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Water Quality Assessment of the 

San Joaquin-Tulare Basins, California; 

Analysis of Available Data on Nutrients and 

Suspended Sediment in Surface Water,—— 

1972-1990

Professional Paper 1587

National Water-Quality Assessment Program

U.S. DEPARTMENT OF THE INTERIOR 

U.S. GEOLOGICAL SURVEY I
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Water Quality Assessment of the 

San Joaquin-Tulare Basins, California: 

Analysis of Available Data on Nutrients and 

Suspended Sediment in Surface Water, 

1972-1990

By Charles R. Kratzer and Jennifer L. Shelton

U.S. GEOLOGICAL SURVEY PROFESSIONAL PAPER 1587

National Water-Quality Assessment Program

1998
U.S. DEPARTMENT OF THE INTERIOR 

BRUCE BABBITT, Secretary

U.S. GEOLOGICAL SURVEY 

CHARLES G. GROAT, Director

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.

Library of Congress Cataloging in Publications Date

Kratzer, Charles R.

Water-quality assessment of the San Joaquin-Tulare Basins, California: Analysis of available data 

on nutrients and suspended sediment in surface water, 1972-1990 / by Charles R. Kratzer and Jennifer 

L. Shelton.

p. c.m. — (U.S. Geological Survey professional paper ; 1587) 

Includes bibliographical references (p. ).

1. Nutrient pollution of water—California—San Joaquin River Watershed. 2. Suspended sediments— 

Environmental aspects—California—San Joaquin River Watershed. 3. Nutrient pollution of water— 

California—Tulare Lake Watershed. 4. Suspended sediments—Environmental aspects—California— 

Tulare Lake Watershed.

I. Shelton, Jennifer L. II. National Water-Quality Assessment Program (U.S. ) III. Title. IV. Series. 

TD427.N87K73 1998

363. 739'42'098948—dc21 97-48536

CIP 

ISBN 0-607-88707-9

For sale by U.S. Geological Survey, Information Services

Box 25286, Federal Center

Denver, CO 80225
FOREWORD

The mission of the U.S. Geological Survey 

(USGS) is to assess the quantity and quality of the 

earth resources of the Nation and to provide information that will assist resource managers and policymakers at Federal, State, and local levels in making sound 

decisions. Assessment of water-quality conditions and 

trends is an important part of this overall mission.

One of the greatest challenges faced by waterresources scientists is acquiring reliable information 

that will guide the use and protection of the Nation's 

water resources. That challenge is being addressed by 

Federal, State, interstate, and local water-resource 

agencies and by many academic institutions. These 

organizations are collecting water-quality data for a 

host of purposes that include: compliance with permits 

and water-supply standards; development of remediation plans for specific contamination problems; operational decisions on industrial, wastewater, or watersupply facilities; and research on factors that affect 

water quality. An additional need for water-quality 

information is to provide a basis on which regionaland national-level policy decisions can be based. Wise 

decisions must be based on sound information. As a 

society we need to know whether certain types of 

water-quality problems are isolated or ubiquitous, 

whether there are significant differences in conditions 

among regions, whether the conditions are changing 

over time, and why these conditions change from 

place to place and over time. The information can be 

used to help determine the efficacy of existing waterquality policies and to help analysts determine the 

need for and likely consequences of new policies.

To address these needs, the U.S. Congress appropriated funds in 1986 for the USGS to begin a pilot program in seven project areas to develop and refine the 

National Water-Quality Assessment (NAWQA) Program. In 1991, the USGS began full implementation of 

the program. The NAWQA Program builds upon an 

existing base of water-quality studies of the USGS, as 

well as those of other Federal, State, and local agencies. 

The objectives of the NAWQA Program are to:

• Describe current water-quality conditions 

for a large part of the Nation's freshwater 

streams, rivers, and aquifers.

• Describe how water quality is changing 

over time.

• Improve understanding of the primary 

natural and human factors that affect 

water-quality conditions.

This information will help support the development 

and evaluation of management, regulatory, and monitoring decisions by other Federal, State, and local 

agencies to protect, use, and enhance water resources.

The goals of the NAWQA Program are being 

achieved through ongoing and proposed investigations 

of 60 of the Nation's most important river basins and 

aquifer systems, which are referred to as study units. 

These study units are distributed throughout the 

Nation and cover a diversity of hydrogeologic settings. 

More than two-thirds of the Nation's freshwater use 

occurs within the 60 study units and more than twothirds of the people served by public water-supply systems live within their boundaries.

National synthesis of data analysis, based on 

aggregation of comparable information obtained from 

the study units, is a major component of the program. 

This effort focuses on selected water-quality topics 

using nationally consistent information. Comparative 

studies will explain differences and similarities in 

observed water-quality conditions among study areas 

and will identify changes and trends and their causes. 

The first topics addressed by the national synthesis are 

pesticides, nutrients, volatile organic compounds, and 

aquatic biology. Discussions on these and other waterquality topics will be published in periodic summaries 

of the quality of the Nation's ground and surface water 

as the information becomes available.

This report is an element of the comprehensive 

body of information developed as part of the NAWQA 

Program. The program depends heavily on the advice, 

cooperation, and information from many Federal, 

State, interstate, Tribal, and local agencies and the 

public. The assistance and suggestions of all are 

greatly appreciated.

Robert M. Hirsch 

Chief Hydrologist
CONTENTS

Abstract..........................................................._ 1

Introduction ..................................................................................................................................................................^ 1

Description of the Study Unit............................................................................................................................................. 2

Physiographic and Geologic Settings................................................................................................................................. 2

Climate...................................................................................................^ 4

Surface Water Hydrology ......................................................................................................................................... 4

Population and Land Use.......................................................................................................................................... 11

Water Use.................................................._ 11

Environmental Framework for Water Quality Assessment................................................................................................. 12

Point Sources............................................................................................................................................................ 12

Nonpoint Sources ..................................................................................................................................................... 12

Water Quality Problems Identified by the State of California.................................................................................. 17

Environmental Settings............................................................................................................................................. 18

Lower San Joaquin River Basin, 1951-1990...................................................................................................................... 20

Sources of Data................................................................................................................................................................... 23

Compilation of Data................................................................................................................................................. 23

Screening of Data..................................................................................................................................................... 24

Analysis Techniques......................................................................................................................................................^ 26

Quality Assurance and Quality Control.............................................................................................................................. 27

Description of Available Data............................................................................................................................................. 28

Timing and Location of Sampling............................................................................................................................ 28

Streamflow at Time of Water Quality Sampling....................................................................................................... 38

Description of Constituent Concentrations by Environmental Setting............................................................................... 41

Differences in Constituent Concentrations Among Environmental Settings............................................................ 41

Concentrations of Constituents in the Lower San Joaquin River............................................................................. 47

Relation to National Conditions ............................................................................................................................... 57

Relation of Nutrient and Suspended Sediment Concentrations to Streamflow.................................................................. 57

Load Estimates ......................................................................... 60

Annual Stream Loads ............................................................................................................................................... 60

Relation of Stream Loads to Upstream Conditions.................................................................................................. 75

Atmospheric Loads................................................................................................................................................... 76

Total Loads in the Lower San Joaquin River Basin.................................................................................................. 78

Trends in Constituent Concentrations ................................................................................................................................ 79

Summary and Conclusions................................................................................................................................................. 86

References Cited......................................................................._ 89

FIGURES

1. Map showing San Joaquin-Tulare Basins, California, study unit..................................................................... 3

2. Map showing mean annual precipitation, San Joaquin-Tulare Basins, California, study unit.......................... 5

3.-5. Graphs showing:

3. Annual mean Streamflow at seven representative sites, San Joaquin-Tulare Basins, California,

study unit, 1950-1991................................................................................................................................ 6

4. Monthly mean Streamflow showing seasonal variation at seven representative sites,

San Joaquin-Tulare Basins, California, study unit, 1950-1991................................................................. 7

5. Unimpaired and measured monthly mean Streamflow, San Joaquin Basin, California, 1979-1992.......... 8

6. Map showing major reservoirs and distribution systems in San Joaquin-Tulare Basins, California,

study unit............................................................................................................................................................ 9

Contents v
Water year hydrologic classifications for the San Joaquin Basin, California, 1950-1992................................. 11

Maps showing:

8. Agricultural diversions from lower San Joaquin River system, California................................................. 13

9. Point source discharges in San Joaquin-Tulare Basins, California, study unit by

type of discharge and amount of discharge................................................................................................. 14

10. Lower San Joaquin River and Grasslands area, California......................................................................... 15

11. Graph showing estimated fertilizer applications of nitrogen and phosphorus in

San Joaquin-Tulare Basins, California, study unit, by county, 1965-1985................................................ 16

12. Graph showing total acres with subsurface agricultural drains in the Grasslands area,

San Joaquin Valley, California, 1950-1991 ................................................................................................ 17

13. Map showing agricultural discharges to lower San Joaquin River system, California............................... 18

14. Map showing impaired water bodies in San Joaquin-Tulare Basins, California, study unit...................... 19

15. Environmental settings in San Joaquin-Tulare Basins, California, study unit:

(A) Environmental settings (B) Locations of environmental settings ......................................................... 20

16. Graph showing comparison of nutrient and suspended-sediment data from the

National Water Information System (NWIS) of the U.S. Geological Survey and STOrage and

RETrieval (STORET) database of the U.S. Environmental Protection Agency for

San Joaquin River near Vernalis, California, 1972-1990............................................................................ 29

17. Graph showing numbers of sites and samples for nutrients and suspended sediment in the final 

National Water-Quality Assessment database, 1972-1990, San Joaquin-Tulare Basins, 

California, study unit................................................................................................................................... 31

18. Map showing long-term water quality monitoring sites in San Joaquin-Tulare Basins,

California, study unit................................................................................................................................... 32

19. Map showing nutrient data sites in San Joaquin-Tulare Basins, California,

study unit, 1972-1990 ................................................................................................................................ 37

20. Graph showing nutrient samples and sampling sites by environmental settings in

San Joaquin-Tulare Basins, California, study unit..................................................................................... 38

21. Map showing suspended sediment data sites in San Joaquin-Tulare Basins, California,

study unit..................................................................................................................................................... 39

22.-33. Graphs showing:

22. Suspended sediment samples and sampling sites by environmental settings in

San Joaquin-Tulare Basins, California, study unit..................................................................................... 40

23. Nutrient and suspended sediment samples and sampling sites for long-term sites by

environmental settings in San Joaquin-Tulare Basins, California, study unit............................................ 41

24. Percent of nutrient and suspended sediment samples collected during the irrigation season at

long-term sites in the San Joaquin Valley, California ................................................................................. 42

25. Percent of streamflow associated with nutrient samples collected at selected sites in

San Joaquin-Tulare Basins, California, study unit..................................................................................... 43

26. Percent of streamflow associated with suspended sediment samples collected at selected sites in

San Joaquin-Tulare Basins, California, study unit..................................................................................... 44

27. Nutrient and suspended sediment concentrations at long-term water quality monitoring sites by

environmental setting in San Joaquin-Tulare Basins, California, study unit, 1972-1990.......................... 45

28. Differences in suspended sediment size among environmental settings, 1972-1990, in

San Joaquin-Tulare Basins, California, study unit..................................................................................... 47

29. Nutrient and suspended sediment concentrations in the San Joaquin River, California,

and its most significant inputs, 1972-1990................................................................................................. 54

30. Comparison of nitrate, total phosphorus, and suspended sediment concentrations,

San Joaquin-Tulare Basins, California, study unit, to national sites, 1993 National Water Summary.

(A) Agricultural areas. (B) Forest areas....................................................................................................... 58

31. Relation between streamflow and nitrate concentrations at selected sites in San Joaquin-Tulare

Basins, California, study unit, 1972-1990.................................................................................................. 59

32. Relation between streamflow and total phosphorus concentrations at selected sites in

San Joaquin-Tulare Basins, California, study unit, 1972-1990................................................................. 61

33. Relation between streamflow and suspended sediment concentrations at selected sites in

San Joaquin-Tulare Basins, California, study unit, 1972-1990 ................................................................ 62

vi Contents
34.-37. Maps showing:

34. Annual nitrate loads in San Joaquin-Tulare Basins, California, study unit,

during wet year (1986) and critically dry year (1988)................................................................................ 70

35. Annual total nitrogen loads in San Joaquin-Tulare Basins, California, study unit,

during wet year (1986) and critically dry year (1988)................................................................................ 71

36. Annual total phosphorus loads in San Joaquin-Tulare Basins, California, study unit,

during wet year (1986) and critically dry year (1988)................................................................................ 72

37. Annual suspended sediment loads in San Joaquin-Tulare Basins, California, study unit,

during wet year (1986) and critically dry year (1988)................................................................................ 73

35.-47. Graphs showing:

38. Annual nitrate, total nitrogen, total phosphorus, and suspended sediment loads at

San Joaquin River near Vernalis site, 1972-1990 ....................................................................................... 75

39. Atmospheric deposition sites and selected drainage basins for load comparisons in

San Joaquin-Tulare Basins, California, study unit..................................................................................... 77

40. Trend in nitrate concentration at San Joaquin River near Vernalis site, 1951-1990................................... 82

41. Potential sources of total nitrogen in the lower San Joaquin River Basin, California, nitrate

loads and concentrations, and nutrient trends in the S an Joaquin River near Vernalis site......................... 83

42. Nitrate concentrations at selected San Joaquin River sites, California, 1972-1990................................... 84

43. Total phosphorus concentrations at selected San Joaquin River sites, California, 1972-1990................... 85

44. Suspended sediment concentrations at selected San Joaquin River sites, California, 1972-1990 ............. 86

45. Nitrate concentrations at representative sites in San Joaquin-Tulare Basins, California,

study unit, 1972-1990................................................................................................................................. 87

46. Total phosphorus concentrations at representative sites in San Joaquin-Tulare Basins,

California, study unit, 1972-1990............................................................................................................... 88

47. Suspended sediment concentrations at representative sites in San Joaquin-Tulare Basins,

California, study unit, 1972-1990............................................................................................................... 89

TABLES

1. Major reservoirs and distribution systems, San Joaquin-Tulare Basins, California, study unit........................ 10

2. Factors affecting nutrient concentrations in the lower San Joaquin River Basin, California,

1950, 1970, and 1990 ......................................................................................................................................... 22

3. Approximate nutrient concentrations from major sources in the lower San Joaquin River Basin,

California, during the late 1980s ........................................................................................................................ 23

4. Number of sites and samples for nutrients and suspended sediments in initial and final databases,

1972-1990, by agency, San Joaquin-Tulare Basins, California, study unit....................................................... 25

5. Number of sites and samples removed from initial database, San Joaquin-Tulare Basins,

California, study unit.......................................................................................................................................... 26

6. Site and basin characteristics of long-term stream water quality sampling sites, San Joaquin-Tulare

Basins, California, study unit............................................................................................................................. 33

7. Summary of Tukey's test on ranks for nutrients and suspended sediment at long-term water quality

monitoring sites, San Joaquin-Tulare Basins, California, study unit................................................................. 47

8. Water quality data for long-term sites, S an Joaquin-Tulare B asins, California, study unit............................... 48

9. Nitrate, total nitrogen, total phosphorus, and suspended sediment load estimates in

San Joaquin-Tulare Basins, California, study unit, 1986-1988......................................................................... 63

10. Nitrate, total nitrogen, total phosphorus, and suspended sediment loads in the lower San Joaquin River,

California, that are unaccounted for by inputs from major tributaries, 1986-1988 ........................................... 74

11. Mean nitrogen loads at atmospheric deposition sites, San Joaquin-Tulare Basins, California,

study unit............................................................................................................................................................ 78

12. Comparison of stream loads and atmospheric deposition loads for total nitrogen in selected drainage

basins, San Joaquin-Tulare Basins, California, study unit, 1986-1988............................................................. 79

13. Estimated loads of total nitrogen and total phosphorus in the lower San Joaquin River Basin,

California, by subbasin for late 1980s................................................................................................................ 80

14. Trends in nutrient and suspended sediment concentrations during the 1980s, San Joaquin-Tulare

Basins, California, study unit............................................................................................................................. 81

Contents vii
CONVERSION FACTORS, VERTICAL DATUM, WATER QUALITY UNITS, 

WATER YEAR, AND ABBREVIATIONS AND ACRONYMS

Conversion Factors

Multiply

acre

acre-foot (acre-ft)

acre-foot per acre (acre-ft/acre)

acre-foot per month (acre-ft/mo)

acre-foot per year (acre-ft/yr)

cubic foot per second (ft3/s)

foot (ft)

inch (in.)

mile (mi)

square mile (mi2)

tons per year (tons/yr)

By

4,047

1,233

1,233

1,233

1,233

0.02832

0.3048

25.4

1.609

2.590

907.18486

To obtain

square meter

cubic meter

cubic meter per acre

square meter per month

square meter per year

cubic meter per second

meter

millimeter

kilometer

square kilometer

kilogram per year

Temperature is given in degrees Celsius (°C), which can be converted to degrees Fahrenheit (°F) by

the following equation:

°F=1.8(°C)+32.

Vertical Datum

Sea level: In this paper, "sea level" refers to the National Geodetic Vertical Datum of 1929—a geodetic datum derived 

from a general adjustment of the first-order level nets of the United States and Canada, formerly called Sea Level Datum of 

1929.

Water Quality Units

Concentrations of constituents in water samples are given in either milligrams per liter (mg/L) or micrograms per liter 

(|ig/L). Milligrams per liter is equivalent to "parts per million" and micrograms per liter is equivalent to "parts per billion."

Water Year

In U.S. Geological Survey papers dealing with surface water supply, the 12-month period October 1 to September 30. 

The water year is designated by the calendar year in which it ends and which includes 9 of the 12 months. For example, the 

year ending September 30, 1992, is called the "1992 water year." In this paper, unless otherwise defined, "years" refer to 

water years.

viii Contents
Abbreviations and Acronyms

BOR, Bureau of Reclamation

CARB, California Air Resources Board

COE, U.S. Army Corps of Engineers

CRWQCB, California Regional Water Quality Control Board

CVP, Central Valley Project

DWR, California Department of Water Resources

EPA, U.S. Environmental Protection Agency

GIRAS, Geographic Information Retrieval and Analysis System

LOWESS, LOcally WEighted Scatterplot Smoothing (technique)

NADP, National Atmospheric Deposition Program

NASQAN, National Stream Quality Accounting Network

NAWQA, National Water-Quality Assessment

NPDES, National Pollutant Discharge Elimination System

NWIS, National Water Information System of the U.S. Geological Survey

NWQL, National Water-Quality Laboratory

QA/QC, Quality assurance/quality control

SAS, Statistical Analysis System

STORET, STOrage and RETrieval database of the U.S. Environmental Protection Agency

SWP, State Water Project

SWRCB, California State Water Resources Control Board

USGS, U.S. Geological Survey

mm, millimeter

mg/L, milligram per liter

(iS/cm, microsiemen per centimeter at 25 degrees Celsius

(ig/L, microgram per liter

Contents ix
Water Quality Assessment of the San Joaquin-Tulare Basins, 

California: Analysis of Available Data on Nutrients and 

Suspended Sediment in Surface Water, 1972-1990

5/Charles R. Kratzer and Jennifer L Shelton

Abstract

Nutrients and suspended sediment in 

surface water of the San Joaquin-Tulare Basins in 

California were assessed using 1972-1990 data 

from the U.S. Geological Survey's National Water 

Information System and the U.S. Environmental 

Protection Agency's STOrage and RETrieval 

database. A database representative of ambient 

surface water conditions was developed by 

excluding sites representing or directly influenced 

by small subsurface agricultural drains, wastewater treatment plant effluents, major water supply 

canals, and reservoirs. Comparisons of nutrient 

and suspended sediment concentrations were 

made among three environmental settings: the San 

Joaquin Valley-west side, the San Joaquin Valleyeast side, and the Sierra Nevada. The primary land 

use is agriculture at the valley sites and forest at the 

Sierra Nevada sites. Soils at the west side valley 

sites are primarily fine-grained alluvial deposits 

from the Coast Ranges; the east side valley sites 

are primarily coarser-grained alluvial deposits 

from the Sierra Nevada.

Nutrient and suspended sediment concentrations in surface water are highest at west side 

sites. Nutrient concentrations in the lower San 

Joaquin River are determined primarily by relatively concentrated inputs from west side agricultural drainage, east side wastewater treatment 

plants and runoff from dairies, and by relatively 

dilute inputs from major east side tributaries. On 

the basis of size distribution and load calculations 

in the San Joaquin River and tributaries, most

suspended sediment in the river comes from west 

side sources.

Nutrient and suspended sediment loads in 

the lower San Joaquin River were much greater in 

a wet year (1986) than in a critically dry year 

(1988). Ratios of 1986 to 1988 loads increased 

with the particulate fraction of each constituent. 

During water years 1986-1988, nonpoint sources 

accounted for at least 81 percent of the total 

nitrogen load and 68 percent of the total phosphorus load from the San Joaquin Basin. The 

overall transport of total nitrogen and total phosphorus from the basin during this time was 

5 percent and 3 percent of the total sources, 

respectively.

Flow-adjusted nitrate concentrations in the 

lower San Joaquin River have increased steadily 

since 1950. This can be attributed to many factors, 

including increases in subsurface agricultural 

drainage, fertilizer application, wastewater treatment plant effluent, and runoff from dairies. Since 

1970, this increase has been due primarily to 

increases of mostly native soil nitrogen in subsurface agricultural drainage. Flow-adjusted 

ammonia concentrations have decreased during 

the 1980s at several sites. These decreases are 

probably related to improved regulation of 

domestic and dairy wastes.

INTRODUCTION

The quality of the nation's ground- and surfacewater resources is being affected by numerous human

Introduction
and natural processes. Existing data generally are 

inadequate to assess the status and trends in water 

quality of large regions of the nation. In 1991, after a 

pilot phase, the U.S. Geological Survey (USGS) began 

to implement the National Water-Quality Assessment 

(NAWQA) Program to integrate information about 

water quality at a wide range of spatial scales, from 

local to national, and to focus on water quality 

conditions that affect large areas of the nation or occur 

frequently within numerous small areas.

In 1991, the San Joaquin-Tulare Basins study 

unit in California was selected as one of the first 20 

NAWQA study units for full-scale implementation. 

Key water quality issues of concern in the study unit 

are concentrations of salinity, trace elements, pesticides, and nutrients in surface water and ground water. 

The highest priority national issues for the first 20 

NAWQA study units are pesticides and nutrients. An 

important first step for each study unit is to review what 

is already known about each of these issues. In particular, the study design and selection of sampling 

locations for each study unit will be influenced by the 

availability and interpretation of existing information 

on the priority constituents. A retrospective report 

consisting of a review and an analysis of existing data 

on nutrients and pesticides for each study unit is one of 

the first major products of the NAWQA Program.

This report presents an analysis of available data 

on nutrients and suspended sediment in surface water 

of the San Joaquin-Tulare Basins study unit. Except for 

Vernalis, the main downstream site on the San Joaquin 

River, data analysis is limited to 1972-1990. The 

purposes of this report are to (1) describe the spatial 

and temporal availability of nutrient and sus-pended 

sediment data in the study unit, and to (2) present a 

preliminary description of the spatial and temporal 

patterns of concentrations and loads in the study unit. 

The information presented in this report was used to 

guide collection and interpretation of data during the 

NAWQA studies.

The nutrients discussed in this report are nitrogen (N) and phosphorus (P), the main nutrients 

responsible for eutrophication in surface water. The 

U.S. Environmental Protection Agency (EPA) has set 

criteria for nitrogen (nitrate and ammonia), but not for 

phosphorus. The maximum allowable level for nitrate 

in drinking water is 10 milligrams per liter (mg/L) as N. 

For ammonia, the ambient water quality criterion to 

protect freshwater aquatic life are calculated using pH 

and temperature of the water at the time of sampling. In 

the study unit, the criterion for ammonia ranges from

less than 0.2 to greater than 50 mg/L, as N. Although 

there are no established water quality criteria for 

suspended sediment, studies have shown that elevated 

concentrations adversely affect fish (U.S. 

Environmental Protection Agency, 1986).

DESCRIPTION OF THE STUDY UNIT

Physiographic and Geologic Settings

The San Joaquin-Tulare Basins study unit has a 

drainage area of 28,500 square miles (mi ) in three 

major physiographic provinces of central California: 

the Sierra Nevada, the San Joaquin Valley, and the 

Coast Ranges (fig. 1). The study unit is divided further 

into the San Joaquin Basin to the north and the hydrologically closed Tulare Basin to the south. During wet 

years, some surface water from the Tulare Basin flows 

into the San Joaquin Basin by overflow from the Kings 

River to the San Joaquin River (by way of Fresno 

Slough). The boundary of the study unit is defined by 

the drainage divides of the Sierra Nevada and Coast 

Ranges (U.S. Geological Survey, 1978).

The Sierra Nevada attain a maximum altitude of 

14,495 feet (ft) at Mount Whitney, the highest point in 

the conterminous United States. In contrast, the San 

Joaquin Valley is a flat structural basin bounded by the 

Sierra Nevada to the east, the Coast Ranges to the west, 

the Tehachapi Mountains to the south, and the 

Sacramento-San Joaquin Delta to the north. Altitudes 

generally range from about 3,000 to 5,000 ft for the 

Coast Ranges, about 5,000 to 8,000 ft for the Tehachapi 

Mountains, and about 8,000 to 14,000 ft for the Sierra 

Nevada. Land-surface altitudes of the valley rise from 

near sea level in the north to 1,000 ft above sea level in 

the southeast.

The bedrock geology of the Sierra Nevada to the 

east of the San Joaquin Valley contrasts sharply with 

that of the Coast Ranges to the west. The Sierra Nevada 

primarily are composed of pre-Tertiary granitic rock 

and are separated from the valley by a foothill belt of 

Mesozoic and Paleozoic marine rocks and Mesozoic 

metavolcanic rocks along the northern one-third of the 

boundary (California Division of Mines and Geology, 

1958, 1959,1964,1965,1966,1967, 1969). The Coast 

Ranges have a core of Franciscan complex of Late 

Jurassic to Late Cretaceous or Paleocene age and of 

ultramafic rocks of Mesozoic age. These rocks are 

overlain by marine and continental sediments of

Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
120°

EXPLANATION

San Joaquin Valley 

Basin boundary 

— — — Study unit boundary

* SAN ~V

Sacramento-Y"1" \ JOAQUIN 

San Joaquin \_ . BASIN _/- „ Delta * s - —-^ ^

projection: Albers. 1st parallel: 29°30' 

cm: 120° 2nd parallel: 45°30'

digital data: U.S. Department of Commerce, 1993

U.S. Environmental Protection Agency, 1982

Figure 1. San Joaquin-Tulare Basins, California, study unit.

Description of the Study Unit 3
Cretaceous to Quaternary age and some Tertiary 

volcanic rocks.

Sediment of the San Joaquin Valley consists of 

interlayered gravel, sand, silt, and clay derived from the 

adjacent mountains and deposited in alluvial-fan, 

flood-plain, flood-basin, lacustrine, and marsh environments. The thickness of the aquifer system formed by 

these sediments averages more than 2,500 ft and 

increases from north to south, with a maximum thickness of more than 9,000 ft at the southern end of the 

valley (Bertoldi and others, 1991). The lithology and 

texture of the sediments reflect their source area and 

manner of deposition. Sediments in the west side 

alluvial fans are coarsest at the heads of the fans and 

consist predominantly of fine-grained silt and clay in 

the rest of the west side of the valley (Laudon and 

Belitz, 1991). In general, sediments derived from the 

Coast Ranges are finer grained than those derived from 

the Sierra Nevada.

Climate

The San Joaquin Valley has an arid to semiarid 

climate that is characterized by hot summers and mild 

winters. The San Joaquin Valley and the eastern slopes 

of the Coast Ranges are in the rainshadow of the Coast 

Ranges. The Sierra Nevada force warm, moist airmasses from the Pacific Ocean aloft. As the airmasses 

cool, the moisture condenses, resulting in heavy 

precipitation on the western slopes. This precipitation, 

occurring as both rainfall and snow, is the major source 

of water in the study unit.

Mean annual precipitation (1911-1960) on the 

San Joaquin Valley floor varies from 5 inches (in.) in 

the south to about 15 in. in the north (fig. 2). Precipitation in the Sierra Nevada, mostly in the form of snow, 

varies from about 20 in. to more than 80 in. at some 

higher altitudes. Precipitation in the Coast Ranges 

(within the study unit) varies from less than 10 in. to 

more than 20 in. As in the valley, precipitation in the 

Sierra Nevada and Coast Ranges increases from south 

to north. Annual precipitation is highly variable; the 

recent drought in California (1987-1992) resulted from 

years of below-normal precipitation in the Sierra 

Nevada. Throughout the study unit, more than 80 

percent of the annual precipitation falls during 

November through April. January is the month of peak 

precipitation in most areas.

Surface Water Hydrology

As expected, mean annual runoff follows the 

same general pattern as precipitation, with the largest 

amounts in the Sierra Nevada followed by the valley 

and Coast Ranges (Gebert and others, 1987). As with 

precipitation, runoff increases from south to north. 

Runoff in the Sierra Nevada varies from about 10 in. to 

more than 40 in. Runoff in the valley varies from less 

than 1 in. to almost 10 in. Runoff is less than 2 in. 

throughout the Coast Ranges.

Annual mean streamflow for 1950-1991 at seven 

representative sites in the study unit is shown in 

figure 3. These include three Sierra Nevada sites, three 

San Joaquin Valley sites, and one Coast Ranges site. All 

sites show the effect of the recent drought years 

(1987-1992) and the relatively wet period preceding 

the drought (1978-1986). As with precipitation, annual 

streamflow is highly variable.

Monthly mean streamflow at the seven representative sites is shown in figure 4. All Sierra Nevada 

sites have peak flows in May and June; this corresponds 

to the peak period of snowmelt runoff. The Mokelumne 

River site has a lower-altitude drainage basin and more 

rain than snow, relative to the other Sierra Nevada sites. 

This probably accounts for the flatter peak period for 

this site.

The peak streamflows at the San Joaquin Valley 

and Coast Ranges sites usually occur during February 

through April. Major reservoir development has altered 

the seasonal patterns at the Merced River near 

Stevinson and San Joaquin River near Vernalis sites, 

and the seasonal patterns are shown before and after 

development of major reservoirs (fig. 4). The postreservoir period at the San Joaquin River near Vernalis 

was a much wetter period. Mean annual flows were 

5,160 cubic feet per second (ft3/s) compared to 3,970 

ft3/s for the prereservoir period and monthly mean 

streamflows were higher in the postreservoir period for 

all months except June (fig. 4). The postreservoir 

seasonal patterns at the Merced (1967-1991) and San 

Joaquin River (1979-1991) sites are influenced by 

winter rainfall (December to March), fish-release 

schedules (April to June), hydropower releases, 

dilution releases to meet Sacramento-San Joaquin 

Delta water quality standards, and upstream agricultural diversions. The Cosumnes River and Los Gatos 

Creek sites are not affected by upstream reservoirs. The 

seasonal pattern for Los Gatos Creek corresponds 

directly to rainfall runoff; the Cosumnes River has a 

combination of rainfall and snowmelt runoff.

Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
EXPLANATION

Line of equal mean annual

precipitation. Interval, in inches

is variable

—— — —— Study unit boundary

35°

40 MILES

0 40 KILOMETERS

Figure 2. Mean annual precipitation, San Joaquin-Tulare Basins, California, study unit. (Modified from Rantz, 1969.)

Description of the Study Unit 5
Station 11303500

San Joaquin River near Vernalis

Mean, 4,375

CD 2-4CD _ o - .E 2

I 2

,400,000,600,200,800,400,000,600,200

800400

0

55504540

35302520

15

10

50

Station 11272500Merced River near StevinsonMean, 656Station 11 224500

~ Los Gatos Creek above Nunez r- Canyon near Coalin -Mean, 5.9-

-

r-nil ^{Vr

1 

1

33

'Tl

U

.

1

-

-

.

n

~L 

__ r

22,00020,000

18,000

16,00014,000

12,000

10,000

8,0006,000

4,0002,000

Station 11335000 

Cosumnes River at Michigan Bar 

-Mean, 5,085

1950 1960 1970 1980 1990

EXPLANATION

Site location 

A Sierra Nevada A San Joaquin Valley A Coast Ranges

35°

0 40 MILES

t,tuu 

4,000 

3,6003,200

2,8002,400

2,000

1,600 1,200 

800

•o 40°

8 °CD (/) fc 1.100

5 1,000

CD 900

£ 800

3 70°

.E 600

g 500

| 400 

I 300

^ 200

CD Q

"CO

i 4,400 

< 4,000

jo 3,600

3,2002,8002,400 2,000

1,600

1,200 

800 400°i

Station 11 31 9500 

~ Mokelumne River near Mokelumne Hill -Mean, 1,017-_-

r

—--

i

H

r

i ;' ;.1. ri: '' *

11

': ' PI ^

i : - J_^

:

K.

5? "'iDii

Station 11 264500 

~ Merced River at Happy Isles Bridge - near Yosemite- Mean, 355

•

--- ——— 

^

j

f Fll

f^:fl

rv " "-1

fill 

^

Jil

1

•

J -

i

S IT J,

\

Station 11 187000 

~ Kern River at Kernville- Mean, 836--_ „;

p

- [-'950

- T> •'" 

H

"

,.- . - n ;: ; >vri p

;

"iftf

1960 1970 1980 199

0 40 KILOMETERS

Figure 3. Annual mean streamflow at seven representative sites, San Joaquin-Tulare Basins, California, study unit, 1950-1991.
11,000

10,000

9,0008,000

7,0006,0005,0004,0003,0002,000

1,000

0

g. 2,200 o 2,000CD

"£ 1,800 '-§ 1,600 

£ 1,400 

~- 1 ,200 

o 1,000

800600400200

0

5550

45

40

35302520

1510

50

Station 11303500San Joaquin River

near Vernalis

Station 11272500 Merced River near 

Stevinson

QPrereservoir 

development

BPostreservoir 

development 1979-1991

QPrereservoir 

development

HPostreservoir• development

1967-1991

Station 11224500 

Los Gatos Creek above Nunez 

Canyon near Coalinga

2,2002,000

1,800

1,6001,4001,2001,000

800600

400200

0

Station 11335000

Cosumnes River at Michigan Bar

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep 

121° 120°

1130350

2,2002,000

1,800

1,6001,4001,2001.000

800600

400

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

EXPLANATION

Site location 

A Sierra Nevada A San Joaquin Valley A Coast Ranges

CDCD 

CD

O

J3

0

_C

I

Ecd2GO

C

cdCD

>.

2,2002,000

1,800

1,6001,4001,2001,000

800600400200

0

2,200

2,000

1,8001,600

1,4001,2001,000

800600400200

0 40 MILES

40 KILOMETERS

Station 11319500 

Mokelumne River near 

Mokelumne Hill

Station 11264500

Merced River at Happy Isles Bridge 

near YosemTte

Station 11187000 

Kern River at Kernville

Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep

•j Figure 4. Monthly mean streamflow showing seasonal variation at seven representative sites, San Joaquin-Tulare Basins, California, study unit, 1950-1991.
1.4

1.2

1.0

0.8

0.6

•£• 0.4

0.2

• Unimpaired flow to valley floor 

in San Joaquin River Basin

O Measured outflow from 

San Joaquin River Basin

Oct Nov Dec Jan Feb Mar Apr May June July Aug Sept 

Month

Figure 5. Unimpaired and measured monthly mean streamflow, San 

Joaquin Basin, California, 1979-1992.

The overall effect of reservoirs and agricultural 

water use on outflow from the San Joaquin Basin is 

shown in figure 5. Monthly mean unimpaired streamflow to the valley floor in the San Joaquin Basin is 

compared with outflow of the San Joaquin River at 

Vernalis, for the postreservoir-development period of 

1979-1992. Unimpaired flow, a term used by the 

California Department of Water Resources (DWR), 

represents the runoff from a basin if the flow of water 

had not been altered (California Department of Water 

Resources, 1987a). The total unimpaired streamflow to 

the valley floor in the San Joaquin Basin (fig. 5) is the 

sum of unimpaired flows on the San Joaquin River at 

Millerton Lake (site 6, fig. 6), Merced River at Lake 

McClure (site 20), Tuolumne River at New Don Pedro 

Reservoir (site 21), Stanislaus River at New Melones 

Reservoir (site 24), and outflow from the Tulare Basin 

by way of Fresno Slough (fig. 6). The unimpaired flow 

provides an estimate of the total water that would be 

expected to reach Vernalis under natural conditions. 

The actual outflow from the San Joaquin Basin (about

3.7 million acre-feet per year [acre-ft/yr] during 1979- 

1992) is much less than the mean unimpaired flow to 

the valley (about 6.1 million acre-ft/yr during the same 

period) mostly because of agricultural water use in the 

basin. The timing of actual outflow (fig. 5) is more 

evenly distributed throughout the year than the 

unimpaired flow to the valley because of the storage 

and release schedules of the four major upstream 

reservoirs, which have a combined total storage 

capacity of almost 6 million acre-feet (acre-ft). 

Reservoir development and water use in the basin have 

shifted the peak outflow from May to March and 

reduced this peak flow from about 1.3 million acre-feet 

per month (acre-ft/mo) to about 0.6 million acre-ft/mo 

during 1979-1992 (fig. 5).

Major reservoirs (capacity more than 75,000 

acre-ft) and distribution systems in the study unit are 

shown in figure 6 and listed in table 1. The only major 

stream in the study unit without a major reservoir is the 

Cosumnes River. Twenty-three of the 25 reservoirs 

listed in table 1 are used at least in part for hydropower 

production. The exceptions are Eastman Lake (site 22) 

and Hensley Lake (site 23), which are used primarily 

for irrigation supply. Overall, 13 of the 25 reservoirs 

are used at least in part for irrigation. Only five of the 

reservoirs have significant municipal uses: Hetch 

Hetchy Reservoir (site 2) is owned and operated by the 

city and county of San Francisco, Pardee Reservoir 

(site 4) is owned and operated by East Bay Municipal 

Utility District for water supply east of San Francisco 

Bay, and San Luis Reservoir (site 19) is jointly owned 

and operated by the DWR and the Bureau of 

Reclamation (BOR) as a major storage reservoir of the 

State Water Project (SWP) and the Central Valley 

Project (CVP) aqueduct systems. In the mid-1990s, 

New Don Pedro (site 21) and New Hogan (site 18) 

reservoirs started to supply municipal water to the 

cities of Modesto and Stockton to supplement 

declining ground water supplies (Garner Reynolds, city 

of Modesto, oral commun., 1996; California 

Department of Water Resources, 1994a).

Water distribution systems shown in figure 6 

include features of the SWP (California Aqueduct, site 

L), the CVP (Delta-Mendota [site I], Friant-Kern [site 

H], and Madera [site J] Canals), and Merced, Modesto, 

Oakdale, South San Joaquin, and Turlock Irrigation 

Districts. These are the major distribution systems for 

agricultural water supply in the study unit. Little municipal water in the study unit is provided by these 

distribution systems; the exception is the city of

8 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
EXPLANATION 

Reservoir and site number 

Distribution system and site

number

Note: names and data for 

reservoirs and distribution 

systems shown in table 1

^VA. —— — —— Study unit boundary

Sacramento J,StOCkton

San Joaquin .

Delta (

40 MILES

40 KILOMETERS

Figure 6. Major reservoirs and distribution systems in San Joaquin-Tulare Basins, California, study unit.

Modesto. The California (site L), Hetch Hetchy (site 

G). and Mokelumne (site F) Aqueducts transport water 

from the San Joaquin Basin to municipal users outside 

the study unit.

Water availability for allocation and regulation in 

the San Joaquin Basin is defined by a water year 

hydrologic classification system. Known as the

60-20-20 water year index, and used by the California 

State Water Resources Control Board (SWRCB), this 

represents the percentage weight given to three variables: the forecasted, unimpaired runoff from April 

through July (60 percent); the forecasted, unimpaired 

runoff from October through March (20 percent); and 

the reservoir carryover storage from the previous water

Description of the Study Unit
Table 1. Major reservoirs and distribution systems, San Joaquin-Tulare Basins, California, study unit

[Major use: 1. irrigation: M. municipal supply; P, hydropower production. Acre-ft. acre-feet; ft3/s, cubic feet per second; mi, mile. California 

Department of Water Resources, 1984, 1987b, 1994a; California State Water Resources Control Board, 1987; Garner Reynolds, city of 

Modesto, oral commun., 1996]

Site No. 

(fig. 6)

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

Site No. 

(fig. 6)

A

B

C

D

E

F

G

H

I

J

K

L

M

n • Year Capacity ... . Reservoir , . ., . -» Waterway completed (thousand acre-ft)

Huntington

Hetch Hetchy

Shaver

Pardee

Salt Springs

Millerton

Isabella

Edison

Pine Flat

Lloyd

Beardsley

Wishon

Courtright

Mammoth Pool

Success

Kaweah

Camanche

New Hogan

San Luis

McClure

New Don Pedro

Eastman

Hensley

New Melones

New Spicer Meadow

Distribution system

1917

1923

1927

1929

1931

1947

1953

1954

1954

1956

1957

1958

1958

1960

1961

1962

1963

1963

1967

1967

1971

1979

1979

1979

1989

89

360

135

210

139

520

570

125

1,000

268

98

128

123

123

85

150

431

325

2,039

1,026

2,030

150

90

2,400

189

Central California Irrigation District Main Canal

Merced Irrigation District Main Canal

Turlock Irrigation District Main Canal

Modesto Irrigation District Main Canal

South San Joaquin Irrigation District Main Canal

Mokelumne Aqueduct

Hetch Hetchy Aqueduct

Friant-Kern Canal

Delta— Mendota Canal

Madera Canal

Oakdale Irrigation District Main Canal

California Aqueduct

Cross Valley Canal

San Joaquin River

Tuolumne River

San Joaquin River

Mokelumne River

Mokelumne River

San Joaquin River

Kern River

San Joaquin River

Kings River

Tuolumne River

Stanislaus River

Kings River

Kings River

San Joaquin River

Tule River

Kaweah River

Mokelumne River

Calaveras River

California Aqueduct/Delta-Mendota Canal

Merced River

Tuolumne River

Chowchilla River

Fresno River

Stanislaus River

Stanislaus River

Year Capacity 

completed (ft3/s)

1880 1,800

1886 2,000

1900 2,100

1904 2,000

1913 950

1929 590

1934 460

1944 4,000

1951 4,600

1952 1,000

'1958 2525

1968 13,100

1975 740

Length 

(mi)

71

21

22

46

32

90

152

152

116

36

36

444

20

Major 

use

P

M,P

P

M,P

P

1,P

1.P

P

1,P

P

P

P

P

P

I,P

I,P

1,P

I,M,P

I.M.P

I,P

I,M,P

I

I

I.P

P

Major 

use

I

I

I

I,M

I

M

M

I

I

I

I

I,M,P

I

North Main Canal. 

2South Main Canal.

year constrained by a maximum allowable value (20 

percent) (California State Water Resources Control 

Board, 1992). Water years 1950-1992 are classified on 

the basis of this index as wet, above normal, below 

normal, dry, or critical (fig. 7).

During the study period, 1972-1990, there were 

seven wet water years, three above normal, three dry, 

and six critical (fig. 7). Thus, it was a period of

extremes. The first six water years of the study period 

were balanced—two wet, one above normal, one dry, 

and two critical. The drought of 1976-1977 was 

followed by a 9-year period dominated by wet water 

years, including the extremely wet water year of 1983. 

Overall, this 9-year period included five wet, two above 

normal, and two dry water years. Following that 9-year 

wet period were six consecutive critical water years.

10 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
0

1 '

1 ,

r—

1 1

— |

1

1

—

1

1

1

1

1

1

1

1

1

1

1

1

1

1

—

1

1

1

1

1

1

1

1

1

1

'

1

1

1

1

—

1

1

1

1

—

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

—

1

1

1

1

1

1

1

1

1

1

1

1

1

1

1

Wet

Above Normal

Below Normal

Drv

Critical

1950 1960 1970 1980 

Figure 7. Water year hydrologic classifications for the San Joaquin Basin, California, 1950-1992.

1990 Classification

Population and Land Use

In 1990, the population of the study unit was 

2,719,958, with about 46 percent in the four largest 

cities: Fresno (453,388), Bakersfield (302,605), 

Stockton (262,046), and Modesto (230,609) 

(California Department of Finance, 1991). Most of the 

rest are in small farming communities in the San 

Joaquin Valley. The Sierra Nevada and the Coast 

Ranges are sparsely populated.

Based on mid-1970s data, the Geographic 

Information Retrieval and Analysis System (GIRAS) 

land-use designations for the study unit included 

39 percent forest land, 32 percent cropland and pasture 

(including orchards and vineyards), 23 percent rangeland, 3 percent barren land, 2 percent urban area, and 

less than 1 percent wetland (U.S. Geological Survey, 

1986). Most of the rangeland is in the Coast Ranges, at 

the valley margin, or in the Tehachapi Mountains (fig. 

1). Little, if any. surface water runoff reaches the valley 

from these areas. The forest land is mostly in the Sierra 

Nevada although some is in the higher altitudes of the 

Coast Ranges. Most forest land is publicly owned, 

primarily as national forests or national parks.

The remnant wetlands in the study unit are less 

than 15 percent of the wetland acreage before settlement of the San Joaquin Valley in the 19th century (San 

Joaquin Valley Drainage Program, 1990). The largest 

remaining wetland area in the study unit is the 

Grasslands (fig. 1). Wetland areas include public lands 

managed by state and federal agencies and privately 

owned duck clubs.

Most of the valley floor is agricultural land. 

Orchards and vineyards are primarily along the east

side of the valley. Wetland areas are in the northern part 

of the valley, and the rangeland areas are in the 

southern part. Cropland and pasture are distributed 

throughout the valley, especially along the west side.

Five counties in the San Joaquin Valley are 

among the nation's 10 highest producers of agricultural commodities, including Fresno (number 1), Kern 

(number 2), and Kings (number 3). Crops accounted 

for 65 percent of the agricultural production in 1987; 

livestock and livestock products accounted for the rest. 

Fruits and nuts accounted for 51 percent of the crop 

value, cotton for 20 percent, and vegetables for 10 

percent (San Joaquin Valley Drainage Program, 1990).

Water Use

The overall consumptive use of water in the 

study unit was about 12.1 million acre-ft in 1990 (W.E. 

Templin, U.S. Geological Survey, written commun., 

1992). About 58 percent of this demand was met with 

surface water and 42 percent with ground water. 

Approximately 38 percent of the surface water (22 

percent of total consumptive use) was imported from 

the Sacramento-San Joaquin Delta through the SWP 

(California Aqueduct) and the CVP (Delta-Mendota 

Canal) (Bureau of Reclamation, 1990; California 

Department of Water Resources, 1991). Of the total 

consumptive water use in the study unit in 1990, 94.9 

percent was for irrigation. Combined with the 

consumptive use of 1.5 percent for livestock, 

agriculture accounted for 96.4 percent of the total use. 

Domestic use (for example, drinking water) accounted 

for only 1.1 percent of the consumptive use in the study

Description of the Study Unit 11
unit, and virtually all this was from ground water (W.E. 

Templin, U.S. Geological Survey, written commun. 

1992). The other 2.5 percent included industrial and 

miscellaneous agriculture.

Total water use in the study unit during 1990, 

including nonconsumptive uses of water, was about 

32.5 million acre-ft (W.E. Templin, U.S. Geological 

Survey, written commun., 1992). Hydropower, the only 

instream water use studied under the USGS water-use 

program, accounted for about three-quarters of the total 

nonconsumptive water use in the study unit (Templin, 

1990). Other significant instream uses, such as 

recreation, fish and wildlife habitat preservation, 

aquaculture, or dilution for water quality improvement, 

have not been quantified. Most of the other nonconsumptive use is irrigation, which includes deep percolation to usable ground water, return flows to surface 

water, and operational spills to surface water. An 

operational spill is excess irrigation water supply that is 

not applied to agricultural lands, but is instead returned 

to a surface water system.

The use of water along the lower, perennial San 

Joaquin River upstream from Vernalis affects water 

quality. During the irrigation season, diversions for 

irrigation often remove most of the river flow (Kratzer 

and Grober, 1991). Main irrigation-season diversions 

from this reach of the river and east side tributaries are 

shown in figure 8 (James and others, 1989; Kratzer and 

others, 1987). Of the 86 diversions shown in figure 8, 

the two largest (West Stanislaus Irrigation District and 

Patterson Water District) account for about 40 percent 

of the total diversions in this area (Kratzer and others, 

1987).

ENVIRONMENTAL FRAMEWORK FOR WATER 

QUALITY ASSESSMENT

Point Sources

Discharges to surface water in the study unit 

include point source discharges with National Pollutant 

Discharge Elimination System (NPDES) permits and 

various nonpoint source discharges. The point source 

discharges are easily identified and quantified through 

records maintained by California state regulatory 

agencies.

Excluding hydropower facilities and fish 

hatcheries, there are 32 point source discharge sites in 

the study unit (fig. 9) with mean discharge rates greater

than 0.5 ft3/s. Of these 32 discharge sites, 18 are 

wastewater treatment plants, 7 are food-processing 

facilities, 3 are manufacturing facilities, 3 are oil- and 

gas-production facilities, and 1 is a sand and gravel 

mining facility. The amounts of discharge from each 

location are also shown in figure 9. Only five of these 

discharge sites average more than 10 ft /s:

Discharge Discharge,

site in tf/s

Modesto Wastewater Treatment Plant 39

Texaco Oil (near Bakersfield) 26

Visalia Wastewater Treatment Plant 19

Turlock Wastewater Treatment Plant 14

Merced Wastewater Treatment Plant 11

The largest cities in the study unit, Fresno and 

Bakersfield, discharge to oxidation ponds followed by 

application to adjacent land and do not have NPDES 

permits for discharging to surface water. The third 

largest city in the study unit, Stockton, discharges to the 

San Joaquin River in the Sacramento-San Joaquin 

Delta, outside of the study unit. The city of Modesto 

discharges to the San Joaquin River only in winter, as 

the wastewater is held in oxidation ponds and applied 

to land adjacent to the ponds during the rest of the year. 

The Turlock and Merced treatment plants discharge to 

the San Joaquin River through the Turlock Irrigation 

District drain lateral number 5 and Owens Creek, 

respectively. The Visalia and Texaco discharges are in 

the Tulare Basin (Kaweah and Kern rivers, 

respectively) and do not affect surface water in the San 

Joaquin Basin.

Nonpoint Sources

Nonpoint source discharges are difficult to 

identify and quantify because they do not have the 

same regulatory requirements as point source discharges. Nevertheless, in this section we will identify 

and, in some cases, quantify several types of nonpoint 

sources in the study unit, particularly in the San 

Joaquin Basin.

The nonpoint source information presented here 

includes fertilizer application and manure production 

in each county, distribution of dairies, acreage of 

subsurface agricultural drains (tile drains), and the 

locations and volumes of agricultural discharges to the 

lower San Joaquin River area (see fig. 10 for area). 

Estimated fertilizer application is based on total fertilizer sales in California, distributed to the county level

12 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins. California 1972-1990
121° 15' 121° 00'

37° 

45'

37° 

30'

37° 

15'

\

' ftiver

f West' 

^ Stanislaus 

^c Irrigation 

s . District

Mean irrigation season 

diversion rate, in cubic feet 

per second

A Less than 1

A 1-5

A 5-25

A Greater than 25

— — —— Study unit boundary

>

Patterson Water' 

District

Turlock Irrigation District lateral 5

Merced Riv£

10 MILES

10 KILOMETERS

projection: Albers. 

cm: 120°

1st parallel: 29°30' 

2nd parallel: 45°30'

digital data: U.S. Environmental Protection Agency, 1994

Figure 8. Agricultural diversions from lower San Joaquin River system, California.

by fertilized acreage in each county (Alexander and 

Smith, 1990). The estimated nitrogen and phosphorus 

fertilizer applications in each county are shown in 

figure 11 for 1965, 1970, 1975, 1980, and 1985 

(Alexander and Smith, 1990). Applications increased 

steadily from 1965 to 1980 and decreased in 1985. This 

pattern reflects the overall acreage in production during

this time within the study unit (California Department 

of Water Resources, 1987b).

The intensive agriculture in the San Joaquin 

Valley relies on relatively high applications of nitrogen 

and phosphorus fertilizers. The estimated amounts of 

fertilizer application shown in figure 11 rank high 

among counties in the nation (Alexander and Smith,

Environmental Framework for Water Quality Assessment 13
----/ '--\ 119° •

/: vA---

EXPLANATION 

Discharge type

1 Wastewater treatment

2 Manufacturing (food products)

3 Manufacturing (other)

4 Oil and gas production

5 Mining (sand and gravel)

Discharge amount, mean 

annual discharge, in 

cubic feet per second 

A Less than 1 

• 1 -5

5-25 

V Greater than 25

Study unit boundary

< !

fcv-- 7 ^ > ' r .'•' '

ev fif Merced, / -> f ^ C

'ar W* Al . X^ ; V V, >

fl «ar v; A!

37° t

-% A2^ 

J* Al

^ c-^^r / ^

40 MILES

40 KILOMETERS

Figure 9. Point source discharges in San Joaquin-Tulare Basins, California, study unit by type of discharge and amount of discharge.

1990). Fresno, Kern, Kings, and Tulare Counties rank San Joaquin, and Merced Counties rank 7, 8, 13, and

1 through 4, respectively, in nitrogen applications in 27, respectively.

1985, and San Joaquin and Merced Counties rank 6 and In 1987, manure produced in the study unit

13, respectively (see fig. 1 for county locations). Fresno contained approximately 137,000 tons of nitrogen and

and Kern Counties rank 1 and 2, respectively, in 

phosphorus applications in 1985, and Kings, Tulare,

30,000 tons of phosphorus (R.B. Alexander, U.S. 

Geological Survey, written cornmun., 1992). The

14 Nutrients and Suspended Sediment in Surface Water, San Joaquin -Tulare Basins, California, 1972-1990
37°45

121°00'

37C 

30

37° 

15'

37° 

00'

Turlock Irrigation 

District lateral 5

"A

^/fiver

Lower

San Joaquin 

River Basin

Stevinson

Newman

Gustine

___ EXPLANATION

| | Wildlife refuge or area 

within the Grasslands

—— - — Study unit boundary

————— Lower San Joaquin River 

Basin boundary

\

J 

\

r

San Luis 

Reservoir

A

Forebay r1 

\

10 MILES

10 KILOMETERS

Los Banos

\Camp 13 Dos Palos 

' Slough

^Panoche 

Drain

projection: Albers. 1st parallel: 29C 30' 

cm: 120° 2nd parallel: 45'30'

digital data: U.S. Environmental Protection Agency, 1994

Figure 10. Lower San Joaquin River and Grasslands area, California.

Environmental Framework for Water Quality Assessment 15
100,000

80

San Joaquin

Stanislaus

Merced Fresno

Madera Tulare

Kings

Kern

San Joaquin Merced Fresno

Stanislaus Madera Tulare

County in the San Joaquin-Tulare Basins

Kings

Kern

Figure 11. Estimated fertilizer applications of nitrogen and phosphorus in San Joaquin-Tulare Basins, California, study unit, by county, 

1965-1985.

counties producing the most nitrogen, in manure, in 

tons per year were Fresno (23,699), Tulare (23,143), 

Merced (21,644), and Stanislaus (20,170). Unlike 

estimates of fertilizer application, these county manure 

production quantities rank only 45, 47, 49, and 52, 

respectively, in the nation.

Information on the area! distribution of dairies in 

the study unit was provided by the California Regional

Water Quality Control Board (CRWQCB). The 

heaviest concentrations of dairies are in Tulare, 

Stanislaus, and Merced Counties. In 1991, these three 

counties had 217,000, 118,000, and 115,000 milk 

cows, respectively (U.S. Department of Agriculture 

and California Department of Food and Agriculture, 

1991). Waste-discharge regulations for dairies 

generally permit discharges to surface water only

16 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
during large storms. However, several unauthorized 

discharges are known to occur in the study unit, and the 

CRWQCB has identified several suspect waterways 

(James and others, 1989; California State Water 

Resources Control Board, 1990, 1991). Because these 

discharges are unauthorized, their magnitude is 

unknown.

The Grasslands area of the San Joaquin Basin 

drains to the San Joaquin River through Salt and Mud 

Sloughs (fig. 10). Subsurface agricultural drains were 

installed in the Grasslands area between 1950 and 1991 

(fig. 12) to relieve areas with shallow, saline water 

tables and to allow for continued agricultural 

productivity. The subsurface drainwater contains high 

levels of nitrates from either fertilizer applications or in 

soil derived from the Coast Ranges. In 1991, the total 

acreage drained by these subsurface drains was about 

58,500 acres (fig. 12).

Most agricultural discharges to the lower, perennial San Joaquin River and the lower reaches of the 

major east side tributaries are shown in figure 13 

(Kratzer and others, 1987; James and others, 1989). Of 

the 104 discharges shown, 87 are tailwater (surface

60

55

50

45

40

o" 

§ 35

X

^ 30

0)

o 

* 25

2

15

10

5

0 

1£

j ii MI

-

-

-

-

-

-

-

r i.m.iinrfiJtl-.ilm

J50 1<

I

I

H

i

j.

3(

i

)

i

P

i

i

-

_L

t

J.

1

1

1

1

1

r^

±

'•

L

J

\

i

-

37

'€

i

'(

E

i

i

)

r

i

F

i i

_LJ

*

—

1

nu

1

3i

i

;

i

i

3(

i

)

i j.

1 1

_L

. !

'

r^

1

1 r

9£

Figure 12. Total acres with subsurface agricultural drains in the 

Grasslands area, San Joaquin Valley, California, 1950-1991.

return flows) and operational spills of surface water 

only, 3 are subsurface agricultural drainage only, and 14 

are a combination of the above. Mean irrigation season

o

discharge is greater than 25 ft /s in five dis-charges: 

Salt Slough, Mud Slough, Orestimba Creek, Hospital 

and Ingram creeks, and Spanish Grant Drain. Except 

for Orestimba Creek, which is entirely surface 

drainage, these discharges are a combination of surface 

and subsurface agricultural drainage. During summer 

low-flow periods, these agricultural discharges account 

for most of the streamflow in the San Joaquin River.

Water Quality Problems Identified by the 

State of California

A water quality assessment of California water 

bodies was developed to report the condition of the 

state's water and to satisfy EPA reporting requirements 

(California State Water Resources Control Board, 

1990). In this assessment, the state classifies the water 

quality of the water bodies, or stretches of water bodies, 

as either good, intermediate, impaired, or unknown. 

The good designation means that the water body 

supports and enhances designated beneficial uses. An 

intermediate designation means that the water body 

generally supports beneficial uses with an occasional 

degradation of water quality. Water bodies were 

qualitatively designated as impaired if they were not 

reasonably expected to attain or maintain applicable 

water quality standards for beneficial uses based on the 

following criteria: (1) designated uses are not 

supported, (2) water quality impairment is moderate to 

severe, (3) designated use is compromised or limited,

(4) aquatic community is known to contain toxic substances in concentrations hazardous to human health,

(5) aquatic community is not fully supported or is 

severely stressed, (6) fish kills are frequent or toxicity 

tests show repeated acute or chronic toxicity, or (7) a 

numerical measurement exceeds a specified criterion or 

objective (California State Water Resources Control 

Board, 1990). The unknown designation is given to 

water bodies with inadequate data.

Water quality was designated as intermediate in 

927 miles (mi) of 20 streams and 56,143 acres of 19 

lakes in the study unit. The state also designated 362 mi 

of 13 streams in the study unit as impaired water bodies 

(fig. 14) (California State Water Resources Control 

Board, 1990). Parts of several water bodies in the study 

unit are impaired. These include the Kings, San 

Joaquin, Merced, Tuolumne, Stanislaus, and

Environmental Framework for Water Quality Assessment 17
121°00'

37° 

45'

N

37° 

30'

37° 

15'

Rive''

Creek %.

^ A .

'ver

Mean irrigation season 

discharge, in cubic feet 

per second 

A Less than 1 

A 1 -5 

A 5-25 

A Greater than 25 

—— — —— Study unit boundary

Turlock Irrigation District lateral 5

Spanish Grant Drain

A

A" A

A

Newman A± 

Slough /

r -j~~\ Merced Ri^tf 

-'"' l_-f i-,

10 MILES

10 KILOMETERS

\

Figure 13. Agricultural discharges to lower San Joaquin River system, California.

Mokelumne rivers, Salt and Mud sloughs, Orestimba 

Creek, and 8,224 acres of the Grasslands (fig. 14).

Environmental Settings

To describe water quality in terms of land 

effects, the study unit was divided into relatively 

homogeneous subunits on the basis of hydrology.

physiography, and geomorphology (fig. 15). The two 

generally distinct surface water basins—the San 

Joaquin Basin and the Tulare Basin—are divided into 

three major physiographic provinces: Coast Ranges, 

San Joaquin Valley, and Sierra Nevada. The valley area 

is analyzed in greatest detail in this report because 

most of the population and agriculture, and therefore, 

water use and activities affecting water quality, are

18 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
38'

SacramentoSan Joaquin Delta

EXPLANATION

| | San Joaquin Valley

I___I Wildlife refuge or area 

within the Grasslands

—— — —— Study unit boundary

————— Impaired part of waterbody

Map 

no.

i

2

3

4

5

6

7

8

9

10

11

12

13

14

Site name

Kings River (lower)

San Carlos River

Panoche Creek

San Joaquin River (lower)

Grasslands marshes

Salt Slough

Mud Slough

Merced River (lower)

Orestimba Creek

Turlock Irrigation District

lateral 5

Tuolumne River (lower)

Stanislaus River (lower)

Lone Tree Creek

Mokelumne River (lower)

Miles 'impaired1

30

1

1

100

8,224 acres

15

14

60

3

5

50

48

15

20

35

119'

40 MILES

40 KILOMETERS

Figure 14. Impaired water bodies in San Joaquin-Tulare Basins, California, study unit.

Environmental Framework for Water Quality Assessment 19
San

Coast Ranges 1

| West Side

Alluvial 1 Ba 

Fans 1 Dep

SAN JOAQUIN-TULARE BAS1 

STUDY UNIT

San Joaquin 1 I 

Vallev 1 Sierra Nevada • Coast Ranges

[NS | A

1 San Joaquin I I 

Valley | Sierra Nevada |

| East Side k \ West Side | | East Side ^

1 1

sin 1 Alluvial 1 Basin 1 

osits 1 Fans 1 Deposits 1

1

Alluvial 1 Basin 1 

Fans 1 Deposits 1

Figure 15. Environmental settings in San Joaquin-Tulare Basins, California, study unit: (A) Environmental settings (6) Locations of 

environmental settings.

located there. Most studies will be done in the valley of 

the San Joaquin Basin, specifically in the perennial 

reach of the San Joaquin River because (1) the 

perennial San Joaquin River is the only surface water 

outlet for the basin, (2) the water quality of the San 

Joaquin River influences water quality in the 

Sacramento-San Joaquin Delta, and (3) the Tulare 

Basin normally does not have a surface water outlet.

The San Joaquin Valley can be divided into the 

areas west and east of the valley trough, or depositional 

axis. The west and east sides can be further subdivided 

into alluvial-fan and basin deposit areas. Although the 

depositional axis of the valley has shifted during 

geologic time, the east side alluvial fans are dominated 

by sediments derived from the Sierra Nevada, and the 

west side alluvial fans are dominated by sediments 

derived from the Coast Ranges. The sediments in the 

basin deposits are a mixture from both Sierra Nevada 

and Coast Ranges sources, reworked and deposited in 

stream channels or shallow lakes and as overbank 

deposits in flood basins. The west side of the Tulare 

Basin valley is not subdivided because of the lack of 

any significant surface water flows.

The contrasting bedrock geology and chemical 

composition of the derived soils of the east and west 

sides of the valley have significant effects on water

quality. Low solubility of the quartz and feldspars that 

make up the bulk of the Sierra Nevada and the granitic 

soils derived from them results in runoff and snowmelt 

with low concentrations of dissolved solids. In 

contrast, the Coast Ranges are composed primarily of 

rocks and sediments of marine origin. The rocks and 

soils derived from the Coast Ranges contain high 

concentrations of trace elements, various nitrogencontaining compounds, and soluble salts including 

calcium, sodium, and magnesium sulfates.

LOWER SAN JOAQUIN RIVER BASIN, 1951-1990

The lower San Joaquin River Basin is defined 

here as the drainage basin of the perennial reach of the 

San Joaquin River from Bear Creek to Vernalis (figs. 1 

and 10). Most discussion of water quality in this report, 

including nitrate trends for 1951-1990, will focus on

^

this drainage area of 7,345 mi . This section provides 

some background on the lower San Joaquin River and 

changes that have occurred in the San Joaquin Basin 

between 1951 and 1990, relative to factors that affect 

nutrient concentrations.

Prior to development of the Delta-Mendota 

Canal in 1951, about 800,000 acres in the lower San 

Joaquin Basin were irrigated with local surface and

20 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
120(1

B

EXPLANATION

San Joaquin Basin 

CD Coast Ranges

San Joaquin Valley 

West side alluvial fans 

West side basin deposits 

East side alluvial fans 

East side basin deposits 

Sierra Nevada

Tulare Basin 

Coast Ranges 

San Joaquin Valley 

West side alluvial fans 

and basin deposits 

East side alluvial fans 

East side basin deposits 

Sierra Nevada

— - — Study unit boundary

Fresno <^t

40 MILES

40 KILOMETERS

Figure 15. Continued.

Lower San Joaquin River Basin, 1951-1990 21
ground water (table 2). Irrigated acreage increased to 

about 1 million acres by 1970 and has remained 

essentially at that level. Irrigation has become more 

efficient since 1951 with increasing use of surface 

return flow recovery systems, laser leveling, and other 

practices. Although no data are available back to 1951, 

we assume that increases in surface return flows due to 

increased irrigated acreage were offset by decreases in 

surface return flows due to increased irrigation 

efficiency and that surface return flows did not increase 

between 1951 and 1990.

In 1950, no subsurface agricultural drainage was 

being discharged to the lower San Joaquin River. By 

1990, the potential subsurface drainage reaching the 

river was about 66 ft3/s (table 2). Until 1985, much of 

this potential discharge to the river was used to flood 

waterfowl areas in the Grasslands (fig. 10) before being 

released to the river, and some nutrients were taken up 

by aquatic plants in the waterfowl areas. Since 1985,

virtually all of the subsurface drainage water has been 

discharged directly to the river due to concerns over the 

accumulation of trace elements (especially selenium) 

in the waterfowl areas.

On the basis of information in NPDES files, the 

amount of wastewater discharged from treatment 

plants to the lower San Joaquin River more than tripled 

from 1950 to 1990 (table 2). Although irrigated acreage 

increased 25 percent from 1950 to 1990, fertilizer 

application increased by about 500 percent for nitrogen 

and 285 percent for phosphorus. During the same 

period, the amount of nitrogen in manure increased by 

64 percent and the amount of phosphorus in manure 

increased by 66 percent (table 2).

The relative nutrient concentrations of the 

sources identified in table 2 are important for identifying the causes of concentration trends, the relation 

of concentrations to streamflow, and the possible 

sources of the loads that were unaccounted-for.

Table 2. Factors affecting nutrient concentrations in the lower San Joaquin River Basin, California, 1950,1970, and 1990

o

[~. approximately; acre-ft. acre-feet: ft /s. cubic feet per second: tons/yr. tons per year]

Factor 1950 1970 1990

Population

Total reservoir storage 1 

Irrigated acreage2 

Sources of irrigation water

Fertilizer application3 

Nitrogen 

Phosphorus

Manure production4 

Nitrogen 

Phosphorus

Wastewater treatment plant 

discharges5' 6

Subsurface agricultural drainage5'7

-215,000

0.5 million acre-ft

800,000 acres

San Joaquin. Merced, 

Tuolumne, and 

Stanislaus Rivers; 

ground water

8,500 tons/yr 

1,900 tons/yr

39,900 tons/yr 

10,200 tons/yr

~16ft3/s

-350,000

2.0 million acre-ft

1,000,000 acres

San Joaquin, Merced,

Tuolumne, and Stanislaus 

Rivers; Delta-Mendota 

Canal; ground water

33,900 tons/yr 

5,200 tons/yr

47.300 tons/yr 

12,700 tons/yr

-43 ft3/s

-47 ft3/s

623,000

6.6 million acre-ft 

-1.000.000 acres

San Joaquin, Merced,

Tuolumne, and Stanislaus 

Rivers; Delta-Mendota 

Canal: ground water

50,900 tons/yr 

7,300 tons/yr

65,600 tons/yr 

16,900 tons/yr

-58 ft3/s

-66 ft3/s

'From California Department of Water Resources 1984, 1987b, 1994a; California State Water Resources Control Board, 1987.

2From California Department of Water Resources 1960, 1983, 1994a; Wall and others, 1981.

3From Alexander and Smith, 1990, and U.S. Environmental Protection Agency, 1990.

4From U.S. Department of Agriculture and California Department of Food and Agriculture, 1991.

-^Expressed as average discharge rates for the entire year. These rates vary considerably throughout the year.

6From information in National Pollutant Discharge Elimination System files, cities of Modesto, Turlock, Merced, and Atwater.

7Assuming a drainage factor of 0.7 acre-feet per acre (Kratzer and others, 1987) for the area of tile drains shown in figure 12. (Harley

Davis, California Regional Water Quality Control Board, Central Valley Region, written commun., 1992) and other reaches of the San

Joaquin River (Kratzer and others, 1987).

22 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Approximate concentrations of nitrate, ammonia, 

orthophosphate, and total phosphorus are given in 

table 3 for dairy runoff, wastewater treatment plant 

effluent, tail water runoff from fertilized fields, and 

subsurface agricultural drainage in the lower San 

Joaquin River Basin. Dairy runoff and wastewater 

treatment plant effluent have high concentrations of 

phosphorus and ammonia relative to tailwater and 

subsurface drainage. Nitrate concentrations are highest 

in subsurface drainage.

The nutrient concentrations shown in table 3 for 

wastewater treatment plant effluent in the lower San 

Joaquin River Basin represent concentrations measured 

in the late 1980s. Since that time, the city of Modesto 

wastewater treatment plant improved aeration in their 

oxidation ponds and expanded their land application 

area. These changes resulted in the improved conversion of ammonia to nitrate and a reduction in phosphorus levels. Median ammonia concentrations in the 

Modesto discharge prior to 1990 were 10 to 20 mg/L; 

in 1994 the median was less than 1 mg/L as N (John 

Amstutz, city of Modesto, California, written 

commun., 1994). Median ammonia concentrations in 

the city of Turlock discharge were 8.2 mg/L as N in 

1991. Median nitrate concentrations in the Modesto 

discharge increased from 1 to 4 mg/L as N prior to 1990 

to about 11 mg/L as N in 1994. Prior to 1989, median 

total phosphorus concentrations in the Modesto 

discharge were 6 to 12 mg/L; after 1989 they were 1 to 

2 mg/L as P. Thus, the recent improvements in wastewater treatment in the lower San Joaquin River Basin 

have resulted in the conversion of ammonia to nitrate 

and the reduction of phosphorus in wastewater 

treatment plant effluent. However, these improvements

occurred around 1990 and do not affect the nutrient 

contributions from wastewater treatment plants during 

1951-1990.

SOURCES OF DATA

Compilation of Data

Water quality data for surface water in the study 

unit for 1972-1990 were compiled from the National 

Water Information System (NWIS) of the USGS and 

the STOrage and RETrieval (STORET) database of the 

EPA. Additional data were entered into the STORET 

database stored on NWIS at the USGS, Sacramento 

office. Sources of additional data include DWR data 

(1988-1990) that had not been entered into STORET 

and suspended sediment data collected by the 

CRWQCB, U.S. Soil Conservation Service, and 

Merced, Modesto, and Turlock Irrigation Districts 

(Westcot and Belden, 1989; U.S. Soil Conservation 

Service, 1989).

In addition to nutrients and suspended sediments, 

retrieved parameters included streamflow, pH, specific 

conductance, dissolved oxygen, total hardness, total 

organic carbon, and chlorophyll a. Nutrient parameter 

codes changed during the study period due to changes 

in laboratory methods or reporting methods (for 

example, nitrate as N versus nitrate as NO3 ), and some 

parameter codes were combined for the long-term 

analysis of nutrient concentrations. Suspended 

sediment codes also were combined to merge the 

STORET suspended solids data with the NWIS

Table 3. Approximate nutrient concentrations from major sources in the lower San Joaquin River Basin, California, during the late 1980s 

[Nutrient concentrations in milligrams per liter as nitrogen or phosphorus; —, no data]

Source

Dairy runoff1

Wastewater treatment plant effluent2 

Tailwater (surface return flow)3

Subsurface agricultural drainage4

Nitrate

0.2

3 

6

25

Ammonia

247

15 

0.1

0.2

Orthophosphate

—

2 

0.2

0.05

Total phosphorus

90

4 

0.4

0.1

Average values from unpublished data for dairy pond water in the central valley of California (Harley Davis, California Regional Water 

Quality Control Board-Central Valley Region, written commun., 1995).

2Flow-weighted averages of median concentrations from city of Turlock (Central Valley Regional Water Quality Control Board, 

unpublished National Pollutant Discharge Elimination System files, 1991) for ammonia (calendar year 1991) and city of Modesto 

unpublished monitoring data (John Amstutz, Modesto Public Works Department, written commun., 1994) for all nutrients (water years 

1987 and 1989).

3Based on median of monthly average data for Orestimba Creek during 1992 and 1993 irrigation seasons (tailwater with some operationalspill water) (U.S. Geological Survey unpublished data, 1992 and 1993).

4Based on California Department of Water Resources (1975).

Sources of Data 23
suspended sediment data. The effect of this 

combination is discussed in the section "Quality 

Assurance and Quality Control." For nutrients, the only 

combinations of significance were nitrate and total 

nitrogen. For orthophosphate, ammonia, total 

phosphorus, and total kjeldahl nitrogen, codes with 

different reporting methods were merged.

For nitrate and total nitrogen, the combinations 

involved substituting different parameters. If dissolved 

nitrate values were not available, values for dissolved 

nitrate plus nitrite, total nitrate, or total nitrate plus 

nitrite were substituted, in that order. Likewise, for the 

total nitrate plus nitrite component of total nitrogen, 

values for dissolved nitrate plus nitrite, total nitrate, or 

dissolved nitrate were substituted, in that order. In most 

cases, these substitutions had no significant effect on 

results.

Screening of Data

The initial database contained 120 NWIS sites 

and 807 STORET sites with nutrient and(or) 

suspended sediment data. Most of the STORET sites 

were sampled by DWR, BOR, USGS, or the CRWQCB 

(table 4). Of the 927 sites, 859 reported nutrient 

samples and 413 reported suspended sediment 

samples. This initial database included 13,753 nutrient 

samples and 9,113 suspended sediment samples.

Several categories of sites were removed from 

the initial database to create a final, screened NAWQA 

database (tables 4 and 5) that would represent the 

ambient surface water conditions in the study unit (in 

each subbasin) and at each sampled site. The removed 

sites include (1) major water supply canals, (2) small, 

individual agricultural drains and evaporation ponds 

(larger drainage systems were kept in the database), 

(3) wastewater treatment plant effluents and sites just 

downstream of effluent discharges, (4) lakes and 

reservoirs, (5) urban runoff sites, (6) sites that have 

inadequate location description, (7) duplicate sites in 

STORET database, and (8) duplicate sites between the 

NWIS and STORET databases. In total, 495 sites 

containing 8,296 nutrient samples, and 2,896 

suspended sediment samples were removed from the 

initial database (table 5).

Many water supply canals were removed from 

the initial database because the water in these canals 

generally does not represent surface runoff from the 

study unit, but is water that has been artificially

transported several miles from its source. Mostly DWR 

data were removed, including data on several sites 

along the California Aqueduct and the Delta-Mendota 

Canal (fig. 14), as well as several smaller irrigationsupply canals. The California Aqueduct and DeltaMendota Canal originate in the Sacramento-San 

Joaquin Delta, downstream of the study unit.

The BOR and DWR have monitored many 

subsurface agricultural drains and evaporation ponds in 

the study unit. These sites represent the quality of 

shallow ground water in relatively small areas; 

therefore, they were deleted from the initial database. 

However, several larger drainage systems collect both 

surface and subsurface agricultural drainage. This 

drainage flows to the San Joaquin River as surface 

water and has a major effect on the water quality of the 

San Joaquin River; therefore, these systems were 

included in the final database. These include the San 

Luis Drain, Panoche Drain, Camp 13 Slough, Salt 

Slough, and Mud Slough (fig. 10).

Sites dominated by wastewater treatment plant 

effluent and by urban runoff were not common in the 

initial database. The four USGS urban-runoff sites in 

the initial database were sampled frequently for 

nutrients and suspended sediment. However, these 

urban-runoff sites were removed from the initial 

database because their small flows discharge to the 

upper San Joaquin River, which generally does not 

flow into the lower, perennial San Joaquin River.

Water quality in lakes and reservoirs is difficult 

to compare with water quality in streams because of the 

effects of water residence time; therefore, lake and 

reservoir sites were removed from the database. This 

removal greatly reduced the number of DWR, EPA, 

and U.S. Army Corps of Engineers (COE) sites and the 

number of COE samples in the final database. The 

removal of unidentified sites—mostly BOR, EPA, 

and California Department of Health Services 

sites—reduced the number of nutrient samples.

Some entries in the STORET database were 

duplicates, or almost duplicates. If identical sites with 

identical data were reported by different agencies, the 

original data and collecting agency were kept in the 

database and the duplicate data were deleted. This was 

common for CRWQCB and DWR data, when identical 

sites or almost identical sites with different data were 

reported by different agencies. These sites were 

combined and assigned to the agency with the most 

data (tables 4 and 5); the samples were apportioned

24 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Table 4. Number of sites and samples for nutrients and suspended sediments in initial and final databases, 1972-1990, by agency, San 

Joaquin-Tulare Basins, California, study unit

Agency Database

Bureau of Reclamation

California Department of Health Services

California Department of Water Resources

California Regional Water Quality Control

Board

Merced Irrigation District

Modesto Irrigation District

Turlock Irrigation District

U.S. Army Corps of Engineers

U.S. Environmental Protection Agency

U.S. Forest Service

U.S. Geological Survey

Total

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Initial

Final

Nutrients

147

27

49

5

362

227

63

0

0

0

0

0

0

0

30

8

86

17

3

3

119

82

859

369

Number of sites

Suspended 

sediment

10

3

0

0

184

109

95

45

5

5

3

3

6

6

30

8

1

0

0

0

79

56

413

235

Number of samples

Total 1

148

28

49

5

364

227

112

45

5

5

3

3

6

6

30

8

87

17

3

3

120

85

927

432

Nutrients

1,444

366

161

36

8,045

2,873

728

0

0

0

0

0

0

0

626

345

282

170

18

18

2,449

1,649

13,753

5,457

Suspended 

sediment

11

4

0

0

2,300

995

939

587

24

24

3

3

18

18

440

270

6

0

0

0

5,372

4,316

9,113

6,217

Sites with nutrient and(or) suspended sediment data.

among the agencies on the basis of the number of 

samples. All nutrient data reported by the CRWQCB 

also were entered into STORET by DWR, and these 

duplicates were deleted.

Duplicate sites and data also occur between the 

STORET and NWIS databases. During the 1970s, 

DWR data often were entered into both the STORET 

and NWIS databases by DWR and USGS, respectively. These sites and samples were removed from the 

USGS list of sites and samples in the database. At sites 

sampled by both DWR and USGS, but primarily by 

USGS, the DWR sites were deleted, and the DWR data 

were combined with the USGS data for the site. The

best example of this is the San Joaquin River near 

Vernalis site, which has an abundance of USGS data. 

Of the 542 DWR nutrient samples reported for this site, 

224 were duplicates and, therefore, were deleted.

The final, screened NAWQA database is 

summarized in table 4. This database, discussed in 

detail in the section "Description of Available Data," 

contains nutrient and(or) suspended sediment data for 

432 sites including 5,457 nutrient samples and 6,217 

suspended sediment samples. The DWR and USGS 

collected most of the data in the final database, 

although the CRWQCB contribution of suspended 

sediment data is significant.

Sources of Data 25
Table 5. Number of sites and samples removed from initial database, San Joaquin-Tulare Basins, California, study unit

[STORET, STOrage and RETrieval database of the U.S. Environmental Protection Agency; NWIS, National Water Information System of 

the U.S. Geological Survey]

Removal category

Agency Water 

supply 

canals

... . . . Unknown 

. . , Waste- Lakes , .. ... n .. . Agncul- . ... sites with Duplicate * , water and Urban . . . .•" . tural t _ „ inadequate sites in 

. . treatment reser- runoff 7. o-rnnrT drains , t . location STORET plants voirs . . t. . 

r descriptions)

Duplicate 

sites 

between 

NWIS and 

STORET

Totals

Number of sites with nutrient and(or) suspended sediment samples

Bureau of Reclamation

California Department of Health Services

California Department of Water Resources

California Regional Water Quality Control Board

U.S. Army Corps of Engineers

U.S. Environmental Protection Agency

U.S. Geological Survey

Totals

13

0

14

0

0

0

2

29

73

0

42

0

0

0

6

121

0

11

5

0

0

0

1

17

0

12

52

1

14

41

3

123

0

0

0

0

0

0

4

4

27

21

5

2

0

28

0

83

6

0

8

64

8

1

0

87

1

0

11

0

0

0

19

31

120

44

137

67

22

70

35

495

Number of nutrient samples

Bureau of Reclamation

California Department of Health Services

California Department of Water Resources

California Regional Water Quality Control Board

U.S. Army Corps of Engineers

U.S. Environmental Protection Agency

U.S. Geological Survey

Totals

47

0

2,106

0

0

0

66

2,219

791

0

2,529

0

0

0

17

3,337

0

29

22

0

0

0

13

64

0

60

159

0

281

41

15

556

0

0

0

0

0

0

396

396

211

36

5

0

0

70

0

322

29

0

25

728

0

1

0

783

0

0

326

0

0

0

293

619

1,078

125

5,172

728

281

112

800

8,296

Number of suspended sediment samples

Bureau of Reclamation

California Department of Health Services

California Department of Water Resources

California Regional Water Quality Control Board

U.S. Army Corps of Engineers

U.S. Environmental Protection Agency

U.S. Geological Survey

Totals

0

0

383

0

0

0

60

443

5

0

473

0

0

0

0

478

0

0

11

0

0

0

0

11

0

0

40

1

170

0

0

211

0

0

0

0

0

0

349

349

2

0

0

19

0

6

0

27

0

0

14

332

0

0

0

346

0

0

384

0

0

0

647

1,031

7

0

1,305

352

170

6

1,056

2,896

ANALYSIS TECHNIQUES

Statistical software programs used to analyze the 

database for this report include PT2, ESTIMATOR, 

Statistical Analysis System (SAS), and STATIT. The 

PT2 and ESTIMATOR (Cohn and others, 1989) 

programs were developed by the Systems Analysis 

Branch of the USGS. PT2 is linked with the 

ARC/INFO Geographic Information System software, 

and results from PT2 can be presented graphically with 

a map of an area. The PT2 program was used to show

sites with data, produce boxplots, analyze trends, and 

present scatterplots and plots of flow versus 

concentration. Two statistical programs—SAS and 

STATIT—were used to test whether concentrations at 

different sites were significantly different. 

ESTIMATOR was used for load calculations.

The trend-analysis program in PT2 performs a 

seasonal Kendall test using an alpha level of 5 percent. 

To use PT2 for trend analysis at a site, (1) the data must 

have spanned most of the period of analysis, and (2) for 

a given seasonal frequency, the beginning and ending

26 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
portions of the record must have sufficient data so that 

most of the possible number of pairwise comparisons 

made in the seasonal Kendall test were present for most 

of the seasons (Lanfear and Alexander, 1990). The PT2 

program initially tries to run a monthly seasonal 

Kendall test. If there are not enough data, it tries a 

bimonthly test and finally a quarterly test.

Constituent concentrations commonly are 

related to streamflow, and trend tests generally are done 

to study changes in concentrations resulting from 

effects other than streamflow. Thus, PT2 uses flow 

adjustment procedures to remove the effect of streamflow variations on concentration trends. PT2 adjusts for 

flow with a LOcally WEighted Scatterplot Smoothing 

(LOWESS) technique. LOWESS is a robust smoothing 

technique that describes the relationship between y and 

x without assuming linearity or normality of the 

residuals (Helsel and Hirsch, 1992). It describes the 

data pattern whose form depends on the smoothing 

coefficient. A smoothing coefficient of 0.5 was used for 

all LOWESS applications in this study. PT2 requires at 

least 25 samples with streamflow values to adjust for 

flow. If a trend test cannot be run with flow adjustment, 

then a concentration-only test is done.

Version 92.11 of ESTIMATOR was used for this 

study; it uses standard output files of streamflow and 

constituent concentration from NWIS as input data 

files. These data are used to develop a relation between 

streamflow and concentration for calculating loads. 

The ESTIMATOR program first runs a calibration 

period for flows and concentrations (Cohn and others, 

1989). Only concentrations with associated streamflows (instantaneous or daily mean) are used in the 

calibration process. For the load-estimation period, 

there must be a streamflow value for every day. The 

ESTIMATOR program provides estimated daily, 

monthly, or annual loads with standard errors and 

standard errors of prediction. Thus, confidence 

intervals for the load estimates can be calculated.

The sign test was used to determine if NWIS and 

STORET data pairs are significantly different. The sign 

test of the STATIT program determines if x is generally 

larger (or smaller, or different) than y for data pairs 

(x{ , vO i=l,...n. It is a fully nonparametric test and may 

be used regardless of the distribution of the differences 

(Helsel and Hirsch, 1992).

In these calculations, Tukey's test was used to 

determine if nutrient and suspended sediment 

concentrations are significantly different at different 

sites. Tukey's test of the SAS statistical program was

run on the ranks of the concentration data. This 

provides a nonparametric multiple comparison of the 

medians of the ranks (Helsel and Hirsch, 1992).

QUALITY ASSURANCE AND QUALITY CONTROL

Quality assurance (QA) and quality control (QC) 

programs of the DWR, BOR, and USGS were 

evaluated. Evaluations include methods of field 

collection, laboratory analysis, and reporting of the 

data. Following the evaluations of QA/QC programs, 

the potential biases introduced by different field and 

laboratory methods are evaluated as they relate to the 

results of data analyses presented in this report.

The DWR began a comprehensive QA/QC 

program in 1988 (California Department of Water 

Resources, 1994b). This program had little impact on 

the DWR data collected and analyzed during the study 

period of this report (1972-1990). All surface water 

samples collected by DWR during the study period 

were grab samples. These samples were collected from 

only one point in the stream cross-section, whereas 

width- and depth-integrated samples were collected 

from throughout the stream cross-section. Most DWR 

samples were analyzed at the DWR Bryte laboratory, 

although other contract labs were used on occasion. 

Although the Bryte laboratory currently has a QA/QC 

program (California Department of Water Resources, 

1994c), it is difficult to evaluate the QA/QC procedures 

that existed for most of the study period. DWR data 

collected prior to 1988 were obtained through 

STORET. DWR data collected after 1988 were not in 

STORET but were obtained directly from DWR by 

computer tape.

Prior to 1984, the BOR Sacramento office did 

not have a comprehensive QA/QC program. All surface 

water samples collected by BOR were grab samples. 

USGS review of nutrient analyses by the BOR 

Sacramento laboratory (M.O. Fretwell, M.J. Fishman, 

and R.T. Iwatsubo, U.S. Geological Survey, written 

commun., 1984) found that organic nitrogen and 

phosphorus were digested by nonstandard procedures. 

As a result, the reported results for total nitrogen and 

total phosphorus were likely to be biased low.

After 1984, the BOR Sacramento office 

collected primarily width- and depth-integrated 

samples for surface water (Bureau of Reclamation, 

1993). The improvements recommended by the USGS 

review resulted in a QA/QC program that included

Quality Assurance and Quality Control 27
better documentation of methods, better chain-ofcustody records for samples, and 25 percent of the total 

samples were collected for QC. The QC samples 

included 10 percent duplicates, 10 percent spikes, and 

5 percent blanks. Thus, BOR data since 1984 should be 

directly comparable to USGS data. BOR data for the 

entire study period were retrieved from STORET.

Details on the general QA/QC program of the 

USGS are given by Fishman and Friedman (1989), 

Friedman and Fishman (1989), and Peart and Thomas 

(1983). Most USGS surface water samples are width 

and depth integrated. Most USGS data evaluated in this 

study were analyzed at the National Water Quality 

Laboratory (NWQL) in Denver and were entered into 

both NWIS and STORET. During the study period, the 

QA/QC program of the NWQL included chain-ofcustody records for samples, documentation of 

methods, and at least 15 percent QC samples.

Despite the attention to QA/QC, there were 

analytical problems for USGS nutrient analyses during 

the study period. From 1973 until May 1990, the 

digestion step of the phosphorus method at the NWQL 

was incomplete for samples with high concentrations 

of suspended sediment (D.A. Rickert, Office of Water 

Quality, U.S. Geological Survey, written commun., 

1992), and the reported values for orthophosphate and 

total phosphorus probably are biased low. A study of 

QA records for the NWQL for total and dissolved 

phosphorus, ammonia, and Kjeldahl nitrogen indicated 

an apparent positive bias (consistently high readings 

compared to standards) for water years 1980 and 1981 

(Alexander and others, 1993). This positive bias affects 

the reported values of orthophosphate, total phosphorus, ammonia, and total nitrogen. However, a comparison of methods used by USGS for nutrient analyses 

during 1965-1982 showed no significant differences 

among the methods (Friedman and Fishman, 1989).

Historical data from STORET could be biased 

due to the preponderance of grab samples. For reasonably well-mixed streams, a grab sample usually is 

sufficient for dissolved species (M.O. Fretwell and R.T. 

Iwatsubo, U.S. Geological Survey, written commun., 

1984; Martin and others, 1992). However, grab samples are usually biased low for suspended sediment and 

the particulate (suspended) fraction of nutrient species. 

This bias would be expected with all non-USGS data, 

except for BOR data collected after 1984.

To evaluate the effects of different field and 

laboratory methods, NWIS and STORET data were 

compared for nitrate, ammonia, total nitrogen, orthophosphate, total phosphorus, and suspended sediment

at the San Joaquin River near Vernalis site (fig. 16). 

These comparisons include only data collected within 

one day of each other. This is the only site in the study 

area with the overlapping NWIS and STORET data 

needed for this comparison. The NWIS and STORET 

data for the nutrient species are not significantly 

different (at the 95-percent confidence level) on the 

basis of the nonparametric sign test. The NWIS 

suspended sediment values are significantly greater 

(p<0.0001) than the STORET suspended solids values 

and the median difference between the NWIS and 

STORET values at Vernalis was 24 mg/L. However, for 

this report, the term "suspended sediment" will be used 

to include suspended solids.

Biases in the NAWQA database primarily affect 

use of the data for trend analyses and load calculations. 

However, the bias affects boxplots of suspended sediment concentrations. The high bias in USGS data for 

orthophosphate, total phosphorus, ammonia, and total 

nitrogen during water years 1980 and 1981 was 

avoided in trend analysis. The mixing of NWIS and 

STORET data for trend analysis of suspended 

sediment concentrations could lead to inappropriate 

trend conclusions. Load calculations of total 

phosphorus using either NWIS or STORET data 

should be considered as minimum estimates. Load 

calculations and boxplots for suspended sediments 

using primarily STORET data also should be 

considered as minimum estimates.

DESCRIPTION OF AVAILABLE DATA

Timing and Location of Sampling

Prior to screening, nutrient and(or) suspended 

sediment data were available for 927 sites in the study 

unit. The removal of duplicate sites, individual 

subsurface agricultural drains, treatment plant 

effluents, water supply systems, lakes, urban runoff 

sites, and unidentified sites reduced this to 432 sites in 

the final NAWQA database. Of these sites, 369 had at 

least one sample analyzed for nutrients between 1972 

and 1990, and 235 had at least one sample analyzed for 

suspended sediment (fig. 17). Data analysis in this 

report is limited to 49 long-term water quality 

monitoring sites (fig. 18, table 6). These sites are 

relatively current (sampled since 1985), and either have 

30 or more nutrient or suspended sediment samples or 

have special spatial importance. Several of these sites 

in the lower San Joaquin River Basin were primarily 

sampled during 1985-1988 as part of either a USGS

28 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
3.0

2.0

1.0

A ' ' 

A Nitrate (milligrams per liter as nitrogen)

0.5 1.0 1.5 2.0 2.5

0.6

CO 

.0 

OS

CO

B Ammonia (milligrams per liter as nitrogen)

D

4.0

2.0

C Total nitrogen (milligrams per liter as nitrogen)

D

n

n D

3.0

1.0 2.0 

STORE! Database

3.0 4.0

Figure 16. Comparison of nutrient and suspended-sediment data from the National Water Information System (NWIS) of the U.S. Geological 

Survey and the STOrage and RETrieval (STORET) database of the U.S. Environmental Protection Agency for San Joaquin River near Vernalis, 

California, 1972-1990. The null hypothesis is that the median of NWIS data equals the median of STORET data.

Description of Available Data 29
0.3

0.2

- D Orthophosphate (milligrams per liter as phosphorus) D

E Total phosphorus (milligrams per liter as phosphorus)

0.2 0.4 0.6

350

300

200

100

F Suspended sediment (milligrams per liter)

D

D

0.8

100 200 

STORE! Database

300 350

Figure 16. Continued.

30 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
500

400

CO

I 300

"o

(5

.a 

E 

.i 200

100

347

I——• STORET

wm NWIS

287

179

Sites with Sites with 

nutrient and/or nutrient 

suspended sediment samples 

samples

Sites with

suspended sediment 

samples

Long term 

sites

7,000

6,000

5,000

4,000

3,000

2,000

1,000

0

B

Nutrient

samples

(At all sites)

Suspended 

sediment 

samples

(At all sites)

Nutrient

samples at

long term sites

Suspended

sediment

samples at

long term sites

Figure 17. Numbers of sites and samples for nutrients and suspended sediment in the final National Water-Quality Assessment database, 

1972-1990, San Joaquin-Tulare Basins, California, study unit. National Water Information System (NWIS) of the U.S. Geological Survey; 

STOrage and RETrieval (STORET) database of the U.S. Environmental Protection Agency.

Description of Available Data 31
EXPLANATION

I | San Joaquin Valley 

4 A NWIS site and number

24 v STORET site and number 

Note: See table 6 for site r

— — —— Study unit boundary

names

40 MILES 

40 KILOMETERS

Figure 18. Long-term water quality monitoring sites in San Joaquin-Tulare Basins, California, study unit. National Water Information System 

(NWIS) of the U.S. Geological Survey; STOrage and RETrieval (STORET) database of the U.S. Environmental Protection Agency

32 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Table 6. Site and basin characteristics of long-term stream water quality sampling sites, San Joaquin-Tulare Basins, California, study unit

[Site ID: unique number for each site. Fifteen digit numbers are based on the geographic location of the site, beginning with the latitude and 

longitude. Eight digit numbers refer to frequently sampled sites along a major stream; the number is assigned in downstream order. 

Acronyms: BOR, Bureau of Reclamation; COE, U.S. Army Corps of Engineers; CRWQCB, California Regional Water Quality Control 

Board, Central Valley Region; DWR, California Department of Water Resources; USGS, U.S. Geological Survey; ft, foot; mi, mile; mi2, 

square mile. See figs. 6, 15 and 18]

Site No. Site name (site ID) Altitude Drainage Environmental 

(ft) area (mi2 ) setting

Major land use1 (Anderson Collecting 

Level II) agency2

1 Kern River at Kernville (111 87000)

2 Kern River below Isabella Dam 

(353830118284801)

3 Kern River near Bakersfield 

(352636118513001)

4 Kings River below North Fork, near 

Trimmer (11218500)

5 Kings River below Pine Flat Dam 

(364948119200601)

6 Kings River below Peoples Weir 

(362912119321201)

7 Tule River near Springville 

(360542118501201)

8 Tule River below Success Dam 

(360324118552401)

9 Kaweah River at Three Rivers 

(362636118540601)

10 Kaweah River below Terminus Dam 

(362448119004201)

Tulare Basin

2,622 1,027 Sierra Nevada

2,435 2,074 Sierra Nevada/reservoirs

Forest—evergreen USGS, DWR 

Forest—evergreen DWR, COE

581 2,406 Sierra Nevada/reservoirs Forest—evergreen DWR

942 1,342 Sierra Nevada Forest—evergreen USGS, DWR, 

COE

557 1,545 Sierra Nevada/reservoirs Forest—evergreen DWR, COE

279 1,742 San Joaquin Valley, east 

side/alluvial

680 247 Sierra Nevada

Agriculture—orchards DWR, USGS 

and vineyards

Forest—evergreen DWR, COE

536 393 Sierra Nevada/reservoirs Forest—evergreen

810 418 Sierra Nevada Forest—evergreen

DWR, COE, 

USGS

DWR, COE

495 561 Sierra Nevada/reservoirs Forest—evergreen DWR, USGS

11 San Joaquin River south fork at Mono Hot 

Springs (371830118574201)

12 San Joaquin River below Kerckhoff 

Powerhouse(370445119333601)

13 San Joaquin River below Friant Dam 

(365900119432401)

14 San Joaquin River near Mendota 

(364836120223601)

15 Fresno River below Hidden Dam 

(370548119532401)

16 San Joaquin River near Stevinson 

(11260815)

17 Panoche Drain near Dos Palos 

(365524120411802)

San Joaquin Basin

6,949 184 Sierra Nevada

564 1,480 Sierra Nevada

150

384

63

141

Forest—evergreen DWR, USGS

Forest—evergreen DWR, USGS

295 1,676 Sierra Nevada/reservoirs Forest—evergreen DWR

(3 ) (3 ) Agriculture—cropland DWR, USGS

and pasture

258 Sierra Nevada/reservoirs Forest—evergreen DWR, COE

4818 S an Joaquin River

integrator site

5 66 San Joaquin Valley, west 

side/alluvial

Agriculture—cropland USGS, DWR, 

and pasture BOR

Agriculture—cropland DWR 

and pasture

Description of Available Data 33
Table 6. Site and basin characteristics of long-term stream water quality sampling sites, San Joaquin-Tulare Basins, California, study 

unit—Continued_____________________________________________________

Major land use1 (Anderson Site No. Site name (site ID) Altitude Drainage 

(ft) area (mi2)

Environmental 

setting Level II)

Collecting 

agency2

69 San Joaquin Valley, west Agriculture—cropland DWR

side/alluvial and pasture

7473 San Joaquin Valley, west Agriculture—cropland USGS, DWR,

side/alluvial and pasture BOR

18 Camp 13 Slough near OroLoma 131 

(365630120451802)

19 Salt Slough near Stevinson (11261100) 65

20 San Joaquin River at Fremont Ford Bridge 56

(371836120554204)

4 1,329 San Joaquin River 

integrator site

Agriculture—cropland DWR, USGS, 

and pasture BOR

21 Mud Slough near Gustine (11262900) 72 7473 San Joaquin Valley, west Agriculture—cropland USGS, BOR 

side/alluvial and pasture

22 Merced River at Happy Isles Bridge 4,020 

(11264500)

23 Merced River near Briceburg (11268200) 1,194

310

181 Sierra Nevada Forest—evergreen USGS, DWR

24 Merced River below Merced Falls 

(373115120195501)

25 Merced River at Milliken Bridge 

(372142120510001)

34 San Joaquin River near Grayson 

(373348121090601)

691 Sierra Nevada Forest—evergreen 

1,062 Sierra Nevada/reservoirs Forest—evergreen

63

26 Merced River near Stevinson (11272500) 55

27 San Joaquin River near Newman 49 

(11274000)

28 Orestimba Creek at Highway 33 105 

(372236121032401)

29 Orestimba Creek at River Road 50 

(372520121000901)

30 Spanish Grant Combined Drain 45 

(372608121015901)

31 San Joaquin River near Patter son 35

(11274570)

32 Olive Avenue Drain (373027121051501) 40

33 Del Puerto Creek at Vineyard Road 88 

(373220121072201)

25

35 Grayson Road Drain (373343 121 102701) 40

36 Tuolumne River at Tuolumne Meadows 8,700 

(375242120173601)

1,3 62 S an Joaquin Valley, east 

side integrator site

1,394 S an Joaquin Valley, east 

side integrator site

43,329 San Joaquin River 

integrator site

87 San Joaquin Valley, west 

side/alluvial

8 11 San Joaquin Valley, west 

side/alluvial

822 San Joaquin Valley, west 

side/alluvial

43,736 San Joaquin River 

integrator site

8 San Joaquin Valley, west 

side/alluvial

8 8 San Joaquin Valley, west 

side/alluvial

44,035 San Joaquin River 

integrator site

4 San Joaquin Valley, west

side/alluvial 

75 Sierra Nevada

Agriculture—orchards 

and vineyards

Agriculture—orchards 

and vineyards

Agriculture—cropland 

and pasture

Agriculture—cropland 

and pasture

Agriculture—cropland 

and pasture

Agriculture—cropland 

and pasture

Agriculture—cropland 

and pasture

Agriculture—orchards 

and vineyards

Agriculture—orchards 

and vineyards

Agriculture—cropland 

and pasture

Agriculture—cropland

and pasture 

Forest—evergreen

USGS, DWR 

DWR, USGS

DWR, USGS

USGS

USGS

DWR, USGS

CRWQCB

CRWQCB

USGS, DWR

CRWQCB

CRWQCB

DWR

CRWQCB 

DWR

34 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Table 6. Site and basin characteristics of long-term stream water quality sampling sites, San Joaquin-Tulare Basins, California, study 

unit—Continued

Site No. Site name (site ID) Altitude

(ft)

Drainage Environmental 

area (mi2) setting

Major land use1 (Anderson Collecting 

Level II) agency2

37 Tuolumne River at LaGrange Bridge 

(374000120274201)

3 8 Tuolumne River at Modesto (11290000)

39 Tuolumne River at Tuolumne City 

(373612121080001)

40 Ingram Creek at River Road 

(373601121132701)

41 Hospital Creek at River Road 

(373638121134301)

42 San Joaquin River at Maze Road 

(11290500)

170 1,542 Sierra Nevada/reservoirs Forest—evergreen DWR, USGS

40

28

52

49

17

43 Stanislaus River Middle Fork at Dardanelle 6,326 

(382030119492401)

44 Stanislaus River below Goodwin Dam 253 

(375106120381201)

45 Stanislaus River at Ripon (113030000) 40

46 Stanislaus River at Koetitz Ranch 25 

(374200121101201)

47 San Joaquin River near Vernalis 13 

(11303500)

48 Mokelumne River near Mokelumne Hill 585 

(381846120430901)

49 Mokelumne River at Woodbridge 15 

(11325500)

1,842 San Joaquin Valley, east 

side integrator site

1,862 San Joaquin Valley, east 

side integrator site

8 11 San Joaquin Valley, west 

side/alluvial

85 San Joaquin Valley, west 

side/alluvial

46,089 San Joaquin River 

integrator site

48 Sierra Nevada

Agriculture—orchards USGS 

and vineyards

Agriculture—orchards DWR, USGS 

and vineyards

Agriculture—cropland CRWQCB 

and pasture

Agriculture—cropland CRWQCB 

and pasture

Agriculture—cropland USGS, DWR 

and pasture

Forest—evergreen DWR, USGS

984 Sierra Nevada/reservoirs Forest—evergreen DWR

1,111 San Joaquin Valley, east 

side integrator site

1,144 San Joaquin Valley, east 

side integrator site

47,345 San Joaquin River 

integrator site

544 Sierra Nevada

657 San Joaquin Valley, east 

side integrator site

Agriculture—orchards USGS 

and vineyards

Agriculture—orchards DWR, USGS 

and vineyards

Agriculture—cropland USGS, DWR 

and pasture

Forest—evergreen DWR

Agriculture—orchards USGS, DWR 

and vineyards __________

1 This is the major land use affecting water quality at the site (for example, at site 25, more than 1,000 of the 1,362 mi2 drainage area is 

forest land, but the major land use affecting water quality is agriculture) (Anderson and others, 1976).

2 Listed in order of importance (number of samples). If USGS is listed first, the site is shown as NWIS site in figure 18. Other sites are 

shown as STORET sites.

3 Most water at this site has been transported from the Sacramento-San Joaquin Delta, more than 100 mi to the north, through the DeltaMendota Canal.

4 The perennial stretch of the San Joaquin River begins with the inflow from Bear Creek just upstream of the Stevinson site. The drainage 

area for the San Joaquin River near Stevinson site is the area drained by Bear Creek. Downstream San Joaquin River sites are adjusted 

accordingly.

5 Area of the Panoche Drainage District.

6 Area of the Pacheco Water District.

7 Area of the combined Salt Slough and Mud Slough drainages, which are interconnected. Drainage can go either way.

8 Drainage area in the valley only. The Coast Ranges usually do not contribute to flows at these sites, especially during the irrigation 

season, and are not included.

Description of Available Data 35
study (nutrients and suspended sediment) or a joint 

CRWQCB-U.S. Soil Conservation Service study 

(suspended sediment).

The final NAWQA database includes 5,457 

nutrient values (70 percent from STORET) and 6,217 

suspended sediment values (69 percent from NWIS). 

The San Joaquin River near Vernalis (site no. 47, 

fig. 18) is the outlet site for the San Joaquin Basin and, 

as a USGS National Stream Quality Accounting 

Network (NASQAN) site, has been sampled 

frequently. It is a combined NWIS and STORET site, 

but because of its wealth of NWIS suspended sediment 

data is considered to be a NWIS site for this report. At 

the Vernalis site, 558 nutrient samples (43 percent from 

NWIS) and 3,518 suspended sediment samples 

(91 percent from NWIS) were taken at the Vernalis site 

during 1972-1990. Without the Vernalis site, the 

STORET database accounts for 71 percent of the 

nutrient samples and 59 percent of the suspended 

sediment samples.

At the 49 long-term sites (fig. 18), 3,397 samples 

were analyzed for nutrients (60 percent from 

STORET) and 5,089 samples for suspended sediments 

(81 percent from NWIS). Excluding samples from the 

San Joaquin River near Vernalis site, these percentages 

change (61 percent STORET samples for nutrients and 

58 percent NWIS samples for suspended sediment).

The 369 sites with nutrient data are shown in 

figure 19 as either NWIS or STORET sites. Sites with 

data from both are given the symbol of the dominant 

data source (for example, NWIS for the San Joaquin 

River near Vernalis site). The 287 STORET sites 

increase the spatial coverage of the 82 NWIS sites, 

particularly in the Sierra Nevada and Coast Ranges 

environmental settings. Distribution of the 369 nutrient 

sites and 5,457 nutrient samples is shown in figure 20 

by environmental setting. These correspond to those 

shown in figures 15 and 16, with the addition of a 

Sierra Nevada reservoirs subcategory and a mainstem 

San Joaquin River category. The reservoirs 

subcategory includes sites in the Sierra Nevada 

foothills just downstream from major reservoirs. The 

San Joaquin River sites integrate the valley east side 

and west side environmental settings. The Sierra 

Nevada, including the Sierra Nevada reservoirs 

category from both basins, accounts for 50 percent of 

the nutrient sites and 37 percent of the nutrient 

samples, and the San Joaquin River sites between 

Mendota Pool (site 14, fig. 18) and Vernalis (site 47) 

account for 6 percent of the sites and 21 percent of the 

samples. Alluvial fans in the valley portion of the San

Joaquin Basin (fig. 15) account for 22 percent of the 

sites and 24 percent of the samples.

The 235 sites with suspended sediment data are 

shown in figure 21. The 179 STORET sites improve the 

spatial coverage provided by the 56 NWIS sites, 

particularly in the Sierra Nevada part of the Tulare 

Basin. The distribution of the 235 sites and 6,217 

samples is shown in figure 22 by environmental 

setting. Only 9 percent of the sites, but 62 percent of the 

samples, are from the San Joaquin River (3,518 

suspended sediment samples were from the Vernalis 

site). Approximately 34 percent of the sites and 13 

percent of the samples are from the Sierra Nevada 

(including the Sierra Nevada reservoirs category). 

Alluvial fans in the San Joaquin Basin account for 34 

percent of the sites and 19 percent of the samples.

The 34 long-term STORET sites (fig. 18) 

improve the spatial coverage provided by the 15 NWIS 

sites, particularly in the Sierra Nevada portion of the 

Tulare Basin and along the upper San Joaquin River. 

The environmental setting distribution of nutrient and 

suspended sediment samples at the 49 long-term sites 

is shown in figure 23. The San Joaquin River sites 

account for 16 percent of the sites, 33 percent of the 

nutrient samples, and 75 percent of the suspended 

sediment samples. The alluvial fans in the San Joaquin 

Basin account for 39 percent of the sites, 28 percent of 

the nutrient samples, and 14 percent of the suspended 

sediment samples. The Sierra Nevada and Sierra 

Nevada reservoirs account for 22 percent of the sites, 

23 percent of the nutrient samples, and 8 percent of the 

suspended sediment samples.

The percentage of samples collected during the 

irrigation season at the long-term sites in the 

agriculture-dominated valley environmental setting is 

shown in figure 24. Although irrigation in the study 

unit generally begins in March, there frequently are 

significant storms in March. Thus, the period when 

water quality in the study unit is primarily affected by 

irrigation return flows is defined as April through 

September (50 percent of the year). There generally is 

not much difference in the sampling frequency 

between irrigation and nonirrigation seasons, except 

for suspended sediment in the west side alluvial fans of 

the San Joaquin Basin. Most suspended sediment 

sampling by the CRWQCB and local water districts 

was done during the summer months. Therefore, most 

suspended sediment data are from this period, and the 

data are biased.

36 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
121°

120°

EXPLANATION

I I San Joaquin Valley 

- N^ A NWIS site 

/ l > v STORET site

~s- \

—— — —— Study unit boundary

40 MILES

40 KILOMETERS

Figure 19. Nutrient data sites in San Joaquin-Tulare Basins, California, study unit, 1972-1990. National Water Information System (NWIS) of 

the U.S. Geological Survey; STOrage and RETrieval (STORET) database of the U.S. Environmental Protection Agency.

Description of Available Data 37
Streamflow at Time of Water Quality Sampling

It is important to know the Streamflow at the time 

of water quality sampling and how it compares to longterm Streamflow. An even distribution of sampling 

across Streamflow regimes is important to represent 

constituent concentrations adequately and for calculating loads. Concentrations of dissolved nutrients 

(nitrate, ammonia, and orthophosphate) are typically 

higher at low streamflows, and sampling that is biased 

towards low streamflows would produce mean nutrient 

concentrations that may be biased high. Also, 

suspended sediment concentrations are typically lower 

at low streamflows, and this biased sampling may 

produce mean suspended sediment concentrations that 

are biased low. For load calculations, it is especially 

important to have sufficient samples at high 

streamflows because most of the annual load is 

transported at high streamflows.

To evaluate the NAWQA database for possible 

bias with regard to streamflows at time of sampling, we 

chose 8 of the 49 long-term monitoring sites as representative. These eight sites include three Sierra Nevada 

sites, three San Joaquin Valley sites (one west side and 

two east side), and two mainstem San Joaquin River 

sites (figs. 25 and 26). For each site, the number of 

nutrient and suspended sediment samples collected 

during each 10 percent of Streamflow for the period of 

sampling were counted. The first 10 percent of streamflow (0 to 10) represents the lowest 10 percent of 

streamflows during the given time period. For evenly 

distributed, unbiased sampling, 10 percent of the 

samples would be collected during each 10 percent of 

Streamflow.

The main concern is possible bias i n sampling at 

the extremes of Streamflow (0-10 and 91-100 percent) 

(figs. 25 and 26). For nutrients, there is a slight bias

c

CD 

O

CD 

D_

40

35 -

30 -

25 -

20 -

15 -

10 -

5 -

L_] Sites (Total = 369) 

• Samples (Total = 5,457)

Environmental Setting

Figure 20. Nutrient samples and sampling sites by environmental settings in San Joaquin-Tulare Basins, California, study unit. See figure 15 

for environmental settings.

38 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
121 120C

EXPLANATION

San Joaquin Valley 

NWIS site

V STORET site 

—— — —— Study unit boundary

VN

^ 

/

>

\

36°-

1y7 fCinS^7 - - i V _,sr

",-^^V V eJv^

Visalia^ ^

-- ,_v v j*S

^ VT Til'e River V V -> 'V

^^ / ! vr K * • F 1 ^ . C

I f* *~ -~~

v - % - ^ |

V. .c \

^ ""n '

.1 .•• \ j

vv y

'W — r ! v

v <s

' ~ ~ &

d*3?

V

*• \

\

(

rue1

VL

j ,

' r

I

v v.

~/f

f **"

Bakersfield

X

40 MILES

35°-

s

40 KILOMETERS

Figure 21. Suspended sediment data sites in San Joaqum-Tulare Basins, California, study unit. National Water Information System (NWIS) 

of the U.S. Geological Survey; STOrage and RETrieval (STORET) database of the U.S. Environmental Protection Agency.

Description of Available Data 39
L_J Sites (Total = 235) 

• Samples (Total = 6,217)

Environmental Setting

Figure 22. Suspended sediment samples and sampling sites by environmental settings in San Joaquin-Tulare Basins, California, study unit. See 

figure 15 for environmental settings.

towards sampling at higher streamflows at the 

Tuolumne River at Modesto (site 38, fig. 18) and the 

San Joaquin River near Newman (site 27), a shortage of 

sampling at the lowest streamflows at the Tule River 

below Success Dam (site 8), and an abundance of 

sampling at the lowest streamflows at the Mokelumne 

River at Woodbridge (site 49). For suspended sediments, there were no samples at the lowest streamflows 

at the Tule River below Success Dam (site 8, fig. 18), 

and an abundance of samples at high streamflows at the 

San Joaquin River near Newman (site 27). For the 

3,471 suspended sediment samples collected at the San 

Joaquin River near Vernalis (site 47) with associated 

streamflow values, there was a slight abundance of 

sampling at the lowest streamflows and a slight shortage of sampling at the highest streamflows. The 

Vernalis site had daily samples for water years 

1973-1982 and reduced sampling (weekly, biweekly, 

or monthly) during the remainder of the study period. 

Thus, statistics for 1973-1982 dominated the summary

for the study period and included the lowest streamflow 

period (1977), but missed the highest streamflow 

period (1983). This explains the bias seen in figure 26 

at the Vernalis site. This bias is removed by reducing 

the Vernalis database to monthly sampling for the study 

period.

In general, the sampling of nutrients and 

suspended sediments at these eight representative sites 

is fairly well distributed across the streamflow regime, 

and the resulting database probably is representative of 

concentrations at these sites. Samples collected at these 

8 sites constitute 26 percent of the nutrient samples 

collected at the 49 long-term sites (16 percent if the San 

Joaquin River at Vernalis site is excluded) and 77 

percent of the suspended sediment samples (29 percent 

if the Vernalis site is excluded). As with most of the 

long-term monitoring sites, these eight sites are 

generally sampled on a regular monthly or quarterly 

schedule, which results in collection of samples that 

represent the overall streamflow regime at these sites.

40 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
80

70

60

50

O "c 

o

0

Q.

- 40

30

20

10

——————— 1 ———————— 1 ———————— 1 ——— 

dH Long term sites (Total = 49)

U~X Nutrient samples (Total = 3,397)

- n Suspended sediment samples

(Total = 5,089)

-

OT

C

3

"ft

^ ~03

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P OT

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2 ® . 03 W

^^ s *~

= > 03

n3 0 "O

> Z 03

^

.E 2 °

^ i_ ~^f

I S g

"^ 77 •-

Tulare Basin

—— i —————— i ——

OT

C

to n3

c •*-

."2 ^

_g "03

"03 0"

% ~TM

'(/} to

"w 0 

0

5 0" ^ —

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£= 0-

=J 03 rn CT 5 s O3 ^

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^> 03

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|ilj ||]

i i

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n3 03

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// . i£/3 //

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/ / /\

/ / - — 1 / /I ^i

———— 1 ——————————

>

ir

_c

cr

03 

O

C

03

tf>

—————

7""ry^/V

/ /

//

/ /

//

/ /

//

/ /

^

; =

EE

= I

— —

- —

EE

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— -

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E — I

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= ;

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San Joaquin Basin

Environmental Setting

Figure 23. Nutrient and suspended sediment samples and sampling sites for long-term sites by environmental settings in San Joaquin-Tulare 

Basins, California, study unit. See figure 15 for environmental settings.

DESCRIPTION OF CONSTITUENT 

CONCENTRATIONS BY ENVIRONMENTAL 

SETTING

Differences in Constituent Concentrations Among 

Environmental Settings

The differences in constituent concentrations 

among environmental settings are illustrated by 

boxplots of nitrate, ammonia, total nitrogen, 

orthophosphate, total phosphorus, and suspended 

sediment at several representative long-term sites 

during 1972-1990 (fig. 27). The environmental settings 

considered are San Joaquin Valley west and east sides 

and Sierra Nevada (fig. 15Z?). Discussion of the Coast 

Ranges environmental setting is not possible due to 

insufficient data. The range of letters from Tukey's test 

on ranks by environmental setting is given in table 7 

and on boxplots in figure 27. Boxplots are useful to 

compare groups of data visually. The boxplots 

produced by PT2 are called 10-90 boxplots. The box 

includes the middle 50 percent of the data, and the

whiskers extend to the 10th and 90th percentiles. The 

PT2 boxplots use a log scale of concentration on the 

y-axis. Likewise, the streamflow values in the PT2 plots 

of constituent concentration versus streamflow are 

plotted on a log scale. Boxplots with a common letter 

are not significantly different at a 0.05 alpha level based 

on Tukey's test on ranks (Helsel and Hirsch, 1992). 

Although only selected long-term sites are shown in 

figure 27, the Tukey's test results (table 7) are based on 

all long-term sites with sufficient data, including 

mainstem San Joaquin River sites.

The valley west side sites include two agricultural drains (Panoche Drain near Dos Palos [site 17, fig. 

18] and Camp 13 Slough near Oro Loma [site 18]), two 

sloughs dominated by surface and subsurface agricultural drainage (Mud Slough near Gustine [site 21] and 

Salt Slough near Stevinson [site 19]), and two creeks 

dominated by surface agricultural drainage during 

irrigation season (Orestimba Creek [sites 28 and 29] 

and Del Puerto Creek at Vineyard Road [site 33]). The 

valley east side sites include the three major tributaries 

to the lower San Joaquin River (Merced River near

Description of Constituent Concentrations by Environmental Setting 41
5 80

.a

E

Q.

CD 70

D)

o 60

O.

<

T3 

0)

O

CD

50

40

" 30

CO 

C/5

"CO

o 20 'o

(D 

D)

& 10

CD O

West side, 

alluvial fans

ED Nutrient samples 

•I Suspended sediment 

samples

East side, 

alluvial fans East side, _ alluvial fans SanJoaqum 

River

Tulare 

Basin

San Joaquin 

Basin

All Valley 

Sites

Environmental Setting

Figure 24. Percent of nutrient and suspended sediment samples 

collected during the irrigation season at long-term sites in the San 

Joaquin Valley, California. See figure 15 for environmental settings.

Stevinson [site 26], Tuolumne River at Modesto [site 

38], and Stanislaus River at Ripon [site 45]), the 

Mokelumne River at Woodbridge (site 49), and one site 

from the Tulare Basin (Kings River below Peoples Weir 

[site 6]) (fig. 18).

The valley west side sites have significantly 

higher concentrations of nitrate, total nitrogen, total 

phosphorus, and suspended sediment than the valley 

east side and Sierra Nevada sites (table 7). This is due 

to the high nitrate concentrations in subsurface 

drainage and the easily erodible fine-grained soils on 

the west side of the valley, which cause suspended 

sediment concentrations to be higher and more 

paniculate forms of nutrients to be transported.

In the agricultural drains on the valley west side, 

nitrate concentrations are especially high, mostly from 

native soil nitrogen in the ground water of the west 

side, which is transported through subsurface 

agricultural drains (Brown, 1975). Most exceed the 

EPA maximum contaminant level for drinking water of 

10 mg/L as N (U.S. Environmental Protection Agency, 

1986); however, these drains are not drinking water 

sources. The other west side sites contain more dilution 

water (operational spills, tail water, natural runoff) and 

thus have lower concentrations.

Subsurface agricultural drains are not a major 

source of total phosphorus and suspended sediment and 

have concentrations comparable to other valley west 

side sites. The easily erodible, fine-grained soils of the 

west side contribute to higher suspended sediment 

concentrations, which carry higher concentrations of 

nutrients relative to the coarser grained east side soils. 

The difference in suspended sediment concentration 

between west side and east side would be even more 

apparent except that most west side values were from 

grab samples that were biased low (fig. 16F), whereas all 

east side values were from width- and depth-integrated 

samples.

Nutrient and suspended sediment concentrations 

are low at all the Sierra Nevada sites (fig. 27). Most of 

the nitrate and orthophosphate concentrations are below 

the reporting level. Much of the variation among Sierra 

Nevada sites is a function of altitude: higher altitude 

sites generally have lower concentrations of nutrients 

and suspended sediment due to less disturbance in the 

drainage basin. Despite the relatively low concentrations 

of nutrients and suspended sediment at Sierra Nevada 

sites, not all sites are significantly lower than valley east 

side sites (table 7). The source of water for valley east 

side sites is the Sierra Nevada, and concentrations of 

nutrients and suspended sediment often are not 

significantly different. The effect of agriculture at the 

valley east side sites is dependent on the season and 

artificial agricultural drainage systems upstream from 

the valley sites.

Contrast in the grain size of suspended sediment 

can be seen by plotting the percentage of suspended 

sediment that is less than 0.062 millimeters (mm) in 

diameter. This is the approximate break between the 

clay and silt fraction, and the sand and gravel fraction. 

The median of suspended sediment less than 0.062 mm 

in diameter at valley west side sites is 96 percent 

(fig. 28). For the San Joaquin River sites, this median is 

92 percent. For valley east side sites, the median is 80 

percent, and for the Sierra Nevada sites it is 54 percent. 

This suggests that most of the suspended sediment in the 

San Joaquin River originates from valley west side 

inputs, despite more than 75 percent of the flow in the 

San Joaquin River originating from east side sources 

(Kratzer and others, 1987). On the basis of the higher 

percentage of fine-grained suspended sediments from 

west side inputs, one would expect higher concentrations of nutrients attached to suspended sediment from 

the west side.

Although only nutrient and suspended sediment 

concentrations are evaluated in this report, the median

42 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
A San Joaquin River sites

• Site 27, San Joaquin River near Newman (1986-1988, 47 samples) 

EH] Site 47, San Joaquin River near Vernalis (1972-1990, 558 samples)

0-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100

Percent of streamflow

25

20

j r15

B San Joaquin Valley sites

• Site 21, Mud Slough near Gustine, (1986-1988, 75 samples)

[ I Site 38, Tuolumne River at Modesto (1986-1988, 45 samples)

ED Site 49, Mokelumne River at Woodbridge (1975-1990, 143 samples)

Nutrient

0-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100

Percent of streamflow

25

20

_ D.

E

CO

J2

03 

O

15

-10

(D 

O

C Sierra Nevada sites

• Site 8, Tule River below Success Dam, (1972-1990, 64 samples)

EH] Site 4, Kings River below North Fork, near Trimmer (1974-1990, 145 samples)

O Site 22, Merced River at Happy Isles Bridge (1972-1990, 171 samples)

Nutrient

0-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100

Percent of streamflow

Figure 25. Percent of streamflow associated with nutrient samples collected at selected sites in San Joaquin-Tulare Basins, California, study 

unit. See figure 18 for site locations.

Description of Constituent Concentrations by Environmental Setting 43
co

25

20

_ 

Q_

E

CO H1-

co 15

- 10

CD 

O

CD 

Q.

A San Joaquin River sites

• Site 27, San Joaquin River near Newman (1986-1988, 41 samples) 

F~~l Site 47, San Joaquin River near Vernalis (1972-1990, 3,471 samples)

Suspended sediment

0-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100

Percent of streamflow

25

20

CO 

_CD 

Q.

CO H1- 

CO 15 "CO 

O

"6 

E 10

CD

E

CD 

0.

B San Joaquin Valley sites

• Site 21, Mud Slough near Gustine (1986-1988, 44 samples)

I I Site 38, Tuolumne River at Modesto (1986-1988, 35 samples)

I 1 Site 49, Mokelumne River at Woodbridge (1975-1990, 111 samples)

Suspended sediment

0-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100

Percent of streamflow

25

20

CO

Q.

E

8 15

io

CD

E

CD 

0.

C Sierra Nevada sites

• Site 8, Tule River below Success Dam (1977-1987, 39 samples)

EH Site 4, Kings River below North Fork, near Trimmer (1978-1990, 93 samples)

I J Site 22, Merced River at Happy Isles Bridge (1972-1990, 96 samples)

Suspended sediment

w 0-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100

Percent of streamflow

Figure 26. Percent of streamflow associated with suspended sediment samples collected at selected sites in San Joaquin-Tulare 

Basins, California, study unit. See figure 18 for site locations.

44 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
75 71 148 108 16

Number of samples 

93 77 71 143 59 40 58 170 40 46 42 116 45 47 148

Nitrate concentration, in milligrams liter, Nper as 

D O

0-•• 

CJD 

EF

'_ San Joaquin Valley 

west side

n n i i 

U U u m

G|H Hll ip in

I M u;J

KL

San Joaquin Valley 

east side

i i i i

1 - 90th percentile 

^mm~ 75th percentile 

^TM1- Median 

*" "r * - 25th percentile

1 - 10th percentile 

- - Reporting level

Nitrate ;

P NO MN P P OP MN LM MN MNI 

P OP OP 0 :

Sierra Nevada

17 18 19 21 28 25 39 46 49 6 11 12 22 36 43 48 1 7 

Site number

9 4

Number of samples 

11 22 81 81 38 27 28 61 21 13 73 11 13 12 72 13 14 83

0.001

JK JK GH KL 

LM LM I J M 

KL

San Joaquin Valley 

east side

KL GH

M I J

KL

Ammonia

LM M JK 

LM

IJ 

KL

HI 

JK

L

I J 

KL

Sierra Nevada

25 39 46 49 6 12 22 36 43 48 1 7 9 4 

Site number

Number of samples 

23 32 104 94 73 53 46 125 33 25 39 116 29 36 33 106 85

10

o '—s

O Q.

C V)

CD E

1 = ' 0.10

o .E

0.01

San Joaquin Valley 

west side

G'H Hf

[•1

San Joaquin Valley 

east side

Total nitrogen

U 

KL

I JK KL

L

Sierra Nevada

JK U

L

17 18 19 21 25 39 46 49 6 11 12 22 36 43 48 1

Site number

Figure 27. Nutrient and suspended sediment concentrations at long-term water quality monitoring sites by environmental setting in San 

Joaquin-Tulare Basins, California, study unit, 1972-1990. Letters on boxplots refer to results of Tukey's test on ranks (table 7). Site numbers 

refer to table 6 and figure 18.

Description of Constituent Concentrations by Environmental Setting 45
Number of samples 

29 36 118 91 15 84 63 63 59 48 37 56 109 36 43 34 72 24 20 90

O Q_

*

C —

8 c5

0 °-

I E

Q. CO

D. 

O

0.1

0.01

0.001

San Joaquin Valley 

east side

90th percentile 

75th percentile 

Median 

25th percentile

10th percentile 

Reporting level

Orthophosphate

HI HI I GH I GH EF FG GH 

I I HI

Sierra Nevada

17 18 19 21 28 25 39 46 49 6 11 12 22 36 43 48 1 7 9 4

Site number

Number of samples 

43 50 119 97 15 84 69 64 142 49 39 56 171 38 45 33 111 11 110

.2o.

2 w -t cc

CD »-^

£ o .-2 '~ 0.1

O CD

in Q.

2 w

o E

w D) 0.01

o =

"cc .E 

o

0.001

San Joaquin Valley 

, wes{ side ,

BF E H

FG

GH

San Joaquin Valley 

, east, side i____i

Total phosphorus

• ill

I HI HI I GH HI GH GH HI

Sierra Nevada

17 18 19 21 28 25 39 46 49 6 11 12 22 36 43 48 1 9 4

Site number

Number of samples 

43 38 66 51 24 24 50 40 48 112 12 11 12 96 12 10 111 22 19 98

81~ 100

c E E cc

51

CD 

Q.

10

0.1

AlB 

CD

AlB 

CD

A'B 

CD

AB 

CD

I

AB 

CD

San Joaquin Valley 

west side,___

San Joaquin Valley 

east side ,

Suspended sediment

_L R •

G G 

• 

G 

iy 

G 

T

G

Sierra Nevada

G G G

17 18 19 21 29 33 26 38 45 49 6 11 12 22 43 48 1 7 9 4

Site number

Figure 27. Continued.

46 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Table 7. Summary of Tukey's test on ranks for nutrients and 

suspended sediment at long-term water quality monitoring sites. 

San Joaquin-Tulare Basins, California, study unit

[Sites with the same letter are not significantly different at the 

95-percent confidence level. A refers to highest concentrations; M 

to lowest concentrations (see figs. 27-29)]______________

Environmental setting

Constituent SanJoaqum 0 , . SanJoaqum 0. 

.... ^ m SanJoaqum .... ^ . Sierra Valley west _. ^ Valley east .. . ' River ' Nevada side side

Nitrate

Ammonia

Total nitrogen

Orthophosphate

Total phosphorus

Suspended 

sediment

Suspended 

sediment size

A-F

A-H

A-D

B-E

A-D

A-D

A-C

B-K

A-I

C-G

A-C

A-D

C-F

A-E

G-M

E-M

G-I

D-I

E-H

F-G

D-H

L-P

G-M

I-L

E-I

G-I

F-G

H

values for specific conductance, pH, dissolved oxygen, 

total hardness, total organic carbon, and chlorophyll a, 

also are given in table 8 for long-term sites.

Concentrations of Constituents in the 

Lower San Joaquin River

Nutrient and suspended sediment concentra-tions 

along the mainstem San Joaquin River and its most 

significant inputs affecting the concentrations are 

shown in figure 29. For all constituents, the east side 

tributaries dilute water in the San Joaquin River;

concentrations in the west side tributaries are equal to 

or greater than those in the mainstem San Joaquin 

River. Also, for all constituents, the dilution by east side 

tributaries is not as great as would be expected from 

mass balance calculations due to other sources of 

agricultural drainage to the mainstem San Joaquin 

River, which are not shown. For nutrients, concentrations are determined primarily by relatively concentrated inputs from west side agricultural drainage, 

discharges from east side wastewater treatment plants 

and dairies, and by relatively dilute inputs from major 

east side tributaries.

For example, nitrogen species, which have low 

concentrations at the upstream San Joaquin River site 

near Stevinson (site 16, fig. 18), increase greatly with 

agricultural drainage input from Salt and Mud sloughs. 

Between Patterson and Vernalis (sites 31 and 47) the 

concentrations are lower, as runoff from east side 

tributaries enters the river (figs. 29A and C). This 

pattern is similar for other constituents in the San 

Joaquin River (Kratzer and others, 1987; Westcot and 

others, 1991; Hill and Gilliom, 1993), including 

selenium, boron, and dissolved solids. Ammonia 

concentrations increase in the river between Newman 

(site 27) and Patterson (site 31), which is not explained 

by the inputs shown in figure 296. This is partly due to 

the Turlock wastewater treatment plant discharge to the 

San Joaquin River through Turlock Irrigation District 

drain lateral number 5 (fig. 13) and partly due to 

discharges from dairies. In calendar year 1991, this 

discharge had a mean ammonia concentration of

CD = 

N "E

w *=

•~ C\J

£ o

c °. 

.E C)

Number of samples 

50 51 45 46 45 47 48 272 45 39 46 90 29 52 51

CD 

CD

-.i 100

CD 

CL

10

W * 

c 0T

90th percentile 

75th percentile 

I- Median

* - 25th percentile

- 10th percentile

San Joaquin

Valley 

west side San Joaquin River

San Joaquin Valley 

east side Sierra Nevada

19 21 16 20 27 31 42 47 26 38 45 49 22

Site number

Figure 28. Differences in suspended sediment size among environmental settings, 1972-1990, in San Joaquin-Tulare Basins, California, study 

unit Letters on boxplots refer to results of Tukey's test on ranks (table 7). Site numbers refer to table 6 and figure 18.

Description of Constituent Concentrations by Environmental Setting 47
o

8.2 mg/L as N and a mean flow of 13.2 ft /s (based on 

NPDES self-monitoring data) (California Regional 

Water Quality Control Board, written commun., 1993).

The concentration pattern of the phosphorus 

species (figs. 29D and E) in the mainstem San Joaquin 

River is similar to that of the nitrogen species (figs. 

29A-C), except that the concentrations at Stevinson 

(site 16) were relatively high before inputs from the 

west side. This pattern also applies to some other 

constituents at this site (Hill and Gilliom, 1993; 

Kratzer and others, 1987), such as molybdenum. The

source of water at Stevinson is a combination of ground 

water accretions, agricultural return flows, wastewater 

treatment plant effluent from Merced and other cities 

through Bear Creek (fig. 10), and runoff from 

rangeland in the lower Bear Creek watershed. Likely 

sources of phosphorus are the rangeland and the 

Merced wastewater treatment plant. Phosphorus levels 

at Stevinson are essentially the same as the levels 

entering from the west side sloughs. There also appears 

to be a significant source of phosphorus to the 

mainstem San Joaquin River between Newman

Table 8. Water quality data for long-term sites, San Joaquin-Tulare Basins, California, study unit

[First line represents median value. Second line shows number of samples, in italics. mg/L, milligram per liter; ug/L, microgram per liter; 

uS/cm, microsiemen per centimeter at 25 degrees Celsius; mm, millimeter; <, less than; —, no data]

Site No Specific

,,. Site name conductance 

Yg,' <^S/cm}

1 Kern River at Kernville

2 Kern River below Isabella Dam

3 Kern River near Bakersfield

4 Kings River below North Fork, near

Trimmer

5 Kings River below Pine Flat Dam

6 Kings River below Peoples Weir

7 Tule River near Springville

8 Tule River below Success Dam

9 Kaweah River at Three Rivers

10 Kaweah River below Terminus Dam

11 San Joaquin River south fork at

Mono Hot Springs

12 San Joaquin River below Kerckhoff

Powerhouse

13 San Joaquin River below Friant

Dam

109

112

111

33

126

47

43

722

34

11

67

50

296

23

214

34

81

21

82

34

27

28

30

48

48

43

PH

7.5

124

7.4

40

7.6

56

7.2

725

7.3

26

7.2

66

8.1

27

7.6

59

7.4

27

7.3

50

7.2

40

7.1

68

7.0

57

Oxygen, 

dissolved 

(mg/L)

10.3

727

10.0

37

10.0

53

10.7

124

10.8

14

9.9

63

10.7

27

10.2

38

10.1

27

10.1

46

8.8

36

10.6

61

11.2

47

Hardness, 

total, 

as CaC03 

(mg/L)

34

7/0

33

53

36

47

14

134

12

33

23

48

100

40

79

55

29

41

33

41

1

27

1

42

14

43

Nitrate, 

dissolved, 

asN 

(mg/L)

0.10

104

0.10

53

<0.10

46

<0.10

755

<0.10

35

0.15

58

<0.10

44

0.16

62

<0.10

42

<0.10

46

<0.10

32

<0.10

54

<0.10

30

Nitrogen, 

ammonia, 

dissolved, 

asN 

(mg/L)

0.02

63

0.05

77

_

—

0.02

75

0.02

13

0.02

13

0.02

72

0.06

14

0.03

13

_

—

—

—

0.02

7

—

—

Nitrogen, 

Kjeldahl. 

total, as N 

(mg/L)

0.21

104

0.30

8

0.30

29

0.27

86

—

—

0.20

33

0.23

7

_

—

0.20

9

0.30

77

0.10

24

0.14

38

0.23

70

48 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
(site 27) and Patterson (site 31) that is not shown in 

figures 29D and E, probably due to discharges from the 

Turlock wastewater treatment plant and dairies.

The pattern of suspended sediment concentrations in the mainstem San Joaquin River (fig. 29F) also 

is similar to nitrogen concentrations. One difference is 

that dilution from east side tributaries does not lower 

the river concentrations between Patterson and Maze 

Road (sites 31 and 42, fig. 18), and only slightly lowers 

the concentrations from Maze Road to Vernalis (sites

42 and 47). This is due to high suspended sediment 

concentrations in several agricultural discharges that 

enter the river from the west side. The seven largest 

west side drains from Newman (site 27) to Vernalis 

(sites 29, 30, 32, 33, 35, 40, and 41, fig. 18) are shown 

in relation to mainstem sites in figure 29F. The median 

suspended sediment concentrations in these seven west 

side agricultural discharges range from 134 to 790 

mg/L, compared with San Joaquin River concentrations of 78 to 100 mg/L in this area. The locations of 

other agricultural discharges are shown in figure 13.

Table 8. Water quality data for long-term sites, San Joaquin-Tulare Basins, California, study unit—Continued

Site 

No. 

(fig. 

18)

1

2

3

4

5

6

7

8

9

10

11

12

13

Site name

Kern River at Kernville

Kern River below Isabella Dam

Kern River near Bakersfield

Kings River below North Fork, near 

Trimmer

Kings River below Pine Flat Dam

Kings River below Peoples Weir

Tule River near Springville

Tule River below Success Dam

Kaweah River at Three Rivers

Kaweah River below Terminus Dam

San Joaquin River south fork at 

Mono Hot Springs

San Joaquin River below Kerckhoff 

Powerhouse

San Joaquin River below Friant 

Dam

Nitrogen, 

total, 

asN 

(mg/L)

0.26

105

0.70

7

0.34

29

0.35 

85

—

0.39 

33

0.31

7

__

—

0.28

9

0.41

17

0.11

25

0.19 

39

0.32 

11

Phosphorus, 

total, 

asP 

(mg/L)

0.02

110

0.04

21

0.04

43

0.01 

107

—

0.04 

49

0.03 

9

0.04

21

0.02

11

0.02

31

0.01

24

0.01

44

0.05 

26

Phosphorus, 

dissolved, 

orthophosphate, 

as P (mg/L)

0.01

68

0.02

36

0.02

39

0.01

84

0.01 

19

0.02 

39

0.02 

24

0.02

34

0.01

19

0.01

14

0.01

14

0.01

25

0.03

24

Carbon, 

organic, 

total 

(mg/L)

2.0

17

_

—

3.2

12

1.7 

19

—

2.5 

11

—

__

—

_

—

_

—

1.2 

9

1.5 

12

—

Sediment, c .. 

_. , ... . . Sediment, Chlorophyll suspended . . 

, ' , x suspended 

a (ug/L) (percent

<0.062mm) lmfl/L'

— 60 5

— 52 111

— — 1

— — 22

— — 6

— — 14

— 61 2 

— 57 95

_ _ I 

— — 26

— — 5 

— — 12

— — 3 

— — 22

— — 6

— — 39

— — 4

— — 19

_ _ —

— — —

— — —

_ _ 2 

_ _ jj

— — 6

_ _ 7

Description of Constituent Concentrations by Environmental Setting 49
Table 8. Water quality data for long-term sites, San Joaquin-Tulare Basins, California, study unit—Continued

Site 

No. 

(fig. 

18)

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

Specific 

Site name conductance

(|iS/cm)

San Joaquin River near Mendota

Fresno River below Hidden Dam

San Joaquin River near Stevinson

Panoche Drain near Dos Palos

Camp 13 Slough near Oro Loma

Salt Slough near Stevinson

San Joaquin River at Fremont Ford

Bridge

Mud Slough near Gustine

Merced River at Happy Isles Bridge

Merced River near Briceberg

Merced River below Merced Falls

Merced River at Milliken Bridge

Merced River near Stevinson

San Joaquin River near Newman

Orestimba Creek at Highway 33

Orestimba Creek at River Road

Spanish Grant Combined Drain

San Joaquin River near Patterson

492

58

155

22

590

92

3.300

73

3,080

71

1,750

191

1,370

188

2,550

136

21

170

43

58

47

28

143

81

189

60

1,190

57

627

34

—

—

1,210

101

PH

7.7

72

7.3

24

8.0

109

7.9

95

7.9

85

7.7

228

7.8

233

8.1

133

6.8

172

7.2

59

7.1

33

7.2

142

7.6

60

8.0

57

8.1

58

—

—

7.8

131

Oxygen, 

dissolved 

(mg/L)

9.7

68

9.2

21

9.0

72

___

—

—

—

7.6

191

8.7

200

9.0

87

10.7

151

10.4

40

10.2

26

8.9

142

8.4

56

9.2

31

9.3

54

—

—

8.4

127

Hardness, 

total, 

as CaC03

(mg/L)

110

58

40

33

130

68

800

62

760

52

380

146

290

137

520

95

6

167

13

25

16

28

46

46

56

57

240

55

190

14

—

—

260

80

Nitrate, 

dissolved, 

asN

(mg/L)

0.52

50

0.14

30

0.20

97

19.2

75

12.7

71

2.9

148

1.3

161

2.2

70S

<0.10

J52

<0.10

34

<0.10

2S

0.84

93

1.3

57

2.0

54

1.5

16

—

—

2.1

SJ

Nitrogen, 

ammonia, 

dissolved, 

asN

(mg/L)

0.01

10

0.06

9

0.05

52

0.26

11

0.06

22

0.12

81

0.07

75

0.09

81

0.03

66

—

—

_

—

0.04

35

0.04

53

0.08

54

—

—

—

—

0.22

51

Nitrogen, 

Kjeldahl, 

total, as N 

(mg/L)

0.50

28

_

—

1.2

70

1.3

23

1.0

32

1.3

104

1.2

115

1.5

95

0.20

113

0.14

25

0.11

8

0.30

73

0.50

57

1.0

53

—

—

—

—

1.2

65

50 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Table 8. Water quality data for long-term sites, San Joaquin-Tulare Basins, California, study unit—Continued

Site 

No.

(fig.

18)

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

Site name

San Joaquin River near Mendota

Fresno River below Hidden Dam

San Joaquin River near Stevinson

Panoche Drain near Dos Palos

Camp 13 Slough near Oro Loma

Salt Slough near Stevinson

San Joaquin River at Fremont Ford 

Bridge

Mud Slough near Gustine

Merced River at Happy Isles Bridge

Merced River near Briceberg

Merced River below Merced Falls

Merced River at Milliken Bridge

Merced River near Stevinson

San Joaquin River near Newman

Orestimba Creek at Highway 33

Orestimba Creek at River Road

Spanish Grant Combined Drain

San Joaquin River near Patterson

Nitrogen, 

total, 

asN

(mg/L)

0.95

28

__

—

1.4 

70

19.6

23

10.7

32

4.4 

104

2.6 

775

4.2 

94

0.25 

116

0.16

25

0.18

8

1.0

73

1.9

57

3.1

53

—

__

—

—

3.4 

65

Phosphorus, 

total, 

asP

(mg/L)

0.15 

42

0.08

9

0.28 

86

0.25

43

0.19 

50

0.27 

779

0.28 

130

0.29 

97

0.01 

750

0.02 

34

0.01

27

0.06

84

0.08

57

0.26

54

0.20 

75

_

—

—

0.38 

79

Phosphorus, 

dissolved, 

orthophosphate, 

as P (mg/L)

0.08

42

0.04

14

0.13 

81

0.05

27

0.04 

34

0.11 

118

0.11 

126

0.13 

97

0.01

74

0.01 

29

0.01

14

0.03 

84

0.05

57

0.13

55

0.08 

14

_

—

—

0.21 

79

Carbon, 

organic, 

total

(mg/L)

4.8 

14

__

—

8.0 

40

8.8

22

7.5 

30

8.9

77

8.1 

60

11 

67

2.1 

33

1.6

7

_

—

—

2.9

42

6.8

41

—

__

—

—

7.4 

42

Sediment, 

Chlorophyll suspended 

a (ug/L) (percent 

<0.062 mm)

— —

_ _

— —

14 91 

41 45

_ _

— —

— —

7.8 95 

43 50

11 94 

49 46

9.2 97 

43 51

— 51 

— 29

— —

_ _

— —

— —

1.4 84

57 45

9.7 91

50 45

— —

_ _

— —

— —

11 97 

49 47

Sediment, 

suspended

(mg/L)

51 

18

6

13

48 

49

136

43

117 

38

144 

66

95

88

130

57

2 

97

2 

7

_

—

10

27

21

50

103

45

—

261

24

154 

75

79 

53

Description of Constituent Concentrations by Environmental Setting 51
Table 8. Water quality data for long-term sites, San Joaquin-Tulare Basins, California, study unit—Continued

Site 

No.

(fig. 

18)

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

Specific 

Site name conductance

((iS/cm)

Olive Avenue Drain

Del Puerto Creek at Vineyard Road

San Joaquin River near Grayson

Grayson Road Drain

Tuolumne River at Tuolumne

Meadows

Tuolumne River at LaGrange Bridge

Tuolumne River at Modesto

Tuolumne River at Tuolumne City

Ingram Creek at River Road

Hospital Creek at River Road

San Joaquin River at Maze Road

Stanislaus River Middle Fork at

Dardanelle

Stanislaus River below Goodwin

Dam

Stanislaus River at Ripon

Stanislaus River at Koetitz Ranch

San Joaquin River near Vernalis

Mokelumne River near Mokelumne

Hill

Mokelumne River at Woodbridge

—

—

1,020

53

—

—

42

44

171

57

269

69

—

—

878

706

44

35

_

—

91

57

113

75

679

431

35

41

47

786

PH

—

—

7.7

85

—

7.3

6

7.0

87

7.5

57

7.3

727

—

—

7.8

739

7.3

46

7.4

72

7.6

57

7.4

779

7.7

555

7.3

44

7.2

788

Oxygen, 

dissolved 

(mg/L)

—

—

8.4

82

—

9.2

34

10.2

77

10.0

49

9.3

727

—

—

8.4

736

9.7

42

10.8

35

9.6

50

9.5

779

8.7

557

10.6

44

10.0

752

Hardness, 

total, 

as CaC03

(mg/L)

—

—

220

37

—

5

28

18

43

53

50

75

50

—

—

190

84

18

33

28

32

37

50

53

57

150

233

12

41

17

775

.... . Nitrogen, Nitrate, 

.. , , ammonia, dissolved, .. . . 

,. dissolved, 

as N .' 

.... as N

(m9/U (mg/L)

— —

— —

2.0 —

32 —

— —

<0.10 —

30 —

<0.10 —

74 —

0.60 0.05

50 50

0.76 0.02

77 19

— —

— —

1.8 0.13

88 55

<0.10 —

28 —

<0.10 —

37 —

0.25 0.03

50 50

0.49 0.03

77 27

1.2 0.07

558 352

<0.10 —

25 —

0.10 0.03

732 54

Nitrogen, 

Kjeldahl, 

total, as N

(mg/L)

—

—

1.5

73

—

0.10

26

0.10

50

0.50

50

0.32

53

—

—

1.3

69

0.10

30

0.20

6

0.40

50

0.34

46

0.88

502

0.11

37

0.30

725

52 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Table 8. Water quality data for long-term sites, San Joaquin-Tulare Basins, California, study unit—Continued

Site 

No. 

(fig. 

18)

32

33

34

35

36

37

38

39

40

41

42

43

44

45

46

47

48

49

Site name

Olive Avenue Drain

Del Puerto Creek at Vineyard Road

San Joaquin River near Gray son

Grayson Road Drain

Tuolumne River at Tuolumne

Meadows

Tuolumne River at LaGrange Bridge

Tuolumne River at Modesto

Tuolumne River at Tuolumne City

Ingram Creek at River Road

Hospital Creek at River Road

San Joaquin River at Maze Road

Stanislaus River Middle Fork at

Dardanelle

Stanislaus River below Goodwin

Dam

Stanislaus River at Ripon

Stanislaus River at Koetitz Ranch

San Joaquin River near Vernalis

Mokelumne River near Mokelumne

Hill

Mokelumne River at Woodbridge

Nitrogen, 

total, 

asN 

(mg/L)

—

—

—

2.8 

13

—

0.13

28

0.21 

53

1.2

50

1.0

53

_

—

—

3.2 

69

0.11

32

0.23

6

0.69 

50

0.82

46

2.2 

501

0.13

32

0.37 

725

Phosphorus, 

total, 

asP 

(mg/L)

—

—

—

0.46 

26

—

0.01

23

0.01 

64

0.05

50

0.09 

69

_

—

—

.33 

84

0.02

44

0.01

23

0.05 

50

0.08

64

0.24 

480

0.02

29

0.02 

142

Phosphorus, 

dissolved, 

orthophosphate, 

as P (mg/L)

—

—

—

0.19

26

—

0.01

11

0.01 

25

0.03

50

0.04 

61

_

—

—

.16

84

0.01

26

0.01

18

0.03 

50

0.03

63

0.11 

362

0.01

9

0.01 

59

Carbon, 

organic, 

total 

(mg/L)

—

—

—

—

—

1.1

9

1.8 

13

2.2

39

3.2 

20

_

—

—

6.1

38

1.0

8

_

—

2.4 

39

3.3

21

5.2 

131

2.1

10

2.3 

43

Sediment, „ .. 

... j j Sediment, Chlorophyll suspended nded

a(ug/L) (percent . r . 

<0.062 mm)

— — 238

— — 16

— — 134 

— — 24

— — 85 

— — 10

— — 790 

— — 24

_ _ —

— — —

— — 2 

— — 11

1.1 86 11

47 39 40

— — 13 

— — 36

— — 650

— — 23

— — 460 

— — 24

7.6 90 94 

49 48 59

— — 4

— — 10

— — —

— — —

1.1 67 20 

49 46 48

— — 17

— — 27

5.8 88 77 

50 272 3.503

— — 2

— — 10

— 81 6 

— 88 112

Description of Constituent Concentrations by Environmental Setting 53
97 148

EXPLANATION

- 90th percentile 

j- 75th percentile 

!- Median

-'- 25th percentile

- 10th percentile 

Reporting level

161 108

Number of samples 

57 54 81 50 88 50 558

10

CD 

D.

W 

03

- Nitrate

E 0.1

0.01

16 19 20 21 26 27 31 

Site number

38 42 45 47

CD 

Q. 

W

03

52 81 77

:Ammonia

0.1

0.01

0.001

16 19

Number of samples 

81 53 54 51 50 55 50 360

20 21 26 27 31 

Site number

38 42 45 47

Figure 29. Nutrient and suspended sediment concentrations in the San Joaquin River, California, and its most significant inputs, 1972-1990. 

Letters on boxplots refer to results of Tukey's test on ranks (table 7). See table 6 for complete site names and figure 19 for site locations. 

Designation of (W) or (E) after some sites refers to whether it is a west side (W) or east side (E) input.

54 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
EXPLANATION

- 90th percentile 

j- 75th percentile 

^- Median

25th percentile

- 10th percentile

70 104 115

Number of samples 

94 57 53 65 50 69 50 501

CD 

Q. 

CO

CO

c

CD

o

o 

o

c

CD 

CD 

O

'c 

"cd 

o

\ r

10

Total nitrogen

CCO -I CO*

°w

0.1

CD li ', ; :. I

E]F

.ECO

coir

16 19 20 21 26 27 31

Site number

38 42 45 47

CD 

Q. 

CO

cd

c

CD 

O

O

o

CD

to

.c

Q. 

CO 

O

.c

Q. 

O

81

0.5

0.1

- Orthophosphate

O 0.001

118 126 91

Number of samples 

57 55 79 50 84 50

DE

^~D"> 

COOJ

coS 

We

clo

16 19 20 21 26 27 

Site number

31 38 42 45

362

D

CO <u 3>

£«

CO CU We

47

Figure 29. Continued.

Description of Constituent Concentrations by Environmental Setting 55
0) 

Q_

CO

E

CO

E

_c

| °-i

"c

0)

o

o 

o 

to

13

o

.c

Q. to 

o

Q.

86 119 130

Number of samples 

97 57 54 79

EXPLANATION

- 90th percentile 

a~ 75th percentile

!- Median

;

J - 25th percentile

- 10th percentile

50 84 50 480

I Total phosphorus E

I!-°CO CQ ro E

0.01

CD >

sir

i

coc

i

.

I-DC

w

^^ 

CO HI "w^

'CCD

coif

16 19 20 21 26 27 31

Site number

38 42 45 47

49 66 88 51 50

Number of samples 

45 24 15 53 16 24 24 40 23 24 59 48 3,503

= 5,000

cu

Q. 

CO

E

CO

J? 1,000

c

0)

o

c 

o 

o

"c

0)

E

T3

0) 

CO

T3

0) 

T3 

C 

0) 

Q. 

CO 

3

C/D

100

10

Suspended sediment

E'F

!§-•!

CO 0)

BC

D1 _

i- CD C.E

J5 CO J> CD CO

CO c O<D

16 19 20 21 26 27 29 30 31 32 33 35 38 40 41 42 45 47

Site number

Figure 29. Continued.

56 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
It should be noted that the values shown in figure 

29F for the west side agricultural drains are total 

suspended solids collected as grab samples; whereas, 

most of the values for the other sites are suspended 

sediment, integrated samples. As the values for the grab 

samples are systematically lower than the integrated 

samples, the effect of the agricultural drains is even 

greater than shown.

Relation to National Conditions

The USGS 1990-1991 National Water Summary 

describes water quality at sites throughout the United 

States, categorized by four upstream land use groups 

(U.S. Geological Survey, 1993). Sites were selected to 

represent the nationwide proportion of agricultural, 

forest, range, and urban land. For each land-use group, 

a national average boxplot is presented for 

concentrations of nitrate, total phosphorus, suspended 

sediment, and other constituents. Drainage areas 

generally are from 1,000 to 3,000 mi2. A site classified 

as agricultural has more than 40 percent area in crop or 

pasture, less than 40 percent in forest, and less than 10 

percent urban. A site classified as forest has more than 

40 percent forest land, less than 40 percent in crop or 

pasture, and less than 10 percent urban.

The nutrient and suspended sediment concentrations at valley sites (fig. 27) represent primarily 

agricultural land use. The west side sites have 

considerably smaller drainage areas than the national 

sites and the east side sites do not strictly meet the 

land-use criteria of the national sites. However, the 

major reservoirs and diversions from these east side 

tributaries as they enter the valley floor make the east 

side sites basically agricultural sites. To provide a 

rough comparison of concentrations in the study unit to 

national conditions, the valley sites (both east and west 

sides) (fig. 27) were merged into composite boxplots of 

nitrate, total phosphorus, and suspended sediment 

concentrations (fig. 30). The median values for the 

10th, 25th, 50th, 75th, and 90th percentiles at valley 

west side and valley east side sites (fig. 27) were used 

to create composite boxplots to represent agricultural 

land in the study unit (fig. 30). The same was done for 

the Sierra Nevada sites to represent forest land in the 

study unit. Urban and range land uses are not 

represented by study unit sites.

A comparison of concentrations of nitrate, total 

phosphorus, and suspended sediment in the study area 

to national average concentrations for agricultural

areas is shown in figure 30A None of the concentrations are substantially different from the national 

averages. Nitrate concentrations are slightly higher; 

total phosphorus and suspended sediment 

concentrations are slightly lower than the national 

averages. For all three constituents, the west side 

concentrations are higher than the national averages, 

and the east side concentrations are lower.

The forested areas of the study unit are in the 

granitic Sierra Nevada and have extensive bedrock and 

thin soils. Runoff from these areas is low in nutrients 

and suspended sediment, and concentrations are 

substantially lower than the national averages 

(fig. 305).

RELATION OF NUTRIENT AND SUSPENDED 

SEDIMENT CONCENTRATIONS TO STREAMFLOW

A good relation of nutrient and suspended 

sediment concentrations to Streamflow is essential to 

load calculations. The eight representative sites from 

the section "Streamflow at Time of Water Quality 

Sampling" are used again. These sites include: (1) three 

Sierra Nevada sites (see table 6; fig. 18), Kings River 

below North Fork, near Trimmer (site 4), Tule River 

below Success Dam (site 8), and Merced River at 

Happy Isles Bridge (site 22); (2) two valley east side 

sites, Tuolumne River at Modesto (site 38), and 

Mokelumne River at Woodbridge (site 49); (3) one 

valley west side site, Mud Slough near Gustine (site 

21); and (4) two sites on the mainstem of the San 

Joaquin River, San Joaquin River near Newman (site 

27) and San Joaquin River near Vernalis (site 47). For 

each of these eight sites, we will discuss the relation 

between Streamflow and concentrations of nitrate, total 

phosphorus, and suspended sediment.

Nitrate concentrations in unmanaged streams 

typically decrease with increasing Streamflow, as the 

base flow is diluted (fig. 31). However, nitrate 

concentrations did not vary much with Streamflow at 

the three Sierra Nevada sites (figs. 31 A, B, and E) or 

one of the valley east side sites (Mokelumne River at 

Woodbridge [site 49; fig. 31G]). At the other valley east 

side site (Tuolumne River at Modesto [site 38; fig. 

31C]), the concentration generally decreased with 

increasing Streamflow. This probably is because of 

increasing dilution of agricultural return flows with 

Sierra Nevada runoff. The exceptions to the general 

trend in figure 31 C were samples collected during the 

low-flow summer of 1988. At the valley west side site

Relation of Nutrient and Suspended Sediment Concentrations to Streamflow 57
10

o

Q. 

CO 

O

03 

D)

0.5

o

o

0.2

0.1

0.05

0.02

0.01

Agricultural areas

————i——I———

Forest areas

— 90th percentile

— 75th percentile

—Median

— 25th percentile

— 10th percentile

A :

1,000 10

500

200 2

100 1

50 0.5

20 0.2

10 0.1

5 0.05

2 0.02

1 0.01

~ca B

1

1.000

500

200

100

50

03 

D)

20

10

T3 

0) 

T3

CO

Nitrate Total Suspended 

phosphorus sediment

Nitrate Total Suspended 

phosphorus sediment

Figure 30. Comparison of nitrate, total phosphorus, and suspended sediment concentrations, San Joaquin-Tulare Basins, California, study 

unit, to national sites, 1993 National Water Summary. (A) Agricultural areas. ^Forest areas.

(Mud Slough near Gustine [site 21; fig. 31F|), nitrate 

concentration generally increased with streamflow. 

This general trend probably is because of an increasing 

proportion of agricultural drainage as it is added to a 

base flow of ground water seepage. At higher flows, 

there is some natural runoff to this site from the Coast 

Ranges, which dilutes the agricultural drainage in Mud 

Slough. Samples collected during the high flow period

of February through April 1986 were exceptions to the 

general trend in figure 3 IF.

The San Joaquin River near Newman site (site 

27) has the common inverse relation between nitrate 

concentration and streamflow (fig. 3 ID). Flows at this 

site come from the Merced River, Salt and Mud 

Sloughs, and the San Joaquin River upstream of the 

sloughs. At higher streamflows, proportionately more

58 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
,^

00 CD

- «

CO CO O

o = 

CD :± 

=*. O

o

CO

lilligrams per liter, as N

o c

k> c

O 01 C

o

o o

b 

o oo

o 

o o 1_

- N:

--=]

-d

_l

fa ^

Et

1 =

f 1!

r 

fl

i i i i r

n^++

t^*+ T T^ -|- +

j-h

++

; + 

'*l

+*

r

1 1

^ CO CO

5 o' S 

S K o o. w = 

5 ^

O o> en

IS |

s?f °

{

: +

-

i i i i 5

oT

CD

=.

Q. 

0>

-r

I i 

b8

+

+

+

-

1 1 I I

o> ro

i i i r

i i i i +

i i i i
flow comes from the Merced River, diluting flows from 

the sloughs that are dominated by agricultural 

drainage.

At the Vernalis site (site 47), the relation is more 

complex (fig. 31//). For flows greater than about

T

1,000 ft /s, the common inverse relation holds.

o

Increases in streamflow above 1,000 ft /s generally 

come from the east side tributaries, which have low 

nitrate concentrations. At flows less than 1,000 ft3/s, 

concentrations increase with streamflow due to two 

factors: (1) water quality at Vernalis is maintained by 

releases of water with low nutrient concentrations from 

the New Melones Reservoir on the Stanislaus River 

(site 24, fig. 6; table 1) to meet water quality criteria for 

specific conductance, and (2) major diversions from 

the San Joaquin River upstream of the Tuolumne River 

remove most of the river flow during low-flow periods 

leaving primarily water from the Tuolumne and 

Stanislaus Rivers (Kratzer and Grober, 1991). Both 

factors reduce the effect of west side agricultural 

drainage at Vernalis.

Total phosphorus concentrations in unmanaged 

streams usually are fairly constant or increase slightly 

with increasing streamflow, depending on the amount 

of total phosphorus attached to suspended sediment. In 

general, the relation between total phosphorus and 

streamflow at the eight representative sites (fig. 32) was 

similar to the relation for nitrate. The main difference 

is the steepness of the curves for Mud Slough (figs. 3 IF 

and 32F) and the San Joaquin River sites (figs. 31 D 

and H; figs. 32 D and //). Unlike nitrate, total 

phosphorus concentrations in subsurface agricultural 

drains are low, and the curves are less steep because of 

relatively lower concentrations of total phosphorus in 

west side agricultural discharges.

Suspended sediment concentrations in streams 

typically increase with streamflow, as higher stream 

velocities dislodge bottom materials and are capable of 

suspending larger-size sediment (fig. 33). This is 

shown at the Sierra Nevada sites on the Kings and 

Merced Rivers (figs. 33A and B). The higher concentrations on the Kings River appear to be primarily due 

to higher streamflows, because the concentration at 

both sites increases at streamflows above 1,000 ft3/s. 

The relation at the third Sierra Nevada site (Tule River 

below Success Dam [site 8], fig. 33F) is affected by the 

reservoir just upstream of the site, because suspended 

sediment settles in the reservoir and alters the typical 

relation.

All suspended sediment samples at the valley 

west side site (Mud Slough near Gustine [site 21]; fig. 

33F) and one valley east side site (Tuolumne River at 

Modesto [site 38]; fig. 33Q were collected during 

1985-1988. This was primarily a period of low 

streamflow except during spring 1986, when high 

streamflows produced higher suspended sediment 

concentrations. The other valley east side site 

(Mokelumne River at Woodbridge [site 49]; fig. 33G) 

displayed a rapid increase in suspended sediment 

concentration at streamflows greater than 1,000 ft3/s.

The relation between suspended sediment and 

streamflows at the two San Joaquin River sites (near 

Newman [site 27] and near Vernalis [site 47]) is not 

typical (figs. 33D and H). Higher streamflows at these 

sites usually indicate more highly concentrated inflows 

from the west side and more diluting streamflows from 

east side tributaries. Because the east side tributaries 

contribute more streamflow, the overall effect on San 

Joaquin River suspended sediment concentrations is a 

slight decrease in concentration with increasing 

streamflow.

LOAD ESTIMATES

Annual Stream Loads

Annual stream loads were estimated using 

ESTIMATOR (version 92.11). The program requires 

daily flow records and enough water quality data to 

develop a quantitative relation between flows and 

constituent concentrations. The standard error of the 

estimated load is calculated to evaluate the accuracy of 

the estimate. In this study, estimates with a standard 

error of less than 30 percent were accepted as 

reasonable. For standard error between 30 and 50 

percent, the estimates are marked as questionable; 

estimates with standard error greater than 50 percent 

are not reported. The standard error of prediction 

allows the calculation of a 95-percent confidence 

interval for the load estimates.

The water quality data used to calculate loads at 

several sites were collected during USGS studies on 

the San Joaquin River during 1986-1988. Reasonable 

load estimates are reported for 23 sites in the study unit 

for nitrate, 15 sites for total nitrogen, 20 sites for total 

phosphorus, and 14 sites for suspended sediment 

(table 9). The water quality data for 14 of the sites for

60 Nutrients end Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
0.25

0.20

0.10

Station 11218500

Site 4

Kings River below North Fork,

near Trimmer 

———— LOWESS smooth

100 1,000 10,000 100,000

Q. 

OT

E

CO 

O)

I

_c 

o

0.25 

°- 20

0.10

B

Station 11264500

Site 22

Merced River at Happy Isles Bridge

———— LOWESS smooth____

10 100 1,000 10,000

rat

o 

01

O

OT

o

Q. 

OT

o

Q. ~ja 

o

o noUl

Station 11290000 

Site 38

Tuolumne River at Modesto 

—— LOWESS smooth

+

10 100 1,000 10,000

r* O

o 

bi

O

0

100

Station 11274000

Site 27

San Joaquin River near Newman

———— LOWESS smooth

0.25

0.20

0.10

E

Station 3603241 18552401 

Site 8

Tule River below Success Dam 

———— LOWESS smooth

0.1 10 100 1,000 10,000

1.0

0.50

Station 11262900

Site 21

Mud Slough near Gustine

———— LOWESS smooth

10 100 1,000

0.25

0.20

0.10

Station 11325500 

Site 49 

Mokelumne River at

Woodbridge 

——— LOWESS smooth

0.1 10 100 1,000 10,000

1.0

0.50

0

H

Station 11303500 

Site 47

San Joaquin River 

near Vernalis 

———— LOWESS smooth

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

Streamflow, in cubic feet per second

Figure 32. Relation between streamflow and total phosphorus concentrations at selected sites in San Joaquin-Tulare Basins, California, 

study unit, 1972-1990. See figure 18 for site locations.

Load Estimates 61
a 31 c: (o 

a. e

Suspended-sediment concentration, in milligrams per liter

s-fj

_. 30

CO

o 

o

0

o 

o

Ol

o

o 

o

IV) 

O

!=V 03

CD 3

— Q.

0

05

o" ->•

g o

- o

5' o

g 8

g; o'

o

T3 

0

0 

O

o

Q. O

O 

O"o

O 

O

1"

a -z.

CO

o 

o

o

o

I I I I

H w eg

O 

O

O

o 

o

o 

o 

o

fc

IV)

Ol 

Ol

o

o 

o

I I I I
Table 9. Nitrate, total nitrogen, total phosphorus, and suspended sediment load estimates in San Joaquin-Tulare Basins, California, study 

unit, 1986-1988

[ft3/s, cubic foot per second; ton/yr, ton per year; —, no data]

Site no. 

(fig. 18} Site name Water 

year

Mean daily 

streamflow

(tf/s)

NITRATE

Load 

(ton/yr)

Standard error of 

load estimate 

(percent)

Load, 

95-percent 

confidence interval 

(ton/yr)

Lower San Joaquin River Basin

16

19

20

21

26

27

31

38

42

45

47

San Joaquin River near Stevinson

Salt Slough near Stevinson

San Joaquin River at Fremont Ford Bridge

Mud Slough near Gustine

Merced River near Stevinson

San Joaquin River near Newman

San Joaquin River near Patterson

Tuolumne River at Modesto

San Joaquin River at Maze Road

Stanislaus River at Ripon

San Joaquin River near Vernalis

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1,824

70.6

27.5

272.7

265.3

264.5

2,273

342.6

288.8

119.6 !

57.7

53.0

860.9

219.8

152.2

3,294

673.1

546.9

3,697

911.5

758.1

1,843

721.8

215.0

6,016

1,820

1,063

1,336

734.5

599.5

7,220

2,505

1,609

231

34

12

860

1,155

1,393

954

1,059

1,270

1,048

324

*335

372

300

219

2,012

1,521

1,587

2,756

2,352

2,216

370

344

146

4,446

3,259

3,036

318

213

144

4,523

3,671

2,868

26

18

22

7.2

5.7

6.3

8.8

8.5

8.9

36

28

34

4.8

4.2

6.5

5.7

6.6

7.5

4.5

4.7

7.1

7.2

8.2

9.5

8.9

9.8

16

4.6

5.7

6.5

3.8

3.6

4.2

108-354

20-47

6.3-18

731-989

1,012-1,298

1,207-1,579

782-1,126

875-1,243

1,039-1,501

210-1,886

116-532

78-592

335 - 409

273 - 327

190-248

1,776-2,248

1,317-1,725

1,347-1,827

2,505 - 3,007

2,127-2,577

1,859-2,573

316-424

288 - 400

118-174

3,638-5,254

2,614 - 3,904

1,967-4,105

288-348

188-238

125 - 163

4,135-4,911

3,367-3,975

2,601-3,135

Other San Joaquin Basin

13 San Joaquin River below Friant Dam 1986

1987

1988

1,346

92.4

109.8

—

9.2

10

—

25

21

—

4.6-14

6.0-11

Load Estimates 63
Table 9. Nitrate, total nitrogen, total phosphorus, and suspended sediment load estimates in San Joaquin-Tulare Basins, California, study 

unit, 1986-1988—Continued

Site no. 

(fig. 18)

22

24

43

44

48

49

1

4

5

8

10

Site name

Merced River at Happy Isles Bridge

Merced River below Merced Falls

Stanislaus River Middle Fork at

Dardanelle

Stanislaus River below Goodwin Dam

Mokelumne River near Mokelumne Hill

Mokelumne River at Woodbridge

Kern River at Kernville

Kings River below North Fork, near

Trimmer

Kings River below Pine Flat Dam

Tule River below Success Dam

Kaweah River below Terminus Dam

Water 

year

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

Mean daily . . Standard error of 

streamflow . . . load estimate 

(tf/s) (t°n/yr) (percent)

539.0

158.5

207.5

1,488

893.7

707.4

188.2

65.1

66.7

1,184

619.4

561.7

1,647

447.3

323.3

1,117

215.7

31.7

Tulare Basin

1,577

458.8

362.5

3,553

823.2

855.9

3,853

1,687

1,234

313.4

89.8

48.0

1,103

232.9

236.3

23

7.6

10

62

30

25

H.6

4.4

4.2

413

58

48

! 29

'8.5

'6.0

'59

17

1 2.2

1 57

—

—

143

39

39

*307

1 209

—

4oo

1 24

48

'50

9.9

^.8

24

25

28

24

26

25

32

32

35

32

16

15

45

43

47

31

27

33

49

—

—

21

19

22

42

49

—

37

30

40

35

28

34

Load, 

95-percent 

confidence interval 

(ton/yr)

11-34

3.6-12

4.4-16

31-93

15-46

13-38

1.6-7.6

0.5-2.3

0.4-2.1

41-185

39-78

33-63

3.1-55

1.4-16

0.4-12

21-97

7.2 - 26

0.7-3.7

1.2-112

—

—

80 - 206

23-56

20-58

45 - 569

3.0-415

—

22-178

8.5-40

1.8-34

15-85

4.1-16

2.7-15

TOTAL NITROGEN

Lower San Joaquin River Basin

16 San Joaquin River near Stevinson 1986

1987

1988

1,824 1

70.6

27.5

,196

148

68

13

9.9

13

874-1,518

72 - 224

55-81

64 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Table 9. Nitrate, total nitrogen, total phosphorus, and suspended sediment load estimates in San Joaquin-Tulare Basins, California, study 

unit, 1986-1988—Continued

Site no. 

(fig. 18)

19

20

21

26

27

31

38

42

45

47

Site name

Salt Slough near Stevinson

San Joaquin River at Fremont Ford Bridge

Mud Slough near Gustine

Merced River near Stevinson

San Joaquin River near Newman

San Joaquin River near Patter son

Tuolumne River at Modesto

San Joaquin River at Maze Road

Stanislaus River at Ripon

San Joaquin River near Vernalis

Water 

year

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

Mean daily 

streamflow 

(ft3/*)

272.7

265.3

264.5

2,273

342.6

288.8

119.6

57.7

53.0

860.9

219.8

152.2

3,294

673.1

546.9

3,697

911.5

758.1

1,843

721.8

215.0

6,016

1,820

1,063

1,336

734.5

599.5

7,220

2,505

1,609

. . Standard error of Load . . .. . 

, , . load estimate (ton/yr) . .. 1 (percent)

1,295

1,604

1,776

2,664

1,490

1,809

793

328

275

810

454

324

4,827

2,371

2,221

6,420

3,820

3,440

1,147

726

277

9,483

5,690

4,472

1,085

605

389

9,594

6,006

4,492

6.1

5.5

6.3

8.9

8.0

9.2

14

11

13

5.4

3.9

6.0

6.4

6.3

7.5

6.6

6.7

10

7.6

7.9

9.1

7.3

7.7

12

11

11

12

3.0

2.3

2.7

Load, 

95-percent 

confidence interval

(ton/yr)

1,133-1,457

1,420-1,788

1,547-2,005

2,177-3,151

1,247-1,733

1,474_2,144

557-1,029

252 - 404

200 - 350

722 - 898

417-491

284 - 364

4,189-5,465

2,067 - 2,675

1,885-2,557

5,560 - 7,280

3,305 - 4,335

2,653 - 4,227

968-1,326

609 - 843

226 - 328

8,069 - 10,897

4,811-6,569

3,271 - 5,673

838-1,332

473 - 737

294 - 484

8,897 - 10,291

5,644 - 6,368

4, 199-4,785

Other San Joaquin Basin

22

43

1

Merced River at Happy Isles Bridge

Stanislaus River Middle Fork at

Dardanelle

Kern River at Kernville

1986

1987

1988

1986

1987

1988

1986

1987

1988

539.0

158.5

207.5

188.2

65.1

66.7

Tulare Basin

1,577

458.8

362.5

274

74

98

1 33

'7.9

'8.5

873

171

115

20

18

20

30

30

34

16

11

12

154 - 394

42 - 106

55-141

13-53

33-12.8

2.7-14.3

584-1,162

131-211

85 - 145

Load Estimates 65
Table 9. Nitrate, total nitrogen, total phosphorus, and suspended sediment load estimates in San Joaquin-Tulare Basins, California, study 

unit, 1986-1988—Continued

Site no. 

(fig. 18)

4

Site name

Kings River below North Fork, near

Trimmer

Water 

year

1986

1987

1988

Mean daily 

streamflow 

(frVs)

3,553

823.2

855.9

Load

(ton/yr)

2,090

352

345

Standard error of 

load estimate 

(percent)

19

12

13

Load, 

95-percent 

confidence interval 

(ton/yr)

1,295-2,885

258 - 446

247 - 443

TOTAL PHOSPHORUS

Lower San Joaquin River Basin

16

19

20

21

26

27

31

38

42

45

47

San Joaquin River near Stevinson

Salt Slough near Stevinson

San Joaquin River at Fremont Ford Bridge

Mud Slough near Gustine

Merced River near Stevinson

San Joaquin River near Newman

San Joaquin River near Patterson

Tuolumne River at Modesto

San Joaquin River at Maze Road

Stanislaus River at Ripon

San Joaquin River near Vernalis

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1,824

70.6

27.5

272.7

265.3

264.5

2,273

342.6

288.8

119.6

57.7

53.0

860.9

219.8

152.2

3,294

673.1

546.9

3,697

911.5

758.1

1,843

721.8

215.0

6,016

1,820

1,063

1,336

734.5

599.5

7,220

2,505

1,609

260

27

14

94

75

73

459

96

82

47

19

15

85

25

18

700

184

182

937

379

323

141

32

17

1,343

512

394

156

50

26

1,270

657

457

18

12

14

5.9

4.5

5.2

11

7.5

7.9

9.1

7.0

8.5

17

9.4

14

10

8.5

10

8.3

7.0

11

19

15

19

8

7.2

11

21

15

17

5.7

4.5

5.3

165 - 355

20-34

10-18

83 - 105

68-82

65-81

357-561

81-111

69-95

38-56

16-22

12-18

55-115

20-30

13-23

551-849

152-216

146-218

779 - 1,095

325-433

245-401

86 - 196

22-42

10-25

1,117-1,569

437 - 587

294 - 494

88 - 224

34-66

17-35

1,109-1,431

590 - 724

404-510

66 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Table 9. Nitrate, total nitrogen, total phosphorus, and suspended sediment load estimates in San Joaquin-Tulare Basins, California, study 

unit, 1986-1988—Continued

Site no. 

(fig. 18) Site name

Water 

year

Mean daily 

streamflow 

(ft3/*)

o-i-i i Load, 

. . Standard error of ... Load i j „• „ 95-percent 

. . . load estimate ... r . . . (ton/yr . ,. confidence interval percent u . . M (ton/yr)

Other San Joaquin Basin

13

22

24

37

43

44

49

1

4

San Joaquin River below Friant Dam

Merced River at Happy Isles Bridge

Merced River below Merced Falls

Tuolumne River at LaGrange Bridge

Stanislaus River Middle Fork at

Dardanelle

Stanislaus River below Goodwin Dam

Mokelumne River at Woodbridge

Kern River at Kernville

Kings River below North Fork, near

Trimmer

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1,346

92.4

109.8

539.0

158.5

207.5

1,488

893.7

707.4

1,566

391.4

107.2

188.2

65.1

66.7

1,184

619.4

561.7

1,117

215.7

31.7

Tulare Basin

1,577

458.8

362.5

3,553

823.2

855.9

! 52

5.0

6.6

9.8

2.5

3.2

20

11

8.1

22

5.7

1.5

6.1

1.4

1.2

'13

8.7

7.2

48

7.4

1.2

67

6.9

4.6

145

15

15

36

16

14

18

18

20

19

17

17

16

14

15

21

21

23

31

16

13

20

14

15

23

15

16

26

16

17

15-89

3.4-6.6

4.8 - 8.4

5.9-13.7

1.5-3.5

1.8-4.6

12-28

7-15

5.3-10.9

15-29

4.1-7.3

1.0-2.0

3.4-8.8

0.8-2.0

0.6-1.8

5-21

6.0-11.4

5.2-9.2

27-69

5.1-9.7

0.8-1.6

35-99

4.7-9.1

3.0-6.2

65 - 225

9-21

9-21

SUSPENDED SEDIMENT

Lower San Joaquin River Basin

16

19

21

San Joaquin River near Stevinson

Salt Slough near Stevinson

Mud Slough near Gustine

1986

1987

1988

1986

1987

1988

1986

1987

1988

1,824

70.6

27.5

272.7

265.3

264.5

119.6

57.7

53.0

172,778

6,662

1,382

46,135

48,485

56,226

24,988

9,786

5,047

29

21

27

16

17

19

15

13

17

68,390-277,166

3,727 - 9,597

635-2,129

30,810-61,460

32,110-64,860

34,446 - 78,006

17,363-32,613

7,200-12,372

3,351-6,743

Load Estimates 67
Table 9. Nitrate, total nitrogen, total phosphorus, and suspended sediment load estimates in San Joaquin-Tulare Basins, California, study 

unit, 1986-1988—Continued

Site no. 

(fig. 18)

26

27

31

38

42

45

47

Site name

Merced River near Stevinson

San Joaquin River near Newman

San Joaquin River near Patterson

Tuolumne River at Modesto

San Joaquin River at Maze Road

Stanislaus River at Ripon

San Joaquin River near Vernalis2

Water 

year

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

Mean daily 

streamflow

(tf/s)

860.9

219.8

152.2

3,294

673.1

546.9

3,697

911.5

758.1

1,843

721.8

215.0

6,016

1,820

1,063

1,336

734.5

599.5

7,220

2,505

1,609

Load 

(ton/yr)

47,969

5,227

3,140

283,988

73,593

69,415

397,777

90,420

74,663

r 75,324

8,294

1,969

621,597

187,810'

131,101

36,864

17,298

11,533

569,064

168,599

114,016

Standard error of 

load estimate 

(percent)

23

7.8

12

13

11

14

16

11

20

32

16

18

15

13

21

10

7.9

11

—

—

—

Load, 

95-percent 

confidence interval 

(ton/yr)

26,300 - 69,638

4,355 - 6,099

2,349-3,931

208,791-359,185

57,250 - 89,935

49,918-88,912

268,225 - 527,329

70,520-110,320

40,770-108,556

27,243 - 123,405

5,547-11,041

1,257-2,681

429,622-813,572

137,215-238,405

68,461 - 193,753

29,333 - 44,395

14,517-20,079

9,086-13,980

—

—

—

Other San Joaquin Basin

22

49

1

4

Merced River at Happy Isles Bridge

Mokelumne River at Woodbridge

Kern River at Kernville

Kings River below North Fork, near

Trimmer

1986

1987

1988

1986

1987

1988

1986

1987

1988

1986

1987

1988

539.0

158.5

207.5

1,117

215.7

31.7

Tulare Basin

1,577

458.8

362.5

3,553

823.2

855.9

3,072

546

657

40,583

2,698

654

193,128

3,731

2,359

_

*8,622

*7,636

16

13

14

21

13

15

25

13

14

_

33

36

2,002-4,142

338 - 704

466 - 848

22,667 - 58,499

1,919-3,477

574-734

89,042-297,214

2,652-4,810

1,628-3,090

_

712-16,532

403 - 14,869

'Questionable load estimates (standard error is 30 to 50 percent).

Suspended sediment loads for San Joaquin River near Vernalis were calculated in National Water Information System (NWIS), not by 

ESTIMATOR (a load calculation program).

68 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
all constituents are primarily from NWIS. The 

streamflow data used in the load calculations are 

entirely from NWIS.

Along with the load estimates, the percent 

standard error and the 95-percent confidence interval 

are given in table 9. Except for Salt Slough at Stevinson 

(site 19), all inputs to the lower San Joaquin River were 

greatest during 1986. The flows at the Salt Slough near 

Stevinson and Mud Slough near Gustine sites (sites 19 

and 21, respectively) are primarily irrigation derived; 

drainage flows can be routed through either slough 

because the sloughs are interconnected. This 

interconnection, along with Mud Slough's drainage 

basin in the normally dry Coast Ranges, accounts for 

the load variation in the sloughs during 1986-1988.

Although Salt and Mud Sloughs account for only 

about 10 percent of flow at Vernalis (Kratzer and 

others, 1987), they contribute nearly half of the nitrate 

load. Nitrate loads carried by other rivers in the study 

unit are small relative to the lower San Joaquin River. 

Nitrate loads in the Kings, Merced, and Stanislaus 

Rivers increase greatly between the Sierra Nevada and 

the valley (table 9).

Nitrate loads in the lower San Joaquin River for 

1986 and 1988 are presented schematically in figure 34 

using the estimates for 11 of the sites given in table 9. 

The schematic shows the difference between loads 

during a wet year (1986) and a critically dry year 

(1988). The nitrate load in the lower San Joaquin River 

near Vernalis during 1986 was more than 50 percent 

greater than the load during 1988 (fig. 34 and table 9). 

The difference between 1986 and 1988 was even 

greater for the Tulare Basin (sites 1, 4, 5, 8, and 10, 

table 9), Mokelumne River (sites 48 and 49), and San 

Joaquin River near Stevinson (site 16). The Stevinson 

site is the upstream boundary for the lower San Joaquin 

River. In 1986, this site received rare, significant flows 

from the upper San Joaquin River and the Kings River. 

Also, Bear Creek (fig. 34) contributed unusually high 

flows to the Stevinson site, including wastewater 

treatment plant effluent from the city of Merced (fig. 1). 

During dry periods, much of the streamflow in Bear 

Creek is diverted by agricultural users and never 

reaches the San Joaquin River.

The 1986 total nitrogen load estimate at Kings 

River below North Fork, near Trimmer (site 4, table 9)

is surprisingly high for a Sierra Nevada site. Like 

nitrate loads, total nitrogen loads for the Merced and 

Stanislaus Rivers increase greatly between the Sierra 

Nevada and the valley. The total nitrogen loads in the 

lower San Joaquin River are shown schematically in 

figure 35. The general pattern is similar to nitrate, with 

the main differences being the relative load at the 

Stevinson site on the San Joaquin River (site 16) in 

1986 and the amount of variation between 1986 and 

1988. The total nitrogen load at Vernalis in 1986 was 

about twice the 1988 load. The 1986 load at Stevinson 

(site 16) was about equal to the load in Salt Slough (site 

19, table 9).

As with nitrate and total nitrogen loads, the total 

phosphorus load in east side tributaries increases 

greatly from the Sierra Nevada to the valley (table 9). 

The total phosphorus loads in the lower San Joaquin 

River system are shown schematically in figure 36. The 

1986 load in the San Joaquin River near Vernalis (site 

47, table 9) was almost three times greater than the 

1988 load. The 1986 load at the upstream boundary site 

at Stevinson (site 16) was greater than the load from 

Mud and Salt Sloughs combined (sites 19 and 21).

As previously mentioned, suspended sediment 

loads increase more with streamflow than do nutrient 

loads. As a result of the greater influence of streamflow 

on suspended sediment concentrations, the 1986 load 

near Vernalis was almost five times greater than in 1988 

(site 47, table 9). The suspended sediment loads in the 

lower San Joaquin River system are shown in figure 37. 

The load at Stevinson (site 16) was high in 1986. As 

with nitrogen loads, the suspended sediment load at 

Salt Slough (site 19) was smaller in 1986 than in 1988.

The load schematics for the lower San Joaquin 

River system (figs. 35-37) show only major inputs. As 

discussed earlier in this report, several smaller inputs 

throughout the system contribute much of the 

unaccounted-for loads between San Joaquin River 

sites. Unaccounted-for nitrate, total nitrogen, total 

phosphorus, and suspended sediment loads during 

1986-1988 are summarized in table 10. These 

unaccounted-for loads represent between 22 and 68 

percent of the difference in estimated loads between 

Stevinson and Vernalis.

Water year 1986 was a wet year, and water year 

1988 was a critically dry year. To put the loads

Load Estimates 69
37° 

45'

37° 

15'

Sacramento-1 ^

~^San Joaquin J 

42

.$

Spanish Grant Drain

121° 00'

EXPLANATION 

Annual nitrate loads, in tons 

per year (as N)

I—I 1986 (wet year)

I I 1988 (critically dry year)

I I Overlap of 1986 and 1988

1,000

-2,000 

3,000

-4,000

5,000

— — — Study unit boundary 

16* Site number and location

Turlock Irrigation District lateral 5

26

27

Wasteway

20

21

1 1 1 5 MILES

5 KILOMETERS

£c°

6

<g*195|

0

Figure 34. Annual nitrate loads in San Joaquin-Tulare Basins, California, study unit, during wet year (1986) and critically dry year (1988). See 

table 9 for site names.

70 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
121° 00'

37° 

45'

^

Sacramento--^ 

San Joaquin )

./"' 

*J

tf'

37° 

15'

5

Spanish Grant Drain

5 MILES

5 KILOMETERS A

EXPLANATION

Annual total nitrogen loads, 

in tons per year (as N)

I—i 1986 (wet year)

tZZ11988 (critically dry year)

H Overlap of 1986 and 1988

(0

o 

oo

- 2,000

- 4,000

- 6,000 

8,000

10,000

— — — Study unit boundary 

16* Site number and location

Turlock Irrigation District lateral 5

26 Merced Riv«r J

27^

Wastewav'

V

Figure 35. Annual total nitrogen loads in San Joaquin-Tulare Basins, California, study unit, during wet year (1986) and critically dry year 

(1988). See table 9 for site names.

Load Estimates 71
37° 

45

Sacramento-^ 

San Joaauin }

37° 

15'

«•

-3s J.'

Spanish Grant Drain

0

121° 00'

5 MILES 0

-i——i o^vj

>

5 KILOMETERS

EXPLANATION 

Annual total phosphorus loads, 

in tons per year (as P)

[—I 1986 (wet year)

I I 1988 (critically dry year)

ETJ Overlap of 1986 and 1988

CO

E _

"o"o

-375 

750 

1,125

1 I_L 1 ,500

— — — Study unit boundary 

16* Site number and location

Turlock Irrigation District lateral 5

*26 Merced W

Wasteway

20'

'"'

6

21 •

-•-

Figure 36. Annual total phosphorus loads in San Joaquin-Tulare Basins, California, study unit, during wet year (1986) and critically dry year 

(1988). See table 9 for site names.

72 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
37° 

45'

37° 

15'

t

Sacramento-^ d?'

San v Joaquin J - N> | ^ ^

^,

42

•V

Spanish Grant Drain

5 MILES

5 KILOMETERS A$

121° 00'

EXPLANATION

Annual suspended sediment 

loads, in tons per year

I I 1986 (wet year)

I I 1988 (critically dry year)

Hisn Overlap of 1986 and 1988

o

0 0

140,000

280,000

420,000

540,000

700,000

— — — Study unit boundary 

16* Site number and location

Turlock Irrigation District lateral 5

I

Wasteway 6

21

Figure 37. Annual suspended sediment loads in San Joaquin-Tulare Basins, California, study unit, during wet year (1986) and critically dry 

year (1988). See table 9 for site names.

Load Estimates 73
Table 10. Nitrate, total nitrogen, total phosphorus, and suspended sediment loads in the lower San Joaquin River, California, that are 

unaccounted for by inputs from major tributaries, 1986-1988

San Joaquin River reach

Stevinson to Fremont

Ford Bridge

Fremont Ford Bridge

to Newman

Newman to Patterson

Patterson to Maze

Road

Maze Road to Vernalis

Total — Stevinson to

Vernalis

Change in 

load in 

reach1 

(ton per 

year)

723

1,058

744

1,690

77

4,292

1986

Unac- _. ... 

. Change in load _. counted- , :. . Change in 

, . . from Stevinson . j. for load .. ,. load in 

.... to Vernalis .1 within , . reach 1 .2 (unaccounted- . reach" . 3 ton per 

. for in reach ) . ton per . . year) year) (percent)

-136

-362

744

1,319

-240

1,325

-3

-8

17

31

-6

31

Nitrate

1,025

462

831

907

412

3,637

1987

Unac- „. - , . 

. Change in load _. counted- , !! . Change in 

. . . from Stevinson . jr. for load . „ .. load in 

... to Vernalis .1 within , . reach .2 (unaccounted- ,

,reach for in reach') (t°n ""

It0npfr (percent) year) 

year) 'p

-129

-163

831

562

200

1,301

-3

-4

23

15

5

36

1,258

317

629

820

-168

2,856

1988

Unac- Change in 

counted- load from 

for load Stevinson to 

within Vernalis 

reach2 (unaccounted- 

(ton per for in reach3) 

year) (percent)

-136

-237

629

674

-312

618

-5

-8

22

24

-11

22

Total Nitrogen

Stevinson to Fremont

Ford Bridge

Fremont Ford Bridge

to Newman

Newman to Patterson

Patterson to Maze

Road

Maze Road to Vernalis

Total — Stevinson to

Vernalis

1,468

2,163

1,593

3.063

111

8,398

172

560

1,593

1.916

-974

3,267

2

7

19

23

-12

39

1,342

881

1,449

1,870

316

5,858

-263

98

1,449

1.144

-289

2,139

-5

2

25

20

-5

37

1,741

412

1,219

1,032

20

4.424

-35

-187

1,219

755

-369

1,383

-1

-4

27

17

-8

31

Total Phosphorus

Stevinson to Fremont

Ford Bridge

Fremont Ford Bridge

to Newman

Newman to Patterson

Patterson to Maze

Road

Maze Road to Vernalis

Total — Stevinson to

Vernalis

199

241

236

406

-73

1,009

105

110

236

266

-228

489

10

11

23

26

-23

48

69

88

195

133

145

630

-7

44

195

102

95

429

-1

7

31

16

15

68

68

100

141

71

63

443

-5

67

141

54

38

295

-1

15

32

12

9

67

Suspended Sediment

Stevinson to Newman

Newman to Patterson

Patterson to Maze

Road

Maze Road to Vernalis

Total — Stevinson to

Vernalis

111,210

113,789

223,820

-52.533

396,286

-7,882

113,789

148,495

-89.397

165.005

-2

29

38

-23

42

66,931

16.827

97,390

-19.211

161.937

3,432

16,828

89,095

-36.508

72,847

2

10

55

-22

45

68.033

5,248

56,438

-17.085

112,634

3.620

5,248

54,475

-28.624

34,719

3

5

48

=25_

31

For example, the change in load in the reach from Maze Road to Vernalis = San Joaquin near Vernalis load — San Joaquin River at Maze 

Road load.

ft

For example, the unaccounted-for load in the reach from Maze Road to Vernalis = San Joaquin River near Vernalis load — Stanislaus River 

at Ripon load — San Joaquin River at Maze Road load. Positive values mean that the load at the downstream site is under-accounted-for by 

inputs from major tributaries. Negative values mean that the load at the downstream site is over-accounted-for by inputs from major 

tributaries. 

"Equals (unaccounted-for load in reach/change in load from Stevinson to Vernalis) x 100.

74 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
6,000

Year

30,000 

z 25,000 

^ 20,000 

>< 15,000

£ 10,000

c 

o

^I;^ ijltli.ii

Year

3,000

2,500

2,000

1,500

1,000

500

—i—i—i—i—i—i—i—r

Total phosphorus

li m fi & j^KiN fe ^ 511 ^l k.

Year

Year

Figure 38. Annual nitrate, total nitrogen, total phosphorus, and 

suspended sediment loads at San Joaquin River near Vernalis site, 

1972-1990.

discussed in this section into a long-term perspective, 

the annual loads of nitrate, total nitrogen, total phosphorus, and suspended sediment at the San Joaquin 

River near Vernalis site during 1972-1990 are shown in 

figure 38. The 1986 loads are in the first quartile 

(highest 25 percent) for nitrate, total nitrogen, and 

suspended sediment and the second highest quartile for 

total phosphorus. The 1988 loads are in the third 

quartile for nitrate, total nitrogen, and total phosphorus 

and the fourth quartile for suspended sediment.

The ratios of wet year loads (1986) to critically 

dry year loads (1988) for nitrate, total nitrogen, total 

phosphorus, and suspended sediment are a function of 

the relation of concentration to streamflow. Suspended 

sediment concentrations increase with streamflow, and 

the ratios of wet year to dry year loads increase as the 

proportions of constituents associated with the particulate fraction increase. The particulate fractions of total 

nitrogen and total phosphorus were calculated from the 

NWIS database using the median of 24 monthly mean 

particulate fractions for 1986 and 1988. The particulate 

fractions and load ratios for the San Joaquin River near 

Vernalis site are:

Constituent

Nitrate

Total nitrogen 

Total phosphorus 

Suspended sediment 

Streamflow

Particulate 

fraction

0

0.14 

0.40

1 

<0.0001

Wet year

(1986) to

dryyear

(1988) ratio

1.58

2.14

2.78

4.99

4.50

Thus, the transport of suspended sediment and 

particulate-associated nutrients increases more with 

streamflow than does the transport of dissolved 

nutrients.

Relation of Stream Loads to Upstream Conditions

Most of the unaccounted-for loads shown in 

table 10 could be attributed to agricultural discharges 

and diversions (see figs. 8 and 13), wastewater treatment plant discharges (see fig. 9), and uncertainty in 

the load estimates (see 95-percent confidence interval 

in table 9). The reach of San Joaquin River from 

Fremont Ford Bridge (site 20, fig. 17) to Newman (site 

27) includes Los Banos Creek and Newman Slough 

(fig. 13), which are potentially significant sources of 

nutrients not attributed to Salt Slough near Stevinson

Load Estimates 75
(site 19), Mud Slough near Gustine (site 21), or the 

Merced River. Los Banos Creek flows from the Coast 

Ranges, through rangeland and wetland areas, and discharges to Mud Slough below the gaging station. Flow 

and load in Los Banos Creek would be most significant 

during wet periods, such as 1986. Newman Slough, 

which carries surface and subsurface agricultural 

drainage from 4,500 acres and wastewater treatment 

plant effluent from the city of Newman during wet 

periods, discharges to the San Joaquin River just upstream of the Merced River (James and others, 1989). 

These sources could account for much of the nutrient 

loads in this reach. In the San Joaquin River from 

Stevinson to Newman, the suspended sediment loads 

are almost completely accounted for by the inputs from 

Mud and Salt sloughs and the Merced River.

The unaccounted-for nutrient and suspended 

sediment loads between Newman and Patterson can be 

attributed primarily to Orestimba Creek, Spanish Grant 

Drain, Turlock Irrigation District lateral number 5 

(fig. 13), and several smaller agricultural discharges. 

Turlock Irrigation District lateral number 5 discharge 

includes effluent from the city of Turlock wastewater 

treatment plant. Unaccounted-for loads between 

Patterson and Maze Road (sites 31 and 42, fig. 18) can 

be attributed primarily to Del Puerto Creek, Hospital 

Creek, Ingram Creek (fig. 13), the city of Modesto 

wastewater treatment plant discharge, and several 

smaller agricultural discharges including Olive Avenue 

Drain and Gray son Road Drain (sites 32 and 35, 

fig. 18).

The Stanislaus River is the only major input 

between Maze Road (site 42, fig. 18) and Vernalis (site 

47). According to the load estimates, there were 

usually losses of nutrients and suspended sediment in 

this reach. These losses can be attributed to agricultural 

diversions and uncertainty in the load estimates.

Loads in the San Joaquin River can be roughly 

assigned as from either west side or east side sources 

based on the estimated loads given in table 9, the 

unaccounted-for loads, and loading estimates for the 

Turlock and Modesto wastewater treatment plants. 

Most nitrate and suspended sediment loads can be 

attributed to west side sources, especially during dry 

years. Total nitrogen and total phosphorus loads cannot 

be clearly attributed to either west side or east side 

sources due to the large unaccounted-for component of 

the total loads (31 to 68 percent, table 10).

Atmospheric Loads

Nitrogen atmospheric deposition data are available from the State Atmospheric Acidity Protection 

Program (California Air Resources Board, 1991) and 

the federal National Atmospheric Deposition Program, 

or NADP (National Atmospheric Deposition Program 

[NRSP-3]/National Trends Network, 1992) for six 

sites in the study unit (sites 1-6, fig. 39). Another state 

site (site 7, fig. 39), outside the study unit, in 

Sacramento, is useful to estimate deposition in the 

northern half of the San Joaquin Valley. No 

atmospheric deposition data were available for 

phosphorus from these data sources. Most total 

phosphorus values measured previously by the NADP 

were less than the reporting level of 0.01 mg/L as P 

(Larry Puckett, U.S. Geological Survey, oral commun., 

1993).

Mean nitrogen loading at each of these sites 

during the sampling periods is shown in table 11. The 

sampling periods vary among sites, but generally 

include water years 1986-1988, plus additional 

months. The total nitrogen loading is the sum of the 

ammonia wet deposition, the nitrate wet deposition, 

and the nitrate dry deposition. The state and federal 

programs reported wet deposition values that are based 

on volume-weighted mean concentrations during 

precipitation. The dry deposition of nitrate is 

calculated from the ratio of dry-to-wet deposition for 

western states (Sisterton, 1990).

The significance of these atmospheric 

deposition values was evaluated by comparing the 

atmospheric deposition of total nitrogen in eight 

selected drainage basins (fig. 39A-H) to the stream 

loads carried from the drainage basins (table 12). This 

deposition in drainage basins is calculated from the 

total nitrogen values in table 1 1 and a qualitative 

assignment of drainage areas (weighting factors in 

table 12) to deposition sites that are based on 

precipitation, elevation, and land use. The eight 

drainage basins (fig. 39) include three Sierra Nevada 

basins (A,B,C), three valley east side basins (D,E,F), 

one valley west side basin (H), and the San Joaquin 

River near Vernalis basin (C-H).

When comparing atmospheric deposition loads 

to stream loads, it is important to consider factors 

affecting the runoff coefficient for the drainage basin 

such as slope, soil characteristics, land use, and the 

manipulation of flow. The runoff coefficient is the 

proportion of total rainfall volume in a watershed that

76 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
EXPLANATION 

Drainage basin for gaging station

^^H Kern River at Kernville

B | Kings River below North Fork

' near Trimmer

C I Merced River at Happy Isles Bridge

CD Merced River near Stevinson

JE I Tuolumne River at Modesto

—i

Stanislaus River at Ripon

San Joaquin River near Vernalis 

(Lower San Joaquin River Basin)

Salt Slough near Stevinson and 

Mud Slough near Gustine

Study unit boundary 

Basin boundary 

Atmospheric deposition site

40 MILES

40 KILOMETERS

Figure 39. Atmospheric deposition sites and selected drainage basins for load comparisons in San Joaquin-Tulare Basins, California, study 

unit.

Load Estimates 77
Table 11. Mean nitrogen loads at atmospheric deposition sites, San Joaquin-Tulare Basins, California, study unit

[CARB, California Air Resources Board; NADP, National Atmospheric Deposition Program, ft, feet; NH4-N, ammonia as N; NO3-N, 

nitrate as N; ton/mi2/yr, ton per square mile per yearj

Site no. Site 

(fig. 39) name

1

2

3

4

5

5

6

6

7

Bakersfield

Lake Isabella

Lindcove

Ash Mountain

Sequoia National Park (Giant Forest)

Sequoia National Park (Giant Forest)

Yosemite National Park

Yosemite National Park

Sacramento

Sampling 

program

CARB

CARB

CARB

CARB

CARB

NADP

CARB

NADP

CARB

Altitude 

(ft)

394

2,658

459

1,798

6,201

6,240

4,577

4,620

112

Sampling 

period

7/85

7/86

7/86

7/8

7/86

10/85

7/85

10/85

7/85

-6/89

-6/89

-6/88

-6/89

-6/89

-9/89

-6/89

-9/89

-6/89

Atmospheric deposition load (ton/mi'Vyr)

NH4-N 

(wet)

0.276

0.104

0.436

0.432

0.408

0.292

0.280

0.354

0.508

N03-N 

(wet)

0.136

0.116

0.252

0.340

0.304

0.263

0.280

0.403

0.240

N03-N 

(dry)

0.053

0.045

0.098

0.133

0.118

0.103

0.109

0.157

0.094

Total 

nitrogen

0.465

0.265

0.786

0.905

0.830

0.658

0.669

0.914

0.842

flows from the watershed as surface water. This 

coefficient defines the link between atmospheric 

deposition and transport in streams. The link is 

expected to be strongest at the Sierra Nevada sites, 

particularly the Merced River at Happy Isles Bridge (C, 

fig. 39). This site is in a small headwaters drainage 

basin of steep granite with no flow manipulation and is 

within 15 mi of an atmospheric deposition sampling 

site. As expected, the atmospheric deposition load of 

nitrogen is nearly equal to the stream load of nitrogen 

in this basin (table 12). The same is true generally for 

the larger, lower-elevation Kings River Basin (basin B, 

fig. 39). although the link between deposition and 

transport is not as strong due to other factors such as 

flow manipulation, lesser slopes, more permeable soils, 

and the extrapolation of atmospheric deposition loads 

from more distant sites.

The west side drainage basin (H in fig. 39 and 

table 12) has the least rainfall and the smallest runoff 

coefficient of the eight basins. In addition, it has a large 

load of total nitrogen from surface and subsurface 

agricultural drainage. Thus, atmospheric deposition 

contributes much less of the stream nitrogen load than 

the Sierra Nevada sites as indicated in table 12.

Conclusions about the relative magnitude of 

atmospheric deposition at the other sites are not 

possible. The link between atmospheric deposition and 

streamflow is weak in the valley due to flat slopes, flow 

manipulation, and agricultural use of precipitation.

Runoff coefficients in the valley are low, and most 

contributions to streamflow are from irrigation return 

flows. Thus, although the deposition load in east side 

tributaries is greater than stream loads (table 12), the 

actual contribution to stream loads is relatively small. 

At Vernalis, the contribution of atmospheric deposition 

is undoubtedly less than at the east side tributary sites 

because loads from the west side are almost exclusively 

land based.

Total Loads in the Lower San Joaquin 

River Basin

Nutrient loads and sources were evaluated for the 

drainage basins shown in figure 39. The shaded area in 

figure 39 (basins C-H) is the drainage basin for the 

lower San Joaquin River, with headwaters in the Bear 

Creek drainage, the eastern portion of drainage 

basin G.

Mean stream loads, point sources (municipal and 

industrial), and nonpoint sources (fertilizer application, 

manure production, subsurface agricultural drainage, 

and atmospheric deposition) are summarized for 

drainage basins C through H (table 13; fig. 39). At the 

Merced River at Happy Isles (basin C), the only 

quantified nutrient source is atmospheric deposition, 

which accounts for most of the total nitrogen and total 

phosphorus stream load leaving the basin. In the other

78 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California. 1972-1990
Table 12. Comparison of stream loads and atmospheric deposition loads for total nitrogen in selected drainage basins, San Joaquin-Tulare 

Basins, California, study unit, 1986-1988

[mi2 , square mile; ton/yr, ton per year]

Drainage basin 

(fig. 39)

Drainage 

area 

(mi2)

Weighting factor for 

atmospheric 

deposition sites

Stream 

load 

(ton/yr)

Atmospheric 

deposition load for 

total nitrogen, as N 

(ton/yr)

A Kern River at Kernville

B Kings River below North Fork, 

near Trimmer

C Merced River at Happy Isles Bridge

C, D Merced River near Stevinson

E Tuolumne River at Modesto

F Stanislaus River at Ripon

C-H San Joaquin River near Vernalis

Sierra Nevada

1,027 ! 0.8 Giant Forest 

0.2 Lake Isabella

1,342

181

1 Q.6 Giant Forest 

0.3 Ash Mountain 

0.1 Lindcove

1 1.0 Yosemite

San Joaquin Valley, East Side

1,394 ! 0.7 Yosemite

0.2 Sacramento 

0.1 Lindcove

1,842

1,111

^.7 Yosemite 

0.2 Sacramento 

0.1 Lindcove

k).7 Yosemite 

0.2 Sacramento 

0.1 Lindcove

H Salt Slough near Stevinson and 

___ Mud Slough near Gustine

San Joaquin River

7,345 ^.6 Yosemite

0.2 Sacramento 

0.1 Lindcove 

O.lBakersfield

San Joaquin Valley, West Side

473 l.OBakersfield

386

929

149

529

717

693

6,697

655

1,070

143

1,020

1,510

862

5,339

2,024 221

Average values from Sequoia National Park (Giant Forest) and Yosemite National Park (table 11).

basins, the mean stream load leaving the basins 

accounts for 5 to 10 percent of the nitrogen sources and 

2 to 5 percent of the phosphorus sources.

The maximum possible contribution of point 

sources to mean stream load is shown in table 13. It was 

assumed that none of the nitrogen or phosphorus from 

point source discharges was diverted at the points 

identified in figure 8, and, therefore, flowed to Vernalis. 

This is an unreasonable assumption, especially during 

the irrigation season of a dry year when most of the San 

Joaquin River upstream of the Tuolumne River 

confluence is diverted.

During 1986-1988, the total transport of nutrients from the lower San Joaquin River Basin (fig. 39)

was about 5 percent of the total sources of total 

nitrogen and about 3 percent of the total sources of total 

phosphorus (table 13). Nonpoint sources accounted for 

at least 81 percent of this nitrogen transport and at least 

68 percent of this phosphorus transport.

TRENDS IN CONSTITUENT CONCENTRATIONS

Trends in concentrations of nitrate, ammonia, 

total nitrogen, orthophosphate, total phosphorus, and 

suspended sediment during the 1980s at the long-term 

water quality monitoring sites (fig. 18) were evaluated 

using the PT2 program. For nitrate and suspended

Trends in Constituent Concentrations 79
Table 13. Estimated loads of total nitrogen and total phosphorus in the lower San Joaquin River Basin, California, by subbasin for late 1980s

[All loads given as ton per year; top number is total nitrogen load, as N, (bold numbers in parentheses represent total phosphorus load, as P); 

ft3/s, cubic foot per second]

Drainage basin 

(see fig. 39)

Merced River at Happy Isles

Bridge (C)

Merced River near Stevinson (D)

Tuolumne River at Modesto (E)

Stanislaus River at Ripon (F)

Mud and Salt Sloughs (H)

San Joaquin River near Patterson

(C, D, H, and part of G)

San Joaquin River near Vernalis

(C, D, E, F, G, and H)

Drainage 

area 

(mi2)

181

1,394

1,842

1,111

473

3,736

7,345

Mean1 

stream 

load, 

1986-1988

149

(5)

529

(43)

717

(63)

693

(77)

2,024

(108)

4,560

(546)

6,697

(795)

Load from point sources

Municipal2

0

(0)

24

(4)

0

(0)

0

(0)

0

(0)

625

(114)

1,254

(228)

Industrial3

0

(0)

0

(0)

0

(0)

0

(0)

0

(0)

28

(25)

28

(25)

Subsurface 

agricultural 

drains4

0

(0)

0

(0)

0

(0)

0

(0)

1,392

(6)

1,449

(6)

1,487

(7)

Load from nonpoint sources

Atmospheric 

deposition5

143

(3)

1,020

(20)

1,510

(30)

862

(17)

221

(4)

2,437

(49)

5,339

(107)

Fertilizer 

application6

0

(0)

2,536

(365)

2,263

(326)

3,888

(560)

13,733

(1,978)

33,623

(4,843)

50,931

(7,335)

Manure 

production7

0

(0)

3,720

(1,004)

3,537

(923)

4,698

(1,196)

9,571

(2,496)

34,153

(8,900)

65,558

(16,928)

^ee table 9.

^Based on information in National Pollutant Discharge Elimination System files (see table 2) and unpublished nutrient data from cities of Turlock and Mode

nitrogen concentration of 22 mg/L as N, total phosphorus concentration of 4 mg/L as P, and total wastewater treatment plant discharge at Vernalis of 58 ft3

3Based on information regarding the industrial discharges shown in figure 9 (Ken Landau, California Regional Water Quality Control Board - Central Valley 

are assumed to be cooling water only, with no nutrient content. A small milk production facility is included, with estimated nutrient concentrations of 36.5 

for total phosphorus (Larry Puckett, U.S. Geological Survey, written commun., 1993). 

4 Assuming a drainage factor of 0.7 acre-feet per acre for the area of tile drains shown in figure 12 (58,489 acres) and other reaches of the San Joaquin River 

Calculations are based on a total nitrogen concentration of 25 mg/L as N for the 58,489 acres and 10 mg/L as N for the 10,010 acres and a total phosphorus 

California Department of Water Resources, 1975). 

5Total nitrogen values are shown in table 12. Most National Atmospheric Deposition Program total phosphorus values were less than 0.01 mg/L as P (Larry 

1993), and a nitrogen-to-phosphorus ratio of 50 was used to calculate total phosphorus concentrations for atmospheric deposition. This results in total phos

depending on the site.

6County data from U.S. Environmental Protection Agency, 1990. Calculations based on proportion of county or county's valley floor area in drainage basin.

7County data from U.S. Department of Agriculture and California Department of Food and Agriculture, 1991. Calculations based on proportion of county or 

8Maximum possible contribution of point sources to mean stream load.
Table 14. Trends in nutrient and suspended sediment concentrations during the 1980s, San Joaquin-Tulare Basins, California, study unit

[Numbers (p-values) represent data from Seasonal Kendall test; trend is considered significant if p-value is less than or equal to 0.05. 

Symbols: A , upward trend, not flow adjusted; ^ , upward trend, flow adjusted; ° , no trend, not flow adjusted; • , no trend, flow 

adjusted; y , downward trend, not flow adjusted; V , downward trend, flow adjusted; <, less than; — , no data]

Site No. Station name (fig. 19)

Nitrate, Ammonia, Nitrogen,

dissolved dissolved total

(1980-1989) (1982-1989) (1982-1989)

Ortho- Total Suspended

phosphate phosphorus sediment

(1982-1989) (1982-1989) (1980-1989)

1

4

16

19

Kern River at Kernville

Kings River below North Fork, near Trimmer

San Joaquin River near Stevinson

Salt Slough near Stevinson

0 (0.30)

0 (0.72)

0 (0.33)

—

y«0.01)

y (<0.01)

—

—

y (0.02)

• (0.07)

—

—

V

O

0

0

(0.02)

(0.11)

(0.94)

(0.17)

V

v (•

A

o

(0.02)

(0.02)

(0.43)

• (0.75)

0 (0.40)

—

—

20 San Joaquin River at Fremont Ford Bridge

21 Mud Slough near Gustine

47 San Joaquin River near Vernalis

49 Mokelumne River at Woodbridge

(<0.01) A

± (<0.01) y (<0.01) • (0.85) 

A (0.05) y (0.03) • (0.67)

— 0(0.12) —

• (0.33) •(0.50) •(0.14)

O (0.57) • (0.76) • (0.68)

sediment, the trend-analysis period was 1980-1989. 

The trend-analysis period for the other constituents was 

1982-1989; laboratory biases were reported for USGS 

data during water years 1980 and 1981. Results of the 

trend analysis are given for 8 of the 49 long-term sites 

(table 14). The other sites did not have enough data 

during this period to report trends. The 95-percent 

confidence level is used as the criteria for significance 

of upward or downward trends. Trends based on the 

seasonal Kendall test are considered significant if the 

p-values are less than or equal to 0.05. Trends that were 

not flow-adjusted (table 14) should be considered with 

caution. The later years of the trend-analysis period 

were much drier than the earlier years. Thus, some of 

the nonflow-adjusted trends, especially upward trends, 

could be primarily due to reduced flows.

Nutrient concentrations, except nitrate, have 

been decreasing at the Kern River site during the 1980s 

despite reduced flows during the trend period 

(table 14). This decrease probably is related to the 

state's continuing effort to improve timber-harvesting 

practices and to minimize degradation of stream quality by domestic wastes and urban runoff. Flow-adjusted 

ammonia concentrations have decreased at several sites 

and probably is related to improved regulation of 

domestic and dairy wastes. The increase in nitrate concentration in the San Joaquin River near Vernalis (site 

47) is caused primarily by increased agricultural return 

flows to the San Joaquin River. This increase in nitrate 

was offset by the decrease in ammonia such that there 

was no trend in the total nitrogen concentration.

A highly significant, flow adjusted, statistical 

trend (p<0.01) of increasing nitrate concentration in the 

San Joaquin River near Vernalis (site 47 [1951-1990]) 

is shown in figure 40. A combination of NWIS and 

STORET data fills some data gaps and provides good 

coverage for the entire 40-year period. The increasing 

nitrate trend could be attributed to several sources 

including subsurface agricultural drainage, runoff from 

fertilizer application (tailwater), wastewater treatment 

plant effluent, and runoff from dairies. The relative 

contributions of these sources can be evaluated by 

nitrate load estimates and differences in nutrient 

concentrations (table 3).

The following information on nutrient sources, 

loads, and trends relating to this increasing nitrate trend 

at Vernalis is shown in figure 41 (A-D):

(A) Nitrogen fertilizer application and nitrogen 

in manure in lower San Joaquin River Basin 

(1951-1990) (table 2).

(B) Five-year running averages (1953-1988) of 

estimated nitrate loads in the San Joaquin 

River Basin near Vernalis, in the combined 

east side tributaries (Merced, Tuolumne, and 

Stanislaus rivers), and in subsurface agricultural drains. Loads in the San Joaquin 

River and east side tributaries were computed by the ESTIMATOR program. The 

east side tributary loads are assumed to be 

related primarily to runoff from fertilizer 

applications. Estimated loads from 

subsurface agricultural drains assume a

Trends in Constituent Concentrations 81
3.2

o>

Q_ 

CO

03

i i i r I i i i i n i r

• National Water Information 

System data

o Storage and Retrieval 

database of the U.S. 

Environmental 

Protection Agency

——- Concentration trend

c

•D

.- 1.6

I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I I

- O

1950 1955 1960 1965 1970 1975 1980 1985 1990

Water year

Figure 40. Trend in nitrate concentration at San Joaquin River near Vernalis site, 1951-1990 (seasonal Kendalltestp-value is less than 0.01).

constant concentration of 25 mg/L as N, a 

drainage factor of 0.7 acre-feet per acre 

(acre-ft/acre), and the subsurface drain 

installation schedule shown in figure 12. 

(Q Five-year running averages of normalized 

nitrate concentrations in the San Joaquin 

River near Vernalis, in east side tributaries, 

and in subsurface drains (1953-1988) were 

calculated by dividing the nitrate loads by 

total annual streamflows in the San Joaquin 

River near Vernalis. Concentrations shown 

for each source represent the portion of 

concentration at Vernalis contributed by the 

source. 

(D) Flow-adjusted nutrient concentration trends

in the San Joaquin River near Vernalis. 

Other sources of nitrate loads and concentrations (fig. 41B and C) include wastewater treatment 

plant discharges, runoff from dairies, and runoff from 

fertilizer applications west of the San Joaquin River. 

These sources were especially important in the early 

1980s because of the effect of water year 1983 on the 

5-year running averages. Water year 1983 was an 

extremely wet year, and unusually large inputs of 

nitrate were probable from the following sources:

(1) inflow from the Tulare Basin through Fresno 

Slough (fig. 1), (2) discharges from the Modesto 

wastewater treatment plant (fig. 9), (3) runoff from 

dairies, and (4) runoff from fertilizer applications west 

of the San Joaquin River.

On the basis of the information summarized in 

figure 41, the source of the nitrate increase during the 

1950s is indeterminate. During the 1960s, phosphorus 

concentrations in the lower San Joaquin River near 

Vernalis decreased (fig. 4ID), and nitrate loads in 

runoff to the lower San Joaquin River from fertilizer 

application (east side tributaries in fig. 4IB) and 

subsurface agricultural drainage (fig. 4IB) increased. 

Thus, increased nitrate in the river was due to increases 

in runoff from fertilizer application and subsurface 

drainage during the 1960s.

Since 1970, phosphorus and ammonia 

concentrations in the river have remained relatively low 

and stable (fig. 41D). Nitrate runoff from fertilizer 

applications (east side tributaries in fig. 4IB) was 

relatively stable. Nitrate loads to the river from 

subsurface agricultural drainage (fig. 4 IB) have 

increased steadily and were the primary cause of the 

increase in concentrations in the river since 1970.

82 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
03

ef TO 50,000

CD CD

en >*

O >-

i % 25,000

c 

o

1 ' ' ' ' ' ' ' ' I ' ' ' ' ' ' ' ' ' I ' ' ' ' ' ' ' ' 

A Potential sources of total nitrogen in lower San Joaquin River Basin

D-Q Fertilizer 

G—O Manure

0

1950 1960 1970 1980 1990

8,000

6,000

TO

- CO

2 ^ 4,000 

I 8.

OT

-£ 2,000

B Estimated nitrate loads in San Joaquin River near Vernalis 

[5-year running averages]

Other sources

Subsurface agricultural drains

East-side tributaries

1950 1960 1970 1980 1990

1.5

OT H n

m i-U

CD

.ti OT

Z E

03 0.5

C 'Normalized1 nitrate concentrations in San Joaquin River near Vernalis 

[5-year running averages]

Other sources

Subsurface agricultural drains

East-side tributaries

San Joaquin River total

1950 1960 1970 1980 1990

D Flow-adjusted nutrient concentration trends in San Joaquin River near Vernalis

Nitrate, as N •———• Total phosporus, as P 

Ammonia, as N Q————0 Orthophosphate, as P

o

1950 1960 1970 1980

Water year

Figure 41. Potential sources of total nitrogen in the lowe- San Joaquin River Basin, California, nitrate loads and concentrations, and nutrient 

trends in the San Joaquin River near Vernalis site. See figure 18 for site locations.

Trends in Constituent Concentrations 83
Nitrate in the subsurface agricultural drainage is 

primarily from the leaching of native soil nitrogen and 

not from fertilizer application (Brown, 1975). A study 

using 15N labeled fertilizer found that only about 5 

percent of the fertilizer applied nitrogen appeared in 

soil extracts (Bureau of Reclamation, 1972). California 

Department of Water Resources (1971) found no 

correlation between fertilizer application and effluent 

nitrogen in subsurface agricultural drains. A mass 

balance for a drained area showed that nitrogen in the 

harvested crops accounted for almost all the applied 

fertilizer nitrogen (Brown, 1975). Despite large 

increases in fertilizer application (table 2), nitrate 

concentrations in the Grasslands area (fig. 10) have

been fairly constant since at least 1967, on the basis of 

DWR monitoring data (California Department of 

Water Resources, 1975, 1986).

The increase in nitrate concentrations during 

1972-1990 also is apparent at most other sites on the 

lower San Joaquin River shown in figure 42. 

Flow-adjusted scatterplots with LOWESS trend lines 

show nitrate, total phosphorus, and suspended 

sediment concentrations at five San Joaquin River sites 

(figs. 42-44). Similar data are shown in scatterplots for 

five representative long-term sites (figs. 45^7). The 

long-term sites are two Sierra Nevada sites (Merced 

River at Happy Isles Bridge [site 22] and Tuolumne 

River at LaGrange Bridge [site 37]), two east side

EXPLANATION

? • Value

• Less than value

—— Concentration trend

5.0 11303500 Site 47, San Joaquin River near Vernalis

1 I I I I I T I \ 1 I I I

I I I I I I I ———— I ———— I ———— I ———— I ———— L

CD 5.0 1 1290500 Site 42, San Joaquin River at Maze Road

5.0

§ 0 

o

o 

o

11274570 Site 31, San Joaquin River near Patterson ——i———i———i———i———i———i———i———i———i———i———r

371836120554204 Site 20, San Joaquin River at Fremont Ford Bridge

To

"E

T3 

CD

3 0

T3 

CO

5 

0 50

U_

0

1 1 1 1 1 1 1 1 1 1 1 1 ' < :> ' 4 4^ '

~~ 1 1 1 i 1 1 1;* ": (. L . - "* 1 1 LI 1 1 1 ~

1 1260815 Site 16, San Joaquin River near Stevinson

i I I i I i ii i I I I

i i i i •"•" ^f—"-— - • "| """""""•"" "|" ill *f I ^p* ••*•••( _ i^^j flip ~|~ ->

1975 1980 1985 1990

Water year

Figure 42. Nitrate concentrations at selected San Joaquin River sites, California, 1972-1990. See figure 18 for site locations. 

84 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
valley sites (Tuolumne River at Tuolumne City [site 39] 

and Stanislaus River at Koetitz Ranch [site 46]), and one 

west side valley site (Salt Slough near Stevinson 

[site 19]).

The increasing nitrate trend at the San Joaquin 

River sites shown in figure 42 probably is due to 

agricultural return flows. All sites appear to have 

increasing concentrations except for the San Joaquin 

River near Stevinson site (site 16), which is upstream of 

most agricultural return flows. The increasing nitrate 

trends at the Vernalis site (site 47) and Fremont Ford 

Bridge (site 20) are statistically significant for the 1972- 

1990 time period (p<0.001 and p=0.012, respectively).

The lack of trends at Vernalis (site 47) for total 

phosphorus and suspended sediment concentrations 

also is apparent at the upstream sites (figs. 43 and 44). 

The Patterson site (site 31) appears to have increasing 

concentrations of total phosphorus (fig. 43) during the 

late 1980s; however, this trend is not statistically 

significant.

The only visual trends for nitrate at the long-term 

sites are an increasing trend at the Salt Slough site and 

a decreasing trend at the Stanislaus River site (site 46 

[fig. 45]). These trends are not statistically significant 

due to the lack of sufficient data during the period. The 

Sierra Nevada site on the Merced River also appears to

EXPLANATION 

« Value

• Less than value

—— Concentration trend

1.0

1 1303500 Site 47, San Joaquin River near Vernalis

\ \ i i i i i i i i i r i i i

i i i i 1 i i i i i i

0) 

CL

CO

CO

1.0

« 1.0

11290500 Site 42, San Joaquin River at Maze Road

i i i i i i i i i i i

J____I____I____I____I____I____I____I____I____I____I____I

11274570 Site 31 , San Joaquin River near Patterson

i r \ r i i i i i i i i i ri i

i i i i i i i i i i i i

Q. 

CO 

O

371836120554204 Site 20, San Joaquin River at Fremont Ford Bridge 1.0 i——i——i——i——i——i——i——\——i——r——\——i——i——i—*n——i——i——i——r

0

1 1 1 1 ~ 1 1 1

CO

^ 11260815 Site 16, San Joaquin River near Stevinson

i

iiiiiiii iiiii i 1,1

* &

i__i__i i__i__i__i__i__i__i__i__i__i

1975 1980 1985 1990

Water year 

Figure 43. Total phosphorus concentrations at selected San Joaquin River sites, California, 1972-1990. See figure 18 for site locations.

Trends in Constituent Concentrations 85
have an increasing trend for nitrate due to the method 

by which values below the detection limit for the 

LOWESS trend line are set to the detection limit by the 

PT2 program. The trend lines for total phosphorus and 

suspended sediment concentrations are basically flat 

for the representative sites that have adequate data 

coverage during the period (figs. 46 and 47). The 

Merced River at Happy Isles Bridge and the Tuolumne 

River at La Grange Bridge sites (sites 22 and 37, 

respectively) could not be flow adjusted for total 

phosphorus and suspended sediment, and only concentration trends are shown for these sites.The Stanislaus 

River at Koetitz Ranch site (site 46) could not be flow 

adjusted for suspended sediment.

SUMMARY AND CONCLUSIONS

The spatial and temporal availability of nutrient 

and suspended sediment data and patterns of 

concentrations and loads in the San Joaquin-Tulare 

Basins for 1972-1990 are described. A database 

representative of ambient surface water conditions was 

developed by excluding sites representing or directly 

influenced by small subsurface agricultural drains, 

wastewater treatment plant effluents, major water 

supply canals, and reservoirs. This database included 

432 sites with data on nutrient and(or) suspended 

sediment concentrations. For this report, data analysis 

was limited to 49 long-term sites with 3,397 nutrient 

samples and 5,089 suspended sediment samples.

EXPLANATION

!' Value 

——— Concentration trend

CD

E

T3

CD 

CO

4QQ 11303500 Site 47, San Joaquin River near Vernalis

g

a o

en

E

CO

.o> 400

E

c

§ o

1 1 1 "1 - ~——— \ —————— 1 ———— 1 ——— ?7T— 1 1 1 1 - - 1 1 1 1

^^^^^.-..v..-..v.,-^.sr..i ------ -: — ..,...,...„.„.-., r „•,'„-,•„•„•,„•„-.,. ......... „ . r ;; ,- " , , ,. , . .,', , ... , - , „. .. „ „ „ . , ., . , ,,„....,.. '7... .-,. ,..,.„. , ;. „ „ . ,'.. .. .., „. .\7. , ,„, .. -.,-.•-,. .......u.-

:. -« -~ •• ••-•••• „ ... ,.iM»" 09 *.*»> , „ ; ' *"";..;.• 

r i i i i i i i i i i i w i i • i i i i " '

1 1290500 Site 42, San Joaquin River at Maze Road

i i i i i i i i i i i i i i i *" i " i~. i

400 11274570 Site 31, San Joaquin River near Patterson

o> 400 371836120554204 Site 20, San Joaquin River at Fremont Ford Bridge

T3

C 

CD 

Q. 

(fl A

400

0

11260815 Site 16, San Joaquin River near Stevinson

1975 1980 1985 1990

Water year

Figure 44. Suspended sediment concentrations at selected San Joaquin River sites, California, 1972-1990. See figure 18 for site locations.

86 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Comparisons of nutrient and suspended sediment concentrations were made among three environmental settings in the study unit: the west side of the 

San Joaquin Valley, the east side of the San Joaquin 

Valley, and the Sierra Nevada. The primary land use is 

agriculture at the valley sites and forest at the Sierra 

Nevada sites. Soils at the western valley sites are primarily fine-grained alluvial deposits from the Coast 

Ranges; the eastern valley sites are primarily coarsergrained alluvial deposits from the Sierra Nevada. Nutrient and suspended sediment concentrations in surface water are highest on the west side of the valley. 

Within the study unit, concentrations of nutrients and 

suspended sediment in agricultural areas are not significantly different from national averages. However, the

concentrations of these constituents in forested areas 

are significantly lower than national averages.

Discharges and diversions of agricultural drainage and reservoir operations create some unusual 

streamflow versus concentration relations in the study 

unit. At the San Joaquin River near Vernalis site, nitrate 

concentrations increase with streamflow at flow rates 

less than 1,000 cubic feet per second, then decrease 

with streamflow at higher flow rates. Suspended 

sediment concentrations decrease slightly with 

streamflow at the Vernalis site. Nutrient concentrations 

in the lower San Joaquin River are determined 

primarily by relatively concentrated inputs from west 

side agricultural drainage, discharges from east side 

wastewater treatment plants and dairies, and by

EXPLANATION

• Value

• Less than value

• Concentration trend

0.45 11264500 Site 22, Merced River at Happy Isles Bridge

374000120274201 Site 37, Tuolumne River at La Grange Bridge

373612121080001 Site 39, Tuolumne River at Tuolumne City

JZ U.O<+

—

Q.

</)

E 

2 0

i i i i i i i i i i i i i i i i i i

f

*r -

i i i i i i i i i i i r" i i i i i i ~

O)

.^ 1 .0

c£

0

"03 

<u 0

c

0

o 

03 1 4

03

'c

O

w 

.5. 0

T3

03

o

0

i i I i i i •' i i -i • i i i i i I I i i

- i i i i i r i i i i i i i i i i i i -

374200121 101201 Site 46, Stanislaus River at Koetitz Ranch

i i i i i i i i i i i i i i i i i i

. ! _;,,,.. » f

I I I I I I I i I I I i I I I i I I ~

1 1261 100 Site 19, Salt Slough near Stevinson

i i i i i i i i i i i i i i i i i i

§ - * . -

- i i i r i i i i i i i i i i i i i i -

1975 1980 1985 1990 

Water year

Figure 45. Nitrate concentrations at representative sites in San Joaquin-Tulare Basins, California, study unit, 1972-1990. See figure 18 for site 

locations.

Summary and Conclusions 87
relatively dilute inputs from major east side tributaries. 

On the basis of size distribution and load calculations 

in the San Joaquin River and tributaries, most 

suspended sediment in the river comes from west side 

sources.

Load calculations were attempted at all 49 longterm sites in the study unit for water years 1986-1988. 

Reasonable estimates of nitrate loads were calculated 

at 23 sites, total nitrogen at 15 sites, total phosphorus at 

20 sites, and suspended sediment at 14 sites. Nutrient

and suspended sediment loads in the lower San Joaquin 

River were much greater in a wet year (1986) than in a 

critically dry year (1988). The ratio of 1986 to 1988 

streamflow was 4.50. Ratios of loads increased with 

particulate fraction of the constituent: 1.58 for dissolved nitrate, 2.14 for total nitrogen, 2.78 for total 

phosphorus, and 4.99 for suspended sediment. During 

water years 1986-1988, nonpoint sources accounted 

for at least 81 percent of the total nitrogen load and 68 

percent of the total phosphorus load leaving the San

•- T!

03 CD

o

CO

8§ 

IE

O C

CO ^

O CD •§-«

0.25 11264500 Site 22, Merced River at Happy Isles Bridge

EXPLANATION 

Value

Less than value 

Concentration trend

. i D

374000120274201 Site 37, Tuolumne River at La Grange Bridge

1975 1980 1985

1

-

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 I 1

V- , «T ,» , • _ „ ;' .. , _

rf! — **s*5 ———— 1 ———— i "rrjrv - . t, .r 1 - 1 . ( ': ? « : t — r-.' ' r '- '• '4 " —— 1 —— • — I 'V I -K • 'V t • i • T '•> I '"Tt

1990

U_ CD O

374200121 101201 Site 46, Stanislaus River at Koetitz Ranch

w -"" 1 1 1 II 1 1 1

°- - * CO «- -

co »,.,„» .. ; '"

E P 0 ~ i i i i i i i ' i

I I I I I I I I I I ,

I I I I I I I " I I I

o =

.C iQ. CD

o S" r> CH 373612121080001 Site 39, Tuolumne River at Tuolumne City

-§_ b u't) i i i ~i —— i — CO 

B D) 

2 =

"S QJ^ jraiHuHIUlK'• 1 •NII|M|||I4I»I .. Illliihw I.— <?W. i . ^-t .n-ii-i y „ „ —— ^ ^" *

tn -E 0 - | | | | I ' I. 1 1

f.l

I I I I I I I I I «- I

I I I I I I I 1 1 1

5 jo 11261100 Site 19, Salt Slough near Stevinson 

o r^ 0.51

0 -

1975 1980 

Water year

1985 1990

Figure 46. Total phosphorus concentrations at representative sites in San Joaquin-Tulare Basins, California, study unit, 1972-1990. See 

figure 18 for site locations.

88 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Joaquin Basin. The overall transport of total nitrogen 

and total phosphorus from the basin during this time 

was 5 percent and 3 percent of the total sources, 

respectively. Atmospheric deposition is probably the 

primary source of nitrogen load at high Sierra Nevada 

sites and is a minor source at sites on the west side of 

the valley. Overall, the atmospheric load is probably a 

small component of nutrient export from the study unit. 

Flow-adjusted nitrate concentrations in the lower 

San Joaquin River have increased steadily since 1950. 

This can be attributed to many factors, including 

increases in subsurface agricultural drainage, fertilizer 

application, wastewater treatment plant effluent, and 

runoff from dairies. Since 1970, this increase has been

c =

O i-

•4= 0>

03 Q_

C £

0) C

O O3

It

(D -,

"

due primarily to increases in subsurface agricultural 

drainage of mostly native soil nitrogen. Flow-adjusted 

ammonia concentrations decreased between 

1982-1989 at Sierra Nevada sites on the Kern and 

Kings Rivers and at valley sites on the lower San 

Joaquin and Mokelumne Rivers. This decrease is 

probably related to improved regulation of domestic 

and dairy wastes.

REFERENCES CITED

Alexander, R.B., and Smith, R.A., 1990, County-level 

estimates of nitrogen and phosphorus fertilizer use in 

the United States, 1945 to 1985: U.S. Geological 

Survey Open-File Report 90-130, 12 p.

EXPLANATION

> Value 

• Less than value 

——— Concentration trend

1 1264500 Site 22, Merced River at Happy Isles Bridge

i i i i i i i i i i i i i i ( i i i

374000120274201 Site 37, Tuolumne River at La Grange Bridge

o b

53

374200121101201 Site 46, Stanislaus River at Koetitz Ranch

i i i i i i i

<jj .® 373612121080001 Site 39, Tuolumne River at Tuolumne City E - 43 —————

o o 

u_ o

w w 

•o E

0) 03

?.S>

(D =

-o c 270 

o> o

i r

i i i i i

i i i i r i r i

i i i i

11261100 ——————Site 19, Salt Slough a near Stevinson

o -

1975 1980 1985 

Water year

1990

Figure 47. Suspended sediment concentrations at representative sites in San Joaquin-Tulare Basins, California, study unit, 1972-1990. See 

figure 18 for site locations.

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Assessment Program, State of Science and Technology 

series, Report 8, p. 8A-1-8A-10.

Templin, W.E., 1990, California water supply and use in 

National Water Summary 1987—Hydrologic events 

and water supply and use: U.S. Geological Survey 

Water-Supply Paper 2350, p. 173-182.

U.S. Department of Agriculture and California Department 

of Food and Agriculture, 1991, California Livestock, 

Cattle: County Estimates of number of head by type, 

California: Sacramento, California, California 

Department of Food and Agriculture, Agricultural 

Statistics Service, 2 p.

U.S. Department of Commerce, 1993, Tiger/line 1992: 

Washington, D.C., Bureau of the Census, Data User 

Services Division [CD-ROM, ISO 9660 format].

U.S. Environmental Protection Agency, 1982, River reach 

file (version 1.0): Washington, D.C., U.S. 

Environmental Protection Agency.

References Cited 91
-1986, Quality criteria for water, 1986: Washington, 

D.C., U.S. Environmental Protection Agency, Office of 

Water Regulation and Standards, EPA 440/5-86-001, 

loose-leaf pages.

-1990, County-level fertilizer sales data: Washington, 

D.C., Office of Policy, Planning, and Evaluation 

(PM-2221).

-1994, River reach file (version 3.0): Washington, D.C.,

U.S. Environmental Protection Agency, Office of 

Water [ARC/INFO export format with DS2 attribute 

set].

U.S. Geological Survey, 1978, Hydrologic unit map—1978: 

State of California: U.S. Geological Survey, scale 

1:500,000, 2 sheets.

———1986, Land use and land cover digital data from

1:250,000- and l:100,000-scale maps: U.S. Geological 

Survey, Data Users Guide 4, 36 p.

——1993, National water summary 1990-91: Hydrologic

events and stream-water quality: U.S. Geological 

Survey Water-Supply Paper 2400, 590 p.

U.S. Soil Conservation Service, 1989, Nonpoint source 

pollution and planning for water-quality improvements 

in western Stanislaus County: U.S. Soil Conservation 

Service, Patterson Field Office, 85 p.

Wall, S.L., Baggett, J., Bauer, E.H., Brown, C.E., Eriksson, 

M., Estes, I.E., Ferchaud, C., Grigg, C.A., Sawyer, G., 

and Thomas, R.W, 1981, Irrigated lands assessment 

for water management: Joint research project: Annual 

Report, 1 January 1980-15 April 1981: Berkeley, 

California, Space Sciences Laboratory, Series, 

University of California, 251 [83] p.

Westcot, D.W., and Belden, K.K., 1989, Quality of agricultural drainage discharging to the San Joaquin River 

from area east of the river in Stanislaus, Merced and 

Madera Counties, California, January 1986 to 

September 1988: California Regional Water Quality 

Control Board, Central Valley Region, 32 p.

Westcot, D.W., Fastenau, R.G., and Enos, C.A., 1991, 

Water quality of the lower San Joaquin River: Lander 

Avenue to Vernalis, October 1989 to September 1990 

(water year 1990): California Regional Water Quality 

Control Board, Central Valley Region, 46 p.

92 Nutrients and Suspended Sediment in Surface Water, San Joaquin-Tulare Basins, California, 1972-1990
Selected Series of U.S. Geological Survey Publications

Books and Other Publications

Professional Papers report scientific data and interpretations 

of lasting scientific interest that cover all facets of USGS investigations and research.

Bulletins contain significant data and interpretations that are of 

lasting scientific interest but are generally more limited in 

scope or geographic coverage than Professional Papers.

Water-Supply Papers are comprehensive reports that present 

significant interpretive results of hydrologic investigations of 

wide interest to professional geologists, hydrologists, and engineers. The series covers investigations in all phases of hydrology, including hydrogeology, availability of water, quality of 

water, and use of water.

Circulars are reports of programmatic or scientific information 

of an ephemeral nature; many present important scientific 

information of wide popular interest. Circulars are distributed 

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Fact Sheets communicate a wide variety of timely information 

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Reports in the Digital Data Series (DDS) distribute large 

amounts of data through digital media, including compact discread-only memory (CD-ROM). They are high-quality, interpretive publications designed as self-contained packages for viewing and interpreting data and typically contain data sets, 

software to view the data, and explanatory text.

Water-Resources Investigations Reports are papers of an 

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Maps

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Information Periodicals

Metal Industry Indicators (Mil's) is a free monthly newsletter that analyzes and forecasts the economic health of five 

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the need for current data. The MIS's are published by commodity as well as by State. A series of international MIS's is also 

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Published on an annual basis, Mineral Commodity Summaries is the earliest Government publication to furnish estimates 

covering nonfuel mineral industry data. Data sheets contain 

information on the domestic industry structure, Government 

programs, tariffs, and 5-year salient statistics for more than 90 

individual minerals and materials.

The Minerals Yearbook discusses the performance of the 

worldwide minerals and materials industry during a calendar 

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"Publications of the U.S. Geological Survey, 1879-1961" 

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Annual supplements for 1982, 1983, 1984, 1985, 1986, and 

subsequent years are available in paperback book form.