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Concentrations of Organic 

Contaminants Detected during 

Managed Flow Conditions, San Joaquin

River and Old River, California, 2001

By James L. Orlando and Kathryn M. Kuivila

Prepared in cooperation with CALFED California Bay−Delta Authority and the 

University of California at Davis

Data Series 120

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2005

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

Box 25286, Denver Federal Center

Denver, CO 80225

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

World Wide Web: http://www.usgs.gov/

Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to 

reproduce any copyrighted materials contained within this report.

Suggested reference:

Orlando, J.L., and Kuivila, K.M., 2005, Concentrations of organic contaminants detected during managed flow 

conditions, San Joaquin River and Old River, California, 2001: U.S. Geological Survey Data Series 120, 13 p.
iii

Contents

Abstract ......................................................................................................................................................... 1

Introduction ................... ................................................................................................................................ 1

Project Design ..................................................................................................................................... 2

Purpose and Scope ............................................................................................................................. 4

Acknowledgments .............................................................................................................................. 4

Procedures and Methods ........................................................................................................................... 4

Description of Sampling Sites .......................................................................................................... 4

Sample Collection ............................................................................................................................... 4

Analysis of Pesticides ........................................................................................................................ 9

Analysis of Wastewater Compounds .............................................................................................11

Analysis of Suspended-Sediment Concentration and Parameters .........................................11

Results ........................... ................................................................................................................................11

Pesticide Concentrations .................................................................................................................11

Wastewater Compounds ..................................................................................................................11

Suspended-Sediment Concentrations and Water Parameters ................................................11

References Cited ........................................................................................................................................ 13

Figures

Figure 1. Map showing locations of sampling sites and flow barriers within the 

San Joaquin Delta ....................................................................................................................... 2

Figure 2. Graph showing San Joaquin River discharge measured at Vernalis, and 

salmon smolt caging periods .................................................................................................... 3

Figure 3. Box plots of water parameter values determined in this study ........................................12

Tables

Table 1. Water-quality sampling sites, Sacramento−San Joaquin Delta, California ................... 3

Table 2. Pesticide concentrations in water samples collected in 2001 .......................................... 5

Table 3. Concentrations of pesticide and wastewater compounds detected in samples 

analyzed by the U.S. Geological Survey’s National Water Quality Laboratory ............. 7

Table 4. Suspended-sediment concentrations and water parameters in water samples 

collected in 2001 ........................................................................................................................ 8

Table 5. Method detection limit, accuracy, and precision data from eight determinations

of the method analytes spiked using 20.0 nanograms-per-liter concentrations in 

Colusa Basin Drain water .........................................................................................................10
iv

Acronyms and Abbreviations

BML Bodega Marine Laboratory (UCD)

Delta San Francisco Bay Delta

GC/MS gas chromatography/mass spectrometry

MDL method detection limit

NWQL National Water Quality Laboratory (USGS)

OCL organic chemistry laboratory (USGS)

SL Sediment Laboratory (USGS)

UCD University of California at Davis

USGS U.S. Geological Survey

VAMP Vernalis Adaptive Management Plan

ng/L nanogram per liter

ft3/s cubic foot per second

mL milliliter

μL microliter

Multiply By To obtain

cubic meter (m3) 264.2 gallon (gal) 

kilogram (kg) 2.205 pound avoirdupois (lb)

kilometer (km) 0.6214 mile (mi)

liter (L) 33.82 ounce, fluid (fl oz)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

 °F = (1.8 × °C) + 32

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83).

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 

25°C).

Conversion Factors and Abbreviations and Acronyms

Conversion Factors 
Abstract

Concentrations of organic contaminants were determined 

in water samples collected at six surface-water sites located 

along the San Joaquin and Old Rivers during April through 

June 2001. Water samples were collected, coincident with 

salmon smolt caging studies conducted by researchers from 

the Bodega Marine Laboratory at the University of California at Davis to characterize exposure of the salmon smolt to 

organic contaminants. Sampling occurred prior to, during, 

and following the implementation of managed streamflow 

conditions on the San Joaquin and Old Rivers as part of the 

Vernalis Adaptive Management Plan. Thirteen pesticides 

were detected in water samples collected during this study, 

and at least five pesticides were detected in each sample. The 

total number of pesticide detections varied little between river 

systems and between sites, but the maximum concentrations 

of most pesticides occurred in San Joaquin River samples. 

The total number of pesticides detected varied little over the 

three time periods. However, during the period of managed 

streamflow, the fewest number of pesticides were detected 

at their absolute maximum concentration. Nine wastewater 

compounds were detected during this study. Suspended-sediment concentrations were similar for the San Joaquin and Old 

Rivers except during the period of managed streamflow conditions, when suspended-sediment concentration was higher at 

sites on the San Joaquin River than at sites on the Old River. 

Values for water parameters (pH, specific conductance, and 

hardness) were lowest during the period of managed flows.

Introduction

Water flow and water quality are thought to be the 

primary factors affecting the survival of juvenile fall-run 

Chinook salmon in the San Joaquin River and the San Francisco Bay Delta (Delta) (San Joaquin River Group Authority, 

2002). A marked decline in the number of adult salmon in the 

San Joaquin River Basin has led to the creation of numerous 

multistakeholder programs designed to stabilize and restore 

salmon populations in this region of California. One of these 

programs, the San Joaquin River Group Authority, has developed and implemented the Vernalis Adaptive Management 

Plan (VAMP), which is designed to support salmon population restoration by improving salmon smolt survival during 

emigration through the San Joaquin River Delta. 

A critical component of the VAMP is the management of 

San Joaquin River and Delta flows during April and May to 

meet established flow targets. This is accomplished by 

(1) constructing flow barriers on key Delta waterways, (2) 

carefully timing the release of water from reservoirs within 

the upper San Joaquin River Basin to augment San Joaquin 

River flows, and (3) reducing Central Valley Water Project water exports from the Delta (San Joaquin River Group 

Authority, 2002). 

Another key element of the VAMP is its support of multiple scientific studies designed to investigate the effects of San 

Joaquin River and Delta flow modifications on salmon smolt 

survival. Previous studies have shown that the survival of 

fall-run Chinook salmon (Oncorhynchus tshawytscha) smolt 

is much greater in the San Joaquin River than in the Old River 

(Herbold and others, 1992; Brandes and Pierce, 1998). The 

overall survival of salmon smolt in the Delta improves during 

high San Joaquin River flows and when the barrier at the head 

of Old River is in place to prevent salmon from entering Old 

River (Brandes and Pierce, 1998; Pierce and Brandes, 1999); 

however, the causes of lower survival rates of salmon smolt in 

Old River are unknown.

One subject of concern is the presence of organic 

contaminants and their potential effects on salmon smolt 

survival. Pesticides are used throughout the Delta and San 

Joaquin River Basin, and approximately 5.2 million kg were 

applied throughout the area in 2001 (California Department of 

Pesticide Regulation, 2001). Numerous studies have detected 

many of these pesticides in surface waters of the region 

(Kuivila and Foe, 1995; MacCoy and others, 1995; Kratzer, 

1997; Dubrovsky, and others, 1998; Kuivila and others, 1999; 

Kuivila and Moon, 2004); however, little is known concerning the effects of these pesticides on the health and survival 

of juvenile Chinook salmon in the San Joaquin River and the 

Delta. Additionally, this region supports a number of large 

urban centers that discharge treated wastewater and associated 

contaminants to the San Joaquin River and its tributaries. 

Concentrations of Organic Contaminants Detected 

during Managed Flow Conditions, San Joaquin River 

and Old River, California, 2001

James L. Orlando and Kathryn M. Kuivila
The effect of streamflow modifications, implemented as 

part of the VAMP, on the transport of organic contaminants 

from agricultural runoff and urban sources in both the San 

Joaquin and Old Rivers is unknown. It is possible that modifications in flow might lead to conditions detrimental to salmon 

smolt survival. As a result, one focus of the VAMP has been 

to study the effects of San Joaquin River flow modifications 

on water quality and related effects on Chinook salmon smolt 

survival.

Project Design

This project was designed to determine if exposure to 

organic contaminants contributes to varying survival rates of 

Chinook salmon smolt emigrating in the Old River and the 

San Joaquin River. To evaluate these potential effects, water 

samples were collected for the analysis of organic contaminants concurrently with salmon-smolt caging studies designed 

to measure smolt biological responses (DNA strand breakage, acetylcholinesterase activity, stress protein expression, 

and cytochrome P450 expression). Six sites were sampled: 

three located on the San Joaquin River and three on Old River 

(fig. 1, table 1). At each of these sites, sets of twelve, hatchery 

raised, salmon smolt were kept in cages for approximately 96 

hours, during three time periods, before, during, and after the 

managed streamflow conditions of the VAMP (fig. 2). The 

discharge shown in figure 2 was recorded at Vernalis, 29 km 

upstream from the head of the Old River. During the VAMP 

period, the mean daily flow measured in the Old River ranged 

from 75 to 692 ft3/s (2.1 to 19.6 m3/s) (San Joaquin River 

Group Authority, 2002).

Figure 1. Map showing locations of sampling sites and flow barriers within the San Joaquin Delta, California.

2 Concentrations of Organic Contaminants, San Joaquin River and Old River, California, 2001

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Figure 2. Graph showing San Joaquin River discharge measured at Vernalis, , California, and salmon smolt caging periods.

Site name USGS site 

identification no.

Latitude

(degree/minute/second)

Longitude

(degree/minute/second)

Old River at Stewart Tract near Lathrop 374910121204301 37°49′10.2′′ 121°20′43.4′′

Old River near Lathrop 374916121223901 37°49′16.3′′ 121°22′39.4′′

Old River at Paradise Cut near Tracy 374813121244901 37°48′13.0′′ 121°24′49.7′′

San Joaquin River near Lathrop 375029121190601 37°50′29.0′′ 121°19′06.6′′

San Joaquin River near Bowman Road Bridge near Lathrop 375154121193101 37°51′54.4′′ 121°19′31.1′′

San Joaquin River near French Camp 375342121194301 37°53′42.4′′ 121°19′43.0′′

Table 1. Water-quality sampling sites, Sacramento−San Joaquin Delta, California.

[Horizontal datum is NAD 83. USGS, U.S. Geological Survey]

Introduction 3

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Water samples for the analysis of pesticides were collected at each of the sites, both when the smolt were emplaced 

(day 1) and when they were removed (day 5). Samples collected on days 1 and 5 were composited for each of the sites in 

an effort to approximate smolt exposure to pesticides during 

each 5-day caging period. Samples were analyzed for 32 current-use pesticides by gas chromatography/mass spectrometry 

(GC/MS) at the U.S. Geological Survey’s (USGS) organic 

chemistry laboratory (OCL) in Sacramento, California. 

Additional samples were collected from two sites, once during 

each sampling period and sent to the USGS’s National Water 

Quality Laboratory (NWQL) in Denver, Colorado, for analysis 

of wastewater compounds and pesticides.

Following exposure in the field, fish were dissected, and 

samples of blood and tissue were collected and analyzed for 

acetylcholinesterase activity, DNA strand breaks, cytochrome 

P450 expression, and stress protein expression. Analyses of 

these effects were conducted by researchers from the Bodega 

Marine Laboratory (BML) at the University California at 

Davis (UCD). Results of these analyses are beyond the scope 

of this report and are not included.

During this study, the USGS assisted UCD with the collection of water samples and conducted chemical analyses of 

all water samples. Water samples were analyzed for pesticides, 

wastewater compounds, suspended-sediment concentration, 

and standard water quality parameters (temperature, pH, conductivity, and hardness). 

Purpose and Scope

This report describes the methods and procedures used 

during sample collection and analysis and presents waterquality data for samples collected during this study. Concentrations of 32 current-use pesticides analyzed in 18 composite 

water samples are presented in table 2. In addition, concentrations of select wastewater compounds and pesticides analyzed 

in six water samples by the NWQL are reported (in table 3) as 

well as suspended-sediment concentration and water quality 

parameters for the water samples (listed in table 4).

Acknowledgments

The authors gratefully acknowledge Wendy Rose of the 

University of California at Davis for organizing this project 

and for her assistance with sample collection. The authors also 

wish to acknowledge Jacqueline Houston, Patricia von Phul, 

Lupe Hererra, and Theresa Pedersen of the USGS for their 

many hours of laboratory work and pesticide analyses. This 

project was funded by the CALFED California Bay−Delta 

Authority under a joint funding agreement with UCD, titled 

“Decreased Survival of Chinook Salmon Smolt in the Old 

River: Biological Responses to Toxicants," and by the USGS’s 

Toxic Substances Hydrology Program.

Procedures and Methods

Description of Sampling Sites

Three sites were chosen on both the San Joaquin River 

and Old River near the southern end of the San Francisco Bay 

Delta, an area used by salmon smolt during migration (fig. 1, 

table 1). Because of the necessity of anchoring the fish cages, 

sites were selected near the river banks, in shallow water and 

often near stands of vegetation. All sites were accessible only 

by boat. Sampling sites were chosen by personnel from the 

U.S. Fish and Wildlife Service and BML.

Sample Collection

Water samples were collected for analysis of pesticide 

and suspended-sediment concentrations and water quality 

parameters (specific conductance, pH, and hardness) at all 

six sites, both at the time of fish emplacement and at retrieval. 

Water samples were collected by submerging a 3-L Teflon 

collection bottle in a weighted steel cage. A single Teflon 

bottle was used at all the sites and was prerinsed between sites 

three times with water from the site about to be sampled and 

(or) with deionized water. All samples were collected from 

the same depth as (0.5 to 1.0 m) and in proximity to the fish 

cages. Immediately after collection, the Teflon bottle was 

shaken for one minute to homogenize the sample, which was 

then poured into a 1-L baked, amber glass bottle containing 100 mL of methylene chloride, one 500-mL glass milk 

bottle for sediment analysis, and one 125-mL plastic bottle for 

analysis of water parameters. Additional 1-L water samples 

were collected only at the farthest downstream sites on both 

the San Joaquin River and Old River once for each caging 

event. These samples were collected for analysis of wastewater compounds and pesticides by the NWQL and required 

a second use of the Teflon bottle sampler at these sites. All 

samples were preserved on ice and transported to the OCL in 

Sacramento within 6 hours of collection. 

4 Concentrations of Organic Contaminants, San Joaquin River and Old River, California, 2001
Sampling site Date (month/day/year) Atrazine Carbaryl Carbofuran Chlorpyrifos Cycloate Diazinon EPTC Metolachlor

Old River at Stewart Tract near Lathrop, California 4/2/01 and 4/6/01 nd nd (6.9) nd nd 17.0 nd 13.4Old River at Stewart Tract near Lathrop, California 5/14/01 and 5/18/01 nd 12.6 nd nd nd 8.3 nd 30.9Old River at Stewart Tract near Lathrop, California 5/31/01 and 6/4/01 nd nd nd nd 11.6 6.7 51.5 27.5Old River near Lathrop, California 4/2/01 and 4/6/01 13.5 nd (10.8) nd nd 54.1 nd 20.2Old River near Lathrop, California 5/14/01 and 5/18/01 nd nd nd nd nd 9.0 nd 24.6Old River near Lathrop, California 5/31/01 and 6/4/01 nd nd nd nd 9.6 5.5 42.3 27.3Old River at Paradise Cut near Tracy, California 4/2/01 and 4/6/01 nd nd 12.7 nd nd 131 nd 16.9Old River at Paradise Cut near Tracy, California 5/14/01 and 5/18/01 nd nd 111 nd nd 9.8 26.3 139Old River at Paradise Cut near Tracy, California 5/31/01 and 6/4/01 nd nd 17.3 nd 8.9 8.4 9.8 211San Joaquin River near Lathrop, California 4/2/01 and 4/6/01 nd 21.4 13.9 nd nd 241 nd 11.0San Joaquin River near Lathrop, California 5/14/01 and 5/18/01 nd 9.8 nd 4.6 nd 10.0 nd 26.7San Joaquin River near Lathrop, California 5/31/01 and 6/4/01 nd nd nd nd 11.9 5.6 38.3 36.4San Joaquin River near Bowman Road Bridge near 

Lathrop, California

4/2/01 and 4/6/01 nd nd (9.3) nd nd 13.9 nd 10.8

San Joaquin River near Bowman Road Bridge near 

Lathrop, California

5/14/01 and 5/18/01 nd 9.9 nd nd nd 8.4 nd 24.7

San Joaquin River near Bowman Road Bridge near 

Lathrop, California

5/31/01 and 6/4/01 nd nd nd nd 13.5 6.8 18.8 41.2

San Joaquin River near French Camp, California 4/2/01 and 4/6/01 nd 11.8 13.3 nd nd 11.3 nd 15.3San Joaquin River near French Camp, California 5/14/01 and 5/18/01 nd 10.2 nd 5.3 (4.3) 9.1 9.1 28.9San Joaquin River near French Camp, California 5/31/01 and 6/4/01 nd nd nd nd 13.1 5.8 nd 42.0

Table 2. Pesticide concentrations in water samples collected in 2001.[All sample types are composites. Samples were analyzed for the following pesticides that were not detected in any samples: Alachlor, Bifenthrin, Butylate, DCPA, Diethatyl-ethyl, Dimethoate, Esfenvalerate, Ethalfluralin, lambda-Cyhalothrin, Malathion, Methidathion, Methyl parathion, 2-keto-molinate, Napropamide, Pebulate, Permethrin, Phosmet, Piperonyl butoxide, and Thiobencarb. Concentrations are in nanograms per liter; m/d/y, month/day/year; nd, not detected; ( ), values are estimated because the compounds were detected at a concentration below the method detection limit]

Procedures and Methods 5
Sampling Site Date (month/day/year) Molinate 4-keto- molinate Prometryn Simazine Trifluralin

Old River at Stewart Tract near Lathrop, California 4/2/01 and 4/6/01 nd nd 86.5 22.9 6.3Old River at Stewart Tract near Lathrop, California 5/14/01 and 5/18/01 (4.0) nd nd 17.4 6.6Old River at Stewart Tract near Lathrop, California 5/31/01 and 6/4/01 16.7 12.5 nd 12.6 (4.3)Old River near Lathrop, California 4/2/01 and 4/6/01 nd nd 114 29.5 5.8Old River near Lathrop, California 5/14/01 and 5/18/01 (6.1) nd nd 15.3 6.5Old River near Lathrop, California 5/31/01 and 6/4/01 11.5 (9.5) nd 14.9 (3.4)Old River at Paradise Cut near Tracy, California 4/2/01 and 4/6/01 nd nd 107 27.3 (4.4)Old River at Paradise Cut near Tracy, California 5/14/01 and 5/18/01 (6.2) nd nd 19.3 (5.0)Old River at Paradise Cut near Tracy, California 5/31/01 and 6/4/01 18.4 12.5 nd 15.6 7.7San Joaquin River near Lathrop, California 4/2/01 and 4/6/01 nd nd 122 26.7 (4.0)San Joaquin River near Lathrop, California 5/14/01 and 5/18/01 8.7 nd nd 19.1 9.4San Joaquin River near Lathrop, California 5/31/01 and 6/4/01 17.6 (11.5) nd 15.5 (4.0)San Joaquin River near Bowman Road Bridge near Lathrop, California 4/2/01 and 4/6/01 nd nd 108 31.0 (4.9)San Joaquin River near Bowman Road Bridge near Lathrop, California 5/14/01 and 5/18/01 (4.4) nd nd 17.8 8.3San Joaquin River near Bowman Road Bridge near Lathrop, California 5/31/01 and 6/4/01 12.5 (11.2) nd 15.3 (4.2)San Joaquin River near French Camp, California 4/2/01 and 4/6/01 nd nd 82.4 64.9 (4.4)San Joaquin River near French Camp, California 5/14/01 and 5/18/01 (7.0) nd nd 14.6 10.1San Joaquin River near French Camp, California 5/31/01 and 6/4/01 35.2 24.4 nd 16.9 (3.8)

Table 2. Pesticide concentrations in water samples collected in 2001

Continued.

[All sample types are composites. Samples were analyzed for the following pesticides that were not detected in any samples: Alachlor, Bifenthrin, Butylate, DCPA, Diethatyl-ethyl, Dimethoate, Esfenvalerate, Ethalfluralin, lambda-Cyhalothrin, Malathion, Methidathion, Methyl parathion, 2-keto-molinate, Napropamide, Pebulate, Permethrin, Phosmet, Piperonyl butoxide, and Thiobencarb. Concentrations are in nanograms per liter; m/d/y, month/day/year; nd, not detected; ( ), values are estimated because the compounds were detected at a concentration below the method detection limit]

6 Concentrations of Organic Contaminants, San Joaquin River and Old River, California, 2001
Table 3. Concentrations of pesticide and wastewater compounds detected in samples analyzed by the U.S. Geological Survey’s 

National Water Quality Laboratory.

[Samples were analyzed for the following compounds that were not detected in any samples: 1,4-Dichlorobenzene, 1-Methylnapthalene, 2,6-Dimethylnapthalene, 2-Methylnapthalene, 3-beta-Coprostanol, 3-Methyl-1(H)-indole, 3-tert-Butyl-4hydroxyanisole, 4-Cumylphenol, 4-n-Octylphenol, 5-Methyl1H-benzotriazle, Acetophenone, Anthracene, Anthraquinone, Benzo(a)pyrene, Benzophenone, beta-Stigmastanol, Bisphenol A, Bromoform, Camphor, 

Carbaryl, Carbazole, Chlorpyrifos, Cotinine, DEET, Dichlorvos, d-Limonene, Ethanol, 2-butoxy-,phosphate, Fluoranthene, Hexahydrohexamethyl cyclopentabenzopyran, Indole, Isoborneol, Isophorone, Isopropylbenzene, Isoquinoline, Menthol, Methyl salicylate, Naphthalene, Nonylphenol,diethoxy-(total), 

Octyphenol,monoethoxy-, Octylphenol,diethoxy-, p-Cresol, para-Nonylphenol-total, Pentachlorophenol, Phenanthrene, Prometon, Pyrene, Skatol, Tetrachloroethylene, Tri(2-chloroethyl)phosphate, Tri(dichlorisopropyl)phosphate, Tributyl phosphate, Triclosan, Triethyl citrate, Triphenyl phosphate, and Tris(2-

butoxyethyl)phosphate. Concentrations are in nanograms per liter; m/d/y, month/day/year; h, hours; m, minutes; E, estimated; * denotes pesticide; <, less 

than]

Compound

Location Old River at Paradise Cut 

near Tracy, CA

San Joaquin River near 

French Camp, CA

Date (m/d/y) 4/6/01 5/14/01 6/4/01 4/6/01 5/14/01 6/4/01

Time (hhmm) 1130 1545 1040 0920 1415 0833

4-tert-Octylphenol < 1,000 E110 < 1,000 < 1,000 E120 < 1,000

Acetyl hexamethyl tetrahydro naphthalene < 500 E61 < 500 < 500 < 500 < 500

beta-Sitosterol E800 E1,300 < 2,000 E700 E1,400 < 2,000

Bromacil* E77 <500 < 500 E59 < 500 < 500

Caffeine < 500 E80 E130 < 500 < 500 < 500

Cholesterol E880 E1,800 < 2,000 E830 E1,400 < 2,000

Diazinon* E12 <500 < 500 E16 < 500 < 500

Metalaxyl* E19 <500 < 500 E11 < 500 < 500

Metolachlor* E35 E160 E72 E26 E51 E48

Phenol E490 <500 E310 E340 < 500 E620

Procedures and Methods 7
Sampling site Date (m/d/y) Time (hhmm)

Suspended 

sediment 

concentration 

(mg/L)

Temperature 

(C°) pH

Specific 

conductance 

(μS/cm)

Hardness

(mg/L as 

CaCO3

)

Old River at Stewart Tract near Lathrop, California 4/2/01 1515 32 17.0 8.10 1015 270Old River at Stewart Tract near Lathrop, California 4/6/01 1230 35 15.5 7.96 900 240Old River at Stewart Tract near Lathrop, California 5/14/01 1645 13 20.5 7.74 316 90Old River at Stewart Tract near Lathrop, California 5/18/01 1128 21 22.1 7.61 338 90Old River at Stewart Tract near Lathrop, California 5/31/01 1210 64 24.5 8.50 646 150Old River at Stewart Tract near Lathrop, California 6/4/01 1130 61 22.0 8.81 730 190Old River near Lathrop, California 4/2/01 1450 39 17.0 8.02 1014 270Old River near Lathrop, California 4/6/01 1200 36 15.5 8.00 902 260Old River near Lathrop, California 5/14/01 1615 16 21.5 7.53 325 100Old River near Lathrop, California 5/18/01 1154 19 22.0 7.66 345 90Old River near Lathrop, California 5/31/01 1229 40 24.0 8.51 649 150Old River near Lathrop, California 6/4/01 1109 48 21.7 8.69 719 170Old River at Paradise Cut near Tracy, California 4/2/01 1415 21 17.0 8.08 962 260Old River at Paradise Cut near Tracy, California 4/6/01 1130 28 15.5 7.99 921 270Old River at Paradise Cut near Tracy, California 5/14/01 1545 20 23.0 7.49 578 150Old River at Paradise Cut near Tracy, California 5/18/01 1225 17 22.6 7.58 526 140Old River at Paradise Cut near Tracy, California 5/31/01 1251 NA 24.5 8.22 842 210Old River at Paradise Cut near Tracy, California 6/4/01 1040 60 21.7 8.32 712 170San Joaquin River near Lathrop, California 4/2/01 1330 20 17.5 8.07 970 260San Joaquin River near Lathrop, California 4/6/01 1030 30 15.5 7.91 916 240San Joaquin River near Lathrop, California 5/14/01 1315 48 19.8 7.52 310 90San Joaquin River near Lathrop, California 5/18/01 0930 48 20.7 7.67 320 90San Joaquin River near Lathrop, California 5/31/01 1018 53 24.0 8.26 645 150San Joaquin River near Lathrop, California 6/4/01 0937 55 21.1 8.78 713 170San Joaquin River near Bowman Road Bridge near Lathrop, California 4/2/01 1300 25 17.5 8.00 983 270San Joaquin River near Bowman Road Bridge near Lathrop, California 4/6/01 1000 47 15.5 7.96 925 260San Joaquin River near Bowman Road Bridge near Lathrop, California 5/14/01 1345 75 20.5 7.52 316 90San Joaquin River near Bowman Road Bridge near Lathrop, California 5/18/01 0904 63 20.5 7.68 326 90San Joaquin River near Bowman Road Bridge near Lathrop, California 5/31/01 1052 NA 25.0 8.48 653 150San Joaquin River near Bowman Road Bridge near Lathrop, California 6/4/01 0905 45 21.1 8.70 697 170San Joaquin River near French Camp, California 4/2/01 1220 40 17.5 7.95 918 240San Joaquin River near French Camp, California 4/6/01 0920 39 15.5 7.97 913 260San Joaquin River near French Camp, California 5/14/01 1415 85 21.5 7.74 313 100San Joaquin River near French Camp, California 5/18/01 0833 61 20.1 7.62 325 100San Joaquin River near French Camp, California 5/31/01 1112 39 24.5 8.62 667 150San Joaquin River near French Camp, California 6/4/01 0833 54 21.4 8.73 665 170

Table 4. Suspended-sediment concentrations and water parameters in water samples collected in 2001. [μg/L, milligram per liter; NA, parameter not available; μS/cm, microsiemens per centimeter; m/d/y, month/day/year; h, hours; m, minutes]

8 Concentrations of Organic Contaminants, San Joaquin River and Old River, California, 2001
Analysis of Pesticides

Water samples collected for the analysis of pesticides 

by the OCL were processed by liquid-liquid extraction. Each 

900-mL water sample was preserved immediately upon collection by pouring the sample into a 1-L amber glass bottle 

containing 100 mL of methylene chloride. Within 24 hours of 

sample collection, the water sample and solvent were transferred to a separatory funnel. The sample bottle was rinsed 

three times with methylene chloride and the rinsate added to 

the separatory funnel, along with 200 μL of terbuthylazine 

surrogate. The entire sample was then extracted three times 

using 100 mL of methylene chloride each time. The methylene chloride extract was then dried with sodium sulfate, 

reduced to 0.5 mL, and solvent-exchanged into ethyl acetate. 

The extract from day 1 was stored in the freezer until the day 

5 sample was extracted; then the two extracts from each site 

were combined. 

For analysis, extracts were amended with internal 

standards and reduced to 200 μL. The extracts were analyzed 

using a Saturn 2000 GC/MS ion trap system (Varian, Inc., 

Walnut Creek, California), for 32 current-use pesticides. The 

details of the instrumental method used for analysis and quality assurance procedures are described in Crepeau and others 

(2000). The major differences between the overall method 

in this study and the previous method (Crepeau and others, 

2000) are the use of liquid–liquid extraction of whole water 

samples instead of solid-phase extraction of filtered samples, 

changes in some analytes, and an overall improvement in 

method detection limits. As liquid–liquid extraction was used 

rather than solid-phase extraction, 12 new analytes were added 

to the method and quantified using calibration standards. 

Other analytical details are recorded in a standard operating 

document on file at the laboratory. 

The analytical method was validated by spiking eight 

replicates of a natural water sample with a mixture of pesticides at a concentration of 20 ng/L to estimate accuracy 

and precision and to determine the method detection limits 

(MDLs). Two unspiked replicate samples were used to determine the background concentrations of the pesticides. The 

water was collected from the Colusa Basin Drain, which has a 

similar water chemistry to the sites sampled in this study.

The MDL was calculated for each pesticide using the 

equation

 MDL = S × t(n−1, 1−α = 0.99)

where 

MDL = method detection limit

S = standard deviation of replicate 

analyses (nanogram per liter) 

n = number of replicate analyses, and

t(n−1, 1−α = 0.99) = 2.998, the Student's t value for 99 

percent confidence level with 7 

degrees of freedom (Eichelberger 

and others, 1988).

MDLs ranged from 2.1 to 11.8 ng/L (table 5). Analytes 

can be identified at concentrations less than the method detection limit, but there is lower confidence in the actual value; 

therefore, these concentrations are reported as estimated 

values.

The accuracy or the mean recovery was calculated as the 

measured concentration divided by the actual spike added, 

expressed as a percentage, and the precision was expressed in 

terms of the percent relative standard deviation of the eight 

replicate water samples. The percent relative standard deviation equals the standard deviation (ng/L) divided by the mean 

observed concentration (ng/L) multiplied by 100. Carbofuran, 

dimethoate, 4-keto molinate, molinate, and thiobencarb were 

detected in the blank sample at concentrations of 9.4 to 211 

ng/L, so the background concentrations were added to the 

matrix spike concentration to determine the mean recovery for these compounds. Mean recoveries for the method 

ranged from 79 to 176 percent (table 5). Five of the seven 

compounds with mean recoveries greater than 120 percent 

were not detected in the environmental samples, but carbaryl 

and carbofuran, which had the highest mean recoveries, were 

detected (table 2). 

Because of the limited number of samples collected 

during this study, no field or laboratory blanks were analyzed. Another study conducted during this same time period, 

involving the same equipment, collection procedures, and 

personnel, included the analysis of ten field blanks and no pesticides were detected (Orlando and others, 2004). 

Procedures and Methods 9
Pesticide

Method

detection limit 

(ng/L)

Mean accuracy

 (percentage

of true

concentration)

Mean observed

concentration

(ng/L)

Matrix plus

background

(ng/L)

Standard

deviation

(ng/L)

Relative

standard 

deviation

(percent)

Alachlor 6.5 113 22.6 20.0 2.2 10

Atrazine 2.1 83 16.6 20.0 0.7 4

Bifenthrin 3.2 91 18.3 20.0 1.1 6

Butylate 3.1 89 17.7 20.0 1.0 6

Carbaryl 8.8 176 35.1 20.0 2.9 8

Carbofuran 11.5 150 44.0 29.4 3.8 9

Chlorpyrifos 3.6 101 20.2 20.0 1.2 6

Cycloate 4.4 105 21.0 20.0 1.5 7

DCPA 2.7 104 20.9 20.0 0.9 4

Diazinon 2.7 90 18.0 20.0 0.9 5

Diethatyl-ethyl 2.4 127 25.4 20.0 0.8 3

Dimethoate 7.1 108 115.0 107.0 2.4 2

EPTC 5.1 96 19.2 20.0 1.7 9

Esfenvalerate 2.3 79 15.9 20.0 0.8 5

Ethalfluralin 5.2 99 19.8 20.0 1.7 9

Lambda-cyhalothrin 3.9 95 19.0 20.0 1.3 7

Malathion 6.3 128 25.6 20.0 2.1 8

Methidathion 4.8 101 20.2 20.0 1.6 8

Methylparathion 4.9 144 28.8 20.0 1.6 6

Metolachlor 4.2 99 19.7 20.0 1.4 7

Molinate 8.0 103 156.0 152.0 2.7 2

2-keto-molinate 7.6 119 23.8 20.0 2.5 11

4-keto-molinate 11.7 98 227.0 231.0 3.9 2

Napropamide 11.8 137 27.4 20.0 3.9 14

Pebulate 5.3 109 21.7 20.0 1.8 8

Permethrin 9.9 111 22.3 20.0 3.3 15

Phosmet 4.6 102 20.4 20.0 1.5 8

Piperonyl butoxide 4.4 126 25.2 20.0 1.5 6

Prometryn 5.1 101 20.1 20.0 1.7 8

Simazine 6.4 120 24.0 20.0 2.1 9

Thiobencarb 5.9 102 92.4 90.2 2.0 2

Trifluralin 5.8 111 22.2 20.0 1.9 9

Table 5. Method detection limit, accuracy, and precision data from eight determinations of the method analytes spiked using 20.0 

nanograms-per-liter concentrations in Colusa Basin Drain water.

[ng/L, nanogram per liter]

10 Concentrations of Organic Contaminants, San Joaquin River and Old River, California, 2001
Analysis of Wastewater Compounds

Water samples collected for analysis of wastewater 

compounds by the NWQL were filtered through baked 0.7-μm 

glass fiber filters within 24 hours of collection and shipped 

on ice to the NWQL for analysis. Samples were analyzed for 

more than 60 compounds using polystyrene-divinylbenzene 

solid-phase extraction and capillary-column gas chromatography/mass spectrometry as reported in Zaugg and others 

(2002).

Analysis of Suspended-Sediment Concentration 

and Parameters

Whole water samples were analyzed for suspendedsediment concentration at the USGS’s Sediment Laboratory 

(SL) in Marina, California. Details of the analytical method 

can be found in Guy (1969). Analytical results of single-blind 

quality control samples provided by SL’s quality assurance 

project showed that laboratory performance during the period 

of this study was satisfactory (U.S. Geological Survey, 2005).

Water parameters (specific conductance, pH, and hardness) were measured in whole water samples at the OCL 

within 24 hours of sample collection. Specific conductance 

and pH were measured using two handheld instruments, (Cole 

Parmer Model 141-61 and Orion Model 250A, respectively), 

as described in the USGS’s national field manual (Wilde and 

Radtke, 1998). Hardness, reported as mg/L of CaCO3, was 

determined using a Hach Model 5-EP titration kit following 

the manufacturer’s guidelines (Hach, 2005). Water temperature was measured in the field at the time of collection using a 

digital thermometer.

Results

Pesticide Concentrations

During this study, 13 current-use pesticides were detected 

in samples collected from six sites along the San Joaquin 

and Old Rivers (table 2). A minimum of five pesticides were 

detected in each sample. One insecticide (diazinon) and 

three herbicides (metolachlor, simazine, and trifluralin) were 

detected in every sample. Maximum concentrations of each 

of the pesticides detected ranged from 5.3 ng/L (chlorpyrifos) 

to 241 ng/L (diazinon). In addition to diazinon, three other 

compoundscarbofuran, metolachlor, and prometrynwere 

detected at high concentrations, with maximum values of 111 

ng/L, 211 ng/L, and 122 ng/L, respectively. 

In general, the number of detections varied little between 

rivers62 detections in Old River samples as compared with 

65 in San Joaquin River samples. A breakdown of pesticide 

detections by site shows that the number of detections per site 

varied by less than 3 percent of the total number of detections. 

In contrast, the maximum concentrations for nine pesticides 

were detected in San Joaquin River samples as compared with 

four in Old River samples.

 The temporal distribution of pesticide detections 

varied little over the three time periods sampled, whereas the 

number of pesticides having their maximum concentration 

detected during the period of managed streamflows was least. 

For the three sampling periods, 39 detections occurred in the 

period prior to the managed flows, 40 during managed flows, 

and 48 after the managed flows. The highest concentrations of 

only three of the 13 pesticides were detected during the managed flow period, whereas the highest concentrations of five 

pesticides were detected in both the before and after periods.

Wastewater Compounds

Samples analyzed at the NWQL contained six wastewater compounds and four pesticides (table 3). Concentrations of 

these compounds ranged from 11 ng/L to 1,800 ng/L, but all 

results are uncertain because the values are below the normal 

laboratory minimum reporting levels. Compounds detected 

at concentrations above the MDL limit, but below the method 

reporting limit, are denoted by an “E” along with the value, 

because they are estimates (Zaugg and others, 2002). The 

pesticide metolachlor was the only compound detected in 

each of the samples. Diazinon and metolachlor were detected 

in both the wastewater and pesticide analyses and the paired 

results are consistent, though they are not directly comparable 

because of differences in sample type and method detection 

limits.

Suspended-Sediment Concentrations and Water 

Parameters

Suspended-sediment concentration was determined for 

34 samples collected during this study (table 4). Suspendedsediment concentrations were similar between river systems 

except during the period of managed streamflow conditions, 

during which suspended-sediment concentrations were much 

higher at sites on the San Joaquin River than at sites on the 

Old River (fig. 3). In samples collected from sites on the Old 

River, suspended-sediment concentrations were generally 

highest in the period following the VAMP and lowest during 

the VAMP. Suspended-sediment concentrations in samples 

collected from the San Joaquin River were generally highest 

during managed flow conditions. 

Water temperature, conductivity, pH, and hardness were 

also measured for all samples, and these values are presented 

in table 4. Values of conductivity, pH, and hardness were lowest at all sites during the managed flow period (fig. 3). 

Results 11
Figure 3. Box plots of water parameter values determined in this study.

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