Front cover: Photographs by Cathy Munday, U.S. Geological Survey.

1. Mud Slough at Highway 140. 

Mud Slough was one of the most significant tributary sources of nutrients, organic carbon, and chlorophyll-a to the San 

Joaquin River during the study.

2. Dairy in San Joaquin River Basin. 

Nitrogen and oxygen isotope data suggested that animal waste was a significant source of nitrate in the San Joaquin 

River during this study.

3. San Joaquin River at Crows Landing.

1

2

3
Sources and Transport of Nutrients, Organic Carbon, 

and Chlorophyll-a in the San Joaquin River 

Upstream of Vernalis, California, during Summer and 

Fall, 2000 and 2001

By Charles R. Kratzer1, Peter D. Dileanis1, Celia Zamora1, Steven R. Silva2, Carol 

Kendall2

, Brian A. Bergamaschi1, and Randy A. Dahlgren3

Sacramento, California

2004

Water-Resources Investigations Report 03-4127

U.S. GEOLOGICAL SURVEY

Prepared in cooperation with the

CALFED BAY-DELTA PROGRAM and

CALIFORNIA DEPARTMENT OF WATER RESOURCES 6427-12

1

U.S. Geological Survey, Sacramento, California

2

U.S. Geological Survey, Menlo Park, California

3

University of California, Davis, California
U.S. DEPARTMENT OF THE INTERIOR

GALE A. NORTON, Secretary

U.S. GEOLOGICAL SURVEY

Charles G. Groat, Director

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.

For additional information write to:

District Chief

U.S. Geological Survey

Placer Hall—Suite 2012

6000 J Street

sacramento, CA 95819-6129

http://ca.water.usgs.gov

Copies of this report can be purchased from:

U.S. Geological Survey

Information Services

Building 810

Box 25286, Federal Center

Denver, CO 80225-0286
Contents iii

Contents

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

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

Study Area............................................................................................................................................................ 4

Methods of Data Collection and Analysis............................................................................................................ 10

Sample Collection and Processing.............................................................................................................. 10

U.S. Geological Survey Methods....................................................................................................... 10

University of California at Davis Methods........................................................................................ 17

Field Measurements and Streamflow.......................................................................................................... 17

Analytical Methods ..................................................................................................................................... 18

U.S. Geological Survey Methods....................................................................................................... 18

Nutrients.................................................................................................................................... 18

Organic Carbon, Ultraviolet Absorbance, and Volatile Suspended Solids .............................. 18

Chlorophyll-a and Pheophytin-a............................................................................................... 19

Suspended Sediment ................................................................................................................. 19

Isotopes ..................................................................................................................................... 19

University of California at Davis Methods........................................................................................ 20

Nutrients.................................................................................................................................... 21

Organic Carbon and Particulate Organic Matter ...................................................................... 21

Chlorophyll-a and Pheophytin-a............................................................................................... 21

Total Suspended Solids............................................................................................................. 21

U.S. Geological Survey Quality Control Samples...................................................................................... 21

Hydrologic Conditions During the Study Period ................................................................................................. 23

Concentrations of Nutrients, Organic Carbon, and Chlorophyll-a ...................................................................... 26

Nitrogen....................................................................................................................................................... 28

Phosphorus .................................................................................................................................................. 28

Organic Carbon ........................................................................................................................................... 33

Chlorophyll-a and Pheophytin-a................................................................................................................. 33

Historical Nutrient Loads in the San Joaquin Basin ............................................................................................ 38

Monthly Loads in the San Joaquin River near Vernalis, 1972–2001 ......................................................... 38

Upstream-to-Downstream Loads in the San Joaquin River, 1986–88........................................................ 41

Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a ....................................................................... 59

Nitrogen....................................................................................................................................................... 59

Phosphorus .................................................................................................................................................. 62

Organic Carbon ........................................................................................................................................... 67

Chlorophyll-a and Pheophytin-a................................................................................................................. 74

Isotopes................................................................................................................................................................. 79

Sources of Particulate Organic Matter ........................................................................................................ 79

Nitrate as a Nutrient Source to Phytoplankton............................................................................................ 79

Sources of Nitrate........................................................................................................................................ 82

Summary and Conclusions................................................................................................................................... 85

References Cited .................................................................................................................................................. 86

Appendixes........................................................................................................................................................... 89
iv Figures

FIGURES

Figure 1. Map showing portion of the San Joaquin Valley and the Sacramento–San Joaquin Delta ............... 3

Figure 2. Map showing San Joaquin Valley portion of the San Joaquin River Basin and site locations ......... 6

Figure 3. Map showing San Joaquin Valley portion of the San Joaquin River Basin, water quality

sampling sites, and land use areas ..................................................................................................... 7

Figure 4. Map showing San Joaquin River Basin and drainage basins for water quality sites......................... 9

Figure 5. Graphs showing precipitation at Modesto, California, streamflow for San Joaquin River 

sampling sites and major east-side tributaries from upstream to downstream, and sample 

collection times, July to October 2000 .............................................................................................. 11

Figure 6. Graphs showing precipitation at Modesto, California, streamflow for minor tributaries with 

gaging stations, and sample collection times, July to October 2000 ................................................. 13

Figure 7. Graphs showing precipitation at Modesto, California, and streamflow for San Joaquin River 

sampling sites and major east-side tributaries from upstream to downstream, and sample 

collection times, June to November 2001.......................................................................................... 14

Figure 8. Graphs showing precipitation at Modesto, California, streamflow for minor tributaries with 

gaging stations, and sample collection times, June to November 2001 ........................................... 16

Figure 9. Graph showing monthly precipitation in downtown Modesto, California, 

December 1971–November 2001 ...................................................................................................... 24

Figure 10. Graphs showing streamflow at San Joaquin River near Vernalis, California.................................... 25

Figure 11. Graph showing water year indexes and corresponding water year types for San Joaquin Basin,

California, 1972–2001 ....................................................................................................................... 26

Figure 12. Graph showing instantaneous streamflow at time of sampling at San Joaquin River sites in 

California ........................................................................................................................................... 27

Figure 13. Graphs showing concentrations of nitrate, inorganic nitrogen, and total nitrogen at San Joaquin 

River sites in California, from upstream to downstream for July through October 2000, with 

streamflow at Vernalis ....................................................................................................................... 29

Figure 14. Graphs showing concentrations of nitrate, inorganic nitrogen, and total nitrogen at San Joaquin 

River sites in California, from upstream to downstream for June through November 2001, with

streamflow at Vernalis ....................................................................................................................... 30

Figure 15. Graphs showing concentrations of orthophosphate and total phosphorus at San Joaquin River sites 

in California, from upstream to downstream for July through October 2000, with streamflow at 

Vernalis.............................................................................................................................................. 31

Figure 16. Graphs showing concentrations of orthophosphate and total phosphorus at San Joaquin River sites 

in California, from upstream to downstream for June through November 2001, with streamflow 

at Vernalis .......................................................................................................................................... 32

Figure 17. Graphs showing concentrations of dissolved organic carbon and suspended organic carbon at 

San Joaquin River sites in California, from upstream to downstream for July through October 

2000, with streamflow at Vernalis..................................................................................................... 34

Figure 18. Graphs showing concentrations of dissolved organic carbon and suspended organic carbon at 

San Joaquin River sites in California, from upstream to downstream for June through November 

2001, with streamflow at Vernalis..................................................................................................... 35

Figure 19. Graph showing concentrations of chlorophyll-a at San Joaquin River sites in California, from 

upstream to downstream for July through October 2000, with streamflow at Vernalis.................... 36

Figure 20. Graphs showing concentrations of chlorophyll-a and pheophytin-a at San Joaquin River sites 

in California, from upstream to downstream for June through November 2001, with streamflow 

at Vernalis .......................................................................................................................................... 37

Figure 21. Graphs showing monthly loads of nitrate, total nitrogen, and total phosphorus at 

San Joaquin River near Vernalis, California, 1972–2001.................................................................. 39
Figures v

Figure 22. Graphs showing flow-adjusted concentrations of nitrate, total nitrogen, and total phosphorus in the 

San Joaquin River near Vernalis, California, 1972–2001.................................................................. 40

Figure 23. Graphs showing monthly loads of nitrate, total nitrogen, and total phosphorus at 

San Joaquin River near Vernalis, California, for 1972–99 (average), 2000, and 2001..................... 42

Figure 24. Graphs showing monthly loads of nitrate at sites in the San Joaquin River, California, upstream 

to downstream for water years 1986–88............................................................................................ 43

Figure 25. Graphs showing monthly loads of total nitrogen at sites in the San Joaquin River, California, 

upstream to downstream for water years 1986–88 ............................................................................ 49

Figure 26. Graphs showing monthly loads of total phosphorus at sites in the San Joaquin River, California,

upstream to downstream for water years 1986–88 ............................................................................ 54

Figure 27. Graphs showing instantaneous loading rates of nitrate, inorganic nitrogen, and total nitrogen at 

San Joaquin River sites from upstream to downstream for July through October 2000, with 

streamflow at Vernalis, California..................................................................................................... 60

Figure 28. Graphs showing instantaneous loading rates of nitrate, inorganic nitrogen, and total nitrogen at 

San Joaquin River sites from upstream to downstream for June through November 2001, with

streamflow at Vernalis, California..................................................................................................... 61

Figure 29. Graphs showing instantaneous loading rates of nitrate, inorganic nitrogen, and total nitrogen in

tributaries from upstream to downstream as a percentage of Vernalis loading rates for July through 

October 2000, with streamflow at Vernalis, California..................................................................... 63

Figure 30. Graphs showing instantaneous loading rates of nitrate, inorganic nitrogen, and total nitrogen 

in tributaries from upstream to downstream as a percentage of Vernalis loading rates for June 

through November 2001, with streamflow at Vernalis, California ................................................... 64

Figure 31. Graphs showing instantaneous loading rates of orthophosphate and total phosphorus at San Joaquin

River sites from upstream to downstream for July through October 2000, with streamflow at 

Vernalis, California............................................................................................................................ 65

Figure 32. Graphs showing instantaneous loading rates of orthophosphate and total phosphorus at San 

Joaquin River sites from upstream to downstream for June through November 2001, with 

streamflow at Vernalis, California..................................................................................................... 66

Figure 33. Graphs showing instantaneous loading rates of orthophosphate and total phosphorus in 

tributaries from upstream to downstream as a percentage of Vernalis loading rates for July 

through October 2000, with streamflow at Vernalis, California ....................................................... 68

Figure 34. Graphs showing instantaneous loading rates of orthophosphate and total phosphorus in 

tributaries from upstream to downstream as a percentage of Vernalis loading rates for June 

through November 2001, with streamflow at Vernalis, California ................................................... 69

Figure 35. Graphs showing instantaneous loading rates of dissolved organic carbon and suspended organic 

carbon at San Joaquin River sites from upstream to downstream for July through October 2000, 

with streamflow at Vernalis, California............................................................................................. 70

Figure 36. Graphs showing instantaneous loading rates of dissolved organic carbon and suspended organic 

carbon at San Joaquin River sites from upstream to downstream for June through November 2001, 

with streamflow at Vernalis, California............................................................................................. 71

Figure 37. Graph showing instantaneous loading rates of dissolved organic carbon in tributaries from 

upstream to downstream as a percentage of Vernalis loading rates for July through 

October 2000, with streamflow at Vernalis, California..................................................................... 72

Figure 38. Graphs showing instantaneous loading rates of dissolved organic carbon and suspended organic 

carbon in tributaries from upstream to downstream as a percentage of Vernalis loading rates for 

June through November 2001, with streamflow at Vernalis, California ........................................... 73

Figure 39. Graph showing instantaneous loading rates of chlorophyll-a at San Joaquin River sites from 

upstream to downstream for July through October 2000, with streamflow at Vernalis, 

California ........................................................................................................................................... 75
vi Figures

Figure 40. Graphs showing instantaneous loading rates of chlorophyll-a and pheophytin-a at San Joaquin 

River sites, from upstream to downstream for June through November 2001, 

with streamflow at Vernalis, California............................................................................................. 76

Figure 41. Graph showing instantaneous loading rates of chlorophyll-a in tributaries from upstream to 

downstream as a percentage of Vernalis loading rates for July through October 2000, with 

streamflow at Vernalis, California..................................................................................................... 77

Figure 42. Graphs showing instantaneous loading rates of chlorophyll-a and pheophytin-a in tributaries 

from upstream to downstream as a percentage of Vernalis loading rates for June through 

November 2001, with streamflow at Vernalis, California................................................................. 78

Figure 43. Graphs showing atomic ratio of carbon to nitrogen in particulate organic matter from 

San Joaquin River sites and Mud Slough in California ..................................................................... 80

Figure 44. Graph showing atomic ratio of carbon to nitrogen versus delta carbon-13 of particulate organic 

matter at San Joaquin River sites, Mud Slough, and other tributaries sampled in 2001 in 

California ........................................................................................................................................... 81

Figure 45. Graphs showing delta nitrogen-15 of total dissolved nitrogen and nitrate in samples from San 

Joaquin River, California, for 2001 ................................................................................................... 81

Figure 46. Graphs showing delta nitrogen-15 of total dissolved nitrogen and particulate organic matter in 

samples from San Joaquin River, California, for 2000...................................................................... 83

Figure 47. Graphs showing delta nitrogen-15 of nitrate and particulate organic matter in samples from San 

Joaquin River, California, for 2001 ................................................................................................... 83

Figure 48 Graph showing delta nitrogen-15 versus delta oxygen-18 of nitrate for San Joaquin River, 

California, and tributary samples for 2001 superimposed on fields of common isotopic 

compositions from different nitrate sources ...................................................................................... 84

Figure 49. Graph showing delta nitrogen-15 versus delta oxygen-18 of nitrate for San Joaquin River, 

California, and tributary samples for 2001 with possible denitrification trend line .......................... 84

Figure 50. Graph showing delta nitrogen-15 of nitrate for San Joaquin River, California, and tributary

samples for 2001................................................................................................................................ 85
Tables vii

TABLES

Table 1. Names, locations, and types of data available for sites in the San Joaquin River Basin, 

California ........................................................................................................................................... 5

Table 2. Basin areas and land use for valley portion of drainage basins within the San Joaquin River 

Basin, California ................................................................................................................................ 8

Table 3. Summary of quality-control replicate data for samples collected in the San Joaquin River 

Basin, California, 2000–2001 ............................................................................................................ 22

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks

in the San Joaquin River Basin, California, in 2000 and 2001 ......................................................... 90

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for 

nutrients, organic carbon, and chlorophyll for San Joaquin River sites in California ...................... 98

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for 

nutrients, organic carbon, and chlorophyll for tributary sites ........................................................... 106
viii Conversion Factors, Vertical Datum and Abbreviations and Acronyms

CONVERSION FACTORS, VERTICAL DATUM AND ABBREVIATIONS AND 

ACRONYMS

CONVERSION FACTORS

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

88); horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27).

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

F = (1.8)C + 32

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

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

micrograms per liter (μg/L).

Abbreviations and Acronyms

‰ per mil

cm centimeter

cm−1 per centimeter

kg/d kilogram per day

L liter

L/mg-centimeter liter per milligram-centimeter

mg milligram

mg/L milligram per liter

mL milliliter

mm millimeter

μg/L microgram per liter

μm micrometer

μS/cm microsiemens per centimeter

nm nanometer

C carbon

DOC dissolved organic carbon

DWR California Department of Water Resources

Multiply By To obtain

inch (in.) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

square mile (mi2) 2.590 square kilometer (km2)

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

acre-foot (acre-ft) 1,233 cubic meter (m3)
Conversion Factors, Vertical Datum and Abbreviations and Acronyms ix

δ delta, the relative difference between the ratio of isotopes in a sample and the ratio of isotopes 

 in some standard

EC electrical conductivity

EDTA ethylenediaminetetraacetic acid

EWI equal width increment

GFF glass fiber filter

Hwy Highway

N nitrogen

NWIS National Water Information System

NWQL National Water Quality Laboratory of the U.S. Geological Survey

P phosphorus

POM particulate organic matter

QA/QC quality assurance and quality control

QC quality control

RPD relative percent difference

SJR San Joaquin River

SOC suspended organic carbon

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

SUVA specific ultraviolet absorbance

TDN total dissolved nitrogen

TMDL Total Maximum Daily Load

UCD University of California at Davis

UCDBL University of California at Davis's Biogeochemistry Laboratory

USGS U.S. Geological Survey

VAMP Vernalis Adaptive Management Plan

VPDB Vienna Pee Dee Belemnite

VSS volatile suspended solids
x Conversion Factors, Vertical Datum and Abbreviations and Acronyms
Abstract 1

Sources and Transport of Nutrients, Organic Carbon, and 

Chlorophyll-a in the San Joaquin River Upstream of 

Vernalis, California, during Summer and Fall, 2000 and 

2001

By Charles R. Kratzer, Peter D. Dileanis, Celia Zamora, Steven R. Silva, Carol Kendall, 

Brian A. Bergamaschi, and Randy A. Dahlgren

ABSTRACT

Oxidizable materials from the San Joaquin 

River upstream of Vernalis can contribute to low 

dissolved oxygen episodes in the Stockton Deep 

Water Ship Channel that can inhibit salmon 

migration in the fall. The U.S. Geological Survey 

collected and analyzed samples at four San 

Joaquin River sites in July through October 2000 

and June through November 2001, and at eight 

tributary sites in 2001. The data from these sites 

were supplemented with data from samples 

collected and analyzed by the University of 

California at Davis at three San Joaquin River sites 

and eight tributary sites as part of a separate study. 

Streamflows in the San Joaquin River were 

slightly above the long-term average in 2000 and 

slightly below average in 2001. Nitrate loads at 

Vernalis in 2000 were above the long-term 

average, whereas loads in 2001 were close to 

average. Total nitrogen loads in 2000 were slightly 

above average, whereas loads in 2001 were 

slightly below average. Total phosphorus loads in 

2000 and 2001 were well below average. These 

nutrient loads correspond with the flow-adjusted 

concentration trends—nitrate concentrations 

significantly increased since 1972 (p < 0.01), 

whereas total nitrogen and total phosphorus 

concentrations did not (p > 0.05). Loading rates of 

nutrients and dissolved organic carbon increased 

in the San Joaquin River in the fall with the release 

of wetland drainage into Mud Slough and with 

increased reservoir releases on the Merced River. 

During August 2000 and September 2001, the 

chlorophyll-a loading rates and concentrations in 

the San Joaquin River declined and remained low 

during the rest of the sampling period. The most 

significant tributary sources of nutrients were the 

Tuolumne River, Harding Drain, and Mud Slough. 

The most significant tributary sources of dissolved 

organic carbon were Salt Slough, Mud Slough, 

and the Tuolumne and Stanislaus Rivers. 

Compared with nutrients and dissolved organic 

carbon, the tributaries were minor sources of 

chlorophyll-a, suggesting that most of the 

chlorophyll-a was produced in the San Joaquin 

River rather than its tributaries. On the basis of the 

carbon-to-nitrogen ratios and the δ13C of 

particulate organic matter in the San Joaquin River 

and tributaries, the particulate organic matter in 

the river was mostly phytoplankton. On the basis 

of the δ15N values of the particulate organic 

matter, and of total dissolved nitrogen and nitrate, 

the nitrate in the San Joaquin River probably was a 

significant nutrient source for the phytoplankton. 

The range of δ15N and δ18O values of nitrate in the 

San Joaquin River and tributaries suggest that 

animal waste or sewage was a significant source of 

nitrate in the river at the time the samples were 

collected.
2 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

INTRODUCTION

The Stockton Deep Water Ship Channel (ship 

channel) was dredged to a depth of about 35 ft to allow 

ocean-going ships to reach the inland Port of Stockton 

(fig. 1). Immediately upstream of the ship channel, the 

San Joaquin River is about 8 to 10 ft deep. At the 

beginning of the ship channel and for about 7 mi 

downstream to Turner Cut (fig. 1), the San Joaquin 

River annually experiences episodes of low dissolved 

oxygen (Lee and Jones-Lee, 2003). These episodes are 

most prolonged and acute in the summer and fall 

months, but also have been observed in other months. 

Dissolved oxygen levels typically fall as low as 2.0 to 

2.5 mg/L (Christopher Foe, California Regional Water 

Quality Control Board, Central Valley Region, written 

commun., 2002). The oxygen deficit can stress and kill 

resident aquatic life and could inhibit the upstream 

migration of fall-run Chinook salmon (Lee and JonesLee, 2003).

The State's basin plan for the Sacramento-San 

Joaquin Delta contains a water quality objective 

requiring oxygen levels to be maintained above 6 mg/L 

in the San Joaquin River between Stockton and Turner 

Cut during September through November and above 

5 mg/L at all other times (California Regional Water 

Quality Control Board, 1998). The 6 mg/L objective 

was adopted to protect the upstream migration of fallrun Chinook salmon. The State of California placed the 

San Joaquin River on the 303(d) list of impaired water 

bodies in 1998 because of low dissolved oxygen levels 

(California State Water Resources Control Board, 

1998). The problem was classified as a high priority for 

correction, and the State committed to complete a 

technical Total Maximum Daily Load (TMDL) in 2003 

and an implementation plan in 2004 (Mark Gowdy, 

California Regional Water Quality Control Board, 

Central Valley Region, written commun., 2003). A 

technical advisory committee was formed to advise the 

State on the development of the TMDL and to oversee 

projects funded by the CALFED Bay-Delta Program 

related to the low dissolved oxygen problem in the 

lower San Joaquin River.

The conceptual model of the dissolved oxygen 

impairment in the ship channel incorporates two 

primary factors—hydrology and upstream loads of 

oxidizable material. Deepening the river decreased the 

efficiency of atmospheric reaeration and increased 

water residence time allowing a larger fraction of the 

imported organic material to be oxidized. If 

streamflows from upstream could be increased, it 

would have two counteracting effects on the 

problem—it would increase the load of upstream 

oxidizable material, but it would reduce the water 

residence time (Mark Gowdy, California Regional 

Water Quality Control Board, Central Valley Region, 

written commun., 2003). The main sources of upstream 

material are the City of Stockton Wastewater Treatment 

Plant (“WWTP” on fig. 1) about one mile upstream of 

the ship channel and the upstream San Joaquin Basin 

(fig. 1). The upstream loads from the San Joaquin 

Basin appear to have the greatest impact on dissolved 

oxygen in the ship channel in summer, and they decline 

in significance in the fall and winter to the City of 

Stockton discharges of treated wastewater containing 

high concentrations of ammonia. 

The primary purpose of this study was to define 

the sources and transport of nutrients, organic carbon, 

and chlorophyll-a in the upstream San Joaquin Basin, 

above Vernalis. A secondary purpose was to compare 

nutrient loads and concentrations from the 1970s and 

1980s to the present (Kratzer and Shelton, 1998). This 

study was funded by the CALFED Bay-Delta Program. 

The sampling in this study was coordinated with an 

independent study conducted in the study area by the 

University of California at Davis (UCD). The UCD 

study was funded by the U.S. Fish and Wildlife Service 

to evaluate the food resources to the Sacramento-San 

Joaquin Delta from the Sacramento and San Joaquin 

Basins. 
Introduction 3

Dry Creek

Los

Banos

Merced

36

30

37

12011930

Turlock

Hospital Creek

Lone Tree Creek

Calaveras River

San Joaquin River

Kings River

Fresno

Slough

Millerton

Lake

Mc Clure

Lake

New Don Pedro

Reservoir

New Melones

Reservoir

Hensley Lake

Tulloch

Reservoir

Fresno River

Bear Creek

Dry Creek

Los Banos Creek

Orestimba Creek

Del Puerto Creek

Ingram Creek

San Luis Drain

Mud Slough

Salt Slough

Merced

River

Tuolumne

Harding Drain

Westport Drain

Spanish

Grant

Drain

River

Stanislaus River

San Joaquin

River

SAN JOAQUIN CO.

CALAVERAS CO.

TUOLUMNE CO.

STANISLAUS CO.

STANISLAUS CO.

MARIPOSA CO.

MERCED CO.

MERCED CO.

MADERA CO.

FRESNO CO.

MADERA CO.

FRESNO CO.

KINGS CO.

Grasslands

Drainage

Project Area

Grasslands

Ecological

Area

SacramentoSan Joaquin

Delta

Stockton

Deep Water

Ship Channel

Port of Stockton

Stockton

WWTP

Lone Tree

Site

Turner

Cut

Vernalis

Stockton

Modesto

12130

37

30

38

12112030

5 10 MILES

0 5 10 KILOMETERS

0

SIERRA NE V ADA

CALIFORNIA

Sacramento

Valley

Sacramento

Basin

COA

S T

RAN

G

E S

San

Joaquin

Basin

Tulare

Basin

San Francisco

SacramentoSan Joaquin

Delta

San Joaquin Valley

Los Angeles

Figure 1. Portion of the San Joaquin Valley and the Sacramento-San Joaquin Delta.
4 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Ammonia, nitrate, and orthophosphate are major 

plant nutrients, and their concentrations are often 

limiting factors in the growth of algal and aquatic plant 

populations. Other forms of nitrogen and phosphorus, 

such as organic compounds containing these elements, 

can be converted to plant nutrients in the aquatic 

environment by microorganisms that use organic 

material as metabolic substrates and release nitrate, 

ammonia, and phosphate as byproducts of aerobic and 

anaerobic respiration. Chlorophyll-a is often used as a 

gross measure of living algal populations and 

pheophytin-a of dead algal populations; these 

populations often account for much of the organic 

carbon in the aquatic system. Samples were collected 

by both the U.S. Geological Survey (USGS) and UCD 

for analysis of biochemical oxygen demand. These 

samples were delivered to either the California 

Regional Water Quality Control Board (Central Valley 

Region) or their contract laboratory and the resulting 

data are not analyzed in this report.

For the sake of brevity, many site names are 

abbreviated in this report from the official names given 

in table 1. For example, the “San Joaquin River at 

Maze Road Bridge near Modesto” (site 24 in table 1) is 

referred to as “SJR at Maze Road,” or sometimes 

simply as “Maze Road.” Tributary sites where there is 

only one site on the tributary will usually be referred to 

by the tributary name; for example, “Hospital Creek 

below confluence of Ingram Creek near Grayson” (site 

23 in table 1) is referred to simply as “Hospital Creek.” 

The authors thank Dr. Peggy Lehman of the 

California Department of Water Resources (DWR) for 

her patience and support on contractual issues related 

to this project. Finally, we acknowledge the steering 

and technical committees of the San Joaquin River 

dissolved oxygen TMDL stakeholder process for their 

technical reviews of this study.

STUDY AREA

The perennial San Joaquin Basin drains 

7,395 mi2, of which 4,320 mi2 are in the Sierra Nevada, 

2,273 mi2 are in the San Joaquin Valley, and 802 mi2

are in the Coast Ranges (fig. 1 inset). On the basis of 

USGS streamflow data for 1951–95, 66 percent of the 

average streamflow in the San Joaquin River comes 

from the three major east-side river basins: the Merced 

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

and the Stanislaus River (21 percent). The remaining 

streamflow in the San Joaquin River comes from the 

Bear Creek Basin; Mud and Salt Sloughs, and 

ephemeral creeks that drain from the west; drainage 

canals that flow directly to the San Joaquin River; and 

occasionally from the upper San Joaquin River above 

Bear Creek during especially high streamflow events 

(fig. 1).

A total of four sites were sampled by the USGS 

during July through October 2000 (sites 7, 12, 18, and 

27 shown in fig. 2 and listed in table 1). These sites 

bracket the major east-side tributaries to the mainstem 

of the San Joaquin River. During June through 

November 2001, the USGS sampled the same four 

mainstem sites plus eight minor tributary sites, 

including four tributaries from the west-side and four 

from the east-side. The west-side sites include Mud 

Slough (site 5, fig. 2) that receives tile drainage from 

97,000 acres (Grasslands Drainage Project Area, fig. 1) 

and includes wetlands (Grasslands Ecological Area) 

and grazing on native vegetation (fig. 3) (Quinn and 

others, 1998). The other three west-side sites (sites 11, 

13, and 23 in fig. 2) generally represent surface runoff 

from row crops and orchards, although Spanish Grant 

Drain and Hospital Creek contain some tile drainage as 

well. The four east-side sites include Harding Drain 

(site 14, fig. 2), which receives treated effluent from the 

City of Turlock wastewater treatment plant in addition 

to excess irrigation water (operational spill) and runoff 

from agricultural areas (fig. 3). The Dry Creek site (site 

20, fig. 2) receives operational spills and agricultural 

return flows from upstream of Modesto, and urban 

runoff from Modesto. The other two east-side sites—

Lone Tree Creek (fig. 1) and Westport Drain (site 17, 

fig. 2)—receive only operational spill and agricultural 

runoff. Data for the Lone Tree Creek site will not be 

interpreted in this report because it discharges to the 

Sacramento-San Joaquin Delta downstream of 

Vernalis.
Study Area 5

Table 1. Names, locations, and types of data available for sites in the San Joaquin River Basin, California

[Site locations in column 4 are in the following order unless otherwise noted: river miles from San Joaquin River; river miles from Vernalis. Water-quality 

samples collected and analyzed by University of California at Davis (UCD) or U.S. Geological Survey (USGS). x, data reported; —, no data reported]

Site 

number 

(See 

fig. 2)

Site name Site identification 

number

Site 

location

 Data at sites

Instantaneous 

streamflow

Continuous 

streamflow

Water

quality

Historic 

loads

Major 

diversion

1 San Joaquin River near Stevinson 111260815

1Department of Water Resources gaging station.

260.5 

2River miles from Vernalis.

— x UCD x —

2 Salt Slough at Highway 165 near Stevinson 11261100 6.8; 64.0 — x UCD x —

3 San Joaquin River at Fremont Ford Bridge 11261500 252.8 — — — x —

4 San Luis Drain, Site B, near Stevinson 11262895 31.8; 9.9; 58.7

3River miles from Mud Slough; river miles from San Joaquin River; river miles from Vernalis.

— x UCD — —

5 Mud Slough near Gustine 11262900 8.0; 56.8 — x UCD/USGS x —

6 Los Banos Creek at Highway 140 4371636120575200

4Lawrence Berkeley Laboratory gaging station.

32.2; 6.0; 54.8 — x UCD — —

7 San Joaquin River upstream of Merced River, near 

Hills Ferry

372006120571701 246.1 — — USGS — —

8 Merced River near Stevinson 111272500 4.8; 50.5 — x — x —

9 Merced River at River Road Bridge near Newman 11273500 1.1; 46.8 — — UCD — —

10 San Joaquin River near Newman 11274000 245.7 — x — x —

11 Orestimba Creek at River Road near Crows 

Landing

11274538 1.0; 37.7 — x UCD/USGS — —

12 San Joaquin River near Crows Landing 11274550 235.5 — x USGS — —

13 Spanish Grant Combined Drain near Patterson 11274554 0.7; 33.4 x — USGS — —

14 Harding Drain at Carpenter Road near Patterson 511274560

5Turlock Irrigation District gaging station.

0.1; 31.2 — x USGS — —

15 San Joaquin River at Patterson Bridge near 

Patterson

111274570 226.3 — x UCD x —

16 Patterson Irrigation District (diversion) 226.2 — — — — x

17 Westport Drain near Modesto 373232121053900 1.0; 22.1 x — USGS — —

18 San Joaquin River at Laird Park near Grayson 373324121090401 216.8 x — USGS — —

19 West Stanislaus Irrigation District (diversion) 211.7 — — — — x

20 Dry Creek at Gallo Bridge below Highway 132 at 

Modesto

373811120590001 60.8; 17.2; 28.4

6River miles from Tuolumne River; river miles from San Joaquin River; river miles from Vernalis.

x — USGS — —

21 Tuolumne River at Modesto 11290000 16.2; 27.4 — x — x —

22 Tuolumne River at Shiloh Road Bridge near 

Grayson

11290200 3.6; 14.8 — — UCD — —

23 Hospital Creek below confluence of Ingram Creek 

near Grayson

373701121121100 0.7; 8.3 x — USGS — —

24 San Joaquin River at Maze Road Bridge near 

Modesto

111290500 24.9 — x UCD x —

25 Stanislaus River at Ripon 11303000 15.7; 18.2 — x — x —

26 Stanislaus River at Caswell State Park near Ripon 374209121103800 8.5; 11.0 — — UCD — —

27 San Joaquin River near Vernalis 11303500 20.0 — x USGS x —
6 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

121

37

30

12030

San Joaquin River

Del Puerto

Creek

EXPLANATION

37

Spanish

Grant

Drain

13

3 7

8

9 10

11

12

15 14

16

17

18

19

20

22 21

23

24

25

26

27

1

2 5

4

6

Streamflow and water quality site

Streamflow and historical loads site

Streamflow, water quality, and historical loads site

Water quality site

Historical loads site

Major diversion site

5 10 MILES

0 5 10 KILOMETERS

0

Modesto

Merced

Los

Banos

Turlock

Los Angeles

San Francisco

CALIFORNIA

San Joaquin

River Basin

San Joaquin

Valley portion

Stanislaus River

Tuolumne River Westport Drain

Orestimba

Creek

Harding Drain

Merced River

Salt Slough

San Luis Drain

Bear Creek

Los Banos Creek

Dry Creek

Dry

Creek

Hospital Creek

Ingram

Creek

Mud Slough

Figure 2. San Joaquin Valley portion of the San Joaquin River Basin and site locations.
Study Area 7

121

37

30

37

12030

12 13

14

15

17 18

22

23

24

26

27

1

2 4

5 6

7

9

11

20

Stanislaus River

Tuolumne River Westport Drain

Orestimba

Creek

Harding Drain

Merced River

Salt Slough

San Luis Drain

Bear Creek

Los Banos Creek

Dry Creek

Dry

Creek

Hospital Creek

Ingram

Creek

Mud Slough

Spanish

Grant

Drain

5 10 MILES

0 5 10 KILOMETERS

0

Del Puerto

Creek

Modesto

Merced

Los

Banos

Turlock

EXPLANATION

Urban

Corn, alfalfa, pasture

Orchards and vineyards

Other agriculture

Native vegetation

Grasslands Ecological Area

Water quality site

Los Angeles

San Francisco

CALIFORNIA

San Joaquin

River Basin

San Joaquin

Valley portion

Figure 3. San Joaquin Valley portion of the San Joaquin River Basin, water quality sampling sites, and land use areas.
8 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

UCD sampled a total of 11 sites in the San 

Joaquin Basin (table 1) during this period, including 

3 mainstem sites, the 3 main east-side tributaries, and 

5 minor tributaries. In addition to sampling Orestimba 

Creek and Mud Slough, UCD also sampled Salt Slough 

(site 2, fig. 2), the San Luis Drain (site 4, fig. 2), and 

Los Banos Creek (site 6, fig. 2). Salt Slough and Los 

Banos Creek receive some releases from wetlands and 

tailwater runoff from agricultural areas. The San Luis 

Drain receives primarily tile drainage from the 

Grasslands Drainage Project Area and some releases 

from wetlands. In this report, the UCD data for these 

11 sites will be presented with the USGS data (Randy 

Dahlgren, University of California, Davis, written 

commun., 2003).

The UCD water quality sampling sites on the 

Merced, Tuolumne, and Stanislaus Rivers (sites 9, 22, 

and 26, respectively; fig. 2) are downstream of gaging 

stations (sites 8, 21, and 25, respectively; fig. 2). 

Streamflows at the water quality sampling sites were 

estimated using travel times in the tributaries from the 

gaging stations (Kratzer and Biagtan, 1997). 

Precipitation in the study area was based on records for 

downtown Modesto.

The 20 sites sampled for water quality in this 

study by UCD or USGS along with land use are shown 

in figure 3. DWR prepares detailed maps of land use on 

the valley floor every six to seven years. The detailed 

categories of land use were aggregated into five general 

categories here for illustrative purposes: urban; corn, 

alfalfa, and pasture; orchards and vineyards; other 

agriculture; and native vegetation. The corn, alfalfa, 

and pasture area includes many of the dairy operations 

in the San Joaquin Basin. The other agriculture area on 

the west-side consists mainly of row crops, whereas the 

south consists mainly of cotton. The Grasslands 

Ecological Area is an area of managed wetlands. These 

wetlands are flooded in the fall and drained in the early 

spring. The percentage of land use in each sampled 

basin (table 1) is listed in table 2. The basin areas for 

the sampled tributaries are shown in figure 4.

Table 2. Basin areas and land use for valley portion of drainage basins within the San Joaquin River Basin, California

[See figure 4 for basin locations. mi2, square mile]

Site 

number 

(See 

figure 4)

Site name1

1To conserve space, site names are slightly abbreviated from the full versions listed in table 1.

 Basin area Land use as percentage of valley basin area 

Total

(mi2)

Valley

(mi2) Urban

Corn, 

alfalfa, and 

pasture

Orchards 

and 

vineyards

Native 

vegetation

Grasslands 

Ecological 

Area

Other 

agriculture

1 San Joaquin River near Stevinson 866 441 7.2 19.7 15.9 34.2 0.0 22.9

2 Salt Slough near Stevinson 492 484 2.8 14.7 1.1 19.5 4.6 57.3

5 Mud Slough near Gustine, California 492 484 2.8 14.7 1.1 19.5 4.6 57.3

6 Los Banos Creek at Highway 140 198 42 2.4 20.6 6.2 43.1 0.2 27.5

9 Merced River at River Road 1,383 245 5.5 15.5 44.0 23.9 0.0 11.1

11 Orestimba Creek at River Road 195 33.3 0.3 15.2 31.4 10.6 0.0 42.5

13 Spanish Grant Drain 33.8 23.9 3.8 26.6 18.2 2.8 0.0 48.7

14 Harding Drain at Carpenter Road 84 84 14.4 51.3 18.8 0.6 0.0 14.9

17 Westport Drain near Modesto 79 79 7.2 28.1 50.8 0.9 0.0 13.0

20 Dry Creek at Gallo Bridge 211 66.1 14.9 30.4 19.2 26.4 0.0 9.2

22 Tuolumne River at Shiloh Road 1,860 149 18.0 20.0 25.8 27.3 0.0 8.9

23 Hospital Creek below Ingram Creek 70.6 16.8 3.4 1.0 18.1 7.1 0.0 70.5

26 Stanislaus River at Caswell State Park 1,144 116 15.4 31.9 31.4 12.9 0.0 8.4

27 San Joaquin River near Vernalis 7,395 2,273 7.1 22.2 19.8 21.6 1.5 27.9
Study Area 9

Stanislaus River

Hospital Creek

Dry Creek

Ingram

Creek

Tuolumne River Westport Drain

Harding Drain

Orestimba Creek

Dry Creek

Merced River

San Luis Drain

Salt Slough

Los Banos Creek

Spanish

Grant

Drain

Del Puerto

Creek

Bear Creek

Mud Slough

10 20 MILES

0 10 20 KILOMETERS

0

Merced

Turlock

Modesto

Los

Banos

EXPLANATION

San Joaquin River near Stevinson

Mud and Salt Sloughs

Los Banos Creek

Merced River at River Road

Orestimba Creek

Spanish Grant Drain

Harding Drain

Westport Drain

Dry Creek

Tuolumne River at Shiloh Road

Hospital and Ingram Creeks

Stanislaus River at Caswell State Park

San Joaquin River near Vernalis

Water quality site

38

121

120

37

1

2 5

9

11

14

17

22

23

26

27

6

13

20

Los Angeles

San Francisco

CALIFORNIA

San Joaquin

River Basin

San Joaquin

Valley portion

Figure 4. San Joaquin River Basin and drainage basins for water quality sites. 
10 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

METHODS OF DATA COLLECTION AND 

ANALYSIS

Sample Collection and Processing

The frequency of sampling during July through 

October 2000 and June through November 2001 by 

USGS at the San Joaquin River sites was every two 

weeks (sites 7, 12, 18, and 27; fig. 2), and every four 

weeks for the minor tributary sites (sites 5, 11, 13, 14, 

17, 20, and 23; fig. 2). UCD generally sampled every 

two weeks throughout the year at their sites (sites 1, 2, 

4, 5, 6, 9, 11, 15, 22, 24, and 26; fig. 2). The sample 

collection times in 2000 relative to precipitation and 

streamflow are shown in figure 5 for the mainstem of 

the San Joaquin River and major east-side tributary 

sites, and in figure 6 for minor tributary sites. The 

equivalent information for 2001 is shown in figures 7

and 8, respectively.

Samples were collected during this study using 

six different methods, depending on the site location 

and streamflow conditions: (1) width- and depthintegrated using a D-77 isokinetic sampler with a 

Teflon nozzle and a 3-L (liter) Teflon bottle (Webb and 

others, 1999); (2) width- and depth-integrated using a 

DH-81 isokinetic sampler with a Teflon nozzle and a 

3-L Teflon bottle (Webb and others, 1999); (3) an 

equally spaced three-point integrated surface grab 

using a 3-L Teflon bottle strapped into a metal cage 

suspended from a rope; (4) a midpoint surface grab 

using the same sampler; (5) a dip sample collected at 

the centroid of flow or at multiple locations along the 

cross section using a 3-L Teflon bottle; and (6) a 

midstream surface grab sample using a collection 

bucket.

U.S. Geological Survey Methods

Samples collected at the SJR near Vernalis 

(site 27) and the SJR at Laird Park (site 18) sites were 

width- and depth-integrated using the D-77 isokinetic 

sampler, whereas the DH-81 isokinetic sampler was 

used at the San Joaquin River upstream of Merced 

River site (site 7). At the SJR near Crows Landing site 

(site 12), samples were collected as equally spaced, 

three-point, integrated surface grabs in a 3-L Teflon 

bottle using the cage sampler suspended from a boat. 

Samples at the minor tributary sites were collected as 

integrated grab samples from a bridge using a 3-L 

Teflon bottle in the cage sampler at Mud Slough 

(site 5) and Harding Drain (site 14), and as wading 

multivertical integrated grabs or midpoint grabs 

depending on streamflow conditions at the other minor 

tributary sites. 

Samples were processed in the field using the 

following protocol. Nine liters was collected at each 

site in three separate 3-L Teflon sample bottles using 

sampling techniques specific to that site. The samples 

were split for analysis of target constituents using a 

cone splitter in 2000 (Radtke and others, 1999), and a 

churn splitter in 2001 (Radtke and others, 1999). 

Sample water for whole-water analyses was poured 

directly from the splitter into the appropriate bottle 

types for analysis of suspended sediment, nutrients, 

volatile suspended solids (VSS), pH, and electrical 

conductivity (EC). The nutrient sample was preserved 

using 1 mL of 4.5N sulfuric acid. Sample water for 

dissolved nutrients and alkalinity was filtered through a 

0.45-μm capsule filter and collected in the appropriate 

bottle types. For chlorophyll-a and pheophytin-a, a 

known volume of sample (ranged from 50 to 150 mL) 

was filtered through a 25-mm glass fiber filter (GFF); 

the filter was placed in a sterile Petri dish, wrapped in 

aluminum foil, and stored and shipped on dry ice. 

Three liters of the total 9-L sample were used for the 

analysis of suspended organic carbon (SOC), dissolved 

organic carbon (DOC), ultraviolet absorbance at 

254 nanometer (nm) wavelength, and stable isotopes. 

The churn splitter used in 2001 was made of 

polyethylene, which could potentially affect the 

concentrations of organic constituents (Wilde and 

others, 1999). Thus, the 3-L Teflon sample bottle used 

for these analytes was not composited in the churn 

splitter, but was poured directly into the appropriate 

bottles for analysis. For SOC and DOC, a 100-mL 

aliquot of sample was filtered through a silver filter. 

For the SOC analysis, the silver filter was retained, 

folded, and placed in aluminum foil and stored on ice 

with the corresponding filtered sample (DOC). A 

100-mL aliquot was filtered through a GFF for the 

ultraviolet absorbance and immediately chilled. The 

remaining sample water was poured into two 1-L 

amber glass bottles for analysis of stable isotopes of 

carbon, nitrogen, and oxygen.
Methods of Data Collection and Analysis 11

San Joaquin River near Stevinson (site 1)

Merced River at River Road (site 9)

San Joaquin River near Crows Landing (site 12)

0

50

100

150

200

250

Streamflow

Sample collection time

0

400

200

600

800

1,000

1,200

1,400

B

C

D

0

400

800

1,200

1,600

Streamflow, in cubic feet per second

2,000

0 8 15 22 29 5 12 19 26 2 9 16 23 30 14 7 21 28

July August September October

2000

0

0.2

0.4

0.6

0.8

1

1.2

Daily precipitation,

in inches per day

Precipitation at Modesto A

Figure 5. Precipitation at Modesto, California, streamflow for San Joaquin River sampling sites and major east-side tributaries from upstream to 

downstream, and sample collection times, July to October 2000. 

(A) Precipitation at Modesto, (B) Streamflow and collection times for San Joaquin River near Stevinson (gaps in streamflow indicate missing data), (C) 

Streamflow and collection times for Merced River at River Road, (D) Streamflow and collection times for San Joaquin River near Crows Landing,
12 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

0 8 15 22 29 5 12 19 26 2 9 16 23 30 14 7 21 28

Tuolumne River at Shiloh Road (site 22)

San Joaquin River at Maze Road (site 24)

Stanislaus River at Caswell State Park (site 26)

San Joaquin River near Vernalis (site 27)

July August September October

2000

E

F

G

H

Streamflow, in cubic feet per second

0

500

1,000

1,500

2,000

2,500

3,000

Streamflow

Sample collection time

0

1,000

2,000

3,000

4,000

0

200

400

600

800

1,000

1,200

0

1,000

2,000

3,000

4,000

0

0.2

0.4

0.6

0.8

1

1.2

Daily precipitation,

in inches per day

Precipitation at Modesto A

Figure 5.—Continued. (E) Streamflow and collection times for Tuolumne River at Shiloh Road, (F) Streamflow and collection times for San Joaquin River at 

Maze Road, (G) Streamflow and collection times for Stanislaus River at Caswell State Park, (H) Streamflow and collection times for San Joaquin River near 

Vernalis. 
Methods of Data Collection and Analysis 13

Streamflow, in cubic feet per second

Salt Slough near Stevinson (site 2) B

Mud Slough near Gustine (site 5) C

Orestimba Creek at River Road (site 11) D

Streamflow

Sample collection time

0

100

200

300

0

50

100

150

200

250

300

350

0

40

80

120

0

0.2

0.4

0.6

0.8

1

1.2

Daily precipitation,

in inches per day

Precipitation at Modesto A

0 8 15 22 29 5 12 19 26 2 9 16 23 30 14 7 21 28

July August September October

2000

Figure 6. Precipitation at Modesto, California, streamflow for minor tributaries with gaging stations, and sample collection times, July to October 2000. 

(A) Precipitation at Modesto, (B) Streamflow and collection times for Salt Slough near Stevinson, (C) Streamflow and collection times for Mud Slough near 

Gustine, (D) Streamflow and collection times for Orestimba Creek at River Road. 
14 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

0

0.2

0.4

0.6

0.8

1 8 15 22 29 6 13 20 27 3 10 17 24 31 14 7 21 28 5 12 26 19 2 9 16 23 30

June July August September October November

2001

Precipitation at Modesto

San Joaquin River near Stevinson (site 1) B

A

Merced River at River Road (site 9) C

San Joaquin River near Crows Landing (site 12) D

0.0

10.0

20.0

30.0

40.0

50.0

60.0

70.0

80.0

90.0

0

100

200

300

400

500

600

700

800

900

1,000

200

0

400

600

800

1,000

1,200

1,400

Streamflow, in cubic feet per second

Streamflow

Sample collection time

Daily precipitation,

in inches per day

Figure 7. Precipitation at Modesto, California, and streamflow for San Joaquin River sampling sites and major east-side tributaries from upstream to 

downstream, and sample collection times, June to November 2001 (gaps in streamflow in 7B, C, E, F, and H indicate missing data).

(A) Precipitation at Modesto, (B) Streamflow and collection times for San Joaquin River near Stevinson, (C) Streamflow and collection times for Merced River 

at River Road, (D) Streamflow and collection times for San Joaquin River near Crows Landing.
Methods of Data Collection and Analysis 15

0

100

200

300

400

500

600

Streamflow, in cubic feet per second

1 8 15 22 29 6 13 20 27 3 10 17 24 31 14 7 21 28 5 12 26 19 2 9 16 23 30

June July August September October November

2001

Tuolumne River at Shiloh Road (site 22) E

San Joaquin river at Maze Road (site 24) F

Stanislaus River at Caswell State Park (site 26)

San Joaquin River near Vernalis (site 27)

G

H

Streamflow

Sample collection time

0

500

1,000

1,500

2,000

2,500

0

200

400

600

800

1,000

500

0

1,000

1,500

2,000

2,500

3,000

3,500

0

0.2

0.4

0.6

0.8

Precipitation at Modesto A

Daily precipitation,

in inches per day

Figure 7.—Continued. (E) Streamflow and collection times for Tuolumne River at Shiloh Road, (F) Streamflow and collection times for San Joaquin River at 

Maze Road, (G) Streamflow and collection times for Stanislaus River at Caswell State Park, (H) Streamflow and collection times for San Joaquin River near 

Vernalis. 
16 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

0

0.2

0.4

0.6

0.8

Precipitation at Modesto A

Salt Slough near Stevinson (site 2) B

0

50

100

150

200

250

Streamflow

Sample collection time

Daily precipitation,

in inches per day

Mud Slough near Gustine (site 5) C

Orestimba Creek at River Road (site 11) D

Harding Drain at Carpenter Road (site 14) E

1 8 15 22 29 6 13 20 27 3 10 17 24 31 14 7 21 28 5 12 26 19 2 9 16 23 30

June July August September October November

2001

Streamflow, in cubic feet per second

0

50

100

150

200

250

300

350

0

20

40

60

80

100

120

140

160

0

50

100

150

200

250

No streamflow data available

after 9/27/01

Figure 8. Precipitation at Modesto, California, streamflow for minor tributaries with gaging stations, and sample collection times, June to November 

2001. 

(A) Precipitation at Modesto, (B) Streamflow and collection times for Salt Slough near Stevinson, (C) Streamflow and collection times for Mud Slough near 

Gustine, (D) Streamflow and collection times for Orestimba Creek at River Road, (E) Streamflow and collection times for Harding Drain at Carpenter Road 

(gap in streamflow indicates missing data).
Methods of Data Collection and Analysis 17

The 3-L Teflon sample collection bottles and the 

churn splitter were cleaned between each site using the 

following protocol. After sampling at a site, the 

collection bottles and the splitter were rinsed with 

deionized water. Approximately 30 mL of dilute 

Liquinox solution was then placed into the bottles and 

splitter, and both were capped and shaken. The 

Liquinox solution was then completely rinsed with 

deionized water. Approximately 30 mL of 5-percent 

hydrochloric acid solution was then added to the bottles 

and splitter, and both were capped and shaken. The 

acid rinsate was emptied into a waste container. The 

final step in the cleaning procedure was to thoroughly 

rinse the collection bottles and churn splitter with 

deionized water. The cone splitter followed the same 

cleaning procedure as the churn splitter, except that the 

appropriate solutions are passed through the splitter. At 

the next site, the 3-L Teflon sample collection bottles 

and splitter were rinsed three times with stream water 

(native water) before collecting or splitting the sample.

University of California at Davis Methods

All samples were collected as midstream grab 

samples using a collection bucket that sampled the 

upper two feet of the water column. The processing 

method for samples collected by UCD included 

holding individual 125-mL amber glass bottles under 

the water being poured from the bucket immediately 

after collection for the analysis of pH, EC, alkalinity, 

nutrients, particulate organic matter (POM), and DOC; 

and a 2-L bottle for collecting the chlorophyll-a, 

pheophytin-a, and total suspended solids samples. The 

cleaning procedure for the collection bucket included 

an 8-percent hydrochloric acid wash and three rinses 

with deionized water. The bucket was also rinsed three 

times with native water prior to sample collection at 

each site.

Field Measurements and Streamflow

Water temperature, dissolved oxygen 

concentrations, and secchi disk (measures water 

transparency) readings were recorded prior to actual 

sample collection at USGS sites. Sample water for the 

determination of pH, EC, and alkalinity was split from 

the cone or churn, and these parameters were measured 

in the field. Water temperature was determined in the 

field at each UCD site, but EC, pH, and alkalinity were 

determined in the laboratory within 24 hours of 

collection.

For most water quality sampling sites, 

streamflows were from gaging stations operated and 

maintained by the USGS, DWR, Lawrence Berkeley 

Laboratory, or Turlock Irrigation District. Of the 20 

water quality sites sampled by USGS and UCD, 11 

have a gaging station at the site, 3 have a gaging station 

upstream of the site, 1 has a gaging station 

downstream, and 5 required instantaneous streamflow 

measurements during each site visit. The sites at gages 

included three DWR gaging stations—SJR near 

Stevinson, SJR near Patterson, and SJR at Maze Road 

(sites 1, 15, and 24; fig. 2); six USGS gaging stations—

Salt Slough near Stevinson, San Luis Drain at Site B, 

Mud Slough near Gustine, Orestimba Creek at River 

Road, SJR near Crows Landing, and SJR near Vernalis 

(sites 2, 4, 5, 11, 12, and 27; fig. 2); a gage operated by 

Lawrence Berkeley Laboratory for the minor tributary 

site, Los Banos Creek at Highway 140 (site 6; fig. 2); 

and a gage operated by Turlock Irrigation District for 

the minor tributary site, Harding Drain at Carpenter 

Road (site14; fig. 2). Three water quality sampling 

sites—Merced River at River Road, Tuolumne River at 

Shiloh Road and Stanislaus River at Caswell State 

Park—are located downstream of gaging stations and 

streamflows were estimated on the basis of travel times 

to the water quality sampling sites (sites 9, 22, and 26; 

fig. 2) (Kratzer and Biagtan, 1997). Streamflows for the 

San Joaquin River upstream of Merced River site were 

estimated using two downstream gages. The SJR at 

Laird Park (site 18; fig. 2) and four minor tributary 

sites—Spanish Grant Drain, Westport Drain near 

Modesto, Dry Creek at Gallo Bridge, and Hospital 

Creek (sites 13, 17, 20, and 23; fig. 2)—do not have 

gaging stations. During three water quality sampling 

visits (September 19, October 3, and November 15) to 

the SJR at Laird Park in 2001, the streamflow 

measurement equipment malfunctioned, and 

streamflow values were estimated using the ratio of the 

measured streamflows at Laird Park to the measured 

streamflows at the upstream DWR gage near Patterson 

for the same parcel of water (using the travel time from 

Kratzer and Biagtan, 1997). The average of these ratios 

was multiplied by the measured streamflow at 

Patterson for the sampling visits when the streamflow 

equipment was malfunctioning.
18 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Analytical Methods 

All samples collected by USGS other than 

isotopes and suspended sediment were shipped 

overnight to the USGS National Water Quality 

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

The isotope samples were first processed and prepared 

at the USGS California District Laboratory in 

Sacramento, California, and then sent to the USGS 

Menlo Park Stable Isotope Laboratory in Menlo Park, 

California, for final analysis. The suspended sediment 

samples were sent to the USGS California District 

Sediment Laboratory in Marina, California, for 

analysis. Samples collected by UCD were analyzed at 

UCD's Biogeochemistry Laboratory (UCDBL) in 

Davis, California.

U.S. Geological Survey Methods

The USGS analytical methods for analysis of 

nutrients, organic carbon, ultraviolet absorbance, VSS, 

chlorophyll-a and pheophytin-a, suspended sediment, 

and isotopes are briefly described here.

Nutrients

The analysis of nutrients at the NWQL included 

the following forms of nitrogen and phosphorus: 

dissolved ammonia, dissolved nitrite, dissolved nitrite 

plus nitrate, dissolved ammonia plus organic nitrogen, 

total ammonia plus organic nitrogen, dissolved 

phosphorus, dissolved orthophosphate, and total 

phosphorus. Ammonia was determined by reacting the 

sample with sodium salicylate, sodium nitroprusside, 

and sodium hypochlorite in an alkaline medium and 

measuring the concentration colorimetrically (Fishman 

and Friedman, 1989). Nitrite was determined from the 

reaction of nitrite ions with sulfanilamide under acidic 

conditions; the concentration was measured 

colorimetrically. The determination of nitrite plus 

nitrate included reducing nitrate to nitrite using a 

copper-cadmium column. The sample was then treated 

with sulfanilamide under acidic conditions, and the 

concentration was measured colorimetrically. The final 

result is the sum of the nitrite originally present plus 

that formed by the reduction of the nitrate (Fishman 

and Friedman, 1989). The determination of ammonia 

plus organic nitrogen included reducing organic 

nitrogen compounds to ammonium ion by digestion 

using sulfuric acid in the presence of mercuric sulfate 

and potassium sulfate. The ammonium ion produced by 

digestion, as well as the ammonium ion originally 

present, was determined by reaction with the same 

reagents as in the ammonia determination previously 

described in an alkaline medium, and the concentration 

was measured colorimetrically (Fishman and 

Friedman, 1989). Orthophosphate was determined by 

first converting all forms of phosphorus to 

orthophosphate by an acid-persulfate digestion. The 

orthophosphate ions were then reacted with ammonium 

molybdenate in acidic solution to form 

phosphomolybdic acid, which upon reduction with 

ascorbic acid produces an intensely colored blue 

complex that is measured colorimetrically (Fishman 

and Friedman, 1989). Total phosphorus was 

determined by the U.S. Environmental Protection 

Agency persulfate-digestion method 365.1 (U.S. 

Geological Survey, 1999). 

Organic Carbon, Ultraviolet Absorbance, and Volatile 

Suspended Solids

The DOC sample was acidified, purged to 

remove inorganic forms of carbon, and oxidized with 

persulfate in an autoclave at 116–130oC. The resultant 

carbon dioxide was measured by nondispersive 

spectrometry (Wershaw and others, 1987). The 

procedure that was used with DOC also was used to 

determine SOC on the silver filter. The determination 

of ultraviolet absorbance involved passing a 1-cm light 

path from a spectrophotometer, set at 254-nm 

wavelength, through the sample and measuring the 

mean ultraviolet absorbance (Eaton and others, 1995). 

The determination of VSS begins with thoroughly 

mixing the unfiltered sample and pouring an 

appropriate volume into a graduated cylinder. This 

volume is then filtered through a glass-fiber filter, and 

the suspended solids are dried, weighed, and ignited at 

550oC for 1 hour. The loss to ignition corresponds to 

the amount of VSS (Fishman and Friedman, 1989).
Methods of Data Collection and Analysis 19

Chlorophyll-a and Pheophytin-a

The NWQL schedule 1508 was used for the 

determination of chlorophyll-a in 2000, whereas the 

NWQL schedule 1637 was used for the determination 

of chlorophyll-a and pheophytin-a in 2001. The 

laboratory procedures for these two schedules vary 

slightly. The procedure for schedule 1508 included 

placing the filter that contained the phytoplankton into 

a tissue grinder and extracting the chlorophylls from 

the algal cells by centrifuging. The chlorophylls were 

then separated from each other and from chlorophyll 

degradation products by thin-layer chromatography. 

The chlorophylls were eluted and measured using a 

spectrofluorometer (Britton and Greeson, 1987). The 

procedure for schedule 1637 included extracting the 

phytoplankton in 100-percent methanol with the aid of 

a tissue grinder and allowing the mixture to steep to 

ensure thorough extraction of the chlorophyll-a. The 

filter slurry was then centrifuged to clarify the solution 

and fluorescence was measured before and after 

acidification with 0.01 N hydrochloric acid. Solutions 

of known concentrations of both chlorophyll-a and 

pheophytin-a were used as calibration factors to 

calculate concentrations (U.S. Environmental 

Protection Agency, 1997). Pheophytin-a was not 

analyzed for samples collected in 2000.

Suspended Sediment

The water-sediment mixture was weighed, then 

the sediment was allowed to settle to the bottom of the 

bottles, and clear water was carefully decanted off to 

leave a water-sediment slurry. At this point, the slurry 

was washed with deionized water through a 0.062-mm 

sieve and put into two crucibles-one for the < 0.062-

mm fraction and one for the > 0.062-mm fraction. 

These two fractions were then filtered separately 

through GFFs, and the two filters were placed into 

evaporating dishes, oven dried, cooled, and weighed 

(Guy, 1973). The total weight of the two fractions was 

used to calculate the suspended sediment concentration 

(in mg/L), and the weight of the < 0.062-mm fraction 

was divided by the total weight to calculate the 

percentage less than 0.062 mm.

Isotopes

Duplicate 1-L samples were collected for isotope 

analysis of POM and total dissolved nitrogen (TDN) at 

four mainstem San Joaquin River sites (sites 5, 10, 16, 

and 25; fig. 2) in 2000 and 2001 and six tributary sites 

(sites 9, 11, 12, 15, 18 and 21; fig. 2) in 2001. These 

samples were first prepared at the USGS California 

District Laboratory and sent to the USGS Menlo Park 

Stable Isotope Laboratory for final analysis. The initial 

processing at the USGS California District Laboratory 

included filtration through a 0.7-μm pore-size GFF 

within 24 hours of collection into 1-L baked amber 

glass bottles. The filters were folded into quarters, 

wrapped in aluminum foil, sealed in plastic bags, and 

stored in a freezer until further processing. The filtered 

water was acidified to pH 2 using concentrated 

hydrochloric acid and stored in a refrigerator at 4oC 

until further processing. 

Further processing of the POM samples began 

with thawing the filters, scraping with a spatula while 

wet, and collecting the scraped material in clean glass 

vials. This removes the POM along with a thin layer of 

the glass fiber filter materials. Hence, because each 

sample contains an unknown amount of glass, the 

absolute elemental values are not representative of the 

organic material and C:N (atomic) ratios are reported 

instead. The samples were then freeze-dried in the vials 

to remove water. After freeze-drying, the samples were 

ground and homogenized in an agate mortar and pestle 

and 20-mg aliquots were weighed into silver cups. The 

open cups were placed in a ceramic rack in a glass 

dessicator jar (with no dessicant and no vacuum grease 

to seal the jar). One drop of organic-free water was 

added to each cup and an open beaker of concentrated 

hydrochloric acid was placed in the bottom of the jar. 

The jar was closed for 6 to12 hours to allow vaporphase acidification to remove carbonates from the 

samples. The rack of samples was then dried at 60oC in 

a convection oven, folded closed and placed in 96-well 

trays for shipment to Menlo Park for final analysis.

The further processing of the filtered samples for 

isotope analysis of TDN began with 200-mL aliquots 

being poured into 1-L flasks and reduced to 25 to 

50 mL by rotary evaporation. This process also 

removes dissolved carbonate from the samples. After 

reduction by rotary evaporation, the samples were 

adjusted to pH 7 by drop-wise addition of sodium 

hydroxide solution. The neutralized samples were 
20 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

poured into clean, glass flasks, then frozen and freeze 

dried. The freeze-dried samples were scraped out of the 

flasks with a clean steel spatula and collected in clean 

glass vials. The collected material was divided into 

40-mg aliquots (using a microbalance), which were 

placed in tin cups. The cups were folded, closed, 

crimped, and placed in 96-well trays for shipment to 

Menlo Park for analysis. 

Upon arrival at the USGS Menlo Park Stable 

Isotope Laboratory, the POM samples were analyzed 

for carbon and nitrogen isotopic and elemental 

composition on a Carlo Erba 1500 or 2500 elemental 

analyzer attached to a Micromass Optima or 

Micromass Isoprime mass spectrometer, in computercontrolled runs of 50 to 100 analyses each. A working 

standard material, ethylenediaminetetraacetic acid 

(EDTA), was analyzed with every run. The standard 

material samples that were analyzed ranged in size in 

order to bracket the environmental sample yield in 

terms of nitrogen and carbon, allowing for correction 

for sample-size linearity of the instrument. The EDTA 

was also analyzed at ten-sample intervals to correct for 

instrument drift over time. Empty silver or tin capsules 

were analyzed as blanks at the beginning and end of the 

run. About 10 percent of the samples were analyzed in 

duplicate. The EDTA standard was calibrated through a 

set of international standards to atmospheric air for 

δ15N and to Vienna Pee Dee Belemnite (VPDB) for 

δ13C. Nitrogen and carbon isotopic compositions are 

expressed in per mil (‰) relative to atmospheric air 

and VPDB, respectively. The calculations are as 

follows:

δ15NAir = {[(15N/14N)s/(15N/14N)Air] - 1} × 1,000

δ13CVPDB = {[(13C/12C)s/(13C/12C)VPDB] - 1} × 1,000

where

Analytical precision (1 standard deviation) for 

the standards was about ±0.15‰ for δ13C and δ15N. In 

2002, the USGS Menlo Park Stable Isotope Laboratory 

initiated a new automated system for simultaneous 

analysis of δ15N and δ18O of nitrate, using a method in 

which bacterial cultures reduce aqueous nitrate to N2O 

(Sigman and others, 2001; Casciotti and others, 2002). 

This development allowed a subset of frozen archived 

2001 samples to be analyzed directly for δ15N and δ18O 

of nitrate.

University of California at Davis Methods

The laboratory quality assurance and quality 

control (QA/QC) for the UCDBL involves standard 

laboratory protocols for spikes, replicates, reference 

standards, setting of control limits, and methods for 

criteria for rejection and data validation. Spikes were 

run at the onset of the project until consistent, and 

acceptable recoveries were obtained. Acceptable 

recovery was set at 85 percent. Approximately 5 to 

10 percent of the UCD samples were replicates. Within 

an analytical run, if replicates were not within 10 to 

20 percent of one another, the samples were 

reanalyzed. Certified nutrient and mineral reference 

standards were used for the determination of nitrate, 

ammonium, and orthophosphate. The reference 

standard was run immediately after instrument 

calibration. The limit of acceptability was ±10 percent 

from the certified value. At the onset of an analytical 

run, a series of distilled-deionized and (or) digested 

matrix blanks were run, after which a standard curve 

was developed from a series of standards defining the 

working range of analysis. The standard curve was 

verified by running the reference standards. The 

standard curve was rejected if it did not determine the 

values of the reference standards within ±10 percent 

and was reanalyzed every 20 to 30 samples to verify 

that no instrument drift had occurred. Drift in excess of 

10 percent resulted in rejection of all values determined 

since the previous standardization. Standards were also 

analyzed at the end of each analytical run.

The UCD water quality samples were analyzed 

for the same constituents as those analyzed by the 

NWQL with the exception of ultraviolet absorbance 

and isotopes. The UCDBL analytical method for 

determination of POM is very similar to the NWQL 

NAir = the international nitrogen 

standard

15N/14N, 13C/12C = ratio of heavy to light isotope 

in the sample or standard

s = sample; and

CVPDB = the international carbon 

standard.
Methods of Data Collection and Analysis 21

method for determination of VSS. The UCDBL 

analytical methods for analysis of nutrients, organic 

carbon, POM, chlorophyll-a and pheophytin-a, and 

total suspended solids are briefly described here.

Nutrients

Samples for nitrate and ammonia were filtered 

through a 0.45-μm Nuclepore membrane filter, and the 

dissolved concentrations were quantified 

simultaneously using an automated membrane 

diffusion and conductivity detection method (Carlson, 

1978; Carlson, 1986). TDN was determined by 

oxidizing a filtered sample (0.45-μm Nuclepore 

membrane) with a 1-percent persulfate oxidant solution 

and then using the same analytical method as for nitrate 

and ammonia (Yu and others, 1994). Dissolved organic 

nitrogen was calculated as the difference between TDN 

and ammonia and nitrate. Samples for total nitrogen 

analysis were analyzed with the same method as TDN. 

Dissolved orthophosphate was determined by a 

spectroscopic method using the stannous chloride 

standard method (Eaton and others, 1995) after the 

sample had been filtered through a 0.45-μm Nuclepore 

membrane. Total phosphorus was determined on 

whole-water samples using the stannous chloride 

standard method following persulfate digestion as 

described for TDN. Total dissolved phosphorus was 

determined on a filtered sample (0.45-μm Nuclepore 

membrane) using the same method as for total 

phosphorus. Dissolved organic phosphorus was 

calculated as the difference between total dissolved 

phosphorus and orthophosphate (Eaton and others, 

1995).

Organic Carbon and Particulate Organic Matter

DOC was analyzed by ultraviolet-enhanced, 

persulfate digestion with infrared detection using a 

Dohrmann 180 DOC instrument (Randy Dahlgren, 

University of California, Davis, written commun., 

2003). For POM samples, a known volume of water 

sample was filtered through a GFF, weighing the filter 

before and after filtration. Following filtration, the filter 

was dried in a desiccator for 24 hours and then weighed 

again. The filter was then ignited at 525oC for four 

hours and the loss in mass was subtracted from the 

precombusted mass to determine the POM present in 

the original sample (Eaton and others, 1995).

Chlorophyll-a and Pheophytin-a

The analytical method for determining 

chlorophyll-a and pheophytin-a concentrations were 

the same as that used in the chlorophyll-a and 

pheophytin-a analyses at the NWQL during the 2001 

study period (laboratory schedule 1637), with the 

exception of the use of 90-percent ethanol instead of 

the 100-percent methanol to extract the pigment (Eaton 

and others, 1995).

Total Suspended Solids

Total suspended solids were quantified by 

filtration of a known volume of water sample through a 

GFF and weighing the filter before and after filtration. 

Following filtration, the filter was dried in a desiccator 

for 24 hours and then weighed again (Randy Dahlgren, 

University of California, Davis, written commun., 

2003).

U.S. Geological Survey Quality Control Samples

The collection of quality control (QC) samples is 

necessary to evaluate the quality of the data. QC 

samples are collected, usually at the field site, in order 

to identify, quantify, and document bias and variability 

in data resulting from the collection, processing, 

shipping, and handling of samples by field and 

laboratory personnel (Wilde and others, 1999). A total 

of 33 QC samples were collected out of a total of 158 

samples (including six environmental samples 

collected at Lone Tree Creek) collected in this study 

(Appendix A). Four different types of field QC samples 

were collected in this study: 9 field blanks, 12 split 

replicates, 8 sequential replicates to compare sampling 

methods (width- and depth-integrated versus midpoint 

grab), and 4 sequential replicates to compare laboratory 

methods (NWQL versus UCDBL). In addition to the 

above QC samples, 15 samples were collected in 2001 

at Mud Slough (4 samples), Orestimba Creek (4 

samples), and SJR near Vernalis (7 samples) by USGS 

and UCD within 2 days of each other. Although not 

truly a replicate, these samples should be close in 

value. A relative percent difference (RPD) is used to 

describe the variability found in replicates. The RPD is 

calculated by taking the absolute value of the difference 

between the environmental and replicate samples and 

dividing by the average of the two samples.
22 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

The primary purpose of the field blanks was to 

identify potential sources of sample contamination and 

to assess the magnitude of contamination with respect 

to environmental concentrations of target analytes 

(Wilde and others, 1999). Of the nine field blanks 

collected, three had detections of DOC above the 

laboratory reporting limit of 0.3 mg/L (Appendix A). 

The field blanks used blank water distributed by the 

NWQL that contained 0.1 mg/L of DOC and the 

analytical reproducibility at this level is about ±0.2 

mg/L. Thus, blanks having concentrations of 0.3 mg/L 

or less for DOC are acceptable (U.S. Geological 

Survey, 2000). The blanks with DOC above 0.3 mg/L 

had concentrations about an order of magnitude below 

the corresponding environmental samples 

(Appendix A).

Split replicates were samples divided into two 

equal subsamples, each of which were submitted for 

identical analyses in order to assess variability from 

sample processing and preservation (Wilde and others, 

1999). The split replicate samples were split from the 

cone splitter in 2000 and from the churn splitter in 

2001. One of the 3-L Teflon sample bottles was poured 

into two sets of bottles directly for SOC, DOC, and 

ultraviolet absorbance analyses in 2001 instead of 

splitting with the plastic churn splitter.

Sequential replicate samples were collected in 

2000 to assess the variability in the UCD grab sampling 

method against the USGS width- and depth-integrated 

sampling method as well as in laboratory performance 

between the NWQL and the UCDBL. The sampling 

design for the collection of sequential replicate samples 

was as follows. During the USGS collection of a water 

quality sample using the width- and depth-integrated 

method, a second sample was collected using the UCD 

midpoint grab method. This second midpoint grab 

sample was considered to be the sequential replicate. 

Both samples were sent to the NWQL for analyses. For 

four of these eight sequential replicates, an additional 

volume of water was collected by midpoint grab and 

was analyzed for the same constituents at the UCDBL. 

Therefore, the sequential replicates were not only used 

to compare the variability in sampling methods, but 

also to compare variability in laboratory methods. 

Table 3. Summary of quality-control replicate data for samples collected in the San Joaquin River Basin, California, 2000–2001

[NWQL, National Water Quality Laboratory; EWI, equal width increment; UCD, University of California at Davis; USGS, U.S. Geological Survey; n, 

number of samples; RPD, relative percent difference; VSS, volatile suspended solids; POM, particulate organic matter. %, percent; —, no data reported] 

Split replicates, 

both analyzed at NWQL

Sequential replicates 

collected by EWI and grab, 

both analyzed at NWQL

Sequential replicates, 

one analyzed at NWQL 

and the other at UCD

Samples collected and analyzed 

within 2 days of each other 

by USGS and UCD

Constituent n

Range of

RPDs 

(%)

Median 

RPDs 

(%)

n

Range of

RPDs 

(%)

Median 

RPDs 

(%)

% with

EWI 

higher

n

Range of

RPDs 

(%)

Median 

RPDs 

(%)

% with

NWQL 

higher

n

Range of

RPDs 

(%)

Median 

RPDs 

(%)

% with 

USGS 

higher

Dissolved nitrate 12 0.0– 4.5 0.6 7 0.5–1.4 0.7 43 4 1.7–10.6 7.8 0 15 1.5–31.9 5.5 53

Total nitrogen 12 0.0– 9.5 2.6 7 0.0–6.7 1.8 57 4 0.7–15.5 1.9 75 15 0.3– 46.0 9.0 20

Dissolved 12 0.0– 8.0 0.0 8 0.0– 8.0 0.0 50 4 3.7–8.6 6.7 25 13 0.0–147.1 14.7 50

orthophosphate

Total phosphorus 12 0.0–5.3 0.9 8 2.3–10.2 4.8 63 4 31.3–54.6 48.9 100 15 2.9–116.2 17.3 53

Dissolved 11 0.0–92.7 3.1 7 0.0– 4.6 2.4 29 4 4.0–77.4 38.8 50 15 0.0–40.0 9.8 54

organic carbon

Suspended 10 0.0–86.4 14.4 7 0.0–82.4 23.5 43 0 — — — 0 — — —

organic carbon

Chlorophyll-a 11 5.0–77.8 16.1 8 2.3–193 11.9 25 4 12.7–190 48.2 50 15 2.0–133.3 19.4 47

Pheophytin-a 10 0.8–78.8 19.4 0 — — — 0 — — — 15 29.8–149.0 102.4 100

VSS/POM 0 — — 0 — — — 2 30.3–53.3 41.8 0 15 2.5–117.0 49.5 13
Hydrologic Conditions During the Study Period 23

The samples collected for the split replicates and 

the sequential replicates to compare sampling methods 

were all analyzed at the NWQL. The median RPDs for 

these samples were less than 5 percent for nutrients and 

DOC and from 10 to 25 percent for SOC, chlorophylla, and pheophytin-a (table 3). For the four sequential 

replicates split between the NWQL and the UCDBL, 

the median RPDs were less than 10 percent for nitrate, 

total nitrogen, and orthophosphate, and between 35 and 

50 percent for total phosphorus, DOC, and chlorophylla. Only two of these four samples had detections to 

compare the NWQL values for VSS with the UCD 

values for POM. These samples had a median RPD of 

41.8 percent. Because there were so few sequential 

replicates for laboratory comparisons, the differences 

between samples collected by USGS and UCD within 

2 days of each other also were evaluated. These 

15 samples were used to address concerns raised by the 

four sequential replicates about mixing USGS and 

UCD data for total phosphorus, DOC, and VSS/POM. 

The concern with total phosphorus analyses and 

potential laboratory bias was somewhat alleviated by 

the additional data as the median RPD dropped from 49 

to 17 percent and the percentage of samples analyzed at 

the NWQL with higher values dropped from 100 to 

53 percent (table 3). Concerns over DOC comparability 

also were reduced as the median RPD dropped from 39 

to 10 percent. The additional data did not alleviate 

concerns regarding mixing VSS and POM data 

however, as the median RPD increased from 42 to 

50 percent and the bias of higher values for POM 

remained. The additional data also pointed out a 

serious problem with mixing USGS and UCD data for 

pheophytin-a as the median RPD was 102 percent and 

all USGS values were higher. 

In conclusion, the nitrogen constituents had low 

variability when analyzed at the NWQL (median RPD 

less than 5 percent) and relatively low variability 

between the NWQL and the UCDBL (median RPD 

less than 10 percent). For the phosphorus constituents 

and for DOC, the variability at the NWQL was also 

less than 5 percent (median RPD), and the variability 

between laboratories was between 10 and 20 percent 

(median RPD). SOC and chlorophyll-a had a 

variability at the NWQL of about 15 percent (median 

RPD), and chlorophyll-a had a variability between 

laboratories of about 20 percent. The variability 

between laboratories for pheophytin-a and VSS/POM 

is unacceptably high (about 100 percent for 

pheophytin-a and 50 percent for VSS/POM). In 

addition, whereas the variability between USGS and 

UCD laboratories appears to be fairly random for 

nutrients, organic carbon, and chlorophyll-a, there was 

a consistent bias for pheophytin-a and the comparison 

of USGS VSS values with UCD POM values. Thus, the 

pheophytin-a values from UCD will not be presented in 

this report and the VSS and POM data will be 

presented as two separate constituents.

HYDROLOGIC CONDITIONS DURING THE 

STUDY PERIOD

The long-term mean annual precipitation in the 

study area is about 10 to 12 in. (Kratzer and Shelton, 

1998). The monthly precipitation in the study area for 

the 30-year period of 1972 to 2001 shown in figure 9 is 

based on precipitation in downtown Modesto. The sixmonth June through November period accounted for 

21 percent of the annual precipitation during the 

30-year period. Some significant precipitation events 

did occur during the 2000 and 2001 sampling periods: 

1.09 in. during October 9–11, 2000, and 0.75 in. during 

November 10–12, 2001.

The streamflow at SJR near Vernalis during June 

through November is much less variable than during 

the rest of the year (fig. 10). In the highly manipulated 

San Joaquin Basin, this time of year is generally a lowflow period influenced primarily by agricultural 

diversions and return flows and hydropower releases 

from the reservoirs. In recent years, significant 

reservoir releases were made during late October to 

attract spawning fall-run Chinook salmon as part of the 

Vernalis Adaptive Management Plan (VAMP) (San 

Joaquin River Group Authority, 2002). The median 

June through November average streamflow near 

Vernalis for the 30-year period was 2,156 ft3/s, with a 

low of 198 ft3/s in 1977 and a high of 14,943 ft3/s in 

1983. During June through November of 2000, the 

average streamflow near Vernalis was 2,419 ft3/s; in 

2001 it was 1,624 ft3/s (fig. 10B). Thus, the June 

through November San Joaquin River streamflows in 

2000 were about 50 percent higher than in 2001.
24 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Water availability in the San Joaquin Basin is 

defined by a water year hydrologic classification 

system known as the 60-20-20 water year index. This 

represents the percentage weight given to three 

variables: the forecasted, unimpaired runoff from April 

through July (60 percent); the forecasted, unimpaired 

runoff from October through March (20 percent); and 

the reservoir carryover storage from the previous water 

year constrained by a maximum allowable value 

(20 percent) (California Department of Water 

Resources, accessed February 20, 2003). Using this 

index, water years 1972–2001 were classified as wet, 

above normal, below normal, dry, or critical (fig. 11). 

"Unimpaired flow" represents the runoff from a basin if 

flow had not been altered (California Department of 

Water Resources, 1987). The total unimpaired 

streamflow to the valley floor in the San Joaquin Basin 

is the sum of unimpaired flows from SJR at Millerton 

Lake, Merced River at Lake McClure, Tuolumne River 

at New Don Pedro Reservoir, Stanislaus River at New 

Melones Reservoir, and outflow from the Tulare Basin 

by way of Fresno Slough (fig. 1). The unimpaired flow 

provides an estimate of the total water that would be 

expected to reach Vernalis under natural conditions. 

The actual outflow from the San Joaquin Basin is about 

40 percent less than the unimpaired flow to the valley, 

mostly because of consumptive agricultural water use 

in the basin (Kratzer and Shelton, 1998). The timing of 

actual outflow is more evenly distributed throughout 

the year than the unimpaired flow to the valley because 

of the storage and release schedules of the four major 

upstream reservoirs. Reservoir development and water 

use in the basin have shifted the peak outflow from 

May to March and cut this peak flow about in half 

(Kratzer and Shelton, 1998).

Figure 9. Monthly precipitation in downtown Modesto, California, December 1971–November 2001.

0.00

1.00

2.00

3.00

4.00

5.00

6.00

7.00

8.00

9.00

10.00

Dec-71Dec-72Dec-73Dec-74Dec-75Dec-76Dec-77Dec-78

Dec-79Dec-80Dec-81Dec-82

Dec-83

Dec-84

Dec-85

Dec-86

Dec-87

Dec-88

Dec-89

Dec-90Dec-91Dec-92Dec-93Dec-94Dec-95

Dec-96

Dec-97

Dec-98Dec-99

Dec-00

Nov-01

Precipitation, in inches per month

Monthly Precipitation at Modesto

December 1971 – November 2001

December – May

June – November
Hydrologic Conditions During the Study Period 25

0

5,000

10,000

15,000

20,000

25,000

30,000

35,000

40,000

45,000

Dec-71

Dec-72

Dec-73

Dec-74

Dec-75

Dec-76

Dec-77

Dec-78

Dec-79

Dec-80

Dec-81

Dec-82

Dec-83

Dec-84

Dec-85

Dec-86

Dec-87

Dec-88

Dec-89

Dec-90

Dec-91

Dec-92

Dec-93

Dec-94

Dec-95

Dec-96

Dec-97

Dec-98

Dec-99

Dec-00

Nov-01

Streamflow, in cubic feet per second

December – May

June – November

Monthly Mean Streamflow at San Joaquin River near Vernalis (site 27)

December 1971 – November 2001

A

Figure 10. Streamflow at San Joaquin River near Vernalis, California. 

(A) Monthly for December 1971–November 2001, and (B) Daily for June through November 2000 and 2001.

0

500

1,000

1,500

2,000

2,500

3,000

3,500

4,000

4,500

Streamflow, in cubic feet per second

2000

2001 Daily Mean Streamflow at San Joaquin River near Vernalis (site 27)

June July August September October November

B
26 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

During the 1972–2001 period, there were 12 wet, 

5 above normal, 4 dry, and 9 critical water years 

(fig. 11. The periods of wet and dry were cyclical 

during the 30-year period. The first six water years of 

the period were balanced—two wet, one above normal, 

one dry, and two critical. The drought of 1976–1977 

was followed by a 9-year period dominated by wet 

water years, including the extremely wet water year of 

1983. Overall, this 9-year period included five wet, two 

above normal, and two dry water years. Following that 

9-year wet period were six consecutive critical water 

years. The last 9 years of the period were again 

dominated by wet water years with 5 wet, 2 above 

normal, a dry, and a critical water year. The 2000 and 

2001 water years were above normal and dry, 

respectively. On the basis of the numeric 60-20-20 

water year index, 2000 (3.38 million acre-ft) was close 

to the 30-year average index of 3.33 million acre-feet, 

while 2001 (2.20 million acre-ft) was considerably 

below the average.

CONCENTRATIONS OF NUTRIENTS, 

ORGANIC CARBON, AND CHLOROPHYLL-A

Concentrations will be interpreted here in terms 

of the range of values and the median values, some 

temporal trends over the sampling period, and some 

upstream to downstream trends. More in-depth analysis 

of tributary sources to the San Joaquin River will be 

presented in the section "Loads of Nutrients, Organic 

Carbon, and Chlorophyll-a." It is important to note that 

considering only concentrations can sometimes be 

misleading with respect to their significance to the 

overall river system because of the magnitude of 

streamflows. For example, SJR near Stevinson had 

some very high concentrations of nutrients, organic 

carbon, and chlorophyll-a on occasion. However, the 

streamflows associated with these high concentrations 

were extremely low, and the river was essentially 

ponded at the site with very low velocities. Further, 

concentrations that were based on individual monthly 

or every two week sampling are connected in the plots 

presented in this section. This connection is made 

merely for the purpose of indicating trends in 

concentrations and should not be implied to represent a 

continuous record of concentrations. Streamflow for 

SJR near Vernalis is shown in each plot to indicate 

streamflow variations in the entire basin. To see the 

relation of concentrations to streamflow at a given site, 

the reader should refer to figures 5 to 8.

Concentrations of nutrients, organic carbon, and 

chlorophyll-a in water samples, collected from July 

through October 2000 and from June through 

November 2001, are presented in Appendixes B and C. 

Appendix B provides laboratory results at sites on the 

San Joaquin River and Appendix C provides laboratory 

results from sites on major and minor tributaries to the 

San Joaquin River. The instantaneous streamflows 

during sampling at the San Joaquin River sites are 

plotted in figure 12. These plots help to show the 

progressive increases in streamflows in the San Joaquin 

River as one moves downstream and that the Merced, 

Tuolumne, and Stanislaus Rivers greatly increase the 

streamflows.

1972 19 1975 80 1985 1990 1995 2000

0

2

4

6

8

Water Year Type

Water year index, in million acre-feet

Critical

Dry

Below Normal

Above Normal

Wet

Figure 11. Water year indexes and corresponding water year types for San Joaquin Basin, California, 1972–2001.
Concentrations of Nutrients, Organic Carbon, and Chlorophyll-a 27

A

1,000

500

0

1,500

2,000

2,500

3,000

7/1 7/15 7/29 8/12 8/26 9/9 9/23 10/7 10/21

Streamflow, instantaneous, in cubic feet per second

2000

0

500

1,000

1,500

2,000

2,500

6/1 6/15 6/29 7/13 7/27 8/10 8/24 9/7 9/21 10/5 10/19 11/2 11/16 11/30

Streamflow, instantaneous, in cubic feet per second

B

2001

3,000

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 12. Instantaneous streamflow at time of sampling at San Joaquin River sites in California. 

(A) July through October 2000, and (B) June through November 2001.
28 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Nitrogen

Ammonia concentrations were below the 

laboratory reporting levels in 59 of the 130 samples 

collected at San Joaquin River sites and in 16 of the 

168 samples collected from tributaries. The median 

concentration of ammonia in the San Joaquin River 

was 0.02 mg/L in 2000 and 0.04 in 2001, with 

maximum concentrations of 0.58 and 0.53 mg/L, 

respectively. The median concentration of ammonia in 

samples collected at tributary sites in 2000 and 2001 

was 0.05 mg/L, with a maximum of 2.43 mg/L. The 

highest concentrations observed were in Harding 

Drain, which receives effluent from the City of Turlock 

Wastewater Treatment Plant.

Nitrate concentrations in the San Joaquin River 

ranged from 0.01 to 8.06 mg/L in 2000 and from 0.02 

to 5.55 mg/L in 2001, with medians of 2.67 and 

2.60 mg/L, respectively. Concentrations at the tributary 

sites ranged from 0.02 to 19.7 mg/L, with a median of 

2.66 mg/L. Concentrations of total nitrogen in the San 

Joaquin River ranged from 1.04 to 11.7 mg/L in 2000 

and from 1.29 to 7.23 mg/L in 2001, with medians of 

3.48 and 3.96 mg/L, respectively. Concentrations in the 

tributaries ranged from 0.37 to 22.9 mg/L, with a 

median of 3.39 mg/L.

With the exception of SJR near Stevinson, most 

nitrogen in the San Joaquin River and the tributaries 

was in the form of nitrate. On average, nitrate 

accounted for 97 percent of the dissolved inorganic 

nitrogen and 72 percent of the total nitrogen in the river 

samples collected downstream of Stevinson. At SJR 

near Stevinson, more of the nitrogen was in the form of 

organic compounds. Dissolved inorganic nitrogen at 

SJR near Stevinson averaged only about 12 percent of 

the total nitrogen. Dissolved organic nitrogen 

accounted for about 67 percent of the total dissolved 

nitrogen and 35 percent of the total nitrogen. At the 

downstream sites in the San Joaquin River, the 

dissolved organic nitrogen accounted for only 

16 percent of the total nitrogen.

Concentrations of nitrate, inorganic nitrogen, and 

total nitrogen generally decreased throughout the 

sampling period at upstream sites in 2000 and 2001 

(figs. 13 and 14). Nitrate concentrations at the Crows 

Landing, Patterson, and Laird Park sites decreased 

from about 4 mg/L to about 2 mg/L; total nitrogen 

decreased from about 6 mg/L to about 2 mg/L. 

Nitrogen concentrations at the two downstream sites, 

Maze Road and Vernalis, did not have a general trend 

over the study period, although concentrations 

fluctuated quite a bit at Maze Road. These sites are 

greatly affected by dilution flows from the Tuolumne 

and Stanislaus Rivers. The dilution of Maze Road 

concentrations in 2001 was not nearly as great as in 

2000 because of relatively high nitrate concentrations 

in the Tuolumne River in 2001. 

Nitrogen concentrations usually decreased in the 

San Joaquin River from Laird Park to Maze Road to 

Vernalis. At the end of the sampling periods in 2000 

and 2001, the concentrations at SJR near Crows 

Landing were actually lower than those at SJR near 

Vernalis. This probably was due to VAMP-related 

reservoir releases on the Merced River and wetland 

releases from the Grasslands Ecological Area to Mud 

Slough. These releases diluted the nitrogen 

concentrations at SJR near Crows Landing. A 

significant precipitation event preceded the last 

sampling visit in 2000 and 2001 as well. 

Phosphorus

Concentrations of orthophosphate in the San 

Joaquin River ranged from 0.04 to 0.34 mg/L in 2000 

and from 0.02 to 0.29 mg/L in 2001, with a median of 

0.12 mg/L for both years. Concentrations at tributary 

sites ranged from below laboratory reporting levels to 

2.27 mg/L, with a median of 0.08 mg/L for both years. 

Total phosphorus concentrations in the San Joaquin 

River ranged from 0.15 to 0.50 mg/L in 2000 and from 

0.18 to 0.56 mg/L in 2001, with medians of 0.26 and 

0.30 mg/L, respectively. Concentrations at tributary 

sites ranged from 0.02 to 2.58 mg/L, with a median of 

0.17 mg/L for both years.

Both orthophosphate and total phosphorus 

concentrations were highly variable throughout the 

monitoring period and did not show any overall 

temporal trends (figs. 15 and 16). Concentrations were 

similar between years for San Joaquin River sites 

downstream of the Merced River. Orthophosphate 

concentrations ranged from about 0.1 to 0.3 mg/L; total 

phosphorus ranged from about 0.2 to 0.5 mg/L.
Concentrations of Nutrients, Organic Carbon, and Chlorophyll-a 29

0

2

4

6

8

10

12

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

Total nitrogen concentration,

in milligrams per liter as N

C

B

0

2

4

6

8

10

12

Inorganic nitrogen concentration,

in milligrams per liter as N

0

2

4

6

8

10

12

Nitrate concentration,

in milligrams per liter as N

A San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Streamflow at San Joaquin River near Vernalis

0

1,000

2,000

3,000

4,000

Streamflow,

in cubic feet per second

Figure 13. Concentrations of nitrate, inorganic nitrogen, and total nitrogen at San Joaquin River sites in California, from upstream to downstream for July 

through October 2000, with streamflow at Vernalis. 

(A) Nitrate, (B) Inorganic nitrogen, (C) Total nitrogen. N, nitrogen.
30 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

0

1

2

3

4

5

6

7

8

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

Total nitrogen concentration,

in milligrams per liter as N

0

1

2

3

4

5

6

7

8

Inorganic nitrogen concentration,

in milligrams per liter as N

B

C

0

1

2

3

4

5

6

7

8

Nitrate concentration,

in milligrams per liter as N

San Joaquin River near Stevinson A

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

0

1,000

2,000

3,000

4,000

Streamflow at San Joaquin River near Vernalis

Streamflow,

in cubic feet per second

Figure 14. Concentrations of nitrate, inorganic nitrogen, and total nitrogen at San Joaquin River sites in California, from upstream to downstream for June 

through November 2001, with streamflow at Vernalis. 

(A) Nitrate, (B) Inorganic nitrogen, (C) Total nitrogen. N, nitrogen.
Concentrations of Nutrients, Organic Carbon, and Chlorophyll-a 31

            

















4OTALPHOSPHORUSCONCENTRATION

INMILLIGRAMSPERLITERAS0

!

"















/RTHOPHOSPHATECONCENTRATION

INMILLIGRAMSPERLITERAS0

3AN*OAQUIN2IVERNEAR3TEVINSON

3AN*OAQUIN2IVERUPSTREAMOF-ERCED2IVER

3AN*OAQUIN2IVERNEAR#ROWS,ANDING

3AN*OAQUIN2IVERNEAR0ATTERSON

3AN*OAQUIN2IVERAT,AIRD0ARK

3AN*OAQUIN2IVERAT-AZE2OAD

3AN*OAQUIN2IVERNEAR6ERNALIS











3TREAMFLOWAT3AN*OAQUIN2IVERNEAR6ERNALIS

3TREAMFLOW

INCUBICFEETPERSECOND

Figure 15. Concentrations of orthophosphate and total phosphorus at San Joaquin River sites in California, from upstream to downstream for July through 

October 2000, with streamflow at Vernalis. 

(A) Orthophosphate, (B) Total phosphorus. P, phosphorus.
32 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

0

1,000

2,000

3,000

4,000

Streamflow,

in cubic feet per second

Streamflow at San Joaquin River near Vernalis

B

0.0

0.1

0.2

0.3

0.4

0.5

0.6

Total phosphorus concentration,

in milligrams per liter as P

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

0.0

0.1

0.2

0.3

0.4

0.5

0.6

Orthophosphate concentration,

in milligrams per liter as P

San Joaquin River near Stevinson A

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 16. Concentrations of orthophosphate and total phosphorus at San Joaquin River sites in California, from upstream to downstream for June through 

November 2001, with streamflow at Vernalis. 

(A) Orthophosphate, (B) Total phosphorus. P, phosphorus.
Concentrations of Nutrients, Organic Carbon, and Chlorophyll-a 33

For San Joaquin River sites downstream of the 

Merced River, phosphorus concentrations were usually 

highest near Patterson and Laird Park, downstream of 

Harding Drain. Concentrations near Crows Landing 

were usually considerably lower than near Patterson 

and at Laird Park, and concentrations at Maze Road 

and near Vernalis were diluted by the Tuolumne and 

Stanislaus Rivers. As with nitrogen concentrations, the 

dilution at Maze Road was much less in 2001 than in 

2000 because of higher phosphorus inputs from the 

Tuolumne River. At the San Joaquin River sites 

upstream of the Merced River and near Crows Landing, 

phosphorus concentrations increased or decreased in 

October in response to wetland releases to Mud Slough 

(increasing concentrations) and VAMP-related 

reservoir releases on the Merced River (decreasing 

concentrations).

Organic Carbon

Dissolved organic carbon (DOC) concentrations 

in the San Joaquin River ranged from 2.3 to 8.8 mg/L 

in 2000 and from 2.5 to 10.3 mg/L in 2001, with a 

median of 3.9 mg/L, both years. Concentrations at the 

tributary sites ranged from 0.7 to 17.6 mg/L, with a 

median concentration of 4.3 mg/L for both years. 

Suspended organic carbon (SOC) concentrations in the 

San Joaquin River ranged from 0.3 to 3.6 mg/L in 2000 

and from 0.8 to 7.9 mg/L in 2001, with medians of 1.1 

and 2.0 mg/L, respectively. Concentrations at the 

tributary sites ranged from <0.2 to >10 mg/L, with a 

median concentration of 1.5 mg/L for both years.

At San Joaquin River sites downstream of the 

Merced River, DOC concentrations usually decreased 

slightly from June and July to September, then 

increased in the fall (figs. 17 and 18). The overall trend 

appears to be closely related to the San Joaquin River 

upstream of Merced River. The increase at this site in 

the fall probably was related to wetland releases from 

the Grasslands Ecological Area to Mud Slough and Los 

Banos Creek (Appendix C). SOC concentrations 

generally decreased from June and July through the 

rest of the sampling period, except for some increases 

at the San Joaquin River sites upstream of the Merced 

River (site 7) and near Crows Landing (site 17) in the 

fall (figs. 17 and 18).

DOC concentrations were highest in the San 

Joaquin River sites upstream of the Merced River and 

generally decreased in downstream order from there. 

SOC concentrations were less variable than DOC, 

except for an unusually high value on August 9, 2001. 

This outlier may represent sampling variability caused 

by a relatively large clump of suspended organic matter 

being collected in the sampler by chance, resulting in a 

nonrepresentative sample with a value higher than 

ambient conditions at the time of sample collection. 

The ultraviolet absorbance at 254-nm is often 

used to infer the qualitative differences in the 

composition of the organic matter in river waters. The 

specific ultraviolet absorbance (SUVA) is the 

ultraviolet absorbance at 254 nm divided by the DOC 

concentration. SUVA is positively correlated with the 

degree of aromatic carbon in the DOC (Bergamaschi 

and others, 2000). The median SUVA at the San 

Joaquin River sites was 0.027 L/mg-cm in 2000 and 

0.028 L/mg-cm in 2001 (Appendix B). The median 

SUVA at the tributary sites was also 0.028 L/mg-cm in 

2001 (Appendix C). Thus, SUVA values in the 

tributaries and in the San Joaquin River were 

essentially the same.

Chlorophyll-a and Pheophytin-a

Chlorophyll-a concentrations at the San Joaquin 

River sites ranged from 5.1 to 377 μg/L in 2000 and 

from 5.4 to 393 μg/L in 2001, with medians of 27.2 and 

29.4 μg/L, respectively. Chlorophyll-a concentrations 

at the tributary sites ranged from 0.2 to 81.5 μg/L, with 

a median of 6.0 μg/L. Pheophytin-a concentrations at 

the four USGS sites on the San Joaquin River ranged 

from 3.7 to 46.5 μg/L in 2001, with a median of 

16.4 μg/L. Pheophytin-a concentrations at the tributary 

sites sampled by USGS ranged from 0.8 to 56.8 μg/L, 

with a median of 6.2 μg/L.

In 2000, chlorophyll-a concentrations in the San 

Joaquin River were highest from July to mid-August, 

then decreased the rest of the sampling period (fig. 19). 

In 2001, chlorophyll-a concentrations increased from 

mid-June to early September, then decreased (fig. 20). 

Pheophytin-a concentrations in 2001 had a trend 

similar to that for chlorophyll-a (fig. 20).
34 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

B

A

Streamflow at San Joaquin River near Vernalis

1,000

0

2,000

3,000

4,000

Streamflow, in cubic feet

per second

0

1

2

3

4

5

6

7

8

9

Dissolved organic carbon concentration,

in milligrams per liter as C

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

0

0.5

1

1.5

2

2.5

3

3.5

4

Suspended organic carbon concentration,

in milligrams per liter as C

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 17. Concentrations of dissolved organic carbon and suspended organic carbon at San Joaquin River sites in California, from upstream to downstream 

for July through October 2000, with streamflow at Vernalis. 

(A) Dissolved organic carbon, (B) Suspended organic carbon. C, carbon.
Concentrations of Nutrients, Organic Carbon, and Chlorophyll-a 35

0

2

4

6

8

10

12

A

B

Streamflow at San Joaquin River near Vernalis

0

1,000

2,000

3,000

4,000

Streamflow, in cubic feet

per second Dissolved organic carbon concentration,

in milligrams per liter as C

0

1

2

3

4

5

6

7

8

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

Suspended organic carbon concentration,

in milligrams per liter as C

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 18. Concentrations of dissolved organic carbon and suspended organic carbon at San Joaquin River sites in California, from upstream to 

downstream for June through November 2001, with streamflow at Vernalis. 

(A) Dissolved organic carbon, (B) Suspended organic carbon. C, carbon.
36 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001



















#HLOROPHYLL
ACONCENTRATIONINMICROGRAMSPERLITER

            



3TREAMFLOWAT3AN*OAQUIN2IVERNEAR6ERNALIS











3TREAMFLOWINCUBICFEETPERSECOND

3AN*OAQUIN2IVERNEAR3TEVINSON

3AN*OAQUIN2IVERUPSTREAMOF-ERCED2IVER

3AN*OAQUIN2IVERNEAR#ROWS,ANDING

3AN*OAQUIN2IVERNEAR0ATTERSON

3AN*OAQUIN2IVERAT,AIRD0ARK

3AN*OAQUIN2IVERAT-AZE2OAD

3AN*OAQUIN2IVERNEAR6ERNALIS

Figure 19. Concentrations of chlorophyll-a at San Joaquin River sites in California, from upstream to downstream for 

July through October 2000, with streamflow at Vernalis. 
Concentrations of Nutrients, Organic Carbon, and Chlorophyll-a 37

0

100

200

300

400

500

10

0

20

30

40

50

Pheophytin-a concentration, in micrograms per liter

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

1,000

0

2,000

3,000

4,000

Streamflow, in cubic feet

per second Chlorophyll-a concentration, in micrograms per liter

A

B

Streamflow at San Joaquin River near Vernalis

Figure 20. Concentrations of chlorophyll-a and pheophytin-a at San Joaquin River sites in California, from upstream to 

downstream for June through November 2001, with streamflow at Vernalis. 

(A) Chlorophyll-a, (B) Pheophytin-a.
38 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

There was very little variation in chlorophyll-a

concentrations from upstream to downstream in 2000 

or 2001, despite diluting flows entering the San 

Joaquin River from the Merced, Tuolumne, and 

Stanislaus Rivers with relatively low chlorophyll-a

concentrations (Appendix C). SJR near Stevinson had 

extremely high concentrations, but at very low 

streamflows as mentioned earlier. Pheophytin-a

concentrations were usually higher at SJR near 

Vernalis and Laird Park than at upstream sites. 

HISTORICAL NUTRIENT LOADS IN THE 

SAN JOAQUIN BASIN

Monthly Loads in the San Joaquin River near 

Vernalis, 1972–2001

Monthly loads of dissolved nitrate (hereinafter, 

nitrate), total nitrogen, and total phosphorus at SJR 

near Vernalis were calculated for the 30-year period in 

this study, 1972–2001, using version 92.11b of the load 

calculation program ESTIMATOR (Cohn and others, 

1989). ESTIMATOR is a log-linear multiple regression 

model of constituent concentration against streamflow 

and time variables. ESTIMATOR uses standard output 

files from the USGS National Water Information 

System (NWIS) database as input data files. These data 

are used to develop a relation between streamflow and 

constituent concentration for calculating loads. The 

ESTIMATOR program first runs a calibration period 

for flows and concentrations. Only concentrations with 

associated streamflows (instantaneous or daily mean) 

are used in the calibration process. For the loadestimation period, there must be a streamflow value for 

each day. The ESTIMATOR program provided 

estimated daily, monthly, or annual loads with standard 

errors and standard errors of prediction. Thus, 

confidence intervals for the load estimates can be 

calculated.

In this study, the data used in ESTIMATOR are 

from the U.S. Environmental Protection Agency's 

STOrage and RETreival (STORET) and NWIS 

databases. The data used are described in Kratzer and 

Shelton (1998) for 1972–90 and in Saleh and others 

(2003) for 1991–2000. For 2001, only data from NWIS 

were used in ESTIMATOR. The calibration period and 

the load-estimation period were both 1972–2001. The 

results reported in Kratzer and Shelton (1998) for the 

SJR near Vernalis for 1972–90 will be slightly different 

than the results reported here for that period because of 

the different calibration period. Similarly, results 

reported in Saleh and others (2003) for the 1980–2000 

period will be different than the results reported here 

for that period.

The annual variations in loads of total nitrogen 

and total phosphorus (fig. 21) closely follow the 

variations in streamflow (fig. 10), while the variations 

in nitrate loads are less pronounced. This is largely a 

function of the particulate fraction of the constituent. 

Total phosphorus has the highest particulate fraction 

(about 0.56 for 1972–2001 data), followed by total 

nitrogen (about 0.36 for 1972–2001 data), while the 

nitrate load is all in the dissolved form (by definition). 

Thus, because suspended sediment concentrations 

increase with streamflow, the ratios of wet year to dry 

year loads should increase with the particulate fraction 

of the constituent. This was the case for 1972–2001, as 

total phosphorus increased the most with streamflow, 

and nitrate the least (fig. 21). Overall, nitrate loads 

increased over time independent of streamflow. This 

increasing nitrate trend is shown as flow-adjusted 

concentrations in figure 22. The highly significant 

statistical trend (p < 0.01) has a slope of 0.025 mg/L 

per year. This is very similar to the slope for the 

40-year period from 1951–90 of 0.028 mg/L per year 

(Kratzer and Shelton, 1998). Much of the nitrate load 

in the San Joaquin River originates in tile drainage 

from the Grasslands Drainage Project Area (fig. 1) that 

is only slightly sensitive to changes in streamflow in 

the San Joaquin River (Kratzer and Shelton, 1998). 

Loads and concentrations of other forms of nitrogen 

and total phosphorus did not increase as did nitrate, and 

thus, there were no statistically significant (at the 

95-percent confidence level) flow-adjusted trends of 

total nitrogen (p = 0.11, slope = 0.0087 mg/L per year) 

and total phosphorus (p = 0.06, slope = – 0.0014 mg/L 

per year) (fig. 22).
Historical Nutrient Loads in the San Joaquin Basin 39

100,000

150,000

50,000

0

200,000

250,000

300,000

350,000

400,000

450,000

Oct-71Oct-72Oct-73Oct-74Oct-75Oct-76Oct-77Oct-78

Oct-79Oct-80Oct-81

Oct-82Oct-83

Oct-84Oct-85

Oct-86

Oct-87

Oct-88

Oct-89

Oct-90Oct-91Oct-92Oct-93Oct-94Oct-95Oct-96Oct-97Oct-98

Oct-99Oct-00Oct-01

Total phosphorus load, in kilograms per month as P

Monthly Loads of Total Phosphorus at San Joaquin River near Vernalis (site 27)

Water Years 1972–2001

C

1,000,000

1,500,000

500,000

0

2,000,000

2,500,000

Total nitrogen load, in kilograms per month as N

Monthly Loads of Total Nitrogen at San Joaquin River near Vernalis (site 27)

Water Years 1972–2001

B

100,000

0

200,000

300,000

400,000

500,000

600,000

700,000

800,000

Nitrate load, in kilograms per month as N

Monthly Loads of Nitrate at San Joaquin River near Vernalis (site 27)

Water Years 1972–2001

A

December–May

June–November

Figure 21. Monthly loads of nitrate, total nitrogen, and total phosphorus at San Joaquin River near Vernalis, California, 1972–2001 (calculated by 

ESTIMATOR). 

(A) Nitrate, (B) Total nitrogen, (C) Total phosphorus. N, nitrogen; P, phosphorus.
40 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

B

Water Year

72 74 76 78 80 82 84 86 88 90 92 94 96 98 00

Flow-adjusted total phosphorus concentration,

in milligrams per liter as P

1.5

1.0

0.5

0.0

C

6

5

4

3

2

1

0

–1

Flow-adjusted total nitrogen concentration,

in milligrams per liter as N

A

6

5

4

3

2

1

0

–1

Flow-adjusted nitrate concentration,

in milligrams per liter as N

National Water Information System database of the U.S. Geological Survey

Storage and Retrieval database of the U.S. Environmental Protection Agency

Concentration trend

Figure 22. Flow-adjusted concentrations of nitrate, total nitrogen, and total phosphorus in the San Joaquin River near Vernalis, California, 

1972–2001. 

(A) Nitrate, (B) Total nitrogen, (C) Total phosphorus. N, nitrogen; P, phosphorus.
Historical Nutrient Loads in the San Joaquin Basin 41

The monthly loads for nitrate, total nitrogen, and 

total phosphorus during the study period, 2000 and 

2001, are compared with the long-term average for the 

previous 28 years (1972–99) in figure 23. The nitrate 

loads in 2000 were generally higher than the long-term 

average, while the 2001 loads were usually close to the 

average. Loads of total nitrogen in 2000 were slightly 

above the long-term average and 2001 loads were 

slightly below the average. Except for March 2000, 

loads of total phosphorus in 2000 and 2001 were below 

the long-term average. The average loads of nitrate, 

total nitrogen, and total phosphorus were generally 

lower during June through November than during the 

rest of the year (fig. 21). 

Upstream-to-Downstream Loads in the San 

Joaquin River, 1986–88

The loads of nitrate, total nitrogen, and total 

phosphorus in the San Joaquin River were evaluated for 

the 1986–88 water years. These years were chosen 

because of the abundance of data available from a 

USGS monitoring program at that time. Eleven sites 

were monitored at least monthly during the three years. 

This provided enough data for the ESTIMATOR 

program to calculate loads for the eleven sites. The 

annual results of loads for the sites and summaries by 

five reaches of the San Joaquin River were presented in 

Kratzer and Shelton (1998); monthly results are 

presented here. Water year 1986 was classified as a wet 

year with an index value of 4.31 million acre-feet; 

water years 1987 and 1988 were both critically dry 

years with index values of 1.86 and 1.48 million acrefeet, respectively. The average index value for the three 

years, 2.55 million acre-feet, is well below the average 

index value for the 1972–2001 period of 3.33 million 

acre-feet. Thus, the 1986–88 period was relatively drier 

than normal overall. The annual loads of nitrate, total 

nitrogen, and total phosphorus in 1986 were in the 

highest third of loads for the 1972–2001 period; loads 

for 1987 were in the middle third; and loads for 1988 

were in the lowest third.

Nitrate loads in the San Joaquin River for 

1986–88 are shown in figures 24A–E by river reach. 

Loads were calculated for six mainstem sites: SJR near 

Stevinson (site 1; fig. 2), SJR at Fremont Ford Bridge 

(site 3; fig. 2), SJR near Newman (site 10; fig. 2), SJR 

near Patterson (site 15; fig. 2), SJR at Maze Road (site 

24; fig. 2), and SJR near Vernalis (site 27; fig. 2). These 

mainstem sites allow us to look at loads in five reaches 

of the San Joaquin River and evaluate unaccounted 

loads. Positive unaccounted loads are inputs in the 

reach that are not accounted for by the site(s) that have 

calculated loads. As of the late 1980s, there were at 

least 104 agricultural discharges to the San Joaquin 

River in the study area (James and others, 1989). 

Negative unaccounted loads are outputs from the San 

Joaquin River in the reach. As of the late 1980s, there 

were at least 86 agricultural diversions from the San 

Joaquin River in the study area (James and others, 

1989). The two largest diversions (Patterson Irrigation 

District and West Stanislaus Irrigation District, sites 16 

and 19; fig. 2) accounted for about 40 percent of the 

total diversions in the study area (Kratzer and others, 

1987; Quinn and Tulloch, 2002).

Salt Slough and Mud Slough accounted for most 

of the nitrate inputs to the San Joaquin River between 

Stevinson and Newman (fig. 24). The occasionally 

significant negative unaccounted load in February 

through April is probably more a function of load 

calculation uncertainty than diversions from the San 

Joaquin River; diversions are relatively low at this time 

of year. The mainstem San Joaquin River sites at 

Fremont Ford Bridge, Newman, Patterson, and Maze 

Road had seasonal patterns of nitrate loads with 

maximum during spring and minimum during fall. The 

unaccounted loads from Newman to Maze Road are all 

positive, indicating that inputs to the San Joaquin River 

exceeded diversions, despite the two large diversions in 

this reach—Patterson Irrigation District and West 

Stanislaus Irrigation District. The inputs from the three 

major east-side tributaries were generally small relative 

to loads in the San Joaquin River. The most significant 

unaccounted nitrate inputs in this reach are probably 

Orestimba Creek, Spanish Grant Drain, Harding Drain, 

Del Puerto Creek, Hospital Creek, the City of Modesto 

wastewater treatment plant discharge, ground-water 

accretions, and several smaller agricultural discharges. 

Harding Drain includes the discharge from the City of 

Turlock wastewater treatment plant. The Modesto plant 

only discharges surface water to the San Joaquin River 

during the winter months.
42 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

20,000

0

40,000

60,000

80,000

100,000

120,000

140,000

160,000

180,000

October

November

December

January

February

March

April

May

June

July

August

September

Total phosphorus load,

in kilograms per month as P

Monthly Total Phosphorus Loads at San Joaquin River near Vernalis (site 27) C

Water Years 1972–2001

0

200,000

400,000

600,000

800,000

1,000,000

1,200,000

1,400,000

Total nitrogen load,

in kilograms per month as N

Monthly Total Nitrogen Loads at San Joaquin River near Vernalis (site 27) B

Water Years 1972–2001

0

100,000

200,000

300,000

400,000

500,000

600,000

700,000

Nitrate load,

in kilograms per month as N

Average of Water Years 1972–99

Water Year 2000

Water Year 2001

Monthly Nitrate Loads at San Joaquin River near Vernalis (site 27) A

Water Years 1972–2001

Figure 23. Monthly loads of nitrate, total nitrogen, and total phosphorus at San Joaquin River near Vernalis, California, for 1972–99 (average), 2000, and 

2001. 

(A) Nitrate, (B) Total nitrogen, (C) Total phosphorus. N, nitrogen; P, phosphorus.
Historical Nutrient Loads in the San Joaquin Basin 43

300,000

200,000

100,000

200,000

100,000

0

300,000

0

300,000

125,000

-125,000

0

0

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

Nitrate load, in kilograms per month as N

San Joaquin River near Stevinson (site 1)

Salt Slough near Stevinson (site 2)

San Joaquin River at Fremont Ford Bridge (site 3)

Unaccountable Load

A

June–November

December–May

200,000

100,000

Figure 24. Monthly loads of nitrate at sites in the San Joaquin River, California, upstream to 

downstream for water years 1986–88. 

(A) Stevinson (site 1) to Fremont Ford Bridge (site 3). 
44 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

325,000

162,500

325,000

325,000

325,000

200,000

-200,000

0

0

0

0

0

San Joaquin River at Fremont Ford Bridge (site 3)

Mud Slough near Gustine (site 5)

Merced River near Stevinson (site 8)

San Joaquin River near Newman (site 10)

Unaccountable Load

B

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

Nitrate load, in kilograms per month as N

162,500

162,500

162,500

Figure 24.—Continued. (B) Fremont Ford Bridge (site 3) to Newman (site 10).
Historical Nutrient Loads in the San Joaquin Basin 45

325,000

100,000

0

325,000

162,500

0

0

Nitrate load, in kilograms per month as N

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

San Joaquin River near Newman (site 10)

C

San Joaquin River near Patterson (site 15)

Unaccountable Load

June–November

December–May

162,500

50,000

–50,000

–100,000

Figure 24.—Continued. (C) Newman (site 10) to Patterson (site 15).
46 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

500,000

0

500,000

0

500,000

0

0

160,000

Nitrate load, in kilograms per month as N

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

San Joaquin River near Patterson (site 15)

Tuolumne River at Modesto (site 21)

San Joaquin River at Maze Road (site 24)

Unaccountable Load

D

June–November

December–May

–80,000

–160,000

250,000

250,000

250,000

80,000

Figure 24.—Continued. (D) Patterson (site 15) to Maze Road (site 24).
Historical Nutrient Loads in the San Joaquin Basin 47

550,000

550,000

0

0

550,000

110,000

0

0

Nitrate load, in kilograms per month as N

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

San Joaquin River at Maze Road (site 24)

Stanislaus River at Ripon (site 25)

San Joaquin River near Vernalis (site 27)

Unaccountable Load

E

June–November

December–May

275,000

275,000

275,000

55,000

–55,000

–110,000

Figure 24.—Continued. (E) Maze Road (site 24) to Vernalis (site 27). N, nitrogen.
48 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Loads of total nitrogen in the San Joaquin River 

for 1986–88 are shown in figures 25A-E by river reach. 

The load of nitrate in the San Joaquin River accounted 

for about 56 percent of the load of total nitrogen. Thus, 

it is not surprising that the pattern of loads of total 

nitrogen is similar to the pattern of loads of nitrate. 

However, although the loads of total nitrogen have the 

same seasonal pattern as nitrate, there is a greater range 

between the minimum and maximum loads, especially 

during a wet year (1986). This range is due to 

proportionately higher particulate nitrogen carried with 

higher streamflows. Thus, although the SJR near 

Stevinson site had a relatively small load of nitrate 

during the exceptionally wet spring of 1986, the load of 

total nitrogen was relatively large. 

Loads of total phosphorus in the San Joaquin 

River for 1986–88 are shown in figures 26A-E by river 

reach. The pattern of loads of total phosphorus is 

similar to total nitrogen, except for the larger variation 

between water years and the reduced significance of 

Salt and Mud Sloughs. Because the total phosphorus in 

the San Joaquin River is about 56-percent particulate, it 

is very much affected by higher streamflows. This is 

reflected in the great difference between the loads in 

the wet year (1986) and the two dry years (1987–88). 

Also, because much of the source of nutrient load in the 

sloughs is tile drainage, and these tile drains have 

relatively low phosphorus concentrations compared 

with those of nitrogen, the contribution of total 

phosphorus from the sloughs is relatively low 

compared with the contributions of loads of nitrate and 

total nitrogen (Kratzer and Shelton, 1998).
Historical Nutrient Loads in the San Joaquin Basin 49

700,000

350,000

0

0

700,000

0

700,000

150,000

0

Total nitrogen load, in kilograms per month as N

San Joaquin River near Stevinson (site 1)

Salt Slough near Stevinson (site 2)

San Joaquin River at Fremont Ford Bridge (site 3)

Unaccountable Load

A

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

350,000

350,000

75,000

–75,000

–150,000

Figure 25. Monthly loads of total nitrogen at sites in the San Joaquin River, California, upstream to 

downstream for water years 1986–88. 

(A) Stevinson (site 1) to Fremont Ford Bridge (site 3). 
50 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

1,100,000

550,000

0

1,100,000

0

1,100,000

0

1,100,000

170,000

0

0

Total nitrogen load, in kilograms per month as N

San Joaquin River at Fremont Ford Bridge (site 3)

Mud Slough near Gustine (site 5)

Merced River near Stevinson (site 8)

San Joaquin River near Newman (site 10)

Unaccountable Load

B

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

550,000

550,000

550,000

85,000

–85,000

–170,000

Figure 25.—Continued. (B) Fremont Ford Bridge (site 3) to Newman (site 10).
Historical Nutrient Loads in the San Joaquin Basin 51

Total nitrogen load, in kilograms per month as N

San Joaquin River near Newman (site 10)

San Joaquin River near Patterson (site 15)

Unaccountable Load

C

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

–250,000

550,000

550,000

250,000

0

0

1,100,000

0

1,100,000

125,000

–125,000

Figure 25.—Continued. (C) Newman (site 10) to Patterson (site 15). 
52 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

1,700,000

0

1,700,000

0

1,700,000

900,000

0

0

Total nitrogen load, in kilograms per month as N

San Joaquin River near Patterson (site 15)

Tuolumne River at Modesto (site 21)

San Joaquin River at Maze Road (site 24)

Unaccountable Load

D

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

–900,000

850,000

850,000

850,000

–450,000

450,000

Figure 25.—Continued. (D) Patterson (site 15) to Maze Road (site 24).
Historical Nutrient Loads in the San Joaquin Basin 53

Total nitrogen load, in kilograms per month as N

1,700,000

850,000

0

1,700,000

0

1,700,000

900,000

0

0

San Joaquin River at Maze Road (site 24)

San Joaquin River near Vernalis (site 27)

Stanislaus River at Ripon (site 25)

Unaccountable Load

E

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

850,000

850,000

450,000

–450,000

–900,000

Figure 25.—Continued. (E) Maze Road (site 24) to Vernalis (site 27). N, nitrogen.
54 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

140,000

70,000

0

140,000

70,000

0

140,000

70,000

45,000

0

0

Total phosphorus load, in kilograms per month as P

San Joaquin River near Stevinson (site 1)

Salt Slough near Stevinson (site 2)

San Joaquin River at Fremont Ford Bridge (site 3)

Unaccountable Load

A

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

22,500

–22,500

–45,000

Figure 26. Monthly loads of total phosphorus at sites in the San Joaquin River, California, upstream to 

downstream for water years 1986–88. 

(A) Stevinson (site 1) to Fremont Ford Bridge (site 3). 
Historical Nutrient Loads in the San Joaquin Basin 55

Total phosphorus load, in kilograms per month as P

200,000

100,000

0

0

0

0

0

200,000

200,000

200,000

40,000

San Joaquin River at Fremont Ford Bridge (site 3)

Mud Slough near Gustine (site 5)

Merced River near Stevinson (site 8)

San Joaquin River near Newman (site 10)

Unaccountable Load

B

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

100,000

100,000

100,000

20,000

–20,000

–40,000

Figure 26.—Continued. (B) Fremont Ford Bridge (site 3) to Newman (site 10). 
56 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001 Total phosphorus load, in kilograms per month as P

200,000

100,000

0

200,000

35,000

-35,000

0

0

San Joaquin River near Newman (site 10)

San Joaquin River near Patterson (site 15)

Unaccountable Load

C

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

100,000

Figure 26.—Continued. (C) Newman (site 10) to Patterson (site 15).
Historical Nutrient Loads in the San Joaquin Basin 57

Total phosphorus load, in kilograms per month as P

325,000

162,500

0

325,000

0

325,000

80,000

0

0

San Joaquin River near Patterson (site 15)

Tuolumne River at Modesto (site 21)

San Joaquin River at Maze Road (site 24)

Unaccountable Load

D

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

162,500

162,500

40,000

–40,000

–80,000

Figure 26.—Continued. (D) Patterson (site 15) to Maze Road (site 24).
58 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001 Total phosphorus load, in kilograms per month as P

325,000

162,500

0

325,000

325,000

325,000

0

0

San Joaquin River at Maze Road (site 24)

Stanislaus River at Ripon (site 25)

San Joaquin River near Vernalis (site 27)

Unaccountable Load

E

June–November

December–May

0ct.

1985

Feb.

1986

June

1986

Oct.

1986

Feb.

1987

June

1987

Oct.

1987

Feb.

1988

June

1988

Month and year

162,500

162,500

162,500

0

–162,500

–325,000

Figure 26.—Continued. (E) Maze Road (site 24) to Vernalis (site 27). P, phosphorus.
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 59

LOADING RATES OF NUTRIENTS, ORGANIC 

CARBON, AND CHLOROPHYLL-A

Instantaneous loading rates of nutrients, organic 

carbon, and chlorophyll-a were calculated for each 

sample that had a streamflow measurement. For 

samples having concentrations less than the laboratory 

reporting level, the concentration was set to half this 

level for the calculation of an instantaneous loading 

rate. Instead of using more robust methods to fit values 

to these samples, a simple substitution of half the 

reporting level produces less bias in the summary 

statistics for concentration at a site than the alternatives 

of zero or the reporting level (Helsel, 1990). It was 

beyond the scope of this study to evaluate the 

possibility of using more robust methods. The 

instantaneous loading rate for a sample was calculated 

as: 

Loading rate (kg/d) = 2.447 × Streamflow (ft3/s) ×

Concentration (mg/L).

As with concentrations, the points representing 

instantaneous loading rates on figures were connected 

for sites to help show the trends in loading rates. This 

does not imply continuous trends in loading rates. 

Also, as for the plots of concentrations, streamflow for 

SJR near Vernalis is shown in each plot of loading rates 

to indicate streamflow variations in the entire basin. 

For streamflow at a given site, refer to figures 5 to 8.

Loading rates in tributaries are presented as a 

percent of the Vernalis loading rate. Because of the 

many diversions from the San Joaquin River during the 

irrigation season (primarily March through 

September), the loading rates are not simply presented 

as the loading rate divided by the Vernalis loading rate. 

To account for the removal of some of the load from 

the San Joaquin River before it reaches Vernalis, the 

following correction was applied to the loading rate in 

the tributary:

Percentage of Vernalis loading rate = 100 × [(tributary 

loading rate × load factor)/Vernalis loading rate]

where, 

Thus, tributaries farther upstream have a 

proportionately lower impact on Vernalis loads than 

tributaries farther downstream. The diversions are 

based on values used in DWR's DSM2-SJR model for 

river reaches in a prototypical dry water year (1985) 

(Quinn and Tulloch, 2002), with values for the same 

water year (1985) for specific diversions between 

reaches (Kratzer and others, 1987). The 1985 

conditions are more representative of water years 2000 

and 2001 than the alternatives of 1989 (critically dry) 

or 1986 (wet).

Nitrogen 

Because nitrate is the dominant form of nitrogen 

in the San Joaquin River system, it explains most of the 

trends in nitrogen. Nitrogen loading rates at the SJR 

upstream of Merced River generally decreased 

throughout the sampling period, except for a slight 

increase in October (for 2000 and 2001) and November 

(for 2001) (figs. 27 and 28). Loading rates at SJR near 

Crows Landing, Patterson, and Laird Park decreased in 

September for both 2000 and 2001. This reduction 

corresponded to the end of irrigation season and 

reduced agricultural drainage from Mud and Salt 

Sloughs and other agricultural drainage inputs. The 

loading rates at SJR near Crows Landing and at Laird 

Park increased in October 2001 with the VAMP-related 

reservoir releases on the Merced River and wetland 

releases into Mud Slough. Loading rates at Maze Road 

and SJR near Vernalis were relatively stable throughout 

the sampling period of both years.

load factor = (Vernalis streamflow - diversions from 

SJR downstream from tributary)/Vernalis 

streamflow.
60 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001 Total nitrogen loading rate, in kilograms per day as N

16,000

14,000

12,000

10,000

8,000

6,000

4,000

2,000

0

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

Inorganic nitrogen loading rate,

in kilograms per day as N

0

16,000

14,000

12,000

10,000

8,000

6,000

4,000

2,000

0

16,000

14,000

12,000

10,000

8,000

6,000

4,000

2,000

Nitrate loading rate,

in kilograms per day as N

Streamflow at San Joaquin River near Vernalis

A

B

C

4,000

3,000

2,000

1,000

0

Cubic feet per second

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 27. Instantaneous loading rates of nitrate, inorganic nitrogen, and total nitrogen at San Joaquin River sites from 

upstream to downstream for July through October 2000, with streamflow at Vernalis, California. 

(A) Nitrate, (B) Inorganic nitrogen, and (C) Total nitrogen. N, nitrogen.
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 61

Total nitrogen loading rate,

in kilograms per day as N

0

16,000

14,000

12,000

10,000

8,000

6,000

4,000

2,000

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

Inorganic nitrogen loading rate,

in kilograms per day as N

0

16,000

14,000

12,000

10,000

8,000

6,000

4,000

2,000

B

C

Nitrate loading rate,

in kilograms per day as N

A

0

16,000

14,000

12,000

10,000

8,000

6,000

4,000

2,000

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Streamflow at San Joaquin River near Vernalis

4,000

3,000

2,000

1,000

0

Cubic feet per second

Figure 28. Instantaneous loading rates of nitrate, inorganic nitrogen, and total nitrogen at San Joaquin River sites from 

upstream to downstream for June through November 2001, with streamflow at Vernalis, California. 

(A) Nitrate, (B) Inorganic nitrogen, and (C) Total nitrogen. N, nitrogen.
62 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Much of the upstream-to-downstream trends in 

loading rates can be explained simply by the increase in 

streamflows from upstream to downstream (fig. 12). 

SJR near Stevinson had very low loading rates of 

nitrogen in both 2000 and 2001 sampling periods, 

despite some very high concentrations. The inputs from 

Mud and Salt Sloughs increased the loading rates from 

SJR near Stevinson to upstream of the Merced River. 

The input of the Merced River, as well as some small 

agricultural drains, increased loading rates at SJR near 

Crows Landing. Loading rates at SJR near Patterson 

and at Laird Park were greater than those at Crows 

Landing because of inputs from Harding Drain and 

agricultural drains. This increase was greatly affected 

by diversions, especially the Patterson Irrigation 

District diversion between Patterson and Laird Park. 

The trend in loading rates from Laird Park to SJR near 

Vernalis was very dependent upon diversions, 

especially the West Stanislaus Irrigation District. 

During that part of the sampling period that took place 

during the irrigation season, the diversions were often 

equal to or greater than discharges in this reach. Thus, 

sometimes the loading rate at SJR near Vernalis was 

actually less than that at Laird Park, despite inputs from 

the Tuolumne and Stanislaus Rivers. This situation 

changed in September when diversions were reduced, 

and the difference in loading rates at SJR near Vernalis 

versus loading rates at Laird Park reflected only the 

inputs between the sites.

The significance of tributary inputs as a 

percentage of the Vernalis loading rate is shown for 

2000 and 2001 in figures 29 and 30. The most 

significant tributary sources of nitrogen were the 

Tuolumne River (13 to 23 percent of Vernalis), Harding 

Drain (5 to 27 percent), Mud Slough (3 to 20 percent), 

Salt Slough (1 to 17 percent), and the Merced River 

(3 to 13 percent). The Stanislaus River and Westport 

Drain also exceeded 10 percent of the Vernalis loading 

rate once each.

Phosphorus 

Loading rates for orthophosphate and total 

phosphorus were fairly stable in 2000 and 2001 at SJR 

near Crows Landing and upstream until the wetlands 

releases into Mud Slough in October and November 

(figs. 31 and 32). Loading rates for orthophosphate at 

San Joaquin River sites downstream of Crows Landing 

were fairly stable in 2000 except for the rise in October. 

Loading rates for total phosphorus in 2000 at 

downstream sites were highly variable before the rise 

in October. Both orthophosphate and total phosphorus 

loading rates at downstream sites (except at Laird Park) 

were fairly stable in 2001 until the October and 

November rise. 

As with nitrogen, SJR near Stevinson had very 

small loading rates of phosphorus. The trends in 

loading rates near Crows Landing are mostly explained 

by loading rates upstream of Merced River from Mud 

and Salt Sloughs. Phosphorus loading rates increased 

greatly from Crows Landing to Patterson with inputs 

from Harding Drain. Phosphorus loading rates at Laird 

Park were greater than near Patterson in 2000, except 

for orthophosphate in July and August. In 2001, 

phosphorus loading rates at Laird Park were less than 

near Patterson, except in June. These loading rates 

generally corresponded to the streamflows at the two 

sites (fig. 12). With lower streamflows in 2001, 

diversions from the San Joaquin River removed a 

greater proportion of the upstream load. Using the 

methodology described earlier in this section, the load 

factors during July through September 2000 for Laird 

Park were 0.76 to 0.94 compared with 0.68 to 0.89 in 

2001. Loading rates for orthophosphate at SJR near 

Vernalis frequently were less than those at upstream 

sites, whereas loading rates for total phosphorus near 

Vernalis were almost always greater than those at 

upstream sites. These occurrences are partly a function 

of the particulate fraction of the phosphorus from the 

Tuolumne and Stanislaus Rivers (average 0.35) versus 

the particulate fraction at Laird Park (average 0.54).
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 63

C

20

10

0

25

5

15

30

Total nitrogen loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

Inorganic nitrogen loading rate

as a percentage of the rate at

San Joaquin River near Vernalis 20

25

15

5

10

0

30

B

20

25

15

5

10

0

30

Nitrate loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

A

4,000

3,000

2,000

1,000

Cubic feet per second

0

Streamflow at San Joaquin River near Vernalis

Salt Slough

Mud Slough

Merced River

Tuolumne River

Stanislaus River

Figure 29. Instantaneous loading rates of nitrate, inorganic nitrogen, and total nitrogen in tributaries from upstream to 

downstream as a percentage of Vernalis loading rates for July through October 2000, with streamflow at Vernalis, California.

(A) Nitrate, (B) Inorganic nitrogen, and (C) Total nitrogen.
64 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

20

10

0

25

5

15

30

Total nitrogen loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

C

Inorganic nitrogen loading rate

as a percentage of the rate at

San Joaquin River near Vernalis 20

10

0

25

5

15

30

B

20

10

0

25

5

15

30

Nitrate loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

A

Streamflow at San Joaquin River near Vernalis 4,000

3,000

2,000

1,000

0

Cubic feet per second

Salt Slough

Mud Slough

Merced River

Orestimba Creek

Spanish Grant Drain

Harding Drain

Westport Drain

Tuolumne River

Hospital Creek

Stanislaus River

Figure 30. Instantaneous loading rates of nitrate, inorganic nitrogen, and total nitrogen in tributaries from upstream to 

downstream as a percentage of Vernalis loading rates for June through November 2001, with streamflow at Vernalis, 

California.

(A) Nitrate, (B) Inorganic nitrogen, and (C) Total nitrogen.
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 65

Streamflow at San Joaquin River near Vernalis

A

B

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

4,000

3,000

2,000

1,000

0

Cubic feet per second Orthophosphate loading rate, in kilograms per day as P

0

1,800

1,600

1,400

1,200

1,000

800

600

400

200

Total phosphorus loading rate, in kilograms per day as P

0

1,800

1,600

1,400

1,200

1,000

800

600

400

200

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

Figure 31. Instantaneous loading rates of orthophosphate and total phosphorus at San Joaquin River sites from 

upstream to downstream for July through October 2000, with streamflow at Vernalis, California.

(A) Orthophosphate, (B) Total phosphorus. P, phosphorus.
66 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

0

100

200

300

400

500

600

700

Orthophosphate loading rate, in kilograms per day as P

0

1,400

1,200

1,000

800

600

400

200

Total phosphorus loading rate, in kilograms per day as P

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

Streamflow at San Joaquin River near Vernalis

A

B

4,000

3,000

2,000

1,000

0

Cubic feet per second

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 32. Instantaneous loading rates of orthophosphate and total phosphorus at San Joaquin River sites from 

upstream to downstream for June through November 2001, with streamflow at Vernalis, California. 

(A) Orthophosphate, (B) Total phosphorus. P, phosphorus. 
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 67

The significance of tributary inputs as a 

percentage of the Vernalis loading rate for 2000 and 

2001 is shown in figures 33 and 34. The most 

significant sources of phosphorus were Harding Drain 

(8 to 76 percent of the Vernalis loading rate), Tuolumne 

River (9 to 51 percent), Mud Slough (0 to 60 percent), 

Stanislaus River (5 to 22 percent), and Salt Slough (1 to 

21 percent). Mud Slough was the main source of 

phosphorus in the San Joaquin River in October both 

years (60 and 36 percent of orthophosphate loading 

rate) during wetland releases. Hospital Creek, which 

had a high suspended sediment concentration 

(3,460 mg/L), contributed 14 percent of the total 

phosphorus loading rate in June. Orestimba Creek, 

Spanish Grant Drain, Westport Drain, and the Merced 

River were always less than 10 percent of the 

phosphorus loading rate to the San Joaquin River. The 

total percentage of the Vernalis loading rate for the 

sampled sites in early September was over 150 percent, 

half coming from Harding Drain. This points out the 

nonconservative nature of orthophosphate. Much of 

this orthophosphate is undoubtedly incorporated into 

phytoplankton before reaching Vernalis.

Organic Carbon 

The DOC loading rates at most San Joaquin 

River sites were fairly stable with a slight decrease 

from June and July through September (figs. 35 and 

36). All San Joaquin River sites except Stevinson 

(site 1) increased in October and November with 

wetland releases and VAMP-related reservoir releases. 

The SOC loading rates at most San Joaquin River sites 

fluctuated only slightly during the sampling period, 

except for Laird Park in 2000 and Vernalis in 2001. 

Two SOC concentrations were responsible for the 

sharp peaks in loading rates: July 25, 2000 at Laird 

Park and August 9, 2001 near Vernalis. SOC is one of 

the more variable measurements and these values could 

be somewhat questionable. The median variability for 

10 split replicates analyzed at NWQL was 14.4 percent, 

with a range of 0.0 to 86.4 percent (table 3). The July 

25 sample at Laird Park had a concentration of 

3.6 mg/L with a split replicate concentration of 3.0 

mg/L.

As for nutrients, DOC loading rates at SJR near 

Stevinson were very low. The sloughs had a relatively 

large contribution to the DOC loading rates in the San 

Joaquin River, especially in October and November. In 

2000, the DOC loading rates at SJR near Patterson 

were similar to the loading rates downstream at Laird 

Park. In 2001, the loading rates at SJR near Patterson 

were considerably greater than the loading rates at 

Laird Park. This was similar to streamflows (fig. 12) 

and was also a function of greater diversion impacts in 

2001 with lower streamflows. DOC loading rates at 

SJR near Vernalis were similar to and usually slightly 

greater than at the Maze Road site. SOC loading rates 

at SJR near Vernalis were similar to Laird Park in 2000, 

but were considerably greater in 2001.

The most significant tributary sources of DOC in 

2000 and 2001 were Salt Slough (4 to 45 percent of the 

Vernalis loading rate), Mud Slough (5 to 36 percent), 

Tuolumne River (12 to 31 percent), and Stanislaus 

River (6 to 24 percent) (figs. 37 and 38). Salt Slough 

was an important source early in the sampling period 

and Mud Slough late in the period. The Merced River 

was 28 percent of the Vernalis DOC loading rate for the 

mid-October sampling during the VAMP-related 

reservoir releases on the Merced. The major tributaries 

do not have SOC data, so only minor tributary sources 

are shown in figure 38. Hospital Creek contributed 

about 13 percent of the Vernalis SOC loading rate in 

June when the creek had a suspended sediment 

concentration of 3,460 mg/L. Mud Slough contributed 

about 17 percent of the SOC loading rate during 

wetland releases in October.
68 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

10

0

15

5

20

25

Total phosphorus loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

20

10

0

30

40

50

60

70

Orthophosphate loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

A

B

Streamflow at San Joaquin River near Vernalis

4,000

3,000

2,000

1,000

0

Cubic feet per second

Mud Slough

Merced River

Tuolumne River

Stanislaus River

Salt Slough

Figure 33. Instantaneous loading rates of orthophosphate and total phosphorus in tributaries from upstream to downstream as 

a percentage of Vernalis loading rates for July through October 2000, with streamflow at Vernalis, California. 

(A) Orthophosphate, (B) Total phosphorus.
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 69

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

Total phosphorus loading rate

as a percentage of the rate at

San Joaquin River near Vernalis 20

10

0

25

5

15

30

35

B

90

80

70

60

50

40

30

20

10

0

Orthophosphate loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

A

4,000

3,000

2,000

1,000

0

Cubic feet per second

Streamflow at San Joaquin River near Vernalis

Mud Slough

Merced River

Orestimba Creek

Spanish Grant Drain

Harding Drain

Westport Drain

Tuolumne River

Hospital Creek

Stanislaus River

Salt Slough

Figure 34. Instantaneous loading rates of orthophosphate and total phosphorus in tributaries from upstream to downstream 

as a percentage of Vernalis loading rates for June through November 2001, with streamflow at Vernalis, California. 

(A) Orthophosphate, (B) Total phosphorus.
70 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

9,000

8,000

7,000

6,000

5,000

4,000

3,000

2,000

1,000

0

Suspended organic carbon loading rate,

in kilograms per day as C

B

25,000

15,000

5,000

0

20,000

10,000

Dissolved organic carbon loading rate,

in kilograms per day as C

A

Streamflow at San Joaquin River near Vernalis 4,000

3,000

2,000

1,000

0

Cubic feet per second

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 35. Instantaneous loading rates of dissolved organic carbon and suspended organic carbon at San Joaquin River sites 

from upstream to downstream for July through October 2000, with streamflow at Vernalis, California.

(A) Dissolved organic carbon (B) Suspended organic carbon. C, carbon.
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 71

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

25,000

5,000

0

15,000

10,000

20,000

Suspended organic carbon loading rate,

in kilograms per day as C

25,000

5,000

0

15,000

10,000

20,000

A

B

Dissolved organic carbon loading rate,

in kilograms per day as C

4,000

3,000

2,000

1,000

0

Cubic feet per second

Streamflow at San Joaquin River near Vernalis

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 36. Instantaneous loading rates of dissolved organic carbon and suspended organic carbon at San Joaquin River sites 

from upstream to downstream for June through November 2001, with streamflow at Vernalis, California. 

(A) Dissolved organic carbon, (B) Suspended organic carbon. C, carbon.
72 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

20

0

10

25

15

5

30

35

40

45

50

Streamflow at San Joaquin River near Vernalis

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

Mud Slough

Merced River

Tuolumne River

Stanislaus River

Salt Slough

4,000

3,000

2,000

1,000

0

Cubic feet per second Dissolved organic carbon loading rate as a percentage of

the rate at San Joaquin River near Vernalis

Figure 37. Instantaneous loading rates of dissolved organic carbon in tributaries from upstream to downstream as a 

percentage of Vernalis loading rates for July through October 2000, with streamflow at Vernalis, California.
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 73

10

12

14

16

18

0

2

4

6

8

Suspended organic carbon

loading rate as a percentage of the rate at

San Joaquin River near Vernalis

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

B

A 40

35

30

25

15

5

0

20

10

Dissolved organic carbon

loading rate as a percentage of the rate at

San Joaquin River neaer Vernalis

Streamflow at San Joaquin River near Vernalis

4,000

3,000

2,000

1,000

0

Cubic feet per second

Mud Slough

Merced River

Orestimba Creek

Spanish Grant Drain

Harding Drain

Westport Drain

Tuolumne River

Hospital Creek

Stanislaus River

Salt Slough

Figure 38. Instantaneous loading rates of dissolved organic carbon and suspended organic carbon in tributaries from 

upstream to downstream as a percentage of Vernalis loading rates for June through November 2001, with streamflow at 

Vernalis, California.

(A) Dissolved organic carbon, (B) Suspended organic carbon.
74 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Chlorophyll-a and Pheophytin-a

Chlorophyll-a loading rates declined at all San 

Joaquin River sites between August 9 and August 23 in 

2000, especially at SJR near Vernalis (fig. 39). 

Reservoir releases on the Tuolumne River that 

increased low chlorophyll-a streamflows from 500 to 

2,000 ft3/s during this period could have flushed 

chlorophyll-a from San Joaquin River sites 

downstream of the Tuolumne, Maze Road and SJR 

near Vernalis. However, loading rates also declined at 

San Joaquin River sites upstream of the Tuolumne 

River. Upstream loading rates and concentrations 

especially declined near Stevinson, where 

concentrations dropped from 377 to 76 μg/L. 

Concentrations near Crows Landing dropped from 58 

to 17 μg/L. Loading rates and concentrations declined 

steadily from the beginning of the sampling at Laird 

Park. Chlorophyll-a loading rates were relatively stable 

after the August decline.

In 2001, there was a general increase in 

chlorophyll-a loading rates at San Joaquin River sites 

from June to a maximum in July through early 

September, then a decline in mid-September (fig. 40). 

This decline in chlorophyll-a loading rates in the San 

Joaquin River occurred about a month later in the year 

than in 2000. Between September 5 and 19 in 2001, 

chlorophyll-a concentrations at Laird Park dropped 

from 59 to 19 μg/L and from 73 to 14 μg/L at SJR near 

Vernalis. As in 2000, chlorophyll-a loading rates were 

relatively low and stable after the decline. Pheophytina loading rates in 2001 were similar to chlorophyll-a

loading rates, except that the peaks and subsequent 

declines occurred about two to four weeks earlier at 

Laird Park and two to four weeks later near Crows 

Landing.

The very high concentrations of chlorophyll-a at 

SJR near Stevinson did result in significant loading 

rates to the San Joaquin River upstream of Merced 

River. Loading rates generally increased in downstream 

order, except that loading rates at Patterson exceeded 

those at Laird Park in June and July of 2001, and 

loading rates at Maze Road occasionally exceeded 

those at Vernalis. However, like SOC, the chlorophyll-a

measurements were relatively variable. So, interpreting 

trends in chlorophyll-a concentrations or loading rates 

is more problematic than with nutrients or DOC. 

Pheophytin-a loading rates increased in downstream 

order.

The most significant tributary sources of 

chlorophyll-a in 2000 and 2001 were Mud Slough (1 to 

15 percent of Vernalis), the Stanislaus River (1 to 

13 percent), and the Tuolumne River (1 to 10 percent) 

(figs. 41 and 42). A late September sample from Mud 

Slough contributed about 10 percent of the pheophytina loading rate at SJR near Vernalis. Generally, 

compared with nutrients and DOC, tributaries were 

minor sources of chlorophyll-a and pheophytin-a

loading rates. The chlorophyll-a in the San Joaquin 

River appeared to be produced primarily in the river. 
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 75

Streamflow at San Joaquin River near Vernalis 4,000

3,000

2,000

1,000

0

250

150

50

0

200

100

Cubic feet per second Chlorophyll-a loading rate, in kilograms per day

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 39. Instantaneous loading rates of chlorophyll-a at San Joaquin River sites from upstream to downstream for 

July through October 2000, with streamflow at Vernalis, California.
76 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

0

120

100

80

60

40

20

Pheophytin-a loading rate, in kilograms per day

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

B

250

150

50

200

100

0

Chlorophyll-a loading rate, in kilograms per day

A

4,000

3,000

2,000

1,000

0

Cubic feet per second

Streamflow at San Joaquin River near Vernalis

San Joaquin River near Stevinson

San Joaquin River upstream of Merced River

San Joaquin River near Crows Landing

San Joaquin River near Patterson

San Joaquin River at Laird Park

San Joaquin River at Maze Road

San Joaquin River near Vernalis

Figure 40. Instantaneous loading rates of chlorophyll-a and pheophytin-a at San Joaquin River sites, from upstream 

to downstream for June through November 2001, with streamflow at Vernalis, California. 

(A) Chlorophyll-a, (B) Pheophytin-a.
Loading Rates of Nutrients, Organic Carbon, and Chlorophyll-a 77

4,000

3,000

2,000

1,000

0

12

10

8

6

4

2

0

Cubic feet per second Chlorophyll-a loading rate as a percentage of the

rate at San Joaquin River near Vernalis

Streamflow at San Joaquin River near Vernalis

Mud Slough

Merced River

Tuolumne River

Stanislaus River

Salt Slough

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2000

Figure 41. Instantaneous loading rates of chlorophyll-a in tributaries from upstream to downstream as a percentage of 

Vernalis loading rates for July through October 2000, with streamflow at Vernalis, California.
78 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

0

1

2

3

4

5

6

7

8

9

10

Pheophytin-a loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

6/1 6/16 7/1 7/16 7/31 8/15 8/30 9/14 9/29 10/14 10/29 11/13 11/28

2001

B

16

14

12

10

8

6

4

2

0

Chlorophyll-a loading rate

as a percentage of the rate at

San Joaquin River near Vernalis

A

Streamflow at San Joaquin River near Vernalis

4,000

3,000

2,000

1,000

0

Cubic feet per second

Mud Slough

Merced River

Orestimba Creek

Spanish Grant Drain

Harding Drain

Westport Drain

Tuolumne River

Hospital Creek

Stanislaus River

Salt Slough

Figure 42. Instantaneous loading rates of chlorophyll-a and pheophytin-a in tributaries from upstream to downstream as a 

percentage of Vernalis loading rates for June through November 2001, with streamflow at Vernalis, California. 

(A) Chlorophyll-a, (B) Pheophytin-a.
Isotopes 79

ISOTOPES

Different sources of nutrients often have 

distinctive isotope ratios. Processes such as nitrification 

and denitrification can alter the isotopic composition of 

reactants and products. The isotopic signatures of both 

source and cycling mechanisms are incorporated in 

algae and other plants. Under favorable circumstances, 

both the source and cycling mechanisms of nutrients 

can be identified with the help of isotopic analysis. In 

this study, elemental and isotopes of nitrogen and 

carbon of POM and TDN were used to address (1) the 

source of POM, (2) the nutrient species responsible for 

phytoplankton growth, and (3) the source of the 

nutrients in the San Joaquin River. Isotope analysis was 

only done on samples collected by USGS.

Sources of Particulate Organic Matter

Four broad categories of POM source materials 

are phytoplankton, macrophyte detritus, soil organic 

matter, and terrestrial plant detritus. The source 

materials generally have overlapping ranges of isotopic 

values and carbon-to-nitrogen (C:N) ratios; however, 

their relative importance may be evaluated by 

considering together isotopic, elemental, chemical, and 

hydrologic data. The one unique and most diagnostic 

measure of the four source categories is the C:N ratio 

of phytoplankton, which ranges between about 5 and 8. 

Other sources of POM have higher C:N ratios. 

Macrophyte detritus ranges from about 10 to 30, soil 

organic matter from about 8 to 15, and terrestrial plant 

detritus >15 (Kendall and others, 2001). 

The average atomic C:N ratio of POM for the 

2000 and 2001 San Joaquin River data was 6.5 and 7.5 

respectively, indicating that the POM was virtually all 

phytoplankton (fig. 43). The C:N ratios that fell above 

the range of phytoplankton values were samples from 

October and November when VAMP-related reservoir 

releases and wetland releases impacted the San Joaquin 

River. These higher C:N ratios reflect inputs from 

terrestrial sources.

Figure 44 illustrates the difference in C:N ratio 

and δ13C of POM in the San Joaquin River and the 

eight tributaries sampled in 2001. The generally higher 

C:N ratios and δ13C values in the tributaries indicate a 

higher fraction of nonphytoplanktonic POM than in the 

San Joaquin River. Of the tributaries sampled, only the 

POM from Mud Slough matched that found in the San 

Joaquin River. This match suggests significant 

phytoplankton growth in the San Joaquin River in 

addition to that entering from its tributaries.

Nitrate as a Nutrient Source to Phytoplankton

Nitrate accounted for about 90 percent of the 

TDN in 2000 and 2001 samples. Samples collected in 

2000 were analyzed only for δ15N of TDN. For 

samples collected in 2001, a new method for 

concurrent analysis of δ15N and δ18O of nitrate at the 

USGS Menlo Park Stable Isotope Laboratory allowed 

the analysis of a subset of archived, frozen samples 

directly for nitrate isotopes. This allowed us to 

determine how well the TDN samples represent the 

isotopic composition of nitrate. Figure 45 shows the 

δ15N values of nitrate and TDN over time for the 2001 

San Joaquin River samples. The TDN samples were 1.9 

±1.1‰ lower than the nitrate on average. The offset 

was the result of organic nitrogen with lower δ15N 

values. In general, the estimated δ15N of nitrate values 

determined from TDN samples were a useful 

representation of the nitrate isotopic values. 
80 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

10

8

6

4

2

0

12

10

8

6

4

2

0

12

C:N ratio of POM C:N ratio of POM

12-July

25-July

8-Aug.

22-Aug.

6-Sept.

19-Sept.

3-Oct.

17-Oct.

Vernalis

(site 27)

Laird Park

(site 18)

Crows Landing

(site 12)

Upstream of

Merced River

(site 7)

Vernalis

(site 27)

Laird Park

(site 18)

Crows Landing

(site 12)

Upstream of

Merced River

(site 7)

Mud Slough

(site 5)

C:N Ratio of Plankton

C:N Ratio of Plankton

13-June

27-June

11-July

25-July

9-Aug.

23-Aug.

5-Sept.

19-Sept.

3-Oct.

17-Oct.

31-Oct.

15-Nov.

2000 A

2001 B

EXPLANATION

EXPLANATION

Figure 43. Atomic ratio of carbon to nitrogen (C:N) in particulate organic matter (POM) from San Joaquin River sites and Mud Slough in 

California. 

(A) San Joaquin River sites in 2000, (B) San Joaquin River sites plus Mud Slough in 2001.
Isotopes 81

14

13

12

11

10

9

8

7

6

5

13 C of POM

C:N ratio

2001

–32 –30 –28 –26 –24 –22

Tributaries

Vernalis (site 22)

Laird Park (site 18)

Crows Landing (site 12)

Upstream of Merced River (site 7)

Mud Slough (site 5)

Figure 44. Atomic ratio of carbon to nitrogen (C:N) versus delta carbon-13 (δ13C) of particulate organic matter (POM) at San Joaquin River 

sites, Mud Slough, and other tributaries sampled in 2001 in California.

8

9

10

11

12

13

14

8

9

10

11

12

13

δ15 N δ15 N

δ15 N δ15 N

4/19 6/8 7/28 9/16

2001

11/5 12/25

4/19 6/8 7/28 9/16

2001

11/5 12/25

4/19 6/8 7/28 9/16

2001

11/5 12/25

4/19 6/8 7/28 9/16

2001

11/5 12/25

4

6

8

10

12

14

16

4

6

8

10

12

14

16

B

A C

TDN

NO3

missing

data

missing

data

missing

data

missing

data

missing

data

TDN

NO3

TDN

NO3

TDN

NO3

Laird Park (site 18)

Vernalis (site 27) Crows Landing (site 12)

Upstream of Merced River (site 7) D

Figure 45. Delta nitrogen-15 (δ15N) of total dissolved nitrogen (TDN) and nitrate (NO3) in 

samples from San Joaquin River, California, for 2001 (gaps indicate missing data). 

(A) Vernalis, (B) Laird Park, (C) Crows Landing, and (D) Upstream of Merced River.
82 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

The δ15N values of POM and TDN for the 2000 

San Joaquin River samples (fig. 46) and POM and 

nitrate for the 2001 San Joaquin River samples (fig. 47) 

showed similar trends over time. When nutrients are 

plentiful, phytoplankton preferentially assimilate an 

isotopically light fraction, thus acquiring a lighter 

isotopic composition than their nutrient source. The 

data suggest that nitrate in the San Joaquin River was a 

significant nutrient source to the phytoplankton and, 

therefore, the phytoplankton either originated in the 

San Joaquin River or entered the river with the nitrate. 

Nitrate and POM data from a recent transect between 

Mud Slough and San Francisco Bay also strongly 

suggest that phytoplankton use nitrate as a significant 

nutrient source (Carol Kendall, U.S. Geological 

Survey, unpub. data from October 2002 transect, 2003).

Sources of Nitrate

Figure 48 shows the δ15N and δ18O values of 

nitrate measured in the San Joaquin River and its 

tributaries superimposed on the fields of common 

isotopic compositions from different nitrate sources 

(Kendall, 1998). All but a few points from the San 

Joaquin River fell within the range of animal waste and 

sewage, whereas most of the tributary values were 

significantly lower in a range suggesting significant 

amounts of soil nitrogen and (or) fertilizer. Of the 

tributaries, the δ15N values of Mud Slough and 

Westport Drain fell mostly within the range of the San 

Joaquin River. 

A possible alternative explanation for the high 

δ15N values in the San Joaquin River is denitrification. 

As nitrate is microbially denitrified, the isotopic 

composition of nitrogen and oxygen of the residual 

nitrate increases in a ratio of approximately 2:1, 

yielding a slope of 0.5 as shown in figure 49. 

Denitrification occurs in anoxic environments and, 

therefore, it does not occur directly in the San Joaquin 

River. On a plot of δ15N versus δ18O of nitrate showing 

San Joaquin River samples plus Mud Slough, the data 

suggest denitrification for a few samples at Mud 

Slough and the SJR upstream of Merced River (fig. 

49). 

Some of the same samples with the highest δ15N 

values had the lowest nitrate concentrations, also 

consistent with a limited amount of denitrification. The 

high δ15N values and relatively high nitrate 

concentrations (Appendix C) at Westport Drain and 

Mud Slough, in contrast with the lower δ15N values at 

other tributaries, suggest source rather than 

denitrification as the primary cause of the high δ15N 

values in those tributaries and in the San Joaquin River 

(fig. 50). The nitrate isotopic data suggest that (1) 

animal waste and (or) sewage represented a significant 

source of nitrate in the San Joaquin River at the time of 

sampling, (2) the measured tributaries did not 

completely account for the nitrate in the San Joaquin 

River, and (3) that nitrate sources were locally variable 

in isotopic composition. 
Isotopes 83

Vernalis (site 27) A C Crows Landing (site 12)

Laird Park (site 18) Upstream of Merced River (site 7) B D

10

15

0

5

20

δ15 N 10

15

0

5

20

δ15N

10

20

15

0

5

25

δ15 N 10

15

0

5

20

δ15 N

6/23 8/12 10/1 11/20

2000

6/23 8/12 10/1 11/20

2000

6/23 8/12 10/1 11/20

2000

6/23 8/12 10/1 11/20

2000

TDN

POM

TDN

POM

TDN

POM

TDN

POM

Figure 46. Delta nitrogen-15 (δ15N) of total dissolved nitrogen (TDN) and particulate 

organic matter (POM) in samples from San Joaquin River, California, for 2000. 

(A) Vernalis, (B) Laird Park, (C) Crows Landing, and (D) Upstream of Merced River.

8

12

0

4

20

16

δ15 N

8

12

0

4

20

16

δ15 N

8

12

0

4

20

16

δ15 N

8

12

0

4

20

16

δ15N

6/1 8/1 10/1 12/1

2001

6/1 8/1 10/1 12/1

2001

6/1 8/1 10/1 12/1

2001

6/1 8/1 10/1 12/1

2001

missing

data

missing

data

missing

data

missing

data missing

data

NO3

NO3

NO3

NO3

POM POM

POM POM

Vernalis (site 27) A C Crows Landing (site 12)

Laird Park (site 18) Upstream of Merced River (site 7) B D

Figure 47. Delta nitrogen-15 (δ15N) of nitrate (NO3) and particulate organic matter (POM) in 

samples from San Joaquin River, California, for 2001 (gaps indicate missing data). 

(A) Vernalis, (B) Laird Park, (C) Crows Landing, and (D) Upstream of Merced River.
84 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

10

-10

0

20

30

40

50

60

70

-10 -5 0 5 10 15 20 25 30 35 40 nitrification

δ18 O of NO3

δ15 N of NO3

NO3 in

precipitation

desert

NO3

deposits

NO3 fertilizer

NH4 in

fertilizer

and rain

manure and

septic waste

soil N

San Joaquin River

Tributaries

Figure 48. Delta nitrogen-15 (δ15N) versus delta oxygen-18 (δ18O) of nitrate (NO3) for San Joaquin River, California, and tributary 

samples for 2001 superimposed on fields of common isotopic compositions from different nitrate sources. 

(From Kendall, 1998).

0

2

10

12

4

6

8

8 9 10 11 12 13 14 15

Vernalis (site 27)

Laird Park (site 18)

Crows Landing (site 12)

Upstream of Merced River (site 7)

Mud Slough (site 5)

2001

δ18 O of NO3

δ15 N of NO3

–2

Figure 49. Delta nitrogen-15 (δ15N) versus delta oxygen-18 (δ18O) of nitrate (NO3) for San Joaquin River, California, and tributary samples for 

2001 with possible denitrification trend line.
Summary and Conclusions 85

SUMMARY AND CONCLUSIONS

Samples were collected and analyzed by USGS 

in July through October 2000 at four San Joaquin River 

sites and in June through November 2001 at the same 

four sites plus eight tributary sites. The data for these 

sites are supplemented in this report with data from 

samples collected and analyzed by UCD from three 

San Joaquin River sites and eight tributary sites as part 

of a separate study. Streamflows in the San Joaquin 

River were slightly above the long-term average in 

2000 and slightly below average in 2001. There were 

several differences in the methods used by USGS and 

UCD for sample collection and laboratory analyses. As 

a result of quality control data comparing the different 

methods, we do not report the UCD pheophytin-a data 

and do not consider the USGS VSS and the UCD POM 

data to be comparable.

The median concentrations at San Joaquin River 

sites in 2000 and 2001 were 2.67 and 2.60 mg/L for 

nitrate, 0.12 mg/L for orthophosphate, 3.9 mg/L for 

DOC, and 27.2 and 29.4 μg/L for chlorophyll-a. The 

median concentrations of all tributary samples in 2000 

and 2001 were 2.66 mg/L for nitrate, 0.08 mg/L for 

orthophosphate, 4.3 mg/L for DOC, and 6.0 μg/L for 

chlorophyll-a. 

Nitrate loads near Vernalis in 2000 were above 

the long-term average, whereas loads in 2001 were 

about average. Total nitrogen loads in 2000 were 

slightly above average, whereas loads in 2001 were 

slightly below average. Total phosphorus loads in 2000 

and 2001 were well below the long-term average. 

These loads correspond with the flow-adjusted 

concentration trends for these constituents—nitrate has 

significantly increased since 1972 (p < 0.01), whereas 

total nitrogen and total phosphorus have not (p > 0.05).

Loading rates of nutrients and organic carbon 

increased in the San Joaquin River in October and 

November with the release of wetland drainage into 

Mud Slough and the increased reservoir releases on the 

Merced River as part of the Vernalis Adaptive 

Management Plan (VAMP). Chlorophyll-a loading 

rates and concentrations declined in the San Joaquin 

River during August in 2000 and September in 2001. 

Irrigation diversions from the San Joaquin River in 

June through August have a significant impact on the 

pattern of upstream to downstream loading rates, 

especially in the reach from Crows Landing to Maze 

Road.

0

2

4

6

8

10

12

14

16

Lonetree

Creek

(see fig. 1)

Hospital

Creek

(site 23)

Dry Creek

(site 20)

Spanish

Grant

Drain

(site 13)

Orestimba Creek

(site 11)

June 13

June 27

July 11

July 25

Aug. 9

Aug. 23

Sept. 5

Sept. 19

Oct. 3

Oct. 17

Oct. 31

Nov. 15

June 13

July 11

Aug 9

Sept. 5

Oct. 3

Oct. 31

SJR sampling trip sites:

Tributary sites:

Vernalis

(site 27)

Laird Park

(site 18)

Crows Landing

(site 12)

Upstream of

Merced River

(site 7)

Mud Slough

(site 5)

δ15 N of NO3

Westport

Drain

(site 17)

2001

Figure 50. Delta nitrogen-15 (δ15N) of nitrate (NO3) for San Joaquin River, California, and tributary samples for 2001. 

SJR, San Joaquin River. 
86 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

The most significant tributary sources of 

nitrogen and phosphorus to the San Joaquin River were 

the Tuolumne River, Harding Drain, and Mud Slough. 

These tributaries individually accounted for as much as 

20 to 27 percent of the nitrogen loading rate at SJR 

near Vernalis, and as much as 51 to 76 percent of the 

phosphorus loading rate near Vernalis during a 

sampling period. The most significant sources of DOC 

were Salt Slough, Mud Slough, and the Tuolumne and 

Stanislaus Rivers. These tributaries accounted for as 

much as 24 to 45 percent of the DOC loading rate at 

SJR near Vernalis. During the VAMP-related reservoir 

releases in October 2000, the Merced River accounted 

for 28 percent of the DOC loading rate at SJR near 

Vernalis. Mud Slough was the only tributary to account 

for as much as 15 percent of the chlorophyll-a loading 

rate near Vernalis; this occurred in September and 

October 2001. Generally, compared with nutrients and 

DOC, tributaries were minor sources of chlorophyll-a

loading rate, suggesting that most of the chlorophyll-a

is produced in the San Joaquin River instead of 

entering from the tributaries.

On the basis of carbon-to-nitrogen ratios and the 

δ13C of POM in the San Joaquin River and tributaries, 

the POM in the San Joaquin River was primarily 

comprised of phytoplankton. Of the tributaries 

sampled, only the POM in Mud Slough had a signature 

consistent with the San Joaquin River. This is 

consistent with the above conclusion that Mud Slough 

was the largest tributary source of chlorophyll-a. On 

the basis of the δ15N values of POM, TDN, and nitrate, 

the nitrate in the San Joaquin River appears to be a 

significant nutrient source to the phytoplankton. The 

range of δ15N and δ18O values of nitrate in the San 

Joaquin River and tributaries suggest that animal waste 

or sewage was a significant source of nitrate in the San 

Joaquin River at the time of sampling. This signature 

was higher in east-side tributaries than in west-side 

tributaries. The west-side sources were more 

suggestive of a soil nitrogen or fertilizer source. 

Denitrification may have been a reason for some high 

δ15N samples in Mud Slough and the SJR upstream of 

Merced River. 

REFERENCES CITED

Bergamaschi, B.A., Fram, M.S., Fujii, R., Aiken, G.R., 

Kendall, C., and Silva, S.R., 2000, Trihalomethanes 

formed from natural organic matter isolates: using 

isotopic and compositional data to help understand 

sources, in Barrett, S.E., Krasner, S.W., and Amy, G.L., 

eds., Natural organic matter and disinfection byproducts, characterization and control in drinking 

water: American Chemical Society Symposium Series 

761, p. 206-222.

Britton, L.J., and Greeson, P.E., eds., 1987, Methods for 

collection and analysis of aquatic biological and 

microbiological samples: U.S. Geological Survey 

Techniques of Water-Resources Investigations, book 5, 

chap. A4, p. 227.

California Department of Water Resources, 1987, California 

Central Valley unimpaired flow data (2d ed.): California 

Department of Water Resources, Division of Planning, 

38 p.

California Department of Water Resources, Division of 

Flood Management, Chronological reconstructed 

Sacramento and San Joaquin Valley water year 

hydrologic classification indices: accessed February 20, 

2003, at URL http://cdec.water.ca.gov/cgiprogs/iodir/WSIHIST

California Regional Water Quality Control Board, Central 

Valley Region, 1998, The water quality control plan 

(basin plan) for the California Regional Water Quality 

Control Board, Central Valley Region (Sacramento 

River Basin and San Joaquin River Basin), (4th ed.).

California State Water Resources Control Board, 1998, 1998 

California 303(d) list and TMDL priority schedule: 

Sacramento, Calif. (approved by U.S. Environmental 

Protection Agency on May 12, 1999).

Carlson, R.M., 1978, Automated separation and 

conductimetric determination of ammonia and 

dissolved carbon dioxide: Analytical Chemistry, v. 50, 

p. 1528-1531.

———, 1986, Continuous flow reduction of nitrate to 

ammonia with granular zinc: Analytical Chemistry, v. 

58, p. 1590-1591.

Casciotti, K.L., Sigman, D.M., Hastings, M.G., Bohlke, J.K., 

and Hilkert, A., 2002, Measurement of the oxygen 

isotopic composition of nitrate in seawater and 

freshwater using the denitrifier method: Analytical 

Chemistry, v. 74, p. 4905-4912.
References Cited 87

Cohn, T.A., DeLong, L.L., Gilroy, E.J., Hirsch, R.M., and 

Wells, D.K., 1989, Estimating constituent loads: Water 

Resources Research, v. 25, no. 5, p. 937-942.

Eaton, A.D., Clesceri, L.S., Greenberg, A.E., 1995, Standard 

methods for the examination of water and wastewater: 

Baltimore, Md., United Book Press, Inc., p. 5-60.

Fishman, M.J., and Friedman, L.C., eds., 1989, Methods for 

determination of inorganic substances in water and 

fluvial sediments: U.S. Geological Survey Techniques 

of Water-Resources Investigations, book 5, chap. A1, 

545 p.

Guy, H.P., 1973, Laboratory theory and methods for 

sediment analysis: U.S. Geological Survey Techniques 

of Water-Resources Investigation, book 5, chap. C1, p. 

17.

Helsel, D.R., 1990, Less than obvious-statistical treatment of 

data below the detection limit: Environmental Science 

and Technology, v. 24, no. 12, p. 1766-1774.

James, E.W., Westcot, D.W., and Gonzalez, J.L., 1989, Water 

diversion and discharge points along the San Joaquin 

River, Mendota Pool Dam to Mossdale Bridge: 

California Regional Water Quality Control Board, 

Central Valley Region, v. 1 (main report), 41 p. and v. 2-

A (appendix A), 198 p.

Kendall, Carol, 1998, Tracing nitrogen sources and cycling 

in catchments, in Kendall, Carol and McDonnell, J.J., 

eds., Isotope tracers in catchment hydrology: Elsevier 

Science, p. 519-576. 

Kendall, Carol, Silva, S.R., and Kelly, V.J., 2001, Carbon 

and nitrogen isotopic compositions of particulate 

organic matter in four large river systems across the 

United States: Hydrological Processes, v. 15, p. 1301-

1346.

Kratzer, C.R., and Biagtan, R.N., 1997, Determination of 

travel times in the lower San Joaquin River Basin, 

California, from dye-tracer studies during 1994-1995: 

U.S. Geological Survey Water-Resources Investigations 

Report 97-4018, 20 p.

Kratzer, C.R., Pickett, P.J., Rashmawi, E.A., Cross, C.L., and 

Bergeron, K.D., 1987, An input-output model of the 

San Joaquin River from the Lander Avenue bridge to 

the Airport Way bridge, Appendix C of San Joaquin 

River Basin Technical Committee Report: Regulation 

of agricultural drainage to the San Joaquin River: 

California State Water Resources Control Board Order 

no. WQ 85-1, 173 p.

Kratzer, C.R., and Shelton, J.L., 1998, Water quality 

assessment of the San Joaquin-Tulare Basins, 

California: Analysis of available data on nutrients and 

suspended sediment in surface water, 1972-1990: U.S. 

Geological Survey Professional Paper 1587, 92 p.

Lee, G.F., and Jones-Lee, Anne, 2003, Synthesis and 

discussion of findings on the causes and factors 

influencing low DO in the San Joaquin River Deep 

Water Ship Channel, CA: including 2002 data: Report 

submitted to SJR DO TMDL [San Joaquin River 

dissolved oxygen total maximum daily load] Steering 

Committee/Technical Advisory Committee and 

CALFED Bay-Delta Program (updated February 26, 

2003), variously paged.

Quinn, N.W.T., McGahan, Joseph, and Delamore, Michael, 

1998, Innovative strategies reduce selenium in 

Grasslands drainage: California Agriculture, v. 52, no. 

5, p. 12-17.

Quinn, N.W.T., and Tulloch, A., 2002, San Joaquin River 

diversion data assimilation, drainage estimation and 

installation of diversion monitoring stations: CALFED 

Project no. ERP-01-N61-02, 55 p.

Radtke, D.B., Horowitz, A.J., Gibs, Jacob, and Wilde, F.D., 

1999, Raw Samples in Wilde, F.D., Radtke, D.B., Gibs, 

Jacob, and Iwatsubo, R.T., eds., National field manual 

for the collection of water quality data: processing of 

water samples: U.S. Geological Survey Techniques of 

Water-Resources Investigations, book 9, chap A5, p. 

23-35.

Saleh, D.K., Domagalski, J.L., Kratzer, C.R., and Knifong, 

D.L., 2003, Organic carbon trends, loads, and yields to 

the Sacramento-San Joaquin Delta, California, water 

years 1980 to 2000: U.S. Geological Survey WaterResources Investigations Report 03-4070, 77 p. Also 

available at http://water.usgs.gov/pubs/wri/wrir034070

San Joaquin River Group Authority, 2002, 2001 annual 

technical report on implementation and monitoring of 

the San Joaquin River Agreement and the Vernalis 

Adaptive Management Plan: Prepared for the California 

State Water Resources Control Board in compliance 

with D-1641, June 2002, variously paged.

Sigman, D. M., Casciotti, K.L., Andreani, M., Barford, C., 

Galanter, M., and Bohlke, J.K., 2001, A bacterial 

method for the nitrogen isotopic analysis of nitrate in 

seawater and freshwater: Analytical Chemistry, v. 73, p. 

4145-4153.

U.S. Environmental Protection Agency, 1997, Method 445.0, 

In vitro determination of chlorophyll a and pheophytin 

a in marine and freshwater algae by fluorescence 

[USEPA report], revised September 1997: accessed 

March 7, 2003, at URL 

http://www.epa.gov/nerlcwww/m445_0.pdf

U.S. Geological Survey, 1999, National Water Quality 

Laboratory technical memorandum 99.05, effective 

January 1999: accessed March 13, 2003, at URL 

http://nwql.usgs.gov/Public/tech_memos/nwql.99-

05.html
88 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

U.S. Geological Survey, , 2000, Frequently asked questions, 

organic analysis and schedules, revised August 2000: 

accessed March 13, 2003, at URL 

http://wwwnwql.cr.usgs.gov/USGS/faqOrganic.html

Webb, W.E., Radtke, D.B., and Iwatsubo, R.T., 1999, 

Surface-water sampling: collection methods at flowingwater and still-water sites in Wilde, F.D., Radtke, D.B., 

Gibs, Jacob, and Iwatsubo, R.T., eds., National field 

manual for the collection of water-quality data; 

collection of water samples: U.S. Geological Survey 

Techniques of Water-Resources Investigations, book 9, 

chap A4, p. 23-59.

Wershaw, R.L., Fishman, M.J., Grabbe, R.R., and Lowe, 

L.E., eds., 1987, Methods for the determination of 

organic substances in water and fluvial sediments: U.S. 

Geological Survey Techniques of Water-Resources 

Investigations, book 5, chap. A3, 80 p.

Wilde, F.D., Schertz, T.L., and Radtke, D.B., 1998, Qualitycontrol samples in Wilde, F.D., Radtke, D.B., Gibs, 

Jacob, and Iwatsubo, R.T., eds., National field manual 

for the collection of water quality data; collection of 

water samples: U.S. Geological Survey Techniques of 

Water-Resources Investigations, book 9, chap. A4, p. 

91-103.

Yu, Z., Northup, R.R., Dahlgren, R.A., 1994, Determination 

of dissolved organic nitrogen using persulfate oxidation 

and conductimetric quantification of nitrate-nitrogen: 

Communications in Soil Science and Plant Analysis, v. 

25, p. 3161-3169.
Appendixes 89

APPENDIXES
90 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks in the San Joaquin River Basin, California, in 2000 

and 2001

[Site names are slightly abbreviated from full versions listed in table 1. RPD, relative percent difference; N, nitrogen; P, phosphorus; C, carbon; SJR, San 

Joaquin River; E, estimated value; EWI, equal width increment; USGS, U.S. Geological Survey; NWQL, National Water Quality Laboratory; UCDBL, 

University of California at Davis Biogeochemistry Laboratory; VSS, volatile suspended solids (NWQL analytical method); POM, particulate organic matter 

(UCDBL analytical method). mg/L, milligram per liter; nm, nanometer; cm-1, per centimeter; μg/L, microgram per liter; mm, millimeter. <, less than; 

>, greater than; NA, not applicable; nc, sample not collected or not analyzed; —, no data] Site number Site name Date Time Ammonia, dissolved (mg/L as N) RPD Ammonia and organic nitrogen, dissolved (mg/L as N)

RPD

 Ammonia and organic nitrogen, 

total (mg/L as N)

RPD

Nitrite, dissolved 

(mg/L as N)

RPD

Nitrate, dissolved 

(mg/L as N)

RPD

Nitrite and nitrate, dissolved 

(mg/L as N)

RPD

Split replicates

5 Mud Slough near Gustine 10/31/01 10:00 0.14 11.8 1.1 0.0 1.4 0.0 0.037 27.7 1.22 0.0 1.26 0.8

10/31/01 10:01 0.12 1.1 1.4 0.028 1.22 1.25

7 SJR upstream of Merced 6/13/01 9:40 < 0.04 NA 0.69 13.5 1.6 6.5 0.079 1.3 5.55 2.0 5.63 2.0

River 6/13/01 9:41 < 0.04 0.79 1.5 0.080 5.44 5.52

11 Orestimba Creek near Crows 10/4/01 15:00 E 0.02 40.0 0.45 14.3 0.91 3.2 0.028 3.6 3.41 0.6 3.44 0.9

Landing 10/4/01 15:01 E 0.03 0.39 0.94 0.027 3.39 3.41

12 SJR near Crows Landing 9/19/00 11:00 <0.02 NA 0.37 8.6 0.79 2.5 0.024 0.0 2.95 0.0 2.97 0.0

9/19/00 11:01 <0.02 0.40 0.81 0.024 2.95 2.97

12 SJR near Crows Landing 9/20/01 10:30 < 0.04 NA 0.30 0.0 0.81 10.5 0.030 0.0 3.36 3.2 3.39 3.2

9/20/01 10:31 < 0.04 0.30 0.90 0.030 3.47 3.50

13 Spanish Grant Drain 7/11/01 12:30 0.31 0.0 0.87 2.3 5.4 3.8 0.095 2.1 5.15 0.0 5.25 0.0

7/11/01 12:31 0.31 0.89 5.2 0.097 5.15 5.25

17 Westport Drain near Modesto 8/7/01 10:30 0.05 0.0 0.31 3.2 0.43 4.6 0.051 1.9 5.90 4.5 5.95 4.5

8/7/01 10:31 0.05 0.32 0.45 0.052 5.64 5.69

18 SJR at Laird Park 7/25/00 18:00 <0.02 NA 0.43 13.0 1.4 6.9 0.077 0.0 4.23 0.2 4.30 0.1

7/25/00 18:01 <0.02 0.49 1.5 0.077 4.22 4.30

18 SJR at Laird Park 8/8/01 13:30 E 0.02 40.0 0.38 0.0 1.2 0.0 0.073 0.0 4.02 1.0 4.09 0.7

8/8/01 13:31 E 0.03 0.38 1.2 0.073 3.98 4.06

20 Dry Creek at Gallo Bridge 9/5/01 13:00 < 0.04 NA 0.49 6.3 0.61 10.3 0.008 13.3 0.34 2.9 0.35 0.0

9/5/01 13:01 < 0.04 0.46 0.55 0.007 0.35 0.35

27 SJR near Vernalis 7/26/01 10:30 < 0.04 NA 0.22 0.0 0.97 8.6 0.041 2.5 2.13 0.0 2.17 0.0

7/26/01 10:31 < 0.04 0.22 0.89 0.040 2.13 2.17

27 SJR near Vernalis 10/4/01 11:00 < 0.04 NA 0.28 10.2 0.51 2.0 0.038 2.6 1.88 0.5 1.92 0.5

10/4/01 11:01 < 0.04 0.31 0.50 0.039 1.89 1.93
Appendix A. 91

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks in the San Joaquin River Basin, California, in 2000 

and 2001–Continued. Site number Total nitrogen (mg/L as N) RPD Orthophosphate, dissolved 

(mg/L as P)

RPD

Total phosphorus 

(mg/L as P)

RPD

Organic carbon, dissolved 

(mg/L as C)

RPD

Organic carbon, suspended 

(mg/L as C)

RPD

Ultraviolet absorbance at 254 nm 

(cm–1)

RPD

Volatile suspended solids 

(mg/L)

RPD

Chlorophyll-a 

(μg/L)

RPD

Pheophytin-a

(μg/L)

RPD

Suspended sediment 

(mg/L)

RPD

 Suspended sediment size 

fraction < 0.062 mm (percent)

RPD

Split replicates

5 2.7 3.8 0.27 0.0 0.45 0.0 11.7 0.9 0.8 0.0 0.341 2.6 8 0.0 13.2 12.9 5.4 35.1 29 NA 82 NA

2.6 0.27 0.45 11.6 0.8 0.350 8 11.6 7.7 nc nc

7 7.2 2.8 0.10 0.0 0.35 0.0 6.3 3.2 2.9 9.8 — NA 9 0.0 28.9 63.2 16.1 55.0 124 NA 94 NA

7.0 0.10 0.35 6.1 3.2 — 9 55.6 28.3 nc nc

11 4.3 2.3 0.11 0.0 0.37 2.7 3.7 0.0 3.7 5.3 0.095 0.0 17 5.7 8.1 5.1 6.3 15.4 239 NA 97 NA

4.4 0.11 0.38 3.7 3.9 0.095 18 7.7 5.4 nc nc

12 3.8 0.0 0.11 0.0 0.25 0.0 3.9 5.3 0.9 11.8 0.101 0.0 <10 NA 30.8 NA nc NA nc NA nc NA

3.8 0.11 0.25 3.7 0.8 0.101 <10 nc nc nc nc

12 4.2 4.7 0.09 0.0 0.21 4.7 3.2 3.1 1.4 15.4 0.102 0.0 6 0.0 15.8 10.7 12.8 21.0 47 NA 47 NA

4.4 0.09 0.22 3.3 1.2 0.102 6 14.2 15.8 nc nc

13 11 9.5 0.13 0.0 1.74 3.5 4.2 NA >10.0 NA nc NA 134 4.6 14.4 42.0 37.8 0.8 1920 NA 98 NA

10 0.13 1.68 nc nc nc 128 9.4 38.1 nc nc

17 6.4 4.8 0.12 8.0 0.17 0.0 6.0 92.7 0.3 28.6 0.069 17.3 1 0.0 2.5 77.8 2.3 78.8 10 NA 93 NA

6.1 0.13 0.17 2.2 0.4 0.058 1 1.1 1.0 nc nc

18 5.8 0.0 0.14 7.4 0.38 2.7 4.2 2.4 3.6 18.2 0.116 0.2 14 15.4 64.4 25.6 nc NA nc NA nc NA

5.8 0.13 0.37 4.3 3.0 0.115 12 49.8 nc nc nc

18 5.3 0.0 0.13 0.0 0.37 5.3 3.6 2.8 >3.3 NA 0.102 0.0 16 13.3 110 28.1 23.4 16.2 86 NA 89 NA

5.3 0.13 0.39 3.5 2.2 0.102 14 82.9 19.9 nc nc

20 0.96 5.4 0.47 0.0 0.56 1.8 7.0 0.0 0.7 13.3 0.240 16.1 4 28.6 1.2 16.1 3.3 39.6 23 NA 88 NA

0.91 0.47 0.55 7.0 0.8 0.282 3 1.4 4.9 nc nc

27 3.1 0.0 0.08 0.0 0.21 0.0 3.2 9.8 2.5 86.4 0.082 0.0 7 0.0 54.2 5.0 17.6 16.7 63 NA 96 NA

3.1 0.08 0.21 2.9 6.3 0.082 7 57.0 20.8 nc nc

27 2.4 0.0 0.11 0.0 0.22 0.0 3.3 3.1 1.0 26.1 0.083 0.0 4 22.2 10.3 10.1 10.3 17.7 46 NA 83 NA

2.4 0.11 0.22 3.2 1.3 0.083 5 11.4 12.3 nc nc
92 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks in the San Joaquin River Basin, California, in 2000 

and 2001—Continued. Site number Site name

Date 

Time 

Ammonia, dissolved

(mg/L as N)

RPD

Ammonia and organic nitrogen, 

dissolved (mg/L as N)

RPD

 Ammonia and organic nitrogen, 

total (mg/L as N)

RPD

Nitrite, dissolved 

(mg/L as N)

RPD

Nitrate, dissolved 

(mg/L as N)

RPD

Nitrite and nitrate, dissolved 

(mg/L as N)

RPD

Total nitrogen 

(mg/L as N)

RPD

Sequential replicates—sampling methods comparison

7 USGS EWI 8/9/00 12:00 < 0.02 NA 0.47 0.0 1.2 22.2 0.083 1.2 2.97 0.7 3.05 0.7 4.3 6.7

7 USGS grab 8/9/00 12:01 < 0.02 0.47 1.5 0.084 2.95 3.03 4.6

7 USGS EWI 10/3/00 12:30 0.04 22.2 0.62 0.0 1.1 10.5 0.041 2.5 1.52 0.7 1.56 0.6 2.6 3.9

7 USGS grab 10/3/00 12:31 0.05 0.62 0.99 0.040 1.51 1.55 2.5

12 USGS EWI 7/25/00 12:00 < 0.02 NA 0.44 4.4 1.5 6.9 0.077 0.0 4.04 0.5 4.12 0.2 5.7 1.8

12 USGS grab 7/25/00 12:01 < 0.02 0.46 1.4 0.077 4.06 4.13 5.6

12 USGS EWI 8/22/00 10:30 0.04 40.0 0.49 2.1 0.96 13.6 0.045 0.0 3.65 1.4 3.69 1.1 4.7 0.0

12 USGS grab 8/22/00 10:31 0.06 0.48 1.1 0.045 3.60 3.65 4.7

18 USGS EWI 7/12/00 13:30 < 0.02 NA 0.47 4.4 1.2 8.7 0.059 8.1 4.19 0.7 4.25 0.7 5.5 1.8

18 USGS grab 7/12/00 13:31 < 0.02 0.45 1.1 0.064 4.22 4.28 5.4

18 USGS EWI 9/7/00 12:20 < 0.02 NA 0.33 3.1 1.1 17.8 0.063 4.9 3.82 0.5 3.88 0.5 5.0 4.1

18 USGS grab 9/7/00 12:21 < 0.02 0.32 0.92 0.060 3.84 3.90 4.8

27 USGS EWI 9/20/00 10:30 < 0.02 NA 0.21 6.9 0.48 3.1 0.025 4.1 1.91 NA 1.94 1.0 2.4 NA

27 USGS grab 9/20/00 10:31 < 0.02 0.23 0.50 0.024 — 1.92 —

27 USGS EWI 10/4/00 10:00 < 0.02 NA 0.20 22.2 0.52 3.9 0.030 3.3 1.93 0.5 1.96 0.5 2.5 0.0

27 USGS grab 10/4/00 10:01 < 0.02 0.25 0.50 0.031 1.94 1.97 2.5
Appendix A. 93

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks in the San Joaquin River Basin, California, in 2000 

and 2001—Continued. Site number Orthophosphate, dissolved (mg/L as P) RPD

Total phosphorus 

(mg/L as P)

RPD

Organic carbon, dissolved 

(mg/L as C)

RPD

Organic carbon, suspended 

(mg/L as C)

RPD

Ultraviolet absorbance at 254 nm 

(cm–1)

RPD

Volatile suspended solids 

(mg/L)

RPD

Chlorophyll-a 

(μg/L)

RPD

Pheophytin-a

(μg/L)

RPD

Suspended sediment 

(mg/L)

RPD

 Suspended sediment size 

fraction < 0.062 mm (percent)

RPD

Sequential replicates—sampling methods comparison

7 0.14 0.0 0.44 2.3 5.0 2.0 1.9 23.5 0.135 0.0 12 8.7 E 35.9 193 — NA — NA — NA

7 0.14 0.45 5.1 1.5 0.135 11 E 0.7 — — —

7 0.17 0.0 0.45 4.6 6.7 4.6 1.7 0.0 0.182 6.2 — NA 26.3 110 — NA 96 NA — NA

7 0.17 0.43 6.4 1.7 0.171 10 7.6 — — —

12 0.08 0.0 0.31 10.2 4.0 0.0 2.4 82.4 0.117 0.9 <10 NA 66.3 13.1 — NA 55 NA — NA

12 0.08 0.28 4.0 1.0 0.118 <10 75.6 — — —

12 0.12 8.0 0.28 3.5 3.9 0.0 0.8 11.8 — NA <10 NA 18.8 9.6 — NA — NA — NA

12 0.13 0.29 3.9 0.9 — — 20.7 — — —

18 0.18 0.0 0.41 2.5 4.2 2.4 1.7 45.5 0.103 1.0 13 7.4 71.8 8.3 — NA 185 NA — NA

18 0.18 0.40 4.3 2.7 0.104 14 78.0 — — —

18 0.20 5.1 0.42 4.9 3.2 3.1 1.3 16.7 0.084 2.4 <10 NA 25.3 2.3 — NA — NA — NA

18 0.19 0.40 3.3 1.1 0.086 — 25.9 — — —

27 0.11 0.0 0.21 4.9 2.3 NA 0.5 NA 0.068 NA <10 NA 10.5 27.9 — NA 58 NA — NA

27 0.11 0.20 — — — <10 13.9 — — —

27 0.10 0.0 0.20 4.9 2.6 3.9 0.3 28.6 0.078 13.7 <10 NA 11.5 10.7 — NA 43 NA — NA

27 0.10 0.21 2.5 0.4 0.068 <10 12.8 — — —
94 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks in the San Joaquin River Basin, California, in 2000 

and 2001—Continued. Site number Laboratory Date 

Time 

Ammonia, dissolved

(mg/L as N)

RPD

Ammonia and organic nitrogen, 

dissolved (mg/L as N)

RPD

 Ammonia and organic nitrogen, 

total (mg/L as N)

RPD

Nitrite, dissolved 

(mg/L as N)

RPD

Nitrate, dissolved 

(mg/L as N)

RPD

Nitrite and nitrate, dissolved 

(mg/L as N)

RPD

Total nitrogen 

(mg/L as N)

RPD

Sequential replicates—laboratory performance comparison

7 NWQL 8/9/00 12:01 < 0.02 NA 0.47 NA 1.5 NA 0.084 NA 2.95 10.6 3.03 NA 4.6 15.5

7 UCDBL 8/9/00 12:02 0.01 — — — 3.28 — 3.94

12 NWQL 7/25/00 12:01 < 0.02 NA 0.46 NA 1.4 NA 0.077 NA 4.06 10.3 4.13 NA 5.6 0.7

12 UCDBL 7/25/00 12:02 0.10 — — — 4.50 — 5.64

12 NWQL 8/22/00 10:31 0.06 50.0 0.48 NA 1.1 NA 0.045 NA 3.60 5.4 3.65 NA 4.7 2.6

12 UCDBL 8/22/00 10:32 0.10 — — — 3.80 — 4.58

18 NWQL 7/12/00 13:31 < 0.02 NA 0.45 NA 1.1 NA 0.064 NA 4.22 1.7 4.28 NA 5.4 1.3

18 UCDBL 7/12/00 13:32 0.08 — — — 4.29 — 5.33
Appendix A. 95

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks in the San Joaquin River Basin, California, in 2000 

and 2001—Continued. Site number Orthophosphate, dissolved (mg/L as P) RPD Total phosphorus 

(mg/L as P)

RPD

Organic carbon, dissolved 

(mg/L as C)

RPD

Organic carbon, suspended 

(mg/L as C)

RPD

Ultraviolet absorbance

at 254 nm (cm–1)

RPD

VSS/POM 

(mg/L)

RPD

Chlorophyll-a 

(μg/L)

RPD

Pheophytin-a

(μg/L)

RPD

Suspended sediment 

(mg/L)

RPD

Suspended sediment size 

fraction <0.062 mm (percent)

RPD

Sequential replicates—laboratory performance comparison

7 0.14 8.6 0.45 54.6 5.1 4.0 1.5 NA 0.135 NA 11 53.3 E 0.7 190 — NA — NA — NA

7 0.155 0.257 4.9 — — 19 29.1 10.3 114 —

12 0.08 6.8 0.28 50.1 4.0 29.9 1.0 NA 0.118 NA <10 NA 75.6 37.2 — NA — NA — NA

12 0.086 0.168 5.4 — — 15 51.9 5.4 48 —

12 0.12 3.7 0.29 31.3 3.9 47.6 0.9 NA — NA — NA 20.7 12.7 — NA — NA — NA

12 0.125 0.212 2.4 — — 13 23.5 4.6 71 —

18 0.18 6.5 0.41 47.6 4.2 77.4 2.7 NA 0.104 NA 14 30.3 78.0 59.1 — NA — NA — NA

18 0.169 0.252 9.5 — — 19 42.4 10.8 164 —
96 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks in the San Joaquin River Basin, California, in 2000 

and 2001—Continued.

Site 

number Date Time

Ammonia, 

dissolved 

(mg/L as N)

Ammonia and 

organic nitrogen, 

dissolved 

(mg/L as N)

Ammonia and 

organic nitrogen, 

total 

(mg/L as N)

Nitrite, dissolved

(mg/L as N)

Nitrite and nitrate, 

dissolved 

(mg/L as N)

Field Blanks

7 7/25/01 10:58 < 0.04 < 0.10 E 0.04 < 0.006 E 0.03

7 8/22/01 10:58 < 0.04 < 0.10 < 0.08 < 0.006 < 0.05

11 9/6/01 14:08 < 0.04 < 0.10 < 0.08 < 0.006 E 0.03

12 10/18/01 10:28 < 0.04 < 0.10 < 0.10 < 0.006 < 0.05

13 9/4/01 11:18 < 0.04 < 0.10 < 0.08 < 0.006 < 0.05

17 10/3/01 11:38 < 0.04 < 0.10 < 0.10 < 0.008 E 0.02

18 8/23/00 11:38 < 0.02 < 0.10 < 0.10 < 0.01 < 0.05

18 9/19/01 11:38 < 0.04 < 0.10 E 0.04 < 0.006 E 0.02

27 8/9/00 16:08 < 0.02 < 0.10 < 0.10 < 0.01 < 0.05
Appendix A. 97

Appendix A. Results of quality control samples for split replicates, sequential replicates, and field blanks in the San Joaquin River Basin, California, in 2000 

and 2001—Continued.

Site 

number Date Time

Orthophosphate, 

dissolved 

(mg/L as P)

Total 

phosphorus 

(mg/L as P)

Organic 

carbon, 

dissolved 

(mg/L as C)

Ultraviolet 

absorbance 

at 254 nm 

(cm–1)

Volatile 

suspended 

solids 

(mg/L)

Chlorophyll-a 

(μg/L)

Pheophytin-a 

(μg/L)

Field Blanks

7 7/25/01 10:58 < 0.02 < 0.004 0.5 < 0.004 < 4 < 0.1 < 0.1

7 8/22/01 10:58 < 0.02 < 0.004 E 0.2 < 0.004 4 — —

11 9/6/01 14:08 < 0.02 < 0.004 0.5 < 0.004 < 4 — —

12 10/18/01 10:28 < 0.02 < 0.004 E 0.2 < 0.004 4 < 0.1 0.1

13 9/4/01 11:18 < 0.02 < 0.004 E 0.2 < 0.004 4 — —

17 10/3/01 11:38 < 0.02 < 0.004 E 0.2 — < 4 < 0.1 0.1

18 8/23/00 11:38 < 0.01 < 0.008 < 0.3 — < 10 — —

18 9/19/01 11:38 < 0.02 < 0.004 < 0.3 < 0.004 < 4 < 0.1 0.1

27 8/9/00 16:08 < 0.01 < 0.008 0.4 — < 10 < 0.1 —
98 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001 Site number Site name Date Time Laboratory Stream flow (ft3/s) Water temperature (C) pH Specific conductance (μS/cm at 25C) Dissolved oxygen (mg/L) Alkalinity (mg/L CaCO3) Secchi disk depth (in.) Ammonia, dissolved (mg/L as N) Nitrate, dissolved (mg/L as N) Inorganic nitrogen, dissolved (mg/L as N) Organic nitrogen, dissolved (mg/L as N)

1 SJR near Stevinson 07/12/00 13:40 UCD E 124 27.8 8.9 413 — — — 0.05 0.37 0.42 0.09

1 SJR near Stevinson 07/26/00 14:15 UCD E 53 27.2 9.1 1060 — — — 0.50 7.29 7.78 1.51

1 SJR near Stevinson 08/09/00 12:46 UCD E 56 26.9 7.9 1110 — — — 0.45 8.06 8.51 1.33

1 SJR near Stevinson 08/23/00 13:42 UCD E 58 26.0 9.1 1030 — — — 0.04 0.32 0.35 0.98

1 SJR near Stevinson 09/06/00 14:15 UCD E 81 22.7 8.5 384 — — — 0.02 0.34 0.36 0.34

1 SJR near Stevinson 09/20/00 15:10 UCD E 16 29.0 8.7 1140 — — — 0.13 0.16 0.29 0.83

1 SJR near Stevinson 10/04/00 13:31 UCD E 22 22.9 8.4 1480 — — — 0.07 0.01 0.09 0.44

1 SJR near Stevinson 10/18/00 13:01 UCD E 38 20.3 8.4 745 — — — < 0.01 0.21 0.22 0.51

1 SJR near Stevinson 06/13/01 09:50 UCD E 14 22.5 7.5 1450 — — — 0.04 0.45 0.49 1.27

1 SJR near Stevinson 06/27/01 12:10 UCD E 18 23.9 8.4 1640 — — — 0.02 0.13 0.15 1.52

1 SJR near Stevinson 07/11/01 09:45 UCD E 43 25.8 8.5 1820 — — — 0.05 0.08 0.13 1.08

1 SJR near Stevinson 07/25/01 14:40 UCD E 21 31.0 8.2 1410 — — — 0.02 0.02 0.05 0.55

1 SJR near Stevinson 08/07/01 13:20 UCD E 17 29.4 9.3 1440 — — — 0.04 0.24 0.28 1.96

1 SJR near Stevinson 08/22/01 13:01 UCD E 23 26.1 9.3 1370 — — — 0.53 1.15 1.68 1.49

1 SJR near Stevinson 09/05/01 13:21 UCD E 24 26.8 8.6 1410 — — — 0.38 0.03 0.40 0.97

1 SJR near Stevinson 09/19/01 11:15 UCD E 11 23.7 8.1 1530 — — — 0.06 0.02 0.08 0.88

1 SJR near Stevinson 10/03/01 10:40 UCD E 31 23.5 8.2 1670 — — — 0.03 0.02 0.04 1.00

7 SJR upstream of Merced 07/26/00 14:00 USGS E 327 28.0 8.3 1660 10.6 130 E 8 < 0.02 4.54 4.75 0.65

7 SJR upstream of Merced 08/09/00 12:00 USGS E 358 26.5 8.5 1350 8.2 140 7 < 0.02 2.97 3.06 0.46

7 SJR upstream of Merced 08/22/00 12:20 USGS E 336 24.5 8.3 1340 8.2 140 8 < 0.02 2.13 2.19 0.48

7 SJR upstream of Merced 09/06/00 12:40 USGS E 284 21.0 8.6 1620 10.2 170 11 < 0.02 2.66 2.71 0.40

7 SJR upstream of Merced 09/19/00 12:30 USGS E 197 25.0 8.2 1340 8.7 150 11 < 0.02 1.28 1.32 0.43

7 SJR upstream of Merced 10/03/00 12:30 USGS E 115 22.0 8.0 1440 8.6 170 13 0.04 1.52 1.60 0.58

7 SJR upstream of Merced 10/17/00 12:30 USGS E 347 19.0 7.9 1180 6.9 170 11 E 0.02 0.80 0.85 0.64

7 SJR upstream of Merced 06/13/01 09:40 USGS E 265 21.0 8.2 2390 8.1 180 — < 0.04 5.55 5.65 0.67

7 SJR upstream of Merced 06/27/01 10:00 USGS E 242 23.0 8.0 1740 6.7 150 6 0.17 4.93 5.18 0.64

7 SJR upstream of Merced 07/11/01 10:20 USGS E 260 24.5 8.2 1860 8.1 150 5 < 0.04 4.08 4.21 0.59

7 SJR upstream of Merced 07/25/01 10:50 USGS E 296 25.5 8.2 1680 7.9 — 7 < 0.04 2.85 2.92 0.39

7 SJR upstream of Merced 08/08/01 10:10 USGS E 243 27.0 8.3 1840 7.4 140 — E 0.03 2.46 2.52 0.41

7 SJR upstream of Merced 08/22/01 10:50 USGS E 286 24.0 8.2 1630 7.5 140 12 < 0.04 2.50 2.58 0.44

7 SJR upstream of Merced 09/05/01 09:30 USGS E 201 23.0 8.2 2270 8.2 190 17 < 0.04 2.50 2.58 0.54

7 SJR upstream of Merced 09/19/01 09:30 USGS E 120 21.5 7.9 2260 8.7 180 11 < 0.04 1.49 1.54 0.50

7 SJR upstream of Merced 10/03/01 10:00 USGS E 197 22.5 7.8 1700 5.5 190 5 < 0.04 0.34 0.38 0.82

7 SJR upstream of Merced 10/17/01 09:30 USGS E 257 19.0 8.0 1350 6.0 180 8 E 0.02 0.39 0.42 0.67

7 SJR upstream of Merced 10/31/01 08:40 USGS E 227 15.5 8.0 11950 7.0 210 11 E 0.03 0.76 0.82 0.67

7 SJR upstream of Merced 11/15/01 09:20 USGS E 575 15.5 8.2 1380 6.6 180 — 0.06 0.74 0.83 0.72

12 SJR near Crows Landing 07/11/00 18:00 USGS 737 27.0 8.5 1080 11.0 140 — < 0.02 3.66 3.73 0.40

12 SJR near Crows Landing 07/25/00 12:00 USGS 612 25.0 8.4 1260 8.6 140 11 < 0.02 4.04 4.13 0.43

12 SJR near Crows Landing 08/08/00 11:00 USGS 644 24.0 8.0 1040 7.5 130 10 0.21 3.47 3.75 0.48

12 SJR near Crows Landing 08/22/00 10:30 USGS 713 23.5 8.1 1020 7.1 130 10 0.04 3.65 3.73 0.45

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for San 

Joaquin River sites in California

[SUVA, specific ultraviolet absorbance; SJR, San Joaquin River; UCD, University of California at Davis; USGS, U.S. Geological Survey; E, estimated. ft3/s, 

cubic foot per second; μS/cm, microsiemens per centimeter; mg/L, milligram per liter; in., inch; nm, nanometer; cm-1, per centimeter; L/mg-cm, liter per 

milligram-centimeter; μg/L, microgram per liter; mm, millimeter; <, less than; >, greater than; —, no data reported]
Appendix B. 99

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for San 

Joaquin River sites in California—Continued Site number Site name Date

 Total nitrogen, dissolved

 (mg/L as N)

 Total nitrogen

 (mg/L as N)

 Orthophosphate, dissolved

(mg/L as P)

 Total phosphorus

 (mg/L as P) 

Organic carbon, dissolved

 (mg/L as C) 

Organic carbon, suspended 

 (mg/L as C)

Ultraviolet absorbance 

at 254 nm (cm–1)

 SUVA

(L/mg-cm)

 Volatile suspended solids

 (mg/L) 

 Particulate organic matter

 (mg/L)

 Chlorophyll-a

 (μg/L)

 Pheophytin-a

 (μg/L)

 Suspended sediment

 (mg/L)

 Suspended sediment, size 

fraction < 0.062 mm (percent)

1 SJR near Stevinson 07/12/00 0.51 1.41 0.04 0.16 4.5 — — — — 24 56.6 — 58 —

1 SJR near Stevinson 07/26/00 9.29 11.6 0.17 0.34 7.4 — — — — 42 286 — 37 —

1 SJR near Stevinson 08/09/00 9.83 11.7 0.06 0.50 7.0 — — — — 50 377 — 54 —

1 SJR near Stevinson 08/23/00 1.33 2.11 0.04 0.19 6.8 — — — — 21 75.5 — 25 —

1 SJR near Stevinson 09/06/00 0.70 1.52 0.08 0.21 3.7 — — — — 12 67.8 — 35 —

1 SJR near Stevinson 09/20/00 1.12 1.74 0.09 0.23 5.2 — — — — 12 15.1 — 17 —

1 SJR near Stevinson 10/04/00 0.52 1.04 0.10 0.21 8.6 — — — — 19 17.1 — 24 —

1 SJR near Stevinson 10/18/00 0.73 1.25 0.09 0.20 4.7 — — — — 15 16.7 — 30 —

1 SJR near Stevinson 06/13/01 1.76 1.92 0.19 0.50 6.7 — — — — 18 120 — 46 —

1 SJR near Stevinson 06/27/01 1.66 2.86 0.07 0.29 6.6 — — — — 18 113 — 34 —

1 SJR near Stevinson 07/11/01 1.22 2.96 0.05 0.23 5.8 — — — — 27 121 — 64 —

1 SJR near Stevinson 07/25/01 0.60 1.61 0.03 0.21 6.5 — — — — 29 85.7 — 33 —

1 SJR near Stevinson 08/07/01 2.24 4.78 0.03 0.20 5.8 — — — — 61 393 — 69 —

1 SJR near Stevinson 08/22/01 3.17 6.35 0.02 0.47 6.2 — — — — 39 348 — 44 —

1 SJR near Stevinson 09/05/01 1.37 3.77 0.07 0.37 5.8 — — — — 45 197 — 49 —

1 SJR near Stevinson 09/19/01 0.96 1.57 0.03 0.19 4.7 — — — — 13 125 — 25 —

1 SJR near Stevinson 10/03/01 1.04 2.76 0.06 0.18 5.3 — — — — 18 80.6 — 22 —

7 SJR upstream of Merced 07/26/00 5.40 6.54 0.09 0.40 5.2 1.9 0.149 0.029 14 — 95.9 — — —

7 SJR upstream of Merced 08/09/00 3.52 4.25 0.14 0.44 5.0 1.9 0.135 0.027 12 — E 35.9 — — —

7 SJR upstream of Merced 08/22/00 2.67 3.48 0.10 0.37 4.8 1.1 — — 14 — 31.4 — — —

7 SJR upstream of Merced 09/06/00 3.11 4.00 0.05 0.26 4.2 1.0 0.114 0.027 <10 — 28.1 — — —

7 SJR upstream of Merced 09/19/00 1.75 2.51 0.11 0.33 6.6 1.5 0.135 0.020 12 — 35.2 — — —

7 SJR upstream of Merced 10/03/00 2.18 2.66 0.17 0.45 6.7 1.7 0.182 0.027 — — 26.3 — 96 90

7 SJR upstream of Merced 10/17/00 1.49 1.55 — 0.43 8.8 1.4 0.240 0.027 <10 — 15.5 — 74 86

7 SJR upstream of Merced 06/13/01 6.32 7.23 0.10 0.35 6.3 2.9 — — 9 — 28.9 16.1 124 94

7 SJR upstream of Merced 06/27/01 5.82 6.61 0.17 0.41 7.1 >3.3 0.169 0.024 16 — 31.2 14.4 163 84

7 SJR upstream of Merced 07/11/01 4.80 5.89 0.12 0.37 — — — 0.025 20 — 27.8 22.9 138 86

7 SJR upstream of Merced 07/25/01 3.31 3.90 0.10 0.36 5.2 >3.3 0.149 0.029 19 — 37.4 13.6 158 85

7 SJR upstream of Merced 08/08/01 2.93 3.79 0.06 0.34 4.7 2.4 0.141 0.030 15 — 48.2 18.2 114 89

7 SJR upstream of Merced 08/22/01 3.02 3.41 0.11 0.33 4.6 3.2 0.133 0.029 18 — 29.4 15.6 143 85

7 SJR upstream of Merced 09/05/01 3.12 3.76 0.08 0.27 4.0 1.7 0.161 0.040 10 — 32.4 30.4 44 86

7 SJR upstream of Merced 09/19/01 2.04 2.62 0.09 0.26 4.6 2.4 0.160 0.035 8 — 29.4 10.8 58 94

7 SJR upstream of Merced 10/03/01 1.20 1.29 0.28 0.55 10.3 1.7 E 0.298 0.030 11 — 23.4 13.3 103 77

7 SJR upstream of Merced 10/17/01 1.09 1.31 0.21 0.45 8.4 1.8 0.239 0.028 14 — 14.4 11.3 90 89

7 SJR upstream of Merced 10/31/01 1.49 1.71 0.16 0.38 8.4 2.2 0.235 0.028 10 — 15.5 12.9 57 94

7 SJR upstream of Merced 11/15/01 1.55 2.07 0.20 0.37 10.1 1.7 E 0.266 0.027 8 — 12.2 3.7 120 82

12 SJR near Crows Landing 07/11/00 4.13 4.82 0.11 0.24 4.5 1.7 0.117 0.026 10 — 64.7 — 71 94

12 SJR near Crows Landing 07/25/00 4.56 5.62 0.08 0.31 4.0 2.4 0.117 0.029 <10 — 66.3 — 55 86

12 SJR near Crows Landing 08/08/00 4.23 5.04 0.12 0.32 4.2 1.1 0.115 0.027 <10 — E 63.8 — — —

12 SJR near Crows Landing 08/22/00 4.18 4.65 0.12 0.28 3.9 0.8 — — — — 18.8 — — —
100 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for San 

Joaquin River sites in California—Continued Site number Site name Date

Time

 Laboratory

 Stream flow 

 (ft3/s)

 Water temperature 

 (C)

 pH 

 Specific conductance

 (μS/cm at 25C)

 Dissolved oxygen

(mg/L) 

 Alkalinity

 (mg/L CaCO3)

 Secchi disk depth 

 (in.)

 Ammonia, dissolved

 (mg/L as N) 

 Nitrate, dissolved

 (mg/L as N)

 Inorganic nitrogen, dissolved

 (mg/L as N)

 Organic nitrogen, dissolved

 (mg/L as N)

12 SJR near Crows Landing 09/06/00 10:30 USGS 708 20.5 8.2 960 8.1 130 10 < 0.02 3.56 3.60 0.31

12 SJR near Crows Landing 09/19/00 11:00 USGS 569 23.5 8.0 910 7.2 140 12 < 0.02 2.95 2.98 0.36

12 SJR near Crows Landing 10/03/00 11:00 USGS 464 21.5 7.7 990 7.7 130 10 < 0.02 2.85 2.88 0.35

12 SJR near Crows Landing 10/17/00 11:20 USGS 1190 18.0 7.8 585 7.8 91 — 0.21 1.24 1.46 0.50

12 SJR near Crows Landing 06/14/01 10:00 USGS 565 22.0 8.2 1330 8.2 130 — < 0.04 4.86 4.95 0.41

12 SJR near Crows Landing 06/28/01 09:50 USGS 562 23.0 8.1 1240 7.4 150 — 0.06 4.93 5.06 0.56

12 SJR near Crows Landing 07/12/01 10:30 USGS 562 24.0 8.5 1320 7.4 150 9 < 0.04 3.83 3.93 0.41

12 SJR near Crows Landing 07/26/01 11:30 USGS 546 24.5 8.3 1330 7.4 — 8 < 0.04 4.05 4.14 0.38

12 SJR near Crows Landing 08/09/01 10:30 USGS 435 26.5 8.3 1420 8.0 160 — E 0.02 3.35 3.43 0.41

12 SJR near Crows Landing 08/23/01 11:00 USGS 531 23.0 8.2 1150 7.8 130 10 < 0.04 4.07 4.13 0.34

12 SJR near Crows Landing 09/06/01 13:00 USGS 361 22.5 8.2 1540 8.9 170 15 < 0.04 4.11 4.19 0.41

12 SJR near Crows Landing 09/20/01 10:30 USGS 354 22.5 8.2 1070 7.5 120 13 < 0.04 3.36 3.41 0.28

12 SJR near Crows Landing 10/04/01 10:30 USGS 371 21.5 7.8 11350 6.4 170 14 < 0.04 1.83 1.88 0.56

12 SJR near Crows Landing 10/18/01 10:20 USGS 773 19.0 8.0 846 7.0 120 22 < 0.04 1.24 1.27 0.37

12 SJR near Crows Landing 11/01/01 10:00 USGS 1190 16.0 7.9 1620 8.8 76 14 < 0.04 1.22 1.25 0.24

12 SJR near Crows Landing 11/16/01 09:20 USGS 1190 15.0 7.8 1840 7.9 120 10 0.04 1.23 1.28 0.49

15 SJR near Patterson 07/12/00 12:50 UCD E 884 25.2 8.1 923 — — — 0.05 3.97 4.02 0.30

15 SJR near Patterson 07/26/00 13:10 UCD E 876 25.1 8.1 1160 — — — 0.08 4.43 4.51 0.53

15 SJR near Patterson 08/09/00 11:45 UCD E 817 24.2 7.8 869 — — — 0.02 3.99 4.01 0.29

15 SJR near Patterson 08/23/00 12:40 UCD E 802 24.4 8.1 946 — — — 0.10 3.47 3.56 0.42

15 SJR near Patterson 09/06/00 13:10 UCD E 902 21.4 8.2 835 — — — 0.08 3.92 4.01 0.02

15 SJR near Patterson 09/20/00 14:20 UCD E 667 25.9 8.0 911 — — — 0.08 3.62 3.70 0.70

15 SJR near Patterson 10/04/00 12:20 UCD E 671 21.1 8.1 851 — — — 0.58 4.11 4.70 0.41

15 SJR near Patterson 10/18/00 11:57 UCD E1460 18.2 8.1 471 — — — 0.30 1.64 1.94 0.44

15 SJR near Patterson 06/13/01 08:50 UCD E 743 21.6 7.9 1280 — — — 0.44 4.09 4.53 0.69

15 SJR near Patterson 06/27/01 10:55 UCD E 691 23.1 8.0 1230 — — — 0.05 4.08 4.14 0.35

15 SJR near Patterson 07/11/01 08:45 UCD E 735 23.1 8.0 1120 — — — 0.11 4.58 4.69 1.68

15 SJR near Patterson 07/25/01 11:40 UCD E 747 25.9 8.1 1210 — — — 0.03 4.07 4.10 0.66

15 SJR near Patterson 08/07/01 11:43 UCD E 664 27.1 8.2 1200 — — — 0.09 3.82 3.91 1.30

15 SJR near Patterson 08/22/01 11:31 UCD E 723 23.6 8.0 1080 — — — 0.11 4.03 4.15 0.95

15 SJR near Patterson 09/05/01 12:03 UCD E 611 24.5 8.2 1100 — — — 0.02 4.37 4.40 0.27

15 SJR near Patterson 09/19/01 10:00 UCD E 475 21.7 8.3 1160 — — — 0.27 3.53 3.79 1.36

15 SJR near Patterson 10/03/01 09:55 UCD E 445 22.1 7.9 1310 — — — 0.34 2.60 2.94 1.57

18 SJR at Laird Park 07/12/00 13:30 USGS E1030 25.5 8.2 1080 10.1 140 E 12 < 0.02 4.19 4.26 0.46

18 SJR at Laird Park 07/25/00 18:00 USGS E 890 28.0 8.8 1220 16.4 300 E 11 < 0.02 4.23 4.31 0.42

18 SJR at Laird Park 08/08/00 13:00 USGS 782 24.5 8.4 1160 11.0 150 12 < 0.02 4.21 4.29 0.39

18 SJR at Laird Park 08/23/00 11:30 USGS 847 23.0 8.1 959 8.1 140 13 < 0.02 3.97 4.05 0.40

18 SJR at Laird Park 09/07/00 12:20 USGS 1090 22.5 8.1 1060 10.3 150 11 < 0.02 3.82 3.89 0.32

18 SJR at Laird Park 09/20/00 13:30 USGS 750 24.5 8.0 974 8.1 150 12 < 0.02 3.75 3.83 0.34

18 SJR at Laird Park 10/04/00 13:00 USGS 663 21.0 8.0 1090 8.6 170 5 0.06 3.40 3.56 0.37

18 SJR at Laird Park 10/18/00 12:30 USGS 1500 18.5 7.8 547 7.5 91 — 0.10 1.63 1.77 0.37

18 SJR at Laird Park 06/13/01 11:30 USGS 761 21.5 8.3 1410 9.1 160 — E 0.03 4.58 4.73 0.47
Appendix B. 101

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for San 

Joaquin River sites in California—Continued Site number Site name Date

 Total nitrogen, dissolved

 (mg/L as N)

 Total nitrogen

 (mg/L as N)

 Orthophosphate, dissolved

(mg/L as P)

 Total phosphorus

 (mg/L as P) 

Organic carbon, dissolved

 (mg/L as C) 

Organic carbon, suspended 

 (mg/L as C)

Ultraviolet absorbance 

at 254 nm (cm–1)

 SUVA

(L/mg-cm)

 Volatile suspended solids

 (mg/L) 

 Particulate organic matter

 (mg/L)

 Chlorophyll-a

 (μg/L)

 Pheophytin-a

 (μg/L)

 Suspended sediment

 (mg/L)

 Suspended sediment, size 

fraction < 0.062 mm (percent)

12 SJR near Crows Landing 09/06/00 3.91 4.46 0.08 0.24 3.4 1.1 0.093 0.027 <10 — 20.1 — — —

12 SJR near Crows Landing 09/19/00 3.34 3.76 0.11 0.25 3.9 0.9 0.101 0.026 <10 — 30.8 — — —

12 SJR near Crows Landing 10/03/00 3.23 3.67 0.12 0.24 3.8 0.3 0.104 0.028 <10 — 20.8 — 52 86

12 SJR near Crows Landing 10/17/00 1.96 1.96 0.12 0.15 4.7 1.1 0.126 0.027 — — 9.3 — 90 86

12 SJR near Crows Landing 06/14/01 5.36 6.23 0.09 0.30 3.9 2.0 0.111 0.028 6 — 49.5 14.0 72 91

12 SJR near Crows Landing 06/28/01 5.62 6.30 0.16 0.35 4.4 2.5 0.135 0.031 12 — 27.8 16.7 53 91

12 SJR near Crows Landing 07/12/01 4.34 5.41 0.11 0.32 4.9 >3.3 0.128 0.026 19 — 26.5 25.9 111 91

12 SJR near Crows Landing 07/26/01 4.52 5.42 0.10 0.27 4.4 2.3 0.121 0.028 13 — 39.4 11.2 107 87

12 SJR near Crows Landing 08/09/01 3.84 4.51 0.12 0.34 3.9 3.2 0.115 0.029 10 — 65.7 21.7 81 90

12 SJR near Crows Landing 08/23/01 4.47 5.21 0.12 0.29 3.6 2.3 0.104 0.029 12 — 13.5 29.0 96 91

12 SJR near Crows Landing 09/06/01 4.60 5.17 0.12 0.27 3.6 1.9 0.113 0.031 6 — 23.7 24.1 51 82

12 SJR near Crows Landing 09/20/01 3.69 4.20 0.09 0.21 3.2 1.4 0.102 0.032 6 — 15.8 12.8 47 47

12 SJR near Crows Landing 10/04/01 2.44 2.63 0.18 0.33 7.1 0.8 0.185 0.026 7 — 15.7 12.1 54 93

12 SJR near Crows Landing 10/18/01 1.64 2.05 0.13 0.31 5.4 2.6 0.150 0.028 11 — 16.2 9.2 108 90

12 SJR near Crows Landing 11/01/01 1.49 1.80 0.07 0.19 3.6 0.9 0.108 0.030 4 — 7.8 3.9 53 81

12 SJR near Crows Landing 11/16/01 1.77 2.11 0.12 0.24 5.9 1.6 0.167 0.028 6 — 8.5 4.0 69 91

15 SJR near Patterson 07/12/00 4.32 4.54 0.27 0.35 4.6 — — — — 17 56.1 — 58 —

15 SJR near Patterson 07/26/00 5.05 5.52 0.31 0.33 6.4 — — — — 19 61.9 — 58 —

15 SJR near Patterson 08/09/00 4.30 4.61 0.27 0.37 3.9 — — — — 16 38.5 — 85 —

15 SJR near Patterson 08/23/00 3.98 4.15 0.21 0.27 4.0 — — — — 13 35.4 — 48 —

15 SJR near Patterson 09/06/00 4.03 4.07 0.22 0.31 3.9 — — — — 9.0 25.0 — 58 —

15 SJR near Patterson 09/20/00 4.41 4.74 0.24 0.39 3.3 — — — — 8.8 11.6 — 33 —

15 SJR near Patterson 10/04/00 5.10 5.17 0.34 0.50 3.9 — — — — 8.8 8.5 — 32 —

15 SJR near Patterson 10/18/00 2.38 2.42 0.19 0.26 3.1 — — — — 12 5.1 — 68 —

15 SJR near Patterson 06/13/01 5.22 5.62 0.19 0.36 4.7 — — — — 17 29.2 — 75 —

15 SJR near Patterson 06/27/01 4.49 4.94 0.19 0.31 7.3 — — — — 16 37.8 — 71 —

15 SJR near Patterson 07/11/01 6.37 6.97 0.16 0.38 5.2 — — — — 15 53.8 — 70 —

15 SJR near Patterson 07/25/01 4.77 5.00 0.13 0.34 4.3 — — — — 18 57.1 — 68 —

15 SJR near Patterson 08/07/01 5.21 5.67 0.26 0.35 3.7 — — — — 19 36.2 — 62 —

15 SJR near Patterson 08/22/01 5.10 5.60 0.19 0.37 3.9 — — — — 14 28.8 — 65 —

15 SJR near Patterson 09/05/01 4.67 4.83 0.22 0.37 3.8 — — — — 9.3 24.5 — 38 —

15 SJR near Patterson 09/19/01 5.15 5.16 0.28 0.41 3.3 — — — — 8.2 14.3 — 39 —

15 SJR near Patterson 10/03/01 4.51 5.36 0.29 0.41 5.2 — — — — 7.4 14.8 — 29 —

18 SJR at Laird Park 07/12/00 4.72 5.45 0.18 0.41 4.2 1.7 0.103 0.025 13 — 71.8 — 185 93

18 SJR at Laird Park 07/25/00 4.73 5.70 0.14 0.38 4.2 3.6 0.116 0.028 14 — 64.4 — 85 81

18 SJR at Laird Park 08/08/00 4.68 5.58 0.17 0.37 3.6 1.1 0.099 0.028 12 — E 43.0 — 76 82

18 SJR at Laird Park 08/23/00 4.45 5.04 0.21 0.41 3.7 0.9 — — <10 — 18.9 — — —

18 SJR at Laird Park 09/07/00 4.21 4.98 0.20 0.42 3.2 1.3 0.084 0.026 <10 — 25.3 — — —

18 SJR at Laird Park 09/20/00 4.17 4.72 0.27 0.44 3.4 1.0 0.092 0.027 <10 — 21.7 — — —

18 SJR at Laird Park 10/04/00 3.93 4.38 0.29 0.47 3.7 0.6 0.102 0.028 <10 — 18.9 — 57 85

18 SJR at Laird Park 10/18/00 2.14 2.67 0.15 0.35 4.0 0.7 0.110 0.028 <10 — 11.8 — 122 74

18 SJR at Laird Park 06/13/01 5.20 5.90 0.29 0.56 3.7 1.7 — — 8 — 20.3 17.6 108 85
102 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for San 

Joaquin River sites in California—Continued Site number Site name Date

Time

 Laboratory

 Stream flow 

 (ft3/s)

 Water temperature 

 (C)

 pH 

 Specific conductance

 (μS/cm at 25C)

 Dissolved oxygen

(mg/L) 

 Alkalinity

 (mg/L CaCO3)

 Secchi disk depth 

 (in.)

 Ammonia, dissolved

 (mg/L as N) 

 Nitrate, dissolved

 (mg/L as N)

 Inorganic nitrogen, dissolved

 (mg/L as N)

 Organic nitrogen, dissolved

 (mg/L as N)

18 SJR at Laird Park 06/27/01 09:50 USGS 600 22.5 7.9 1270 7.6 160 11 0.05 4.67 4.84 0.36

18 SJR at Laird Park 07/11/01 11:50 USGS 680 24.0 8.4 1110 11.1 140 14 < 0.04 4.12 4.22 0.35

18 SJR at Laird Park 07/25/01 13:00 USGS 665 26.0 8.5 1220 10.7 — 19 < 0.04 4.63 4.72 0.32

18 SJR at Laird Park 08/08/01 13:30 USGS 575 26.5 8.4 1360 13.6 180 14 E 0.02 4.02 4.11 0.36

18 SJR at Laird Park 08/22/01 13:30 USGS 672 24.0 8.3 1240 7.8 150 12 < 0.04 3.55 3.66 0.32

18 SJR at Laird Park 09/05/01 11:30 USGS 487 23.0 8.5 1300 11.3 160 35 < 0.04 4.32 4.42 0.35

18 SJR at Laird Park 09/19/01 11:30 USGS E 494 — 7.9 1180 — 170 13 < 0.04 4.19 4.29 0.36

18 SJR at Laird Park 10/03/01 11:40 USGS E 434 22.0 7.9 1260 8.0 170 16 < 0.04 3.07 3.17 0.43

18 SJR at Laird Park 10/17/01 08:40 USGS 790 18.5 7.8 1080 7.6 160 15 0.07 2.70 2.82 0.50

18 SJR at Laird Park 10/31/01 09:30 USGS 1320 16.5 7.8 1687 8.3 86 23 < 0.04 2.08 2.13 0.24

18 SJR at Laird Park 11/15/01 11:00 USGS E 1250 16.0 8.1 877 8.0 120 18 < 0.04 1.52 1.57 0.49

24 SJR at Maze Road 07/12/00 12:13 UCD E 1450 24.7 8.0 712 — — — 0.02 3.13 3.15 0.18

24 SJR at Maze Road 07/26/00 11:30 UCD E 1440 23.7 8.1 615 — — — 0.01 2.40 2.41 0.48

24 SJR at Maze Road 08/09/00 10:47 UCD E 1410 23.5 8.1 700 — — — < 0.01 2.98 2.99 0.14

24 SJR at Maze Road 08/23/00 11:35 UCD E 2260 22.0 8.0 426 — — — 0.01 1.66 1.68 0.10

24 SJR at Maze Road 09/06/00 11:30 UCD E 1980 19.7 8.2 539 — — — 0.01 2.42 2.43 0.06

24 SJR at Maze Road 09/20/00 12:00 UCD E 1950 23.7 7.9 464 — — — 0.06 2.03 2.09 0.47

24 SJR at Maze Road 10/04/00 11:40 UCD E 1690 20.0 8.2 555 — — — 0.14 2.41 2.55 0.30

24 SJR at Maze Road 10/18/00 11:15 UCD E 2360 18.3 8.2 489 — — — 0.19 1.81 1.99 0.43

24 SJR at Maze Road 06/13/01 08:00 UCD E 988 21.4 8.0 1020 — — — 0.10 2.50 2.60 0.78

24 SJR at Maze Road 06/27/01 10:20 UCD E 957 22.4 8.0 931 — — — 0.04 3.66 3.70 0.27

24 SJR at Maze Road 07/11/01 07:45 UCD E 820 23.9 8.2 942 — — — 0.04 3.83 3.87 1.17

24 SJR at Maze Road 07/25/01 11:37 UCD E 885 24.9 8.0 915 — — — 0.03 4.41 4.44 0.56

24 SJR at Maze Road 08/07/01 11:00 UCD E 945 26.7 8.3 815 — — — 0.06 3.02 3.08 1.69

24 SJR at Maze Road 08/22/01 10:58 UCD E 972 23.2 8.1 819 — — — 0.05 3.07 3.11 0.35

24 SJR at Maze Road 09/05/01 11:26 UCD E 920 24.1 8.6 945 — — — 0.05 2.45 2.50 0.38

24 SJR at Maze Road 09/19/01 09:10 UCD E 1020 21.7 8.1 817 — — — 0.04 2.91 2.95 0.85

24 SJR at Maze Road 10/03/01 09:20 UCD E 1020 22.0 7.9 880 — — — 0.09 2.70 2.79 2.41

27 SJR near Vernalis 07/12/00 17:30 USGS 1870 26.0 8.6 600 11.7 93 — < 0.02 2.22 2.26 0.27

27 SJR near Vernalis 07/26/00 15:30 USGS 1860 25.5 9.0 550 12.9 79 10 < 0.02 1.56 1.60 0.22

27 SJR near Vernalis 08/09/00 16:00 USGS 1770 26.0 8.6 615 12.8 88 19 < 0.02 1.98 2.02 0.27

27 SJR near Vernalis 08/23/00 09:30 USGS 2610 22.0 8.0 430 8.3 66 17 < 0.02 1.38 1.41 0.19

27 SJR near Vernalis 09/07/00 10:30 USGS 2270 20.0 8.0 504 8.5 72 17 < 0.02 1.84 1.87 0.19

27 SJR near Vernalis 09/20/00 10:30 USGS 2270 23.0 7.6 459 7.7 86 12 < 0.02 1.91 1.95 0.20

27 SJR near Vernalis 10/04/00 10:00 USGS 2090 19.5 8.0 510 8.3 94 10 < 0.02 1.93 1.97 0.19

27 SJR near Vernalis 10/18/00 10:00 USGS 2690 18.0 7.8 490 8.1 86 — E 0.03 1.60 1.65 0.25

27 SJR near Vernalis 06/14/01 12:00 USGS 1550 22.5 8.6 752 10.2 100 — < 0.04 2.00 2.05 0.20

27 SJR near Vernalis 06/28/01 11:50 USGS 1480 22.5 8.4 659 9.4 95 13 < 0.04 1.97 2.03 0.21

27 SJR near Vernalis 07/12/01 10:00 USGS 1300 22.5 8.9 661 11.3 100 15 < 0.04 1.82 1.88 0.18

27 SJR near Vernalis 07/26/01 10:30 USGS 1360 25.5 8.7 719 11.8 — — < 0.04 2.12 2.19 0.20 

27 SJR near Vernalis 08/09/01 11:00 USGS 1200 26.0 8.5 744 10.2 170 5 E 0.03 1.92 1.99 0.24

27 SJR near Vernalis 08/23/01 10:30 USGS 1380 23.0 8.3 732 9.5 100 — < 0.04 2.01 2.07 0.22
Appendix B. 103

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for San 

Joaquin River sites in California—Continued Site number Site name Date Total nitrogen, dissolved (mg/L as N)

 Total nitrogen

 (mg/L as N)

 Orthophosphate, dissolved

(mg/L as P)

 Total phosphorus

 (mg/L as P) 

Organic carbon, dissolved

 (mg/L as C) 

Organic carbon, suspended 

 (mg/L as C)

Ultraviolet absorbance 

at 254 nm (cm–1)

 SUVA

(L/mg-cm)

 Volatile suspended solids

 (mg/L) 

 Particulate organic matter

 (mg/L)

 Chlorophyll-a

 (μg/L)

 Pheophytin-a

 (μg/L)

 Suspended sediment

 (mg/L)

 Suspended sediment, size 

fraction < 0.062 mm (percent)

18 SJR at Laird Park 06/27/01 5.20 5.99 0.22 0.43 3.6 3.2 0.107 0.030 11 — 38.5 18.7 116 86

18 SJR at Laird Park 07/11/01 4.57 5.70 0.14 0.36 3.7 > 3.3 0.106 0.029 20 — 36.7 46.5 115 88

18 SJR at Laird Park 07/25/01 5.04 5.80 0.06 0.31 3.4 > 3.3 0.104 0.031 13 — 62.3 25.4 109 86

18 SJR at Laird Park 08/08/01 4.47 5.29 0.13 0.37 3.6 > 3.3 0.102 0.028 16 — 110 23.4 86 89

18 SJR at Laird Park 08/22/01 3.98 4.84 0.10 0.33 3.1 2.3 0.091 0.029 14 — 53.6 27.3 111 82

18 SJR at Laird Park 09/05/01 4.77 5.80 0.09 0.24 2.7 2.0 0.095 0.035 10 — 59.1 18.2 38 69

18 SJR at Laird Park 09/19/01 4.65 5.26 0.18 0.34 3.2 1.3 0.090 0.028 6 — 18.5 20.3 59 83

18 SJR at Laird Park 10/03/01 3.60 3.96 0.14 0.30 4.3 0.8 0.115 0.027 5 — 14.8 15.2 60 79

18 SJR at Laird Park 10/17/01 3.32 3.68 0.20 0.37 5.3 1.9 0.145 0.027 94 — 15.7 10.3 — —

18 SJR at Laird Park 10/31/01 2.37 2.75 0.17 0.29 3.8 1.2 0.094 0.025 18 — 7.6 7.5 62 82

18 SJR at Laird Park 11/15/01 2.06 2.45 0.14 0.29 5.6 1.8 0.150 0.027 10 — 9.4 5.0 71 85

24 SJR at Maze Road 07/12/00 3.34 3.67 0.14 0.25 4.2 — — — — 18 41.3 — 98 —

24 SJR at Maze Road 07/26/00 2.89 3.12 0.10 0.19 3.9 — — — — 14 37.6 — 50 —

24 SJR at Maze Road 08/09/00 3.13 3.44 0.14 0.19 3.4 — — — — 11 36.7 — 46 —

24 SJR at Maze Road 08/23/00 1.78 2.00 0.10 0.15 2.4 — — — — 11 15.0 — 64 —

24 SJR at Maze Road 09/06/00 2.49 2.74 0.13 0.20 3.5 — — — — 8.0 17.5 — 56 —

24 SJR at Maze Road 09/20/00 2.56 3.17 0.12 0.21 2.3 — — — — 7.2 5.8 — 44 —

24 SJR at Maze Road 10/04/00 2.84 3.04 0.14 0.20 2.8 — — — — 7.8 7.2 — 36 —

24 SJR at Maze Road 10/18/00 2.42 2.46 0.18 0.25 3.7 — — — — 12 5.6 — 74 —

24 SJR at Maze Road 06/13/01 3.38 4.56 0.12 0.28 3.3 — — — — 15 37.0 — 63 —

24 SJR at Maze Road 06/27/01 3.97 4.83 0.14 0.25 2.6 — — — — 18 42.1 — 98 —

24 SJR at Maze Road 07/11/01 5.04 5.50 0.15 0.39 3.9 — — — — 20 68.9 — 110 —

24 SJR at Maze Road 07/25/01 5.00 5.99 0.12 0.30 3.8 — — — — 22 45.4 — 96 —

24 SJR at Maze Road 08/07/01 4.77 5.21 0.13 0.29 3.6 — — — — 21 45.4 — 80 —

24 SJR at Maze Road 08/22/01 3.46 3.78 0.12 0.29 3.1 — — — — 15 25.2 — 75 —

24 SJR at Maze Road 09/05/01 2.88 3.12 0.09 0.27 3.1 — — — — 12 48.7 — 41 —

24 SJR at Maze Road 09/19/01 3.81 4.10 0.11 0.22 2.5 — — — — 8.0 23.5 — 46 —

24 SJR at Maze Road 10/03/01 5.20 5.39 0.15 0.28 3.3 — — — — 6.7 13.5 — 32 —

27 SJR near Vernalis 07/12/00 2.53 3.01 0.12 0.26 3.4 0.6 0.084 0.025 <10 — 50.3 — 63 89

27 SJR near Vernalis 07/26/00 1.82 2.42 0.08 0.16 2.8 0.8 0.084 0.029 <10 — 38.6 — 36 84

27 SJR near Vernalis 08/09/00 2.29 2.78 0.10 0.20 2.7 0.5 0.068 0.025 <10 — E 45.2 — 23 81

27 SJR near Vernalis 08/23/00 1.60 1.94 0.09 0.21 2.5 0.5 — — <10 — 10.8 — 84 80

27 SJR near Vernalis 09/07/00 2.06 2.48 0.10 0.22 2.5 0.6 0.070 0.028 <10 — — — 37 80

27 SJR near Vernalis 09/20/00 2.15 2.42 0.11 0.21 2.3 0.5 0.068 0.030 <10 — 10.5 — 58 90

27 SJR near Vernalis 10/04/00 2.16 2.48 0.10 0.20 2.6 0.3 0.078 0.030 <10 — 11.5 — 43 78

27 SJR near Vernalis 10/18/00 1.90 2.24 0.10 0.24 3.0 — 0.089 0.030 <10 — 7.9 — 72 88

27 SJR near Vernalis 06/14/01 2.25 2.86 0.08 0.24 2.8 1.1 0.071 0.025 5 — 31.2 27.0 49 89

27 SJR near Vernalis 06/28/01 2.24 2.86 0.10 0.23 2.7 1.8 0.080 0.030 7 — 21.7 26.1 63 87

27 SJR near Vernalis 07/12/01 2.06 2.78 0.08 0.24 2.7 3.0 0.078 0.029 12 — 25.4 33.8 58 89

27 SJR near Vernalis 07/26/01 2.39 3.14 0.08 0.21 3.2 2.5 0.082 0.026 7 — 54.2 17.6 63 93

27 SJR near Vernalis 08/09/01 2.23 2.68 0.09 0.24 2.7 7.9 0.080 0.030 7 — 49.8 23.0 54 88

27 SJR near Vernalis 08/23/01 2.29 2.72 0.09 0.25 3.0 0.8 0.073 0.024 11 — 31.5 28.9 167 41
104 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for San 

Joaquin River sites in California—Continued Site number Site name Date

 Laboratory

 Stream flow 

 (ft3/s)

 Water temperature 

 (C)

 pH 

 Specific conductance

 (μS/cm at 25C)

 Dissolved oxygen

(mg/L) 

 Alkalinity

 (mg/L CaCO3)

 Secchi disk depth 

 (in.)

 Ammonia, dissolved

 (mg/L as N) 

 Nitrate, dissolved

 (mg/L as N)

 Inorganic nitrogen, dissolved

 (mg/L as N)

 Organic nitrogen, dissolved

 (mg/L as N)

27 SJR near Vernalis 09/06/01 USGS 1230 22.0 8.4 790 9.3 120 27 < 0.04 1.98 2.03 0.26

27 SJR near Vernalis 09/20/01 USGS 1290 21.0 8.2 584 — 98 17 < 0.04 2.47 2.52 0.20

27 SJR near Vernalis 10/04/01 USGS 1300 21.5 7.7 1702

1Laboratory value.

8.2 110 — < 0.04 1.88 1.94 0.26

27 SJR near Vernalis 10/18/01 USGS 1580 19.0 8.0 690 8.1 120 22 < 0.04 1.84 1.88 0.25

27 SJR near Vernalis 11/01/01 USGS 2390 16.5 7.9 1507 8.6 78 20 < 0.04 1.52 1.56 0.20

27 SJR near Vernalis 11/16/01 USGS 2170 15.0 7.7 668 8.4 97 — 0.04 1.41 1.46 0.30
Appendix B. 105

Appendix B. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for San 

Joaquin River sites in California—Continued Site number Site name Date Total nitrogen, dissolved (mg/L as N)

 Total nitrogen

 (mg/L as N)

 Orthophosphate, dissolved

(mg/L as P)

 Total phosphorus

 (mg/L as P) 

Organic carbon, dissolved

 (mg/L as C) 

Organic carbon, suspended 

 (mg/L as C)

Ultraviolet absorbance 

at 254 nm (cm–1)

 SUVA

(L/mg-cm)

 Volatile suspended solids

 (mg/L) 

 Particulate organic matter

 (mg/L)

 Chlorophyll-a

 (μg/L)

 Pheophytin-a

 (μg/L)

 Suspended sediment

 (mg/L)

 Suspended sediment, size 

fraction < 0.062 mm (percent)

27 SJR near Vernalis 09/06/01 2.29 2.87 0.07 0.19 2.9 2.4 0.076 0.026 7 — 73.2 32.9 29 83

27 SJR near Vernalis 09/20/01 2.72 3.24 0.11 0.23 2.6 1.1 0.080 0.031 6 — 14.1 17.4 50 73

27 SJR near Vernalis 10/04/01 2.20 2.43 0.11 0.22 3.3 1.0 0.083 0.025 4 — 10.3 10.3 46 83

27 SJR near Vernalis 10/18/01 2.13 2.44 0.12 0.23 3.5 1.2 0.091 0.026 7 — 15.9 11.1 57 82

27 SJR near Vernalis 11/01/01 1.76 1.99 0.10 0.21 3.1 1.1 0.077 0.025 6 — 5.4 5.8 56 80

27 SJR near Vernalis 11/16/01 1.76 2.06 0.11 0.20 4.0 0.8 0.111 0.028 6 — 6.1 5.0 58 87
106 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

i

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for 

tributary sites

[SUVA, specific ultraviolet absorbance; UCD, University of California at Davis; USGS, U.S. Geological Survey; E, estimated; Rd., road; Cr., creek; S.P., State 

Park. ft3/s, cubic foot per second; μS/cm, microsiemens per centimeter; mg/L, milligram per liter; in., inch; nm, nanometer; cm-1, per centimeter; L/mg-cm, 

liter per milligram-centimeter; μg/L, microgram per liter; mm, millimeter; <, less than; >, greater than; —, no data reported] Site number Site name Date Time Laboratory Stream flow (ft3/s) Water Temperature (C) pH Specific conductance (μS/cm at 25C) Dissolved Oxygen (mg/L) Alkalinity (mg/L CaCO3) Secchi disk depth (in.)

 Ammonia, dissolved

 (mg/L as N) 

 Nitrate, dissolved

 (mg/L as N)

Inorganic nitrogen, dissolved

 (mg/L as N)

Organic nitrogen, dissolved

 (mg/L as N)

2 Salt Slough near Stevinson 07/12/00 13:50 UCD 225 26.1 7.6 905 — — — 0.34 3.67 4.02 0.33

2 Salt Slough near Stevinson 07/26/00 14:30 UCD 171 26.2 8.0 969 — — — 0.29 4.06 4.34 0.80

2 Salt Slough near Stevinson 08/09/00 12:58 UCD 205 25.5 7.7 775 — — — 0.06 2.27 2.33 0.27

2 Salt Slough near Stevinson 08/23/00 13:55 UCD 164 24.9 8.0 901 — — — 0.04 1.66 1.70 0.24

2 Salt Slough near Stevinson 09/06/00 14:30 UCD 101 22.4 8.3 1070 — — — 0.03 1.13 1.16 0.26

2 Salt Slough near Stevinson 09/20/00 15:25 UCD 85 28.1 8.2 2190 — — — 0.02 0.25 0.27 0.38

2 Salt Slough near Stevinson 10/04/00 13:46 UCD 85 21.4 8.1 1180 — — — 0.05 0.50 0.55 0.13

2 Salt Slough near Stevinson 10/18/00 13:14 UCD 116 19.7 8.3 1260 — — — 0.04 0.28 0.32 0.46

2 Salt Slough near Stevinson 06/13/01 10:00 UCD 135 20.5 7.8 1230 — — — 0.10 3.61 3.71 0.89

2 Salt Slough near Stevinson 06/27/01 12:30 UCD 205 23.0 7.9 927 — — — 0.09 1.77 1.85 0.98

2 Salt Slough near Stevinson 07/11/01 10:00 UCD 196 23.3 7.8 917 — — — 0.10 2.18 2.28 1.33

2 Salt Slough near Stevinson 07/25/01 13:36 UCD 187 29.1 8.1 1020 — — — 0.10 1.92 2.01 0.41

2 Salt Slough near Stevinson 08/07/01 13:40 UCD 153 29.7 7.9 1040 — — — 0.03 1.15 1.18 0.60

2 Salt Slough near Stevinson 08/22/01 13:19 UCD 195 23.4 7.9 956 — — — 0.06 1.26 1.32 0.90

2 Salt Slough near Stevinson 09/05/01 13:45 UCD 51 26.2 8.4 1570 — — — 0.05 0.17 0.22 0.35

2 Salt Slough near Stevinson 09/19/01 11:30 UCD 53 22.7 8.0 1580 — — — 0.04 0.14 0.18 0.78

2 Salt Slough near Stevinson 10/03/01 10:45 UCD 45 21.3 7.9 1730 — — — 0.05 0.19 0.24 0.64

4 San Luis Drain, Site B 07/12/00 14:20 UCD E 67 27.2 8.4 3400 — — — 0.12 12.5 12.6 0.06

4 San Luis Drain, Site B 07/26/00 15:00 UCD E 57 27.9 8.5 3700 — — — 0.07 15.4 15.5 3.08

4 San Luis Drain, Site B 08/09/00 13:26 UCD E 55 27.4 8.3 3450 — — — 0.01 10.8 10.8 0.11

4 San Luis Drain, Site B 08/23/00 14:20 UCD E 57 26.4 8.5 3020 — — — 0.02 8.59 8.60 0.80

4 San Luis Drain, Site B 09/06/00 15:00 UCD E 47 22.4 8.5 3510 — — — 0.05 13.6 13.7 0.31

4 San Luis Drain, Site B 09/20/00 15:55 UCD E 21 30.1 8.6 4520 — — — 0.04 13.5 13.5 1.65

4 San Luis Drain, Site B 10/04/00 14:20 UCD 21 23.6 8.4 4190 — — — 0.36 10.6 11.0 0.29

4 San Luis Drain, Site B 10/18/00 13:45 UCD 19 21.0 8.3 3440 — — — 0.20 12.5 12.7 1.42

4 San Luis Drain, Site B 06/13/01 10:25 UCD 61 21.1 8.0 4180 — — — 0.12 19.5 19.6 0.05

4 San Luis Drain, Site B 06/27/01 13:20 UCD 50 24.4 8.3 3650 — — — 0.04 11.9 11.9 0.09

4 San Luis Drain, Site B 07/11/01 10:40 UCD 59 25.1 8.2 3580 — — — 0.03 13.4 13.4 0.58

4 San Luis Drain, Site B 07/25/01 13:41 UCD 56 26.2 8.1 4230 — — — 0.17 15.5 15.6 2.29

4 San Luis Drain, Site B 08/07/01 14:10 UCD 61 29.3 8.6 3510 — — — 0.03 9.90 9.93 0.67

4 San Luis Drain, Site B 08/22/01 13:34 UCD 53 25.2 8.5 3380 — — — 0.24 10.5 10.7 0.79

4 San Luis Drain, Site B 09/05/01 14:15 UCD 33 27.9 8.4 3410 — — — 0.14 8.57 8.71 1.80

4 San Luis Drain, Site B 09/19/01 12:20 UCD 17 24.4 8.4 4400 — — — 0.06 9.46 9.52 3.41

4 San Luis Drain, Site B 10/03/01 10:55 UCD 9 23.7 8.1 3880 — — — 0.09 4.27 4.36 1.30

5 Mud Slough near Gustine 07/12/00 14:25 UCD 74 26.8 8.4 3220 — — — 0.07 11.1 11.2 0.32

5 Mud Slough near Gustine 07/26/00 15:10 UCD 63 27.2 8.5 3590 — — — 0.04 13.6 13.6 2.02

5 Mud Slough near Gustine 08/09/00 13:38 UCD 64 26.3 8.3 3110 — — — 0.02 9.10 9.12 0.22

5 Mud Slough near Gustine 08/23/00 14:40 UCD 60 25.8 8.5 2860 — — — 0.01 8.03 8.04 0.70

5 Mud Slough near Gustine 09/06/00 15:10 UCD 56 22.4 8.5 3120 — — — 0.04 11.6 11.6 0.24

5 Mud Slough near Gustine 09/20/00 15:59 UCD 53 28.5 7.9 2200 — — — 0.08 5.32 5.40 0.31
Appendix C. 107

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for 

tributary sites—Continued Site number Site name

Date

 Total nitrogen, dissolved

 (mg/L as N)

 Total nitrogen

 (mg/L as N)

 Orthophosphate, dissolved

(mg/L as P)

 Total phosphorus

 (mg/L as P) 

Organic carbon, dissolved

 (mg/L as C) 

Organic carbon, suspended 

 (mg/L as C)

Ultraviolet absorbance 

at 254 nm (cm–1)

 SUVA

(L/mg-cm)

 Volatile suspended solids

 (mg/L) 

 Particulate organic matter

 (mg/L)

 Chlorophyll-a

(μg/L)

 Pheophytin-a

(μg/L)

 Suspended sediment

 (mg/L)

 Suspended sediment, size 

fraction < 0.062 mm (percent)

2 Salt Slough near Stevinson 07/12/00 4.35 4.52 0.13 0.28 13.5 — — — — 25 14.2 — 152 —

2 Salt Slough near Stevinson 07/26/00 5.14 5.40 0.19 0.31 6.4 — — — — 28 24.6 — 146 —

2 Salt Slough near Stevinson 08/09/00 2.60 2.84 0.18 0.30 4.7 — — — — 30 16.4 — 169 —

2 Salt Slough near Stevinson 08/23/00 1.94 2.28 0.16 0.26 4.9 — — — — 28 14.2 — 165 —

2 Salt Slough near Stevinson 09/06/00 1.42 1.64 0.08 0.17 5.0 — — — — 10 16.1 — 70 —

2 Salt Slough near Stevinson 09/20/00 0.65 0.93 0.11 0.23 4.7 — — — — 10 11.9 — 43 —

2 Salt Slough near Stevinson 10/04/00 0.68 0.85 0.10 0.21 5.3 — — — — 18 10.2 — 85 —

2 Salt Slough near Stevinson 10/18/00 0.78 1.03 0.10 0.23 5.1 — — — — 23 10.2 — 135 —

2 Salt Slough near Stevinson 06/13/01 4.60 5.31 0.15 0.50 6.6 — — — — 30 12.5 — 148 —

2 Salt Slough near Stevinson 06/27/01 2.83 2.93 0.19 0.34 5.6 — — — — 25 16.3 — 181 —

2 Salt Slough near Stevinson 07/11/01 3.61 4.28 0.17 0.52 5.1 — — — — 33 23.0 — 215 —

2 Salt Slough near Stevinson 07/25/01 2.43 2.88 0.16 0.42 5.1 — — — — 28 15.1 — 152 —

2 Salt Slough near Stevinson 08/07/01 1.78 2.24 0.16 0.28 4.0 — — — — 23 23.5 — 93 —

2 Salt Slough near Stevinson 08/22/01 2.22 2.42 0.16 0.38 3.8 — — — — 22 13.0 — 115 —

2 Salt Slough near Stevinson 09/05/01 0.57 0.82 0.17 0.27 4.6 — — — — 9.3 9.4 — 30 —

2 Salt Slough near Stevinson 09/19/01 0.96 1.09 0.10 0.18 4.2 — — — — 11 12.5 — 74 —

2 Salt Slough near Stevinson 10/03/01 0.89 1.90 0.10 0.28 5.3 — — — — 13 9.3 — 56 —

4 San Luis Drain, Site B 07/12/00 12.7 13.0 0.01 0.02 7.0 — — — — 16 31.0 — 40 —

4 San Luis Drain, Site B 07/26/00 18.6 19.1 0.02 0.02 8.2 — — — — 15 20.8 — 31 —

4 San Luis Drain, Site B 08/09/00 10.9 11.4 0.01 0.03 6.6 — — — — 18 53.9 — 33 —

4 San Luis Drain, Site B 08/23/00 9.40 9.60 < 0.01 0.04 6.7 — — — — 17 30.9 — 26 —

4 San Luis Drain, Site B 09/06/00 14.0 14.2 < 0.01 0.03 5.9 — — — — 19 75.5 — 50 —

4 San Luis Drain, Site B 09/20/00 15.2 16.2 0.01 0.02 5.1 — — — — 13 12.4 — 34 —

4 San Luis Drain, Site B 10/04/00 11.2 11.4 < 0.01 0.03 5.7 — — — — 22 20.7 — 42 —

4 San Luis Drain, Site B 10/18/00 14.1 14.7 0.01 0.02 6.0 — — — — 12 14.0 — 26 —

4 San Luis Drain, Site B 06/13/01 19.7 22.9 0.01 0.07 5.6 — — — — 20 62.2 — 47 —

4 San Luis Drain, Site B 06/27/01 12.0 12.6 < 0.01 0.12 6.4 — — — — 12 55.1 — 58 —

4 San Luis Drain, Site B 07/11/01 14.0 14.9 0.01 0.02 8.1 — — — — 15 24.5 — 39 —

4 San Luis Drain, Site B 07/25/01 17.9 19.5 < 0.01 0.08 5.3 — — — — 18 47.9 — 37 —

4 San Luis Drain, Site B 08/07/01 10.6 11.5 0.01 0.03 5.3 — — — — 19 57.1 — 30 —

4 San Luis Drain, Site B 08/22/01 11.5 11.6 0.01 0.03 4.7 — — — — 14 32.8 — 21 —

4 San Luis Drain, Site B 09/05/01 10.5 11.4 0.01 0.03 5.4 — — — — 12 16.8 — 20 —

4 San Luis Drain, Site B 09/19/01 12.9 13.6 < 0.01 0.06 4.7 — — — — 10 10.8 — 16 —

4 San Luis Drain, Site B 10/03/01 5.66 5.79 0.01 0.02 5.2 — — — — 13 17.8 — 25 —

5 Mud Slough near Gustine 07/12/00 11.5 11.6 0.01 0.03 7.1 — — — — 18 33.7 — 57 —

5 Mud Slough near Gustine 07/26/00 15.6 15.7 0.04 0.06 8.2 — — — — 17 20.4 — 52 —

5 Mud Slough near Gustine 08/09/00 9.34 9.56 0.01 0.05 8.3 — — — — 23 62.9 — 61 —

5 Mud Slough near Gustine 08/23/00 8.74 9.00 0.01 0.04 6.6 — — — — 20 47.3 — 44 —

5 Mud Slough near Gustine 09/06/00 11.8 12.2 <0.01 0.05 5.6 — — — — 13 60.1 — 45 —

5 Mud Slough near Gustine 09/20/00 5.71 6.43 0.03 0.17 6.9 — — — — 13 13.6 — 35 —
108 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for 

tributary sites—Continued Site number Site name

Date

Time

 Laboratory

 Stream flow 

 (ft3/s)

 Water Temperature 

 (C)

 pH 

 Specific conductance

(μS/cm at 25C)

 Dissolved Oxygen

 (mg/L) 

 Alkalinity

 (mg/L CaCO3)

 Secchi disk depth 

 (in.)

 Ammonia, dissolved

 (mg/L as N) 

 Nitrate, dissolved

 (mg/L as N)

Inorganic nitrogen, dissolved

 (mg/L as N)

Organic nitrogen, dissolved

 (mg/L as N)

5 Mud Slough near Gustine 10/04/00 14:27 UCD 87 22.8 7.8 1550 — — — 0.13 2.40 2.53 0.20

5 Mud Slough near Gustine 10/18/00 13:53 UCD 197 20.5 8.2 1107 — — — 0.10 1.56 1.66 1.35

5 Mud Slough near Gustine 06/13/01 10:35 UCD 68 21.1 8.1 4110 — — — 0.06 19.7 19.8 0.84

5 Mud Slough near Gustine 06/27/01 12:50 UCD 63 23.3 8.4 4110 — — — 0.04 17.1 17.1 1.67

5 Mud Slough near Gustine 07/10/01 09:50 USGS 79 27.0 8.1 3730 8.8 — 18 < 0.04 11.3 11.4 0.61

5 Mud Slough near Gustine 07/25/01 14:05 UCD 64 29.1 8.2 4120 — — — 0.14 14.7 14.9 2.03

5 Mud Slough near Gustine 08/08/01 10:20 USGS 67 — 8.6 3170 — 120 17 E 0.02 10.2 10.3 0.60

5 Mud Slough near Gustine 08/22/01 13:41 UCD 60 25.2 8.5 3260 — — — 0.05 9.11 9.17 0.57

5 Mud Slough near Gustine 09/06/01 12:00 USGS 50 24.0 8.5 2010 8.5 140 17 < 0.04 7.53 7.65 0.84

5 Mud Slough near Gustine 09/19/01 12:05 UCD 46 24.1 8.4 2500 — — — 0.05 3.64 3.69 1.71

5 Mud Slough near Gustine 10/04/01 11:30 USGS 105 23.0 7.6 11590 8.2 200 19 < 0.04 0.65 0.68 1.18

5 Mud Slough near Gustine 10/31/01 10:00 USGS 133 18.0 8.0 11900 5.9 210 23 0.14 1.22 1.40 0.96

6 Los Banos Creek at Hwy 140 07/12/00 14:50 UCD 2 32.9 8.1 1090 — — — 0.03 0.04 0.07 0.69

6 Los Banos Creek at Hwy 140 07/26/00 15:24 UCD 6 30.2 8.4 885 — — — <0.01 0.02 0.02 1.19

6 Los Banos Creek at Hwy 140 08/09/00 13:50 UCD 3 29.1 7.9 1360 — — — <0.01 0.43 0.43 0.81

6 Los Banos Creek at Hwy 140 08/23/00 14:48 UCD 3 30.3 8.4 1320 — — — 0.32 1.67 1.99 0.44

6 Los Banos Creek at Hwy 140 09/06/00 15:24 UCD 12 24.6 8.2 1150 — — — 0.11 0.52 0.63 0.98

6 Los Banos Creek at Hwy 140 09/20/00 16:20 UCD 6 27.8 7.5 553 — — — 0.02 0.74 0.76 0.39

6 Los Banos Creek at Hwy 140 10/04/00 14:40 UCD 27 23.1 7.4 576 — — — 0.01 0.02 0.03 0.61

6 Los Banos Creek at Hwy 140 10/18/00 14:07 UCD 38 22.0 8.2 631 — — — 0.08 0.13 0.20 0.90

6 Los Banos Creek at Hwy 140 06/13/01 10:50 UCD 7 20.7 7.7 1191 — — — 0.12 2.77 2.89 1.79

6 Los Banos Creek at Hwy 140 06/27/01 13:30 UCD 4 23.9 7.9 982 — — — 0.01 1.20 1.21 1.81

6 Los Banos Creek at Hwy 140 07/11/01 11:15 UCD 6 24.6 7.7 1330 — — — 0.05 0.08 0.14 1.92

6 Los Banos Creek at Hwy 140 07/25/01 13:15 UCD 13 27.5 8.1 1640 — — — 0.30 0.46 0.75 1.67

6 Los Banos Creek at Hwy 140 08/07/01 14:45 UCD 5 34.2 8.7 1420 — — — 0.03 0.22 0.25 0.93

6 Los Banos Creek at Hwy 140 08/22/01 13:57 UCD 14 28.1 8.2 1390 — — — 0.20 1.37 1.57 1.15

6 Los Banos Creek at Hwy 140 09/05/01 14:27 UCD 8 28.1 8.2 1040 — — — 0.28 1.02 1.30 0.85

6 Los Banos Creek at Hwy 140 09/19/01 12:45 UCD 3 24.6 8.5 1190 — — — 0.06 0.09 0.15 1.34

6 Los Banos Creek at Hwy 140 10/03/01 11:15 UCD 45 23.5 7.5 836 — — — 0.01 0.44 0.45 4.84

9 Merced River at River Rd. 07/12/00 13:20 UCD E 182 25.8 7.9 259 — — — 0.03 2.97 3.00 0.07

9 Merced River at River Rd. 07/26/00 14:10 UCD E 137 27.4 8.0 293 — — — 0.03 3.67 3.70 0.33

9 Merced River at River Rd. 08/09/00 12:22 UCD E 140 24.8 7.7 245 — — — <0.01 2.77 2.77 0.19

9 Merced River at River Rd. 08/23/00 13:18 UCD E 153 25.3 8.0 234 — — — 0.03 2.78 2.81 0.15

9 Merced River at River Rd. 09/06/00 14:10 UCD E 153 22.4 8.0 198 — — — 0.03 2.73 2.76 0.08

9 Merced River at River Rd. 09/20/00 14:50 UCD E 156 27.2 7.9 236 — — — 0.03 2.66 2.70 0.06

9 Merced River at River Rd. 10/04/00 13:10 UCD E 139 19.8 8.0 286 — — — 0.07 3.36 3.43 0.19

9 Merced River at River Rd. 10/18/00 12:36 UCD E 797 16.7 7.7 41 — — — 0.06 0.13 0.19 0.08

9 Merced River at River Rd. 06/13/01 09:30 UCD E 158 21.4 8.0 249 — — — 0.06 2.27 2.33 0.03

9 Merced River at River Rd. 06/27/01 11:30 UCD E 158 22.9 7.6 276 — — — 0.03 2.68 2.71 0.42

9 Merced River at River Rd. 07/11/01 09:15 UCD E 125 23.0 8.2 274 — — — 0.23 3.43 3.65 0.41

9 Merced River at River Rd. 07/25/01 12:57 UCD E 122 25.8 8.1 334 — — — 0.04 3.25 3.29 0.45

9 Merced River at River Rd. 08/07/01 12:05 UCD E 85 27.8 7.9 322 — — — 0.04 3.66 3.69 0.41

9 Merced River at River Rd. 08/22/01 12:05 UCD E 98 23.7 8.1 334 — — — 0.03 3.45 3.48 0.17
Appendix C. 109

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for 

tributary sites—Continued Site number Site name

Date

 Total nitrogen, dissolved

 (mg/L as N)

 Total nitrogen

 (mg/L as N)

 Orthophosphate, dissolved

(mg/L as P)

 Total phosphorus

 (mg/L as P) 

Organic carbon, dissolved

 (mg/L as C) 

Organic carbon, suspended 

 (mg/L as C)

Ultraviolet absorbance 

at 254 nm (cm–1)

 SUVA

(L/mg-cm)

 Volatile suspended solids

 (mg/L) 

 Particulate organic matter

 (mg/L)

 Chlorophyll-a

(μg/L)

 Pheophytin-a

(μg/L)

 Suspended sediment

 (mg/L)

 Suspended sediment, size 

fraction < 0.062 mm (percent)

5 Mud Slough near Gustine 10/04/00 2.73 3.27 0.16 0.29 9.2 — — — — 16 11.8 — 52 —

5 Mud Slough near Gustine 10/18/00 3.01 3.35 0.38 0.43 8.0 — — — — 10 7.2 — 30 —

5 Mud Slough near Gustine 06/13/01 20.6 20.7 0.01 0.07 5.4 — — — — 21 58.8 — 50 —

5 Mud Slough near Gustine 06/27/01 18.8 19.0 < 0.01 0.12 6.7 — — — — 8.3 55.4 — 34 —

5 Mud Slough near Gustine 07/10/01 12.0 12.5 < 0.02 0.08 3.9 2.7 0.138 0.035 9 — 6.1 14 36 83

5 Mud Slough near Gustine 07/25/01 16.9 17.4 < 0.01 0.02 5.5 — — — — 20 55.4 — 40 —

5 Mud Slough near Gustine 08/08/01 10.9 11.5 < 0.02 0.05 5.0 2.1 0.127 0.025 9 — 43.3 12 25 25

5 Mud Slough near Gustine 08/22/01 9.73 10.8 <0.01 0.06 5.1 — — — — 16 31.3 — 34 —

5 Mud Slough near Gustine 09/06/01 8.49 8.93 E 0.09 0.16 6.3 1.8 0.186 0.030 8 — 17.9 14 22 94

5 Mud Slough near Gustine 09/19/01 5.40 5.89 0.06 0.19 6.9 — — — — 8.0 13.7 — 24 —

5 Mud Slough near Gustine 10/04/01 1.86 2.36 0.51 0.82 14.0 2.1 0.424 0.030 6 — 18.9 12 24 46

5 Mud Slough near Gustine 10/31/01 2.36 2.66 0.27 0.45 12.0 0.8 0.341 0.028 8 — 13.2 5.4 29 82

6 Los Banos Creek at Hwy 140 07/12/00 0.76 1.09 0.12 0.27 7.9 — — — — 14 66.7 — 49 —

6 Los Banos Creek at Hwy 140 07/26/00 1.21 1.80 0.35 0.49 16.1 — — — — 33 50.1 — 132 —

6 Los Banos Creek at Hwy 140 08/09/00 1.24 1.60 0.25 0.30 9.6 — — — — 16 13.9 — 53 —

6 Los Banos Creek at Hwy 140 08/23/00 2.43 3.04 0.30 0.38 10.6 — — — — 27 19.6 — 161 —

6 Los Banos Creek at Hwy 140 09/06/00 1.61 1.84 0.19 0.27 13.3 — — — — 12 15.1 — 71 —

6 Los Banos Creek at Hwy 140 09/20/00 1.15 1.88 0.27 0.77 10.9 — — — — 11 9.7 — 20 —

6 Los Banos Creek at Hwy 140 10/04/00 0.63 1.15 0.41 0.91 15.1 — — — — 13 11.0 — 17 —

6 Los Banos Creek at Hwy 140 10/18/00 1.10 1.16 0.32 0.52 17.6 — — — — 6.7 3.2 — 24 —

6 Los Banos Creek at Hwy 140 06/13/01 4.68 5.40 0.16 0.57 12.3 — — — — 29 66.1 — 135 —

6 Los Banos Creek at Hwy 140 06/27/01 3.02 3.57 0.05 0.31 7.5 — — — — 20 41.0 — 110 —

6 Los Banos Creek at Hwy 140 07/11/01 2.06 3.28 0.30 0.64 11.1 — — — — 29 65.5 — 91 —

6 Los Banos Creek at Hwy 140 07/25/01 2.43 3.36 0.04 0.08 14.4 — — — — 27 33.7 — 64 —

6 Los Banos Creek at Hwy 140 08/07/01 1.18 2.73 0.19 0.37 12.9 — — — — 32 47.5 — 82 —

6 Los Banos Creek at Hwy 140 08/22/01 2.72 3.62 0.08 0.36 8.1 — — — — 23 33.1 — 98 —

6 Los Banos Creek at Hwy 140 09/05/01 2.15 3.16 0.10 0.35 5.6 — — — — 20 17.3 — 123 —

6 Los Banos Creek at Hwy 140 09/19/01 1.49 2.08 0.51 0.63 8.8 — — — — 4.6 9.1 — 11 —

6 Los Banos Creek at Hwy 140 10/03/01 5.29 6.54 0.36 0.62 8.3 — — — — 8.0 15.4 — 16 —

9 Merced River at River Rd. 07/12/00 3.08 3.14 0.04 0.07 2.0 — — — — 2.2 1.0 — 5 —

9 Merced River at River Rd. 07/26/00 4.03 4.57 0.04 0.06 2.0 — — — — 2.3 0.7 — 4 —

9 Merced River at River Rd. 08/09/00 2.96 3.06 0.05 0.08 2.0 — — — — 2.5 1.4 — 4 —

9 Merced River at River Rd. 08/23/00 2.96 2.98 0.04 0.06 2.3 — — — — 2.4 1.3 — 5 —

9 Merced River at River Rd. 09/06/00 2.84 2.84 0.02 0.04 1.7 — — — — 1.0 0.7 — 6 —

9 Merced River at River Rd. 09/20/00 2.75 2.82 0.03 0.05 1.8 — — — — 1.1 0.8 — 5 —

9 Merced River at River Rd. 10/04/00 3.62 3.58 0.05 0.06 2.0 — — — — 2.1 0.8 — 2 —

9 Merced River at River Rd. 10/18/00 0.27 0.37 0.01 0.04 2.6 — — — — 3.2 1.1 — 14 —

9 Merced River at River Rd. 06/13/01 2.36 2.41 0.02 0.05 0.7 — — — — 2.4 3.1 — 7 —

9 Merced River at River Rd. 06/27/01 3.13 3.42 0.03 0.08 2.2 — — — — 2.1 3.0 — 9 —

9 Merced River at River Rd. 07/11/01 4.06 4.46 0.07 0.09 2.0 — — — — 3.3 2.2 — 18 —

9 Merced River at River Rd. 07/25/01 3.74 3.94 0.04 0.11 2.4 — — — — 4.8 5.6 — 12 —

9 Merced River at River Rd. 08/07/01 4.10 4.82 0.03 0.06 1.9 — — — — 2.6 1.7 — 5 —

9 Merced River at River Rd. 08/22/01 3.65 3.97 0.03 0.07 1.8 — — — — 2.2 1.5 — 8 —
Appendix C. 110

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for 

tributary sites—Continued Site number Site name

Date

Time

 Laboratory

 Stream flow 

 (ft3/s)

 Water Temperature 

 (C)

 pH 

 Specific conductance

(μS/cm at 25C)

 Dissolved Oxygen

 (mg/L) 

 Alkalinity

 (mg/L CaCO3)

 Secchi disk depth 

 (in.)

 Ammonia, dissolved

 (mg/L as N) 

 Nitrate, dissolved

 (mg/L as N)

Inorganic nitrogen, dissolved

 (mg/L as N)

Organic nitrogen, dissolved

 (mg/L as N)

9 Merced River at River Rd. 09/05/01 12:33 UCD E 49 24.7 7.9 330 — — — 0.04 2.92 2.95 0.42

9 Merced River at River Rd. 09/19/01 10:45 UCD E 175 22.3 8.0 215 — — — 0.05 2.25 2.31 0.55

9 Merced River at River Rd. 10/03/01 10:20 UCD E 96 21.0 7.9 344 — — — 0.04 3.05 3.09 0.62

11 Orestimba Creek at River Rd. 07/12/00 13:10 UCD 11 23.2 8.1 643 — — — 0.02 4.52 4.54 0.19

11 Orestimba Creek at River Rd. 07/26/00 13:40 UCD 13 23.4 8.2 661 — — — 0.15 6.27 6.42 0.40

11 Orestimba Creek at River Rd. 08/09/00 12:07 UCD 27 22.5 7.9 498 — — — <0.01 2.44 2.44 0.13

11 Orestimba Creek at River Rd. 08/23/00 13:01 UCD 11 22.4 8.2 635 — — — 0.03 4.03 4.06 0.42

11 Orestimba Creek at River Rd. 09/06/00 13:40 UCD 23 19.6 8.3 446 — — — 0.08 2.03 2.11 0.07

11 Orestimba Creek at River Rd. 09/20/00 14:35 UCD 28 25.9 8.1 436 — — — 0.08 1.64 1.72 0.70

11 Orestimba Creek at River Rd. 10/04/00 12:49 UCD 11 18.1 8.1 450 — — — 0.06 0.90 0.96 0.06

11 Orestimba Creek at River Rd. 10/18/00 12:08 UCD 81 18.3 8.2 438 — — — 0.05 0.54 0.59 0.33

11 Orestimba Creek at River Rd. 06/13/01 10:00 USGS 100 20.5 8.2 667 8.3 120 4 0.10 2.66 2.79 0.30

11 Orestimba Creek at River Rd. 06/27/01 11:15 UCD 17 21.9 8.1 738 — — — 0.05 5.36 5.41 0.24

11 Orestimba Creek at River Rd. 07/10/01 12:40 USGS 19 — 7.9 860 6.4 — 4 0.06 5.56 5.82 0.50

11 Orestimba Creek at River Rd. 07/25/01 12:36 UCD 9.7 26.3 8.3 811 — — — 0.09 5.99 6.08 0.70

11 Orestimba Creek at River Rd. 08/08/01 12:40 USGS 12 — 8.3 1800 — 130 — E0.02 4.61 4.66 0.26

11 Orestimba Creek at River Rd. 08/22/01 11:54 UCD 10 20.6 8.1 846 — — — 0.10 3.84 3.94 0.68

11 Orestimba Creek at River Rd. 09/05/01 12:18 UCD 7.3 22.5 8.1 925 — — — 0.12 5.05 5.16 0.82

11 Orestimba Creek at River Rd. 09/19/01 10:25 UCD 1.4 19.3 8.1 1210 — — — 0.05 7.06 7.11 2.04

11 Orestimba Creek at River Rd. 10/04/01 15:00 USGS 11 20.5 7.9 1968 5.2 140 — E0.02 3.41 3.46 0.43

11 Orestimba Creek at River Rd. 10/31/01 15:40 USGS 78 17.0 8.2 1743 9.0 98 12 E0.02 0.84 0.87 0.22

13 Spanish Grant Drain 06/13/01 13:00 USGS 13 23.0 7.9 1280 6.9 190 4 0.08 6.35 6.54 0.72

13 Spanish Grant Drain 07/11/01 12:30 USGS 28 — 7.8 971 7.2 120 3 0.31 5.15 5.56 0.56

13 Spanish Grant Drain 08/06/01 12:30 USGS 29 24.0 8.2 927 7.4 170 5 0.08 6.11 6.27 0.54

13 Spanish Grant Drain 09/04/01 11:10 USGS 17 27.5 8.0 892 — 130 9 E0.08 E5.45 E 5.41 E 0.82

13 Spanish Grant Drain 10/02/01 10:20 USGS 2.0 21.0 7.9 1815 7.6 120 7 0.04 1.61 1.69 0.27

13 Spanish Grant Drain 10/30/01 09:50 USGS <0.01 17.0 7.7 1778 4.0 120 — E0.04 1.00 1.07 0.38

14 Harding Drain at Carpenter Rd. 06/13/01 16:00 USGS 57 22.0 7.8 454 7.9 100 >32 2.43 4.18 7.26 0.67

14 Harding Drain at Carpenter Rd. 07/12/01 10:10 USGS 85 22.0 8.0 458 8.2 — >29 0.33 4.47 5.04 0.35

14 Harding Drain at Carpenter Rd. 08/06/01 10:30 USGS 106 21.5 17.8 1558 6.2 140 >36 1.86 6.81 9.35 0.84

14 Harding Drain at Carpenter Rd. 09/04/01 13:10 USGS 82 24.0 8.1 467 — 150 >32 E1.02 E7.68 E9.43 E0.78

14 Harding Drain at Carpenter Rd. 10/02/01 12:30 USGS — 22.5 7.8 438 7.4 140 >60 1.05 6.82 8.63 0.65

14 Harding Drain at Carpenter Rd. 10/30/01 12:00 USGS — 19.0 8.0 875 6.0 220 — 2.10 11.6 15.4 0.90

17 Westport Drain near Modesto 06/14/01 12:30 USGS 36 23.5 8.2 1230 9.1 86 >23 E0.04 5.21 E 5.32 0.21

17 Westport Drain near Modesto 07/12/01 13:00 USGS 76 24.0 8.0 307 8.4 — — 0.22 5.59 5.87 0.29

17 Westport Drain near Modesto 08/07/01 10:30 USGS 18 23.0 8.0 320 8.8 94 >24 0.05 5.90 6.00 0.26

17 Westport Drain near Modesto 09/05/01 10:20 USGS 20 21.5 8.2 309 8.1 120 — E0.04 3.29 3.38 0.25

17 Westport Drain near Modesto 10/03/01 11:30 USGS 13 22.5 8.0 679 7.1 200 >13 0.11 8.77 8.99 0.42

17 Westport Drain near Modesto 11/01/01 11:00 USGS 2.9 15.0 8.3 1957 9.8 300 >8 0.04 18.5 18.7 0.66

20 Dry Creek at Gallo Bridge 06/15/01 10:00 USGS 93 20.0 7.7 104 7.7 58 10 < 0.04 0.40 0.46 0.67

20 Dry Creek at Gallo Bridge 07/13/01 09:20 USGS 70 25.0 7.5 113 7.8 35 19 < 0.04 0.63 0.69 0.53

20 Dry Creek at Gallo Bridge 08/07/01 14:40 USGS 92 25.5 7.4 759 7.2 44 — E0.04 0.32 0.37 0.57

20 Dry Creek at Gallo Bridge 09/05/01 13:00 USGS 99 23.0 8.1 84 7.7 38 — < 0.04 0.34 0.37 0.47
Appendix C. 111

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for 

tributary sites—Continued Site number Site name

Date

 Total nitrogen, dissolved

 (mg/L as N)

 Total nitrogen

 (mg/L as N)

 Orthophosphate, dissolved

(mg/L as P)

 Total phosphorus

 (mg/L as P) 

Organic carbon, dissolved

 (mg/L as C) 

Organic carbon, suspended 

 (mg/L as C)

Ultraviolet absorbance 

at 254 nm (cm–1)

 SUVA

(L/mg-cm)

 Volatile suspended solids

 (mg/L) 

 Particulate organic matter

 (mg/L)

 Chlorophyll-a

(μg/L)

 Pheophytin-a

(μg/L)

 Suspended sediment

 (mg/L)

 Suspended sediment, size 

fraction < 0.062 mm (percent)

9 Merced River at River Rd. 09/05/01 3.37 3.66 0.02 0.43 1.7 — — — — 1.5 1.6 — 6 —

9 Merced River at River Rd. 09/19/01 2.86 2.97 0.02 0.05 1.4 — — — — 2.1 1.7 — 8 —

9 Merced River at River Rd. 10/03/01 3.71 3.72 0.02 0.06 1.7 — — — — 1.4 1.5 — 3 —

11 Orestimba Creek at River Rd. 07/12/00 4.74 4.99 0.13 0.17 3.7 — — — — 27 2.0 — 170 —

11 Orestimba Creek at River Rd. 07/26/00 6.82 6.95 0.12 0.17 3.2 — — — — 29 4.0 — 214 —

11 Orestimba Creek at River Rd. 08/09/00 2.57 2.74 0.08 0.14 2.5 — — — — 37 6.0 — 306 —

11 Orestimba Creek at River Rd. 08/23/00 4.48 4.71 0.10 0.14 3.9 — — — — 22 2.9 — 144 —

11 Orestimba Creek at River Rd. 09/06/00 2.17 2.25 0.08 0.16 2.7 — — — — 12 6.6 — 122 —

11 Orestimba Creek at River Rd. 09/06/00 5.85 6.25 — — — — — — — — — — — —

11 Orestimba Creek at River Rd. 09/20/00 2.42 2.61 0.06 0.19 2.5 — — — — 14 5.8 — 118 —

11 Orestimba Creek at River Rd. 10/04/00 1.02 1.14 0.07 0.11 2.8 — — — — 11 2.1 — 51 —

11 Orestimba Creek at River Rd. 10/18/00 0.92 1.03 0.05 0.10 3.2 — — — — 17 5.6 — 164 —

11 Orestimba Creek at River Rd. 06/13/01 3.09 3.99 0.12 0.48 4.8 0.4 0.392 0.082 21 — 9.2 13 521 96

11 Orestimba Creek at River Rd. 06/27/01 5.65 5.72 0.12 0.15 3.5 — — — — 41 18.9 — 328 —

11 Orestimba Creek at River Rd. 07/10/01 6.32 7.06 0.11 0.36 3.7 4.6 0.104 0.028 23 — 0.8 1.5 273 96

11 Orestimba Creek at River Rd. 07/25/01 6.78 7.06 0.10 0.58 2.7 — — — — 31 1.1 — 198 —

11 Orestimba Creek at River Rd. 08/08/01 4.92 5.57 0.13 0.33 2.4 2.5 0.070 0.029 24 — 5.2 3.4 272 99

11 Orestimba Creek at River Rd. 08/22/01 4.62 5.21 0.06 0.31 3.4 — — — — 24 2.4 — 165 —

11 Orestimba Creek at River Rd. 09/05/01 5.98 6.35 0.07 0.28 3.1 — — — — 13 3.1 — 114 —

11 Orestimba Creek at River Rd. 09/19/01 9.15 9.81 0.05 0.17 3.7 — — — — 4.3 2.3 — 27 —

11 Orestimba Creek at River Rd. 10/04/01 3.89 4.35 0.11 0.37 3.7 3.7 0.095 0.026 17 — 8.1 6.3 239 97

11 Orestimba Creek at River Rd. 10/31/01 1.09 1.43 0.04 0.18 3.1 1.4 0.087 0.028 6 — 1.6 3.6 125 95

13 Spanish Grant Drain 06/13/01 7.26 8.37 0.18 0.46 9.9 0.2 0.470 0.047 13 — 11.8 18 245 93

13 Spanish Grant Drain 07/11/01 6.12 10.6 0.13 1.74 4.2 >10 — — 134 — 14.4 38 1920 98

13 Spanish Grant Drain 08/06/01 6.81 8.79 0.14 0.46 3.8 2.5 0.111 0.029 26 — 5.4 4.0 464 91

13 Spanish Grant Drain 09/04/01 E6.23 E6.73 E0.18 0.36 7.4 2.4 0.176 0.024 16 — 4.5 8.3 177 88

13 Spanish Grant Drain 10/02/01 1.96 2.25 0.03 0.18 3.1 1.8 0.094 0.030 8 — 6.4 10 109 94

13 Spanish Grant Drain 10/30/01 1.45 1.97 0.07 0.18 5.1 1.6 0.124 0.024 10 — 6.7 4.6 36 98

14 Harding Drain at Carpenter Rd. 06/13/01 7.93 8.33 1.90 2.05 4.6 0.9 0.098 0.021 E2 — 4.4 10 12 73

14 Harding Drain at Carpenter Rd. 07/12/01 5.39 5.56 0.44 0.49 3.1 1.4 0.074 0.024 6 — 1.7 6.2 25 69

14 Harding Drain at Carpenter Rd. 08/06/01 10.2 10.5 0.77 0.84 3.5 0.6 0.079 0.023 6 — 13.3 8.3 37 37

14 Harding Drain at Carpenter Rd. 09/04/01 E10.2 E10.4 E0.91 0.94 4.0 0.4 0.093 0.023 4 — 1.9 3.0 10 82

14 Harding Drain at Carpenter Rd. 10/02/01 9.28 9.38 0.62 0.71 3.4 0.5 0.078 0.023 E3 — 6.3 5.5 14 76

14 Harding Drain at Carpenter Rd. 10/30/01 16.3 16.6 2.27 2.58 5.2 0.5 0.101 0.019 4 — 4.5 4.5 15 81

17 Westport Drain near Modesto 06/14/01 5.53 5.67 0.07 0.13 4.9 0.8 0.076 0.016 E2 — 1.7 3.1 21 63

17 Westport Drain near Modesto 07/12/01 6.16 6.51 0.14 0.20 2.4 1.6 0.064 0.027 8 — 1.8 6.4 44 89

17 Westport Drain near Modesto 08/07/01 6.26 6.38 0.12 0.17 6.0 0.3 0.069 0.012 E1 — 2.5 2.3 10 93

17 Westport Drain near Modesto 09/05/01 3.63 3.86 0.10 0.16 3.1 0.7 0.052 0.017 4 — 1.4 3.4 26 83

17 Westport Drain near Modesto 10/03/01 9.41 9.39 0.06 0.10 2.6 0.4 E0.057 0.022 E<1 — 0.5 1.4 11 50

17 Westport Drain near Modesto 11/01/01 19.4 19.5 0.60 0.59 5.2 <0.2 0.144 0.028 E2 — 0.2 0.8 — —

20 Dry Creek at Gallo Bridge 06/15/01 1.13 1.54 0.50 0.71 8.7 2.4 0.276 0.032 6 — 3.7 7.3 59 64

20 Dry Creek at Gallo Bridge 07/13/01 1.22 1.42 0.58 0.66 7.9 1.5 0.285 0.036 8 — 1.7 3.9 33 70

20 Dry Creek at Gallo Bridge 08/07/01 0.94 1.09 0.53 0.66 7.5 0.6 0.340 0.045 E3 — 2.0 3.9 27 68

20 Dry Creek at Gallo Bridge 09/05/01 0.84 0.96 0.46 0.56 7.0 0.7 0.240 0.034 4 — 1.2 3.3 23 88
112 Sources and Transport of Nutrients, Organic Carbon, Chlorophyll-a in the San Joaquin River Upstream of Vernalis, CA, during Summer, Fall, 2000 and 2001

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for 

tributary sites—Continued Site number Site name

Date

Time

 Laboratory

 Stream flow 

 (ft3/s)

 Water Temperature 

 (C)

 pH 

 Specific conductance

(μS/cm at 25C)

 Dissolved Oxygen

 (mg/L) 

 Alkalinity

 (mg/L CaCO3)

 Secchi disk depth 

 (in.)

 Ammonia, dissolved

 (mg/L as N) 

 Nitrate, dissolved

 (mg/L as N)

Inorganic nitrogen, dissolved

 (mg/L as N)

Organic nitrogen, dissolved

 (mg/L as N)

20 Dry Creek at Gallo Bridge 10/03/0 14:20 USGS 90 21.0 7.3 88 6.8 34 >22 < 0.04 0.25 0.28 0.48

20 Dry Creek at Gallo Bridge 11/01/0 15:30 USGS 7.4 16.0 7.6 1 104 10.6 36 >13 < 0.04 0.28 0.30 0.20

22 Tuolumne River at Shiloh Rd. 07/12/0 12:20 UCD E 620 24.3 7.7 165 — — — 0.06 1.55 1.62 0.07

22 Tuolumne River at Shiloh Rd. 07/26/0 12:20 UCD E 732 22.7 7.8 116 — — — 0.02 0.98 1.00 0.22

22 Tuolumne River at Shiloh Rd. 08/09/0 11:11 UCD E 497 27.9 7.7 198 — — — 0.02 1.75 1.76 0.10

22 Tuolumne River at Shiloh Rd. 08/23/0 12:10 UCD E1633 20.3 7.6 65 — — — 0.02 0.33 0.35 0.07

22 Tuolumne River at Shiloh Rd. 09/06/0 12:20 UCD E 851 20.2 7.9 128 — — — 0.02 0.55 0.57 0.04

22 Tuolumne River at Shiloh Rd. 09/20/0 12:20 UCD E1129 22.9 7.6 100 — — — 0.03 0.52 0.55 0.09

22 Tuolumne River at Shiloh Rd. 10/04/0 11:47 UCD E 974 19.1 7.7 121 — — — 0.03 0.84 0.87 0.06

22 Tuolumne River at Shiloh Rd. 10/18/0 11:27 UCD E 551 17.1 8.1 171 — — — 0.02 1.34 1.35 0.24

22 Tuolumne River at Shiloh Rd. 06/13/0 08:20 UCD E 234 21.0 8.1 314 — — — 0.08 3.50 3.58 0.11

22 Tuolumne River at Shiloh Rd. 06/27/0 10:40 UCD E 213 22.4 7.6 295 — — — 0.06 2.37 2.43 0.05

22 Tuolumne River at Shiloh Rd. 07/11/0 08:15 UCD E 182 22.9 8.2 298 — — — 0.04 2.88 2.92 0.47

22 Tuolumne River at Shiloh Rd. 07/25/0 12:05 UCD E 277 26.0 8.2 251 — — — 0.03 1.76 1.79 0.35

22 Tuolumne River at Shiloh Rd. 08/07/0 11:20 UCD E 277 27.7 7.8 227 — — — 0.03 1.63 1.66 0.46

22 Tuolumne River at Shiloh Rd. 08/22/0 11:15 UCD E 296 23.1 8.0 226 — — — < 0.01 1.85 1.86 0.35

22 Tuolumne River at Shiloh Rd. 09/05/0 11:41 UCD E 286 23.7 7.8 236 — — — 0.01 1.87 1.88 0.44

22 Tuolumne River at Shiloh Rd. 09/19/0 09:30 UCD E 296 21.1 8.1 234 — — — 0.02 1.70 1.72 0.44

22 Tuolumne River at Shiloh Rd. 10/03/0 09:35 UCD E 324 20.8 7.9 236 — — — 0.04 1.65 1.69 0.40

23 Hospital Cr. below Ingram Cr. 06/14/0 15:30 USGS 26 29.0 8.3 — 6.8 140 1 < 0.04 4.00 4.10 0.37

23 Hospital Cr. below Ingram Cr. 07/11/0 09:40 USGS 18 21.0 8.0 1070 7.3 — 2 0.61 5.67 6.51 1.79

23 Hospital Cr. below Ingram Cr. 08/09/0 10:30 USGS 23 22.5 18.0 11120

1Laboratory value.

8.4 140 1 0.46 5.98 6.71 0.54

23 Hospital Cr. below Ingram Cr. 09/07/0 10:30 USGS 0.86 19.0 8.1 1870 7.6 210 5 0.18 11.8 12.4 0.64

23 Hospital Cr. below Ingram Cr. 10/05/0 10:00 USGS 4.9 19.0 8.1 11350 8.9 180 >7 < 0.04 4.05 4.18 0.44

23 Hospital Cr. below Ingram Cr. 11/02/0 09:30 USGS 1.7 14.0 8.0 1937 9.6 110 >5 < 0.04 3.33 3.37 0.45

26 Stanislaus River at Caswell 07/12/0 11:40 UCD E 400 22.1 7.6 97 — — — 0.02 0.42 0.45 0.08

26 Stanislaus River at Caswell 07/26/0 11:00 UCD E 462 22.1 7.8 93 — — — 0.05 0.42 0.47 0.06

26 Stanislaus River at Caswell 08/09/0 10:20 UCD E 391 21.5 7.5 89 — — — 0.04 0.44 0.48 0.10

26 Stanislaus River at Caswell 08/23/0 10:35 UCD E 391 21.0 7.8 94 — — — 0.05 0.42 0.48 0.05

26 Stanislaus River at Caswell 09/06/0 11:00 UCD E 391 17.1 7.8 94 — — — 0.07 0.51 0.57 0.04

26 Stanislaus River at Caswell 09/20/0 11:30 UCD E 380 21.1 7.7 110 — — — 0.05 0.38 0.43 0.22

26 Stanislaus River at Caswell 10/04/0 11:04 UCD E 384 18.1 7.8 99 — — — 0.07 0.41 0.48 0.12

26 Stanislaus River at Caswell 10/18/0 10:35 UCD E 597 16.2 8.0 104 — — — 0.02 0.52 0.54 0.17

26 Stanislaus River at Caswell 06/13/0 07:35 UCD E 564 19.1 7.8 75 — — — 0.03 0.28 0.30 0.04

26 Stanislaus River at Caswell 06/27/0 09:30 UCD E 571 19.4 7.5 72 — — — 0.03 0.31 0.33 0.02

26 Stanislaus River at Caswell 07/11/0 07:00 UCD E 536 20.4 7.8 74 — — — 0.06 0.23 0.29 0.07

26 Stanislaus River at Caswell 07/25/0 10:53 UCD E 452 22.2 7.9 84 — — — 0.03 0.17 0.20 0.18

26 Stanislaus River at Caswell 08/07/0 10:32 UCD E 393 22.8 7.6 85 — — — 0.04 0.38 0.42 0.23

26 Stanislaus River at Caswell 08/22/0 10:22 UCD E 362 19.8 7.8 83 — — — 0.01 0.23 0.24 0.16

26 Stanislaus River at Caswell 09/05/0 10:45 UCD E 348 20.7 7.6 85 — — — 0.03 0.26 0.29 0.45

26 Stanislaus River at Caswell 09/19/0 08:20 UCD E 306 19.6 7.7 93 — — — 0.05 0.27 0.32 0.14

26 Stanislaus River at Caswell 10/03/0 08:50 UCD E 293 22.8 7.8 112 — — — 0.05 0.61 0.66 0.22
Appendix C. 113

i

Appendix C. All data (University of California at Davis and U.S. Geological Survey) for 2000 and 2001 for nutrients, organic carbon, and chlorophyll for 

tributary sites—Continued Site number Site name

Date

 Total nitrogen, dissolved

 (mg/L as N)

 Total nitrogen

 (mg/L as N)

 Orthophosphate, dissolved

(mg/L as P)

 Total phosphorus

 (mg/L as P) 

Organic carbon, dissolved

 (mg/L as C) 

Organic carbon, suspended 

 (mg/L as C)

Ultraviolet absorbance 

at 254 nm (cm–1)

 SUVA

(L/mg-cm)

 Volatile suspended solids

 (mg/L) 

 Particulate organic matter

 (mg/L)

 Chlorophyll-a

(μg/L)

 Pheophytin-a

(μg/L)

 Suspended sediment

 (mg/L)

 Suspended sediment, size 

fraction < 0.062 mm (percent)

20 Dry Creek at Gallo Bridge 10/03/01 0.76 0.80 0.33 0.42 6.7 0.4 E.252 0.038 E 1 — 1.4 2.7 9 74

20 Dry Creek at Gallo Bridge 11/01/01 0.50 0.62 0.18 0.21 3.8 — 0.130 0.034 E 3 — 0.4 0.8 — —

22 Tuolumne River at Shiloh Rd. 07/12/00 1.69 1.71 0.08 0.12 2.3 — — — — 3.6 1.1 — 15 —

22 Tuolumne River at Shiloh Rd. 07/26/00 1.22 1.27 0.07 0.11 1.9 — — — — 3.0 0.7 — 9 —

22 Tuolumne River at Shiloh Rd. 08/09/00 1.87 1.94 0.10 0.12 2.2 — — — — 2.3 0.5 — 5 —

22 Tuolumne River at Shiloh Rd. 08/23/00 0.42 0.49 0.04 0.06 1.6 — — — — 2.9 0.9 — 9 —

22 Tuolumne River at Shiloh Rd. 09/06/00 0.62 0.71 0.07 0.10 1.9 — — — — 1.9 0.8 — 9 —

22 Tuolumne River at Shiloh Rd. 09/20/00 0.64 0.75 0.05 0.07 1.7 — — — — 3.0 0.8 — 15 —

22 Tuolumne River at Shiloh Rd. 10/04/00 0.93 0.94 0.05 0.07 1.8 — — — — 3.0 1.0 — 11 —

22 Tuolumne River at Shiloh Rd. 10/18/00 1.59 1.91 0.04 0.07 1.6 — — — — 3.6 1.0 — 15 —

22 Tuolumne River at Shiloh Rd. 06/13/01 3.69 3.74 0.13 0.17 4.1 — — — — 3.1 2.4 — 10 —

22 Tuolumne River at Shiloh Rd. 06/27/01 2.48 2.70 0.15 0.35 3.3 — — — — 3.6 4.3 — 14 —

22 Tuolumne River at Shiloh Rd. 07/11/01 3.39 4.00 0.23 0.29 3.1 — — — — 2.4 2.4 — 8 —

22 Tuolumne River at Shiloh Rd. 07/25/01 2.13 2.30 0.15 0.17 2.5 — — — — 3.9 3.3 — 11 —

22 Tuolumne River at Shiloh Rd. 08/07/01 2.12 2.20 0.14 0.19 3.3 — — — — 3.1 3.2 — 8 —

22 Tuolumne River at Shiloh Rd. 08/22/01 2.21 2.25 0.16 0.24 2.4 — — — — 4.6 3.7 — 20 —

22 Tuolumne River at Shiloh Rd. 09/05/01 2.32 2.36 0.16 0.22 2.1 — — — — 2.2 2.1 — 9 —

22 Tuolumne River at Shiloh Rd. 09/19/01 2.16 2.27 0.11 0.17 1.9 — — — — 2.7 2.5 — 12 —

22 Tuolumne River at Shiloh Rd. 10/03/01 2.09 2.15 0.11 0.18 2.0 — — — — 3.2 3.2 — 12 —

23 Hospital Cr. below Ingram Cr. 06/14/01 4.47 9.38 0.16 2.27 7.7 >10 0.119 0.015 126 — 81.5 57 3460 95

23 Hospital Cr. below Ingram Cr. 07/11/01 8.30 10.4 0.17 0.91 4.8 >5.0 0.098 0.020 66 — 16.7 18 1160 94

23 Hospital Cr. below Ingram Cr. 08/09/01 7.25 9.35 0.17 0.87 3.4 >5.0 0.102 0.030 46 — 12.1 6.5 998 94

23 Hospital Cr. below Ingram Cr. 09/07/01 13.0 13.3 0.19 0.32 4.3 3.5 0.105 0.024 9 — 10.0 6.2 134 97

23 Hospital Cr. below Ingram Cr. 10/05/01 4.62 5.01 0.15 0.29 4.7 0.6 0.107 0.023 7 — 16.9 20 77 75

23 Hospital Cr. below Ingram Cr. 11/02/01 3.82 4.45 0.15 0.38 5.0 2.6 0.146 0.029 15 — 4.2 7.6 286 86

26 Stanislaus River at Caswell S.P. 07/12/00 0.53 0.54 0.04 0.06 1.1 — — — — 2.7 1.1 — 8 —

26 Stanislaus River at Caswell S.P. 07/26/00 0.53 0.57 0.05 0.08 1.9 — — — — 3.2 1.4 — 10 —

26 Stanislaus River at Caswell S.P. 08/09/00 0.57 0.63 0.05 0.08 1.8 — — — — 3.6 1.2 — 11 —

26 Stanislaus River at Caswell S.P. 08/23/00 0.53 0.59 0.06 0.09 2.1 — — — — 3.3 0.8 — 10 —

26 Stanislaus River at Caswell S.P. 09/06/00 0.62 0.71 0.08 0.13 2.1 — — — — 1.8 0.7 — 8 —

26 Stanislaus River at Caswell S.P. 09/20/00 0.65 0.73 0.06 0.09 1.9 — — — — 1.9 0.7 — 8 —

26 Stanislaus River at Caswell S.P. 10/04/00 0.59 0.60 0.14 0.18 2.3 — — — — 2.4 0.8 — 5 —

26 Stanislaus River at Caswell S.P. 10/18/00 0.71 0.86 0.06 0.08 1.9 — — — — 2.2 0.9 — 4 —

26 Stanislaus River at Caswell S.P. 06/13/01 0.35 0.39 0.03 0.07 1.5 — — — — 3.4 2.4 — 13 —

26 Stanislaus River at Caswell S.P. 06/27/01 0.35 0.52 0.03 0.10 1.5 — — — — 8.1 7.5 — 40 —

26 Stanislaus River at Caswell S.P. 07/11/01 0.37 0.53 0.04 0.07 1.6 — — — — 3.3 1.1 — 11 —

26 Stanislaus River at Caswell S.P. 07/25/01 0.38 0.40 0.05 0.09 1.7 — — — — 3.5 0.9 — 8 —

26 Stanislaus River at Caswell S.P. 08/07/01 0.65 1.00 0.04 0.07 1.7 — — — — 2.5 1.0 — 5 —

26 Stanislaus River at Caswell S.P. 08/22/01 0.40 0.47 0.04 0.09 1.5 — — — — 2.9 1.4 — 8 —

26 Stanislaus River at Caswell S.P. 09/05/01 0.74 1.02 0.05 0.10 1.5 — — — — 1.5 1.2 — 6 —

26 Stanislaus River at Caswell S.P. 09/19/01 0.46 0.49 0.06 0.10 1.6 — — — — 1.3 1.2 — 8 —

26 Stanislaus River at Caswell S.P. 10/03/01 0.88 1.08 0.04 0.06 1.6 — — — — 1.4 1.2 — 6 —