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Cover photo: Orestimba Creek at River Road Bridge near Crows Landing. (Effluent emerging from pipe can be seen near 

the center of the top photograph. A hydrologic technician measures stream depth near the effluent.) Photographed by 

Jason T. May, U.S. Geological Survey.
Occurrence, Distribution, Instantaneous 

Loads, and Yields of Dissolved Pesticides 

in the San Joaquin River Basin, California, 

During Summer Conditions, 1994 and 2001

By Larry R. Brown, Sandra Y. Panshin, Charles R. Kratzer, Celia Zamora, and 

JoAnn M. Gronberg

Prepared in cooperation with the Central Valley Regional Water Quality Control Board

Scientific Investigations Report 2004-5083

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: 2004

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

Box 25286, Denver Federal Center

Denver, CO 80225

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

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

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

endorsement by the U.S. Government.

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

reproduce any copyrighted materials contained within this report.

Suggested citation:

Brown, L.R., Panshin, S.Y., Kratzer, C.R., Zamora, Celia, and Gronberg, J.M., 2004, Occurrence, distribution, instantaneous loads, and yields of dissolved pesticides in the San Joaquin River Basin, California, during summer conditions, 

1994 and 2001: U.S. Geological Survey Scientific Investigations Report 2004-5083, 53 p. 
iii

Contents

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

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

Purpose and Scope ................................................................................. 2

Study Area .......................................................................................... 5

Methods ................................................................................................... 5

Sampling Design .................................................................................... 5

Field Method and Sample Processing ............................................................ 7

Analytical Methods ................................................................................. 7

Quality Control Procedures ........................................................................ 7

Field Blank Samples .............................................................................. 8

Replicate Samples ................................................................................. 8

Spiked Samples .................................................................................... 8

Assessment of Quality Assurance ............................................................... 12

Statistical Methods for Assessing Patterns in Application, Occurrence, and 

Distribution of Pesticides .................................................................. 12

Instantaneous Pesticide Loads .................................................................. 14

Results and Discussion ................................................................................. 15

Patterns in Application ........................................................................... 15

Patterns in Occurrence and Distribution ......................................................... 20

Instantaneous Loads .............................................................................. 45

Summary and Conclusion .............................................................................. 50

References Cited .......................................................................................... 51
iv

Figures

Figure 1. Map showing basins and sites sampled in June 1994 and June and August 2001, 

in the lower San Joaquin River Basin ................................................... 4

Figure 2. Map showing sites sampled in the valley portion of the lower 

San Joaquin River Basin .................................................................. 6

Figure 3. Cluster analysis of Jaccards distances, which are based on the presence or 

absence of pesticide applications in the study basins in (A) June 1994, 

(B) June 2001, and (C) August 2001 ...................................................... 13

Figure 4. Graphs showing site scores on the first three axes from a principal 

components analysis of pesticide application in the 28 days preceding 

sampling in June 1994 ..................................................................... 18

Figure 5. Graphs showing site scores on the first three axes from a principal 

components analysis of pesticide application in the 28 days preceding 

sampling in June 2001 ..................................................................... 19

Figure 6. Graphs showing site scores on the first three axes from a principal 

components analysis of pesticide application in the 28 days preceding 

sampling in August 2001 .................................................................. 20

Figure 7. Cluster analysis of Jaccards distances, which are based on the presence or 

absence of dissolved pesticides in water samples in (A) June 1994, 

(B) June 2001, and (C) August 2001 ...................................................... 38

Figure 8. Graphs showing site scores on the first three axes from a principal 

components analysis of dissolved pesticide concentrations in June 1994 ......... 40

Figure 9. Graphs showing site scores on the first three axes from a principal 

components analysis of dissolved pesticide concentrations in June 2001 ......... 41

Figure 10. Graphs showing site scores on the first three axes from a principal 

components analysis of dissolved pesticide concentrations in August 2001 ...... 42

Figure 11. Graphs showing site scores on the first two axes from principal 

components analysis of instantaneous pesticide loads in June 1994, 

June 2001, and August 2001 ............................................................... 45

Figure 12. Graphs showing site scores on the first two axes from principal 

components analysis of instantaneous pesticide yields in June 1994, 

June 2001, and August 2001 ............................................................... 47
v

Tables

Table 1. Sites sampled in 1994 and 2001 in the San Joaquin River Basin, California ......... 2

Table 2. Pesticide, CAS number, and reporting limits ............................................. 3

Table 3. Percentages of land use on the east side and west side of the study area 

in the mid-1990s ........................................................................... 7

Table 4. Relative percent difference (RPD) and absolute difference (in micrograms 

per liter) for pesticides collected in environmental and replicate samples 

in 1994 and 2001 ........................................................................... 9

Table 5. Summary of quality control data in 2001 for three spiked samples. .................. 10

Table 6. Mean, median, and standard deviation of recoveries of laboratory spikes in 

pesticide-grade purified water ............................................................ 11

Table 7. Number of basins in which a pesticide was applied, the total amount applied 

in the 28 days before water samples were collected, and the number of basins 

for which the pesticide was detected in the water sample ........................... 16

Table 8. Loadings of pesticides on axes from principal component 

analysis (PCA) of pesticide application intensity (pounds per square mile) ......... 17

Table 9. Streamflow and dissolved pesticide concentrations for sites sampled 

during June 1994 in the San Joaquin River Basin ....................................... 21

Table 10. Streamflow and dissolved pesticide concentrations for sites sampled 

during June 2001 in the San Joaquin River Basin .................................... 25

Table 11. Streamflow and dissolved pesticide concentrations for sites sampled 

during August 2001 in the San Joaquin River Basin .................................... 30

Table 12. Chemical and physical properties of detected pesticides and pesticides 

applied in the basin, but not detected in water samples .............................. 36

Table 13. Number of pesticide detections at each site .......................................... 37

Table 14 Loadings of pesticides on axes from a principal component analysis (PCA) 

of pesticide concentrations in tributary basins for each sampling period ......... 39

Table 15. Loadings of pesticides on axes from a principal component analysis 

(PCA) of pesticide instantaneous loads in tributary basins for each 

sampling period .............................................................................. 44

Table 16. Loadings of pesticides on axes from a principal component analysis 

(PCA) of pesticide instantaneous yields in tributary basins for each 

sampling period .............................................................................. 46

Table 17. Adjusted instantaneous loads for sites contributing to instantaneous 

pesticide loads at the San Joaquin River near Vernalis in June 1994 ............... 48
vi

Conversion Factors, Datum, and Abbreviations

CONVERSION FACTORS 

Multiply By To obtain

cubic foot per second (ft3/s) 0.02832 cubic meter per second 

liter (L) 1.057 quart

mile (mi) 1.609 kilometers

square mile (mi2) 2.590 square kilometers

pound, avoirdupois (lb) 0.4536 kilogram 

Temperature in degrees Fahrenheit (oF) may be converted to degrees Celsius (oC) as follows:

o

C=(oF-32)/1.8.

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

25oC).

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

or micrograms per liter (μg/L). 

DATUM

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88). Horizontal coordinate information is referenced to the North American Datum of 1983 

(NAD 83). 

ABBREVIATIONS

CMC criterion maximum concentration

GC/MS gas chromatograpy/mass spectrometry

> greater than

Koc organic carbon normalized adsorption coefficient

LRL laboratory reporting level

< less than

LT/MDL long-term method detection limit

mg milligram

MDL method detection limit

μm micrometer

μg/L microgram per liter

PCA principal components analysis

RPD relative percent difference

NWQL National Water Quality Laboratory

TMDL total maximum daily load

USGS U.S. Geological Survey

WSID Westside Irrigation District
Occurrence, Distribution, Instantaneous Loads, and Yields 

of Dissolved Pesticides in the San Joaquin River Basin, 

California, During Summer Conditions, 1994 and 2001

By Larry R. Brown, Sandra Y. Panshin, Charles R. Kratzer, Celia Zamora, and JoAnn M. Gronberg

Abstract

Water samples were collected from 22 drainage basins 

for analysis of 48 dissolved pesticides during summer flow 

conditions in 1994 and 2001. Of the 48 pesticides, 31 were 

reported applied in the basin in the 28 days preceding the June 

1994 sampling, 25 in the 28 days preceding the June 2001 

sampling, and 24 in the 28 days preceding the August 2001 

sampling. The number of dissolved pesticides detected was 

similar among sampling periods: 26 were detected in June 

1994, 28 in June 2001, and 27 in August 2001. Concentrations 

of chlorpyrifos exceeded the California criterion for the protection of aquatic life from acute exposure at six sites in June 

1994 and at five sites in June 2001. There was a single exceedance of the criterion for diazinon in June 1994. The number 

of pesticides applied in tributary basins was highly correlated 

with basin area during each sampling period (Spearman’s 

r = 0.85, 0.70, and 0.84 in June 1994, June 2001, and August 

2001, respectively, and p < 0.01 in all cases). Larger areas 

likely include a wider variety of crops, resulting in more varied pesticide use. Jaccard’s similarities, cluster analysis, principal components analysis, and instantaneous load calculations 

generally indicate that west-side tributary basins were different 

from east-side tributary basins. In general, west-side basins 

had higher concentrations, instantaneous loads, and instantaneous yields of dissolved pesticides than east-side basins, 

although there were a number of exceptions. These differences 

may be related to a number of factors, including differences 

in basin size, soil texture, land use, irrigation practices, and 

stream discharge.

Introduction

Agriculture in the San Joaquin Valley of California is 

both productive and valuable. The availability of water for 

irrigation, the Mediterranean climate, and the long growing 

season have combined to make it one of the most intensively 

farmed and economically important agricultural regions in the 

United States. In 2000, the agricultural industry of California 

produced a gross cash income of 27 billion dollars and supplied more than half the nation’s fruits, nuts, and vegetables 

(California Department of Food and Agriculture 2001). Much 

of this production occurred in the San Joaquin Valley.

This intensive agricultural activity includes widespread 

and intensive use of various pesticides. The occurrence and 

concentrations of these pesticides and their effects on water 

quality have been a long-standing concern in the region, especially their potential toxicity to aquatic organisms (Foe and 

Connor, 1991; Foe, 1995; de Vlaming and others, 2000; Werner and others, 2000). Many recent studies have focused on 

storm transport of pesticides applied to orchard crops during 

the winter (Kuivila and Foe, 1995; Kratzer, 1997; Domagalski 

and others, 1997; Kratzer, 1999; Kratzer and others, 2002), 

providing important insights into pesticide transport processes 

and effects on water quality, especially during winter storms. 

Other studies have conducted periodic sampling at a limited 

number of sites (MacCoy and others, 1995; Domagalski, 

1997; Panshin and others, 1998; Domagalski and Munday, 

2003), documenting temporal variability in the occurrence and 

concentrations of dissolved pesticides. However, these studies 

have not sufficiently documented geographic variability in the 

occurrence of dissolved pesticides during the summer irrigation season (April–August), a period of high pesticide use. 

Understanding geographic variability is important, particularly 

in the context of understanding source loads with regard to 

total maximum daily loads (TMDLs).
2 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 1. Sites sampled in 1994 and 2001 in the San Joaquin River Basin, California.

[Site codes are the sampling sites shown in fig.1; WSID, Westside Irrigation District; mi2, square mile] 

USGS 

station number

Site

code

Station name Drainage basin

area–valley floor

(mi2)

Year 

sampled

371521120390800 E1 Bear Creek at Bert Crane Road near Merced 317 1994, 2001

11260815 S1 San Joaquin River near Stevinson 866 1994, 2001

11261100 G1 Salt Slough at Highway 165 near Stevinson 492a 1994, 2001

371636120575200 G2 Los Banos Creek at Highway 140 198 2001

11262900 G3 Mud Slough near Gustine 492a 1994, 2001

372424120432800 E2 Livingston Canal at Livingston Treatment Plant near Livingston 44 1994, 2001

372323120481700 E3 Highline Canal Spill near Hilmar 46 1994, 2001

11270900 E4 Merced River below Merced Falls Dam near Snelling 0 1994

11273500 E5 Merced River at River Road Bridge near Newman 321 1994, 2001

371903120585400 W1 Newman Wasteway at Highway 33 near Gustine 9 1994, 2001

11274538 W2 Orestimba Creek at River Road near Crows Landing 11 1994, 2001

11274554 W3 Spanish Grant Combined Drain near Patterson 22 1994, 2001

11274560 E6 Harding Drain at Carpenter Road near Patterson 84 1994, 2001

11274570 S2 San Joaquin River at Patterson Bridge near Patterson 3,770 1994, 2001

373232121053900 E7 Westport Drain near Modesto 79 1994, 2001

373027121051401 W4 Olive Avenue Drain near Patterson 8 1994, 2001

11274653 W5 Del Puerto Creek at Vineyard Road near Patterson 8 1994, 2001

373621121102801 S3 San Joaquin River below WSID pump above Tuolumne River near Westley 4,145 1994, 2001

11290000 E8 Tuolumne River at Modesto 299 1994

11290200 E9 Tuolumne River at Shiloh Road Bridge near Grayson 319 2001

373842121131800 W6 Hospital Creek at River Road near Patterson 5 1994, 2001

373747121125200 W7 Ingram Creek at River Road near Patterson 11 1994, 2001

11303000 E10 Stanislaus River at Ripon near Patterson 127 1994

374209121103800 E11 Stanislaus River at Caswell State Park near Ripon 160 2001

11303500 S4 San Joaquin River near Vernalis 7,395 1994, 2001 a

Salt Slough and Mud Slough are interconnected by manmade structures, and so, share the same drainage. 

Purpose and Scope

This report documents the occurrence, distribution, and 

instantaneous loads of dissolved pesticides in the surface 

waters of the San Joaquin River Basin during summer flow 

conditions in 1994 and 2001. Distribution was assessed by 

evaluating patterns in pesticide concentrations, instantaneous 

loads, and instantaneous yields among the sites sampled. To 

the extent possible, the occurrence, distribution, and instantaneous loads of dissolved pesticides were compared with 

available data on land use and pesticide applications in order 

to provide insights into sources and transport mechanisms for 

the chemicals detected. Samples were collected at 22 sites in 

June 1994 (table 1) and at 22 sites in June and August 2001 

(table 1) for analysis of 48 dissolved pesticides (table 2) . 

These sites included various tributaries and several nested 

subbasins of the perennial mainstem San Joaquin River. 

The tributaries were selected to characterize water inputs 

from subbasins with physiography, land use, and pesticide 

applications typical of tributary inputs to the San Joaquin 

River. Subbasins of the San Joaquin River were selected to 

characterize changes in water quality resulting from surface 

water inputs (fig. 1). The site at the San Joaquin near Vernalis 

integrates the effects of all upstream inputs. This study focuses 

on geographic variability of pesticide application, occurrence, distribution, instantaneous loads, and instantaneous 

yields. Information on temporal variability in pesticides during 

the April to August, 2001 sampling period is available in 

Domagalski and Munday (2003).
Introduction 3

Table 2. Pesticide, CAS number, and reporting limits.

[CAS, Chemical Abstracts Service; LRL, Laboratory Reporting Level; m, only method reporting limit available; MRL, Method Detection Limit; 

ΝΑ, not analyzed; μg/L, microgram per liter]

Pesticide CAS number

LRL 

2001

(μg/L)

MRL

1994

(μg/L)

2,6-Diethylaniline 579-66-8 0.002 0.003

Acetochlor 34256-82-1 .004 .002

Alachlor 15972-60-8 .002 .002

Atrazine 1912-24-9 .007 .001

Atrazine, deethyl 6190-65-4 .006 .002

Azinphos-methyl 86-50-0 .05 .001

Benfluralin 1861-40-1 .01 .002

Butylate 2008-41-5 .002 m .002

Carbaryl 63-25-2 .041 .003

Carbofuran 1563-66-2 .02 .003

Chlorpyrifos 2921-88-2 .005 .004

Cyanazine 21725-46-2 .018 .004

Dacthal (DCPA) 1861-32-1 .003 .002

DDE, p,p′- 72-55-9 .003 .006

Diazinon 333-41-5 .005 .002

Dieldrin 60-57-1 .005 .001

Disulfoton 298-04-4 .021 .017

EPTC 759-94-4 .002 .002

Ethalfluralin 55283-68-6 .009 .004

Ethoprophos 13194-48-4 .005 .003

Fonofos 944-22-9 .003 .003

HCH, alpha- (alpha-BHC) 319-84-6 .005 .002

HCH, gamma- (Lindane) 58-89-9 .004 .004

Linuron 330-55-2 .035 .002

Malathion 121-75-5 .027 .005

Methyl parathion 298-00-0 .006 .006

Metolachlor 51218-45-2 .013 .002

Metribuzin 21087-64-9 .006 .004

Molinate 2212-67-1 .002 .004

Napropamide 15299-99-7 .007 .003

Parathion 56-38-2 .007 .004

Pebulate 1114-71-2 .002 .004

Pendimethalin 40487-42-1 .01 .004

Permethrin, cis- 54774-45-7 .006 .005

Phorate 298-02-2 .011 .002

Prometon 1610-18-0 .015 .018

Propachlor 1918-16-7 .01 .007

Propanil 709-98-8 .011 .004

Propargite 2312-35-8 .023 .013

Pronamide 23950-58-5 .004 .003

Simazine 122-34-9 .011 .005

Tebuthiuron 34014-18-1 .016 .01

Terbacil 5902-51-2 .034 .007

Terbufos 13071-79-9 .017 .013

Terbuthylazine 5915-41-3 .1 m ΝΑ

Thiobencarb 28249-77-6 .005 .002

Triallate 2303-17-5 .002 .001

Trifluralin 1582-09-8 .009 .002
4 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Figure 1. Basins and sites sampled in June 1994 and June and August 2001, in the lower San Joaquin River Basin. See table 1 for site 

codes. 

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Methods 5

Study Area

The perennial San Joaquin River Basin drains an area 

of 19,023 km2 (7,345 mi2). Of this area, 59 percent is in the 

Sierra Nevada, 11 percent is in the Coast Ranges, and 30 percent is in the San Joaquin Valley. The Sierra Nevada and Coast 

Ranges portions of the drainage are predominantly forested 

land. Virtually all irrigated agriculture and most pesticide 

applications occur in the San Joaquin Valley portion of the 

drainage; thus, this study focuses on the San Joaquin Valley 

portion of the perennial San Joaquin River Basin (fig. 2). The 

water distribution system within the valley floor area is complex. As of the late 1980s, there were at least 86 agricultural 

diversions and 104 agricultural discharges to the San Joaquin 

River (Kratzer and Shelton, 1998).

Climate in the San Joaquin Valley is arid-to-semiarid. 

Precipitation, which falls primarily as snow in the Sierra 

Nevada during November through April, is highly variable 

from year to year. The years sampled in this study, 1994 and 

2001, were considered critically dry and dry, respectively, 

due to limited precipitation (California Department of Water 

Resources, accessed January 20, 2004). The surface hydrology of the San Joaquin River drainage has been altered 

substantially to store and distribute surface water derived from 

snowmelt in the Sierra Nevada. Every major river system in 

the study area has one or more reservoirs. This water is subsequently used for irrigated agriculture and a variety of other 

urban and environmental uses. On the basis of U.S. Geological 

Survey (USGS) streamflow records for 1951 to 1990, 

67 percent of the flow of the perennial San Joaquin River 

is from the three large eastern tributaries: the Merced River 

(15 percent), the Tuolumne River (30 percent), and the 

Stanislaus River (22 percent). Bear Creek, Mud and Salt 

Sloughs, ephemeral streams draining the Coast Ranges, and 

drainage canals that flow directly to the San Joaquin River, 

contribute the remaining 33 percent of streamflow.

Because of geological differences between the Sierra 

Nevada and Coast Ranges, the texture of the soils is different 

between the east side and west side of the valley (Gronberg 

and others, 1998; Panshin and others, 1998). Sediments on 

the eastern side of the valley are generally highly permeable, medium- to coarse-grained sands with low total organic 

carbon. Soils on the eastern side of the valley tend to be finest 

near the valley trough and coarser near the upper parts of the 

alluvial fans. Soils on the western side of the valley tend to be 

finer textured with higher clay content and lower permeability 

than soils on the eastern side of the valley. The west side of the 

valley also tends to be steeper on average than the east side of 

the valley, resulting in steeper gradient in creeks and 

agricultural drains.

These differences in soils and topography have contributed to differences in agricultural land use (table 3). The west 

side of the valley is dominated by row crops (48 percent) 

along with relatively small percentages of orchards 

(7 percent) and vineyards (<1 percent). In contrast, orchards 

are the dominant agricultural land use on the east side of the 

valley (24 percent) and row crops constitute only about 18 

percent. The soils, topography, and related cropping patterns 

also seem to influence irrigation practices and potential agricultural return flows. Drip and flood irrigation tend to be more 

common on the east side of the valley, where they are used primarily on orchards and vineyards. These methods allow water 

to percolate into the soil and generally produce little irrigation 

return flow. Furrow irrigation tends to be more common on 

the west side of the valley, where it is used on row crops. This 

method produces more irrigation return flow because all of 

the applied water does not percolate into the soil. Suspended 

sediment concentrations can be fairly high in irrigation return 

flow from furrow irrigation. Unfortunately, irrigation practices 

and associated return flows are not quantified, so any relation 

between irrigation practices and pesticide transport is somewhat speculative.

The southernmost part of the basin differs from the 

remainder of the basin in several important ways. This area 

includes extensive managed wetlands in addition to agricultural uses. Even though the tributaries in this area are considered to be on the west side of the valley, they are very low 

gradient. For these reasons, these tributaries (Salt Slough, Mud 

Slough, and Los Banos Creek) are coded differently than the 

other west-side tributaries (figs. 1 and 2, table 1).

Methods

Sampling Design

Pesticide sampling in June 1994 occurred from 18 to 

24 June in conjunction with a dye study (Kratzer and Biagitin, 1997) resulting in a Lagrangian design. This means that 

each parcel of water sampled was estimated to reach the San 

Joaquin near Vernalis (site code S4) at the same time. Sampling in 2001 was not Lagrangian, but was completed within 

two days on each occasion. In both years, water samples were 

collected from each of 22 sites. Of these, 19 sites were common to both years (table 1). Additional water samples (replicates) were collected at some sites as described in the section 

on quality assurance procedures. The 18 tributary sites sampled each year (sites not on the San Joaquin River in table 1) 

were selected to characterize water inputs from subbasins 

having physiography, land use, and pesticide applications 

typical of tributary inputs to the San Joaquin River. The four 

sites on the San Joaquin River were the same both years and 

were selected to characterize changes in water quality related 

to tributary inputs.
6 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

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Figure 2. Sites sampled in the valley portion of the lower San Joaquin River Basin. See table 1 for site codes.
Methods 7

Table 3. Percentages of land use on the east side and west side of the study area in the mid-1990s. 

[Data obtained from the California Department of Water Resources 1995, 1996, 1997a,b. Data for the basins in the southern part of the study area are included in 

the west side. Percentages do not total 100 because of rounding. <, smaller than]

Land use East side basins West side basins

Idle agricultural land 2 1

Native vegetation 23 24

Orchards−citrus <1 <1

Orchards−other 24 7

Pasture 16 14

Rice 1 1

Row crops 18 48

Semiagricultural1 3 1

Urban 10 3

Vineyards 4 <1 1

Farmsteads, livestock feed lots, dairies, and poultry farms.

Field Method and Sample Processing

Discrete water samples were collected for analyses of 

pesticides. Most samples were collected as either flow- and 

width-integrated samples using a D-77 isokinetic sampler 

with Teflon nozzle and 3-L Teflon bottle (Shelton, 1994) or as 

equally spaced three-point integrated samples collected with 

a 3-L Teflon bottle strapped into a metal cage and suspended 

from a rope. Exceptions included wide channels where five 

points were integrated rather than three (S3 and S4); Del 

Puerto Creek (W5), which was only wide enough for a midpoint grab with a 3-L Teflon bottle; and the Stanislaus River 

at Caswell State Park near Ripon (E11), where a dip sample 

was collected from the part of the channel carrying most of 

the flow. Data collected using these other methods have been 

compared with data from integrated samples, and the data are 

comparable (Domagalski and Munday, 2003; Zamora and others, 2003). Samples were stored on ice and processed (filtered 

and extracted) within three days of collection. 

A 1-L aliquot was processed from each water sample. All 

aliquots were filtered (0.7 μm, glass fiber filter) to remove suspended solids. Pesticides were extracted from the 1-L aliquot 

by passing the sample through a 500-mg C-18 solid-phase 

extraction cartridge. The cartridge was then dried by passing 

carbon dioxide or nitrogen gas through it. In 1994, samples 

were filtered and extracted at the USGS California District 

laboratory. In 2001, whole water was sent to the USGS, 

National Water Quality Laboratory (NWQL) in Denver, 

Colorado where filtering and extraction were conducted. The 

cartridges were analyzed for extracted pesticides at NWQL.

Analytical Methods

The samples extracted using the C-18 cartridge were 

analyzed for 48 pesticides and pesticide metabolites (table 2) 

by gas chromatography/mass spectrometry (GC/MS). The 

pesticides were eluted from the C-18 cartridge using 

hexane-isopropanol (in a ratio of 3:1). The eluate was analyzed by GC/MS in the selected ion-monitoring mode using 

three characteristic ions for each pesticide. Zaugg and others 

(1995) and Lindley and others (1996) provide a complete 

description of the method.

Most analytical results were reported as laboratory 

reporting level (LRL). The LRL is generally equal to twice the 

annually determined long-term method detection limit 

(LT-MDL). The LRL controls false negative error. The probability of falsely reporting a nondetection for a sample that 

contained an analyte at a concentration equal to or greater than 

the LRL is predicted to be no more than 1 percent (Childress 

and others, 1999). The remaining analytes are reported in 

terms of the method detection limit (MDL) defined as the 

smallest measured concentration of a constituent that may be 

reliably measured (<1 percent chance of a false positive) by a 

given analytical method. 

Quality Control Procedures

Quality control samples were collected and analyzed to 

evaluate possible contamination of samples and recovery efficiency and reproducibility of the pesticide analyses, given the 

sampling, transport, and analytical procedures. A total of 22 

environmental samples were collected in 1994 and a total of 

22 environmental samples were collected in 2001. Two types 

of field quality control samples were evaluated: field blanks (1 

in 1994 and 3 in 2001) and field replicates (2 in 1994 and 5 in 

2001). Laboratory quality control samples consisted of spiked 

environmental samples (1 in 1994 and 3 in 2001) (Mueller and 

others, 1997).

Two quality control samples were collected by the California Regional Water Quality Control Board in June 1994 in 

conjunction with this study, but could not be used. The spiked 

sample collected used a spiking solution that was too concentrated, and this spiking solution contaminated the associated 

blank.
8 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Field Blank Samples

Field blanks were collected to estimate bias from 

contamination of the samples. Field blanks were processed 

in the field after an environmental sample was processed and 

equipment was cleaned in the field to determine whether the 

cleaning procedure following each sample collection was 

adequate to prevent cross-contamination and to determine 

whether the sample was exposed to atmospheric contamination 

during sampling. Field blanks consisted of certified organicfree water that was poured from the 3-L Teflon bottle, through 

the sample splitting device, into a 1-L glass sample bottle. The 

blanks were then extracted and analyzed in the same manner 

as a regular sample.

One field blank was analyzed in 1994, and three were 

analyzed in 2001. The field blank from 1994 contained no 

pesticides at detectable levels. One of the field blanks from 

2001 contained metolachlor at an estimated concentration of 

0.005 μg/L. This concentration is much lower than the LRL 

of 0.013 μg/L. No other pesticides were detected in any of the 

2001 field blanks. The low rate of detection in the data from 

the four field blanks indicates that no systematic contamination was caused by the sampling or cleaning procedures. 

Replicate Samples

Replicate samples were collected to assess the variability 

caused by sample collection, field processing, and laboratory 

analysis procedures. The replicates were sequential, duplicate 

samples; that is, one sample (the environmental sample) was 

collected, then a second sample (the replicate) was collected 

while the first sample was being processed. The replicate was 

processed in a manner identical to the environmental sample. 

Two pairs of replicates were analyzed in 1994, and five pairs 

were analyzed in 2001 (table 4). Because multiple pesticides 

were analyzed in each environmental sample, there was a total 

of 92 individual pesticide analyses performed in 1994 and a 

total of 235 individual pesticide analyses performed in 2001.

The simplest level of analysis of these replicates 

addresses the issue of detection or nondetection of a specific 

pesticide in the environmental sample and its corresponding 

replicate. Ideally, if a pesticide is not detected in the environmental sample, it should not be detected in the paired replicate. This pairing of nondetections occurred in 82 percent of 

the 1994 analyses, and in 75 percent of the 2001 analyses. 

Conversely, if the pesticide is detected in the environmental 

sample, it should also be detected in the paired replicate. This 

pairing of detections occurred in 15 percent of the 1994 analyses, and in 24 percent of the 2001 analyses. In 1994, 3 percent 

of the analyses (3 pesticides in 1 sample, out of 92 analyses 

performed) detected a pesticide in either the environmental 

sample or the replicate, but not in both. In 2001, this value was 

less than 1 percent (2 pesticides in 1 sample, out of 235 analyses performed). In all of these cases of pairing a detection with 

a nondetection, the detected value was relatively low (less than 

0.016 μg/L) relative to the LRL, and in two of the cases, the 

detected concentration was less than the MDL.

For cases where the pesticide is detected in the environmental sample and the replicate, assessment of the difference 

in concentration between the environmental sample and the 

paired replicate is important. This assessment is performed 

by calculating the absolute difference and the relative percent 

difference between the two values. The relative percent difference (RPD) is defined as:

 RPD = |CSample – CReplicate|/[(CSample + CReplicate)/2] × 100%, 

where

CSample = concentration of pesticide in the environmental 

sample, 

CReplicate = concentration of pesticide in the replicate.

When the pesticide was detected in both the replicate and 

the environmental sample, a median RPD of 8 percent was calculated for both the 1994 (n = 14) and the 2001 (n = 56) data. 

Thus, when a pesticide was detected in both the environmental 

sample and the replicate, the values were very close. For all 

the replicate data, it is important to remember that most of 

these concentrations are very low; therefore, a small absolute 

difference in the concentrations of the environmental sample 

and the replicate sample can lead to a large relative percent 

difference between the two values. Minimum, maximum, and 

median values for the absolute difference and relative percent 

difference of all pesticides are presented in table 4.

Spiked Samples

Spiked samples are used to measure bias caused by 

analyte degradation or sample matrix interference on the 

analyses of specific constituents. Spiked samples (spikes) consisted of an environmental sample to which a known amount 

of certain analytes had been added. Each spike had a corresponding environmental sample, collected at the same time, 

to which nothing was added. The June 1994 spiked sample 

had the solution added in the field. The June and August 

2001 spikes had the analytes added at NWQL. The percentage recovery of each pesticide in the spikes was determined 

by calculating the concentration of that pesticide in the spiked 

sample, subtracting the amount in the environmental sample, 

and dividing by the expected concentration in the spiked 

sample and multiplying by 100. The expected concentration 

was what would be detected if the pesticide were not present 

in the environmental sample, assuming 100 percent recovery 

from the spiked sample.
Methods 9

Table 4. Relative percent difference (RPD) and absolute difference (in micrograms per liter) for pesticides collected in environmental 

and replicate samples in 1994 and 2001.

[For 1994, n = 2 pair; for 2001, n = 5 pairs; ND, not detected in either sample; DET, detected in both samples; E, concentration estimated in both samples]

Pesticide Year Comments Minimum

RPD

Maximum 

RPD

Median 

RPD

Minimum

absolute

difference

Maximum

absolute

difference

Median

absolute

difference

Alachlor 1994 1 ND, 1 DET 0 20.7 10.3 0 0.006 0.003

Atrazine 1994 1 ND, 1 DET 0 3.2 1.6 0 .002 .001

2001 1 ND, 3 DET 0 13.3 7.7 0 .002 .001

Atrazine, deethyl 1994 1 ND 0 0 0 0 0 0

2001 3 ND, 1 E 0 40 0 0 .001 0

Azinphos-methyl 1994 1 ND, 1 E 0 8.3 4.2 0 .02 .01

Carbaryl 1994 1 ND, 1 E 0 19.2 9.6 0 .007 .0035

2001 1 ND, 4 E 0 19.2 8 0 .007 .001

Chlorpyrifos 1994 1 ND, 1 DET 0 11.8 5.9 0 .03 .015

2001 2 ND, 3 DET 0 25 4.7 0 .002 .001

Diazinon 1994 1 ND 0 0 0 0 0 0

2001 1, ND, 2 DET, 2 E 0 9.2 0 0 .007 0

Dieldrin 2001 2 ND, 3 DET 0 38.7 0 0 .012 0

EPTC 1994 2 DET 4 111.9 57.9 .02 .033 .0265

2001 1 ND, 4 DET 0 8.9 3.5 0 .004 .003

Ethalfluralin 2001 4 ND, 1 DET 0 5.9 0 0 .004 0

Fonofos 2001 4 ND, 1 E 0 0 0 0 0 0

Lindane 2001 4 ND, 1 E 0 0 0 0 0 0

Malathion 2001 3 ND, 2 E 0 18.2 0 0 .001 0

Metolachlor 1994 2 DET 2.9 7.7 5.3 .001 .004 .0025

2001 5 DET 1.9 14.9 6.7 .002 .141 .005

Metribuzin 1994 1 ND 0 0 0 0 0 0

2001 2 ND, 3 DET 0 25 6.5 0 .005 .001

Molinate 2001 3 ND, 2 DET 0 9.1 0 0 .002 0

Napropamide 2001 2 ND, 3 DET 0 30.7 5.1 0 .231 .001

DDE, p,p′ 1994 1 ND, 1 DET 0 11.8 5.9 0 .001 .0005

2001 2 ND, 2 DET, 1 E 0 37.5 10.5 0 .006 .001

Pendimethalin 2001 4 ND, 1 DET 0 12.2 0 0 .01 0

Prometon 2001 4 ND, 1 E 0 22.2 0 0 .001 0

Propargite 1994 1 ND, 1 DET 0 19.8 9.9 0 .018 .009

2001 1 ND, 4 DET 0 29.5 1.6 0 .054 .002

Simazine 1994 2 DET 6 6.5 6.2 .001 .004 .0025

2001 1 ND, 3 DET, 1 E 0 16.7 7.4 0 .002 .001

Trifluralin 1994 1 ND, 1 DET 0 6.1 3 0 .03 .015

2001 2 ND, 3 DET 0 14.6 1.5 0 .152 .006
10 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 5. Summary of quality control data in 2001 for three spiked 

samples.

[E, recovery not calculated because concentration was reported as an estimate]

Pesticide Minimum

recovery

Maximum

recovery

Median

recovery

2,6-Diethylaniline 88 101 97

Acetochlor 106 127 119

Alachlor 104 128 107

Atrazine 107 118 116

Atrazine, deethyl E E E

Azinphos-methyl E E E

Benfluralin 69 103 79

Butylate 86 96 87

Carbaryl E E E

Carbofuran E E E

Chlorpyrifos 90 106 102

Cyanazine 113 123 119

Dacthal (DCPA) 105 113 111

DDE, p,p′- 46 76 52

Diazinon 96 102 98

Dieldrin 74 114 80

Disulfoton 77 100 94

EPTC 79 115 98

Ethalfluralin 102 135 104

Ethoprophos 93 124 113

Fonofos 88 100 95

HCH, alpha- (alpha-BHC) 92 115 113

HCH, gamma- (Lindane) 96 118 112

Linuron 95 117 107

Malathion 95 102 100

Methyl parathion 80 88 83

Metolachlor 83 117 108

Metribuzin 101 115 108

Molinate 91 98 92

Napropamide 107 133 109

Parathion 109 116 111

Pebulate 91 97 95

Pendimethalin 82 115 104

Permethrin, cis- 55 80 59

Phorate 87 114 96

Prometon 106 118 111

Propachlor 102 111 110

Propanil 97 115 114

Propargite 94 139 105

Pronamide 101 112 108

Simazine 98 105 99

Tebuthiuron 105 134 114

Terbacil E E E

Terbufos 92 103 94

Thiobencarb 98 104 100

Triallate 92 101 92

Trifluralin 78 128 79

One spike was analyzed in 1994; however, data from this 

spike were unusable because of an error in recording the lot 

number of the spiking solution. Three spikes were analyzed 

in 2001 (table 5). For these spikes, the median percentage 

recoveries range from 79 to 119 percent, with the exception 

of p,p′-DDE (52 percent) and cis-permethrin (59 percent). 

Recoveries were not calculated for pesticides that had estimated concentrations (carbaryl, carbofuran, deethylatrazine, 

azinphos-methyl, and terbacil).

NWQL regularly performs quality control checks on 

analytical procedures. These checks consist of spiking each of 

the measured pesticides into pesticide-grade purified water to 

a concentration of 0.1 μg/L. The results from these checks are 

listed in table 6. In general, the results were similar to those 

obtained from the spiked environmental samples (table 5). 

Both p,p′-DDE and cis-permethrin were biased low in the 

laboratory quality control checks and in the spiked environmental samples. Recoveries of most of the other pesticides 

(34) ranged from 80 to 108 percent. However, there were 

a number of notable results. Carbofuran and carbaryl had 

relatively good mean and median recoveries (87–110 percent), 

but had very high standard deviations (79 and 110, respectively) (table 6). Low recoveries (44–78 percent) were found 

for several pesticides (table 6) that had estimated concentrations or median recoveries of 79 percent or less in the spiked 

environmental samples (table 5). The pesticides that had 

estimated values in the spiked environmental samples included 

deethylatrazine (44 percent), azinphos-methyl (73 percent), 

and terbacil (78 percent). The pesticides that had median 

recoveries of 79 percent or less in the spiked environmental 

samples included benfluralin (65 percent), disulfoton 

(43 percent), ethalfluralin (76 percent), pendimethalin (66 

percent), phorate (67 percent), propargite (66 percent), and 

trifluralin (66 percent). Although recoveries for these pesticides were biased low, the standard deviations for these pesticides also were low indicating limited variability (table 6).

For most pesticides, the analytical method generally 

yields consistent results for spiked samples. Low spike recoveries indicate that the pesticide has an increased chance of not 

being detected in environmental samples when it is present at 

low, but nominally detectable concentrations. 
Methods 11

Table 6. Mean, median, and standard deviation of recoveries of laboratory spikes in pesticide-grade purified water.

[μg/L, microgram per liter]

Pesticide

Amount

spiked

(μg/L)

Total number 

of samples Mean Median Standarddeviation

2,6-Diethylaniline 0.1 295 94 92 12

Acetochlor .1 295 97 96 11

Alachlor .1 295 95 95 10

Atrazine .1 295 96 95 11

Atrazine, deethyl .1 295 45 44 15

Azinphos-methyl .1 295 78 73 33

Benfluralin .1 295 66 65 11

Butylate .1 295 90 88 10

Carbaryl .1 295 109 87 110

Carbofuran .1 295 110 94 79

Chlorpyrifos .1 295 90 90 11

Cyanazine .1 295 93 93 24

Dacthal (DCPA) .1 295 100 99 11

DDE, p,p′- .1 295 63 64 8

Diazinon .1 295 95 95 8

Dieldrin .1 295 91 89 11

Disulfoton .1 295 41 43 27

EPTC .1 295 91 91 13

Ethalfluralin .1 295 76 76 13

Ethoprophos .1 295 83 83 14

Fonofos .1 295 87 90 15

HCH, alpha (alpha-BHC) .1 295 90 91 13

HCH, gamma- (Lindane) .1 295 97 97 12

Linuron .1 295 103 100 27

Malathion .1 295 87 84 16

Methyl parathion .1 295 87 84 19

Metolachlor .1 295 99 97 12

Metribuzin .1 295 84 84 12

Molinate .1 295 92 91 10

Napropamide .1 295 88 86 15

Parathion .1 295 89 85 21

Pebulate .1 295 93 91 10

Pendimethalin .1 295 69 66 15

Permethrin, cis- .1 295 42 42 8

Phorate .1 295 66 67 18

Prometon .1 295 92 92 12

Pronamide .1 295 90 90 15

Propachlor .1 295 99 97 15

Propanil .1 295 100 99 15

Propargite .1 295 74 66 28

Simazine .1 295 87 88 15

Tebuthiuron .1 295 110 108 22

Terbacil .1 295 77 78 23

Terbufos .1 295 70 73 16

Thiobencarb .1 295 94 95 8

Triallate .1 295 89 89 8

Trifluralin .1 295 66 66 13
12 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Assessment of Quality Assurance

Overall, the quality control samples showed that no systematic contamination was caused by the sampling or cleaning 

procedures. The results are reproducible on the basis of results 

from replicate samples. Measured concentrations are likely 

biased low for a number of pesticides that are based on spiked 

environmental samples and laboratory spikes into pesticidegrade purified water. However, variability in concentration is 

low for these potentially biased analyses so that the relative 

concentrations when compared among sites (that is, which 

sites are higher or lower than others) are likely correct. Finally, 

high variability for carbofuran and carbaryl, despite good 

mean and median recoveries, suggests caution in interpreting 

results for those chemicals. All quality control results should 

be considered when interpreting the concentration data.

Statistical Methods for Assessing Patterns in 

Application, Occurrence, and Distribution of 

Pesticides

Cluster analysis and principal components analysis 

(PCA) were utilized to determine if there were patterns in 

pesticide application, occurrence and distribution among the 

study basins (statistical techniques explained below). Pesticide application data (California Department of Pesticide 

Regulation, 2002) were obtained for each study basin (table 1) 

for the 28 days preceding the first day of sampling for each 

sample period. The 28-day time period was determined by 

the most measurable precipitation preceding any sampling 

period. Applications were analyzed as both presence/absence 

and application intensity (pounds active ingredient per square 

mile). Basin areas for large east-side tributary rivers were 

based on basin areas in the valley. Because Salt Slough and 

Mud Slough are interconnected, this basin was analyzed as 

a single site. Merced River below Merced Falls (E4) was 

omitted from the analysis because it was sampled as a reference site, above the valley, and thus was considered to have no 

upstream basin area for the purposes of this analysis.

Occurrence and distribution data were obtained from the 

chemical analysis of the water samples. A pesticide was considered present if it was detected at a concentration above the 

reporting level (MDL in 1994 and LRL in 2001). Pesticides 

that had reported estimated concentrations below the reporting 

level were not considered present. Concentrations of dissolved 

pesticides were compared to several water quality criteria 

(table 2). Pesticide presence/absence data were analyzed by 

cluster analysis. Concentration data, instantaneous load data, 

and instantaneous yield data were analyzed with PCA.

Presence/absence data were analyzed using Jaccards 

similarities followed by a group average linkage method cluster analysis. Jaccards similarity is calculated as, 

2C/(A+B+C), where A is the number of pesticides found only 

at site 1, B is the number of pesticides found only at site 2, and 

C is the number of pesticides found at both sites. Jaccards similarity varies from 1 (all pesticides shared) to 0 (no pesticides 

shared). Clustering, in general, is a group of methods that produce a hierarchical arrangement of sites on the basis of their 

similarity (see Gauch, 1982). The method starts with each 

sample assigned to a cluster with a single member, and then 

uses a distance measure to group similar clusters into larger 

clusters until a final single cluster contains all the samples. 

In this analysis the distance is 1 – (Jaccards similarity). Thus, 

more similar sites are closer in distance and cluster together. 

The results are portrayed graphically as a dendrogram (see 

fig. 3 as an example). The similarity of different groups can be 

assessed by observing the “percentage information remaining” 

at branching points. All information is present when individual 

sites are considered and no information remains when all sites 

have been combined into a single group.

Application intensity was analyzed using PCA. The basic 

purpose of PCA is to produce a reduced number of independent composite variables (principal component axes) that summarize the relations of a larger number of correlated variables 

(Gauch, 1982). The associations of the original variables to 

the derived composite variables are known as loadings and 

are analogous to correlations. So, variables with high loadings 

on a principal component axis are highly correlated with each 

other, increasing or decreasing together. The eigenvalue is a 

calculated value for each axis that represents the percentage of 

variance in the data explained by that axis. The first few principal component axes usually summarize most of the variation in a data set. In this study, only principal component axes 

with eigenvalues greater than one are interpreted. This cutoff 

is commonly used to identify the PCA axes with the greatest 

explanatory value (McCune and Grace, 2002).

Principal components analysis is most appropriate for 

data meeting certain statistical assumptions. The analysis 

assumes that the data are normally distributed (bell-shaped 

curve around the mean). When data do not satisfy this assumption, the data can be transformed to better meet the assumption of normality. The data in this study were characterized 

by many low and moderate values and a few high values. The 

data values were transformed with the function 

log10(value +1), to improve normality.
Methods 13

Figure 3. Cluster analysis of Jaccards distances, which are based on the presence or absence of 

pesticide applications in the study basins in (A) June 1994, (B) June 2001, and (C) August 2001. See 

table 1 for site codes. Percentage information remaining varies from 100, starting with the individual 

sites, and decreases to 0 as the sites are clustered into a single group.

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14 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Only pesticides applied in more than seven basins (more 

than one-third) were used in the PCA. PCA was also used to 

analyze concentrations, instantaneous loads, and instantaneous 

yields. Instantaneous loads were calculated by multiplying the 

concentration at a site by the discharge. This gives the mass 

of pesticide being transported by the stream at the time the 

sample was taken. It was not possible to calculate cumulative 

loads because continuous discharge data and periodic pesticide 

data were not available for many of the sites. Instantaneous 

yields were calculated by dividing the instantaneous load by 

the basin area. Standardizing by area provides a more meaningful comparison of basins of widely differing sizes. As for 

application intensities, only pesticides detected in more than 

seven basins were used in the PCA. However, the San Joaquin 

mainstem sites (S1–4) were not included in the PCA analyses 

of instantaneous loads and instantaneous yields. The high 

discharges at the mainstem sites resulted in very high calculated instantaneous loads that obscured patterns among the 

tributary sites. Also, nondetections were assigned a value of 

zero for the analyses of instantaneous loads and instantaneous 

yields because assigning a value of one-half the detection limit 

to a site having high discharge sometimes resulted in values 

higher than at sites where pesticides were actually detected. 

This added source of variation is undesirable for PCA. For 

the analysis of concentrations, nondetections were assigned a 

value of one-half the reporting limit, and the data were transformed, as in the application intensity analysis. 

The low bias for some pesticides noted in the quality control procedures (tables 5 and 6) should not have a significant 

effect on the results of PCA. PCA is being used in this study to 

evaluate patterns of correlation among pesticides. Therefore, 

the relative value at a sitewhich sites have high values and 

which sites have low valuesis more important than the 

absolute concentration in determining the resulting patterns.

Instantaneous Pesticide Loads

The data were used to address two objectives. First, we 

determined the major sources of pesticides detected at the 

San Joaquin River near Vernalis (S4) during the June 1994 

study period. Second, we compared the instantaneous loads 

from upstream tributaries with the instantaneous loads at the 

San Joaquin River near Vernalis to determine if the total basin 

instantaneous load could be estimated from instantaneous 

loads in the tributaries during the June 1994 study period. 

These types of analyses are most appropriately applied to data 

collected in a Lagrangian manner. This means that the same 

parcel of water is sampled as it moves downstream through 

the system. Because only the 1994 sampling was conducted in 

a Lagrangian manner, only the 1994 data are analyzed in this 

fashion.

The first objective was addressed by examining and 

comparing the instantaneous loads from each of the tributaries. 

The second objective was addressed by summing the instantaneous loads from the San Joaquin River near Stevinson (S1) 

with instantaneous loads from the east-side tributaries and the 

west-side tributaries. The east-side tributaries included the 

Merced River (E5), Harding Drain (E6), Westport Drain (E7), 

Tuolumne River (E8), and Stanislaus River (E10). The westside sites included Newman Wasteway (W1), Orestimba Creek 

(W2), Spanish Grant Drain (W3), Olive Avenue Drain (W4), 

Del Puerto Creek (W5), Hospital Creek (W6), and Ingram 

Creek (W7). The southern tributaries were included with 

the west-side sites for this analysis and included Salt Slough 

(G1) and Mud Slough (G3). Los Banos Creek (G2) was not 

included because it was dry at the time of sampling. For the 

purposes of these calculations, samples which did not have 

detections of a particular pesticide were assigned a 

concentration value equal to one-half the MDL. 

Instantaneous loads were calculated for all pesticides at 

each site. The data were screened to determine which pesticides to examine in more detail. The pesticides that were 

examined in detail met all three of the following criteria: (1) 

the pesticide was detected at San Joaquin River near Vernalis 

(the integrator site); (2) the pesticide was detected at five or 

more sites; and (3) at least one sample had a concentration 

greater than or equal to 0.1 μg/L. Five pesticides met all the 

criteria: alachlor, EPTC, metolachlor, molinate, and trifluralin. 

These pesticides exhibited good recoveries in spiked samples, 

except trifluralin (tables 5 and 6), which was biased low. 

Despite the bias, calculation of instantaneous loads should still 

be useful in identifying the basins contributing more or less 

of the pesticide to the San Joaquin River near Vernalis. The 

bias primarily affects calculations of the actual mass of the 

pesticide present, not the relative importance of the different 

sources.
Results and Discussion 15

Results and Discussion 

Patterns in Application

Of the 48 pesticides analyzed, 31 were reported applied 

in the San Joaquin River Basin upstream of Vernalis in 1994 

(table 7). Fewer pesticides were applied preceding the June 

(25 pesticides) and August (24 pesticides) 2001 sampling periods. The amounts applied varied between years and between 

the two sampling periods in 2001 (table 7). More than 1,000 lb 

of active ingredient were applied for 19 pesticides in June 

1994, 15 in June 2001, and 12 in August 2001. The number 

of pesticides applied in individual tributary basins ranged 

from 5 to 19 in 1994, from 4 to 16 in June 2001, and from 3 

to 14 in August 2001. Newman Wasteway (W1) always had 

the minimum number of pesticides applied. The maximum 

number of pesticides was applied in the Westport Drain (E7) 

and Tuolumne River at Modesto (E8) basins in 1994 and in 

the Tuolumne River at Shiloh Road (E9) (June) and Stanislaus 

River at Caswell State Park (E11) (June and August) in 2001. 

The number of pesticides applied in tributary basins was 

highly correlated with basin area during each sampling period 

(Spearman’s r = 0.85, 0.70, and 0.84 in June 1994, June 2001, 

and August 2001, respectively p < 0.01 in all cases). Larger 

areas likely include a wider variety of crops, resulting in more 

varied pesticide use.

Jaccards similarities ranged widely in June 1994 

(0.16–0.96), June 2001 (0.08 and 0.96), and August 2001

(0.13–1.00). The results of the cluster analysis (fig. 3) reflected 

the relation between basin size and number of pesticides 

applied. In June 1994 and June 2001, the mainstem San 

Joaquin River sites and large east-side and southern tributary 

sites occurred together in clusters with greater than 50 percent 

of the information remaining (fig. 3). June 1994 differed 

from June 2001 in that all of the smaller east-side drains also 

occurred in the cluster (fig. 3). In June 1994, Jaccards similarities between sites in the cluster ranged from a minimum 

of 0.42 (E1 and S4) to a maximum of 0.96 (S2 and S3). In 

June 2001, only Westport Drain (E7) of the smaller tributaries, clustered with the larger basins (fig. 3). In June 2001, 

Jaccards similarities between sites in the cluster ranged from a 

minimum of 0.36 (E7 and S1) to a maximum of 0.96 (S3 and 

S4). In August 2001, the mainstem San Joaquin River basins 

clustered with some of the southern basins, but the large eastside basins formed a separate cluster with Harding Drain (E6) 

and Westport Drain (E7) (fig. 3). Jaccards similarities ranged 

from 0.50 to 1.00 in the mainstem cluster and from 0.50 to 

0.90 in the cluster of east-side sites. Most of the smaller basins 

exhibited no obvious pattern between sampling periods, with 

the following exceptions: Del Puerto Creek (W4) and Olive 

Avenue Drain (W5) were always very similar to each other 

(Jaccards similarity from 0.67 to 0.89) as were Livingston 

Canal (E2) and Highline Canal (E3) (Jaccards similarity from 

0.50 to 0.75).

These patterns in similarity are not surprising given 

the correlation between basin size and number of pesticides 

applied. The larger basins cluster together because the larger 

basins tend to have at least small applications of a wide variety 

of pesticides. The mainstem San Joaquin River basins are 

expected to cluster closely because they are nested within 

each other and only gain or lose a few pesticides between the 

upstream and downstream sites. The smaller basins cluster less 

regularly because fewer pesticides were applied and not all the 

same pesticides were applied in each basin, during the preceding 28 days. This variability presumably relates to the specific 

land uses and needs within those basins. Some of these differences might become less obvious if longer application periods 

were considered, assuming that there is some probability of 

small applications of additional pesticides within a longer time 

period.

The results of the principal components analyses (table 8

and figs. 4–6) provided information regarding similarities 

in application intensity among sites. In 1994, the first seven 

principal component (PC) axes had eigenvalues that were 

greater than one, but only the first three principal component 

axes had high loadings (>0.50) for more than two pesticides 

(table 8). Plots of basin scores on the first three PC axes 

(fig. 4) gave results similar to the cluster analysis (fig. 3A). The 

mainstem, southern, and east-side basins tended to have PC 

axis 1 scores of around zero or greater with a fairly restricted 

range of scores on PC axis 2. The small west-side basins had 

negative scores on PC axis 1 and a wide range of scores on 

PC axis 2. The separation of sites on PC axis 1 was mainly 

due to higher applications of pebulate and trifluralin combined 

with no or lower applications of butylate, cyanazine, methyl 

parathion, pendimethalin, cis-permethrin, and simazine in 

west-side basins compared with the other basins. PC axis 2 

separated basins having higher applications of propargite from 

basins having higher applications of carbaryl, chlorpyrifos, 

and gamma-HCH. PC axis 3 mainly separated basins having higher applications of azinphos-methyl, ethalfluralin, and 

metolachlor from basins having lower applications of those 

chemicals. Neither PC axis 2 nor PC axis 3 exhibited any 

strong geographic pattern.
16 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 7. Number of basins in which a pesticide was applied, the total amount applied in the 28 days before water samples were

 collected, and the number of basins for which the pesticide was detected in the water sample.

[A total of 22 basins were sampled during each sampling period. D, number of samples with concentrations above the MDL (Method Detection Limit) in 1994 

and LRL (Laboratory Reporting Level) in 2001; E, number of samples with estimated concentrations below the reporting limit; lb, pound; <, less than]

Pesticide

June 1994 June 2001 August 2001

Basins 

where 

applied

Total 

amount 

applied

(lb)

Basins

where 

detected

Basins 

where 

applied

Total amount 

applied

(lb)

Basins 

where 

detected

Basins 

where 

applied

Total 

amount 

applied

(lb)

Basins 

where 

detected

Alachlor 4 927 7D 5 691 0 0 0 1D

Atrazine 0 0 14D 0 0 12D, 5E 0 0 8D, 9E

Azinphos-methyl 18 4,054 6D 9 295 2E 12 4,002 0

Butylate 12 25,577 4D 7 3,657 0 7 528 0

Carbaryl 18 7,726 9D 18 12,332 1D, 12E 13 1,772 11E

Carbofuran 2 78 1D 0 0 0 5 88 0

Chlorpyrifos 19 15,793 11D, 1E 19 13,386 13D, 2E 20 34,289 15D, 1E

Cyanazine 13 5,542 5D 0 0 0 4 117 9D, 2E

Dacthal (DCPA) 0 0 1D, 1E 0 0 0 0 0 1D

DDE, p,p′- 0 5D, 1E 0 0 6D, 3E 0 0 6D

Diazinon 20 7,952 10D 12 916 11D, 10E 14 2,561 15D, 2E

Dieldrin 0 0 3D 0 0 4D 0 0 4D

Disulfoton 4 172 0 0 0 0 4 117 0

EPTC 13 28,548 17D 9 3,297 17D, 2E 9 2,264 16D

Ethalfluralin 13 3,093 5D 7 229 1D 0 0 1D

Ethoprophos 0 0 0 0 0 1D, 1E 0 0 1D

Fonofos 7 970 0 0 0 1D, 1E 0 0 0

HCH, alpha- (alpha-BHC) 0 0 0 0 0 1D 0 0 1D

HCH, gamma- (Lindane) 10 27 0 6 72 3D, 1E 4 <1 2D, 2E

Linuron 4 25 0 0 0 0 0 0 0

Malathion 7 217 0 11 1,647 1E 12 5,279 12E

Methyl parathion 10 1,854 0 11 3,590 1D, 1E 7 625 0

Metolachlor 17 18,137 15D 17 9,958 16D, 5E 9 1,448 16D, 5E

Metribuzin 3 14 2D 5 373 2D 3 43 1D

Molinate 8 8,550 12D 7 8,251 10D, 2E 0 0 3D

Napropamide 11 191 4D 4 130 5D, 1E 6 165 1D, 1E

Parathion 5 50 0 0 0 0 0 0 0

Pebulate 9 9,755 5D 5 590 0 4 96 0

Pendimethalin 9 1,307 0 10 1,002 0 6 83 3D

Permethrin, cis- 13 1,035 0 16 2,410 0 20 4,225 0

Phorate 5 1,713 0 6 329 0 5 465 0

Prometon 0 0 0 0 0 5E 0 0 0

Pronamide 1 7 0 3 16 1D 2 13 0

Propachlor 0 0 0 0 0 1E 0 0 1E

Propanil 2 891 0 7 6,494 0 6 2,941 0

Propargite 17 11,653 4D, 1E 20 28,394 5D 21 135,686 13D, 2E

Simazine 11 2,823 22D 12 1,554 10D, 9E 12 2,395 6D, 10E

Tebuthiuron 0 0 1E 0 0 1E 0 0 1E

Thiobencarb 6 6,520 4D 6 10,700 1D, 2E 0 0 1D

Trifluralin 20 13,856 13D 18 9,682 11D, 4E 14 2,563 10D, 2E
Results and Discussion 17

Table 8. Loadings of pesticides on axes from principal component analysis (PCA) of pesticide application intensity (pounds per square 

mile).

[, loading <0.5]

PCA

axis 1

PCA

axis 2

PCA

axis 3

PCA

axis 4

PCA

axis 5

PCA

axis 6

PCA

axis 7

June 1994 

Azinphos-methyl   0.60 — — — —

Butylate 0.81   — — — —

Carbaryl — 0.56  — — — —

Chlorpyrifos — .78  — — − 0.50 —

Cyanazine .70 —  — — — —

Diazinon — —  — — — —

EPTC — —  0.59 — — —

Ethalfluralin — — .51 — — — —

HCH, gamma- (Lindane) — .51 — — — — —

Methyl parathion- .60 — — — — .53 —

Metolachlor — — .72 — — — —

Molinate — — — — 0.54 — —

Napropamide — — — — .51 — —

Pebulate −.70 — — — — — —

Pendimethalin .64 — — — — — 0.54

Permethrin, cis- .88 — — — — — —

Propargite — −.69 — — — — —

Simazine .71 — — — — — —

Trifluralin − .80 — — — — — —

Percent variance explained: 27.2 15.5 14.6 10.0 7.7 6.3 5.5

June 2001 

Azinphos-methyl — — − .66 — — 

Carbaryl — — — .57 — 

Chlorpyrifos — — — .54 — 

Diazinon — .69 — — — 

EPTC — .67 — — — 

Malathion .69 — — — — 

Methyl parathion — .56 — — — 

Metolachlor .68 — — — — 

Pendimethalin .50 — − .75 — — 

Permethrin, cis- .55 −.57 — — — 

Propargite .76 — — — — 

Simazine — −.55 — — — 

Trifluralin — — — — — 

Percent variance explained: 24.1 18.8 14.8 12.8 9.3 

August 2001 

Azinphos-methyl — — .67 — 

Carbaryl — .69 .67 — 

Chlorpyrifos .89 — — — 

Diazinon — — — .72 

EPTC — .77 — — 

Malathion — — — − .84 

Metolachlor — — — — 

Permethrin, cis- .93 — — — 

Propargite .87 — — — 

Simazine .78 — — — 

Trifluralin .79 — — — 

Percent variance explained: 34.3 18.0 15.4 14.1 
18 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

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Figure 4. Site scores on the first three axes from a principal components analysis of pesticide application in the 28 days preceding 

sampling in June 1994. See table 1 for site codes. The arrows indicate the direction of increasing application of particular pesticides.

The PCA of June 2001 application intensity (table 8, 

fig. 5) largely reflected the results of the cluster analysis 

(fig. 3B) but also exhibited differences because of the amounts 

applied. Five of the PC axes had eigenvalues greater than one, 

but only the first two were loaded highly for more than two 

pesticides. No pesticides were highly loaded on PC axis 5. A 

plot of PC axes 1 and 2 showed a tight group of basins with 

negative scores on both axes. This group included most of the 

basins in the cluster of mainstem, southern, and large eastside tributary basins identified by cluster analysis (fig. 3B). 

The main differences in the PCA grouping were the inclusion of Newman Wasteway (W1) and Livingston Canal (E2) 

in the group and the absence of the Merced River at River 

Road (E5). There were few applications of any pesticides in 

the Newman Wasteway and Livingston Canal basins, which 

tended to group them with the large cluster that had low application intensities for many pesticides. The Merced River at 

River Road varied from the other mainstem and large east-side 

basins mainly because of heavy application of propargite. 

PC axis 3 mainly separates the Orestimba Creek Basin from 

the others because it had the highest applications of pendimethalin and azinphos-methyl. In contrast to June 1994, PC 

axis 1 did not separate west-side basins from the others. The 

main geographic separation occurred on PC axis 2, which 

shows west-side basins having higher scores than the other 

basins. This relationship corresponds to higher applications 

of diazinon, EPTC, and methyl parathion and lower applications of cis-permethrin and simazine in west-side basins 

compared with the other basins. Although there is some 

overlap in the pesticides contributing to the geographic separation (cis-permethrin, simazine, and methyl parathion), there 

are differences as well. In June 1994, butylate, cyanazine, 

pendimethalin, pebulate, and trifluralin were also important 

(fig. 4). These pesticides were not important in June 2001, but 

diazinon and EPTC were important.
Results and Discussion 19

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Figure 5. Site scores on the first three axes from a principal components analysis of pesticide application in the 28 days preceding 

sampling in June 2001. See table 1 for site codes. The arrows indicate the direction of increasing application of particular pesticides.

Just as the cluster analysis did not show a single large 

cluster in August 2001 (fig. 3C), the PCA of application intensity did not reveal any closely associated groups of similar 

basins (fig. 6). Only the first four PC axes had eigenvalues 

greater than one and only the first PC axis was loaded heavily for more than two pesticides (table 8). PC axis 1 separated 

basins on the basis of application intensity of five pesticides 

used in nearly all of the basins. There seemed to be no strong 

geographic pattern; however, the three highest scores are all 

for east-side basins (E3, E5, E7). In contrast, PC axis 2 scores 

showed a strong geographic pattern with six west-side basins 

(W2–W7) having no or little application of carbaryl and 

EPTC. Neither of these pesticides were important in geographic differences in June 1994. EPTC contributed to geographic variation in June 2001, but carbaryl did not. PC axis 

3 separated basins on the basis of applications of azinphosmethyl and carbaryl, but similar to PC axes 1 and 2, there was 

no strong grouping of sites.

There were not any consistent strong patterns in application intensity. Although the June 1994 analysis showed a clear 

separation of east-side and west-side sites on PCA axis 1, 

which explains the greatest proportion of variance in the data 

(table 8), a similar pattern was not apparent in 2001. East-side 

and west-side basins had widely overlapping distributions of 

scores on PCA axis 1 in both June and August 2001. There 

was separation of west-side basins from other basins in 2001 

on the basis of PC axis 2 scores; however, PC axis 2 explains 

less of the variance of the data (table 8) suggesting that other 

factors were more important than geography in determining 

application rates. Also, the pesticides that were important in 

separating the west-side basins from the other basins varied 

among sample periods. The lack of a consistent strong pattern 

between years and between months should not be surprising 

given the wide variety of factors likely affecting application 

patterns. Such factors include changing cropping patterns in 

different basins, changing price and availability of specific 

pesticides, and outbreaks of different pests.
20 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

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Figure 6. Site scores on the first three axes from a principal components analysis of pesticide application in the 28 days preceding 

sampling in August 2001. See table 1 for site codes. The arrows indicate the direction of increasing application of particular pesticides.

Patterns in Occurrence and Distribution

In 1994, 26 pesticides were detected at least once, including pesticides having estimated concentrations below the 

reporting level (tables 7 and 9). In June 2001, 28 pesticides 

were detected at least once, including pesticides having estimated concentrations below the reporting level (tables 7 and 

10). In August 2001, 27 pesticides were detected at least once, 

including pesticides having estimated concentrations below 

the reporting level (tables 7 and 11). Two pesticides detected 

during each sampling period are breakdown products of pesticides. Deethylatrazine is derived from atrazine and p,p′-DDE 

is derived from DDT (these chemicals are included in the term 

pesticide throughout this report).

Only chlorpyrifos exceeded any of the water quality criteria considered in this study (table 2), except for one 

exceedance of the California CMC (criterion maximum concentration) for diazinon during June 2001 at Hospital Creek 

(W6). In June 1994, four (W2, W3, W4, and W5) of seven 

west-side sites exceeded the California CMC for chlorpyrifos 

of 0.020 μg/L. Hospital Creek (W6) and one site on the San 

Joaquin River (S3) were at the CMC. In June 2001, there were 

five exceedances of the chlorpyrifos CMC, including three 

east-side tributaries (E5, E9, and E11) and two west-side tributaries (W2 and W7). There were no exceedances in August 

2001.
Results and Discussion 21

Table 9. Streamflow and dissolved pesticide concentrations for sites sampled during June 1994 in the San Joaquin River Basin.

[E, estimated concentration; WSID, Westside Irrigation District; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than]

Site

code Station name Date Time

Streamflow

(ft3/s)

Alachlor

concentration 

(μg/L)

Atrazine

concentration

(μg/L)

Atrazine, 

deethyl

concentration

(μg/L)

Azinphosmethyl 

concentration 

(μg/L)

Butylate 

concentration

(μg/L)

Carbaryl

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road 

near Merced

 06/18/1994 1100 68.2 <0.002 <0.001 <0.002 <0.001 0.007 <0.003

S1 San Joaquin River near Stevinson 06/20/1994 1830 17.3 <.002 .008 <.002 <.001 <.002 <.003

G1 Salt Slough at Highway 165 near 

Stevinson

 06/21/1994 0600 187 <.002 <.001 <.002 <.001 <.002 <.003

G3 Mud Slough near Gustine 06/21/1994 0400 28 <.002 .022 E.010 <.001 <.002 E.015

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 06/20/1994 1300 44.2 <.002 <.001 <.002 <.001 <.002 <.003

E3 Highline Canal Spill near Hilmar 06/21/1994 0220 15.3 <.002 <.001 <.002 <.001 <.002 <.003

E4 Merced River below Merced Falls 

Dam near Snelling

 06/18/1994 0900 1,680 <.002 <.001 <.002 <.001 <.002 <.003

E5 Merced River at River Road 

Bridge near Newman

 06/22/1994 0400 141 <.002 <.001 <.002 <.001 <.002 <.003

W1 Newman Wasteway at Highway 33 

near Gustine

 06/22/1994 0100 10 .009 .036 E.005 E.013 <.002 E.170

W2 Orestimba Creek at River Road 

near Crows Landing

 06/22/1994 1645 9.6 <.002 .017 E.005 E.079 <.002 <.003

W3 Spanish Grant Combined Drain 

near Patterson

 06/22/1994 2100 35 <.002 .022 E.005 E1.000 <.002 E.021

E6 Harding Drain at Carpenter Road 

near Patterson

 06/22/1994 2300 35 <.002 .008 E.012 <.001 .008 E.390

S2 San Joaquin River at Patterson 

Bridge near Patterson

 06/23/1994 0530 487 <.002 .011 E.008 E.077 <.002 E.150

E7 Westport Drain near Modesto 06/23/1994 1100 15.2 <.002 <.001 <.002 <.001 .002 <.003

W4 Olive Avenue Drain near Patterson 06/23/1994 0630 6.2 .032 .063 <.002 E.250 <.002 E.040

W5 Del Puerto Creek at Vineyard 

Road near Patterson

 06/23/1994 0830 7.8 .520 .040 E.006 <.001 <.002 <.003

S3 San Joaquin River below WSID 

pump above Tuolumne River 

near Westley

 06/23/1994 2200 347 .021 .013 E.005 E.046 <.002 E.028

E8 Tuolumne River at Modesto 06/23/1994 0400 121 <.002 .007 <.002 <.001 .004 E.010

W6 Hospital Creek at River Road near 

Patterson

 06/23/1994 2330 32.1 .240 .048 <.002 <.001 <.002 <.003

W7 Ingram Creek at River Road near 

Patterson

 06/24/1994 0030 11.1 .130 .023 E.008 <.001 <.002 E.053

E10 Stanislaus River at Ripon near 

Patterson

 06/23/1994 1800 499 <.002 <.001 <.002 <.001 <.002 <.003

S4 San Joaquin River near Vernalis 06/24/1994 1100 1,110 .014 .009 E.004 <.001 <.002 <.003
Results and Discussion 22

Table 9. Streamflow and dissolved pesticide concentrations for sites sampled during June 1994 in the San Joaquin River BasinContinued.

[E, estimated concentration; WSID, Westside Irrigation District; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than]

Site

code Station name Date Time

Carbofuran

concentration

(μg/L)

Chlorpyrifos

concentration

(μg/L)

Cyanzine

concentration

(μg/L)

Dacthal

concentration 

(μg/L)

DDE, p,p’-

concentration

(μg/L)

Diazinon 

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road near 

Merced

 06/18/1994 1100 <0.003 E0.003 <0.004 <0.002 <0.006 0.005

S1 San Joaquin River near Stevinson 06/20/1994 1830 <.003 <.004 .130 <.002 <.006 <.002

G1 Salt Slough at Highway 165 near 

Stevinson

 06/21/1994 0600 <.003 <.004 <.004 <.002 <.006 <.002

G3 Mud Slough near Gustine 06/21/1994 0400 <.003 <.004 .150 .006 <.006 .012

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 06/20/1994 1300 <.003 <.004 <.004 <.002 <.006 <.002

E3 Highline Canal Spill near Hilmar 06/21/1994 0220 <.003 <.004 <.004 <.002 <.006 <.002

E4 Merced River below Merced Falls 

Dam near Snelling

 06/18/1994 0900 <.003 <.004 <.004 E.001 <.006 <.002

E5 Merced River at River Road Bridge 

near Newman

 06/22/1994 0400 <.003 <.004 <.004 <.002 <.006 <.002

W1 Newman Wasteway at Highway 33 

near Gustine

 06/22/1994 0100 <.003 <.004 .026 <.002 <.006 .011

W2 Orestimba Creek at River Road near 

Crows Landing

 06/22/1994 1645 <.003 .270 <.004 <.002 .018 <.002

W3 Spanish Grant Combined Drain near 

Patterson

 06/22/1994 2100 E.01 .029 <.004 <.002 .006 .016

E6 Harding Drain at Carpenter Road 

near Patterson

 06/22/1994 2300 <.003 .014 <.004 <.002 <.006 .030

S2 San Joaquin River at Patterson 

Bridge near Patterson

 06/23/1994 0530 <.003 .030 .049 <.002 <.006 .011

E7 Westport Drain near Modesto 06/23/1994 1100 <.003 .015 <.004 <.002 <.006 <.002

W4 Olive Avenue Drain near Patterson 06/23/1994 0630 <.003 .270 <.004 <.002 .009 <.002

W5 Del Puerto Creek at Vineyard Road 

near Patterson

 06/23/1994 0830 <.003 .037 <.004 <.002 E.003 .019

S3 San Joaquin River below WSID 

pump above Tuolumne River near 

Westley

 06/23/1994 2200 <.003 .020 <.004 <.002 <.006 .009

E8 Tuolumne River at Modesto 06/23/1994 0400 <.003 .012 .049 <.002 <.006 <.002

W6 Hospital Creek at River Road near 

Patterson

 06/23/1994 2330 <.003 .020 <.004 <.002 .027 .009

W7 Ingram Creek at River Road near 

Patterson

 06/24/1994 0030 <.003 .007 <.004 <.002 .012 .009

E10 Stanislaus River at Ripon near 

Patterson

 06/23/1994 1800 <.003 <.004 <.004 <.002 <.006 <.002

S4 San Joaquin River near Vernalis 06/24/1994 1100 <.003 <.004 <.004 <.002 <.006 <.002
Results and Discussion 23

Table 9. Streamflow and dissolved pesticide concentrations for sites sampled during June 1994 in the San Joaquin River BasinContinued.

[E, estimated concentration; WSID, Westside Irrigation District; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than]

Site

code Station name Date Time

Dieldrin

concentration

(μg/L)

EPTC

concentration

(μg/L)

Ethalfluralin

concentration

(μg/L)

Fonofos

concentration

(μg/L)

Metolachlor

concentration

(μg/L)

Metribuzin

concentration 

(μg/L)

Molinate

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road 

near Merced

 06/18/1994 1100 <0.001 E40.000 <0.004 <0.003 0.004 <0.004 0.006

S1 San Joaquin River near Stevinson 06/20/1994 1830 <.001 .130 <.004 <.003 .110 <.004 .100

G1 Salt Slough at Highway 165 near 

Stevinson

 06/21/1994 0600 <.001 <.002 <.004 <.003 <.002 <.004 <.004

G3 Mud Slough near Gustine 06/21/1994 0400 <.001 .012 <.004 <.003 <.002 <.004 .690

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 06/20/1994 1300 <.001 <.002 <.004 <.003 <.002 <.004 <.004

E3 Highline Canal Spill near Hilmar 06/21/1994 0220 <.001 <.002 <.004 <.003 <.002 <.004 <.004

E4 Merced River below Merced Falls 

Dam near Snelling

 06/18/1994 0900 <.001 <.002 <.004 <.003 <.002 <.004 .016

E5 Merced River at River Road Bridge 

near Newman

 06/22/1994 0400 <.001 .013 <.004 <.003 .034 <.004 <.004

W1 Newman Wasteway at Highway 33 

near Gustine

 06/22/1994 0100 <.001 .180 <.004 <.003 .180 <.004 <.004

W2 Orestimba Creek at River Road 

near Crows Landing

 06/22/1994 1645 .012 .340 .120 .120 .560 .012 <.004

W3 Spanish Grant Combined Drain 

near Patterson

 06/22/1994 2100 <.001 .140 .018 .028 .170 <.004 .015

E6 Harding Drain at Carpenter Road 

near Patterson

 06/22/1994 2300 <.001 .022 <.004 <.003 .005 <.004 <.004

S2 San Joaquin River at Patterson 

Bridge near Patterson

 06/23/1994 0530 <.001 .110 <.004 .005 .071 <.004 .099

E7 Westport Drain near Modesto 06/23/1994 1100 <.001 .051 <.004 <.003 <.002 <.004 <.004

W4 Olive Avenue Drain near Patterson 06/23/1994 0630 <.001 .510 <.004 <.003 .054 <.004 <.004

W5 Del Puerto Creek at Vineyard Road 

near Patterson

 06/23/1994 0830 <.001 .320 .036 <.003 .110 <.004 .008

S3 San Joaquin River below WSID 

pump above Tuolumne River 

near Westley

 06/23/1994 2200 <.001 .100 <.004 .006 .087 <.004 .079

E8 Tuolumne River at Modesto 06/23/1994 0400 <.001 .020 <.004 <.003 .280 <.004 .027

W6 Hospital Creek at River Road near 

Patterson

 06/23/1994 2330 .013 .660 .073 .017 .053 .032 .090

W7 Ingram Creek at River Road near 

Patterson

 06/24/1994 0030 .012 .140 .190 .006 .076 <.004 .041

E10 Stanislaus River at Ripon near 

Patterson

 06/23/1994 1800 <.001 <.002 <.004 <.003 <.002 <.004 <.004

S4 San Joaquin River near Vernalis 06/24/1994 1100 <.001 .034 <.004 <.003 .064 <.004 .030
24 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 9. Streamflow and dissolved pesticide concentrations for sites sampled during June 1994 in the San Joaquin River BasinContinued.

[E, estimated concentration; WSID, Westside Irrigation District; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than]

Site

code Station name Date Time

Napro

pamide

concentration

(μg/L)

Pebulate

concentration

(μg/L)

Propargite

concentration

(μg/L)

Simazine

concentration

(μg/L)

Tebuthiuron

concentration

(μg/L)

Thiobencarb

concentration

(μg/L)

Trifluralin 

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road 

near Merced

 06/18/1994 1100 <0.003 <0.004 <0.013 0.008 <0.010 <0.002 0.006

S1 San Joaquin River near Stevinson 06/20/1994 1830 <.003 <.004 <.013 .043 <.010 <.002 <.002

G1 Salt Slough at Highway 165 near 

Stevinson

 06/21/1994 0600 <.003 <.004 E.006 .053 <.010 <.002 <.002

G3 Mud Slough near Gustine 06/21/1994 0400 <.003 <.004 <.013 .061 <.010 .077 .018

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 06/20/1994 1300 <.003 <.004 <.013 .007 <.010 <.002 <.002

E3 Highline Canal Spill near Hilmar 06/21/1994 0220 <.003 <.004 <.013 .035 <.010 <.002 <.002

E4 Merced River below Merced Falls 

Dam near Snelling

 06/18/1994 0900 <.003 <.004 <.013 .007 <.010 .004 <.002

E5 Merced River at River Road 

Bridge near Newman

 06/22/1994 0400 <.003 <.004 <.013 .016 <.010 <.002 <.002

W1 Newman Wasteway at Highway 

33 near Gustine

 06/22/1994 0100 <.003 <.004 <.013 .073 <.010 <.002 .010

W2 Orestimba Creek at River Road 

near Crows Landing

 06/22/1994 1645 .033 .098 .430 .054 <.010 <.002 .140

W3 Spanish Grant Combined Drain 

near Patterson

 06/22/1994 2100 .019 .054 1.100 .069 <.010 <.002 .100

E6 Harding Drain at Carpenter Road 

near Patterson

 06/22/1994 2300 <.003 <.004 <.013 .024 <.010 <.002 <.002

S2 San Joaquin River at Patterson 

Bridge near Patterson

 06/23/1994 0530 <.003 <.004 .031 .039 <.010 .007 .013

E7 Westport Drain near Modesto 06/23/1994 1100 <.003 <.004 <.013 .030 <.010 <.002 .016

W4 Olive Avenue Drain near Patterson 06/23/1994 0630 <.003 <.004 .100 .065 <.010 <.002 .510

W5 Del Puerto Creek at Vineyard 

Road near Patterson

 06/23/1994 0830 <.003 <.004 <.013 .050 <.010 <.002 .035

S3 San Joaquin River below WSID 

pump above Tuolumne River 

near Westley

 06/23/1994 2200 <.003 .016 <.013 .042 <.010 .004 .018

E8 Tuolumne River at Modesto 06/23/1994 0400 <.003 <.004 <.013 .030 <.010 <.002 <.002

W6 Hospital Creek at River Road near 

Patterson

 06/23/1994 2330 .056 .033 <.013 .059 E.006 <.002 .350

W7 Ingram Creek at River Road near 

Patterson

 06/24/1994 0030 .069 .053 <.013 .037 <.010 <.002 .430

E10 Stanislaus River at Ripon near 

Patterson

 06/23/1994 1800 <.003 <.004 <.013 .024 <.010 <.002 <.002

S4 San Joaquin River near Vernalis 06/24/1994 1100 <.003 <.004 <.013 .033 <.010 <.002 .019
Results and Discussion 25

Table 10. Streamflow and dissolved pesticide concentrations for sites sampled during June 2001 in the San Joaquin River Basin. 

[E, estimated concentration; ft3/s, cubic feet per second; M, deleted due to interferences; μg/L, microgram per liter; <, less than; ND, no data] 

Site

code Station name Date Time

Streamflow

(ft3/s)

Atrazine

concentration

(μg/L)

Atrazine, 

deethyl

concentration

(μg/L)

Azinphosmethyul 

concentration

(μg/L)

Carbaryl 

concentration 

(μg/L)

Chlorpyrifos

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road near Merced 06/20/2001 0830 2.9 <0.007 <0.006 <0.050 <0.041 0.018

S1 San Joaquin River near Stevinson 06/20/2001 1110 1.3 .008 <.006 <.050 <.041 <.005

G1 Salt Slough at Highway 165 near Stevinson 06/20/2001 1040 201 .014 E.002 <.050 E.022 .008

G2 Los Banos Creek at Highway 140 06/20/2001 0910 7.4 .015 <.006 <.050 E.015 <.005

G3 Mud Slough near Gustine 06/20/2001 0950 62.0 .016 <.006 <.050 <.041 E.004

E2 Livingston Canal at Livingston Treatment 

Plant near Livingston

 06/20/2001 1010 0 <.007 <.006 <.050 <.041 <.005

E3 Highline Canal Spill near Hilmar 06/20/2001 1110 4.25 E.001 <.006 E.019 <.041 E.003

E5 Merced River at River Road Bridge near 

Newman

06/20/2001 1340 180 <.007 <.006 <.050 <.041 .025

W1 Newman Wasteway at Highway 33 near 

Gustine

 06/20/2001 1200 6.1 E.006 <.006 <.050 E.002 .013

W2 Orestimba Creek at River Road near Crows 

Landing

 06/20/2001 1150 12.9 .013 <.006 <.050 E.004 .149

W3 Spanish Grant Combined Drain near 

Patterson

 06/20/2001 1350 21.0 .018 <.006 E.013 E.310 .009

E6 Harding Drain at Carpenter Road near 

Patterson

 06/21/2001 1120 61.5 E.004 E.004 <.050 E.007 .012

S2 San Joaquin River at Patterson Bridge near 

Patterson

 06/20/2001 0910 336 .009 E.003 <.050 E.002 <.005

E7 Westport Drain near Modesto 06/21/2001 0940 21.2 <.007 <.006 <.050 E.002 <.005

W4 Olive Avenue Drain near Patterson 06/21/2001 0950 ND .021 E.003 <.050 E.004 .007

W5 Del Puerto Creek at Vineyard Road near 

Patterson

06/20/2001 1440 6.4 .013 E.004 <.050 E.013 <.005

S3 San Joaquin River below WSID pump 

above Tuolumne River near Westley

06/21/2001 1120 502 .008 <.006 <.050 <.041 .009

E9 Tuolumne River at Shiloh Road Bridge near 

Grayson

06/21/2001 1230 177 E.004 <.006 <.050 E.002 .021

W6 Hospital Creek at River Road near Patterson 06/21/2001 1400 4.1 .016 E.003 <.050 E.012 <.005

W7 Ingram Creek at River Road near Patterson 06/21/2001 1310 15 .027 <.006 <.050 E.040 0.021

E11 Stanislaus River at Caswell State Park near 

Ripon

06/21/2001 1300 550 <.007 <.006 <.050 .041 .100

S4 San Joaquin River near Vernalis 06/21/2001 1220 1,368 E.005 <.006 <.050 <.041 .010
26 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 10. Streamflow and dissolved pesticide concentrations for sites sampled during June 2001 in the San Joaquin River Basin—Continued. 

[E, estimated concentration; ft3/s, cubic feet per second; M, deleted due to interferences; μg/L, microgram per liter; <, less than; ND, no data] 

Site

code Station name Date Time

DDE, p,p′-

concentration

(μg/L)

Diazinon

concentraton

(μg/L)

Dieldrin

concentration

(μg/L)

EPTC

concentration

(μg/L)

Ethalfluralin

concentration

(μg/L)

Ethoprophos

concentration 

(μg/L)

E1 Bear Creek at Bert Crane Road near 

Merced

 06/20/2001 0830 <0.003 E0.002 <0.005 0.003 <0.009 <.005

S1 San Joaquin River near Stevinson 06/20/2001 1110 E.001 E.003 <.005 .007 <.009 <.005

G1 Salt Slough at Highway 165 near 

Stevinson

 06/20/2001 1040 <.003 .006 <.005 .015 <.009 <.005

G2 Los Banos Creek at Highway 140 06/20/2001 0910 <.003 E.003 <.005 .035 <.009 <.005

G3 Mud Slough near Gustine 06/20/2001 0950 <.003 E.003 <.005 .003 <.009 <.005

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 06/20/2001 1010 <.003 <.005 <.005 <.002 <.009 <.005

E3 Highline Canal Spill near Hilmar 06/20/2001 1110 <.003 E.001 <.005 <.002 <.009 <.005

E5 Merced River at River Road Bridge 

near Newman

 06/20/2001 1340 <.003 .007 <.005 .002 <.009 <.005

W1 Newman Wasteway at Highway 33 

near Gustine

 06/20/2001 1200 .003 E.004 <.005 .011 <.009 <.005

W2 Orestimba Creek at River Road near 

Crows Landing

 06/20/2001 1150 .009 E.004 .007 .048 <.009 E.003

W3 Spanish Grant Combined Drain near 

Patterson

 06/20/2001 1350 .010 .029 .007 .072 <.009 .033

E6 Harding Drain at Carpenter Road 

near Patterson

 06/21/2001 1120 <.003 .038 <.005 .010 <.009 <.005

S2 San Joaquin River at Patterson Bridge 

near Patterson

 06/20/2001 0910 E.002 .007 <.005 .008 <.009 <.005

E7 Westport Drain near Modesto 06/21/2001 0940 M E.002 <.005 E.001 <.009 <.005

W4 Olive Avenue Drain near Patterson 06/21/2001 0950 <.003 .006 <.005 .053 <.009 <.005

W5 Del Puerto Creek at Vineyard Road 

near Patterson

 06/20/2001 1440 .005 .008 <.005 .047 <.009 <.005

S3 San Joaquin River below WSID 

pump above Tuolumne River near 

Westley

 06/21/2001 1120 E.001 .007 <.005 .011 <.009 <.005

E9 Tuolumne River at Shiloh Road 

Bridge near Grayson

 06/21/2001 1230 <.003 .026 <.005 E.002 <.009 <.005

W6 Hospital Creek at River Road near 

Patterson

 06/21/2001 1400 .019 .180 .037 .077 <.009 <.005

W7 Ingram Creek at River Road near 

Patterson

 06/21/2001 1310 .013 E.004 .009 .116 .070 <.005

E11 Stanislaus River at Caswell State Park 

near Ripon

 06/21/2001 1300 <.003 .030 <.005 <.002 <.009 <.005

S4 San Joaquin River near Vernalis 06/21/2001 1220 <.003 E.004 <.005 .004 <.009 <.005
Results and Discussion 27

Table 10. Streamflow and dissolved pesticide concentrations for sites sampled during June 2001 in the San Joaquin River Basin—Continued.

[E, estimated concentration; ft3/s, cubic feet per second; M, deleted due to interferences; μg/L, microgram per liter; <, less than; ND, no data] 

Site

code Station name Date Time

Fonofos 

concentration

(μg/L)

HCH, 

alphaconcentration

(μg/L)

HCH,

gammaconcentration

(μg/L)

Malathion

concentration

(μg/L)

Methyl

parathion

concentration

(μg/L)

Metolachlor

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road 

near Merced

06/20/2001 0830 <0.003 <0.005 <0.004 <.027 <0.006 E0.009

S1 San Joaquin River near Stevinson 06/20/2001 1110 <.003 <.005 <.004 <.027 <.006 .329

G1 Salt Slough at Highway 165 near 

Stevinson

 06/20/2001 1040 <.003 <.005 <.004 <.027 <.006 .119

G2 Los Banos Creek at Highway 140 06/20/2001 0910 <.003 <.005 <.004 <.027 <.006 .051

G3 Mud Slough near Gustine 06/20/2001 0950 <.003 <.005 <.004 <.027 <.006 .088

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 06/20/2001 1010 <.003 <.005 <.004 <.027 <.006 <.013

E3 Highline Canal Spill near Hilmar 06/20/2001 1110 <.003 <.005 <.004 <.027 <.006 E.002

E5 Merced River at River Road Bridge 

near Newman

 06/20/2001 1340 <.003 <.005 <.004 <.027 <.006 E.005

W1 Newman Wasteway at Highway 33 

near Gustine

 06/20/2001 1200 <.003 <.005 <.004 <.027 <.006 .044

W2 Orestimba Creek at River Road 

near Crows Landing

 06/20/2001 1150 <.003 <.005 <.004 <.027 E.004 .271

W3 Spanish Grant Combined Drain 

near Patterson

 06/20/2001 1350 .004 <.005 <.004 <.027 .069 .820

E6 Harding Drain at Carpenter Road 

near Patterson

 06/21/2001 1120 <.003 .011 .025 <.027 <.006 .015

S2 San Joaquin River at Patterson 

Bridge near Patterson

 06/20/2001 0910 <.003 <.005 <.004 <.027 <.006 .104

E7 Westport Drain near Modesto 06/21/2001 0940 <.003 <.005 <.004 <.027 <.006 E.004

W4 Olive Avenue Drain near Patterson 06/21/2001 0950 <.003 <.005 .007 <.027 <.006 .097

W5 Del Puerto Creek at Vineyard Road 

near Patterson

 06/20/2001 1440 <.003 <.005 <.004 E.017 <.006 .705

S3 San Joaquin River below WSID 

pump above Tuolumne River 

near Westley

 06/21/2001 1120 <.003 <.005 .005 <.027 <.006 .133

E9 Tuolumne River at Shiloh Road 

Bridge near Grayson

 06/21/2001 1230 <.003 <.005 <.004 <.027 <.006 .018

W6 Hospital Creek at River Road near 

Patterson

 06/21/2001 1400 <.003 <.005 <.004 <.027 <.006 .088

W7 Ingram Creek at River Road near 

Patterson

 06/21/2001 1310 E.001 <.005 E.002 <.027 <.006 1.080

E11 Stanislaus River at Caswell State 

Park near Ripon

 06/21/2001 1300 <.003 <.005 <.004 <.027 <.006 E.004

S4 San Joaquin River near Vernalis 06/21/2001 1220 <.003 <.005 <.004 <.027 <.006 .048
28 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 10. Streamflow and dissolved pesticide concentrations for sites sampled during June 2001 in the San Joaquin River Basin—Continued.

[E, estimated concentration; ft3/s, cubic feet per second; M, deleted due to interferences; μg/L, microgram per liter; <, less than; ND, no data] 

Site

code Station name Date Time

Metrobuzin

concentration

(μg/L)

Molinate

concentration

(μg/L)

Napropamide

concentration

(μg/L)

Prometron

concentration

(μg/L)

Pronamide

concentration

(μg/L)

Propachlor

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road 

near Merced

 06/20/2001 0830 <0.006 <0.002 <0.007 <0.015 <0.004 <0.010

S1 San Joaquin River near Stevinson 06/20/2001 1110 <.006 <.002 E.005 <.015 <.004 <.010

G1 Salt Slough at Highway 165 near 

Stevinson

 06/20/2001 1040 <.006 .013 <.007 <.015 .005 <.010

G2 Los Banos Creek at Highway 

140

 06/20/2001 0910 <.006 <.005 <.007 E.002 <.004 <.010

G3 Mud Slough near Gustine 06/20/2001 0950 <.006 .170 <.007 E.002 <.004 <.010

E2 Livingston Canal at Livingston 

Treatment Plant near 

Livingston

 06/20/2001 1010 <.006 <.002 <.007 <.015 <.004 <.010

E3 Highline Canal Spill near Hilmar 06/20/2001 1110 <.006 <.005 <.007 <.015 <.004 <.010

E5 Merced River at River Road 

Bridge near Newman

 06/20/2001 1340 <.006 E.001 <.007 <.015 <.004 <.010

W1 Newman Wasteway at Highway 

33 near Gustine

 06/20/2001 1200 <.006 E.001 <.007 E.003 <.004 <.010

W2 Orestimba Creek at River Road 

near Crows Landing

 06/20/2001 1150 <.006 .006 <.007 <.015 <.004 <.010

W3 Spanish Grant Combined Drain 

near Patterson

 06/20/2001 1350 <.112 <.002 .090 <.015 <.004 <.010

E6 Harding Drain at Carpenter Road 

near Patterson

 06/21/2001 1120 <.006 <.002 <.007 <.015 <.004 <.010

S2 San Joaquin River at Patterson 

Bridge near Patterson

 06/20/2001 0910 <.006 .008 <.007 <.015 <.004 <.010

E7 Westport Drain near Modesto 06/21/2001 0940 <.006 <.002 .007 <.015 <.004 <.010

W4 Olive Avenue Drain near 

Patterson

 06/21/2001 0950 <.006 .011 <.007 <.015 <.004 <.010

W5 Del Puerto Creek at Vineyard 

Road near Patterson

 06/20/2001 1440 <.006 .016 .072 <.015 <.004 <.010

S3 San Joaquin River below WSID 

pump above Tuolumne River 

near Westley

 06/21/2001 1120 <.006 .004 <.007 E.002 <.004 <.010

E9 Tuolumne River at Shiloh Road 

Bridge near Grayson

 06/21/2001 1230 <.006 <.002 <.007 <.015 <.004 E.010

W6 Hospital Creek at River Road 

near Patterson

 06/21/2001 1400 .009 .021 .868 <.015 <.004 <.010

W7 Ingram Creek at River Road near 

Patterson

 06/21/2001 1310 .049 .023 .025 E.004 <.004 <.010

E11 Stanislaus River at Caswell State 

Park near Ripon

 06/21/2001 1300 <.006 <.002 <.007 <.015 <.004 <.010

S4 San Joaquin River near Vernalis 06/21/2001 1220 <.006 .002 <.007 <.015 <.004 <.010
Results and Discussion 29

Table 10. Streamflow and dissolved pesticide concentrations for sites sampled during June 2001 in the San Joaquin River Basin—Continued.

[E, estimated concentration; ft3/s, cubic feet per second; M, deleted due to interferences; μg/L, microgram per liter; <, less than; ND, no data] 

Site

code Station name Date Time

Propargite

concentration

(μg/L)

Simazine

concentration

(μg/L)

Terbuthiuron

concentration

(μg/L)

Thiobencarb

concentration

(μg/L)

Trifluralin

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road 

near Merced

 06/20/2001 0830 0.055 <0.011 <0.016 <0.005 <0.009

S1 San Joaquin River near Stevinson 06/20/2001 1110 <.023 E.011 <.016 <.005 .016

G1 Salt Slough at Highway 165 near 

Stevinson

 06/20/2001 1040 <.023 .013 <.016 <.005 .055

G2 Los Banos Creek at Highway 

140

 06/20/2001 0910 <.023 .013 E.007 <.005 <.009

G3 Mud Slough near Gustine 06/20/2001 0950 <.023 E.009 <.016 .110 <.009

E2 Livingston Canal at Livingston 

Treatment Plant near 

Livingston

 06/20/2001 1010 <.023 <.011 <.016 <.005 <.009

E3 Highline Canal Spill near Hilmar 06/20/2001 1110 .045 E.004 <.016 E.002 <.009

E5 Merced River at River Road 

Bridge near Newman

 06/20/2001 1340 .100 E.004 <.016 <.005 E.003

W1 Newman Wasteway at Highway 

33 near Gustine

 06/20/2001 1200 <.023 .049 <.016 <.005 E.007

W2 Orestimba Creek at River Road 

near Crows Landing

 06/20/2001 1150 .036 .013 <.016 <.005 .123

W3 Spanish Grant Combined Drain 

near Patterson

 06/20/2001 1350 <.500 .026 <.016 <.005 .220

E6 Harding Drain at Carpenter Road 

near Patterson

 06/21/2001 1120 <.023 E.008 <.016 <.005 E.009

S2 San Joaquin River at Patterson 

Bridge near Patterson

 06/20/2001 0910 <.066 .011 <.016 <.005 .011

E7 Westport Drain near Modesto 06/21/2001 0940 <.069 E.006 <.016 <.005 .011

W4 Olive Avenue Drain near 

Patterson

 06/21/2001 0950 <.023 .014 <.016 E.003 .237

W5 Del Puerto Creek at Vineyard 

Road near Patterson

 06/20/2001 1440 <.023 .022 <.016 <.005 .134

S3 San Joaquin River below WSID 

pump above Tuolumne River 

near Westley

 06/21/2001 1120 <.023 E.009 <.016 <.005 .010

E9 Tuolumne River at Shiloh Road 

Bridge near Grayson

 06/21/2001 1230 <.023 E.008 <.016 <.005 <.009

W6 Hospital Creek at River Road 

near Patterson

 06/21/2001 1400 <.023 .013 <.016 <.005 1.120

W7 Ingram Creek at River Road near 

Patterson

 06/21/2001 1310 .062 .013 <.016 <.005 .405

E11 Stanislaus River at Caswell State 

Park near Ripon

06/21/2001 1300 <.023 <.011 <.016 <.005 <.009

S4 San Joaquin River near Vernalis 06/21/2001 1220 <.023 E.007 <.016 <.005 E.006
30 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 11. Streamflow and dissolved pesticide concentrations for sites sampled during August 2001 in the San Joaquin River Basin. 

[E, estimated concentration; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than; ΝD, no data] 

Site

code Station name Date Time

Streamflow

(ft3/s)

Alachlor

concentration

(μg/L)

Atrazine

concentration

(μg/L)

Atrazine,

deethyl

concentration

(μg/L)

Carbaryl

concen

tration

(μg/L)

Chlorpyrifox

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road near 

Merced

08/01/2001 0850  <0.002 <0.007 <0.006 <0.041 <0.005

S1 San Joaquin River near Stevinson 08/02/2001 1310 1.0 <.002 .012 <.006 <.041 E.005

G1 Salt Slough at Highway 165 near 

Stevinson

08/01/2001 1240 177 <.002 .009 <.006 E.009 .009

G2 Los Banos Creek at Highway 140 08/01/2001 0940 9.2 <.002 .008 <.006 <.041 <.005

G3 Mud Slough near Gustine 08/01/2001 1030 68.2 <.002 .011 E.006 <.041 .008

E2 Livingston Canal at Livingston Treatment 

Plant near Livingston

08/01/2001 1000 0 <.002 <.007 <.006 <.041 .005

E3 Highline Canal Spill near Hilmar 08/01/2001 1020 .2 <.002 <.007 <.006 <.041 <.005

E5 Merced River at River Road Bridge near 

Newman

08/01/2001 0840 132 <.002 <.007 <.006 <.041 <.005

W1 Newman Wasteway at Highway 33 near 

Gustine

08/01/2001 1120 14 <.002 .008 <.006 E.008 .013

W2 Orestimba Creek at River Road near 

Crows Landing

08/01/2001 1110 9.6 <.002 .010 <.006 E.009 .009

W3 Spanish Grant Combined Drain near 

Patterson

08/01/2001 1320 29.0 <.002 .008 <.006 E.064 .007

E6 Harding Drain at Carpenter Road near 

Patterson

08/02/2001 1020 139 <.002 E.003 <.006 <.041 .008

S2 San Joaquin River at Patterson Bridge 

near Patterson

08/02/2001 0900 400 <.002 E.005 <.006 E.008 .006

E7 Westport Drain near Modesto 08/02/2001 0930 29.4 <.002 E.002 <.006 E.006 .015

W4 Olive Avenue Drain near Patterson 08/02/2001 0920 17.3 <.002 E.006 <.006 E.010 .006

W5 Del Puerto Creek at Vineyard Road near 

Patterson

08/01/2001 1420 4.6 <.002 .007 E.005 E.005 .007

S3 San Joaquin River below WSID pump 

above Tuolumne River near Westley

 0802/2001 1200 468 <.002 E.004 <.006 E.008 .006

E9 Tuolumne River at Shiloh Road Bridge 

near Grayson

08/02/2001 1130 213 <.002 E.003 E.005 E.006 .012

W6 Hospital Creek at River Road near 

Patterson

08/02/2001 1500 .6 .037 E.003 <.006 <.041 <.005

W7 Ingram Creek at River Road near 

Patterson 08/02/2001

 1410 21.2 <.002 E.003 <.006 E.012 <.005

E11 Stanislaus River at Caswell State Park 

near Ripon

08/02/2001 1010 367 <.002 <.007 <.006 <.041 .005

S4 San Joaquin River near Vernalis 08/02/2001 1040 1,220 <.002 E.003 E.005 <.041 .008
Results and Discussion 31

Table 11. Streamflow and dissolved pesticide concentrations for sites sampled during August 2001 in the San Joaquin River Basin—

Continued.

[E, estimated concentration; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than; ND, no data] 

Site

code Station name Date Time

Cyanazine

concentration

(μg/L)

DCPA

concentration

(μg/L)

DDE, p,p′-

concentration

(μg/L)

Diazinon

concentration

(μg/L)

Dieldrin

concentration

(μg/L)

EPTC

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road near 

Merced

 08/01/2001 0850 <0.018 <0.003 <0.003 <0.005 <0.005 <0.002

S1 San Joaquin River near Stevinson 08/02/2001 1310 4.340 <.003 <.004 <.005 <.005 .029

G1 Salt Slough at Highway 165 near 

Stevinson

 08/01/2001 1240 .063 <.003 <.003 .042 <.005 .014

G2 Los Banos Creek at Highway 140 08/01/2001 0940 E.011 <.003 <.003 .007 <.005 .257

G3 Mud Slough near Gustine 08/01/2001 1030 E.010 <.003 <.003 .007 <.005 .050

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 08/01/2001 1000 <.018 <.003 <.003 <.005 <.005 <.002

E3 Highline Canal Spill near Hilmar 08/01/2001 1020 <.018 <.003 <.003 E.004 <.005 <.002

E5 Merced River at River Road Bridge 

near Newman

 08/01/2001 0840 <.018 <.003 <.003 <.005 <.005 <.002

W1 Newman Wasteway at Highway 33 

near Gustine

 08/01/2001 1120 <.018 <.003 E.005 .036 .007 .072

W2 Orestimba Creek at River Road near 

Crows Landing

 08/01/2001 1110 <.018 .005 E.016 .022 .010 .078

W3 Spanish Grant Combined Drain near 

Patterson

 08/01/2001 1320 <.018 <.003 E.009 .034 .009 .047

E6 Harding Drain at Carpenter Road 

near Patterson

 08/02/2001 1020 <.018 <.003 <.003 .013 <.005 <.002

S2 San Joaquin River at Patterson Bridge 

near Patterson

 08/02/2001 0900 .056 <.003 <.003 .030 <.005 .014

E7 Westport Drain near Modesto 08/02/2001 0930 <.018 <.003 <.003 E.004 <.005 .002

W4 Olive Avenue Drain near Patterson 08/02/2001 0920 .069 <.003 <.003 .038 <.005 .022

W5 Del Puerto Creek at Vineyard Road 

near Patterson

 08/01/2001 1420 .024 <.003 .004 .010 <.005 .049

S3 San Joaquin River below WSID 

pump above Tuolumne River near 

Westley

 0802/2001 1200 .051 <.003 <.003 .020 <.005 .014

E9 Tuolumne River at Shiloh Road 

Bridge near Grayson

 08/02/2001 1130 <.018 <.003 <.003 .009 <.005 .005

W6 Hospital Creek at River Road near 

Patterson

 08/02/2001 1500 .035 <.003 .004 .022 .013 .010

W7 Ingram Creek at River Road near 

Patterson

 08/02/2001 1410 .019 <.003 .011 .011 <.005 .008

E11 Stanislaus River at Caswell State Park 

near Ripon

 0802/2001 1010 <.018 <.003 <.003 <.005 <.005 <.002

S4 San Joaquin River near Vernalis 08/02/2001 1040 .020 <.003 <.003 .012 <.005 .007
32 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 11. Streamflow and dissolved pesticide concentrations for sites sampled during August 2001 in the San Joaquin River Basin—

Continued.

[E, estimated concentration; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than; ND, no data]

Site

code Station name Date Time

Ethalfluralin

concentration

(μg/L)

Ethoprophos

concentration

(μg/L)

HCH, alphaconcentration

(μg/L)

HCH, 

gammaconcentration

(μg/L)

Malathion

concentration

(μg/L)

Metolachlor

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road near 

Merced

 08/01/2001 0850 <0.009 <0.005 <0.005 <0.004 <0.027 0.031

S1 San Joaquin River near Stevinson 08/02/2001 1310 <.009 <.005 <.005 <.004 <.027 1.380

G1 Salt Slough at Highway 165 near 

Stevinson

 08/01/2001 1240 <.009 <.005 <.005 <.004 E.016 .146

G2 Los Banos Creek at Highway 140 08/01/2001 0940 <.009 <.005 <.005 <.004 <.027 .039

G3 Mud Slough near Gustine 08/01/2001 1030 <.009 <.005 <.005 <.004 <.027 .173

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 08/01/2001 1000 <.009 <.005 <.005 <.004 <.027 <.013

E3 Highline Canal Spill near Hilmar 08/01/2001 1020 <.009 <.005 <.005 <.004 <.027 <.013

E5 Merced River at River Road Bridge 

near Newman

 08/01/2001 0840 <.009 <.005 <.005 <.004 <.027 E.010

W1 Newman Wasteway at Highway 33 

near Gustine

 08/01/2001 1120 <.009 <.005 <.005 <.004 E.010 .198

W2 Orestimba Creek at River Road near 

Crows Landing

 08/01/2001 1110 <.009 .007 <.005 <.004 E.009 .235

W3 Spanish Grant Combined Drain near 

Patterson

 08/01/2001 1320 <.009 <.005 <.005 <.004 E.006 .844

E6 Harding Drain at Carpenter Road 

near Patterson

 08/02/2001 1020 <.009 <.005 .019 .029 <.027 E.004

S2 San Joaquin River at Patterson Bridge 

near Patterson

 08/02/2001 0900 <.009 <.005 <.005 .006 E.004 .145

E7 Westport Drain near Modesto 08/02/2001 0930 <.009 <.005 <.005 <.004 E.005 .031

W4 Olive Avenue Drain near Patterson 08/02/2001 0920 <.009 <.005 <.005 E.004 <.027 .204

W5 Del Puerto Creek at Vineyard Road 

near Patterson

 08/01/2001 1420 <.009 <.005 <.005 <.004 E.010 .210

S3 San Joaquin River below WSID 

pump above Tuolumne River near 

Westley

 0802/2001 1200 <.009 <.005 <.005 E.003 <.027 .108

E9 Tuolumne River at Shiloh Road 

Bridge near Grayson

 08/02/2001 1130 <.009 <.005 <.005 <.004 E.005 E.009

W6 Hospital Creek at River Road near 

Patterson

 08/02/2001 1500 <.009 <.005 <.005 <.004 E.004 .217

W7 Ingram Creek at River Road near 

Patterson

 08/02/2001 1410 .063 <.005 <.005 <.004 E.021 .746

E11 Stanislaus River at Caswell State Park 

near Ripon

 0802/2001 1010 <.009 <.005 <.005 <.004 E.012 E.009

S4 San Joaquin River near Vernalis 08/02/2001 1040 <.009 <.005 <.005 <.004 E.020 .052
Results and Discussion 33

Table 11. Streamflow and dissolved pesticide concentrations for sites sampled during August 2001 in the San Joaquin River Basin—

Continued.

[E, estimated concentration; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than; ND, no data]

Site

code Station name Date Time

Metribuzin

concentration

(μg/L)

Molinate

concentration

(μg/L)

Napropamide

concentration

(μg/L)

Pendimethalin

concentration

(μg/L)

Propachlor

concentration

(μg/L)

Propargite

concentration

μg/L)

E1 Bear Creek at Bert Crane Road near 

Merced

08/01/2001 0850 <0.006 <0.002 <0.007 <0.010 <0.010 0.026

S1 San Joaquin River near Stevinson 8/02/2001 1310 <.006 <.002 <.007 <.010 <.010 <.023

G1 Salt Slough at Highway 165 near 

Stevinson

 8/01/2001 1240 <.006 <.004 <.007 <.010 <.010 E.021

G2 Los Banos Creek at Highway 140 8/01/2001 0940 <.006 <.002 <.007 <.010 <.010 <.023

G3 Mud Slough near Gustine 8/01/2001 1030 <.006 .024 <.007 <.010 <.010 <.023

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

 8/01/2001 1000 <.006 <.002 <.007 <.010 <.010 <.023

E3 Highline Canal Spill near Hilmar 8/01/2001 1020 <.006 <.002 <.007 <.010 <.010 <.023

E5 Merced River at River Road Bridge 

near Newman

 8/01/2001 0840 <.006 <.002 <.007 <.010 <.010 .025

W1 Newman Wasteway at Highway 33 

near Gustine

 8/01/2001 1120 <.006 .007 <.007 <.010 <.010 .051

W2 Orestimba Creek at River Road near 

Crows Landing

 8/01/2001 1110 <.006 .006 E.006 .118 <.010 .538

W3 Spanish Grant Combined Drain near 

Patterson

 8/01/2001 1320 .016 <.006 .020 .087 <.010 .234

E6 Harding Drain at Carpenter Road 

near Patterson

 8/02/2001 1020 <.006 <.002 <.007 <.010 <.010 2.400

S2 San Joaquin River at Patterson Bridge 

near Patterson

 8/02/2001 0900 <.006 <.002 <.007 .014 <.010 .054

E7 Westport Drain near Modesto 8/02/2001 0930 <.006 <.002 <.007 <.010 <.010 .398

W4 Olive Avenue Drain near Patterson 08/02/2001 0920 <.006 <.002 <.007 <.010 <.010 .040

W5 Del Puerto Creek at Vineyard Road 

near Patterson

08/01/2001 1420 <.010 <.005 <.007 <.010 <.010 .073

S3 San Joaquin River below WSID 

pump above Tuolumne River near 

Westley

08/02/2001 1200 <.006 <.002 <.007 <.010 <.010 <.023

E9 Tuolumne River at Shiloh Road 

Bridge near Grayson

08/02/2001 1130 <.006 <.002 <.007 <.010 E.010 .470

W6 Hospital Creek at River Road near 

Patterson

08/02/2001 1500 <.006 <.002 <.007 <.010 <.010 .173

W7 Ingram Creek at River Road near 

Patterson

08/02/2001 1410 <.006 <.002 <.007 <.010 <.010 .353

E11 Stanislaus River at Caswell State Park 

near Ripon

08/02/2001 1010 <.006 <.002 <.007 <.010 <.010 E.020

S4 San Joaquin River near Vernalis 08/02/2001 1040 <.006 <.002 <.007 <.010 <.010 <.023
34 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 11. Streamflow and dissolved pesticide concentrations for sites sampled during August 2001 in the San Joaquin River Basin—

Continued.

[E, estimated concentration; ft3/s, cubic feet per second; μg/L, microgram per liter; <, less than; ND, no data]

Site

code

Station name Date Time Simazine

concentration

(μg/L)

Terbuthiuron

concentration

(μg/L)

Thiobencarb

concentration

(μg/L)

Trifluralin

concentration

(μg/L)

E1 Bear Creek at Bert Crane Road near 

Merced

08/01/2001 0850 <0.011 <0.016 <0.005 <0.009

S1 San Joaquin River near Stevinson 08/02/2001 1310 .015 <.016 <.005 <.009

G1 Salt Slough at Highway 165 near 

Stevinson

08/01/2001 1240 E.008 <.016 <.005 .026

G2 Los Banos Creek at Highway 140 08/01/2001 0940 .011 E.007 <.005 E.007

G3 Mud Slough near Gustine 08/01/2001 1030 E.010 <.016 .014 <.009

E2 Livingston Canal at Livingston 

Treatment Plant near Livingston

08/01/2001 1000 <.011 <.016 <.005 <.009

E3 Highline Canal Spill near Hilmar 08/01/2001 1020 <.011 <.016 <.005 <.009

E5 Merced River at River Road Bridge near 

Newman

08/01/2001 0840 <.011 <.016 <.005 <.009

W1 Newman Wasteway at Highway 33 near 

Gustine

08/01/2001 1120 .020 <.016 <.005 .163

W2 Orestimba Creek at River Road near 

Crows Landing

08/01/2001 1110 .015 <.016 <.005 .031

W3 Spanish Grant Combined Drain near 

Patterson

08/01/2001 1320 .016 <.016 <.005 .180

E6 Harding Drain at Carpenter Road near 

Patterson

08/02/2001 1020 <.011 <.016 <.005 <.009

S2 San Joaquin River at Patterson Bridge 

near Patterson

08/02/2001 0900 E.007 <.016 <.005 .014

E7 Westport Drain near Modesto 08/02/2001 0930 E.009 <.016 <.005 <.009

W4 Olive Avenue Drain near Patterson 08/02/2001 0920 E.010 <.016 <.005 .067

W5 Del Puerto Creek at Vineyard Road near 

Patterson

08/01/2001 1420 E.011 <.016 <.005 .070

S3 San Joaquin River below WSID pump 

above Tuolumne River near Westley

0802/2001 1200 E.009 <.016 <.005 .013

E9 Tuolumne River at Shiloh Road Bridge 

near Grayson

08/02/2001 1130 .014 <.016 <.005 <.009

W6 Hospital Creek at River Road near 

Patterson

08/02/2001 1500 E.007 <.016 <.005 .051

W7 Ingram Creek at River Road near 

Patterson

08/02/2001 1410 E.006 <.016 <.005 .087

E11 Stanislaus River at Caswell State Park 

near Ripon

0802/2001 1010 <.011 <.016 <.005 <.009

S4 San Joaquin River near Vernalis 08/02/2001 1040 E.009 <.016 <.005 E.008
Results and Discussion 35

The relation between the number of basins where a 

pesticide was applied and the number of basins where the 

dissolved pesticide was detected in water was variable. A 

number of pesticides were detected in water that had not been 

applied in the San Joaquin River Basin during the 28 days 

before sampling (table 7). Atrazine and deethylatrazine were 

two of the most commonly detected pesticides in water, but 

there were no recorded applications of atrazine within 28 days 

of any of the sampling periods. Dacthal, dieldrin, p,p′-DDE, 

and tebuthiuron were detected during all sampling periods 

despite no application, except dacthal, which was not detected 

in June 2001. In June and August 2001, alpha-HCH (alphaBHC), ethoprophos, and propachlor were detected despite no 

application. In June 2001, prometon was detected. In August 

2001, alachlor, ethalfluralin, gamma-HCH, and thiobencarb 

were detected although there was no application in the 28-day 

presample period; however, these pesticides were applied 

preceding the June 2001 sampling and were also detected 

in the June samples. Domagalski and Munday (2003) also 

noted detections of pesticides with no agricultural applications during regular periodic sampling at 12 sites in the San 

Joaquin River Basin during April to August 2001. Domagalski 

and Munday (2003) attributed these detections to winter-time 

applications, nonagricultural use, or interbasin transfers of 

irrigation water that included irrigation return flows containing 

dissolved pesticides.

The chemical and physical properties of the pesticides 

(table 12) also are important. Koc is the organic carbon normalized adsorption coefficient, and pesticides having high log Koc

values will sorb to the soil, making it less likely that they will 

be immediately transported to the surface water. Pesticides 

with a short hydrolysis half-life will degrade quickly if they do 

reach the water. Runoff potential is a categorical aggregate of 

the influence of water solubility, soil half-life, and Koc on the 

likelihood of pesticide transport to surface water (Goss, 1992). 

Most of the pesticides detected, even though not applied in the 

previous 28 days, have half-lives of greater than 28 days with 

medium to large runoff potentials (table 12). Several also have 

high log Koc values (>3), including dacthal, p,p′-DDE, dieldrin, ethalfluralin, and both forms of HCH (table 12). These 

characteristics make it likely that these pesticides will persist 

in the environment well after application and eventually reach 

surface waters at a later time. 

Several pesticides that were applied in the 28 days previous to sampling were not detected in water during at least 

one sampling period (table 7). In 17 of 28 cases the applications were less than 1,000 lb of active ingredient for the entire 

San Joaquin River Basin (alachlor, butylate, carbofuran, 

disulfoton, lindane, linuron, malathion, methyl parathion, 

parathion, pebulate, phorate, pronamide, and propanil). In the 

remaining cases, the applications were greater than 1,000 lb of 

active ingredient (azinphos-methyl, butylate, methyl parathion, pendimethalin, cis-permethrin, phorate, and propanil). 

The large applications of azinphos-methyl, permethrin, and 

propanil are particularly notable (table 7).

Although it is expected that applications and detections 

do not correspond exactly, the lack of detections of pesticides 

applied in large amounts is somewhat surprising. The chemical and physical properties of azinphos-methyl and permethrin 

can explain why these pesticides were not detected in surface 

water despite their high application. Azinphos-methyl has 

a high value for log Koc (3.00, table 12) relative to the other 

pesticides, and a short hydrolysis half-life (23 hours, table 12). 

In the case of azinphos-methyl, the short hydrolysis half-life 

is probably the more important factor. Permethrin has a small 

runoff potential, and thus is unlikely to be transported offsite. 

The lack of detections of propanil can be better explained 

by the location of its application rather than its chemical 

and physical properties. Propanil was used only in east-side 

subbasins. As mentioned earlier, the physiography of the east 

side, as well as the irrigation methods used there, likely lead 

to less transport of pesticides to surface water than on the west 

side.

The number of dissolved pesticides detected at any 

concentration varied considerably among basins (total detections in table 13). The larger difference between quantifiable 

and total detections in 2001 compared with 1994 was due to 

the use of the laboratory reporting level (LRL) in 2001 rather 

than the method detection limit (MDL) to define quantifiable 

detections. The LRL is more conservative, but reduces the 

likelihood of reporting false negatives. There was no clear 

pattern in frequencies of detections across years and seasons in 

a particular basin. Unlike pesticide applications, there was not 

a strong relation between the detection of dissolved pesticides 

in tributary basins (quantifiable detections) and basin size. 

In 1994 there was a significant negative correlation between 

basin size and quantifiable detections (Spearman’s r = – 0.53, 

p < 0.05). The same trend was evident in 2001, but the correlations were not statistically significant (Spearman’s r = – 0.36 

and – 0.43, p > 0.05). 
36 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 12. Chemical and physical properties of detected pesticides and pesticides applied in the basin, but not detected in water 

samples. 

[All runoff potentials are from Goss (1992); Koc, organic carbon normalized adsorption coefficient; mg/L, milligram per liter; >, greater than; ND, no data] 

Analyte Solubility

(mg/L) Log Koc

Hydrolysis

half-life

at pH 7

Runoff potential

Alachlor 1

1.30E+2 2

2.23 3None at 30 days Medium

Atrazine 1

3.00E+1 2

2.00 4

1,771 years Large

Azinphos-methyl 1

3.00E+1 2

3.00 323 hours Medium

Butylate 1

4.00E+1 2

2.60 3Stable ND

Carbaryl 1

3.20E+1 22.48 415 days Medium

Carbofuran 1

6.50E+2 31.46 48.2 weeks Large

Chlorpyrifos 1

3.00E−1 23.78 435.3 days Small

Cyanazine 2

1.70E+2 22.28 3Stable Medium

Dacthal (DCPA) 2

5.00E−1 23.70 ND Medium

DDE, p,p′- 1

4.00E−2 45.29 2Stable ND

Diazinon 1

3.80E+1 51.60–2.63 4184 days Large

Dieldrin 1

1.70E−1 44.08–4.55 410.5 years ND

Disulfoton 1

2.50E+1 22.78 41.2–103 days Large

EPTC 1

3.70E+2 42.38 3Stable Medium

Ethalfluralin 2

3.00E−1 23.60 3Stable after 31 days Medium

Ethoprophos 2

7.50E+2 21.85 3Stable Medium

Fonofos 2

1.69E+1 22.94 474–127 days Large

HCH, alpha- (alpha-BHC) 1

1.00E0 43.28 6207 days ND

HCH, gamma- (Lindane) 1

8.00E0 23.04 6207 days ND

Linuron 1

6.50E+1 22.60 ND Large

Malathion 1

1.45E+2 23.26 49 days (pH 6) Small

Methyl parathion 1

2.50E+1 23.71 672 days Medium

Metolachlor 2

5.30E+2 22.30 4>200 days Large

Metribuzin 2

1.22E+3 21.78 ND Large

Molinate 2

9.70E+2 22.28 ND Medium

Napropamide 2

7.40E+1 42.83 ND Large

Parathion 1

1.50E+1 23.70 43.5 weeks (pH 6.0) ND

Pebulate 1

6.00E+1 42.80 ND Medium

Pendimethalin 2

2.75E−1 23.70 ND Medium

Permethrin, cis- 2

6.00E−3 25.00 ND Small

Phorate 1

4.00E+1 23.00 496 hours Large

Prometon 1

7.50E+2 22.18 ND Large

Pronamide 2

1.50E+1 22.90 ND Large

Propachlor 1

6.00E+2 21.90 ND Medium

Propanil 1

3.00E+2 22.17 ND Medium

Propargite 2

5.00E−1 23.60 ND Medium

Simazine 1

5.00E0 42.14 ND Large

Tebuthiuron 2

2.50E+3 42.79 4>64 days Large

Thiobencarb 2

2.80E+1 22.95 ND Medium

Trifluralin 1

5.00E−1 42.94–4.49 ND Medium

1

Suntio and others (1988)

2

Wauchope and others (1992)

3

U.S. Environmental Protection Agency (1997)

4

Montgomery (1993)

5

Howard (1991)

6

Howard and others (1991)
Results and Discussion 37

Table 13. Number of pesticide detections at each site. 

[Quantifiable detections indicate that the pesticide concentration exceeded reporting limits used in that year. Total detections includes pesticides reported as 

estimated concentrations below the reporting limit. WSID, Westside Irrigation District; , no data] 

Site 

code Station name

 June 1994 June 2001 August 2001

Quantifiable

detections

Total 

detections

Quantifiable

detections

Total 

detections

Quantifiable

detections

Total 

detections

 E1 Bear Creek at Bert Crane Road near Merced 4 8 3 5 2 2

 S1 San Joaquin River near Stevinson 6 6 5 8 6 6

 G1 Salt Slough at Highway 165 near Stevinson 1 2 9 11 7 11

 G2 Los Banos Creek at Highway 140   4 8 4 8

 G3 Mud Slough near Gustine 10 11 5 9 7 10

 E2 Livingston Canal at Livingston Treatment Plant near 

Livingston

 0 1 0 0 1 1

 E3 Highline Canal Spill near Hilmar 1 1 1 8 0 1

 E4 Merced River below Merced Falls Dam near Snelling 1 4    

 E5 Merced River at River Road Bridge near Newman 3 3 4 8 1 2

 W1 Newman Wasteway at Highway 33 near Gustine 9 11 4 11 10 13

 W2 Orestimba Creek at River Road near Crows Landing 15 16 10 14 14 17

 W3 Spanish Grant Combined Drain near Patterson 14 18 14 15 14 15

 E6 Harding Drain at Carpenter Road near Patterson 8 9 7 11 5 7

 S2 San Joaquin River at Patterson Bridge near Patterson 15 15 7 10 9 13

E7 Westport Drain near Modesto 5 5 2 8 4 9

 W4 Olive Avenue Drain near Patterson 10 11 9 12 7 11

W5 Del Puerto Creek at Vineyard Road near Patterson 11 12 8 12 8 13

S3 San Joaquin River below WSID pump above 

Tuolumne River near Westley

 11 15 8 11 6 10

E8 Tuolumne River at Modesto 8 9    

E9 Tuolumne River at Shiloh Road Bridge near Grayson   5 8 5 11

W6 Hospital Creek at River Road near Patterson 16 17 11 13 8 12

W7 Ingram Creek at River Road near Patterson 17 17 13 18 8 12

E10 Stanislaus River at Ripon near Patterson 1 1    

E11 Stanislaus River at Caswell State Park near Ripon   2 3 1 4

S4 San Joaquin River near Vernalis 7 8 4 8 5 10

The cluster analysis of pesticide detections (fig. 7) 

showed a very different pattern than the analysis of application (fig. 3). During all three sampling periods all the west-side 

basins clustered together at greater than 50 percent information remaining. Three or four of the San Joaquin mainstem 

sites also occurred in this cluster during each sampling period. 

The southern tributaries also tended to be associated with this 

cluster, but not consistently. The ranges in similarities within 

these clusters were similar among the sample periods. In 

1994, Jaccards similarities ranged from 0.23 (W2 and G3) to 

0.83 (W6 and W7). In June 2001, similarities between sites 

in the cluster varied from 0.29 (G2 and W3) to 0.89 (S3 and 

W4). In August 2001, Jaccards similarities ranged from 0.27 

(W2 and S4, W3 and S4) to 0.89 (S2 and W4). The east-side 

tributaries showed no consistent clustering patterns. When all 

sites are considered, Jaccards similarities ranged from 0.06 

to 1.00 in June 1994, from 0 to 0.89 in June 2001, and from 

0 to 0.89 in August 2001. The values of 0 and 1.00 were due 

mainly to similarities between sites where only one or two 

pesticides were present. The first four PC axes of all three 

PCA of concentrations of dissolved pesticides in the tributaries had eigenvalues greater than one (table 14). Greater than 

50 percent of the variance was explained by the first two PC 

axes for all three sampling periods. In all sampling periods, 

only one or two pesticides loaded highly on PC axes 3 and 4 

(table 11). In 1994, molinate loaded highly on PC axis 3, and 

EPTC and metolachlor loaded highly on PC axis 4. In June 

2001, molinate loaded highly on PC axis 3, and chlorpyrifos 

and simazine loaded highly on PC axis 4. In August 2001, 

chlorpyrifos and propargite loaded highly on PC axis 3, and 

cyanazine and metolachlor loaded highly on PC axis 4.
38 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Figure 7. Cluster analysis of Jaccards distances, which are based on the presence or absence of dissolved pesticides in water 

samples in (A) June 1994, (B) June 2001, and (C) August 2001. See table 1 for site codes. Percentage information remaining varies from 

100, starting with the individual sites, and decreases to 0 as the sites are clustered into a single group.

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Results and Discussion 39

Table 14. Loadings of pesticides on axes from a principal component analysis (PCA) of pesticide concentrations in tributary basins for 

each sampling period.

[Only PCA axes with eigenvalues greater than one are shown; , loading less than 0.50]

PCA axis 1 PCA axis 2 PCA axis 3 PCA axis 4

June 1994

Atrazine 0.83  — 

Atrazine, deethyl .61 −0.70  

Carbaryl  −.69  

Chlorpyrifos .52 .63  

Diazinon .53 −.76  

EPTC —   0 .72

Metolachlor   — −.51

Molinate   −0.80 

Simazine .80   

Trifulralin .60   

Percent variance explained: 3.50 25.30 12.70 11.20

June 2001 

Atrazine .86   

Chlorpyrifos    .80

Diazinon  −.87 — 

EPTC .97 —  

Metolachlor .76 .52  

Molinate   −.89 

Simazine —   − .61

Trifulralin .84 − .52  

Percent variance explained: 4.60 19.00 16.00 13.30

August 2001

Atrazine .59 − .62  

Chlorpyrifos   .80 

Cyanazine    .53

Diazinon .87   

EPTC  − .84  

Metolachlor .75   −.57

Propargite   .69 

Trifulralin .84   —

Percent variance explained: 33.90 19.40 17.30 14.10

Plots of PC axis scores for the 1994 sampling period 

(fig. 8) revealed more distinct site groupings than expected 

on the basis of clustering results (fig. 7A). The large cluster of west-side tributaries, including an east-side (E6) and 

southern (G3) tributary, was still apparent, but the eastern 

tributaries also formed a tight group. The separation of 

the two groups was due mainly to high concentrations of 

atrazine, chlorpyrifos, deethylatrazine, diazinon, simazine, and 

trifluralin in the west-side tributaries and nondetections or low 

concentrations in the other tributaries. Harding Drain (E6) 

differed from the west-side tributaries with respect to concentrations of carbaryl, chlorpyrifos, deethylatrazine, and 

diazinon (fig. 8 and table 9). Harding Drain transports water 

from the city of Turlock’s wastewater treatment plant, which 

might account for differences from other east-side tributaries. 

Mud Slough (G3) differed from all the other sites because of a 

large concentration of molinate (fig. 8 and table 9). Molinate is 

used on rice, which is grown primarily in the Salt Slough and 

Mud Slough drainages (Domagalski and Munday, 2003).
40 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

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Figure 8. Site scores on the first three axes from a principal components analysis of dissolved pesticide concentrations in June 1994. 

See table 1 for site codes. The arrows indicate the direction of increasing concentration of particular pesticides.

Similar to 1994, plots of PC axis scores for the June 

2001 sampling period (fig. 9) revealed a different pattern than 

expected on the basis of clustering results (figure 7B). The 

east-side tributaries formed a very tight group on the basis of 

nondetections or low detections of the commonly detected 

pesticides (fig. 9 and table 10). The west-side and southern 

tributaries exhibited considerable variability along PC axis 1 

on the basis of concentrations of atrazine, EPTC, metolachlor, 

and trifluralin. PC axis 2 mainly separated Hospital Creek 

(W6) from the other basins (fig. 9) because of higher concentrations of diazinon and trifluralin and lower concentration 

of metolachlor, relative to the other west-side and southern 

tributaries (table 10). As in 1994, Mud Slough (G3) was different from the other basins because of a high concentration of 

molinate. Domagalski and Munday (2003) also documented 

high concentrations of molinate in the Mud Slough drainage as 

well as in the Salt Slough drainage.

The PC axis plots for August 2001 (fig. 10) were 

different in several ways from the plots for June 1994 and 

June 2001. The west-side tributaries had some variability 

along both PC axis 1 and PC axis 2. There was also variation among the east-site tributaries along PC axis 3. As for 

the other two sample periods, PC axis 1 mainly separated the 

east-side tributaries from the other tributaries (fig. 10) on the 

basis of nondetections or low concentrations of the commonly 

detected pesticides. The variation along PC axis 2 was due to 

differences in concentrations of atrazine and EPTC. PC axis 3 

highlighted high concentrations of chlorpyrifos and propargite 

in three east-side tributaries—Harding Drain (E6), Westport 

Drain (E7), and the Tuolumne River (E9)compared with the 

other east-side tributaries. The concentrations in these tributaries were similar or higher than the concentrations in the three 

west-side tributariesNewman Wasteway (W1), Orestimba 

Creek (W2), and Spanish Grant Drain (W3)with the highest 

concentrations of these pesticides (table 11).
Results and Discussion 41

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Figure 9. Site scores on the first three axes from a principal components analysis of dissolved pesticide concentrations in June 2001. 

See table 1 for site codes. The arrows indicate the direction of increasing concentration of particular pesticides.

The differences between application and detection clusters suggest that different factors are driving the two processes. 

Application appears to be driven primarily by basin size, 

which is likely a surrogate for diversity of land use. All else 

being equal, detected pesticides should mirror the application pattern. This is clearly not occurring because the relation 

between basin size and pesticides applied is much weaker 

in the detection data in addition to the differences in clustering. The tight clustering of west-side basins (fig. 7) suggests 

that there is some similarity in land use or post-application 

practices that determine transport processes. The PCA results 

also suggest differences in transport processes. The analyses 

of application intensity (figs. 4–6) show differences between 

east-side and west-side basins in terms of which pesticides 

are applied in the greatest amounts. In contrast, the PCAs 

of concentrations mainly reflect pesticides detected in high 

concentrations in west-side tributaries. These pesticides are 

either not detected in east-side tributaries or are only detected 

at low concentration. Similarly, Domagalski and Munday 

(2003) found that overall frequency of detection of pesticides 

was higher in west-side basins during their periodic sampling 

during April to August 2001. 
42 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

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Figure 10. Site scores on the first three axes from a principal components analysis of dissolved pesticide concentrations in August 

2001. See table 1 for site codes. The arrows indicate the direction of increasing concentration of particular pesticides.

The differences between east-side and west-side basins 

are likely related to many factors. Unfortunately, the data are 

inadequate to identify many of these factors quantitatively; 

however, some qualitative observations are possible. It seems 

likely that land use, irrigation practices, and stream size might 

all be important factors. As noted earlier, row crops are the 

dominant agricultural land use on the west side of the valley 

(48 percent). On the east side of the valley, row crops are less 

important (18 percent). Row crops are generally irrigated by 

furrow irrigation, but drip and flood irrigation are more common in orchards, pastures, and vineyards, which are important 

east-side land uses. Irrigation practices (drip or flood) and the 

coarser-grained soils on the east side of the valley, likely result 

in much of the applied irrigation water infiltrating into the 

groundwater. Therefore, there is probably relatively little agricultural return water to transport pesticides. Conversely, higher 

use of furrow irrigation and steeper land gradients combined 

with less permeable fine-grained soils on the west side of the 

valley likely result in greater quantities of agricultural return 

water. The fine-grained, poorly drained soils of the west-side 

basins also appear to act as efficient reservoirs for long-lived 

chemicals such as dacthal, dieldrin, and DDT and its metabolites, including p,p′-DDE (Periera and others 1996; Brown 

1997). The steeper gradients of the west-side streams result in 

greater sediment loads and greater transport of the soil-bound 

chemicals into surface waters. In addition, tile drains are more 

common in the west-side basins, particularly the Mud Slough 

Basin. Tile drains result in fairly short groundwater residence 

times and tile drainage might carry some of the more longerlived, water soluble pesticides. Finally, any pesticide-laden 

agricultural return water that does eventually reach the larger 

east-side rivers will be diluted by reservoir releases, while 

most of the west-side basins contain primarily agricultural 

drainage water from April to August, although some operational spill occurs at times. Given these differences, it is not 

surprising that the west-side basins tend to have the highest 

concentrations.
Results and Discussion 43

The PCA of instantaneous pesticide loads (table 15) gave 

somewhat different results than the PCA of pesticide concentrations (table 14). The loadings of the pesticides were different and more of the variance was explained by PC axis 1 in the 

analysis of instantaneous loads (tables 14 and 15). In general, 

the same pesticides had high loadings on PC axis 1, but PC 

axis 1 included additional pesticides in the analysis of instantaneous loads. The differences between the instantaneous load 

and concentration analyses are most obvious in plots of site 

scores on the first two PC axes (figs. 8–11). In all cases, the 

clear separation of the east-side tributaries from the west-side 

and southern tributaries is lost when instantaneous loads are 

considered (fig. 11). The east-side tributaries tend to have 

lower instantaneous loads than the other sites, but not always.

A notable difference between the concentration (fig. 8) 

and instantaneous load results (fig. 11) in June 1994 is the 

change of position for the Tuolumne River (E8). This large 

east-side tributary had low pesticide concentrations, but a high 

discharge resulting in large instantaneous loads and the fifth 

highest score on PC axis 1 (fig. 11). The most interesting difference in June 2001 was that PC axis 2 summarized variation 

in instantaneous loads of chlorpyrifos and diazinon among 

east-side tributaries (fig. 11) rather than separating a single 

tributary, Hospital Creek (W6), from all the others (fig. 9) 

on the basis of pesticide concentrations. Another noticeable 

difference was the relative change in positions on PC axis 1 

of Salt Slough (G1) and Hospital Creek (W6) in the analysis 

of instantaneous loads (fig. 11) compared with the analysis of 

concentrations (fig. 9). Similar differences occurred in August 

2001 with Salt Slough having the highest score on PC axis 1 

on the basis of loads (fig. 11) compared with a score similar to 

several west-side sites when only concentrations were considered (fig. 10). As in June 2001, in August 2001, PC axis 

2 of the load analysis described differences among east-side 

tributaries (fig. 11), whereas PC axis 2 of the concentration 

analysis emphasized differences among west-side and southern tributaries (fig. 10).

A further contrast is provided by considering the analysis of instantaneous yields. Greater than 50 percent of the 

variance was explained by PC axis 1 for each of the three 

sampling periods (table 16). The pesticides loading highly on 

PC axis 1 were very similar to those found to load heavily on 

PC axis 1 of the instantaneous load analysis for each sampling 

period, but there were some minor differences (tables 15 and 

16). In all cases, the separation of west-side tributaries from 

the east-side tributaries noted in the analyses of concentrations (figs. 8–10) was reestablished (fig. 12). In all cases, the 

west-side tributaries had the highest instantaneous yields. 

There were a few minor exceptions with Newman Wasteway 

(W1) grouping with the other sites in June 2001 and Del 

Puerto Creek (W5) and Hospital Creek (W6) grouping with 

the other sites in August 2001. The major difference between 

the concentration and instantaneous yield analyses was that the 

southern tributaries grouped with the west-side tributaries in 

the analysis of concentrations and with the east-side tributaries 

in the analysis of instantaneous yields.

The contrasting patterns found when using concentration, 

instantaneous load, or instantaneous yield data are important 

to water quality management in several ways. First, when 

considering the biological effects of dissolved pesticides, concentration is the measure that is most important. Organisms 

experience concentrations, not instantaneous loads. Therefore, 

the high concentrations found in west-side basins suggest that 

these basins are the most stressful for aquatic life as has been 

found by other researchers (Foe and Connor, 1991; Foe, 1995). 

Conversely, when managing for a TMDL at some downstream 

location, a small instantaneous load represented by a toxic, 

but low discharge, water body, might be insignificant to the 

TMDL compared with the instantaneous load represented by 

a large volume tributary having lower concentrations of the 

regulated pesticide. However, the cumulative load from such 

small discharges cannot be ignored. This is especially true 

of the San Joaquin River Basin where agricultural drainage 

water can constitute a substantial part of the flow at the San 

Joaquin River near Vernalis (S4). Finally, in understanding the 

processes, it is important to consider instantaneous yields. By 

standardizing instantaneous loads by unit area, instantaneous 

yields give an indication of the importance of transport processes. In general, the PCA analysis did not show any strong 

geographic patterns in application intensity (figs. 4–6) that 

would affect instantaneous yields. The strong pattern in instantaneous yields suggests that pesticides are much more likely to 

enter surface waters on the west side of the valley compared 

with the east side of the valley. These results might be important in identifying areas where source control might be of the 

most benefit. Clearly, concentration, instantaneous loads, and 

instantaneous yields might each be important to consider, 

depending on the regulatory or management context.
44 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 15. Loadings of pesticides on axes from a principal component analysis (PCA) of pesticide instantaneous loads in tributary basins 

for each sampling period.

[Only PCA axes with eigenvalues greater than one are shown. , loading less than 0.50]

PCA axis 1 PCA axis 2 PCA axis 3 PCA axis 4

June 1994

Atrazine 0.87   

Atrazine, deethyl .64 −0.71  

Carbaryl .60 −.61  

Chlorpyrifos .55   −0.54

Diazinon .73 −.52  

EPTC   −0.57 

Metolachlor  .53  

Molinate .58   .60

Simazine   .81 

Trifulralin .56 .50  

Percent variance explained: 33.20 21.40 13.90 11.70

June 2001 

Atrazine .92   

Chlorpyrifos  .93  

Diazinon  .93  

EPTC .89   

Metolachlor .89   

Molinate .59  −.78 

Simazine .85   

Trifulralin .81  — 

Percent variance explained: 52.90 22.90 13.50 

August 2001 

Atrazine .90   

Chlorpyrifos  .84  

Cyanazine .80   

Diazinon .77 .59  

EPTC .72   

Metolachlor .82   

Propargite  .73 .50 

Trifulralin .75  .55 

Percent variance explained: 49.10 21.10 12.60 
Results and Discussion 45

Figure 11. Site scores on the first two axes from principal components analysis of instantaneous pesticide loads in June 1994, June 

2001, and August 2001. See table 1 for site codes. The arrows indicate the direction of increasing instantaneous loads of particular 

pesticides.

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Instantaneous Loads

Alachlor, EPTC, metolachlor, molinate, and trifluralin 

met the criteria for detailed analysis in 1994 (table 17). 

Samples in 1994 were collected in a Lagrangian manner; 

therefore, the same parcel of water was being sampled all the 

way downstream. However, water in the San Joaquin River 

Basin is used extensively for irrigation in June, and much of 

the water and pesticides from the upstream tributaries do not 

reach Vernalis because of diversions. Therefore, the loads of 

pesticides from the different tributaries were weighted in the 

following equation according to a loading factor (table 17) that 

took into account the diversions from the San Joaquin River 

downstream from each tributary:

Percent of Vernalis load = [(tributary load ×

loading factor)/Vernalis load] × 100

Sites upstream of the two largest diversions (Patterson Irrigation District and West Stanislaus Irrigation District) had 

much lower loading factors (that is, less of the load makes 

it to Vernalis) than sites downstream of these diversions. 

The Merced River below Merced Falls (E4) and the Bear 

Creek (E1) sites also had large diversions before reaching the 

mainstem of the San Joaquin River.
46 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 16. Loadings of pesticides on axes from a principal component analysis (PCA) of pesticide instantaneous yields in tributary basins 

for each sampling period.

[Only PCA axes with eigenvalues greater than one are shown; —, loading less than 0.50]

PCA axis 1 PCA axis 2 PCA axis 3

June 1994 

Atrazine 0.97  

Atrazine, deethyl  0.91 —

Carbaryl  .79 

Chlorpyrifos .55  −0.76

Diazinon .90  

EPTC .60  

Metolachlor .69  

Molinate .92  

Simazine .94  

Trifulralin .93  

Percent variance explained: 55.29 17.93 11.13

June 2001 

Atrazine .95  

Chlorpyrifos  .69 

Diazinon  .92 

EPTC .98  

Metolachlor .85  

Molinate .78  

Simazine .66  

Trifulralin .86  

Percent variance explained: 55.02 18.77 

August 2001 

Atrazine .73 −.63 

Chlorpyrifos .67  

Cyanazine  .86 

Diazinon .91  

EPTC .90  

Metolachlor .74  

Propargite   −.92

Trifulralin .93  

Percent variance explained: 52.67 17.99 14.37
Results and Discussion 47

Figure 12. Site scores on the first two axes from principal components analysis of instantaneous pesticide yields in June 1994, June 

2001, and August 2001. See table 1 for site codes. The arrows indicate the direction of increasing instantaneous yields of particular 

pesticides.

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The sum of these adjusted loads from the contributing 

tributaries accounted for most of the loads measured at the San 

Joaquin River near Vernalis. Sums of loads from the tributaries 

range from 50 percent (molinate) to 105 percent (trifluralin) 

of measured loads at the San Joaquin River near Vernalis. 

The sums of the measured loads in this study are not expected 

to equal 100 percent because of unmeasured diversions and 

discharges in the system. As of the late1980s, there were at 

least 86 agricultural diversions and 104 agricultural discharges 

to the San Joaquin River (Kratzer and Shelton, 1998). Westside sites accounted for most of the alachlor (79 percent), 

EPTC (84 percent), molinate (35 percent), and trifluralin 

(100 percent). East-side sites contribute most (51 percent) of 

the metolachlor load. 

In 1994, Hospital Creek (49 percent), Del Puerto Creek 

(19 percent), and Ingram Creek (9 percent) were the 

largest sources of alachlor. The Del Puerto Creek Basin 

received applications totaling 569 lb of alachlor (71.1 lb/mi2) 

in the 28 days preceding sampling. However, the Hospital 

Creek and Ingram Creek Basins had no alachlor applied in the 

6 months preceding sampling. The alachlor detected may have 

resulted from an even earlier application or unreported application. In March 1994, 448 lb of alachlor were applied just 

outside the boundary of the Ingram Creek Basin, near the sampling site. Hospital Creek and Ingram Creek are unique among 

west-side tributaries. They have a much higher suspended 

sediment load and more irrigation tailwater than other sites. 

These factors could cause higher concentrations and loads of 

pesticides if pesticides stored in the soil are later transported to 

these tributaries with sediment and dissolve into the water. 
48 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Table 17. Adjusted instantaneous loads for sites contributing to instantaneous pesticide loads at the San Joaquin River near Vernalis in 

June 1994.

[g/d, grams per day]

Site 

code Station name Date

Sample 

loading 

factor

Alachlor EPTC Metolachlor

Load 

(g/d)

Percentage 

of Vernalis 

load

Load 

(g/d)

Percentage

of Vernalis

load

Load

(g/d)

Percentage

of Vernalis

load

S4 San Joaquin River near Vernalis 06/24/1994 1 38.0264 100.0000 92.3498 10.0000 173.8349 100.0000

S1 San Joaquin River near Stevinson 06/20/1994 .38 .0161 .0423 2.0913 2.2645 1.7695 1.0179

West-side sites 

G1 Salt Slough at Highway 165 

near Stevinson

06/21/1994 .40 .1830 .4813 .1830 .1982 .1830 .1053

G3 Mud Slough near Gustine 06/21/1994 .41 .0281 .0739 .3371 .3650 .0281 .0162

W1 Newman Wasteway at Highway 33 

near Gustine

06/22/1994 .45 .0991 .2606 1.9821 2.1463 1.9821 1.1402

W2 Orestimba Creek at River Road 

near Crows Landing

06/22/1994 .51 .0120 .0315 4.0734 4.4108 6.7091 3.8595

W3 Spanish Grant Combined Drain 

near Patterson

06/22/1994 .52 .0445 .1171 6.2350 6.7515 7.5710 4.3553

W4 Olive Avenue Drain near Patterson 06/23/1994 .73 .3527 .9275 5.6210 6.0866 .5952 .3424

W5 Del Puerto Creek at Vineyard Road 

near Patterson

06/23/1994 .73 7.2453 19.0533 4.4586 4.8280 1.5327 .8817

W6 Hospital Creek at River Road 

near Patterson

06/23/1994 .99 18.6632 49.0795 51.3237 55.5754 4.1215 2.3709

W7 Ingram Creek at River Road 

near Patterson

06/24/1994 .99 3.4957 9.1929 3.7646 4.0765 2.0436 1.1756

Total of west-side sites 3.1236 79.2176 77.9785 84.4382 24.7662 14.2470

East-side sites 

E5 Merced River at River Road Bridge 

near Newman

06/22/1994 .45 .1553 .4083 2.0184 2.1856 5.2789 3.0367

E6 Harding Drain at Carpenter Road 

near Patterson

06/22/1994 .56 .0480 .1261 1.0551 1.1426 .2398 .1380

E7 Westport Drain near Modesto 06/23/1994 .73 .0272 .0714 1.3847 1.4995 .0272 .0156

E8 Tuolumne River at Modesto 06/23/1994 .99 .2931 .7708 5.8625 6.3482 82.0753 47.2145

E10 Stanislaus River at Ripon near 

Patterson

06/23/1994 .99 1.2088 3.1790 1.2088 1.3090 1.2088 .6954

Total of east-side sites 1.7323 4.5556 11.5297 12.4848 88.8300 51.1002

Sum of Stevinson and west-side and east-side sites. 31.8720 83.8156 91.5994 99.1875 115.3658 66.3651
Results and Discussion 49

Table 17. Adjusted instantaneous loads for sites contributing to instantaneous pesticide loads at the San Joaquin River near Vernalis in 

June 1994—Continued.

[g/d, grams per day]

Site 

code Station name Date

Sample 

loading 

factor

Molinate Trifluralin

Load (g/d) Percentage of 

Vernalis load Load (g/d) Percentage of Vernalis load

S4 San Joaquin River near Vernalis 06/24/1994 1 81.4851 10.0000 51.6072 10.0000

S1 San Joaquin River near Stevinson 06/20/1994 .38 1.6087 1.9742 .0161 .0312

West-side sites 

G1 Salt Slough at Highway 165 near Stevinson 06/21/1994 .40 .3661 .4492 .1830 .3547

G3 Mud Slough near Gustine 06/21/1994 .41 19.3832 23.7874 .5056 .9798

W1 Newman Wasteway at Highway 33 near 

Gustine

 06/22/1994 .45 .0220 .0270 .1101 .2134

W2 Orestimba Creek at River Road near Crows 

Landing

 06/22/1994 .51 .0240 .0294 1.6773 3.2501

W3 Spanish Grant Combined Drain near 

Patterson

 06/22/1994 .52 .6680 .8198 4.4535 8.6297

W4 Olive Avenue Drain near Patterson 06/23/1994 .73 .0220 .0271 5.6210 1.8918

W5 Del Puerto Creek at Vineyard Road near 

Patterson

 06/23/1994 .73 .1115 .1368 .4877 .9450

W6 Hospital Creek at River Road near Patterson 06/23/1994 .99 6.9987 8.5889 27.2171 52.7390

W7 Ingram Creek at River Road near Patterson 06/24/1994 .99 1.1025 1.3530 11.5627 22.4053

Total of west-side sites 28.6980 35.2187 51.8181 10.4086

East-side sites 

E5 Merced River at River Road Bridge near 

Newman

 06/22/1994 .45 .3105 .3811 .1553 .3009

E6 Harding Drain at Carpenter Road near 

Patterson

 06/22/1994 .56 .0959 .1177 .0480 .0929

E7 Westport Drain near Modesto 06/23/1994 .73 .0543 .0666 .4344 .8418

E8 Tuolumne River at Modesto 06/23/1994 .99 7.9144 9.7127 .2931 .5680

E10 Stanislaus River at Ripon near Patterson 06/23/1994 .99 2.4177 2.9670 1.2088 2.3424

Total of east-side sites 1.7928 13.2452 2.1396 4.1460

Sum of Stevinson and west-side and east- side sites. 41.0995 5.4380 53.9738 104.5858
50 Occurrence, Distribution, Instantaneous Loads, and Yields of Dissolved Pesticides, San Joaquin River Basin, Calif.

Hospital Creek (56 percent) and Spanish Grant Drain 

(7 percent) were the largest sources of EPTC. Neither of these 

basins reported agricultural application of EPTC during the 6 

months preceding sampling. As for alachlor, earlier applications of EPTC, unreported application, or inter-basin transport 

might account for these loads.

Mud Slough (24 percent) was the largest source of the 

molinate load. As noted earlier, applications of pesticides to 

Mud and Salt Sloughs were combined because the basins are 

interconnected by water management infrastructure. In the 

28 days preceding sampling, 3,439 lb (7.0 lb/mi2) of molinate 

were applied to the combined basin. Molinate is used primarily on rice. Within the study area, this crop is only grown 

in significant amounts in the Mud and Salt Slough Basins 

(Domagalski and Munday, 2003).

Tributaries contributing large portions of the trifluralin 

load included Hospital Creek (53 percent), Ingram Creek 

(22 percent), Spanish Grant Drain (9 percent), and Olive 

Avenue Drain (11 percent). All of these basins had applications of trifluralin in the 28 days preceding sampling. Hospital Creek had 53 lb applied (10.7 lb/mi2

). Ingram Creek had 

384 lb applied (34.9 lb/mi2). Spanish Grant Drain had 274 lb 

applied (12.5 lb/mi2). Olive Avenue Drain had 29 lb applied 

(3.7 lb/mi2).

The Tuolumne River at Modesto (47 percent) was the 

major source of metolachlor. During the 28 days before sampling, 746 lb of metolachlor were applied in the basin 

(2.9 lb/mi2). The agreement between the tributary loads 

and measured loads at the San Joaquin River near Vernalis 

(S4) was very good in 1994, as would be expected with the 

Lagrangian sampling design. 

Summary and Conclusion

Of the 48 pesticides analyzed in this study, 31 were 

reported applied in the 28 days preceding the June 1994 

sampling, 25 in the 28 days preceding the June 2001 sampling, 

and 24 in the 28 days preceding the June 2001 sampling. The 

number of pesticides applied in tributary basins was highly 

correlated with basin area, resulting in the larger basins forming a distinct cluster of sites with similar applications of a variety of pesticides. Smaller basins had fewer pesticides applied 

and often not the same pesticides as neighboring basins. The 

PCA analysis of application intensity indicated that the westside tributary basins generally were different from all the other 

basins in June 1994 and 2001; however, this geographic pattern was not apparent in August 2001.

The number of dissolved pesticides detected was similar 

among sampling periods with 26 detected in June 1994, 28 in 

June 2001, and 27 in August 2001 (table 7). Concentrations 

of chlorpyrifos equaled or exceeded the California CMC at 

six sites in June 1994 and five sites in June 2001. There was 

a single exceedance of the California CMC for diazinon in 

June 2001. A number of pesticides that were not applied in 

the 28 days preceding sampling were detected during each 

sampling period. These detections were likely due to earlier 

applications. There also were pesticides that were applied in 

the 28 days preceding sampling that were not detected during 

sampling. These nondetections likely were due to a combination of the chemical and physical characteristics of the 

particular pesticide and to a variety of other land use and water 

use factors.

Unlike pesticide applications, there was not a strong 

relationship between basin area and the number of pesticides 

detected. Cluster analysis revealed high similarity among 

west-side basins (fig. 7). The PCA results generally showed 

east-side and west-side basins forming distinct groups owing 

to high concentrations of pesticides in west-side basins and 

low concentrations or nondetections of pesticides in eastside basins. These differences in concentrations may be due 

to differences in land use, soil characteristics, and irrigation 

practices that result in greater irrigation return flows in the 

west-side basins. The distinction between west-side and eastside basins became less clear when instantaneous loads were 

considered owing to the higher discharges in some east-side 

basins. High discharge can cause even a low concentration 

to result in a significant load. Consideration of instantaneous 

yields indicated that more pesticide is transported out of westside basins per unit area than out of east-side basins. These 

contrasts between results for concentrations, instantaneous 

loads, and instantaneous yields are important to managers and 

regulators depending on their focus. High concentrations are 

important when considering toxicity to biota. Instantaneous 

loads may be just as important in the regulatory context of 

TMDLs. Instantaneous yields may indicate where management practices may be most effective.

The analysis of June 1994 loads that were based on 

Lagrangian sampling generally showed good concordance 

between tributary loads and the integrated load at the San 

Joaquin River near Vernalis. Tributary loads were often associated with large applications of particular pesticides within the 

basin. In general, west-side basins accounted for the largest 

percentages of loads at the San Joaquin near Vernalis, but this 

was not always the case.

In conclusion, there were geographic differences in 

pesticide concentrations, instantaneous loads, and instantaneous yields within the valley portion of the San Joaquin 

River Basin. In general, west-side basins were different from 

east-side basins; however, there were exceptions in each of 

the analyses. The factors generating these differences between 

basins could not be rigorously quantified, but likely include 

basin size, land use, soil characteristics, irrigation practices, 

and differences in stream discharge.
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