Water Quality in the

Sacramento River Basin

California, 1994–98

U.S. Department of the Interior

U.S. Geological Survey

Circular 1215
POINTS OF CONTACT AND ADDITIONAL INFORMATION

Front cover: Aerial view of the Sacramento River in the Sacramento Valley (Rand Schaal, Ph.D., pilot and 

photographer). 

Back cover: Left, Collection of water samples during high flow conditions on the Sacramento River; right, Collection 

of samples of aquatic organisms and assessment of habitat conditions at a northern California headwaters stream. 

The companion Web site for NAWQA summary reports:

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

Sacramento River Basin contact and Web site:

Joseph Domagalski

U.S. Geological Survey

Water Resources Division

Placer Hall, 6000 J Street, 

Sacramento, CA 95819-6129

e-mail: joed@usgs.gov

http://water.wr.usgs.gov/sac_nawqa/index.html

National NAWQA Program:

Chief, NAWQA Program

U.S. Geological Survey

Water Resources Division

12201 Sunrise Valley Drive, MS 413

Reston, VA 20192

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

River Basin Assessments

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)

Eastern Iowa Basins (Circular 1210)

Georgia-Florida Coastal Plain (Circular 1151)

Hudson River Basin (Circular 1165)

Kanawha-New River Basins (Circular 1204)

Lake Erie-Lake Saint Clair Drainages (Circular 1203)

Las Vegas Valley Area and the Carson and Truckee River Basins

(Circular 1170)

Lower Illinois River Basin (Circular 1209)

Long Island-New Jersey Coastal Drainages (Circular 1201)

Lower Susquehanna River Basin (Circular 1168)

Mississippi Embayment (Circular 1208)

Ozark Plateaus (Circular 1158)

Potomac River Basin (Circular 1166)

Puget Sound Basin (Circular 1216)

Other NAWQA summary reports

Red River of the North Basin (Circular 1169)

Rio Grande Valley (Circular 1162)

San Joaquin-Tulare Basins (Circular 1159)

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 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)

National Assessments

The Quality of Our Nation’s Waters—Nutrients and 

Pesticides (Circular 1225)
U.S. GEOLOGICAL SURVEY CIRCULAR

Water Quality in the Sacramento River Basin, 

California,1994–98

1215

By Joseph L. Domagalski,1 Donna L. Knifong,1 Peter D. Dileanis,1 Larry R. 

Brown,1 Jason T. May,2 Valerie Connor,3 and Charles N. Alpers1

1

U.S. Geological Survey, Placer Hall, 6000 J Street, Sacramento, CA 95819-6129

2

California State University Foundation, 6000 J Street, Sacramento, CA 95819-6063

3

Central Valley Regional Water Quality Control Board, 3443 Routier Road, Sacramento, CA 95827-3098
Library of Congress Cataloging-in-Publications Data

The use of firm, trade, and brand names in this report is for identification purposes only and

does not constitute endorsement by the U.S. Government.

Free on application to the

U.S. Geological Survey

Information Services

Box 25286 Federal Center

Denver, CO 80225

Or call: 1-888-ASK-USGS

U.S. DEPARTMENT OF THE INTERIOR

BRUCE BABBITT, Secretary

U.S. GEOLOGICAL SURVEY

Charles G. Groat, Director

2000

Water-quality assessment of the Sacramento River Basin, California, 1994–98 / by Joseph L. Domagalski...[et 

al.].

p. cm. -- (U.S. Geological Survey Circular ; 1215)

Includes bibliographical references.

ISBN 0-607-95419-1 (alk. paper)

1. Water quality--California--Sacramento River Watershed. I. Domagalski, Joseph L. II. Geological Survey 

(U.S.) III. Series.

TD224.C3 W393 2000

363.739’42’097945--dc21

00-049453
CONTENTS

Contents III

NATIONAL WATER-QUALITY ASSESSMENT PROGRAM ............................................................IV

SUMMARY OF MAJOR FINDINGS................................................................................................... 1

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

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

INTRODUCTION TO THE SACRAMENTO RIVER BASIN................................................................ 3

Land-Use Effects on Water Quality and Stream Habitat.............................................................. 4

Water Use in California ................................................................................................................ 5

Effects of Hydrologic Conditions on Study Results...................................................................... 5

Study Design Focuses on Land Use............................................................................................ 6

MAJOR FINDINGS ............................................................................................................................ 7

Surface Water .............................................................................................................................. 7

NATIONAL PERSPECTIVE—Nutrients in a National Context .................................................... 8

Pesticides in Surface Water ......................................................................................................... 9

Pesticides of Historical Use ....................................................................................................... 10

NATIONAL PERSPECTIVE—Organophosphate Insecticides in Agricultural and 

Urban Streams in a National Context..................................................................................... 11

Metals in Water and Streambed Sediment ................................................................................ 12

Mercury in Water and Streambed Sediment.............................................................................. 14

Ambient Toxicity Monitoring by California State Agencies ......................................................... 17

Aquatic Biology .......................................................................................................................... 19

NATIONAL PERSPECTIVE—Aquatic Biology in a National Context ....................................... 21

Ground Water............................................................................................................................. 22

STUDY UNIT DESIGN .................................................................................................................... 25

GLOSSARY..................................................................................................................................... 27

REFERENCES ................................................................................................................................ 29

APPENDIX—WATER QUALITY DATA FROM THE SACRAMENTO RIVER BASIN 

IN A NATIONAL CONTEXT.......................................................................................................... 31
NATIONAL WATER-QUALITY ASSESSMENT PROGRAM

IV National Water-Quality Assessment Program 

Sacramento River Basin 

1991–95

1994–98

1997–2001

Not yet scheduled

High Plains Regional

Ground Water Study, 

1999–2004

NAWQA Study Units— 

Assessment schedule

THIS REPORT summarizes major findings about water quality in the Sacramento River Basin that emerged from 

an assessment conducted between 1994 and 1998 by the U.S. Geological Survey (USGS) National Water-Quality 

Assessment (NAWQA) Program. Water quality is discussed in terms of local and regional issues and compared to 

conditions found in all 36 NAWQA study areas, called Study Units, assessed to date. Findings are also explained in 

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

organisms. The NAWQA Program was not intended to assess the quality of the Nation's drinking water, such as by 

monitoring water from household taps. Rather, the assessments focus on the quality of the resource itself, thereby 

complementing many ongoing Federal, State, and local drinking-water monitoring programs. The comparisons 

made in this report to drinking-water standards and guidelines are only in the context of the available untreated 

resource. Finally, this report includes information about the status of aquatic communities and the condition of instream habitats as elements of a complete water-quality assessment.

Many topics covered in this report reflect the concerns of officials of State and Federal agencies, water-resource 

managers, and members of stakeholder groups who provided advice and input during the Sacramento River Basin 

assessment. Basin residents who wish to know more about water quality in the areas where they live will find this 

report informative as well. 

THE NAWQA PROGRAM seeks to improve scientific and public understanding of water quality in the Nation’s 

major river basins and ground-water systems. Better understanding facilitates effective resource managment, 

accurate identification of water-quality priorities, and successful development of strategies that protect and restore 

water quality. Guided by a nationally consistent study design and shaped by ongoing communication with local, 

State, and Federal agencies, NAWQA assessments support the investigation of local issues and trends while 

providing a firm foundation for understanding water quality at regional and national scales. The ability to integrate 

local and national scales of data collection and analysis is a unique feature of the USGS NAWQA Program.

The Sacramento River Basin is one of 51 water-quality assessments initiated since 1991, when the U.S. 

Congress appropriated funds for the USGS to begin the NAWQA Program. As indicated on the map, 36 

assessments have been completed, and 15 more assessments will conclude in 2001. Collectively, these assessments 

cover about one-half of the land area of the United States and include water resources that are available to more 

than 60 percent of the U.S. population.
Summary of Major Findings 1 

SUMMARY OF MAJOR FINDINGS

Major Findings

0 20 40 MILES

0 20 40 KILOMETERS

Urban

Cropland and pasture

Range land

Forest land

Water

Barren land

Yolo Bypass

Land use

Study area boundary

EXPLANATION

121

122

123

41

40

39

Redding

Red

Bluff

Chico

Colusa

Sacramento

Putah Creek

American River

Yuba River

Lake Oroville

Deer Cre ek

M

Pit River cCloud River

Big

Chico Creek

Creek Arcade

Cache Creek

Colusa Basin Drain

Sacramento

River Butte Creek

Feather River

Sacramento

Slough

Shasta Lake

CALIFORNIA

Clear

Lake

Stream and River Highlights

The water quality of the Sacramento River and 

its major tributaries supports most beneficial 

uses most of the time, including drinking and 

irrigation water, recreation, and protection of fish 

and other aquatic life. Most of the water in the 

Sacramento River and its major tributaries, such 

as the Feather and American rivers, is derived 

from melting snow that enters the rivers by managed discharges of water from reservoirs. 

Because the snow is pure, much of the Sacramento River and its large tributaries have low 

concentrations of dissolved minerals. Although 

water quality of the Sacramento River is good 

most of the year, seasonal events, such as agricultural runoff or runoff from historical mining 

operations, may affect this quality. Variable climatic conditions and variation in amounts of 

rainfall, coupled with competing demands for 

water uses, affect the aquatic ecology of this 

basin. Management of the major rivers for the 

migration and reproduction of chinook salmon 

and other salmonid fish is a major concern in the 

Sacramento River Basin.

• Pesticides can affect the suitability of water for 

drinking and can also be toxic to aquatic organisms. In previous years, the concentrations of 

pesticides used on rice were sufficiently high to 

affect the health of aquatic life in streams draining the rice growing areas and to contribute to 

taste and odor problems for treated drinking 

water withdrawn from the lower Sacramento 

River. The concentrations of rice pesticides in 

agricultural streams and major rivers are now at 

acceptable levels.

• Phosphorus, a plant nutrient related to algal 

growth, was elevated in most samples collected in 

agricultural and urban streams.

• Mercury from historical mining activities has been 

a pervasive and prevalent problem of the Sacramento River Basin and downstream locations. 

Mercury concentrations in water exceeded recommended guidelines for the protection of aquatic life 

during this study. 

• Salmonid fish reproduce in mountain streams, with 

subsequent migration to marine waters and final 

migration back to the mountain streams for 

reproduction. Water management projects 

(reservoirs and dams) have blocked the normal 

migration routes, forcing fish to move to less 

desirable habitats, thus affecting their 

reproduction. 

The Sacramento River Basin Study Unit has a wide range of land uses that encompass 

about 70,000 square kilometers in California. The large cropland and pasture area is 

known as the Sacramento Valley. The Sacramento River is the largest river in California 

and supplies drinking and irrigation water to communities and farms in both northern and 

southern California. In 1995, over 2.2 million people lived within the Study Unit boundary, 

with more than 1 million in the Sacramento metropolitan area.

• Organophosphate insecticides, a group of pesticides used in agricultural 

and urban areas, enter the 

Sacramento River from 

multiple sources at 

concentrations that exceed 

recommended criteria for 

protection of aquatic life. 

Although the concentrations in agricultural and 

urban streams sometimes 

exceed amounts that are 

toxic to zooplankton 

in laboratory tests, the 

toxicity is greatly reduced 

or eliminated when 

concentrations of these 

pesticides are diluted by 

the Sacramento River. 
2 Water Quality in the Sacramento River Basin

Small Streams Major Rivers

Agricultural Urban Mining

Selected Indicators of Stream-Water Quality

Mixed

Land Uses

—

Nitrate2

Pesticides1

Trace

elements4

Semivolatile organics7

Organochlorines6

Percentage of samples with concentrations greater

than or equal to health-related national guidelines for

drinking water, protection of aquatic life, or contact

recreation

Percentage of samples with concentrations less than

health-related national guidelines for drinking water,

protection of aquatic life, or contact recreation

Percentage of samples with no detection

Not assessed

—

Mercury5

1 Insecticides, herbicides, and pesticide metabolites, sampled in water.

2

3 Total phosphorus, sampled in water.

5 Total mercury in unfiltered water samples.

Organochlorine compounds including DDT and PCBs, sampled in fish tissue.

7 Miscellaneous industrial chemicals and combustion by-products, sampled in sediment.

Phosphorus3

Selected Indicators of Ground-Water Quality

Shallow Ground Water Supply Wells

Urban Agricultural Domestic Public

Nitrate2

Pesticides1

Radon

Volatile

organic compounds3

—

Percentage of samples with concentrations greater

than or equal to health-related national guidelines for 

drinking water

Percentage of samples with concentrations less than

health-related national guidelines for drinking water

Percentage of samples with no detection

Not assessed

—

—

—

—

— —

—

1 Insecticides, herbicides, and pesticide metabolites, sampled in water.

2 Nitrate (as nitrogen), sampled in water.

3 Solvents, refrigerants, fumigants, and gasoline compounds, sampled

in water.

the valley and from infiltration of rain, rivers, and irrigation on the valley floor. Ground water is affected by 

agricultural and urban land uses. 

• Bentazon, a herbicide applied to rice fields, was 

detected in 71 percent of shallow wells sampled in the 

rice-growing area, despite having been suspended from 

use since 1989. Bentazon concentrations measured in 

this study did not exceed any existing drinking-water 

standard. To protect rivers from pesticide contamination, the rice-field water is required, by means of 

mechanical controls, to remain on the fields for about 

1 month. During that time, pesticide levels decrease by 

various processes, but evaporation of the water may 

increase the salinity of the shallow ground water by 

leaving salts behind. 

• Urban growth of the Sacramento metropolitan area has 

affected ground-water quality. Nitrate concentrations 

are elevated but are below drinking-water standards in 

most wells. 

• Some of the most heavily used portion of the southeastern Sacramento Valley aquifer was shown to generally have good water quality suitable for drinking and 

other uses. Only about 3 percent of the ground-water 

samples collected had nitrate or trichloroethene concentrations that exceeded a drinking-water standard. 

Radon concentrations exceeded guidelines in most of 

the domestic wells sampled.

Major Influences on Ground Water

• Agricultural and urban land-use practices

• Soil and aquifer properties 

• Optimal temperature of rivers for fish migration is maintained most of the time, but temperature management 

can be difficult during a drought. 

• Reservoirs have affected habitats of bottom-dwelling 

aquatic insect populations downstream from the dams. 

This may affect the food supply for critical life stages of 

fish.

• Nonnative fish and other nonnative aquatic species have 

affected streams in the Sacramento Valley. Nonnative 

species may outcompete native species, resulting in new 

aquatic community assemblages, thus creating an imbalance in formerly stable ecosystems.

Major Influences on Streams and Rivers

• Year-to-year variation in precipitation amounts

• Runoff from agricultural, urban, and mining areas

• Existence and maintenance of water-supply and floodcontrol projects 

Ground-Water Highlights

Ground water of the Sacramento Valley accumulated 

in aquifers from precipitation in low hills surrounding 
Introduction to the Sacramento River Basin 3

INTRODUCTION TO THE SACRAMENTO RIVER BASIN

Sacramento

Red

Bluff

40 MILES

0 40 KILOMETERS

0 20

20

121

122

123

41

40

39

Headwaters, McCloud River

Farming in the central valley

Acid mine drainage in Spring Creek

Farming in the Central Valley

Lake Clementine Dam

Drainage from the abandoned 

Reddington Mercury Mine

Sacramento

Valley (north

Central Valley)

(south Central Valley)

Sacramento

River Basin 

San Joaquin–

Sacramento Delta

CALIFORNIA

PACIFIC OCEAN

The Sacramento River Basin 

occupies nearly 70,000 square 

kilometers (km2) in the north 

central part of California (fig. 1). 

The Sacramento River is the largest 

river in California, with an average 

annual runoff of 27 billion cubic 

meters (m3) (Domagalski and 

Brown, 1998). The basin includes 

all or parts of six landforms or 

physiographic provinces—the 

Great Basin, the Middle Cascade 

Mountains, the Sierra Nevada, the 

Klamath Mountains, the Coast 

Ranges, and the Sacramento Valley 

(fig. 1). The Sacramento Valley is 

the low-lying province of the basin; 

the other provinces are mountainous. Land use in the mountainous regions of the basin is 

principally forest, although forest 

Figure 1. Physiographic provinces in the Sacramento River Basin. Physiographic provinces are regions defined principally by 

geologic and topographic features.
4 Water Quality in the Sacramento River Basin

Redding

Chico

0 20 40 MILES

0 20 40 KILOMETERS

Source: California Division of Mines and Geology

Copper mine

Lead mine

Zinc mine

EXPLANATION

Colusa

Freeport

Red Bluff

Sacramento

Tehama

Verona

Putah Creek

Folsom

Lake

River

American

Lake 

Berryessa

Cache Creek

Bear River

Clear

Lake

Yuba River

Feather River

Colusa Basin Drain

Lake

Oroville

Sacramento River

Stony Creek

Cottonwood Creek

Shasta

Lake

M

Pit River

cCloud River Keswick

Reservoir

121

122

123

41

40

39

Sacramento

Valley

and rangeland are mixed in regions 

of the Coast Ranges and the Great 

Basin. Domagalski and others 

(1998) have provided more 

information on the physiographic 

provinces of the Sacramento River 

Basin. 

The Sacramento Valley is the 

northern portion of the Central 

Valley of California and is fully 

contained in the Study Unit. The 

Sacramento Valley has the greatest 

population of any part of the basin, 

and it is there that the greatest 

effects or potential effects on surface and ground water are likely to 

occur from land-use activities. The 

Sacramento Valley is also the area 

of greatest water use in the basin. 

Land-Use Effects on 

Water Quality and 

Stream Habitat

The Sacramento Valley supports 

a diverse agricultural economy, 

much of which depends on the 

availability of irrigation water. 

Water is collected in reservoirs at 

several locations within the mountains surrounding the Sacramento 

Valley and is released according to 

allocations for agricultural, urban, 

and environmental needs. The 

reservoirs also are managed for 

flood control. The reservoirs 

provide flood protection and allow 

the storage of water during dry 

years, but the placement of dams at 

the reservoirs has blocked 

migration routes for salmonid fish.

More than 8,000 km2

 of the 

Sacramento Valley are irrigated. 

The major crops are rice, fruits, 

nuts, tomatoes, sugar beets, corn, 

alfalfa, and wheat. Dairy products 

also are an important agricultural 

commodity. The land areas 

adjacent to the Sacramento Valley 

are mostly forested (fig. 1). 

The largest cities of the basin are 

in the Sacramento Valley and 

include Chico, Red Bluff, Redding, 

and Sacramento. The Sacramento 

metropolitan area is home to more 

than 1 million people, which is 

nearly half of the total population 

(U.S. Department of Commerce, 

1992) in the basin. 

Previous mining for copper, 

lead, and zinc (fig. 2) in the 

Klamath Mountains has resulted in 

acid mine drainage (drainage of 

acidic waters from mines) into part 

of Keswick Reservoir, which is 

located immediately downstream 

from Shasta Lake. The drainage 

includes both mined metals and 

nonmined metals such as cadmium. 

Mercury that was used in previous 

mining within the Coast Ranges 

(fig. 3) enters the Sacramento 

Valley through Cache and Putah 

creeks. Although neither creek 

flows directly into the Sacramento 

River during low-flow conditions, 

the load of mercury can be transported to downstream receiving 

waters, including the San Francisco 

Bay, during stormwater runoff 

Figure 2. Locations of copper, lead, and zinc mines. The most severe case of 

drainage of acidic waters from mines has been in the region near Shasta Lake.
Introduction to the Sacramento River Basin 5 

Colusa

Freeport

Red Bluff

Redding

Sacramento

Tehama

Verona

0 20 40 MILES

0 20 40 KILOMETERS

121

122

123

41

40

39

Source: California Division of Mines and Geology

Mercury mine

Gold mine

EXPLANATION

Putah Creek

Folsom

Lake

River

American

Lake 

Berryessa

Cache Creek

Bear River

Clear

Lake

Yuba River

Feather River

Colusa Basin Drain

Sacramento River

Stony Creek

Cottonwood Creek

Shasta

Lake

Pit Rive r

Lake

Oroville

Sacramento

Valley

conditions. Mercury also can enter the Sacramento 

River from the Sierra Nevada, where it was used in 

historical gold mining (fig. 3).

Water Use in California

Water storage, transportation, and allocation in 

California are strategically managed to take into 

account the wide diversity of the State’s geography and 

physiography. Water is stored in nonpopulated areas of 

California and then transferred by natural stream 

channels or man-made canals to areas of demand. 

Reservoirs within the Sacramento River Basin have 

been constructed in the mountainous areas just adjacent 

to the valley. All major rivers of the Sacramento River 

Basin have one or more reservoirs, which were 

constructed during the late 1940s to late 1960s mainly 

for flood control. Storage capacity of the reservoirs is 

managed to capture runoff from winter storms. However, stored water is not used solely in the Sacramento 

River Basin; it is transported to other locations in 

California and is a major source of supply for Los 

Angeles and other southern California communities.

Total water use in the Sacramento River Basin is 

about 18 billion cubic meters per year (m3

/yr). Allocations of water for agricultural, urban, and environmental uses are made according to the California water 

plan (California Department of Water Resources, 1998) 

but are modified on the basis of the yearly conditions of 

reservoir storage. For example, during drought years, 

total allocations are decreased. Pie charts in figure 4 

show the percentage of allocations during average 

years of rainfall for 1995 and projected for 2020. Of 

those allocations, surface water provides 82 percent 

and ground water 18 percent of the total demand. 

During drought years, surface water drops to about 

75 percent and ground water rises to about 25 percent 

of total demand.

Effects of Hydrologic Conditions on 

Study Results

The average annual precipitation for the entire 

Sacramento River Basin is 914 millimeters (mm), most 

of which falls as rain or snow during November 

through March. Because little or no rain falls during the 

summer growing season, irrigation is required for 

successful agriculture. Most of the water-quality 

samples for the Sacramento River Basin study were 

collected between the fall of 1995 and the spring of 

Figure 3. Locations of gold and mercury mines. The era of 

gold mining began in 1849 after the discovery of placer 

deposits in the American River.

Figure 4. Water allocations for average rainfall years for 

1995 and projected for 2020. 

1995 Average

2020 Average

(Projected)

Urban

Agricultural

Environmental

Sacramento Valley Water Allocation

EXPLANATION

5% 8%

40%

55% 53%

39%
6 Water Quality in the Sacramento River Basin

1,000

0

2,000

3,000

4,000

Oct

Dec

Feb

Apr

June

Aug

Oct

Dec

Feb

Apr

June

Aug

Oct

Dec

Feb

Apr

Oct

June

Aug

Annual mean discharge

Daily mean discharge

Samples collected

Daily mean discharge,

in cubic meters per second

1995 1996 1997 1998

Highest historical

streamflow

Site: Yuba River near Marysville

1998, which covered a series of 

wet winters. Precipitation amounts 

in northern California are variable 

and dependent on the location of 

the Pacific jet stream. The average 

annual rainfall at the city of 

Sacramento is about 460 mm. 

Since the 1940s, however, as little 

as 140 mm and as much as 915 mm 

have been recorded in a year. 

Two major hydrological events 

occurred during the period of this 

study. The first, a major flood, 

occurred during the winter of 

1996–97. Flooding began on 

January 1, 1997, and affected a 

major part of the Sacramento River 

downstream from Shasta Lake as 

well as tributaries to the 

Sacramento River, especially the 

Feather and Yuba rivers. Some 

streams, such as the Yuba River, 

had the highest recorded streamflow following the rainfall 

associated with the flood of 

January 1, 1997 (fig. 5). The 

second major hydrological event 

was the El Niño episode of 

1997–98. The term “El Niño” 

refers to an “ocean–atmosphere 

phenomenon” during which wind 

and ocean current in the equatorial 

Pacific result in warmer-thannormal water along the North and 

South American Pacific coasts. El 

Niño winters frequently bring 

higher-than-normal precipitation in 

northern California because of a 

southward shift of the storm tracks 

and jet stream over North America.

Study Design Focuses 

on Land Use

Chemical and biological samples 

were collected from rivers and 

streams within, or downstream 

from, forested, urban, agricultural, 

and mining areas to assess overall 

quality and effects of specific landuse practices. In most cases, river 

or stream sampling sites were 

located in the Sacramento 

Valley—the region of both the 

highest water use and where many 

potential effects on water quality 

had occurred and are likely to 

occur. At some sites, water samples 

were collected monthly and during 

storms to assess the effects of 

storm runoff on contaminant 

transport. Other sites were sampled 

only monthly, usually during 

normal flows. Shallow ground 

water was sampled from three 

areas—the highly used part of the 

southeastern Sacramento Valley 

aquifer, downstream from rice 

fields, and downstream from the 

recently urbanized area of 

metropolitan Sacramento. 

Domestic wells (existing wells) 

were sampled for the southeastern 

Sacramento Valley aquifer study 

area, whereas monitoring wells 

(drilled for this study) were 

sampled for the rice and urban 

land-use study areas. 

Figure 5. Yuba River hydrograph. The highest recorded discharge for the lower Yuba River occurred shortly after a large 

rainfall on January 1, 1997.
MAJOR FINDINGS

Major Findings 7 

Nitrite plus nitrate concentration, in milligrams per liter

EPA primary drinking water 

 standard, 10 milligrams per liter

Sacramento River at Bend Bridge

Sacramento River at 

Colu

Yuba Ri

Feather Ri

Sacramento 

Slough

Colusa Basin Drain

Sacramento River at 

Verona

Cache Creek

Arcade 

Creek

American River

Sacramento River at Freep

Yolo Bypass

2.0

1.0

0

0.5

2.5

1.5

Maximum

Median

Minimum

Agricultural site

Mining site

Urban site

Agricultural site

Agricultural site

Urban site

Sacramento River at Bend Bridge

Sacramento River at 

Colusa

Yuba River

Feather River

Sacramento Slough

Colusa Basin Drain

Sacramento River at Verona

Cache 

Creek

Arcade 

Creek

American River

Sacramento River at Freeport

Yolo Bypass

Dissolved solids, in milligrams per liter

100

0

200

300

400

500

600

700

Maximum

Median

Minimum

EPA secondary 

 drinking-water 

 standard g Minin site

Surface Water

Water of the Sacramento River and its major tributaries is generally of good quality; the source is snow 

that melts and collects in upstream reservoirs and is 

released in response to water needs or flood control. 

The amount of dissolved solids in the Sacramento 

River and its major tributaries (Yuba, Feather, and 

American rivers) was low at all of the sampled locations (fig. 6). Higher median concentrations of dissolved solids occurred at agricultural sites such as 

the Sacramento Slough and Colusa Basin Drain, but 

those are diluted upon mixing with Sacramento 

River water (Domagalski and Dileanis, 2000). Nutrient concentrations such as nitrate also were low 

throughout the Sacramento River Basin (Domagalski 

and Dileanis, 2000) (fig. 7), and drinking-water 

standards for nitrate were not exceeded during the 

course of this study. At some locations, algae 

attached to streambed material was abundant, 

indicating that further investigation of nutrient 

dynamics and their consequences to the streams of 

this watershed is warranted. Excess algal growth, 

which is usually related to higher-than-normal 

nutrient inputs to streams, is a water-quality concern 

when the algae affect the aquatic community 

(because of dissolved oxygen depletion). No such 

effects were observed in the Sacramento River or its 

major tributaries. Excess algae also can contribute to 

taste and odor problems in drinking water.

Some stream segments are listed as “impaired” by 

various contaminants (U.S. Environmental Protection Agency, accessed January 2, 2000). An impairment means that a standard of water quality for 

beneficial uses (for example, as a source of drinking 

water or for recreation or industrial use) is not being 

met. The impaired water bodies shown in figure 8 are 

mainly affected by nonpoint sources of contaminants 

from agriculture or from a combination of point and 

nonpoint sources from abandoned mines. Waterquality objectives are usually not met only during 

conditions of stormwater-driven runoff. The Clean 

Water Act requires States to maintain a listing of 

Figure 6. Concentrations of dissolved solids at the fixed sites. 

The highest concentrations were measured at the agricultural, 

mining, and urban sites. (EPA, Environmental Protection 

Agency)

Figure 7. Concentrations of nitrite plus nitrate at the 

fixed sites. The highest concentrations were measured at 

the mining and urban sites. 
8 Water Quality in the Sacramento River Basin

Streams Draining

Mixed Land-Use Areas

Streams Draining

Urban Areas

Highest (greater than 2.9)

Medium (0.64 to 2.9)

Lowest (less than 0.64)

Average annual concentration of total nitrogen,

 in milligrams per liter

Average annual total nitrogen input, in kilograms 

 per square kilometer by county for 1995–98. Inputs 

 are from fertilizer, manure, and the atmosphere.

NAWQA Study Unit boundary

Greater than 2,801

672 to 2,801 

Less than 672 

EXPLANATION

Sacramento

River Basin

Streams Draining

Agricultural Areas

Nutrient concentrations in the streams of mixed land-use and agricultural regions of the Sacramento River 

Basin tend to be lower relative to those measured in other areas of the United States with similar fertilizer 

applications within their watersheds. The maps show nitrogen; phosphorus concentrations have a very similar pattern. Elevated concentrations of nitrogen or phosphorus can stimulate nuisance growth of algae. The 

nutrient concentrations tend to be less than those of adjacent areas in California, agricultural areas of the 

Pacific Northwest, and large areas of the midcontinent region. In contrast to mixed land-use streams, nutrient concentrations of the urban stream are among the highest of similar urban streams throughout the United 

States. The lower concentrations in streams of mixed land-use probably can be attributed to dilution by 

streamflow. The Sacramento River and its major tributaries are derived from melting snow, which has low 

nutrient concentrations. These rivers tend to dilute the agricultural drainage, and therefore nutrient concentrations remain low in the major rivers. In addition, some instream processes remove nutrients, such as algal 

growth that incorporates nutrients in algae biomass. The urban stream, Arcade Creek, is entirely within an 

urbanized area, and all runoff to the stream is affected by that urban land use. The only inputs of water to 

Arcade Creek are from impacted land. The range in nutrient concentrations for all NAWQA Study Units is 

shown in the Appendix.

NUTRIENTS IN A NATIONAL CONTEXT
Major Findings 9 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

 

28

 

29

30

31

32

33

34

35

36

Impaired water bodies

Yolo Bypass

NAWQA Study Unit boundary

American River, lower

Arcade Creek

Berryessa Lake

Cache Creek

Chicken Ranch Slough

Clear Lake

Colusa Basin Drain

Davis Creek Reservoir

Dolly Creek

Elder Creek

Elk Grove Creek

Fall River

Feather River

French Ravine

Harley Gulch

Horse Creek

Humbug Creek

James Creek

Kanaka Creek

Keswick Reservoir

Little Backbone Creek

Little Cow Creek

Little Grizzly Creek

Morrison Creek

Natomas East Main Drain

Pit River

Sacramento River

 (Red Bluff to Delta)

Sacramento River

 (Shasta Dam to Red Bluff)

Shasta Lake

Spring Creek

Strong Ranch Slough

Sulphur Creek

Town Creek

West Squaw Creek

Whiskeytown Reservoir

Willow Creek (Whiskeytown)

EXPLANATION

0 20 40 MILES

0 20 40 KILOMETERS

36

30

35

34

21

28

29

16

33

12

26

22

20

15

1

2

3

4

5

6

7 8

9

10

11

24

31

18 25

32 13

19

17

14

23

27

Sacramento Valley

121

122

123

41

40

39

Clear

Lake

Lake 

Berryessa

Folsom

Lake

Lake

C

Oroville olusa Basin Drain

Sacramento River

Feather River

Bear River

Yuba River

American River

Shasta

Lake

Pit River

impaired water bodies for the purpose of establishing a Total Maximum Daily Load (TMDL). A 

TMDL is a plan to restore the beneficial uses of the stream or to 

otherwise correct the impairment. 

The most prevalent listings in the 

Sacramento River Basin are for 

organophosphate pesticides and 

mercury, for which TMDLs 

currently are being considered. 

Pesticides in 

Surface Water

The concentrations of molinate and 

other pesticides (used in rice farming) 

measured during this study in the 

Colusa Basin Drain or in the 

Sacramento River, represent a 

significant improvement over 

concentrations measured in 

previous years (Domagalski, 

2000). The major pesticides 

that have been used on rice are 

molinate, thiobencarb, and 

carbofuran. Rice farming 

requires that fields be flooded 

with water throughout the 

growing season. Molinate and 

thiobencarb are applied to control aquatic grasses and weeds, 

whereas carbofuran is applied 

to control insects. During the 

late 1970s, the levels of rice 

pesticides in the Colusa Basin 

Drain were sometimes acutely 

toxic to fish such as carp (Cyprinus carpio) (Bennett and 

others, 1998). The toxicity was 

attributed to molinate. 

In the early 1980s, consumers of drinking water in the 

city of Sacramento reported an 

objectionable taste, which was 

attributed to thiobencarb. A 

management program was 

enacted to reduce the levels of 

these pesticides in streams. 

The plan requires that ricefield water be retained on 

fields for 1 month following 

pesticide application to allow 

concentrations in water to be 

reduced through mechanisms 

such as volatilization, biological processes, or sunlightinduced degradation. Sampling of rice pesticides during 

this study showed that concentrations occasionally were in 

excess of management 

objectives in agricultural 

streams but always were very 

low in the Sacramento River 

(fig. 9). A target concentration 

Figure 8. Impaired water bodies of the Sacramento River Basin according to the 

California 303(d) list (U.S. Environmental Protection Agency, accessed January 2, 2000). 

Impaired water bodies require the implementation of a management plan called a Total 

Maximum Daily Load (TMDL) to bring the water body into compliance with existing 

standards. Most of the impairments are the result of pesticides from agricultural or urban 

use, or from metals derived from historical mining operations.
10 Water Quality in the Sacramento River Basin NoDe Jan 14

Feb 18

Mar 18

Apr 9

Apr 24

May 9

May 23

June 17

July 10July 28

Aug 26

Sept 18

Oct 30

Nov 12

Dec 17

Jan 21

Feb 26

0

2

4

6

8

10

12

14

16

18

20

Molinate, in micrograms per liter

 Freeport

of 13 micrograms per liter (μg/L) 

of molinate in water was chosen for 

management of this herbicide. That 

level was chosen to protect the 

crustacean Neomysis mercedis, an 

important part of the food chain for 

young fish (Harrington, 1990). 

Concentrations in agricultural 

streams exceeded the target at least 

during 1 month of the year. Concentrations in the Sacramento 

River were always below those 

reported to be harmful to N. 

mercedis (Domagalski, 2000). 

Pesticides also are transported to 

the Sacramento River, its tributaries, and agricultural drainage 

canals during winter storms 

(Kuivila and Foe, 1995; MacCoy 

and others, 1995; Domagalski, 

1996). The pesticide that is 

considered a major problem for 

stormwater-driven transport is 

diazinon because of its toxicity to 

aquatic organisms and its high 

detection frequency. Diazinon is 

toxic to some species of zooplankton, such as Ceriodaphnia dubia, at 

low concentrations (0.35 μg/L) 

(Amato and others, 1992). The 

zooplankton species C. dubia, is 

used in laboratory assays to test 

water for toxicity (U.S. Environmental Protection Agency, 

1991a,b). Diazinon is applied to 

orchard crops, especially almonds, 

prunes, and stone fruits, during 

December and January to protect 

trees from insects that lay eggs in 

the trees during the winter and 

hatch the following spring. Toxic 

concentrations in tributaries to the 

Sacramento River can occur when 

agricultural areas contribute storm 

runoff; toxic concentrations rarely 

occur in the Sacramento River 

itself (MacCoy and others, 1995). 

Diazinon was present in 

stormwater runoff at a number of 

sites in 1994 (Domagalski, 1996), 

and in nonstorm flows during 1996 

through 1998. In the 1994 study, 

the Feather River was shown to be 

the greatest source of diazinon to 

the Sacramento River during a single storm, but other streams probably contributed to the diazinon 

load in the Sacramento River as 

well. This depended in part on the 

timing of diazinon applications and 

the location of greatest rainfall. 

The results of the routine samplings for diazinon during stable 

flow conditions at Arcade Creek 

near Del Paso Heights, Colusa 

Basin Drain at Road 99E near 

Knights Landing, and Sacramento 

River at Freeport are shown in 

figure 10. No stormwater runoff 

samples were collected. The highest concentrations during this 

NAWQA study occurred at Arcade 

Creek near Del Paso Heights, an 

urban site. Concentrations of diazinon in Arcade Creek that are 

toxic to C. dubia can occur in any 

season and result from household 

pesticide use and urban runoff. A 

standard for diazinon of 0.08 μg/L 

was proposed by the International 

Commission for the Great Lakes. 

As figure 10 shows, that standard 

was frequently exceeded at the 

Arcade Creek near Del Paso 

Heights site.

Pesticides of 

Historical Use

Pesticides that are no longer 

used, such as DDT, can still be 

detected in streambed sediments 

and the tissues of aquatic organisms because of their persistent 

chemical characteristics. Concentrations of pesticides such as DDT 

and its breakdown products tended 

to be low to nondetectable in the 

Figure 9. Concentrations of molinate at the Colusa Basin Drain at Road 

99E near Knights Landing and Sacramento River at Freeport sites. The 

water in the Colusa Basin Drain is primarily agricultural drainage.
Major Findings 11 

ORGANOPHOSPHATE INSECTICIDES IN 

AGRICULTURAL AND URBAN STREAMS IN A NATIONAL CONTEXT

Streams Draining

Agricultural Areas

13

4

5

3

7

20

24

60

58

4 36

3 5

30

19

14 76 11

74

33

23

100

20

20

58

9

6

28

8

4 6

5

39

4

3

33

7

50

6 50

16

17

4

5

7

13 8

6 3

14

11 3

10

3

5

3

14

6

4

6

15

45

5

21 35

46

7

Streams Draining

Urban Areas

 Streams Draining

Mixed Land-Use Areas Highest 25 percent 

Middle 50 percent 

Lowest 25 percent

Sum of insecticide concentrations

Aquatic-life guidelines

Bold outline indicates exceedance by one or more

 insecticides. Number is percentage of samples

 that exceeded a guideline within a 1-year period.

Insecticide use, in kilograms per square kilometer

 of agricultural land

NAWQA Study Unit boundary

Urban areas

Highest (greater than 9.6)

Medium (3.7–9.6)

Lowest (less than 3.7)

No reported use

EXPLANATION

Sacramento

River Basin

Organophosphate insecticides such as diazinon, chlorpyrifos, and malathion are toxic at low concentrations to 

some aquatic organisms. Some species of zooplankton are affected by diazinon concentrations as low as 

0.35 μg/L. Diazinon levels at the urban stream, Arcade Creek, were elevated at various times of the year and 

exceeded recommended criteria for the protection of aquatic life for every measurement taken. Those levels were 

among the highest in the Nation. Most of the diazinon measured at the Arcade Creek site probably originated 

from household use throughout the watershed. Runoff from yards from either rainwater or irrigation water contributes to the loading of diazinon to stormwater drains that ultimately discharge into the creek. Diazinon enters 

agricultural drainage mainly in stormwater runoff because it is sprayed on orchards during the rainy winter season. Previous studies have shown that concentrations of diazinon in agricultural streams can be elevated less than 

a day after rainfall. Although diazinon concentrations of agricultural streams also were among the highest in the 

Nation, only one sample from those streams taken in this study exceeded recommended criteria. The range in 

diazinon concentrations for all NAWQA Study Units is shown in the Appendix.
12 Water Quality in the Sacramento River Basin

S

 (large river site)

Probable toxic effects to 

G

0

0.2

0.4

0.6

0.8

1

1.2

1 4.

Diazinon, in micrograms per liter

Nov 

Dec 

Jan

Jan 29

Feb 7

Feb 21

Mar 7

Mar 21

Apr 10Apr 23

May 12May 23May 27

June 13June 26

July 11July 21

Aug 8

Aug 29

Sept 5

Sept 26

Oct 8

Oct 17

Nov 7

Nov 14

Dec 19

Jan 9

Feb 17

Apr 23

streambed sediments of the Sacramento River (MacCoy and Domagalski, 1999). Concentrations were 

higher in the streambed sediment 

of agricultural and urban streams. 

At some agricultural sites, and the 

urban site on Arcade Creek, the 

concentrations of DDT or its 

breakdown products in streambed 

sediment exceeded the Canadian 

sediment quality guidelines. The 

Canadian guidelines are designed 

to limit the accumulation of specific contaminants in organisms to 

levels below those that may adversely affect aquatic life (Canadian Council of Ministers of the 

Environment, 1995). 

Concentrations of DDT or its 

breakdown products such as 

p,p′-DDE, or other organochlorine 

insecticide residues, were very low 

in the tissues of aquatic organisms 

collected in the Sacramento River 

and its large tributaries (fig. 11). 

Concentrations of p,p′-DDE in the 

tissues of aquatic organisms collected from agricultural drainage 

sites were higher (fig. 11). The 

levels found in tissues of aquatic 

organisms from the agricultural 

drainage sites probably do not pose 

a health risk for humans but are 

above criteria developed by the 

New York State Department of 

Environmental Conservation 

(Newell and others, 1987) for 

protection of fish-eating wildlife 

such as birds. No national criteria 

exist to protect fish-eating wildlife 

from organochlorine compounds 

such as DDT or its breakdown 

products; New York’s are the 

only criteria available for comparison. The levels of p,p′-DDE 

found in the tissue of aquatic 

organisms tended to be relatively 

high when compared with other 

NAWQA Study Units. The range 

in concentrations for DDT and 

its breakdown products for all 

NAWQA Study Units is shown 

in the Appendix.

Metals in Water and 

Streambed Sediment

Acid mine drainage has been 

a serious environmental problem 

in the northern portion of the 

Sacramento River Basin (Alpers 

and others, 2000a,b). Several 

streams are listed as impaired 

(fig. 8) because of high concentrations of metals such as cadmium, copper, lead, and zinc. 

Metals concentrations in previous years have been toxic to fish 

in the upper Sacramento River 

near and downstream from 

Redding (Alpers and others, 

2000a,b). Recent mitigation 

efforts at one of the more contaminated sites in the Spring 

Creek drainage near Shasta Lake 

have significantly lowered concentrations of metals in the Sacramento River, and no toxic 

effects to fish were observed 

during the course of this investigation (Alpers and others, 

2000a,b). However, elevated 

levels of metals such as copper 

in streambed sediment can still 

be measured in the upper Sacramento River Basin downstream 

from Redding (MacCoy and 

Domagalski, 1999). Copper and 

other metals may still affect 

aquatic organisms. 

Figure 10. Concentrations of diazinon at the Colusa Basin Drain at Road 99E near 

Knights Landing, Arcade Creek near Del Paso Heights, and Sacramento River at 

Freeport sites. The highest concentrations were in the urban stream, Arcade Creek.
Major Findings 13 

Colusa

Verona

Freeport

Yuba River

Bear River

A

merican River

East Canal

Colusa Basin Drain

Jack Slough

Cache Creek

Cottonwood Creek

Stony Creek

Arcade Creek

McCloud River

Deer Creek

Feather River

600

700

500

400

300

200

100

0

p,p'-DDE, in micrograms per kilogram (wet weight)

Sacramento Valley

Agricultural Drainage

Sites

Downstream from

Coast Ranges

Urban Reference

New York State criterion for 

protection of fish-eating wildlife

Sacramento

River

Downstream from

Sierra Nevada

Trace Metals in Aquatic 

Organisms

For the NAWQA Program, looking for trace metals includes sampling streambed sediment and 

tissues of aquatic organisms. In 

theory, the transfer of metals from 

the streambed sediment into 

aquatic organisms can be understood by knowing the concentrations and geochemical forms of the 

trace metals in both the sediment 

and biota, as long as the feeding 

behaviors of the organisms are also 

understood. A predictive model of 

metals in tissue that is based on the 

amounts in streambed sediment 

could be developed from these 

studies. In practice, this becomes 

difficult because the actual bioavailability of metals in sediment 

can vary from site to site. For 

example, the concentrations measured in aquatic organisms may not 

be fully assimilated into the cellular material of the organism but 

rather may be present as undigested material or even attached to 

external body parts. Because metals contamination from acid mine 

drainage is an important waterquality issue for the upper Sacramento River Basin, and knowledge 

of the actual bioavailability of metals in the mine drainage is essential 

for current and future management 

of the mine waste, a collaborative 

study was completed by the Sacramento River Basin NAWQA Program and the National Research 

Program of the USGS (Cain and 

others, 2000). In that study, biologists examined streambed sediment 

and the cytosol from the caddisfly, 

an aquatic insect widely distributed 

in the upper Sacramento River and 

part of the food chain for a variety 

of fishes, including salmonid species. Cytosol is cellular material 

that can be isolated from aquatic 

insects. Biologists analyzed both 

whole body samples and cytosol 

samples for metals. Metal concentrations in cytosol provide a good 

indication of the potential effects 

on aquatic organisms from acid 

mine drainage. Aquatic insects also 

were sampled in a nearby reference 

stream that was unaffected by acid 

mine drainage. Elevated levels of 

cadmium, copper, lead, and zinc, 

derived from acid mine drainage, 

could clearly be distinguished in 

the cytosol samples, and it was 

shown that metals from the acid 

mine drainage were transported at 

least 120 kilometers downstream 

from the mine sources.

Figure 11. Conentrations of p,p′-DDE (a DDT breakdown product) in biota from the Sacramento River Basin. The use of DDT in 

the United States was terminated in 1972.
14 Water Quality in the Sacramento River Basin

Mountain sources

ELEMENTAL MERCURY

VOLATILIZATION

AND DEPOSITION METHYLMERCURY

TRANSPORT

DEMETHYLATION

METHYLATION

 BIOMAGNIFICATION

THROUGH FOOD WEB

SEDIMENT

RESUSPENSION

INORGANIC MERCURY

INORGANIC MERCURY METHYLMERCURY

METHYLMERCURY

METHYLMERCURY DEPOSITION 

AND RUNOFF

BIOMAGNIFICATION DEPENDS

ON MERCURY METHYLATION

SEDIMENTATION SEDIMENTATION

OUTFLOW

TO OCEAN

ATMOSPHERIC

DEPOSITION

INORGANIC MERCURY

DEPOSITION 

AND RUNOFF

OUTFLOW

TO OCEAN

Mercury in Water and 

Streambed Sediment

Mercury is currently considered 

the most serious water-quality 

problem in the Sacramento River, 

some tributaries of the Sacramento 

River, and downstream locations 

including the San Francisco Bay 

(Domagalski, 1998). Mercury can 

enter streams or aquatic systems 

through either atmospheric deposition or transport from geological 

or man-made sources (fig. 12). 

Several processes contribute to the 

subsequent bioaccumulation of 

mercury in fish tissue. Because of 

the presence of mercury in the tissue of certain fish species, advisories have been posted for several 

water bodies, and more advisories 

are planned, both within the Sacramento River Basin and in the San 

Francisco Bay. Specific advisories 

for fish species and locations are 

listed on the California Office of 

Environmental Health Hazards 

Assessment Web site at 

http://www.oehha.org/fish.html. 

A recent study (Davis and others, 

2000) documented mercury levels 

of concern to human health in sport 

fish collected in the lower 

Sacramento and Feather rivers.

Although atmospheric mercury 

is the principal cause of mercury 

contamination of water bodies in 

other parts of the United States, 

especially the midwestern and 

eastern United States, the cause is 

different in California. Geologic 

and anthropogenic sources, especially from historical mining for 

both mercury and gold, are the 

main reasons for mercury problems 

in the Sacramento River Basin 

(Domagalski, 1998). Mercury was 

mined in the Coast Ranges near 

Clear Lake and at locations east 

and south of Clear Lake (fig. 3), 

and it was used in the recovery of 

gold from ore and stream deposits 

during the late 19th century (fig. 3). 

Decades of gold mining in the 

Sierra Nevada have resulted in the 

deposition of mercury in the 

streambed sediments of the gold 

mining region. The release of 

mercury from ore to streambed 

sediments in the mercury mining 

regions of the Coast Ranges also 

Figure 12. Mercury pathways in aquatic systems. 
Major Findings 15 

Mc

Cloud River

Deer 

Creek

Bend BridgeBend Bridge

Woodson Bridge

Big Chico Creek

Butte City

ColusaColusa

VeronaVerona

FreeportFreeport

Yolo Bypass

Yuba RiverYuba River

Bear RiverBear River

Feather RiverFeather River

A

merican River

A

merican River

Jack Slough

East 

Canal

Colusa Basin Drain

Colusa Basin Drain

Sacramento Slough

Cottonwood 

Creek

Cottonwood 

Creek

Elder 

Creek

Thomes 

Creek

Stony Creek

Stony Creek

Cache 

Creek

Cache 

Creek

Arcade 

Creek

Reference

Sites

Sacramento River

Sites

Sacramento

Valley Sites

Coast Ranges

Drainage Sites

Urban

Site

0.1

0.05

0

0.15

0.2

0.25

0.3

0.4

0.35

0.45 

Mercury, in micrograms per gram

Sampled 1995

Sampled 1997

Sierra Nevada

Drainage Sites

Average amount

 of mercury in rocks

 on the earth's surface

has occurred (Hunerlach and 

others, 1999). The construction of 

reservoirs in the lower Sierra 

Nevada between 1948 and 1968 

has had the positive effect of 

reducing the amount of mercury 

transported downstream (Slotton 

and others, 1997). Reservoirs trap 

mercury because suspended sediment, the principal means by which 

it is transported, tends to settle to 

the bottom. This trapping of mercury will have future implications 

on the management of these reservoirs, including potential dam 

removal. Some dams are being 

considered for removal in order to 

restore habitat for fish. Residual 

mercury from mining operations is 

present in the streambed sediments 

downstream from the Sierra 

Nevada reservoirs, as indicated by 

the NAWQA Program for the 

Sacramento River Basin. Concentrations of mercury in the streambed sediments of 24 sites sampled 

during the NAWQA Program are 

shown in figure 13. The highest 

concentrations of mercury in 

streambed sediment were measured in samples collected from 

sites downstream from the Sierra 

Nevada and the Coast Ranges. 

Sites on the Sacramento River 

downstream from the Feather River 

tended to have higher mercury 

concentrations relative to sites 

sampled upstream from the confluence of these two rivers because 

of historical gold mining. 

The U.S. Environmental Protection Agency (EPA) has recommended water-quality criteria for 

mercury to protect aquatic life and 

human health. A recommended criterion of 12 nanograms per liter 

(ng/L) of total mercury in water 

was proposed by the EPA in 1985 

(Marshack, 1995). That criterion is 

supposed to limit the amount of 

mercury accumulation in fish tissue 

and thereby protect human health. 

The 12-ng/L criterion was 

exceeded mainly during runoff 

conditions at all fixed sites during

the timeframe of this investigation. 

In 1999, the recommended level 

was revised to 50 ng/L (U.S. 

Environmental Protection Agency,

Figure 13. Concentrations of mercury in streambed sediment at select locations of the Sacramento River Basin.
16 Water Quality in the Sacramento River Basin

Feb 28

Mar 20

Feb 12

Apr 16

May 20

June 3

Dec 9

Jan 13

Feb 11

Apr 8

100

0

200

300

400

500

600

0

20

40

60

80

100

120

Suspended sediment concentration, in milligrams per liter Suspended sediment concentration, in milligrams per liter

Mercury concentration in unfiltered water, in nanograms per 

1999). The 50-ng/L level was 

exceeded only at Cache Creek at 

Rumsey, Sacramento River at 

Colusa, and the Yolo Bypass at 

Interstate 80. Continued monitoring of mercury levels in fish tissue will be required to determine if 

the 50-ng/L criteria is effective. 

Time series plots of mercury and 

suspended sediment for the Sacramento River at Colusa are shown in 

figure 14. The higher concentrations of mercury correlate well 

with suspended sediment because 

much of the load of total mercury 

is transported with the suspended 

material (Alpers and others, 

2000b).

Methylmercury is the most 

bioaccumulative form of mercury 

in the environment because it 

builds up in organisms more 

readily than other forms of 

mercury. It is a toxic form of 

mercury that can bioaccumulate in 

the tissues of aquatic organisms 

and cause human health problems 

if fish with high levels are consumed. Methylmercury usually is 

formed by bacterially mediated 

reactions in sediments. Concentrations in water were measured at 

selected sites on the Sacramento 

River and at sites receiving agricultural drainage to assess the effects 

of agricultural activities on the 

production or the levels of 

methylmercury. 

Concentrations of methylmercury in unfiltered water are 

shown in figure 15. The highest 

median concentration was 

0.19 ng/L, which represents the 

samples collected at the Colusa 

Basin Drain at Road 99E near 

Knights Landing site. There is no 

water-quality standard in 

California or in any other State that 

is based on methylmercury 

concentrations in water. However, 

a concentration at or below 

0.1 ng/L of methylmercury has 

been suggested as being representative of pristine water (Rudd, 

1995). That concentration is typical 

of rivers upstream from wetland 

environments and away from 

mercury sources (Rudd, 1995). The 

median methylmercury concentrations for the Sacramento River sites 

were slightly above 0.1 ng/L and 

maximum concentrations approach 

2 ng/L. It is not known how or if 

those levels of methylmercury in 

water contribute to elevated levels 

of mercury in fish tissue.

There was a seasonal component 

to methylmercury concentrations 

for the sites at which they were 

measured for this study. The lowest 

concentrations were measured 

during middle to late summer 

(fig. 16). Higher concentrations 

tended to be measured during the 

autumn to winter months. The 

magnitude of the concentrations 

may also have been related to 

precipitation and runoff conditions. 

The highest concentrations for the 

period of this study were measured 

during January and February of 

1997 and were attributed to the 

January 1997 flood. During the 

subsequent El Niño winter of 

1997–98, higher-than-normal 

amounts of rain were recorded for 

much of the Sacramento River 

Basin, although there was no single 

storm of the magnitude of the 

January 1997 flood. Methylmercury concentrations increased 

during the El Niño winter, but not 

to the extent of the flood of the 

previous year. The effect of these 

methylmercury concentrations on 

downstream water bodies, such as 

the San Francisco Bay, has not 

been determined.

Figure 14. Mercury and suspended sediment concentrations for the Sacramento 

River at Colusa site. Mercury concentrations increase with sediment concentrations 

because mercury is attached to sediment particles.
Major Findings 17 

Sacramento River

at Colusa

Colusa Basin Drain

at Road 99E

near Knights Landing

Sacramento Slough near

Knights Landing

Sacramento River

at Verona

Sacramento River

at Freeport

Methylmercury, in nanograms per liter

2 5.

2.0

1.5

1.0

0.5

0

Ambient Toxicity Monitoring by 

California State Agencies

Ambient toxicity testing uses laboratory bioassays 

to assess the effect of contaminants on aquatic life. 

Essentially, the tests answer the question: Can specific types of fish, invertebrates, and algae species 

continue to live, grow, and reproduce in water samples collected from water bodies? The EPA protocols 

(U.S. Environmental Protection Agency, 1991a,b) for 

conducting chronic toxicity tests on freshwater species include representatives from three phyla and 

trophic levels. The three species are the fathead minnow, a small planktonic crustacean (C. dubia), and a 

planktonic green alga (Selenastrum capricornutum). 

These three species have been used to evaluate ambient water quality in the Sacramento River Basin since 

1986. California regulatory agencies rely on the tests 

for evaluating compliance with narrative toxicity 

objectives, which state that “all waters shall be maintained free of toxic substances in concentrations that 

produce detrimental physiological responses in aquatic 

life” (Marshack, 1995). Testing has changed from conducting broad watershed surveys that determine the 

spatial and temporal distribution of toxicity to conducting detailed follow-up studies that couple toxicity 

testing with a Toxicity Identification Evaluation (TIE) 

to identify specific chemicals and land uses responsible for toxicity. Water-quality data from the NAWQA 

Program are useful in determining the exposure of 

aquatic organisms to specific groups of contaminants 

such as organophosphate pesticides. Results from 

13 years of monitoring suggest that the EPA toxicity 

tests are powerful tools for assessing water quality.

The toxicity testing program in the Sacramento 

River watershed was the first indicator of the potential 

water-quality problems currently associated with pesticide runoff from urban areas and orchards. Using C. 

dubia tests, pulses of toxicity have been detected over 

a 10-year period throughout the Sacramento Valley in 

waters that receive drainage from orchards (de 

Vlaming and others, 2000). The toxicity has been 

linked to diazinon applied to dormant orchards and 

chlorpyrifos applied to nondormant orchards. C. dubia

also was effective in identifying toxicity attributed to 

drainage from rice fields. Rice-field drainage also was 

toxic to two important local species, larval striped bass 

and an invertebrate, N. mercedis. The invertebrate toxicity was caused by methyl parathion and carbofuran. 

As mentioned previously, a rice management program 

has eliminated the toxicity to all three species. C. 

dubia toxicity is detected throughout the year in waters 

that receive drainage from urban areas (fig. 10). This 

toxicity is attributed to diazinon and chlorpyrifos. 

Although most toxicity has been detected with C. 

dubia and linked to insecticides, other examples of 

ambient water toxicity have been identified. In areas of 

the Sacramento Valley that receive acid mine drainage, 

toxicity to S. capricornutum and C. dubia has been 

linked to copper and zinc. Mine remediation projects 

have reduced both metal concentrations and toxicity. 

Concentrations of copper and zinc measured in this 

NAWQA Program confirm that metal concentrations 

are below toxic levels (Alpers and others, 2000b). 

S. capricornutum toxicity has been documented in 

Figure 15. Concentrations of methylmercury at select 

locations in the Sacramento River Basin. Methylmercury is the 

form of mercury most likely to accumulate in aquatic species 

such as fish.
18 Water Quality in the Sacramento River Basin

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

2

Methylmercury in unfiltered water, in nanograms per liter M

Feb

Mar

Apr

June

Aug

Sept

Oct

Dec

Jan

Feb

Mar

Apr

May

June

Aug

Oct

Nov

Dec

Jan

Feb

Mar

Apr

May

June

1996 1997 1998

Sacramento River at Colusa

Sacramento Slough

Colusa Basin Drain

Sacramento River at Verona

Sacramento River at Freeport

waters that receive agricultural or 

urban runoff. Some of the toxicity 

can be attributed to the herbicide 

diuron, also detected in samples 

collected by the NAWQA Program; 

however, additional unidentified 

toxicants are present. Fathead minnow toxicity has been traced to 

ammonia originating from dairies 

and wastewater treatment plants. 

Taken together, the results of the 

last decade reveal that all three testing procedures, in association with 

TIEs and chemical analyses, have 

been effective for the identification 

of an array of toxicants originating 

from various sources. In several 

cases, alternative land-use practices 

or management strategies have 

improved water quality, as demonstrated by toxicity test monitoring. 

Because resources are not available 

for monitoring the complete array 

of potential contaminants, toxicity 

testing is a useful tool for focusing 

on chemicals present in a water 

body at toxic levels. 

NAWQA Participation 

with Local WaterQuality Programs

All NAWQA Study Units maintain communication and program 

coordination with a liaison committee of outside parties interested 

in water quality within the respective basins. During the early part of 

this NAWQA study, two significant 

programs were taking shape that 

involved new approaches to understanding and promoting the better 

management of water quality in the 

Sacramento River Basin. 

In 1994, Congress recognized 

the need to develop a coordinated, 

technically sound, adequately 

funded program that would focus 

on establishing toxic pollutant 

standards for the Sacramento River 

Basin. Congress then appropriated 

funds for the Sacramento River 

Toxic Pollutant Control Program 

(SRTPCP) and has continued to 

support the program. 

The long-term objective of the 

SRTPCP is to develop and 

implement a program that will bring 

the Sacramento River and its tributaries into compliance with waterquality standards for toxic pollutants and thereby protect beneficial 

uses. A second objective of the 

SRTPCP is to help form a viable 

organization of watershed stakeholders. The stakeholder organization is intended to address not 

only the related toxic-pollutant 

issues of the watershed, but also the 

broader water-quality and watershed issues that must be resolved to 

protect and enhance surface and 

ground water throughout the basin. 

The broader program to be conducted by this stakeholder organization has been named the Sacramento River Watershed Program 

(SRWP). The SRWP, although 

initiated with funding provided 

under the SRTPCP, is much broader 

in scope than the SRTPCP. The 

SRWP is intended to provide a 

forum to address a broad array of 

water-quality-related issues within 

the watershed, not just issues on 

toxic pollutants. Other issues that 

may be addressed under the broader 

watershed program include, but are 

not limited to, conventional water 

quality (including sediment, 

temperature, and dissolved solids), 

habitat, endangered species, 

streamflow, and ground-water 

issues. 

The NAWQA Program participates in various committees of the 

SRWP, including the monitoring 

committee, to share data. Data from 

the NAWQA Program are shared 

with the SRWP and are used to help 

interpret the current water-quality 

conditions and to help guide the 

continued management of the water 

resources of the Sacramento River 

Basin.

Figure 16. Seasonal changes of methylmercury concentrations. The highest 

concentrations were measured during high streamflow and following rainfall.
Major Findings 19 

Feb 13

Apr 24

May 30

June 27

July 11

Aug 29

Sept 20

Oct 23

Nov 22

Dec 12

Feb 20

Mar 20

Apr 22

May 30

June 25

July 23

Aug 21

Sept 17

Oct 22

Nov 19

Jan 14

Feb 18

Apr 9

0

5

10

15

20

25

Water temperature, in degrees Celsius

Sacramento River above Bend Bridge near Red Bluff

Sacramento River at Colusa

Sacramento River at Verona

Sacramento River at Freeport

1996 1997 1998

Sites listed in downstream order

Aquatic Biology

Changes in land use in the Sacramento River Basin have had major 

effects on the streams in the basin 

and on the aquatic communities dependent on them. Riparian forests 

and wetlands have been removed 

or degraded. Water development 

activities, particularly construction of dams and reservoirs, have 

altered natural flow and water temperature. The seasonal nature of 

higher temperatures along a stretch 

of the Sacramento River downstream from Shasta Lake is shown 

in figure 17. Water diversions for 

irrigation result in less water in the 

Sacramento River and rapidly 

increasing temperatures that are 

potentially harmful to certain fish 

in the spring and summer, especially downstream from the site on 

the Sacramento River above Bend 

Bridge near Red Bluff. 

Collectively, these changes in 

streams have resulted in corresponding changes in native ecological communities, including 

species extirpation and population 

declines in remaining native 

species (Moyle and Nichols, 1974; 

Brown and Moyle, 1993; Brown, 

2000). These declines have resulted 

in the listing of a number of animal 

and plant species as threatened or 

endangered under State or Federal 

law. 

Native fish species are still 

common in Sacramento 

River Basin streams

Thirty-five species of fish were 

collected, including 12 species 

native to California. Statistical 

techniques were used to categorize 

sites on the basis of similar fish 

groupings. Four species of fish 

were collected at mountain 

streams—rainbow trout, brown 

trout, riffle sculpin, and chinook 

salmon. These species are generally associated with cold, clear 

water and are considered intolerant of other environmental conditions such as warm water. Only 

brown trout is an introduced 

species. Rainbow trout were collected at all sites and were the most 

abundant species, representing 74 

percent of the fish collected.

Fish were also sampled at sites 

below the mountains but above the 

valley floor. Those sites are 

referred to as the foothill sites. 

Twenty-one species of fish, 

including 13 native species, were 

collected at the nine sites in the 

foothill group. None of the 

introduced species was abundant, 

and no introduced species 

represented more than 3 percent of 

the fish collected. Native minnows, 

hardhead, Sacramento pikeminnow, speckled dace, California 

roach, and Sacramento sucker 

dominated sites in this group.

Twenty-four species of fish, 

including nine native species, were 

collected at the three large river 

sites, which are located at low elevations on the larger rivers. Native 

species tended to be more abundant. The most abundant native 

species were Sacramento pikeminnow, Sacramento sucker, tule 

perch, and prickly sculpin. No 

introduced species exceeded 

7 percent of the catch. 

Agricultural land sites within the 

Sacramento Valley were dominated 

by introduced species and included 

sites on natural and artificial waterways that were heavily influenced 

by agricultural land uses or water 

management activities. Twenty 

species were collected at these 

sites, including only three native 

species.

Figure 17. Temperature of the Sacramento River at select locations. Seasonal 

increases are caused by diversion of river water for irrigation. 
20 Water Quality in the Sacramento River Basin

0

20

40

60

80

100

0

20

40

60

80

100

Agricultural land

Large river

Foothill

Mountain 

Native Fish

0

4

6

8

12

14

Fish with Anomalies

Percentage Percentage Percentage

0

2

1

3

4

Tolerant Species

Nu

mber

Intolerant Species

The group of fish at the agricultural land sites had the lowest percentage of native fish, the lowest 

percentage of intolerant fish, and 

the highest percentage of fish with 

external anomalies (fig. 18), indicating degraded environmental conditions. Intolerant fish are defined 

as those that are not adaptable to 

human alterations to the environment and thus decline in numbers 

when these alterations occur. The 

agricultural land site group also 

had a low number of native species 

compared with the large river and 

foothill site groups. In summary, 

the fish site data indicate that the 

agricultural land site group had the 

most degraded environmental conditions, the foothill and mountain 

site groups had the best conditions, 

and the large river site group had 

somewhat intermediate conditions. 

Previous studies of fish community structure in California have 

established correlations between 

the increasing numbers of introduced fish species in Central Valley 

streams and the disturbances 

caused by human activities (Moyle 

and Nichols, 1974; Brown and 

Moyle, 1993; Brown, 2000). 

Environmental disturbances associated with human activities 

include changes in water quality, 

streamflow, and habitat. Changes in 

streamflow, in particular changes in 

quantity and timing, have been 

identified as very important determinants of the structure of 

California fish communities (Baltz 

and Moyle, 1993; Moyle and Light, 

1996a,b; Brown, 2000). 

Differences in water quantity 

and water management have subsequent effects on water quality 

and habitat. Although these observations do not provide definitive 

support for the primary importance 

of streamflow in maintaining populations of native fish species, such 

relations and their effects on native 

fishes warrant consideration whenever changes in water management 

are being considered. Assessments 

of resident fish communities may 

be useful in determining the 

effectiveness of such changes in 

restoring natural ecological 

functions.

Streams without large 

reservoirs supported higher 

abundance of aquatic 

insects than streams with 

large reservoirs

Aquatic insect communities 

were compared at 23 locations 

including sites on two streams, Big 

Chico and Deer creeks, which have 

no major dams. Most streams sampled as part of this NAWQA Program have at least one major water 

project that affects a portion of the 

natural channels. Big Chico and 

Deer creeks are, therefore, unique 

in this study in that their flows are 

largely unregulated. Statistical 

analyses of the aquatic insect communities show that some sites on 

Deer and Big Chico creeks have 

more species and greater abundances of benthic macroinvertebrates compared with sites 

downstream from dams on the 

other streams sampled. Further 

research is needed to verify and 

evaluate these relations.

Populations of anadromous 

salmonids, including steelhead, 

rainbow trout, and chinook salmon, 

have declined throughout the Central Valley, resulting in protection 

of the remaining populations under 

Federal and State endangered species legislation (Yoshiyama and 

others, 1998). The reasons for the 

declines are complex and interactive; however, the construction of 

dams and reservoirs on California 

streams and rivers is widely recognized as one of the important factors (Yoshiyama and others, 1998). 

Dams and reservoirs block established migration routes, causing 

fish to reproduce in less desirable 

habitats. Another ecological effect 

from dams and reservoirs can be 

Figure 18. Characteristics of fish 

from ecological studies. 
Major Findings 21 

Biological indicators of water and habitat quality for 6 sites in the Sacramento River Basin were compared 

with similar data from 140 sites from NAWQA Study Units throughout the Nation. Because the rankings have 

not been calibrated for Sacramento River Basin streams, they should not be interpreted as designating “good” 

and “bad” water quality in streams. The sites simply score higher or lower in relation to other NAWQA sites, 

which represent a wide range of environmental settings.

The Yuba River site ranked among the least degraded sites nationally for all three indicators. The consistently low scores for this site can be attributed to abundant native fishes and the presence of healthy invertebrate and algal communities associated with cool water and abundant riffle habitats. The Arcade Creek and 

Colusa Basin Drain sites ranked among the most degraded sites nationally for all three indicators. This score 

may have to do more with the harsh nature of the physical environment than with water quality. Flow at these 

sites fluctuates widely because of storm runoff and variation in urban runoff. Biological communities in such 

streams tend to have few species, resulting in low indicator scores. Local determination of habitat and water 

quality is better accomplished using locally derived data, as has been demonstrated for Central Valley fish 

(Brown, 2000; May and Brown, 2000) and invertebrate communities (Brown and May, 2000a,b). 

1

Represents 140 sites from NAWQA Study Units throughout the United States with algal, invertebrate 

(primarily insects, worms, crayfish, clams), and fish data. “Mixed” indicates a combination of agricultural, 

urban, and other use.

 

Comparisons of biological indicators of water quality from Sacramento River Basin sites with other 

sites with biological data from the NAWQA Program1

Site Name National Land Use 

Category 1

Fish

Status

Invertebrate 

Status

Algal

Status

Colusa Basin Drain at Road 99E near 

Knights Landing Agriculture

Sacramento River at Colusa Mixed

Yuba River near Marysville Mixed

Feather River near Nicolaus Mixed

American River at Sacramento Mixed

Arcade Creek near Del Paso Heights Urban

Highest 25 percent nationally (comparatively more degraded)

Middle 50 percent nationally

Lowest 25 percent nationally (comparatively less degraded)

AQUATIC BIOLOGY IN A NATIONAL CONTEXT
22 Water Quality in the Sacramento River Basin

Percentage of wells with one or more detected pesticides

0

10

20

30

40

50

60

70

80

90

100

Southeastern

Sacramento Valley

Rice

Land Use

Urban

Land Use

changes in downstream populations of aquatic insects. This is 

potentially important to anadromous and resident fish populations 

because aquatic insects are a critical food source for nearly all species of fish at some life stage. 

The implication of this study is 

that construction of dams and reservoirs in the foothills has either 

submerged the productive habitat 

in Central Valley streams or altered 

them indirectly through downstream effects on ecological conditions. The importance of other 

downstream effects, such as disruption of sediment transport, has been 

recognized for anadromous salmonids. As a result of this recognition, 

a variety of projects are underway 

or are being proposed to improve 

conditions for anadromous fishes 

and to restore ecological processes 

in general.

Ground Water

Ground-water quality was investigated in the portion of the aquifer 

of the southeastern Sacramento 

Valley used for domestic purposes 

or irrigation and in the shallow portion of the aquifer below the valley’s two major land uses—rice 

cultivation and land that had been 

urbanized from 5 to 25 years ago. 

The southeastern Sacramento 

Valley was chosen for investigation 

because it is in that region that 

domestic and irrigation usage of 

ground water is highest. Although 

ground water is used in other parts 

of the valley, its usage is not as 

great as in the southeastern 

Sacramento Valley. 

The ground-water quality of 

some areas of the Sacramento 

Valley, such as the southwestern 

portion, is not entirely suitable for 

human or agricultural use because 

of the presence of elevated 

concentrations of boron, fluoride, 

chloride, nitrate, and sulfate (Hull, 

1984; Davisson and Criss, 1993). 

The study conducted in the southeastern Sacramento Valley aquifer 

was designed to address the suitability of a portion of the aquifer. 

Specifically, only existing domestic 

wells were sampled. 

Out of 31 wells sampled, only 

one sample exceeded the drinking 

water standard for nitrate. The 

median concentration of nitrate 

was 1.3 mg/L. Previous NAWQA 

investigations have found a median 

nitrate concentration of 0.48 mg/L 

in major aquifers throughout the 

United States (Nolan and Stoner, 

2000). Therefore, the wells sampled in this study have nitrate 

values above the national median. 

One or more pesticides were 

detected in 9 of 31, or 29 percent, 

of the wells of the southeastern 

Sacramento Valley (fig. 19). Simazine was detected in three wells, 

but the concentrations were very 

low and were not close to any 

drinking-water standard. Bentazon 

was one of the more frequently 

detected pesticides. Bentazon is a 

herbicide that was used on rice, but 

its use was suspended in 1989 

pending a review; then, in 1992, it 

was formally banned by the 

California Department of Pesticide 

Regulation (Miller-Maes and 

others, 1993). All bentazon concentrations were below drinkingwater standards. 

Volatile organic chemicals 

(VOCs) are not causing any apparent water-quality problems in the 

shallow aquifer of the southeastern 

Sacramento Valley. In one of the 

wells sampled, which is downgradient from a known point 

source, eight different VOCs were 

detected. One of those VOCs 

(trichloroethene, measured at 

5.5 μg/L) exceeded current 

drinking-water standards (primary 

MCL is 5 μg/L).

The effects of rice cultivation—one of the most prevalent 

agricultural practices in the Sacramento Valley—on ground water 

were examined by drilling and 

sampling 28 new wells (fig. 20). 

The wells were drilled to completion near the water table so that the 

agricultural effects on the most 

Figure 19. Percentage of wells having one or more 

detected pesticides for the three ground-water studies.
Major Findings 23 

recent water that entered the 

ground could be assessed. Rice cultivation requires that fields be 

flooded for the duration of the 

growing season, which lasts from 

May through September.

Pesticides were more frequently 

detected in the wells of the rice 

land-use study area compared with 

other regions outside the rice study 

area. One or more pesticides were 

detected in 25 of 28 (89 percent) of 

the wells sampled (fig. 19). The 

most frequently detected pesticide 

of the rice study was bentazon, a 

herbicide used in rice fields until 

suspension in 1989 and a formal 

ban in 1992. Although no observed 

concentrations exceeded drinkingwater standards, the high detection 

frequency, almost 10 years since 

the last known use, suggests that 

bentazon is easily transported to 

ground water and does not readily 

degrade in ground water. Molinate, 

another herbicide used on rice, was 

detected in 7 out of 28 wells. 

Thiobencarb, also a herbicide, was 

found in three wells; carbofuran, an 

insecticide used on rice, was 

detected in four. Herbicides and 

insecticides are applied to rice at 

the same time, shortly after planting in May. The most heavily used 

pesticides on rice are molinate, 

thiobencarb, and carbofuran. 

Therefore, it is not surprising to see 

these compounds in the ground 

water under the rice land-use 

region. None of the pesticide concentrations that were measured 

exceeded any known water-quality 

standard.

 Nutrient concentrations tended 

to be low in the ground water under 

the rice fields. The median nitrate 

concentration was 2 mg/L, and no 

concentrations exceeded a 

drinking-water standard. The 

median nitrate concentration 

measured in previous NAWQA 

investigations in agricultural land 

use settings was 3.4 mg/L (Nolan 

and Stoner, 2000).

Dissolved solids were elevated 

in rice fields relative to the other 

ground water sampled in this study. 

The elevated concentrations are 

most likely related to evaporation 

of irrigation water, which leaves 

behind salt. The effects of these 

increases in dissolved solids on 

deeper portions of the aquifer are 

unknown. 

The effects of recent urbanization on the quality of shallow 

ground water were investigated as 

part of this NAWQA study 

(fig. 21). The chosen metropolitan 

area was that of the city and surrounding counties of Sacramento. 

The part of the metropolitan area 

developed between 5 and 25 years 

ago was chosen for the investigation because it was assumed that 

the water quality of older urban 

land might have degraded water 

quality because it was developed 

prior to the passage of the Clean 

Water Act and the period of more 

recent environmental awareness. 

Trichloromethane was the most 

frequently detected volatile organic 

chemical (16 of 19 wells). The concentrations were always very low 

and did not exceed any drinkingwater standards. The presence of 

trichloromethane can be attributed 

to lawn irrigation using water 

treated by chlorination. One or 

more pesticides were detected in 6 

of 19 (32 percent) of the wells sampled in the urban land-use study 

(fig. 19). Atrazine, or its degradation product, was the most frequently detected pesticide in the 

shallow ground water under the 

recently urbanized area. The 

Figure 20. Drilling and installing a new monitoring well in the rice-growing 

region of the Sacramento Valley. 
24 Water Quality in the Sacramento River Basin

occurrence of atrazine in ground 

water could not be attributed to 

either current urban land use or 

past agricultural production. All 

atrazine concentrations were below 

drinking-water standards.

 An examination of the nitrate 

data revealed the highest potential 

contamination of ground water 

from recent urban development. 

Although no wells had concentrations of nitrate above the drinkingwater standard, one well had a concentration of 8 mg/L, and 5 of the 

19 (26 percent) of the sampled 

wells had concentrations that 

exceeded 5 mg/L. The median concentration of nitrate was 2.4 mg/L. 

The median concentration of 

nitrate in ground water under urban 

areas measured in previous 

NAWQA investigations was 

1.6 mg/L (Nolan and Stoner, 

2000). 

With the exception of arsenic, 

trace elements generally were not 

found to be a problem from the 

perspective of human toxicity. 

Some wells did have high concentrations of iron and manganese. 

The primary drinking-water 

standard for cadmium (5 μg/L) was 

exceeded in three wells of the rice 

land-use study. The source of that 

cadmium is unknown. Arsenic 

exceeded the current drinkingwater standard of 50 μg/L in one 

urban well and approached the 

drinking-water standard in three 

other wells. Arsenic would be more 

problematic if the drinking-water 

standard were lowered to 5 μg/L, as 

proposed by the EPA (U.S. 

Environmental Protection Agency, 

2000). At that level, the standard 

would be exceeded in 53 percent of 

the urban wells, 39 percent of the 

rice land-use wells, and 48 percent 

of the domestic wells sampled in 

the southeastern Sacramento 

Valley. Iron and manganese dissolve when oxygen is absent in the 

ground water. Although generally 

nontoxic, these two metals can 

limit the beneficial uses of the 

ground water because they may 

precipitate when the ground water 

is exposed to air. The precipitation 

can be severe enough to adversely 

affect household uses of water as 

well as plumbing. 

Radon concentrations exceeded 

the EPA proposed drinking-water 

standard of 300 picocuries per liter 

in 90 percent of the domestic wells 

sampled. The median concentration from wells sampled in the 

southeastern Sacramento Valley 

was 495 picocuries per liter. Radon 

is a colorless gas formed from the 

radioactive decay of radium. 

Radium is produced by the radioactive decay of uranium, which has 

a half-life of 4.4 billion years, 

whereas the half-life of solid 

radium is 1,620 years. Radon, on 

the other hand, has a half-life of 

only 3.8 days. Because radon is a 

gas, it moves easily in underground 

geologic environments and readily 

enters ground water. Regions of the 

country with geologic formations 

containing granite, volcanic rocks, 

certain types of shale known as 

dark shale, and some sedimentary 

and metamorphic rocks are more 

likely to have soil or ground water 

enriched in radon. Those conditions exist in the Sacramento River 

Basin. The health effects of consuming water containing radon at 

levels determined in this study have 

not been identified.

Figure 21. Drilling and installation of a new monitoring well in the Sacramento 

metropolitan area. This study of shallow ground water was the first of its kind within 

the Sacramento metropolitan area. 
Study Unit Design 25 

STUDY UNIT DESIGN

0

0 40 MILES

40 KILOMETERS

0

0 40 MILES

40 KILOMETERS

0

0 40 MILES

40 KILOMETERS

Basic

Intensive

Special studies

Bed sediment

Bed sediment and 

 aquatic biota

Stream sites

Urban

Agriculture

Orchards

Forest and rangeland

Water bodies

Wetlands

Barren land

Land use

EXPLANATION

Intensive

Synoptic studies

Stream ecology sites

Sierra Nevada

Klamath Mountains

Eastern Cascades foothills

Chaparral and woodlands

Central Valley

Cascades

Snake River High Desert

Northern Basin and Range

Water bodies

Ecological regions

EXPLANATION

Southeastern Sacramento Valley

Rice land use

Urban land use

Ground-water sites

High infiltration rates, deep

 soils, well to excessively 

 drained

Moderate infiltration rates,

 moderately deep to deep

 soils

Slow infiltration rates,

 has a layer that impedes

 downward movement of

 water

Very slow infiltration rates,

 shallow soils over nearly

 impervious material

Soil types

EXPLANATION

1

2 3

5 4 6

12

11

10

9

7,8

Stream Chemistry

Basic and Intensive Fixed Sites (see 

Glossary) were selected to assess the 

occurrence of dissolved compounds 

and select compounds associated with 

solid materials in stream water or 

streambed sediment. Basic Fixed Sites 

were sampled less frequently and for 

fewer compounds than Intensive Fixed 

Sites. 

Basic and Intensive Fixed Sites

1. Sacramento River above Bend Bridge 

near Red Bluff

2. Sacramento River at Colusa

3. Yuba River at Marysville

4. Feather River near Nicolaus

5. Cache Creek at Rumsey

6. Colusa Basin Drain at Road 99E near 

Knights Landing

7. Sacramento Slough near Knights 

Landing

8. Sacramento River at Verona

9. Arcade Creek near Del Paso Heights

10. American River at Sacramento

11. Sacramento River at Freeport

12. Yolo Bypass at Interstate 80 near West 

Sacramento

Special Studies

A study of metals transport from an 

acid mine drainage site and a generalized study of mercury transport along a 

reach of the Sacramento River downstream from Shasta Lake were 

completed. 

Stream Ecology

Ecological assessments were completed along mountain to valley 

reaches (synoptic studies) of 3 streams, 

at 7 of the 12 Basic Fixed Sites, and at 

1 reference site to determine variations 

in the community structure of aquatic 

biota. 

Ground-Water Chemistry

Surveys of water quality in a used portion of the Sacramento Valley aquifer 

and the effects of agricultural and 

urban land uses on water quality were 

completed.
26 Water Quality in the Sacramento River Basin

SUMMARY OF DATA COLLECTION IN THE SACRAMENTO RIVER BASIN, 1994–98

Study

component What data were collected and why Types of sites sampled Number of sites

Sampling frequency and period

Stream Chemistry

Basic Fixed 

Sites— 

General water 

chemistry

Streamflow, nutrients, major ions, suspended sediment, 

water temperature, specific conductance, organic carbon, 

trace metals, mercury, dissolved oxygen, alkalinity and 

pH; to describe concentrations, loads, and seasonal variations.

Large rivers, most with continuous streamflow measurements available; streams 

with continuous streamflow measurements that drain forested, agricultural, 

and mining areas.

8 Monthly, 02/97–04/98

Intensive Fixed 

Sites— 

Agricultural 

and large 

river

In addition to the above constituents, 84 pesticides; to 

describe concentrations and seasonal variations.

One agricultural stream that drains 

primarily agricultural areas; one large 

river site near the mouth of the basin.

3 Monthly, 02/96–04/98; 

Monthly for pesticides, 

11/96–03/97 and 

08/97–04/98; twice per 

month for pesticides 

04/97–07/97

Intensive Fixed 

Sites—Urban

The same constituents as Basic Fixed Sites and Intensive 

Fixed Sites and, in addition, 85 volatile organic compounds; to describe concentrations and seasonal variations.

One stream that drains a primarily urbanized area.1 Monthly for pesticides and 

volatile organic chemicals, 

11/96–12/96 and 

01/98–04/98; twice 

monthly for pesticides, 

01/97–11/97. Storm 

sampling for volatile 

organic chemicals, 04/96 

and 10/96

Contaminants 

in streambed 

sediments

Trace elements and organic compounds; to determine 

presence of potentially toxic compounds attached to 

streambed sediments.

Depositional zones of large rivers and 

select tributaries, including fixed sites.

17 in 1996; 19 

in 1997

One sampling for trace 

elements and organic 

compounds in 1995; one 

sampling for trace 

elements in 1997

Contaminants 

in tissues of 

aquatic 

organisms

Asiatic clams and bottom-feeding fish were collected to 

determine the presence of contaminants that can accumulate in tissues of aquatic organisms. The tissue samples 

were analyzed for trace elements and organic compounds.

Fixed sites and other select sites of large 

rivers and select tributaries.

17 One sampling in 1997

Stream Ecology

Intensive 

Assessments

Fish, macroinvertebrates, and algae; to assess biological 

communities and habitat in streams representing primary 

ecological regions.

Sites at or near a fixed site or at a pristine or 

reference location.

9 Three samplings, 1996–98

Synoptic 

Studies

Fish, macroinvertebrates, and algae; to determine spatial 

distribution and communnity structure of aquatic species 

and habitat.

Sites along an elevation gradient from the 

Sierra Nevada to the Sacramento Valley.

14 Two samplings, 1997–98

Ground-Water Chemistry

Aquifer 

Survey

Major ions, nutrients, pesticides, trace elements, volatile 

organic compounds, and radon; to describe the overall 

water quality and natural chemistry in a surficial aquifer.

Domestic wells in the southeastern Sacramento Valley.31 wells Once in 1996

Land-Use 

Effects— 

Agriculture 

(rice)

Major ions, nutrients, trace elements, and pesticides; to 

describe the water quality and natural chemistry in a 

surficial aquifer in an agricultural setting.

Newly drilled monitoring wells completed 

near the water table in a surficial aquifer 

beneath or near rice fields.

28 wells Once in 1997

Land-Use 

Effects— 

Urban

Major ions, nutrients, pesticides, trace elements, volatile 

organic compounds, and radon; to describe the overall 

water quality and natural chemistry in a surficial aquifer.

Newly drilled monitoring wells completed 

near the water table in a surficial aquifer 

beneath a recently urbanized area.

19 wells Once in 1998

Special Studies

Sacramento 

River Trace 

Metals Study

Trace elements measured in whole water, filtered water, 

ultrafiltered water, and on colloids.

Sacramento River and select tributaries 

including an acid mine drainage site.

19 During selected high flow 

and low-flow stream 

conditions, 07/96–06/97
Glossary 27

GLOSSARY 

Amalgamation—The dissolving or blending of a metal 

(commonly gold and silver) in mercury to separate it 

from its parent material. 

Aquatic guidelines—Specific levels of water quality which, 

if reached, may adversely affect aquatic life. These are 

nonenforceable guidelines issued by a governmental 

agency or other institution. 

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 Waterquality guidelines and Water-quality standards. 

Aquifer—A water-bearing layer of soil, sand, gravel, or 

rock that will yield usable quantities of water to a well. 

Basic Fixed Sites—Sites on streams at which streamflow is 

measured and samples are collected for temperature, 

salinity, suspended sediment, major ions and metals, 

nutrients, and organic carbon to assess the broad-scale 

spatial and temporal character and transport of 

inorganic constituents of stream water in relation to 

hydrologic conditions and environmental settings.

Bed sediment—The material at 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 biological sequestering of a 

substance at a higher concentration than that at which it 

occurs in the surrounding environment or medium. 

Also, the process whereby a substance enters organisms 

through the gills, epithelial tissues, dietary, or other 

sources. 

Bioavailability—The capacity of a chemical constituent to 

be taken up by living organisms either through physical 

contact or by ingestion. 

Criterion—A standard rule or test on which a judgment or 

decision can be based. 

Dissolved solids—Amount of minerals, such as salt, that are 

dissolved in water; amount of dissolved solids is an 

indicator of salinity or hardness. 

Drainage basin—The portion of the surface of the earth that 

contributes water to a stream through overland runoff, 

including tributaries and impoundments. 

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 contamination 

levels for public water systems required to protect the 

public welfare; guidelines have no regulatory status and 

are issued in an advisory capacity. 

Ecological studies—Studies of biological communities and 

habitat characteristics to evaluate the effects of physical 

and chemical characteristics of water and hydrologic 

conditions on aquatic biota and to determine how 

biological and habitat characteristics differ among 

environmental settings in NAWQA Study Units. 

Ecoregion—An area of similar climate, landform, soil, 

potential natural vegetation, hydrology, or other 

ecologically relevant variables. 

Ecosystem—The interacting populations of plants, animals, 

and microorganisms occupying an area, plus their 

physical environment. 

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. 

Habitat—The part of the physical environment where plants 

and animals live. 

Hydrograph—Graph showing variation of water elevation, 

velocity, streamflow, or other property of water with 

respect to time. 

Intensive Fixed Sites—Basic Fixed Sites with increased 

sampling frequency during selected seasonal periods 

and analysis of dissolved pesticides for 1 year. 

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. 

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 stream water 

and ground water. One thousand micrograms per liter 

equals 1 milligram per liter (mg/L). 

Nitrate—An ion consisting of nitrogen and oxygen (NO3

-

). 

Nitrate is a plant nutrient and is very mobile in soils. 

Nonpoint source—A pollution source that cannot be 

defined as originating from discrete points such as pipe 

discharge. Areas of fertilizer and pesticide applications, 

atmospheric deposition, manure, and natural inputs 

from plants and trees are types of nonpoint source 

pollution. 

Nutrient—An element or compound essential for animal 

and plant growth. Common nutrients in fertilizer 

include nitrogen, phosphorus, and potassium. 
28 Water Quality in the Sacramento River Basin

Organochlorine compound—Synthetic organic 

compounds containing chlorine. As generally used, the 

term refers to compounds containing mostly or 

exclusively carbon, hydrogen, and chlorine. Examples 

include organochlorine insecticides, polychlorinated 

biphenyls, and some solvents containing chlorine. 

Organophosphate insecticides—A class of insecticides 

derived from phosphoric acid. They tend to have high 

acute toxicity to vertebrates. Although readily 

metabolized by vertebrates, some metabolic products 

are more toxic than the parent compound. 

Phosphorus—A nutrient essential for growth that can play a 

key role in stimulating aquatic growth in lakes and 

streams. 

Plankton—Floating or weakly swimming organisms whose 

migration is controlled by waves and currents. Animals 

of the group are called zooplankton and the plants are 

called phytoplankton. 

Point source—A source at a discrete location such as a 

discharge pipe, drainage ditch, tunnel, well, 

concentrated livestock operation, or floating craft. 

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. 

Radon—A naturally occurring, colorless, odorless, 

radioactive gas formed by the disintegration of the 

element radium; damaging to human lungs when 

inhaled. 

Recharge—Water that infiltrates the ground and reaches the 

saturated zone. 

Runoff—Excess rainwater or snowmelt that is transported to 

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

Semivolatile organic compound (SVOC)—Operationally 

defined as a group of synthetic organic compounds that 

are solvent-extractable and that can be determined by 

gas chromatography/mass spectrometry. SVOCs 

include phenols, phthalates, and polycyclic aromatic 

hydrocarbons (PAHs). 

Suspended sediment—Particles of rock, sand, soil, and 

organic detritus carried in suspension in the water 

column, in contrast to sediment that moves on or near 

the streambed. 

Tolerant species—Those species that are adaptable to 

(tolerant of) human alterations to the environment and 

often increase in number when human alterations occur. 

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.

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, 

fumigants, some inert ingredients in pesticides, and 

some by-products of chlorine disinfection. 

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. 

Watershed—See Drainage basin. 

Water table—The point below the land surface where 

ground water is first encountered and below which the 

earth is saturated. Depth to the water table varies widely 

across the country. 

Wetlands—Ecosystems whose soil is saturated for long 

periods seasonally or continuously, including marshes, 

swamps, and ephemeral ponds. 
References 29

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30 Water Quality in the Sacramento River Basin

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Water-Quality Data in a National Context 31 

Streams in agricultural areas 

Streams in urban areas

Streams and rivers draining mixed land uses 

Shallow ground water in agricultural areas

Shallow ground water in urban areas 

Major aquifers 

Detected concentration in Study Unit

Frequencies of detection, in percent. Detection frequencies 

were not censored at any common reporting limit. The lefthand column is the study-unit frequency and the right-hand 

column is the national frequency 

Not measured or sample size less than two

Study-unit sample size. For ground water, the number of 

samples is equal to the number of wells sampled

National ranges of detected concentrations, by land use, in 36 

NAWQA Study Units, 1991–98—Ranges include only samples

in which a chemical was detected

Drinking-water quality (applies to ground water and surface water)

Protection of aquatic life (applies to surface water only)

Prevention of eutrophication in streams not flowing directly into 

lakes or impoundments

No benchmark for drinking-water quality

No benchmark for protection of aquatic life

*

**

66 38

CHEMICALS IN WATER

Concentrations and detection frequencies, Sacramento River 

Basin, 1994–98—Detection sensitivity varies among chemicals and, 

thus, frequencies are not directly comparable among chemicals

Lowest

25 percent

Middle

50 percent

Highest

25 percent

National water-quality benchmarks

National benchmarks include standards and guidelines related to 

drinking-water quality, criteria for protecting the health of aquatic life, and 

a goal for preventing stream eutrophication due to phosphorus. Sources 

include the U.S. Environmental Protection Agency and the Canadian 

Council of Ministers of the Environment.

|

|

|

--

This appendix is a summary of chemical concentrations 

and biological indicators assessed in the Sacramento 

River Basin. Selected results for this basin are graphically 

compared to results from as many as 36 NAWQA Study 

Units investigated from 1991 to 1998 and to national 

water-quality benchmarks for human health, aquatic life, or 

fish-eating wildlife. The chemical and biological indicators 

shown were selected on the basis of frequent detection, 

detection at concentrations above a national benchmark, 

or regulatory or scientific importance. The graphs illustrate 

how conditions associated with each land use sampled in 

the Sacramento River Basin compare to results from 

across the Nation, and how conditions compare among 

the several land uses. Graphs for chemicals show only 

detected concentrations and, thus, care must be taken to 

evaluate detection frequencies in addition to concentrations when comparing study-unit and national results. For 

example, molinate concentrations in Sacramento River 

Basin agricultural streams were similar to the national 

distribution, but the detection frequency was much higher 

(100 percent compared to 7 percent).

CONCENTRATION, IN MICROGRAMS PER LITER

 0.0001 0.001 0.01 0.1 1 10 100 1,000 

Study-unit frequency of detection, in percent

National frequency of detection, in percent

Pesticides in water—Herbicides

Study-unit sample size

12

Bentazon (Basagran, Bentazone) ** 50 17 | 22 0 1 | 29 4 12 | 26

71 4 | 28 5 3 | 19 16 2 | 25

2,4-D (Aqua-Kleen, Lawn-Keep, Weed-B-Gone) 

18 15 | | 22 28 18 | | 29 4 11 | | 26

0 <1 | 28 0 1 | 19 0 <1 | 24

DCPA (Dacthal, chlorthal-dimethyl) * **

52 18 21 83 30 30 4 20 26

0 1 28 0 1 19 0 <1 31

Diuron (Crisuron, Karmex, Diurex) ** 68 13 | 22 86 22 | 29 54 20 | 26

7 4 | 28 0 3 | 19 0 2 | 31

EPTC (Eptam, Farmarox, Alirox) * **

57 21 21 13 4 30 15 19 26

0 1 28 0 1 19 0 <1 31

Metolachlor (Dual, Pennant) 

90 81 | | 21 80 64 | | 30 77 83 | | 26

0 18 | 28 0 9 | 19 0 5 | 31

Molinate (Ordram) * **

100 7 21 3 3 30 69 5 26

25 1 28

0 <1 31

Prometon (Pramitol, Princep) **

14 44 | 21 97 86 | 30 0 60 | 26

0 12 | 28 0 21 | 19 0 5 | 31

Simazine (Princep, Caliber 90) 95 61 | | 21 73 77 | | 30 58 74 | | 26

36 21 | 28 5 18 | 19 10 5 | 31

Thiobencarb (Bolero, Saturn, Benthiocarb) * ** 90 4 21 3 2 30 50 2 26

11 <1 28 0 <1 19

APPENDIX—WATER-QUALITY DATA FROM THE SACRAMENTO 

RIVER BASIN IN A NATIONAL CONTEXT

For a complete view of Sacramento River Basin data and for additional information about specific benchmarks used, visit our Web site at 

http://water.usgs.gov/nawqa/. Also visit the NAWQA Data Warehouse for access to NAWQA data sets at http://water.usgs.gov/nawqa/data. 
32 Water Quality in the Sacramento River Basin

CONCENTRATION, IN MICROGRAMS PER LITER

 0.0001 0.001 0.01 0.1 1 10 100 1,000 

Study-unit frequency of detection, in percent

National frequency of detection, in percent

Pesticides in water—Insecticides

Study-unit sample size

Volatile organic compounds (VOCs) in ground water

These graphs represent data from 16 Study Units, sampled from 1996 to 1998

Study-unit frequency of detection, in percent

National frequency of detection in percent Study-unit sample size

CONCENTRATION, IN MICROGRAMS PER LITER

 0.001 0.01 0.1 1 10 100 1,000 10,000 

Other insecticides detected 

Azinphos-methyl (Guthion, Gusathion M) * 

p,p'-DDE 

Propargite (Comite, Omite, Ornamite) * **

Insecticides not detected

Aldicarb (Temik, Ambush, Pounce) 

Aldicarb sulfone (Standak, aldoxycarb) 

Aldicarb sulfoxide (Aldicarb breakdown product) 

Dieldrin (Panoram D-31, Octalox, Compound 497) 

Disulfoton (Disyston, Di-Syston) **

Ethoprop (Mocap, Ethoprophos) * **

Fonofos (Dyfonate, Capfos, Cudgel, Tycap) **

alpha-HCH (alpha-BHC, alpha-lindane) **

gamma-HCH (Lindane, gamma-BHC) 

3-Hydroxycarbofuran (Carbofuran breakdown product) * **

Methiocarb (Slug-Geta, Grandslam, Mesurol) * **

Methomyl (Lanox, Lannate, Acinate) **

Methyl parathion (Penncap-M, Folidol-M) **

Oxamyl (Vydate L, Pratt) **

Parathion (Roethyl-P, Alkron, Panthion, Phoskil) * 

cis-Permethrin (Ambush, Astro, Pounce) * **

Phorate (Thimet, Granutox, Geomet, Rampart) * **

Propoxur (Baygon, Blattanex, Unden, Proprotox) * **

Terbufos (Contraven, Counter, Pilarfox) **

Trifluralin (Treflan, Gowan, Tri-4, Trific) 

52 21 | | 21 33 13 | | 30 0 17 | | 26

0 1 | 28 0 1 | 19 0 <1 | 31

Other herbicides detected

Alachlor (Lasso, Bronco, Lariat, Bullet) **

Atrazine (AAtrex, Atrex, Atred, Gesaprim) 

Benfluralin (Balan, Benefin, Bonalan) * **

Bromacil (Hyvar X, Urox B, Bromax) 

Bromoxynil (Buctril, Brominal) * 

Cyanazine (Bladex, Fortrol) 

Deethylatrazine (Atrazine breakdown product) * **

Dichlorprop (2,4-DP, Seritox 50, Lentemul) * **

2,6-Diethylaniline (Alachlor breakdown product) * **

MCPA (Rhomene, Rhonox, Chiptox) 

Metribuzin (Lexone, Sencor) 

Napropamide (Devrinol) * **

Norflurazon (Evital, Predict, Solicam, Zorial) * **

Oryzalin (Surflan, Dirimal) * **

Pebulate (Tillam, PEBC) * **

Pendimethalin (Pre-M, Prowl, Stomp) * **

Pronamide (Kerb, Propyzamid) **

Propanil (Stam, Stampede, Wham) * **

Tebuthiuron (Spike, Tebusan) 

Triclopyr (Garlon, Grandstand, Redeem, Remedy) * **

Herbicides not detected

Acetochlor (Harness Plus, Surpass) * **

Acifluorfen (Blazer, Tackle 2S) **

Butylate (Sutan +, Genate Plus, Butilate) **

Chloramben (Amiben, Amilon-WP, Vegiben) **

Clopyralid (Stinger, Lontrel, Transline) * **

2,4-DB (Butyrac, Butoxone, Embutox Plus, Embutone) * **

Dacthal mono-acid (Dacthal breakdown product) * **

Dicamba (Banvel, Dianat, Scotts Proturf) 

Dinoseb (Dinosebe) 

Ethalfluralin (Sonalan, Curbit) * **

Fenuron (Fenulon, Fenidim) * **

Fluometuron (Flo-Met, Cotoran) **

Linuron (Lorox, Linex, Sarclex, Linurex, Afalon) * 

MCPB (Thistrol) * **

Neburon (Neburea, Neburyl, Noruben) * **

Picloram (Grazon, Tordon) 

Propachlor (Ramrod, Satecid) **

Propham (Tuberite) **

2,4,5-T **

2,4,5-TP (Silvex, Fenoprop) **

Terbacil (Sinbar) **

Triallate (Far-Go, Avadex BW, Tri-allate) * 

CONCENTRATION, IN MICROGRAMS PER LITER

 0.0001 0.001 0.01 0.1 1 10 100 1,000 

Study-unit frequency of detection, in percent

National frequency of detection, in percent Study-unit sample size

Carbaryl (Carbamine, Denapon, Sevin) 

43 9 | | 21 100 46 | | 30 27 16 | | 26

0 <1 | 28 0 2 | 19 0 1 | 31

Carbofuran (Furadan, Curaterr, Yaltox) 100 11 | | 21 3 3 | | 30 23 10 | | 26

14 2 | 28 0 1 | 19 0 1 | 31

Chlorpyrifos (Brodan, Dursban, Lorsban) 29 18 | | 21 73 37 | | 30 4 20 | | 26

0 1 | 28 0 1 | 19 0 <1 | 31

Diazinon (Basudin, Diazatol, Neocidol, Knox Out) 

71 16 | | 21 100 70 | | 30 35 39 | | 26

0 <1 | 28 0 2 | 19 0 2 | 31

Malathion (Malathion) 33 5 | | 21 53 21 | | 30 8 6 | | 26

0 <1 | 28 0 <1 | 19 0 <1 | 31

CONCENTRATION, IN MICROGRAMS PER LITER

 0.0001 0.001 0.01 0.1 1 10 100 1,000 

Study-unit frequency of detection, in percent

National frequency of detection, in percent Study-unit sample size

Methyl tert-butyl ether (MTBE) 

-- 4 | 0 11 16 | 19 3 6 | 31

Trichloroethene (TCE) 

-- 3 | 0 0 8 | 19 13 5 | 31
Water-Quality Data in a National Context 33 

CONCENTRATION, IN MILLIGRAMS PER LITER

 0.001 0.01 0.1 1 10 100 1,000 10,000 100,000 

CONCENTRATION, IN MILLIGRAMS PER LITER

 0.001 0.01 0.1 1 10 100 1,000 10,000 100,000 

Nutrients in water

Study-unit frequency of detection, in percent

National frequency of detection, in percent Study-unit sample size

Dissolved solids in water

Study-unit frequency of detection, in percent

National frequency of detection, in percent Study-unit sample size

Trichloromethane (Chloroform) 

-- 35 | 0 84 51 | 19 10 30 | 31

Other VOCs detected

Bromodichloromethane (Dichlorobromomethane) 

Carbon disulfide * 

Chloromethane (Methyl chloride) 

Dichlorodifluoromethane (CFC 12, Freon 12) 

1,2-Dichloroethane (Ethylene dichloride) 

1,1-Dichloroethane (Ethylidene dichloride) * 

cis-1,2-Dichloroethene ((Z)-1,2-Dichloroethene) 

Ethenylbenzene (Styrene) 

Iodomethane (Methyl iodide) * 

Tetrachloroethene (Perchloroethene) 

Tetrachloromethane (Carbon tetrachloride) 

1,1,1-Trichloroethane (Methylchloroform) 

Trichlorofluoromethane (CFC 11, Freon 11) 

1,2,4-Trimethylbenzene (Pseudocumene) * 

VOCs not detected

tert-Amylmethylether (tert-amyl methyl ether (TAME)) * 

Benzene 

Bromobenzene (Phenyl bromide) * 

Bromochloromethane (Methylene chlorobromide) 

Bromoethene (Vinyl bromide) * 

Bromomethane (Methyl bromide) 

2-Butanone (Methyl ethyl ketone (MEK)) * 

n-Butylbenzene (1-Phenylbutane) * 

sec-Butylbenzene * 

tert-Butylbenzene * 

3-Chloro-1-propene (3-Chloropropene) * 

1-Chloro-2-methylbenzene (o-Chlorotoluene) 

1-Chloro-4-methylbenzene (p-Chlorotoluene) 

Chlorobenzene (Monochlorobenzene) 

Chlorodibromomethane (Dibromochloromethane) 

Chloroethane (Ethyl chloride) * 

Chloroethene (Vinyl chloride) 

1,2-Dibromo-3-chloropropane (DBCP, Nemagon) 

1,2-Dibromoethane (Ethylene dibromide, EDB) 

Dibromomethane (Methylene dibromide) * 

trans-1,4-Dichloro-2-butene ((Z)-1,4-Dichloro-2-butene) * 

1,2-Dichlorobenzene (o-Dichlorobenzene) 

1,3-Dichlorobenzene (m-Dichlorobenzene) 

1,4-Dichlorobenzene (p-Dichlorobenzene) 

1,1-Dichloroethene (Vinylidene chloride) 

trans-1,2-Dichloroethene ((E)-1,2-Dichlorothene) 

Dichloromethane (Methylene chloride) 

1,2-Dichloropropane (Propylene dichloride) 

2,2-Dichloropropane * 

1,3-Dichloropropane (Trimethylene dichloride) * 

trans-1,3-Dichloropropene ((E)-1,3-Dichloropropene) 

cis-1,3-Dichloropropene ((Z)-1,3-Dichloropropene) 

1,1-Dichloropropene * 

Diethyl ether (Ethyl ether) * 

Diisopropyl ether (Diisopropylether (DIPE)) * 

1,2-Dimethylbenzene (o-Xylene) 

1,3 & 1,4-Dimethylbenzene (m-&p-Xylene) 

1-4-Epoxy butane (Tetrahydrofuran, Diethylene oxide) * 

Ethyl methacrylate * 

Ethyl tert-butyl ether (Ethyl-t-butyl ether (ETBE)) * 

1-Ethyl-2-methylbenzene (2-Ethyltoluene) * 

Ethylbenzene (Phenylethane) 

Hexachlorobutadiene 

1,1,1,2,2,2-Hexachloroethane (Hexachloroethane) 

2-Hexanone (Methyl butyl ketone (MBK)) * 

Isopropylbenzene (Cumene) * 

p-Isopropyltoluene (p-Cymene) * 

Methyl acrylonitrile * 

Study-unit frequency of detection, in percent

National frequency of detection in percent Study-unit sample size

CONCENTRATION, IN MICROGRAMS PER LITER

 0.001 0.01 0.1 1 10 100 1,000 10,000 

Methyl-2-methacrylate (Methyl methacrylate) * 

4-Methyl-2-pentanone (Methyl isobutyl ketone (MIBK)) * 

Methyl-2-propenoate (Methyl acrylate) * 

Methylbenzene (Toluene) 

Naphthalene 

2-Propanone (Acetone) * 

2-Propenenitrile (Acrylonitrile) 

n-Propylbenzene (Isocumene) * 

1,1,2,2-Tetrachloroethane * 

1,1,1,2-Tetrachloroethane 

1,2,3,4-Tetramethylbenzene (Prehnitene) * 

1,2,3,5-Tetramethylbenzene (Isodurene) * 

Tribromomethane (Bromoform) 

1,1,2-Trichloro-1,2,2-trifluoroethane (Freon 113) * 

1,2,4-Trichlorobenzene 

1,2,3-Trichlorobenzene * 

1,1,2-Trichloroethane (Vinyl trichloride) 

1,2,3-Trichloropropane (Allyl trichloride) 

1,2,3-Trimethylbenzene (Hemimellitene) * 

Ammonia, as N * **

65 84 54 86 86 36 34 75 230

36 78 28 89 71 18 77 70 31

Dissolved ammonia plus organic nitrogen, as N * ** 83 78 54 100 74 36 16 62 230

11 28 28 39 30 18 0 24 31

Dissolved nitrite plus nitrate, as N ** 94 95 | 54 100 97 | 36 88 91 | 230

82 81 | 28 72 74 | 18 94 71 | 31

Orthophosphate, as P * **

98 79 54 97 72 36 67 74 230

96 59 28 100 52 18 100 61 31

Total phosphorus, as P * ** 100 92 | 54 100 90 | 37 85 88 | 230

Dissolved solids * ** 100 100 56 100 100 38 100 100 229

100 100 28 100 100 19 100 100 31
34 Water Quality in the Sacramento River Basin

Fish tissue from streams in agricultural areas

Fish tissue from streams in urban areas

Fish tissue from streams draining mixed land uses

Sediment from streams in agricultural areas 

Sediment from streams in urban areas 

Sediment from streams draining mixed land uses

Protection of fish-eating wildlife (applies to fish tissue)

Protection of aquatic life (applies to bed sediment)

No benchmark for protection of fish-eating wildlife

No benchmark for protection of aquatic life

|

|

**

CHEMICALS IN FISH TISSUE

AND BED SEDIMENT

Concentrations and detection frequencies, Sacramento River 

Basin, 1994–98—Detection sensitivity varies among chemicals and, 

thus, frequencies are not directly comparable among chemicals. 

Study-unit frequencies of detection are based on small sample sizes; 

the applicable sample size is specified in each graph

Lowest

25 percent

Middle

50 percent

Highest

25 percent

National benchmarks for fish tissue and bed sediment

National benchmarks include standards and guidelines related to 

criteria for protection of the health of fish-eating wildlife and aquatic 

organisms. Sources include the U.S. Environmental Protection Agency, 

other Federal and State agencies, and the Canadian Council of 

Ministers of the Environment

*

CONCENTRATION, IN MICROGRAMS PER KILOGRAM

(Fish tissue is wet weight; bed sediment is dry weight)

 0.1 1 10 100 1,000 10,000 100,000 

CONCENTRATION, IN MICROGRAMS PER KILOGRAM

(Fish tissue is wet weight; bed sediment is dry weight)

 0.1 1 10 100 1,000 10,000 100,000 

National ranges of concentrations detected, by land use, in 36 

NAWQA Study Units, 1991–98—Ranges include only samples

in which a chemical was detected

Detected concentration in Study Unit

Frequencies of detection, in percent. Detection frequencies 

were not censored at any common reporting limit. The lefthand column is the study-unit frequency and the right-hand 

column is the national frequency

Not measured or sample size less than two

Study-unit sample size

66 38

--

12

Organochlorines in fish tissue (whole body)

and bed sediment

Study-unit frequency of detection, in percent

National frequency of detection, in percent Study-unit sample size

Study-unit frequency of detection, in percent

National frequency of detection, in percent Study-unit sample size

Other trace elements detected

Selenium 

Zinc 

Trace elements not detected

Lead

CONCENTRATION, IN PICOCURIES PER LITER

Trace elements in ground water

Arsenic 

100 58 | 28 100 36 | 19 90 37 | 31

Cadmium 

11 2 | 28 0 1 | 19 -- <1 | 0

Chromium 

96 85 | 28 100 79 | 19 -- 73 | 0

Radon-222 

-- 99 | 0 -- 100 | 0 100 97 | 31

Uranium 

86 64 | 28 58 35 | 19 -- 33 | 0

Study-unit frequency of detection, in percent

National frequency of detection, in percent Study-unit sample size

CONCENTRATION, IN MICROGRAMS PER LITER

 0.01 0.1 1 10 100 1,000 10,000 100,000 

 0.01 0.1 1 10 100 1,000 10,000 100,000 

o,p'+p,p'-DDD (sum of o,p'-DDD and p,p'-DDD) * 

100 49 2 -- 69 0 0 50 2

67 27 | 3 -- 50 | 1 0 20 | 8

p,p'-DDE * **

100 90 2 -- 94 0 50 92 2

100 48 3 -- 62 1 38 39 8

o,p'+p,p'-DDE (sum of o,p'-DDE and p,p'-DDE) * 100 90 2 -- 94 0 50 92 2

100 48 | 3 -- 62 | 1 38 39 | 8

Total DDT (sum of 6 DDTs) **

100 90 | 2 -- 94 | 0 50 93 | 2

100 49 3 -- 66 1 38 41 8

Dieldrin (Panoram D-31, Octalox) * 

100 53 2 -- 42 0 0 38 2

0 13 | 3 -- 30 | 1 0 9 | 8
Water-Quality Data in a National Context 35 

Other SVOCs detected

Acenaphthene 

Acenaphthylene 

Anthracene 

Benz[a]anthracene 

Benzo[a]pyrene 

Benzo[b]fluoranthene **

Benzo[ghi]perylene **

Benzo[k]fluoranthene **

Butylbenzylphthalate **

Chrysene 

p-Cresol **

Di-n-butylphthalate **

Di-n-octylphthalate **

Diethylphthalate **

1,6-Dimethylnaphthalene **

Dimethylphthalate **

9H-Fluorene (Fluorene) 

Indeno[1,2,3-cd]pyrene **

2-Methylanthracene **

4,5-Methylenephenanthrene **

1-Methylphenanthrene **

Naphthalene 

Phenanthrene 

Pyrene 

SVOCs not detected

Acridine **

C8-Alkylphenol **

Azobenzene **

Benzo[c]cinnoline **

2,2-Biquinoline **

4-Bromophenyl-phenylether **

4-Chloro-3-methylphenol **

bis(2-Chloroethoxy)methane **

2-Chloronaphthalene **

2-Chlorophenol **

4-Chlorophenyl-phenylether **

Dibenz[a,h]anthracene 

Dibenzothiophene **

1,2-Dichlorobenzene (o-Dichlorobenzene) **

1,3-Dichlorobenzene (m-Dichlorobenzene) **

1,4-Dichlorobenzene (p-Dichlorobenzene) **

1,2-Dimethylnaphthalene **

3,5-Dimethylphenol **

2,4-Dinitrotoluene **

2-Ethylnaphthalene **

Isophorone **

Isoquinoline **

1-Methyl-9H-fluorene **

1-Methylpyrene **

Nitrobenzene **

CONCENTRATION, IN MICROGRAMS PER KILOGRAM, DRY WEIGHT N-Nitrosodi-n-propylamine **

 0.1 1 10 100 1,000 10,000 100,000 

CONCENTRATION, IN MICROGRAMS PER KILOGRAM, DRY WEIGHT

 0.1 1 10 100 1,000 10,000 100,000 

Study-unit frequency of detection, in percent

National frequency of detection, in percent

Study-unit frequency of detection, in percent

National frequency of detection, in percent

Semivolatile organic compounds (SVOCs)

in bed sediment

Study-unit sample size

Study-unit sample size

Other organochlorines detected

o,p'+p,p'-DDT (sum of o,p'-DDT and p,p'-DDT) *

Organochlorines not detected

Chloroneb (Chloronebe, Demosan) * **

DCPA (Dacthal, chlorthal-dimethyl) * **

Endosulfan I (alpha-Endosulfan, Thiodan) * **

Endrin (Endrine) 

gamma-HCH (Lindane, gamma-BHC, Gammexane) * 

Total-HCH (sum of alpha-HCH, beta-HCH, gamma-HCH, and delta-HCH) **

Heptachlor epoxide (Heptachlor breakdown product) * 

Heptachlor+heptachlor epoxide (sum of heptachlor and heptachlor epoxide) **

Hexachlorobenzene (HCB) **

Isodrin (Isodrine, Compound 711) * **

p,p'-Methoxychlor (Marlate, methoxychlore) * **

o,p'-Methoxychlor * **

Mirex (Dechlorane) **

PCB, total 

Pentachloroanisole (PCA) * **

cis-Permethrin (Ambush, Astro, Pounce) * **

trans-Permethrin (Ambush, Astro, Pounce) * **

CONCENTRATION, IN MICROGRAMS PER KILOGRAM

(Fish tissue is wet weight; bed sediment is dry weight)

 0.1 1 10 100 1,000 10,000 100,000 

Study-unit frequency of detection, in percent

National frequency of detection, in percent Study-unit sample size

Dieldrin+aldrin (sum of dieldrin and aldrin) ** 100 52 | 2 -- 42 | 0 0 38 | 2

0 13 3 -- 29 1 0 9 8

Toxaphene (Camphechlor, Hercules 3956) * ** 50 12 2

0 1 2

0 <1 3

Anthraquinone **

0 21 3 -- 83 1 12 39 8

9H-Carbazole **

33 19 3 -- 76 1 0 33 8

2,6-Dimethylnaphthalene **

100 65 3 -- 74 1 62 77 8

bis(2-Ethylhexyl)phthalate **

100 91 3 -- 99 1 100 95 8

Fluoranthene 

100 66 | 3 -- 97 | 1 88 78 | 8

Phenol **

100 81 3 -- 82 1 100 80 8
36 Water Quality in the Sacramento River Basin

Biological indicator value, Sacramento River Basin, by land 

use, 1994–98

Biological status assessed at a site

National ranges of biological indicators, in 16 NAWQA Study 

Units, 1994–98

Streams in undeveloped areas

Streams in agricultural areas

Streams in urban areas

Streams in mixed-land-use areas

75th percentile

25th percentile

BIOLOGICAL INDICATORS

Higher national scores suggest habitat disturbance, water-quality 

degradation, or naturally harsh conditions. The status of algae, 

invertebrates (insects, worms, and clams), and fish provide a 

record of water-quality and stream conditions that waterchemistry indicators may not reveal. Algal status focuses on the 

changes in the percentage of certain algae in response to 

increasing siltation, and it often correlates with higher nutrient 

concentrations in some regions. Invertebrate status averages 11 

metrics that summarize changes in richness, tolerance, trophic 

conditions, and dominance associated with water-quality 

degradation. Fish status sums the scores of four fish metrics 

(percent tolerant, omnivorous, non-native individuals, and percent 

individuals with external anomalies) that increase in association 

with water-quality degradation

 0 10 20 30 40 50 60 70 80 90 100

CONCENTRATION, IN MICROGRAMS PER GRAM

(Fish tissue is wet weight, bed sediment is dry weight)

 0.01 0.1 1 10 100 10,000 1,000 

Study-unit frequency of detection, in percent

National frequency of detection, in percent

Trace elements in fish tissue (livers) and 

bed sediment

Study-unit sample size

 0 5 10 15 20

N-Nitrosodiphenylamine **

Pentachloronitrobenzene **

Phenanthridine **

Quinoline **

1,2,4-Trichlorobenzene **

2,3,6-Trimethylnaphthalene **

 Algal status indicator

Undeveloped

Agricultural

Urban

Mixed

 Invertebrate status indicator

Undeveloped

Agricultural

Urban

Mixed

 Fish status indicator

Undeveloped

Agricultural

Urban

Mixed

Arsenic * 

100 56 2 -- 38 0 100 76 2

100 99 | 5 -- 98 | 1 100 97 | 20

Cadmium * 

100 77 2 -- 72 0 50 95 2

80 98 | 5 -- 100 | 1 100 98 | 20

Chromium * 100 62 2 -- 72 0 50 54 2

100 100 | 5 -- 99 | 1 100 100 | 20

Copper * 100 100 2 -- 100 0 100 100 2

100 100 | 5 -- 99 | 1 100 100 | 20

Lead * 

50 11 2 -- 41 0 50 41 2

100 100 | 5 -- 100 | 1 100 99 | 20

Mercury * 

100 71 2 -- 59 0 100 80 2

100 82 | 5 -- 97 | 1 100 93 | 20

Nickel * **

50 42 2 -- 44 0 50 50 2

100 100 5 -- 100 1 100 100 20

Selenium * 100 99 2 -- 100 0 100 99 2

100 100 | 5 -- 100 | 1 100 100 | 20

Zinc * 

100 100 2 -- 100 0 100 100 2

100 100 | 5 -- 99 | 1 100 100 | 20
Coordination with agencies and organizations in the Sacramento River Basin was integral to the success of this 

water-quality assessment. We thank those who served as members of our liaison committee. 

Federal Agencies

U.S. Environmental Protection Agency

U.S. Fish and Wildlife Service

Bureau of Reclamation

National Marine Fisheries Service

State Agencies

California Regional Water Quality Control Board

California Department of Water Resources

California Department of Fish and Game

California Division of Mines and Geology

California State Water Resources Control Board

Other

University of California, Davis

We also thank the following organizations for contributing to this effort. 

We are grateful to the Sacramento River Watershed Program (SRWP) and the Sacramento Regional County 

Sanitation District (SRCSD). The SRWP was initiated in 1995, just as the NAWQA Program initiated most of the 

water-quality sample collection activities in the basin. The SRWP has the following mission statement: “To ensure 

that current and potential uses of the watershed’s resources are sustained, restored, and where possible, 

enhanced, while promoting the long-term social and economic vitality of the region.” The current SRWP 

membership includes a diverse group of stakeholders interested in water quality of the Sacramento River Basin. 

The infrastructure of the SRWP provides a unique means of achieving the NAWQA goals of coordination. The 

SRCSD anticipated the need for a more comprehensive approach to water-quality management of the Sacramento 

River Basin. As a result, the SRCSD was instrumental in developing the Sacramento River Toxic Pollutant Control 

Program and was a partner with the Sacramento River Basin NAWQA Program in a detailed study of trace metals 

in the Sacramento River system. Other agencies contributing to or helping to facilitate funding for that study include 

the California State Water Resources Control Board, the U.S. Environmental Protection Agency, and the National 

Marine Fisheries Service.

A COORDINATED EFFORT
Domagalski and others— Water Quality in the Sacramento River Basin

U.S. Geological Survey Circular 1215

National Water-Quality Assessment (NAWQA) Program

Sacramento River Basin

NAWQA

Sacramento

Sacramento R

Feather R

Yu b a R

Cache Cr

American R