Microbial and Dissolved Organic Carbon 

Characterization of Stormflow in the 

Santa Ana River at Imperial Highway, 

Southern California, 1999–2002

By John A. Izbicki, M. Isabel Pimentel, Menu Leddy1, and Brian Bergamaschi

In cooperation with the

Orange County Water District

1

Orange County Water District

Scientific Investigations Report 2004-5116

U.S. Department of the Interior

U.S. Geological Survey
U.S. Geological Survey, Reston, Virginia: 2004

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

Box 25286, Denver Federal Center

Denver, CO 80225-0286

U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

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:

Izbicki, J.A., Pimentel, M.I., Leddy, M., and Bergamaschi, B., 2004, Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River at Imperial Highway, Southern California, 1999–2002: U.S. Geological Survey Scientific Investigations Report 2004–5116, 71 p.
iii

Contents

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

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

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

Previous Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Description of the Santa Ana River Basin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

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

Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Sampled Stormflows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Analytical Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Total Coliforms and Fecal Indicator Bacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Historical Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Total Coliforms and Fecal Indicator Bacteria Concentrations during Stormflow. . . . . . . . . 13

Phospholipid Fatty Acids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Phospholipid Fatty Acid Concentrations and Compositions during Stormflow. . . . . . . . . . . 20

Comparison with Phospholipid Fatty Acids from Other Sources. . . . . . . . . . . . . . . . . . . . . . . 23

16S rRNA Gene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Amplicon Size and Diversity during Stormflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Comparison with Amplicons from Other Sources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Dissolved Organic Carbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Dissolved Organic Carbon Concentrations during Stormflow . . . . . . . . . . . . . . . . . . . . . . . . . 31

Dissolved Organic Carbon Compositions during Stormflow . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Ultraviolet Absorbance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Excitation/Emission Spectroscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Dissolved Organic Carbon Fractionation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Total Coliform Bacteria, Fecal Coliform Bacteria, and Dissolved Organic Carbon

Concentrations in Shallow Ground Water during Stormflow . . . . . . . . . . . . . . . . . . . . . . . 41

Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

References Cited . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Appendixes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
iv

Figures

Figure 1. Map showing Santa Ana River Basin, southern California, and location of 

selected stream gages and sample-collection sites . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Figure 2. Map showing land use in the Santa Ana River Basin, southern California, 1990. . . . . . 5

Figure 3. Graphs showing sampled stormflows, precipitation, and stream discharge

for the Santa Ana River at Imperial Highway, southern California,

during the 1999–2000, 2000–01, and 2001–02 rainy seasons.. . . . . . . . . . . . . . . . . . . . 7

Figure 4. Graph showing monthly median total and fecal coliform bacteria 

concentrations in the Santa Ana River at Imperial Highway, 

southern California, January 1986 to March 1994. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Figure 5. Graphs showing total coliform and fecal indicator bacteria 

(Escherichia coli and enterococci) concentrations in the Santa Ana River 

at Imperial Highway, southern California, during the first stormflow 

of the 1999–2000, 2000–01, and 2001–02 rainy seasons.. . . . . . . . . . . . . . . . . . . . . . . . 14

Figure 6. Graphs showing total coliform and fecal indicator bacteria 

(Escherichia coli and enterococci) concentrations in Mill Creek 

at Chino-Corona Road, and in the Santa Ana River at Imperial Highway, 

southern California, November 12, 2001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Figure 7. Graphs showing total coliforms, fecal coliforms, Escherichia coli, 

and enterococci concentrations as a function of suspended-sediment 

concentration in stormflow in the Santa Ana River at Imperial 

Highway, southern California, 2000–01 and 2001–02 rainy seasons. . . . . . . . . . . . . . 17

Figure 8. Graph showing suspended-sediment concentrations as a function

of streamflow during stormflow conditions in the Santa Ana River 

at Imperial Highway, southern California, 2000–01 and 2001–02

rainy seasons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Figure 9. Graphs showing phospholipid fatty acid concentrations as a function

of streamflow, and of total coliform bacteria, and Escherichia

coli concentrations in stormflow in the Santa Ana River at 

Imperial Highway, 1999–2000 and 2001–02 rainy seasons. . . . . . . . . . . . . . . . . . . . . . 21

Figure 10. Graphs showing selected phospholipid fatty acid (PLFA) structural groups

as a function of total phospholipid fatty acid concentration in stormflow

in the Santa Ana River, 1999–2000 and 2001–02 rainy seasons. . . . . . . . . . . . . . . . . . 22

Figure 11. Graphs showing total coliform bacteria and total phospholipid fatty 

acid (PLFA) concentrations as a function of streamflow, and 

changes in diversity of PLFA and the 16S rRNA gene during 

the November 12–14, 2001, stormflow, Santa Ana River (SAR) 

at Imperial Highway, southern California . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Figure 12. Graph showing the first principal component as a function of the 

second principal component for the 10 most common phospholipid

fatty acids in stormflow in the Santa Ana River at Imperial Highway, 

southern California, 1999–2000 and 2001–02 rainy seasons.. . . . . . . . . . . . . . . . . . . . 26

Figure 13 .Graphs showing amplicons from Terminal-Restriction Fragment 

Length Polymorphism analysis of the 16S rRNA gene with 

polymerase chain reaction amplification using universal eubacterial 

primers and PCR amplification using eubacterial primers and digestion

with DdeI restriction endonuclease for selected stormflow samples

from the Santa Ana River at Imperial Highway, southern California, 

November 12–14, 2001. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
v

Figure 14. Graphs showing amplicons from Terminal-Restriction Fragment Length 

Polymorphism analysis of the 16S rRNA gene with polymerase chain 

reaction amplification using universal eubacterial primers and PCR 

amplification using eubacterial primers and digestion with DdeI

restriction endonuclease for selected samples from the Santa Ana 

River Basin, southern California. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Figure 15. Graphs showing changes in dissolved organic carbon concentration and

ultraviolet absorbance at 254 nanometers during the first stormflows

of the 1999–2000, 2000–01, and 2001–02 rainy seasons, Santa Ana 

River at Imperial Highway, southern California. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Figure 16. Graphs showing selected full-spectrum ultraviolet absorbance 

scans, Santa Ana River at Imperial Highway, 1999–2000, 2000–01,

and 2001–02 rainy seasons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Figure 17. Graphs showing dissolved organic carbon as a function of UV254, and UV285 

as a function of UV254, in stormflow in the Santa Ana River at 

Imperial Highway, southern California, 1999–2000, 2000–01, 

and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
vi

Tables

Table 1. Summary of stormflow sample collection in the Santa Ana River at Imperial 

Highway, southern California, 1999–2000, 2000–01, 2001–02 rainy seasons. . . . . . . 8

Table 2. Summary of historical bacteria concentrations and bacteria concentrations 

measured during pre-stormflow and stormflow conditions in the 

Santa Ana River at Imperial Highway, southern California . . . . . . . . . . . . . . . . . . . . . 11

Table 3. Description of selected phospholipid fatty acid structural groups . . . . . . . . . . . . . . . . . . 19

Table 4. Eigenvectors composing the first and second principal components of 

phospholipid fatty acid structural groups and the 10 most common 

fatty acids in stormflow in the Santa Ana River atImperial Highway, 

1999–2000, and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Table 5. Total phospholipid fatty acid concentrations and percent of total PLFA 

for the 10 most commonly detected fatty acids in selected samples

from the Santa Ana River basin, southern California . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Table 6. Equations describing the relation between dissolved organic carbon 

and ultraviolet absorbance in early-season and late-season stormflows

in the Santa Ana River, California . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Table 7. Dissolved organic carbon concentrations and hydrophobic-acid, 

hydrophobic-neutral, hydrophilic-acid, and transhydrophilic-acid 

fractions of dissolved organic carbon in stormflow samples collected 

from the Santa Ana River at Imperial Highway and from Mill Creek

at Chino-Corona Road, southern California, 2001–02 rainy season . . . . . . . . . . . . . . 42

Appendixes

Appendix A.Total coliforms, fecal coliforms, Escherichia coli, enterococci, 

and suspended-sediment concentrations for stormflow in the 

Santa Ana River at Imperial Highway, in Mill Creek, and in 

shallow ground water from the Santa Ana River Basin, 

southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons. . . . . . . . . . . . 50

Appendix B1. Total phospholipid fatty acid concentrations and 

selected fatty acid structural groups in stormflow in the 

Santa Ana River at Imperial Highway, southern California, 

1999–2000 and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Appendix B2. Normal saturated phospholipid fatty acids in stormflow

in the Santa Ana River at Imperial Highway, southern California, 

1999–2000 and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Appendix B3. Mid-chain branched saturated phospholipid fatty acids 

in stormflow in the Santa Ana River at Imperial Highway, 

southern California, 1999–2000 and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . 55
vii

Appendix B4. Terminally branched saturated phospholipid fatty acids)

in stormflow in the Santa Ana River at Imperial Highway, 

southern California, 1999–2000 and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . 57

Appendix B5. Monoenoic phospholipid fatty acids in stormflow in 

the Santa Ana River at Imperial Highway, southern California, 

1999–2000 and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Appendix B6. Branched monoenoic phospholipid fatty acids in 

stormflow in the Santa Ana River at Imperial Highway, 

southern California, 1999–2000 and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . 60

Appendix B7. Polyenoic phospholipid fatty acids in stormflow 

in the Santa Ana River at Imperial Highway, southern California,

1999–2000 and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Appendix C. Dissolved organic carbon and ultraviolet absorption

data for stormflow in the Santa Ana River at the diversion 

downstream from Imperial Highway and at the subsurface

collection and recharge system, southern California, 

1999–2000, 2000–01, and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Appendix D. Data for field parameters, major ions, and nutrients in the 

Santa Ana River at the diversion downstream from Imperial 

Highway, southern California, 1999–2000, 2000–01,

and 2001–02 rainy seasons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
viii

Conversion Factors, Datum, and Abbreviations

CONVERSION FACTORS

Temperature in degrees Celsius (οC) may be converted to degrees Fahrenheit (οF) as follows:

oF=1.8 oC+32.

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

25οC).

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

micrograms per liter (μg/L). 

DATUM

Sea level: In this report, “sea level” refers to the National Geodetic Vertical Datum of 1929 

(NGVD of 1929)—a geodetic datum derived from a general adjustment of the first-order level nets 

of both the United States and Canada, formerly called Sea Level Datum of 1929.

ABBREVIATIONS

ABI Applied Biosystems

bp base pairs

CaCO3 calcium carbonate

CFU/100mL colony forming units per 100 milliliters

CH4 methane

CM-1 absorbance per centimeter length

CO2 carbon dioxide

DDMMSS degrees, minutes, seconds

DBP disinfection by product

DNA deoxyribonucleic acid

DOC dissolved organic carbon

EEM excitation/emission spectroscopy

GIS geographic information system

HAA haloacetic acids

HCL hydrochloric acid

Multiply By To obtain

acre-foot (acre-ft) 1,233 cubic meter

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

foot (ft) 0.3048 meter

inch (in.) 2.54 centimeter

inch (in.) 25.4 millimeter

mile (mi) 1.609 kilometer

square mile (mi2) 12.590 square kilometer
ix

μL microliter

μM micromole

μS/cm microsiemen per centimeter at 25οC

mL milliliters

MPN most probable number

MTBE methyl-tert-butyl ether

MTF multi-tube fermentation

2N normality of two

N2 nitrogen gas

Na2HPO4 sodium phosphate

NaOH sodium hydroxide

ng nanogram

nm nanometer

NPOC nonpurgeable organic carbon

OCWD Orange County Water District

PCR polymerase chain reaction

PLFA phospholipid fatty acid

pmole/g picomole per gram

pmole/L picomole per liter

PO4 phoshate

rpm revolutions per minute

SAR Santa Ana River

SARWQH Santa Ana River Water Quality and Health (study)

SCARS subsurface collection and recharge system

16S rRNA a bacterial ribosomal ribonucleic acid

SO4 sulfate

SUVA specific ultraviolet absorbance

THM trihalomethane

T-RFLP Terminal-Restriction Fragment Length Polymorphism

UVA ultraviolet absorption

UV254 ultraviolet absorption at 254 nanometers

UV285 ultraviolet absorption at 285 nanometers

QSU quinine sulfate unit

Organizations

OCWD Orange County Water District

SCAG Southern California Association of Governments

USGS U.S. Geological Survey
Microbial and Dissolved Organic Carbon Characterization 

of Stormflow in the Santa Ana River at Imperial Highway, 

Southern California, 1999–2002

By John A. Izbicki, M. Isabel Pimentel, Menu Leddy, and Brian Bergamaschi

Abstract

The Santa Ana River drains about 2,670 square miles of 

densely populated coastal southern California, near Los 

Angeles. Almost all the flow in the river, more than 

200,000 acre-feet annually, is diverted to ponds where it 

infiltrates and recharges underlying aquifers pumped to supply 

water for more than 2 million people. Base flow in the river is 

almost entirely treated municipal wastewater discharged from 

upstream treatment plants and, in the past, stormflow was 

considered a source of high-quality water suitable for use as a 

source of ground-water recharge that would dilute poorer 

quality water recharged during base flow.

Stormflow in the Santa Ana River at the Imperial 

Highway diversion contains total coliform bacteria 

concentrations as high as 3,400,000 colonies per 100 mL 

(milliliters). Fecal indicator bacteria concentrations, including 

fecal coliforms, Escherichia coli, and enterococci, were as high 

as 310,000, 84,000, and 102,000 colonies per 100 mL, 

respectively. Although concentrations were high owing to 

urban runoff during the first stormflow of the rainy season, the 

highest concentrations occurred during the recessional flows of 

the first stormflow of the rainy season after streamflow 

returned to pre-storm conditions. Molecular indicators of 

microbiological organisms in stormflow, including 

phospholipid fatty acid (PLFA) and genetic data, show that the 

diversity of the total microbial population decreases during 

stormflow while fecal indicator bacteria concentrations 

increase. This suggests that the source of the bacteria must be 

poorly diverse and dominated by only a few types of bacteria. 

Although direct runoff of fecal indicator bacteria from urban 

areas occurs, this process cannot explain the very high 

concentrations of fecal indicator bacteria in runoff from 

upstream parts of the basin characterized by urban, agricultural 

(including more than 300,000 head of dairy cattle), and other 

land uses. Although other explanations are possible, fecal 

indicator bacteria concentrations and molecular 

microbiological data indicate accumulation and extended 

survival of bacteria in streambed sediments, and subsequent 

mobilization of those sediments and associated bacteria during 

stormflow. Both PLFA and genetic data indicate that water 

from dairy-waste storage ponds was not present during 

sampled stormflows. This is consistent with the relatively dry 

conditions and the absence of large stormflows during the 

study.

Dissolved organic carbon (DOC) concentrations in 

stormflow ranged from 3 to 15.3 mg/L. In general, 

concentrations increased during stormflow and were 

distributed across the stormflow hydrograph in a manner 

similar to that of fecal indicator bacteria. DOC concentrations 

typically remained high for several days after flow returned to 

pre-storm conditions. Ultraviolet absorbance, excitation 

emission spectroscopy, and sequential fractionation of DOC 

using XAD-8 and XAD-4 resins showed that the composition 

of DOC changed rapidly during stormflow. Hydrophobic and 

hydrophilic acids were the largest fraction of DOC composing 

between 27 and 45 percent and between 24 and 37 percent of 

the DOC, respectively.

The fraction of DOC composed of hydrophobic acids 

decreased due to urban runoff and increased during the 

recession of the first stormflow of the rainy season; the 

hydrophilic-acid fraction generally decreased throughout the 

stormflow hydrograph; the transhydrophilic-acid fraction did 

not vary greatly during stormflow; and the hydrophobic-neutral 

fraction increased from low values in base flow to almost

30 percent of the DOC after more soluble and more mobile 

hydrophobic and hydrophilic acids were washed from urban 

areas. Comparison of ultraviolet absorbance data with data 

collected during previous studies shows that the optical 

properties and, presumably, the composition of the DOC were 

different in this study than DOC collected during wetter 

periods.

Samples of shallow ground water collected during 

stormflow from beneath recharge facilities along the Santa Ana 

River show that most fecal indicator bacteria and DOC were 

removed as water infiltrated into the streambed.
2 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Introduction

The Santa Ana River drains about 2,670 square miles 

(mi2) of the densely populated coastal area of southern 

California south of Los Angeles (fig. 1). Base flow in the river 

is maintained largely by the discharge of treated municipal 

wastewater from upstream wastewater-treatment plants 

(Burton and others, 1998). Almost all the flow in the Santa Ana 

River, more than 200,000 acre-feet (acre-ft) of water annually, 

is diverted to ponds where it infiltrates and recharges aquifers 

underlying Orange County. Pumpage from these aquifers is the 

primary source of water supply for about 2 million people. 

Although wastewater discharged to the river is highly treated, 

there may be public health issues associated with the long-term 

use of water from the Santa Ana River for ground-water 

recharge to aquifers pumped for public supply.

Stormflow has long been considered a source of highquality water, suitable for dilution of water recharged from the 

river during base flow. Recent work (Izbicki and others, 2000) 

has shown that stormflow in the Santa Ana River may contain 

increased concentrations of pesticides, trace elements, and 

other contaminants–although these contaminants do not 

typically exceed respective public health goals. Stormflow in 

the Santa Ana River also may include runoff from urban and 

agricultural areas that may contain high concentrations of 

microbiological organisms that can degrade water quality.

Purpose and Scope

The purpose of this study was to measure changes in the 

concentration of total coliforms and fecal indicator bacteria in 

the Santa Ana River during stormflow. Measured changes 

were related to changes in selected molecular indicators of 

microbiological organisms, such as phospholipid fatty acid 

(PLFA) and the profile obtained from analysis of 

deoxyribonucleic acid (DNA), to determine if sources having 

greatly different microbial populations were contributing to 

stormflow during different parts of the hydrograph. In 

addition, changes in the concentration and composition of 

dissolved organic carbon (DOC) were measured due to (1) the 

possible association of organic carbon with fecal material, 

(2) health concerns associated with carbon of wastewater 

origin in water used to recharge aquifers pumped for public 

supply, and (3) concerns about the reactivity of the DOC and 

potential for disinfection by-product formation when 

recharged water is extracted and chlorinated for public supply.

This study was done by the U. S. Geological Survey 

(USGS) in cooperation with the Orange County Water District 

(OCWD) as part of the Santa Ana River Water Quality and 

Health (SARWQH) study. The purpose of the SARWQH 

study was to evaluate the use of the Santa Ana River as the 

primary source of recharge for aquifers underlying Orange 

County, California. 

Previous Studies

Contamination of surface water and ground water by fecal 

bacteria is a public health concern due to the potential for 

transmission of disease through contact or ingestion. Urban 

areas are especially sensitive to microbial contamination 

because, during stormflow, water and fecal material may run 

directly into streams from city streets and sewers without 

retention and filtration by soils. Concern over microbial 

contamination of surface water is especially high in southern 

California where runoff from large urban areas drains directly 

to the ocean (Schiff and Stevenson, 1996, Nobel and others, 

2000, Leecaster and Weisberg, 2001; Schiff and Kinney, 2001, 

Schiff and others, 2001). Recent closure of recreational 

beaches due to bacterial contamination has resulted in 

economic losses and concern about the quality of runoff from 

urban areas.

The chemical and microbiological quality of surface 

water in southern California may be of greater concern in areas 

where surface water is used directly for public supply or to 

recharge aquifers pumped for public supply. These issues have 

been addressed as part of the Santa Ana River Water Quality 

and Health study (SARWQH study) by Orange County Water 

District. Historical changes in water quality in the Santa Ana 

River were studied by Burton and others (1998). The chemical 

quality of stormflow, with respect to pesticides, selected trace 

elements, and dissolved organic carbon, was studied by Izbicki 

and others (2000). Although microbial data have been 

collected from the Santa Ana River by the Orange County 

Health Department from 1986 to 1994 (Orange County Health 

Department, written commun., 1999), the rapid, short-term 

changes in microbial quality resulting from stormflow runoff 

in the Santa Ana River previously have not been studied.

To address potential public health effects, the chemical 

and microbiological quality of water recharged from the Santa 

Ana River to aquifers underlying Orange County that are used 

for public supply also has been studied as part of the 

SARWQH study. Similar studies have been done in parts of 

Los Angeles County (Leenheer and others, 2001; Schroeder 

and Anders, 2002) and other areas where treated wastewater is 

used to recharge aquifers pumped for public supply.
Introduction 3

Pacific Ocean

Big Bear

Lake

Lake

Elsinore

San Jacinto River

River

Cucamonga Creek

Chino Cr

San Antonio Wash

15

5

10

215

405

605

91

Orange

County

Los Angeles

County

Riverside

County

San Bernardino

County

1,2

SCARS 4,5 3 7

8 6

Los Angeles

San Diego

San

Francisco

Santa Ana

Basin

California

Pacific Ocean

Base from U.S. Geological Survey

digital elevation data, 1999

Albers Equal-Area Conic Projection

0 10 20 MILES

0 10 20 KILOMETERS

Basin boundary

County line

Prado

Dam

Santa

Ana

SAN GABRIEL MTS

SAN BERNARDINO MTS

SAN JACINTO MTS

SANTA ANA MTS

CHINO HILLS

Santa Ana River

drainage basin

San

Bernardino

Riverside

EXPLANATION

Stream gage

Sample-collection site—

Number corresponds to sample location in text

1

2

3

4

5

6

7

8

SCARS

Santa Ana River at the diversion downstream

from Imperial Highway (11075620)

Stormdrain tributary to Santa Ana River at Imperial Highway

and Santa Ana River at Imperial Highway (11075600)

Santa Ana River streambed upstream from Imperial Highway

Santa Ana River upstream from Prado Dam

Prado wetland soil

Dairy waste pond near Pine Avenue

Mill Creek at Chino-Corona Road

Cucamonga Creek near Mira Loma

Subsurface collection and recharge system

Figure 1. Santa Ana River Basin, southern California, and location of selected stream gages and sample-collection sites.
4 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Public health issues related to the use of water from the 

Santa Ana River to recharge aquifers pumped for public supply 

are complex. Part of the SARWQH study focused on travel 

time from recharge to wells (Davisson and others, 1996, 

Gamlin and others, 2001; Herndon and others, 2003) and the 

percentage of wastewater in water extracted by the wells. 

Other parts of the SARWQH study focused on the 

concentration and composition of carbon of wastewater origin 

(Reinhard and others, 1996; Ding and others, 1999) in water 

extracted by public supply wells. The concentration and 

composition of DOC in water used to recharge aquifers are of 

additional concern in the Santa Ana River Basin and in other 

areas because of the potential for DOC to form disinfection byproducts, such as trihalomethanes (THMs) or haloacetic acids 

(HAA), during chlorination (Reckhow and others, 1990; 

California Department of Water Resources, 1994, Krazner and 

others, 1996; Fujii and others, 1998; Rostad, 2002, Rostad and 

others, 2000).

In addition to the SARWQH study, the Santa Ana River 

is one of the USGS National Water-Quality Assessment 

(NAWQA) study units, and ground-water and surface-water 

quality within the basin are studied as part of that ongoing 

program (Belitz, 1999).

Description of the Santa Ana River Basin

Streams of the Santa Ana River drainage basin, which are 

part of the Santa Ana River hydrologic unit, discharge to the 

west into the Pacific Ocean. The Santa Ana River hydrologic 

unit is approximately 2,670 mi2 and encompasses parts of San 

Bernardino, Riverside, Los Angeles, and Orange Counties

(fig. 1). The study area topography ranges from steep, rugged 

mountains with peaks as high as 11,500 ft above sea level, to 

broad alluvial valleys and a coastal plain. Warm, dry summers 

and cool, moist winters characterize the climate of the study 

area, and average annual precipitation ranges from about 

12 inches (in.) near the coast to about 18 in. in the inland 

valleys. Annual precipitation totals can exceed 40 in. in some 

of the higher mountains. Most precipitation occurs during the 

“winter” rainy season between November and March.

The Santa Ana River Basin has undergone major 

development in recent years, and has experienced a rapid 

increase in population. In 1990, the population was greater 

than 4.5 million (Santa Ana Regional Water Quality Control 

Board, 1995). Land use in the area ranges from dense urban 

development in the coastal plain and inland valleys to 

undeveloped wilderness in the high mountains (fig. 2). In 

1995, approximately 340 animal-confinement facilities having 

over 340,000 animals, mostly dairy cows, operated within the 

Santa Ana River Basin (Santa Ana Regional Water Quality 

Control Board, 1995). Most of these are in the area just north 

of Prado Dam that is drained by Chino and Cucamonga creeks 

(fig. 1).

The Santa Ana River Basin can be divided into an upper 

and a lower basin at Prado Dam (fig. 1). Prado Dam is operated 

according to a complex set of procedures intended to minimize 

flood damage in the lower part of the basin and to maximize 

the availability of surface water for ground-water recharge 

(U.S. Army Corps of Engineers, 1994). To minimize adverse 

effects on endangered species in the riparian habitat upstream 

from Prado Dam, water is not stored behind the dam during 

much of the dry season (U.S. Army Corps of Engineers, 1994). 

Storage of water behind Prado Dam during the wet season 

typically includes temporary flooding of the riparian habitat 

upstream from the dam after stormflows until water can be 

released downstream for ground-water recharge. In wet years, 

the upstream area may be flooded throughout most of the rainy 

season and into the dry season as late as June. In dry years, 

water may be stored only briefly behind the dam after 

stormflow. When water is stored behind the dam, releases may 

be increased prior to large stormflows to increase available 

storage for flood control. Releases are frequently decreased 

while runoff is occurring downstream from the dam to 

minimize damage to urban areas from flooding and to 

maximize storage of stormflow for subsequent release for 

ground-water recharge.

Local water is extensively managed for public supply, 

and additional water is imported into the study area from 

northern California and the Colorado River. Most of the water 

used for public supply upstream from Prado Dam is discharged 

to the Santa Ana River, its tributaries, or adjacent shallow 

ground water as treated municipal wastewater. Nearly half of 

the base flow of the Santa Ana River is treated to remove 

nitrate by a series of artificial wetlands upstream from Prado 

Dam, and nearly all of the flow (including stormflow) in the 

river, more than 200,000 acre-ft annually, is diverted near 

Imperial Highway by the Orange County Water District to 

recharge underlying aquifers. Only water from larger 

stormflows that exceed the capacity of the diversion facility is 

not diverted for recharge.

Acknowledgments

This study, by the U.S. Geological Survey, was funded by 

the Orange County Water District, Fountain Valley, Calif., as 

part of their Santa Ana River Water Quality and Health study 

(SARWQH). The authors thank the U.S. Army Corps of 

Engineers for precipitation and stage data for Prado Dam; John 

Vandenbergh of the Orange County Water District for data on 

surface flow at the diversion downstream from Imperial 

Highway; Minoo Ghajar, of the Orange County Public Health 

Department, for the analysis of total coliforms and fecal 

indicator bacteria. The authors also thank Katherine Patel, 

Mike Weihner, Gregory Woodside, and Nira Yamachika of the 

Orange County Water District, and the scientific review panel 

of the SARWQH study for sharing their expertise and for their 

input throughout this study.
Introduction 5

Basin boundary County line

LAND USE

Open space, recreation,

vacant or undeveloped Agriculture—Cropland

and pasture

Agriculture—Livestock Surface water

Urban—Industrial,

transportation and military

Urban—Commercial

Urban—Residential

Land-use data from SCAG Land Use,

1990 and 1993 GIS coverage

Base from U.S. Geological Survey

digital elevation data, 1999

Albers Equal-Area Conic Projection

0 10 20 MILES

0 10 20 KILOMETERS

Figure 2. Land use in the Santa Ana River Basin, southern California, 1990.
6 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Approach

Eight stormflows were sampled on the Santa Ana River 

between January 25, 2000, and March 8, 2002. Discrete 

samples were collected to characterize conditions in the river 

prior to stormflow, on the rising limb of the stormflow 

hydrograph, near the peak flow, and during the recession of the 

stormflow hydrograph. Bacteria samples were collected from 

the bridge at Imperial Highway using depth-integrated 

samplers. Equipment used for the collection and handling of 

bacteria samples was sterilized in an autoclave prior to use and 

sterile procedures were used to ensure that samples intended 

for microbial analysis were not contaminated during collection 

and handling. Additional samples were collected more 

frequently from automated samplers at the diversion point 

about one-quarter of a mile downstream from the bridge at 

Imperial Highway. The automated samplers were not used for 

microbiological samples because sterile collection and 

handling of samples was not possible using these samplers; 

however, samples from the automated samplers were analyzed 

for nonmicrobial and less expensive parameters, such as field 

parameters, some chemical constituents, or optical property 

data such as ultraviolet absorbance. Data collected from the 

automated samplers helped verify that large changes in the 

chemical composition of stormflow did not occur between 

sample-collection intervals at the bridge farther upstream. All 

samples were processed in the field at the time of collection 

and shipped to laboratories for analysis within 24 hours of 

sample collection.

Concentrations of total coliforms and fecal indicator 

bacteria—including fecal coliforms, Escherichia coli (E. coli), 

and enterococci—were evaluated across the stormflow 

hydrograph. Phospholipid fatty acid (PLFA) and genetic data 

(deoxyribonucleic acid, DNA) were used to determine if 

sources having greatly different microbial populations were 

contributing to stormflow runoff during different parts of the 

hydrograph. PLFA and genetic data were not used to identify 

specific organisms that may, or may not, have been present in 

a sample; instead, bacterial concentrations were compared 

with changes in PLFA, genetic profile, and dissolved organic 

carbon (DOC) concentrations to determine if there was an 

association between bacteria and DOC. Changes in DOC 

composition during stormflow were evaluated on the basis of 

optical properties, such as ultraviolet absorption and 

excitation-emission spectroscopy, and selected operationallydefined fractions. Changes in DOC composition also are 

important owing to concern about carbon of wastewater origin 

in water recharged to aquifers and the potential of the DOC to 

form disinfection by-products if chlorinated prior to 

distribution for public supply.

Sample pH, specific conductance, and alkalinity were 

measured in the field. Samples for total coliforms and fecal 

indicator bacteria were placed in coolers and chilled and 

delivered to the Orange County Public Health Laboratory 

within 24 hours for analysis. Samples for DOC, and optical 

property analysis were field filtered through baked glass-fiber 

filters, placed in coolers, chilled, and shipped overnight 

delivery to a USGS Laboratory in Sacramento within 24 hours 

of collection for analysis. Samples for PLFA analysis were 

placed in coolers, chilled, and shipped overnight delivery to a 

commercial laboratory within 24 hours of collection for 

analysis. Samples for Terminal-Restriction Fragment Length 

Polymorphism (T-RFLP) analysis were placed in coolers, 

chilled, and delivered to Orange County Water District 

laboratories within 24 hours of collection for analysis.

Sampled Stormflows

Eight stormflows were sampled at Imperial Highway 

during the 1999–2000, 2000–01, and 2001–02 rainy seasons 

(fig. 3). The data-collection period was drier than average and 

the 2001–02 rainy season was the driest rainy season on record 

(Los Angeles Times, 2002). The small amount of precipitation 

that did occur was typically of short duration, and not widely 

distributed across the basin. As a result, stormflows were 

generally smaller in magnitude and shorter in duration than 

were stormflows sampled between 1995 and 1998 by Izbicki 

and others (2000). Precipitation and flow statistics associated 

with sampled stormflows are summarized in table 1.

Sample collection included the first stormflow of each 

rainy season. The first stormflow in the 1999–2000 and

2000–01 rainy seasons was later than usual and occurred in 

January. Sample collection also included late-season 

stormflows that occurred under a wide range of antecedent 

conditions-such as the February 11–15, 2001, stormflow that 

was preceded by relatively dry conditions that allowed highly 

mobile or soluble material to accumulate in the basin; or the 

March 5–7, 2001, stormflow that was preceded by a series of 

larger storms that washed highly mobile or soluble material 

from the basin. Although detention ponds intended to control 

runoff from dairies in the basin were filled to near capacity as 

a result of that series of storms, widespread failure of detention 

ponds was not reported during the 2000–01 rainy season. 

During this study, only small amounts of water were 

stored behind Prado Dam after stormflow for later release to 

the river and the diversion at Imperial Highway farther 

downstream. As a result, with the exception of the 

March 5–7, 2001, stormflow, most stormflows sampled as part 

of this study were discrete events and water was not greatly 

altered by mixing with water stored from previous stormflows 

or by leaching of organic material from the flooded riparian 

habitat behind the dam.
Approach 7

0

1

2

3

4

5

1999

1999–2000 rainy season

2000

10,000

10

1,000

100

0

1

2

3

4

5

2000–01 rainy season

STREAMFLOW, IN CUBIC FEET PER SECOND

DAILY PRECIPITATION, IN INCHES

2000 2001

10,000

10

1,000

100

Nov Dec Feb Jan Mar Apr

0

1

2

3

4

5

2001–02 rainy season

Storms sampled Daily precipitation totals

Mean daily discharge at the diversion downstream from Imperial Highway

2001 2002

10,000

10

1,000

100

EXPLANATION

Figure 3. Sampled stormflows, precipitation, and stream discharge for the Santa Ana River at Imperial Highway, southern California, during the 1999–2000, 

2000–01, and 2001–02 rainy seasons.
8 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Table 1. Summary of stormflow sample collection in the Santa Ana River at Imperial Highway, southern California, 1999–2000, 2000–01, 2001–02 rainy 

seasons

[Data provided by Orange County Public Health Department; in., inches; ft3/s, cubic feet per second; >, greater than]

1Accurate measurement of flow was not possible because of mechanical problems at the diversion at Imperial Highway 

Sample collection dates

Rainfall at

Prado Dam 

(in.)

Peak flow at 

Imperial Highway 

(ft3/s)

Peak flow

below Prado Dam 

(ft3/s)

Comments

01/25/00 to 01/26/00 0.62 569 401 First stormflow of rainy season

02/12/00 to 02/13/00 .79 644 307

02/22/00 to 02/27/00 2.04 >9001 3,900 Preceded by a large storm

01/10/01 to 01/14/01 2.38 4,111 4,100 First stormflow of rainy season

02/11/01 to 02/15/01 2.27 5,400 5,800 Preceded by dry conditions

03/05/01 to 03/07/01 .5 618 505 Preceded by a series of larger storms

11/12/01 to 11/14/01 .43 399 372 First stormflow of rainy season

03/06/02 to 03/08/02 .25 256 295
Approach 9

Analytical Methods

Total coliforms, fecal coliforms, Escherichia coli (E. 

coli), and enterococci were analyzed within 24 hours of 

collection by the Orange County Public Health Laboratory, 

Anaheim, California. During the 1999–2000 and 2000–01 

rainy seasons, samples were analyzed at dilutions ranging from 

1:10 to 1:10,000 using a combination of three procedures:

(1) multi-tube fermentation (MTF) for total coliforms, 

(2) Colilert-18 with Quanti-tray 2000 (IDEXX Laboratories 

Inc., Westbrook, Maine) for fecal coliforms and E. coli, and 

(3) Enterolert (IDEXX Laboratories Inc., Westbrook, Maine) 

for enterococci. Results are Most Probable Number per 100 

milliliters (MPN/100ml). Because E. coli numbers were greater 

than fecal coliform bacteria numbers, the analytical methods 

were changed after the 2000–01 rainy season. During the 

2001–02 rainy season, samples were analyzed at similar 

dilutions using m-Endo LES agar for total coliforms (American 

Public Health Association, 1998 9222 B), M-FC agar for fecal 

coliforms (American Public Health Association, 1998), 

modified m-TEC agar for E. coli (U.S. Environmental 

Protection Agency, 2000), and m-EI agar for enterococci 

(American Public Health Association, 1998). Results for the 

2001–02 rainy season are reported as colonies per 100 mL. 

Field blanks showed no evidence of contamination from 

sample collection equipment.

Phospholipid fatty acid analyses were done by Microbial 

Insights, Rockford, Tenn. Analysis for fatty acid methyl esters 

was done using standard protocol (Microbial ID Inc., 1992; 

Cavigelli and others, 1995). Lipids were saponified using 

3.25N NaOH in methanol, heated, and then methylated using 

3.25N HCl in methanol and extracted in a mixture of methyltert-butyl ether (MTBE) and hexane. After extraction and 

separation the organic phase was washed using dilute NaOH 

and the methylated fatty acids were analyzed by gas 

chromatography (Microbial ID Inc., 1992; Cavigelli and 

others, 1995). Blank samples collected from the automated 

samplers during the 1999–2000 rainy season showed small 

amounts of contamination from the automated sampling 

equipment. PLFA samples collected during the 2001–02 rainy 

season were collected from the bridge upstream of Imperial 

Highway using depth-dependent sample collection equipment. 

No evidence of contamination was observed in these samples. 

Genetic profiles of the microbial communities from 

stormflow samples were done using a combination of PCR 

(polymerase chain reaction) and Terminal Restriction 

Fragment Length Polymorphism (T-RFLP) by Orange County 

Water District. Bacterial cells suspended in a 3-liter water 

sample were separated from particulate material by adding a 

1 percent solution of Na2HPO4 and shaking the sample for 

15 minutes. Debris was allowed to settle for about 30 minutes, 

following which 500 ml of the sample was removed and 

bacterial cells were concentrated by centrifugation at 

8,000 rpm for 60 minutes. Total deoxyribonucleic acid (DNA) 

from the resulting bacterial pellet was extracted using the 

UltraClean Soil DNA isolation kit (MoBio Laboratories Inc., 

Solana Beach, California), as specified by the manufacturer, 

and was stored at −20οC for further analysis. To obtain a 

genetic profile from as many different species as possible, PCR 

was used to amplify a portion of the 16S rhibosomal 

ribonucleic (rRNA) gene. “Universal” PCR primers (AvanissAghajani, and others 1996; Brunk and others, 1996) were used 

to amplify the hypervariable region of the 16S rRNA that 

results in amplicons (amplified PCR products) that range from 

480 to 500 base pairs (bp) in size. The forward “Universal” 

primer was synthesized with fluorescent 5-

hexachlorofluorscein (Hex) labeled at the 5' end (IDT, 

Coraville, Iowa). Amplification was done using a GeneAmp 

PCR system 9600 (Applied Biosystems, ABI, Foster City, 

California) with the following concentration of PCR 

components in a final volume of 100 μL: 1X PCR buffer with 

1.5 μM MgCl2 (ABI), 200 μM each deoxynucleotide 

triphosphate (dNTP, ABI), 0.2 μM of each primer, 2.5 units of 

Amplitaq Polymerase (ABI) and approximately 2–4 ng of total 

DNA. The cycling protocal used 95οC for 11 minutes for initial 

denaturation, 35 cycles of 94οC for 1 minute, 55οC for 

1 minute, 72οC for 3 minutes, and a final extension of 72οC for 

10 minutes. Approximately 10–30 ng of PCR amplicons 

derived from each sample were digested using 10Units of Ddel

restriction ednonuclease (New England Biolabe, Beverly, 

Massachusetts) in a total volume of 20 μL for 1 hour at 37οC to 

obtain a T-RFLP pattern of the different species present in the 

sample. The size of the amplicons was determined by capillary 

electrophoresis using a 310 Genetic Analyzer (ABI) as follows: 

2 μL of the restricted amplicons were mixed with 12.5 μL of a 

mixture of deionized formamide and Tamara 500 internal size 

standard (ABI). The mixture was then denatured at 94οC for 

5 minutes and immediately chilled on ice prior to 

electrophoresis using the Genescan mode (ABI). The size of 

the restricted amplicons were determined by comparison with 

Tamara internal size standard using the Local Southern method 

in the Genescan software, version 2.1 (ABI). Only the 5' end of 

the restricted amplicons are fluorescently labeled: therefore, 

digestion of the amplicons with restriction enzymes results in 

only one band even if multiple cut sites exist. The sensitivity of 

this method is limited to about one base pair.
10 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Dissolved organic carbon and optical-property 

measurements were done by the USGS, Sacramento, 

California (Bird and others, 2003). Dissolved organic carbon 

was measured on filtered samples using a Shimadzu 

TOC-5000A organic carbon analyzer calibrated using 

potassium hydrogen phthalate standards prepared in organicfree water, with standard concentrations bracketing the 

concentration of the samples. Aliquots of sample (4.5 mL) 

were acidified using 30 μL of 2N HCL and sparged using N2

for 3 minutes to remove inorganic carbon as CO2. The nonpurgeable organic carbon (NPOC) was analyzed by direct 

injection of liquid sample into a high-temperature (680οC) 

combustion tube packed with a platinum catalyst, and the CO2

produced was detected using a nondispersive infrared 

photometric cell. Each analysis represents the mean of three 

injections, standard deviation of the three injections ranged 

from 0.002 to 0.145 mg/L. Precision of the technique is 

reported to be between 0.3 and 2.9 percent of the total 

concentration (Bird and others, 2003). 

Optical measurements made as part of this study included 

UV Absorbance and excitation/emission spectroscopy (EEM). 

Samples were gravity filtered to reduce DOC contamination by 

lysing algae or bacterial cells during mechanical filtration. 

UV measurements were done from 190 to 310 nm using a PE 

Lambda 3B UV/VIS spectrophotometer having a 1-centimeter 

path-length cell. EEM measurements were done by irradiating 

the sample across 255 to 600 nm range of wavelengths and 

simultaneously recording the emitted fluorescence across 250 

to 700 nm range of wavelengths. EEM measurements were 

done using a SPEX Fluorimax-3 excitation/emission 

fluorometer.

Separation of dissolved organic carbon (DOC) into 

operationally defined fractions and measurements on those 

fractions was done by George Aiken, USGS, Boulder, 

Colorado. Operationally defined fractions of DOC were 

defined by their ability to pass-through or sorb on a column of 

XAD-8 or XAD-4 resins under different pHs (Aiken and 

others, 1992). The fractions measured include hydrophobic 

acids, hydrophilic acids, transhydrophilic acids, and the 

hydrophobic-neutral fractions of the DOC. Hydrophobic acids 

are defined as that portion of DOC that sorbs on a column of 

XAD-8 resin at pH 2 and is eluted at pH 13. Hydrophilic acids 

are defined as that portion of DOC that passes-through 

columns of XAD-8 and XAD-4 resins at pH 2. 

Transhydrophilic acids are defined as that portion of DOC that 

does not sorb on XAD-8 resin at pH 2, sorbs on XAD-4 resin 

at pH 2, and is eluted from the XAD-4 resin using NaOH at 

pH 13. The hydrophobic-neutral fraction is defined as the 

fraction of DOC that sorbs and cannot be eluted from XAD-8 

and XAD-4 resin at pH 13. Once separated, the DOC and 

optical properties of the hydrophobic, hydrophilic, and 

transhydrophobic acid fractions were measured using 

analytical techniques similar to those described in the previous 

paragraph. Because the hydrophobic neutral fraction cannot be 

eluted, its concentration was calculated as the difference 

between the total DOC concentration and the DOC 

concentrations of the eluted fractions at pH 2 (hydrophobic 

acids) and pH 11 (hydrophyllic acids plus transhydrophyllic 

acids). Because small amounts of DOC may be contributed 

from the XAD-4 resins during the fractionation proceedure, at 

low DOC concentrations the four fractions do not necessarily 

sum to 100 percent.

Total Coliforms and Fecal Indicator 

Bacteria

Historical Data

Total and fecal coliform bacteria concentrations at 

Imperial Highway measured on a weekly to monthly basis by 

Orange County Public Health Department from January 1986 

to March 1994 provide a baseline to evaluate stormflow data 

collected as part of this study. During that period, total 

coliform bacteria concentrations ranged from 130 colonies per 

100 mL to greater than the maximum quantification level of 

16,000 colonies per 100 mL. Fecal coliform bacteria 

concentrations ranged from 20 colonies per 100 mL to greater 

than the maximum quantification level of 16,000 colonies per 

100 mL (table 2). High concentrations of total and fecal 

coliform bacteria were measured in both the dry season and the 

rainy season, and concentrations in excess of the maximum 

quantification level occurred in all months of the year and were 

not well correlated with streamflow.

Despite variability in individual samples, monthly 

historical median total and fecal coliform bacteria 

concentrations were higher toward the end of the dry season 

and decreased during the rainy season (fig. 4). The reason for 

high median values during the dry season is not clear. Flow in 

the Santa Ana River during the dry season is maintained by 

discharge of highly treated municipal wastewater having low 

bacteria concentrations. There is scant surface runoff during 

the dry season and few discharges from other sources. It may 

be possible that total coliform and fecal coliform bacteria 

survive and grow in the shallow warm water or bed of the 

Santa Ana River and its tributary streams during this time. 

Growth of fecal coliform bacteria has been observed in 

environmental settings (Francy and others, 1996) and may be 

a special concern in shallow, concrete-lined channels tributary 

to the Santa Ana River. Some of these channels have yearround flow and are highly productive, supporting dense algal 

growth during the latter part of the dry season. Improperly 

treated wastewater, small amounts of urban runoff associated 

with lawn watering and other uses, windblown material from 

agricultural areas, or fecal material from other sources could 

inoculate these channels with fecal bacteria and produce 

elevated concentrations of fecal bacteria in the Santa Ana 

River farther downstream.
Total Coliforms and Fecal Indicator Bacteria 11

Table 2. Summary of historical bacteria concentrations and bacteria concentrations measured during pre-stormflow and stormflow conditions in the Santa Ana 

River at Imperial Highway, southern California

[Historical data collected and analyzed by Orange County Public Health Laboratory; data from this study collected by U.S. Geological Survey and analyzed by 

Orange County Public Health Laboratory; shallow ground water collected from Orange County Water District subsurface-collection and recharge system (SCARS) 

about 4 feet below the bed of the off-channel recharge facility along the Santa Ana River about 1 mile downstream from Imperial Highway; bacteria results 

reported as colonies per 100 mL; ft3/s, cubic feet per second; <, less than; >, greater than; —, no data]

Historical data Data from this study

January 1986 to March 1994 January 2000 to March 2002

Dry season

(April–September)

Rainy season

(October–March) Prestormflow

Stormflow,

including

recessional

flow

Shallow

ground

water <200 ft3

/s <200 ft3/s >200 ft3/s

Flow Minimun 44 52 200 231 224 —

Median 169 173 280 357 491 —

Maximum 446 199 4,500 537 5,400 —

Total Coliforms Minimun 170 300 130 1,100 200 <10

Median 9,000 9,000 5,000 2,650 25,000 50

Maximum >16000 >16000 >16000 8,000 3,400,000 130

Fecal Coliforms Minimun <20 80 <20 <10 25 <10

Median 600 700 500 25 4,000 <10

Maximum >16000 >16000 >16000 1,700 310,000 10

Escherichia coli Minimun — — — 100 40 <10

Median — — — 210 3,080 <10

Maximum — — — 700 84,000 <10

Enterococci Minimun — — — 120 <10 <10

Median — — — 120 5,800 10

Maximum — — — 940 100,000 20
12 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

100

1,000

10,000

100,000

MONTH

BACTERIA, IN COLONIES

PER 100 MILLILITERS

Total coliforms

Fecal coliforms

January

December

April

July

October

Rainy season

Dry season

Figure 4. Monthly median total and fecal coliform bacteria concentrations in the Santa Ana River at Imperial Highway, southern California, January 1986 to 

March 1994. (Data provided by the Orange County Public Health Department.)
Total Coliforms and Fecal Indicator Bacteria 13

Historical data collected across a wide range of flows 

suggest that total and fecal coliform bacteria concentrations 

were lower during the rainy season. During the rainy season the 

median total and fecal coliform bacteria concentrations during 

low flows (less than 200 ft3/s) were slightly higher than 

concentrations measured during higher flows (table 2). 

However, available historical data had an upper quantification 

limit; as a result, concentrations greater than 16,000 colonies 

per 100 mL were not evaluated and maximum concentrations 

are not known. In addition, samples were collected at weekly 

or greater time intervals that do not allow for the evaluation of 

short-term changes in water quality that occur during 

stormflow. Short-term changes in microbial concentrations 

during stormflow were addressed as part of this study.

Total Coliforms and Fecal Indicator Bacteria 

Concentrations during Stormflow

Total and fecal coliform bacteria concentrations in 

stormflow from the Santa Ana River at Imperial Highway were 

as high as 3,400,000 and 310,000 colonies per 100 mL, 

respectively. E. coli and enterococci concentrations were as 

high as 84,000 and 100,000 colonies per 100 mL, respectively 

(table 2, Appendix A). In general, total coliform and fecal 

indicator bacteria concentrations increased during stormflow, 

although decreases in total coliform and fecal indicator bacteria 

concentrations were recorded during the March 6–8, 2002, 

stormflow. Precipitation and subsequent runoff were small in 

magnitude during that stormflow, and streamflow actually 

decreased at Imperial Highway as a result of regulation at 

Prado Dam. In most stormflows, total coliforms, fecal 

coliforms, E. coli, and enterococci concentrations were well 

correlated. During the 2000–01 rainy season, E. coli

concentrations exceeded fecal coliform bacteria concentrations 

in some samples—especially at higher concentrations. This 

should not occur because E. coli is one of many fecal coliform 

bacteria: as discussed previously, analytical methods were 

changed during the 2001–02 rainy season to correct this 

problem.

Total coliform and fecal indicator bacteria concentrations 

during the first stormflows of the winter rainy season were 

higher than concentrations during stormflows later in the 

season. Changes in bacterial concentrations during the first 

stormflows of the rainy season followed a similar pattern 

regardless of the magnitude of the stormflow (fig. 5). In 

general, total coliform and fecal indicator bacterial 

concentrations increased rapidly as runoff from urban areas 

downstream from Prado Dam contributed to stormflow, and 

concentrations then declined slightly after bacteria were 

washed from urban streets and drains. After a period of several 

hours, bacterial concentrations increased to their highest values 

as parts of the basin upstream from Prado Dam contributed to 

stormflow. The basin is extensively urbanized upstream from 

Prado Dam, but it is unlikely that runoff from urban areas 

upstream from the dam can account for total coliform and fecal 

indicator bacteria concentrations that are as much as an order 

of magnitude greater than concentrations measured during 

runoff from urban areas downstream from the dam (fig. 5). 

Other sources of bacterial contamination also must be present. 

The basin also contains numerous dairies in the Chino and 

Cucamonga Creek areas, as well as other land uses, that may 

contribute to increased bacteria concentrations during 

stormflow. Data collected as part of this study also show that 

total coliform and fecal indicator bacteria concentrations in the 

Santa Ana River at Imperial Highway remained high even after 

flow in the river had returned to pre-storm levels.

The highest bacteria concentrations were measured 

November 12–14, 2001, during the first stormflow of the 

2001–02 rainy season; although precipitation was only about 

0.5 in., it was very intense and most of the water fell during a 

brief interval. Orange County Water District personnel 

sampling downstream from dairy operations—on Mill Creek at 

Chino-Corona Road, a tributary to the Santa Ana River about 

11 mi upstream from Imperial Highway—recorded total 

coliform bacteria concentrations as high as 7,300,000 colonies 

per 100 mL during this stormflow (fig. 6). Fecal coliform 

bacteria, E. coli, and enterococci concentrations were similarly 

elevated, having concentrations of 530,000, 90,000, and 

1,210,000 colonies per 100 mL, respectively. The bacteria 

concentrations at Imperial Highway were highest about 14 

hours after the highest concentrations at the Mill Creek site. 

Samples were not collected along the main stem of the Santa 

Ana River during this stormflow, and contributions from urban 

areas along the main stem of the Santa Ana River during this 

stormflow are not known.

Total coliforms and fecal indicator bacteria 

concentrations in stormflows that occurred later in the rainy 

season were variable and did not follow a consistent pattern 

during stormflow. For example, bacteria concentrations and 

their distribution across the stormflow hydrograph during large 

stormflows preceded by extended dry periods, such as the 

February 11–15, 2001, stormflow, were similar to those 

measured during the first stormflow of the rainy season. In 

contrast, bacteria concentrations actually decreased during 

small late-season stormflows that were preceded by other 

stormflows that may have washed bacteria from the basin. 
14 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

0

20

40

60

80

100

10

100

1,000

10,000

11/11/01 11/15/01 11/12/01 11/13/01 11/14/01

1

100

10,000

1,000

10

1,000,000

100,000

10,000,000

BACTERIA, IN COLONIES

PER 100 MILLILITERS

Total coliforms E. coli Enterococci

Percent is percentage of

streamflow derived from

runoff downstream

from Prado Dam

EXPLANATION

STREAMFLOW, IN CUBIC

FEET PER SECOND PERCENT

10

100

1,000

10,000

0

20

40

60

80

100

1/10/01 1/11/01 1/12/01 1/13/01 1/14/01

Percent is percentage of

streamflow derived from

runoff downstream

from Prado Dam

1

100

10,000

1,000

10

1,000,000

100,000

10,000,000

PERCENT

STREAMFLOW, IN CUBIC

FEET PER SECOND PERCENT

0

20

40

60

80

100

STREAMFLOW, IN CUBIC

FEET PER SECOND

BACTERIA, IN MOST PROBABLE NUMBER PER 100 MILLILITERS

1/23/00 1/24/00 1/26/00 1/27/00 1/25/00

Percent is percentage of

streamflow derived from

runoff downstream

from Prado Dam

1

100

10,000

1,000

10

1,000,000

100,000

10,000 10,000,000

10

1,000

100

Figure 5. Total coliform and fecal indicator bacteria (Escherichia coli and enterococci) concentrations in the Santa Ana River at Imperial Highway, southern 

California, during the first stormflow of the 1999–2000, 2000–01, and 2001–02 rainy seasons.
Total Coliforms and Fecal Indicator Bacteria 15

11/12/01 11/13/01

0

20

40

60

80

100

10

1

100

1,000

10,000

100,000

1,000,000

10,000,000

10

1

100

1,000

10,000

100,000

1,000,000

10,000,000

Santa Ana River at Imperial Highway

STREAMFLOW, IN CUBIC FEET PER SECOND

BACTERIA, IN COLONIES PER 100 MILLILITERS

PERCENT

DATE

EXPLANATION

Percent is percentage of

streamflow derived from

runoff downstream

from Prado Dam

10

100

1,000

10,000

Total coliforms E. coli Enterococci

Mill Creek at Chino-Corona Road

(Streamflow data from Cucamonga Creek near Mira Loma)

10

100

1,000

10,000

Figure 6. Total coliform and fecal indicator bacteria (Escherichia coli and enterococci) concentrations in Mill Creek at Chino-Corona Road, and in the Santa Ana 

River at Imperial Highway, southern California, November 12, 2001. (Samples collected by Orange County Water District; bacteria data from Orange County 

Health Department.)
16 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Several researchers have shown that fecal indicator 

bacteria may be present at large concentrations in streambed 

sediments (Von Donsel and Geldreich, 1971; Myers and 

others, 1998) and these bacteria may survive for extended 

periods in those sediments (Burton and others, 1987). Matson 

and others (1978) theorized a conceptual model of bacteria 

mobilization that includes storage of fecal bacteria in 

streambed sediments and scouring of sediment and associated 

bacteria as velocities increase during stormflow. Total 

coliforms and fecal indicator bacteria concentrations in the 

Santa Ana River at Imperial Highway increased with 

suspended-sediment concentrations, consistent with the model 

of Matson and others (1978), until suspended-sediment 

concentrations exceeded about 500 mg/L (fig. 7). The higher 

suspended-sediment concentrations occurred during the larger 

stormflows, and suspended sediment mobilized during these 

stormflows eventually exceeded the available bacteria. Total 

coliforms and fecal indicator bacteria concentrations were 

lower, per unit of suspended sediment, during the first 

stormflow of the rainy season (fig. 7) because suspendedsediment concentrations were higher during the first stormflow 

of the rainy season (fig. 8). The model of Matson and others 

(1978) is consistent with low bacteria concentrations measured 

during smaller stormflows when streamflow velocities are not 

large enough to re-suspend streambed sediments. The model is 

not consistent with high total coliforms and fecal indicator 

bacteria concentrations that persist in the Santa Ana River for 

several days after streamflow returned to pre-storm conditions. 

The data show that sediment disturbed and re-deposited after 

stormflow continues to contribute these bacteria to the river 

until a new equilibrium is established between the streambed 

and overlying water. This results suggests that the model 

initially proposed by Matson and others (1978) could be 

modified to include a period after the cessation of stormflow 

when recently disturbed sediment equilibrate with the 

overlying water. Because accumulation and survival of 

bacteria in streambed sediments was not measured as part of 

this study, data are not available to test the suitability of the 

modified model.

Phospholipid Fatty Acids

Fatty acids are components of all living cells. At the 

cellular level, they may be used for energy storage or they may 

be part of cellular organelles and structures where they 

participate in metabolic activity (Tunlid and White, 1992). 

Fatty acids that contain phosphorous, known as phospholipid 

fatty acid (PLFA), are commonly found in cell walls and in the 

membranes of cellular organelles where they participate in 

activities such as nutrient uptake and waste removal. Specific 

PLFAs are associated with specific metabolic activities and 

may be indicators of the types of organisms present (Edlund 

and others, 1985; Dowling and others, 1986; White and others, 

1996; Paul and Clark, 1996). Because PLFAs contain 

phosphorous, they are rapidly degraded in the environment and 

are typically associated with living (or recently living) 

organisms (White and others, 1979; White, 1994). Because 

PLFAs can be measured at very low concentrations (in the 

picomole range) they can be used to identify changes in 

microbial populations in environmental settings (Vestal and 

White, 1989). Total PLFA concentrations also are an indicator 

of total microbial biomass. However, concentrations do not 

necessarily relate directly to other measures of cellular 

populations, such as most probable number or colonies per 

100 mL, used to quantify fecal indicator bacteria because 

microorganisms differ greatly in size and large organisms may 

contain larger quantities of PLFAs than smaller 

microorganisms. 

Fatty acids have a wide range of compositions, and a 

shorthand notation has been developed to identify specific 

fatty acids (Paul and Clark, 1996). This notation follows the 

form 

X:YωZ,

where

For unsaturated fatty acids, the stereochemistry of the 

carbon chain is described by the suffixes c, cis (this is the most 

common form, and the suffix is usually omitted from the shorthand notation), or t, trans. For fatty acids having branched 

carbon chains, i describes isomethyl branching (second C from 

the methyl end), a describes anteisomethyl branching (third 

from the methyl end); and Me, follows position of the methyl 

branching. The prefix cy, identifies a cyclopropane ring within 

the carbon chain. Fatty acids can be categorized into common 

structural groups (table 3). The groups are useful to categorize 

the wide diversity of fatty acids and describe changes that are 

occurring within the fatty acid assemblages.

X is the number of carbon atoms,

Y is the number of carbon-carbon double bonds,

ω is the end of the molecule, and

Z is the number of carbon atoms between the terminal 

double bond and the methyl end of the 

molecule. 
Phospholipid Fatty Acids 17

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

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

SUSPENDED SEDIMENT,

IN MILLIGRAMS PER LITER

SUSPENDED SEDIMENT,

IN MILLIGRAMS PER LITER

SUSPENDED SEDIMENT,

IN MILLIGRAMS PER LITER

SUSPENDED SEDIMENT,

IN MILLIGRAMS PER LITER

TOTAL COLIFORMS,

IN COLONIES PER 100 MILLILITERS

FECAL COLIFORMS,

IN COLONIES PER 100 MILLILITERS

ESCHERICHIA COLI,

IN COLONIES PER 100 MILLILITERS

ENTEROCOCCI,

IN COLONIES PER 100 MILLITERS

EXPLANATION

First stormflow of the rainy season All other stormflows

1,000,000

10,000

100

1

1,000,000

10,000

100

1

10,000,000

100,000

1,000

10

1,000,000

10,000

100

1

500 mg/L500 mg/L

500 mg/L

500 mg/L

Figure 7. Total coliforms, fecal coliforms, Escherichia coli, and enterococci concentrations as a function of suspended-sediment concentration in stormflow in 

the Santa Ana River at Imperial Highway, southern California, 2000–01 and 2001–02 rainy seasons.
18 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

10

100

1,000

10,000

100 1,000 10,000

STREAMFLOW,

IN CUBIC FEET PER SECOND

SUSPENDED SEDIMENT,

IN MILLIGRAMS PER LITER

All other stormflows

First stormflow

EXPLANATION

Figure 8. Suspended-sediment concentrations as a function of streamflow during stormflow conditions in the Santa Ana River at Imperial Highway, southern 

California, 2000–01 and 2001–02 rainy seasons.
Phospholipid Fatty Acids 19

Table 3. Description of selected phospholipid fatty acid (PLFA) structural groups

[Standard nomenclature used for fatty-acid names follows the form X:YωZ, where X is the number of carbon atoms, Y is the number of carbon-carbon double 

bonds, ω is the end of the molecule, and Z is the number of carbon atoms between the terminal double bond and the methyl end of the molecule, i, iso methyl 

branching, and Me, methyl branching]

Structural group Representative fatty acid Shorthand notation

Monoenoic CH3(CH2)5CH=CH(CH2)7COOH 16:1ω7

Branched CH3CH(CH2)4CH=CH(CH2)7COOH i17:1ω7

monoenoic |

CH3

Polyenoic CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH 18:2ω7

Normal CH3(CH2)14COOH 16:0 

saturated

Terminally CH3CH(CH2)12COOH i16:0

branched |

saturated CH3

Mid-chain CH3(CH2)2 CH(CH2)10COOH 10Me16:0

branched |

saturated CH3
20 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Although researchers in previous studies have identified 

marker fatty acids and associated these compounds with 

specific organisms or groups of organisms (Edlund and others, 

1985; Dowling and others, 1986; Paul and Clark, 1996, White 

and others, 1996), even a brief review of the available literature 

shows a number of inconsistencies in the approach. Recent 

work by Haack and others (1994) showed that even in 

simplified model microbial communities, many fatty acids are 

not specific to individual organisms but rather are found in a 

wide range of different organisms having similar metabolic 

processes. In this study, changes in the relative abundance of 

specific fatty acids or fatty acid structural groups were used to 

show changes in the types and diversity of microorganisms 

present during different parts of the stormflow hydrograph and 

throughout the rainy season without inferring the presence of 

specific organisms.

Phospholipid Fatty Acid Concentrations and 

Compositions during Stormflow

Phospholipid fatty acid concentrations and composition 

were measured during five stormflows during the 1999–2000 

and 2001–02 rainy seasons (Appendix B). Additional samples 

for comparison with stormflow samples were collected from 

other sources such as storm drains, bed material from the Santa 

Ana River, and a dairy-waste storage pond (table 5, later in this 

report).

Total PLFA concentrations in samples from the Santa Ana 

River at Imperial Highway ranged from 18,200 to 

725,000 picomoles per liter (pmole/L). In general, total PLFA 

concentrations were lower in samples collected prior to the 

beginning of stormflow. However, pre-storm concentrations 

were dependent on antecedent conditions, and samples 

collected prior to the onset of stormflow, when antecedent 

conditions were relatively wet, had higher PLFA 

concentrations than did samples collected after relatively dry 

periods. Total PLFA concentrations increased with increases in 

streamflow and total coliform and fecal indicator bacteria 

concentrations (fig. 9). Concentrations were distributed 

through the stormflow hydrograph in a similar manner to 

bacterial concentrations. In the same manner as total coliforms 

and fecal indicator bacteria (E. coli), PLFA concentrations 

commonly remained high during the recessional flows of the 

first stormflow of the rainy season—even after flow had 

returned to pre-storm conditions.

More than 80 PLFAs were identified in samples collected 

as part of this study (Appendix B). Monoenoic 

(monounsaturated) fatty acids, normal saturated fatty acids, 

and polyenoic (polyunsaturated) fatty acids composed most of 

the total fatty acids measured. Structurally more complex fatty 

acids having branched or ring structures composed, on average, 

less than 12 percent of the total fatty acids measured. Changes 

in fatty acid groups and individual fatty acids within those 

groups reflect the complex changes in the total microbial 

population (not just total coliform and fecal indicator bacteria 

measured as part of this study) present within the Santa Ana 

River that occur as water from different sources having 

different microbial populations contributes to stormflow. 

As total PLFA concentrations increased, the monoenoic 

fatty acid fraction increased (fig. 10), and in some samples the 

two most common monoenoic fatty acids, 16:1ω7 and 18:1ω7, 

composed more than half of the total PLFAs. For this to occur 

the source of bacteria contributing these fatty acids must be 

poorly diverse and the total microbial population must be 

dominated by only a few types of bacteria. As total fatty acid 

concentrations increased, normal saturated and polyenoic fatty 

acid concentrations generally decreased. However, there was 

more variability in the relation between the polyenoic PLFA 

fraction, total PLFA concentrations, and stormflow than in the 

monoenoic or normal fatty acid fractions (fig. 10). For 

example, during the first stormflows of the winter rainy season, 

the polyenoic fatty acid fraction initially increased as runoff 

from urban areas downstream from Prado Dam contributed to 

stormflow, and in some stormflows the polyenoic fraction 

composed as much as 40 percent of the total PLFA during that 

time. The polyenoic fatty acid fraction subsequently decreased 

to less than 20 percent of the total PLFA during the recessional 

flows when runoff from areas upstream from Prado Dam was 

present and the total PLFA was composed largely of a few 

monoenoic fatty acids. Even though much of the basin 

upstream from Prado Dam is urbanized, the fatty acids (and 

consequently the total bacterial population) present in the Santa 

Ana River during the recession of the early season stormflows 

are different from the fatty acids present in urban runoff 

contributed by areas downstream from Prado Dam.

Changes in PLFA composition during stormflow were 

expressed as changes in the diversity of the 10 most common 

fatty acids using the Simpson reciprocal and Shannon-Wiener 

indexes (Goodman, 1975). The indexes are calculated as 

follows:

Simpson reciprocal index (D) = 1/Σ(Pi

2),

Shannon-Wiener index (H) = −Σ(Pi ln[Pi]),

where 

P is the number of organisms (or, in this case, the fatty 

acid fraction) of each type i observed.
Phospholipid Fatty Acids 21

1,000

10,000

100,000

1,000,000

1,000

10,000

100,000

1,000,000

1,000

10,000

100,000

1,000,000

0 200 400 600 800

STREAMFLOW, IN CUBIC FEET PER SECOND

All other data

First stormflow of the rainy season

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

TOTAL COLIFORMS, IN COLONIES PER 100 MILLILITERS

1 100 10,000 1,000,000

ESCHERICHIA COLI, IN COLONIES PER 100 MILLILITERS

TOTAL PHOSPHOLIPID FATTY ACIDS, IN PICOMOLES PER LITER

EXPLANATION

Figure 9. Phospholipid fatty acid concentrations as a function of streamflow, and of total coliform bacteria, and Escherichia coli concentrations in stormflow in 

the Santa Ana River at Imperial Highway, 1999–2000 and 2001–02 rainy seasons.
22 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

0

20

40

60

80

100

10,000 100,000 1,000,000

TOTAL PHOSPHOLIPID FATTY ACIDS,

IN PICOMOLES PER LITER

MONOENOIC FATTY ACIDS,

IN PERCENT OF TOTAL PLFAs

All other data

First stormflow of the rainy season

0

10

20

30

40

0

10

20

30

40

NORMAL SATURATED FATTY ACIDS,

IN PERCENT OF TOTAL PLFAs

POLYENOIC FATTY ACIDS,

IN PERCENT OF TOTAL PLFAs

EXPLANATION

Figure 10. Selected phospholipid fatty acid (PLFA) structural groups as a function of total phospholipid fatty acid concentration in stormflow in the Santa Ana 

River, 1999–2000 and 2001–02 rainy seasons.
Phospholipid Fatty Acids 23

Both the Simpson reciprocal and Shannon-Weiner indices 

increase with increasing diversity and decrease with decreasing 

diversity. The indexes provide a convenient way to compare 

changes in fatty acid composition representative of changes in 

the total bacterial population during stormflow, with changes in 

total coliform and fecal indicator bacteria measured during 

stormflow. For example, as total PLFA concentrations and 

total coliform concentrations increased during the recessional 

of the November 12–14, 2001, stormflow, PLFA diversity 

decreased (fig. 11). The decrease in diversity presumably 

results from a source present within the Santa Ana River 

largely dominated by only a few bacteria species that contains 

high concentration of total coliforms.

Comparison with Phospholipid Fatty Acids from Other 

Sources

Principal component analysis was used to compare 

stormflow data with samples collected from other sources. 

Principal component analysis is a multivariate statistical 

technique that transforms a set of inter-correlated variables into 

a new coordinate system (Kshirsagar, 1972; Morrison, 1976; 

Gnanadesikan, 1977). The transformed variables are 

uncorrelated linear combinations of the original variables 

known as principal components. Principal components have a 

mean of zero and the same variance as the original data set. The 

values of the principal components are known as scores, and 

the scores are calculated on the basis of the contribution of each 

variable to the total variance (Preisendorfer and others, 1981). 

The magnitude and direction (plus or minus) of each variable 

to the principal component score is described by an 

eigenvector. 

The eigenvectors describing the first and second principal 

components for the 10 most common fatty acids in stormflow 

are listed in table 4. The first principal component explained 

almost 40 percent of the total variance and contained large 

positive eigenvectors for a monoenoic (18:1ω9), two saturated 

(18:0, 16:0), and three polyenoic fatty acids (20:5ω3, 18:2ω6, 

and 18:3ω3); and large negative eigenvectors for two 

monoenoic (16:1ω7, and 16:1ω5) and a terminally branched 

saturated fatty acid (i15:0). The second principal component 

explained about 20 percent of the total variance and contained 

large positive eigenvectors for a terminally branched (i15:0), a 

polyenoic (18:2ω6), and a monoenoic (16:1ω5) fatty acid; and 

large negative eigenvectors for a polyenoic (20:5ω3) and a 

monoenoic (16:1ω7) fatty acids.

A plot of the first principal component as a function of the 

second principal component (fig. 12) shows that samples from 

the recessional flows of the first stormflows of the rainy season 

had negative scores for both the first and second principal 

components. These scores are consistent with decreases in fatty 

acids having large positive eigenvectors for both the first and 

second principal components (such as the monoenoic fatty acid 

18:1ω9 and the polyenoic fatty acids 18:2ω6 and 18:3ω3), and 

increases in fatty acids having large negative eigenvectors for 

the first and second principal component (such as the 

monoenoic fatty acid 16:1ω7) (table 4). In contrast, the first 

principal component was positive and the second principal 

component was negative for samples collected from the Santa 

Ana River when urban runoff predominated. These scores are 

consistent with decreases in fatty acids having large negative 

eigenvectors for the first principal component and large 

positive eigenvectors for the second principal component (such 

as the normal saturated fatty acid i15:0), and increases in fatty 

acids having large positive eigenvectors for the first principal 

component and large negative eigenvectors for the second 

principal component (such as the polyenoic fatty acid 20:5ω3). 

The results of the principal component analysis reflect changes 

in the composition of the total PLFA and, presumably, changes 

in the total microbial population they represent during 

stormflow.

Samples from selected sources in the Santa Ana River 

Basin show a wide range of fatty acid concentrations and 

compositions (table 5). Some of the samples have distinctive 

fatty acid composition that could be useful in the identification 

of bacteria from these sources.

The highest fatty acid concentrations in water, about 

100,000 pmole/L, were from Cucamonga Creek, downstream 

from dairy operations, and from a dairy-waste storage pond 

(table 5). The two most common fatty acids in water from 

Cucamonga Creek were the monoenoic fatty acids 18:1ω7 and 

16:1ω7. The sample from the dairy-waste pond contained high 

concentrations of terminally branched saturated fatty acids 

i14:0, i15:0, and a15:0—which, with the exception of i15:0 

(shown in table 5), were not among the 10 most commonly 

detected fatty acids in stormflow. 

The lowest concentrations, between about 5,000 and 

24,000 pmole/L, were from an urban stormdrain tributary to the 

Santa Ana River near the Imperial Highway diversion. 

Although the fatty acid composition of water from the 

stormdrain varied widely throughout the rainy season, several 

samples contained high concentrations of the monoenoic fatty 

acid 18:1ω7 and the polyenoic fatty acid 20:5ω3.
24 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Total Coliforms

Total PLFA

EXPLANATION

Simpson's reciprocal index

Species richness

Shannon-Weiner index

0

20

40

60

80

100

PERCENT

Percent is percentage of

streamflow derived from

runoff downstream

from Prado Dam

11/12/01 11/13/01 11/14/01

SAR at the diversion

downstream from

Imperial Highway

STREAMFLOW, IN CUBIC

FEET PER SECOND

TOTAL COLIFORMS, IN COLONIES

PER 100 MILLILITERS AND

PLFA, IN PICOMOLES PER LITER

10

100

1,000

10,000

10

1

100

1,000

10,000

100,000

1,000,000

10,000,000SIMPSON'S RECIPROCAL INDEX AND SPECIES RICHNESS

(note scale change)

0

20

40

60

80

100

0

5

10

PLFA

0

1

2

3

4

5

0

1

2

SHANNON-WEINER BIODIVERSITY INDEX

(note scale change)

0

1

2

3

4

5

PCR-Ddel with restriction endonucleases

PCR-amplification only

0

5

10

15

20

Figure 11. Total coliform bacteria and total phospholipid fatty acid (PLFA) concentrations as a function of streamflow, and changes in diversity of PLFA and the 

16S rRNA gene during the November 12–14, 2001, stormflow, Santa Ana River (SAR) at Imperial Highway, southern California. (PCR, polymerase chain reaction; 

16S rRNA, a bacterial ribosomal ribonucleic gene.)
Phospholipid Fatty Acids 25

Table 4. Eigenvectors composing the first and second principal components of phospholipid fatty acid structural groups and the 10 most common fatty acids in 

stormflow in the Santa Ana River at Imperial Highway, 1999–2000, and 2001–02 rainy seasons

[Fatty acids listed in order of average abundance; ↑, expected increase in fatty acid fraction; ↓, expected decrease in fatty acid fraction; —, no data]

Phospholipid

fatty acid

First

principal

component

Second

principal

component

Recessional flow,

first stormflow

of rainy season

Urban runoff,

first stormflow

of rainy season

 16:1ω7 −0.37 −0.40 ↑ —

 18:1ω7 −.08 −.05 — —

i16:0 .28 −.16 — —

 18:1ω9 .43 .22 ↓ —

 20:5ω3 .30 −.43 — ↑

 18:2ω6 .30 .42 ↓ —

 18:3ω3 .30 .16 ↓ —

 i15:0 −.31 .52 — ↓

 16:1ω5 −.34 .31 — —

 18:0 .32 .08 — —
26 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

–5

5

–5

0

5

FIRST PRINCIPAL COMPONENT, UNITLESS

SECOND PRINCIPAL COMPONENT, UNITLESS

First stormflow of the rainy season

All other data

Recessional

flows

Urban

runoff

EXPLANATION

Figure 12. The first principal component as a function of the second principal component for the 10 most common phospholipid fatty acids in stormflow in the 

Santa Ana River at Imperial Highway, southern California, 1999–2000 and 2001–02 rainy seasons.
Phospholipid Fatty Acids 27

Table 5. Total phospholipid fatty acid (PLFA) concentrations and percent of total PLFA for the 10 most commonly detected fatty acids in selected samples from 

the Santa Ana River basin, southern California

[Data collected by U.S. Geological Survey and analyzed by Microbial Insights, Inc.; DDMMSS, degrees, minutes, seconds; PLFA structural-group concentrations 

in percent of total PLFA concentration; pmole/L, picomoles per liter; pmole/g, picomoles per gram; SAR baseflow, Santa Ana River baseflow sample; urban drain, 

stormdrain tribuary to the Santa Ana River at Imperial Highway; SAR streambed, Santa Ana River streambed upstream from Imperial Highway; Prado wetland 

soil, wetland soil sample at Prado Dam; dairy waste pond, dairy waste pond near Pine Avenue; Cucamonga Creek baseflow, Cucamonga Creek near MiraLoma; 

Cucamonga Creek algae, Cucamonga Creek near Mira Loma algea sample; NA, not applicable; —, no data]

Sample Site 

No.

Latitude 

(DDMMSS)

Longitude 

(DDMMSS)

Sample

date

Total PLFA 

(pmole/g)

Total PLFA 

(pmole/L)

Terminally 

branched 

saturated 

(percent of 

total PLFA)

Monoenoic 

(percent 

of total 

PLFA)

Branched 

monoenoic 

(percent 

of total 

PLFA)

Mid-chain 

branched 

saturated 

(percent of 

total PLFA)

Normal 

saturated 

(percent 

of total 

PLFA)

Polyenoic 

(percent 

of total 

PLFA)

SAR baseflow 1 335123 1174723 08/29/01 NA 59,600 7.7 33 1.0 1.3 28 29

Urban drain 2 335122 1174718 12/09/99 NA 5,150 3.2 40 1.5 1.2 18 36

Urban drain 2 335122 1174718 03/02/00 NA 23,900 2.3 26 .6 3.3 22 47

Urban drain 2 335122 1174718 08/29/01 NA 17,200 4.5 40 1.6 3.6 25 25

SAR streambed 3 335223 1174448 12/09/99 3,690 NA 13.1 34 3.7 7.2 21 20

SAR streambed 3 335223 1174448 03/02/00 13,200 NA 9.3 29 2.8 4.8 22 33

SAR streambed 3 335223 1174448 08/29/01 107,000 NA 4.2 28 .3 .5 45 22

Prado wetland soil 5 335323 1173817 12/09/99 6,700 NA 16.0 36 5.4 5.0 22 17

Prado wetland soil 5 335323 1173817 03/02/00 3,080 NA 13.7 37 5.2 11 16 18

Prado wetland soil 5 335323 1173817 08/29/01 25,000 NA 10.9 33 2.0 5.5 22 26

Dairy waste pond 6 335645 1173922 08/29/01 NA 97,000 21.7 23 1.1 1.8 32 20

Cucamonga Creek 

baseflow

8 335858 1173555 12/09/99 NA 101,000 6.6 36 1.4 2.7 23 30

Cucamonga Creek 

algae

8 335858 1173555 08/29/01 342,000 NA 9.3 17 .7 .3 27 45

[Percent of total PLFA for the 10 most commonly detected fatty acids; standard nomenclature used for fatty-acid names follows the form 

X:YωZ, where X is the number of carbon atoms, Y is the number of carbon-carbon double bonds, ω is the end of the molecule, and Z is the 

number of carbon atoms between the terminal double bond and the methyl end of the molecule, i, isomethyl branching.]

Sample Site 

No. Date 16:1ω7 18:1ω7 i16:0 18:1ω9 20:5ω3 18:3ω3 16:1ω5 18:0 18:2ω6 i15:0

SAR baseflow 1 08/29/01 19.4 9.7 3.7 6.7 5.6 — 2.5 2.2 4.6 1.5

Urban drain 2 12/09/99 11.2 25.7 .5 12.8 7.7 2.5 .0 3.8 4.5 .5

Urban drain 2 03/02/00 12.8 8.0 .5 5.0 20.9 6.5 .8 3.5 8.1 .6

Urban drain 2 08/29/01 11.1 22.7 1.0 8.3 4.2 — 1.8 4.8 4.6 .6

SAR streambed 3 12/09/99 11.4 12.0 2.1 6.6 1.4 1.3 2.8 3.0 2.3 5.4

SAR streambed 3 03/02/00 23.9 2.4 2.2 2.8 2.0 — 1.2 .9 3.4 .7

SAR streambed 3 08/29/01 10.1 12.2 1.7 6.2 1.4 1.9 3.3 3.1 4.0 3.6

Prado wetland soil 5 12/09/99 7.0 9.0 1.0 5.9 .3 2.9 3.5 2.0 18.2 3.0

Prado wetland soil 5 03/02/00 9.1 12.1 2.2 6.5 .7 .7 4.2 2.5 4.3 4.2

Prado wetland soil 5 08/29/01 16.6 8.4 1.5 14.3 1.6 — 4.9 1.7 4.3 3.5

Dairy waste pond 6 08/29/01 11.2 8.3 2.4 10.1 .3 — 2.1 4.6 5.5 4.5

Cucamonga Creek 

baseflow

8 12/09/99 14.5 18.3 1.1 6.1 2.3 11.7 1.2 1.6 4.9 2.9

Cucamonga Creek 

algae

8 08/29/01 4.6 7.5 6.3 29.6 .2 — 1.4 1.2 9.3 1.6
28 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

The highest fatty acid concentration extracted from solid 

material, slightly greater than 340,000 picomoles per gram 

(pmole/g), was from algae sampled from the concrete-lined 

channel of Cucamonga Creek (table 5). This sample contained 

high concentrations of the monoenoic fatty acid 18:1ω9 but 

low concentrations of other commonly detected monoenoic 

fatty acids such as 16:1ω7 and 18:1ω7. The algae sample was 

very low in the polyenoic fatty acid 20:5ω3. Fatty acids in 

streambed material varied widely in concentration and 

composition. Concentrations were higher, about 

100,000 pmole/g, in streambed material collected prior to the 

beginning of the rainy season, and were as low as 

3,000 pmole/g in streambed material collected later in the rainy 

season. Fatty acid composition in streambed material was 

variable, but the sample collected prior to the beginning of the 

rainy season contained large amounts of the monoenoic fatty 

acid 16:1ω7.

Comparison of the principal component scores in table 4

with the fatty acid composition from selected sources (table 5) 

showed that the fatty acid composition of the first stormflow of 

the rainy season, when urban runoff from the area downstream 

from Prado Dam predominated, was similar to the fatty acid 

composition of samples collected from urban stormdrains. 

Some of the fatty acids present during the recessional flow of 

the first stormflow of the rainy season also could be explained 

by contributions from urban stormdrains. However, a 

combination of fatty acids from urban stormdrains (urban drain 

baseflow) and material mobilized from the bed of the Santa 

Ana River (SAR streambed) would be required to account for 

the large amounts of the monoenoic fatty acid 16:1ω7 present 

during these recessional flows. Fatty acids associated with 

streambed sediments during the latter part of the sampled 

stormflows may reflect recently disturbed streambed 

sediments equilibrating with the overlying water consistent 

with the proposed modifications to the model of Matson and 

others (1978). 

The algae sample had a high concentration of fatty acid 

18:1ω9. This fatty acid actually decreased during the recession 

of the first stormflow of the rainy season, suggesting that large 

amounts of algal material was not present in the Santa Ana 

River at that time—even though this material should be readily 

scoured from the concrete-lined channel of Cucamonga Creek 

during stormflow.

The sample from the dairy-waste pond had high 

concentrations of terminally branched saturated fatty acids 

such as i14:0, i15:0, and a15:0—which, only i15:0, is among 

the 10 most commonly detected fatty acids in the sampled 

stormflows. Concentrations of these fatty acids did not show a 

consistent increase or decrease during different parts of the 

stormflow hydrographs from this study, suggesting that direct 

release of material from dairy waste ponds did not occur during 

the sampled stormflows. This is consistent with field 

observations that showed that the sampled stormflows were 

not large and did not exceed the design criteria of the wastestorage ponds.

Data collected as part of this study show changes in the 

fatty acid composition of stormflow, presumably resulting 

from changing microbiological assemblages, as runoff was 

contributed from different sources within the basin. Additional 

data collection covering a greater range of stormflow 

conditions, which would include additional characterization of 

the fatty acid composition from different sources in the basin 

and characterization of seasonal changes in fatty acid 

composition, would be required to draw definitive conclusions 

about the sources of the fatty acids and the total microbial 

population they represent in the Santa Ana River during 

stormflow.

16S rRNA Gene

Genetic-based methods increasingly have been used to 

determine sources of fecal contamination in water (Bernstein 

and others, 2002; Hartel and others, 2002; Kern and others, 

2002; Wheeler and others, 2002; Bernhard and Field, 2000). 

The genes that compose the 16S rRNA gene has been 

characterized (Paul and Clark, 1996) and widely used for 

genetic studies of bacteria in water (Samadpour, 2002) and 

soils (Bruce, 1997; Liu and others, 1997; Dunbar and others, 

2000). The 16S rRNA gene can be isolated and specific 

regions of the gene, such as the hypervariable region, can be 

amplified using PCR (polymerase chain reaction). The base 

pair sequence in the hypervariable region is different in 

different bacterial species and, in a mixture of bacteria, species 

can be identified on the basis of their unique base pair sequence 

in that region.

One of the more common approaches for the 

interpretation of this type of data is to compare the pattern of 

the 16S rRNA gene with known patterns from organisms in a 

database developed from known sources (Samadpour, 2002). 

The development of such a database is often expensive and 

time consuming and was beyond the scope of this study. 

Databases developed from other geographic areas were not 

used because the spatial and temporal range over which these 

databases can be successfully used for the identification of 

bacteria is unknown (Hartel and others, 2002). In this study, 

fragment length patterns from the 16S rRNA gene isolated 

from different samples of stormflow using TerminalRestriction Fragment Length Polymorphism (T-RFLP) are 

representative of the genetic material from the entire microbial 

population. These data were not compared to libraries of 

genetic data from different organisms to identify specific 

organisms from specific sources, but rather these data were 

used to determine if the microbial community changed during 

the stormflow hydrograph and if total coliform and fecal 

indicator bacteria measured during different times within the 

hydrograph were associated with a similar or dissimilar 

bacteria populations—and were presumably from a similar or 

dissimilar source.
16S rRNA Gene 29

Amplicon Size and Diversity during Stormflow

Two methods were used to create the genetic profiles 

analyzed in this study. In the first method, a segment of the 

hypervariable region of the 16S rRNA gene, consisting of 

about 500 base-pairs, was amplified using universal eubacterial 

primers (Avaniss-Aghajani and others, 1996; Brunk and others, 

1996). The forward primer was labeled using a fluorescent dye 

and the total DNA was amplified using Polymerase Chain 

Reaction (PCR). In the second method, the labeled amplicons 

(PCR products) were digested into smaller fragments using 

DdeI restriction endonuclease according to a procedure known 

as Terminal Restriction Fragment Length Polymorphism

(T-RFLP). Digestion of the amplicons produced fragments of 

different size due to differences in the sequence of base pairs 

that compose the DNA. The genetic material is more finely 

subdivided during the digestion step and each fragment is 

believed to represent a different bacterial species. As a result, 

the T-RFLP analysis produces a genetic profile of the microbial 

community present in the water sample.

The undigested PCR products for three selected samples 

collected during the November 12–14, 2001, stormflow are 

shown in figure 13A. The samples represent base flow 

(streamflow prior to the onset of stormflow), urban runoff 

(from that part of the basin downstream from Prado Dam), and 

the recessional part of the stormflow hydrograph (streamflow 

at this time consists largely of runoff from areas upstream from 

Prado Dam and increasing amounts of base flow as flows 

decrease), and are representative of the changes in the 

microbial community across the stormflow hydrograph.

The undigested PCR products consisted of DNA 

fragments ranging in length from 422 to 483 base pairs. 

Comparison of the fragments in the three samples from the 

November 12–14, 2001, stormflow shows that of the 29 

different fragments detected only 2, having lengths of 427 and 

429 base pairs, were present in all three samples. The fragment 

having 429 base pairs was commonly detected in other 

stormflows sampled as part of this study, but the fragment 

having 427 base pairs was not commonly present in the lateseason stormflows sampled as part of this study. Six of the 

twenty-nine fragments detected were unique to base flow, 

6 were unique to urban runoff, and 10 were unique to the 

recession flow of the hydrograph and presumably represent 

organisms found only during those parts of the stormflow 

hydrograph. The data show large changes in the genetic profile, 

and the microbial community it represents, during stormflow.

More fragments, that were smaller in length, ranging from 

28 to 493 base pairs, were detected from the digested samples 

(fig. 13B) using T-RFLP. Fragments in the digested samples 

should not be larger than fragments present in the undigested 

samples. The absence of the longer fragments in the undigested 

samples may result from reduced sensitivity of the capillary 

electrophoresis technique when fewer fragments having 

greater individual peak height are present in the sample. 

Endonuclease digestion provided a finer discrimination of the 

genetic material from different bacteria—although it was more 

labor intensive. Additional digestion using another restriction 

enzyme may have yielded even more fragments and provided 

even finer discrimination of the genetic material. Of the ninetyfour different fragments detected only 4, having lengths of 240, 

241, 244, and 268 base pairs, were present in all three samples. 

These fragments were commonly detected in samples collected 

throughout the November 12–14, 2001, stormflow, but all were 

unexplainably absent in the last sample collected at 08:00 from 

the recession of this stormflow on November 14, 2001. Forty 

of the ninety-four fragments detected were unique to base flow, 

20 were unique to urban runoff, and 20 were unique to the 

recessional flow. The base-flow sample and the urban-runoff 

sample had the largest number of fragments in common, and 

the sample from the recession of the stormflow hydrograph had 

the fewest fragments in common with the other samples shown 

in red in figure 13. Even though streamflow returned to prestorm conditions by the end of the sample collection period, the 

genetic material sampled had not returned to pre-storm 

conditions. In the same manner demonstrated by the undigested 

PCR products, these data suggest large changes in the genetic 

material, and in the microbial community it represents, during 

stormflow.

PCR products, with and without digestion, showed 

increasing dominance of a few fragments during the recession 

of the November 12–14, 2001, stormflow (fig. 13). The effect 

is large and during recessional flow several fragments were 

present at concentrations, as indicated by peak height of the 

capillary electrophoresis, that were an order of magnitude 

larger than measured during base flow or during urban runoff. 

In the same manner shown by the PLFA data, the genetic 

profile data are consistent with bacterial contributions from 

sources that have only a limited diversity of bacteria.

Quantitative measures of fragment diversity, including 

species richness (calculated as the number of fragments 

present), Simpsons’s reciprocal index, and the ShannonWeiner index, were calculated from the number of fragments 

present and the peak height in a manner similar to that used for 

calculating phospholipid fatty acid diversity. These measures 

of diversity are shown for the entire November 12–14, 2001, 

stormflow in figure 11. For T-RFLP-with endonuclease 

digestion-species richness, Simpson's reciprocal index, and the 

Shannon-Weiner index decrease, indicating decreased 

diversity during stormflow. The lowest diversity was present 

during the recessional flows. Results were similar for PLFA 

and T-RFLP, with endonuclease digestion suggesting that 

similar conclusions can be drawn about changes in bacterial 

diversity and sources during stormflow, using either type of 

data. Indexes of diversity calculated on the basis of fragments 

obtained without endonuclease digestion increase during 

stormflow, and conclusions about the changes in the microbial 

community would be different using these data. It is likely that 

the genetic profile data without endonuclease digestion are too 

imprecise to adequately characterize changes in the microbial 

community during stormflow.
30 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

11/12/01, at 20:30 hrs

11/12/01, at 20:30 hrs

401 411 421 431 441 451 461 471 481 491 501

1 101 201 301 401 501

AMPLICON LENGTH, IN BASE-PAIRS

AMPLICON LENGTH, IN BASE-PAIRS

11/13/01, at 12:15 hrs

0

1,000

2,000

3,000

11/12/01, at 18:00 hrs

11/13/01, at 12:15 hrs

B

A

11/12/01, at 18:00 hrs

0

5,000

10,000

15,000

0

1,000

2,000

3,000

0

10,000

20,000

30,000

0

5,000

10,000

15,000

PEAK HEIGHT

(note scale change)

PEAK IHEIGHT

(note scale change)

0

50,000

100,000

150,000

Number of amplicons = 11

Simpson's reciprocal index = 3.52

Shannon-Weiner index = 1.57

Number of amplicons = 18

Simpson's reciprocal index = 0.68

Shannon-Weiner index = 1.54

Number of amplicons = 54

Simpson's reciprocal index = 17.1

Shannon-Weiner index = 3.34

Number of amplicons = 33

Simpson's reciprocal index = 13.4

Shannon-Weiner index = 3.00

Number of amplicons = 27

Simpson's reciprocal index = 4.88

Shannon-Weiner index = 2.14

Number of amplicons = 10

Simpson's reciprocal index = 4.41

Shannon-Weiner index = 1.77 (Base flow)

(Recessional flow)

(Urban runoff)

(Base flow)

(Recessional flow)

(Urban runoff)

Figure 13. Amplicons from Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis of the 16S rRNA gene with (A) polymerase chain reaction 

(PCR) amplification using universal eubacterial primers and (B) PCR amplification using eubacterial primers and digestion with DdeI restriction endonuclease for 

selected stormflow samples from the Santa Ana River at Imperial Highway, southern California, November 12–14, 2001.
Dissolved Organic Carbon 31

Comparison with Amplicons from Other Sources

Genetic profiles from stormflow were compared with 

profiles obtained with and without endonuclease digestion 

from a small number of samples from different sources. These 

sources included samples of dairy-pond wastes, algae from the 

Cucamonga Creek stormflow channel, and base flow discharge 

from an urban storm drain (fig 14). These samples are not 

intended to be inclusive of all possible sources in the Santa Ana 

River Basin but are representative of several possible sources 

of bacterial contamination.

Fragments from none of the three sources matched the 

very large peaks present in urban runoff and during the 

recession of the November 12–14, 2001 stormflow. However, 

a combination of urban runoff and algae could produce the very 

large peaks present in the recessional stormflow obtained from 

both PCR amplication without digestion and PCR amplication 

with digestion (T-RFLP). The PLFA data suggest that algae did 

not contribute to stormflow fatty acid composition, and 

T-RFLP analysis of streambed material were not available to 

determine if the resuspension of streambed sediments and 

associated bacteria could contribute to the material sampled 

during stormflow.

The large peaks present in stormflow are notably absent in 

the sample from the dairy-waste pond. These data support the 

suggestion that a direct release of dairy waste did not occur 

during the November 12–14, 2001 stormflow, which is 

consistent with field observations that suggest that dairy-waste 

ponds did not contribute to runoff during this period.

Dissolved Organic Carbon

Some dissolved organic carbon (DOC) within stormflow 

may be derived from the same sources as are fecal bacteria and, 

therefore, an understanding of the sources and changes in 

composition of DOC may help delineate the sources of fecal 

bacteria during stormflow. In addition, knowledge of the 

source and composition of DOC is important because there are 

other health concerns associated with DOC in stormflow. For 

example, it may be desirable to minimize the amount of DOC 

owing to the potential for disinfection by-product (DBP) 

formation during the chlorination of drinking water and to 

minimize the DOC of wastewater origin in water recharged 

from the Santa Ana River due to health concerns associated 

with this material.

Dissolved Organic Carbon Concentrations during 

Stormflow

The DOC concentrations in samples collected prior to the 

beginning of stormflow ranged from 4.2 to 7.6 mg/L, with a 

median concentration of 5.3 mg/L (Appendix C). 

Concentrations in samples collected prior to the beginning of 

stormflow were highest later in the rainy season. These values 

are similar to DOC concentrations in base flow in the Santa 

Ana River measured by Izbicki and others (2000). DOC 

concentrations of 3 to 5 mg/L are typical for surface water in 

arid regions (Thurman, 1986); however, because base flow in 

the Santa Ana River is primarily treated wastewater, the DOC 

concentration is largely controlled by the concentration of the 

wastewater discharges. Some increase in DOC concentrations 

in the Santa Ana River may occur as water flows through 

artificial wetlands used to remove nitrate upstream from Prado 

Dam. Gray and others (1996) showed that nitrate removal 

within these wetlands changed the composition of DOC in the 

Santa Ana River.

During this study, DOC concentrations in stormflow 

ranged from 3.0 to 15.0 mg/L, with a median concentration of 

6.7 mg/L. These values are similar to historical (1977–86) 

DOC concentrations in the Santa Ana River during the rainy 

season (Burton and others, 1998) and slightly lower than DOC 

concentrations in stormflow measured by Izbicki and others 

(2000). DOC concentrations increased during most stormflows 

and concentrations were higher during early season 

stormflows. The highest concentrations were measured during 

the recession of the first stormflows of the rainy season when 

stormflow was dominated by runoff from the area upstream 

from Prado Dam (fig. 15), similar to the distribution of total 

and fecal coliform bacteria concentrations in stormflow. The 

elevated DOC concentrations also persisted in the Santa Ana 

River for several days—frequently remaining high even after 

streamflow returned to pre-storm conditions. Similar results 

were obtained for stormflow samples collected from the Santa 

Ana River during 1995–98 (Izbicki and others, 2000). In 

general, DOC concentrations in late-season stormflows were 

lower than concentrations in the first stormflow of the rainy 

season. However, if antecedent conditions were dry, DOC 

concentrations in late-season stormflows were higher and 

approached concentrations measured during the first stormflow 

of the rainy season.
32 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

AMPLICON LENGTH, IN BASE-PAIRS

0

3,000

6,000

0

3,000

6,000

0

3,000

6,000

Urban base flow

Algae from Cucamonga Creek

Number of amplicons = 43

Simpson's recprocal index = 15.9

Shannon-Weiner index = 3.1

1 101 201 301 401 501

Number of amplicons = 35

Simpson's reciprocal index = 0.94

Shannon-Weiner index = 3.1

Dairy-waste pond

Number of amplicons = 61

Simpson's reciprocal index = 12.0

Shannon-Weiner index = 3.3

B

PEAK HEIGHT

401 411 421 431 441 451 461 471 481 491 501

AMPLICON LENGTH, IN BASE-PAIRS

Dairy-waste pond Number of amplicons = 13

Simpson's reciprocal index = 5.0

Shannon-Weiner index = 1.9

0

5000

10,000

15,000

20,000

0

5000

10,000

15,000

20,000

0

5000

10,000

15,000

20,000

Urban base flow

Algae from Cucamonaga Creek

Number of amplicons = 16

Simpson's reciprocal index = 7.6

Shannon-Weiner index = 2.3

Number of amplicons = 18

Simpson's reciprocal index = 7.2

Shannon-Weiner index = 2.3

A

PEAK HEIGHT

Figure 14. Amplicons from Terminal-Restriction Fragment Length Polymorphism (T-RLFP) analysis of the 16S rRNA gene with (A) polymerase chain reaction 

(PCR) amplification using universal eubacterial primers and (B) PCR amplification using eubacterial primers and digestion with DdeI restriction endonuclease for 

selected samples from the Santa Ana River Basin, southern California.
Dissolved Organic Carbon 33

0

20

40

60

80

100

11/11/01 11/15/01 11/12/01 11/13/01 11/14/01

UV absorbance at

254 nanometers

Dissolved organic

carbon

EXPLANATION

Percent is percentage of

streamflow derived from

runoff downstream

from Prado Dam

0.0

0.2

0.4

0.6

0.8

1.0

0

5

10

15

20

DISSOLVED ORGANIC CARBON,

IN MILLIGRAMS PER LITER

UV ABSORBANCE

AT 254 NANOMETERS

PERCENT

STREAMFLOW, IN CUBIC

FEET PER SECOND

10

100

1,000

10,000

0

20

40

60

80

100

1/10/01 1/11/01 1/12/01 1/13/01 1/14/01

Percent is percentage of

streamflow derived from

runoff downstream

from Prado Dam

DISSOLVED ORGANIC CARBON,

IN MILLIGRAMS PER LITER

0

5

10

15

20

PERCENT

0.0

0.2

0.4

0.6

0.8

1.0

UV ABSORBANCE

AT 254 NANOMETERS

10

100

1,000

10,000

STREAMFLOW, IN CUBIC

FEET PER SECOND PERCENT

1/23/00 1/24/00 1/26/00 1/27/00 1/25/00

Percent is percentage of

streamflow derived from

runoff downstream

from Prado Dam

NO DOC DATA

0

20

40

60

80

100

0.0

0.2

0.4

0.6

0.8

1.0

UV ABSORBANCE

STREAMFLOW, IN CUBIC

AT 254 NANOMETERS

FEET PER SECOND

10,000

10

1,000

100

Figure 15. Changes in dissolved organic carbon (DOC) concentration and ultraviolet (UV) absorbance at 254 nanometers during the first stormflows of the 

1999– 2000, 2000–01, and 2001–02 rainy seasons, Santa Ana River at Imperial Highway, southern California.
34 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Dissolved Organic Carbon Compositions during 

Stormflow

Characterization of the composition of DOC may help 

identify its origin and allow predictions about its fate in the 

environment. Thorough characterization of DOC is a complex 

task requiring a hierarchical analytical approach that may 

determine, among other things, (1) operationally defined 

organic fractions, (2) functional-group characteristics, 

(3) molecular weight, and (4) the concentrations of specific 

organic compounds (Leenheer and Huffman, 1976; Barber, 

1992). This hierarchical approach is time consuming, labor 

intensive, and expensive. Given the number of samples 

collected and the rapid changes in DOC during stormflow, such 

a rigorous approach was beyond the scope of this study.

As part of this study, a simplified approach that utilizes 

changes in the optical properties of water was used to 

characterize DOC for most samples collected in this study. 

Exposure to specific wavelengths of light can cause changes in 

DOC compounds at the atomic level. These changes include 

the transition of electrons to higher energy levels, rotational or 

vibrational changes within bonds, or changes in the spin of 

atomic nuclei (Hart and Schuetz, 1972). Such changes result in 

the absorbance and fluorescence of energy that is related to the 

presence of specific functional groups within complex carbon 

molecules. Optical properties of DOC are especially useful for 

identification of aromatic (benzene-like ring-structures) and 

aliphatic (carbon compounds that do not contain benzene-like 

ring structures). Interpretation of optical data is complex and 

not quantitative. Simple molecules such as methane (CH4) 

have several absorption bands, and more complex molecules 

may absorb and fluoresce light energy at many wavelengths. 

Most natural DOC is complex and some material is more 

aromatic, containing many benzene-like ring structures, while 

other material is more aliphatic (less aromatic), containing 

fewer benzene-like ring structures.

To assist in the characterization of DOC, optical data were 

supplemented with measurements of specific fractions of DOC 

during the 2001–02 rainy seasons. Ultraviolet absorbance 

spectra were measured on the DOC fractions, but individual 

compounds within each fraction were not determined.

Ultraviolet Absorbance

Dissolved organic carbon absorbance within the UV range 

[220–800 nanometers (nm)] is usually associated with 

unsaturated molecules such as those containing carbon-carbon 

double bonds, carbon-oxygen double bonds, or carbon-carbon 

double bonds in complex aromatic (benzene-like) ring 

structures (Gutsche and Pasto, 1975). Carbon-carbon double 

bonds within aromatic rings generally absorb near 254 nm and 

carbon-oxygen double bonds generally absorb near 285 nm 

(Gutsche and Pasto, 1975). However, the exact absorbance 

wavelength changes with the length and complexity of the 

associated carbon molecules and other structures. As a result, 

ultraviolet absorbance spectra do not show pronounced peaks 

at wavelengths corresponding to specific functional groups but 

instead are smooth curves. The shape of these curves can vary 

significantly in individual samples (fig. 16).

UV absorbance spectra can be used to quantify the 

concentrations of individual compounds in simple mixtures; 

however, absorbance data are not quantitative for solutions 

containing complex mixtures of natural and anthropogenic 

compounds. Nitrate and iron also absorb within the UV range, 

and some interference due to these constituents has been 

observed in stormflow samples from the Santa Ana River 

(Izbicki and others, 2000). For example, comparison of the 

UV spectra for early season base flow samples collected on 

January 25, 2000, at 0915 and January 10, 2001, at 1540 shows 

a large difference in UV absorbance in the range of 190 to 

about 230 nm (fig. 16). Much of this difference can be 

attributed to differences in nitrate concentrations, which were 

3.7 and 6.6 mg/L as nitrogen, respectively (Appendix D). 

Because nitrate concentrations in the Santa Ana River decrease 

during stormflow, and because nitrate does not greatly affect 

UV absorbance at higher wavelengths (such as 254 and 

285 nm), interference from nitrate is small for most stormflow 

samples. UV absorbance data have been used in previous 

studies as a surrogate for DOC concentrations (California 

Department of Water Resources, 1994) and, despite their lack 

of specificity, UV absorbance data have been used as an 

indicator of DOC composition (Krazner and others, 1996; 

Izbicki and others, 2000). 

Ultraviolet absorbance was measured between 190 and 

310 nm as part of this study (fig. 16); however, for 

convenience, most analysis was done on data collected at 

254 and 285 nm. As previously discussed, these wavelengths 

correspond to the peak absorbance of carbon-carbon double 

bonds and carbon-oxygen double bonds, respectively. 

Ultraviolet absorbance at 254 nm (UV254) in pre-stormflow 

conditions from the Santa Ana River at Imperial Highway 

ranged from 0.092 to 0.240, with a median absorbance of 

0.130. Ultraviolet absorbance at 254 nm in stormflow ranged 

from 0.102 to 0.649, with a median absorbance of 0.237. UV254

was generally well correlated with DOC and increased in a 

similar manner as urban runoff and other sources contributed to 

stormflow (fig. 15). Ultraviolet absorbance at 285 nm (UV285) 

was smaller in magnitude but generally well correlated with 

UV254, having a Spearman rank correlation coefficient of

ρ = 0.99.
Dissolved Organic Carbon 35

Early-season base flow—11/12/01 at 18:00

Late-season base flow—03/06/02 at 18:30

Early-season urban runoff—11/12/01 at 20:30

Early-season recessional flow—11/13/01 at 12:15

Shallow ground water—11/14/01 at 09:15

2001–02 rainy season

Early-season base flow—01/10/01 at 15:40

Early-season urban runoff—01/11/01 at 03:00

Early-season recessional flow—01/12/01 at 00:30

Late-season reservoir release—03/06/01 at 04:00

2000–01 rainy season

285

190 200 210 220 230 240 250 260 270 280 290 300 310

WAVELENGTH, IN NANOMETERS

ABSORBANCE

Early-season base flow—01/25/00 at 09:15

Late-season base flow—02/12/00 at 00:00

Early-season urban runoff—01/25/00 at 10:40

Early-season recessional flow—01/26/00 at 10:40

Late-season reservoir release—02/25/00 at 03:00

1999–2000 rainy season

254 285

254

254 285

0

1

2

3

4

5

6

7

190 200 210 220 230 240 250 260 270 280 290 300 310

WAVELENGTH, IN NANOMETERS

ABSORBANCE

0

1

2

3

4

5

6

7

190 200 210 220 230 240 250 260 270 280 290 300 310

WAVELENGTH, IN NANOMETERS

ABSORBANCE

0

1

2

3

4

5

6

7

Figure 16. Selected full-spectrum ultraviolet (UV) absorbance scans, Santa Ana River at Imperial Highway, 1999–2000, 2000–01, and 2001–02 rainy seasons.
36 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

UV254 absorbance data are compared with DOC 

concentrations in figure 17. The slope of the lines shown in 

figure 17 have units of DOC in mg/L per absorbance at 

254 nm, and the inverse of the slope is conceptually similar to 

specific UV absorbance (SUVA) discussed in some studies. 

The data show that there is less UV254 absorbance per unit 

carbon in early season stormflows than in other stormflows. 

This is consistent with less aromaticity (fewer benzene-like 

ring structures) in DOC from this stormflow. The equation of 

the line through the data was not significantly different from 

the equation used to describe the relation between DOC and 

UV254 absorbance in early season stormflows sampled during 

1995–98 in the Santa Ana River at Imperial Highway by 

Izbicki and others (2000) (table 6). This result suggests that the 

DOC in early season stormflows is similar to DOC sampled 

previously in similar stormflows.

Despite occurring more than 2 months after the usual start 

of the rainy season, the January 10–14, 2001, stormflow was 

the first stormflow of that winter's rainy season. The 

composition of DOC during this stormflow was different from 

that of the November 12–14, 2001, stormflow and early-season 

stormflows sampled by Izbicki and others (2000), and was 

more similar to the composition of DOC in late-season 

stormflows. Organic carbon that accumulated in the basin 

during the previous dry season had not been washed off during 

previous stormflows, but had apparently changed in 

composition and become more aromatic, resembling the DOC 

of other late-season stormflows sampled as part of this study. 

This could occur as a result of the decomposition of simpler, 

straight-chain, aliphatic carbon compounds such as sugars, 

starches, and waxes common in plant material.

The equations in table 6 describe the slope of DOC in lateseason stormflows, which is significantly less than the slope 

estimated for similar late-season stormflow data collected by 

Izbicki and others (2000), and reflect more carbon-carbon 

double bonds per unit carbon than do previously collected data. 

Data collected as part of this study were collected under dryer 

conditions than data collected previously by Izbicki and others 

(2000). Under the wetter conditions that prevailed during 

1995–98, the reservoir behind Prado Dam contained water 

during the later part of the rainy season. Soils and vegetation 

within the flooded area contributed DOC to water held behind 

the dam and downstream reaches of the Santa Ana River. 

Under the dryer conditions that prevailed during this study, the 

reservoir behind Prado Dam did not contain water and did not 

contribute DOC to late-season stormflows.

Comparison of UV254 and UV285 data (fig. 17) shows that 

DOC in the January 10–14, 2001, stormflow has optical 

properties, and presumably composition, that is more similar to 

late-season stormflows rather than the first stormflow of the 

2000–01 rainy season. This result is consistent with alteration 

of the organic carbon prior to the beginning of the rainy season. 

The slopes of the early-season equations are not significantly 

different from the slope estimated from similar data collected 

by Izbicki and others (2000). The optical-property data suggest 

that the composition of DOC of the early season stormflows 

sampled as part of this study are similar to the composition of 

early season stormflows sampled from the Santa Ana River at 

Imperial Highway between 1995 and 1998 by Izbicki and 

others (2000). 

Excitation/Emission Spectroscopy

In addition to absorbance at selected wavelengths, 

dissolved organic matter also fluoresces when irradiated at 

different wavelengths. The technique used in this study to 

measure this property is known as excitation/emission (EEM) 

spectroscopy, and the resulting spectra is a three-dimensional 

map of fluorescence intensity as a function of excitation 

wavelength and emission wavelength. Like UV absorbance, 

EEM spectra of natural DOC is a continuum that does not show 

peaks at specific wavelengths that correspond to specific 

functional groups or compounds. However, various 

researchers have identified fluorescence at specific 

wavelengths that may be associated with proteins (Traganza, 

1969; Coble and others, 1990) and humic substances (Coble 

and others, 1990; Mopper and Shultz, 1993). Other researchers 

have used EEM spectra for tracking aromatic structures, and 

unsaturated structures containing carbonyl groups that exhibit 

strong EEM signals (Kresovitskii and Bolotin, 1988; Skoog 

and others, 1998).

The intensity of the fluorescence at different excitation 

and emission wavelengths changed in patterns that were 

similar from stormflow to stormflow. Numerical approaches 

that interpret changes in EEM spectra as mixtures from 

selected source waters (Marhaba and others, 2000) have been 

used in the Santa Ana River Basin (Brian Bergamaschi, USGS, 

written commun., 2003). However, quantitative, numerical 

interpretation of EEM spectra was beyond the scope of this 

study and no attempt was made to identify specific compounds 

or functional groups within the dissolved organic matter that 

contributed to the spectra.

More than 160 excitation/emission spectra were 

measured on samples collected from eight stormflows during 

the 1999–2000, 2000–01, 2001–02 rainy seasons. Stormflow 

samples show a distinct series of changes in fluorescence 

intensity at different excitation and emission wavelengths as 

runoff from different sources enters the Santa Ana River 

during different parts of the stormflow hydrograph. This 

sequence is illustrated by selected EEM spectra from three 

sampled stormflows (fig. 18). The stormflows are discussed 

from the smallest to the largest stormflow.
Dissolved Organic Carbon 37

0.0

0.2

0.4

0.6

0.8

0

5

10

15

20

25

0.0 0.2 0.4 0.6 0.8

UV ABSORBANCE AT 254 NANOMETERS

UV ABSORBANCE AT 285 NANOMETERS DISSOLVED ORGANIC CARBON,

IN MILLIGRAMS PER LITER

Early-season stormflows

DOC = 1.8 + 27.9 UV254

Late-season stormflows

DOC = 5.3 + 3 UV254

January 10–14, 2001,

stormflow

Shallow ground water

Base flow

Early-season stormflows

Late-season stormflows

January 10–14, 2001, stormflow

Shallow ground water

EXPLANATION

Analysis of covariance R2 = 0.88

Shallow ground water

Base flow

Late-season stormflows

UV285 = -0.02 + 0.82 UV254

UV285 = 0.01 + 0.65 UV254

Early-season stormflows

Increasing

absorbance per

unit carbon

Analysis of covariance R2 = 0.98

Figure 17. Dissolved organic carbon (DOC) as a function of UV254, and UV285 as a function of UV254, in stormflow in the Santa Ana River at Imperial Highway, 

southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons. UV, ultraviolet.
38 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Table 6. Equations describing the relation between dissolved organic carbon (DOC) and ultraviolet (UV) absorbance in early-season and late-season stormflows 

in the Santa Ana River, California

[1995–98 data modified from Izbicki and others, 2000; DOC, dissolved organic carbon; UV254, ultraviolet absorbance at 254 nanometers; UV285, ultraviolet 

absorbance at 285 nanometers]

Data-collection

period Early-season stormflows Late-season stormflows

1995–98 DOC = 1.9 + 28.1 UV254 DOC = 1.9 + 23.2 UV254

2000–02 DOC = 1.8 + 27.9 UV254 DOC = 5.3 + 3 UV254

1995–98 UV285 = 0.78 UV254 − 0.01 UV285 = 0.69 UV254

2000–02 UV285 = 0.82 UV254 − 0.02 UV285 = 0.01 + 0.65 UV254
Dissolved Organic Carbon 39

400 300

300 400 500 600 700

0

50E+05

10E+06

15E+06

20E+06 1/10/01

at 15:40 hrs

1/11/01

at 01:00 hrs

1/12/01

at 00:30 hrs

11/12/01

at 15:55 hrs

11/12/01

at 20:30 hrs

11/14/01

at 10:00 hrs

3/6/02

at 18:30 hrs

3/7/02

at 06:00 hrs

3/7/02

at 20:00 hrs

1/14/01

at 12:00 hrs

1/10–14/2001 Stormflow 11/12–14/2001 Stormflow

EXPLANATION

3/6–8/2002 Stormflow

Base flow

DOC = 4.6 mg/L

UV254 = 0.11

Streamflow =

275 cubic feet

per second

Streamflow =

234 cubic feet

per second

Streamflow =

255 cubic feet

per second

Streamflow =

456 cubic feet

per second

Streamflow =

380 cubic feet

per second

Streamflow =

224 cubic feet

per second

Streamflow =

3,840 cubic feet

per second

Streamflow =

367 cubic feet

per second

Streamflow =

260 cubic feet

per second

Streamflow =

237 cubic feet

per second

End of sample

collection

DOC = 8.1 mg/L

UV254 = 0.37

80%Urban runoff

DOC = 6.1 mg/L

UV254 = 0.18

DOC = 10.1 mg/L

UV254 = 0.59

Base flow

DOC = 4.8 mg/L

UV254 = 0.13

40 % Urban runoff

DOC = 13.4 mg/L

UV254 = 0.41

End of sample

collection

DOC = 11.5 mg/L

UV254 = 0.34

Base flow

DOC = 4.3 mg/L

UV254 = 0.10

10 % Urban runoff

DOC = 5.6 mg/L

UV254 = 0.14

End of sample

collection

DOC = 4.6 mg/L

UV254 = 0.11

400 300

300 400 500 600 700

50E+05

0

10E+06

15E+06

20E+06

400300 0

50E+05

10E+06

15E+06

20E+06

300 400 500 600 700

400

300

0

50E+05

10E+06

15E+06

20E+06

300 400 500 600 700

0

50E+05

10E+06

15E+06

20E+06

300 400 500 600 700

300

600

600 300

0

50E+05

10E+06

15E+06

20E+06

300 400 500 600 700

600 300

0

50E+05

10E+06

15E+06

20E+06

300 400 500 600 700

0

50E+05

10E+06

15E+06

20E+06

300 400 500 600 700

600

300

0

50E+05

10E+06

15E+06

20E+06

300 400 500 600 700

600 300

0

50E+05

10E+06

15E+06

20E+06

300 400 500 600 700

600

300

EXCITATION

WAVELENGTH,

EMISSION WAVELENGTH, IN NANOMETERS

IN NANOMETERS

INTENSITY, IN QUININE

SULFATE UNITS

DOC Dissolved organic carbon

UV254 Ultraviolet absorbance

at 254 nanometers

mg/L milligrams per liter

hrs hours

Figure 18. Selected excitation/emission spectra for three stormflows in the Santa Ana River at Imperial Highway, southern California.
40 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Data collected during the March 6–8, 2002, stormflow 

(fig. 18) show that EEM spectra are sensitive to even small 

changes in DOC concentrations and composition. This lateseason stormflow was one of the smallest stormflows sampled 

during this study and only 0.25 in. of precipitation was 

measured at Prado Dam. DOC concentrations ranged from 

4.3 to 7.6 mg/L (Appendix C), and changes in total and fecal 

coliform bacteria concentrations during this stormflow were 

small (Appendix A). DOC and bacteria concentrations were 

difficult to relate to stormflow, because most of the 

precipitation fell near the coast with only small, scattered 

showers farther inland that produced almost no runoff from 

upstream parts of the basin, and because flow in the Santa Ana 

River decreased as a result of regulation at Prado Dam. Despite 

the small amount of precipitation and subsequent runoff, and 

only small changes in the DOC concentrations, there are 

measurable changes in the intensity and shape of the EEM 

spectra as runoff from urban areas downstream from Prado 

Dam entered the Santa Ana River on March 7 at 0600 (fig. 18). 

For example, samples collected prior to the onset of stormflow 

on March 6 at 1830 have relatively high intensity at excitation 

wavelengths near 285 nm and emission wavelengths near 

375 nm that give the spectra a pronounced “shoulder” in that 

region (fig. 18). This shoulder is not present in the EEM 

spectra from samples collected on March 7 at 0600 when 

runoff from urban areas was present. By 2000 on March 7, the 

EEM spectra from DOC in the river had returned to pre-storm 

conditions (fig. 18). 

Data collected during the November 12–14, 2001, 

stormflow show a pattern similar to that observed during the 

March 6–8, 2002, stormflow. This was the first stormflow of 

the 2001–02 rainy season and, although only 0.5 in. of 

precipitation was measured at Prado Dam, most precipitation 

fell during a short period at the beginning of the storm and 

precipitation occurred throughout the basin. DOC 

concentrations ranged from 4.8 to 13.5 mg/L (Appendix C). 

The changes in total and fecal coliform bacteria concentrations 

were large during this stormflow and during the recession of 

this stormflow. Total coliform bacteria concentrations were as 

high as 3,400,000 colonies per 100 mL and fecal coliform 

bacteria concentrations were as high as 310,000 colonies per 

100 mL (Appendix A). These were the highest concentrations 

measured in the Santa Ana River at Imperial Highway during 

this study. The EEM spectra from samples collected prior to 

the storm on November 12 at 1555 (fig. 18) were similar in 

magnitude to the samples collected prior to the 

March 6–8, 2002, stormflow and to most other samples 

collected prior to the beginning of stormflow; the spectra for 

the November 12, at 1555, samples had the distinctive 

“shoulder” near an excitation wavelength of 280 nm and an 

emission wavelength near 350 nm. The intensity and shape of 

the EEM spectra changed by November 12, at 2030, when 

runoff from urban areas downstream from Prado Dam and 

associated DOC were present. Unlike the March 6–8, 2002, 

stormflow, the EEM spectra did not return to pre-storm 

conditions at any time during the sampling period. This is 

because DOC from runoff from urban areas upstream from 

Prado Dam continued to dominate the EEM spectra even 

though streamflow returned to pre-storm conditions. Total and 

fecal coliform bacteria concentrations also remained high 

throughout the stormflow sample-collection period.

Changes in EEM spectra for samples collected during the 

January 10–14, 2001, stormflow are similar to changes 

measured on samples collected during the November 12–14, 

2001, stormflow (fig. 18)—but the EEM spectra are lower in 

intensity, presumably owing to the lower DOC concentrations. 

Despite the lower DOC concentrations and lower EEM 

intensities, the sample collected January 11 at 0100 had the 

highest percentage of runoff from urban areas downstream 

from Prado Dam (slightly more than 80 percent) of all samples 

collected during this study. These samples illustrate that there 

is not a 1 to 1 correspondence between runoff from selected 

sources and the DOC concentration of water from that source. 

However, the EEM spectra suggest that the composition of 

DOC in stormflow may remain relatively constant despite 

changing antecedent conditions that may change the 

concentration. The intensity and shape of the EEM spectra for 

samples collected during the January 10–14, 2001, stormflow 

did not return to pre-storm conditions during the samplecollection period; similarly total and fecal coliform bacteria 

concentrations remained high during the sample-collection 

period in a pattern similar to that of the November 12–14, 

2001, stormflow.

Dissolved Organic Carbon Fractionation

Operational fractions of DOC, defined by their ability to 

pass-through or sorb on XAD8 or XAD4 resins under different 

pHs (Aiken and others, 1992), were measured for two 

stormflows sampled during the 2001–02 rainy season. The 

fractions include hydrophobic acids, hydrophilic acids, 

transhydrophilic acids, and the hydrophobic-neutral fractions 

of the DOC.

The hydrophobic-acid fraction typically consists of 

aliphatic carboxylic acids having five to nine carbons, one- and 

two-ring aromatic carboxylic acids, one- and two-ring phenols, 

and aquatic humic and fulvic substances (Aiken and others, 

1992). Hydrophobic acids typically account for about 

30 percent of the DOC in natural water but may account for as 

much as 50 to 90 percent of the DOC in highly colored water 

(Thurman, 1986).
Dissolved Organic Carbon 41

The hydrophilic-acid fraction typically consists of more 

readily soluble compounds and may contain sugar acids, 

alcohols, polyfunctional organic acids, and aliphatic acids with 

five or fewer carbon atoms (Thurman, 1986; Aiken and others, 

1992). This fraction contains fewer aromatic compounds; 

therefore, it should contain relatively fewer THM and DBP 

precursors in comparison with the hydrophobic-acid fraction 

(Fujii and others, 1998).

The hydrophobic acids were the largest fraction within 

the DOC during both base flow and stormflow, composing 

about 33 percent (median value) of the DOC during the two 

sampled stormflows (table 7). The DOC concentration and the 

percent hydrophobic acid increased during both stormflows 

and composed as much as 45 percent of the DOC during the 

recessional flow of the November 12–14, 2001, stormflow. 

The highest concentrations were present during the recessional 

flow. Hydrophilic acids were the next largest fraction within 

the DOC. The concentrations and percent of total DOC were 

similar for hydrophobic and hydrophilic acids for pre-storm 

samples; however, the hydrophilic-acid fraction decreased 

during stormflow to slightly more than 20 percent of the total 

DOC—although concentrations of hydrophilic acids 

subsequently increased during the recessional flows of both 

sampled stormflows. These results are consistent with 

increased aromaticity in DOC composition in the recession of 

stormflows in Santa Ana River inferred from UV absorbance 

measurements by Izbicki and others (2000) and with 

UV absorbance data presented in this report (fig. 17). The 

transhydrophilic-acid fraction remained relatively constant, 

between 21 and 13 percent of the DOC, during stormflow, 

although concentrations increased with increasing DOC 

concentrations (table 7). The hydrophobic-neutral fraction 

varied widely during stormflow, ranging between 2 and 

29 percent of the total DOC. The highest hydrophobic-neutral 

fractions were present in samples collected during the 

transition from stormflow dominated by urban runoff from the 

area downstream from Prado Dam to the recessional flows 

dominated by runoff from the area upstream from Prado Dam. 

Motor oils and many other relatively insoluble contaminants 

associated with runoff from city streets may be within this 

fraction. These compounds composed a large fraction of the 

DOC on the rising limb of the hydrograph after hydrophobic 

acids from urban areas downstream from Prado Dam were 

washed from the basin.

Total Coliform Bacteria, Fecal 

Coliform Bacteria, and Dissolved 

Organic Carbon Concentrations in 

Shallow Ground Water during 

Stormflow

Samples of shallow ground water were collected during 

stormflow in the 2001–02 rainy season from the subsurfacecollection and recharge system (SCARS) operated by OCWD 

and analyzed for fecal indicator bacteria, DOC concentrations 

and optical properties. The SCARS system collects water by 

gravity drainage through three, 1,000-foot-long, 

6-inch-diameter perforated pipes buried about 4 ft below the 

bed of the OCWD off-channel recharge facility along side of 

the Santa Ana River about 1 mi. downstream from Imperial 

Highway (Gregory Woodside, Orange County Water District, 

unpub. data, 2001).

Total coliform bacteria concentrations in shallow ground 

water collected from the SCARS during two stormflows 

during the 2001–02 rainy season were low and ranged from 

less than the detection limit of 10 to 130 colonies per 100 mL 

(Appendix A). Smaller changes in concentrations were 

measured for fecal coliforms, E. coli, and enterococci bacteria, 

which rarely exceeded the detection limit of 10 colonies per 

100 mL (Appendix A). Similarly, DOC concentrations 

measured in shallow ground water collected from the SCARS 

during two stormflows during the 2001–02 rainy season were 

low and ranged from 1.4 to 2.4 mg/L (Appendix C). DOC 

concentrations showed only small increases during 

stormflows. UV absorbance values also were low. These 

results suggest that most bacteria and much of the DOC are 

removed as water infiltrates through the bed of the Santa Ana 

River.
42 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Table 7. Dissolved organic carbon (DOC) concentrations and hydrophobic-acid, hydrophobic-neutral, hydrophilic-acid, and transhydrophilic-acid fractions of 

dissolved organic carbon in stormflow samples collected from the Santa Ana River at Imperial Highway and from Mill Creek at Chino-Corona Road, southern 

California, 2001–02 rainy season

[Samples from the Santa Ana River at Imperial Highway collected by the U.S. Geological Survey, samples from Mill Creek at Chino–Corona Road collected by 

Orange County Water District; all samples analyzed by the U.S. Geological Survey laboratory in Boulder, Colorado; results for dissolved organic carbon may 

differ slighty from results in Appendix C; mg/L, milligrams per liter; percent, percent of dissolved organic carbon; —, no data]

Sample

date Time

Dissolved 

organic

carbon

Hydrophobicacid-fractionHydrophobicneutral-fractionHydrophilicacid-fractionTranshydrophilicacid-fraction

(mg/L) (mg/L) (percent) (mg/L) (percent) (mg/L) (percent) (mg/L) (percent)

Santa Ana River at Imperial Highway

11/12/01 1800 5.9 2.2 37 0.1 2 2.2 37 1.2 21

11/12/01 2030 10.6 4.1 39 .3 3 2.7 25 1.7 16

11/12/01 2240 7.5 2.2 30 1.8 24 1.9 25 1.1 15

11/13/01 0100 6.9 1.9 27 2.0 29 1.8 26 1.0 14

11/13/01 0340 5.9 1.9 33 .8 13 1.8 30 1.1 18

11/13/01 1215 18.5 7.9 43 2.0 11 4.3 23 3.2 17

11/14/01 0800 12.4 5.6 45 .9 7 3.1 25 2.1 17

03/06/02 1830 4.5 1.5 33 .8 17 1.4 32 .8 17

03/07/02 0650 4.9 1.7 34 .8 17 1.5 30 .8 17

03/07/02 1030 5.2 1.8 34 .9 18 1.5 29 .8 15

03/07/02 1330 5.3 1.5 29 1.2 22 1.5 28 .9 17

03/07/02 1630 5.0 1.5 30 1.1 21 1.4 28 .8 15

03/07/02 2300 5.1 1.6 32 .9 18 1.5 29 .8 15

03/08/02 0700 8.6 3.2 37 2.0 23 2.1 24 1.1 13

Mill Creek at Chino-Corona Road

11/12/01 1720 5.2 1.4 26 .2 4 2.1 41 .9 17

11/12/01 1945 5.8 1.6 28 .5 8 2.2 38 .9 16

11/12/01 2015 34.4 15.5 45 3.4 10 7.6 22 5.2 15

11/12/01 2030 35.0 15.4 44 3.9 11 7.7 22 5.3 15

11/12/01 2045 43.5 20.4 47 4.4 10 9.1 21 6.5 15

11/12/01 2100 28.7 12.9 45 3.2 11 6.3 22 4.3 15

11/12/01 2115 29.8 — — — — — — — —

11/12/01 2130 27.6 — — — — — — — —

11/12/01 2145 25.9 11.9 46 1.3 5 8.3 32 4.1 16

11/12/01 2200 23.3 10.5 45 1.9 8 6.5 28 3.7 16

11/12/01 2245 28.0 12.9 46 3.4 12 6.2 22 4.2 15
Conclusions 43

Conclusions

Total and fecal indicator bacteria concentrations increased 

in the Santa Ana River at Imperial Highway during stormflow. 

Total coliform bacteria concentrations in stormflow were as 

high as 3,400,000 colonies per 100 mL. Fecal coliforms, 

Escherichia coli, and enterococci concentrations were as high 

as 310,000, 84,000, and 100,000 colonies per 100 mL, 

respectively. The highest concentrations were measured during 

the first stormflow of the winter rainy season. Although runoff 

from urban areas downstream from Prado Dam contributed 

high concentrations of fecal indicator bacteria, the 

concentrations measured in the recessional flows of the first 

stormflow of the rainy season—when runoff was derived from 

areas upstream from Prado Dam—were as much as an order of 

magnitude higher. High concentrations of fecal indicator 

bacteria persisted even after the river returned to prestormflows and were not likely to have resulted solely from 

urban runoff.

The highest total and fecal coliform bacteria 

concentrations (7,300,000 and 530,000 colonies per 100 mL, 

respectively) measured by OCWD personnel as part of this 

study were from Mill Creek, downstream from dairy operations 

and upstream from Prado Dam. Although bacteria 

concentrations were not measured in the main stem of the Santa 

Ana River upstream from Prado Dam or other tributaries, 

runoff from this area directly contributes to high bacteria 

concentrations measured farther downstream.

Direct runoff of fecal bacteria occurs during stormflow, 

especially from urban areas, but the occurrence and distribution 

of the highest total and fecal coliform indicator bacteria 

concentrations in stormflow also may fit a conceptual model 

proposed by Matson and others (1978). In this model, bacteria 

accumulate and survive for extended periods in streambed 

sediments and are mobilized as those sediments are scoured 

when flow velocities increase during stormflow. However, data 

collected as part of this study show that high bacteria 

concentrations persist after flow returns to pre-storm 

conditions. To explain the persistence of bacteria, the model 

initially proposed by Matson and others (1978) could be 

modified to include a period after the cessation of stormflow 

when recently disturbed sediment equilibrates with the 

overlying water. 

Because accumulation and survival of bacteria in 

streambed sediments was not measured as part of this study, 

data are not available to test the suitability of the model 

directly. However, molecular microbiological data, including 

phospholipid fatty acid (PLFA) and genetic profile data, 

collected as part of this study provide information on changes 

in the microbial population that occur during stormflow and the 

nature of the source responsible for these changes. These data 

are consistent with the proposed modifications to Matson and 

others (1978) model.

More than 80 phospholipid fatty acids, reflecting specific 

metabolic processes by different bacteria that comprise the 

total microbial population, were detected in stormflow. PLFA 

concentrations ranged from 18,200 to 725,000 picomoles per 

liter and increased with bacteria concentrations. Fatty acid 

concentrations were distributed in a similar manner to bacteria 

during stormflow and concentrations often remained high after 

flow returned to pre-storm conditions. In general, fatty acids 

decreased in diversity and were dominated by a few monoenoic 

fatty acids as concentrations increased—especially during the 

recessional flow of the first stormflow of the rainy season. The 

source of bacteria contributing fatty acids to the total bacterial 

population sampled during stormflow must be poorly diverse 

and dominated by only a few types of bacteria. Samples from 

specific sources within the Santa Ana River Basin suggest that 

changes in fatty-acid concentrations measured during 

stormflow could be explained by fatty-acid concentrations in 

runoff from urban storm drains and streambed material. Fatty 

acids associated with dairy-waste storage ponds were not 

commonly measured in stormflows sampled during this study.

Genetic profiles from the hypervariable region within the 

16S rRNA gene, amplified using polymerase chain reaction 

(PCR) analyzed without and with endonuclease digestion 

(T-RFLP) showed decreases in the diversity of the total 

microbial population with increasing total and fecal coliform 

bacteria concentrations during stormflow. Results of 

quantitative analysis of the genetic profiles obtained with 

endonuclease digestion (T-RFLP) were similar to the results 

obtained on the basis of the PLFA data. However, the genetic 

profile data are more specific than PLFA data and indicate a 

wide range of bacterial organisms that are unique to different 

parts of the stormflow hydrograph and, presumably, to runoff 

from different sources in the basin. Quantitative analysis of the 

genetic profile data obtained without endonuclease digestion 

produced different results from either the analysis of PLFA 

data or the genetic profiles obtained using T-RFLP. This result 

suggests that the digestion of the larger fragments is necessary 

to obtain an accurate genetic profile of the changes in microbial 

community that occur during stormflows containing runoff and 

bacteria from different sources. Development of a library of the 

genetic make-up and base-pair sequences of bacteria from 

different sources and comparison of stormflow data to this 

library, a technique commonly known as microbial “source 

tracking” was beyond the scope of this study, but comparison 

of genetic profiles from dairy-waste storage ponds showed that 

organisms from the waste pond were not present in stormflow.
44 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

The DOC concentration and composition changed rapidly 

during stormflow and did not return to pre-storm conditions 

during the sample-collection period but typically remained 

high for several days after the storm ceased. Comparison of 

ultraviolet absorbance data with similar data collected between 

1995 and 1998 suggests that the composition of DOC from 

many stormflows sampled as part of this study was different 

from the composition of DOC in stormflows sampled 

previously from the Santa Ana River. This may limit 

interpretations from this study to similar dry periods, and 

additional data collection may be required before 

interpretations can be extended to wetter periods. 

Total coliform bacteria, fecal indicator bacteria, and 

DOC concentrations in shallow ground water during the 

2001–02 rainy season were low and showed only small 

changes during stormflows. These data suggest that most 

bacteria and much of the DOC are removed as water infiltrates 

through the bed of the Santa Ana River.

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Appendixes
50 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Appendix A. Total coliforms, fecal coliforms, Escherichia coli, enterococci, and suspended-sediment concentrations for stormflow in the Santa Ana River at 

Imperial Highway, in Mill Creek, and in shallow ground water from the Santa Ana River Basin, southern California, 1999–2000, 2000–01, and 2001–02 rainy 

seasons—Continued

Station

No. Date Time

Streamflow

(ft3/s)

Total coliforms 

(MPN/100 mL)

Fecal 

coliforms 

(MPN/100 mL)

Escherichia 

coli

(MPN/100 mL)

Enterococci

(MPN/100 mL)

Suspended

sediment

(in mg/L)

11075600 11/18/1999 0830 — 16,000 — 31 86 —

11075600 12/07/1999 0935 — 800 — 160 63 —

11075600 01/25/2000 1035 566 17,000 — 5,500 4,600 —

11075600 01/25/2000 1200 506 5,000 — 1,700 3,900 —

11075600 01/25/2000 1330 454 3,000 — 2,000 1,900 —

11075600 01/25/2000 1600 471 9,000 — 2,600 2,100 —

11075600 01/26/2000 0750 426 900,000 — 17,000 14,000 —

11075600 01/26/2000 1130 435 500,000 — 9,800 9,200 —

11075600 01/26/2000 1530 426 170,000 — 7,700 9,200 —

11075600 02/12/2000 0240 319 30,000 — 1,800 7,700 —

11075600 02/12/2000 0440 627 50,000 — 8,700 17,000 —

11075600 02/12/2000 0710 521 23,000 — 5,200 9,800 —

11075600 02/12/2000 0930 415 50,000 — 3,900 6,100 —

11075600 02/12/2000 1230 376 30,000 — 2,200 5,800 —

11075600 02/12/2000 1630 346 30,000 — 2,100 2,600 —

11075600 02/13/2000 0900 363 30,000 — 1,200 3,400 —

11075600 02/22/2000 2300 — 50,000 — 3,300 8,200 —

11075600 02/23/2000 0800 — 24,000 — 3,900 6,100 —

11075600 02/23/2000 0940 — 50,000 — 4,400 8,700 —

11075600 02/23/2000 1140 — 23,000 — 3,900 4,900 —

11075600 02/23/2000 1300 — 30,000 — 4,900 6,900 —

11075600 02/23/2000 1520 — 30,000 — 4,400 9,800 —

11075600 02/23/2000 1740 — 13,000 — 4,400 9,800 —

11075600 02/24/2000 0830 — 23,000 — 3,900 7,300 —

11075600 02/25/2000 1130 632 14,000 — 3,100 4,600 —

11075600 01/10/2001 1600 276 8,000 130 210 230 68

11075600 01/10/2001 1800 307 7,000 500 550 910 98

11075600 01/10/2001 2300 466 23,000 1,700 2,100 4,100 101

11075600 01/11/2001 0400 1,300 80,000 30,000 7,300 15,000 1100

11075600 01/11/2001 1020 650 17,000 8,000 7,300 >24,000 607

11075600 01/11/2001 1530 475 23,000 1,400 3,900 9,200 215

11075600 01/12/2001 0020 3,840 300,000 30,000 6,900 >24,000 4,900

11075600 01/12/2001 0840 1,620 230,000 8,000 12,000 >24,000 977

11075600 01/12/2001 1400 1,000 110,000 5,000 8,200 >24,000 657

11075600 01/14/2001 1200 367 130,000 5,000 2,400 1,900 119

11075600 02/11/2001 1900 401 1,100 <20 20 52 19

11075600 02/12/2001 0130 396 3,000 <20 73 120 20

11075600 02/12/2001 0430 409 1,700 <20 85 220 18

Appendix A. Total coliforms, fecal coliforms, Escherichia coli, enterococci, and suspended-sediment concentrations for stormflow in the Santa Ana River at 

Imperial Highway, in Mill Creek, and in shallow ground water from the Santa Ana River Basin, southern California, 1999–2000, 2000–01, and 2001–02 rainy 

seasons

[Indicator bacteria measured as most probable number per 100 milliliters (MPN/100 mL), except for storms on 11/2001 and 3/2002, which are in Colony Forming 

Units per 100 milliliters (CFU/100 mL); 11075600, Santa Ana River at Imperial Highway; Mill Creek, Mill Creek at Chino-Corona Road; SCARS, subsurface 

collection and recharge system; samples collected by U.S.Geological Survey and analyzed by Orange County Public Health Laboratory; streamflow data 

collected by the Orange County Water District; ft3/s, cubic feet per second; mg/L, milligrams per liter; <, less than; >, greater than; ≥, greater than or equal to; 

—, no data] 
Appendix A 51

11075600 02/12/2001 0720 2,000 30,000 40 1,800 4,100 216

11075600 02/12/2001 1100 1,030 22,000 60 5,800 17,000 640

11075600 02/12/2001 1430 1,690 23,000 260 3,100 9,200 546

11075600 02/12/2001 2130 1,890 17,000 330 2,900 4,400 —

11075600 02/13/2001 0430 3,490 8,000 1,400 2,400 6,900 1,850

11075600 02/13/2001 1200 5,400 50,000 8,000 8,200 >24,000 2,240

11075600 02/13/2001 1700 4,970 80,000 23,000 9,800 >24,000 1,690

11075600 02/14/2001 1000 2,480 70,000 11,000 13,000 >24,000 1,140

11075600 02/15/2001 1000 604 23,000 3,000 3,100 2,200 2,280

11075600 03/05/2001 1100 537 5,000 1,700 690 120 34

11075600 03/06/2001 0100 529 50,000 1,700 1,400 1,100 30

11075600 03/06/2001 0300 602 17,000 13,000 1,400 1,200 39

11075600 03/06/2001 0600 614 5,000 2,300 2,100 1,100 49

11075600 03/06/2001 1230 530 — — — — 42

11075600 03/06/2001 1700 536 5,000 1,300 880 210 29

11075600 03/07/2001 0900 562 11,000 1,700 960 440 36

11075600 11/12/2001 1800 231 ≥3,600 ≥330 ≥180 940 65

11075600 11/12/2001 2030 339 430,000 57,000 30,000 89,000 749

11075600 11/12/2001 2240 377 ≥100,000 24,000 6,600 22,000 163

11075600 11/13/2001 0100 297 41,000 ≥8,800 2,100 11,000 119

11075600 11/13/2001 0340 288 46,000 ≥4,600 1,500 5,100 116

11075600 11/13/2001 1215 351 3,400,000 310,000 84,000 100,000 238

11075600 11/14/2001 0800 263 270,000 32,000 6,500 8,600 134

11075600 03/06/2002 1830 255 2,300 40 90 110 55

11075600 03/07/2002 0650 224 2,300 90 110 140 19

11075600 03/07/2002 1030 234 3,900 170 100 210 14

11075600 03/07/2002 1330 240 2,400 210 80 80 12

11075600 03/07/2002 1630 238 2,600 50 40 40 11

11075600 03/07/2002 2300 238 200 10 70 <10 13

11075600 03/08/2002 0700 244 4,500 120 70 210 12

Mill Creek 11/12/2001 1720 — ≥31,000 ≥680 ≥230 230,000 —

Mill Creek 11/12/2001 1945 — ≥6,900 6,000 2,300 230,000 —

Mill Creek 11/12/2001 2015 — 5,700,000 530,000 90,000 1,210,000 —

Mill Creek 11/12/2001 2030 — 5,100,000 520,000 50,000 780,000 —

Mill Creek 11/12/2001 2045 — 7,300,000 500,000 67,000 680,000 —

Mill Creek 11/12/2001 2100 — 5,600,000 200,000 44,000 640,000 —

Mill Creek 11/12/2001 2115 — 5,200,000 250,000 44,000 530,000 —

Mill Creek 11/12/2001 2130 — 4,700,000 230,000 42,000 320,000 —

Mill Creek 11/12/2001 2145 — 5,900,000 200,000 65,000 220,000 —

Mill Creek 11/12/2001 2200 — 1,600,000 43,000 5,300 82,000 —

Mill Creek 11/12/2001 2245 — 630,000 170,000 18,000 210,000 —

SCARS 11/12/2001 1950 — <10 <10 <10 <10 —

Appendix A. Total coliforms, fecal coliforms, Escherichia coli, enterococci, and suspended-sediment concentrations for stormflow in the Santa Ana River at 

Imperial Highway, in Mill Creek, and in shallow ground water from the Santa Ana River Basin, southern California, 1999–2000, 2000–01, and 2001–02 rainy 

seasons—Continued

Station

No. Date Time

Streamflow

(ft3

/s)

Total coliforms 

(MPN/100 mL)

Fecal 

coliforms 

(MPN/100 mL)

Escherichia 

coli

(MPN/100 mL)

Enterococci

(MPN/100 mL)

Suspended

sediment

(in mg/L)
52 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

SCARS 11/12/2001 2100 — 60 <10 <10 <10 —

SCARS 11/12/2001 2250 — 130 10 <10 20 —

SCARS 11/13/2001 0140 — 130 <10 <10 10 —

SCARS 11/13/2001 0410 — 50 10 <10 20 —

SCARS 11/13/2001 0905 — 40 <10 <10 10 —

SCARS 11/13/2001 1240 — 40 <10 <10 <10 —

SCARS 11/13/2001 1620 — 20 <10 <10 10 —

SCARS 11/14/2001 0915 — 90 <10 <10 <10 —

SCARS 03/06/2002 1830 — 10 <10 <10 <10 —

SCARS 03/07/2002 0715 — 10 <10 <10 <10 —

SCARS 03/07/2002 1100 — <10 <10 <10 <10 —

SCARS 03/07/2002 1330 — 20 <10 <10 <10 —

SCARS 03/07/2002 1700 — <10 <10 <10 <10 —

SCARS 03/07/2002 2330 — 10 <10 <10 <10 —

SCARS 03/08/2002 0700 — <10 <10 <10 <10 —

Appendix A. Total coliforms, fecal coliforms, Escherichia coli, enterococci, and suspended-sediment concentrations for stormflow in the Santa Ana River at 

Imperial Highway, in Mill Creek, and in shallow ground water from the Santa Ana River Basin, southern California, 1999–2000, 2000–01, and 2001–02 rainy 

seasons—Continued

Station

No. Date Time

Streamflow

(ft3

/s)

Total coliforms 

(MPN/100 mL)

Fecal 

coliforms 

(MPN/100 mL)

Escherichia 

coli

(MPN/100 mL)

Enterococci

(MPN/100 mL)

Suspended

sediment

(in mg/L)
Appendix B1 53

Appendix B1. Total phospholipid fatty acid (PLFA) concentrations and selected fatty acid structural groups in stormflow in the Santa Ana River at Imperial 

Highway, southern California, 1999–2000 and 2001–02 rainy seasons

[Data collected by U.S. Geological Survey and analyzed by Microbial Insights, Inc.; PLFA structural-group concentrations in percent of total PLFA concentration; 

pmole/L, picomoles per liter; 11075620, Santa Ana River at the diversion downstream from Imperial Highway; 11075600, Santa Ana River at Imperial Highway]

Station

No. Date Time Total PLFA 

(pmole/L)

Community structure (percent of total PLFA)

Terminally

branched

saturates

Monoenoic Branched

monoenoic

Mid-chain

branched

saturates

Normal

saturated Polyenoic

11075620 01/25/00 0915 99,100 3.8 40 1.1 1.0 17 37

11075620 01/25/00 1040 130,000 4.8 40 1.2 1.1 16 36

11075620 01/25/00 1240 140,000 5.4 42 1.4 1.1 17 33

11075620 01/25/00 1440 193,000 6.1 47 1.6 1.0 17 27

11075620 01/25/00 1640 109,000 4.6 48 1.2 1.1 16 28

11075620 01/25/00 2240 393,000 5.7 57 1.6 .9 17 18

11075620 01/26/00 0740 525,000 4.8 48 1.3 .8 14 15

11075620 01/26/00 1530 725,000 7.0 60 2.0 1.1 15 15

11075620 02/12/00 0130 135,000 8.9 50 2.9 2.1 17 19

11075620 02/12/00 0300 146,000 9.4 49 3.0 2.0 17 19

11075620 02/12/00 0430 192,000 8.5 46 2.5 2.5 17 24

11075620 02/12/00 0440 123,000 8.6 51 2.8 2.2 16 19

11075620 02/12/00 0930 98,600 9.2 48 3.2 2.2 17 20

11075620 02/12/00 0930 113,000 9.6 49 3.3 2.3 16 20

11075620 02/12/00 1400 213,000 10.5 47 3.1 2.7 17 20

11075620 02/12/00 2130 189,000 10.4 47 3.2 2.4 17 20

11075620 02/22/00 2200 197,000 10.9 47 3.6 4.5 16 19

11075620 02/23/00 0730 181,000 10.7 48 3.4 4.4 16 17

11075620 02/23/00 1200 190,000 10.2 45 3.2 4.2 17 21

11075620 02/23/00 1430 178,000 10.0 43 3.3 4.4 17 22

11075620 02/23/00 1600 179,000 10.4 44 3.3 4.4 16 22

11075620 02/23/00 2200 155,000 10.0 45 3.1 4.8 17 21

11075620 02/24/00 0100 201,000 11.1 45 3.4 4.7 17 19

11075620 02/24/00 0700 177,000 10.8 43 2.9 5.3 17 21

11075620 02/27/00 0300 126,000 10.7 41 2.9 4.0 18 23

11075600 11/12/01 1800 18,200 9.2 38 1.2 1.8 25 24

11075600 11/12/01 2030 155,000 9.9 40 1.7 1.8 20 26

11075600 11/12/01 2240 44,900 9.3 42 1.6 1.7 19 27

11075600 11/13/01 0100 48,500 10.2 41 1.2 1.4 21 25

11075600 11/13/01 0340 38,100 8.8 42 1.3 2.1 20 26

11075600 11/13/01 1215 155,000 8.8 54 1.0 1.0 18 17

11075600 11/14/01 0800 55,900 9.8 50 1.1 1.7 21 17

11075600 03/06/02 1830 19,600 5.0 36 .7 4.2 23 32

11075600 03/07/02 0650 19,300 3.6 34 1.3 4.0 20 37

11075600 03/07/02 1030 25,600 6.4 36 .9 4.7 23 29

11075600 03/07/02 1330 37,000 4.1 33 .7 3.8 24 35

11075600 03/07/02 1630 22,100 7.2 40 1.0 4.7 24 23

11075600 03/07/02 2300 16,700 4.6 36 1.0 4.2 23 31

11075600 03/08/02 0700 12,100 .0 41 .0 1.0 24 34
54 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Appendix B2. Normal saturated phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 

1999–2000 and 2001–02 rainy seasons

[Data collected by the U.S. Geological Survey and analyzed by Microbial Insights, Inc.; individual PLFA concentrations in percent of total PLFA; standard 

nomenclature used for fatty-acid names where the numbers before and after the colon indicate the numbers of carbon atoms and carbon-carbon double bonds, 

respectively; pmole/L, picomoles per liter; 11075620, Santa Ana River at the diversion downstream from Imperial Highway; 11075600, Santa Ana River at 

Imperial Highway]

Station No. Date Time Total PLFA 

pmole/L 14:0 15:0 16:0 17:0 18:0

11075620 01/25/00 0915 99,100 0.2 0.5 14 0.5 2.1

11075620 01/25/00 1040 130,000 .3 .6 13 .6 2.2

11075620 01/25/00 1240 140,000 .6 .6 14 .5 1.9

11075620 01/25/00 1440 193,000 1.0 .7 13 .5 1.6

11075620 01/25/00 1640 109,000 .2 .5 13 .5 1.9

11075620 01/25/00 2240 393,000 .5 .6 14 .4 1.4

11075620 01/26/00 0740 525,000 .4 .5 12 .4 1.2

11075620 01/26/00 1530 725,000 .4 .7 13 .4 1.0

11075620 02/12/00 0130 135,000 1.7 .9 13 .5 1.4

11075620 02/12/00 0300 146,000 1.8 .9 13 .5 1.5

11075620 02/12/00 0430 192,000 1.0 .9 12 .5 1.8

11075620 02/12/00 0440 123,000 1.3 .8 12 .5 1.4

11075620 02/12/00 0930 98,600 2.1 .9 12 .4 1.4

11075620 02/12/00 0930 113,000 2.0 .8 12 .5 1.4

11075620 02/12/00 1400 213,000 1.7 .9 12 .5 1.6

11075620 02/12/00 2130 189,000 1.8 .9 13 .5 1.6

11075620 2/22/00 2200 197,000 1.4 .8 11 .5 1.7

11075620 02/23/00 0730 181,000 1.5 .8 11 .5 1.9

11075620 02/23/00 1200 190,000 1.5 .8 12 .5 2.1

11075620 02/23/00 1430 178,000 1.3 .8 12 .6 2.1

11075620 02/23/00 1600 179,000 1.3 .7 12 .5 2.0

11075620 02/23/00 2200 155,000 1.0 .8 12 .6 2.2

11075620 02/24/00 0100 201,000 1.4 .9 12 .5 2.3

11075620 02/24/00 0700 177,000 1.4 .8 12 .6 2.4

11075620 02/27/00 0300 126,000 1.3 .9 12 .5 3.1

11075600 11/12/01 1800 18,200 1.9 .9 19 .8 2.5

11075600 11/12/01 2030 155,000 1.7 .8 14 .7 2.6

11075600 11/12/01 2240 44,900 1.4 .7 14 .6 2.4

11075600 11/13/01 0100 48,500 2.0 .8 16 .6 2.4

11075600 11/13/01 0340 38,100 1.3 .8 15 .7 2.4

11075600 11/13/01 1215 155,000 1.9 .7 14 .4 1.4

11075600 11/14/01 0800 55,900 2.3 .8 15 .5 1.8

11075600 03/06/02 1830 19,600 .9 .6 17 .7 3.7

11075600 03/07/02 0650 19,300 .3 .4 16 .9 2.7

11075600 03/07/02 1030 25,600 1.5 .6 17 .5 2.9

11075600 03/07/02 1330 37,000 .8 .4 14 .4 8.1

11075600 03/07/02 1630 22,100 1.1 .7 19 .6 2.1

11075600 03/07/02 2300 16,700 .4 .5 19 .7 2.7

11075600 03/08/02 0700 12,100 .0 .0 19 1.7 3.5
Appendix B3 55

Appendix B3. Mid-chain branched saturated phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 

1999–2000 and 2001–02 rainy seasons—Continued

Station 

No. Date Time Total PLFA 

(pmole/L)

14:0a

(14.41)

15:0 

(15.48)

10me15:0 

(15.57)

16:0 

(16.07)

10me16:0 

(16.43)

11me16:0 

(16.47)

12me16:0 

(16.5)

11075620 01/25/00 0915 99,100 — — — — 0.9 — —

11075620 01/25/00 1040 130,000 — — — — .9 — —

11075620 01/25/00 1240 140,000 — — — — 1.0 — —

11075620 01/25/00 1440 193,000 — — — — .9 — —

11075620 01/25/00 1640 109,000 — — — — .9 — —

11075620 01/25/00 2240 393,000 — — — — .8 — —

11075620 01/26/00 0740 525,000 — — — — .6 — —

11075620 01/26/00 1530 725,000 — — — — .8 — —

11075620 02/12/00 0130 135,000 — — — — 1.0 — 0.0

11075620 02/12/00 0300 146,000 — — — — .9 — .0

11075620 02/12/00 0430 192,000 — — — — 1.2 — .2

11075620 02/12/00 0440 123,000 — — — — 1.0 — .0

11075620 02/12/00 0930 98,600 — — — — 1.1 — .0

11075620 02/12/00 0930 113,000 — — — — .9 — .0

11075620 02/12/00 1400 213,000 — — — — 1.3 — .1

11075620 02/12/00 2130 189,000 — — — — 1.1 — .0

11075620 02/22/00 2200 197,000 — — — 0.1 2.0 — .1

11075620 02/23/00 0730 181,000 — — — .1 1.8 — .1

11075620 02/23/00 1200 190,000 — — — .0 1.7 — .1

11075620 02/23/00 1430 178,000 — — — .1 1.7 — .1

11075620 02/23/00 1600 179,000 — — — .0 1.7 — .2

11075620 02/23/00 2200 155,000 — — — .1 1.8 — .1

11075620 02/24/00 0100 201,000 — — — .1 1.8 — .1

11075620 02/24/00 0700 177,000 — — — .7 1.7 — .2

11075620 02/27/00 0300 126,000 — — — .0 1.1 — .0

11075600 11/12/01 1800 18,200 — — — — .8 0.4 —

11075600 11/12/01 2030 155,000 — — — — .9 .1 —

11075600 11/12/01 2240 44,900 — — — — .7 .0 —

11075600 11/13/01 0100 48,500 — — — — .5 .0 —

11075600 11/13/01 0340 38,100 — — — — .8 .2 —

11075600 11/13/01 1215 155,000 — — — — .5 .2 —

11075600 11/14/01 0800 55,900 — — — — .6 .2 —

11075600 03/06/02 1830 19,600 .7 — 1.3 .0 .3 .2 —

11075600 03/07/02 0650 19,300 .3 — .5 .1 .4 .3 —

11075600 03/07/02 1030 25,600 1.2 — 1.0 .1 .3 .2 —

11075600 03/07/02 1330 37,000 .5 — 1.0 .1 .2 .1 —

11075600 03/07/02 1630 22,100 1.0 — .8 .1 .3 .2 —

11075600 03/07/02 2300 16,700 .4 — .7 .1 .4 .2 —

11075600 03/08/02 0700 12,100 .0 — .0 .0 .0 .0 —

Appendix B3. Mid-chain branched saturated phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 

1999–2000 and 2001–02 rainy seasons

[Data collected by the U.S. Geological Survey and analyzed by Microbial Insights, Inc.; individual PLFA concentrations in percent of total PLFA; standard 

nomenclature used for fatty-acid names follows the form X:YωZ, where X is the number of carbon atoms, Y is the number of carbon-carbon double bonds, ω is 

the end of the molecule, and Z is the number of carbon atoms between the terminal double bond and the methyl end of the molecule, a, anteiso methyl branching, 

me, methyl branching; number in parentheses is effective carbon chain length; pmole/L, picomoles per liter; 11075620, Santa Ana River at the diversion 

downstream from Imperial Highway; 11075600, Santa Ana River at Imperial Highway; —, no data]
56 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Appendix B3. Mid-chain branched saturated phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 

1999–2000 and 2001–02 rainy seasons—Continued

Station 

No. Date Time 17:0a

(17.05)

17:0 

(17.11)

10me17:0 

(17.47)

11me17:0 

(17.46)

18:2 

(17.47)

12me17:0/1

8:2 (17.473)

10me18:0 

(18.38)

12me18:00 

(18.43)

11075620 01/25/00 0915 — — — — — — 0.2 —

11075620 01/25/00 1040 — — — — — — .2 —

11075620 01/25/00 1240 — — — — — — .2 —

11075620 01/25/00 1440 — — — — — — .1 —

11075620 01/25/00 1640 — — — — — — .2 —

11075620 01/25/00 2240 — — — — — — .2 —

11075620 01/26/00 0740 — — — — — — .1 —

11075620 01/26/00 1530 — — — — — — .2 —

11075620 02/12/00 0130 — — 1.0 — — — .2 —

11075620 02/12/00 0300 — — .9 — — — .2 —

11075620 02/12/00 0430 — — .9 — — — .2 —

11075620 02/12/00 0440 — — 1.0 — — — .2 —

11075620 02/12/00 0930 — — .8 — — — .2 —

11075620 02/12/00 0930 — — 1.1 — — — .2 —

11075620 02/12/00 1400 — — 1.0 — — — .3 —

11075620 02/12/00 2130 — — 1.0 — — — .3 —

11075620 02/22/00 2200 0.2 — .6 — 1.0 — .5 0.2

11075620 02/23/00 0730 .2 — .5 — 1.0 — .5 .2

11075620 02/23/00 1200 .1 — .6 — 1.0 — .5 .2

11075620 02/23/00 1430 .2 — .6 — 1.1 — .5 .1

11075620 02/23/00 1600 .2 — .7 — 1.0 — .6 .1

11075620 02/23/00 2200 .2 — .6 — 1.0 — .7 .2

11075620 02/24/00 0100 .2 — .6 — 1.0 — .7 .2

11075620 02/24/00 0700 .2 — .6 — 1.1 — .7 .2

11075620 02/27/00 0300 .0 — 1.0 — 1.0 — .8 .0

11075600 11/12/01 1800 — — .0 — — 0.7 .0 —

11075600 11/12/01 2030 — — .2 — — .4 .2 —

11075600 11/12/01 2240 — — .3 — — .4 .3 —

11075600 11/13/01 0100 — — .2 — — .4 .2 —

11075600 11/13/01 0340 — — .3 — — .5 .3 —

11075600 11/13/01 1215 — — .0 — — .3 .0 —

11075600 11/14/01 0800 — — .2 — — .5 .2 —

11075600 03/06/02 1830 — 0.0 .3 0.4 — .8 .2 0.0

11075600 03/07/02 0650 — .2 .4 .5 — .9 .3 .1

11075600 03/07/02 1030 — .1 .2 .5 — .9 .2 .1

11075600 03/07/02 1330 — .1 .2 .6 — .9 .1 .0

11075600 03/07/02 1630 — .2 .4 .5 — .9 .2 .1

11075600 03/07/02 2300 — .2 .3 .4 — 1.0 .3 .1

11075600 03/08/02 0700 — .0 .0 .0 — 1.0 .0 .0
Appendix B4 57

Appendix B4 Terminally Branched Saturates (TerBrSats) phospholipid fatty acids in stormflow from the Santa Ana River at Imperial Highway, southern 

California, 1999–00 and 2001–02 rainy seasons—Continued

Station

No. Date Time Total PLFA 

(pmole/L)

i14:0

(13.62)

i15:0 

(14.63)

a15:0 

(14.70)

i16:0 

(15.63)

i17:0 

(16.62)

a17:0/

17:1ω8c

(16.70)

11075620 01/25/00 0915 99,100 0.0 0.9 0.7 0.7 0.4 1.2

11075620 01/25/00 1040 130,000 .0 1.1 .9 .8 .4 1.6

11075620 01/25/00 1240 140,000 .0 1.4 1.2 .9 .4 1.5

11075620 01/25/00 1440 193,000 .3 1.8 1.5 .9 .4 1.3

11075620 01/25/00 1640 109,000 .0 1.0 .9 .9 .4 1.5

11075620 01/25/00 2240 393,000 .1 1.6 1.5 .8 .3 1.3

11075620 01/26/00 0740 525,000 .1 1.9 1.8 .9 .3 1.5

11075620 01/26/00 1530 725,000 .1 2.0 1.7 1.0 .3 1.9

11075620 02/12/00 0130 135,000 .8 3.1 2.4 1.0 .5 1.2

11075620 02/12/00 0300 146,000 .9 3.3 2.6 1.0 .5 1.2

11075620 02/12/00 0430 192,000 .4 2.4 2.4 1.2 .5 1.7

11075620 02/12/00 0440 123,000 .5 2.7 2.4 1.1 .5 1.5

11075620 02/12/00 0930 98,600 1.0 3.0 2.4 1.1 .5 1.2

11075620 02/12/00 0930 113,000 1.2 3.1 2.5 1.0 .5 1.2

11075620 02/12/00 1400 213,000 .8 3.2 2.9 1.3 .6 1.6

11075620 02/12/00 2130 189,000 .9 3.3 2.9 1.3 .5 1.6

11075620 02/22/00 2200 197,000 .7 3.4 3.2 1.3 .8 1.6

11075620 02/23/00 0730 181,000 .6 3.3 3.2 1.2 .7 1.6

11075620 02/23/00 1200 190,000 .6 3.0 3.0 1.2 .7 1.6

11075620 02/23/00 1430 178,000 .6 2.9 2.7 1.4 .7 1.7

11075620 02/23/00 1600 179,000 .5 3.0 2.8 1.5 .8 1.8

11075620 02/23/00 2200 155,000 .4 2.8 2.9 1.4 .8 1.8

11075620 02/24/00 0100 201,000 .7 3.2 3.4 1.3 .8 1.7

11075620 02/24/00 0700 177,000 .6 3.0 3.4 1.3 .8 1.7

11075620 02/27/00 0300 126,000 .6 3.1 3.5 1.1 .8 1.7

11075600 11/12/01 1800 18,200 .6 2.8 2.1 2.2 .9 .8

11075600 11/12/01 2030 155,000 .9 3.0 2.7 1.6 .8 1.0

11075600 11/12/01 2240 44,900 .5 2.6 2.5 2.0 .8 1.0

11075600 11/13/01 0100 48,500 .6 2.9 2.8 2.4 .7 .9

11075600 11/13/01 0340 38,100 .5 2.6 2.3 1.9 .8 .8

11075600 11/13/01 1215 155,000 .6 2.9 2.6 1.8 .4 .6

11075600 11/14/01 0800 55,900 .9 3.2 2.5 2.0 .6 .7

11075600 03/06/02 1830 19,600 .2 1.8 1.3 .7 .5 .5

11075600 03/07/02 0650 19,300 .0 1.1 .7 .6 .6 .6

11075600 03/07/02 1030 25,600 .4 2.6 1.8 .8 .4 .4

11075600 03/07/02 1330 37,000 .1 1.6 1.2 .5 .3 .3

11075600 03/07/02 1630 22,100 .2 2.7 2.0 .9 .5 .9

11075600 03/07/02 2300 16,700 .0 1.4 .9 .8 .6 .9

11075600 03/08/02 0700 12,100 .0 .0 .0 .0 .0 .0

Appendix B4 Terminally branched saturated phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–

2000 and 2001–02 rainy seasons

[Data collected by the U.S.Geological Survey and analyzed by Microbial Insights, Inc; individual PLFA concentrations in percent of total PLFA; standard 

nomenclature used for fatty-acid names follows the form X:YωZ, where X is the number of carbon atoms, Y is the number of carbon-carbon double bonds, 

ω is the end of the molecule, and Z is the number of carbon atoms between the terminal double bond and the methyl end of the molecule, t, trans, i, iso methyl 

branching, a, anteiso methyl branching; number in parentheses is effective carbon chain length; pmole/L, picomoles per liter; 11075620, Santa Ana River at the 

diversion downstream from Imperial Highway; 11075600, Santa Ana River at Imperial Highway]
58 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Appendix B5. Monoenoic phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–2000 and 

2001–02 rainy seasons—Continued

Station No. Date Time Total PLFA 

(pmole/L)

15:

1ω6c

(14.80)

16:

1ω9c

(15.69)

16:

1ω7c

(15.75)

16:

1ω7t

(15.78)

16:

1ω5c

(15.83)

16:

1ω13t

(15.90)

11075620 01/25/00 0915 99,100 — 1.1 21 0.3 1.8 —

11075620 01/25/00 1040 130,000 — 1.2 21 .3 1.9 —

11075620 01/25/00 1240 134,000 — 1.3 23 .3 2.2 —

11075620 01/25/00 1440 193,000 — 1.2 28 .3 2.3 —

11075620 01/25/00 1640 109,000 — 1.0 26 .3 2.3 —

11075620 01/25/00 2240 393,000 — 1.0 34 .4 1.9 —

11075620 01/26/00 0740 525,000 — .8 29 .3 1.6 —

11075620 01/26/00 1530 725,000 — .8 35 .0 2.6 —

11075620 02/12/00 0130 135,000 0.4 1.5 28 .4 3.0 0.3

11075620 02/12/00 0300 146,000 .4 1.5 28 .4 3.0 .3

11075620 02/12/00 0430 192,000 .4 1.2 25 .4 2.3 .2

11075620 02/12/00 0440 123,000 .4 1.3 29 .4 2.9 .3

11075620 02/12/00 0930 98,600 .4 1.4 28 .4 2.8 .4

11075620 02/12/00 0930 113,000 .4 1.6 28 .4 2.8 .3

11075620 02/12/00 1400 213,000 .4 1.4 25 .4 3.0 .2

11075620 02/12/00 2130 189,000 .4 1.5 25 .4 3.0 .3

11075620 02/22/00 2200 197,000 .3 1.4 24 .5 2.7 —

11075620 02/23/00 0730 181,000 .4 1.3 26 .6 2.7 —

11075620 02/23/00 1200 190,000 .4 1.3 24 .5 2.5 —

11075620 02/23/00 1430 178,000 .3 1.2 21 .4 2.8 —

11075620 02/23/00 1600 179,000 .3 1.3 22 .4 3.1 —

11075620 02/23/00 2200 155,000 .3 1.3 22 .6 2.7 —

11075620 02/24/00 0100 201,000 .3 1.3 23 .6 2.7 —

11075620 02/24/00 0700 177,000 .3 1.3 22 .6 2.4 —

11075620 02/27/00 0300 126,000 .3 1.4 22 .7 2.0 —

11075600 11/12/01 1800 18,200 .0 1.5 17 .5 2.3 —

11075600 11/12/01 2030 155,000 .2 1.5 13 .4 2.3 —

11075600 11/12/01 2240 44,900 .0 1.3 16 .4 2.3 —

11075600 11/13/01 0100 48,500 .0 1.2 19 .5 2.3 —

11075600 11/13/01 0340 38,100 .2 1.3 17 .4 2.2 —

11075600 11/13/01 1215 155,000 .2 1.0 30 .0 1.8 —

11075600 11/14/01 0800 55,900 .2 1.3 25 .0 2.2 —

11075600 03/06/02 1830 19,600 .0 1.1 20 .4 1.8 —

11075600 03/07/02 0650 19,300 .0 .9 14 .3 1.4 —

11075600 03/07/02 1030 25,600 .1 1.1 21 .3 1.9 —

11075600 03/07/02 1330 37,000 .0 .9 20 .2 1.4 —

11075600 03/07/02 1630 22,100 .1 1.2 23 .4 2.3 —

11075600 03/07/02 2300 16,700 .0 1.1 18 .4 2.0 —

11075600 03/08/02 0700 12,100 .0 .0 18 .0 2.0 —

Appendix B5. Monoenoic phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–2000 and

2001–02 rainy seasons

[Data collected by the U.S. Geological Survey and analyzed by Microbial Insights, Inc.; individual PLFA concentrations in percent of total PLFA; standard 

nomenclature used for fatty-acid names follows the form X:YωZ, where X is the number of carbon atoms, Y is the number of carbon-carbon double bonds, ω is the 

end of the molecule, and Z is the number of carbon atoms between the terminal double bond and the methyl end of the molecule, c, cis, cy, cyclopropane ring 

within the carbon chain, t, trans; number in parentheses is effective carbon chain length; pmole/L, picomoles per liter; 11075620, Santa Ana River at the diversion 

downstream from Imperial Highway; 11075600, Santa Ana River at Imperial Highway]
Appendix B5 59

Appendix B5. Monoenoic phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–2000 and 2001–

02 rainy seasons—Continued

Station No. 17:

1ω8c

(16.74)

17:

1ω6c

(16.78)

cy

17:0 

(16.80)

17:1 

(16.90)

17:

1ω6c

(16.78)

18:

1ω7c

(17.75)

18:

1ω7t

(17.79)

18:

1ω6c

(17.86)

18:

1ω5c

(17.84)

19:

1ω6c

(18.78)

cy

19:0 

(18.81)

11075620 — — 0.3 — 0.4 14 — — — — 0.5

11075620 — — .3 — .4 15 — — — — .6

11075620 — — .4 — .4 14 — — — — .6

11075620 — — .3 — .4 14 — — — — .5

11075620 — — .4 — .5 17 — — — — .6

11075620 — — .3 — .4 18 — — — — .4

11075620 — — .3 — .4 15 — — — — .4

11075620 — — .5 — .5 20 — — — — .5

11075620 — 0.5 .5 — — 14 — — 0.2 — .6

11075620 — .5 .5 — — 14 — — .2 — .5

11075620 — .5 .4 — — 14 — — .2 — .6

11075620 — .5 .5 — — 15 — — .2 — .6

11075620 — .5 .5 — — 13 — — .2 — .6

11075620 — .4 .4 — — 14 — — .2 — .5

11075620 — .5 .6 — — 15 — — .2 — .8

11075620 — .5 .6 — — 15 — — .2 — .6

11075620 — .5 .9 — — 14 0.3 — .3 — 1.3

11075620 — .5 .7 — — 14 .4 — .2 — 1.1

11075620 — .5 .7 — — 13 .4 — .3 — 1.0

11075620 — .4 .7 — — 15 .3 — .3 — 1.1

11075620 — .4 .8 — — 15 .3 — .3 — 1.2

11075620 — .5 .8 — — 14 .4 — .3 — 1.3

11075620 — .5 .8 — — 14 .4 — .3 — 1.1

11075620 — .5 .8 — — 14 .2 — .2 — 1.0

11075620 — .4 .5 — — 13 .5 — .1 — .6

11075600 0.5 .4 .6 — — 14 — 0.0 .3 — 1.1

11075600 .7 .5 .6 — — 18 — .2 .5 — 1.8

11075600 .8 .4 .6 — — 18 — .0 .4 — 1.5

11075600 .7 .4 .6 — — 15 — .0 .2 — 1.0

11075600 .7 .4 .6 — — 18 — .0 .3 — 1.2

11075600 .5 .3 .4 — — 18 — .0 .2 — .7

11075600 .5 .4 .6 — — 19 — .0 .2 — .9

11075600 .3 .3 .3 0.0 — 11 — .0 .3 — .3

11075600 .4 .4 .8 .1 — 15 — .0 .3 — .7

11075600 .3 .3 .2 .1 — 10 — .0 .2 — .3

11075600 .2 .2 .2 .1 — 9 — .0 .3 — .2

11075600 .0 .3 .3 .1 — 12 — .0 .4 — .3

11075600 .0 .3 .3 .1 — 13 — .2 .2 — .4

11075600 .0 .0 .0 .0 — 21 — .0 .0 — .0
60 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Appendix B6. Branched monoenoic phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–2000 

and 2001–02 rainy seasons—Continued

Station No. Date Time Total PLFA 

(pmole/L)

15:1

(14.35)

15:1 

(14.41)

15:1 

(14.46)

16:1 

(15.41)

16:1 

(15.41)

17:1ω7 

(16.34)

19:1 

(18.03)

11075620 01/25/00 0915 99,100 — 0.2 — — — 0.4 0.5

11075620 01/25/00 1040 130,000 — .3 — — — .5 .5

11075620 01/25/00 1240 140,000 — .5 — — — .5 .4

11075620 01/25/00 1440 193,000 — .8 — — — .5 .3

11075620 01/25/00 1640 109,000 — .3 — — — .5 .4

11075620 01/25/00 2240 393,000 — .6 — — — .6 .4

11075620 01/26/00 0740 525,000 — .5 — — — .5 .3

11075620 01/26/00 1530 725,000 — .8 — — — .7 .4

11075620 02/12/00 0130 135,000 — 1.6 0.3 — — .7 .4

11075620 02/12/00 0300 146,000 — 1.6 .3 — — .7 .4

11075620 02/12/00 0430 192,000 — 1.0 .4 — — .7 .4

11075620 02/12/00 0440 123,000 — 1.4 .3 — — .7 .4

11075620 02/12/00 0930 98,600 — 1.8 .3 — — .7 .4

11075620 02/12/00 0930 113,000 — 1.9 .3 — — .6 .4

11075620 02/12/00 1400 213,000 — 1.4 .4 — — .8 .5

11075620 02/12/00 2130 189,000 — 1.5 .4 — — .8 .4

11075620 02/22/00 2200 197,000 0.1 1.3 .3 — 0.2 1.1 .5

11075620 02/23/00 0730 181,000 .0 1.4 .4 — .1 1.1 .5

11075620 02/23/00 1200 190,000 .0 1.2 .4 — .1 1.0 .5

11075620 02/23/00 1430 178,000 .0 1.1 .3 — .2 1.0 .6

11075620 02/23/00 1600 179,000 .0 1.1 .3 — .3 1.1 .5

11075620 02/23/00 2200 155,000 .0 1.0 .3 — .1 1.1 .6

11075620 02/24/00 0100 201,000 .0 1.4 .4 — .1 1.1 .5

11075620 02/24/00 0700 177,000 .0 1.2 .4 — .2 1.0 .2

11075620 02/27/00 0300 126,000 .0 1.5 .3 — .2 .9 .0

11075600 11/12/01 1800 18,200 — — — — — .6 .6

11075600 11/12/01 2030 155,000 — — — — — .7 1.0

11075600 11/12/01 2240 44,900 — — — — — .8 .8

11075600 11/13/01 0100 48,500 — — — — — .6 .6

11075600 11/13/01 0340 38,100 — — — — — .6 .7

11075600 11/13/01 1215 155,000 — — — — — .6 .5

11075600 11/14/01 0800 55,900 — — — — — .5 .6

11075600 03/06/02 1830 19,600 — — — 0.0 .0 .4 .3

11075600 03/07/02 0650 19,300 — — — .2 .0 .5 .5

11075600 03/07/02 1030 25,600 — — — .2 .1 .3 .3

11075600 03/07/02 1330 37,000 — — — .1 .1 .2 .3

11075600 03/07/02 1630 22,100 — — — .2 .1 .3 .4

11075600 03/07/02 2300 16,700 — — — .1 .0 .4 .5

11075600 03/08/02 0700 12,100 — — — .0 .0 .0 .0

Appendix B6. Branched monoenoic phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–2000 

and 2001–02 rainy seasons

[Data collected by the U.S. Geological Survey and analyzed by Microbial Insights, Inc.; individual PLFA concentrations in percent total PLFA; standard 

nomenclature used for fatty-acid names follows the form X:YωZ, where X is the number of carbon atoms, Y is the number of carbon-carbon double bonds, ω is the 

end of the molecule, and Z is the number of carbon atoms between the terminal double bond and the methyl end of the molecule; number in parentheses is 

effective carbon chain length; pmole/L, picomoles per liter; 11075620, Santa Ana River at the diversion downstream from Imperial Highway; 11075600, Santa 

Ana River at Imperial Highway; —, no data]
Appendix B7 61

Appendix B7. Polyenoic phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–2000 and 2001–02 

rainy seasons—Continued

Station 

No. Date Time

Total 

PLFA 

(pmole/L)

16:2 

(15.58)

18:4ω3 

(17.11)

poly18 

(17.30)

18:3ω6 

(17.41)

18:4ω3 

(17.45)

18:2 

(17.47)

18:2a

(17.52)

18:2b

(17.57)

18:2ω6 

(17.59)

18:3ω3 

(17.63)

18:

10ω9c

(17.69)

18:2c

(18.53)

11075620 01/25/00 0915 99,100 0.8 — 0.3 0.4 2.0 1.1 — — 6.0 3.7 8.0 —

11075620 01/25/00 1040 130,000 .7 — .3 .4 1.5 .9 — — 7.5 3.6 7.9 —

11075620 01/25/00 1240 140,000 .9 — .2 .4 1.9 .9 — — 5.2 3.9 7.0 —

11075620 01/25/00 1440 193,000 .8 — .2 .4 1.5 1.1 — — 4.6 3.0 5.5 —

11075620 01/25/00 1640 109,000 .7 — .3 .5 1.6 1.3 — — 4.3 2.9 5.6 —

11075620 01/25/00 2240 393,000 .4 — .1 .3 .5 1.0 — — 4.0 2.3 4.3 —

11075620 01/26/00 0740 525,000 .3 — .1 .2 .4 .8 — — 3.4 2.0 3.6 —

11075620 01/26/00 1530 725,000 .4 — .1 .3 .6 1.0 — — 2.6 1.7 3.3 —

11075620 02/12/00 0130 135,000 — — — — 1.1 — — — 3.4 2.2 4.3 —

11075620 02/12/00 0300 146,000 — — — — 1.1 — — — 3.4 2.2 4.4 —

11075620 02/12/00 0430 192,000 — — — — .7 — — — 8.3 2.6 5.7 —

11075620 02/12/00 0440 123,000 — — — — 1.2 — — — 4.0 2.1 4.7 —

11075620 02/12/00 0930 98,600 — — — — 2.0 — — — 2.8 2.5 4.0 —

11075620 02/12/00 0930 113,000 — — — — 1.3 — — — 3.6 2.2 4.1 —

11075620 02/12/00 1400 213,000 — — — — .7 — — — 5.6 2.6 5.0 —

11075620 02/12/00 2130 189,000 — — — — 1.0 — — — 4.5 2.5 4.8 —

11075620 02/22/00 2200 197,000 .6 0.2 — 1.0 — — — — 3.1 1.9 4.4 —

11075620 02/23/00 0730 181,000 .7 .2 — 1.1 — — — — 2.9 2.3 4.7 —

11075620 02/23/00 1200 190,000 .6 .2 — 1.0 — — — — 4.5 2.6 5.8 —

11075620 02/23/00 1430 178,000 .5 .2 — .8 — — — — 5.9 2.7 5.7 —

11075620 02/23/00 1600 179,000 .6 .2 — .9 — — — — 5.0 2.7 5.7 —

11075620 02/23/00 2200 155,000 .6 .2 — 1.1 — — — — 3.7 2.5 5.6 —

11075620 02/24/00 0100 201,000 .6 .2 — 1.0 — — — — 3.4 2.2 5.3 —

11075620 02/24/00 0700 177,000 .6 .2 — 1.0 — — — — 4.6 2.4 5.8 —

11075620 02/27/00 0300 126,000 .9 .3 — 1.0 — — — — 2.7 2.1 5.5 —

11075600 11/12/01 1800 18,200 — — — — — — 2.1 — 3.9 4.4 6.5 —

11075600 11/12/01 2030 155,000 — — — — — — 1.6 — 9.5 2.9 7.8 —

11075600 11/12/01 2240 44,900 — — — — — — 1.5 — 8.7 3.0 7.1 —

11075600 11/13/01 0100 48,500 — — — — — — 1.5 — 7.5 3.0 6.2 —

11075600 11/13/01 0340 38,100 — — — — — — 1.9 — 7.5 3.6 6.4 —

11075600 11/13/01 1215 155,000 — — — — — — 1.4 — 5.1 2.3 4.2 —

11075600 11/14/01 0800 55,900 — — — — — — 1.7 — 3.5 2.4 4.4 —

11075600 03/06/02 1830 19,600 — — — — — — 1.5 — 4.5 2.2 6.0 —

11075600 03/07/02 0650 19,300 — — — — — — 2.0 — 5.3 3.7 7.4 —

11075600 03/07/02 1030 25,600 — — — — — — 1.3 — 6.3 3.2 5.8 —

11075600 03/07/02 1330 37,000 — — — — — — 1.0 — 9.6 2.0 7.6 —

11075600 03/07/02 1630 22,100 — — — — — — 1.8 — 3.8 2.2 5.1 —

11075600 03/07/02 2300 16,700 — — — — — — 2.5 — 4.0 2.2 5.7 —

11075600 03/08/02 0700 12,100 — — — — — — 2.3 — 4.6 3.2 7.9 —

Appendix B7. Polyenoic phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–2000 and 2001–02 

rainy seasons

[Data collected by the U.S. Geological Survey and analyzed by Microbial Insights, Inc.; individual PLFA concentrations in percent total PLFA; standard 

nomenclature used for fatty-acid names follows the form X:YωZ, where X is the number of carbon atoms, Y is the number of carbon-carbon double bonds, ω is the 

end of the molecule, and Z is the number of carbon atoms between the terminal double bond and the methyl end of the molecule, c, cis, a, anteiso methyl 

branching; number in parentheses is effective carbon chain length; pmole/L, picomoles per liter; 11075620, Santa Ana River at the diversion downstream from 

Imperial Highway; 11075600, Santa Ana River at Imperial Highway; —, no data]
62 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Appendix B7. Polyenoic phospholipid fatty acids (PLFA) in stormflow in the Santa Ana River at Imperial Highway, southern California, 1999–2000 and 2001–02 

rainy seasons—Continued

Station 

No. Date Time

20:

4ω6 

(19.15)

20:

5ω3 

(19.19)

20:

3 

(19.98)

20:

3ω6 

(19.40)

20:

2ω3 

(19.60)

20:

1ω11c

(19.66)

20:

1ω9c

(19.68)

20:

1ω7c

(19.75)

20:0 

(20.00)

22:

4ω6 

(21.18)

22:

5ω6 

(21.06)

22:

5ω3 

(21.23)

22:

6ω3 

(21.14)

22:0 

(22.00)

23:0 

(23.00)

24:0 

(24.00)

11075620 01/25/00 0915 1.2 11.9 — 0.4 0.2 — 0.4 — 0.3 — — 0.2 — 0.3 — 0.3

11075620 01/25/00 1040 1.4 9.7 — .4 .2 — .4 — .3 — — .2 — .4 — .3

11075620 01/25/00 1240 1.3 9.0 — .3 .2 — .4 — .3 — — .2 — .3 — .2

11075620 01/25/00 1440 1.0 7.6 — .2 .2 — .3 — .2 — — .2 — .3 — .2

11075620 01/25/00 1640 1.1 8.2 — .2 .2 — .4 — .3 — — .1 — .3 — .2

11075620 01/25/00 2240 .9 3.2 — .2 .1 — .1 — .2 — — .1 — .2 — .2

11075620 01/26/00 0740 .8 2.7 — .2 .1 — .1 — .2 — — .1 — .2 — .1

11075620 01/26/00 1530 .8 3.1 — .1 .1 — .2 — .1 — — .1 — .1 — .1

11075620 02/12/00 0130 1.1 6.1 0.1 .1 — — — — .2 0.1 — — — .2 — .1

11075620 02/12/00 0300 1.1 5.9 .1 .1 — — — — .2 .1 — — — .3 — .2

11075620 02/12/00 0430 1.1 4.9 .2 .2 — — — — .2 .2 — — — .2 — .2

11075620 02/12/00 0440 1.0 5.6 .1 .1 — — — — .2 .1 — — — .2 — .1

11075620 02/12/00 0930 .9 7.5 .1 .2 — — — — .2 .1 — — — .1 — .1

11075620 02/12/00 0930 1.0 6.7 .1 .1 — — — — .2 .1 — — — .2 — .1

11075620 02/12/00 1400 1.1 3.7 .1 .1 — — — — .3 .0 — — — .3 — .2

11075620 02/12/00 2130 1.1 4.6 .1 .1 — — — — .3 .0 — — — .2 — .2

11075620 02/22/00 2200 1.8 3.5 .1 .1 .1 0.5 — 0.1 .3 .1 — — — .4 0.1 .3

11075620 02/23/00 0730 1.5 2.8 .1 .1 .0 .0 — .1 .3 .1 — — — .3 .0 .3

11075620 02/23/00 1200 1.7 3.0 .2 .1 .1 .0 — .0 .3 .2 — — — .4 .0 .3

11075620 02/23/00 1430 1.7 2.7 .2 .1 .1 .0 — .0 .3 .2 — — — .4 .2 .3

11075620 02/23/00 1600 1.9 3.0 .2 .1 .1 .0 — .0 .4 .2 — — — .4 .0 .3

11075620 02/23/00 2200 1.9 3.3 .2 .2 .1 .0 — .0 .3 .2 — — — .4 .1 .3

11075620 02/24/00 0100 1.8 3.2 .2 .2 .1 .0 — .1 .3 .2 — — — .3 .1 .3

11075620 02/24/00 0700 1.7 2.7 .2 .1 .1 .0 — .0 .3 .1 — — — .4 .1 .3

11075620 02/27/00 0300 5.9 4.0 .2 .2 .1 .0 — .0 .2 .3 — — — .2 .0 .2

11075600 11/12/01 1800 1.9 3.7 — — — .0 .0 1.2 .4 — — — — — — —

11075600 11/12/01 2030 1.5 1.8 — — — .2 .4 .3 .4 — — — — — — —

11075600 11/12/01 2240 2.2 2.8 — — — .3 .5 .3 .4 — — — — — — —

11075600 11/13/01 0100 2.0 3.0 — — — .3 .0 .9 .4 — — — — — — —

11075600 11/13/01 0340 1.8 2.6 — — — .3 .0 1.0 .5 — — — — — — —

11075600 11/13/01 1215 1.2 2.2 — — — .0 .0 .3 .2 — — — — — — —

11075600 11/14/01 0800 1.3 2.5 — — — .2 .0 .7 .3 — — — — — — —

11075600 03/06/02 1830 2.1 10.8 — — .2 .2 .5 .3 .5 .0 0.5 .4 1.8 .3 .2 —

11075600 03/07/02 0650 2.7 11.2 — — .2 .4 1.1 .0 .3 .1 .4 .5 1.2 .3 .2 —

11075600 03/07/02 1030 1.4 7.6 — — .1 .2 .4 .2 .5 .0 .3 .2 1.0 .2 .2 —

11075600 03/07/02 1330 1.5 10.7 — — .1 .2 .4 .2 .7 .0 .2 .2 .6 .3 .1 —

11075600 03/07/02 1630 1.3 5.5 — — .3 .2 .8 .1 .3 .0 .3 .2 .9 .3 .2 —

11075600 03/07/02 2300 2.5 9.1 — — .4 .3 .7 .3 .3 .1 .5 .3 1.3 .4 .2 —

11075600 03/08/02 0700 2.8 9.8 — — .0 .0 1.8 .0 .0 .0 .0 .0 1.6 .0 .0 —
Appendix C 63

Appendix C. Dissolved organic carbon (DOC) and ultraviolet absorption (UVA) data for stormflow in the Santa Ana River at the diversion downstream from 

Imperial Highway and at the subsurface collection and recharge system (SCARS), southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—

Continued

Station name Station No. Date Time DOC

(mg/L)

UV254

(cm-1)

UV285

(cm-1)

Santa Ana River at the diversion downstream from Imperial Highway 11075620 01/25/2000 0915 — 0.116 0.088

11075620 01/25/2000 1040 — .187 .138

11075620 01/25/2000 1130 — .188 .140

11075620 01/25/2000 1240 — .157 .120

11075620 01/25/2000 1440 — .150 .114

11075620 01/25/2000 1640 — .145 .111

11075620 01/25/2000 1940 — .189 .137

11075620 01/25/2000 2240 — .269 .194

11075620 01/26/2000 0140 — .319 .231

11075620 01/26/2000 0740 — .377 .275

11075620 01/26/2000 1040 — .423 .308

11075620 01/26/2000 1340 — .389 .283

11075620 01/26/2000 1530 — .368 .268

11075620 02/12/2000 0000 6.3 .157 .115

11075620 02/12/2000 0130 5.8 .154 .114

11075620 02/12/2000 0300 5.3 .161 .119

11075620 02/12/2000 0430 5.5 .167 .123

11075620 02/12/2000 0600 5.4 .164 .125

11075620 02/12/2000 0730 6.7 .196 .147

11075620 02/12/2000 0930 5.3 .169 .125

11075620 02/12/2000 1130 6.1 .172 .128

11075620 02/12/2000 1400 5.7 .144 .106

11075620 02/12/2000 1630 6.1 .165 .129

11075620 02/12/2000 1900 5.9 .150 .111

11075620 02/12/2000 2130 5.5 .136 .102

11075620 02/13/2000 0030 5.8 .157 .121

11075620 02/13/2000 0330 5.7 .148 .112

11075620 02/13/2000 0630 5.5 .176 .132

11075620 02/13/2000 0930 6.4 .184 .139

11075620 02/22/2000 2220 6.1 .198 .154

11075620 02/23/2000 0730 5.9 .186 .146

11075620 02/23/2000 0830 5.8 .190 .147

11075620 02/23/2000 0930 5.9 .198 .155

11075620 02/23/2000 1030 5.8 .192 .149

11075620 02/23/2000 1200 5.7 .187 .145

11075620 02/23/2000 1300 5.2 .168 .132

11075620 02/23/2000 1430 4.7 .159 .127

11075620 02/23/2000 1600 5.1 .184 .145

11075620 02/23/2000 1900 5.3 .187 .146

11075620 02/23/2000 2200 6.4 .184 .142

Appendix C. Dissolved organic carbon (DOC) and ultraviolet absorption (UVA) data for stormflow in the Santa Ana River at the diversion downstream from 

Imperial Highway and at the subsurface collection and recharge system (SCARS), southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons

[11075620, Santa Ana River at the diversion downstream from Imperial Highway; 11075600, Santa Ana River at Imperial Highway; samples collected by the U.S. 

Geological Survey (USGS) and analyzed by the USGS Sacramento lab; DOC, dissolved organic carbon; UV254, ultraviolet absorption at 254 nanometers; UV285, 

ultraviolet absorption at 285 nanometers; mg/L, milligrams per liter; cm-1, absorbance per centimeter length; —, no data]
64 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Santa Ana River at the diversion downstream from Imperial Highway 11075620 02/24/2000 0100 — 0.184 0.142

11075620 02/24/2000 0400 6.2 .177 .138

11075620 02/24/2000 0700 6.2 .178 .139

11075620 02/24/2000 1000 5.9 .183 .143

11075620 02/24/2000 1900 5.5 .351 .287

11075620 02/25/2000 0300 5.4 .358 .296

11075620 02/25/2000 1100 5.2 .346 .283

11075620 02/25/2000 1900 5.9 .303 .244

11075620 02/26/2000 0300 5.2 .316 .256

11075620 02/26/2000 1100 6.0 .292 .234

11075620 02/26/2000 1900 7.0 .271 .216

11075620 02/27/2000 0300 6.7 .268 .212

11075620 02/27/2000 1100 6.7 .240 .189

11075620 01/10/2001 1540 4.6 .110 .076

11075620 01/10/2001 1710 4.6 .114 .080

11075620 01/10/2001 1900 6.6 .180 .124

11075620 01/10/2001 2100 7.2 .234 .166

11075620 01/10/2001 2300 6.6 .201 .143

11075620 01/11/2001 0100 6.1 .184 .132

11075620 01/11/2001 0300 5.1 .268 .211

11075620 01/11/2001 0500 5.4 .267 .204

11075620 01/11/2001 0700 8.2 .331 .253

11075620 01/11/2001 1100 7.5 .355 .272

11075620 01/11/2001 1400 8.5 .359 .272

11075620 01/11/2001 1700 9.4 .306 .222

11075620 01/11/2001 2000 11 .343 .249

11075620 01/11/2001 2300 12 .557 .435

11075620 01/12/2001 0030 10 .590 .467

11075620 01/12/2001 0330 9.9 .649 .524

11075620 01/12/2001 0630 9.7 .522 .404

11075620 01/12/2001 0930 9.2 .591 .481

11075620 01/12/2001 1230 8.7 .585 .466

11075620 01/12/2001 1530 9.1 .545 .425

11075620 01/12/2001 2130 8.8 .562 .445

11075620 01/13/2001 0330 8.8 .452 .349

11075620 01/13/2001 0930 8.5 .472 .367

11075620 01/13/2001 1530 8.3 .429 .333

11075620 01/13/2001 2130 8.2 .411 .313

11075620 01/14/2001 0330 8.0 .400 .306

11075620 01/14/2001 0930 8.1 .384 .295

11075620 01/14/2001 1200 8.1 .368 .278

11075620 02/11/2001 1900 5.7 .128 .088

11075620 02/12/2001 0200 5.5 .130 .090

Appendix C. Dissolved organic carbon (DOC) and ultraviolet absorption (UVA) data for stormflow in the Santa Ana River at the diversion downstream from 

Imperial Highway and at the subsurface collection and recharge system (SCARS), southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—

Continued

Station name Station No. Date Time DOC

(mg/L)

UV254

(cm-1)

UV285

(cm-1)
Appendix C 65

Santa Ana River at the diversion downstream from Imperial Highway 11075620 02/12/2001 0400 5.6 0.137 0.095

11075620 02/12/2001 0600 5.3 .162 .114

11075620 02/12/2001 0800 3.0 .192 .147

11075620 02/12/2001 1000 4.6 .218 .162

11075620 02/12/2001 1200 4.6 .211 .158

11075620 02/12/2001 1500 4.3 .220 .168

11075620 02/12/2001 1800 6.9 .341 .257

11075620 02/12/2001 2100 5.6 .232 .172

11075620 02/13/2001 0000 6.8 .319 .237

11075620 02/13/2001 0300 5.6 .255 .187

11075620 02/13/2001 0600 6.5 .292 .219

11075620 02/13/2001 0900 6.7 .347 .264

11075620 02/13/2001 1200 6.1 .384 .295

11075620 02/13/2001 1700 5.8 .431 .340

11075620 02/13/2001 2200 6.1 .404 .315

11075620 02/14/2001 0300 6.8 .385 .298

11075620 02/14/2001 0800 5.9 .416 .327

11075620 02/14/2001 1300 6.0 .371 .289

11075620 02/14/2001 1800 6.1 .415 .328

11075620 02/15/2001 0800 5.7 .332 .258

11075620 02/15/2001 1100 5.7 .328 .256

11075620 03/5/2001 1100 7.6 .240 .175

11075620 03/6/2001 0120 8.1 .251 .184

11075620 03/6/2001 0230 7.1 .247 .179

11075620 03/6/2001 0400 8.8 .259 .181

11075620 03/6/2001 0530 7.3 .228 .165

11075620 03/6/2001 0700 7.3 .224 .163

11075620 03/6/2001 0830 7.6 .232 .169

11075620 03/6/2001 1000 7.6 .236 .172

11075620 03/6/2001 1230 8.0 .237 .173

11075620 03/6/2001 1700 7.9 .232 .168

11075620 03/6/2001 2300 8.1 .229 .168

11075620 03/7/2001 0500 8.0 .232 .170

11075620 11/12/2001 1545 4.8 .127 .089

11075620 11/12/2001 1555 4.8 .124 .095

11075620 11/12/2001 1745 6.1 .170 .113

11075620 11/12/2001 1800 5.0 .124 .062

11075620 11/12/2001 1845 5.0 .113 .076

11075620 11/12/2001 1915 4.3 .114 .081

11075620 11/12/2001 2015 12 .376 .254

11075620 11/12/2001 2045 13 .418 .278

11075620 11/12/2001 2145 12 .394 .267

11075620 11/12/2001 2230 13 .412 .281

Appendix C. Dissolved organic carbon (DOC) and ultraviolet absorption (UVA) data for stormflow in the Santa Ana River at the diversion downstream from 

Imperial Highway and at the subsurface collection and recharge system (SCARS), southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—

Continued

Station name Station No. Date Time DOC

(mg/L)

UV254

(cm-1)

UV285

(cm-1)
66 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Santa Ana River at the diversion downstream from Imperial Highway 11075620 11/12/2001 2330 11 0.367 0.259

11075620 11/13/2001 0030 12 .359 .248

11075620 11/13/2001 0130 9.6 .261 .182

11075620 11/13/2001 0230 7.8 .218 .151

11075620 11/13/2001 0330 6.9 .182 .130

11075620 11/13/2001 0430 7.0 .195 .158

11075620 11/13/2001 0530 7.0 .182 .128

11075620 11/13/2001 0630 6.5 .173 .121

11075620 11/13/2001 0730 6.3 .166 .123

11075620 11/13/2001 1015 13 .400 .266

11075620 11/13/2001 1600 15 .522 .344

11075620 11/13/2001 2200 14 .420 .278

11075620 11/14/2001 0400 11 .366 .241

11075620 11/14/2001 1000 11 .344 .229

Santa Ana River at Imperial Highway 11075600 11/12/2001 1800 4.2 .092 .062

11075600 11/12/2001 2030 13 .318 .215

11075600 11/12/2001 2240 8.6 .197 .140

11075600 11/13/2001 0100 6.9 .153 .100

11075600 11/13/2001 0340 6.3 .143 .097

11075600 11/13/2001 1215 15 .473 .302

11075600 11/14/2001 0800 11 .328 .204

Santa Ana River at the diversion downstream from Imperial Highway 11075620 03/06/2002 1830 4.3 .099 .069

11075620 03/07/2002 0600 5.6 .141 .094

11075620 03/07/2002 0800 5.7 .143 .097

11075620 03/07/2002 1130 5.5 .140 .094

11075620 03/07/2002 1330 5.3 .129 .088

11075620 03/07/2002 1530 5.2 .129 .088

11075620 03/07/2002 1730 4.8 .118 .081

11075620 03/07/2002 2000 4.6 .108 .075

11075620 03/07/2002 2300 4.5 .102 .070

11075620 03/08/2002 0200 5.5 .129 .087

11075620 03/08/2002 0500 6.7 .159 .104

11075620 03/08/2002 0800 7.6 .195 .125

11075620 03/08/2002 1100 7.6 .189 .122

Subsurface collection and recharge system SCARS 11/12/2001 1950 1.4 .041 .028

SCARS 11/12/2001 2100 1.4 .042 .024

SCARS 11/12/2001 2250 2.1 .043 .028

SCARS 11/13/2001 0140 2.1 .043 .030

SCARS 11/13/2001 0410 2.4 .042 .029

SCARS 11/13/2001 0905 2.2 .044 .027

SCARS 11/13/2001 1242 1.5 .041 .029

SCARS 11/13/2001 1620 2.2 .042 .029

Appendix C. Dissolved organic carbon (DOC) and ultraviolet absorption (UVA) data for stormflow in the Santa Ana River at the diversion downstream from 

Imperial Highway and at the subsurface collection and recharge system (SCARS), southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—

Continued

Station name Station No. Date Time DOC

(mg/L)

UV254

(cm-1)

UV285

(cm-1)
Appendix C 67

Subsurface collection and recharge system SCARS 11/14/2001 0915 1.7 0.052 0.032

SCARS 03/07/2002 0715 1.6 .040 .027

SCARS 03/07/2002 1100 1.6 .039 .026

SCARS 03/07/2002 1330 1.6 .042 .028

SCARS 03/07/2002 1700 1.6 .040 .027

SCARS 03/07/2002 2330 1.6 .039 .026

SCARS 03/08/2002 0700 1.5 .039 .027

Appendix C. Dissolved organic carbon (DOC) and ultraviolet absorption (UVA) data for stormflow in the Santa Ana River at the diversion downstream from 

Imperial Highway and at the subsurface collection and recharge system (SCARS), southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—

Continued

Station name Station No. Date Time DOC

(mg/L)

UV254

(cm-1)

UV285

(cm-1)
68 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

Appendix D. Data for field parameters, major ions, and nutrients in the Santa Ana River at the diversion downstream from Imperial Highway (11075620), 

southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—Continued

Station

No. Date Time

Streamflow

(ft3/s)

pH

(standard 

units)

Specific

conductance

(μS/cm)

Alkalinity

(mg/L as 

CaCO3)

Sulfate,

dissolved

(mg/L as 

SO4)

Chloride,

dissolved

(mg/L)

Nitrate,

dissolved

(mg/L as N)

Nitrite,

dissolved

(mg/L as N)

Bromide,

dissolved

(mg/L)

Phosphate,

ortho, 

dissolved

(mg/L as PO4)

11075620 01/25/2000 0915 492 6.8 807 152 95 100 3.7 <0.02 <0.4 0.5

11075620 01/25/2000 1040 565 6.9 768 137 110 87 3.3 <.02 <.4 <.3

11075620 01/25/2000 1130 512 6.9 744 138 95 82 3.2 <.02 <.4 .4

11075620 01/25/2000 1240 492 6.9 782 144 100 90 3.6 <.02 .4 .3

11075620 01/25/2000 1440 471 7.5 791 — — — 3.6 <.02 — —

11075620 01/25/2000 1640 457 7.2 788 — — — 3.7 <.02 — —

11075620 01/25/2000 1940 424 7.4 820 153 — — 4.4 .03 — —

11075620 01/25/2000 2240 431 7.2 551 102 — — 3.1 .04 — —

11075620 01/26/2000 0140 433 7.3 563 103 — — 3.4 .05 — —

11075620 01/26/2000 0740 426 7.3 758 130 95 79 4.2 .09 <.4 .5

11075620 01/26/2000 1040 437 7.2 807 131 130 87 4.3 .11 <.4 .4

11075620 01/26/2000 1340 432 7.2 779 131 100 84 4.2 .13 <.4 .6

11075620 01/26/2000 1530 426 7.9 799 133 120 84 4.3 .14 <.4 .4

11075620 02/12/2000 0000 321 7.9 756 157 95 80 5.4 .09 <.4 .4

11075620 02/12/2000 0130 319 7.9 766 160 — 78 5.1 .08 — —

11075620 02/12/2000 0300 323 8.0 686 150 — 77 5.0 .08 — —

11075620 02/12/2000 0430 620 7.8 495 94 75 47 2.9 .06 <.4 <.3

11075620 02/12/2000 0600 629 7.9 510 95 85 49 3.0 .06 <.4 <.3

11075620 02/12/2000 0730 460 8.0 603 110 90 58 3.6 .08 <.4 .3

11075620 02/12/2000 0930 415 8.0 670 130 90 67 4.2 .09 <.4 <.3

11075620 02/12/2000 1130 385 7.3 690 140 90 68 4.2 .09 <.4 <.3

11075620 02/12/2000 1400 366 8.0 763 150 100 79 4.4 .10 <.4 .5

11075620 02/12/2000 1630 346 8.0 731 150 90 77 4.4 .10 .7 2

11075620 02/12/2000 1900 333 8.0 743 150 85 79 4.6 .10 .4 <.3

11075620 02/12/2000 2130 324 7.9 758 160 95 81 4.8 .09 .9 1

11075620 02/13/2000 0030 340 7.9 709 140 90 75 4.4 .09 <.4 <.3

11075620 02/13/2000 0330 334 7.9 728 150 95 79 4.5 .10 <.4 .5

11075620 02/13/2000 0630 334 7.9 711 150 95 75 4.2 .10 1.0 .4

11075620 02/13/2000 0930 357 7.8 702 140 95 72 4.0 .10 <.4 .3

11075620 02/22/2000 2220 — 7.8 462 99 50 44 2.0 .08 <.4 .5

11075620 02/23/2000 0730 — 7.9 422 89 50 45 2.2 .08 <.4 .5

11075620 02/23/2000 0830 — 7.9 422 91 45 38 1.9 .07 <.4 .4

11075620 02/23/2000 0930 — — — — 50 42 2.0 .08 <.4 .4

11075620 02/23/2000 1030 — 7.9 424 91 50 40 1.9 .07 <.4 .5

11075620 02/23/2000 1200 — 7.9 362 76 50 35 1.6 .06 <.4 .3

11075620 02/23/2000 1300 — 7.8 336 66 45 30 3.3 1.1 <.4 .3

11075620 02/23/2000 1430 — 7.9 301 59 50 29 1.3 .04 <.4 .3

11075620 02/23/2000 1600 — 7.9 381 70 60 34 .07 <.02 <.4 .5

11075620 02/23/2000 1900 — 7.1 518 94 3 1.7 2.5 .07 <.4 <.3

11075620 02/23/2000 2200 — 7.2 552 110 100 60 2.4 .07 <.4 <.3

11075620 02/24/2000 0100 — 7.4 474 100 70 49 2.6 .09 <.4 .3

11075620 02/24/2000 0400 — 7.3 501 100 70 54 2.5 .08 .5 .2

11075620 02/24/2000 0700 — 7.3 486 110 70 51 2.5 .06 <.4 .2

Appendix D. Data for field parameters, major ions, and nutrients in the Santa Ana River at the diversion downstream from Imperial Highway (11075620), 

southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons

[Samples analyzed by U.S. Geological Survey Geochemical lab in San Diego; 11075620, Santa Ana River at the diversion downstream from Imperial Highway; 

alkalinity measured as filtered incremental titration; ft3/s, cubic feet per second; μS/cm, microsiemens per centimeter at 25 degrees Celsius; mg/L, milligrams per 

liter; E, Estimated value; <, less than; —, no data]
Appendix D 69

11075620 02/24/2000 1000 — 7.6 475 98 60 47 <0.02 <0.02 <0.4 <0.3

11075620 02/24/2000 1900 464 7.8 469 99 55 43 2.3 .06 <.4 .5

11075620 02/25/2000 0300 460 8.0 477 100 55 42 2.2 .07 <.4 .4

11075620 02/25/2000 1100 460 7.9 473 100 60 43 2.2 .10 <.4 .5

11075620 02/25/2000 1900 452 7.9 505 110 70 46 2.3 .10 <.4 .3

11075620 02/26/2000 0300 450 7.7 556 120 75 51 2.4 .14 <.4 <.3

11075620 02/26/2000 1100 456 7.9 547 120 70 50 2.4 .14 <.4 .6

11075620 02/26/2000 1900 452 7.8 576 120 75 53 2.5 .16 <.4 .3

11075620 02/27/2000 0300 447 7.9 597 130 75 56 2.5 .18 <.4 .4

11075620 02/27/2000 1100 443 7.9 607 130 75 56 2.6 .17 <.4 .3

11075620 01/10/2001 1540 275 8.5 971 — 100 110 6.6 .04 <.4 .5

11075620 01/10/2001 1710 284 8.3 965 — 100 100 7.5 <.04 <.4 <.6

11075620 01/10/2001 1900 386 8.3 860 — 91 88 5.2 <.04 <.4 <.6

11075620 01/10/2001 2100 499 8.2 629 — 76 63 3.8 <.02 <.2 <.3

11075620 01/10/2001 2300 466 8.2 648 — 87 64 3.7 <.02 <.2 <.3

11075620 01/11/2001 0100 456 8.4 628 — 90 70 3.9 .04 <.2 <.3

11075620 01/11/2001 0300 1570 8.0 244 — 36 21 1.5 .02 <.2 <.3

11075620 01/11/2001 0500 1550 8.0 306 — 53 27 1.3 .02 <.2 <.3

11075620 01/11/2001 0700 957 7.8 418 — 82 40 1.5 .02 <.2 <.3

11075620 01/11/2001 1100 700 8.1 475 — 80 38 2.1 .04 <.2 <.3

11075620 01/11/2001 1400 600 7.9 472 — 78 39 2.4 .04 <.2 <.3

11075620 01/11/2001 1700 500 7.8 541 — 84 48 3.3 .05 <.2 .4

11075620 01/11/2001 2000 1450 7.7 543 — 78 49 3.5 .03 <.2 <.3

11075620 01/11/2001 2300 3410 7.8 425 — 53 40 2.6 .05 <.2 <.3

11075620 01/12/2001 0030 3840 7.8 402 — 47 37 2.6 .04 <.2 <.3

11075620 01/12/2001 0330 4110 7.8 371 — 41 32 2.4 .02 <.2 <.3

11075620 01/12/2001 0630 2340 7.8 401 — 51 35 2.3 .04 <.2 <.3

11075620 01/12/2001 0930 1410 7.9 408 — 51 36 2.6 .05 <.2 <.3

11075620 01/12/2001 1230 1170 7.9 417 — 48 37 2.7 .04 <.4 .03

11075620 01/12/2001 1530 1030 7.8 415 — 50 37 2.6 .04 .3 <.3

11075620 01/12/2001 2130 434 7.6 457 — 61 42 2.8 .08 <.2 .3

11075620 01/13/2001 0330 414 7.8 577 — 85 59 2.9 <.02 <.2 <.3

11075620 01/13/2001 0930 395 7.8 574 — 85 58 2.8 <.02 <.2 <.3

11075620 01/13/2001 1530 384 7.8 571 — 82 56 2.8 .06 <.2 .3

11075620 01/13/2001 2130 376 7.9 573 — 78 57 2.8 <.02 <.2 <.3

11075620 01/14/2001 0330 372 8.0 603 — 83 64 2.9 .04 <.4 <.3

11075620 01/14/2001 0930 371 7.9 572 — 77 57 2.9 <.02 <.2 <.3

11075620 01/14/2001 1200 367 7.9 572 — 75 56 2.9 <.02 <.2 <.3

11075620 02/11/2001 1900 401 8.3 985 — 100 110 5.5 .16 <.4 <.6

11075620 02/12/2001 0200 395 8.2 987 — 100 100 5.9 .15 <.4 <.6

11075620 02/12/2001 0400 401 8.3 989 — — 100 — .15 — —

11075620 02/12/2001 0600 691 8.1 606 — 65 61 3.3 .10 <.4 <.6

11075620 02/12/2001 0800 2100 7.8 184 — 25 15 .79 .02 <.2 <.3

11075620 02/12/2001 1000 1550 7.9 289 — 44 25 1.2 <.02 <.2 <.3

11075620 02/12/2001 1200 1030 8.0 415 — 58 38 2.1 .06 <.2 <.3

11075620 02/12/2001 1500 1690 7.8 196 — 32 16 .65 <.02 <.2 <.3

11075620 02/12/2001 1800 756 8.0 443 — 86 40 1.3 .03 <.2 <.3

11075620 02/12/2001 2100 1800 8.1 404 — 65 35 1.5 .04 <.2 <.3

Appendix D. Data for field parameters, major ions, and nutrients in the Santa Ana River at the diversion downstream from Imperial Highway (11075620), 

southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—Continued

Station

No. Date Time

Streamflow

(ft3/s)

pH

(standard 

units)

Specific

conductance

(μS/cm)

Alkalinity

(mg/L as 

CaCO3)

Sulfate,

dissolved

(mg/L as 

SO4)

Chloride,

dissolved

(mg/L)

Nitrate,

dissolved

(mg/L as N)

Nitrite,

dissolved

(mg/L as N)

Bromide,

dissolved

(mg/L)

Phosphate,

ortho, 

dissolved

(mg/L as PO4)
70 Microbial and Dissolved Organic Carbon Characterization of Stormflow in the Santa Ana River, Southern California

11075620 02/13/2001 0000 854 8.0 487 — 90 43 1.4 0.03 <0.2 <0.3

11075620 02/13/2001 0300 2480 8.1 634 — 100 60 2.8 .05 <.4 <.6

11075620 02/13/2001 0600 4510 8.0 499 — 65 47 2.5 .04 <.2 <.3

11075620 02/13/2001 0900 5050 8.0 480 — 56 44 2.6 .06 <.2 <.3

11075620 02/13/2001 1200 5400 8.0 386 — 46 34 2.0 .05 <.2 <.3

11075620 02/13/2001 1700 4970 8.0 326 — 36 28 1.9 .05 <.2 <.3

11075620 02/13/2001 2200 4550 8.0 321 — 35 27 1.8 .04 <.2 <.3

11075620 02/14/2001 0300 2570 8.0 344 — 40 28 1.9 .03 <.2 <.3

11075620 02/14/2001 0800 2480 8.0 344 — 38 28 1.8 .03 <.2 <.3

11075620 02/14/2001 1300 1080 8.0 401 — 48 33 1.8 .04 .3 <.3

11075620 02/14/2001 1800 593 8.1 413 — 50 35 1.9 .04 <.2 <.3

11075620 02/15/2001 0800 611 8.0 498 — 66 43 1.9 .05 <.2 <.3

11075620 02/15/2001 1100 601 7.9 489 — 63 41 1.9 .04 <.2 <.3

11075620 03/05/2001 1100 537 8.1 635 140 77 62 2.8 .12 <.2 .4

11075620 03/06/2001 0120 530 8.0 655 140 75 63 2.6 .25 <.4 <.6

11075620 03/06/2001 0230 542 8.1 623 130 68 59 2.7 .18 <.4 .5

11075620 03/06/2001 0400 615 8.1 614 130 73 58 2.7 .13 <.4 .2

11075620 03/06/2001 0530 618 8.1 577 120 70 52 2.5 .15 <.2 .3

11075620 03/06/2001 0700 610 8.1 588 120 69 54 2.6 .11 <.2 .3

11075620 03/06/2001 0830 600 8.1 641 140 74 61 3.4 .11 <.2 .4

11075620 03/06/2001 1000 591 8.1 672 140 78 68 3.0 .01 <.2 .3

11075620 03/06/2001 1230 530 8.1 696 140 79 65 3.1 .13 <.2 .5

11075620 03/06/2001 1700 536 8.3 719 150 92 70 3.0 <.1 <.4 .4

11075620 03/06/2001 2300 538 8.3 720 160 81 73 3.5 .23 <.2 .6

11075620 03/07/2001 0500 574 8.2 723 150 84 72 3.4 .26 <.2 .5

11075620 11/12/2001 1545 234 8.7 960 — 120 110 6.0 <.05 <.2 .3

11075620 11/12/2001 1555 234 8.7 962 — 110 110 5.3 <.05 <.2 .8

11075620 11/12/2001 1800 231 8.6 865 — 120 110 5.3 <.05 <.2 .8

11075620 11/12/2001 1845 232 8.5 993 — 120 110 5.4 <.05 <.2 .5

11075620 11/12/2001 1915 245 8.5 978 — 110 110 4.8 <.05 <.2 .7

11075620 11/12/2001 1945 249 — — — 120 110 4.8 <.05 <.2 .7

11075620 11/12/2001 2015 269 8.3 656 — 93 78 4.7 <.05 <.2 <.3

11075620 11/12/2001 2045 383 8.2 648 — 80 66 4.2 <.05 <.2 <.3

11075620 11/12/2001 2115 388 — — — 81 64 4.1 <.05 <.2 .3

11075620 11/12/2001 2145 383 8.2 669 — 87 69 4.3 <.05 <.2 <.3

11075620 11/12/2001 2230 380 8.1 684 — 96 70 4.0 <.05 <.2 <.3

11075620 11/13/2001 0030 296 8.1 751 — 110 77 4.2 <.05 <.2 <.3

11075620 11/13/2001 0130 295 8.2 814 — 110 89 4.3 <.05 .4 .7

11075620 11/13/2001 0230 293 — — — 120 98 4.6 <.05 <.2 .8

11075620 11/13/2001 0330 290 8.2 922 — 120 100 4.5 <.05 <.2 1.0

11075620 11/13/2001 0430 287 8.3 939 — 120 100 4.6 <.05 <.2 .8

11075620 11/13/2001 0530 290 8.2 939 — 120 100 4.6 <.05 <.2 .8

11075620 11/13/2001 0630 291 8.2 946 — 120 110 4.7 <.05 <.2 .7

11075620 11/13/2001 0730 308 8.2 920 — -- 110 4.8 <.05 <.2 .8

11075620 11/13/2001 1015 330 8.1 886 — 100 100 5.8 <.05 .2 .7

11075620 11/13/2001 2200 263 8.2 947 — 100 76 4.4 <.05 <.2 .3

Appendix D. Data for field parameters, major ions, and nutrients in the Santa Ana River at the diversion downstream from Imperial Highway (11075620), 

southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—Continued

Station

No. Date Time

Streamflow

(ft3/s)

pH

(standard 

units)

Specific

conductance

(μS/cm)

Alkalinity

(mg/L as 

CaCO3)

Sulfate,

dissolved

(mg/L as 

SO4)

Chloride,

dissolved

(mg/L)

Nitrate,

dissolved

(mg/L as N)

Nitrite,

dissolved

(mg/L as N)

Bromide,

dissolved

(mg/L)

Phosphate,

ortho, 

dissolved

(mg/L as PO4)
Appendix D 71

11075620 03/06/2002 1830 255 8.5 1,040 — 130 120 6.7 0.05 <1 <1

11075620 03/07/2002 0630 224 8.2 1,030 — 120 110 5.7 .07 <1 1.0

11075620 03/07/2002 0800 229 8.2 1,000 — 120 110 5.7 .06 <1 <2

11075620 03/07/2002 0930 234 8.3 994 — 110 110 5.8 .07 <1 <2

11075620 03/07/2002 1130 236 8.5 1,000 — 120 120 5.9 .06 <1 <.5

11075620 03/07/2002 1330 240 8.6 997 — 110 120 7.2 .07 <1 .5E

11075620 03/07/2002 1530 238 8.8 1,000 — 120 120 6.4 .06 <1 .4E

11075620 03/07/2002 1730 237 8.7 1,020 — 120 120 6.5 .06 <1 .5

11075620 03/07/2002 2000 237 8.6 1,020 — 120 120 6.8 .06 <1 .5

11075620 03/07/2002 2300 238 8.3 1,020 — 120 120 6.9 .06 <1 .6

11075620 03/08/2002 0200 243 8.3 994 — 120 120 6.6 .06 <1 .4E

11075620 03/08/2002 0500 244 8.2 987 — 120 120 6.4 .07 <1 .4E

11075620 03/08/2002 0800 244 8.2 983 — 120 110 6.3 .08 <1 .4E

11075620 03/08/2002 1100 247 8.4 984 — 120 110 6.2 .10 <1 .6

Appendix D. Data for field parameters, major ions, and nutrients in the Santa Ana River at the diversion downstream from Imperial Highway (11075620), 

southern California, 1999–2000, 2000–01, and 2001–02 rainy seasons—Continued

Station

No. Date Time

Streamflow

(ft3/s)

pH

(standard 

units)

Specific

conductance

(μS/cm)

Alkalinity

(mg/L as 

CaCO3)

Sulfate,

dissolved

(mg/L as 

SO4)

Chloride,

dissolved

(mg/L)

Nitrate,

dissolved

(mg/L as N)

Nitrite,

dissolved

(mg/L as N)

Bromide,

dissolved

(mg/L)

Phosphate,

ortho, 

dissolved

(mg/L as PO4)