Water-Resources Investigations Report 03–4274

Prepared in cooperation with

Idaho Department of Environmental Quality

U.S. Department of the Interior

U.S. Geological Survey

Assessment of Fish Assemblages and Minimum

Sampling Effort Required to Determine Biotic

Integrity of Large Rivers in Southern Idaho, 2002
Cover: U.S. Geological Survey employees electrofishing in the Salmon River near Challis, Idaho (photo by 

William H. Clark, Idaho Department of Environmental Quality)
Assessment of Fish Assemblages 

and Minimum Sampling Effort 

Required to Determine Biotic 

Integrity of Large Rivers in 

Southern Idaho, 2002

By Terry R. Maret and Douglas S. Ott

Prepared in cooperation with 

Idaho Department of Environmental Quality

Water-Resources Investigations Report 03–4274

U.S. Department of the Interior

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

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

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

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

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

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

endorsement by the U.S. Government.

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

reproduce any copyrighted materials contained within this report.

Maret, T.R., and Ott, D.S., 2004, Assessment of Fish Assemblages and Minimum Sampling Effort Required to 

Determine Biotic Integrity of Large Rivers in Southern Idaho, 2002: U.S. Geological Survey Water-Resources 

Investigations Report 03 –4274, 16 p.
Contents iii

Contents

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

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

Purpose and scope. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

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

Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Site selection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Fish collection and processing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Analytical methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Results of fish assemblages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Fish metrics and index scores . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Sampling effort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Sampling variability . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Minimum sampling effort. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Summary and conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

References cited. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Figures

1. Map showing location of study area, Environmental Monitoring and Assessment 

Program (EMAP) sampling sites, and bioregions in southern Idaho, 2002 . . . . . . . . . . . 4

2. Number of subreaches in relation to percent cumulative fish species collected 

over a sampling distance of 40 channel widths in 14 river reaches in southern 

Idaho, 2002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

3. Number of subreaches in relation to number of fish species collected over a 

sampling distance of 100 channel widths in the Snake River at Heise and near 

Marsing, and in the Payette River near Emmett, southern Idaho, 2002 . . . . . . . . . . . . . . 11 

4. Number of fish in relation to percent cumulative species collected over a 

sampling distance of 40 channel widths in 14 river reaches in southern Idaho, 

2002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

5. Mean number of fish collected over a sampling distance equal to 40 channel 

widths in 10 equidistant subreaches in 14 river reaches in southern Idaho, 2002 . . . . . 12

6. Cumulative Index of Biotic Integrity scores over a sampling distance equal to 

100 channel widths in 10 equidistant subreaches in the Snake River at Heise and 

near Marsing, and in the Payette River near Emmett, southern Idaho, 2002 . . . . . . . . . 13
iv Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002

Tables

1. Basin and site characteristics for all sites sampled for the Environmental Monitoring 

and Assessment Program, southern Idaho, 2002. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2. Fish species collected at all sites sampled for the Environmental Monitoring and 

Assessment Program, southern Idaho, 2002. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

3. Fish metrics and final Index of Biotic Integrity (IBI) scores, number of fish collected, 

total number of species, number of native species, and Zoogeographic Integrity

Coefficient (ZIC) index values for all sites sampled for the Environmental Monitoring 

and Assessment Program, southern Idaho, 2002. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

4. Index of Biotic Integrity (IBI) scores and number of fish species and individuals 

collected at three sites in a reach length of 100 times the channel width sampled for 

the Environmental Monitoring and Assessment Program, southern Idaho, 2002. . . . . . 13

Conversion Factors and Datum

Multiply By To obtain

centimeter (cm)

kilometer (km)

meter (m)

millimeter (mm)

To convert 

 

°C (degrees Celsius) to 

 

°F (degrees Fahrenheit), use the following equation:

°F=(1.8°C) + (32)

Sea level: In this report, “sea level” refers to the National Geodetic Vertical Datum of 1929—a 

geodetic datum derived from a general adjustment of the first-order level nets of the United 

States and Canada, formerly called Sea Level Datum of 1929. 

0.3937

0.6214

3.281

0.03937

inch (in.)

mile (mi)

foot (ft)

inch (in.)
Assessment of Fish Assemblages and 

Minimum Sampling Effort Required to 

Determine Biotic Integrity of Large Rivers 

in Southern Idaho, 2002

By Terry R. Maret and Douglas S. Ott

Abstract

Abstract. 

A critical issue surrounding biomonitoring in large rivers 

(fifth- through seventh-order) is the minimum sampling-reach 

distance required to collect an adequate number of fish to represent the fish assemblage within a reach. Excessive sampling 

effort (excessive reach length) is costly in terms of work 

hours, reduces the number of sites that can be visited, can 

compromise field-crew safety, can be logistically unfeasible, 

and can cause unnecessary injury to captured fish. On the 

other hand, inadequate sampling effort can produce considerable variability in multiple samples collected at a site and may 

underrepresent the species or river condition present.

During the summer of 2002, the U.S. Geological Survey, 

in cooperation with the Idaho Department of Environmental 

Quality, determined the minimum sampling effort required to 

characterize fish assemblages at 17 large-river sites in southern Idaho. The study was done as part of the U.S. Environmental Protection Agency’s Environmental Monitoring and 

Assessment Program. Electrofishing methods and multiple 

gear types were used to collect sample populations of fish in 

river reach lengths representing 40 and 100 times the wetted 

channel width. Minimum sampling effort was assessed by 

comparing the relation between reach length and the number 

of species collected, total individuals collected, and final 

Index of Biotic Integrity (IBI) scores.

Thirty-two species of fish in the families Catostomidae, 

Centrarchidae, Cottidae, Cyprinidae, Ictaluridae, Percidae, 

and Salmonidae were collected. Of these, 12 alien species 

were collected, representing about 38 percent of all species 

collected during the study.

A reach length of 30 to 40 times the wetted channel 

width was determined to be sufficient for collecting an adequate number of fish to estimate species richness and evaluate 

biotic integrity. At most sites, about 250 fish were needed to 

effectively represent 95 percent of the species present. Fiftythree percent of the sites assessed, using an IBI developed specifically for large Idaho rivers, received scores of less than 50, 

indicating poor biotic integrity.

Introduction

Introduction. 

Large rivers are the least ecologically understood and 

most poorly studied of any inland water resource and are perhaps the most affected by human activity (Dynesius and Nilsson, 1994; Simon and Sanders, 1999). Large-river investigations have been hampered by sampling difficulty and the lack 

of operational theoretical models related to conservation of 

biological resources (Reash, 1999; Galat and Zweimuller, 

2001). The development of North America’s rivers has supported many important human uses and needs, including navigation, flood control, hydropower, irrigation, waste disposal, 

and recreation. However, these uses have not come without a 

cost, especially in the depletion of native aquatic biodiversity 

and subsequent decline in native fish.

The primary causes for declines or extinctions of native 

fish include habitat alteration, pollution, hybridization, introduced species, and overharvest (Li and others, 1987; Miller 

and others, 1989). Many endemic fish species of the Western 

United States are endangered, threatened, or of special concern as a result of these human activities (Warren and Burr, 

1994).

There are few published studies on large-river fish 

assemblages in Idaho. The fishery studies completed on the 

Snake River and its major tributaries are primarily agency 

reports assessing sportfishery populations (Maret, 1995). 

Idaho Power Company relicensing efforts have resulted in the 

compilation of anecdotal historical and recent data on fish species occurrences on the Snake River and its tributaries downstream from Shoshone Falls (Chandler and Radko, 2001). The 

U.S. Geological Survey (USGS) has provided recent (1993–
2 Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002

2003) fishery data collected from a number of large rivers in 

Idaho as part of the National Water-Quality Assessment 

(NAWQA) Program and Statewide Surface-Water-Quality 

Trend Network to evaluate the status and trends of fish 

assemblages (data accessed at http://idaho.usgs.gov/

projects/fish/index.html).

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,” more emphasis is being placed on 

development of biocriteria in State water-quality standards. 

Increasingly, biological monitoring programs and biocriteria 

development have expanded to include large rivers. The western U.S. Environmental Protection Agency (USEPA) Environmental Monitoring and Assessment Program (EMAP) recently 

has focused on evaluating ecological conditions of nonwadeable rivers; river conditions will be evaluated on the basis of a 

random site-selection design (Peck and others, 2002). The 

Index of Biotic Integrity (IBI) is used by many Federal and 

State agencies to assess fish assemblage structure and function 

because it serves as an indicator of historical and current conditions of a stream system (Karr, 1991). The Idaho Department of Environmental Quality (IDEQ) recently published 

monitoring protocols and an IBI that uses aquatic organisms 

and habitat measures to evaluate large rivers in Idaho (Grafe, 

2002; Mebane and others, 2003). Zaroban and others (1999) 

classified Northwest fish species according to various 

attributes (for example, pollution sensitivity, temperature tolerance, feeding and habitat groups) to facilitate evaluation of 

surface-water resource conditions.

Regulatory agencies responsible for monitoring large 

numbers of waterbodies need consistent and cost-effective 

sampling methods for accurately and precisely measuring 

biotic integrity. A critical issue surrounding river biomonitoring is the minimum sampling-reach length required to adequately represent the fish assemblage. Because collection 

methods and sampling effort vary widely among national and 

State assessment programs (Flotemersch and Cormier, 2001), 

and because few studies have quantitatively evaluated the 

optimum electrofishing distance for large-river fisheries, no 

standard reach length currently is generally accepted. The 

NAWQA Program prescribes a sampling distance of 500 to 

1,000 m for large rivers and the use of multiple gear (such as 

boat and backpack electrofishing) to more effectively sample 

different habitats within a representative reach (Meador and 

others, 1993). Hughes and others (2002) determined that a 

sampling distance of 85 to 100 times the average wetted channel width would be necessary to collect a sample population 

representing 95 percent of the fish species present in Oregon 

raftable rivers that were 10 to 150 m wide. However, their 

assessment did not evaluate the collection effort and the 

resulting IBI scores that are needed to determine aquatic life 

use support. On the basis of the Oregon study findings, the 

western USEPA EMAP protocols require a sampling reach 

length of 100 times the wetted channel width (100X) and use 

of boat electrofishing gear for large Western rivers (Peck and 

others, 2002). Given this requirement, sampling reaches can 

be longer than 10 km, which could compromise the safety of 

the field crew, owing to an overextended workday. Also, 

because the sampling locations are chosen at random, these 

long reaches may not be logistically feasible to sample 

because of difficult access. In addition, electrofishing such 

long reach lengths could cause unnecessary injury to captured 

fish, especially to sensitive or federally listed species such as 

bull trout (Salvelinus confluentus) and chinook salmon (Oncorhynchus tshawytscha).

Geomorphology would be the primary determinant of 

sampling reach length and the associated instream habitats 

consisting of geomorphic channel units (for example, riffles, 

pools, and runs). Inclusion of at least one meander wavelength, based on 20X the wetted channel width (Leopold and 

others, 1964) in a sampling reach is necessary to ensure that 

representative habitats are sampled. These criteria are recommended for determining the length of sampling reach needed 

to represent fish assemblages (Lyons, 1992). In addition, the 

USEPA Rapid Bioassessment Protocols recommend sampling 

all habitats within a distance of 40X of boatable waters (Flotemersch and Cormier, 2001).

Hughes and others (2002) gave a number of reasons why 

sampling reaches consisting of 20 to 40X may not be adequate 

to effectively represent fish assemblages in large Western rivers. One of the reasons is that efficient collections in Western 

rivers may be compromised by swift water, more mobile fish, 

and hazardous obstructions. Evaluating the effects of electrofishing sampling effort is important to study design, development of site-scale sampling protocols, and quantification of 

ecological changes and patterns over time (Cao and others, 

2002; Meador and others, 2003). Sampling distances that 

equal or exceed the threshold at which a desired attribute 

(such as species richness) becomes asymptotic are more likely 

to produce similar results than would additional sampling, 

which would yield comparatively little new information 

(Lyons, 1992). Excessive sampling effort is costly in terms of 

work hours and reduces the number of sites that can be visited, whereas inadequate sampling effort can produce considerable variability in multiple samples collected at a site and 

may underrepresent the species or river condition present.

Purpose and Scope

This report characterizes fish assemblages collected for 

the USEPA’s EMAP in southern Idaho and identifies the minimum sampling effort (minimum reach length) required to collect a sample population of fish representing the greatest percentage of species within a reach. The data were collected at 

17 sites in large (fifth- through seventh-order) rivers during 

the summer (July 25 through October 2) of 2002. Fish assemblages were characterized using various metrics that have 

proven beneficial for evaluating water-quality conditions in 

Idaho rivers. Minimum sampling effort was assessed by comparing the relation between reach length and the number of 

species collected, total individuals collected, and final IBI 
Methods 3

scores. This assessment will provide IDEQ with information 

on the status of the fisheries in southern Idaho and the level of 

effort necessary to provide fish assemblage data adequate to 

evaluate the biotic integrity of Idaho’s large rivers.

Description of Study Area

The study area (fig. 1) comprises the main-stem Snake 

River and its major tributaries and the main-stem Salmon and 

Bear Rivers in southern Idaho. The study area is located primarily in the Snake River Basin/High Desert and Northern 

Basin and Range Ecoregions (Omernik and Gallant, 1986). 

The IDEQ has classified this area of Idaho as part of the 

Basins Bioregion on the basis of similarities in aquatic species 

and landscape features (Grafe, 2002).

Climate in most of the study area is semiarid and annual 

precipitation ranges from 25 to 50 cm. Precipitation occurs 

primarily as snow, and peak flows generally result from spring 

snowmelt.

Range and forest land are the predominant land uses, and 

more than 60 percent of the land is federally owned. Populated 

areas and agricultural lands are located primarily adjacent to 

main-stem rivers and major tributaries to access water for irrigation and domestic supply purposes. Migrating fish face 

many obstacles along the Snake River. Shoshone Falls near 

Twin Falls, Idaho, is higher than Niagara Falls (more than 65 

m high) and is a natural barrier to upstream movement of fish 

(fig. 1). Flow in the Snake River is highly regulated by dams 

and diversions. Eighteen large dams currently regulate the 

Snake River in the study area. 

Most rivers in Idaho are presumed or explicitly designated to support coldwater biota (Grafe, 2002). Rivers in predominantly range and forest land basins of southern Idaho are 

typified by coarse substrate (gravel and cobbles), a variety of 

low- to high-gradient (0.01–1.0 percent) habitats, and generally sparse macrophyte growth. Rivers in agricultural basins 

are typified by more fine-grained substrate, low-gradient habitats, and abundant macrophyte growth. Wetted channel widths 

ranged from about 8 to 193 m at all sampling sites, excluding 

site 8, which was almost dry at the time of sampling (table 1). 

Sampling site elevation above sea level ranged from 670 to 

1,850 m. Because of drought conditions, southern Idaho river 

flows were about 60 to 80 percent of the long-term average 

during the sampling period (Brennan and others, 2003).

Acknowledgments

Numerous individuals from the USGS assisted in collecting and processing data during the course of this study: 

Ross G. Dickinson, Jon E. Hortness, Dorene E. MacCoy, 

Michael A. Nolevanko, Robert E. Reaves, and Kenneth D. 

Skinner. Sean Woodhead of IDEQ assisted with fish sampling 

at the Rock Creek site. Colleague reviews by William H. 

Clark, Cyndi S. Grafe, Dorene E. MacCoy, Michael R. Meador, and Christopher A. Mebane improved the quality of the 

manuscript. Special thanks are extended to Donald W. Zaroban for assisting with the identification and vouchering of 

fish specimens and to Robert E. Hughes and Philip R. Kaufman for their help in training field crews in sampling methods. 

Funding for this work was provided by the USGS and the 

IDEQ. 

Methods

Methods. 

Site Selection

Sites selected for sampling were provided by the IDEQ. 

Site selection was based on a random selection process of 

Idaho rivers in the Basins Bioregion of southern Idaho that 

were equal to or greater than fifth order on 1:100,000-scale 

hydrographic maps (C.S. Grafe, Idaho Department of Environmental Quality, written commun., 2002). About 50 candidate sites representing a diverse set of river sizes and physical 

and chemical habitats were selected. About 10 sites were eliminated immediately from this list for reasons related primarily 

to safety and access. The Snake River at Heise (site 1) was 

hand selected (HSSD) to represent a main-stem Snake River 

reference site that was not in the original random list provided. 

Field reconnaissance of the remaining 40 sites by USGS and 

IDEQ resulted in 17 sites (fig. 1 and table 1) selected for sampling that met the criteria given by Grafe (2002) and Peck and 

others (2002). Other biological and habitat data were collected 

concurrently by IDEQ at all sites but are not summarized in 

this report.

Fish Collection and Processing

Fish were collected at 17 large-river sites during lowflow conditions (July 25 through October 2) in 2002 following 

USEPA EMAP protocols (Peck and others, 2002, table 1). All 

collections and identifications were made by USGS personnel 

using a team of scientists familiar with fish species of Idaho. 

All personnel involved with fish sampling were trained in 

electrofishing techniques and EMAP sampling protocols. 

Fourteen reaches that included one duplicate reach (total of 13 

sites) were electrofished over a reach length representing 40X 

(Peck and others, 2001). Three sites were electrofished at a 

reach length representing 100X to evaluate information gained 

by additional sampling effort (Peck and others, 2002): Snake 

River at Heise, Snake River near Marsing, and Payette River 

near Emmett. The Big Lost River above Mackay Reservoir 

(site 8) was intermittent, resulting in an assessed reach length 

of about 15 m. For this reason, this site was not included in 

any of the final data assessments. All reaches sampled were 

divided into 10 continuous subreaches of equal length (noted 

as A through J). The data for each subreach were recorded 

separately to calculate statistical relations between sampling 
4 Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002

0 40

0

80 MILES

40 80 KILOMETERS

Base from U.S. Geological Survey digital data; 1972; 1:2,000,000,

Transverse Mercator projection; Factor at central meridian: 0.99960;

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

Bioregions modified from U.S. Environmental Protection Agency

digital data; Region 10 Ecoregions; 1991; 1:2,000,000

Salmon River

Weiser

River

Payette

River

Snake

River

Snake

River

Owyhee

River

Bruneau

River

West

Fork

Big

River

Lost

American

Falls

Reservoir

Snake

River

Bear

River

Blackfoot

River PortneufRiver

Bear

Lake

Jackson

Lake

Owyhee

Reservoir

Brownlee

Reservoir

Salmon

River

1

2

3

4 5

6

8

16

7

9

10 13

15

14

12

11

17

Shoshone Falls

118° 116° 114° 112° 110°

46°

44°

42°

EXPLANATION

West Fork Bruneau River

 near Grasmere

Snake River near Walters

 Ferry

Snake River near Marsing

Owyhee River below Red

 Canyon

Payette River near Emmett

Weiser River near Weiser

Salmon River near Challis

Salmon River near Salmon

10

11

12

13

14

15

16

17

Snake River at Heise

Snake River near Shelley

Blackfoot River near Blackfoot

Bear River below Alexander

 Reservoir

Portneuf River near Topaz

Portneuf River near Pocatello

Rock Creek at Twin Falls

Big Lost River above Mackay

 Reservoir

Snake River at Hagerman

1

2

3

4

5

6

7

8

9

 Bioregions

 Basins

 Central and south mountains

 Northern mountains

 EMAP sampling sites

WASHINGTON

UTAH

WYOMING

MONTANA

IDAHO

NEVADA

OREGON

Columbia

River

Salmon

River

Snake

River

Figure 1. Location of study area, Environmental Monitoring and Assessment Program (EMAP) sampling sites, and bioregions in

southern Idaho, 2002.
Table 1. Basin and site characteristics for all sites sampled for the Environmental Monitoring and Assessment Program (EMAP), southern Idaho, 2002[Site locations shown in figure 1; no., number; ID, identification; m, meters; HSSD, hand selected]

1Reach sampled at 100 times the wetted channel width. 3 Channel composed of intermittent pools.2Spatial duplicate. 4Temporal duplicate.

Site no. Site name

EMAP

site ID Latitude Longitude

Stream 

order

Elevation

(m above 

sea level)

Average 

wetted 

channel 

width 

(m)

Reach 

length 

(m)

E

fi

ge

11 Snake River at Heise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . HSSD 43°35'48" 111°36'59" 6 1,530 110 11,000 raft 

2 Snake River near Shelley. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 43°22'10" 112°10'02" 6 1,400 130 5,200 raft 3 Blackfoot River near Blackfoot. . . . . . . . . . . . . . . . . . . . . . . . . . 9 43°10'04" 112°19'34" 6 1,350 18 720 raft 4 Bear River below Alexander Reservoir near Soda Springs . . . . . 37 42°38'45" 111°41'56" 5 1,720 40 1,600 raft 

5 Portneuf River near Topaz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 42°37'25" 112°06'37" 5 1,500 15 600 raft 

6 Portneuf River near Pocatello . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 42°48'24" 112°22'47" 5 1,350 12 480 raft 7 Rock Creek at Twin Falls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 42°33'19" 114°28'51" 5 1,100 8 320 tote 

27 Rock Creek at Twin Falls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 42°33'36" 114°29'37" 5 1,100 8 320 tote 38 Big Lost River above Mackay Reservoir near Mackay. . . . . . . . 17 44°00'36" 113°47'11" 5 1,850 3 15 bac

9 Snake River at Hagerman . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 42°42'35" 114°50'24" 7 880 193 7,700 jet 

10 West Fork Bruneau River near Grasmere . . . . . . . . . . . . . . . . . . 77 42°20'02" 115°38'52" 5 1,140 14 560 bac11 Snake River near Walters Ferry . . . . . . . . . . . . . . . . . . . . . . . . . . 115 43°19'49" 116°35'40" 7 700 130 5,200 jet 

112 Snake River near Marsing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 43°28'27" 116°46'30" 7 680 150 15,000 jet 

1, 412 Snake River near Marsing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 43°28'27" 116°46'30" 7 680 150 15,000 jet 

13 Owyhee River below Red Canyon. . . . . . . . . . . . . . . . . . . . . . . . 32 42°16'37" 116°50'29" 5 1,340 22 880 bac

114 Payette River near Emmett . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 43°52'34" 116°31'08" 6 720 60 6,000 raft 

15 Weiser River near Weiser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 44°14'54" 116°57'31" 6 670 25 1,000 raft 16 Salmon River near Challis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 44°36'00" 114°11'10" 6 1,490 40 1,600 raft 17 Salmon River near Salmon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 45°09'35" 113°54'48" 6 1,190 50 2,000 raft 
6 Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002

effort and species collection. A Global Positioning System 

and laser range finder were used to determine sampling locations. All sampling was limited to 1 day per site, which 

included both travel and collection time. Total collection time 

in the field to sample reach lengths of 30 to 40X was about 3 

to 6 hours and, to sample reach lengths of 100X, was about 10 

to 14 hours.

The selection of electrofishing methods depended primarily on river access and size (width and depth of channel). 

Electrofishing was concentrated near the riverbanks. Where 

possible, after two consecutive subreaches were sampled, collections were alternated to the opposite bank. This ensured 

that habitats from both banks were sampled throughout the 

reach. Collection methods attempted to capture all fish species 

from habitats at each sampling site.

Because of the wide variety of field conditions encountered, four electrofishing gear types were used for a single 

pass through a reach (see table 1 for gear type used for each 

site). These included backpack (3 sites), tote barge (1 site), 

raft (10 sites), and jet boat (3 sites). Backpack and tote barge 

collections were made in an upstream direction to most effectively capture fish encountered. The backpack unit (SmithRoot model 12) and the tote barge (Smith-Root model VI-A, 

direct current (DC) pulsator and 5,000-watt, 240-volt generator) both were operated with one anode and one netter. The 

raft and jet boat also were equipped with a Smith-Root model 

VI-A, DC pulsator and a 5,000-watt, 240-volt generator with 

one or two bow-mounted anode electrodes made of a circular 

array of 6.5-mm steel cable extending in front of the bow. The 

jet boat hull served as the cathode, and an array of aluminum 

conduit composed the port and starboard cathode droppers on 

the raft. Fish collections from the raft and jet boat were made 

while the vessel floated in a downstream direction and one 

netter was positioned in the bow of the boat. When large numbers of easily identifiable fish, for example, common carp 

(Cyprinus carpio) and largescale suckers (Catostomus macrocheilus), were too numerous to net while boat electrofishing, 

they were tallied visually. The motorized jet boat was particularly useful at low-gradient sites where wind inhibited floating 

in a downstream direction. There was no effort to concentrate 

extra sampling effort at specific habitat types while floating 

(riffles, pools, woody snags, etc.). Electrofishing DC usually 

varied between 30 and 60 pulses per second and 400 to 1,000 

volts, depending on conductivity of the water. Electrofishing 

time ranged from 0.3 to 1.8 hours for sites sampled at 40X, 

except site 8, which consisted of a few intermittent pools. 

Electrofishing time for the three sites sampled at 100X ranged 

from 1.3 to 3.8 hours.

Captured fish were placed in an aerated livewell and processed immediately after sampling each subreach to reduce 

stress to the fish. When necessary, fish were anesthetized with 

a dilute solution of clove oil and ethanol. All fish were identified to species, counted, and measured (minimum and maximum total length). The presence of external anomalies (deformities, eroded fins, lesions, and tumors) also was recorded. 

Specimens of selected species were retained for reference and 

verification of field identifications. Species too large for collection jars were photographed before being returned to 

the river. A voucher collection from these samples is located 

in the Orma J. Smith Museum of Natural History, Albertson 

College, Caldwell, Idaho. Prior to sampling, an Idaho Department of Fish and Game scientific collection permit, number 

F–18–87, was obtained by William H. Clark of IDEQ. 

Donald W. Zaroban, fish curator for the Orma J. Smith 

Museum of Natural History, provided taxonomic confirmation 

for selected specimens. For calculation of the IBI, rainbow 

trout (Oncorhynchus mykiss) were considered alien upstream 

from Shoshone Falls, which historically limited their 

upstream distribution in the Columbia and Snake River system 

(Behnke, 1992). Where distinguishable, hatchery fish were 

excluded from IBI calculations (Mebane and others, 2003).

Two sites were selected for duplicate sampling to evaluate spatial and temporal variability in collection methods. At 

Rock Creek at Twin Falls (site 7), fish were collected during 

the same week on different reaches of equal length that were 

about 2 km apart. At the Snake River near Marsing (site 12), 

fish were collected on the same reach at the beginning and end 

of the sampling period.

Analytical Methods

Fish assemblages were analyzed using abundances of 

individuals and species and an IBI developed by Mebane and 

others (2003). Geographic origin (native or alien), tolerance to 

pollution, and temperature preferences were assigned to each 

species (table 2) following guidelines outlined by Zaroban and 

others (1999). General tolerances and temperature preferences 

were gleaned from reference literature and from the authors’ 

experience in observing how species distributions and abundances changed with increased temperatures, turbidity, sedimentation, and nutrient concentrations.

The IBI developed specifically for evaluating conditions 

of large rivers in the Pacific Northwest (table 3) consists of 10 

metrics: number of coldwater native species, number of cottid 

age classes, percent sensitive native individuals, percent coldwater individuals, percent tolerant individuals, number of 

alien species, percent common carp individuals, number of 

salmonid age classes, catch per unit effort (fish captured per 

minute of electrofishing), and percent selected anomalies 

(deformities, eroded fins, lesions, and tumors). Because only 

minimum and maximum lengths are required for EMAP, number of cottid and salmonid age classes could not be determined accurately; therefore, these two metrics were not used. 

However, as suggested by Mebane and others (2003), percent 

sculpins can be substituted for number of cottid age classes in 

the IBI calculations. These nine metrics were standardized by 

scoring them continuously from 0 to 1, then weighted as necessary to produce an IBI score ranging from 0 to 100. According to Mebane and others (2003), sites with IBI scores 

between 75 and 100 exhibit high biotic integrity and minimal 

disturbance and support an abundant and diverse assemblage 
Methods 7

Table 2. Fish species collected at all sites sampled for the Environmental Monitoring and Assessment Program, southern Idaho, 2002

[Assignment of geographic origin, tolerance to pollution, and temperature preference of fish were taken from Zaroban and others (1999); 

sites of occurrence shown in figure 1 and described in table 1]

Family

Common name Species Origin1

Tolerance 

to 

pollution2 Temperature

preference Sites of occurrence 

Catostomidae

bluehead sucker Catostomus discobolus N I cool 2, 6

bridgelip sucker3 Catostomus columbianus N T cool 7, 10, 11, 12, 14, 15, 16, 17

largescale sucker3 Catostomus macrocheilus N T cool

7, 9, 10, 11, 12, 13, 14, 15, 16, 

17

mountain sucker Catostomus platyrhynchus N I cool 5, 10, 14, 17

Utah sucker Catostomus ardens N T cool 1, 2, 3, 4, 6

Centrarchidae

black crappie Pomoxis nigromaculatus A T warm 12, 15

bluegill Lepomis macrochirus AT warm 15

largemouth bass Micropterus salmoides AT warm 15

pumpkinseed Lepomis gibbosus A T cool 15

smallmouth bass Micropterus dolomieui A I cool 11, 12, 13, 14, 15

white crappie Pomoxis annularis AT warm 15

Cottidae

mottled sculpin Cottus bairdi N I cold 1, 2, 3, 4, 5, 6, 7, 10, 13, 16, 17

Paiute sculpin Cottus beldingi N I cold 1, 2, 6, 13

shorthead sculpin3 Cottus confusus N S cold 14, 16

Cyprinidae

common carp Cyprinus carpio A T warm 2, 3, 4, 5, 6, 7, 9, 11, 12, 14, 15

chiselmouth Acrocheilus alutaceus N I cool 7, 10, 11, 12, 13, 14, 15, 16

fathead minnow Pimephales promelas AT warm 2

leatherside chub Gila copei N I cool 3

longnose dace Rhinichthys cataractae N I cool 1, 2, 3, 6, 10, 13, 14, 15, 16, 17

northern pikeminnow3 Ptychocheilus oregonensis N T cool 9, 10, 11, 12, 14, 15, 16, 17

peamouth Mylocheilus caurinus N I cool 12

redside shiner Richardsonius balteatus N I cool 2, 3, 4, 5, 6, 7, 9, 10, 17
8 Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002

Table 2. Fish species collected at all sites sampled for the Environmental Monitoring and Assessment Program, southern Idaho, 2002—

Continued

of native coldwater species; sites with scores between 50 and 

74 exhibit moderate biotic integrity where alien species are 

more frequent and the assemblage is dominated by coolwater, 

native species; sites with scores <50 exhibit poor biotic integrity where coldwater and sensitive species are rare or absent 

and where tolerant fish predominate. For a more detailed 

description of index development, metric response, and application, see the report by Mebane and others (2003).

Major faunal shifts in many streams in the Western 

United States are the result of alien fish species. Often, alien 

fish species are better adapted than native species to thrive in 

altered habitats (Moyle, 1994). The status of fish assemblages 

is related to the extent of habitat disturbance and the occurrence of native versus alien species. The Zoogeographic Integrity Coefficient (ZIC) index, derived from the ratio of the 

number of native species to the total number of species, was 

used to evaluate the degree of habitat disturbance, whereby a 

value of 1 indicates an undisturbed environment and a value of 

0 indicates a highly disturbed environment (Elvira, 1995).

Various statistical relations between sampling effort and 

species collection were calculated to evaluate information 

gained from additional collection effort in successive subreaches. At the three sites sampled at 100X, all possible combinations of four contiguous subreaches (total of seven possible combinations) totaling 40X were assessed and compared 

with results for the entire reach. These comparisons were useful for evaluating whether additional collection effort beyond 

40X would change the overall assessment of biotic integrity. 

All statistical and graphical analyses were performed using 

SYSTAT (Wilkinson, 1999). Significant differences between 

medians of sample groups were determined with the nonparametric Mann-Whitney t-test. Differences were considered statistically significant when p <0.05.

1 N, native; A, alien. 4 Federally listed as threatened. 2 I, intermediate species; S, sensitive species; T, tolerant species. 5 Cutthroat trout X rainbow trout hybrids collected at sites. 3 Native in the Snake River downstream from Shoshone Falls.

Cyprinidae—Continued

speckled dace Rhinichthys osculus N I cool 1, 2, 3, 4, 5, 6, 7, 10, 16, 17

Utah chub Gila atraria N T cool 3, 7, 9

Ictaluridae

channel catfish Ictalurus punctatus A T warm 11, 12, 14, 15

tadpole madtom Noturus gyrinus AT warm 15

Percidae

yellow perch Perca flavescens A I cool 4, 11, 12

Salmonidae

brown trout Salmo trutta A I cold 1, 2, 5, 6, 7

chinook salmon3, 4 Oncorhynchus tshawytscha N S cold 16

cutthroat trout 5 Oncorhynchus clarki N S cold 1, 2

 mountain whitefish Prosopium williamsoni N I cold 1, 2, 8, 9, 10, 14, 16, 17

rainbow trout3 Oncorhynchus mykiss N S cold 1, 2, 6, 7, 9, 16, 17

Family

Common name Species Origin1

Tolerance 

to 

pollution2 Temperature

preference Sites of occurrence 
Table 3. Fish metrics and final Index of Biotic Integrity (IBI) scores, number of fish collected, total number of species, number of native species, and Zoog

Coefficient (ZIC) index values for all sites sampled for the Environmental Monitoring and Assessment Program, southern Idaho, 2002

[No., number; TFF, too few fish to calculate index score]

1 See figure 1. 3Temporal duplicate. 5 Includes deformities, e2Spatial duplicate. 4 No. of fish collected per minute electrofishing. 6Ratio of native to total 

Site No.1

Metrics 1 2 3 4 5 6 7 27 8 9 10 11 12 312 13 

IBI scores

 No. of coldwater native 

species. . . . . . . . . . . . . . 4 4 1 1 1 2 2 2 1 2 2 0 0 0 2 2 

 Percent sculpin . . . . . . . . 3.0 6.0 7.0 4.0 1.0 6.0 9.0 18.0 0.0 0.0 7.0 0.0 0.0 0.0 16.0 1 Percent sensitive native 

individuals. . . . . . . . . . . 12.0 1.0 0.0 0.0 0.0 0.0 2.0 15.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1

 Percent coldwater 

individuals. . . . . . . . . . . 98.0 21.0 7.0 4.0 2.0 7.0 35.0 61.0 100 1.0 9.0 0.0 0.0 0.0 16.0 1

 Percent tolerant 

individuals. . . . . . . . . . . 1.0 26.0 52.0 24.0 28.0 62.0 31.0 24.0 0.0 94.0 25.0 52.0 69.0 47.0 2.0 4

 No. of alien species . . . . . 2 4 1 2 2 3 2 1 0 1 0 4 4 4 1 3  Percent common carp

individuals. . . . . . . . . . . 0.0 0.3 12.2 14.2 28.3 0.8 0.4 0.0 0.0 1.5 0.0 18.1 35.7 12.1 0.0 6

 Catch per unit effort4 . . . 8.7 1.3 0.3 0.5 0.3 1.3 3.3 5.5 4.0 0.1 0.7 0.0 0.0 0.0 0.4 1

 Percent selected 

anomalies5 . . . . . . . . . . 0.0 0.0 0.6 0.8 0.0 0.0 0.4 2.5 0.0 0.0 0.0 0.2 1.1 0.0 0.9 0

 Final IBI score 69 51 23 27 27 34 55 67 TFF 20 56 10 5 13 51 3

Other metrics

 No. of fish collected. . . . . 1,050 358 164 394 304 358 260 241 3 581 214 409 356 967 109 6 No. of native species . . . . 7 8 7 4 4 6 6 8 1 6 10 4 5 3 5 7  Total no. of species . . . . . 9 13 8 6 6 10 9 9 1 7 10 8 9 7 6 1 ZIC6 . . . . . . . . . . . . . . . . 0.78 0.62 0.88 0.67 0.67 0.60 0.67 0.89 TFF 0.71 1.00 0.50 0.56 0.43 0.83 0
10 Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002

Results of Fish Assemblages

Results of Fish Assemblages. . 

Thirty-two species of fish in the families Catostomidae, 

Centrarchidae, Cottidae, Cyprinidae, Ictaluridae, Percidae, 

and Salmonidae were collected (table 2). Twelve alien species 

representing about 38 percent of all species were collected. 

Many of these alien species such as sunfish (Centrarchidae), 

common carp (Cyprinidae), and catfish (Ictaluridae) are 

adapted for warmwater habitats, especially those habitats created by impoundments. The most commonly collected species 

(collected at 10 or more sites) were largescale sucker, mottled 

sculpin, common carp, longnose dace, and speckled dace. 

Common carp, a tolerant alien, was collected at about 65 percent (11 of 17) of the sites. According to Mebane and others 

(2003), the presence of carp indicates degraded conditions in 

Pacific Northwest rivers.

The presence of smallmouth bass, an alien piscivore, in 

the Snake River (sites 11 and 12), Owyhee River (site 13), and 

Payette and lower Weiser Rivers (sites 14 and 15) indicates a 

potential hazard to native fish such as cyprinids, cottids, and 

juvenile salmonids. Miller and others (1989) indicated that 

alien fish species were a factor in 68 percent of North American fish extinctions. Hughes and others (2002) also noted this 

concern about the widespread occurrence of smallmouth bass 

in many rivers in Oregon. The presence of channel catfish, a 

warmwater-adapted species, also indicates that these river 

reaches no longer offer coldwater habitat for many native fish. 

Small native benthic fish (sculpins and dace) commonly were 

collected with boat electrofishing, although the abundances of 

these species likely were underrepresented by jet boat or raft 

electrofishing. For example, the percent sculpins collected by 

jet boat or raft never exceeded 7 percent at any site (table 3). 

Mebane and others (2003) found that the percent sculpins collected by multiple gear (raft and backpack electrofisher) at six 

sites on the Salmon River, a minimally disturbed large river in 

Idaho, averaged about 30 percent.

The number of fish collected at all sites (excluding site 

8) ranged from 82 to 1,050 (table 3). Only three mountain 

whitefish were collected from the Big Lost River above 

Mackay Reservoir (site 8). This site was almost dry; only a 

few intermittent pools remained.

Two relatively rare species were collected—bluehead 

suckers at the Snake River near Shelley (site 2) and Portneuf 

River near Pocatello (site 6), and a leatherside chub at Blackfoot River near Blackfoot (site 3). Federally listed chinook 

salmon juveniles were collected only from the Salmon River 

near Challis (site 16). 

Fish Metrics and Index Scores

Final IBI scores for all sites ranged from 5 (Snake River 

near Marsing, site 12) to 73 (Salmon River near Challis, site 

16) (table 3). The unusually low IBI scores for the Snake 

River near Marsing and Walters Ferry (site 11) likely were due 

to recent fish kills as a result of excessively high water temperatures (J.C. Dillon, Idaho Department of Fish and Game, oral 

commun., 2002). IBI scores for about 53 percent (9 of 16) of 

the sites, excluding site 8 with only 3 fish, were <50, indicating poor biotic integrity (Mebane and others, 2003). Typically, 

few or no coldwater or sensitive species were collected at 

these sites, and the assemblage was composed predominately 

of tolerant cool or warmwater species. Although analysis of 

human factors responsible for these poor biotic conditions is 

beyond the scope of this study, reports by Maret (1995, 1997) 

summarize land and water uses affecting fish populations in 

southern Idaho. No sites sampled during this study received 

high IBI scores (>75). Sites where salmonids were collected 

may have received a slightly higher IBI score if age classes 

had been determined. Distinguishing salmonid age classes for 

future EMAP assessments would more fully utilize the IBI 

developed for Idaho rivers.

The Weiser River near Weiser (site 15) received the lowest ZIC index value of 0.36 and one of the lowest IBI scores 

(11), indicating a highly disturbed environment. The highest 

total number of species (14) was collected at this site; however, only 5 of these species were native. Most of the species 

collected at this site were warmwater-adapted aliens such as 

black crappie, white crappie, bluegill, largemouth bass, common carp, channel catfish, and tadpole madtom. West Fork 

Bruneau River near Grasmere (site 10) and the two Salmon 

River sites (16 and 17) received high ZIC index values of 1.0, 

indicating no habitat disturbance. These same sites also 

received some of the highest IBI scores, ranging from 56 to 

73.

Sampling Effort

On the basis of 14 reaches sampled at 40X, fish collected 

in an average of 7.5 subreaches (30 channel widths) represented about 95 percent of the species present in the entire 

reach (fig. 2). Collections in three different reaches sampled at 

100X also supported this finding. Few, if any, additional species were collected after sampling 30 to 40X (three to four 

subreaches) the channel width at those sites representing 

100X (fig. 3). One additional species, a longnose dace, was 

collected in the last subreach in the Snake River at Heise (site 

1). As expected, the asymptote was reached after minimum 

sampling effort (30 to 40X) at reaches characterized by few 

species, homogeneous physical habitat, and slow velocities 

(for example, Snake River near Marsing, site 12). Contrary to 

these findings, Hughes and others (2002) determined that 

more than twice the distance (about 85 channel widths) was 

needed to collect 95 percent of the fish species in Oregon rivers. In another study, Patton and others (2000) determined that 

a mean of 22X (a 100-m reach length) was required to collect 
11

90 percent of the species in small, wadeable, Wyoming 

streams.

For the present study, about 250 fish represented 95 percent of the species in a reach (fig. 4). This number is remarkably similar to that of Hughes and others (2002), who determined that at least 225 fish were necessary to represent 95 

percent of the species in a reach. On the basis of the number of 

fish collected from the 14 reaches sampled at 40X, about 8.5 

subreaches (34 channel widths) would need to be electrofished 

to collect 250 fish (fig. 5). Mean catch rates (number of fish 

captured) were very similar among subreaches; no large differences in catch rates between upstream and downstream 

subreaches were apparent. Additional information from the 

three reaches sampled at 100X also showed that a minimum of 

about 250 fish could be collected by sampling any of the seven 

subreach combinations equaling 40X (table 4).

The mean (± standard error) catch rates for the reaches 

sampled at 40X and 100X were 28.9 ± 2.3 (n=14) and 90.3 

± 10.9 (n=3) individuals per subreach, respectively. This catch 

rate is about 3 times higher than that of Hughes and others 

(2002), whose mean (± standard error) catch rate was 24.6 

± 2.5 individuals per subreach for 45 Oregon river reaches 

sampled at 100X. Reasons for this large difference in catch 

rate are unclear but could be related to differences in river 

conditions or fish abundances. Perhaps Oregon reaches were 

more difficult to sample because of faster velocities or more 

complex physical habitats. According to Hughes and others 

(2002), the mean gradient for 45 streams sampled in Oregon 

was 0.8 percent (range 0.2 to 2.6 percent). Gradients for raft 

sites sampled in this study were highest at Payette River near 

Emmett (0.3 percent), Snake River at Heise (0.4 percent), and 

Salmon River near Challis and Salmon (0.6 percent). Gradients at most other boat sites sampled generally were less than 

0.1 percent. These comparisons indicate that streams sampled 

in southern Idaho were of lower gradient (more “flat water”) 

than those sampled by Hughes and others (2002). This may, at 

least in part, explain the higher catch rate of fish in this study 

than in the study of Hughes and others (2002). Another reason 

for the difference could be the type of collection gear; rafts 

were the only gear used for the Oregon study, whereas four 

gear types were used for this study. The mean catch rate by 

using a raft was similar to the mean catch rate by using all 

gear types in this study and, on average, still resulted in more 

fish collected per subreach than did the Oregon study. The 

mean (± standard error) catch rates by raft for the reaches 

sampled at 40X and 100X were 28.0 ± 2.6 (n=8) and 87.1 

± 9.0 (n=2) individuals per subreach, respectively.

Cumulative IBI scores determined for subreaches sampled at the three sites representing 100X showed little variability (fig. 6). Almost no change in the IBI score occurred 

after four subreaches (40X) were sampled. Mean IBI scores 

for subreaches sampled at 20X were not significantly different 

(p=0.45, n=14) from scores for subreaches sampled at 40X. 

PERCENT CUMULATIVE SPECIES

NUMBER OF SUBREACHES

100

90

80

70

60

50

40

30

20

10

0

12345 789 6 10

Mean Standard

error

Figure 2. Number of subreaches in relation to percent cumulative

fish species collected over a sampling distance of 40 channel

widths in 14 river reaches in southern Idaho, 2002.

NUMBER OF SPECIES

NUMBER OF SUBREACHES

12

11

10

9

8

7

6

5

4

3

2

12345 789 6 10

Snake River at Heise

Snake River near Marsing

Payette River near Emmett

Figure 3. Number of subreaches in relation to number of fish species

collected over a sampling distance of 100 channel widths in the Snake

River at Heise and near Marsing, and in the Payette River near

Emmett, southern Idaho, 2002.

Methods
12 Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002 PERCENT CUMULATIVE SPECIES

NUMBER OF FISH

100

90

80

70

60

50

40

30

20

10

0

50 100 200 250 300 150 350

Mean Standard

error

Figure 4. Number of fish in relation to percent cumulative species

collected over a sampling distance of 40 channel widths in 14 river

reaches in southern Idaho, 2002. NUMBER OF FISH

NUMBER OF SUBREACHES

350

300

250

200

150

100

50

0

12345 789 6 10

Mean Standard

error

Figure 5. Mean number of fish collected over a sampling distance

equal to 40 channel widths in 10 equidistant subreaches in 14 river

reaches in southern Idaho, 2002.

However, the fish population collected in a reach sampled at 

20X, or five subreaches in a 40X reach, represented only 

about 80 percent of all the species in the reach (fig. 2). A summary of all possible contiguous subreaches equaling 40X at 

the three sites representing 100X showed little difference in 

IBI scores (table 4). IBI score ranges were 66 to 71 for the 

Snake River at Heise, 12 to 15 for the Snake River near Marsing, and 21 to 34 for the Payette River near Emmett.

Methods. 

Sampling Variability

Two duplicate samples showed some spatial or temporal 

variability. The spatial duplicate samples collected at Rock 

Creek at Twin Falls (site 7) at 40X received final IBI scores of 

55 and 67. The same number of fish species (9) was collected 

at each site, and the total number of fish collected at each site 

was 241 and 260. Temporal samples collected at the beginning 

and end of the sampling period (about 3 months between visits) over a reach length of 100X at the Snake River near Marsing (site 12) showed little difference in IBI scores of 5 and 13. 

However, the number of species ranged from 9 to 7, and the 

total number of fish collected each time was 356 and 967. 

Even though more than 600 additional fish were collected at 

the end of the sampling period, the IBI scores still indicated 

poor biotic integrity. This large difference in the number of 

fish may have been related to river conditions, water clarity, 

and the lack of abundant macrophyte growth at the end of the 

sampling period, which made it easier to observe and collect 

more fish.

Minimum Sampling Effort

Results of this assessment of sampling efficiency using 

multiple gear types in a wide range of rivers in southern Idaho 

showed that a reach length of 30 to 40X the wetted channel 

width is generally sufficient to collect an adequate number of 

fish to estimate species richness and to evaluate biotic integrity using an IBI approach. This conclusion is contingent on a 

catch rate similar to that achieved in this study. Using channel 

widths listed in table 1, the median reach lengths of 30 and 

40X equate to sampling distances of 1,200 and 1,600 m, 

respectively. These distances are similar to the 1,600-m (1.6-

km) sampling distance that Lyons and others (2001) recommended for large rivers in Wisconsin.
Summary and Conclusions 13

Table 4. Index of Biotic Integrity (IBI) scores and number of 

fish species and individuals collected at three sites in a reach 

length of 100 times the channel width sampled for the 

Environmental Monitoring and Assessment Program, 

southern Idaho, 2002

[Data are for the seven possible contiguous subreach combinations 

equaling 40 times the channel width; No., number; locations shown 

in figure 1] 

Site 

No. Site name

SubreachIBI 

score

No. of 

fish 

species

No. 

of 

fish

1 Snake River at Heise

A – D 71 8 447

B–E 70 8 372

C–F 68 8 377

D–G 70 7 497

E–H 66 8 424

F–I 67 8 391

G–J 68 9 357

Mean 69 8 409

12 Snake River near 

Marsing

A–D 13 7 511

B–E 13 6 612

C–F 13 6 695

D–G 13 6 583

E–H 12 6 383

F–I 13 6 283

G–J 15 6 214

Mean 13 6 469

14 Payette River near 

Emmett

A–D 29 11 236

B–E 27 9 258

C–F 30 9 229

D–G 21 7 202

E–H 24 7 220

F–I 27 7 261

G–J 34 7 336

Mean 27 8 249

Results from this study also suggest that a sample population of fish collected in a minimum reach length of 20X 

might be sufficient to evaluate fish assemblages using the IBI 

but would represent only about 80 percent of all the species 

present in the reach. Depending on monitoring needs and 

objectives, it may not be cost effective to spend additional 

sampling effort at a site to collect rare species. Because the 

IBI score is based primarily on the relative abundances of the 

most abundant species, the addition of a few rare species 

would not greatly influence the final score. However, in most 

cases, about 250 fish would need to be collected to effectively 

represent 95 percent of the species present.

Summary and Conclusions

Summary and Conclusions. 

Fish sampling was conducted at 17 large-river sites during low-flow conditions (July 25 through October 2) in 2002 

following U.S. Environmental Protection Agency Environmental Monitoring Assessment Program (EMAP) protocols. 

Site selection was based on a random selection process of 

Idaho rivers in the Basins Bioregion of southern Idaho that 

were equal to or greater than fifth order on 1:100,000-scale 

hydrographic maps. Fourteen reaches, which included one 

duplicate (total of 13 sites) were electrofished over a reach CUMULATIVE INDEX OF BIOTIC INTEGRITY SCORE

NUMBER OF SUBREACHES

100

90

80

70

60

50

40

30

20

10

0

12345 789 6 10

Snake River at Heise

Snake River near Marsing

Payette River near Emmett

Figure 6. Cumulative Index of Biotic Integrity scores over a sampling

distance equal to 100 channel widths in 10 equidistant subreaches in

the Snake River at Heise and near Marsing, and in the Payette River

near Emmett, southern Idaho, 2002.
14 Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002

length representing 40 times (40X) the wetted channel width. 

The remaining three sites were electrofished at a reach length 

representing 100X the wetted channel width to evaluate information gained by additional sampling effort. All reaches sampled were divided into 10 continuous subreaches of equal 

length to enable calculation of statistical relations between 

sampling effort and species collection. Because of the wide 

variety of field conditions encountered, four electrofishing 

methods were used that consisted of a single pass through a 

reach. All fish were identified to species, counted, and measured (minimum and maximum total length). External anomalies (deformities, eroded fins, lesions, and tumors) also were 

recorded. 

Fish assemblages were analyzed on the basis of abundances of individuals and species and the Index of Biotic 

Integrity (IBI). Geographic origin (native or alien), tolerance 

to pollution, and temperature preferences were assigned to 

each species. The Zoogeographic Integrity Coefficient (ZIC), 

an index derived from the ratio of the number of native species 

to the total number of species, was used to evaluate the degree 

of habitat disturbance. Various statistical relations between 

sampling effort and species collection were calculated to evaluate information gained from additional collection effort in 

successive subreaches.

Thirty-two species of fish in the families Catostomidae, 

Centrarchidae, Cottidae, Cyprinidae, Ictaluridae, Percidae, 

and Salmonidae were collected. Twelve alien species representing about 38 percent of all species were collected. Many 

of these alien species such as sunfish (Centrarchidae), common carp (Cyprinidae), and catfish (Ictaluridae) are adapted 

for warmwater habitats, especially those habitats created by 

impoundments. About 53 percent (9 of 16 sites, excluding site 

8 with only 3 fish), received IBI scores of <50, which indicates poor biotic integrity. These sites typically contained few 

or no coldwater or sensitive species, and the assemblage was 

composed of predominantly tolerant cool or warmwater species. No sites received high IBI scores (>75). West Fork Bruneau River near Grasmere and the two Salmon River sites near 

Challis and Salmon received high ZIC index values of 1.0, 

indicating no habitat disturbance.

On the basis of 14 reaches sampled at 40X, fish collected 

in about 7.5 subreaches (30 channel widths) represented about 

95 percent of the species present in the entire reach. Collections in three different reaches sampled at 100X also supported this finding. Few, if any, additional species were collected after sampling 30 to 40X (three to four subreaches) the 

channel width at those sites representing 100X. In most cases, 

about 250 fish were needed to effectively represent 95 percent 

of the species present. On the basis of the number of fish collected from the 14 reaches sampled at 40X, about 8.5 subreaches (34 channel widths) would need to be electrofished to 

collect 250 fish. Additional information from the three reaches 

sampled at 100X also showed that a minimum of about 250 

fish could be collected by sampling any of the seven subreach 

combinations equaling 40X. The mean (± standard error) 

numbers of fish captured in the reaches sampled at 40X and 

100X were 28.9 ± 2.3 (n=14) and 90.3 ± 10.9 (n=3) individuals per subreach, respectively.

Results of this assessment of sampling efficiency using 

multiple gear types in a wide range of rivers in southern Idaho 

showed that a reach length of 30 to 40X the wetted channel 

width is generally sufficient to collect an adequate number of 

fish to estimate species richness and to evaluate biotic integrity using an IBI approach. This conclusion is contingent on a 

catch rate similar to that achieved in this study. Analyses also 

suggested that, in most cases, about 250 fish would need to be 

collected to effectively represent 95 percent of the species 

present. Median reach lengths of 30 and 40X equate to sampling distances of 1,200 and 1,600 m, respectively.

Results from this study may be applicable to other semiarid, fifth- through seventh-order southern Idaho rivers that are 

sampled during summer low-flow conditions. Several conclusions reached during this study would benefit future EMAP 

studies: (1) The wide range of river conditions encountered in 

southern Idaho made it impractical to rely on one gear type or 

collection method to effectively sample all sites. The flexibility to choose gear type most appropriate for stream conditions 

likely improved capture efficiency. Reliance on only one gear 

type (for example, raft) may restrict capture efficiency at sites 

where wading methods may be more effective. (2) It is of paramount importance that the field crew include an experienced 

fishery biologist familiar with a variety of electrofishing methods and the handling and identification of regional fish fauna. 

(3) Large-river work in the West demands that crew members 

be trained and skillful in the use of rafts and jet boats in highvelocity rivers. (4) It would be desirable to determine salmonid and cottid age classes within the sampling reach to more 

effectively utilize the IBI developed specifically for Idaho rivers. (5) A thorough reconnaissance of each candidate site prior 

to sampling would provide critical information that is desirable for an effective and safe sampling effort.

References Cited

References Cited. 

Behnke, R.J., 1992, Native trout of western North America: 

Bethesda, Md., American Fisheries Society Monograph 

6, 275 p.

Brennan, T.S., Lehmann, A.K., Campbell, A.M., O'Dell, I., 

and Beattie, S.E., 2003, Water resources data, Idaho, 

water year 2002, v. 1, Great Basin and Snake River 

Basin above King Hill: U.S. Geological Survey Water 

Data Report ID–02–1, 419 p.

Cao, Y., Larsen, D.P., Hughes, R.M., Angermeier, P.L., and 

Patton, T.M., 2002, Sampling effort affects multivariate 

comparisons of stream assemblages: Journal of the 

North American Benthological Society, v. 21, no. 4, p. 

701–714.

Chandler, J.A., and Radko, M., 2001, Introduction and overview, in Chandler, J.A., ed., Chapter 1. Feasibility of 

reintroduction of anadromous fish above or within the 
References Cited 15

Hells Canyon Complex, technical appendix E.3.1–2 for 

Hells Canyon Complex Hydroelectric Project FERC No. 

1971: Boise, Idaho Power Company, 20 p.

Dynesius, M., and Nilsson, C., 1994, Fragmentation and flow 

regulation of river systems in the northern third of the 

world: Science, v. 266, p. 753–762.

Elvira, B., 1995, Native and exotic freshwater fishes in Spanish river basins: Freshwater Biology, v. 33, p. 103–108.

Flotemersch, J.E., and Cormier, S.M., 2001, Comparisons of 

boating and wading methods used to assess the status of 

flowing waters: Cincinnati, Ohio, U.S. Environmental 

Protection Agency, National Exposure Research Laboratory, EPA/600/R–00/108, 93 p.

Galat, D.L., and Zweimuller, I., 2001, Conserving large-river 

fishes: is the highway analogy an appropriate paradigm: 

Journal of the North American Benthological Society, v. 

20, no. 2, p. 266–279.

Grafe, C.S., Mebane, C.A., McIntyre, M.J., Essig, D.A., 

Brandt, D.H., and Mosier, D.T., 2002, The Idaho Department of Environmental Quality water body assessment 

guidance, second edition—final: Boise, Idaho Department of Environmental Quality, [variously paged].

Hughes, R.M., Kaufman, P.R., Herlihy, A.T., Intelmann, S.S., 

Corbett, S.C., Arbogast, M.C., and Hjort, R.C., 2002, 

Electrofishing distance needed to estimate fish species 

richness in raftable Oregon rivers: North American Journal of Fisheries Management, v. 22, p. 1229–1240.

Karr, J.R., 1991, Biological integrity: a long-neglected aspect 

of water resource management: Ecological Applications 

v. 1, no. 1, p. 66–84.

Leopold, L.B., Wolman, M.G., and Mill, J.P., 1964, Fluvial 

processes in geomorphology: San Francisco, Calif., 

W.H. Freeman Press, 522 p.

Li, H.W., Schreck, C.B., Bond, C.E., and Rexstad, E., 1987, 

Factors influencing changes in fish assemblages of 

Pacific Northwest streams, in Matthews, W.J., and Heins, 

D.C., eds., Community and evolutionary ecology of 

North American stream fishes: Norman, Okla., University of Oklahoma Press, p. 193–202.

Lyons, J., 1992, The length of stream to sample with a towed 

electrofishing unit when fish species richness is estimated: North American Journal of Fisheries Management, v. 12, p. 198–203.

Lyons, J., Piette, R.R., and Niermeyer, K.W., 2001, Development, validation, and application of a fish-based index of 

biotic integrity for Wisconsin’s large warmwater rivers: 

Transactions of the American Fisheries Society, v. 130, 

p. 1077–1094.

Maret, T.R., 1995, Water-quality assessment of the upper 

Snake River Basin, Idaho and western Wyoming—summary of aquatic biological data for surface water through 

1992: U.S. Geological Survey Water-Resources Investigations Report 95–4006, 59 p.

——— 1997, Characteristics of fish assemblages and related 

environmental variables for streams of the upper Snake 

River Basin, Idaho and western Wyoming, 1993–95: 

U.S. Geological Survey Water-Resources Investigations Report 97–4087, 50 p.

Meador, M.R., Cuffney, T.E., and Gurtz, M.E., 1993, Methods 

for sampling fish communities as part of the National 

Water-Quality Assessment Program: U.S. Geological 

Survey Open-File Report 93–104, 40 p.

Meador, M.R., McIntyre, J.P., and Pollock, K.H., 2003, 

Assessing the efficacy of single-pass backpack electrofishing to characterize fish community structure: Transactions of the American Fisheries Society, v. 132, p. 39–

46.

Mebane, C.A., Maret, T.R., and Hughes, R.M., 2003, An index 

of biological integrity (IBI) for Pacific Northwest Rivers: 

Transactions of the American Fisheries Society, v. 132, 

p. 239–261.

Miller, R.R., Williams, J.D., and Williams, J.E., 1989, Extinction of North America fishes during the past century: 

Fisheries, v. 14, no. 6, p. 22–38.

Moyle, P.B., 1994, Biodiversity, biomonitoring, and the structure of stream fish communities, in Loeb, S.L., and Spacie, A., eds., Biological monitoring of aquatic systems: 

Boca Raton, Fla., Lewis Publishers, p. 171–186.

Omernik, J.M., and Gallant, A.L., 1986, Ecoregions of the 

Pacific Northwest: Corvallis, Oreg., U.S. Environmental 

Protection Agency, EPA 600/3–86/033, 39 p.

Patton, T.M., Hubert, W.A., Rahel, F.J., and Gerow, K.G., 

2000, Effort needed to estimate species richness in small 

streams on the Great Plains in Wyoming: North American Journal of Fisheries Management, v. 20, p. 394–398.

Peck, D.V., Averill, D.K., Lazorchak, J.M., and Klemm, D.J., 

eds., 2002, Environmental monitoring and assessment 

program—surface waters: western pilot study: field 

operations manual for non-wadeable rivers and streams 

(Draft): Corvalis, Oreg., U.S. Environmental Protection 

Agency, 198 p.

Peck, D.V., Lazorchak, J.M., and Klemm, D.J., eds., 2001, 

Environmental monitoring and assessment program—

surface waters: western pilot study: field operations manual for wadeable streams (Draft): Corvalis, Oreg., U.S. 

Environmental Protection Agency, 242 p.

Reash, R.J., 1999, Considerations for characterizing Midwestern large-river habitats, in Simon, T.P., ed., Assessing the 

sustainability and biological integrity of water resources 

using fish communities, chapter 17: Boca Raton, Fla., 

CRC Press, p. 463–473.

Simon, T.P., and Sanders, R.E., 1999, Applying an Index of 

Biotic Integrity based on Great-River fish communities: 

considerations in sampling and interpretation, pages 

475–505, in Simon, T.P., ed., Assessing the sustainability 

and biological integrity of water resources using fish 
16 Fish Assemblages and Minimum Sampling Effort to Determine Biotic Integrity, Large Rivers, Southern Idaho, 2002

communities: Boca Raton, Fla., CRC Press, Lewis Publishers, 671 p.

Strahler, A.N., 1957, Quantitative analysis of watershed geomorphology: Transactions of the American Geophysical 

Union, v. 38, p. 913–920.

Warren, M.L., Jr., and Burr, B.M., 1994, Status of freshwater 

fishes of the United States—overview of an imperiled 

fauna: Fisheries, v. 19, no. 1, p. 6–18.

Wilkinson, L., 1999, SYSTAT for Windows—statistics, version 9.0: Evanston, Ill., SPSS, Inc., 660 p.

Zaroban, D.W., Mulvey, M.P., Maret, T.R., Hughes, R.M., and 

Merritt, G.D., 1999, Classification of species attributes 

for Pacific Northwest freshwater fishes: Northwest Science, v. 73, no. 2, p. 81–93.
Biotic Integrity of Large Rivers in Southern Idaho, 2002—Water-Resources Investigations Report 03–4274

Maret and Ott—Assessment of Fish Assemblages and Minimum Sampling Effort Required to Determine