U.S. Department of the Interior USGS Fact She

U.S. Geological Survey 1 D

Kootenai

River

Pend Oreille

River

Spokane

River

Coeur

d'Alene

Lake

River

Salmon River

Snake

Blackfoot

River

River

Bear

River

American Falls Reservoir

Snake

River

Boise

EXPLANATION

Water chemistry

Water chemistry and

 habitat parameters

 for macroinverte-

 brates

Water chemistry,

 contaminants for

 fish, and habitat

 parameters for

 macroinvertebrates

Map identification

 number, refer to

 table at right for

 site name

52

SAMPLING SITES AND

TYPE OF ANALYSIS

1

2

3

4

5

6

7

48

51

49

50

52

44

45

39 47 46

40 42

41

37

43

36

32

27

26

33

38 35

34

25

28 29

30 23

10 11

12

14

15

13

17

9 8

18 16

53

19

21 20 24

22

31

Figure 1. Locations of sampling sites comprising the Idaho statewide surface-water

quality monitoring program.

Clearwater River

BACKGROUND

In 1990, the U.S. Geological Survey 

(USGS), in cooperation with the Idaho 

Division of Environmental Quality (formerly Idaho Department of Health and 

Welfare, Division of Environmental Quality), implemented a statewide waterquality monitoring program in response 

to Idaho’s antidegradation policy as required by the Clean Water Act (CWA). 

The objective was to provide water-quality managers with a coordinated statewide program to detect trends in surfacewater quality.

The program design included chemical analyses of water samples collected 

at 56 sites on the Bear, Clearwater, 

Kootenai, Pend Oreille, Salmon, Snake, 

and Spokane Rivers and their tributaries 

(fig. 1). Samples were collected every

year (1990 through 1995) at 5 sites 

(annual sites), every other year at 19 sites 

(biennial sites), and every third year at 

32 sites (triennial sites). Each year, 25 of 

the 56 sites were sampled. During water 

years 1990–95 (October 1, 1989, to September 30, 1995), samples were collected 

bimonthly. Onsite analyses consisted of 

discharge, specific conductance, pH, 

temperature, dissolved oxygen, bacteria 

(fecal coliform and fecal streptococci), 

and alkalinity. Laboratory analyses consisted of major ions, nutrients, trace elements, turbidity, and suspended sediment. 

Analytical results from the fi

sites sampled during water ye

are presented in a report by O

Berenbrock (1994).

CHANGES TO THE PRO

In 1996, biological analy

added to the monitoring prog

effectively assess the status a

stream quality in Idaho. So th

cal analyses could be added w

creasing program costs, anal

elements in water were dropp

yses of major ions and alkali

PREPARED IN COOPERATION WITH THE IDAHO DIVISION OF ENVIRONMENTAL QUALITY

Changes to Idaho’s Statewide Surface-Water Quality 

Monitoring Program Since 1995

Table 1. Sampling sites that compose the Idaho statewide surface-water qu

monitoring program

Site Site

No. Site name No. Site name

1. Kootenai River at Porthill 26. Beaver Creek at Spence

2. Clark Fork River below Cabinet Gorge Dam, 27. Big Lost River near Chi

near Cabinet 28. Big Wood River near Be

3. Priest River near Priest River 29. Silver Creek near Picabo

4. North Fork Coeur d’Alene River at 30. Malad River near Goodi

Enaville 31. Bruneau River near Hot 

5. South Fork Coeur d’Alene River near 32. Snake River near Murph

Pinehurst 33. Boise River near Twin S

6. St. Joe River at Calder 34. Boise River below Diver

7. Spokane River near Post Falls 35. Boise River at Glenwoo

8. Snake River near Heise 36. Boise River near Parma

9. Snake River at Lorenzo 37. Snake River at Nyssa

10. Teton River near St. Anthony 38. South Fork Payette Rive

11. Henrys Fork near Rexburg 39. North Fork Payette Rive

12. Willow Creek near Ririe 40. North Fork Payette Rive

13. Blackfoot River near Blackfoot 41. Payette River near Payet

14. Snake River near Blackfoot 42. Weiser River near Weise

15. Portneuf River at Topaz 43. Snake River at Weiser

16. Marsh Creek near McCammon 44. Pahsimeroi River at Elli

17. Portneuf River at Pocatello 45. Salmon River at Salmon

18. Snake River near Minidoka 46. Lemhi River near Lemh

19. Snake River at Milner 47. Johnson Creek at Yellow 

20. Snake River near Kimberly 48. Little Salmon River at R

21. Blue Lakes Spring 49. Snake River near Anaton

22. Rock Creek at Daydream Ranch 50. Lapwai Creek near Lapw

23. Box Canyon Springs 51. South Fork Clearwater R

24. Salmon Falls Creek near Hagerman 52. Palouse River near Potla

25. Camas Creek at Red Road 53. Bear River at Idaho-Uta
2

reduced to one set of samples collected 

during base-flow conditions in September. Discharge, specific conductance, pH, 

temperature, turbidity, dissolved oxygen, 

bacteria, nutrients, and suspended sediment continue to be analyzed. Temperature is recorded continuously during summer months (June to September) at sites 

where samples are collected for biological analyses.

The resulting water-quality monitoring program consisted of 53 sites (fig. 1). 

Forty of these sites were designated as 

biological sampling sites. Because of limited funding, sites at which biological 

data were collected were divided among 

three regions—southeastern, southwestern, and northern. These sites are sampled once over a 3-year rotation in each 

of the three regions. The first rotation of 

sampling in the southeastern and southwestern regions was completed during 

1996–97. Sampling in the northern region 

is scheduled for summer/fall 1998.

The frequency of water-chemistry 

sample collection was changed from 

bimonthly during October to September, 

to monthly during April through September, when recreational uses are the most 

intensive. Biological sampling was targeted for summer/fall low-flow conditions, when coldwater biota (a primary 

beneficial use) are most limited as a 

result of reduced streamflow, which 

causes thermal stress and habitat loss.

WHY THE CHANGES?

The original water-quality monitoring program, consisting of conventional 

water-chemistry analyses, was not adequate for beneficial-use assessment. More 

quantitative measurements of biotic integrity were needed to assess the status 

of designated beneficial uses. Because 

aquatic biological communities integrate 

stream-chemistry and habitat changes resulting from human activities in a river 

basin, measuring the biotic integrity of 

these communities will provide an effective approach for evaluating trends in 

surface-water quality. Collection of 

aquatic biological data also will provide a 

better understanding of the structure and 

composition of biological communities 

in large rivers (such as the Snake River) 

in Idaho, information that currently is 

lacking.

Ultimately, this improved surfacewater quality monitoring program will 

better meet the goals of the CWA by providing more information for addressing 

water-resource management issues such 

as the Total Maximum Daily Load process. This process involves the State of 

Idaho developing pollution control strategies for water-quality limited water bodies. Data collected during the surfacewater quality monitoring program will 

be used to prioritize water bodies for 

treatment and to evaluate the effectiveness of this pollution abatement process.

BIOLOGICAL DATA COLLECTION

Data collected at biological sampling 

sites consisted of macroinvertebrates, fish, 

and associated stream-habitat parameters. 

Biological data were collected following 

protocols designed for the National WaterQuality Assessment (NAWQA) Program 

(Crawford and Luoma, 1993; Cuffney and 

others, 1993a, 1993b; Meador and others, 

1993a, 1993b; Plafkin and others, 1989).

Application of 

NAWQA protocols provides 

nationally consistent and standardized methods for collecting and analyzing biological 

data, which ensures comparability of existing and future 

data. 

Fish were 

collected from 

all habitats in a 

representative riffle reach. W

fish-tissue and fish-liver com

ples were analyzed for 26 org

pounds and 22 inorganic com

respectively. In addition, the 

fish species were counted, an

were measured and examined 

nal anomalies (for example, 

lesions, tumors, and parasite

invertebrate and fish commu

ment for each site was comp

various community attributes

tolerances, and temperature p

RESULTS TO DATE FOR 

SELECTED SITES

Temperature

According to Idaho Wat

Standards and Wastewater T

Standards (Idaho Departmen

and Welfare, 1985), tempera

designated for coldwater bio

use must be “22 degrees Cel

less with a maximum daily a

greater than 19 degrees C.” D

97, the daily average tempera

was exceeded at sites on Mar

(site 16) and the Blackfoot, P

Boise Rivers (sites 15, 17, an

Biologists assess fish communities using electrofishing techniques

on the Portneuf River, Idaho. Some fish are sent to laboratories

where their tissue is analyzed for the presence of pollutants

(photograph by T. R. Maret)

Sampling for benthic inverteb

Big Lost River, Idaho (photog

Maret)
3

FECAL COLIFORM, COLONIES

PER 100 MILLILITERS

1,000

800

600

400

200

0

Figure 3. Fecal coliform analy

samples collected at selected 

during 1996–97. (See figure 1 

tions; see table 1 for site name

53 11 14

SITE NUM

17 22 

6

6 6

6

6

DISSOLVED NITRATE, IN

MILLIGRAMS PER LITER

2.5

2.0

1.5

1.0

0.5

0

Figure 4. Dissolved nitrate a

water samples collected at se

in Idaho during 1996–97. (Se

site locations; see table 1 for 

53 11 14

SITE NUM

17 22 

6

6 6

6

14

tively; fig. 2). Because of the significance 

of this temperature information and its 

potential effect on beneficial use, continuous-temperature monitoring will be expanded to include all 1998 statewide surface-water quality monitoring sites.

Bacteria

Fecal coliform is an indicator of fecal 

contamination by warmblooded animals 

and can indicate the presence of pathogenic micro-organisms. Concentrations 

of fecal coliform bacteria in water designated for primary contact recreation 

(swimming, water skiing, or skin/scuba 

diving) cannot exceed 500 colonies per 

100 milliliters (mL) of water at any time, 

and concentrations in only 10 percent 

of the total samples collected over a 

30-day period can exceed 200 colonies 

per 100 mL (Idaho Department of Health 

and Welfare, 1985). Concentrations of 

fecal coliform bacteria in water designated for secondary contact recreation 

(fishing, boating, or wading) cannot exceed 800 colonies per 100 mL at any 

time, and concentrations in only 10 percent of the total samples collected over a 

30-day period can exceed 400 colonies 

per 100 mL (Idaho Department of Health 

and Welfare, 1985). Fecal coliform concentrations exceeded primary contact recreation standards in samples from the 

Portneuf River at Pocatello, Rock Creek 

at Daydream Ranch, Boise River near 

Parma, and Bear River at Idaho-Utah 

State line (sites 17, 22, 36, and 53, 

respectively); and exceeded secondary 

contact recreation standards in samples 

from the Portneuf River at Pocatello and 

Boise River near Parma (sites 17 and 36, 

respectively; fig. 3).

Nutrients

Nitrate is an important nutrient for 

aquatic plants. Common human sources 

of nitrate are agricultural fertilizers, manure from livestock feedlots and dairycattle operations, and effluent from sewage-treatment plants. A nitrate concentration of 0.3 milligram per liter (mg/L) is 

considered the limit for preventing nuisance growths of algae and aquatic plants 

in streams (Idaho Department of Health 

and Welfare, 1985). Concentrations of 

dissolved nitrate in samples from the 

Portneuf River at Pocatello, Rock Creek 

at Daydream Ranch, Boise River near 

Number of samples

Individual data point

75th percentile plus 1.5 

75th percentile

Median

25th percentile

25th percentile minus 1

Primary contact recrea

 (Idaho Department o

 Welfare, 1985)

Secondary contact recr

 (Idaho Department o

 Welfare, 1985)

Interquartile range

(IQR)

EXPLANATION FOR BOX

(Figures 3, 4)

14

DAILY AVERAGE WATER TEMPERATURE, IN DEGREES CELSIUS

25

20

15

10

May June July Aug. Sept.

Figure 2. Water temperature analyzed in

samples collected at selected sites in

Idaho during 1996–97. (See figure 1 for

site locations; see table 1 for site names)

Site 13

Site 16

25

20

15

10

5

Site 17

Site 15

Site 27

1996

Site 35

Site 36

Site 22

Site 28

June July Aug. Sept.

1997

Coldwater biota maximum daily

average water temperature

25

20

15

10

5

25

20

15

10

Periods of

missing record

Periods of

missing record
4

MERCURY, IN MICROGRAMS

PER GRAM, WET WEIGHT

0.12

0.10

0.08

0.06

0.04

0.02

0

Figure 5. Mercury analyzed in livers of

fish collected at selected sites in Idaho

during 1993 and 1996. (See figure 1 for

site locations; see table 1 for site names)

14 37 11

SITE NUMBER

36 17 22 27

U.S. Fish and Wildlife Service

guideline (Eisler, 1987)

Laboratory

detection

level

Parma, Snake River at Nyssa, and Bear 

River at Idaho-Utah State line (sites 17, 

22, 36, 37, and 53, respectively) 

exceeded 0.3 mg/L (fig. 4).

Fish Tissue

Preliminary results of analyses of 

fish tissue for seven sites are presented in 

figure 5. Mercury was detected in the tissue (livers) of fish at all sites sampled 

during 1996 but did not exceed the U.S. 

Fish and Wildlife Service guideline of 

0.1 microgram per gram, wet weight, for 

the protection of fish-eating birds and 

wildlife (fig. 5). Total PCBs were 

detected in whole-body samples of fish 

at 5 of 7 sites sampled during 1996. In 

1993, PCB concentrations in tissue of 

fish from the Portneuf River at Pocatello 

(site 17), which were collected as part of 

the NAWQA Program, exceeded the 

National Academy of Sciences/National 

Academy of Engineering guideline of 

500 micrograms per kilogram, wet 

weight, for the protection of fish-eating 

birds and wildlife. Analytical results of 

fish-tissue samples collected during 1997 

were not yet available when this report 

was written.

FUTURE PLANS

All water-chemistry and biological 

data will continue to be published annually in the USGS Water Resources Data 

report for Idaho. The first rotation of biological sampling in all three regions will 

be completed in 1998. A complete analysis of the statewide surface-water quality 

monitoring program is planned to identify sites that best characterize basin conditions.

REFERENCES CITED

Crawford, J.K., and Luoma, S.N., 1993, 

Guidelines for studies of contaminants in biological tissue for the 

National Water-Quality Assessment 

Program: U.S. Geological Survey 

Open-File Report 92– 494, 69 p.

Cuffney, T.F., Gurtz, M.E., and Meador, 

M.R., 1993a, Guidelines for processing and quality assurance of 

benthic invertebrate samples collected as part of the National WaterQuality Assessment Program: U.S. 

Geological Survey Open-File 

Report 93–407, 80 p.

———1993b, Methods for collecting 

benthic invertebrate samples as 

part of the National Water-Quality 

Assessment Program: U.S. Geological Survey Open-File Report 

93–404, 66 p.

Eisler, Ronald, 1987, Mercury hazards 

to fish, wildlife, and invertebrates, 

a synoptic review: U.S. Fish and 

Wildlife Service Biological Report 

85 (1.10), 90 p.

Idaho Department of Health and Welfare, 

1985, Idaho water quality standards 

and wastewater treatment requirements: Boise, Idaho De

Health and Welfare, Di

Environmental Quality, 

Meador, M.R., Cuffney, T.F.

M.E., 1993a, Methods 

fish communities as par

National Water-Quality 

Program: U.S. Geologi

Open-File Report 93–1

Meador, M.R., Hupp, C.R., 

T.F., and Gurtz, M.E., 1

ods for characterizing s

tat as part of the Nation

Quality Assessment Pro

Geological Survey Ope

Report 93–408, 48 p.

O’Dell, Ivalou, and Berenbro

1994, Idaho’s surface-w

monitoring program—r

five sites sampled durin

years 1990–93: U.S. Ge

Survey Fact Sheet FS–9

Plafkin, J.L., Barbour, M.T., 

K.D., Gross, S.K., and H

R.M., 1989, Rapid bioa

protocols for use in stre

rivers—benthic macroi

and fish: Washington, D

Environmental Protecti

Office of Water Report 

89–001.

—Ivalou O’Dell, Terry R. Maret

Susan E. Moore

For more information, contac

Ivalou O’Dell

U.S. Geological Survey, WR

230 Collins Road

Boise, ID 83702

(208) 387-1300

Cutthroat trout, a popular sportfish found

in Idaho, also are considered a sensitive

indicator of stream conditions (photograph

© 1996 by W. H. Mullins and published

with permission)