlated with specific 

conductance. Urban land use also appears to increase nutrient 

concentrations in the lower Boise River. Maret (1997) found 

that specific conductance and percentage of fine sediment in 

streams and rivers of southern Idaho were highly correlated 

with agricultural land use. The suspended-sediment criterion 

of 80 mg/L for no more than 14 days (Rowe and others, 2003) 

was exceeded most frequently at the downstream-most site at 

Parma. Total nitrogen concentrations at Glenwood, Middleton, 

and Parma exceeded National background concentrations 

of 1.0 mg/L (U.S. Geological Survey, 1999). Middleton and 

Parma had more than twice the median flow-adjusted total 

nitrogen concentrations compared to undeveloped basins 

across the country (0.26 mg/L; Clark and others, 2000). 

Glenwood, Middleton, and Parma also exceeded the flowadjusted total phosphorus concentrations for undeveloped 

basins (0.02 mg/L; Clark and others, 2000). 

Table 4. Median, minimum, and maximum values of instantaneous water-quality measurements and select constituent concentrations from sites on the 

lower Boise River, southwestern Idaho, 1994–2002.

[Derived from MacCoy (2004). Subbasins shown in figure 1. Abbreviations: USGS, U.S. Geological Survey; oC, degrees Celsius; mg/L, milligram per liter; 

μS/cm, microsiemen per centimeter; Min., minimum, Max., maximum]

Water-quality 

sampling site

USGS

station 

No.

Subbasins

Temperature

(oC)

Dissolved 

oxygen 

(mg/L)

pH 

(standard 

units)

Specific 

conductance 

(μS/cm)

Suspended 

sediment 

(mg/L)

Total 

nitrogen

 (mg/L as N)

Total 

phosphorus 

(mg/L as P)

Median 

(Min.-Max.)

Median 

(Min.-Max.)

Median 

(Min.-Max.)

Median 

(Min.-Max.)

Median 

(Min.-Max.)

Median 

(Min.-Max.)

Median 

(Min.-Max.)

Diversion 13203510 Upstream of 

Eagle Island 

Basin

9.2 11.6 7.6 75 4 0.26 0.04

(1.6 - 18.8) (9.1 - 14.6) (6.6 - 8.5) (51 - 107) (1 - 38) (0.15 - 0.51) (0.01 - 0.09)

Glenwood 13206000 Upstream of 

Eagle Road 

Basin

11.5 11.4 8.0 90 5 0.45 0.09

(2.8 - 23.0) (8.4 - 15.8) (7.8 - 8.9) (52 - 197) (1 - 107) (0.18 - 1.90) (0.02 - 0.38)

Middleton 13210050 Upstream of 

Middleton 

Basin

12 11.7 8.0 136 6 0.89 0.15

(2.7 - 22.5) (8.8 - 15.7) (6.7 - 9.1) (74 - 314) (2 - 211) (0.38 - 3.51) (0.03 - 0.85)

Parma 13213000 Upstream of 

Boise River 

Mouth Basin

12.1 10.2 8.0 343 45 2.17 0.3

(3.4 - 31.5) (6.7 - 16.2) (7.3 - 8.9) (128 - 585) (8 - 245) (0.62 - 5.33) (0.08 - 0.55)

Fish Communities and Related Environmental Conditions 15
In natural stream environments, the 

temperature regime varies longitudinally 

and can be modified by land-management 

activities that influence channel width, riparian 

canopy cover, pool volume, runoff timing, 

and instream flow. Temperature has been 

an influential parameter in determining fish 

community structure (Poole and Berman, 2001; 

Poole and others, 2004), and it is vital to the 

understanding of the fish community in the 

lower Boise River. The State’s daily maximum 

temperature standards of 22°C and 13°C 

(Idaho Department of Environmental Quality, 

2001) to protect cold water biota and salmonid 

spawning, respectively, were exceeded most 

frequently at Middleton and Parma (MacCoy, 

2004). Continuous long-term monitoring of 

temperature is needed in the lower Boise River 

to monitor compliance with these standards. 

The City of Boise and the USGS began 

continuous temperature monitoring at selected 

sites on the lower Boise River in 2004 as part of 

a modeling effort; data from those monitoring 

efforts have not yet been published. For more 

information on the Idaho State water-quality 

standards for temperature refer to http://www.

deq.idaho.gov/water/data_reports/surface_

water/monitoring/temperature-index.cfm.

Occurrence and Status of Fish in the 

Lower Boise River

Occurrence

Fish species that have been collected in 

the lower Boise River from the studies listed in 

table 1 are summarized in appendix A. Table 5

summarizes the occurrence of each species 

by river mile from USGS and IDFG sampling 

events. All USGS data and only that from 

the first pass of the IDFG depletion sampling 

are summarized in appendix A and used in 

summary statistics. Water-quality and habitat 

conditions have changed in the basin since the 

first study was completed in 1974 by the IDFG. 

Therefore, the species listed for a given location 

in table 5 may not occur at that location today. 

For example, in 1988 and 1992, IDFG sampled 

common carp near Glenwood Bridge. Studies 

since that time have not found common carp at 

that site. The occurrence of fish species found 

near Middleton and near the mouth also is a 

result of only one sampling event at each USGS 

sampling site between 1995 and 1996 (table 1); 

a different community may occur at these sites 

today (2004).

Twenty-two species of fish distributed among 7 families have been 

identified in the lower Boise River: 3 Salmonidae (2 trout and 1 whitefish), 

2 Cottidae (sculpins), 3 Catostomidae (suckers), 7 Cyprinidae (minnows), 

4 Centrarchidae (sunfishes), 2 Ictaluridae (catfishes), and 1 Cobitidae (loach) 

(table 5). 

Mountain whitefish (fig. 5) is the most widely distributed salmonid, 

having been collected from downstream of Barber Dam to the mouth. Brown 

trout (Salmo trutta, fig. 6) have been collected downstream of Barber Dam 

to Eagle Road Bridge; although rainbow trout (fig. 7) are the least distributed 

of the salmonids, having been collected downstream of Barber Dam to 

Middleton. 

Figure 5. Mountain whitefish (Prosopium williamsoni).

Figure 6. Brown trout (Salmo trutta).

Figure 7. Rainbow trout (Oncorhynchus mykiss).

16  Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Table 5. Occurrence of fish species in the lower Boise River, southwestern Idaho, 1988–2004.

[Data for this chart from studies listed in table 1. Abbreviations; WTF, wastewater-treatment facility; HWY, highway]

 Fish species

Major dams, drains, 

canals between 

each river mile

Diversion 

Dam, New 

York Canal, 

Barber Dam

Ridenbaugh 

Canal

City Canal, 

Settlers 

Canal 

diversion 

dam

Thurman 

Mill Canal, 

WTF input

 Farmers 

Union 

Canal

Dry Creek 

Canal

WTF input, 

Thurman 

Drain

River mile 64 59 57.5 52 50 47.5 46.4 45 43

Lucky Peak 

Dam Barber Dam Loggers Creek

Diversion 

above 

Americana 

Blvd

Lander 

WTF

Glenwood 

Bridge

Top of 

Eagle 

Island

West Boise 

WTF Eagle Road

Salmonidae Salmo trutta Brown trout

Prosopium williamsoni Mountain whitefish

Onchorhynchus mykiss Wild rainbow trout

Cottidae Cottus bairdi Mottled sculpin

Cottus confusus Shorthead sculpin

Catostomidae Catostomus columbianus Bridgelip sucker

Catostomus macrocheilus Largescale sucker

Catostomus platyrhynchus Mountain sucker

Cyprinidae Cyprinus carpio Commom carp

Acrocheilus alutaceus Chiselmouth

Ptychocheilus oregonensis Northern pikeminnow

Richardsonius balteatus Redside shinner

Rhinichthys cataractae Longnose dace

Rhinichthys umatilla Umatilla dace

Gila bicolor Tui chub

Centrarchidae Lepomis gibbosus Pumpkinseed

Leponis macrochirus Bluegill

Micropterus salmoides Largemouth bass

Micropterus dolomieui Smallmouth bass

Ictaluridae Ictalurus punctatus Channel catfish

Noturus gyrinus Tadpole madtom

Cobitidae Misgurnus anguillicaudatus Oriental weatherfish

Fish Communities and Related Environmental Conditions 17
Fish species 

Major dams, drains, 

canals between 

each river mile

Dry Creek, 

Middleton 

Canal, Phyllis 

Canal, Warm 

Springs Canal

Phyllis Canal, 

Warm Springs 

Canal

Caldwell Highline 

Canal, Fifteenmile 

Creek, Mill Slough, 

Willow Creek, 

Mason Creek, Noble 

Drain, Notus Canal

Indian Creek, 

Conway Gulch, 

Eureka Canal, 

WTF input

Dixie 

Slough

River mile 38 34 31 21 14 5 3.8 2

Bottom Eagle 

Island Star Middleton HWY 95 at Caldwell Notus HWY 95 near Parma Parma gage

Fort Boise 

National 

Wildlife 

Refuge

Salmonidae Salmo trutta Brown trout

Prosopium williamsoni Mountain whitefishOnchorhynchus mykiss?? Wild rainbow trout

Cottidae Cottus bairdi Mottled sculpin

Cottus confusus Shorthead sculpin

Catostomidae Catostomus columbianus Bridgelip sucker

Catostomus macrocheilus Largescale suckerCatostomus platyrhynchus Mountain sucker

Cyprinidae Cyprinus carpio Commom carp

Acrocheilus alutaceus ChiselmouthPtychocheilus oregonensis Northern pikeminnowRichardsonius balteatus Redside shinnerRhinichthys cataractae Longnose daceRhinichthys umatilla Umatilla daceGila bicolor Tui chub

Centrarchidae Lepomis gibbosus Pumpkinseed

Leponis macrochirus BluegillMicropterus salmoides Largemouth bassMicropterus dolomieui Smallmouth bass

Ictaluridae Ictalurus punctatus Channel catfish

Noturus gyrinus Tadpole madtom

Cobitidae Misgurnus 

anguillicaudatus

Oriental weatherfish

Table 5. Occurrence of fish species in the lower Boise River, southwestern Idaho, 1988–2004.—Continued[Data for this chart from studies listed in table 1. Abbreviations; WTF, wastewater-treatment facility; HWY, highway]

18  Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Both mottled (Cottus bairdi) and shorthead (Cottus 

confusus) sculpin (fig. 8) have been found only downstream 

of Barber Dam to Glenwood Bridge. Both largescale 

sucker (Catostomus macrocheilus, fig. 9) and bridgelip 

sucker (Catostomus columbianus, fig. 10) were found at all 

locations sampled, whereas mountain suckers (Catostomus 

platyrhynchus) were collected only from Glenwood Bridge to 

Middleton. 

Most minnow species were widely distributed. Common 

carp, northern pikeminnow (Ptychocheilus oregonensis, 

fig. 11), redside shiner (Richardsonius balteatus), longnose 

dace (Rhinichthys cataractae) and Umatilla dace (Rhinichthys

Umatilla) were found at all sampling sites from Glenwood 

Bridge to the mouth. One minnow, chiselmouth (Acrocheilus 

alutaceus), was collected at all sampling sites downstream of 

Barber Dam. 

Of the sunfish, bluegill were found from Glenwood 

Bridge to Star, smallmouth bass (Micropterus dolomieu) 

(fig. 12) were found from Middleton to the mouth, and 

largemouth bass were found from Glenwood Bridge to the 

mouth. Catfish were found in the lower reaches: channel 

catfish from Caldwell to the mouth, and tadpole madtom 

(Noturus gyrinus) from Star to Middleton. 

The oriental weather fish (loach) is an invasive species 

that probably was introduced in the drains of the lower Boise 

River from tropical fish aquariums; it has been found from 

Glenwood to Middleton. The species is native to northeastern 

Asia and central China. They prefer still or slow-moving 

shallow waters in which they can burrow into the mud. 

They are tolerant to a wide range of water temperatures and 

conditions. For example, their ability to absorb oxygen from 

the air allows them to survive in water that is low in oxygen 

content. Moreover, the species has few predators and high 

production rates (Gulf States Marine Fisheries Commission: 

accessed March 2005, at http://nis.gsmfc.org/nis_factsheet.

php?toc_id=192).

Figure 8. Shorthead sculpin (Cottus confusus) and mottled sculpin 

(Cottus bairdi).

Figure 9. Largescale sucker (Catostomus macrocheilus).

Figure 10. Bridgelip sucker (Catostomus columbianus).

Figure 11. Northern pikeminnow (Ptychocheilus oregonensis).

Figure 12. Smallmouth bass (Micropterus dolomieu).

Fish Communities and Related Environmental Conditions 19
Status

Fish metrics and the associated IBI scores have been 

summarized in table 6 for reaches in the lower Boise River 

sampled during low-flow periods (November to April) and 

from least-disturbed rivers in southern Idaho. Sampling 

events for low-flow periods were chosen for IBI comparison 

to eliminate any sampling bias due to the inability to capture 

fish during high flows. Although all 10 metrics are similarly 

weighted, the occurrence of cold water species, sculpin, and 

common carp, or the occurrence of tolerant species, tended to 

drive the IBI scores either lower or higher. For example, the 

lack of sculpin species, as well as the decrease in cold water 

and sensitive species, decreased the overall IBI score. The 

occurrence of common carp at reach 3 in 1988 and 1992, and 

reaches 7 and 9 in 1996, also decreased the IBI scores. The 

percentage of anomalies also were highest at reach 3 in 2003, 

but this metric did not appear to have a profound effect on the 

IBI score. 

IBI scores were higher for reaches 1 through 5 in 2003 

(average IBI score of near 81) than in 1988 (average IBI 

score of near 62), which may indicate improved water-quality 

conditions in the upper reaches. The IBI scores from four 

least-disturbed sites ranged from 65 (intermediate biotic 

integrity) at the South Fork Snake River near Heise in 2003 

to 99 (high biotic integrity) at the South Fork Payette River 

near Lowman in 2001. The median IBI score for all four 

least-disturbed sites was 81, indicating high biotic integrity 

(table 6). The dominant metrics driving the IBI scores at the 

least-disturbed sites were percentage of sculpin and cold 

water species. No carp were found at the least-disturbed sites, 

although tolerant individuals were found at all sites except the 

South Fork Payette River near Lowman.

Overall, the IBI scores for the lower Boise River 

(calculated since 1988, n=26, median of 67, intermediate 

biotic integrity) were lower than those for the least-disturbed 

sites. The IBI scores of 11 and 40 (indicating poor biotic 

integrity) at the Mouth and Middleton, respectively, were 

much lower than the scores at the least-disturbed sites. 

Additional sampling in the lower Boise River would be 

required to better characterize the biotic integrity of the 

system, particularly in the lower reaches where findings are 

based on a small number of samples.

Most IBI score classifications for sites with multiple 

years of data remained similar except for reach 3 (fig. 13). In 

this reach, IBI scores increased from 36 (poor biotic integrity) 

in 1988 to 73 (intermediate biotic integrity) in 2003. Median 

IBI scores calculated for reaches 1 and 2 sampled between 

1988 and 2003 were greater than 75, indicating high biotic 

integrity, and for reaches 4 and 5 were near 60, indicating 

intermediate biotic integrity. 

IBI scores were compared to some water-quality and 

habitat features measured between 1994 and 2002 (tables 3

and 4). Maximum instantaneous values of water temperature 

were negatively correlated with IBI scores (Spearman’s rank 

correlation coefficient >0.5, n=10, α=0.1). A significantly 

negative correlation was found between IBI scores and 

maximum instantaneous values of specific conductance and 

suspended sediment (Spearman’s rank correlation coefficient 

>0.80, n=10, α <0.5). Recent habitat measures such as 

embeddedness and bankful width were similar throughout the 

lower Boise River (table 3) and did not correlate well with IBI 

scores. 

A dramatic longitudinal shift occurs in feeding groups 

from upstream to downstream in the lower Boise River

(fig. 14, appendix A). Communities numerically dominated 

by piscivores (fish feeding on other fish) and invertivores 

(fish feeding on invertebrates), and those dominated by 

omnivores (fish feeding on both plant and animals) and 

herbivores (fish feeding on primarily plants) were compared 

between reaches for the samples collected in 1996. There 

was a decrease in piscivores and invertivores in reaches 3, 

7, and 9. Only 20 percent of the fish species in reach 9 fed 

on macroinvertebrates or other fish. MacCoy (2004) found 

little difference in macroinvertebrate abundance from reach 1 

to reach 9, but did identify differences in macroinvertebrate 

tolerance levels and feeding habits. In reach 1, the 

macroinvertebrate community consisted of only 2 percent 

tolerant species and was primarily filterers. Filterers spend 

most of their life cycle on the surface of coarse substrate, 

using specialized web and filtering mechanisms to feed on 

suspended detritus, and they are readily available for fish to 

consume (Voshell, 2002). The macroinvertebrate community 

in reach 9 consisted of near 50 percent tolerant species, and 

the community was primarily gatherers. Gatherers eat fine 

detritus that has fallen out of suspension and is located either 

on bottom sediment or between coarse substrate (Voshell, 

2002). These species may not be readily available for fish to 

consume because they usually reside between course substrate 

or burrow into bottom sediment.

Subbasin areas were similar except for the upstream 

of Mouth subbasin that included an additional 1,000 mi2 of 

land (table 7). No significant correlation was found between 

basin area and IBI scores. However, specific land-use metrics 

calculated for each lower Boise River subbasin appear to 

correlate with IBI scores. Area of developed land, impervious 

surface area, and number of major diversions increased in a 

downstream direction (table 7) and had a significant negative 

correlation with IBI scores (Spearman rank correlation 

coefficient >0.9, n=7, α<0.05). Additional fish-community 

data in the downstream reaches would help to test the relation 

between land use and fish community.

20 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Table 6. Selected metrics and Index of Biological Integrity scores calculated for fish samples collected during low-flow periods (November to April) from the lower Boise River and least disturbed sites 

in southwestern Idaho.[Reach locations are shown in figure 1 and table 2. Data for U.S. Geological Survey fish samples can be found online at http://id.water.usgs.gov/projects/fish/index.html. Reach: *, least-disturbed sites. Abbreviations: DELT, deformities, eroded fins, lesions, or tumors; ND, no data collected]

Reach No. or 

site name Month Year

Number of 

cold native 

species

Percentage 

of sculpin

Percentage 

of sensitive 

native 

individuals

Percentage 

of cold 

individuals

Percentage 

of tolerant 

individuals

 Number 

of nonindiginous 

species

Percentage 

of carp

Salmonid 

age 

classes 

(no 

whitefish)

Cold 

individuals 

per minute

Percentage 

of DELT 

anomolies

Index of 

Biological 

Integrity

1 Jan. 1988 3 22 2 79 9 1 0 3 ND ND 81

Dec. 1996 4 50 30 98 0 1 0 3 ND ND 89Nov. 2003 4 79 80 97 1 1 0 5 15 0 93

2 Jan. 1988 3 1 0 16 9 1 0 2 ND ND 54

Apr. 1992 3 45 2 56 13 1 0 2 5 ND 76Mar. 1995 4 28 21 59 11 0 0 ND ND ND 92Dec. 1996 4 45 14 74 16 2 0 2 12 0 78Nov. 2003 5 45 25 91 7 1 0 6 9 0 89

3 Jan. 1988 3 1 0 6 35 3 1 ND ND ND 36

Mar. 1992 2 0 0 20 80 1 1 1 3 ND 33Feb. 1995 2 0 4 28 51 1 0 ND 4 ND 48Dec. 1996 4 2 2 31 48 1 0 2 2 0 57Dec. 2001 4 8 3 77 16 2 0 2 12 2 68Nov. 2003 5 15 4 69 26 2 0 3 4 3 73

4 Jan. 1988 3 1 5 67 31 1 0 6 ND ND 70

Mar. 1992 2 0 3 43 53 1 0 5 3 ND 55Mar. 1995 2 0 5 83 17 1 0 ND ND ND 62Dec. 1996 2 0 2 70 27 2 0 4 4 1 65Nov. 2003 3 0 9 90 8 2 0 4 6 1 72

5 Jan. 1988 3 4 4 38 37 1 0 7 ND ND 67

Mar. 1992 2 0 0 6 62 1 0 2 ND ND 35Feb. 1995 2 0 6 44 20 0 0 2 5 1 67Dec. 1996 2 0 9 81 11 2 0 2 ND 1 60Nov. 2003 3 0 27 84 16 2 0 5 5 ND 77

7 Dec. 1996 2 0 0 26 28 2 8 ND 3 1 399 Dec. 1996 1 0 0 8 80 2 2 0 0 2 11

*Henry’s Fork River 

near St. Anthony

Sept. 1999 3 7 0 78 1 3 0 6 10 1 78

*South Fork Snake 

River near Heise

Sept. 2003 3 2 10 83 13 3 0 3 3 2 65

*South Fork Payette 

River near Lowman

July 2001 3 73 91 92 0 0 0 4 3 0 99

*Boise River near 

Twin Springs

Sept. 2004 5 7 19 46 35 0 0 5 2 0 84

Fish Communities and Related Environmental Conditions 21
Table 7. Subbasin areas, selected land-use metrics, and fish Index of Biotic Integrity scores for selected sampling events on the lower Boise River, 

southwestern Idaho, 2000–03.

[Subbasins and reach locations are shown in figure 1 and table 2. Subbasin area: including 2,690 mi2 upstream of Lucky Peak Dam. Abbreviations: WTF, 

wastewater- treatment facility; mi2, square mile; IBI, Index of Biotic Integrity]

Fish 

sampling 

reach No.

Fish sampling reach name Subbasin

Subbasin 

area 

(mi2)

2001 

developed 

land 

(mi2)

2000-01 

impervious 

surface 

(mi2)

2001 

number

of major 

diversions

 IBI score 

(year 

sampled)

1 Downstream of Barber Dam Upstream of Eagle Island 2,710 0.12 1.70 5 93 (2003)

2 Upstream of Lander WTF Upstream of Eagle Island 2,770 14.8 14.3 13 89 (2003)

3 Downstream of Lander WTF 73 (2003)

4 Upstream of West Boise WTF Upstream of Eagle Road 2,777 17.6 16.5 19 72 (2003)

5 Downstream of West Boise WTF 77 (2003)

7 Middleton Upstream of Middleton 2,894 27.5 25.8 31 39 (1996)

9 Mouth Upstream of mouth 3,910 79.9 73.9 57 11 (1996)

Figure 13. Fish index of biological integrity scores by year 

calculated for low-flow sampling events (November to April) in 

seven reaches of the lower Boise River, 1988–2003. 

(Reach numbers correspond to the reaches identified in figure 1 and 

table 2.)

Reach 9

0

20

40

60

80

100

0

20

40

60

80

100

0

20

40

60

80

100

0

20

40

60

80

100

19881990199219941996199820002002

YEAR

19881990199219941996199820002002

Reach 5 Reach 7

Reach 3 Reach 4

Reach 1 Reach 2

YEAR

FISH INDEX OF BIOLOGICAL INTEGRITY SCORE

Figure 14. Percentages of invertivores and piscivores versus 

percentages of omnivores and herbivores derived from 1996 fish 

collections in the lower Boise River, southwestern Idaho.

id3093_figure14

Invertivores and piscivores

Omnivores and herbivores

REACH 9

 RM 2

REACH 7

 RM 31

REACH 5

 RM 45.5

REACH 4

 RM 46.5

REACH 3

RM 47

REACH 2

 RM 52

REACH 1 

RM 59

0

20

40

60

80

100

PERCENTAGE OF TOTAL INDIVIDUALS

22 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Fish Communities Upstream and Downstream of 

Wastewater-Treatment Facilities

Most of the fish-community data have been collected 

upstream and downstream of the Lander and West Boise 

WTFs (reaches 2 through 5; fig. 1). Data available for reaches 

1 through 5 allowed for a more in-depth analysis of fishcommunity responses to water-quality and habitat variables. 

Table 6 provides individual metrics and IBI scores for sites 

upstream and downstream of WTFs.

The median IBI scores calculated from 1988 through 

2003 at reaches 3 and 5 downstream of WTFs (53 and 67, 

respectively) were lower than reaches 2 and 4 upstream of

the WTFs (78 and 65, respectively). Of the sites upstream 

and downstream of WTFs, the average IBI score upstream 

of Lander WTF, reach 2, was the only site with high biotic 

integrity (fig. 13). More tolerant fish species were found 

downstream of WTFs, with the average percentage of tolerant 

species increasing from reaches 2 to 3 (11 to 43 percent), and 

reaches 4 to 5 (27 to 29 percent). The difference in tolerant 

species between reaches 4 and 5 was small and these sites 

are considered to support similar fish communities. The 

average percentage of cold water species decreased from 

reach 2 to 3 (from 59 to 38 percent) and from reach 4 to 5 

(from 71 to 50 percent). Percentage of sculpin had the most 

dramatic longitudinal decrease for an individual metric. The 

average (1988–2003) percentage of sculpin in reach 1 was 

close to 50 percent of the fish community and decreased 

to an average of 33 percent in reach 2 and decreased even 

further to an average of 4 percent in reach 3. Sculpin have not 

been found since 1988 at reaches 4 and 5, and were found 

in very low numbers. The decrease in the sculpin population 

in the downstream reaches may be a factor of a combination 

of habitat loss, predation, and water-quality degradation. 

There was an increase in percentage of sculpin between 

1988 and 2003 in reach 3 that suggests a slight improved 

water quality (fig. 15). There also was an increase in the 

IBI score in reach 3 from 36 (poor biotic integrity) in 1988 

to 73 (intermediate biotic integrity) in 2003. The City of 

Boise changed from chlorination/declorination treatment of 

wastewater to ultraviolet treatment at the Lander WTF in 1995 

(Robbin Finch, City of Boise, written commun., 2003), which 

may have had an impact on the sculpin population. Sculpin 

were not found in the downstream Lander WTF sample in 

August 2004 (appendix A). Previous samples from this reach 

were taken during low-flow periods (December to March) 

suggesting that sculpin may have flow or seasonal preferences 

in habitat. Although similar changes to wastewater treatment 

were made at the West Boise WTF in 2000, sculpin have not 

been found upstream or downstream of this facility.

Sculpin and other benthic small-bodied fish have been 

used as sentinel species for environmental monitoring because 

they may be sensitive to chemical or other stressors. They are 

not subject to fishing harvest and stocking which confound 

the analyses of game fish. Sculpin have a limited home range 

(less than 50 m and respond to local conditions (Brown and 

Downhower, 1982; Gray, 2004; Petty and Grossman, 2004). In 

contrast, the home range of large-bodied fish such as suckers 

or mountain whitefish can be more than 50 km making it 

difficult to relate exposure to responses (Pettit and Wallace, 

1975; Baxter, 2002).

Analysis of Mountain Whitefish Condition

Mountain whitefish comprise a large portion of the 

fish biomass in the lower Boise River. The species has been 

classified as a cold water native, but it is intermediate in 

its sensitivity to degraded water-quality conditions such as 

siltation, elevated temperatures, and low dissolved-oxygen 

concentrations (Zaroban and others, 1999). Several studies 

have documented the adverse effects of elevated summer 

temperatures and suspended sediment on mountain whitefish. 

For example, in laboratory experiments with adult fish, 

increasing lethality was observed at temperatures greater 

than about 23oC (Ihnat and Buckley, 1984). In July 2002, a 

large kill of mountain whitefish occurred in the Snake River 

near Waters Ferry, Idaho, following several days during 

which the maximum daily temperatures in the river exceeded 

26oC (Idaho Department of Environmental Quality, 2003). 

Mountain whitefish also showed avoidance behavior and gill 

damage following exposures to elevated suspended sediments 

during a sluicing operation in Wyoming in which sediment 

concentrations increased to 500 times the background 

concentration (Bergsted and Bergersen, 1997). In contrast, 

when exposed to elevated concentrations of suspended 

sediment that were within the natural range in an Alberta 

River, mountain whitefish showed no avoidance behavior 

(Reid and others, 2002).

id3093_figure15

Upstream,

 reach 2

Downstream,

 reach 3

0

10

20

30

40

50

1988 1992 1995 1996 2001 2003

PERCENTAGE OF SCULPIN

SELECTED YEAR OF DATA ANALYSIS

Figure 15. Changes in the occurrence of sculpin upstream and 

downstream of Lander Wastewater Treatment Facility, lower Boise River, 

southwestern Idaho, 1988–2003.

Fish Communities and Related Environmental Conditions 23
Because lower Boise River mountain whitefish are 

somewhat sensitive to degraded water quality and account 

for a large portion of the fish biomass, additional analyses of 

length and weight data were made to determine the relative 

“health” of the population. The relation of mountain whitefish 

length and weight observed in the lower Boise River from 

sites upstream of Middleton is compared to those from leastdisturbed rivers in southern Idaho and to mountain whitefish 

collected from throughout their natural range in the northern 

United States and Canada (Rogers and others, 1996) to give 

a relative “condition” of individual fish. Condition indexes or 

standard weight equations are considered most representative 

if they are developed by using a large portion of the population 

across the geographical range (Murphy and others, 1991). 

Rogers and others (1996) developed a North American 

standard weight equation for mountain whitefish using more 

than 13,000 fish from their range in the northern United States 

and two Canadian provinces. Condition equations were 

developed from the lower Boise River and least-disturbed 

rivers using regression analysis of log-transformed mountain 

whitefish total lengths and weights (fig. 16). The lower Boise 

River equation (log . 10W = + 5 624 3. l 229 og10 L)was very 

similar to both the North American standard equation 

(log . 10W = + 5 086 3. l 036 og10 L) and the least-disturbed 

site equation (log . 10W = -4 057 + 2. l 623 og10 L). Lower 

Boise River mountain whitefish appear to be slightly smaller 

than those from the least-disturbed sites in southern Idaho 

(fig. 17). Based on their abundance and their relative weight, 

the general condition of the mountain whitefish in the lower 

Boise River appears to be high, although mountain whitefish 

are uncommon downstream of Middleton. Possible factors that 

may limit mountain whitefish populations in the downstream 

reaches include water-quality conditions such as high 

temperatures and increased siltation. 

Least disturbed streams

North American standard equation

Lower Boise River

Least disturbed streams

LOG10 VALUE OF MOUNTAIN WHITEFISH LENGTH, IN MILLIMETERS

LOG10 VALUE OF MOUNTAIN WHITEFISH WEIGHT, IN GRAMS

1

1.5

2

2.5

3

2.1 2.2 2.3 2.4 2.5 2.6

Figure 16. Comparison of relative weight equations calculated for mountain whitefish collected from the lower Boise River 

with the North American standard weight equation for mountain whitefish and measurements from least-disturbed rivers in 

southern Idaho.

North American standard weight equation for mountain whitefish from Rogers and others (1996).

24 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Data Limitations and Potential Future 

Investigations 

Based on several metrics and an overall IBI of the lower 

Boise River, the fish community upstream of the Lander 

WTF is similar to that of least-disturbed rivers in southern 

Idaho. Downstream of the Lander WTF, the apparent range 

expansion of sculpin over the last decade may indicate longterm improvements in water quality. However, important 

limitations apply to the analysis of this limited dataset. The 

main analytical tools, an IBI model to evaluate the overall 

fish community and relative weight equations to evaluate fish 

community “health,” are useful but crude in their predictive 

power to asses the effect of pollutants on the fish population.

Future assessments of status or changes in fish 

community and health in the lower Boise River would benefit 

from more robust assessments of the distribution of benthic 

species such as sculpin and direct assessment of fish health. 

Measures related to energy expenditure, energy storage, 

and survival of fish populations can be obtained with little 

additional effort (Munkittrick and McMaster, 2000). Measures 

of bioaccumulation and biomarkers of chemical exposure 

can be important measures for waters that receive complex 

point and non-point discharges. These measures have been 

successfully used in the monitoring and assessment of fish 

health in rivers receiving organic effluents and in targeting 

similar species found in the lower Boise River (KloepperSams and others, 1994a, 1994b; Swanson and others, 1994; 

Gibbons and others, 1998). 

Recent studies have shown that rivers receiving urban and 

agricultural effluent, such as the lower Boise River, may be 

influenced by wastewater chemicals that include detergents, 

disinfectants, fragrances, fire retardants, nonprescription 

drugs, and pesticides (Barnes and others, 2002; Kolpin and 

others, 2002; Sprague and Battaglin, 2004). Some of these 

chemicals may mimic hormones, causing effects in fish 

that may not be obvious in conventional monitoring, such 

as reduced reproductive health or reduced defense against 

disease (Thorpe and others, 2001; van der Oost and others, 

2003; Brown and others, 2004). Three sites on the lower 

Boise River (downstream of Diversion Dam, upstream of 

id3093_figure17

Lower Boise River

y = 0.000002x

3.23

R2 = 0.98

N = 2306

Least-disturbed sites

y = 0.00009x

2.63

R2 = 0.93

N = 154

0

100

200

300

400

500

600

100 150 200 250 300 350 400

LENGTH, IN MILLIMETERS

WEIGHT, IN GRAMS

Figure 17. Mountain whitefish length and weight relations for the lower Boise River and least-disturbed sites in southern Idaho, 

1988–2004.

Data Limitations and Potential Future Investigations 25
Middleton, and downstream of Parma) were selected as part 

of a national assessment of wastewater chemicals (Barnes 

and others, 2002). Results of this study found no antibiotics 

or human pharmaceutical compounds at these sites in water 

but did detect hormones and other organic wastewater 

chemicals. Bioaccumulation of these chemicals is unknown 

in the lower Boise River. Preliminary results of a recent 

USGS study have identified these types of chemicals in 

Colorado streams (Sprague and Battaglin, 2004) and have 

indicated their potential endocrine disruption effects on 

fish. The USGS conducted a reconnaissance of endocrinedisrupting compounds in rivers across the United States 

and concluded that sites containing these compounds may 

affect the endocrine system of resident fish (Goodbred 

and others, 1997). In a survey of fish contamination in the 

Columbia River, mountain whitefish tended to have higher 

concentrations of mercury and some pesticides than did other 

fish (U.S. Environmental Protection Agency, 2002). This 

finding suggests that different species also may have different 

uptake rates and reactions to pollutants. Considering the above 

factors, a more comprehensive evaluation of fish health that 

includes both indicators of exposure and potential effects 

of endocrine-disrupting chemicals could provide important 

information about the effects of pollutants on fish populations 

in the lower Boise River.

Summary

Within the last century, the lower Boise River 

downstream of Lucky Peak Dam in southwestern Idaho has 

been transformed from a meandering, braided, gravel-bed 

river that supported large runs of salmon to a channelized, 

regulated, urban river that provides flood control and irrigation 

water to more than 1,200 square miles of land. In some places, 

the river is one-half the width it was before it was dammed. 

The lower Boise River fish communities are impacted by 

flow alterations, habitat loss, and poor water quality. As water 

demand increases for urban, domestic, and agricultural uses, 

so does the impact on the fish communities. The river’s flow 

is regulated by upstream dams and downstream irrigation 

returns. In fact, the current flow in the lower Boise River is 

opposite to that of pre-dam era, with lower flows in the winter 

and higher flows in the summer. The lack of higher flows 

to recruit and move gravel for riffle habitat and to mobilize 

fine sediment has caused embeddedness throughout the river 

that measures between 50 and 75 percent. The quality of 

water decreases in a downstream direction with increasing 

temperatures and nutrient and sediment concentrations. 

Although rainbow trout are stocked at a rate of 56,000 fish per 

year in the lower Boise River, the lack of colder temperatures 

downstream has reduced natural spawning of this species. 

Fish data from the U.S. Geological Survey (USGS) and 

Idaho Department of Fish and Game (IDFG) collected since 

1974 were combined to report the status of fish communities 

in the lower Boise River. Twenty-two species representing 

7 families of fish have been identified in the lower Boise 

River: 3 salmonids (trout and whitefish), 2 cottids (sculpins), 

3 catostomids (suckers), 7 cyprinids (minnows), 4 centrarchids 

(sunfish), 2 ictalurids (catfish), and one cobitidae (loach). Of 

these, 13 are native species, 5 are cold water species, 9 are 

cool water species, and 8 are warm water species. Most of 

the warm water species are found in the lower reaches of the 

river. Of the salmonid species, mountain whitefish have been 

found throughout the lower Boise River, and rainbow and 

brown trout have been found upstream of Eagle Road. Sculpin, 

a cold water, bottom-feeding fish, has been found only in the 

upstream reaches upstream of Glenwood Bridge. Suckers 

have been found throughout the river, and tolerant species 

such as carp, northern pikeminnow, bass, and catfish have 

been found primarily in the lower reaches. Index of Biotic 

Integrity (IBI) scores calculated for USGS and IDFG sampling 

events between 1988 and 2004 decreased in a downstream 

direction, with two of the lowest scores (indicating poor 

biotic integrity) measured at Middleton (40) and near the 

mouth (11), respectively. IBI scores for each sampling reach 

remained similar over time except for the reach downstream 

of the Lander WTF. The IBI scores for the reach downstream 

of the Lander WTF (reach 5) increased from a score of 36 in 

1988, indicating poor biotic integrity, to 73 in 2003, indicating 

intermediate biotic integrity. The increase in IBI score at 

this site may be an indication of increased water quality and 

reflects the increased number of sculpin found in 2003. IBI

scores for all sites were negatively correlated with maximum 

instantaneous water temperature, specific conductance, and 

suspended sediment; as well as the basin land-use metrics of 

area of developed land, impervious surface area, and number 

of major diversions within a subbasin. Fish communities 

downstream of Middleton consisted primarily of tolerant 

species and omnivorous feeders, whereas fish communities in 

the upstream most reach downstream of Barber Dam consist 

of only 2 percent tolerant species and were piscivores and 

invertivores.

Fish communities downstream of the Lander WTF 

generally had lower IBI scores, an increase in tolerant species, 

and a decrease in percentage of cold water species. Sculpin 

were not found downstream of Glenwood Bridge in the lower 

Boise River, possibly due to decreases in habitat and water 

quality. Length-weight relations for mountain whitefish, 

an indicator used to determine the condition of the species’ 

population in the lower Boise River, were similar to those 

found both in regional populations and in least-disturbed rivers 

in southern Idaho.

26  Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
The fish communities in the lower Boise River have 

changed in response to changes in habitat, land use, and 

water quality. As the human population increases in the lower 

Boise River Basin, the demand for both high-quality water 

and recreation in and around the river will affect aquatic 

communities, especially fish communities. Frequent and 

comprehensive monitoring of the lower Boise River fish 

communities will help to identify impacts and to sustain this 

beneficial resource.

Land use in the lower Boise River Basin is changing 

rapidly from a rural/agricultural community to an urban/

residential community, and these changes may affect the lower 

Boise River fish community. Future assessments of status 

or changes in fish community and health in the lower Boise 

River should focus on the distribution of benthic species such 

as sculpin and the direct assessment of fish health. A more 

comprehensive evaluation of fish health that includes both 

indicators of exposure and potential effects of endocrinedisrupting chemicals could provide important information 

about the effects of pollutants on fish populations in the lower 

Boise River.

Acknowledgments

The author would like to thank Jeff Dillon of the Idaho 

Department of Fish and Game (IDFG) for providing data 

and technical input for this report. Technical reviews by 

Karen Murray, Chris Mebane, and Terry Maret of the U.S. 

Geological Survey (USGS) greatly improved the quality 

of this report. Thank you to all of the USGS, IDFG, City 

of Boise, and Idaho Department of Environmental Quality 

personnel who helped with fish collection and data analysis. 

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References Cited  31
Appendix A. Relative percentage of abundance of fish species in the lower Boise River, Idaho.

[Origin: I, introduced; N, native. Tolerance: I, intermediate; S, sensitive; T, tolerant. Adult trophic guild: Classification of species from Zaroban and others, 

1999; inv., invertivore, pisc, piscivore; omni, omnivore; herb, herbivore. Abbreviations: IFG, Idaho Fish and Game; USGS, U.S. Geological Survey; WTF, 

wastewater-treatment facility; –, no species found]

Date Collecting 

agency

Species

Brown trout 

(Salmo 

trutta)

Mountain 

whitefish 

(Prosopium 

williamsoni)

Wild 

rainbow trout 

(Onchorhychus 

mykiss)

Mottled 

sculpin 

(Cottus 

bairdi)

Shorthead 

sculpin 

(Cottus 

confusus)

Sculpin 

(Cottus sp.)

Origin I N N N N N

Tolerance I I S I S I

Temperature preference Cold Cold Cold Cold Cold Cold

Adult trophic guild inv/pisc inv inv/pisc inv inv inv

Site location

Downstream Barber Dam Jan. 1988 IDFG 1.3 72.7 2.7 – – 12.7

Downstream Barber Dam Dec. 1996 USGS 1.3 39.8 7.2 27.5 22.5

Downstream Barber Dam Nov. 2003 USGS .2 11.9 5.4 4.4 74.8 –

Upstream Lander WTF Jan. 1988 IDFG .1 15.5 .3 – – .4

Upstream Lander WTF Mar. 1992 IDFG 2.1 38.4 2.1 – – 28.9

Upstream Lander WTF Mar. 1995 USGS 29.9 1.8 8.8 18.8 –

Upstream Lander WTF Dec. 1996 USGS .4 28.4 .6 31.4 13.5 –

Upstream Lander WTF Nov. 2003 USGS 2.3 38.1 6.0 15.8 19.1 9.7

Downstream Lander WTF Jan. 1988 IFG – 5.5 – – – .5

Downstream Lander WTF Mar. 1992 IFG – 19.6 .2 – – –

Downstream Lander WTF Feb. 1995 USGS .3 24.2 1.3 – – –

Downstream Lander WTF Dec. 1996 USGS .8 27.6 .8 .8 1.2 –

Downstream Lander WTF Dec. 2001 USGS 1.1 66.4 1.4 6.6 1.4 –

Downstream Lander WTF Nov. 2003 USGS 1.8 48.6 3.5 10.6 .4 3.9

Downstream Lander WTF Aug. 2004 USGS 5.3 17.2 2.4 – – –

Upstream West Boise WTF Jan. 1988 IFG .3 61.6 5.1 – – .3

Upstream West Boise WTF Mar. 1992 IFG .7 39.5 3.3 – – –

Upstream West Boise WTF Mar. 1995 USGS .4 77.3 5.2 – – –

Upstream West Boise WTF Dec. 1996 USGS .6 67.4 1.7 – – –

Upstream West Boise WTF Nov. 2003 USGS 3.2 78.8 8.5 – – –

Downstream West Boise WTF Jan. 1988 IFG .3 32.0 2.7 – – 3.7

Downstream West Boise WTF Mar. 1992 IFG – 5.3 .4 – – –

Downstream West Boise WTF Mar. 1995 USGS – 36.7 8.5 – – –

Downstream West Boise WTF Dec. 1996 USGS 2.1 69.8 9.4 – – –

Downstream West Boise WTF Nov. 2003 USGS 2.1 55.5 26.6 – – –

North channel Eagle Island Jan. 1988 IFG .2 .9 – – – .9

Middleton Dec. 1996 USGS – 25.9 .2 – – –

Middleton Aug. 1997 USGS – 2.0 – – – –

Above Star Road Jan. 1988 IFG – 6.6 .7 – – –

Caldwell Aug. 1997 USGS – 2.5 – – – –

Near mouth Dec. 1996 USGS – 8.3 – – – –

Near mouth Aug. 1997 USGS – 1.8 – – – –

– – –

32 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Appendix A. Relative percentage of abundance of fish species in the lower Boise River, Idaho.—Continued

[Origin: I, introduced; N, native. Tolerance: I, intermediate; S, sensitive; T, tolerant. Adult trophic guild: Classification of species from Zaroban and others, 

1999; inv., invertivore, pisc, piscivore; omni, omnivore; herb, herbivore. Abbreviations: IFG, Idaho Fish and Game; USGS, U.S. Geological Survey; WTF, 

wastewater treatment facility; –, no species found]

Date

Species

Bridgelip 

sucker 

(Catostomus 

columbianus)

Largescale 

sucker 

(Catostomus 

macrocheilus)

Mountain 

sucker 

(Catostomus 

platyrhynchus)

Sucker 

(Catostomus

sp.)

Common carp 

(Cyprinus

carpio)

Chiselmouth 

(Acrocheilus 

alutaceus)

Longnose 

dace 

(Rhinichthys 

cataractae)

Origin N N N N I N N

Tolerance T T I T T I I

Temperature preference Cool Cool Cool Cool Warm Cool Cool

Adult trophic guild herb omni herb herb/omni omni herb inv

Site location

Downstream Barber Dam Jan. 1988 – – – 10.0 – – –

Downstream Barber Dam Dec. 1996 – – – – – 0.4 –

Downstream Barber Dam Nov. 2003 0.4 0.5 – – – – –

Upstream Lander WTF Jan. 1988 – – – 9.1 – .1 –

Upstream Lander WTF Mar. 1992 – – – 16.3 – – –

Upstream Lander WTF Mar. 1995 3.9 6.9 1.1 – – – 9.7

Upstream Lander WTF Dec. 1996 5.7 9.4 – – 0.1 – 4.0

Upstream Lander WTF Nov. 2003 1.4 5.1 – – – – –

Downstream Lander WTF Jan. 1988 – – – 28.1 1.1 .1 –

Downstream Lander WTF Mar. 1992 – – – 79.0 .9 – –

Downstream Lander WTF Feb. 1995 9.4 42.9 .5 – – – 5.2

Downstream Lander WTF Dec. 1996 12.2 34.6 .8 – – .4 10.6

Downstream Lander WTF Dec. 2001 5.0 10.2 .6 – – – 5.2

Downstream Lander WTF Nov. 2003 5.3 17.7 – 1.1 – – .7

Downstream Lander WTF Aug. 2004 3.0 39.1 – – – – 10.1

Upstream West Boise WTF Jan. 1988 – – – 30.6 – .7 –

Upstream West Boise WTF Mar. 1992 – – – 52.6 – – –

Upstream West Boise WTF Mar. 1995 3.3 13.3 – – – – .4

Upstream West Boise WTF Dec. 1996 5.8 13.3 .3 – – – .9

Upstream West Boise WTF Nov. 2003 1.1 5.8 – 1.1 – – 1.3

Downstream West Boise WTF Jan. 1988 – – – 37.3 – – –

Downstream West Boise WTF Mar. 1992 – – – 57.4 – 2.7 –

Downstream West Boise WTF Mar. 1995 .3 19.4 2.9 – – .6 10.9

Downstream West Boise WTF Dec. 1996 2.1 8.8 – – – 1.5

Downstream West Boise WTF Nov. 2003 1.4 12.1 – – – – –

North channel Eagle Island Jan. 1988 – – – 76.5 – 1.6 –

Middleton Dec. 1996 2.8 17.9 1.9 – 7.5 .5 7.8

Middleton Aug. 1997 10.2 12.3 – – .3 37.2 14.9

Above Star Road Jan. 1988 – – – 14.5 – 17.5 –

Caldwell Aug. 1997 8.9 16.7 – – 2.5 9.9 –

Near mouth Dec. 1996 48.8 26.4 – – 2.5 – 10.7

Near mouth Aug. 1997 31.2 33.5 – – 3.2 6.3 –

Appendix A  33
Appendix A. Relative percentage of abundance of fish species in the lower Boise River, Idaho.—Continued

[Origin: I, introduced; N, native. Tolerance: I, intermediate; S, sensitive; T, tolerant. Adult trophic guild: Classification of species from Zaroban and others, 

1999; inv., invertivore, pisc, piscivore; omni, omnivore; herb, herbivore. Abbreviations: IFG, Idaho Fish and Game; USGS, U.S. Geological Survey; WTF, 

wastewater treatment facility; –, no species found]

Date

Species

Umatilla 

dace 

(Rhinichthys 

umatilla1)

Dace 

(Rhinichthys

sp.)

Northern 

pikeminnow 

(Ptychocheilus 

oregonensis)

Redside shiner 

(Richardsonius 

balteatus)

Tui chub 

(Gila 

bicolor)

Pumpkinseed 

(Lepomis 

gibbosus)

Bluegil 

(Leponis 

macrochirus)

Origin N N N N N I I

Tolerance I I T I T T T 

Temperature preference Cool Cool Cool Cool Warm Warm Warm

Adult trophic guild inv inv inv/pisc inv omni inv/pisc inv/pisc

Site location

Downstream Barber Dam Jan. 1988 – – – 0.7 – – –

Downstream Barber Dam Dec. 1996 1.3 – – .0 – – –

Downstream Barber Dam Nov. 2003 1.1 – 0.5 .8 – – –

Upstream Lander WTF Jan. 1988 – – .1 74.2 – – –

Upstream Lander WTF Mar. 1992 1.6 – – 10.5 – – –

Upstream Lander WTF Mar. 1995 17.5 – .2 1.4 – – –

Upstream Lander WTF Dec. 1996 5.6 – .9 – – – –

Upstream Lander WTF Nov. 2003 1.4 – .6 .6 – – –

Downstream Lander WTF Jan. 1988 – – 1.1 58.7 – – 4.8

Downstream Lander WTF Mar. 1992 – – .3 – – – –

Downstream Lander WTF Feb. 1995 15.6 – – .8 – – –

Downstream Lander WTF Dec. 1996 2.8 – .8 6.5 – – –

Downstream Lander WTF Dec. 2001 1.4 – – – – – –

Downstream Lander WTF Nov. 2003 4.3 – 1.8 – – – –

Downstream Lander WTF Aug. 2004 4.7 – 1.8 16.0 – – –

Upstream West Boise WTF Jan. 1988 – 1.4 – – – – –

Upstream West Boise WTF Mar. 1992 – – – 3.9 – – –

Upstream West Boise WTF Mar. 1995 .0 – .1 – – – –

Upstream West Boise WTF Dec. 1996 1.7 – – .3 – – –

Upstream West Boise WTF Nov. 2003 – – – – – – –

Downstream West Boise WTF Jan. 1988 – 1.2 1.1 21.7 – – –

Downstream West Boise WTF Mar. 1992 – 1.5 3.8 28.3 – – –

Downstream West Boise WTF Mar. 1995 13.5 – .3 7.0 – – –

Downstream West Boise WTF Dec. 1996 2.9 – .6 2.6 – – –

Downstream West Boise WTF Nov. 2003 – – 1.4 – – – –

North channel Eagle Island Jan. 1988 – 3.2 2.3 14.5 – – –

Middleton Dec. 1996 35.3 – – – – – –

Middleton Aug. 1997 6.3 8.8 6.8 .1

Above Star Road Jan. 1988 – 4.6 5.1 51.1 – – –

Caldwell Aug. 1997 .8 – – – – – –

Near mouth Dec. 1996 .8 – – – – – –

Near mouth Aug. 1997 – – 5.9 – 10.9 0.5 –

34 Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Appendix A. Relative percentage of abundance of fish species in the lower Boise River, Idaho.—Continued

[Origin: I, introduced; N, native. Tolerance: I, intermediate; S, sensitive; T, tolerant. Adult trophic guild: Classification of species from Zaroban and others, 

1999; inv., invertivore, pisc, piscivore; omni, omnivore; herb, herbivore. Abbreviations: IFG, Idaho Fish and Game; USGS, U.S. Geological Survey; WTF, 

wastewater treatment facility; –, no species found]

Date

Species

Total 

abundance

Largemouth 

bass 

(Micropterus 

salmoides)

Smallmouth 

bass 

(Micropterus 

dolomieui)

Channel 

catfish 

(Ictalurus 

punctatus)

Tadpole 

madtom 

(Noturus 

gyrinus)

Oriental 

weatherfish 

(Misgurnus 

anguillicaudatus)

Origin I I I I I

Tolerance T I T T T 

Temperature preference Warm Cool Warm Warm Warm

Adult trophic guild pisc pisc inv/pisc inv/pisc omni

Site location

Downstream Barber Dam Jan. 1988 – – – – – 150

Downstream Barber Dam Dec. 1996 – – – – – 236

Downstream Barber Dam Nov. 2003 – – – – – 826

Upstream Lander WTF Jan. 1988 – – – – – 702

Upstream Lander WTF Mar. 1992 – – – – – 190

Upstream Lander WTF Mar. 1995 – – – – – 565

Upstream Lander WTF Dec. 1996 – – – – – 806

Upstream Lander WTF Nov. 2003 – – – – – 514

Downstream Lander WTF Jan. 1988 – – – – – 2,929

Downstream Lander WTF Mar. 1992 – – – – – 647

Downstream Lander WTF Feb. 1995 – – – – – 385

Downstream Lander WTF Dec. 1996 – – – – – 246

Downstream Lander WTF Dec. 2001 0.8 – – – – 363

Downstream Lander WTF Nov. 2003 .4 – – – – 282

Downstream Lander WTF Aug. 2004 – – – – 0.6 169

Upstream West Boise WTF Jan. 1988 – – – – – 294

Upstream West Boise WTF Mar. 1992 – – – – – 152

Upstream West Boise WTF Mar. 1995 – – – – – 842

Upstream West Boise WTF Dec. 1996 8.1 – – – – 347

Upstream West Boise WTF Nov. 2003 .3 – – – – 378

Downstream West Boise WTF Jan. 1988 .1 – – – – 748

Downstream West Boise WTF Mar. 1992 .6 – – – – 714

Downstream West Boise WTF Mar. 1995 – – – – – 341

Downstream West Boise WTF Dec. 1996 – 0.3 – – – 341

Downstream West Boise WTF Nov. 2003 1.0 – – – – 290

North channel Eagle Island Jan. 1988 – – – – – 442

Middleton Dec. 1996 .2 – – – – 425

Middleton Aug. 1997 .9 .1 0.1 .1 974

Above Star Road Jan. 1988 – – – – – 607

Caldwell Aug. 1997 – – 0.5 – – 203

Near mouth Dec. 1996 2.5 – – – – 121

Near mouth Aug. 1997 .9 4.1 1.8 – – 221

1Rhinichthys umatilla is not classified in Zaroban and other (1999), classified in Wydoski and Whitney (2003).

Appendix A  35
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36  Fish Communities and Related Environmental Conditions of the Lower Boise River, Idaho, 1974-2004
Manuscript approved for publication, May 14, 2006

Prepared by the U.S. Geological Survey Publishing Network, 

Publishing Service Center, Tacoma, Washington

Bill Gibbs 

Donita Parker

Linda Rogers

Sharon Wahlstrom

For more information concerning the research in this report, contact 

Director, Idaho Water Science Center

U.S. Geological Survey

230 Collins Road

Boise, Idaho 83702

http://id.water.usgs.gov
SIR 2006–5111 MacCoy

Fish Communities and Related Environmental Conditions of the 

Lower Boise River, Southwestern Idaho, 1974-2004