Analysis of Pesticides in Surface Water and 

Sediment from Yolo Bypass, California, 

2004–2005

by Kelly L. Smalling, James L. Orlando, and Kathryn M. Kuivila

Scientific Investigations Report 2005-5220

Sacramento, California

2005
U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

P. Patrick Leahy, Acting Director

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

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

Box 25286, Denver Federal Center

Denver, CO 80225-0286

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

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

imply endosement 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:

Smalling, K.L., Orlando, J.L., and Kuivila, K.M., 2005, Analysis of Pesticides in Surface Water and Sediment from Yolo 

Bypass, California, 2004–2005: U.S. Geological Survey Scientific Investigations Report 2005-5220, 20 p.
Contents

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

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

Hydrology ................................................................................................................................................................... 1

Pesticide Use and Transport................................................................................................................................... 2

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

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

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

Sample Collection and Analytical Methods ................................................................................................................. 5

Sample Collection..................................................................................................................................................... 5

Water.................................................................................................................................................................. 5

Suspended Sediment....................................................................................................................................... 7

Bed Sediment.................................................................................................................................................... 7

Analysis of Dissolved Pesticides ........................................................................................................................... 7

Analysis of Pesticides Associated with Bed and Suspended Sediments....................................................... 7

Quality Assurance and Quality Control ................................................................................................................. 9

Method Detection Limits ......................................................................................................................................... 9

Sediment Organic Carbon Analysis..................................................................................................................... 10

Analysis of Suspended Sediments and Water-Quality Parameters............................................................... 11

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

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

Bed and Suspended-Sediment Concentrations ................................................................................................ 14

Suspended-Sediment Concentrations and Water-Quality Parameters ........................................................ 18

Sediment Organic Carbon ..................................................................................................................................... 18

Conclusions...................................................................................................................................................................... 18

References.......................................................................................................................................................................20

iii
Figures

Figure 1. Input sources and locations of sampling sites within the Yolo Bypass, 

California ........................................................................................................................................3

Figure 2. Map of 10 sampling locations along a transect conducted in the Yolo Bypass, 

California on March 3, 2004.........................................................................................................6

Figure 3. Discharge following a significant rainfall–runoff event at three inputs to the 

Yolo Bypass....................................................................................................................................7

Tables

Table 1. 2003 Pesticide application amounts for the five source watersheds to the 

Yolo Bypass, California. .............................................................................................................. 4

Table 2. Surface water, suspended and bed sediment sampling sites in the Yolo Bypass and its 

tributaries, California, and sample matrix collected...............................................................5

Table 3. Mean recovery of pesticides from matrix spikes (n = 9) using various bed (n = 5) and 

suspended (n = 4) sediment and method detection limits (MDL) .........................................8

Table 4. Method detection limits for pesticides analyzed in surface water in 2001 and 2002......10

Table 5. Pesticide concentrations (ng/L) detected in surface water samples collected in 2004 

from six source watersheds and two sites within the Yolo Bypass, California................11

Table 6. Pesticide concentrations detected in surface water samples from a Yolo Bypass, 

California, transect on March 3, 2004......................................................................................14

Table 7. .Total organic carbon and pesticide concentrations in bed sediment samples 

collected September 21, 2004, from the Yolo Bypass, California........................................15

Table 8. Total organic carbon and pesticide concentrations detected in water and suspended 

sediments collected from the Yolo Bypass, California, in 2004 and 2005 ..........................16

Table 9. Suspended sediment concentrations and water-quality parameters for samples for 

Yolo Bypass, California ..............................................................................................................19

iv
Conversion Factors

Multiply By Obtain

kilogram (kg) 2.205 pound avoirudupois (lb)

kilometer (km) 0.6214 mile (mi)

meter (m) 3.281 foot (ft)

gram (g) 0.03527 ounce, avoirdupois (oz)

liter (L) 33.82 ounce, fluid (oz)

NOTE TO USGS USERS:, Use of hectare (ha) as an alternative name for square hectometer (hm2) is 

restricted to the measurement of small land or water areas. Use of liter (L) as a special name for cubic 

decimeter (dm3) is restricted to the measurement of liquids and gases. Metric ton (t) as a name for megagram (Mg) should be restricted to commercial usage, and no prefixes should be used with it.

Datum: Horizontal coordinate information is referenced to North American Datum of 1983, NAD83

Abbreviations

dms, degrees, minutes, seconds

ft3/s, cubic foot per second

g, gram

km, kilometer

km2, square kilometer

L, liter

L/min, liter per minute

lb, pound

m, meter

mi, mile

mg, milligram

mgL, milligram per liter

mL, milliliter

na, not available

nd, not detected

ng, nanogram

N2, nitrogen gas

ng/g, nanogram per gram

ng/L, nanogram per liter

μg/kg, microgram per kilogram

μm, micrometer

μL, microliter

μS/cm, microsiemens per centimeter

v
Acronyms

atm, atmospheres

DCM, dichloromethane

EPA, U.S. Environmental Protection Agency

GC/MS, gas chromatograph/mass spectrometer

GPC/HPLC, gel permeation chromatography/high pressure liquid chromatography

HCl, hydrochloric acid

KL, Knights Landing

MASE, microwave-assisted solvent extraction

MDL, method detection limits

PAH, polycyclic aromatic hydrocarbon

rpm, revolutions per minute

SPE, solid-phase extraction cartridge

SD, standard deviation

v/v, volume-to-volume

USGS, U.S. Geological Survey

vi
Abstract

Inputs to the Yolo Bypass are potential sources of pesticides 

that could impact critical life stages of native fish. To assess the 

direct inputs during inundation, pesticide concentrations were 

analyzed in water, in suspended and bed-sediment samples collected from six source watersheds to the Yolo Bypass, and from 

three sites within the Bypass in 2004 and 2005. Water samples 

were collected in February 2004 from the six input sites to the 

Bypass during the first flood event of the year representing pesticide inputs during high-flow events. Samples were also collected along a transect across the Bypass in early March 2004 

and from three sites within the Bypass in the spring of 2004 

under low-flow conditions. Low-flow data were used to understand potential pesticide contamination and its effects on native 

fish if water from these areas were used to flood the Bypass in 

dry years. To assess loads of pesticides to the Bypass associated 

with suspended sediments, large-volume water samples were 

collected during high flows in 2004 and 2005 from three sites, 

whereas bed sediments were collected from six sites in the fall 

of 2004 during the dry season.

Thirteen current-use pesticides were detected in surface 

water samples collected during the study. The highest pesticide 

concentrations detected at the input sites to the Bypass corresponded to the first high-flow event of the year. The highest pesticide concentrations at the two sites sampled within the Bypass 

during the early spring were detected in mid-April following a 

major flood event as the water began to subside. The pesticides 

detected and their concentrations in the surface waters varied 

by site; however, hexazinone and simazine were detected at all 

sites and at some of the highest concentrations.

Thirteen current-use pesticides and three organochlorine insecticides were detected in bed and suspended sediments collected in 2004 and 2005. The pesticides detected and 

their concentrations varied by site and sediment sample type. 

Trifluralin, p,p′-DDE, and p,p′-DDT were highest in the bed 

sediments, whereas oxyfluorfen and thiobencarb were highest 

in the suspended sediments. With the exception of the three 

organochlorine insecticides, suspended sediments had higher 

pesticide concentrations compared with bed sediments, indicating the potential for pesticide transport throughout the Bypass, 

especially during high-flow events. Understanding the distribution of pesticides between the water and sediment is needed to 

assess fate and transport within the Bypass and to evaluate the 

potential effects on native fish.

Introduction

Fisheries studies in the late 1990s suggest that the Yolo 

Bypass provides a habitat to 42 fish species, of which 15 are 

native (Sommer and others, 2002). A few of the species found 

in the Bypass are year-round residents in the perennial waters of 

the Bypass; however, most use the Bypass either as a migration 

corridor or as a rearing or spawning habitat during the winter and early spring when it floods. Recent studies have shown 

that Chinook salmon increased in size substantially faster in the 

Yolo Bypass than in the Sacramento River (Sommer and others, 

2001). This increase in growth rate was attributed to the warmer 

waters in the Bypass and its greater abundance and quality of 

food compared with that of the Sacramento River (Sommer and 

others, 2002; Sommer and others, 2001). It has been proposed 

to flood the Bypass annually or during the drier months to give 

native fish productive waters year-round. The Bypass is a complex, engineered floodplain designed to channel water away 

from low lying areas and into the basin during high-flow events, 

whereas waters from agricultural and urban sources can be used 

to flood the Bypass in dry years as a management practice for 

native fish populations. However, the impact of nonpoint source 

contamination of pesticides to native fish within the Bypass is 

still largely unknown.

Hydrology

The Yolo Bypass is a 60-km long, 24,000-hectare leveed 

basin designed in the early 1930s to divert flood waters of the 

Sacramento River away from Sacramento and other nearby 

low-lying communities. The Bypass floods in 7 out of 10 years 

in the winter or spring and is designed to withstand flows up 

to 500,000 ft3/s. When flows on the Sacramento River exceed 

roughly 60,000 ft3/s at the Fremont Weir, water begins to spill 

into the Bypass. When the Bypass is fully inundated, the wetted area of the Sacramento–San Joaquin Delta system approximately doubles. Historically, the floodplain has been inundated as early as October and as late as June with a typical peak 

between January and March.

Analysis of Pesticides in Surface Water and Sediment 

from Yolo Bypass, California, 2004–2005

by Kelly L. Smalling, James L. Orlando, and Kathryn M. Kuivila

1
The Yolo Bypass receives water from six sources that vary 

greatly during low-flow and high-flow conditions, making the 

hydrology of the system complex (fig. 1). The watersheds that 

drain into the Yolo Bypass include, Willow Slough (697 km2), 

Putah Creek (1,685 km2), Cache Creek (2,957 km2), Knights 

Landing Ridge Cut (4,374 km2), and the Sacramento and 

Feather Rivers (61,299 km2) at the Fremont Weir (fig. 1). The 

Bypass itself is relatively small, only 243 km2; however, under high-flow conditions, the watershed includes all the basins 

mentioned previously and increases in size to 71,255 km2.

During high-flow conditions, the primary input to the 

Bypass is the Fremont Weir, which conveys flood water from 

the Sacramento River, the Feather River, and the Sutter Bypass. 

Water flowing into the Bypass at the Freemont Weir initially 

flows through the Toe Drain (fig. 1), a riparian channel running along the eastern edge of the Bypass, and then spills onto 

the floodplain when flows through the small channel exceed 

3,500 ft3/s (Sommer and others, 2002). Minor inundations of 

the Bypass also may occur during high flows on Cache Creek, 

Putah Creek, Willow Slough, and Knights Landing Ridge Cut, 

without the overtopping of Fremont Weir.

During low-flow conditions, the Yolo Bypass receives most 

of its water from four watersheds: Putah Creek, Cache Creek, 

Knights Landing Ridge Cut, and Willow Slough. Water from 

Putah Creek and Cache Creek is shunted off for irrigation as it 

enters the Bypass and eventually drains into the Toe Drain on the 

eastern edge of the floodplain. Water from Cache Creek enters 

a leveed settling basin and is slowly drained through a series of 

ditches across the Bypass into the Toe Drain. When the settling 

basin exceeds capacity, water flows into the Bypass over a large 

concrete ‘step ladder’ spillway. During the dry summer months, 

Cache Creek, which is dry upstream of the settling basin, is not 

a source of surface water to the Bypass. Also during the summer, the Toe Drain, which connects to a complex network of 

channels and ditches used for irrigation, becomes the primary 

source of perennial water into the Bypass. Knights Landing 

Ridge Cut is an artificial overflow channel that connects the 

lower end of the Colusa Basin Drain to the Bypass. The Colusa 

Basin Drain is a 70-mi long channel running along the western 

edge of the Sacramento River. Under low-flow conditions, the 

drain discharges directly to the Sacramento River; however, under high-flow conditions, water in the drain is shunted through 

Knights Landing Ridge Cut to the Bypass (Jones and Stokes, 

2001). The Willow Slough watershed, which is the smallest 

watershed connected to the Bypass, drains principally agricultural areas immediately west of the Bypass. Willow Slough also 

conveys effluent from the city of Davis’s wastewater treatment 

plant.

Pesticide Use and Transport

Historically, corn, melons, rice, safflower, and tomatoes 

have been the predominant crops grown inside the Yolo Bypass, 

whereas the major crops grown in the areas surrounding the 

Bypass include alfalfa, beans, nuts (almonds and walnuts), 

orchards, and rice. The variety of crops grown in the region gives 

rise to the use of many different types of herbicides and insecticides. Of the 38 current-use pesticides analyzed in the study, 17 

were used in the Yolo Bypass watershed (table 1). Molinate and 

thiobencarb, two thiocarbamate herbicides, are used extensively 

on rice, both within and outside the Yolo Bypass (Crepeau and 

Kuivila, 2000). Greater than 500,000 lb (active ingredient) each 

of molinate and thiobencarb were applied to rice fields within 

the Bypass high-flow watershed in 2003 (California Department 

of Pesticide Regulation, 2003). Other pesticides used in these 

watersheds include chlorpyrifos, diazinon, hexazinone, metolachlor, oxyfluorfen, and trifluralin (California Department of 

Pesticide Regulation, 2003) (table 1).

Pesticide use in the watersheds surrounding the Bypass 

has a direct impact on the Bypass itself, especially under highflow conditions or during the first rainfall of the season, as 

sediments move from the fields to the creeks. High flows from 

the input watersheds may increase bound suspended-sediment 

loads to the Bypass, increasing depositional rates of sediment 

pesticides in some areas. The influx of dissolved pesticides into 

the bypass during high-flow events may have an impact on local fish populations. Limited information is available regarding 

the long-term effects of pesticide exposure to fish in the Bypass 

during high-flow years when the pesticide flux from the surrounding watersheds is greatly increased.

A conceptual model of pesticide transport and fate suggests three potential sources of contamination to the Bypass. 

During inundation, dissolved pesticides as well as pesticides 

sorbed to suspended sediments are present in the surface water used to flood the Bypass. A third potential source of exposure is pesticides applied directly to soils within the Bypass. 

Understanding the fate of pesticides in the Yolo Bypass will 

help fisheries biologists assess the potential risks of long-term 

exposure to juvenile and adult fish.

Project Design

The project was designed to measure the concentrations 

of pesticides entering the Yolo Bypass during a high-flow event 

and to determine the types and amounts of pesticides present 

within the Bypass itself. A variety of pesticide classes was analyzed in surface water and in bed and suspended sediments to 

achieve the goals of this study. Modifications to our previous 

sediment method were made to add new compounds and decrease method detection limits for some analytes, especially 

the pyrethroids owing to their aquatic toxicity at extremely low 

levels.

Surface waters were sampled during two different phases 

for this study. The first phase of sampling (or high flow) was designed to measure the direct inputs of pesticides during an event 

in February 2004 that represents the Bypass when it floods. The 

second sampling phase (or low flow) was designed to compare 

pesticide concentrations in the Toe Drain and Putah Creek in 

late March and April 2004 because water from these sites may 

be used to flood the Bypass in dry years in support of native fish 

populations.

2
Figure 1. Input sources and locations of sampling sites within the Yolo Bypass, California.

#

#

#

#

#

#

#

#

#

A

Yolo Bypass

Sacramento

Davis

Woodland

Cache Creek Inflow to Settling

Basin near Woodland, CA

Woodland R1

Toe Drain at Yolo Bypass Willow Slough Bypass at County near West Sacramento, CA

Rd 105 near Davis, CA

Knights Landing Ridge Cut

near Knights Landing, CA

Sacramento Slough near

Knights Landing, CA

Sacramento River at

Knights Landing, CA

Fremont Weir

0 2.5 5 MILES

0 4 8 KILOMETERS

CALIFORNIA

Sutter Bypass

Colusa Basin Drain

Cache Creek

Ridge Cut Slough

Sacramento River

Willow Slough

Putah Creek

Feather River

39

3850

3840

3830

3820

122 12150 12140 12130 12120

South Fork Putah Creek at

Mace Rd near Davis, CA

Yolo Bypass

Rangers Demonstration Pond

office in

wildlife area

EXPLANATION

Yolo Bypass 

Wildlife Area

Urban Area

Yolo Bypass

Fremont Weir

Highway

Sampling Site

3
Another element of this study assessed both the transport 

of pesticides associated with suspended sediments to the Bypass 

and those associated with agricultural soils in and around the 

Bypass. Large volume water samples were collected for the isolation of suspended sediments in February 2004 and January 

2005 during high-flow events from three source watersheds 

(Putah Creek, Willow Slough, and Knights Landing Ridge Cut), 

and bed sediment samples were collected in September 2004 

after pesticide application when the Bypass was dry. All water 

and sediment samples were analyzed for pesticides at the U.S. 

Geological Survey’s (USGS) California Water Science Center 

laboratory in Sacramento, California (Sacramento laboratory).

Purpose and Scope

This report describes the methods and procedures used 

during sampling, extraction, and analysis of pesticides at 

various sites (fig. 1) and presents water and sediment data 

for samples collected during this study. Several pyrethroid 

insecticides were added to the sediment method, and modifications were made to decrease analytical detection limits. 

Concentrations of 27 current-use pesticides were analyzed in 

48 water samples, and total organic carbon and concentrations 

of 41 pesticides were analyzed in 10 sediment samples. In 

addition, suspended-sediment concentrations and water-quality parameter data are presented, as well as method detections 

limits for pesticides analyzed in water and sediments. During 

this study, the USGS was responsible for the initiation of field 

sampling, collection of surface water and suspended sediments 

and all chemical analyses. Larry Walker and Associates, a 

consulting firm in Davis, California, conducted the bed-sediment sampling in 2004. Water and sediment samples were analyzed for pesticides and total organic carbon at the USGS’s 

California Water Science Center organic chemistry laboratory 

in Sacramento, California.

Acknowledgments

The authors acknowledge Lisa Jacobson, Stephanie Smith, 

and Patrick Nicholas of the USGS for their many hours of sampling, laboratory work, and pesticide analysis. We also thank the 

personnel from the California Department of Water Resources 

and Dave Feliz of the California Department of Fish and Game 

for help with water sampling and Aramand Ruby for collecting the bed-sediment samples analyzed in the study. This project was funded by the California Resources Agency/California 

Bay-Delta Authority (Contract # 4600002755) and the USGS 

Federal–State Cooperative Program.

Table 1 2003 Pesticide application amounts for the five source watersheds to the Yolo Bypass, California. 

[For the Yolo Bypass high-flow watershed, the total application amounts equal the sum of the watersheds listed 

below for the entire Bypass. Values are in pounds per year. Pesticide application amounts are in pounds per 

year active ingredient. KL, Knights Landing] 

Pesticide Cache Creek Putah Creek KL Ridge Cut Willow Slough Sacramento and 

Feather Rivers

Bifenthrin 43 0 670 25 600 

Carbaryl 630 62 1,100 170 4,200 

Chlorpyrifos 5,340 2,400 25,000 5,500 92,000 

DCPA 0 0 440 0 400 

Diazinon 1,540 1,100 8,200 1,700 52,000 

EPTC 1,300 0 3,800 0 4,300 

Hexazinone 1,270 1,300 7,700 5,400 27,000 

Methidathion 0 0 1,200 0 6,400 

Metolachlor 2,600 1,800 11,000 5,900 3,200 

Molinate 0 1,100 150,000 7,000 370,000 

Napropamide 580 250 3,100 370 4,800 

Oxyfluorfen 3,600 1,100 15,000 1,700 12,000 

Pendimethalin 360 210 5,900 240 6,000 

Simazine 1,820 650 2,500 210 19,000 

Tau-fluvalinate 0 0 36 0 36 

Thiobencarb 2,000 0 250,000 14,000 280,000 

4
Sample Collection and Analytical 

Methods

Sample Collection

Sites were selected on each of the major surface water 

inputs to the Yolo Bypass. Samples were collected from six 

sites: Sacramento River at Knights Landing, (abbreviated as 

Sacramento River), Sacramento Slough near Knights Landing 

(Sacramento Slough), Cache Creek Inflow to the Settling Basin 

near Woodland (Cache Creek), South Fork of Putah Creek at 

Mace Rd near Davis (Putah Creek), Knights Landing Ridge 

Cut near Knights Landing (KL Ridge Cut), and Willow Slough 

Bypass at County Rd 105 near Davis (Willow Slough) (table 2, 

fig. 1). All sites are located as close to the Bypass as feasible 

(fig. 1). Additional samples were collected from three sites located within the Bypass: Toe Drain at Yolo Bypass near West 

Sacramento (Toe Drain), Woodland R1 (Woodland), and Yolo 

Bypass Demonstration Pond (Yolo pond) (table 2, fig. 1), and 

nine stations along a transect across the Bypass with Toe Drain 

as the 10th station along the transect (table 2, fig. 2).

Primary field sampling began in mid-February of 2004 following a significant rainfall and runoff event in the area, and 

continued through the end of April 2004 (fig. 3). Water for the 

high-flow sampling was collected from February 19 to March 

11 on a weekly basis from the six inputs to the Bypass. Surface 

water for the low-flow sampling was collected weekly between 

March 17 and April 21 from the two sites within the bypass 

(Yolo Pond and Toe Drain) and Putah Creek. On March 3, water 

was collected from 10 stations along a single transect across the 

width of the Bypass (fig. 2). Suspended-sediment samples were 

collected on February 20 from Putah Creek and KL Ridge Cut.

Bed-sediment samples were collected in September 2004 

by personnel from a local environmental consulting firm (Larry 

Walker Associates, Davis, California). Samples were collected 

at four input sites (Cache Creek, KL Ridge Cut, Putah Creek, 

and Willow Slough) and two sites within the Bypass (Woodland 

and Toe Drain) (Larry Walker Associates, 2005).

In January 2005, water and suspended-sediment samples 

were collected once during a significant rainfall runoff event at 

the KL Ridge Cut and Willow Slough sites.

Water

Samples were collected for analysis of pesticides, suspended-sediment concentrations, and water-quality parameters 

(pH, specific conductance, and temperature) at all sites except 

Woodland. Water samples were collected as mid-channel grabs 

from bridges using a weighted, two-bottle sampler. Sample water was collected at a depth of approximately 0.5 m directly into 

one 1-L baked, glass bottle and one 500-mL glass milk bottle 

for pesticide and suspended-sediment concentration analyses, 

respectively. Samples were immediately placed on ice and 

transported to the Sacramento laboratory. Whole water samples collected for analysis of suspended-sediment concentration were shipped within 1 month of collection to the USGS’s 

Sediment Laboratory in Marina, California. Samples were also 

collected for pesticide analysis from nine stations and the Toe 

Drain site along one transect located immediately south of the 

Interstate 80 causeway within the Bypass (fig. 2). Water was 

collected by hand-dipping 1-L baked, amber glass bottles just 

below the water surface at 10 stations spaced equally across the 

Bypass. These samples were preserved on ice and transported 

to the Sacramento laboratory.

Table 2 Surface water, suspended and bed sediment sampling sites in the Yolo Bypass and its tributaries, California, and sample matrix 

collected.

[Horizontal Datum is NAD 83. dms, degrees, minutes, seconds; km, kilometer]

Site name USGS site 

identification no. Latitude (dms) Longitude (dms)

Distance to 

Bypass (km) Sample matrix collected

Cache Creek Inflow to Settling 

Basin near Woodland

384340121434401 38° 43’ 40” 121° 43’ 48” 9.2 Water, bed sediment

Knights Landing Ridge Cut near 

Knights Landing

384455121414001 38° 44’ 55” 121° 41’ 40” 3.9 Water, suspended and bed 

sediment

Sacramento River at Knights 

Landing

11391000 38° 47’ 06” 121° 39’ 16” 9.1 Water

Sacramento Slough near Knights 

Landing

11391100 38° 48’ 11” 121° 42’ 59” 2 Water

South Fork Putah Creek at Mace 

Rd near Davis

383109121414601 38° 31’ 09” 121° 41’ 46” 3.5 Water, suspended and bed 

sediment

Toe Drain at Yolo Bypass near 

West Sacramento

383425121350201 38° 34’ 25” 121° 35’ 02” Within Bypass Water and bed sediment

Willow Slough Bypass at County 

Rd 105 near Davis

383524121403401 38° 35’ 24” 121°40’ 34” 4.7 Water, suspended and bed 

sediment

Woodland R1 Within Bypass Bed sediment

Yolo Bypass Demonstration Pond Within Bypass Water

5
§¦ ̈I 80

Yolo Bypass

Willow Slough

Yolo Bypass

Rangers office in Demonstration Pond

wildlife area

Putah Creek

Toe Drain Ship

Channel

Sacramento River

Willow Slough Bypass at County

Rd 105 near Davis, CA

South Fork Putah Creek at

Mace Rd near Davis, CA

Toe Drain at Yolo Bypass

near West Sacramento, CA

9 7 8

6 3 4 5 2 1

10

# Sampling Site

X Transect Site

0 1 2 4 MILES

0 1.25 2.5 5 KILOMETERS

3832

3830

3828

12135

3836

3834

12140

EXPLANATION

Yolo Bypass

Yolo Bypass Wildlife Area

Highway

Figure 2. Map of 10 sampling locations along a transect conducted in the Yolo Bypass, California on March 3, 2004.

6
Suspended Sediment

Large volume water samples were collected at three sites 

(KL Ridge Cut, Putah Creek, and Willow Slough) and processed 

to isolate suspended sediments. At each site, approximately 200 

L of water were collected using a peristaltic pump equipped 

with a stainless steel and Teflon inlet hose. Water was pumped 

at multiple stations across each channel profile, and at each station the inlet hose was suspended at multiple depths through the 

water column. All samples were collected and transported in 

20-L stainless steel soda kegs to the Sacramento laboratory.

Bed Sediment

Bed-sediment samples were collected from four input sites 

and two sites within the Bypass (table 2). Sediment was collected from the top 2 centimeters of undisturbed stream bottom 

in areas of active deposition in 500-mL pre-cleaned glass jars. 

Samples were then shipped on ice to the Sacramento laboratory 

and stored frozen at –20 °C until analysis.

Analysis of Dissolved Pesticides

Water samples were filtered through baked 0.7 μm glass 

fiber filters within 24 hours of collection. Terbuthylazine 

was added to each sample as a recovery surrogate to provide 

quantitative data on extraction efficiency and the samples were 

extracted onto C8 solid phase extraction cartridges. The cartridges were dried using compressed carbon dioxide, frozen, 

and stored for up to 6 months at –20 °C. Prior to analysis, the 

cartridges were thawed, eluted using 9 mL of ethyl acetate, and 

concentrated for analysis. Deuterated polycyclic aromatic hydrocarbon (PAH) compounds were used as an internal standard 

and included d10-acenaphthene, d10-phenanthrene, and d10-pyrene. All extracts were analyzed for 27 pesticides using a Varian 

Saturn 2000 gas chromatograph mass spectrometer (GC/MS) 

with ion trap detection. Details of the analytical method are described in Crepeau and others (2000).

Analysis of Pesticides Associated with Bed and 

Suspended Sediments

Large volume water samples were processed to isolate suspended-sediment particles using a Westfalia continuous-flow 

centrifuge, within 6 hours of collection. During this process, 

sample water was passed through the centrifuge at a rate of 2 

L/min using a peristaltic pump. This flow rate has been shown 

to be optimal for the collection of suspended-sediment particles 

(Horowitz and others, 1989). In addition, a single 1-L water 

sample was collected from the centrifuge effluent and analyzed 

for dissolved pesticides.

Feb. 5 Feb. 19 Mar. 4 

2004

Mar. 18 Apr. 1 Apr. 15 

Fremont Weir Discharge, in cubic feet per second 

Cache Creek and Putah Creek discharge, in cubic feet per second 

High-Flow

Sampling

Low-Flow

Sampling

20,000 80,000

Cache Creek 

Putah Creek 

Fremont Weir 

60,000

40,000

20,000

0

15,000

5,000

0

10,000

Figure 3. Discharge following a significant rainfall–runoff event at three inputs to the Yolo Bypass during 2004 high 

and low-flow sampling events.

7
 Following centrifugation, the concentrated sediment and 

sediment-water slurry were removed from the stainless steel 

centrifuge bowls and further dewatered by centrifuging for 20 

minutes at 10,000 rpm using a high speed refrigerated centrifuge 

(Sorvall RC-5B centrifuge, DuPont Company, Wilmington, 

Delaware). The water separated from the samples during this 

step was decanted, and the remaining sediments were placed in 

precleaned glass jars and stored frozen until analysis.

The sediments were analyzed using the method described 

by LeBlanc and others (2004) with slight modifications to lower 

the MDL and limit matrix interference. The modified method, 

discussed in detail in this section, includes six compounds not 

analyzed in the original method and excludes three previously 

analyzed compounds. To avoid cross contamination and artifacts associated with drying and to increase extraction efficiency of the MASE, wet sediments were used (Jayaraman and others, 2001). Approximately 5 g of sediment (dry weight) were 

fortified with a labeled surrogate recovery solution containing 

400-ng 13C-labeled trifluralin, chlorpyrifos, p,p′-DDE, and permethrin (cis/trans mixture) (Cambridge Isotope Laboratories 

Inc., Andover, Massachusetts). The amount of moisture in the 

sediment was set at 50 percent prior to MASE by adding between 0.2 and 1.5 mL of organic free deionized water depending 

on the moisture content of each sediment sample. The sediment 

samples were extracted two times with a mixture of dichloromethane (DCM) and acetone (50:50 v/v) using an MSP 1000 

(CEM Corporation, Mathews, North Carolina). Details of the 

MASE procedure are described in Leblanc and others (2004).

Following extraction, the samples were decanted through 

glass funnels packed with approximately 30 g of sodium sulfate 

to remove excess water. Extracts were reduced at 25 °C and 

0.6 atm to 0.75 mL using a Turbovap II (Zymark Corporation, 

Hopkinton, Maryland). Sediment matrix was removed by passing the sample extract via vertical flow under gravity through 

two stacked solid-phase extraction (SPE) cartridges containing 

different sorbents. A 6 mL, 500 mg, nonporous, graphitized 

carbon SPE (Restek Corporation, Bellefonte, Virginia) was 

stacked on top of a 500 mg Alumina SPE (Varian Inc., Palo 

Alto, California) and washed with 10 mL of DCM to remove 

cartridge impurities. The organic rich, colored sample extract 

was added to the cartridges, rinsed in tandem with 10 mL of 

DCM, and collected as fraction 1 (F1). The carbon SPE was 

removed and the Alumina SPE was eluted with 10 mL of ethyl 

acetate and DCM (50:50 v/v) and collected as fraction 2 (F2). 

With the exception of the triazines/triazinones, carbamates, and 

napropamide, most pesticide classes were eluted primarily in 

the F1 with minimal carryover into the F2. Only molinate and 

methidathion split between the F1 and F2. Because the F2 contained more sample matrix than the F1, the two fractions were 

analyzed separately to reduce interferences with the pyrethroids 

in the first fraction and improve the (MDLs). Concentrations 

of each analyte were calculated in each fraction separately and 

then summed together to give a final reported value.

Both fractions were evaporated separately under a gentle 

stream of highly purified nitrogen gas (N-evap, Organomation 

Associates, Berlin, Massachusetts) to 0.5 mL and exchanged 

into ethyl acetate. Sulfur, found only in the F1 extracts, was 

removed using a gel permeation/high pressure liquid chromatography (GPC/HPLC) system. The F1 and F2 extracts were 

reduced under a gentle stream of N2 to 0.2 mL, and 40 μL of the 

deuterated internal PAH standard was added. The extracts were 

analyzed by GC/MS for a suite of 41 pesticides.

Five pyrethroids were added to the method, which included deltamethrin, fenpropathrin, phenothrin, resmethrin, and 

tau-fluvalinate (table 3). Diethylatyl-ethyl and azinphos-methyl 

were the two compounds removed from the original method 

developed by LeBlanc and others (2004).

Table 3 Mean recovery of pesticides from matrix spikes (n 

= 9) using various bed (n = 5) and suspended (n = 4) sediment 

and method detection limits (MDL).

[All MDLs were determined in Cache Creek sediment only (n = 7). 

μg/kg, microgram per kilogram; SD, standard deviation; MDL, method 

detection limit; NA, not available]

Mean ± SD (%) MDL (ng/g)

Triazines/Triazones

Atrazine1 85.0 ± 5.1 1.7

Hexazinone 114 ± 12.7 2.3

Prometryn1 89.3 ± 9.0 1.9

Simazine1 91.3 ± 7.8 1.4

Anilines

Ethalfluralin1 82.8 ± 8.9 1.2

Pendamethalin 105 ± 5.1 1.5

Trifluralin 88.9 ± 13.6 1.1

Chloacetanilides

Alachlor1 86.1 ± 10.9 1.4

Metolachlor1 85.1 ± 5.6 1.7

Carbamates

Carbaryl 103 ± 8.0 2.2

Carbofuran1 102 ± 13.0 5.3

Thiocarbamates

Butylate1 60.0 ± 6.6 1.1

Cycloate1 66.6 ± 5.5 0.8

EPTC1 62.3 ± 8.1 1.4

Molinate 62.9 ± 7.7 0.6

Pebulate1 60.6 ± 6.9 0.9

Thiobencarb 93.9 ± 10.7 1.6

8
Table 3 Mean recovery of pesticides from matrix spikes (n 

= 9) using various bed (n = 5) and suspended (n = 4) sediment 

and method detection limits (MDL).

[All MDLs were determined in Cache Creek sediment only (n = 7). 

μg/kg, microgram per kilogram; SD, standard deviation; MDL, method 

detection limit; NA, not available]

Mean ± SD (%) MDL (ng/g)

Organochlorines

p,p’-DDD 85.4 ± 12.7 1.3

p,p′-DDE 85.1 ± 9.1 1.5

p,p′-DDT 85.2 ± 12.4 1.9

Organophosphates

Chlorpyrifos 82.5 ± 6.0 0.8

Diazinon1 85.1 ± 14.8 0.6

Malathion1 94.4 ± 7.8 2.2

Methidathion1 102 ± 10.5 1.5

Methylparathion1 103 ± 7.4 2

Phosmet1 93.8 ± 17.0 2.4

Pyrethroids

Bifenthrin 84.2 ± 15.1 2.3

Cyfluthrin1 81.5 ± 7.3 7.9

Cypermethrin1 86.0 ± 14.1 5.6

Deltamethrin1 88.5 ± 15.1 1.1

Esfevalerate1 80.1 ± 6.6 1.8

Fenpropathrin1 85.3 ± 17.9 1.4

Lambda-Cyhalothrin1 77.1 ± 9.8 1.6

Permethrin1 79.0 ± 12.8 1.2

Sumithrin1 92.8 ± 16.3 2.9

Tau-fluvalinate 83.5 ± 14.9 1.1

Miscellaneous

DCPA 82.4 ± 8.4 1.5

Napropamide 98.2 ± 8.5 1.6

Oxuflurofen 92.7 ± 10.5 2.5

Piperonyl butoxide1 106 ± 10.0 1.3

1Pesticides not detected in this study.

Quality Assurance and Quality Control

Dissolved pesticide concentrations were validated against 

a comprehensive set of quality control parameters including laboratory and field blanks, matrix spikes, replicate samples, and 

surrogate recovery. Laboratory and field blanks were analyzed 

every 10–20 samples for a total of 6 in 2004 and 1 in 2005. No 

pesticides were detected in any of the blanks. Replicate samples 

(6) were analyzed constituting approximately 10 percent of the 

samples and were within 25 percent agreement for all pesticides 

detected. Matrix spikes were analyzed in approximately 10 percent of the samples as part of the described method validation 

with recoveries ranging from 80 to 120 percent. Terbuthylazine 

was used as a recovery surrogate to assess the efficiency of sample extraction. The average percentage recovery and standard 

deviation of the recovery surrogate were calculated for each 

site. Sample data were excluded if the recovery of terbuthylazine was outside the mean plus or minus two standard deviations.

Sediment matrix spikes, method blanks, and replicate 

samples were also processed for quality control purposes. 

During final method testing, 200 ng of each pesticide listed in 

table 3 was spiked into five bed sediment and four suspendedsediment samples. Matrix spike percentage recoveries ranged 

from 60 to 114 percent (table 3). Replicate samples constituted 

approximately 10 percent of the total samples analyzed, and the 

differences between replicates were less than 25 percent for all 

pesticides detected. No pesticides were detected in any blank 

sample run with each batch of five sediment samples. Recovery 

of the sediment surrogate mixture was used to monitor the efficiency of each extraction. The average percentage recoveries of 

13C-labeled trifluralin, chlorpyrifos, p,p′-DDE, and permethrin 

(cis/trans mixture) were 92.0 ± 10.2, 93.0 ± 9.0, 87.5 ± 13.3 and 

95.2 ± 10.0, respectively.

Method Detection Limits

Surface water method detection limits were validated in a 

previous study (Orlando and others, 2004) using the EPA procedure (U.S. Environmental Protection Agency, 1992; table 4). 

Water used for the MDLs was collected in 2001 and 2002 from 

the San Joaquin River near Vernalis (USGS site ID number 

11303500), which has similar water chemistry to the sites sampled in the study.

9
Table 4 Method detection limits for pesticides analyzed 

in surface water in 2001 and 2002.

[The method detection limits for pesticides analyzed in surface 

water in 2001 and 2002 are taken from Orlando and others, 2004. 

Method detection limits not available for Bifenthrin, Cyfluthrin, 

Cypermethrin, Deltamethrin, Esfenvalerate, Fenpropathrin, Lambdacyhalothrin, Resmethrin, Permethrin, Phenothrin, p,p′-DDD, 

p,p′-DDE, p,p′-DDT, Tau-fluvalinate; ng/L, nanogram per liter]

Pesticide Method detection limit (ng/L)

Alachlor1 2.1

Atrazine1 4.2

Butylate1 1.8

Carbaryl 4.2

Carbofuran1 3.3

Chlorpyrifos1 4.2

Cycloate1 1.5

DCPA1 1.2

Diazinon 3.6

EPTC 4.5

Ethalfluralin1 2.4

Hexazinone 5.7

Malathion1 2.1

Methidathion 5.4

Methyl parathion1 4.2

Metolachlor 3.3

Molinate 2.7

Napropamide 7.2

Oxyfluorfen 4.2

Pebulate1 0.6

Pendimethalin 2.4

Phosmet1 4.2

Piperonyl butoxide1 3.3

Prometryn1 2.7

Simazine 6.9

Thiobencarb 3.9

Trifluralin 3.0

MDLs for the sediment samples were determined using 

seven replicates of Cache Creek sediment collected for this 

study. Cache Creek was chosen because it had low background 

pesticide concentrations and was similar in organic carbon 

content to the other sites. A mixture containing approximately 

50 ng of each analyte (approximately10 ng/g dry weight) was 

added to the sediment and carried through the entire procedure. 

The method detection limits for each compound in sediment 

and water are listed in tables 3 and 4.

The MDL was calculated for each pesticide using the following equation: 

MDL = S × t (n–1, 1–a = 0.99)

where:

MDL = method detection limit (μg/kg)

S = standard deviation of replicate samples

n = number of replicates

t = value of Student’s t statistic at 6 degrees of freedom 

and 99 percent confidence level

MDLs for sediment ranged from 0.6 to 7.9 μg/kg (table 3), 

whereas MDLs for dissolved pesticides ranged from 0.6 to 7.2 

ng/L (table 4). Analytes can be identified at concentrations less 

than the MDL with a lower confidence in the actual value; therefore, these concentrations are reported as estimated values.

Sediment Organic Carbon Analysis

Suspended and bed sediments were analyzed for organic 

carbon content using a Perkin Elmer CHNS/O analyzer (Perkin 

Elmer Corporation, Norwalk, Connecticut). Sediments were 

combusted at 925 °C in silver boats after being exposed to 

concentrated HCl fumes in a desiccator for 24 hours to remove 

inorganic carbon. Before analysis, sediments were dried to a 

constant weight at 100 °C for 3 hours. Acetanilimide was used 

for instrument calibration of elemental carbon and nitrogen.

1Pesticides not detected in this study

10
Analysis of Suspended Sediments and WaterQuality Parameters

Whole water samples were analyzed for suspended-sediment concentration at the U.S. Geological Survey Sediment 

Laboratory in Marina, California. Details of the analytical 

method can be found in Guy (1969). Analytical results of 

single-blind quality control samples provided by the USGS’s 

Sediment Laboratory Quality Assurance Project show that laboratory performance during the period of this study was satisfactory (U.S. Geological Survey, 2005).

Water parameters (pH, specific conductance, and water 

temperature) were measured in whole-water samples on site or 

at the Sacramento laboratory within 24 hours of sample collection. Specific conductance and pH were measured using two 

handheld instruments, (Cole Parmer Model 141-61 and Orion 

Model 250A, respectively), following methods described in 

the USGS’s National Field Manual (Wilde and Radtke, 1998). 

Water temperature was measured in the field at the time of 

collection using a digital thermometer.

Results

Dissolved Pesticide Concentrations

In this study, 13 current-use pesticides were detected 

in surface water samples collected from the six input sites 

to the Bypass and the two sites within the Bypass (table 2). 

Hexazinone and simazine were detected in samples collected 

from every site and were the highest in early February at KL 

Ridge Cut and Willow Slough, respectively, in 2004. Willow 

Slough, KL Ridge Cut, and Toe Drain had the highest pesticide 

concentrations compared with the other sites with values ranging from 5 to 2,500 ng/L (table 5).

Table 5 Pesticide concentrations detected in surface water samples collected in 2004 from six source watersheds and two sites 

within the Yolo Bypass, California.

[Site names are abbreviated; for complete names, see table 2. Pesticide concentrations in nanogram per liter. Samples were analyzed for the following pesticides that were not detected: Alachlor, Atrazine, Butylate, Carbofuran, Chlorpyrifos, Cycloate, DCPA, Ethalfluralin, Malathion, Methyl parathion, Pebulate, 

Phosmet, Piperonyl butoxide, and Prometryn. hh:mm, hours:minutes; mm/dd/yy, month/day/year; nd, not detected; ( ), concentrations less than MDL and are 

estimated values]

Site Date 

(mm/dd/yy)

Time 

(hh:mm) Carbaryl Diazinon EPTC Hexazinone Methidathion

Metolachlor Molinate

Cache Creek 2/19/04 14:00 nd nd nd 19.4 nd nd nd

2/26/04 09:10 nd nd nd 46.4 nd 3.5 nd

3/04/04 10:50 nd nd nd 7.7 nd nd nd

3/11/04 11:00 nd nd nd 6.0 nd nd nd

Knights Landing Ridge Cut 2/19/04 14:35 nd 157 nd 947 39.5 22.8 12.5

2/26/04 08:40 nd 41.7 nd 315 nd 10.4 27.7

3/04/04 11:05 nd 40.8 nd 409 nd 26.9 20.4

3/11/04 11:15 nd 20.7 nd 271 nd 23.3 23.7

Putah Creek 2/19/04 10:45 nd nd nd 15.2 nd nd nd

2/26/04 10:15 nd nd nd 10.8 nd nd nd

3/04/04 09:20 nd nd nd nd nd nd nd

3/11/04 11:15 nd nd nd nd nd nd nd

3/17/04 11:10 nd nd nd nd nd nd nd

3/23/04 10:45 nd nd nd nd nd nd nd

3/29/04 10:45 nd nd nd nd nd nd nd

4/05/04 08:50 nd nd nd nd nd nd nd

4/12/04 12:00 nd nd nd nd nd 8.6 nd

4/21/04 12:10 nd nd nd 14.9 nd nd nd

11
Site Date 

(mm/dd/yy)

Time 

(hh:mm) Carbaryl Diazinon EPTC Hexazinone Methidathion

Metolachlor Molinate

Sacramento River 2/19/04 15:00 nd 28.1 nd 31.6 nd nd nd

2/26/04 08:05 nd nd nd 32.3 nd (1.7) nd

3/04/04 11:35 nd 4.1 nd 17.3 nd 4.0 nd

3/11/04 11:45 nd (3.4) nd 10.9 nd nd nd

Sacramento Slough 2/19/04 15:25 nd 11.9 11.4 328 nd 24.5 33.3

2/26/04 07:35 nd nd nd 17.5 nd nd nd

3/04/04 12:00 nd (0.2) nd 22.7 nd nd nd

3/11/04 12:20 nd nd nd 15.0 nd 3.9 nd

Toe Drain 3/11/04 09:30 nd 10.1 nd 167 nd 20.8 15.4

3/17/04 13:05 nd 4.0 nd 87.5 nd 24.2 8.6

3/23/04 12:15 nd 5.7 nd 56.9 nd 22.1 nd

3/29/04 12:00 41.3 nd nd 57.9 nd 113 nd

4/05/04 09:40 nd (0.9) nd 66.1 nd 55.1 nd

4/12/04 13:05 nd nd nd 70.9 nd 265 nd

4/21/04 13:10 nd nd 32.0 196 367 9.4

Willow Slough 2/19/04 12:50 nd 12.2 nd 2539 nd 28.9 nd

2/26/04 09:50 nd 96.4 nd 1556 nd 49.5 nd

3/04/04 10:19 nd nd nd 369 nd 13.5 nd

3/11/04 10:35 nd nd nd 318 nd 10.7 nd

Yolo Pond 2/19/04 11:45 nd 16.0 nd 89.8 nd nd nd

3/17/04 12:00 nd nd nd 174 nd 7.2 nd

3/23/04 11:30 nd nd nd 314 nd 9.6 nd

3/29/04 11:30 nd nd nd 365 nd 9.9 nd

4/05/04 09:25 nd nd nd 352 nd 9.9 nd

4/12/04 12:30 nd nd nd 403 nd 11.6 nd

4/21/04 12:40 nd nd nd 368 nd 6.3 nd

Table 5 Pesticide concentrations detected in surface water samples collected in 2004 from six source watersheds and two sites 

within the Yolo Bypass, California—Continued.

[Site names are abbreviated; for complete names, see table 2. Pesticide concentrations in nanogram per liter. Samples were analyzed for the following pesticides that were not detected: Alachlor, Atrazine, Butylate, Carbofuran, Chlorpyrifos, Cycloate, DCPA, Ethalfluralin, Malathion, Methyl parathion, Pebulate, 

Phosmet, Piperonyl butoxide, and Prometryn. hh:mm, hours:minutes; mm/dd/yy, month/day/year; nd, not detected; ( ), concentrations less than MDL and are 

estimated values]

12
Site Date

(mm/dd/yy)

Time

(hh:mm) Napropamide Oxyfluorfen Pendimethalin Simazine Thiobencarb Trifluralin

Cache Creek 02/19/04 14:00 nd nd nd 43.3 nd nd

02/26/04 09:10 nd nd nd 24.4 nd 9.8

03/04/04 10:50 nd nd nd 30.5 nd nd

03/11/04 11:00 nd nd nd 20.8 nd nd

Knights Landing Ridge Cut 02/19/04 14:35 38.4 nd 8.0 604 27.3 nd

02/26/04 08:40 nd nd nd 457 30.9 9.1

03/04/04 11:05 nd nd nd 394 32.4 12.4

03/11/04 11:15 nd nd nd 266 25.3 nd

Putah Creek 02/19/04 10:45 nd nd nd 41.9 nd nd

02/26/04 10:15 nd nd nd 84.0 nd nd

03/04/04 09:20 nd nd nd 35.3 nd nd

03/11/04 10:15 nd nd nd 35.1 nd nd

03/17/04 11:10 nd nd nd 39.6 nd nd

03/23/04 10:45 nd nd nd 33.6 nd nd

03/29/04 10:45 nd nd nd 30.3 nd nd

04/05/04 08:50 nd nd nd 28.0 nd nd

04/12/04 12:00 nd nd nd 29.4 nd 11.2

04/21/04 12:10 nd nd nd 26.8 nd 4.1

Sacramento River 02/19/04 15:00 nd nd nd 106 nd nd

02/26/04 08:05 nd nd nd 27.1 nd nd

03/04/04 11:35 nd nd nd 43.0 nd nd

03/11/04 11:45 nd nd nd 15.9 nd nd

Sacramento Slough 02/19/04 15:25 nd 48.6 nd 84.8 24.6 5.4

02/26/04 07:35 nd nd nd nd nd nd

03/04/04 12:00 nd nd nd 49.1 nd nd

03/11/04 12:20 nd nd nd 22.4 nd nd

Toe Drain 03/11/04 09:30 nd nd nd 164 nd 4.1

03/17/04 13:05 nd nd nd 90.1 15.3 9.4

03/23/04 12:15 nd nd nd 51.7 12.1 9.1

03/29/04 12:00 nd nd 9.7 44.2 nd 4.4

04/05/04 09:40 nd nd 21.0 73.8 8.8 nd

04/12/04 13:05 nd nd 8.5 50.7 10.3 6.5

04/21/04 13:10 nd nd nd 45.9 12.8 12.5

Willow Slough 02/19/04 12:50 nd 39.5 nd 85.6 nd 66.4

02/26/04 09:50 78.8 71.1 nd 148 nd 56.8

03/04/04 10:19 nd 15.3 nd 36.3 18.4 12.5

03/11/04 10:35 nd 30.6 nd 23.8 9.3 9.8

Yolo Pond 02/19/04 11:45 nd nd nd nd nd nd

03/17/04 12:00 nd nd nd 61.7 nd nd

03/23/04 11:30 nd nd nd 49.0 nd nd

03/29/04 11:30 nd nd nd 34.0 nd 4.8

04/05/04 09:25 nd nd nd 24.4 nd nd

04/12/04 12:30 nd nd nd 20.0 nd nd

04/21/04 12:40 nd nd nd 26.0 nd nd

Table 5 Pesticide concentrations detected in surface water samples collected in 2004 from six source watersheds and two sites 

within the Yolo Bypass, California—Continued.

[Site names are abbreviated; for complete names, see table 2. Pesticide concentrations in nanogram per liter. Samples were analyzed for the following pesticides that were not detected: Alachlor, Atrazine, Butylate, Carbofuran, Chlorpyrifos, Cycloate, DCPA, Ethalfluralin, Malathion, Methyl parathion, Pebulate, 

Phosmet, Piperonyl butoxide, and Prometryn. hh:mm, hours:minutes; mm/dd/yy, month/day/year; nd, not detected; ( ), concentrations less than MDL and are 

estimated values]

13
The spatial distribution of dissolved pesticides detected in 

and around the Bypass varied by watershed and sampling location. The highest number of pesticides detected—10 out of 

13—were detected at KL Ridge Cut and the Toe Drain between 

February and April of 2004. Cache Creek, Putah Creek, and the 

Sacramento River, on the other hand, had the lowest number of 

pesticides detected and some of the lowest pesticide concentrations.

Seven pesticides were detected in water samples collected 

during the March 2004 transect (table 6 and fig. 2). Hexazinone 

and simazine were detected at all stations across the transect 

and at the highest concentrations. Stations 3, 4, 5, and 6 had 

significantly higher pesticide concentrations compared with the 

other stations. Molinate, thiobencarb, and diazinon were detected only at stations 3–6, whereas concentrations of hexazinone 

and simazine were also elevated compared with the other stations. The pesticide signature at stations 3–6 corresponds to a 

KL Ridge Cut ‘fingerprint’ indicating a definitive pulse of water 

characteristic of KL Ridge Cut that was detected downstream 

within the Bypass.

Table 6 Pesticide concentrations detected in surface water samples from a Yolo Bypass, California, transect 

on March 3, 2004.

[See fig. 2 for site locations. Pesticide concentrations in nanogram per liter. Samples were analyzed for the following pesticides 

that were not detected: Alachlor, Atrazine, Butylate, Carbaryl, Carbofuran, Chlorpyrifos, Cycloate, DCPA, EPTC, Ethalfluralin, 

Malathion, Methidathion, Methyl parathion, Napropamide, Oxyfluorfen, Pebulate, Pendimethalin, Phosmet, Piperonyl butoxide, 

and Prometryn; nd, not detected; ng/L, nanogram per liter]

Site no. Diazinon Hexazinone Metolachlor Molinate Simazine Thiobencarb Trifluralin

1 nd 34.8 nd nd 59.6 nd 4.1

2 nd 42.9 14.5 nd 58.7 nd 5.5

3 43.4 377 32.2 22.0 341 24.2 6.9

4 53.8 413 35.8 24.4 411 26.9 6.9

5 36.6 277 27.6 16.7 251 24.1 5.1

6 33.6 309 25.8 17.6 279 20.6 4.6

7 nd 29.7 8.1 nd 17.5 nd 3.6

8 nd 26.5 8.2 nd 20.9 nd nd

9 nd 26.3 9.0 nd 21.0 nd nd

10 nd 31.7 14.9 nd 30.9 nd 3.8

Bed and Suspended-Sediment Concentrations

Six bed-sediment samples and four suspended-sediment 

samples collected in 2004 and 2005 were analyzed for pesticides, and 13 current-use pesticides and 3 organochlorine insecticides were detected (tables 7 and 8). Thiobencarb, a thiocarbamate insecticide used on rice, was detected most frequently 

in bed and suspended sediments and at some of the highest 

concentrations (1.4 to 24.3 μg/kg dry weight). Another currentuse herbicide, oxyfluorfen, was detected at the highest concentration in Willow Slough suspended sediment (50.1 μg/kg), 

whereas the organochlorine insecticide p,p′-DDE, a degradate 

of DDT, was detected at the highest concentration in the Putah 

Creek bed-sediment sample (147 μg/kg). Bifenthrin, carbaryl, 

DCPA, and napropamide, on the other hand, were detected at 

the lowest concentrations and frequency across all sites. The 

three organochlorine insecticides were detected at low concentrations in all suspended-sediment samples, whereas only p,p′-

DDD was detected at low concentrations in most of the bed 

sediment samples.

14
Table 7 Total organic carbon and pesticide concentrations in bed sediment samples collected September 21, 2004, from the Yolo Bypass, California.

[Site names are abbreviated; for complete names, see table 2. Concentrtations are in μg/kg dry weight. Samples were analyzed for the following pesticides that were not detected: Alachlor, Atrazine, Bifenthrin, Butylate, Carbofuran, Cycloate, Cyfluthrin, Cypermethrin, Diazinon, Deltamethrin, EPTC, Esfenvalerate, Ethalfluralin, Fenpropathrin, Hexazinone, Lambda-cyhalothrin, Malathion, Methidathion, Methyl parathion, Pebulate, Pendimethalin, Permethrin, Phenothrin, Phosmet, Piperonyl butoxide, Prometryn, Resmethrin, Simazine, Tau-fluvalinate; nd, not detected; ( ), concentrations less than MDL and are estimated values.

Site Organic carbon (%) Carbaryl Chlorpyrifos- DCPA Metolachlor Molinate Napropamide- Oxyflurofen Thiobencarb- Trifluralin p,p′-DDD p,p′-DDE p,p′-DDT

Cache Creek 1.5 nd nd nd nd nd nd nd (1.4) nd nd nd nd

Putah Creek 0.9 7.7 nd 2.6 (0.4) nd 2.7 15.8 nd 24 15.8 147 41.1Knights Landing 

Ridge Cut

1.3 nd nd nd (1.2) 1.1 nd nd 2.5 (0.1) (0.5) nd nd

Toe Drain 0.8 nd nd nd nd 0.8 nd nd 5.6 (0.2) (0.6) nd ndWoodland 0.6 nd 3.9 nd nd nd nd nd 8.8 (0.3) 1.5 nd ndWillow Slough 1.8 nd 2.4 nd nd nd nd nd 3.1 nd 2.2 3 nd

15
Table 8 Total organic carbon and pesticide concentrations detected in water and suspended sediments collected from the Yolo Bypass, California, in 2004 and 2005.

[ng/L, nanogram per liter (for concentrations detected in water); μg/kg, microgram per kilogram (for suspended sediments)] 

Site Date (mm/dd/yy) Time (hh:mm) Sample type Organic carbon (%) Bifenthrin Chlorpyrifos Diazinon Hexazinone Methidathion Metolachlor Molinate Oxyfluorfen

Knights Landing Ridge Cut 2/20/04 15:30 Water na nd nd 160 987 30.3 32.2 24.2 56.6

1/3/05 11:00 Water na nd nd nd 300 nd 21.9 8.12 14.7

Putah Creek 2/20/04 13:20 Water na nd nd nd 14.4 nd nd nd ndWillow Slough 1/3/05 13:00 Water na nd nd nd 9210 nd 74.9 nd 27.1Knights Landing Ridge Cut 2/20/04 15:30 Suspended sediment 1.2 nd nd nd nd nd (0.4) 2.4 16.3

1/3/05 11:00 Suspended sediment 1.3 nd (0.5) nd nd nd (1.29) 4.5 26.4

Putah Creek 2/20/04 13:20 Suspended sediment 1.5 nd nd nd nd nd nd nd ndWillow Slough 1/3/05 13:00 Suspended sediment 2.1 (1.7) 1.3 nd 9.4 nd 3.9 nd 50.1

16
Site Date (mm/dd/yy) Time (hh:mm) Sample type Organic carbon (%) Pendimethalin Simazine Tau-fluvalinate Thiobencarb Trifluralin p,p′-DDD p,p′-DDE p,p′-DDT

Knights Landing Ridge Cut 2/20/04 15:30 Water na 11.1 511 nd 26.9 9.6 nd nd nd

1/03/05 11:00 Water na 9.5 189 nd nd nd nd nd nd

Putah Crk 2/20/04 13:20 Water na nd 45.6 nd nd nd nd nd ndWillow Slough 1/03/05 13:00 Water na 3.8 128 nd nd 17.4 nd nd ndKnights Landing Ridge Cut 2/20/04 15:30 Suspended sediment 1.2 2.7 nd 1.4 11.7 (0.9) (0.9) 2.8 nd

1/03/05 11:00 Suspended sediment 1.3 8.3 nd 11.1 24.3 2.4 2.4 2.8 1.9

Putah Creek 2/20/04 13:20 Suspended sediment 1.5 1.7 nd nd nd 1.5 (1.1) 4.3 (1.3)Willow Slough 1/03/05 13:00 Suspended sediment 2.1 2.8 nd 2.7 1.7 5 1.5 4 ndTable 8 Total organic carbon and pesticide concentrations detected in water and suspended sediments collected from the Yolo Bypass, California, in 2004 and 2005—Continued..[ng/L, nanogram per liter (for concentrations detected in water); μg/kg, microgram per kilogram (for suspended sediments)] 

17
Suspended sediments had a greater number of detections 

and higher pesticide concentrations compared with the corresponding bed sediment samples, with the exception of Putah 

Creek. Tau-fluvalinate, a pyrethroid insecticide, was detected in 

the suspended sediments collected from KL Ridge Cut in 2004 

and 2005 and from Willow Slough in 2005. With the exception of p,p′-DDE, pesticide concentrations from 2005 KL Ridge 

Cut suspended-sediment samples were higher than those from 

2004. The only pesticide not detected in 2004 that showed up at 

very low concentrations in 2005 (< 2 μg/kg) was p,p′-DDT.

When the large volume water samples were processed for 

suspended sediments in 2004 and 2005, the centrifuge effluent was also analyzed for dissolved pesticides. Hexazinone and 

simazine were detected at the highest concentrations in these 

water samples similar to the surface water samples collected at 

each site (table 8). The more hydrophobic compounds, such as 

the pyrethroids and the organochlorine insecticides, were detected only in suspended sediments, whereas the more water 

soluble compounds, such as simazine, were detected only in the 

water. Seven of the sixteen compounds detected were found in 

both the water and the suspended sediments.

Suspended-Sediment Concentrations and 

Water-Quality Parameters

Suspended-sediment concentrations were determined for 

the 44 out of the 46 water samples collected during this study 

(table 9). Suspended-sediment concentrations varied between 

sites and over time. The trend observed in suspended-sediment 

concentrations for the six inputs to the Bypass was greater for 

Cache Creek than for Willow Slough followed by KL Ridge 

Cut, Sacramento River, Putah Creek, and Sacramento Slough. 

The highest concentrations of suspended sediments were observed on either February 19 or February 26, 2004. Suspendedsediment concentrations at the inputs to the Bypass generally 

increased during the first flood of water and then slowly decreased over time. Toe Drain and the Yolo Pond, the two lowflow sampling sites within the Bypass, had the highest concentrations on March 29, 2004, and April 21, 2004, respectively. 

Yolo Pond generally had the lowest suspended-sediment concentrations, ranging from 5 to 93 mg/L.

Water temperature, conductivity, and pH also were measured for the 46 water samples collected, and these values are 

presented in table 9. The pH was similar between sites and over 

time, whereas the conductivity varied by location and sampling 

time. The average temperature at each site increased steadily 

over the 2-month sampling period.

Sediment Organic Carbon

Sediment organic carbon was measured in both bed and 

suspended-sediment samples in 2004 and 2005 (tables 7 and 8). 

The amount of organic carbon ranged from 0.6 to 2.1 percent 

and was generally higher in the suspended sediments compared 

with the bed sediments.

Conclusions

This project was designed to assess the potential exposure of native fish in the Bypass to pesticides during high and 

low-flow events. One step was to modify the existing sediment 

analytical method to achieve lower method detection limits and 

increased recoveries while adding more analytes. The modifications to the sediment method discussed in the report decreased 

matrix interferences in both bed and suspended sediments, and 

for some compounds, especially the pyrethroids, decreased the 

method detection limits. Tau-fluvalinate, a pyrethroid insecticide, was one of the six new compounds added and was detected at very low concentrations in suspended sediments from 

KL Ridge Cut and Willow Slough.

Representative samples were analyzed from the possible 

sources of pesticide contamination to the Bypass which includes surface water and suspended sediments from the source 

watersheds, as well as resuspension of pesticides bound to bed 

sediments within the Bypass. Hexazinone and simazine were 

detected most frequently in the surface water from all sites, 

whereas thiobencarb and oxyfluorfen were detected at some of 

the highest concentrations in bed and suspended sediments from 

most sites. The highest number of pesticides was detected in the 

suspended sediments compared with bed sediments and surface 

water. With the exception of a few compounds, the same pesticides were detected in the sediment and the water, and correlate 

with the agricultural use in each of the different watersheds. To 

successfully optimize the Yolo Bypass as a fisheries habitat, it 

is important to understand the fate and transport of pesticides to 

the Bypass under high and low-flow events.

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Sampling

site

Date

(mm/dd/yy)

Time

(hh:mm)

Suspended 

sediment 

concentration

(mg/L)

pH

Specific 

conductance

(μS/cm)

Water

temperature

(°C)

Cache Creek 2/19/04 14:00 1026 7.56 302 12.7

2/26/04 19:10 1683 7.63 227 10.4

3/4/04 10:50 613 7.92 365 10.2

3/11/04 11:00 1167 8.37 257 14.7

Knights Landing Ridge Cut 2/19/04 14:35 420 7.34 284 14.0

2/26/04 08:40 524 7.49 400 11.6

3/04/04 11:05 210 7.96 370 10.9

3/11/04 11:15 171 8.14 540 17.1

1/30/05 11:00 na 7.07 302 na

Sacramento River 2/19/04 15:00 435 6.97 101 12.0

2/26/04 08:05 123 7.31 134 10.3

3/04/04 11:35 195 8.02 132 9.8

3/11/04 11:45 182 8.44 151 13.1

Sacramento Slough 2/19/04 15:25 174 7.05 460 13.3

2/26/04 07:35 81 7.28 132 10.4

3/04/04 12:00 71 7.89 135 11.6

3/11/04 12:20 19 8.16 149 15.4

Willow Slough 2/19/04 12:50 318 7.31 280 12.7

2/26/04 09:50 920 7.38 146 10.6

3/04/04 10:19 206 8.05 580 10.5

3/11/04 10:35 196 8.67 896 16.0

1/03/05 01:00 na 7.01 162 na

 Putah Creek 2/19/04 10:45 250 7.37 314 10.7

2/26/04 10:15 258 7.65 302 11.0

3/04/04 09:20 32 8.28 335 10.6

3/11/04 10:15 34 8.60 343 13.5

3/17/04 11:10 21 8.58 338 15.7

3/23/04 10:45 21 8.04 342 15.0

3/29/04 10:45 28 7.65 340 13.8

4/05/04 08:50 36 6.97 395 13.6

4/12/04 12:00 24 7.95 530 18.8

4/21/04 12:10 231 7.95 530 16.5

Toe Drain 3/11/04 09:30 84 8.29 411 16.0

3/17/04 13:05 76 8.40 605 na

3/23/04 12:15 50 7.89 623 18.5

3/29/04 12:00 477 7.98 712 18.0

4/05/04 09:40 86 8.12 818 16.0

4/12/04 13:05 100 7.98 732 20.2

4/21/04 13:10 149 7.90 559 16.4

Yolo Pond 2/19/04 11:45 5 7.56 561 14.4

3/17/04 12:00 23 8.55 558 22.3

3/23/04 11:30 59 7.93 737 17.7

3/29/04 11:30 55 7.92 748 22.5

4/05/04 09:25 52 8.91 918 12.2

4/12/04 12:30 67 8.31 980 20.1

4/21/04 12:40 93 8.41 1075 19.5

Table 9. Suspended sediment, concentratons, and water-qualituy parameters for samples from the Yolo Bypass, California.

[Woodland R1 site not sampled for these constituents. hh:mm, hours:minutes; mm/dd/yy, month/day/year; mg/L, milligram per liter; μS/com, microsiemends per centimeter; na, not analyzed]

19
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