Water Quality in the Northern Rockies 

Intermontane Basins

Idaho, Montana, and Washington, 1999–2001

U.S. Department of the Interior

U.S. Geological Survey

Circular 1235
Points of Contact and Additional Information

The companion web site for NAWQA summary reports:

http://water.usgs.gov/nawqa/nawqa_sumr.html

Other NAWQA summary reports

River Basin Assessments

Acadian-Pontchartrain Drainages (Circular 1232)

Albemarle-Pamlico Drainage Basin (Circular 1157)

Allegheny and Monongahela River Basins (Circular 1202)

Apalachicola-Chattahoochee-Flint River Basin (Circular 1164)

Central Arizona Basins (Circular 1213)

Central Columbia Plateau (Circular 1144)

Central Nebraska Basins (Circular 1163)

Connecticut, Housatonic and Thames River Basins (Circular 1155)

Cook Inlet Basin (Circular 1240)

Delaware River Basin (Circular 1227)

Delmarva Peninsula (Circular 1228)

Eastern Iowa Basins (Circular 1210)

Georgia-Florida Coastal Plain (Circular 1151)

Great and Little Miami River Basins (Circular 1229) 

Great Salt Lake Basins (Circular 1236)

Hudson River Basin (Circular 1165)

Island of Oahu (Circular 1239)

Kanawha - New River Basins (Circular 1204)

Lake Erie - Lake Saint Clair Drainages (Circular 1203)

Long Island - New Jersey Coastal Drainages (Circular 1201)

Lower Illinois River Basin (Circular 1209)

Lower Susquehanna River Basin (Circular 1168)

Lower Tennessee River Basin (Circular 1233)

Las Vegas Valley Area and the Carson and Truckee River Basins (Circular 1170)

Mississippi Embayment (Circular 1208)

Mobile River Basin (Circular 1231)

New England Coastal Basins (Circular 1226)

Ozark Plateaus (Circular 1158)

Potomac River Basin (Circular 1166)

Puget Sound Basin (Circular 1216)

Red River of the North Basin (Circular 1169)

Rio Grande Valley (Circular 1162)

Sacramento River Basin (Circular 1215)

San Joaquin-Tulare Basins (Circular 1159)

Santa Ana Basin (Circular 1238)

Santee River Basin and Coastal Drainages (Circular 1206)

South-Central Texas (Circular 1212)

South Platte River Basin (Circular 1167)

Southern Florida (Circular 1207)

Trinity River Basin (Circular 1171)

Upper Colorado River Basin (Circular 1214)

Upper Illinois River Basin (Circular 1230)

Upper Mississippi River Basin (Circular 1211)

Upper Snake River Basin (Circular 1160)

Upper Tennessee River Basin (Circular 1205)

Western Lake Michigan Drainages (Circular 1156)

White River Basin (Circular 1150)

Willamette Basin (Circular 1161)

Yakima River Basin (Circular 1237)

Yellowstone River Basin (Circular 1234)

National Assessments

The Quality of Our Nation‘s Waters—Nutrients and Pesticides (Circular 1225)

Northern Rockies Intermontane Basins contact 

and web site:

USGS State Representative

U.S. Geological Survey

Water Resources Discipline

230 Collins Rd.

Boise, ID 83702 e-mail: dc_id@usgs.gov

http://id.water.usgs.gov/nrok/

National NAWQA Program:

Chief, NAWQA Program

U.S. Geological Survey

Water Resources Division

12201 Sunrise Valley Drive, M.S. 413

Reston, VA 20192

http://water.usgs.gov/nawqa/

Front cover: Spokane River near Spokane, Washington (Photograph by Lan Tornes). 

Back cover: Left, Mining-affected tributary to the South Fork Coeur d’Alene River (Photograph by Lan Tornes); 

Center, Lake Pend Oreille (Photograph by Lan Tornes); Right, Collecting fish samples (Photograph by Terry 

Maret). 
U.S. Department of the Interior

U.S. Geological Survey

Water Quality in the Northern Rockies 

Intermontane Basins, Idaho, Montana, 

and Washington, 1999–2001

By Gregory M. Clark, Rodney R. Caldwell, Terry R. Maret, Craig L. Bowers, 

DeAnn M. Dutton, and Michael A. Beckwith

Circular 1235
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 sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

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.

Suggested citation:

Clark, Gregory M., Caldwell, Rodney R., Maret, Terry R., Bowers, Craig L., Dutton, DeAnn M., and Beckwith, Michael 

A., 2004, Water quality in the Northern Rockies Intermontane Basins, Idaho, Montana, and Washington, 1999–2001: 

Reston, Va., U.S. Geological Survey Circular 1235, 35 p.

Library of Congress Cataloging-in-Publication Data

Water quality in the Northern Rockies Intermontane Basins, Idaho, Montana, and Washington, 1999–2001 / 

 Gregory M. Clark ... [et. al.].

 p. cm. -- (Circular ; 1235)

 Includes bibliographical references.

 ISBN 0-607-94067-0

 1. Water quality -- Clark Fork Watershed (Mont. and Idaho). 2. Water quality -- 

 Pend Oreille River Watershed. 3. Water quality -- Spokane River Watershed (Idaho and Wash.). 

 I. Clark, G. M. (Gregory M.), 1958-. II. Geological Survey (U.S.) III. U.S. Geological Survey 

 circular ; 1235.

 TD223.7.W38 2003

 363.739’42’0979--dc22 2003063064
iii

Contents

National Water-Quality Assessment Program ......................................................... iv

What kind of water-quality information does the NAWQA Program provide? ............... v

Introduction to this Report .............................................................................. vi

Summary of Major Findings .............................................................................. 1

Stream and River Highlights ..................................................................... 1

Ground-Water Highlights ........................................................................... 2

Introduction to the Northern Rockies Intermontane Basins ....................................... 3

Major Findings ............................................................................................. 6

Historical mining activities have degraded water-quality 

conditions in numerous streams .................................................................. 6

Nutrient concentrations in streams generally are low ....................................... 11

Fish in the Spokane River contain polychlorinated biphenyls (PCBs) 

at elevated concentrations ........................................................................ 13

The Spokane River also contains low concentrations of pesticides 

and volatile organic compounds .................................................................. 14

Ground water in aquifers used for drinking-water supply in Spokane, 

Coeur d’Alene, and Missoula is generally of good quality .................................... 15

Study Unit Design ....................................................................................... 18

Stream Chemistry and Ecology .................................................................. 18

Ground-Water Chemistry ........................................................................ 18

References Cited .......................................................................................... 20

Glossary ................................................................................................... 23

Appendix ................................................................................................... 25
iv

National Water-Quality Assessment Program

The quality of the Nation’s water resources is integrally linked to the long-term availability of 

water that is clean and safe for drinking and recreation and also suitable for industry, irrigation, and habitat for fish and wildlife. Recognizing the need for long-term, nationwide assessments of water resources, the U.S. Congress has appropriated funds since 1991 for the USGS to 

conduct the National Water-Quality Assessment (NAWQA) Program. Scientists in the NAWQA 

Program work with partners in government, research, and public interest groups to assess the 

spatial extent of water-quality conditions, how water quality changes with time, and how human 

activities and natural factors affect water quality. This information is useful for guiding watermanagement and protection strategies, research, and monitoring in different hydrologic and 

land-use settings across the Nation.

The Northern Rockies Intermontane Basins is one of 51 water-quality assessments initiated 

since 1991. Together, the 51 major river basins and aquifer systems, referred to as “Study 

Units,” include water resources used by more than 60 percent of the population in watersheds 

that cover about half of the land area of the conterminous United States. Timing of the assessments varies because of the Program’s rotational design, in which one-third of all Study Units 

are intensively investigated for 3 to 4 years, with trends assessed every 10 years. As indicated 

on the map, the Northern Rockies Intermontane Basins is part of the third set of intensive investigations, which began in 1997.

1991–95

1994–98

1997–2001

Not yet scheduled

HighPlains Regional

GroundWaterStudy,

1999–2004

Northern Rockies

Intermontane Basins

NAWAQA Study Units—

Assessment schedule
v

What kind of water-quality information does the NAWQA 

Program provide?

Water-quality assessments by a single program cannot possibly address all of the Nation’s 

water-resources needs and issues. Therefore, it is necessary to define the context within which 

NAWQA information is most useful. 

• Total resource assessment—NAWQA assessments are long-term and interdisciplinary, 

and include information on water chemistry, hydrology, land use, stream habitat, and 

aquatic life. Assessments are not limited to a specific geographic area or water-resource 

problem at a specific time. Therefore, the findings describe the general health of the total 

water resource, as well as emerging water issues, thereby helping managers and decision 

makers to set priorities.

• Source-water characterization—Assessments focus on the quality of the available, 

untreated resource and thereby complement (rather than duplicate) Federal, State, and 

local programs that monitor drinking water. Findings are compared to drinking-water 

standards and health advisories as a way to characterize the resource.

• Compounds studied—Assessments focus on chemical compounds that have well-established methods of investigation. It is not financially or technically feasible to assess all 

the contaminants in our Nation’s waters. In general, the NAWQA Program investigates 

those pesticides, nutrients, volatile organic compounds, and metals that have been or are 

currently used commonly in agricultural and urban areas across the Nation. A complete 

list of compounds studied is on the NAWQA Web site at http://water.usgs.gov/nawqa.

• Detection compared to risk—Compounds are measured at very low concentrations, 

often 10 to 100 times lower than Federal or State standards and health advisories. Detection of compounds, therefore, does not necessarily translate to risks to human health or 

aquatic life. However, these analyses are useful for identifying and evaluating emerging 

issues, as well as for tracking contaminant levels over time.

• Multiple scales—Assessments are guided by a nationally consistent study design and 

uniform methods of sampling and analysis. Findings thereby pertain not only to water 

quality of a particular stream or aquifer but also contribute to the larger picture of how 

and why water quality varies regionally and nationally. This consistent, multiscale 

approach helps to determine if a water-quality issue is isolated or pervasive. It also 

allows direct comparisons of how human activities and natural processes affect water 

quality in the Nation’s diverse environmental settings. 
vi

Introduction to this Report

This report contains the major findings of a 1999–2001 assessment of water quality in the 

Northern Rockies Intermontane Basins. It is one of a series of reports by the National WaterQuality Assessment (NAWQA) Program that present major findings in 51 major river basins 

and aquifer systems across the Nation. 

In these reports, water quality is discussed in terms of local, State, and regional issues. Conditions in a particular basin or aquifer system are compared to conditions found elsewhere and 

to selected national benchmarks, such as those for drinking-water quality and the protection of 

aquatic organisms. 

This report is intended for individuals working with water-resource issues in Federal, State, or 

local agencies, universities, public interest groups, or in the private sector. The information will 

be useful in addressing a number of current issues, such as the effects of agricultural and urban 

land use on water quality, human health, drinking water, source-water protection, hypoxia and 

excessive growth of algae and plants, pesticide registration, and monitoring and sampling strategies. This report is also for individuals who wish to know more about the quality of streams 

and ground water in areas near where they live, and how that water quality compares to the 

quality of water in other areas across the Nation.

The water-quality conditions in the Northern Rockies Intermontane Basins summarized in this 

report are discussed in detail in other reports that can be accessed from (http://id.water.usgs.

gov/nrok/index.html). Detailed technical information, data and analyses, collection and analytical methodology, models, graphs, and maps that support the findings presented in this report in 

addition to reports in this series from other basins can be accessed from the national NAWQA 

Web site (http://water.usgs.gov/nawqa). 

“ Understanding river and 

aquifer interaction often 

is critically linked to the 

consumptive needs of our citizenry, stream aquatic life, and 

riparian health, and ultimately 

our quality of life. Focused 

USGS scientific studies are 

assisting state and local government to protect water quality, manage water resources, 

and preserve natural systems 

such as the Spokane River and 

Spokane Valley-Rathdrum 

Prairie Aquifer in Washington 

and Idaho.”

— John L. Roland, Hydrogeologist

Spokane River Basin Remediation 

Coordinator, 

Washington State Department of 

Ecology 
Summary of Major Findings

1

Stream and River Highlights

Hard-rock mining, agriculture, urbanization, logging, 

and other activities have altered water quality and aquatic 

biological communities in streams and rivers of the Northern Rockies Intermontane Basins. Concentrations of trace 

elements in streambed sediment exceed guidelines established for the protection of aquatic life in many streams in 

the Clark Fork-Pend Oreille and Spokane River Basins. Fish 

and invertebrate communities also show adverse effects from 

elevated concentrations of trace elements. Concentrations of 

the nutrients nitrogen and phosphorus in streams are generally low; however, some concentrations approach or exceed 

recommended goals for preventing nuisance plant growth in 

streams. Excessive nutrients and potential eutrophication are 

a concern for Flathead Lake, Lake Pend Oreille, and Coeur 

d’Alene Lake, where residential and commercial development 

and recreational uses are increasing rapidly. 

• Concentrations of arsenic, cadmium, copper, lead, 

mercury, and zinc in streambed sediment exceeded 

guidelines for the protection of aquatic life (by as 

much as 40 times for some elements at some sites). 

Concentrations of copper in sediment from the upper 

Clark Fork, and concentrations of arsenic, cadmium, 

mercury, lead, and zinc in sediment from the South 

Fork Coeur d’Alene and Coeur d’Alene Rivers were 

among the highest in more than 1,200 streams sampled 

by the NAWQA Program across the Nation. Concentrations of trace elements in livers of fish and in 

tissue of invertebrates in mining-affected streams were 

elevated above natural background levels, and the 

abundance and diversity of fish and invertebrate species were greatly reduced. Trace-element concentrations in sportfish fillets, however, were generally low, 

with none in excess of U.S. Environmental Protection 

Agency (USEPA) human-health screening values for 

fish consumption (p. 7−10).

• The load, or mass, of trace elements transported 

in streams is highly variable, depending on annual 

precipitation and streamflow. During 1999 and 2000, 

an average of about 8,900 lb/yr (pounds per year) of 

cadmium, 500,000 lb/yr of lead, and 1.4 million lb/yr 

of zinc entered Coeur d’Alene Lake from the Coeur 

d’Alene River. The lake retained about 48 percent of 

the cadmium, 91 percent of the lead, and 30 percent of 

the zinc; the remaining trace elements were transported 

through the lake and into the Spokane River (p. 8). 

• Nutrient concentrations in streams generally were 

low, often below minimum reporting levels. Only 2 of 

10 streams sampled routinely (the South Fork Coeur 

d’Alene River near Pinehurst, Idaho, and the Spokane 

0

0

20

20

40 MILES

40 KILOMETERS

EXPLANATION

Forest (75%)

Range (11%)

Agricultural (8%)

Land cover and percentage of total area

Water (3%)

Barren (2%)

Urban (1%)

EXPLANATION

Clark Fork/Pend Oreille River Basin

Spokane River Basin

Washington

Oregon

Montana

Idaho

River at Seven Mile Bridge near Spokane, Washington) 

contained a median concentration of total nitrogen 

higher than a national background concentration of 

0.26 mg/L (milligrams per liter) for relatively undisturbed sites. The Clark Fork at Turah Bridge, Montana, 

South Fork Coeur d’Alene River near Pinehurst, Idaho, 

and Spokane River at Seven Mile Bridge near Spokane, Washington, contained a median concentration 

of total phosphorus higher than a national background 

concentration of 0.02 mg/L for relatively undisturbed 

sites. Elevated concentrations of total nitrogen and 

phosphorus in the South Fork Coeur d’Alene River 

near Pinehurst and in the Spokane River at Seven Mile 

Bridge near Spokane are attributable to sewage-treatment effluent. Elevated concentrations of chlorophylla, which are indicative of algal growth on streambeds 

and moderate nutrient enrichment, were measured 

in the Spokane, Flathead, and Bitterroot Rivers (p. 

11−12). 

• Concentrations of polychlorinated biphenyls (PCBs) in 

fillet and whole-body samples of fish from the Spokane 

River near Spokane exceeded recommended limits for 

 Major Influences on Water Quality in Streams and Rivers

Annual variability in precipitation and streamflow

Runoff from historical mining 

Urban runoff and sewage-treatment effluent
Ground-Water Highlights

Ground water accounts for about 19 percent of the total 

water used in the Northern Rockies Intermontane Basins and 

is the primary source of water for municipal, domestic, and 

industrial supplies. The Spokane Valley/Rathdrum Prairie and 

Missoula/Bitterroot basin-fill aquifers underlying Spokane, 

Coeur d’Alene, and Missoula currently supply drinking water 

for about 70 percent of the population in the basins and have 

been designated as sole-source aquifers by the USEPA. In general, the quality of water in these sole-source aquifers reflects 

minimal evidence of human activities despite continued urban 

development. These sole-source aquifers are particularly 

vulnerable to contamination, however, because of a relatively 

shallow water table, porous aquifer materials, and relatively 

rapid rates of recharge, and in some places they already contain low concentrations of trace elements and organic chemicals. 

• Arsenic concentrations exceeded the USEPA drinking-water standard of 10 μg/L (micrograms per liter) 

in only 3 of 31 wells sampled in the basin-fill aquifers 

underlying the Spokane/Coeur d’Alene area and in 

none of 30 wells sampled in the basin-fill aquifers 

underlying the Missoula/Bitterroot area. None of the 61 

wells sampled contained nitrate concentrations exceeding the USEPA drinking-water standard of 10 mg/L 

(p. 15−16). 

• Radon concentrations in ground-water samples ranged 

from 253 to 3,050 pCi/L (picocuries per liter) with the 

highest concentrations found along the relatively thin 

margins of the aquifers in the Spokane/Coeur d’Alene 

area and along the western edge of the Bitterroot Valley. Only one sample contained a radon concentration 

less than the USEPA proposed drinking-water standard of 300 pCi/L, and none of the samples contained 

concentrations exceeding 4,000 pCi/L, a less stringent 

standard being proposed by some States in cooperation 

with the USEPA (p. 16).

• Volatile organic compounds (VOCs) were detected in 

19 of 61 samples collected from the basin-fill aquifers, 

and pesticides were detected in 15 samples; 5 samples 

(8 percent) contained mixtures of VOCs and pesticides. 

Nearly all detected compounds, however, were at low 

concentrations; none exceeded or even approached 

established drinking-water standards and guidelines 

(p. 17).

• The Spokane River exchanges water with the underlying aquifer between Coeur d’Alene Lake and Spokane. 

In the upstream part of the reach, water from the river 

seeps to the aquifer; the exchange reverses farther 

downstream near Spokane, where ground water discharges back to the river. Concentrations of dissolved 

zinc in some near-river alluvial wells were slightly 

elevated (about 75 μg/L) as a result of recharge from 

the Spokane River; however, the concentrations in the 

aquifer rapidly decreased with distance from the river. 

Concentrations of other trace elements in near-river 

wells were near or below minimum reporting levels, 

and all were below drinking-water standards and guidelines (p. 10−11). 

 Major Influences on Ground-Water Quality

Soil and aquifer properties

Natural water-rock interactions

Urban land use and development 

Trace elements

in sediment1

Trace elements

in fish tissue1

Nutrients

Urban Undeveloped Mining Mixed Land Uses

Organochlorines

in tissue2

Small streams Major rivers

Selected Indicators of Surface-Water Quality

Proportion of samples with detected concentrations greater than or

equal to health-related national guidelines for drinking water,

protection of aquatic life, or desired goal for preventing nuisance

plant growth

Proportion of samples with detected concentrations less than healthrelated national guidelines for drinking water, protection of

aquatic life, or desired goal for preventing nuisance plant growth

Proportion of samples with no detections

1 Arsenic, mercury, and metals.

2 DDT and PCBs.

Proportion of samples with detected concentrations greater than or equal to

health-related national guidelines for

drinking water

Proportion of samples with detected concentrations less than health-related

national guidelines for drinking water

Proportion of samples with no detections

1 Solvents, refrigerants, fumigants, and gasoline compounds.

Selected Indicators of Ground-Water Quality

Domestic

Supply Wells

Trace

elements

Arsenic

Volatile

organics1

Nutrients

Pesticides

Radon

human consumption and for the protection of fish-eating wildlife. PCB concentrations in samples of wholebody fish from the Spokane River ranked among the 

upper 25 percent of concentrations in fish from more 

than 700 streams sampled by the NAWQA Program 

nationwide. No other organochlorine compounds in 

fish tissue exceeded human health or wildlife protection guidelines (p. 13).

2 Water Quality in the Northern Rockies Intermontane Basins
Introduction to the Northern Rockies Intermontane Basins

3

The Northern Rockies Intermontane Basins encompass 31,500 square 

miles (mi2) in western Montana, northern Idaho, and northeastern Washington 

(fig. 1). The study unit includes two 

major river basins: the Clark Fork−Pend 

Oreille River Basin (about 79 percent of 

the unit) and the Spokane River Basin 

(about 21 percent). Most of the study 

area lies within the Northern Rocky 

Mountains physiographic province. 

Topography ranges from high, mountainous areas where elevations exceed 

10,000 feet (ft) to large, flat valleys at 

elevations as low as 1,000 ft (Maret 

and Dutton, 1999). The unit contains 

numerous large natural lakes, including Flathead Lake (the largest natural 

freshwater lake in the Western United 

States), Lake Pend Oreille (one of the 

deepest lakes in the United States), and 

Priest and Coeur d’Alene Lakes, which 

are used extensively for fishing, boating, 

and other recreational activities.

Hydrologic conditions affect 

water quality in streams and 

ground water

Water quality in streams, rivers, 

and shallow ground water often varies 

in response to hydrologic conditions; 

thus, information on streamflow and 

other hydrologic conditions is critical 

for assessing water quality. For example, 

when precipitation and runoff are below 

average, streamflow is lower than normal, and concentrations of suspended 

sediment and constituents that attach to 

Figure 1. Natural geologic and topographic features in combination with land-use activities, such as mining, influence 

water-quality conditions in the Northern Rockies Intermontane Basins. 

Oreille

Coeur

Coeur

d'Alene

Lake

Lake

Pend

Oreille

Spokane

Flathead

Flathead

Lake

Clark

Fork Clark

Blackfoot

Bitterroot River

Fork

River

River

d'Alene

River

River

Pend

River

Priest

Lake

Spokane

Coeur

d'Alene

Missoula

Kalispell

Butte

Kellogg

WASHINGTON

IDAHO

IDAHO

MONTANA

Rugged, mountainous terrain with 

intermontane valleys is characteristic 

of much of the study unit.

Historical mining has affected water quality and 

aquatic life in many streams where erosion and 

runoff continue to transport trace elements that 

have accumulated in sediment.

Some of the largest and deepest 

natural lakes in the Western United 

States, such as Lake Pend Oreille, 

are contained in the Northern 

Rockies Intermontane Basins.

Urban areas, accounting for only 

1 percent of the land area, are 

growing rapidly around the citities of Missoula, Coeur d’Alene, 

and Spokane, and rely on clean 

supplies of ground water.
STREAMFLOW, IN CUBIC FEET PER SECOND

1999 2000 2001

WATER YEAR

50,000

50,000

30,000

10,000

7,000

5,000

3,000

1,000

700

500

300

100

30,000

10,000

7,000

5,000

3,000

1,000

O N D J F M A M J J A S O N D J F M A M J J A S O N D J F M A M J J A S

75th percentile

25th percentile

Daily mean

Water years 1970–2001

Clark Fork at St. Regis, Montana

Spokane River at Post Falls, Idaho

Figure 2. Streamflows were generally average during 1999−2000. Streamflows 

during 2001 were only about 40−60 percent of the 30-year historical average. 

sediment particles, such as phosphorus 

and some trace elements, often are lower 

than average. In contrast, concentrations 

of dissolved constituents, particularly 

those contributed by ground water and 

sewage-treatment effluent, commonly 

are higher than average when precipitation and streamflow are low. During 

1999 and 2000, streamflow at most sites 

was about average. Water year 2001 

was drier than normal, and streamflow 

at all sites was typically about 40 to 60 

percent of the 30-year historical average 

(fig. 2). 

Average annual precipitation in 

the Study Unit ranges from less than 15 

inches in many of the mountain valleys 

of western Montana to more than 100 

inches (primarily in the form of snow) 

in mountainous regions of northwestern 

Montana. The magnitude and quality of 

streamflow generally are determined by 

the amount of water derived from the 

winter snowpack. Streamflow typically 

is highest during the spring and lowest during the fall and winter; average 

annual runoff (the volume of water leaving a basin per unit of basin area) ranges 

from less than 5 inches at lower elevations to more than 50 inches at higher 

elevations (Tornes, 1997). 

Land-use activities, such as 

mining, affect water quality in 

the basins

The Northern Rockies Intermontane Basins primarily are forested 

(about 75 percent); the remaining land 

is agricultural (8 percent), rangeland (11 

percent), urban (1 percent), and other 

uses (5 percent). Agricultural activities 

occur primarily in the upper Clark Fork, 

the Bitterroot and Flathead River Basins 

in Montana, and in tributary basins of 

the Spokane River. Although urban land 

accounts for only 1 percent of the study 

unit, cities such as Missoula, Coeur 

d’Alene, and Spokane are growing 

rapidly. From 1990 to 2000, the total 

population in the counties containing 

these three cities grew by an average of 

22 percent (U.S. Census Bureau, 2000). 

Water quality in streams, rivers, 

lakes, and shallow ground water is 

affected by land-use activities, including 

mining, urban development, agriculture, 

and municipal and industrial discharge 

of wastewater. Mining activities have 

had a major effect on water quality; 

about 1,600 active and abandoned hardrock mines of various sizes have been 

documented (Maret and Dutton, 1999). 

In the upper Clark Fork Basin, mine tailings have been transported and deposited along more than 150 miles (mi) of 

river channel and flood plain from Butte 

to near Missoula (Andrews, 1987). Similarly, tailings discharged directly to the 

South Fork Coeur d’Alene River have 

been transported and deposited along 

60 mi of the river channel and flood 

plain of the Coeur d’Alene River, on 

the bottom of Coeur d’Alene Lake, and 

out of the lake into the Spokane River 

(Grosbois and others, 2001). These tailings typically contain elevated concentrations of arsenic, cadmium, copper, 

lead, and zinc. Toxic effects of these 

trace elements have led to numerous 

fishkills in the upper Clark Fork since 

1984 (Phillips and Lipton, 1995) and a 

depleted population of benthic invertebrates in Coeur d’Alene Lake (Woods 

and Beckwith, 1997). 

High-elevation, headwater streams 

in forested watersheds have generally 

excellent water quality and healthy 

biological communities, except in some 

areas affected by logging, mining, and 

recreation. Historical logging practices 

common to some forested areas in the 

Northern Rockies Intermontane Basins 

often introduced large amounts of sediment to streams, primarily from massive 

soil erosion and severely destabilized 

streambanks and channels (Woods and 

Beckwith, 1997). Forest fires also can 

influence water quality; runoff from 

burned areas transports eroded sediment 

and ash to streams. 

4 Water Quality in the Northern Rockies Intermontane Basins
Figure 3. Agriculture accounts for 81 percent of the water used in the Study Unit, primarily in the Clark Fork−Pend Oreille River Basin. Although ground water accounts for only 

19 percent of the water used in the study unit, it accounts for 70 percent of the drinkingwater supply. 

WATER WITHDRAWALS, IN MILLIONS OF GALLONS PER DAY

PERCENTAGE OF TOTAL WITHDRAWALS

1,200

1,000

800

600

400

200

0

80

70

60

50

40

30

20

10

0

TOTAL

WITHDRAWALS

PUPLIC

SUPPLY

DOMESTIC INDUSTRIAL AGRICULTURAL

Surface water

Ground water

Spokane

River

Basin

Clark Fork/

Pend Oreille

River Basin

Main-stem dams on the Clark 

Fork, Flathead, and Spokane 

Rivers regulate streamflows 

for hydroelectric-power 

generation and flood control. 

These dams change the 

natural hydrologic patterns of 

rivers and act as barriers to 

fish passage.

In lower elevation areas, water 

quality is affected by land-use activities involving livestock grazing, dryland 

and irrigated agriculture, and urban 

development. Runoff from agricultural 

land commonly contributes sediment, 

nutrients, and pesticides to streams. 

Runoff from urban areas commonly contributes nutrients, bacteria, pesticides, 

organic chemicals, and trace elements to 

streams and aquifers. Nutrients (primarily nitrogen and phosphorus) are of 

special concern for Coeur d’Alene Lake, 

Flathead Lake, and Lake Pend Oreille 

because of the potential for eutrophication and excessive algal growth in these 

low-productivity lakes. Other sources of 

nutrients to streams include municipal 

wastes, septic-system effluent, and soil 

erosion from logging. 

Surface water is used primarily 

for irrigation and ground water 

is used primarily for drinkingwater and industrial supplies

Total water use reported during 

2000 in the Study Unit averaged about 

1,350 million gallons per day (fig. 3). 

Irrigation, primarily from surface-water 

sources in the Clark Fork–Pend Oreille 

River Basin, accounted for about 81 percent of the total water use. Although surface-water sources provide most of the 

water for agricultural use, ground water 

is the main source for public, domestic, 

and industrial supplies. Although ground 

water accounts for only about 19 percent 

of the total water used in the basins, it 

accounts for about 70 percent of the 

drinking-water supply. As the population 

in the Study Unit continues to grow, the 

amount of ground water used for public 

supply also will continue to grow. 

On the Clark Fork and the Flathead 

and Spokane Rivers, 16 dams regulate 

streamflow for hydroelectric-power 

generation and flood control (Maret and 

Dutton, 1999). The dams, however, also 

alter the natural hydrologic patterns of 

rivers and act as barriers to fish passage.

Ground water is vulnerable to 

contamination

Principal aquifers used for water 

supply in the basins are in basin-fill 

deposits along most reaches of large 

rivers and major tributaries. These basinfill aquifers are composed primarily of 

gravel, sand, silt, and clay derived from 

glacial outburst floods, glacial debris, 

alluvial fans, stream transport, and 

lakebed sediment. The heterogeneous 

nature of these unconsolidated materials results in a large range of hydraulic 

properties, which in turn results in variable productivity of wells. 

The Spokane Valley/Rathdrum 

Prairie and Missoula/Bitterroot basinfill aquifers underlying Spokane, Coeur 

d’Alene, and Missoula currently supply 

drinking water to about 70 percent of the 

population in the Study Unit and have 

been designated as sole-source aquifers 

by the USEPA. These aquifers provide 

the only economically available supply 

of drinking water for these cities. The 

aquifers are particularly vulnerable to 

contamination, however, because of a 

relatively shallow water table, porous 

aquifer materials, and relatively rapid 

rates of recharge. 

Introduction 5
6 Water Quality in the Northern Rockies Intermontane Basins

Major Findings

Historical mining 

activities have degraded 

water-quality conditions 

in numerous streams

Mining has been central to the 

economy of many communities in 

Montana and Idaho since the late 1800s. 

In the past, mining activities yielded 

large volumes of metal-rich tailings that 

were commonly deposited in nearby 

streams or along their banks and flood 

plains. In a comprehensive investigation 

of mining in the Coeur d’Alene River 

Basin by the U.S. Bureau of Fisheries 

in 1932, Dr. M.M. Ellis found “that as 

far as fisheries are concerned, the mine 

wastes poured in the South Fork of 

the Coeur d’Alene River have reduced 

50 miles of the South Fork and Main 

Coeur d’Alene River to a barren stream 

practically without fish fauna, fish food, 

or plankton, and with enormous lateral 

supplies of potentially toxic materials which will continue to poison the 

In the early 20th century, mining drove 

the economic, social, and political 

development in the region, and a number of towns resembled those of the 

industrialized East. Mining also affected 

the natural environment, however, as 

mining wastes and contamination, such 

as raw sewage from mining settlements, were deposited directly into 

streams.

0

0

10

10

30

30

20

20

40

40

50 MILES

50 KILOMETERS

EXPLANATION

1 to 19

20 to 50

Greater than 50

MINING CLAIMS PER SECTION

1

7

SAMPLE TYPES COLLECTED

AND SITE NUMBER

Sediment and fish tissue

Sediment only

Coeur d'Alene

Lake

Lake Pend

Oreille Flathead

Lake

Hungry

Horse

Reservoir

Priest Lake

114°

49°

115°

116°

117°

49°

118°

48°

118°

117° 47°

116°

115°

46°

114°

113°

46°

47°

48°

113°

Spokane Coeur d'Alene

Missoula

Kalispell

Butte

Pend Oreille

River

Coeur

Spokane

Flathead

Clark

Fork

Clark

Blackfoot

Bitterroot

River

Fork

River River

d'Alene

River

River

South Fork

St River Regis

1

12

15

2

3

4

5

6

7

8

9

10

11

14

13

16 21

17

18

19

20

22

MONTANA IDAHO

WASHINGTON

Figure 4. Concentrations of some trace 

elements in streambed sediment at some 

sites exceeded guidelines for the protection of aquatic life by as much as 40 

times. The highest concentrations of trace 

elements were from streams within, or 

downstream from, USEPA Superfund sites 

affected by historical mining.

CONCENTRATION OF TRACE ELEMENTS IN STREAMBED

SEDIMENT, IN MICROGRAMS PER GRAM, DRY WEIGHT 10,000

5,000

1,000

500

100

50

10

5

1

0.5

0.1

0.05

0.01 ARSENIC CADMIUM COPPER LEAD MERCURY ZINC

19

18

2

6

14

20

8

16

8

19 8

14

18

2

1

8

20

1

1

14

2

14

1

18

19

20

18

14

2

19

20

8

18

2

22

8

20

6

19

14

1

Probable effect level (PEL)

Concentration exceeding PEL

Relatively pristine site

18 Site number on map
Major Findings 7

Mining contributes to elevated 

concentrations of trace elements in streambed sediment 

Potentially harmful concentrations 

of trace elements have accumulated 

in streambed sediment in numerous 

streams in the Clark Fork−Pend Oreille 

and Spokane River Basins. Concentrations of six trace elements (arsenic, 

cadmium, copper, lead, mercury, and 

zinc) exceeded sediment-quality guidelines for protection of aquatic life (PEL) 

in the Clark Fork near Galen and Turah, 

Montana (sites 1 and 2); the South Fork 

Coeur d’Alene River near Pinehurst, 

Idaho (site 18); the Coeur d’Alene 

River near Harrison, Idaho (site 19); 

and the Spokane River near Post Falls, 

Idaho (site 20) (fig. 4). These sites are 

downstream from areas that have been 

heavily affected by historical mining 

and designated as USEPA Superfund 

Concentrations of some trace elements associated with 

mining were among the highest in streambed sediment 

sampled across the Nation

Concentrations of arsenic, cadmium, copper, lead, 

mercury, and zinc in more than 50 percent of the streambed-sediment samples collected in the Clark Fork-Pend 

Oreille and Spokane River Basins exceeded national 

median concentrations for these trace elements in more 

than 1,200 samples collected by the NAWQA 

Program from all land-use settings in 48 

major river basins. Concentrations of each 

of these trace elements in more than 30 

percent of the samples ranked among the 

highest 10 percent of national concentrations. Concentrations of copper in streambed sediment from the Clark Fork near 

Galen and at Turah and concentrations of 

arsenic, cadmium, mercury, lead, and zinc 

in streambed sediment from the South Fork 

and Coeur d’Alene Rivers were among the 

highest 1 percent of national concentrations. 

Percentage of concentrations in the upper 50 percentile

Percentage of concentrations in the upper 10 percentile

Percentage of concentrations in the upper 1 percentile

100

90

80

70

60

50

40

30

20

10

0

Arsenic Cadmium Copper Mercury Lead Zinc

PERCEN

TA

GE OF SA

MPLES

TRACE ELEMENT

are subsequently redeposited in stream 

sediment, lake bottoms, and flood plains. 

It has been estimated that mining has 

introduced more than 100 million tons 

of metal-enriched tailings to both the 

Clark Fork (Andrews, 1987) and the 

South Fork Coeur d’Alene River Basins 

(Long, 1998). 

waters of the Coeur d’Alene River for 

a considerable period of time” (Ellis, 

1940). Although most mining activities 

in the basins have been discontinued 

or curtailed, and practices to minimize 

the adverse effects have been improved, 

erosion and runoff continue to transport 

and disperse tailings downstream, which 

Trace elements in streambed sediment - How toxic?

Trace-element concentrations in streambed sediment, such as those shown 

in figure 4, are compared with a probable effect level, or PEL, established as 

a Canadian Sediment Quality Guideline (Canadian Council of Ministers of 

the Environment, 1999) for the protection of aquatic life. According to the 

guideline, trace-element concentrations in bulk sediment exceeding the PEL 

frequently are associated with adverse biological effects. NAWQA samples 

represent the fine-grained fraction of bed sediment only (less than 63 micrometers), which, in general, contains higher concentrations of trace elements than 

bulk sediment does. NAWQA samples, therefore, may somewhat overstate the 

problem based on bulk-sediment criteria, and caution should be used in applying the criteria to values close to the PEL.
8 Water Quality in the Northern Rockies Intermontane Basins

sites. Although these streams are not 

used as a source for drinking water, the 

frequent and elevated occurrence of 

trace elements in sediment is a potential 

concern for wildlife, recreational use, 

and fish consumption. Concentrations of 

trace elements were lowest in streambed 

sediment from near-pristine areas of the 

Middle Fork Flathead River in Montana, 

and the St. Joe River at Red Ives in 

Idaho. 

Trace elements are transported 

downstream in the Clark Fork 

and Coeur d’Alene River Basins 

and accumulate in lakes

Transport of trace-element contaminants in the Clark Fork and Coeur 

d’Alene River Basins can be substantial. 

For example, about 34,000 pounds (lb) 

of copper, 6,000 lb of lead, and 56,000 

lb of zinc were transported annually in 

the Clark Fork at Turah during water 

years 1999−2001 (site 2 in fig. 4). These 

loads actually may underestimate average rates of transport because precipitation, runoff, and streamflow were near 

or below normal during those years 

(streamflows ranged from 63 to 113 

percent of normal compared with the 15-

year period 1986−2001). Precipitation 

and runoff, which wash contaminated 

sediment from source areas into streams, 

control the transport and subsequent 

downstream distribution. For example, 

during water year 1997, when the annual 

mean streamflow in the Clark Fork 

was about 180 percent of the historical 

average, about 5 to 7 times more copper 

(220,000 lb), lead (38,000 lb), and zinc 

(320,000 lb) were transported in the 

Clark Fork at Turah than during water 

years 1999−2001 (Lambing, 1998). 

Excessive amounts of trace elements also can enter streams during 

storms and periods of high snowmelt 

runoff. For example, high flows in the 

Coeur d’Alene River following a heavy 

rain on snowpack in February 1996 

transported about 1.4 million lb of lead 

into Coeur d’Alene Lake in 1 day (Beckwith, 1996), which is about 4 times the 

average annual load of lead (360,000 

lb) transported into the lake during 

1999−2001 (Clark, 2003). 

Large quantities of trace elements 

are transported to and deposited on the 

bottom of Coeur d’Alene Lake (Horowitz and others, 1993; Bookstrom and 

others, 2001; Woods, 2001). About 82.5 

million tons of trace-element-enriched 

sediment, covering about 85 percent 

of the lakebed, have been deposited in 

Coeur d’Alene Lake since the late 1800s 

(Horowitz and others, 1995). Median 

concentrations of arsenic, cadmium, 

lead, mercury, and zinc in surficial 

lakebed sediment samples collected during the early 1990s from enriched areas 

of the lake exceeded sediment-quality 

guidelines for the protection of aquatic 

life by as much as 10 times (Woods and 

Beckwith, 1997). 

Trace elements continue to accumulate in Coeur d’Alene Lake. About 

8,900 lb of total cadmium, 500,000 lb 

of total lead, and 1.4 million lb of total 

zinc entered Coeur d’Alene Lake each 

year during 1999−2000 from the Coeur 

d’Alene River (Clark, 2003). Not all 

of these trace elements, however, are 

retained in the lake. For example, about 

4,600 lb of cadmium and 980,000 lb 

of zinc, or about 52 and 70 percent 

of the annual loads entering the lake 

were transported from the lake, primarily in a dissolved form, and into the 

Spokane River during 1999−2000 (fig. 

5). Because lead is less soluble than 

cadmium and zinc in water, the lake is 

more efficient in retaining lead, which 

adheres to sediment particles that settle 

to the lakebed. During 1999−2000, only 

about 44,000 lb/yr, or about 9 percent of 

the lead entering the lake, was transported from the lake into the Spokane 

River. Elevated concentrations of trace 

elements in streambed sediment in 

the Spokane River near Post Falls and 

farther downstream (Beckwith, 2002) 

most likely result from transport through 

Coeur d’Alene Lake. Likewise, elevated 

concentrations of trace elements (above 

natural background levels) in streambed 

sediment from the Pend Oreille River 

downstream from Lake Pend Oreille 

(Beckwith, 2002) indicate trace-element 

transport throughout the length of the 

Clark Fork and through the lake. 

Figure 5. During 1999−2000, Coeur d’Alene 

Lake retained about 46 percent of the 

combined load of cadmium, lead, and 

zinc entering the lake. The remainder 

was transported out of the lake and into 

the Spokane River. The lake is especially 

efficient at retaining lead, which adheres 

to sediment particles and is subsequently 

deposited on the lake bottom.

Runoff from storm events and snowmelt 

can transport large quantities of sediment containing elevated concentrations 

of trace elements into the Coeur d’Alene 

River and Coeur d’Alene Lake. About 85 

percent of the lakebed is covered with 

trace-element-enriched sediment, which 

can be toxic to benthic organisms.

Cadmium

Lead

Zinc

ANNUAL LOAD, IN POUNDS PER YEAR 2,000,000

1,500,000

1,000,000

500,000

0

Inflow to Coeur

d'Alene Lake

Outflow from Coeur

d'Alene Lake
Major Findings 9

CONCENTRATION OF TRACE ELEMENTS IN FISH

LIVERS, IN MICROGRAMS PER GRAM, DRY WEIGHT 10,000

5,000

1,000

500

100

50

10

5

1

0.5

0.1

0.05

ARSENIC CADMIUM COPPER LEAD MERCURY ZINC 0.01

16

8

14

1

14

18

8

17

16 4

14

8

14

8

18

5

14

8

22

8

18

14

62%

50%

56%

50%

75%

38%

56%

Relatively pristine site

NAWQA national median

concentration

Site number from figure 4

Percentage of concentrations

equal to or exceeding

NAWQA national median

16

Trace-element contamination 

may be adversely affecting 

aquatic life

Streambeds provide habitat for 

many aquatic organisms. Streambed 

sediment contaminated with trace elements can be toxic to aquatic invertebrates (worms, clams, and insect larvae) 

or can provide a sublethal source of 

exposure causing bioaccumulation in 

invertebrate tissues and a concentrated 

source of trace elements in the diet 

of fish (Woodward and others, 1995). 

Previous studies in the upper Clark Fork 

have documented adverse effects of 

trace elements, including bioaccumulation in insect communities (Axtmann 

and others, 1997), fishkills (Phillips and 

Lipton, 1995), and reduced fish diversity 

and populations (Marr and others, 1995).

Trace-element concentrations 

in the tissue of aquatic biota 

are elevated

Tissue samples from caddisfly 

larvae and fish indicate that elevated 

concentrations of trace elements in water 

and streambed sediment contribute to 

elevated concentrations in biota. Data 

from the Coeur d’Alene River Basin 

showed that concentrations of cadmium, 

lead, and zinc in tissues of caddisfly 

larvae were statistically correlated with 

concentrations of trace elements in the 

sediment and water, all of which were 

related to upstream mining activity 

(Maret and others, 2003). Concentrations of trace elements in caddisflies 

were highest at sites in the basin affected 

by historical mining. For example, 

concentrations of lead in caddisflies 

from the South Fork Coeur d’Alene 

River at Silverton were almost 100 times 

higher than the median lead concentration in caddisflies from three unaffected 

reference sites on the St. Regis River in 

Montana. 

Historical mining activities also 

have affected concentrations of trace elements in fish, as measured in fish livers. 

For example, the highest concentrations 

of cadmium, lead, and zinc were in liver 

samples of fish from the mining-affected 

South Fork Coeur d’Alene River near 

Pinehurst (fig. 6) (Maret and Skinner, 

2000). Consistent with trace elements 

in streambed sediment, concentrations 

of trace elements were lowest in liver 

samples of fish from relatively pristine 

areas of the Middle Fork Flathead River, 

Montana, and the St. Joe River at Red 

Ives, Idaho. Concentrations of some 

trace elements, however, were elevated 

in streams relatively unaffected by 

mining. Specifically, concentrations of 

copper and mercury were highest in livers of fish from Rock Creek, a tributary 

of the Clark Fork near Clinton, Montana 

(site 4), and the Bitterroot River near 

Missoula, Montana (site 5). Copper and 

mercury in streambed sediment at these 

two relatively unaffected sites were low; 

therefore, elevated concentrations in the 

fish-liver samples probably reflect fish 

migration into tributaries from the Clark 

Fork, where the trace elements originally were bioaccumulated. 

In contrast to trace-element concentrations in liver samples, concentrations 

in sportfish (trout and whitefish) fillets 

were relatively low. No fillet samples 

from fish collected in the Study Unit 

contained concentrations in excess of 

USEPA human-health screening values 

for fish consumption (Maret and Skinner, 2000). This finding is noteworthy 

because mercury, in particular, is known 

to bioaccumulate in muscle tissue of 

fish and subsequently is passed through 

the food chain to predatory wildlife and 

humans (Wiener and Spry, 1996). 

Figure 6. Concentrations of trace elements in liver samples of fish collected from the 

Northern Rockies Intermontane Basins generally ranked in the top 50 percentile of concentrations in fish collected from 462 streams nationwide by the NAWQA Program. Concentrations of cadmium, copper, and lead in fish from some sites exceeded the NAWQA 

national median by more than 10 times. 

Trace-element concentrations in fish and 

invertebrates were higher in streams 

affected by mining compared with concentrations in nonaffected streams. Miningaffected streams also contained fewer 

individuals, fewer native fish species, and 

less diversity in the biological community 

than did nonaffected streams.
10 Water Quality in the Northern Rockies Intermontane Basins

Species diversity is reduced in 

mining-affected streams

 Elevated concentrations of trace 

elements also have contributed to 

reduced diversity and abundance of 

native fish and invertebrate species and 

increased abundance of nonnative fish 

species. For example, sculpins, which 

are sensitive to pollution, were scarce 

or nonexistent at mining-affected sites 

(Maret and MacCoy, 2002). Although 

trout also were less abundant at miningaffected sites, they still were collected 

at sites, such as the South Fork Coeur 

d’Alene River near Pinehurst, where 

concentrations of dissolved trace elements in water exceeded USEPA chronic 

water-quality criteria for the protection of aquatic life (Hornig and others, 

1988). Invertebrate species sensitive to 

pollution, such as stoneflies, mayflies, 

and caddisflies, were not as common at 

mining-affected sites as at sites unaffected by mining (Maret and others, 

2003). Specifically, the median density 

of invertebrates at the mining-affected 

sites (about 400 individuals per square 

foot) was significantly lower than at 

reference sites (about 770 individuals 

per square foot). Fewer than 150 invertebrate individuals per square foot were 

present at the mining-affected sites at 

the mouth of Canyon Creek in the South 

Fork Coeur d’Alene River Basin and at 

the South Fork Coeur d’Alene River at 

Silverton. 

Trace-element contamination in the Spokane River is a 

concern

Elevated concentrations of trace 

elements in the Spokane River are of 

priority concern to water-quality managers (Grosbois and others, 2001). In 

2000, the State of Idaho and the USEPA 

developed and issued a total maximum 

daily load (TMDL) to allocate trace-element loading in the Spokane River Basin 

in Idaho. The Washington State Department of Ecology also has placed the 

Spokane River on its EPA 303(d) list for 

trace-element concentrations in violation 

of Washington’s water-quality criteria 

(Washington State Department of Ecology, 2000b). 

Trace-element concentrations in 

water were highest within impoundments or low-velocity sections of the 

river near the outlet of Coeur d’Alene 

Lake, where fine-grained sediment is 

trapped (Grosbois and others, 2001). 

Concentrations generally decreased 

with increased distance downstream 

from Coeur d’Alene Lake as a result of 

sedimentation and mixing with more 

dilute inflows. Concentrations of arsenic, cadmium, lead, mercury, and zinc in 

streambed sediment from the Spokane 

River near Post Falls exceeded sediment-quality guidelines for the protection of aquatic life and were between 3 

ELEVATION, IN FEET ABOVE NATIONAL

GEODETIC VERTICAL DATUM OF 1929

FEET

FROM

RIVER

2,070

2,036

2,002

1,968

1,934

1,900 3,500

900

475

200

100

60

42

14

<1

Recharge

<1 <1

Median zinc concentration, in micrograms per liter,

water year 2001

Well

Water level

13

EXPLANATION

0

0

1

1

2 MILES

2 KILOMETERS WASHIN

G

T

O

N

ID

A

H

O

Spokane

city limits

Spokane River

A

A'

Spokane River near Post Falls

(site 20, figure 4)

Spokane Valley/Rathdrum Prairie

sole source aquifer

Ground water influenced by river

Losing river reach (river water seeping to ground water)

Gaining river reach (ground water discharging to river)

Direction of regional ground-water flow

EXPLANATION

Spokane River

A A'

Figure 7. Water containing elevated concentrations of zinc are transported from the 

Spokane River to the underlying Spokane Valley/Rathdrum Prairie aquifer. The extent of 

the river’s broader influence on the water quality of the aquifer, however, is minimal as 

most of the effect is limited to a several-hundred-foot margin along the river. 
Major Findings 11

and 14 times higher than the concentrations downstream near Spokane. 

Trace-element concentrations in 

water and sediment in the Spokane River 

have raised human health concerns 

about potential contamination of the 

underlying Spokane Valley/Rathdrum 

Prairie aquifer, which supplies drinking 

water to the cities of Coeur d’Alene and 

Spokane and the surrounding area. During high stream discharge, the Spokane 

River may lose more than 500 cubic 

feet per second (ft3/s) of its flow to the 

aquifer between Coeur d’Alene Lake 

and Spokane (Bolke and Vaccaro, 1981; 

Gearhart and Buchanan, 2000). Seepage 

from the Spokane River to the aquifer 

transports dissolved trace elements, primarily zinc, into the aquifer. Movement 

of trace elements in ground water within 

Mean annual concentration,

in milligrams per liter

Less than 0.6

0.6 to 3.0

Greater than 3.0

Nitrogen input, in

pounds per acre

Less than 6

6 to 25

Greater than 25

Mean annual concentration,

in milligrams per liter

Less than 0.05

0.05 to 0.3

Greater than 0.3

Phosphorus input, in

pounds per acre

Less than 2

2 to 5

Greater than 5

TOTAL NITROGEN

TOTAL PHOSPHORUS

Nutrient concentrations in the Northern 

Rockies Intermontane Basins were among 

the lowest when compared with 479 streams 

sampled by the NAWQA Program that drain 

undeveloped, urban, agricultural, and mixed 

land-use basins across the Nation. Concentrations of total nitrogen at 9 of 10 sites in this 

Study Unit were among the lowest 10 percent 

nationally; concentrations in the Spokane 

River at Seven Mile Bridge near Spokane 

were among the lowest 30 percent. Concentrations of total phosphorus were among 

the lowest 10 percent nationally at 7 of the 

10 sites and among the lowest 25 percent at 

all 10 sites. The relatively low concentrations are due primarily to low chemical use 

and population density; inputs of nitrogen 

and phosphorus from fertilizer, manure, and 

sewage-treatment effluent were some of the 

lowest in the Nation. 

a 200-ft margin of the river, which has 

been reported by Marti and Garrigues 

(2001), could affect water-supply wells 

near the river. 

Zinc concentrations rapidly 

decreased in the alluvial aquifer with 

distance from the Spokane River 

(Caldwell and Bowers, 2003) (fig. 7). 

Most of the water lost from the Spokane River to the aquifer appears to 

travel along the path of the river and 

discharges back to the river along a 

gaining reach near Spokane. Although 

dissolved zinc concentrations in some 

near-river wells were elevated as a result 

of recharge from the Spokane River, 

concentrations of other trace elements 

were below drinking-water standards 

and guidelines, and most were below 

minimum reporting levels. 

Nutrient concentrations 

in streams generally are 

low

Concentrations of nutrients (nitrogen and phosphorus) in streams primarily reflect land use in the upstream 

watershed and generally are highest 

downstream from agricultural and 

urban areas and lowest downstream 

from undeveloped land, forests, and 

rangeland (Mueller and Helsel, 1996). 

Concentrations of total nitrogen and 

phosphorus considered to be natural (or 

“background”) are 0.26 and 0.02 mg/L, 

calculated from samples collected from 

63 streams draining relatively undeveloped, pristine basins across the Nation 

Nutrient concentrations in many streams were among 

the lowest in the Nation
12 Water Quality in the Northern Rockies Intermontane Basins

(Clark and others, 2000). Such values 

often serve as reference levels against 

which effects of human activities, such 

as applications of fertilizers and discharge of sewage treatment effluent, can 

be assessed. 

Concentration benchmarks also 

have been established to control nuisance filamentous algal growth. For 

example, the USEPA established a 

desired national goal of 0.1 mg/L of 

total phosphorus for the prevention of 

nuisance growth in streams and other 

flowing waters not discharging directly 

to lakes or impoundments. More regionalized benchmarks proposed by Watson 

and others (2000) for the Clark Fork in 

western Montana to control nuisance 

filamentous algal growth are 0.02 and 

0.3 mg/L of total phosphorus and nitrogen. 

Nutrient concentrations in streams 

generally were low, often below minimum reporting levels. Low concentrations probably are attributable to a 

relatively sparse population, the relatively small amount of agricultural land 

(8 percent of Study Unit), and the large 

amount of forests and rangeland (86 

percent of Study Unit). Samples from 

only 2 of 10 stream sites, South Fork 

Coeur d’Alene River near Pinehurst and 

Spokane River at Seven Mile Bridge 

near Spokane, contained median total 

nitrogen concentrations larger than 

the national background concentration 

for relatively undisturbed sites (0.26 

mg/L) or the regional benchmark for 

the prevention of nuisance algal growth 

(0.3 mg/L). Median concentrations at 

these two sites were 0.34 and 0.74 mg/L. 

Samples from only three sites, Clark 

Fork at Turah Bridge, South Fork Coeur 

d’Alene River near Pinehurst, and Spokane River at Seven Mile Bridge near 

Spokane, contained median concentrations of total phosphorus (0.03 mg/L) 

higher than the background concentration for relatively undisturbed sites and 

the regional benchmark for the prevention of nuisance algal growth (both 

0.02 mg/L). Elevated concentrations 

of total nitrogen and total phosphorus 

in the South Fork Coeur d’Alene River 

near Pinehurst and the Spokane River 

at Seven Mile Bridge are attributable to 

sewage effluent. The concentrations of 

total nitrogen (greater than 2 mg/L) and 

phosphorus (greater than 0.1 mg/L) were 

particularly elevated in the Spokane 

River during low flow, when treated 

wastewater from the city of Spokane 

composed as much as 10 percent of 

the stream discharge measured in the 

Spokane River at Seven Mile Bridge 

(Beckwith, 2003). 

Despite low concentrations 

of nutrients, some streams are 

impaired by algal growth

Growth of periphyton algae (an 

attached algal community living on 

stream bottoms) indicated nutrient 

enrichment at 3 of 10 stream sites; algae 

density was highest at the Spokane River 

at Seven Mile Bridge. Specifically, densities of periphyton algae and concentrations of algal chlorophyll-a (the pigment 

responsible for photosynthesis in algae) 

were more than twice as high at the 

Spokane River at Seven Mile Bridge 

than at any other site. The chlorophyll-a

concentration at the Spokane River at 

Seven Mile Bridge was 94 milligrams 

per square meter (mg/m2) (MacCoy and 

Maret, 2003), which closely approaches 

100 mg/m2, the chlorophyll-a concentration typically associated with a nuisance 

level of periphyton growth (Welch and 

others, 1989). Periphyton algae and 

chlorophyll-a also were elevated in the 

Bitterroot River near Missoula and the 

Flathead River at Perma but did not 

exceed 100 mg/m2 at either site. 

Lakes trap large quantities of 

nutrients 

The effects of urban development 

and an increasing population on nutrient enrichment in lakes in the Northern 

Rockies Intermontane Basins are of 

increasing concern. Development can 

increase nutrient loads through runoff 

from lawns as well as from municipal 

wastewater-treatment facilities. Subsequent nutrient enrichment in lakes can 

result in increased growth of nuisance 

aquatic plants, loss of water clarity, 

and reduced dissolved-oxygen concentrations in the lower water column. 

Low dissolved oxygen near the sediment/water interface can severely stress 

benthic organisms and bottom-dwelling 

fish and release potentially toxic trace 

elements into the water. Lakes also can 

dramatically affect downstream water 

quality through retention of incoming 

sediment, nutrients, and contaminants. 

The amount of constituents retained in 

lakes reflects a combination of physical 

and hydrologic characteristics such as 

circulation patterns and sedimentation of 

incoming materials, as well as biological processes such as nutrient uptake by 

algae. 

Annual loads of nitrogen and phosphorus delivered to, and released from, 

Coeur d’Alene Lake, Flathead Lake, and 

Lake Pend Oreille differ substantially. 

Specifically, Coeur d’Alene Lake and 

Lake Pend Oreille generally retain less 

than 15 percent of the annual loads of 

total nitrogen they receive, whereas 

Flathead Lake retains about one-third of 

the annual load of nitrogen it receives 

(Woods, in press). The greater retention 

of nitrogen in Flathead Lake is caused 

by its circulation patterns, which result 

in a longer hydraulic residence time and 

greater uptake of incoming nitrogen. 

The retention of phosphorus is substantially greater than retention of nitrogen 

because phosphorus tends to attach to 

inorganic and organic particles, which 

settle to the lakebeds; about one-half 

and three-fourths of annual incoming loads of phosphorus are retained 

in Coeur d’Alene and Flathead Lakes, 

respectively. Phosphorus retention in 

Lake Pend Oreille is less; only about 15 

percent of the total phosphorus received 

annually is retained. Circulation patterns in Lake Pend Oreille tend to move 

water and sediments from the inflow 

of the Clark Fork directly northward 

toward the Pend Oreille River outflow, 

thus minimizing mixing in the southern 

part of the lake. Thermal stratification, 

adsorption/desorption reactions, nutrient 

uptake by phytoplankton, and organic 

respiration and decay are other important processes that affect nutrient cycling 

in these lakes (Woods, in press).
Major Findings 13

Fish in the Spokane River 

contain polychlorinated 

biphenyls (PCBs) at elevated concentrations 

Organic contamination of bed 

sediment and fish has occurred in the 

Spokane River as a result of many years 

of industrial and wastewater discharge 

to streams in the Spokane area (Washington State Department of Ecology, 

1995; Maret and Dutton, 1999; Maret 

and MacCoy, 2002). NAWQA sampling, conducted in partnership with 

the Washington State Department of 

Ecology, identified elevated concentrations of PCBs ranging from 140 to 500 

μg/kg in whole-body tissue samples of 

suckers from four sites in the Spokane 

River (MacCoy, 2001). These concentrations exceeded the 110-μg/kg criterion 

established to protect fish-eating wildlife 

(Newell and others, 1987). Concentrations in sportfish fillets (rainbow trout 

and whitefish) ranged from 70 to 1,610 

μg/kg, far exceeding 5 μg/kg, a fish-tissue concentration established by the 

USEPA for human consumption (U.S. 

Environmental Protection Agency, 

1999). A comparison of data collected 

in a 1993 study (Washington State 

Department of Ecology, 1995) with data 

collected in 1999 as part of the NAWQA 

Program determined that concentrations 

of PCBs in fish did not decline significantly between 1993 and 1999. On the 

basis of these findings, the Washington 

State Department of Ecology issued a 

health advisory in March 2001 recommending restrictions on consumption 

of fish from selected reaches of the 

Spokane River.

Although concentrations of total 

PCBs in fish tissue of whole-body 

fish samples from the Spokane River 

exceeded the 110-μg/kg (microgram 

per kilogram) criterion for the protection of fish-eating wildlife (Newell and 

others, 1987), they were not among the 

Although PCBs in whole-body tissue samples of fish from the Spokane 

River were high, they were not among the highest nationally

PCBs IN TISSUE SA

MPLES OF WHOLE-BODY FISH,

IN

MICROGRA

MS PER KILOGRA

M, WET WEIGHT

All NAWQA

STREAMS

(703 samples)

NAWQA

URBAN STREAMS

(101 samples)

40

100,000

50,000

5,000

10,000

1,000

500

100

Spokane

River

samples

Fish-eating wildlife

criterion, 110 μg/kg

Outliers

75th percentile

50th percentile

(median)

25th percentile

10th percentile

90th percentile

Sum of total PCB concentrations in whole-body

fish samples from urban streams

Lowest 50 percent (all with no detections)

Second highest 25 percent

Highest 25 percent

highest concentrations nationally. When 

compared with other whole-body tissue 

samples of fish collected by NAWQA 

from more than 700 streams draining 

watersheds that represent a variety of 

land uses, PCBs in the Spokane River 

fish samples (140 to 500 μg/kg) were 

higher than the national median (50th 

percentile concentration). However, 

concentrations of PCBs in fish from the 

Spokane River were much lower than 

concentrations in fish collected from 

some urban and agricultural streams in 

the northeastern United States. Concentrations in some of these samples 

exceeded 10,000 μg/kg.

 PCBs — What are they? 

PCBs are a group of similar, 

manufactured, organochlorine 

chemicals. Their primary use was 

to insulate electrical equipment 

such as high-voltage transformers, 

but they also were used in a wide 

variety of other materials. PCBs 

are long lived in the environment 

and accumulate in the bodies of 

fish and other animals, where 

they can be toxic. They have been 

implicated as potential carcinogens and as human endocrine disruptors. Manufacture of PCBs in 

the United States ended in 1977, 

but because of their environmental 

persistence, significant amounts of 

PCBs remain in the environment.
14 Water Quality in the Northern Rockies Intermontane Basins

The Spokane River also 

contains low concentrations of pesticides and 

volatile organic compounds 

Out of 47 pesticides and 84 VOCs 

analyzed, 12 pesticides (or pesticide 

breakdown products) and 15 VOCs were 

detected (fig. 8) in water samples collected from the Spokane River near Post 

Falls and at Seven Mile Bridge. Nearly 

all of the detections were at very low 

concentrations and none exceeded established USEPA water-quality standards 

and guidelines. 

The herbicide triallate, used on 

barley and wheat, was detected in 40 

percent of 22 water samples collected 

from the Spokane River during the 

spring and summer of 1999 and 2000. 

The herbicide atrazine was the only 

other pesticide detected in more than 10 

percent of the samples. The herbicides 

EPTC (0.019 μg/L), trifluralin (0.031 

μg/L), and pendimethalin (0.019 μg/L) 

were the only pesticides detected at 

quantifiable concentrations; all other 

pesticide detections were reported as 

estimates because of their extremely low 

concentration.

VOCs detected in the Spokane 

River belong to three general classes: 

fuel-related, trihalomethanes, and solvents. These classes of VOCs are common in storm water and shallow ground 

water in urban areas across the Nation 

(Lopes and Bender, 1998). Toluene, 

benzene, chloroform, and acetone were 

detected in more than 50 percent of 12 

samples collected from the Spokane 

River during February through October 

1999. Similar to pesticide detections in 

the Spokane River, most VOC detections were reported as estimates because 

of their low concentrations. MTBE was 

detected in two samples at a concentration of 0.3 μg/L, well below the 20- to 

40-μg/L drinking-water advisory issued 

by the USEPA (U.S. Environmental 

Protection Agency, 1997). 

0.004(e)

0.004(e)

0.019

0.003(e)

0.005(e)

0.004(e)

0.004(e)

0.031

0.003(e)

0.003(e)

0.019

0.002(e)

0.26

0.18

0.13

15

0.04(e)

0.02(e)

0.01(e)

0.04(e)

0.04(e)

0.01(e)

0.01(e)

0.3

0.04(e)

0.01(e)

0.01(e)

Triallate

Atrazine

Prometon

Diazinon

EPTC

Carbaryl

Dacthal

Trifluralin

Deethylatrazine

Lindane

Pendimethalin

Simazine

0.002(e)

Herbicide or herbicide

breakdown product

Insecticide or insecticide

breakdown product

Maximum concentration

detected, in micrograms

per liter; (e) indicates

estimated value

FREQUENCY OF DETECTION, AS

PERCENTAGE OF SAMPLES

PESTICIDES

(22 samples)

VOLATILE ORGANIC

COMPOUNDS

(12 samples)

Toluene

Benzene

0 10 20 30 40 50 60 70 80 90 100

0 5 10 15 20 25 30 35 40 45 50

Chloroform

Acetone

m-,p-Xylene

Tetrachloroethene

1,1,1-Trichloroethane

Trichloroethene

Bromodichloromethane

1,2,4-Trimethylbenzene

Ethylbenzene

Methyl tert-butyl

ether (MTBE)

1,4-Dichlorobenzene

p-Isopropyltoluene

Styrene

Figure 8. Twelve different pesticides and fifteen different VOCs were 

detected in water samples from the Spokane River. In general, the detections 

were at extremely low concentrations. 
Major Findings 15

Ground water in aquifers 

used for drinking-water 

supply in Spokane, Coeur 

d’Alene, and Missoula is

generally of good quality

Ground water in basin-fill aquifers 

in the Spokane Valley and surrounding 

area and the Missoula/Bitterroot Valleys 

is of good quality and generally acceptable for most purposes (fig. 9). These 

aquifers serve as principal sources of 

drinking water (two areas within these 

aquifers are designated as sole-source 

aquifers; fig. 10) in northeastern Washington, northern Idaho, and southwestern Montana. These aquifers are highly 

susceptible to contamination, however, 

because of agricultural activities and 

urban development, in combination with 

permeable overlying soils that allow 

water and contaminants to readily move 

downward to the water table. 

Even though the basin-fill aquifers are susceptible to contamination, 

relatively few constituent concentrations exceeded USEPA drinking-water 

standards and guidelines. The elevated 

concentrations of trace elements, such 

as arsenic and radon, in a few of the 

samples most likely resulted from natural processes rather than human activities. Arsenic, which occurs naturally in 

rocks and soils, exceeded the USEPA 

drinking-water standard of 10 μg/L in 

CONSTITUENT CONCENTRATION,

IN MILLIGRA

MS PER LITER

CONSTITUENT CONCENTRATION,

IN MICROGRA

MS PER LITER

CONSTITUENT CONCENTRATION,

IN PICOCURIES PER LITER

Zinc

Iron

Arsenic

Orthophosphorus

Radon

Sodium

Hardness

Nitrate

Fluoride

Chloride

Sulfate

Manganese

5

1

10,000

5,000

1,000

500

100

50

10

0.5

0.1

0.05

0.01

Dissolved solids

5

1

10,000

5,000

1,000

500

100

50

10

0.5

0.1

0.05

0.01

0

0

10

10

30

30

20

20

40

40

50 MILES

50 KILOMETERS

IDAHO MONTANA

WASHINGTON

Coeur

d'Alene

Lake

Lake

Pend

Oreille Flathead

Lake

Spokane Coeur d'Alene

Missoula

Kalispell

Butte

Spokane

Clark

Bitterroot

River

River

Detectable concentrations in the Spokane

and Coeur d'Alene area aquifers

Detectable concentrations in the Missoula

and Bitterroot Valley aquifers

Standard or guideline

EXPLANATION

Spokane and Coeur d'Alene

area aquifers

Missoula and Bitterroot

Valley aquifers

Figure 9. Water quality in basin-fill aquifers in the Spokane/Coeur d’Alene area 

and in the Missoula/Bitterroot Valleys is 

good. Few constituents exceed established Federal drinking-water standards 

or guidelines. Alluvial aquifers are 

susceptible to contamination because 

of porous soils, shallow depths to water, 

and relatively rapid rates of recharge. 
16 Water Quality in the Northern Rockies Intermontane Basins

samples collected from three wells (12 

to 31 μg/L) in Spokane/Coeur d’Alene 

area aquifers (fig. 9). Concentrations of 

iron and (or) manganese, also naturally 

occurring minerals, exceeded USEPA 

secondary drinking-water regulations 

developed for taste, odor, and aesthetic 

effects, in five wells in the Spokane/

Coeur d’Alene area aquifers and in one 

well in the Missoula/Bitterroot Valley 

aquifers. 

Radon concentrations ranged from 

253 to 3,050 pCi/L; concentrations in 

all but one of the samples from 61 wells 

exceeded the proposed USEPA drinking-water standard of 300 pCi/L (U.S. 

Environmental Protection Agency, 

2000). A less stringent standard has 

been proposed that would raise the 

acceptable concentration of radon in 

individual water systems to 4,000 pCi/L. 

No samples from the Spokane/Coeur 

d’Alene area or Missoula/Bitterroot Valley basin-fill aquifers contained radon at 

concentrations that exceeded this limit. 

Radon in ground water is related to rock 

type and typically is elevated in igneous 

and metamorphic rocks. For example, 

concentrations in excess of 1,000 pCi/L 

were measured along the relatively thin 

margins of the Spokane, Coeur d’Alene, 

and Bitterroot Valleys, which are underlain by granitic bedrock aquifers. 

Nitrate, which is derived primarily from fertilizers used on farmland 

and residential areas, was found in 90 

percent of ground-water samples, but 

concentrations were low (medians of 

0.26 and 0.40 mg/L in the Spokane/

Coeur d’Alene area and Missoula/Bitterroot Valley aquifers). In fact, only 

seven samples, all from wells in the 

Spokane/Coeur d’Alene area aquifers, 

contained concentrations of nitrate of 2 

mg/L or greater — a “background” or 

natural concentration above which possible contamination from human sources 

is indicated (Mueller and Helsel, 1996). 

No concentrations exceeded the USEPA 

drinking-water standard of 10 mg/L; the 

maximum nitrate concentration of 7.6 

mg/L was measured in an agricultural 

area in the Little Spokane River Valley 

north of Spokane.

 What is Radon?

Radon is a colorless, odorless, radioactive gas that occurs naturally through the 

radioactive decay of radium in igneous and metamorphic rocks. It commonly 

enters buildings through foundation cracks, dirt floors, and floor drains and 

can dissolve in ground water. Radon in ground water is carried into buildings served by water-supply wells, where it is subsequently released into air 

during everyday use and potentially becomes a cause of lung cancer (U.S. 

Environmental Protection Agency, 2000). Some States, in cooperation with the 

USEPA, are developing multimedia mitigation programs to reduce concentrations of radon in indoor air. One of the recommendations of these programs is 

to limit radon concentrations in individual water systems to 4,000 pCi/L. 

Radon concentrations in basin-fill 

aquifers were among the highest in 

the Nation

Radon concentrations in 

about 90 percent of the groundwater samples collected from the 

Spokane/Coeur d’Alene area and 

Missoula/Bitterroot Valley basinfill aquifers exceeded 420 pCi/L, 

the NAWQA national median 

for nearly 2,500 ground-water 

samples collected from 1991 

to 2001. Igneous and metamorphic rocks, which are sources 

of radon-bearing minerals, are 

common throughout the Northern Rocky Mountains. Radon is 

similarly elevated in aquifers in 

other parts of the Rocky Mountain region such as the Upper 

61

2,495 Number of

samples

75th percentile

50th percentile

(median)

25th percentile

10th percentile

90th percentile

RA

DON CONCENTRATION, IN PICOCURIES PER LITER 2,500

2,000

1,500

1,000

500

0

NORTHERN

ROCKIES

INTERMONTANE

BASINS SAMPLES

ALL

NAWQA

SAMPLES
Major Findings 17

Pesticides and volatile organic 

compounds occur relatively 

infrequently and at low concentrations in ground water

Pesticides and VOCs were detected 

relatively infrequently in ground water 

in the Spokane/Coeur d’Alene area and 

the Missoula/Bitterroot Valley basin-fill 

aquifers. Specifically, at least one pesticide compound was detected in 15 wells 

and at least one VOC was detected in 19 

wells. Mixtures of pesticides and VOCs 

were detected in five wells (fig. 10); 

however, all concentrations were well 

below USEPA drinking-water standards 

and guidelines. 

Fourteen different pesticides were 

detected at least once in the Spokane/

Coeur d’Alene area and the Missoula/

Bitterroot Valley basin-fill aquifers. The 

most commonly detected compounds 

were the herbicide prometon (four detections) and the insecticide carbofuran 

and (or) its breakdown products (five 

detections). Prometon, used primarily for nonagricultural purposes such 

as domestic and commercial applications along roadsides and as an asphalt 

additive, is most common in ground 

water in urban areas (Kolpin and others, 1998). Prometon is one of the 

most frequently detected pesticides in 

ground water nationally (Squillace and 

others, 2002). Carbofuran (and[or] its 

breakdown products), which is used on 

fruits, vegetables, and forests to control 

a variety of insects, was detected only in 

an area of heavy agricultural land use in 

the Little Spokane River Valley north of 

Spokane. Concentrations of carbofuran 

were about 1,000 times less than the current USEPA drinking-water standard of 

40 μg/L (U.S. Environmental Protection 

Agency, 2001). 

The number of pesticides detected 

and their concentrations in the Spokane/

Coeur d’Alene area and the Missoula/

Bitterroot Valley basin-fill aquifers 

generally were less than those in ground 

water sampled nationwide. Specifically, 

none of the pesticide concentrations in 

the basin-fill aquifers exceeded 0.2 μg/L, 

whereas concentrations in 9 percent of 

nearly 1,500 NAWQA samples collected 

Spokane

Missoula

Stevensville

Hamilton

0

0

10

10

20

20

30 MILES

30 KILOMETERS

Basin-fill aquifer

Sole-source aquifer

Pesticides detected

VOCs detected

Both detected

Neither detected

Spokane and

Coeur d'Alene

area aquifers

Missoula and

Bitterroot

Valley

aquifers

EXPLANATION

Figure 10. Pesticides were detected in 15 of 61 basin-fill 

aquifer wells in the Spokane/Coeur d’Alene and Missoula/Bitterroot Valleys; VOCs were detected in 19 wells; 

and both pesticides and VOCs were detected in 5 wells. 

All of the pesticides and VOCs detected were at concentrations less than USEPA drinking-water standards and 

guidelines.

from 1992 to 1999 exceeded 0.2 μg/L 

(Squillace and others, 2002). 

Trihalomethanes, a class of 

compounds that are formed during the 

disinfection of microbes in drinking 

water, were among the most frequently 

detected VOCs and were detected in 

seven wells. Chloroform, the most common trihalomethane, was detected in five 

wells; the maximum concentration was 

0.54 μg/L. Other frequently detected 

VOCs included tetrachloroethene (or 

PERC) and 1,1,1-trichloroethane. These 

two compounds are used in dry cleaning and as degreasing solvents and 

were detected in four and three wells, 

respectively. Although PERC has been 

detected at concentrations exceeding 

the 5-μg/L drinking-water standard in 

samples collected by Missoula County 

within the Missoula urban area, concentrations in samples collected during 

this study (maximum was 0.3 μg/L) 

were well below the USEPA drinkingwater standard. Methyl tert-butyl ether 

(or MTBE), a gasoline oxygenate of 

environmental concern, was not detected 

in ground-water samples during this 

study. Although MTBE is not used as a 

fuel additive in the State of Washington, 

it has been detected in ground water 

in the Spokane area (Washington State 

Department of Ecology, 2000a) and in 

other areas throughout the United States 

(Delzer and Ivahnenko, 2003).
Study Unit Design

The NAWQA study design for the Northern Rockies Intermontane Basins includes assessments of the physical and 

chemical characteristics of surface and ground water and the ecological conditions in streams. Information was collected on 

stream chemistry and ecology and ground-water chemistry using nationally consistent protocols and methods (Gilliom and 

others, 1995). Thus, water-quality findings in the Study Unit can be compared with findings in other basins and be placed in 

a regional and national context.

Stream Chemistry and Ecology

Assessment of stream chemistry focused 

on how water quality of rivers varies in different 

seasons, under different hydrologic conditions, 

and in response to different types of land use. 

Samples were collected at 10 monitoring sites for 

about 2 years and were analyzed for major ions, 

nutrients, trace elements, and suspended sediment. Selected streams were sampled intensively 

for VOCs and(or) pesticides. Ecological assessments focused on the effects of land use on stream 

ecology, especially as demonstrated by contaminants in fish tissue and streambed sediment and 

by the numbers and kinds of aquatic organisms. 

Fish-tissue and streambed-sediment samples were 

collected at general stream-chemistry sites and at 

additional stream sites for a basinwide assessment 

of trace elements and organic compounds. Special 

ecological studies were conducted in the Spokane 

and St. Regis River Basins to evaluate the effects 

of mining on stream ecology and contaminants in 

the Spokane River. 

Ground-Water Chemistry 

Ground-water assessments focused on 

water quality of two major basin-fill aquifers 

that are the principal sources of drinking water 

in their areas and include two areas designated 

by the USEPA as sole-source aquifers: the 

Spokane Valley/Rathdrum Prairie aquifer in 

northeastern Washington and northern Idaho, 

and the Missoula aquifer in southwestern 

Montana. These aquifers are highly susceptible to contamination because of agricultural activities and urban development, in 

combination with permeable overlying soils 

that allow water and contaminants to readily 

move downward to the water table. In addition, a ground-water/surface-water interaction 

study was conducted to examine the effects 

of recharge from the Spokane River on the 

hydrologic and chemical characteristics of the 

adjacent alluvial aquifer.

EXPLANATION

General extent of basin-fill aquifers in the Study Unit

Extent of the basin-fill aquifers sampled

Spokane River ground-water/surface-water interaction

study

Well sampled

0

0

25

25

50 MILES

50 KILOMETERS

Lake

Pend Oreille

Coeur

d'Alene

Lake

Flathead

Lake

Pend Oreille

Spokane

River

Coeur d'Alene

River

Clark

Fork

Clark

Fork

River Bitterroot

River Blackfoot

River St Joe

River

MONTANA

IDAHO

WASHINGTON

EXPLANATION

Northern Rockies

Canadian Rockies

Montana Valley and

Foothill Prairies

Columbia Plateau

ECOREGIONS SAMPLE COLLECTED

General chemistry, general ecology, streambed

sediment, and fish tissue monitoring site

Streambed sediment

and/or fish tissue site

Synoptic site

Ecoregions modified from Omernik and Gallant, 1986

0

0

25

25

50 MILES

50 KILOMETERS

Lake

Pend Oreille

Coeur d'Alene Lake

Flathead Lake

Pend Oreille

River

Spokane River

Coeur d'Alene River

Clark

Fork

Clark

Fork

River Bitterroot

River Blackfoot

River St Joe

MONTANA

IDAHO

WASHINGTON

18 Water Quality in the Northern Rockies Intermontane Basins
Study

component What data are collected and why Types of sites sampled Number of sites sampled Sampling frequency and period

Stream Chemistry

General 

chemistry of 

streams and 

rivers

Streamflow, dissolved oxygen, 

pH, alkalinity, specific conductance, temperature, nutrients, 

major ions, trace elements, and 

suspended sediment to assess 

occurrence and distribution.

Streams draining basins ranging 

in size from about 100 to 11,000 

square miles, reflecting forest 

and mixed land use, and widely 

distributed geographically within 

the Study Unit.

10 Approximately monthly from 

April 1999 through June 2001

Pesticides 

and VOCs in 

streams and 

rivers

Above constituents plus 

pesticides and volatile organic 

compounds in water.

Bitterroot R. near Missoula, 

Spokane R. near Post Falls, and 

Spokane R. at Seven Mile Bridge.

Spokane R. near Post Falls and 

Spokane R. at Seven Mile Bridge.

3

2

Monthly during the growing season, 1999 − 2000

During low streamflow conditions, 1999 

Contaminants 

in streambed 

sediment and 

fish tissue

Trace elements and organic 

compounds to assess occurrence 

and distribution in streambed 

sediment and fish tissue.

General stream-chemistry sites 

plus additional sites for good 

geographic distribution and variety 

in land-use types.

22 (Streambed 

sediment)

16 (Fish tissue)

Once, June − September 1998

Once, June – September 1998

Stream Ecology

General 

ecology of 

streams and 

rivers

Fish, invertebrates, algae, and 

associated physical habitats to 

assess stream conditions and 

biological community conditions. Interannual variability at 

two sites described.

Locations correspond with general 

stream-chemistry sites and represent a variety of land uses.

10

2

Once, July – September 1999

Annually for one reach 1999–

2001

Three reaches sampled in 1999

Synoptic 

study of mining effects 

on biological 

communities

Same as above plus trace elements in sediment, water, and 

biota to assess extent and magnitude of mining contamination. 

Areas of mining land use and 

background sites representing 

forested land in the Coeur d’Alene 

Basin and St. Regis River Basins.

18 Once, July – September 2000

Synoptic 

study of contaminants in 

the Spokane 

River 

Fish, invertebrates, and algae 

to assess biological conditions. 

Organic compounds and trace 

elements in streambed sediment 

and fish and insect tissue to assess contamination from mining 

and urban sources.

Spokane River upstream from, 

within, and downstream from the 

city of Spokane.

4 Once, July – August 1999

Ground-Water Chemistry

Basin-fill 

aquifer survey, Spokane/

Coeur 

d’Alene area

Major ions, trace elements, nutrients, radionuclides, pesticides, 

radon, VOCs, and isotopes to assess water quality in the Spokane 

Valley/Rathdrum Prairie solesource aquifer and surrounding 

basin-fill aquifers.

Primarily domestic wells completed in unconsolidated basin-fill 

deposits.

31 Once, May – August 1999

Basin-fill 

aquifer 

survey, 

Missoula/

Bitterroot 

Valleys

Same as above to assess water 

quality in the Missoula solesource aquifer and surrounding 

basin-fill aquifers.

Primarily domestic wells completed in unconsolidated basin-fill 

deposits.

30 Once, May – June 2001

Surfacewater/

ground-water 

interaction 

study

Major ions, trace elements, and 

stable isotopes to assess the 

effect of local recharge from the 

Spokane River on the Spokane 

Valley/Rathdrum Prairie aquifer.

Spokane River near Post Falls 

gaging station and monitoring 

wells completed in unconsolidated 

alluvial deposits.

Spokane River 

plus 25 monitoring wells.

River sampled about monthly 

1999–2001. Wells sampled up to 

nine times between June 2000 and 

August 2001.

Study Unit Design 19
References Cited

Andrews, E.D., 1987, Longitudinal dispersion of trace elements in the Clark Fork River, Montana, in Averett, R.C., 

and McKnight, D.M., eds., Chemical quality of water and 

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20 Water Quality in the Northern Rockies Intermontane Basins
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References Cited 21
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22 Water Quality in the Northern Rockies Intermontane Basins
Glossary

Alluvial aquifer - A water-bearing deposit of unconsolidated 

material (sand and gravel) left behind by a river or other flowing water. 

Aquatic-life criteria - Water-quality guidelines for protection 

of aquatic life. Often refers to U.S. Environmental Protection 

Agency water-quality criteria for protection of aquatic organisms. See also Water-quality guidelines and Water-quality 

criteria. 

Background concentration - A concentration of a substance in 

a particular environment that is indicative of minimal influence 

by human (anthropogenic) sources. 

Bedrock - General term for consolidated (solid) rock that 

underlies soils or other unconsolidated material. 

Bed sediment - The material that temporarily is stationary in 

the bottom of a stream or other watercourse. 

Benthic invertebrates - Insects, mollusks, crustaceans, worms, 

and other organisms without a backbone that live in, on, or 

near the bottom of lakes, streams, or oceans. 

Bioaccumulation - The net accumulation of a substance by an 

organism as a result of uptake from all environmental sources, 

including gills, epithelial tissues, and dietary sources. 

Breakdown product - A compound derived by chemical, biological, or physical action upon a pesticide. The breakdown is 

a natural process that may result in a more toxic or a less toxic 

compound and a more persistent or less persistent compound. 

Concentration - The amount or mass of a substance present 

in a given volume or mass of sample. Usually expressed as 

micrograms per liter (water sample) or micrograms per kilogram (sediment or tissue sample). 

Cubic foot per second (ft3/s, or cfs) - Rate of water discharge 

representing a volume of 1 cubic foot passing a given point 

during 1 second, equivalent to approximately 7.48 gallons per 

second or 448.8 gallons per minute or 0.02832 cubic meter per 

second. 

Detection limit - The minimum concentration of a substance 

that can be identified, measured, and reported within 99-percent confidence that the analyte concentration is greater than 

zero; determined from analysis of a sample in a given matrix 

containing the analyte. 

Discharge - Rate of fluid flow passing a given point at a given 

moment in time, expressed as volume per unit of time. 

Dissolved constituent - Operationally defined as a constituent 

in water that passes through a 0.45-micrometer filter. 

Drainage area - The drainage area of a stream at a specified 

location is that area, measured in a horizontal plane, which is 

enclosed by a drainage divide. 

 23

Drinking-water standard or guideline - A threshold concentration in a public drinking-water supply, designed to protect 

human health. As defined here, standards are U.S. Environmental Protection Agency regulations that specify the maximum contaminant levels for public water systems required to 

protect the public welfare; guidelines have no regulatory status 

and are issued in an advisory capacity. 

Eutrophication - The process by which water becomes 

enriched with plant nutrients, most commonly phosphorus and 

nitrogen. 

Ground water - In general, any water that exists beneath the 

land surface, but more commonly applied to water in fully 

saturated soils and geologic formations. 

Herbicide - A chemical or other agent applied for the purpose 

of killing undesirable plants. See also Pesticide. 

Human health advisory - Guidance provided by U.S. Environmental Protection Agency, State agencies, or scientific 

organizations, in the absence of regulatory limits, to describe 

acceptable contaminant levels in drinking water or edible fish. 

Insecticide - A substance or mixture of substances intended to 

destroy or repel insects. 

Load - General term that refers to a material or constituent in 

solution, in suspension, or in transport; usually expressed in 

terms of mass or volume. 

Maximum contaminant level (MCL) - Maximum permissible 

level of a contaminant in water that is delivered to any user of 

a public water system. MCLs are enforceable standards established by the U.S. Environmental Protection Agency. 

Mean - The average of a set of observations, unless otherwise 

specified. 

Median - The middle or central value in a distribution of data 

ranked in order of magnitude. The median is also known as the 

50th percentile. 

Micrograms per liter (μg/L) - A unit expressing the concentration of constituents in solution as weight (micrograms) of solute per unit volume (liter) of water; equivalent to one part per 

billion in most streamwater and ground water. One thousand 

micrograms per liter equals 1 mg/L. 

Milligrams per liter (mg/L) - A unit expressing the concentration of chemical constituents in solution as weight (milligrams) of solute per unit volume (liter) of water; equivalent 

to one part per million in most streamwater and ground water. 

One thousand micrograms per liter equals 1 mg/L. 

Minimum Reporting Level - Smallest measured concentration 

of a constituent that may be reliably reported using a given 

analytical method.
24 Water Quality in the Northern Rockies Intermontane Basins 

Nutrient - Element or compound essential for animal and plant 

growth. Common nutrients in fertilizer include nitrogen, phosphorus, and potassium. 

Organochlorine compound - Synthetic organic compounds 

containing chlorine. As generally used, term refers to compounds containing mostly or exclusively carbon, hydrogen, 

and chlorine. Examples include organochlorine insecticides, 

polychlorinated biphenyls, and some solvents containing 

chlorine. 

Pesticide - A chemical applied to crops, rights of way, lawns, 

or residences to control weeds, insects, fungi, nematodes, 

rodents, or other “pests.” 

Picocurie (pCi) - One trillionth (10-12) of the amount of radioactivity represented by a curie (Ci). A curie is the amount of 

radioactivity that yields 3.7 x 1010 radioactive disintegrations 

per second (dps). A picocurie yields 2.22 disintegrations per 

minute (dpm), or 0.037 dps. 

Polychlorinated biphenyls (PCBs) - A mixture of chlorinated 

derivatives of biphenyl, marketed under the trade name Aroclor with a number designating the chlorine content (such as 

Aroclor 1260). PCBs were used in transformers and capacitors 

for insulating purposes and in gas pipeline systems as a lubricant. Further sale for new use was banned by law in 1979. 

Probable effect level (PEL) - A guideline established by the 

Canadian Council of Ministers of the Environment for the 

protection of aquatic life in streambed sediment. According to 

the guideline, trace-element concentrations in bulk sediment 

exceeding the PEL frequently are associated with adverse 

biological effects.

Radon - A naturally occurring, colorless, odorless, radioactive gas formed by the disintegration of the element radium; 

damaging to human lungs when inhaled. 

Runoff - Excess rainwater or snowmelt that is transported to 

streams by overland flow, tile drains, or ground water. 

Sole-source aquifer - A ground-water system that supplies at 

least 50 percent of the drinking water to a particular human 

population; the term is used to denote special protection 

requirements under the Safe Drinking Water Act and may be 

used only by approval of the U.S. Environmental Protection 

Agency. 

Streamflow - A type of channel flow applied to that part of 

surface runoff in a stream, whether or not it is affected by 

diversion or regulation. 

Synoptic - A short-term investigation of specific water-quality 

conditions during selected seasonal or hydrologic conditions 

to provide improved spatial resolution for critical water-quality conditions.

Tailings - Rock that remains after processing ore to remove the 

valuable minerals. 

Total Maximum Daily Load (TMDL) - The amount of a particular pollutant that a particular stream, lake, estuary, or other 

water body can ‘handle’ without violating State water-quality 

standards.

Trace element - An element found in only minor amounts 

(concentrations less than 1.0 milligram per liter) in water or 

sediment; includes arsenic, cadmium, chromium, copper, lead, 

mercury, nickel, and zinc. 

Tributary - A river or stream flowing into a larger river, stream, 

or lake. 

Urban site - A site that has greater than 50 percent urbanized 

and less than 25 percent agricultural area. 

Volatile organic compounds (VOCs) - Organic chemicals that 

have a high vapor pressure relative to their water solubility. 

VOCs include components of gasoline, fuel oils, and lubricants, as well as organic solvents, refrigerants, fumigants, 

some inert ingredients in pesticides, and some byproducts of 

chlorine disinfection. 

Water-quality criteria - Specific levels of water quality which, 

if reached, are expected to render a body of water unsuitable 

for its designated use. Commonly refers to water-quality criteria established by the U.S. Environmental Protection Agency. 

Water-quality criteria are based on specific levels of pollutants 

that would make the water harmful if used for drinking, swimming, farming, fish production, or industrial processes. 

Water-quality guidelines - Specific levels of water quality which, if reached, may adversely affect human health or 

aquatic life. These are nonenforceable guidelines issued by a 

governmental agency or other institution. 

Water-quality standards - State-adopted and U.S. Environmental Protection Agency-approved ambient standards for 

water bodies. Standards include the use of the water body and 

the water-quality criteria that must be met to protect the designated use or uses. 

Water year - The continuous 12-month period, October 1 

through September 30, in U.S. Geological Survey reports dealing with surface-water supply. The water year is designated 

by the calendar year in which it ends and which includes 9 of 

the 12 months. Thus, the year ending September 30, 1980, is 

referred to as water year 1980. 

Yield - The mass of material or constituent transported by a 

river in a specified period of time, divided by the drainage area 

of the river basin. 
Appendix 25

Appendix—Water-Quality Data from the Northern Rockies 

Intermontane Basins in a National Context

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Coordination with agencies and organizations in the Northern Rockies Intermontane Basins was 

integral to the success of this water-quality assessment. We thank those who served as members of 

our liaison committee. 

Federal Agencies

Bureau of Indian Affairs

National Park Service

U.S Army Corps of Engineers

U.S. Bureau of Land Management

U.S. Environmental Protection Agency

U.S. Fish and Wildlife Service

U.S. Forest Service

State Agencies

Idaho Department of Environmental 

Quality

Idaho Department of Water Rescources

Idaho Fish and Game

Montana Bureau of Mines

Montana Department of Environmental 

Quality

Montana Fish, Wildlife, and Parks

Washington Department of Ecology

Washington Department of Fish and 

Wildlife

Washington Department of Natural 

Resources

Local Agencies

City of Missoula

Panhandle Health District

Spokane County

Spokane County Conservation District

Universities

Eastern Washington University

Montana State University

University of Idaho

University of Montana

Other public and private organizations

Clark Fork - Pend Oreille Coalition

Coeur d’Alene Tribe

Confederated Salish and Kootenai Tribe

Flathead Basin Commission

Silver Valley Natural Resources Trustees

Spokane River Association

Tri-State Water Quality Council

Kalispel Tribe

We thank the following individuals for contributing to this effort. 

Lan Tornes for his early efforts in getting this project up and running.

Rick Backsen, Fred Bailey, Lee Chambers, Lawrence Deweese, Angela Frandsen, Keith Hein, Dorene MacCoy, Doug Ott, Karen 

Payne, Stephan Porter, Ken Skinner, Terry Short, and Zachary Taylor for their assistance in data collection.

John Lambing, John Roland, and Michael Woodside for their technical reviews of the manuscript.

Richard Helton and Phillip Redman for preparation of illustrations.

Linda Channel for editorial reviews and report processing.

The numerous property owners that allowed the use of their property by the USGS for access to specific stream reaches, the 

installation of monitoing wells, or the sampling of existing wells.
Clark and others— Water Quality in the Northern Rockies Intermontane Basins 

U.S. Geological Survey Circular 1235

National Water-Quality Assessment (NAWQA) Program

Northern Rockies Intermontane Basins

NAWQA

Coeur

d'Alene

Lake

Lake

Pend Oreille

Flathead

Spokane Lake Coeur

d'Alene

Missoula

Kalispell

Butte

Clark

Fork

Clark

Fork

Coeur d'Alene R.

Spokane

River

IDAHO

OREGON

MONTANA

WASHINGTON