Water Quality in the

San Joaquin-Tulare Basins

California, 1992–95

U.S. Department of the Interior

U.S. Geological Survey Circular 1159

science for a changing world
A COORDINATED EFFORT

Chief, NAWQA Program

U.S. Geological Survey

Water Resources Division

12201 Sunrise Valley Drive, M.S. 4

Reston, VA 20192

FOR ADDITIONAL INFORMATION ON THE

NATIONAL WATER-QUALITY ASSESSMENT (NAWQA) PROGRAM:

Coordination among agencies and organizations is an integral part of the NAWQA Program. We tha

following agencies and organizations who directly participated in the San Joaquin–Tulare Basins program

Front cover: Yosemite National Park.

(Photograph by Sylvia V. Stork, U.S. Geological Survey)

Back cover: Ground-water sampling in vineyards in eastern Fresno County, and

 Ecological survey at a site on the San Joaquin River.

(Photographs by Neil M. Dubrovsky, U.S. Geological Survey)

Aquatic Habitat Institute

Bureau of Reclamation, Mid Pacific Region

California Department of Fish and Game

California Department of Food and Agriculture, Agriculture

Resources Board

California Department of Health Services, Office of Drinking

Water

California Department of Pesticide Regulation,

Environmental Monitoring Branch

California Department of Water Resources

California Regional Water Quality Control Board, Central

Valley Region

California State Water Resources Control Board

California State University, Fresno, School of Engineering

California Waterfowl Association

Environmental Defense Fund

Kenneth D. Schmidt and Associates, Groundwater Quality

Consultants

Kern County Water Agency

Kings River Conservation District

Larry Walker Associates, Inc., Environmental Engineering

and Management

Merced County Association of Governments

Merced County Department of Agriculture

Merced Irrigation District

Metropolitan Water District of Southern California

Modesto Irrigation District

National Park Service

San Joaquin River Flood Control Association

San Luis and Delta-Mendota Water Authority

Stanford University, Department of Geological and

Environmental Sciences

Turlock Irrigation District

United Anglers of California

U.S. Army Corps of Engineers

U.S. Department of Agriculture, Water Management

Research Laboratory

U.S. Environmental Protection Agency

U.S. Fish and Wildlife Service

U.S. Natural Resources Conservation Service

University of California, Farm and Home Advisors O

University of California, Davis, Department of Land, 

Water Resources

Water Resources Center

Westlands Water District

San Joaquin–Tulare Basins Study Unit, contact:

District Chief

U.S. Geological Survey

Water Resources Division

Placer Hall

6000 J Street

Sacramento, CA 95819-6129

Information on the NAWQA Program is also available on the Internet via the World Wide Web. Yo

connect to the NAWQA Home Page using the Universal Resources Locator (URL):

http://wwwrvares.er.usgs.gov/nawqa/nawqa_home.html

The San Joaquin–Tulare Basins Study Unit’s Home Page is at URL:

http://water.wr.usgs.gov/sanj_nawqa/
U.S. GEOLOGICAL SURVEY CIRCULAR

Water Quality in the San Joaquin–Tulare

Basins, California, 1992–95

1159

By Neil M. Dubrovsky, Charles R. Kratzer, Larry R. Br

JoAnn M. Gronberg, and Karen R. Burow

CONTENTS

National Water-Quality Assessment

Program ........................................................ 

Summary of major issues and

findings ......................................................... 

Environmental setting and hydrologic

conditions ..................................................... 

Major issues and findings .............................. 

Water-quality conditions in a national

context ........................................................... 

Study design and data collection .................. 

Summary of compound detections and

 concentrations ............................................. 

References......................................................... 

Glossary ............................................................ 
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

U.S. DEPARTMENT OF THE INTERIOR

BRUCE BABBITT, Secretary

U.S. GEOLOGICAL SURVEY

Thomas J. Casadevall, Acting Director

1998

Dubrovsky, Neil M.

 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

/ by Neil M. Dubrovsky, Charles R. Kratzer, Larry R. Brown, Jo Ann

M. Gronberg, Karen R. Burow .

p. cm. — (U.S. Geological Survey Circular : 1159)

 Includes bibliographical references (p. ).

 ISBN 0-607-89190-4

 1. Water quality—California—San Joaquin River Watershed.

 2. Water quality—California—Tulare Lake Watershed. I. Dubrovsky, N. M.

 II. Series.

 TD224.C3W369 1998

363.739’42’09794—dc21 98-12058

CIP
U.S. Geological Survey Circular 

NATIONAL WATER-QUALITY ASSESSMENT PROGRAM

“The scientific and

technical informatio

contained in this rep

provides valuable

assistance in

California’s efforts t

better understand an

implement program

to address water

resource issues—no

only in the San

Joaquin–Tulare

Basins, but througho

the state.”

Walt Pettit,

Executive Director

California State W

Resources Contro

Board

Began in 1991

Began in 1994

Began in 1997

Not scheduled yet

EXPLANATION

Knowledge of the quality of the Nation's streams and aquifers is important because

of the implications to human and aquatic health and because of the significant costs

associated with decisions involving land and water management, conservation, and

regulation. In 1991, the U.S. Congress appropriated funds for the U.S. Geological

Survey (USGS) to begin the National Water-Quality Assessment (NAWQA) Program

to help meet the continuing need for sound, scientific information on the areal extent

of the water-quality problems, how these problems are changing with time, and an

understanding of the effects of human actions and natural factors on water quality

conditions.

The NAWQA Program is assessing the water-quality conditions of more than 50 of

the Nation's largest river basins and aquifers, known as Study Units. Collectively,

these Study Units cover about one-half of the United States and include sources of

drinking water used by about 70 percent of the U.S. population. Comprehensive

assessments of about one-third of the Study Units are ongoing at a given time. Each

Study Unit is scheduled to be revisited every decade to evaluate changes in waterquality conditions. NAWQA assessments rely heavily on existing information collected by the USGS and many other agencies as well as the use of nationally consistent study designs and methods of sampling and analysis. Such consistency simultaneously provides information about the status and trends in water-quality conditions

in a particular stream or aquifer and, more importantly, provides the basis to make

comparisons among watersheds and improve our understanding of the factors that

affect water-quality conditions regionally and nationally.

This report is intended to summarize major findings that emerged between 1992

and 1995 from the water-quality assessment of the San Joaquin–Tulare Basins Study

Unit and to relate these findings to water-quality issues of regional and national concern. The information is primarily intended for those who are involved in waterresource management. Indeed, this report addresses many of the concerns raised by

regulators, water-utility managers, industry representatives, and other scientists, engineers, public officials, and members of stakeholder groups who provided advice and

input to the USGS during this NAWQA Study-Unit investigation. Yet, the information

contained here may also interest those who simply wish to know more about the quality of water in the rivers and aquifers in the area where they live.

Robert M. Hirsch, Chief Hydrologist
2 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

SUMMARY OF MAJOR ISSUES AND FINDINGS

This report summarizes the major findings of the National Water-Quality Assessment

(NAWQA) for the San Joaquin–Tulare Basins, California. The brief statements of the

major findings that follow are expanded on later in this report (p. 6–19). Comparisons of

data within this Study Unit with data from all 20 Study Units nationwide are given in

descriptive (p. 20–23) and tabular (p. 26–31) formats. Additional information on the

methods, approaches, and findings of all the investigations of the San Joaquin–Tulare

Basins NAWQA studies is available in the technical reports listed on pages 32–33.

Though this report is an integral part of a national study, it also is intended to serve as a

stand-alone resource for anyone interested in water quality in California.

The California Water Resources

Control Board has set a goal of

zero toxicity in surface water in the

San Joaquin River system. This

goal is based on concerns for

maintenance of anadromous fish,

endangered fish in the

Sacramento–San Joaquin Delta,

and human health. Toxicity may

result from several causes, but

generally has been attributed to

pesticides from agricultural

nonpoint sources. High concentrations of organophosphate

insecticides, resulting from application to some orchards during the

winter, are of particular concern.

(p. 6–9)

A wide variety of pesticides occur in the San Joaquin River and its tributa

some at concentrations high enough to adversely impact aquatic life.

• Forty-nine pesticides were detected in the San Joaquin River and thr

subbasins, 22 of which were detected in more than 20 percent of the sa

Available drinking-water standards were not exceeded, but the concent

of seven pesticides exceeded the criteria for the protection of aquatic li

• Pesticide occurrence is related to the timing and spatial distribution 

pesticide application; the most frequent occurrence and highest concen

generally coincide with the time of heaviest agricultural application.

• Crop type and basin characteristics affect spatial and seasonal variab

pesticide occurrence.

• The main source of organophosphate insecticides is the application t

dormant orchards. Concentrations of organophosphate insecticides in r

are high, and highly variable, during winter storms. Peak diazinon conc

trations in Orestimba Creek, in the Merced and the Tuolumne Rivers, a

the main stem of the San Joaquin River frequently exceeded levels that 

acutely toxic to some aquatic life.

• Diazinon and other pesticides were also found to be transported to th

Tuolumne River in stormwater runoff from the Modesto urban area.

Long-banned organochlorine

insecticides, such as DDT, are

bound to soil particles in areas of

past application. The soils and

associated bound pesticides are

transported to streams by soil

erosion during natural or irrigationrelated runoff. Once in the stream,

organochlorine insecticides are

taken up by organisms and bioaccumulated through the food

chain. These compounds have

been shown to be harmful to wildlife and humans that consume

them. (p. 10–11)

Long-banned organochlorine insecticides continue to be transported to str

by soil erosion of contaminated agricultural fields, resulting in contamina

suspended sediment, bed sediment, and aquatic organisms.

• Concentrations of organochlorine insecticides, such as DDT, toxaphe

chlordane, in tissues of clams and fish from the San Joaquin River and 

western tributaries, were high relative to national values obtained in the 

and 1980s.

• Concentrations of DDT compounds in fine-grained bed sediments an

samples are correlated, suggesting that bioaccumulation is taking place

• Most whole-water concentrations of p,p ́-DDT, chlordane, dieldrin, 

toxaphene exceeded chronic criteria for the protection of freshwater aq

life.

• Runoff from winter storms will continue to deliver a substantial load 

sediment-bound organochlorine insecticides to the San Joaquin River, e

irrigation-induced soil erosion is reduced.

Toxicity to Aquatic Organisms in Streams Attributed to Pesticides

Potential for Adverse Effects on Biota from Pesticides in Bed Sediment and Biota

Nutrient Concentrations in the San Joaquin River Generally Support the Beneficial Us

Designated beneficial uses for

the San Joaquin River include

drinking water and the aquatic

ecosystem. Nitrate and

ammonia criteria have been set

Some nitrate and ammonia concentrations exceed criteria in some small

tributaries, but generally do not limit beneficial uses in the main stem of t

Joaquin River.

• Mud and Salt Sloughs account for only about 10 percent of the strea

but contribute nearly half the nitrate load in the San Joaquin River.

CALIF
U.S. Geological Survey Circular 1159 

SUMMARY OF MAJOR ISSUES AND FI

Development of water resources in

the San Joaquin River drainage,

including the Sacramento-San

Joaquin Delta, has been accompanied by large-scale changes in

the aquatic ecosystems, including

fish populations. Anadromous

salmon have declined, along with

other migratory and resident native

fish species. Though there are

likely multiple reasons for declines

in native fish species, the roles of

water chemistry and habitat degradation have never been addressed

on a basinwide basis. (p. 14–15)

Fish communities in the San Joaquin River and its tributaries change in re

to water chemistry and habitat quality in a pattern suggesting that human

activities, including agriculture, are important factors in controlling the di

bution and abundance of fish species. Fish communities in the lower San J

River were highly degraded compared with other NAWQA Study Units, a

stream habitat at some sites.

• Introduced fish species outnumber native fish species by almost 2 to 

• In the lower San Joaquin River drainage, four groups of sites can be 

on the basis of fish communities. Native species were most common ne

foothill dams and were gradually replaced by different groups of introd

species in downstream areas where land use is dominated by agricultur

other human activities.

• The Stanislaus River appeared to provide the best habitat for native 

of the three major tributaries studied, possibly because of the way flow 

managed in the Stanislaus River compared with that of the Tuolumne a

Merced Rivers.

• Fish communities provide a useful assessment of overall stream hea

San Joaquin Valley streams. Though the analysis cannot separate the

individual effects of water chemistry (including toxicity) and habitat qu

both appear to be important.

Habitat Disruption and Water Chemistry Have Adversely Affected Native Fish Populatio

Ground water is the primary

source of drinking water for the

majority of the population in the

eastern San Joaquin Valley.

Millions of pounds of pesticides

and fertilizer have been used on

agricultural land in the valley. Prior

data have shown ground-water

contamination by agricultural

nonpoint sources. (p. 16–19)

Nitrate concentrations in ground water frequently exceeded drinking wate

standards; however, pesticide concentrations rarely exceeded drinking-wat

standards, with the notable exception of 1,2,-dibromo-3-chloropropane (D

• Nitrate concentrations in ground water in the eastern San Joaquin Va

exceeded the U.S. Environmental Protection Agency (USEPA) drinking

standard in about one fourth of the domestic water-supply wells sample

• Nitrate concentrations in shallow ground water were related to the ov

agricultural land-use setting; concentrations varied among different agr

tural land-use settings and were linked to fertilizer application, physica

characteristics of the sediment, and biochemical processes in ground w

• Nitrate concentrations in ground water have increased since the 1950s

1950 to 1980, the largest source of nitrate—nitrogen fertilizer—also inc

from 114 to 745 million pounds per year.

• Pesticides were detected in about two-thirds of the ground-water sam

collected from domestic water supply wells, but concentrations of most

pesticides were low—less than 0.1 microgram per liter (μg/L).

• DBCP concentrations exceed the USEPA drinking-water standard of

0.2 μg/L in 20 percent of the domestic water supply wells sampled. Dat

monitoring wells show that DBCP concentrations generally decrease w

depth and are highly variable near the water table.

• Pesticide concentrations in ground water generally have not increased 

last decade on the basis of a small number of wells sampled (19) during

1986–87 and again in 1995. Direct comparison of the data is difficult be

of changes in detection limits.

Drinking-Water Supplies From Ground Water Have Been Degraded by Fertilizers and Pest

by USEPA to protect these beneficial uses. The San Joaquin River

Basin has many sources of nitrate

and ammonia: fertilizer and

manure, subsurface agricultural

drains, dairies, and wastewatertreatment plants. (p. 12–13)

• Nitrate concentrations in the San Joaquin River have been increasing 

the last 40 years, but concentrations are still well below the drinking-w

standard.

• Ammonia criteria were frequently exceeded in Turlock Irrigation Di

lateral 5, and occasionally in Orestimba Creek and Spanish Grant Drai

of the samples collected in the main stem of the San Joaquin River exc

criteria during 1993–95.
4 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

ENVIRONMENTAL SETTING AND HYDROLOGIC CONDITIONS

TOTAL

PUBLIC SUPPLY

2,304,000 POPULATION

SERVED

DOMESTIC SUPPLY

704,000 POPULATION

SERVED

COMMERCIAL

INDUSTRIAL

AND MINING

IRRIGATION

AND LIVESTOCK

THERMOELECTRIC

16,000

12,000

14,000

0

2,000

4,000

6,000

8,000

10,000

WATER WITHDRAWALS,

IN MILLIONS OF GALLONS PER DAY

SURFACE WATER

GROUND WATER 93%

100%

5% <1% <1% <1% 0

The San Joaquin–Tulare Basins NAWQA Study Unit is

located in central California and includes the San Joaquin

Valley, the eastern slope of the Coast Ranges, and the

western slope of the Sierra Nevada.

The Sierra Nevada are predominantly forested land, and

the Coast Ranges and the foothills of the Sierra Nevada are

rangeland. Almost the entire valley floor is used for

agricultural land. In 1987, about 10.5 million acres in the

San Joaquin Valley was farmland (San Joaquin Valley

Drainage Program, 1990, p. 50). Abundant water, combined

with the long growing season, results in an exceptionally

productive agricultural economy in the San Joaquin Valley.

In 1987, approximately 10.2 percent of the total value of

agricultural production in the United States came from

California, 49 percent of which, or $6.82 billion, was from

the San Joaquin Valley.

Thirty-eight percent of the surface water is imported from

the Sacramento–San Joaquin Delta through the DeltaMendota Canal and California Aqueduct (U.S. Bureau of

Reclamation, 1990; California Department of Water

Resources, 1991). Most of the rest of the surface water is

from the Sierra Nevada. Surface water from the Sierra

Nevada is of very high quality, but major changes in water

quality occur when surface water enters the San Joaquin

Valley. These changes are primarily due to the large amount

Irrigation of agricultural land on the valley flo

primary use of water in the San Joaquin–Tul

Basins.

EXPLANATION

LAND USE

Urban

Agriculture

Rangeland

Forest

Tundra

Other

Cosumnes River

Calaveras River

Stanislaus River

Merced River

Chowchilla River

Tuolumne River

Fresno River

Fresno Slough Kings River

Kaweah River

Mokelumne River

LosGatos C reek

Tule River

Kern River

San Joaquin

River Delta - Mendota Canal

Los

Banos

Creek

Madera Canal

California

Aqueduct

Friant - Kern

Canal

35

36

37

38

121 120

COAST RANGES

SIERRA NEVADA

SAN

JOAQUIN

BASIN

TULARE

BASIN

15,000

0

5,000

10,000

AREA, IN SQUARE MILES

URBAN OR

BUILT-UP LAND

AGRICULTURAL

LAND

RANGELAND

FOREST LAND

WATER

WETLAND

BARREN LAND

TUNDRA

TOTAL LAND AREA = 31,200 square miles

of irrigated agriculture, which affects the quality of 

surface and ground water in the valley.

Irrigation return water may reach surface water as 

runoff (tailwater), as water from subsurface drainage

systems installed to control the water table, or as gro

water discharged through riverbeds. The result can b

increased concentrations of dissolved solids, nutrien

pesticides, and, in some areas, trace elements. Irriga

the largest source of recharge to the regional aquifer, 

ground-water recharge can contain higher concentra

dissolved solids than natural recharge in the past. Th

recharge also may contain elevated concentrations o

nutrients, pesticide residues, and trace elements.
U.S. Geological Survey Circular 1159 

ENVIRONMENTAL SETTING AND HYDROLOGIC COND

EXPLANATION

RANGE OF HISTORICAL DATA,

 WATER YEARS (WY) 1961-1990

MEDIAN

WY 1992

WY 1993

WY 1994

WY 1995

PRECIPITATION

 SITE

DISCHARGE

 SITE

0

60

20

40

MONTHLY MEAN

DISCHARGE, IN THOUSAND

CUBIC FEET PER SECOND

San Joaquin 

near V

0

15

5

10

PRECIPITATION, IN INCHES

San Joaquin-Tulare Basins

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

MONTH MONTH

Representative of the entire study area

0

40

20

PRECIPITATION, IN INCHES

0

8

2

4

6

MONTHLY MEAN

DISCHARGE, IN THOUSAND

CUBIC FEET PER SECOND

Calaveras

Big Trees

Mokelumne River near Mokelum

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

MONTH MONTH

Representative of the Sierra Nevada area

0

10

5

PRECIPITATION, IN INCHES

0

3

1

2

MONTHLY MEAN

DISCHARGE, IN HUNDRED

CUBIC FEET PER SECOND

Los Gatos 

above 

C

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

Panoche 2 W

O N D J F M A M J J 

No Data for 

March 1993

MONTH MONTH

Representative of the Coast Ranges area

Calaveras

Big Trees

Mokelumne River

near Mokelumne Hill

San Joaquin

River near

Vernalis

Panoche 2 W

Los Gatos

Creek above

Nunez Canyon

The distribution of precipitation, and consequently runoff,

in the San Joaquin–Tulare Basins is highly influenced by

topography. Mean annual precipitation on the valley floor

ranges from less than 5 inches in the south to 15 inches in the

north. Precipitation in the Coast Ranges varies from less than

10 inches (at Panoche 2 W) to more than 20 inches. Average

annual precipitation in the Sierra Nevada, mostly in the form

of snow, ranges from about 20 inches in the lower foothills to

more than 80 inches at some higher elevation sites

(Calaveras Big Trees).

Hydrologic conditions during the intensive data collection

phase (1992–95 water years [WYs]) of the San Joaquin–

Tulare Basins NAWQA were variable. Precipitation in WYs

1993 and 1995 was above the 1961–90 average of

19.4 inches (42 and 70 percent, respectively). The 1992 and

1994 WYs were slightly below average (16 and 26 percent,

respectively). Approximately 80 percent of the annual

precipitation normally occurs from November to March. The

temporal distribution of precipitation during the inte

data collection phase followed this pattern, with slig

greater departure from average during drier years.

Total streamflows at the San Joaquin River near V

site, during WYs 1992–94, were 48 to 78 percent be

average, whereas streamflow during WY 1995 was 9

percent above average. Eighty-five percent of the stre

normally occurs from November to March in the Co

Ranges, reflecting the pattern of precipitation. In the 

Nevada, and in the San Joaquin–Tulare Basins as a w

only 40 to 50 percent of the streamflow occurs from

November to March; the greater proportion of the

streamflow comes from snowmelt stored in the reser

which is not released until later in the spring. During 

intensive data-collection period there was little depa

(less than 10 percent) from these temporal patterns, e

1995 at the San Joaquin River near Vernalis where m

the streamflow occurred during the spring.

Hydrologic conditions during the intensive data-collection phase were highly variable.
6 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

MAJOR ISSUES AND FINDINGS—Pesticides in the San Joaquin River Basin

0 100 200 

APPLICATION, IN THOUSAND POUNDS ACTIVE INGREDIEN

Simazine

Diazinon

EPTC

Dacthal

Metolachlor

Chlorpyrifos

Cyanazine

Diuron

Carbaryl

Trifluralin

Pebulate

Alachlor

Propargite

Molinate

Fonofos

Malathion

Napropamide

Methomyl

Pronamide

 PESTICIDE

TRUCK CROPS

BEANS

ALFALFA

COTTON

RICE

ALM

VIN

CO

OT

Pesticide criteria for the

protection of aquatic life were

frequently exceeded

Although USEPA drinking-water

standards were not exceeded, criteria

for the protection of freshwater aquatic

life were exceeded in 37 percent of the

stream samples (Panshin and others, in

press). Concentrations of seven pesticides exceeded criteria for aquatic

life; these are the herbicides diuron

and trifluralin; and the insecticides

azinphos-methyl, carbaryl, chlorpyrifos, diazinon, and malathion. Forty

percent of these exceedances are

attributed solely to diazinon.

The exceedance of a water-quality

criteria indicates a strong probability

that aquatic species are being

adversely affected. Aquatic life criteria

are determined by exposing test

organisms to water containing only

one pesticide at a time. Most of the

samples tested in this study contained

mixtures of more than 7, and as many

as 22, different pesticides. The toxicity

of combinations of pesticides is largely

unknown, but there is some potential

for additive or interactive effects.

Pesticides were detected in all but

one of the 143 surface-water samples

collected during calendar year 1993

from four sites—Orestimba Creek,

Salt Slough, Merced River, and San

Joaquin River near Vernalis. These

sites were selected to evaluate how the

concentrations of dissolved pesticides

vary in contrasting parts of the basin

and during different seasons (Panshin

and others, in press).

Forty-nine of the 83 pesticides

analyzed for were detected. The most

commonly occurring ones were the

herbicides simazine, dacthal, metolachlor, and EPTC, and the insecticides

diazinon and chlorpyrifos. Concentrations of the detected pesticides usually

were low, but highly variable: median

concentrations of the six most frequently detected pesticides ranged

from 0.004 μg/L for dacthal to 0.050

μg/L for simazine, and 10 pesticides

had maximum concentrations greater

than 1 μg/L. Over half of the pesticides

detected have no established aquaticlife criteria, and the potential for these

compounds to induce toxicity, endocrine disruption, or impaired immune

response is not well known.

Detections of pesticides in

surface waters are related to

where and when pesticides

are applied

The California Department of

Pesticide Regulation maintains

detailed information on pesticide

application. This information includes

type of compound, location, date,

amount applied, and target crop for

each pesticide application. The vast

majority of pesticide applicati

Study Unit is for agricultural u

Seventy percent (38 of 54) 

pesticides with known applica

were detected. Detection frequ

also related to the amount of p

applied; 4 of the 6 most comm

detected pesticides were amon

most heavily applied of the pe

analyzed: chlorpyrifos, diazin

EPTC, and simazine.

There is often a correspond

between the time a pesticide w

applied and when, and at what 

centration, it was detected (Pa

and others, in press). The max

application and occurrence ge

coincided for 19 pesticides (fo

example, EPTC), usually duri

summer irrigation season. In c

several pesticides (for exampl

pyrifos) attained their maximu

centration in streams during w

runoff rather than at the time o

maximum application. This in

that, in some cases, winter run

more efficient than irrigation r

flows at transporting pesticide

the site of application to a stre

During the autumn there is ne

rainfall nor irrigation, resultin

relatively few detections.

Selected subbasins sampled in the

San Joaquin River Basin.

The diversity of crops and pesticides applied is large in the San Joaquin R

(California Department of Pesticide Regulation, 1994).

Orestimba

Creek

Basin

Salt

Slough

Basin

Merced

River

Basin
U.S. Geological Survey Circular 1159 

MAJOR ISSUES AND FINDINGS—Pesticides in the San Joaquin Rive

Crop type and basin

characteristics affect spatial

and seasonal variability of

pesticide occurrence

Orestimba Creek is typical of the

small western tributaries to the San

Joaquin River where streamflow is

predominantly agricultural runoff

during the summer, but may also

include large amounts of runoff from

the nonagricultural Coast Ranges

during the winter. A greater variety of

pesticides were detected here (28

herbicides and 12 insecticides) compared with the other sites. During the

winter, high concentrations of some

pesticides occur for brief periods

because of transport by rainfall runoff

(see the following section and

Domagalski and others, 1997). During

the irrigation season, a large number of

pesticides—usually greater than

15—were detected (Panshin and

others, in press). Pesticides detected

more frequently in Orestimba Creek

than at the other sites include DDE,

dieldrin, fonofos, napropamide, and

Some pesticides were detected frequently in samples from all three subbas

other pesticides were detected in samples from only one or two subbasins

Data for monthly pesticide application in the San Joaquin River Basin and concentration in samples in the San Joaquin River near Vernalis show that the occurrence

and application are often related in the summer, whereas the concentration may

peak in the winter in spite of heavier application in the summer.

propargite. The presence of these

pesticides is attributed to past or present application primarily on dry beans

and truck crops.

Salt Slough drains a low-lying part

of the San Joaquin Valley, which

80

20

0

40

60

APPLIED

DISCHARGE

DETECTED

NOT DETECTED

30

10

0

20

J FMAMJ J ASOND

J FMAMJ J ASOND

1993

DISCHARGE, IN THOUSAND CUBIC FEET PER SECOND

CHLORPYRIFOS APPLICATION, 

IN THOUSAND POUNDS

ACTIVE INGREDIENT

EPTC APPLICATION, IN THOUSAND

POUNDS ACTIVE INGREDIENT

1993

10

8

6

4

2

0

10

8

6

4

2

0

0.06

0.20

0

0

EPTC CONCENTRATION,

IN MICROGRAMS PER LITER 0.05

0.10

0.15

CHLORPYRIFOS CONCENTRATION,

IN MICROGRAMS PER LITER 0.02

0.04

0 100 50

Simazine

Diazinon

EPTC

Dacthal

Metolachlor

Chlorpyrifos

Cyanazine

Atrazine

Diuron

Carbaryl

Trifluralin

DDE, p,p’-

Pebulate

Alachlor

Propargite

Molinate

Fonofos

Malathion

Napropamide

Dieldrin

Methomyl

Pronamide

PESTICIDE

0 100 50

DETECTION FREQUENCY, IN PERCENT

0 50

Orestimba Creek Salt Slough Merced Riv

includes large areas of wetland

cotton; the slough does not hav

significant upland area within i

and its streamflow is dominate

agricultural drainage much of 

Twenty-five herbicides and eig

insecticides were detected at th

Pesticides detected more frequ

Salt Slough than at other sites 

atrazine, cyanazine, diuron, EP

malathion, and molinate. The p

of these pesticides is attri-bute

application primarily on cotton

alfalfa, and truck crops.

The Merced River is one of 

tributaries that carry runoff fro

Sierra Nevada year round, ofte

reservoir release, and runoff fr

cultural areas during the summ

Although 26 pesticides were d

in this river, the frequency of d

and concentrations were usual

lower than corresponding leve

other two basins. This relative

occurrence is due to a combin

factors: the generally coarse-g

soils of the eastern San Joaqui

result in little surface runoff du

rainfall or irrigation; and pesti

that do reach the Merced Rive

diluted by the release of the re

pesticide-free water from a res

the Sierra Nevada foothills.
8 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

MAJOR ISSUES AND FINDINGS—Sources and Transport of Pesticides in the San Joaquin River Ba

Stanislaus

River

Basin

Tuolumne

River

Basin

Merced

River

Bear Basin

Creek

Basin Orestimba

Creek

Basin

The organophosphate insecticide

diazinon is used for many agricultural

and urban applications. The main agricultural application of diazinon in the

San Joaquin River Basin occurs during

the winter to control wood-boring

insects in dormant almond orchards.

This application period coincides with

the rainy season.

Concentrations of diazinon

during storm runoff

frequently exceeded toxic

levels

Diazinon concentrations during

winter storm runoff in Orestimba

Creek, and in the Merced, Tuolumne,

and San Joaquin Rivers frequently

exceeded 0.35 μg/L, a concentration

shown to be acutely toxic to water fleas

(Kuivila and Foe, 1995; Domagalski

and others, 1997; Kratzer, 1997).

Although this level is acutely

toxic to water fleas,

the effect on other

organisms is largely

unknown. Concentrations in the Stanislaus

River never exceeded

0.35 μg/L. On the

basis of daily samples

from the San Joaquin

River during 1991–94,

diazinon concentrations only exceeded

0.35 μg/L during January and February

storm runoff (MacCoy and others, 1995).

Transport of

diazinon in the San

Joaquin River is

related to timing of

diazinonapplication

and storms

The main factors

involved in the transport

of diazinon in the San

Joaquin River are the

timing of diazinon applications and the occurrence

of sizable storms during

January and February.

During 1991–93, 74 percent of diazinon transport

in the San Joaquin River

occurred during January

and February. In 1994, about half of

the diazinon application in agricultural areas of the San Joaquin River

Basin occurred during two dry periods

preceding sampled storms during

January and February. The ove

amount of diazinon transporte

San Joaquin River during thes

was only about 0.05 percent o

amount applied during the pre

dry periods.

Diazinon concentrations at the San Joaquin River near Vernalis exceeded concentrations to

life (0.35 microgram per liter) only during January and February because of storm runoff.

Almond orchard spraying (photograph by Dave Kim,

California Department of Pesticide Regulation).

San Joaquin River Basin s

boundaries of Orestimba C

Creek, Merced River, Tuolu

and Stanislaus River Basin

orchards shown in green).

About half of the total agricultural application 

1994 occurred during two dry periods preced

D J F M

1993 1994

0

1.0

0.2

0.4

0.6

0.8

PRECIPITATION, IN INCHES PER DAY

January

1994

Storm

February

1994

Storm

PRECIPITATIO

DIAZINON

 APPLICATIO

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

1991 1992 1993 1994

YEAR

2

0

4

6

8

1

1.2

0.2

0

0.4

0.6

0.8

1.0

DIAZINON CONCENTRATION,

IN MICROGRAMS PER LITER

DISCHARGE

CONCENTRATION
U.S. Geological Survey Circular 1159 

MAJOR ISSUES AND FINDINGS—Sources and Transport of Pesticides in the San Joaquin Rive

A dye-tracer study was done during

the February 1994 storm to estimate

traveltimes in the San Joaquin River

system (Kratzer and Biagtan, 1997).

On the basis of storm sampling during

1993–94 and estimated traveltimes,

ephemeral west-side creeks probably

were the main diazinon source early

during the storms, whereas the

Tuolumne and Merced Rivers and eastside drainages directly to the San

Joaquin River were the main sources

later (Domagalski and others, 1997;

Kratzer, 1997).

More pesticides were

detected in runoff from urban

areas than from agricultural

areas in the Tuolumne River

Basin, but pesticide transport

was usually greater in runoff

from agricultural areas

The occurrence, concentrations, and

transport of dissolved pesticides in

storm runoff were compared in the

Tuolumne River Basin for two land

uses: agricultural areas and the

Modesto urban area. Both storms

followed the main application period

of pesticides on dormant almond

orchards. Six pesticides were detected

in runoff from agricultural areas, and

15 pesticides were detected in runoff

from urban areas. Chlorpyrifos,

diazinon, DCPA, metolachlor, and

simazine were detected in almost every

sample. Median concentrations were

higher in runoff from urban areas for

Most diazinon in the San Joaquin River comes from west-side creeks, 

Tuolumne and Merced Rivers, and direct drainage from the east side

Sampling a storm drain during

February 1995 storm (photograph by

Charles R. Kratzer, U.S. Geological

Survey).

all pesticides except napropamide and

simazine. The lower occurrence and

concentrations in agricultural runoff

was partly attributed to dilution by

nonstorm base flow in the Tuolumne

River and by storm runoff from

nonagricultural land (primarily native

vegetation) (Kratzer, in press).

Transport of chlorpyrifos, diazinon,

metolachlor, napropamide, and

simazine was greater from agricultural

areas than from urban areas. Transport

of DCPA was about the same from

agricultural and urban areas. The main

source of transport for the oth

pesticides could not be determ

In most cases, the occurren

relative concentrations of pes

storm runoff from agricultura

urban areas were related to pe

applications. Some pesticides 

frequently, and in relatively h

concentrations, in the storm d

not relate to reported use. How

unlike agricultural use, report

pesticide use in urban areas is

incomplete and only includes 

licensed pest control operator

More pesticides were detected, and generally in higher concentrations, 

runoff from urban areas compared with storm runoff from agricultural ar

0

100

20

40

60

80

DETECTION

FREQUENCY,

IN PERCENT

Benfluralin

Carbaryl

Chlorpyrifos

DCPA

Diazinon

Disulfoton

EPTC

Malathion

Metolachlor

Napropamide

Pendimethalin

Prometon

Propanil

Simazine

Trifluralin

 PESTICIDE

EXPLANA

0.001

1

0.002

0.005

0.01

0.02

0.05

0.1

0.2

0.5

MEDIAN CONCENTRATION,

IN MICROGRAMS 

PER LITER

 

7 8 9 10 11 12 

FEBRUARY 1994

0

6

1

2

3

4

5

DIAZINON LOAD, IN POUNDS

ACTIVE INGREDIENT PER DAY

MERCED RIVER

OTHER EAST-SIDE CRE

 AND BEAR CREEK

BEAR CREEK

SAN JOAQUIN RIVER 

 TOTAL

WEST-SIDE CREEKS

WEST-SIDE CREEKS

 AND OTHER

 EAST-SIDE CREEKS

STANISLAUS RIVER

TUOLUMNE RIVER

OTHER EAST-SIDE

 CREEKS
10 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

MAJOR ISSUES AND FINDINGS—DDT and Other Persistent Organochlorine Pesticides in Sus

Sediment, Bed Sediment, and Tissue of Biota

5 MILES

0 5 KILOMETERS

0

EAST-S

WEST-

MUD A

 SLOU

SAN JO

 RIVER 

EAST-S

WEST-

MUD A

EXPLAN

Stanislaus River

Tuolumne River

Merced 

Hospital

Creek

San

River 

Mud

Los Banos

Slough

Joaquin

Ingram

Creek

Del Puerto Creek

Orestimba Creek

Turlock Irrigati

District Lateral 

Olive Ave.

Drain

Spanish

Grant

Drain

Newman

Wasteway

Creek

Organochlorine insecticides, such as

DDT and toxaphene, were used

extensively in the San Joaquin Valley

to control agricultural pests. The use of

such compounds was banned in the

1970s in the United States because of

detrimental effects on wildlife, such as

the bald eagle and peregrine falcon.

These chemicals are persistent in the

environment because they degrade

slowly and are tightly bound to soil

particles. Contaminated soils from

agricultural and urban areas containing

these compounds are still entering

streams because of soil erosion. Once

contaminated soil has entered a stream

as sediment, it becomes available to a

variety of small aquatic organisms,

such as insects that obtain food from

the water or bed sediment. These

organisms then are eaten by larger

organisms, resulting in the contaminants being passed up the food chain

in processes known as bioaccumulation. This process can result in

concentrations of organochlorine

compounds in fish and other biota that

are harmful to wildlife and humans

that consume them.

Concentrations of DDT and

organochlorine insecticides

in aquatic organisms and bed

sediment still exceed

guidelines for protection of

fish-eating wildlife

Studies done during the 1970s and

1980s documented contamination of

both stream bed sediments and aquatic

organisms in the San Joaquin River

system. In those studies, levels of

organochlorine insecticides in the San

Joaquin Valley were high compared

with other parts of the Nation, and

levels in aquatic organisms exceeded

guidelines for the protection of fisheating wildlife in several areas (Brown,

1997). In October 1992, samples of

tissue of aquatic organisms and finegrained bed sediment were collected at

18 sites and analyzed to determine

whether the distribution or

concentrations of organochlorine

insecticides had changed from the

earlier studies.

Mud and Salt Sloughs sites (2 sites)

Compound Tissue Bed Sediment

Total DDT 79–342 1–7

Dieldrin ND–6 ND

The concentration and variety of organochlorine insecticides in tissue and 

were highest in west-side sites, intermediate in the San Joaquin River sites

east-side sites. (Red values – exceeded guidelines for the protection of fish

[National Academy of Sciences and National Academy of Engineering, 197

analyzed; tissue and sediment values in micrograms per kilogram, wet and 

respectively; ND – not detected).

DDT in tissue (of clams and fi

in bed sediment, suggesting th

bioaccumulation was taking pl

(Brown, 1997).

The results of these compar

indicate that, though these inse

concentrations might be declin

they may adversely impact aqu

organisms, and hence other wi

the San Joaquin Valley for yea

come. An additional potential 

of these compounds has been r

by recent studies that suggest t

organochlorine insecticides ca

harmful to the hormone (endo

and immune systems of wildli

humans at much lower concen

than was previously thought (C

and Clement, 1992).

Concentrations of organochlorine

insecticides in aquatic organisms and

bed sediment were highest in the small

western tributaries to the San Joaquin

River and in the lower part of the San

Joaquin River (Brown, 1997). Concentrations in these areas were still high

compared to national values from the

1970s and 1980s. Concentrations in

tissue and sediment at the west-side

sites were among the highest encountered at NAWQA Study Units. Comparison of 1992 data with data that

were available for some sites showed

evidence of a decline in concentrations

in tissue at those sites. Bed-sediment

concentrations appeared similar to

historical data, but the historical data

were collected using different

methods, making direct comparisons

difficult. There was a strong

correlation between concentrations of

East-side sites (8 sites)

Compound Tissue Bed Sediment

Total DDT 6–101 ND–50

Chlordane ND ND–9

.

West-side sites (3 sites)

Compound Tissue Bed Sediment

Total DDT 509–2,192 109–415

Toxaphene ND–2,000 ND–630

Dieldrin ND–10 1–10

Dacthal 11–360 ND–32

PCBs ND–57 ND

Permethrin NA ND–31

San Joaquin River sites (3 sites)

Compound Tissue Bed Sediment

Total DDT 50–510 ND–13

Toxaphene ND–160 ND

Dieldrin ND–5 ND

Dacthal ND–33 ND

PCBs ND–57 ND
U.S. Geological Survey Circular 1159 

MAJOR ISSUES AND FINDINGS—DDT and Other Persistent Organochlorine Pesticides in Sus

Sediment, Bed Sediment, and Tissue 

drinking-water standards (California

Department of Water Resources,

1995).

Although controlling

irrigation-induced soil erosion will reduce the transport

of organochlorine insecticides, it will not eliminate

organochlorine insecticides

from the San Joaquin River

because of transport during

winter storms

Estimated loads of

organochlorine insecticides for the entire irrigation season exceeded

estimated loads for the

January 1995 storm by

about 2 to 4 times for

suspended transport and

about 3 to 11 times for

total transport. However,

because the average

winter runoff is 2 to 4

times the runoff during

the January 1995 storm,

average winter transport

of organochlorine

insecticides may be

Large amounts of

sediment-bound DDT and

other organochlorine

insecticides are transported from small westside tributaries to the San

Joaquin River during

winter storms

NAWQA did studies on the

west-side tributaries and main

stem of the San Joaquin River to

determine the processes controlling transport of sedimentbound pesticides. Samples of

suspended sediment were analyzed for 15 organochlorine

insecticides to compare transport

during the irrigation season (June

1994) with transport during

winter storm runoff (January

1995) (Kratzer, 1998).

The most frequently detected

organochlorine insecticides

during both the winter storm runoff

and irrigation season were p,p ́-DDE,

p,p ́-DDT, p,p ́-DDD, dieldrin, toxaphene, and chlordane. Aldrin, endrin,

mirex, and lindane also were detected

during the winter storm runoff; lindane

was also detected during the irrigation

season.

Median concentrations of total

DDT, chlordane, dieldrin, and toxaphene on suspended sediment were

slightly greater during the irrigation

season than during winter storm runoff. However, streamflows, suspendedsediment concentrations, and instantaneous loads were substantially greater

during the winter storm runoff.

Most of the calculated whole-water

concentrations of p,p ́-DDT, chlordane, dieldrin, and toxaphene

exceeded the USEPA chronic criteria

for the protection of freshwater aquatic

life (U.S. Environmental Protection

Agency, 1986). In addition, 6 of 16

toxaphene and 1 of 16 p,p ́-DDT

concentrations exceeded USEPA acute

criteria for the protection of freshwater

aquatic life (U.S. Environ-mental

Protection Agency, 1986), and 5 of 16

chlordane and 1 of 16 toxaphene

concentrations exceeded California

similar to irrigation season tran

The average winter transport is 

dependent on long-term season

variations in suspended-sedime

organochlorine insecticide con

trations, both of which are unk

Nevertheless, these findings ind

that runoff from winter storms 

continue to deliver a significant 

sediment-bound organochlorin

insecticides to the San Joaquin 

for an indeterminate amount of 

even if irrigation-induced soil e

is reduced.

Loads of total DDT were substantially greater in

samples collected during winter runoff compared

with samples collected during irrigation season

at all sites except Hospital Creek.

Most whole-water concentration

toxaphene exceeded the USEP

chronic criterion for protection o

freshwater aquatic life.

0.01 10,000 0.1 1 10 100 1,000

INSTANTANEOUS LOADS

OF TOTAL DDT,

IN GRAMS PER DAY

Spanish Grant Drain

San Joaquin

River

Newman

Wasteway

Orestimba

Creek

Olive Avenue

Drain

Del Puerto

Creek

Ingram

Creek

Hospital Creek

IRRIGATION SEASON

WINTER RUNOFF

SAMPLING SITE

0.0001 0.001 0.01 0.1 

CALCULATED WHOL

CONCENTRATION OF T

IN MICROGRAMS P

USEPA

Chronic

Criterion

USEP

Acut

Criteri

Detected

Not detected 

Not detected 

Detected

IRRIGATION SEASO

WINTER RUNOFF

Newman

Wasteway

Olive Avenue

Drain

Spanish

Grant Drain

Orestimba

Creek

Del Puerto

Creek

Ingram

Creek

Hospital

Creek

San Joaquin

River

SAMPLING SITE

Orestimba Creek during a winter storm (left) a

season (right) (photographs by Sylvia V. Stork 

R. Kratzer, U.S. Geological Survey, respective
12 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

MAJOR ISSUES AND FINDINGS—Nutrients in the San Joaquin River

5 MILES

0 5 KILOMETERS

0

121 15' 121 00'

37 

45'

37 

15'

Merced Riv

Los Banos Creek

Mud Slough

Newman Wasteway

Sa

Orestimba Creek

Ingram

Creek

Tuolumne

River

Hospital

SacramentoSan Joaquin

Delta

Stanislaus River

San Joaquin River

Turlock Irrigation District lateral 5

Spanish Grant Drain

Creek

Del Puerto Creek

STANISLAUS CO

STANISLAUS CO

MERCED CO

MERCED CO

SAN JOAQUIN CO

5,000

ANNUAL NITRATE 

 TONS PER YEA

4,000

3,000

2,000

1,000

0

Width of color bar

Tons per year as N

1986 (wet year)

1988 (dry year)

OVERLAP OF 1

 AND 1988

STUDY UNIT B

SITE LOCATIO

San Joaquin River

near Vernalis

San Joaquin River

at Patterson

San Joaquin River

near Newman

Modesto

Nitrogen and phosphorus are

essential nutrients for aquatic plants.

However, in high concentrations, they

can cause excessive plant growth

(eutrophication) and toxicity to infants

(“blue baby syndrome” or methemoglobinemia from ingestion of nitrate).

The USEPA has set criteria for the

nitrate and ammonia forms of nitrogen,

but not for phosphorus. The maximum

contaminant level (MCL) for nitrate in

drinking water is 10 milligrams per

liter as nitrogen (mg/L as N) (U.S.

Environmental Protection Agency,

1986).

The USEPA also has established

criteria for maximum ammonia concentrations in surface water on the

basis of chronic and acute exposure of

aquatic organisms to un-ionized

ammonia (U.S. Environmental Protection Agency, 1986). These criteria vary

inversely with pH and temperature.

The chronic criteria range from about

0.2 to 2 mg/L as N for the range of pH

(7.5–8.5) and temperatures (5–25°C)

generally found in surface water in the

San Joaquin Valley.

Mud and Salt Sloughs

account for nearly half of the

nitrate in the San Joaquin

River

Nutrient concentrations in the lower

San Joaquin River are determined

primarily by relatively concentrated

inputs from west-side agricultural

drainage, east-side wastewatertreatment plants and runoff from

dairies, and relatively dilute inputs

from major east-side tributaries. Mud

and Salt sloughs receive a part of their

flow from subsurface drains that drain

about 60,000 acres of agricultural land.

Although the sloughs account for only

about 10 percent of the streamflow in

the San Joaquin River near Vernalis,

the subsurface drainage is very high in

nitrate (about 25 mg/L as N), and the

sloughs contribute nearly one-half the

nitrate (Kratzer and Shelton, in press).

The nitrate transported in the San

Joaquin River during a wet year (1986)

was about 50 percent more than that

transported in a dry year (1988).

The nitrate MCL was exceeded in

Spanish Grant Drain, Turlock

Irrigation District lateral 5, and

Orestimba Creek in 15, 11, and 9

percent, respectively, of samples

collected between April 1993 and

March 1995. However, these tributaries are not designated as drinkingwater sources. The MCL was not

exceeded during this period in the

main stem of the San Joaquin River, a

designated drinking-water source.

Nitrate concentrations in the

San Joaquin River have been

increasing during the last 40

years

Increasing nitrate concentrations in

the San Joaquin River could be

attributed to several sources,

including subsurface agricultu

drainage, runoff from fertilizer

applications, wastewater-treatm

plant effluent, and runoff from 

The relative contribution of th

sources was evaluated with est

of nitrate loads and with trend

ammonia and phosphorus

concentrations. Wastewater- tr

plant effluent and runoff from 

have especially high concentra

ammonia and phosphorus, yet

concentrations of ammonia an

phosphorus in the San Joaquin 

generally declined or remained 

while nitrate concentrations st

increased.

During both dry and wet years, much of the nitrate load in the San Joaquin 

be attributed to subsurface agricultural drainage discharged to Mud and Sa
U.S. Geological Survey Circular 1159 

MAJOR ISSUES AND FINDINGS—Nutrients in the San Joaqu

The source of the nitrate increase

during the 1950s was indeterminate.

During the 1960s, runoff from fertilizer applications (primarily in eastside basins) and subsurface agricultural drainage were the probable

sources of the increase. Since 1970,

subsurface agricultural drainage has

been the primary cause of the

increasing nitrate trend (Kratzer and

Shelton, in press). Other studies have

determined that the nitrate in the subsurface agricultural drainage primarily

comes from the leaching of native soil

nitrogen and not from fertilizer application (Brown, 1975). Other sources of

nitrate loads were especially important

in the early 1980s because of the effect

of an extremely wet year (1983) on the

5-year running averages. The

unusually large inputs of nitrate in

1983 were probably from (1) inflow

from the Tulare Basin through the

Fresno Slough, (2) discharge from

wastewater-treatment plants, (3) runoff

from dairies, and (4) runoff from

fertilizer applications west of the San

Joaquin River (Kratzer and Shelton, in

press). Despite this long-term increase

in the San Joaquin River, nitrate

concentrations are still well below the

USEPA drinking-water standard.

Ammonia criteria were

frequently exceeded in

Turlock Irrigation District

lateral 5 and occasionally

exceeded in Orestimba Creek

and Spanish Grant Drain

On the basis of monthly samples

collected during 1985–88, ammonia

concentrations in the San Joaquin

River increased from Newman to

Patterson, then declined from

Patterson to Vernalis as a result of

dilution by the Tuolumne and Stanislaus Rivers (Kratzer and Shelton, in

press). The increase from Newman to

Patterson is attributed to relatively

concentrated inputs, such as Turlock

Irrigation District lateral 5, Orestimba

Creek, and Spanish Grant Drain. Most

of the flow in Turlock Irrigation

District lateral 5 is effluent from the

Turlock wastewater-treatment plant,

especially during the nonirrigation

season. Ammonia concentrations

exceeded the USEPA chronic criteria

in 2 of the 51 samples collected at the

San Joaquin River at Patterson during

1985–88.

Ammonia concentrations in Turlock

Irrigation District lateral 5, Orestimba

Creek, and Spanish Grant Drain

exceeded the USEPA chronic criteria

in 76, 14, and 5 percent, respectively,

of samples collected between April

1993 and March 1995. None of the

samples collected at the San Joaquin

River at Patterson during April 1993 to

March 1995 had ammonia concentrations that exceeded the USEPA chronic

criteria, but some concentrations were

just under the criteria.

Unlike nitrate, ammonia concentrations at the San Joaquin River near

Vernalis did not increase from 1974 to

1990. Instead, ammonia concentrations increased until 1984, then

declined. This decrease was probably

due to a combination of factors,

including conversion of ammonia to

nitrate by improved wastewate

treatment, reduced discharges 

wastewater-treatment plants du

sequence of dry years during t

1980s and expanded use of lan

disposal, and reduced inputs fr

dairies during the sequence of 

years (Kratzer and Shelton, in 

The flow-adjusted nitrate concentration in the San Joaquin River has incre

about 0.3 to 1.4 milligrams per liter (mg/L) over the last four decades.

Nitrate loads in the San Joaquin River from subsurface agricultural drains 

increased steadily since the 1950s.

Nitrate concentration in the Sa

Joaquin River have steadily inc

while ammonia concentration h

declined since 1984.

3.2

1.6

0

1950 1960 1970 1980 

FLOW-ADJUSTED 

NITRATE CONCENTRATION,

IN MILLIGRAMS PER LITER, AS N

WATER YEAR

TREND

USGS

STORET

1950 1960 1970 1980 

8,000

6,000

4,000

2,000

0

ESTIMATED NITRATE LOADS IN SAN JOAQUIN RIVER NEAR VERNALIS

 (5-year running averages)

OTHER SOURCES

SUBSURFACE AGRICULTURAL DRAINS

EAST-SIDE TRIBUTARIES

San Joaquin River

 total

NITRATE, IN TONS PER YEAR, AS N 

1970 191975 1980 1985

YEAR

2

1

FLOW-ADJUSTED NITRATE,

IN MILLIGRAMS PER LITER, AS N

0 

NITRATE

AMMONIA
14 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

MAJOR ISSUES AND FINDINGS—Fish Communities, Stream Habitat, and

Water Quality in the San Joaquin River Drainage

Nativ

San J

 Ma

Large

 an

Catfi

Sma

Othe

 sp

San J

 Ma

Lowe

Stan

Uppe

5 10 MILES

0 5 10

0

Ripon

Modesto

Vernalis

Patterson

Gustine

Riverbank

Knights Ferry

Waterford

Merced

Merced River Orestimba Creek

Tuolumne River San Joaquin River

Stanislaus River

SC CF AL

0

60

20

40

MEAN PERCENTAGEOF MAXIMUM VALUE

Lower Tributary 

Habitat variables FisFish community Habitat variables

SC CF AL

0

60

20

40

MEAN PERCENTAGEOF MAXIMUM VALUE

San Joaquin Main Stem group

SC CF AL

0

60

20

40

MEAN PERCENTAGEOF MAXIMUM VALUE

Stanislaus River group Upper Tributary 

SC CF AL

0

60

20

40

MEAN PERCENTAGEOF MAXIMUM VALUE

Habitat variables Fish community FisHabitat variables

 KILOMETERS

EXPLAN

FISH 

SITE G

Human activities, including development of water resources, agriculture,

and urbanization in the San Joaquin–

Tulare Basins, have been accompanied by large-scale changes in aquatic

ecosystems. Populations of anadromous salmon have declined, along

with other migratory and resident

native species. Though there are likely

many reasons for the decline, the roles

of water chemistry and habitat degradation have not been assessed on a

basin-wide scale. Fish communities

were sampled in the San Joaquin–

Tulare Basins to determine their status

and whether they provided useful indications of water chemistry and habitat

conditions.

Introduced fish species

outnumber native species

almost 2 to 1, indicating

impaired habitat or water

chemistry or both

Assessments of fish communities

were made at 32 sites during August

and September from 1993 to 1995.

Fish were collected and identified to

species, and habitat and waterchemistry data were collected at each

site (Meador and others, 1993a,b).

A total of 34 species of fish

were collected. Twelve

species were native to

California and 22 species

were introduced from

outside California. Native

species were generally

more abundant at higher

elevation sites in the valley, the

foothills, and the Sierra Nevada.

Introduced species were generally

more abundant at lower elevation sites

on the valley floor. High percentages

of introduced species are considered

an indication of impaired water chemistry and habitat conditions (Hughes

and Gammon, 1987; Karr, 1991).

Using the fish data collected, groups

of sites with similar relative abundances of fish species were defined

using statistical techniques. This

analysis was done twice: once for the

20 low-elevation sites most likely to be

affected by human activities, and once

for all of the 32 sites sampled.

The 20 low-elevation sites were all

in the lower San Joaquin River drainage, downstream from the major foothills reservoirs. Four groups of sites

were identified on the basis of fish

communities, water chemistry, and

habitat quality: a San Joaquin Main

Stem group, a Lower Tributary group,

a Stanislaus River group, and an Upper

Tributary group.

The San Joaquin Main Stem group

was characterized by high percentages

of introduced species tolerant of harsh

environmental conditions, particularly

the fathead minnow, red shiner,

threadfin shad, and inland silverside

(all referred to as the San Joaquin

Main Stem species). The San Joaquin

Main Stem group included eight sites

on the main stem of the San Joaquin

River and on small western an

southern tributary streams. Sp

conductance (an indicator of s

which was highest at these site

good indicator of general wate

chemistry and of the influence 

irrigation return flows in the S

Joaquin River drainage. Fish

cover—the percentage of area 

provides cover from predators

lowest at these sites. Environm

degradation, as indicated by in

specific conductance and decre

fish cover, was related to huma

activities such as agricultural l

The Lower Tributary group wa

characterized by high percenta

introduced largemouth bass, re

sunfish, and white catfish. The

were located in the lower and 

At the 20 lower elevation sites, fish communities, habitat, and water chemi

significantly among the site groups. (SC – Specific conductance; CF – Cov

AL – Agricultural land).
U.S. Geological Survey Circular 1159 

MAJOR ISSUES AND FINDINGS—Fish Communities, Stream Hab

Water Quality in the San Joaquin River D

 reaches of the Merced and

Tuolumne Rivers, but only the

farthest downstream site on

the Stanislaus River. Values

of specific conductance, fish

cover, and agricultural land

use were intermediate

between the Upper Tributary

and San Joaquin Main Stem

groups.

The Upper Tributary

group included the farthest

upstream site on the Stanislaus and Merced Rivers,

and the two farthest upstream sites on the

Tuolumne River. These

sites were characterized by high

percentages of the native species:

Sacramento squawfish, hardhead,

Sacramento sucker, and prickly sculpin. Specific conductance and agricultural land use were lowest at these

sites, and fish cover was highest.

The two middle sites on the Stanislaus River formed a separate group

characterized by high percentages of

introduced smallmouth bass and native

tule perch. Water chemistry and habitat

were similar to the Upper Tributary

sites.

The second analysis, which was

based on the fish data from all 32 sites,

also resulted in four groups of sites: a

San Joaquin Main Stem group, a Foothill group, a Lower Tributary group,

and a Sierra Nevada group. The San

Joaquin Main Stem group was identical and the Lower Tributary group very

similar to the groups obtained using 20

sites. The Foothill group included all

but one site in the previously defined

Upper Tributary group, the Stanislaus

River group, and additional sites

located upstream from the foothill reservoirs. These sites were characterized

by native Sacramento squawfish, hardhead, tule perch, scul-pins, and introduced smallmouth bass. The Sierra

Nevada group was dominated by

native rainbow trout and introduced

brown trout. Water chemistry and habitat conditions were very different

among site groups, as would be

expected in a study that included

the San Joaquin main stem sit

consistent with these patterns.

Environmental degradation 

human activities may have bee

stressful to resident fish as indi

the high incidence of external

abnormalities, such as parasite

lesions, at the Lower Tributary 

(21 percent) and San Joaquin m

stem sites (17 percent). The in

of abnormalities was much low

Stanislaus River (3 percent) an

Tributary sites (3 percent). In o

areas of the country, an incide

external abnormalities greater 

percent is considered an indica

impaired conditions (Hughes a

Gammon, 1987; Karr, 1991).

The rarity of native fishes a

Lower Tributary and San Joaqu

stem sites may not be irreversi

High discharges in 1995 in the 

and Tuolumne Rivers were acc

nied by higher percentages of 

and migratory native species. S

cal analysis of data from sites 

in more than one year indicate

fish communities in 1993 and 

were very similar, but in 1995 

very different from the other y

Also, the greater abundance of 

species in the Stanislaus River

larly tule perch, at downstream 

compared with the other easte

taries, suggests that the higher 

flows favor native species. Fur

monitoring during different flo

ditions could help determine c

tions necessary to reestablish n

fish communities.

small, cold, high-elevation streams and

large, warm, low-elevation rivers.

Thus, these groups are most indicative

of large-scale, natural gradients and

less related to environmental impairment than the groups obtained from

the analysis of 20 low-elevation sites.

Native species are more

successful in the major

eastern tributaries when

flows are higher

Overall environmental quality is

reflected by fish communities: native

species are common at the least altered

sites, and tolerant introduced species

are common at the most altered sites.

However, the influences of water

chemistry and habitat on fish communities could not be separated

because both sets of variables were

related to land use (Brown and others,

in press). Additional variables may

also contribute to this

pattern. Dissolved pesticide concentrations sometimes reached levels toxic

to some invertebrates,

primarily at sites in the

San Joaquin Main Stem

group. Similarly, concentrations of organochlorine

insecticides in sediments

and tissues of biota were

highest at sites in the San

Joaquin Main Stem group

(Brown, 1997). The

dominance of tolerant

introduced species at

This site on the Stanislaus River has good rip

habitat, instream habitat, and water chemistry

(photograph by Larry R. Brown, U.S. Geologic

Riparian and instream habitats are good at Orestimba

Creek, but because water chemistry is poor and

fluctuations in flow are substantial, the site had a high

percentage of introduced fish species (photograph by

Larry R. Brown, U.S. Geological Survey).
16 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

MAJOR ISSUES AND FINDINGS—Effect of Agriculture on Ground Water, Eastern San Joaquin Vall

Ground water is the source of drinking water for most of the population of

the eastern San Joaquin Valley. Each

year, millions of pounds of nitrate (in

fertilizer and manure) and pesticides

are applied to cropland. Some of these

chemicals infiltrate to the water table,

degrade the water quality, and potentially cause a public health risk.

The quality of ground water in the

alluvial fans of the eastern San Joaquin

Valley was assessed by collecting data

from three sets of wells: 30 domestic

wells representative of the regional

aquifer, 60 shallow domestic wells in

three well-defined and contrasting

agricultural land-use settings, and 20

multilevel monitoring wells in a

3.5-mile transect along a ground-water

flow path (see p. 24–25).

Nitrate concentrations in

ground water in the eastern

San Joaquin Valley often

exceeded the drinking-water

standard

Nitrate concentrations in 24 percent

(21 of 88) of the domestic wells sampled during 1993–95 in the regional

aquifer survey and land-use studies of

the eastern San Joaquin Valley

exceeded the drinking-water standard

of 10 mg/L established by the USEPA.

Furthermore, ground-water samples

from 77 percent of the wells had

nitrate concentrations greater than

2 mg/L, which is believed to represent

background concentrations (Mueller

and Helsel, 1996). These findings indicate that ground-water quality has

been degraded over a large part of this

aquifer because of the input of nitrate

from human activity.

Ground-water samples collected in

1995 from the 30 domestic wells in the

regional aquifer survey (median well

depth 182 feet) had a median nitrate

concentration of 4.6 mg/L; 5 of the 30

wells (17 percent) exceeded the

USEPA drinking-water standard. The

median concentration of 4.6 mg/L was

higher than the median of 2.4 mg/L for

ground water in similar alluvial settings with agricultural land use nationwide (Mueller and others, 1995).

Nitrate concentrations in ground

water sampled during 1993–95 from

shallow domestic wells (median well

depth 150 feet) were compared among

three contrasting agricultural land-use

settings. These 60 wells (three sets of

20) represent a part of the aquifer that

is usually used as a domestic water

supply. Nitrate concentrations were the

highest in samples from the wells in

the almond land-use setting, whereas

concentrations were the lowest in samples from wells in the vineyard landuse setting. Nitrate concentrations

were intermediate in samples from a

grouped land-use setting of corn,

alfalfa, and vegetables. Median nitrate

concentrations in the three land-use

settings were greater than or equal to

the median in the regional aqu

vey; therefore, some of the oth

use settings in the eastern San 

Valley must have generally low

nitrate concentrations than the

agricultural settings.

Nitrate concentrations 

samples from shallow

domestic wells were re

to nitrate application,

sediment texture, and

potential for nitrate rem

by chemical reactions

Sources of nitrate from agri

ture—fertilizer and manure—w

estimated for a 0.25-mile-radiu

centered at each well in each o

three agricultural land-use sett

Nitrate concentrations in groun

in the three land-use settings w

related to estimates of the amo

nitrogen applied: the greatest a

of nitrogen was applied in the 

land-use setting; a slightly low

amount was applied in the cor

alfalfa, and vegetable land-use 

and the smallest amount was ap

the vineyard land-use setting (

and others, in press, a). The es

amount of nitrogen applied to 

ual sites was not strongly relat

nitrate concentrations in groun

samples from the wells, howev

These results indicate that estim

the amount of nitrogen applied 

fair indicator of nitrate concen

for an area; however, the estim

not a good predictor of concen

in an individual well.

This lack of predictability p

is due to several factors. The a

Characteristic Vineyard Almond

alfa

e

Median nitrate concentration, in milligrams per liter

(number of samples that exceeded the USEPA drinkingwater standard in parenthesis)

Low

4.6

(3)

High

10

(8)

Inte

Source: nitrogen applied within a 0.25-mile radius Low

7,300 lb

High

19,900 lb16

Susceptibility: sediment texture High High 

Susceptibility: potential for nitrate removal by chemical

reactions (nitrate reduction) Low Intermediate 

Nitrate concentrations in 24 percent of

domestic wells exceeded USEPA

drinking-water standards (RAS – regional

aquifer survey; VIN – vineyard land use;

ALM – almond land use; CAV – corn,

alfalfa, and vegetable land use).

Nitrate sources and aquifer susceptibility vary in the three agricultural land-u

RAS VIN ALM CAV

TYPE OF WELL

0.01

100

0.02

0.05

0.1

0.2

0.5

1

2

5

10

20

50

NITRATE, IN MILLIGRAMS PER LITER

Drinkingwater

standard

National

background

levels
U.S. Geological Survey Circular 1159 

MAJOR ISSUES AND FINDINGS—Effect of Agriculture on Ground Water, Eastern San Joaqui

of coarse-grained sediments (sand- or

gravel-sized) in the subsurface, which

is referred to as sediment texture, is a

major factor in the susceptibility of a

site to nitrate contamination. The sediment texture influences the rates of

infiltration and ground-water flow in

the aquifer, which controls how rapidly

water at the surface, with high nitrate

concentrations, can infiltrate the soil

and move downward to a well in the

aquifer. The sediment textures in the

almond and vineyard land-use settings

were generally coarse-grained and

conducive to rapid infiltration and

ground-water flow. The sediment texture in the corn, alfalfa, and vegetable

land-use setting was generally finegrained with abundant clay, resulting

in slow rates of infiltration and groundwater flow.

These contrasts in sediment texture,

considered along with the contrasts in

the amount of nitrogen applied, indicate that nitrate concentrations in

ground water were highest where high

susceptibility and high amounts of

nitrogen applied occurred together (the

almond land-use setting); nitrate concentrations in ground water were lowest where the amount of nitrogen

applied was low, even though the susceptibility was high (the vineyard landuse setting); and nitrate concentrations

in ground water were intermediate

where the amount of nitrogen applied

was high, but the susceptibility was

low (the corn, alfalfa, and vegetable

land-use setting) (Burow and others, in

press, a).

Nitrate in ground water can also be

removed by biochemical reactions

such as nitrate reduction, in which

nitrate is converted to nitrogen gas.

These biochemical reactions can happen in ground water that has very low

concentrations of dissolved oxygen.

The chemical traits that indicate a

potential for nitrate reduction, such as

low dissolved-oxygen concentrations

and high concentrations of iron and

manganese, existed in ground-water

samples from the corn, alfalfa, and

vegetable land-use setting. The few

samples that have these chemical traits

do in fact have low or nondetectable

nitrate concentrations. In contrast,

there is little evidence of nitrate reduction in samples from the almond and

vineyard land-use settings. Therefore,

ground water in parts of the corn,

alfalfa, and vegetable land-use setting

is less susceptible to nitrate contamination than ground water in the other two

land-use settings because nitrate may

be removed by biochemical processes.

The presence of fine-grained sediment textures and evidence of nitrate

reduction at some sites in the corn,

alfalfa, and vegetable land-use setting

are a result of its location on the lowest

parts of the eastern alluvial fans, near

the boundary between the alluvial fans

and basin, where sediments were

deposited by different sedimentary

processes. As a result, sediment texture and chemical conditions in the

corn, alfalfa, and vegetable land-use

setting are more variable than in the

almond and vineyard land-use settings.

This high variability makes it difficult

to generalize the conclusions from the

overall data set to specific sites.

Nitrate concentrations in

ground water have increased

in the eastern San Joaquin

Valley

Analyses of several thousand

ground-water samples were compiled

from USGS and USEPA data bases to

evaluate the long-term changes in

nitrate concentrations. Data fro

in the eastern San Joaquin Val

were less than or equal to 200 

deep indicate that median nitra

centrations increased significa

from the 1950s to the 1960s, a

the 1970s to the 1980s. From 

1980, the amount of nitrogen f

applied in the eastern San Joaq

ley counties increased from 11

million pounds per year, an inc

554 percent. The number of da

other confined-animal feedlots

hence manure production, also 

increased greatly during this p

However, estimates indicate th

gen fertilizer is the largest sou

nitrate in the eastern San Joaqu

ley (Gronberg and others, in pr

course, this generalization may 

the case for areas where the so

may be attributed to confined-

feedlots located close together

As indicated by a much sma

better controlled data set, nitra

concentrations increased over l

a decade. Of the 30 wells in th

regional aquifer survey in the 

San Joaquin Valley that were s

in 1995, 23 also had been sam

during 1986–87. The median n

concentration of this subset of 

domestic wells increased from

2.4 mg/L during 1986–87 to 4

in 1995 (Burow and others, in

press, b). The increase in

Fertilizer use and median nitrate concentration in ground water have gener

increased over the past four decades.

1950 1960 1970 1980 1990 200

YEAR

0

7

2

4

6

MEDIAN NITRATE CONCENTRATION,

IN MILLIGRAMS PER LITER

4

DECADE, (666) NUMBER OF SAMPLES

ESTIMATED FERTILIZER USE

23 WELLS SAMPLED DURING 

 1986-87 AND IN 1995

(618) (1,038) (1,010) (666)
18 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

MAJOR ISSUES AND FINDINGS—Effect of Agriculture on Ground Water, Eastern San Joaquin Vall

0

25

50

75

100

125

150

175

200

225

250

275

DEPTH BELOW LAND SURFACE, IN FEET

0 

0 1,00

6.4

1977

3.0

1991

<0.03

1956

<0.03

1992 <0.03

1992

1.3

1989

2.0

1970

<0.03

NA

<0.03

NA

<0.03

1965

0.86

NA

0.3

1979

0.03

1961

<0.03

1940

0.86

1963

<0.03

1947

<0.03

1947

2.6

1986

2.8

1992

0.46

1954

0.29

1954

EXPLANATION

ESTIMATED CONCENTRATIONS OF NITRATE

 RECHARGE DATE

DBCP CONCENTRATION,

 IN MICROGRAMS PER LITER

ESTIMATED RECHARGE DATE

1990s

1980s

1970s

1960s

Pre-1960s

Greater than 10 milligrams per liter

3 to 10 milligrams per liter

Less than 3 milligrams per liter

 

water table

Pesticides were detected in

69 percent of the groundwater samples collected from

domestic wells in the eastern

San Joaquin Valley

Pesticides were detected in 61

of the 88 domestic wells sampled

during 1993–95 (69 percent), but

concentrations of most pesticides were low—less than

0.1 μg/L. Although 25 pesticides

were detected, only 5 pesticides

were detected in more than

10 percent of the samples:

simazine, 1,2-dibromo-3-

chloropropane (DBCP), atrazine,

desethylatrazine (a

transformation product of

atrazine), and diuron. The

greatest number of pesticides

were detected in ground-water

samples from wells in the

vineyard land-use setting, where

17 different pesticides were

detected in 80 percent of the s

Pesticides were detected least 

55 percent of samples) in grou

water samples from wells in th

alfalfa, and vegetable land-use 

although the number of pestici

detections were not significant

different among the three land

settings.

Simazine, atrazine, diuron, and DBCP 

common pesticides in the eastern San 

Valley, California (atrazine detections i

desethylatrazine).

SIMAZINE ATRAZINE DIURON 

SELECTED PESTICIDE

0

100

20

40

60

80

DETECTION FREQUENCY, IN PERCENT

VINEYARD LAND USE

ALMOND LAND USE

CORN, ALFALFA, AND VEGETA

 LAND USE

REGIONAL AQUIFER SURVEY 

Monitoring wells installed along the ground-water flow path in the vineyard land-use settin

that DBCP and nitrate concentrations generally are lowest in older water and are high but 

in the younger water (<, less than).

nitrate concentration is

likely attributed to

increased fertilizer use

from 1950 to 1980.

Analyses of samples

from the 20 multilevel

monitoring wells in the

vineyard land-use setting

indicated that nitrate

concentrations have

generally increased over

the last four decades. In

addition to analyses for

nitrate and pesticides, the

estimated date when the

ground water sampled

from these wells was recharged was determined

by measuring concentrations of chlorofluorocarbons (CFC). CFC

concentrations in

samples from the deepest

wells indicate that the

deepest ground water

had entered the aquifer

prior to 1960. Nitrate

concentrations in the

pre-1960 water are generally less than

3 mg/L. In general, ground-water age

increases with depth below land

surface, whereas nitrate concentrations

decrease with depth. The highest

nitrate concentrations occur in shallow

ground water that was recharged

during 1977 to 1992. Because typical

domestic well depths in the vicinity of

the monitoring well transect are about

90 to 130 feet below land surface,

these data suggest that nitrate

concentrations could increase in

domestic wells in the vineyard

land-use setting.

Taken together, these studies offer

compelling evidence that nitrate concentrations in the ground water in the

eastern San Joaquin Valley have

increased over the last four decades;

prediction of future change is problematic because of the decrease in the

amount of fertilizer application over

the last decade.
U.S. Geological Survey Circular 1159 

MAJOR ISSUES AND FINDINGS—Effect of Agriculture on Ground Water, Eastern San Joaqui

wells (less than 90 feet deep), 

(or desethylatrazine) was detec

five of the six shallow wells, a

DBCP was detected in four of 

shallow wells. Although plaus

explanations exist for the high 

concentrations in young groun

current data are insufficient to 

the source of the high DBCP

concentrations. These data sug

ground water from domestic w

the vineyard land-use setting w

likely continue to contain DBC

simazine, and atrazine (or

desethylatrazine).

The occurrence of DBCP and

simazine in the three agricultural landuse settings is generally consistent

with the available information on the

use of these pesticides (Burow and others, in press, a). In contrast, atrazine

and diuron detections were not consistent with their reported use, possibly

because of their application on rightsof-way for weed control.

The number of pesticide detections

was related to characteristics that dictate the relative susceptibility of

ground water beneath the three landuse settings. The greatest number of

pesticide detections occurred in the

vineyard land-use setting. The number

of pesticide detections per sample was

correlated with the coarse-grained sediment texture and dissolved-oxygen

concentrations. Furthermore, samples

from 15 of the 18 (83 percent) wells

with nitrate concentrations exceeding

the USEPA drinking-water standard

also contained at least one pesticide. In

the vineyard land-use setting, concentrations of DBCP and nitrate were positively correlated, indicating that

ground-water samples with the highest nitrate concentrations also had the

highest DBCP concentrations.

DBCP concentrations

exceeded the USEPA

drinking-water standard in 20

percent of the ground-water

samples collected from

domestic wells in the eastern

San Joaquin Valley

Concentrations of DBCP, a soil

fumigant banned since 1977, exceeded

the USEPA drinking-water standard of

0.2 μg/L in 18 of the 88 (or 20 percent)

domestic wells sampled during 1993–

95. Ten of the DBCP samples that

exceeded the USEPA standards were

from wells in the vineyard land-use

setting, where DBCP was used to combat nematodes. In contrast, DBCP was

not detected in any of the samples

from the wells in the corn, alfalfa, and

vegetable land-use setting. The soil

fumigant 1,2-dibromoethane (also

called EDB or ethylene dibromide)

was the only other pesticide detected at

a concentration that exceeded a

USEPA drinking-water standard,

although only six of the pesticides

detected in ground water in the eastern

San Joaquin Valley have drinkingwater standards. EDB was detected in

one ground-water sample.

Pesticide concentrations in

domestic wells were

consistent over time (1986–87

to 1995) but were higher in

monitoring wells near the

water table than at greater

depths

Of the 30 domestic wells sampled as

part of the regional aquifer survey in

1995, 19 had been sampled for pesticides during 1986–87. Samples from

both periods were tested for 21

pesticides and 37 volatile organic

compounds (VOC), but the laboratory

methods of analyses were different for

the two time periods. An increase from

13 pesticide detections during 1986–

87 to 23 pesticide detections in 1995

can be attributed to the use of an

analytical method that was 10 times

more sensitive than the method used

during 1986–87 (Burow and others, in

press, b). If the data are adjusted to the

same level of sensitivity, the number of

pesticide detections is similar for the

two periods: 10 detections during

1986–87 and 7 detections in 1995.

Concentrations of pesticides generally

were lower in 1995 than during

1986–87. Although the number of

wells resampled is small, and the age

of the sampled ground water has not

been determined, there is no evidence

that the pesticide concentrations or the

number of pesticides detected during

1986–87 increased in 1995.

Analyses of samples from the 20

multilevel monitoring wells in the

vineyard land-use setting show that

DBCP concentrations generally

decreased with depth and were highly

variable near the water table. Pesticides were detected most frequently

near the water table in ground water

that was recharged after 1980.

Simazine was detected in all six

ground-water samples from shallow

The number of pesticide detect

similar during 1986–87 and 199

(red – concentration remained t

or decreased; blue – concentra

increased; white – indeterminat

estimated. <, less than; μg/L,

micrograms per liter)

Pesticide 1986-87

concentration

(μg/L)

conc

(μ

Atrazine <0.1 

<0.1 0

0.1 0

<0.1 0

<0.1 

0.4 0

<0.1 0

0.2 0

Simazine <0.1 0

0.2 

<0.1 0

0.1 0

<0.1 0

0.1 

<0.1 0

0.2 0

0.1 <

0.2 0

DBCP <3.0 

1,2-dichloropropane

6.4 

Prometon <0.1 0

<0.1 0

Cyanazine <0.1 0

EDB <0.2 

Dicamba 0.01 <

0.01 <

Dichlorprop 0.01 <
20 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

WATER-QUALITY CONDITIONS IN A NATIONAL CONTEXT—Stream-Water Quality

Seven major water-quality characteristics were evaluated for stream sites i

NAWQA Study Unit. Summary scores for each characteristic were comput

sites that had adequate data. Scores for each site in the San Joaquin–Tular

Study Unit were compared with scores for all sites sampled in the 20 NAW

Study Units during 1992–95. Results are summarized by percentiles; high

percentile values generally indicate poorer quality compared with other N

sites. Water-quality conditions at each site also are compared to established 

for protection of aquatic life. Applicable criteria are limited to nutrients an

pesticides in water and semivolatile organic compounds (SVOC), organoc

pesticides, and PCBs in sediment. (Methods used to compute rankings and 

aquatic-life criteria are described by Gilliom and others, in press.)

FISH COMMUNITY DEGRADATION

High percentages of fish at sites 

fixed-site network were nonnati

omnivores, diseased or deforme

tolerant of human-caused stream

degradation. Disease or deformi

includes external parasites, tumo

skeletal deformities. All sites re

the poorest score for percentage 

native species and percentage of 

with external anomalies. Fish co

ities at all sites were scored as h

degraded when compared with f

communities at other sites acros

Nation.

STUDY AREA showing inset

Greater than the 75th percentile

(among the highest 25 percent

of NAWQA stream sites)

Between the median and the 75th percentile

Between the 25th percentile and the median

Less than the 25th percentile

(among the lowest 25 percent

of NAWQA stream sites)

EXPLANATION

Ranking of stream quality relative to all

NAWQA stream sites — Darker colored

circles generally indicate poorer quality.

Bold outline of circle indicates one or more

aquatic life criteria were exceeded.

STREAM HABITAT DEGRADATIO

Physical characteristics of strea

have substantial effects on wate

chemistry and aquatic life. On t

of stream modification, bank er

bank stability, and riparian veg

density, sites in the Study Unit 

moderately to highly degraded 

compared with other sites in the 

There are no standards or guidel

apply to stream habitat.

Stanislaus River

Tuolumne River

Merced River

San

River

Salt

Mud Los Banos

Slough

Slough

Joaquin

Del Puerto Creek

Orestimba Creek

Turlock Irrigation

District Lateral 5

Creek

Stanislaus River

Tuolumne River

Merced River

San

River

Salt

Mud Los Banos

Slough

Slough

Joaquin

Del Puerto Creek

Orestimba Creek

Turlock Irrigation

District Lateral 5

Creek
U.S. Geological Survey Circular 1159 

Stanislaus River

Tuolumne River

Merced River

San

River

Salt

Mud Los Banos

Slough

Slough

Joaquin

Del Puerto Creek

Orestimba Creek

Turlock Irrigation

District Lateral 5

Creek

Stanislaus River

Tuolumne River

Merced River

San

River

Salt

Mud Los Banos

Slough

Slough

Joaquin

Del Puerto Creek

Orestimba Creek

Turlock Irrigation

District Lateral 5

Creek

Stanislaus River

Tuolumne River

Merced River

San

River

Salt

Mud Los Banos

Slough

Slough

Joaquin

Del Puerto Creek

Orestimba Creek

Turlock Irrigation

District Lateral 5

Creek

SEMIVOLATILE ORGANIC

COMPOUNDS in bed

sediment

Few SVOCs were detected

in the Study Unit. Those

detected were usually

found at low concentrations, and values were low

compared with other sites

in the Nation. Criteria for

protection of aquatic life

were not exceeded.

CONCLUSIONS

The Study Unit is in poor condition compared wi

other 19 Study Units in the categories of fish co

munities, PCBs, and organochlorines in stream

sediment and fish tissue, and pesticides in the w

Several sites exceeded guidelines and criteria, 

the occurrence of nonnative fish species and fi

with external anomalies were especially high in 

Study Unit. Stream habitat and nutrient

concentrations in water were close to the media

the 20 Study Units. Only the occurrence and

concentrations of SVOCs in sediment were low

relative to the other Study Units.

NUTRIENTS in water

Nutrient concentrati

the Study Unit rang

very low to one of t

highest in the Natio

high concentrations 

sites that are downs

from agricultural dr

or wastewater-treatm

plant discharge. Am

concentrations exce

guidelines for fish t

at three sites in the S

Unit.

PESTICIDES in water

Concentrations of di

pesticides in the Stud

were among the high

NAWQA sites natio

For many pesticides

Study Unit had the m

imum concentration 

Study Units. All site

exceeded the aquatic

criteria for at least on

pesticide at least 17 

of the time. Howeve

drinking-water-quali

standards were not ex

TRACE ELEMENTS in bed

sediment

Concentrations of trace

elements in bed sediment

generally were higher than

concentrations found in

other NAWQA Study

Units.

ORGANOCHLORINE

PESTICIDES and PCBs in

bed sediment and biological

tissue

Concentrations of

organochlorine chemicals

in the Study Unit,

particularly DDT compounds and toxaphene,

were high in bed sediment

and tissues of fish or clams.

Levels at some sites were

among the highest in the

Nation.

Stanislaus River

Tuolumne River

Merced River

San

River

Salt

Mud Los Banos

Slough

Slough

Joaquin

Del Puerto Creek

Orestimba Creek

Turlock Irrigation

District Lateral 5

Creek

Stanislaus River

Tuolumne River

Merced River

San

River

Salt

Mud Los Banos

Slough

Slough

Joaquin

Del Puerto Creek

Orestimba Creek

Turlock Irrigation

District Lateral 5

Creek

WATER-QUALITY CONDITIONS IN A NATIONAL CONTEXT—Stream-Water 
22 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

WATER-QUALITY CONDITIONS IN A NATIONAL CONTEXT—Ground-Water Quality

Five major water-quality characteristics were evaluated for ground-water studie

NAWQA Study Unit. Ground-water resources were divided into two categorie

(1) drinking-water aquifers, and (2) shallow ground water underlying agricultu

urban areas. Summary scores were computed for each characteristic for all aqui

shallow ground-water areas that had adequate data. Scores for each aquifer and 

ground-water area in the San Joaquin-Tulare Basins Study Unit were compare

scores for all aquifers and shallow ground-water areas sampled in the 20 NAW

Study Units during 1992–95. Results are summarized by percentiles; higher pe

values generally indicate poorer quality compared with other NAWQA ground

studies. Water-quality conditions for each drinking-water aquifer also are com

with established drinking-water standards and criteria for protection of human 

(Methods used to compute rankings and evaluate standards and criteria are desc

Gilliom and others, in press.)

NITRATE

Nitrate concentrations in shallow

ground water from domestic

wells in agricultural areas were

among the highest of all

NAWQA Study Units. The water

quality was different in areas with

different crops. Drinking-water

standards were exceeded in 40

percent of the wells in the almond

area, and in only 15 percent of

wells in the vineyard area.

EXPLANATION

REGIONAL AQUIFER SURVEY (RAS)

 (includes all land uses)

 Unspecified land use

Almonds land use (ALM)

Vineyards land use (VIN)

Corn, alfalfa, vegetables land use (CA

Ranking of ground-water quality relative t

all NAWQA ground-water studies — Darke

colored circles generally indicate poorer

quality. Bold outline of circle indicates that

one or more standards or criteria were

exceeded.

Greater than the 75th percentile

 (among the highest 25 percent

 of NAWQA ground-water studies)

Between the median and the 75th percentile

Between the 25th percentile and the median

Less than the 25th percentile

 (among the lowest 25 percent

 of NAWQA ground-water studies)

RAS

ALM

CAV

VIN

RADON

Radon concentrations were

relatively high when compared

with other NAWQA Study Units.

No current water-quality

standards exist for this element.

RAS

VIN

CAV

ALM

All of these land-use settings represent both 

ground water areas and drinking-water aquif

national comparison purposes, these land-us

settings were compared with the summary sc

other drinking-water aquifers.
U.S. Geological Survey Circular 1159 

WATER-QUALITY CONDITIONS IN A NATIONAL CONTEXT—Ground-Water 

PESTICIDES

Pesticides were detected in more

than 50 percent of ground-water

samples in the Study Unit. All

aquifer areas sampled had levels

above the national median for

NAWQA studies, but were not

among the highest in the Nation.

No drinking-water standards were

exceeded, except for DBCP (see

VOC results below).

VOLATILE ORGANIC COMPOUNDS

VOCs were detected in 27 percent

of the wells overall, and the percent detection in most of the areas

was greater than the median for

all NAWQA Study Units. The

high rate of VOC detection and

the exceedance of the drinkingwater standard in 40 percent of

the wells in the vineyard area are

largely the result of the detection

of the banned soil fumigant

DBCP.

CONCLUSIONS

Ground-water quality in the San Joaq

Tulare Basins is generally poor comp

with the other Study Units. Nitrate

concentrations were higher than the

national median and frequently exce

drinking-water standards in all of the 

areas sampled. Pesticides were frequently detected and the rate of dete

was above the national median. No

drinking-water standards were excee

The rate of detection for VOCs was h

compared to the other Study Units

because of the frequent detection of

DBCP. No drinking-water standards 

exceeded except for DBCP, and in o

sample, EDB.

DISSOLVED SOLIDS

Concentrations of dissolved

solids in the eastern alluvial fans

generally were higher than the

median for all NAWQA Study

Units; however, dissolved solids

in areas where corn, alfalfa, and

vegetables are grown were among

the highest. The dissolved-solids

standard is for aesthetics—

appearance and smell—and

though often exceeded, no health

threat is indicated.

ALM

CAV

VIN

RAS

ALM

CAV

VIN

RAS

RAS

VIN

CAV

ALM
24 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

STUDY DESIGN AND DATA COLLECTION

and interpretation of specialized studies. In general, 

questions addressed by each study component becam

focused during each of the 3 years of intensive data

collection (September 1992 to August 1995).

Sampling sites were selected to represent major, largescale contrasts in ecoregions, land use, and hydrogeology.

Most of the data were collected in the predominantly agricultural San Joaquin Valley because factors likely to impact

water quality are concentrated in this area. This focus was

consistent with the first two topics selected for study at the

national level by the NAWQA Program: pesticides and

nutrients.

Studies were designed to provide multiple lines of evidence to describe water quality conditions (Gilliom and

others, 1995). To this end, investigations of surface-water

chemistry, contaminants in sediment and in tissues of aquatic

organisms, and aquatic ecology took place at the same sites,

if possible. The studies also were designed to provide information on water quality over a range of complementary

temporal and geographic scales. The time scale of surfacewater investigations varied from once-a-year, to once-amonth, to several times a day. The geographic scale of the

ground-water investigations ranged from sampling 30 wells

distributed over 2,000 square miles to sampling four wells

within 200 feet. Each scale of study revealed relations

between water quality and causal factors not apparent at

larger or smaller scales.

At all levels of study, relevant ancillary information, such

as land use, soil and aquifer properties, fertilizer-use rate,

and locations of dairies, was collected to help explain the

chemical and ecological data. Detailed information, such as

change in streamflow during a winter storm or the timing of

use of a particular pesticide, was also used for both design

Location of steam ecology sites. Location of ground-water chemistry sites.

Location of stream chemistry sites.

EXPLANATION

LAND USE

Urban

Agriculture

Rangeland

Forest

Tundra

Other

STREAM

CHEMI

SITES

Basic

Intens

Syno

20 4

0 20 40 K

0

EXPLANATION

PHYSIOGRAPHY

Eastern

 alluvial fans

Western

 alluvial fans

Sierra Nevada

Coast Ranges

GROUN

CHEMI

Regio

 Aquif

Viney

 land 

Almo

 land 

Corn

 land 

Flow 

Regio

 Aquif

Viney

 land 

Almo

 land 

Corn

 or ve

 land 

Flow Path

Study Area

20 40 MILES

0 20 40 KILOMETERS

0
U.S. Geological Survey Circular 1159 

STUDY DESIGN AND DATA COLL

SUMMARY OF DATA COLLECTION IN THE SAN JOAQUIN-TULARE BASINS STUDY UNIT, 1992–95

Study

component What data were collected and Why Types of sites sampled Numberof sites

Sampling fr

and pe

Stream Chemistry

Basic Fixed Sites

(BFS)—general water

chemistry

Streamflow, nutrients, major chemical constituents, organic carbon, suspended sediment, water temperature, specific conductance, pH, and dissolved oxygen to describe

concentrations and seasonal variations.

Representative of a variety of agricultural land uses, and the basin

outflow.

10 Monthly plu

Jan. 1993–D

Intensive Fixed

Sites (IFS)—

pesticides

In addition to the above constituents, approximately 83 dissolved pesticides to describe concentrations and seasonal

variations.

Subset of basic sites representing

contrasting physiographic

areas, and the basin outflow.

4 twice weekly 

Jan. 1993–D

Synoptic

sites—water

chemistry

Streamflow, pesticides, water temperature, specific conductance, pH, and dissolved oxygen to describe concentrations

and spatial distributions.

Basic sites and others representing

agricultural and urban land

uses.

23 (low

flow)

Once Jun

Contaminants in

bed sediments

 Total PCBs, 32 organochlorine pesticides, 63 semivolatile

organic compounds, and 44 trace elements to determine

occurrence and spatial distribution.

Depositional zones of all basic and

intensive sites, plus additional

synoptic sites.

17 Once Oct

Contaminants in

aquatic biota

Total PCBs, 30 organochlorine pesticides, and 24 trace elements

were analyzed to determine occurrence and spatial distribution. Clams and whole fish for organic contaminants. Clams,

fish livers, or crayfish for trace elements.

 Same sites as for contaminants in

bed sediment where tissue

could be collected.

18 Once Oct.–N

Stream Ecology

Intensive assessmentsAssess communities of fish, macroinvertebrates, and algae at

each site; and quantitatively describe stream habitat for these

organisms.

Subset of BFS (9 of 10) plus a site

in Yosemite National Park.

3

4

6

3 reaches/sit

1 reach/year

1 reach in 

Synoptic studies Similar to the above, one reach per site, for areal comparison of

habitat and community composition, nutrient samples collected.

Subset of BFS plus others. 32 Once in eithe

199

Ground-Water Chemistry

Regional Aquifer

Survey—eastern alluvial fans

 Major chemical constituents, nutrients, 83 pesticides, 60 volatile organic compounds, and radon to determine occurrence

of these constituents in this region.

Domestic wells in the eastern alluvial fans, San Joaquin Valley.30 Once in 

Land-use

effects—corn,

alfalfa, and vegetable row

crops

Major chemical constituents, nutrients, 83 pesticides, 60 volatile

organic compounds, and radon to describe the effects of agricultural land use on shallow ground water, eastern alluvial

fans.

Shallow domestic wells;

Shallow monitoring wells;

>50 percent corn, alfalfa, and vegetables grown in rotation within

a 0.25-mile radius.

20

10

Once in 

Land-use effects—

almond

orchards

Major chemical constituents, nutrients, 83 pesticides, 60 volatile

organic compounds, and radon to describe the effects of agricultural land use on shallow ground water, eastern alluvial

fans.

Shallow domestic wells;

Shallow monitoring wells;

>50 percent almond orchards

within 0.25 mile radius.

20

10

Once in 

Land-use

effects—vineyards

Major chemical constituents, nutrients, 83 pesticides, 60 volatile

organic compounds, and radon to describe the effects of agricultural land use on shallow ground water, eastern alluvial

fans.

Shallow domestic wells;

Shallow monitoring wells;

>50 percent vineyards within

0.25-mile radius.

20

10

Once in 

Chemical and

physical processes along

ground-water

flow paths

Major chemical constituents, nutrients, 83 pesticides, 60 volatile

organic compounds, radon, transformation products of 1,2-

dibromo-3-chloropropane, and constituents used to estimate

date when ground water was recharged.

 20 wells at 6 sites along an

approximate ground-water flow

path beneath vineyard land use

in eastern alluvial fan, San

Joaquin Valley.

20 Once in 

Once in 

Special Studies

Dissolved pesticide transport in

winter storms

Dissolved pesticides and streamflow were measured along with

a dye traveltime study to assess the variability of concentrations during storms and the impact on the basin outflow. Specific agricultural and urban areas were assessed.

2 IFS, 3 western valley sites, and

basin outflow.

5 eastern valley sites, 3 agricultural drains, and basin outflow.

5 urban sites, 3 agricultural drains,

7 eastern valley sites, and basin

outflow.

6

9

16

Jan.–Feb

Jan.–Feb

Feb.–Mar

Transport of sediment-bound

pesticides

Sediment-bound pesticides, dissolved pesticide, suspended sediment, and streamflow to compare winter and irrigation season transport.2 Coast Ranges sites, 2 agricultural drains, 7 western valley

sites, and basin outflow.

8

12

June 1

Jan. 19

Aquatic ecology–-

Merced River,

Yosemite

National Park

Assessment of algal community, chlorophyll-a and ash-free dry

mass, and supporting data on nutrients, major constituents,

trace elements, and organic contaminants in bed sediment

and tissue.

Synoptic sites. 8 Sept. 1
26 Water Quality in the San Joaquin–Tulare Basins, 1992–95

SUMMARY OF COMPOUND DETECTIONS AND CONCENTRATIONS—Analysis And Detection of Pesticides

Organic Compounds, and Nutrients in Ground and Surface Waters of the San Joaquin–Tulare Basins Study Un

Herbicide

(Trade or common

name)

Rate

of

detection b

Concentration, in μg/L

0.001 0.01 0.1 1 10 100 1,000

The following tables summarize data collected for NAWQA studies from 1992–95 by showing results for the San J

Tulare Basins Study Unit compared to the NAWQA national range for each compound detected. The data were collected a

variety of places and times. In order to represent the wide concentration ranges observed among Study Units, logarithmic 

used to emphasize the general magnitude of concentrations (such as 10, 100, or 1000), rather than the precise number. The 

dataset used to construct these tables is available upon request.

Concentrations of herbicides, insecticides, volatile organic compounds, and nutrients detected in ground and surface water

Joaquin–Tulare Basins Study Unit. [mg/L, milligrams per liter; μg/L, micrograms per liter; pCi/L, picocuries per liter; %, perc

than; - -, not measured; trade names may vary]

EXPLANATION

Range of surface-water detections in all 20 Study Units

Detection in the San Joaquin–Tulare Basins Study Unit

Range of ground-water detections in all 20 Study Units

Drinking water standard or guideline a

Freshwater-chronic criterion for the protection of aquatic life a

Herbicide

(Trade or common

name)

Rate

of

detection b

Concentration, in μg/L

0.001 0.01 0.1 1 

Ethalfluralin (Sonalan, Sonalen)

13%

<1%

Linuron (Lorox,

Linex, Sarclex)

<1%

0%

MCPA (Agritox,

Agroxone)

3%

0%

Metolachlor (Dual,

Pennant)

44%

1%

Metribuzin (Lexone,

Sencor)

3%

0%

Molinate (Ordram) 9%

0%

Napropamide

(Devrinol)

24%

1%

Norflurazon (Evital,

Solicam, Telok)

8%

2%

Oryzalin (Surflan,

Dirimal, Ryzelan)

8%

0%

Pebulate (Tillam) 11%

0%

Pendimethalin

(Prowl, Stomp)

4%

0%

Prometon (Gesagram, prometone)

3%

1%

Pronamide (Kerb,

propyzamid)

3%

0%

Propachlor (Ramrod,

propachlore)

<1%

0%

Propanil (Stampede,

Surcopur)

<1%

0%

Alachlor (Lasso) 9%

0%

2,6-Diethylaniline

(Alachlor metabolite)

<1%

0%

Atrazine (AAtrex,

Gesaprim)

27%

7%

Deethylatrazinec

(Atrazine metabolite)

<1%

7%

Benfluralin (Balan,

Benefin, Bonalan)

2%

0%

Bromacil (Hyvar X,

Urox B, Bromax)

8%

0%

Butylate (Sutan,

Genate Plus, butilate)

4%

<1%

Cyanazine (Bladex,

Fortrol)

34%

1%

2,4-D (2,4-PA) 12%

0%

2,4-DB (Butyrac,

Embutox)

1%

0%

DCPA (Dacthal, chlorthal-dimethyl)

22%

<1%

Dichlorprop (2,4-DP,

Seritox 50, Kildip)

3%

0%

Dinoseb (DNBP, DN

289, Premerge)

0%

2%

Diuron (Karmex,

Direx, DCMU)

54%

12%

EPTC (Eptam) 43%

1%
U.S. Geological Survey Circular 1159 

SUMMARY OF COMPOUND DETECTIONS AND CONCENTRATIONS—Analysis And Detection of Pestici

Organic Compounds, and Nutrients in Ground and Surface Waters of the San Joaquin–Tulare Basin

Simazine (Aquazine,

Princep, GEsatop)

95%

34%

Tebuthiuron (Spike,

Perflan)

2%

0%

Terbacilc (Sinbar) <1%

1%

Thiobencarb (Bolero,

Saturn, benthiocarb)

2%

0%

Triallate (Far-Go) <1%

<1%

Triclopyr (Garlon,

Grazon, Crossbow)

1%

0%

Trifluralin (Treflan,

Trinin, Elancolan)

30%

<1%

Insecticide

(Trade or common

name)

Rate

of

detection b

Concentration, in μg/L

Aldicarbc (Temik) 1%

0%

Azinphos-methylc

(Guthion, Gusathion)

12%

0%

Carbarylc (Sevin,

Savit)

25%

1%

Carbofuranc

(Furadan, Curaterr)

5%

0%

Chlorpyrifos (Dursban, Lorsban)

52%

<1%

p,p’-DDE (p,p’-DDT

metabolite)

14%

<1%

Diazinon 71%

<1%

Dieldrin (Panoram D31, Octalox)

10%

1%

Disulfotonc (Disyston, Dithiosystox)

<1%

0%

Ethoprop (Mocap,

Prophos)

<1%

<1%

Fonofos (Dyfonate) 10%

0%

alpha-HCH (alphaBHC, alpha-lindane)

4%

0%

gamma-HCH 4%

0%

Malathion (maldison,

malathon, Cythion)

8%

1%

0.001 0.01 0.1 1 10 100 1,000

Methomyl (Lannate,

Nudrin)

5%

0%

Methyl parathion

(Penncap-M)

<1%

0%

cis-Permethrinc

(Ambush, Pounce)

<1%

0%

Propargite (Comite,

Omite, BPPS)

20%

0%

Terbufos (Counter) <1%

0%

Volatile organic

compound

(Trade or common

name)

Rate

of

detection b

Concentration, in μg/L

1,2,3-Trichloropropane (Allyl trichloride)

--

7%

1,2,4-Trimethylbenzene (Pseudocumene)

--

2%

1,2-Dibromo-3-chloropropaned (DBCP)

--

21%

1,2-Dibromoethaned

(EDB)

--

1%

1,2-Dichloropropane

(Propylene dichloride)

--

6%

Dichloromethane

(Methylene chloride)

--

1%

Methylbenzene (Toluene)

--

2%

total Trihalomethanes --

2%

Trichloroethene

(TCE)

--

2%

Trichlorofluoromethane

(CFC 11)

--

2%

Volatile organic

compound

(Trade or common

name)

Rate

of

detection b

Concentration, in μg/L

Tetrachloroethene

(Perchloroethene)

--

3%

0.01 0.1 1 10 

0.01 0.1 1 10 100 

Insecticide

(Trade or common

name)

Rate

of

detection b

Concentration, in μg/L

0.001 0.01 0.1 1 

Herbicide

(Trade or common

name)

Rate

of

detection b

Concentration, in μg/L

0.001 0.01 0.1 1 10 100 1,000
28 Water Quality in the San Joaquin–Tulare Basins, 1992–95

SUMMARY OF COMPOUND DETECTIONS AND CONCENTRATIONS—Analysis And Detection of Pesticides

Organic Compounds, and Nutrients in Ground and Surface Waters of the San Joaquin–Tulare Basins Study Un

Dissolved ammonia 94%

56%

Dissolved ammonia

plus organic nitrogen

as nitrogen

77%

6%

Dissolved phosphorus as phosphorus

96%

85%

Dissolved nitrite plus

nitrate

95%

97%

Radon 222 --

100%

Other Rate

of

detection b

Concentration, in pCi/L

1 10 100 1,000 

Nutrient

(Trade or common

name)

Rate

of

detection b

Concentration, in mg/L

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

Herbicides, insecticides, volatile organic compounds, and nutrients not detected in ground and surface waters of the San J

Basins Study Unit.

Herbicides

2,4,5-T

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

Acetochlor (Harness Plus,

Surpass)

Acifluorfen (Blazer, Tackle

2S)

Bentazon (Basagran, Bentazone, Bendioxide)

Bromoxynil (Buctril, Brominal)

Chloramben (Amiben,

Amilon-WP, Vegiben)

Clopyralid (Stinger, Lontrel, Reclaim, Transline)

Dacthal mono-acid

(Dacthal metabolite)

Dicamba (Banvel, Dianat,

Scotts Proturf)

Fenuron (Fenulon, Fenidim)

Fluometuron (Flo-Met,

Cotoran, Cottonex, Meturon)

MCPB (Thistrol)

Neburon (Neburea, Neburyl, Noruben)

Picloram (Grazon, Tordon)

Propham (Tuberite)

Insecticides

3-Hydroxycarbofuran

(Carbofuran metabolite)

Aldicarb sulfone (Standak,

aldoxycarb, aldicarb metabolite)

Aldicarb sulfoxide (Aldicarb metabolite)

Methiocarb (Slug-Geta,

Grandslam, Mesurol)

Oxamyl (Vydate L, Pratt)

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

Phorate (Thimet, Granutox, Geomet, Rampart)

Propoxur (Baygon, Blattanex, Unden, Proprotox)

Volatile organic

compounds

1,1,1,2-Tetrachloroethane

(1,1,1,2-TeCA)

1,1,1-Trichloroethane

(Methylchloroform)

1,1,2,2-Tetrachloroethane

1,1,2-Trichloro-1,2,2-trifluoroethane (Freon 113, CFC

113)

1,1,2-Trichloroethane

(Vinyl trichloride)

1,1-Dichloroethane (Ethylidene dichloride)

1,1-Dichloroethene

(Vinylidene chloride)

1,1-Dichloropropene

1,2,3-Trichlorobenzene

(1,2,3-TCB)

1,2,4-Trichlorobenzene

1,2-Dichlorobenzene

(o-Dichlorobenzene,

1,2-DCB)

1,2-Dichloroethane (Ethylene dichloride)

1,3,5-Trimethylbenzene

(Mesitylene)

1,3-Dichlorobenzene

(m-Dichlorobenzene)

1,3-Dichloropropane

(Trimethylene dichloride)

1,4-Dichlorobenzene

(p-Dichlorobenzene,

1,4-DCB)

1-Chloro-2-methylbenzene

(o-Chlorotoluene)

1-Chloro-4-methylbenzene

(p-Chlorotoluene)

2,2-Dichloropropane

Benzene

Bromobenzene

(Phenyl bromide)

Bromochloromethane

(Methylene chlorobromide)

Bromomethane

(Methyl bromide)

Chlorobenzene

(Monochlorobenzene)

Chloroethane

(Ethyl chloride)

Chloroethene

(Vinyl chloride)

Chloromethane

(Methyl chloride)

Dibromomethane

(Methylene dibromide)

Dichlorodifluoromethane

(CFC 12, Freon 12)

Dimethylbenzenes

(Xylenes (total))

Ethenylbenzene (Styrene)

Ethylbenzene

(Phenylethane)

Hexachlorobutadiene

Isopropylbenzene

(Cumene)

Methyl tert-butyl ethere

(MTBE)

Naphthalene

Tetrachloromethane

(Carbon tetrachloride)

cis-1,2-Dichloroethene

((Z)-1,2-Dichloroethene)

cis-1,3-Di

((Z)-1,3-D

n-Butylbe

(1-Phenyl

n-Propylb

(Isocumen

p-Isopropy

(p-Cymen

sec-Butylb

tert-Butyl

trans-1,2-

((E)-1,2-D

trans-1,3-

((E)-1,3-D

Nutrient

No nonde
U.S. Geological Survey Circular 1159 

SUMMARY OF COMPOUND DETECTIONS AND CONCENTRATIONS—Analysis And Detection of Pestici

Organic Compounds, and Nutrients in Ground and Surface Waters of the San Joaquin–Tulare Basin

1-Methylphenanthrene

--

6%

1-Methylpyrene --

6%

2,6-Dimethylnaphthalene

--

78%

2,6-Dinitrotoluene --

6%

2-Methylanthracene --

6%

4,5-Methylenephenanthrene

--

11%

9H-Carbazole --

6%

9H-Fluorene --

6%

Acridine --

6%

Anthracene --

17%

Anthraquinone --

6%

Benz[ a ]anthracene --

28%

Benzo[ a ]pyrene --

17%

Benzo[ b ]fluoranthene

--

33%

Benzo[ k ]fluoranthene

--

33%

Butylbenzylphthalate --

28%

Chrysene --

33%

Di- n -butylphthalate --

78%

Concentrations of semivolatile organic compounds, organochlorine compounds, and trace elements detected in fish and cla

bed sediment of the San Joaquin–Tulare Basins Study Unit. [μg/g, micrograms per gram, in dry weight; μg/kg, micrograms 

in dry weight for semivolatile organic compounds and organochlorine compounds in bed sediment, and in wet weight for or

compounds in fish and clam tissue; %, percent; <, less than; - -, not measured; trade names may vary]

Semivolatile organic

compound

Rate of

detection b

Concentration, in μg/kg

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

Semivolatile organic

compound

Rate of

detection b

Concentration, in μg/kg

0.1 10 100 1,1

Di- n -octylphthalate --

6%

Dibenz[ a,h ]

anthracene

--

6%

Diethylphthalate --

17%

Fluoranthene --

35%

Indeno[1,2,3- cd ]

pyrene

--

11%

Phenanthrene --

33%

Phenol --

56%

Pyrene --

35%

bis(2-Ethylhexyl)phthalate

--

94%

p-Cresol --

28%

Organochlorine

compound

(Trade name)

Rate

of

detection b

Concentration, in μg/kg

total-Chlordane 0%

6%

DCPA (dacthal, chlorthal-dimethyl)

28%

6%

p,p’-DDE 89%

72%

total-DDT 89%

72%

Dieldrin (Panoram D31, Octalox)

17%

17%

0.01 0.1 1 10 100 

EXPLANATION

Range of detections in fish and clam tissue in all 20 Study Units

Detection in bed sediment or fish tissue in the San Joaquin–Tulare Basins Study Unit

Range of detections in bed sediment in all 20 Study Units

Guideline for the protection of aquatic life f

Detection in clam tissue in the San Joaquin–Tulare Basins Study Unit
30 Water Quality in the San Joaquin–Tulare Basins, 1992–95

SUMMARY OF COMPOUND DETECTIONS AND CONCENTRATIONS—Analysis And Detection of Pesticides

Organic Compounds, and Nutrients in Ground and Surface Waters of the San Joaquin–Tulare Basins Study Un

PCB, total 11%

0%

cis-Permethrin

(Ambush, Pounce)

--

6%

trans-Permethrin

(Ambush, Pounce)

--

6%

Toxaphene (camphechlor)

11%

6%

Arsenic 94%

100%

Cadmium 62%

56%

Chromium 94%

100%

Copper 100%

100%

Lead 38%

100%

Mercury 69%

100%

Nickel 88%

100%

Selenium 75%

100%

Zinc 100%

100%

Organochlorine

compound

(Trade name)

Rate

of

detection b

Concentration, in μg/kg

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

Trace element Rate

of

detection b

Concentration, in μg/g

0.01 0.1 1 10 1
U.S. Geological Survey Circular 1159 

SUMMARY OF COMPOUND DETECTIONS AND CONCENTRATIONS—Analysis And Detection of Pestici

Organic Compounds, and Nutrients in Ground and Surface Waters of the San Joaquin–Tulare Basin

Semivolatile organic compounds, organochlorine compounds, and trace elements not detected in fish and clam tissue and b

of the San Joaquin–Tulare Basins Study Unit.

Semivolatile organic

compounds

1,2,4-Trichlorobenzene

1,2-Dichlorobenzene (oDichlorobenzene, 1,2-

DCB)

1,2-Dimethylnaphthalene

1,3-Dichlorobenzene (mDichlorobenzene)

1,4-Dichlorobenzene (pDichlorobenzene, 1,4-

DCB)

1,6-Dimethylnaphthalene

1-Methyl-9H-fluorene

2,2-Biquinoline

2,3,6-Trimethylnaphthalene

2,4-Dinitrotoluene

2-Chloronaphthalene

2-Chlorophenol

2-Ethylnaphthalene

3,5-Dimethylphenol

4-Bromophenyl-phenylether

4-Chloro-3-methylphenol

4-Chlorophenyl-phenylether

Acenaphthene

Acenaphthylene

Azobenzene

Benzo [c] cinnoline

Benzo [g,h,i] perylene

C8-Alkylphenol

Dibenzothiophene

Dimethylphthalate

Isophorone

Isoquinoline

N-Nitrosodi-n-propylamine

N-Nitrosodiphenylamine

Naphthalene

Nitrobenzene

Pentachloronitrobenzene

Phenanthridine

Quinoline

bis (2-Chloroethoxy)methane

Organochlorine

compounds

Aldrin (HHDN, Octalene)

Chloroneb (chloronebe,

Demosan, Soil Fungicide

1823)

Endosulfan I (alphaEndosulfan, Thiodan,

Cyclodan, Beosit, Malix,

Thimul, Thifor)

Endrin (Endrine)

Heptachlor epoxide (Heptachlor metabolite)

Heptachlor (Heptachlore,

Velsicol 104)

Hexachlorobenzene (HCB)

Isodrin (Isodrine, Compound 711)

Mirex (Dechlorane)

Pentachloroanisole (PCA,

pentachlorophenol metabolite)

alpha-HCH (alpha-BHC,

alpha-lindane, alphahexachlorocyclohexane,

alpha-benzene hexachloride)

beta-HCH (beta-BHC,

beta-hexachlorocyclohexane, alpha-benzene

hexachloride)

delta-HCH (delta-BHC,

delta-hexachlorocyclohexane, delta-benzene

hexachloride)

gamma-HCH (Lindane,

gamma-BHC, Gammexane, Gexane, Soprocide,

gamma-hexachlorocyclohexane, gamma-benzene

hexachloride, gamma-benzene)

o,p’-Methoxychlor

p,p’-Methoxychlor (Marlate, methoxychlore)

Trace elem

No nondetect

a

 Selected water-quality standards and guidelines (Gilliom and others, in press).

b Rates of detection are based on the number of analyses and detections in the Study Unit, not on national data. Rates of detection for h

insecticides were computed by only counting detections equal to or greater than 0.01 μg/L in order to facilitate equal comparisons 

compounds, which had widely varying detection limits. For herbicides and insecticides, a detection rate of “<1%” means that all d

than 0.01 μg/L, or the detection rate rounds to less than one percent. For other compound groups, all detections were counted and m

limits for most compounds were similar to the lower end of the national ranges shown. Method detection limits for all compounds 

summarized in (Gilliom and others, in press).

c

 Detections of these compounds are reliable, but concentrations are determined with greater uncertainty than for the other compounds 

as estimated values (Zaugg and others, 1995).

d In the San Joaquin–Tulare Basins Study Unit, 152 ground-water samples were analyzed for 1,2-dibromo-3-chloropropane (DBCP) a

1,2-dibromoethane (EDB) at lower detection limits (0.03 and 0.04 μg/L, respectively). DBCP was detected in 50 of these samples 

detected in one sample.

e The guideline for methyl tert-butyl ether is between 20 and 40 μg/L; if the tentative cancer classification C is accepted, the lifetime he

be 20 μg/L (Gilliom and others, in press).

f

 Selected sediment-quality guidelines (Gilliom and others, in press).

(These tables were designed and built by Sarah Ryker, Jonathan Scott, and Alan Haggland.)
32 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

REFERENCES

Brown, R.L., 1975, The occurrence

and removal of nitrogen in

subsurface agricultural drainage

from the San Joaquin Valley,

California: Water Research, v. 9,

no. 5/6, p. 529–546.

Brown, L.R., 1997, Concentrations of

chlorinated organic compounds in

biota and bed sediment in streams

of the San Joaquin Valley,

California: Archives of

Environmental Contamination

and Toxicology, v. 33, no. 4, p.

357–368.

Brown, L.R., Kratzer, C.R., and

Dubrovsky, N.M., in press,

Integrating chemical, water

quality, habitat and fish

assemblage data from the San

Joaquin River drainage,

California, in Smith, C.S., and

Scow, K., eds., Integrated

Assessment of Ecosystem Health:

Ann Arbor, Mich., Ann Arbor

Press.

Burow, K.R., Shelton, J.L., and

Dubrovsky, N.M., in press, a,

Occurrence of nitrate and pesticides in ground water beneath

three agricultural land-use

settings in the eastern San

Joaquin Valley, California,

1993–1995: U.S. Geological

Survey Water Resources

Investigations Report 97-4284.

Burow, K.R., Stork, S.V., and

Dubrovsky, N.M., in press, b,

Nitrate and pesticides in ground

water in the eastern San Joaquin

Valley, California: Occurrence

and trends: U.S. Geological

Survey Water Resources

Investigations Report 98-4040.

California Department of Pesticide

Regulation, [1994], Pesticides use

data for 1993. (Digital data for

review at the California

Department of Pesticide

Regulation, Sacramento, Calif.)

California Department of Water

Resources, 1991, Management of

the California State Water

Project: California Department of

Water Resources Bulletin 132-91,

370 p.

———1995, Compilation of federal

and state drinking water standards

and criteria: [Sacramento, Calif.],

Division of Local Assistance,

Quality Assurance Technical

Document series, no. 3, 56 p.

Colborn, Theo, and Clement, Coralie,

(eds.), 1992, Chemically-induced

alterations in sexual and

functional development—The

wildlife/human connection:

Princeton, N.J., Princeton

Scientific Publishing, Advances

in Modern Environmental

Toxicology series, v. 21, 403 p.

Domagalski, J.L., Dubrovsky, N.M.,

and Kratzer, C.R., 1997,

Pesticides in the San Joaquin

River, California—Inputs from

dormant sprayed orchards:

Journal of Environmental Quality,

v. 26, no. 2, p. 454–465.

Gilliom, R.J., Alley, W.M., and Gurtz,

M.E., 1995, Design of the

National Water-Quality

Assessment Program—

Occurrence and distribution of

water-quality conditions: U.S.

Geological Survey Circular 1112,

33 p.

Gilliom, R.J., Mueller, D.K., and

Nowell, L.H., in press, Methods

for comparing water quality

conditions among National

Water-Quality Assessment Study

Units, 1992-1995: U.S.

Geological Survey Open-File

Report 97-589.

Gronberg, J.M., Dubrovsky, N.M.,

Kratzer, C.R., Domagalski, J.L.,

Brown, L.R., and Burow, K.R., in

press, Environmental setting of

the San Joaquin-Tulare Basins,

California: U.S. Geological

Survey Water-Resources

Investigations Report 97-4205.

Hughes, R.M., and Gammon, J.R.,

1987, Longitudinal changes in

fish assemblages and water

quality in the Willamette River,

Oregon: Transactions of t

American Fisheries Socie

v. 116, p. 196-209.

Karr, J.R., 1991, Biological

integrity—A long neglect

aspect of water resource m

ment: Ecological Applica

v. 1, p. 66–84.

Kratzer, C.R., 1997, Transport 

diazinon in the San Joaqu

Basin, California: U.S.

Geological Survey Open-

Report 97-411, 22 p.

———1998, Transport of sed

bound organochlorine pe

to the San Joaquin River,

California: U.S. Geologic

Survey Open-File Report 

30 p.

Kratzer, C.R., in press, Pestici

storm runoff from agricul

and urban areas in the Tu

River Basin in the vicinit

Modesto, California: U.S

Geological Survey Water

Resources Investigations 

98-4017.

Kratzer, C.R., and Biagtan, R.

1997, Determination of tr

times in the lower San Jo

River Basin, California, f

dye-tracer studies during 

1995: U.S. Geological Su

Water-Resources Investig

Report 97-4018, 20 p.

Kratzer, C.R., and Shelton, J.L

press, Water-quality asses

of the San Joaquin-Tulare 

California: Analysis of av

data on nutrients and susp

sediment in surface water

1990: U.S. Geological Su

Professional Paper 1587, 

Kuivila, K.M., and Foe, C.G., 

Concentrations, transport 

biological effects of dorm

spray pesticides in the Sa

Francisco Estuary, Califo

Environmental Toxicolog

Chemistry, v. 14, no. 7,

p. 1141–1150.
REFER

U.S. Geological Survey Circular 1159 

MacCoy, D.E., Crepeau, K.L., and

Kuivila, K.M., 1995, Dissolved

pesticide data for the San Joaquin

River at Vernalis and the

Sacramento River at Sacramento,

California, 1991–94: U.S.

Geological Survey Open-File

Report 95-110, 27 p.

Madison, R.J., and Brunett, J.O., 1985,

Overview of the occurrence of

nitrate in ground water in the

United States, in U.S. Geological

Survey, National Water Summary

1984—Hydrologic events,

selected water-quality trends, and

ground-water resources: U.S.

Geological Survey Water-Supply

Paper 2275, p. 93–105.

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

Gurtz, M.E., 1993a, Methods for

sampling fish communities as part

of the National Water-Quality

Assessment Program: U.S.

Geological Survey Open-File

Report 93-104, 40 p.

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

T.F., and Gurtz, M.E., 1993b,

Methods for assessing stream

habitat as part of the National

Water-Quality Assessment

Program: U.S. Geological Survey

Open-File Report 93-408, 48 p.

Mueller, D.K., and Helsel, D.R., 1996,

Nutrients in the Nation’s

waters—Too much of a good

thing?: U.S. Geological Survey

Circular 1136, 24 p.

Mueller, D.K., Hamilton, P.A., Helsel,

D.R., Hitt, K.J., and Ruddy, B.C.,

1995, Nutrients in ground water

and surface water of the United

States: An analysis of data

through 1992: U.S. Geological

Survey Water-Resources

Investigations Report 95-4031,

74 p.

National Academy of Sciences and

National Academy of

Engineering, 1973 [1974], Water

quality criteria, 1972: U.S.

Environmental Protection

Agency, EPA R3-73-033, 594 p.

Panshin, S.Y., Dubrovsky, N.M.,

Gronberg, J.M., and Domagalski,

J.L., in press, Occurrence and

distribution of dissolved

pesticides in the lower San

Joaquin River Basin, California:

U.S. Geological Survey WaterResources Investigations Report

98-4032.

San Joaquin Valley Drainage Program,

1990, A management plan for

agricultural subsurface drainage

and related problems on the

westside San Joaquin Valley:

Final report of the San Jo

Valley Drainage Program

[Sacramento, Calif.], San 

Valley Drainage Program

U.S. Bureau of Reclamation, 1

Report of operations: U.S

of Reclamation, Mid-Pac

Region, Central Valley

Operations Coordinating 

42 p.

U.S. Environmental Protection

Agency, 1986, Quality cri

water 1986 (“Gold Book”

Environmental Protection

Agency, Office of Water

Regulations and Standard

440/5-85-001.

Zaugg, S.D., Sandstrom, M.W

S.G., and Fehlberg, K.M.

Methods of analysis by th

Geological Survey Nation

Water Quality Laboratory

Determination of pesticid

water by C-18 solid-phas

extraction and capillary-c

gas chromatography/mas

spectrometry with selecte

monitoring: U.S. Geologi

Survey Open-File Report 

49 p.
34 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

GLOSSARY

Algae—chlorophyll-bearing nonvascular, primarily aquatic species that

have no true roots, stems, or leaves;

most algae are microscopic, but some

species can be as large as vascular

plants.

Alluvial aquifer—A water-bearing

deposit of unconsolidated material

(sand and gravel) left behind by a river

or other flowing water.

Alluvium—Deposits of clay, silt,

sand, gravel or other particulate rock

material left by a river in a streambed,

on a flood plain, delta, or at the base

of a mountain.

Ammonia—A compound of nitro-gen

and hydrogen (NH3) that is a common

byproduct of animal waste. Ammonia

readily converts to nitrate in soils and

streams.

Anomalies—As related to fish,

externally visible skin or subcutaneous disorders, including

deformities, eroded fins, lesions, and

tumors.

Aquatic life criteria—Water-quality

guidelines for protection of aquatic

life. Often refers to U.S.

Environmental Protection Agency

water-quality criteria for protec-tion of

aquatic organisms. See Water-quality

guidelines, Water-quality criteria, and

Freshwater chronic criteria.

Aquifer—A water-bearing layer of

soil, sand, gravel, or rock that will

yield usable quantities of water to a

well.

Background concentration—A

concentration of a substance in a

particular environment that is

indicative of minimal influence by

human (anthropogenic) sources.

Base flow—Sustained, low flow in a

stream; ground-water discharge is the

source of base flow in most places.

Basic Fixed Sites—Sites on streams

at which streamflow is measured and

samples are col-lected 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.

Basin—See Drainage basin.

Bed sediment—The material that

temporarily is stationary in the bottom

of a stream or other watercourse.

Bed sediment and tissue

studies—Assessment of concentrations and distributions of trace

elements and hydrophobic organic

contaminants in streambed sedi-ment

and tissues of aquatic organ-isms to

identify potential sources and to assess

spatial distribution.

Benthic invertebrates—Insects,

mollusks, crustaceans, worms, and

other organisms without a back-bone

that live in, on, or near the bottom of

lakes, streams, or oceans.

Biota—Living organisms.

Chlordane—Octachloro-4,7-

methanotetrahydroindane. An

organochlorine insecticide no longer

registered for use in the United States.

Technical chlordane is a mixture in

which the primary components are cisand trans-chlordane, cis- and transnonachlor, and heptachlor.

Chlorofluorocarbons—A cla

volatile compounds consisting 

carbon, chlorine, and fluorine.

Commonly called freons, whic

been used in refrigeration

mechanisms, as blowing agent

fabrication of flexible and rigid 

and, until several years ago, as

propellants in spray cans.

Community—In ecology, the 

that interact in a common area

Concentration—The amount 

of a substance present in a giv

volume or mass of sample. Us

expressed as micrograms per l

(water sample) or micro- gram

kilogram (sediment or tissue s

Confluence—The flowing tog

two or more streams; the place 

a tributary joins the main strea

Contamination—Degradation 

water quality compared to orig

natural conditions due to huma

activity.

Criterion—A standard rule or 

which a judgment or decision 

based.

Cubic foot per second—(ft3/s

is the rate of water discharge

representing a volume of a 1 c

foot passing a given point duri

second, equivalent to approxi-

7.48 gallons per second or 448

gallons per minute or 0.02832 

meter per second.

Degradation products—Com

resulting from trans-formation 

organic substance through che

photochemical, and(or) bioche

reactions.

The terms in this glossary were compiled from numerous sources. Some definitions have been mo

and may not be the only valid ones for these terms.
GLO

U.S. Geological Survey Circular 1159 

Denitrification—A process by which

oxidized forms of nitrogen such as

nitrate (NO3

-

) are reduced to form

nitrites, nitrogen oxides, ammonia, or

free nitrogen: com-monly brought

about by the action of denitrifying

bacteria and usually resulting in the

escape of nitrogen to the air.

Detection limit—The concentra-tion

below which a particular analytical

method cannot deter-mine, with a high

degree of certainty, a concentration.

DDT—dichloro-diphenyl-trichloroethane. An organochlorine insect-icide

no longer registered for use in the

United States.

Dieldrin—An organochlorine

insecticide no longer registered for use

in the United States. Also a

degradation product of the insecticide

aldrin.

Discharge—Rate of fluid flow

passing a given point at a given

moment in time, expressed as volume

per unit of time.

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 con-tributes

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; guide-lines

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.

Effluent—Outflow from a partic-ular

source, such as a stream that flows

from a lake or liquid waste that flows

from a factory or sewage-treatment

plant.

Environmental setting—Land area

characterized by a unique combination of natural and human-related

factors, such as row-crop cultivation

or glacial-till soils.

Ephemeral stream—A stream or part

of a stream that flows only in direct

response to precipitation or snowmelt.

Its channel is above the water table at

all times.

Erosion—The process whereby

materials of the Earth's crust are

loosened, dissolved, or worn away and

simultaneously moved from one place

to another.

Eutrophication—The process by

which water becomes enriched with

plant nutrients, most com-monly

phosphorus and nitrogen.

Fertilizer—Any of a large nu

natural or synthetic materials,

including manure and nitrogen

phosphorus, and potassium co

pounds, spread on or worked i

to increase its fertility.

Fish community—See Comm

Flow path—An underground 

for ground-water movement,

extending from a recharge (int

zone to a discharge (output) zo

as a shallow stream.

Freshwater chronic criteria—

highest concentration of a con

nant that freshwater aquatic or

can be exposed to for an exten

period of time (4 days) withou

adverse effects. See Water-qua

criteria.

Fumigant—A substance or m

of substances that produce gas

fume, or smoke intended to de

insects, bacteria, or rodents.

Ground water—In general, an

that exists beneath the land sur

but more commonly applied to 

in fully saturated soils and geo

formations.

Habitat—The part of the phys

environment where plants and 

live.

Herbicide—A chemical or oth

agent applied for the purpose o

killing undesirable plants. See 

Pesticide.

Hydrograph—Graph showing

variation of water elevation, v

streamflow, or other property 

with respect to time.
36 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

GLOSSARY

Insecticide—A substance or mix-ture

of substances intended to destroy or

repel insects.

Intensive Fixed Sites—Basic Fixed

Sites with increased sampling frequency during selected seasonal

periods and analysis of dissolved

pesticides for 1 year. Most NAWQA

Study Units have one to two integrator

Intensive Fixed Sites and one to four

indicator Intensive Fixed Sites.

Invertebrate—An animal having no

backbone or spinal column. See also

Benthic invertebrates.

Irrigation return flow—The part of

irrigation applied to the surface that is

not consumed by evapotranspiration

or uptake by plants and that migrates

to an aquifer or surface-water body.

Land-use study—A network of

existing shallow wells in an area

having a relatively uniform land use.

These studies are a subset of the

Study-Unit Survey and have the goal

of relating the quality of shallow

ground water to land use. See StudyUnit Survey.

Leaching—The removal of materials

in solution from soil or rock to ground

water; refers to movement of

pesticides or nutrients from land

surface to ground water.

Load—General term that refers to a

material or constituent in solu-tion,

suspension, or in transport; usually

expressed in terms of mass or volume.

Main stem—The principal course of a

river or a stream.

Maximum contaminant level

(MCL)—Maximum permissible level

of a contaminant in water that is

delivered to any user of a public water

system. MCL's are enforceable

standards established by the U.S.

Environmental Protection Agency.

Mean—The average of a set of

observations, unless otherwise

specified.

Mean discharge (MEAN)—The

arithmetic mean of individual daily

mean discharges during a specific

period, usually daily, monthly, or

annually.

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.

Metabolite—A substance pro-duced

in or by biological processes.

Method detection limit—The

minimum concentration of a substance that can be accurately identified and measured with present

laboratory technologies.

Micrograms per liter (μg/L)—A unit

expressing the concentration of

constituents in solution as weight

(micrograms) of solute per unit

volume (liter) of water; equivalent to

one part per billion in most

streamwater and ground water. One

thousand micrograms per liter equals 1

mg/L.

Milligrams per liter (mg/L)—A unit

expressing the concentration of

chemical constituents in solu-tion as

weight (milligrams) of solute per unit

volume (liter) of water; equivalent to

one part per million in most

streamwater and ground water. One

thousand micrograms per liter equals 1

mg/L.

Monitoring well—A well designed

for measuring water levels and testing

ground-water quality.

Mouth—The place where a stream

discharges to a larger stream, a lake,

or the sea.

Nitrate—An ion consisting of

nitrogen and oxygen (NO3

-

). N

a plant nutrient and is very mo

soils.

Nonpoint source—A pollutio

that cannot be defined as origi

from discrete points such as pi

discharge. Areas of fertilizer a

pesticide applications, atmosp

deposition, manure, and natura

from plants and trees are types 

nonpoint source pollution.

Nutrient—Element or compo

essential for animal and plant 

Common nutrients in fertilizer 

nitrogen, phos-phorus, and pot

Organochlorine compound—

Synthetic organic compounds

containing chlorine. As genera

used, term refers to compound

containing mostly or exclusive

carbon, hydrogen, and chlorin

Examples include organo-chlo

insecticides, polychlor-inated

biphenyls, and some solvents

containing chlorine.

Organochlorine insecticide—

of organic insecticides con-tai

high percentage of chlorine. In

dichlorodi-phenylethanes (suc

DDT), chlorinated cyclodiene

as chlordane), and chlorinated 

zenes (such as lindane). Most

organochlorine insecticides we

banned because of their carcin

genicity, tendency to bioaccu-

and toxicity to wildlife.

Organophosphate insecticide

class of insecticides derived fr

phosphoric acid. They tend to 

high acute toxicity to verte-bra

Although readily metab-olized 

vertebrates, some metabolic pr

are more toxic than the parent

compound.
GLO

U.S. Geological Survey Circular 1159 

Pesticide—A chemical applied to

crops, rights of way, lawns or

residences to control weeds, insects,

fungi, nematodes, rodents or other

"pests."

Phosphorus—A nutrient essential for

growth that can play a key role in

stimulating aquatic growth in lakes

and streams.

Precipitation—Any or all forms of

water particles that fall from the

atmosphere, such as rain, snow, hail,

and sleet.

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.

Relative abundance—The number of

organisms of a particular kind present

in a sample relative to the total

number of organisms in the sample.

Riparian—Areas adjacent to rivers

and streams with a high density,

diversity, and productivity of plant

and animal species relative to nearby

uplands.

Runoff—Excess rainwater or snowmelt that is transported to streams by

overland flow, tile drains, or ground

water.

Sediment—Particles, derived from

rocks or biological materials, that have

been transported by a fluid or other

natural process, sus-pended or settled

in water.

Semivolatile organic compound

(SVOC)—Operationally defined as a

group of synthetic organic compounds that are solvent-extractable

and can be determined by gas

chromatography/mass spectrometry.

SVOCs include phenols, phthalates,

and polycyclic aromatic hydrocarbons

(PAH).

Species—Populations of orga-nisms

that may interbreed and pro-duce

fertile offspring having simi-lar

structure, habits, and functions.

Specific conductance—A measure of

the ability of a liquid to conduct an

electrical current.

Streamflow—A type of channel flow,

applied to that part of sur-face runoff

in a stream whether or not it is

affected by diversion or regulation.

Stream reach—A continuous part of

a stream between two specified points.

Study Unit—A major hydrologic

system of the United States in which

NAWQA studies are focused. Study

Units are geograph-ically defined by a

combination of ground- and surfacewater features and generally

encompass more than 4,000 square

miles of land area.

Study Unit Survey—Broad

assessment of the water-quality

conditions of the major aquifer

systems of each Study Unit. The

Study-Unit Survey relies primarily on

sampling existing wells and, wherever

possible, on existing data collected by

other agencies and programs.

Typically, 20 to 30 wells are sampled

in each of three to five aquifer

subunits.

Subsurface drain—A shallow 

installed in an irrigated field to

intercept the rising ground-wa

and maintain the water table a

acceptable depth below the lan

surface.

Surface water—An open bod

water, such as a lake, river, or 

Suspended (as used in tables 

chemical analyses)—The amo

(concentration) of undissolved

material in a water-sediment m

It is associated with the materi

retained on a 0.45-micro-mete

Suspended sediment—Partic

rock, sand, soil, and organic d

carried in suspension in the wa

column, in contrast to sedimen

moves on or near the streambe

Suspended-sediment

concentration—The velocityweighted concentration of susp

sediment in the sampled zone 

the water surface to a point

approximately 0.3 foot above 

expressed as milligrams of dry

sediment per liter of water-sed

mixture (mg/L).

Synoptic sites—Sites sampled 

a short-term investigation of s

water-quality conditions durin

selected seasonal or hydro-log

conditions to provide improve

resolution for critical water-qu

conditions.

Total DDT—The sum of DDT 

metabolites (breakdown produ

including DDD and DDE.

Trace element—An element f

only minor amounts (concen-t

less than 1.0 milligram per lite

water or sediment; includes ar

cadmium, chromium, copper, 

mercury, nickel, and zinc.
38 Water Quality in the San Joaquin–Tulare Basins, California, 1992–95

GLOSSARY

Urban Site—A site that has greater

than 50 percent urbanized and less

than 25 percent agricul- tural area.

Volatile organic compounds

(VOC)—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 criteria—Specific

levels of water quality which, if

reached, are expected to render a body

of water unsuitable for its designated

use. Commonly refers to water-quality

criteria estab-lished by the U.S.

Environmental Protection Agency.

Water-quality criteria are based on

specific levels of pollutants that would

make the water harmful if used for

drinking, swimming, farming, fish

produc-tion, or industrial processes.

Water-quality guidelines—Specific

levels of water quality which, if

reached, may adversely affect human

health or aquatic life. These are

nonenforceable guide-lines issued by a

governmental agency or other

institution.

Water-quality standards—Stateadopted and U.S. Environmental

Protection Agency-approved ambi-ent

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.

Water year—The continuous 

month period, October 1 throu

September 30, in U.S. Geolog

Survey reports dealing with th

surface-water supply. The wa

is designated by the calendar 

which it ends and which inclu

the 12 months. Thus, the year 

September 30, 1980, is referre

the "1980" water year.

Wetlands—Ecosystems who

saturated for long periods sea

or continuously, including ma

swamps, and ephemeral pond

Withdrawal—The act or pro

removing; such as removing w

from a stream for irrigation or 

water supply.
Dubrovsky and others • Water Quality in the San Joaquin-Tulare Basins

USGS Circular 1159 • 1998

National Water-Quality Assessment (NAWQA) Program

San Joaquin-Tulare Basins

NAWQA

Stockton

Fresno

Bakersfield

StanislausRiver

Tuolumn e Rive r

Merced R.

Kings River

Kern Riv er

California Aqueduct

San Joaquin River

CALIFORNIA