Trends in Nutrient Concentrations, Loads, and Yields in

Streams in the Sacramento, San Joaquin, and Santa Ana

Basins, California, 1975–2004

Scientific Investigations Report 2010–5228

National Water-Quality Assessment Program

U.S. Department of the Interior

U.S. Geological Survey
Cover: General land-use map of California showing boundaries of the Sacramento, 

San Joaquin, and Santa Ana Basins (see figure 6 in report for detail).
Trends in Nutrient Concentrations, Loads, and Yields in 

Streams in the Sacramento, San Joaquin, and Santa Ana 

Basins, California, 1975–2004

By Charles R. Kratzer, Robert H. Kent, Dina K. Saleh, Donna L. Knifong, Peter D. Dileanis, and 

James L. Orlando

National Water-Quality Assessment Program

Scientific Investigations Report 2010–5228

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2011

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Suggested citation:

Kratzer, C.R., Kent, R.H., Saleh, D.K., Knifong, D.L., Dileanis, P.D., and Orlando, J.L., 2011, Trends in nutrient 

concentrations, loads, and yields in streams in the Sacramento, San Joaquin, and Santa Ana Basins, California, 

1975–2004: U.S. Geological Survey Scientific Investigations Report 2010-5228, 112 p.

.
iii

Foreword

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local information needs and decisions related to water-quality management and policy (http://water.usgs.gov/nawqa). The NAWQA 

Program is designed to answer: What is the condition of our Nation’s streams and groundwater? How are conditions changing over 

time? How do natural features and human activities affect the quality of streams and groundwater, and where are those effects most 

pronounced? By combining information on water chemistry, physical characteristics, stream habitat, and aquatic life, the NAWQA 

Program aims to provide science-based insights for current and emerging water issues and priorities. From 1991–2001, the NAWQA 

Program completed interdisciplinary assessments and established a baseline understanding of water-quality conditions in 51 of the 

Nation’s river basins and aquifers, referred to as Study Units (http://water.usgs.gov/nawqa/studyu.html). 

In the second decade of the Program (2001–2012), a major focus is on regional assessments of water-quality conditions and trends. 

These regional assessments are based on major river basins and principal aquifers, which encompass larger regions of the country 

than the Study Units. Regional assessments extend the findings in the Study Units by filling critical gaps in characterizing the quality 

of surface water and groundwater, and by determining status and trends at sites that have been consistently monitored for more than 

a decade. In addition, the regional assessments continue to build an understanding of how natural features and human activities 

affect water quality. Many of the regional assessments employ modeling and other scientific tools, developed on the basis of data 

collected at individual sites, to help extend knowledge of water quality to unmonitored, yet comparable areas within the regions. 

The models thereby enhance the value of our existing data and our understanding of the hydrologic system. In addition, the models 

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nonpoint and point sources of contamination, land conversion, and altering flow and (or) pumping regimes, are likely to affect water 

conditions within a region.

Other activities planned during the second decade include continuing national syntheses of information on pesticides, volatile organic 

compounds (VOCs), nutrients, selected trace elements, and aquatic ecology; and continuing national topical studies on the fate of 

agricultural chemicals, effects of urbanization on stream ecosystems, bioaccumulation of mercury in stream ecosystems, effects of 

nutrient enrichment on stream ecosystems, and transport of contaminants to public-supply wells.

The USGS aims to disseminate credible, timely, and relevant science information to address practical and effective water-resource 

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The USGS recognizes that a national assessment by a single program cannot address all water-resource issues of interest. External 

coordination at all levels is critical for cost-effective management, regulation, and conservation of our Nation’s water resources. 

The NAWQA Program, therefore, depends on advice and information from other agencies—Federal, State, regional, interstate, 

Tribal, and local—as well as nongovernmental organizations, industry, academia, and other stakeholder groups. Your assistance and 

suggestions are greatly appreciated.

 Matthew C. Larsen

Acting Associate Director for Water
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Contents

Foreword ........................................................................................................................................................iii

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

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

Description of Study Area ............................................................................................................................2

Physiography and Geology .................................................................................................................5

Water Resources ..................................................................................................................................6

Sacramento Basin .......................................................................................................................6

San Joaquin Basin.....................................................................................................................11

Santa Ana Basin ........................................................................................................................11

Land Use...............................................................................................................................................12

Analysis Techniques....................................................................................................................................14

Loads and Yields .................................................................................................................................14

Standard Error of Prediction....................................................................................................15

Loading Factors..........................................................................................................................15

Unmodeled Load Sources and (or) Sinks ..............................................................................16

Stepwise Multiple Linear Regression .............................................................................................16

Trends ..................................................................................................................................................17

Trends in Flow-Adjusted Concentrations...............................................................................17

Trends in Measured Concentrations ......................................................................................18

Sources of Data for Nutrient Concentrations and Flow in Streams....................................................18

Data Sources.......................................................................................................................................18

Database Issues..................................................................................................................................19

Combining Multiple Parameters into a Single Constituent.................................................19

Combining Multiple Sites into a Single Site ..........................................................................19

Censoring Levels in NWIS........................................................................................................19

Data Thinning..............................................................................................................................27

Influence of Sample Collection and Analytical Methods....................................................27

Sites with Sufficient Data for Trends and Loads ...........................................................................27

Sources of Ancillary Data...........................................................................................................................37

Point Sources of Nutrients................................................................................................................37

Sacramento Basin .....................................................................................................................37

San Joaquin Basin.....................................................................................................................39

Santa Ana Basin ........................................................................................................................39

Nonpoint Sources of Nutrients.........................................................................................................40

Atmospheric Deposition ...........................................................................................................40

Sacramento Basin ............................................................................................................40

San Joaquin Basin............................................................................................................44

Santa Ana Basin ...............................................................................................................44

Fertilizer Application .................................................................................................................44

Manure Production ...................................................................................................................45

Tile Drainage...............................................................................................................................45

Data for Stepwise Multiple Linear-Regression Analysis .............................................................45
vi

Results ...........................................................................................................................................................46

Nutrient Sources, 1985–2004.............................................................................................................46

Point Sources .............................................................................................................................46

Sacramento Basin ............................................................................................................47

San Joaquin Basin............................................................................................................47

Santa Ana Basin ...............................................................................................................47

Nonpoint Sources......................................................................................................................51

Sacramento Basin ............................................................................................................51

San Joaquin Basin............................................................................................................52

Santa Ana Basin ...............................................................................................................52

Estimated Stream Nutrient Loads, 1975–2004................................................................................55

Sacramento Basin .....................................................................................................................56

San Joaquin Basin.....................................................................................................................61

Santa Ana Basin ........................................................................................................................68

Average Annual Nutrient Yields for the 1985–2004 Period by Subbasin ...................................70

Relations Between Nutrient Yields and Nutrient Sources and Subbasin Characteristics ....73

Trends in Nutrient Concentrations, 1975–2004...............................................................................74

Trends in Flow-Adjusted Concentrations ..............................................................................74

Sacramento Basin ............................................................................................................74

San Joaquin Basin............................................................................................................91

Santa Ana Basin ...............................................................................................................93

Trends in Measured Concentrations ......................................................................................95

Sacramento Basin ............................................................................................................95

San Joaquin Basin............................................................................................................97

Santa Ana Basin ...............................................................................................................99

Long-Term Nitrate Concentrations, 1905–2004 ..............................................................................99

Sacramento Basin .....................................................................................................................99

San Joaquin Basin...................................................................................................................101

Santa Ana Basin ......................................................................................................................102

Management Strategies Implemented in the Santa Ana Basin ........................................................103

Summary and Conclusions.......................................................................................................................103

Acknowledgments.....................................................................................................................................105

References Cited........................................................................................................................................105

Data CD (in report cover)..........................................................................................................................111

Contents—Continued
vii

Figures

Figure 1. Maps showing location of the Sacramento, San Joaquin, and Santa Ana

Basins, California ........................................................................... 3

Figure 2. Map showing physiographic sections in Sacramento, San Joaquin, and Santa

Ana Basins, California ..................................................................... 5

Figure 3. Graphs showing long-term precipitation and flow in Sacramento, San Joaquin,

and Santa Ana Basins, California ......................................................... 7

Figure 4. Graphs showing water-year hydrologic classifications for 1901–2004 for

Sacramento Basin, and San Joaquin Basin, California ................................. 9

Figure 5. Illustration showing schematic diagram of major tributaries, diversions, and

wastewater treatment-plant discharges for the Sacramento Basin, and San

Joaquin Basin, California .................................................................. 10

Figure 6. Map showing general land use in Sacramento, San Joaquin, and Santa Ana

Basins, California ........................................................................... 13

Figure 7. Maps showing sites in Sacramento, San Joaquin, and Santa Ana Basins,

California, with sufficient data for analyses of flow-adjusted trends and (or)

loads of nitrate, ammonia, total nitrogen, orthophosphate, and total

phosphorus, 1975–2004 ..................................................................... 30

Figure 8. Maps showing drainage subbasins for sites in Sacramento, San Joaquin, and 

Santa Ana Basins, California, with sufficient data for analyses of flow-adjusted

trends and(or) loads of nitrate, ammonia, total nitrogen, orthophosphate, and

total phosphorus, 1975–2004 ............................................................... 33

Figure 9. Graphs showing number of samples in final database by data source for

nitrate, ammonia, total nitrogen, orthophosphate, and total phosphorus for

water years 1975–1984, 1985–1992, and 1993–2004 for Sacramento, San

Joaquin, and Santa Ana Basins, California ............................................. 36

Figure 10. Map showing locations of point sources of nutrients in Sacramento, San

Joaquin, and Santa Ana Basins, California, with average discharge rates for

1985, 1993, and 2004 ........................................................................ 38

Figure 11. Map showing locations of sites in Sacramento, San Joaquin, and Santa Ana

Basins, California, with atmospheric-deposition data ................................. 41

Figure 12. Graphs showing total nitrogen and total phosphorus loads from point sources

to Sacramento River, 1985–2004, San Joaquin River, 1985–2004, and Santa Ana

River, 1975–2004.............................................................................. 48

Figure 13. Graphs showing contributions from wastewater treatment plants and

non-wastewater discharges to flow in the Santa Ana River, 1975–2000 ............ 49

Figure 14. Graph showingammonium and nitrate in the effluent of selected wastewater

treatment plants of the Santa Ana Basin, October 1971–September 2003............ 50

Figure 15. Graph showing total inorganic nitrogen concentrations in effluent from the

Rialto wastewater treatment plant, 1993–2003 .......................................... 51

Figure 16. Graph of estimated total nitrogen loads from atmospheric deposition in the

Sacramento (valley only), San Joaquin (valley only), and Santa Ana (basin

only) Basins, California, 1985–2004 ...................................................... 51

Figure 17. Graphs showing fertilizer application in Sacramento, San Joaquin, and Santa

Ana Basins, California, for nitrogen, and phosphorus, 1987–2004 ..................... 53

Figure 18. Graphs showing manure production in Sacramento, San Joaquin, and Santa

Ana Basins, California, for nitrogen, and phosphorus, 1982–2002 ..................... 54
viii

Figure 19. Graph showing oxides of nitrogen in air samples collected from the

Riverside-Rubidoux air sampling site, California, during the study period............ 55

Figure 20. Graph showing estimated daily loads and measured instantaneous loads of

nitrate for San Joaquin River near Vernalis, 1975–2004................................. 56

Figure 21. Graphs showing nitrate loads for mainstem sites in the Sacramento Basin:

Sacramento River at Delta, at Keswick, near Red Bluff, near Hamilton City,

upstream of Colusa Basin Drain, at Verona, and at Freeport, 1975–2004, with

standard error of prediction and timing of data collection ........................... 57

Figure 22. Graphs showing ammonia loads for mainstem sites in the Sacramento Basin:

Sacramento River at Keswick, at Verona, and at Freeport, 1975–2004, with

standard error of prediction and timing of data collection ........................... 58

Figure 23. Graphs showing total nitrogen loads for mainstem sites in the Sacramento

Basin: Sacramento River at Keswick, near Red Bluff, near Hamilton City, at

Verona, and at Freeport, 1975–2004, with standard error of prediction and

timing of data collection .................................................................. 59

Figure 24. Graphs showing orthophosphate loads for mainstem sites in the Sacramento

Basin: Sacramento River at Delta, at Keswick, near Red Bluff, near Hamilton

City, upstream of Colusa Basin Drain, at Verona, and at Freeport, 1975–2004,

with standard error of prediction and timing of data collection ..................... 60

Figure 25. Graphs showing total phosphorus loads for mainstem sites in the Sacramento

Basin: Sacramento River at Delta, at Keswick, near Red Bluff, near Hamilton

City, upstream of Colusa Basin Drain, at Verona, and at Freeport, 1975–2004,

with standard error of prediction and timing of data collection ..................... 62

Figure 26. Graphs showing unmodeled load sources and (or) sinks for the Sacramento

River from Verona to Freeport (adjusted by loading factors) for total nitrogen,

and total phosphorus, 1985–2004 ......................................................... 63

Figure 27. Graphs showing nitrate loads for mainstem sites in the San Joaquin Basin:

San Joaquin River near Patterson, at Maze Road, and near Vernalis,

1975–2004, with standard error of prediction and timing of data collection ......... 64

Figure 28. Graphs showing ammonia loads for mainstem sites in the San Joaquin Basin:

San Joaquin River near Patterson, at Maze Road, and near Vernalis,

1975–2004, with standard error of prediction and timing of data collection ......... 64

Figure 29. Graphs showing total nitrogen loads for mainstem sites in the San Joaquin

Basin: San Joaquin River near Stevinson, near Patterson, at Maze Road, and

near Vernalis, 1975–2004, with standard error of prediction and timing of data

collection .................................................................................... 65

Figure 30. Graphs showing orthophosphate loads for mainstem sites in the San Joaquin

Basin: San Joaquin River near Stevinson, near Patterson, at Maze Road, and

near Vernalis, 1975–2004, with standard error of prediction and timing of data

collection .................................................................................... 65

Figure 31. Graphs showing total phosphorus loads for mainstem sites in the San Joaquin

Basin: San Joaquin River near Stevinson, near Patterson, at Maze Road, and

near Vernalis, 1975–2004, with standard error of prediction and timing of data

collection .................................................................................... 66

Figure 32. Graphs showing unmodeled load sources and(or) sinks in the San Joaquin

River from Stevinson to Patterson (adjusted by loading factors) for total

nitrogen, and total phosphorus, 1985–2004 ............................................. 66

Figures—Continued
ix

Figure 33. Graphs showing unmodeled load sources and(or) sinks in the San Joaquin

River from Patterson to Maze Road (adjusted by loading factors) for total

nitrogen, and total phosphorus, 1985–2004 ............................................. 67

Figure 34. Graphs showing unmodeled load sources and(or) sinks in the San Joaquin

River from Maze Road to Vernalis (adjusted by loading factors) for total

nitrogen, and total phosphorus, 1985–2004 ............................................. 67

Figure 35. Graphs showing loads for the Santa Ana River downstream of Prado Dam for

nitrate, ammonia, total nitrogen, orthophosphate, and total phosphorus,

1975–2004, with standard error of prediction and timing of data collection ......... 68

Figure 36. Graph showing unmodeled load sources and(or) sinks in the Santa Ana River

from MWD Crossing to downstream of Prado Dam for nitrate, for 1985–2004 ...... 69

Figure 37. Maps showing average yields of total nitrogen in subbasins of the Sacramento

and San Joaquin Basins, California, for total nitrogen, 1985–2004 .................. 71

Figure 38. Maps showing average yields for total phosphorus in subbasins of the

Sacramento and San Joaquin Basins, 1985–2004 ....................................... 72

Figure 39. Graphs showing flow-adjusted concentrations in the Sacramento River at

Freeport, California, for nitrate, ammonia, total nitrogen, orthophosphate, and

total phosphorus, 1975–2004 ............................................................... 80

Figure 40. Map showing trends in flow-adjusted concentrations of nitrate in the

Sacramento Basin and San Joaquin Basin, California, 1975–2004, 1985–2004,

and 1993–2004 .............................................................................. 81

Figure 41. Map showing trends in flow-adjusted concentrations of ammonia in the

Sacramento Basin and San Joaquin Basin, California, 1975–2004, 1985–2004,

and 1993–2004 .............................................................................. 83

Figure 42. Map showing trends in flow-adjusted concentrations of total nitrogen in the

Sacramento Basin and San Joaquin Basin, California, 1975–2004, 1985–2004,

and 1993–2004 .............................................................................. 85

Figure 43. Map showing trends in flow-adjusted concentrations of orthophosphate in the

Sacramento Basin and San Joaquin Basin, California, 1975–2004, 1985–2004,

and 1993–2004 .............................................................................. 87

Figure 44. Map showing trends in flow-adjusted concentrations of total phosphorus in

the Sacramento Basin and San Joaquin Basin, California, 1975–2004,

1985–2004, and 1993–2004 .................................................................. 89

Figure 45. Graph showing flow-adjusted concentrations in the San Joaquin River near

Vernalis for nitrate, ammonia, total nitrogen, orthophosphate, and total

phosphorus, 1975–2004 ..................................................................... 92

Figure 46. Graph showing flow-adjusted and measured concentrations in the Santa Ana

River downstream of Prado Dam for nitrate, ammonia, total nitrogen,

orthophosphate, and total phosphorus, 1975–2004 .................................... 93

Figure 47. Graphs showing measured nutrient concentrations for Colusa Basin Drain in

the Sacramento Basin for nitrate, ammonia, total nitrogen, orthophosphate,

and total phosphorus, 1975–2004 ......................................................... 95

Figure 48. Graph showing measured nutrient concentrations for Fremont Weir in the

Sacramento Basin for nitrate, ammonia, total nitrogen, orthophosphate, and

total phosphorus, 1975–2004 ............................................................... 96

Figure 49. Graph showing measured nitrate concentrations for Camp 13 Slough in the

San Joaquin Basin, 1975–2004 ............................................................ 97

Figures—Continued
x

Figure 50. Graphs showing measured nutrient concentrations for San Joaquin River at

Fremont Ford in the San Joaquin Basin for nitrate, ammonia, total nitrogen,

orthophosphate, and total phosphorus, 1975–2004 .................................... 98

Figure 51. Graph showing wastewater and storm-flow components of flow in the Santa

Ana River downstream of Prado Dam, 1975–2004 ....................................... 99

Figure 52. Graphs showing measured nitrate concentrations for Sacramento Basin sites

with long-term data: Sacramento River near Red Bluff, 1905–2004, Sacramento

River at Colusa, 1930–2004, Sacramento River upstream of Colusa Basin Drain,

1930–2004, Feather River at Oroville, 1905–2004, Feather River near Nicolaus,

1930–2004, Sacramento River at Verona, 1905–2004,American River at Nimbus,

1905–2004, and Sacramento River at Freeport, 1930–2004..............................100

Figure 53. Graph showing measured nitrate concentrations for San Joaquin Basin sites

with long-term data: Merced River below Merced Falls, 1930–2004, Tuolumne

River at LaGrange, 1905–2004, Stanislaus River below Goodwin Dam,

1930–2004, and San Joaquin River near Vernalis, 1908–2004...........................101

Figure 54. Graphs showing measured nitrate concentrations for Santa Ana Basin sites

that have long-term data: Santa Ana River near Mentone, 1908–2001; Warm

Creek near San Bernardino, 1930–2004; Santa Ana River at MWD Crossing,

1930–2001; and Santa Ana River downstream of Prado Dam, 1908–2004 ............102

Figures—Continued

Tables

Table 1. Combination of parameters to create a long-term database for nitrate,

ammonia, total nitrogen, orthophosphate, and total phosphorus. ..................... 20

Table 2. Combination of water-quality sites and flow sites to create a long-term

database for evaluating trends and loads for nitrate, ammonia, total nitrogen,

orthophosphate, and total phosphorus.................................................... 21

Table 3. Changes in nutrient detection and reporting limits over time at the U.S.

Geological Survey National Water Quality Laboratory ................................. 24

Table 4. Site names and primary geographic setting (mountain, valley, or basin) for all

54 sites in final database: official names and simplified names for use in this

report.......................................................................................... 28

Table 5. Wet and dry deposition factors applied to National Atmospheric Deposition

Program data to estimate total atmospheric deposition of total nitrogen for

subbasins in the Sacramento, San Joaquin, and Santa Ana Basins, 1985–2004 ... 42

Table 6. Results from stepwise multiple linear regression of basin yields versus basin

nutrient sources and characteristics, and correlation matrix for the 11 variables

in the stepwise multiple linear regression................................................ 75

Table 7. Summary of trends in flow-adjusted nutrient concentrations in the Sacramento,

San Joaquin, and Santa Ana Basins, 1975–2004, 1985–2004, and 1993–2004......... 76
xi

Conversion Factors, Datums, and Abbreviations and Acronyms

Conversion Factors

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2)

acre 0.4047 hectare (ha)

acre 0.4047 square hectometer (hm2) 

acre 0.004047 square kilometer (km2)

square foot (ft2) 929.0 square centimeter (cm2)

square foot (ft2) 0.09290 square meter (m2)

square mile (mi2) 259.0 hectare (ha)

square mile (mi2) 2.590 square kilometer (km2) 

Volume

cubic foot (ft3) 28.32 cubic decimeter (dm3) 

cubic foot (ft3) 0.02832 cubic meter (m3) 

acre-foot (acre-ft) 1,233 cubic meter (m3)

acre-foot (acre-ft) 1.233 cubic hectometer (hm3)

acre-foot per year (acre-ft/yr) 1.233 cubic hectometer per year (hm3/yr) 

Flow rate

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

Mass

pound, avoirdupois (lb) 0.4536 kilogram (kg) 

ton, short 907.2 kilogram (kg) 

ton per month (ton/mo) 907.2 kilogram per month (kg/mo)

ton per year (ton/yr) 907.2 kilogram per year (kg/yr)

ton per square mile per year 

(ton/mi2/yr)

350.3 kilogram per square kilometer per year 

(kg/km2/yr)

Application rate

pounds per acre per year 

[(lb/acre)/yr] 1.121 kilograms per hectare per year [(kg/ha)/yr]

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

°C=(°F-32)/1.8.

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).

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 (NAVD 88).

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

Altitude, as used in this report, refers to distance above the vertical datum.
xii

Conversion Factors, Datums, and Abbreviations and 

Acronyms—Continued

Abbreviations and Acronyms

AAPFCO Association of American Plant Food Control Officials

AMLE adjusted maximum-likelihood estimator

ARB California Air Resources Board

CADMP California Acid Deposition Monitoring Program of ARB

CASTNET Clean Air Status and Trends Network of USEPA

CBD Colusa Basin Drain

DWR California Department of Water Resources

FAC flow-adjusted concentration

IEUA Inland Empire Utility Agency

LRL laboratory reporting level

LT-MDL long-term minimum detection limit

MDL minimum detection limit

MLR multiple linear regression

MRL minimum reporting level

N nitrogen

NADP National Atmospheric Deposition Program

NAWQA National Water-Quality Assessment

NH3 or NH3 ammonia

NLCDe 1992 National Land Cover Dataset, August 2005 enhanced version

NO3 or NO3 nitrate

NPDES National Pollutant Discharge Elimination System

NWIS National Water Information System

NWQL National Water Quality Laboratory

OP orthophosphate

P phosphorus

RIX Rapid Infiltration and Extraction facility (in Colton)

RWQCB(CVR) California Regional Water Quality Control Board, Central Valley Region

RWQCB(SAR) California Regional Water Quality Control Board, Santa Ana Region

SEP standard error of prediction

SAR Santa Ana River

SARI Santa Ana Regional Interceptor pipeline

SJR San Joaquin River

SRCSD Sacramento Regional County Sanitation District

SRWP Sacramento River Watershed Program

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

SWRCB California State Water Resources Control Board

TN total nitrogen

TP total phosphorus

UCD University of California at Davis

USBR U.S. Bureau of Reclamation

USEPA U.S. Environmental Protection Agency

USGS U.S. Geological Survey

WWTP wastewater treatment plant
Trends in Nutrient Concentrations, Loads, and Yields in 

Streams in the Sacramento, San Joaquin, and Santa Ana 

Basins, California, 1975–2004

By Charles R. Kratzer, Robert H. Kent, Dina K. Saleh, Donna L. Knifong, Peter D. Dileanis, and 

James L. Orlando

Abstract 

A comprehensive database was assembled for the 

Sacramento, San Joaquin, and Santa Ana Basins in California 

on nutrient concentrations, flows, and point and nonpoint 

sources of nutrients for 1975–2004. Most of the data on 

nutrient concentrations (nitrate, ammonia, total nitrogen, 

orthophosphate, and total phosphorus) were from the U.S. 

Geological Survey’s National Water Information System 

database (35.2 percent), the California Department of Water 

Resources (21.9 percent), the University of California at 

Davis (21.6 percent), and the U.S. Environmental Protection 

Agency’s STOrage and RETrieval database (20.0 percent). 

Point-source discharges accounted for less than 1 percent 

of river flows in the Sacramento and San Joaquin Rivers, but 

accounted for close to 80 percent of the nonstorm flow in the 

Santa Ana River. Point sources accounted for 4 and 7 percent 

of the total nitrogen and total phosphorus loads, respectively, 

in the Sacramento River at Freeport for 1985–2004. Point 

sources accounted for 8 and 17 percent of the total nitrogen 

and total phosphorus loads, respectively, in the San Joaquin 

River near Vernalis for 1985–2004. The volume of wastewater 

discharged into the Santa Ana River increased almost threefold over the study period. However, due to improvements in 

wastewater treatment, the total nitrogen load to the Santa Ana 

River from point sources in 2004 was approximately the same 

as in 1975 and the total phosphorus load in 2004 was less than 

in 1975. Nonpoint sources of nutrients estimated in this study 

included atmospheric deposition, fertilizer application, manure 

production, and tile drainage. The estimated dry deposition 

of nitrogen exceeded wet deposition in the Sacramento and 

San Joaquin Valleys and in the basin area of the Santa Ana 

Basin, with ratios of dry to wet deposition of 1.7, 2.8, and 9.8, 

respectively. Fertilizer application increased appreciably from 

1987 to 2004 in all three California basins, although manure 

production increased in the San Joaquin Basin but decreased 

in the Sacramento and Santa Ana Basins from 1982 to 2002. 

Tile drainage accounted for 22 percent of the total nitrogen 

load in the San Joaquin River near Vernalis for 1985–2004.

Nutrient loads and trends were calculated by using the 

log-linear multiple-regression model, LOADEST. Loads 

were calculated for water years 1975–2004 for 22 sites in the 

Sacramento Basin, 15 sites in the San Joaquin Basin, and 6 

sites in the Santa Ana Basin. The average annual load of total 

nitrogen and total phosphorus for 1985–2004 in subbasins in 

the Sacramento and San Joaquin Basins were divided by their 

drainage areas to calculate average annual yield. Total nitrogen 

yields were greater than 2.45 tons per square mile per year 

[(tons/mi2)/yr] in about 61 percent of the valley floor in the 

San Joaquin Basin compared with only about 12 percent of the 

valley floor in the Sacramento Basin. Total phosphorus yields 

were greater than 0.34 (tons/mi2)/yr in about 43 percent of 

the valley floor in the San Joaquin Basin compared with only 

about 5 percent in the valley floor of the Sacramento Basin. In 

a stepwise multiple linear-regression analysis of 30 subbasins 

in the Sacramento and San Joaquin Basins, the most important 

explanatory variables (out of 11 variables) for the response 

variable (total nitrogen yield) were the percentage of land use 

in (1) orchards and vineyards, (2) row crops, and (3) urban 

categories. For total phosphorus yield, the most important 

explanatory variable was the amount of fertilizer application 

plus manure production.

Trends were evaluated for three time periods: 1975–

2004, 1985–2004, and 1993–2004. Most trends in flowadjusted concentrations of nutrients in the Sacramento Basin 

were downward for all three time periods. The decreasing 

nutrient trends in the American River at Sacramento and the 

Sacramento River at Freeport for 1975–2004 were attributed 

to the consolidation of wastewater in the Sacramento 

metropolitan area in December 1982 to a discharge point 

downstream of the Freeport site. Unlike the Sacramento Basin, 

most trends in flow-adjusted concentrations of nitrate and total 

nitrogen in the San Joaquin Basin were upward, especially 

over the 1975–2004 time period. The upward trend in nitrate 

and total nitrogen at the San Joaquin River near Vernalis site 

for 1975–2004 was due to many factors, including increases 

in tile drainage, fertilizer application, and manure production. 

The opposite trends for nitrate compared to total nitrogen for 
2 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

1993–2004 at the Salt Slough site (downward trends) and the 

Mud Slough site (upward trends) was due to the re-routing 

of all tile drainage to Mud Slough starting in October 

1996 with the Grasslands Bypass Project. Most trends in 

flow‐adjusted concentrations of ammonia, orthophosphate, and 

total phosphorus in the San Joaquin Basin were downward. 

Because of the significant upward trend in flow at the Santa 

Ana River downstream of Prado Dam site over the study 

period (1975–2004), quantitative trends in measured nutrient 

concentrations were evaluated. These trends generally were 

downward and were attributed to improvements in wastewater 

treatment.

Introduction

The nutrients discussed in this report are forms of 

nitrogen (N) and phosphorus (P), the main nutrients for the 

growth of algal and aquatic plant populations. The forms of 

N and P considered in this report include nitrate, ammonia, 

total nitrogen (TN), orthophosphate, and total phosphorus 

(TP). 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. The 

U.S. Environmental Protection Agency (USEPA) has set 

enforceable criteria for nitrogen (nitrate and ammonia forms), 

but not for phosphorus. The maximum contaminant level 

of 10 mg/L for nitrate (as N) in drinking water is based on 

the ability of excessive nitrate to restrict oxygen transport 

in the bloodstream. Infants under the age of 4 months lack 

the enzyme necessary to correct this condition and can die 

from methemoglobinemia (commonly known as “blue-baby 

syndrome”). The ambient water-quality criteria for ammonia 

are based on the protection of aquatic organisms such as 

fish. The criteria vary with acidity and water temperature, 

as these factors affect the proportion of total ammonia in 

the more toxic un-ionized form (NH3) versus the less toxic 

ionized form (NH4

+). At 25 °C the crossover point (where their 

proportions are equal) between NH3 and NH4

+ is at pH 9.24. 

The concentration of NH3 decreases about 10-fold for every 

decrease of 1 pH unit, such that at pH 7.0 NH3 makes up only 

0.57 percent of the total ammonia. For most surface waters in 

this study (pH ranged from 7 to 9, temperature ranged from 

10 to 30 °C), the chronic ammonia criteria would range from 

about 0.2 to 6 mg/L as N. The natural conversion of ammonia 

to nitrate (called nitrification) in streams removes oxygen 

from water and, therefore, can adversely affect fish. Although 

USEPA has not established an enforceable criterion for 

phosphorus, in order to control algae growth, they recommend 

that the TP concentration not exceed 0.1 mg/L as P in streams 

that do not discharge directly to lakes or reservoirs.

The main concern with nutrients in the Sacramento, San 

Joaquin, and Santa Ana Basins (fig. 1) is over the effects on 

downstream uses. In the Sacramento Basin, the main concern 

is over the nutrients as a food source in the Sacramento–San 

Joaquin Delta. In the San Joaquin Basin, there is a concern 

over how the algal growth creates an area of hypoxia in the 

Stockton Deep Water Ship Channel area (near Stockton in 

fig. 1B) and the impact of the algal growth on water-treatment 

costs. In the Santa Ana Basin, the nitrate in the river is 

of concern as much of the water is used to recharge the 

groundwater downstream, which subsequently is used as a 

source of drinking water.

The primary objectives of this report are to (1) determine 

trends in nutrient concentrations and loads at selected sites 

in the Sacramento, San Joaquin, and Santa Ana Basins 

in California, and (2) describe the factors affecting those 

trends. Trends were evaluated for nitrate, ammonia, TN, 

orthophosphate, and TP. The Sacramento, San Joaquin, and 

Santa Ana Basins are study units of the U.S. Geological 

Survey (USGS) National Water-Quality Assessment 

(NAWQA) Program. Similar analyses of nutrient trends 

are being conducted for study units across the country as 

part of the trends program of NAWQA. The time periods 

evaluated for trends in this study were water years 1975–2004, 

1985–2004, and 1993–2004. The first two time periods were 

selected by the authors to illustrate 30-year and 20-year trends 

in California streams. The later time period, 1993–2004, was 

a common time period selected by authors of all the NAWQA 

trend reports across the United States (Sprague and others, 

2009). This time period (1993–2004) corresponded with 

the time period of NAWQA sampling in the study units and 

allowed for a comparison of trends across the Nation for the 

same time period.

Description of Study Area

The Sacramento Basin covers about 27,000 mi2 in 

north-central California, the San Joaquin Basin about 

11,400 mi2 in central California, and the Santa Ana Basin 

about 2,700 mi2 in southern coastal California (fig. 1). The 

Sacramento River is the largest and longest river in California; 

the San Joaquin River the second longest; and the Santa Ana 

River is the largest stream system in southern California.
Description of Study Area 3

IP-002261_fig 01a

Folsom

Lake

American

Arcade Creek

River

Clear

Lake

Colusa Basin Drain

Glenn-Colusa Canal

Teham a- Colusa Canal

Cottonwood Creek

Yolo

Bypass

Shasta

Lake

Pit

River

Feather River

Lake

Oroville New Bullards Bar

Reservoir

Keswick 

Reservoir

Yuba River

Stony Creek

Butte Slough

Sutter Bypass

Mill Creek

Deer Creek

Sacramento River

McCloud River

Bear River

Cache Creek

Sacramento

Slough

Sierra

Nevada

Coast

Ranges

Sacramento

Basin

San Joaquin

Basin

San JoaquinTulare Basins

Santa

Ana

Basin

San

Francisco

Los

Angeles

San

Diego

SacramentoSan Joaquin

Delta

Central Valley

123°

122°

121°

39°

40°

41°

0 20 40 MILES

0 20 40 KILOMETERS

KLAMATH

MOUNTAINS

MOUNT SHASTA

KLAMATH

MOUNTAINS

MIDDLE

CASCADE

MOUNTAINS

Butte 

Basin

A.

Sacramento

Verona

Freeport

Knights Landing

Marysville

Woodland

Wheatland

Nicolaus

Yuba

City

Chico

Hamilton City

Gridley

Colusa

Redding

Delta

Woodland

Red Bluff

Figure 1. Location of the (A) Sacramento, (B), San Joaquin, and (C) Santa Ana Basins, California.
4 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 01b

Grasslands

Drainage 

Project Area

Merced River

Tuolumne River

Stanislaus River

New Melones 

Lake

New Don Pedro

Reservoir

Lake

Modesto McClure San

Joaquin

River

San Joaquin River

Millerton

Lake

Friant Kern

Canal

Madera Canal

Bear Cr

121°

120°

37°

38°

0 10 MILES 5

0 10 KILOMETERS 5

Orestimba

Ceek

Mud Slough

San Luis Drain

Camp 13

Slough

Panoche

Drain

Salt Slough

Yosemite

National

Park

San Luis

Reservoir

California

Aqueduct

Delta

Mendota

Canal

Merced

Atwater

Stevinson

Los

Banos

Vernalis

Patterson

Turlock

Sierra

Nevada

Coast

Ranges

Sacramento

Basin

San Joaquin

Basin

San JoaquinTulare Basins

Santa

Ana

Basin

San

Francisco

Los

Angeles

San

Diego

SacramentoSan Joaquin

Delta

Central Valley

B.

Figure 1.—Continued
Description of Study Area 5

IP-002261_fig 01c

Sierra

Nevada

Coast

Ranges

Sacramento

Basin

San Joaquin

Basin

San JoaquinTulare Basins

Santa

Ana

Basin

San

Francisco

Los

Angeles

San

Diego

SacramentoSan Joaquin

Delta

Central Valley

Cucamonga Cr

Chino Cr

Santa

Ana River

San

Jacinto

River

Lake

Elsinore

Temescal Creek

118°

117°

34°

0 10 20 MILES

0 10 20 KILOMETER

Coastal

Basin

Inland

Basin

San Jacinto

Basin

San Gabriel

Mountains

San Bernardino

Mountains

San Jacinto

Mountains

Santa Ana

Mountains

Prado

Dam

Seven Oaks

Dam

Chino Dairy

Preserve

Chino

San

Bernardino

Riverside

Santa

Ana

Huntington Beach

Warm Cr

Prado

Wetlands

Pacific

Ocean

C.

Figure 1.—Continued

Physiography and Geology

The Sacramento Basin includes parts of six 

physiographic sections—the Great Basin, the Middle Cascade 

Mountains, the Sierra Nevada, the Klamath Mountains, the 

Coast Ranges, and the Sacramento Valley (the northern part 

of the California Trough) (fig. 2; Fenneman and Johnson, 

1946). The Great Basin area is a volcanic tableland with 

altitudes of 4,000–5,000 ft. This area is drained by the Pit 

River. The Middle Cascade Mountains are the southernmost 

extent of the Cascades, a volcanic range extending north to 

Canada. The Sierra Nevada is composed primarily of preTertiary granitic rocks and is separated from the valley by 

a foothill belt of Mesozoic and Paleozoic marine rocks and 

Mesozoic metavolcanic rocks. The Klamath Mountains form 

a complex series of rocks dating from the early Paleozoic 

to the present and include accreted terrains, oceanic crust, 

and subduction-zone complexes. The Coast Ranges consist 

primarily of marine sediment and form a series of northwestto-southeast trending ridges and valleys associated with 

faulting and folding. The Sacramento Valley is part of the 

northwestward-trending asymmetric-structural trough (the 

northern part of the California Trough in fig. 2) of the Central 

Valley that has been filled with sediment that is as thick 

as 10 mi in portions of the valley. Most of the soils in the 

Sacramento Valley are fine grained with low permeability. 

Undefined

California Coast Ranges

California Trough

Great Basin

Klamath Mountains

Middle Cascade Mountains

Mexican Highlands

Salton Trough

Sierra Nevada

Sonoran Desert

Los Angeles Ranges

0 50 100 MILES

0 50 100 KILOMETERS

Physiographic Sections 

EXPLANATION

Sacramento

Basin

San Joaquin

Basin

Santa

Ana

Basin

Figure 2. Physiographic sections in Sacramento, San Joaquin, 

and Santa Ana Basins, California.
6 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

The crests of the Middle Cascade Mountains are about 

14,000 ft (Mt. Shasta), the Sierra Nevada about 10,000 ft, 

the Klamath Mountains about 8,000 ft, and the Coast Ranges 

about 7,000 ft. Altitudes in the Sacramento Valley range from 

about 1,000 ft in the north to near sea level in the south at the 

Sacramento–San Joaquin Delta.

The San Joaquin Basin includes parts of three 

physiographic sections—Coast Ranges, the San Joaquin Valley 

(central part of the California Trough), and the Sierra Nevada 

(fig. 2; Fenneman and Johnson, 1946). The boundary of the 

San Joaquin Basin is defined by the drainage divides of the 

Coast Ranges, the San Joaquin River, and the Sierra Nevada 

on the west, south, and east, respectively, and the Sacramento–

San Joaquin Delta to the north. The Tulare Basin to the 

south is closed hydrologically for surface water (endorheic) 

and is not included in this study. In addition, the diversion 

of water out of the upper San Joaquin River for irrigation 

via the Madera and Friant–Kern canals has caused sections 

of the San Joaquin River to go dry in most years since the 

completion of Friant Dam (at Millerton Lake in fig. 1B) and 

the canals in 1951. Thus, in this study the only focus is on the 

7,395 mi2 basin of the perennial San Joaquin River. Hereafter, 

this will be referred to as the San Joaquin Basin in this report. 

The crests of the Coast Ranges in this perennial San Joaquin 

Basin are about 4,000 ft, and the Sierra Nevada are about 

13,000 ft. The altitude of the San Joaquin Valley ranges from 

about 1,000 ft in the south to near sea level in the north at the 

Sacramento–San Joaquin Delta.

Geologically, the Coast Ranges, San Joaquin Valley, and 

Sierra Nevada in the San Joaquin Basin are similar to their 

counterparts in the Sacramento Basin. The composition of the 

sediments of the San Joaquin Valley reflects the source area 

and manner of deposition. Alluvial deposits on the eastside 

of the valley were derived primarily from the weathering 

of granitic intrusive rocks of the Sierra Nevada, with lesser 

contributions from the sedimentary rocks of the foothills. 

These alluvial deposits are highly permeable, medium- to 

coarse-grained sands that form broad alluvial fans where the 

streams enter the valley. The alluvial deposits on the westside 

of the valley tend to be of finer texture relative to those of 

the eastside because they are derived from the Coast Ranges. 

In the valley trough, stream-channel deposits are flanked by 

basin deposits of varying extent. These basin deposits are 

interbedded lacustrine, marsh, overbank, and stream-channel 

sediments deposited by the numerous sloughs and meanders 

of the major rivers. These deposits generally have high clay 

content and low permeability (Davis and Hall, 1959).

The Santa Ana Basin is all within one physiographic 

section—the Los Angeles Ranges (fig. 2). The Santa Ana 

Basin is characterized by prominent mountains as high as 

10,000 ft that rise steeply from the relatively flat-lying coastal 

plain and inland valleys. The Santa Ana River begins in the 

San Bernardino Mountains and flows more than 100 mi to the 

Pacific Ocean near Huntington Beach. The 2,700 mi2 area of 

the Santa Ana Basin includes three distinct subbasins—the 

Inland Basin, the San Jacinto Basin, and the Coastal Basin 

(fig. 1C). In this study, the focus is on the 1,400 mi2 of the 

Inland Basin from the San Bernardino Mountains to Prado 

Dam. Only inputs to the Inland Basin normally affect water 

quality in the Santa Ana River downstream of Prado Dam; the 

site used for trend analysis in this study. The Coastal Basin is 

downstream of Prado Dam and does not affect water quality 

at the trend site. Streamflow from the San Jacinto Basin 

normally terminates at Lake Elsinore and only torrential rains 

or extended wet cycles have produced rare overflows down 

Temescal Creek to the Santa Ana River (California Regional 

Water Quality Control Board, Santa Ana Region, 1975, 1995). 

Thus, the Inland Basin hereinafter is referred to as the Santa 

Ana Basin.

Water Resources

In addition to descriptions of the general hydrology of the 

Sacramento, San Joaquin, and Santa Ana Basins, this section 

will provides details about major tributaries and diversions 

needed to interpret loads, yields, and trends described in this 

report. In the Sacramento and San Joaquin Basins especially, 

diversions for agriculture and flood control have major 

impacts on the transport of nutrients. 

Sacramento Basin

The Sacramento Basin has a variety of climates with 

an overall average annual precipitation of 36 in., mostly 

occurring during the months of November through March, 

as indicated by monthly precipitation values (fig. 3). The 

Great Basin province has cold, snowy winters with only 

12 in. annual precipitation. The Middle Cascade Mountains 

and Sierra Nevada provinces average up to 80 in. of 

precipitation on their western slopes. Precipitation in the 

Klamath Mountains province is among the highest in northern 

California, approaching 140 in. in some locations. However, 

most of the major rivers of the Klamath Mountains drain to 

the Pacific Ocean instead of the Sacramento Basin. Annual 

precipitation in the Coast Ranges is variable, but can reach as 

much as 60 in. in places. The Sacramento Valley has an aridto-semiarid climate characterized by hot summers and mild 

winters, with average annual precipitation ranging from 14 to 

25 in.

All major rivers of the Sacramento Basin—Sacramento, 

Feather, American, and Yuba—have impoundments just 

upstream of the margin of the Sacramento Valley. The 

reservoirs are managed to collect snowmelt and to provide 

flood protection. The upper Sacramento River, the McCloud 

River, and the Pit River supply water to Shasta Lake, 

which has a capacity of 4,552,000 acre-ft. Lake Oroville 

on the Feather River has a capacity of 3,538,000 acre-ft. 
Description of Study Area 7

86420

1210

4,0003,5003,0002,5002,0001,5001,0005000

1974

1975

1976

1977

1978

1979

1980

1981

1982

1983

1984

1985

1986

1987

1988

1989

1990

1991

1992

1993

1994

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

Precipitation - Riverside (NOAA Riverside Fire Station site)Discharge - NWIS data for Santa Ana River below Prado Dam, CA (11074000)

PRECIPITATION, IN INCHES PER MONTH PRECIPITATION, IN INCHES PER MONTH PRECIPITATION, IN INCHES PER MONTH

9876543210

10 45,000

40,00035,00030,00025,00020,00015,00010,0005,0000

1974

1975

1976

1977

1978

1979

1980

1981

1982

1983

1984

1985

1986

1987

1988

1989

1990

1991

1992

1993

1994

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

Precipitation - Modesto (Modesto Irrigation District site)Discharge - NWIS data for San Joaquin River  near Vernalis, CA (11303500)

86420

1816141210

250,000200,000150,000100,00050,0000

PrecipitationDischarge

1974

1975

1976

1977

1978

1979

1980

1981

1982

1983

1984

1985

1986

1987

1988

1989

1990

1991

1992

1993

1994

1995

1996

1997

1998

1999

2000

2001

2002

2003

2004

Precipitation - Chico (NOAA Chico University site)Discharge - NWIS data for Sacramento River at Freeport, CA (11447650) +  Yolo Bypass near Woodland, CA (11453000)

DISCHARGE, IN CUBIC FEET PER SECOND DISCHARGE, IN CUBIC FEET PER SECOND DISCHARGE, IN CUBIC FEET PER SECOND

ABC

Figure 3. Long-term precipitation and flow in (A) Sacramento, (B) San Joaquin, and (C) Santa Ana Basins, California.
8 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Folsom Lake, on the American River, has a capacity of 

974,500 acre-ft. New Bullards Bar Reservoir, on the 

Yuba River, has a capacity of 966,100 acre-ft (California 

Department of Water Resources, 2009a). Water is released 

from the reservoirs during spring and summer to provide 

irrigation water to agricultural communities in the Sacramento 

and San Joaquin Valleys. These reservoirs also provide 

drinking water to residents of the Central Valley and 

southern California and are used to lower the salinity of the 

Sacramento–San Joaquin Delta by dilution. Water entering 

the reservoirs is of high quality, so the focus of this study 

was on downstream impacts. Environmental uses (defined by 

California Department of Water Resources (DWR) as wild 

and scenic river flows, required delta outflow, instream flows, 

and water use in managed wetlands) accounted for 58 percent 

of water use in the Sacramento Basin in 2000; agricultural 

use accounted for 38 percent; and urban use accounted for 

5 percent (California Department of Water Resources, 2005a). 

The water availability in the Sacramento Basin is 

characterized by a water-year index used by the State of 

California for water allocation and regulation (fig. 4A). The 

index used for the Sacramento Basin is known as the 40-30-30 

water-year index (California Department of Water Resources, 

2009b). This index is calculated by summing 40 percent of the 

current unimpaired runoff from April through July, 30 percent 

of the current unimpaired runoff from October through March, 

and 30 percent of the previous water-year’s index (with a 

maximum of 10.0). Unimpaired runoff represents the natural 

water production of a river basin, unaltered by upstream 

diversions, storage, and export of water to or import of water 

from other basins. For the Sacramento Basin, the unimpaired 

runoff is the sum of the runoff in the Sacramento River near 

Red Bluff, the Feather River inflow to Lake Oroville, the Yuba 

River about 15 mi northeast of Marysville, and the American 

River inflow to Folsom Lake (fig. 1A). Proceeding from wet 

to dry conditions, the water years are classified as wet, above 

normal, below normal, dry, or critical. The classifications for 

1901–2004 are shown in figure 4A. This record shows high 

variability with periods of wetter conditions alternating with 

periods of drier conditions. The average flow leaving the 

Sacramento Basin (Sacramento River at Freeport plus the Yolo 

Bypass) to the delta is about 27,000 ft3/s.

The three largest agricultural diversion points on the 

Sacramento River in downstream order are: (1) the TehamaColusa and Corning Canals diversion at the Red Bluff 

Diversion Dam (about 2 mi downstream of Red Bluff), 

(2) the Glenn-Colusa Canal diversion point at Hamilton City 

(west of Chico), and (3) the Sutter Mutual Water Company 

and Reclamation District 108 diversion points downstream 

of Colusa (west of Yuba City) (fig. 5). The Tehama-Colusa 

and Corning Canals diversion is operated by the Bureau of 

Reclamation (Reclamation) as part of the Central Valley 

Project (Bureau of Reclamation, 2007a). In 1989, these 

canals provided water for about 100,000 acres of agricultural 

land and about 20,000 acres of wildlife refuge land (Bureau 

of Reclamation, 2007a). During 1993–2004, these canals 

diverted from 205,000 to 363,000 acre-ft of water annually 

during the peak irrigation season of April through October 

(Bureau of Reclamation, 2007b). This amounted to less 

than 1–13 percent of the flow in the Sacramento River near 

Red Bluff based on monthly rates. The Glenn-Colusa Canal 

diversion started in 1883 and is operated by the Glenn-Colusa 

Irrigation District (Glenn-Colusa Irrigation District, 2007). 

The maximum diversion of water is 3,000 ft3/s, which is 

used to irrigate about 141,000 acres of agricultural land. 

During 1993–2004, this diversion ranged from 520,000 to 

760,000 acre-ft annually during the peak irrigation season 

of April through October (Bureau of Reclamation, 2007b). 

This amounted to 1–26 percent of the flow in the Sacramento 

River at Vina based on monthly rates. The Sutter Mutual 

Water Company and Reclamation District 108 divert water 

to irrigate about 47,000 acres of agricultural land on the east 

side of the river and 48,000 acres of agricultural land on the 

west side of the Sacramento River, respectively (Schantz and 

others, 2002; California Bay-Delta Authority, 2007). During 

1993–2004, these diversions for irrigation ranged from 

238,000 to 380,000 acre-ft annually during the peak irrigation 

season from April through October (Bureau of Reclamation, 

2007b). This amounted to less than 1 to 18 percent of the flow 

in the Sacramento River at Colusa based on monthly rates. 

Together these three diversion points diverted 2–43 percent 

of the Sacramento River flow near Red Bluff during the 

April through October period based on monthly rates for 

1993–2004. Downstream of the Colusa Basin Drain (CBD), 

the Sacramento Basin becomes complicated by the potentially 

large diversion into the Yolo Bypass, plus the large and 

sometimes ungaged inputs from the Feather River, Sacramento 

Slough, and CBD (fig. 5).

In addition to the spring and summer diversions for 

agricultural use, the diversions in the Sacramento Basin for 

flood control in the winter and spring can be especially large. 

The Sacramento Basin has a bypass system where high flows 

are diverted to the Sutter Bypass and the Yolo Bypass, around 

the Freeport gage and returned to the Sacramento River 

downstream of Freeport in the delta (fig. 5). The Sacramento 

River has six main diversion points into the bypasses. From 

upstream to downstream these flood-control diversions are 

Moulton Weir, Colusa Weir, Tisdale Weir, Fremont Weir, 

Knights Landing Ridge Cut, and Sacramento Weir (fig. 5). In 

the reach of river from Hamilton City to Colusa, the Moulton 

and Colusa Weirs can divert more than one-half the river flows 

into the Sutter Bypass during high winter and spring flows. 

For example, in February 1998, the Moulton Weir diverted 

9,592 ft3/s and Colusa Weir diverted 45,250 ft3/s from the 

river to the bypass (data from DWR Water Data Library, 

accessed April 2, 2008, at URL: http://wdl.water.ca.gov/

hydstra/index.cfm). This amounted to 61 percent of the river 

flow at Hamilton City, upstream of the diversions. Tisdale 

Weir diverts high winter and spring flows from the river to 

the Sutter Bypass between Colusa and upstream of CBD. 
Description of Study Area 9

IP-002261_fig 04

0

1

2

3

4

5

6

7

8

Wet

Above Normal

Below Normal

Dry

Critical

1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 Classification

SAN JOAQUIN BASIN

WATER YEAR INDEX,

IN MILLION ACRE-FEET

0

2

4

6

8

10

12

14

16

18

Wet

Above Normal

Below Normal

Dry

Critical

1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 Classification

SACRAMENTO BASIN

WATER YEAR INDEX,

IN MILLION ACRE-FEET

A

B

Figure 4. Water-year hydrologic classifications for 1901–2004 for (A) Sacramento Basin, and (B) San Joaquin Basin, 

California.

In February 1998, Tisdale Weir diverted an additional 

16,450 ft3/s from the river (data from DWR Water Data 

Library, accessed April 2, 2008, at URL: http://wdl.water.

ca.gov/hydstra/index.cfm). This represents about 36 percent of 

the flow that was left in the river at Colusa after the Moulton 

and Colusa Weirs had removed 61 percent of the upstream 

flow, leaving about 25 percent of flow that had been measured 

at Hamilton City upstream of the diversions. 

At Knights Landing, the Sacramento River flood control 

and drainage systems converge creating increased hydrologic 

complexity. The CBD discharges to the Sacramento River 

near Knights Landing when the water levels in the CBD are 

higher than the river. However, when the river levels are 

higher, CBD discharges to Knights Landing Ridge Cut instead 

(fig. 5; Schemel and others, 2002). This flow is ungaged and 

flows to the Yolo Bypass and around the Freeport gage. Thus, 

drainage from CBD does not always affect water quality at 

Freeport. Where the Sutter Bypass intersects the Sacramento 

River downstream of Knights Landing, it generally crosses 

the river and flows into the Yolo Bypass at the Fremont 

Weir. Sacramento Slough is a drainage canal in the Sutter 

Bypass that discharges its drainage from Butte Basin (and 

Butte Creek) into the Sacramento River (fig. 5). However, at 

high river levels, Sacramento Slough is not able to discharge 

into the river, and the area becomes flooded and most of 

the drainage eventually ends up in the Yolo Bypass. At high 

flows, most of the Feather River ends up in the Yolo Bypass, 

and the lower portion of the Feather River ends up in the 

backwater of the Sacramento River. For this reason, estimates 

of Feather River near Nicolaus flows were made by adding 

flows for the Feather River at Gridley (between Lake Oroville 

and the Yuba River confluence) to flows for the Yuba River 

near Marysville and the Bear River near Wheatland (fig. 1A). 

Downstream of Verona and just upstream of the American 

River confluence, is the Sacramento Weir (fig. 5). This is a 

rarely used flood‐control weir just upstream of the City of 

Sacramento. However, in February 1986 and in January 1997, 

23,920 and 19,700 ft3/s were diverted into the Yolo Bypass at 

this weir, respectively (data from National Water Information 

System [NWIS]).
10 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Figure 5. Schematic diagram of mMajor tributaries, diversions (agricultural and flood control), and wastewater 

treatment-plant discharges for the (A) Sacramento Basin, and (B) San Joaquin Basin, California.

IP_002261_figure_05

(A) (B)

Red Bluff Tehama-Colusa &

Corning Canals

Glenn-Colusa

Canal

Hamilton City

Moulton Weir

Colusa Weir

Colusa

Tisdale Weir

Sutter Mutual & 

RD 108 above 

CBD

Verona

Freeport

Butte Creek Sutter Bypass

Sacramento 

Slough

Colusa Basin 

Drain

Knights 

Landing 

Ridge Cut

Sacramento 

Weir

American R

Yolo Bypass

Feather R

Yuba R

Bear R

Stevinson

Patterson

Vernalis

Stanislaus R

Maze 

Road

Tuolumne R

W Stanislaus ID

Patterson ID

Modesto WWTP

Turlock WWTP

Merced R

Mud Slough

Salt Slough

Fremont Weir

WWTP - wastewater treatment plant

ID - irrigation district

RD - reclamation district

CBD - Colusa Basin Drain

R - river
Description of Study Area 11

San Joaquin Basin

The perennial San Joaquin Basin has an overall longterm average annual precipitation of 28 in. (13 in. in the 

valley portion only), most occurring from November through 

March (National Center for Atmospheric Research, 2003). The 

eastern slopes of the Coast Ranges and the San Joaquin Valley 

are in the rain shadow of the Coast Ranges. Warm, moist air 

masses from the Pacific Ocean are forced aloft by the Sierra 

Nevada. The air masses cool, and the moisture condenses, 

resulting in heavy precipitation on the western slopes of the 

Sierra Nevada. This precipitation, occurring as rainfall and 

snow, is the major source of water entering the San Joaquin 

Basin. Annual precipitation in the valley ranges from 7 in. 

in the south to 15 in. in the north. Precipitation in the Coast 

Ranges ranges from less than 10 in. to more than 20 in. 

Precipitation in the Sierra Nevada ranges from about 20 in. in 

the lower foothills to more than 80 in. at some high-altitude 

sites.

All major rivers of the perennial San Joaquin Basin—

Merced, Tuolumne, and Stanislaus—have impoundments 

just upstream of the margin of the San Joaquin Valley 

(fig. 1B). Lake McClure, on the Merced River, has a capacity 

of 1,026,000 acre-ft. New Don Pedro Reservoir, on the 

Tuolumne River, has a capacity of 2,030,000 acre-ft. New 

Melones Lake, on the Stanislaus River, has a capacity of 

2,400,000 acre-ft (California Department of Water Resources, 

2009). These reservoirs are managed for irrigation water 

supply, hydroelectric power production, recreation, and some 

municipal water supply. Water entering the reservoirs is of 

high quality, so the focus of this study was on downstream 

impacts. For the entire San Joaquin Basin in 2000, agriculture 

accounted for about 57 percent of water use, environmental 

uses accounted for 38 percent, and urban use accounted for 

5 percent (California Department of Water Resources, 2005a).

Water availability in the San Joaquin Basin is 

characterized by a water-year index that differs slightly from 

the one for the Sacramento Basin (fig. 4B). The index used 

for the basin is known as the 60-20-20 water-year index 

(California Department of Water Resources, 2009b). Sixty 

percent of the current unimpaired runoff from April through 

July, 20 percent of the current unimpaired runoff from 

October through March, and 20 percent of the previous water 

year’s index (with a maximum of 4.5) are summed. For the 

San Joaquin Basin, the unimpaired runoff is the sum of the 

runoff in the Stanislaus River inflow to New Melones Lake, 

Tuolumne River inflow to New Don Pedro Reservoir, Merced 

River inflow to Lake McClure, and San Joaquin River (SJR) 

inflow to Millerton Lake. The classifications for 1901–2004 

are shown in figure 4B. As was observed for the Sacramento 

Basin, this record indicates high variability with periods of 

wetter conditions alternating with periods of drier conditions. 

The average flow leaving the San Joaquin Basin to the delta is 

about 4,500 ft3/s.

Surface water in the San Joaquin Basin is reused multiple 

times because there are more than 100 diversion and return 

flow points in use in agricultural areas (Kratzer and Shelton, 

1998). Thus, a large proportion of water entering the San 

Joaquin Basin may never enter the delta through the SJR. 

The two largest agricultural diversions—Patterson Irrigation 

District and West Stanislaus Irrigation District—can each 

divert more than half the flow in the river during low-flow 

summer periods (fig. 5). Unlike the Sacramento River, the SJR 

does not have a bypass system, and the high winter and spring 

flows stay in the main channel (except when levees breach 

during extreme high flow events).

Santa Ana Basin

The Santa Ana Basin has a Mediterranean climate with 

hot, dry summers and cooler, wetter winters. Average annual 

precipitation ranges from about 10 to 24 in. in the coastal plain 

and inland valleys, and from 24 to 48 in. in the San Gabriel 

and San Bernardino Mountains. Groundwater is the primary 

source of water supply in the watershed, meeting about 

two-thirds of the total water demand of about 1.2 million 

acre-ft/yr (Santa Ana Watershed Project Authority, 1998). 

Imported water from northern California and the Colorado 

River meet about one-quarter of the total consumptive 

demand. Urban use in the watershed in 2000 accounted for 

75 percent of water use; agriculture comprised the remaining 

25 percent (Belitz and others, 2004). Withdrawal rates of 

local groundwater far exceeded natural recharge throughout 

the study period. Consequently, engineered groundwater 

recharge is an important and recognized beneficial use of the 

Santa Ana River (SAR). Dissolved solids (salts) and nutrients 

(specifically inorganic nitrogen) have been identified as the 

primary water-quality concerns associated with this source of 

recharge (California Regional Water Quality Control Board, 

Santa Ana Region, 1995). 

Historically, it is believed that the SAR flowed 

continuously throughout most of the year. But by 1969, water 

diversions and groundwater pumping had severely diminished 

natural flow in the river (California Regional Water Quality 

Control Board, Santa Ana Region, 1995). Currently, the high 

degree of urbanization in the basin creates a disconnection 

between landscape and water quality in the river. Flow from 

the upper Santa Ana Basin commonly is diverted to detention 

basins and seldom reaches the valley floor, even during storm 

events. As a result, the majority of flow in the lower basin 

originates from treated wastewater (Burton and others, 1998), 

with additional, but significant periodic inputs from storms. 

Currently, nearly all this domestic wastewater is tertiary 

treated (Izbicki and others, 2000) to meet water-quality 

objectives established by the California Regional Water 

Quality Control Board, Santa Ana Region (RWQCB(SAR); 

1995). Nevertheless, nutrient concentrations in the treated 

effluent are higher than natural sources of flow. 
12 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Land Use

Land use in the mountainous regions of the Sacramento 

Basin is principally forest, although forest and rangeland are 

mixed in regions of the Coast Ranges and the Great Basin 

(fig. 6). The land uses of the Sacramento Valley are dominated 

by agriculture. In 2000, about 2,000 mi2 of the Sacramento 

Valley were irrigated (California Department of Water 

Resources, 2001). Orchards—principally walnut, almond, 

prune, and peach—are along river channels to take advantage 

of well-drained soils. Rice is one of the principal crops 

because of the relatively impermeable soils of the valley and 

the availability of irrigation water from the Sacramento River.

The major population centers of the Sacramento 

Basin are in the Sacramento Valley. The total population 

of the Sacramento Basin in 2000 was about 2.59 million 

(California Department of Water Resources, 2005a), with 

about 1.84 million of that in the metropolitan Sacramento 

area (defined here as the area within a 40-mi radius of the 

State Capitol in the six-county region considered by the 

Sacramento Area Council of Governments) at the southern 

end of the Sacramento Valley (Sacramento Area Council of 

Governments, 2002). Other cities in the Sacramento Basin 

with a population more than 50,000 include Redding (81,000) 

and Chico (60,000) (U.S. Census Bureau, 2001a).

In the San Joaquin Basin, the Sierra Nevada is 

predominantly forested land, the Coast Ranges and the 

foothills of the Sierra Nevada primarily are rangeland, and 

the San Joaquin Valley is dominated by agriculture (fig. 6). 

In 2000, about 1,000 mi2 of the perennial San Joaquin Basin 

and about 4,500 mi2 of the entire San Joaquin-Tulare Basins 

were irrigated (California Department of Water Resources, 

2001). The distribution of crops in the valley generally reflects 

the distribution of soil texture and chemistry. Orchards and 

vineyards primarily are grown on the well-drained alluvial 

fan soils of the eastside. Cotton, a salt tolerant crop, is the 

principal crop grown on the basin deposits at the southern 

end of the basin. Row crops, such as beans, are primarily 

grown on the alluvial fans of the westside. Land along the 

SJR on the eastside primarily is used for corn, alfalfa, pasture, 

and dairies. In 1999, the total gross value of agricultural 

production in the entire San Joaquin Valley was about 

$14.5 billion (Kuminoff and others, 2000). This represented 

about 7.6 percent of the U.S. agricultural production and 

about 58 percent of California’s total agricultural production, 

compared to 11 percent of California’s total agricultural 

production from the Sacramento Basin and less than 1 percent 

from the Santa Ana Basin (Kuminoff and others, 2000; U.S. 

Department of Agriculture, 2004). The major products (in total 

value) in the San Joaquin Valley were livestock and livestock 

products (30 percent), fruits and nuts (26 percent), field 

crops (25 percent), and vegetables and melons (13 percent) 

(Kuminoff and others, 2000).

As with the Sacramento Basin, the major population 

centers of the San Joaquin Basin are located in the valley. The 

total 2000 population of the perennial San Joaquin Basin is 

about 729,000 (U.S. Census Bureau, 2001b–2001e). Cities 

with populations or more than 50,000 in the basin include 

Modesto (189,000), Merced (64,000), and Turlock (56,000) 

(U.S. Census Bureau, 2001a). Population growth in the basin 

for 1980–2000 was about 64 percent, compared to 43 percent 

in California and 31 percent in the United States (U.S. Census 

Bureau, 2001a). 

Land use in the entire Santa Ana Basin during the last 

decade of the study period was about 35 percent urban; 

10 percent agricultural; and 55 percent open space consisting 

primarily of undeveloped highlands that are steep and 

relatively impervious (Belitz and others, 2004). Land use 

in the Inland Basin is about 33 percent urban; 8 percent 

agricultural; and 59 percent open space (Southern California 

Association of Governments, 1997). The primary agricultural 

area in the Inland Basin is the Chino Dairy Preserve (fig. 1C). 

The number of dairy cows in this area increased from about 

152,000 in 1975 to about 228,000 in 1985 (Wildermuth 

Environmental, 1998). Recently, the number of dairy farms in 

the Chino Dairy Preserve has decreased due to urban pressures 

(Vitko, 2005). The open space in the Inland Basin primarily is 

mountains that are steep and remain undeveloped. The Santa 

Ana Basin is rapidly urbanizing, and agricultural land use in 

the Inland Basin, and in the Santa Ana Basin as a whole, is 

decreasing. The RWQCB(SAR) (1975) reported agricultural 

land use equivalent to about 20 percent of the Santa Ana Basin 

in 1975, which is about twice the percentage documented for 

1993 (Southern California Association of Governments, 1997). 

The entire Santa Ana Basin is home to about 6 million 

people; about 2.6 million of these people live in the Inland 

Basin (California Department of Finance, 2000). Population 

densities and land-use percentages in the Inland Basin are 

intermediate to those in the highly urbanized Coastal Basin 

and the less-developed San Jacinto Basin and, as a result, 

are similar to those in the Santa Ana Basin as a whole. 

In 2000, the population density in the entire 2,700 mi2 of 

Santa Ana Basin there was 2,360 people/mi2 compared to 

1,870 people/ mi2 in the Inland Basin (California Department 

of Finance, 2000). Around the beginning of the study 

period, in 1970, these densities were 920 people/mi2 and 

760 people/ mi2, respectively. 
Description of Study Area 13

IP_002261_figure_06

0 50 100 MILES

0 50 100 KILOMETERS

EXPLANATION

Open Water

Perennial Ice/Snow

Urban/Residential/Commerical/Transportation

Bare rock/quarry/transitional

Forest

Shrubland

Orchard/Vineyard/Other

Grassland/Herbaceous

Pasture/Hay

Row Crops

Small Grains

Fallow

Urban/Recreational Grasses

Wetlands

Santa

Ana

Basin

San Joaquin

Basin

Sacramento

Basin

Figure 6. General land use in Sacramento, San Joaquin, and Santa Ana Basins, California.
14 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Analysis Techniques

Long-term changes over time (trends) in nutrient 

concentrations and loads can be used to evaluate changes in 

nutrient sources or management activities within a watershed. 

However, concentrations and loads of nutrients are influenced 

by the amount of flow at the time of sampling. This influence 

is strong especially for sediment-associated nutrients like 

TP more than for primarily dissolved nutrients like nitrate 

(Kratzer and Shelton, 1998). In point-source dominated basins 

(such as the Santa Ana), the input of nutrients is relatively 

constant; increases in flow likely will result in decreased 

concentrations due to dilution. In nonpoint-source dominated 

basins (such as the Sacramento and San Joaquin), nutrient 

inputs from storm runoff likely will increase some nutrient 

concentrations with flow. Trends in the measured nutrient 

concentrations give an indication of the water-quality changes 

that riverine habitats have experienced and are important with 

regards to biotic impacts. However, in order to determine 

whether a stream has experienced a trend in water quality due 

to changes in watershed activities, the effect of flow magnitude 

must be removed from the measured concentrations. 

This is done by calculating flow-adjusted concentrations 

(FAC), which give insight into whether a trend in measured 

concentrations is a “true” trend in the nutrient sources or 

simply reflects a trend in flow due to climatological or 

hydrologic changes. Various statistical techniques (described 

herein) were used to estimate nutrient loads and yields, relate 

yields to nutrient sources and subbasin characteristics, and to 

determine trends in nutrient concentrations. 

Loads and Yields

Loads were determined for sites sampled from 1975 

to 2004, where possible in this study. Loads were estimated 

using the program LOADEST, which is incorporated into the 

statistical package, S-PLUS (Slack and others, 2003; Runkel 

and others, 2004; Insightful Corporation, 2005). Monthly 

loads were estimated for sites with sufficient data for 1975–

2004. In general terms, a load is an integrated mass flux over 

some time interval {t

a, tb}:

() () () ,

where

is the total load,

is the instantaneous load,

is a unit conversion factor,

is the instantaneous measured concentration, 

and

is the instantaneous flow.

b b

a a

t t

t t

L l t dt kc t q t dt

L

l

k

c

q

= = ∫ ∫ (1)

LOADEST is a log-linear multiple-regression model 

of constituent concentration against flow, decimal-time, and 

seasonal variables. The presence of multi-collinearity and 

censoring of data can cause difficulties for multiple regression. 

Multi-collinearity occurs when one or more independent 

variables are highly correlated and can lead to misspecified 

model coefficients. LOADEST eliminates this by centering the 

independent variables. To account for the presence of censored 

data, an adjusted maximum-likelihood estimator (AMLE) was 

used to calculate model coefficients. The AMLE procedure 

also corrects for first-order bias in the standard maximumlikelihood regression coefficients and incorporates a factor that 

minimizes the bias that can occur when estimated logarithms 

of concentration are retransformed to original units (Cohn, 

2005). For sites without censored data, the AMLE is identical 

to ordinary least squares. For most sites in this study, the 

following seven-parameter version of the LOADEST model 

was used:

2

0 1 2

2

34 5

6

ln ( ) ln ( / ) [ln ( / )]

( ) ( ) sin (2 )

+ cos (2 ) ,

where

ln is the natural logarithm function,

is the measured concentration, in milligrams

per liter,

is the measured daily mea

c c

c c

C QQ QQ

tt tt t

t

C

Q

=β +β +β

+β − +β − +β π

β π +ε

0

1 2

3 4

n flow, in cubic feet

per second,

is time, in decimal years,

, are centering variables for flow and time,

is a constant,

, describe the relation between concentration 

and flow,

, describe the re

c c

t

Q t

β

β β

β β

5 6

lation between concentration

and time, independent of flow,

, describe seasonal variation in concentration data,

and

is residual error, assumed to be normally

distributed with zero mean and variance ε

β β

ε

σ 2

.

(2)

A calibration period for flow and concentration using 

only concentrations with associated flow values is run first. 

In this study, we used the entire time period of water-quality 

data during 1975–2004 as the calibration period. For the 

load-estimation period, there must be a flow value for each 

day. In addition to monthly loads, the output from LOADEST 

includes the average daily flux, the variance of the average 

daily flux, the 95 percent confidence interval for the average 

daily flux, and the standard error of prediction (SEP) for the 

average daily flux. The variance is a measure of the variability 

in the model prediction due to parameter uncertainty. 
Analysis Techniques 15

Mathematically, it is the square of the standard error. The SEP 

is a measure of the expected difference between the model 

prediction and the true load that flowed past the site, reflecting 

parameter uncertainty and natural variability. Thus, the SEP 

is always larger than the standard error. The SEP (expressed 

as a percent of the estimated load) is plotted for each month 

along with the estimated loads in this report. The 95-percent 

confidence interval for the load estimates from LOADEST 

are constructed using SEP (Timothy Cohn, U.S. Geological 

Survey, written commun., 2004). For a normal distribution, 

this 95-percent confidence interval is ±1.96 SEP. However, 

LOADEST assumes a log-normal distribution of loads. To 

calculate the 95-percent confidence interval, we reparametrize 

the estimated monthly load (see μLN below) and SEP (see σLN

2 

below):

{ }

[ ]

[ ] [ ]

LN

2 2

2

C.I. exp[μ 1.96 ],exp[μ 1.96 ] ,

where

C.I. is 95-percent lognormal confidence interval,

is ln 1+(SEP) /(estimated load from LOADEST) ,

μ is ln estimated load from LOADEST /2,

and

exp is e , 

LN LN LN LN

LN

LN

= −σ +σ

σ    

− σ

( )

where e is the base of natural logarithm

=2.718.... .

(3)

In some cases, not enough data were available to run the 

seven-parameter LOADEST model (eq. 2), but enough data 

were available to run a less rigorous five-parameter model. 

This model includes the β0, β1, β3, β5, and β6 terms from 

equation 2. LOADEST loads were estimated for the Feather 

River near Nicolaus site using an estimated flow record, and 

loads for CBD and Sacramento Slough were estimated using 

the average instantaneous loads during periods with flow 

records (see section, “Water Resources”).

 Yields were calculated for subbasins by dividing the 

estimated loads by the subbasin area. Unlike the temporal 

analysis of loads, yields were evaluated in only a spatial 

context in this report. The average annual yields for 

1985–2004 were used to make spatial comparisons in the 

Sacramento and San Joaquin Basins. Comparison of yields 

among subbasins allows identification of areas with the largest 

impacts on nutrient concentrations and loads downstream. On 

the mainstem Sacramento and San Joaquin Rivers, yields also 

were calculated for the areas between sampling sites on the 

mainstem river using the differences in loads between sites. 

TN yields were divided into four categories: <0.57, 0.57–1.51, 

1.51–2.45, and >2.45 (tons/mi2)/yr. The Redfield ratio of TN 

to TP found in phytoplankton on a mass basis (7.2:1) was 

used to devise categories for TP (Hall and others, 2005). Thus, 

the TN yield categories were divided by 7.2 to create four 

categories for TP yields: <0.08, 0.08–0.21, 0.21–0.34, and 

>0.34 (tons/mi2)/yr.

Standard Error of Prediction

The SEP was used as the primary determinant of the 

quality of load estimates made by using LOADEST. SEP 

values greater than 30 percent were considered questionable 

and SEP values greater than 50 percent were not used in 

this report except where noted. The SEP is affected by 

several factors: (1) the range of flow conditions covered 

by the calibration database, (2) gaps in data during the 

calibration period especially at the beginning or end of 

the load-estimation period, (3) shortage of data, and (4) 

inconsistencies in the flow versus concentration relations.

If sufficient concentration data were not available during 

high-flow periods, these times of potentially high loads 

usually will have especially high SEP values. Although not 

as big of a problem for long-term load estimates, the same 

is true of especially low-flow periods. When the calibration 

period for LOADEST does not have concentration data at 

the beginning and ending of the periods picked for load 

estimates, these periods also will have especially high SEP 

values. In these cases, the load estimates are being made for 

periods outside of the calibration period. An overall shortage 

of concentration data usually will result in high SEP values 

throughout the load estimation period. Also, short-term factors 

such as hysteresis are not accounted for by the LOADEST 

model. With hysteresis, the concentrations at the same flow 

on the ascending limb of a storm hydrograph typically are 

higher than on the descending limb. Donato and MacCoy 

(2005) found that the phosphorus loads on the Boise River 

in Idaho measured during high flow were underestimated by 

LOADEST by about 40 percent, and measured loads during 

low flow were overestimated. Thus, LOADEST does better at 

estimating long-term loads (monthly or annual) than shortterm loads (daily).

Loading Factors

To account for losses of water (and therefore loads) in 

the Sacramento and San Joaquin Basins due to diversions (see 

section, “Water Resources”), loading factors were developed 

to modify the loads from upstream sites on a monthly basis 

(table CD-1). This loading factor is the fraction of the load 

that is transported from the upstream site to the downstream 

site. In mathematical terms, this loading factor is 1 minus the 

fraction of the upstream load that is diverted before being 

transported to the downstream site. These factors were used 

in the analysis of loads and yields in the Sacramento and San 

Joaquin Basins in this report.

In the Sacramento Basin, loading factors were developed 

to account for the large spring and summer agricultural 

diversions between Red Bluff and upstream of Colusa Basin 

Drain. Loading factors also were developed to account for 

the large winter and spring flood-control diversions between 
16 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Hamilton City and Freeport. A sample calculation of a 

monthly loading factor for the Sacramento Basin is presented 

here for January 1997 for the reach between Verona and 

Freeport:

[ ]

1 (diversions between Verona and Loading Factor Freeport as fraction of Freeport flow)

1 (19,700 / 87,110) 1 0.23 0.77,

where

19,700 = average monthly diversion for flood control 

at Sacramento Weir 

  − =    

= − =− =

(from NWIS, in 

cubic foot per second), and

87,110 = average monthly flow in Sacramento River 

at Freeport (from NWIS, in cubic foot 

per second).

In this case the loading factor is 0.77 and the fraction 

diverted is 0.23.

In the San Joaquin Basin, loading factors were developed 

to account for agricultural diversions between Stevinson and 

Vernalis (Kratzer and others, 2004). A sample calculation of a 

monthly loading factor for the San Joaquin Basin is presented 

here for July 2002 for the reach between Patterson and Maze 

Road:

[ ]

[ ]

1 (diversions between Patterson 

Loading Factor and Maze Road as fraction of 

Maze flow)

1 (346.6 16.0 18.2) / 687

1 (380.8 / 687) 1 0.55 0.45,

where

346.6 = average monthly diversion between Patterso

  −

=  

 

=− + +

= − =− =

n

and Tuolumne River (from Kratzer

and others, 1987; Quinn and Tulloch, 2002; 

 in cubic foot per second),

16.0 = average monthly diversion from Tuolumne 

 River downstream of the flow gage 

(from Kratzer and others, 1987; in cubic 

 foot per second),

 18.2 = average monthly diversion between Tuolumne 

 River and Maze Road (from Kratzer and others, 

 1987; Quinn and Tulloch, 2002; in cubic 

 foot per second),

687 = average monthly flow in SJR at Maze Road 

 (from DWR Water Data Library; in cubic

foot per second.

In this case the loading factor is 0.45 and the fraction 

diverted is 0.55.

Unmodeled Load Sources and (or) Sinks

In the results of this study, many references are made to 

the unmodeled load sources and(or) sinks or the unmodeled 

areas between mainstem sites. This term is defined here to aid 

the interpretation of these results. This term means that these 

loads or areas could not be quantified with LOADEST due to 

a shortage of data. However, in most cases, we know about 

significant sources (point or nonpoint) or sinks (agricultural or 

flood-control diversions) that occur between mainstem sites. 

The loads for these sources and(or) sinks were evaluated by 

the difference in modeled loads for mainstem reaches. The 

loads were then compared to known, but unmodeled, sources 

and(or) sinks for interpreting potential sources of these loads. 

In addition, these unmodeled loads also were used to calculate 

yields for these unmodeled areas. These yields were used in 

the stepwise multiple linear-regression analysis of yields as a 

function of nutrient sources and subbasin characteristics.

Unmodeled sources in the Sacramento Basin also include 

the major agricultural tributaries on the westside (CBD) and 

the eastside (Sacramento Slough) of the Sacramento Valley. 

The DWR maintains flow records for the CBD for days when 

the CBD discharges to the Sacramento River. These flows 

were combined with water-quality data to produce a record of 

instantaneous loads for 1993–2004, which were then averaged 

to produce an average annual yield. These yields were not 

representative of all TN and TP produced in the CBD subbasin 

for the year; only TN and TP that actually discharged to 

the Sacramento River at Knights Landing. Likewise, DWR 

maintains a record of flows at Sacramento Slough. However, 

these flows were reported as zero or missing when the water 

level in Sacramento Slough was lower than the level of the 

Sacramento River. Unlike CBD, these flows were not released 

elsewhere and although LOADEST could not be used for this 

site due to the missing flow record, load estimates were made 

by averaging the instantaneous loads for 1993–2004.

Stepwise Multiple Linear Regression

The differences in yields between subbasins in the 

Sacramento and San Joaquin Basins were evaluated for 

the average 1985–2004 yield estimates. The major factors 

responsible for differences in yields between subbasins were 

evaluated in this report using a stepwise multiple linearregression (MLR) model in S-PLUS (Helsel and Hirsch, 1992; 

Insightful Corporation, 2005). The average annual yield of TN 

and TP for 1985–2004 by subbasin in the Sacramento and San 

Joaquin Basins (or unmodeled areas between mainstem sites) 

was the response variable in the MLR. These average yields 

were related to 11 explanatory variables including nutrient 

sources (fertilizer application and manure production, and 

atmospheric deposition) and subbasin characteristics (various 

land covers, soil types, and runoff factor). Point sources and 

tile drainage were included in the analysis by reducing the 
Analysis Techniques 17

subbasin yields accordingly. The stepwise MLR process in 

S-PLUS evaluated explanatory variables iteratively in the 

forward and backward directions.

The decision to add or remove variables was based on 

the Mallow’s Cp statistic and the Akaike’s Information Criteria 

statistic. Mallow’s Cp statistic is a criterion based on the 

number of variables and mean-square-error for the model. The 

Akaike’s Information Criteria statistic is the likelihood version 

of the Cp statistic and includes a measure of model error and a 

penalty for too many explanatory variables (Helsel and Hirsch, 

1992). In S-PLUS, the stepwise MLR program calculates 

the Cp statistic for the current model, as well as those for all 

possible reduced and augmented models, then adds or removes 

the variable that reduces Cp the most. Outliers are identified 

in the program by the Cook’s distance value, a measure of 

the influence of individual observations on the regression 

coefficients (Insightful Corporation, 2005). An adjusted R2

value is produced for the resulting MLR equation. An adjusted 

R2 is the coefficient of determination (R2) adjusted for the 

number of explanatory variables in the MLR. The MLR model 

with the highest adjusted R2 is the one with the lowest meansquare-error. Unfortunately, the adjusted R2 always increases 

with the number of explanatory variables, and thus is not a 

good determinant of the best model. A p-value also is provided 

for each variable in the stepwise MLR process. This value is 

the probability of obtaining the test statistic or less, in this case 

the t-statistic, when the null hypothesis is true. In the case of a 

MLR the null hypothesis is that the coefficient for the variable 

is zero. Thus, for the significance level of 0.05 used in this 

report, a p-value less than 0.05 means that the coefficient is 

significantly different from zero.

For the regression coefficients to be directly relevant to 

the significance of each explanatory variable, all variables 

(response and explanatory) need to be standardized or centered 

(Helsel and Hirsch, 1992; Wise and others, 2007). This was 

done before fitting the MLR equation by subtracting the mean 

for each variable and dividing by the standard deviation. 

Each standardized regression coefficient then represents the 

change in the response of yield in standardized units to a unit 

change in the standardized explanatory variable. Because 

standardized regression coefficients are independent of scale 

units, they are useful in interpreting the results from MLR 

analysis. Standardizing the data also reduces the effect of 

multi-collinearity (degree to which one or more explanatory 

variables are related).

Trends

Flow-adjusted trends are the trends in concentrations that 

would have occurred in the absence of natural variations in 

flow. Non-flow-adjusted trends are the trends resulting from 

natural and human factors. Monotonic, flow-adjusted trends, 

were estimated with parametric multiple-regression analysis 

using the statistical program LOADEST. The dependent 

variable was concentration, and the independent variables 

were various functions of flow, decimal time, and season. The 

trends were determined using the model coefficient of the 

decimal-time term, with a coefficient significantly different 

from zero indicating the presence of a significant trend.

Trends in Flow-Adjusted Concentrations

For trends in FACs, the results of the decimal-time 

factors were used in the seven-parameter LOADEST model 

(eq. 2) to determine significant trends and their slopes 

(Langland and others, 2006). The trend in FAC (in percent 

difference relative to a starting time, t

0) is calculated from: 

[ ] [ ]

0

FAC trend =100 (exp[ ] 1),

where

exp = e , where e is the base of the natural

logarithm (=2.718....),

is an estimate for the flow-adjusted change

in ln (C) between a starting time t and 

any subsequent ti

FA

FA

τ −

τ

2 2

3 04 0

3 4

me =

( )+ ( ) ( ) and,

ln, , , are defined in equation 2.

c c

c

t

tt tt t t

t

β− β − − −    

β β

(4) 

In this report, the slope of the trend in FAC is expressed 

in terms of percent per year. This is merely the value from 

equation 4 divided by the time period of the trend (t – t

0). The 

result in equation 4 gives the direction and slope for the trend 

in FAC, but not the significance of the trend. The p-value, or 

significance level, for the trend in FAC is calculated from a 

two-tailed test using the Student’s t distribution:

t

t

p-value = 2[1 ( statistic, )],

where

p-value is the probability of obtaining the computed

test statistics when the null hypothesis is

true,

is the value of the Student's cumulativedistribution functio

F t df

F t

−

n for the calculated

value of the statistic and the given

degrees of freedom,

statistic is equal to (see eq. 4) divided by the

standard error of , and

is the degrees of freedom (equals number

of o

FA

FA

t

t

df

τ

τ

bservations minus number of 

parameters in model).

(5)

In this study, a p-value of less than 0.05 is considered to 

represent significant relations. For some sites without enough 

data to run the seven-parameter LOADEST model, a less 

rigorous five-parameter model was run. In these cases, only 

the β3 term occurs in equation 4 for defining the trend in FAC.
18 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

To plot the FAC over time, the residuals (distance from 

the LOESS trend line) from the flow versus concentration 

plot (with their time) were added to the mean measured 

concentration over time. A LOESS fit is a nonparametric 

smoothing that minimizes the influence of outliers on the 

trend line. It is a generalization of running means which gets 

a predicted value at each point by fitting a weighted linear 

regression where the weights decrease with distance from the 

point of interest. Connecting these predicted values produces 

a smooth curve (Insightful Corporation, 2005). Thus, the trend 

analysis for FACs was essentially an analysis of the change 

in the flow-water quality relation over time. If the flow record 

is trend free, then the results of this analysis of residuals 

becomes an efficient means of detecting and estimating 

the magnitude of trends in water quality caused by factors 

other than flow. In LOADEST these residuals were created 

by selecting a model using the Q, Q2, sine of decimal-time, 

and cosine of decimal-time variables (with coefficients β0, 

β 1, β 2, β 5, and β 6 in eq. 2), but not the decimal-time and 

decimal-time-squared variables. One of the output files in 

LOADEST was the flow-adjusted residuals of concentration. 

These residuals were added to the mean of the measured 

concentrations and plotted as the FAC. 

Trends in Measured Concentrations

If a water-quality sampling site had a significant trend 

in flow over the trend period, then trends in the residuals for 

the flow versus concentration relation would not translate 

necessarily to a trend in the distribution of the water-quality 

constituent. In these cases, it was more appropriate to report a 

trend in the measured concentrations. This was done for one 

site in this study—SAR downstream of Prado Dam. The SAR 

flow increased significantly over the study period as it was 

dominated by wastewater inputs instead of runoff inputs from 

the watershed, and as the population increased rapidly. 

A trend in measured concentrations can be estimated 

by performing a Mann Kendall test, or by regressing the 

measured concentrations on time without a flow term. In this 

study, the Mann Kendall test was used to determine trends in 

measured flows and concentrations for the SAR downstream 

of Prado Dam site. The Mann Kendall test computes Kendall’s 

tau non-parametric correlation coefficient and its test of 

significance for any pair of x, y data. Thus, if x is time, the 

test is a test for trend in the y variable. The computer program 

provided with Helsel and others (2006) was used for the 

Mann Kendall test, with a level of 0.05. For flow at the SAR 

downstream of Prado Dam site, the trend in mean monthly 

flow was evaluated instead of mean daily flow, owing to the 

limitation of the computer program to 500 pairs of x, y data.

Sources of Data for Nutrient 

Concentrations and Flow in Streams

Several sources of data, primarily in electronic form, 

were considered in this study. In addition to combining data 

from several sources, several similar water-quality parameters 

and sites were combined in this study to attempt to create 

the best long-term database for analysis of trends and loads. 

Data were retrieved for 1975–2004 for all sites. The influence 

of different sample collection and analytical methods on the 

long-term database was considered, as were issues relating to 

data frequency, detection limits, and reporting levels.

Data Sources

Although water-quality data were retrieved for 

many other parameters (field parameters, organic carbon, 

chlorophyll, and selected minerals), the parameters evaluated 

in this study were selected forms of nitrogen (nitrate, 

ammonia, and TN) and phosphorus (orthophosphate and TP). 

The data compilation emphasized the dissolved forms of 

nitrate, ammonia, and orthophosphate. The final water-quality 

database used for this study included data from the following 

electronic sources: U.S. Environmental Protection Agency’s 

STOrage and RETrieval database (STORET), U.S. Geological 

Survey’s National Water Information System (NWIS) 

database, DWR, University of California at Davis (UCD), 

Sacramento River Watershed Program (SRWP), Sacramento 

Regional County Sanitation District (SRCSD), and the 

California Regional Water Quality Control Board, Central 

Valley Region (RWQCB(CVR)). All available data for sites 

of interest were included from the USGS, DWR, and UCD 

databases. Data from the other sources were used as needed to 

fill in gaps in time for sites of interest. The STORET database 

provided data for the 1975–1988 time period primarily, as 

after 1988 most of the agencies that were providing data to 

STORET stopped doing so. This included data provided by 

DWR, Bureau of Reclamation, and California State Water 

Resources Control Board (SWRCB) primarily. Data provided 

by these agencies in STORET are simply identified as 

STORET data and not by agency because in many cases more 

than one agency entered the same data. Thus, in removing 

these duplicates, it was difficult to identify the true collecting 

agency. 

 All USGS data used in this study came from the NWIS 

database. Data identified as DWR came from various sources. 

The 1988–1998 data primarily came from the individual 

districts of the DWR (Northern, Central, San Joaquin, and 

Southern Districts) as Microsoft® Excel spreadsheets, and for 

the period after 1998, most of the DWR data were obtained 

from the Water Data Library, at URL: http://wdl.water.ca.gov/
Sources of Data for Nutrient Concentrations and Flow in Streams 19

index.cfm. Some DWR data also were obtained from a 

database maintained by the Interagency Ecological Program, 

available at URL: http://bdat.ca.gov/index.html. The UCD 

data were obtained from Dr. Randy Dahlgren as an Microsoft®

Excel spreadsheet. The UCD data were collected from several 

sites in the Sacramento and San Joaquin Basins for 1999–

2004. The SRWP and the SRCSD data were obtained from 

Larry Walker and Associates. All or part of the SRWP data for 

eight sites were included in the database as were the SRCSD 

data for two sites in the Sacramento Basin (Sacramento 

River at Verona and American River at Nimbus Dam). The 

RWQCB(CVR) data for one site in the San Joaquin Basin 

(SJR at Fremont Ford) were obtained from their database at 

URL: http://www.swrcb.ca.gov/rwqcb5/programs/agunit/

swamp/MER538.xls.

Historical nitrate data were acquired for eight Sacramento 

Basin sites, four San Joaquin Basin sites, and three Santa 

Ana Basin sites. Data for 1905–07, 1908, and 1930–32 were 

obtained from three USGS studies (Van Winkle and Eaton, 

1910; Stabler, 1911; California Department of Public Works, 

Division of Water Resources, 1931). Data for these sites 

between 1932 and 1975 were from either NWIS or STORET. 

Database Issues

Combining Multiple Parameters into a Single 

Constituent

The forms of nitrogen and phosphorus were reported in 

multiple ways by different agencies and over different time 

periods. To create a long-term database for these parameters, 

several parameters were combined to create the final database 

(table 1). Although much of the data on nitrate are reported 

as nitrate plus nitrite, hereinafter this will be referred to 

as “nitrate.” In addition, at the pH values found in most 

samples, the majority of the ammonia will be found in the 

form of ammonium ion, hereinafter this will be referred to as 

“ammonia.” The final database used for trends and loads of 

nitrate (called NO3 in the database), ammonia (NH3), TN, 

orthophosphate (OP), and TP is included in the cover of this 

report as table CD-1 on the Data CD.

For NO3, NH3, OP, and TP, if a value was censored (<), 

the < designation was kept in the database. It usually was 

necessary to calculate TN by adding total kjeldahl nitrogen 

(total ammonia and organic nitrogen) and nitrate (table 1). 

When one or both of these two numbers was a censored value, 

the following rules applied, with x representing total kjeldahl 

nitrogen and y representing nitrate (Mueller and Spahr, 2006):

TN x y (if there were no < 's, simply add)

TN x y

if y x; TN x y/2

if y x; TN y

TN x y

if y x; TN x

if y x; TN y

= +

= +<

< =+

> =<

=< + <

< =<

> =<

A few exceptions to these rules occurred with the nitrate 

values, as many times the dissolved nitrate value (NWIS 

parameter code 00631) had considerably higher values than 

the whole-water nitrate value (NWIS parameter code 00630). 

The USGS National Water Quality Laboratory (NWQL) 

discontinued the analysis of whole-water nitrate in 1993, 

owing to difficulties with the analytical technique (Rickert, 

1992). Thus, in these cases the 00631 value was used for both 

NO3 and in calculating TN.

Combining Multiple Sites into a Single Site

As with parameters, sites also were combined to create 

the long-term database. For several sites, different agencies 

sampled water quality at slightly different sites. Additionally, 

the water-quality sites were often at slightly different sites 

than the corresponding flow gaging station. A listing of these 

combinations of sites is provided in table 2 for sites where at 

least one of the combined sites was 0.5 river miles or more 

away from the other sites. Sites were combined only if: (1) no 

known substantial factors existed affecting water quality 

between water-quality sites, and (2) no known substantial 

factors existed affecting flow between the water-quality and 

gaging sites. 

Censoring Levels in NWIS

The definition of censoring level in NWIS changed 

over the study period. Prior to 1992, the NWQL typically 

censored data at the minimum reporting level (MRL). This 

level was the smallest measured concentration that could be 

reliably reported by using a given analytical method (Oblinger 

Childress and others, 1999). From 1992 to 1998, the NWQL 

censored data at the minimum detection limit (MDL), adopting 

the approach used by USEPA. The MDL was the minimum 

concentration that could be measured and reported with a 

99-percent confidence that the concentration was greater than 

zero. At the MDL, the risk of a false positive was predicted to 

be less than or equal to 1 percent. A false positive means that 

the constituent was reported as present when it was not.
20 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 Table 1. Combination of parameters to create a long-term database for nitrate, ammonia, total nitrogen, orthophosphate, and total phosphorus.

[Abbreviations: NWIS, National Water Information System; STORET, U.S. Environmental Protection Agency STOrage and RETrieval data warehouse; mg/L, milligrams per liter]

Combined 

parameter name

Combined 

parameter

code

NWIS/STORET

parameter codes 

combined

Description of NWIS/STORET

parameter codes

Equation for combining

parameters1

NITRATE NO3 71851 Dissolved nitrate, in mg/L as NO3 NO3 = {71851, 0.2259, 1; 00618, 1.0, 2; 00631, 1.0, 3; 00620, 

(mg/L as N) 00618 Dissolved nitrate, in mg/L as N 1.0, 4; 71850, 0.2259, 5; 00630, 1.0, 6}

00631 Dissolved nitrate + nitrite, in mg/L as N00620 Total nitrate, in mg/L as N71850 Total nitrate, in mg/L as NO300630 Total nitrate + nitrite, in mg/L as N

AMMONIA NH3 00608 Dissolved ammonia, in mg/L as N NH3 = {00608, 1.0, 1; 71846, 0.7765, 2}

(mg/L as N) 71846 Dissolved ammonia, in mg/L as NH4TOTAL TKN 00625 Total ammonia + organic nitrogen, in mg/L as N TKN = {00625, 1.0, 1; 00635, 1.0, 2}KJELDAHL 00635 Total ammonia + organic nitrogen, in mg/L as NNITROGEN(mg/L as N)TOTAL TN 62855 Nitrogen, total, whole water, acidified, mg/L as N TN = {62855, 1.0, 1; [TKN + (00630, 1.0, 1; 00631, 1.0, 2; , NITROGEN 00625 Total ammonia + organic nitrogen, in mg/L as N 71851, 0.2259, 3; 00618, 1.0, 4; 00620, 1.0, 5}(mg/L as N) 00635 Total ammonia + organic nitrogen, in mg/L as N

00630 Total nitrate + nitrite, in mg/L as N00631 Dissolved nitrate + nitrite, in mg/L as N71851 Dissolved nitrate, in mg/L as NO300618 Dissolved nitrate, in mg/L as N00620 Total nitrate, in mg/L as N

ORTHO- OP 00671 Dissolved orthophosphate, in mg/L as P OP = {00671, 1.0, 1; 00660, 0.3261, 2; 00666, 1.0, 3}

PHOSPHATE 00660 Dissolved orthophosphate, in mg/L as PO4 (mg/L as P) 00666 Dissolved phosphorus, in mg/L as PTOTAL TP 00665 Total phosphorus, in mg/L as P TP = {00665, 1.0, 1; 71886, 0.3261, 2}

PHOSPHORUS 71886 Total phosphorus, in mg/L as PO4

(mg/L as P)

1 For example (71851, 0.2259, 1) means 71851 is the parameter code; 0.2259 is a conversion factor to convert NO3 as NO3 to NO3 as N; and 1 is the priority code defined as the order in which a parameter is 

used (e.g., priority 1 is used first, priority 2 is used if priority 1 is not available and so on). 
Sources of Data for Nutrient Concentrations and Flow in Streams 21

Table 2. Combination of water-quality sites and flow sites to create a long-term database for evaluating trends and loads for nitrate, 

ammonia, total nitrogen, orthophosphate, and total phosphorus.

[Abbreviations: RM, river mile; USGS, U.S. Geological Survey; STORET, STOrage and RETreival database; DWR, California Department of Water Resources; 

UCD, University of California at Davis; SRWP, Sacramento River Watershed Program; SRCSD, Sacramento Regional County Sanitation District]

Combined water-quality site name Water-quality sites included 

(site ID)

Flow site 

(site ID) Site agency Description of site

Sacramento Basin

Sacramento River at Keswick 11370500 11370500 USGS

RSAC568 STORET 0.5 RM upstream of gage

403633122264301 USGS 0.5 RM upstream of gage

A2101000 STORET; DWR 0.6 RM upstream of gage

Sacramento R at Court Road UCD 2.3 RM downstream of gage

Cottonwood Creek near Cottonwood 11376000 11376000 USGS

11375970 USGS 2.6 RM upstream of gage

A0352050 STORET; DWR 2.6 RM upstream of gage

Cottonwood Cr at Cottonwood UCD 2.6 RM upstream of gage

Sacramento River near Red Bluff 11377100 11377100 USGS

SRABB SRWP at USGS gage

11377200 USGS 2.8 RM downstream of gage

A0278500 STORET; DWR 2.8 RM downstream of gage

Sac R at Bend Ferry Road UCD 2.8 RM downstream of gage

Mill Creek near Los Molinos 11381500 11381500 USGS

A441100 DWR at USGS gage

A0442300 STORET; DWR 2.8 RM downstream of gage

A0442050 STORET; DWR 4.3 RM downstream of gage

Deer Creek near Vina 11383500 11383500 USGS

Deer Cr at Leiniger Road UCD 5.5 RM downstream of gage

A0432101 STORET; DWR 8.2 RM downstream of gage

Stony Creek below Black Butte Dam 11388000 USGS

A3111000 STORET; DWR at USGS gage

Stony Creek at Orland UCD 8.4 RM downstream of gage

Sacramento River at Colusa 1138950 1138950 USGS

A0242000 STORET; DWR at USGS gage

SRCOL SRWP 0.6 RM downstream of gage

Sacramento River above Colusa 11390500 USGS

 Basin Drain 11390650 USGS 28.3 RM downstream of gage

A0223002 STORET; DWR 28.3 RM downstream of gage

Colusa Basin Drain near Knights 

Landing

11390890 No Flow Data USGS

A0294710 STORET; DWR at USGS site

COLDR SRWP at USGS site

Colusa Basin Dr at Knights Lndg UCD 2.9 RM downstream of USGS site

Sacramento River at Fremont Weir 11391020 No Flow Data USGS

A0217000 STORET; DWR at USGS site

A0219501 STORET; DWR 0.6 RM upstream of USGS site

Sac R at Knights Landing UCD 5.6 RM upstream of USGS site
22 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Table 2. Combination of water-quality sites and flow sites to create a long-term database for evaluating trends and loads for nitrate, 

ammonia, total nitrogen, orthophosphate, and total phosphorus.—Continued

[Abbreviations: RM, river mile; USGS, U.S. Geological Survey; STORET, STOrage and RETreival database; DWR, California Department of Water Resources; 

UCD, University of California at Davis; SRWP, Sacramento River Watershed Program; SRCSD, Sacramento Regional County Sanitation District]

Combined water-quality site name Water-quality sites included 

(site ID)

Flow site 

(site ID) Site agency Description of site

Sacramento Basin—Continued

Sacramento Slough near Knights 11391100 No Flow Data USGS

 Landing A0292500 STORET; DWR at USGS site

SACSL SRWP at USGS site

Sacramento Sl at Karnack UCD 1.0 RM upstream of USGS site

Yuba River near Marysville 11421000 11421000 USGS

A0615000 STORET; DWR at USGS gage

11421500 USGS 4.0 RM downstream of gage

Yuba R at Simpson Lane UCD 4.0 RM downstream of gage

Bear River near Wheatland 11424000 11424000 USGS

A0655000 DWR at USGS gage

Bear R at Forty Mile Road UCD 4.5 RM downstream of gage

Feather River near Nicolaus 11425000 No Flow Data USGS

A0510300 DWR 1.2 RM upstream of USGS site

FRNIC SRWP 1.2 RM upstream of USGS site

Sacramento River at Verona 11425500 11425500 USGS

A021500 DWR 0.6 RM upstream of USGS gage

A021120 STORET; DWR 7.6 RM upstream of USGS gage

SRVET SRWP 7.6 RM upstream of USGS gage

Sacramento R at Veterans Bridge SRCSD 7.6 RM upstream of USGS gage

WB008403413741 STORET 7.6 RM upstream of USGS gage

SR1 STORET 7.6 RM upstream of USGS gage

Arcade Creek near Del Paso 11447360 11447360 USGS

 Heights ARCNW SRWP 4.6 RM downstream of USGS gage

American River at Sacramento 11447000 USGS at USGS water-quality site

A0714010 STORET; DWR 0.7 RM upstream of USGS wq site

11446500 USGS 15.3 RM upstream of USGS wq site

San Joaquin Basin

Mud Slough near Gustine 11262900 11262900 USGS

Mud Slough at Kesterson UCD 0.3 RM upstream of gage

B0040000 DWR 3.8 RM downstream of gage

Merced River near Stevinson 11272500 11272500; 

B05125

USGS; DWR

372142120510001 STORET; USGS 7.0 RM upstream of gage

B0513100 DWR 7.0 RM upstream of gage

11273500 USGS 3.7 RM downstream of gage

Merced R at River Road UCD 3.7 RM downstream of gage

Orestimba Creek at River Road 11274538 11274538 USGS

Orestimba Cr at River Rd UCD at USGS gage

B0873500 B0873500 DWR 4.3 RM upstream of USGS gage
Sources of Data for Nutrient Concentrations and Flow in Streams 23

However, at the MDL concentration there is a 50-percent 

chance of a false negative; however, one-half of the time 

a sample with a true concentration would be reported as 

not being detected. Thus, to reduce this occurrence of false 

negatives, the NWQL began to report censored data at a 

laboratory reporting level (LRL) in 1998 (Oblinger Childress 

and others, 1999). The LRL is twice the long-term MDL 

(LT-MDL) defined by the NWQL, specific to analytical 

methods. The approach used to define the LT-MDL is similar 

to the approach used to define the MDL, except that it 

requires more quality-assurance and quality-control samples. 

Because it is designed to capture more sources of variability, 

the LT-MDL usually is slightly higher than the MDL. In 

this new censoring approach of the NWQL, concentrations 

that fall between the LT-MDL and the LRL are labeled as 

“estimated.” The LT-MDL is reassessed each year based on the 

quality-assurance and quality-control data and the probability 

of a false positive is predicted to be less than or equal to 

1 percent.

Because most of the data reported by DWR, STORET, 

and UCD used either a MRL or MDL censoring level, 

estimated values are reported as concentrations greater than 

the MRL, and values less than the LRL were changed to less 

than the LT-MDL where these values were available. Although 

the NWIS database does not show these LT-MDL values, the 

NWQL has information on these values in published method 

reports, technical memoranda, and at the NWQL web page at 

URL: http://wwwnwql.cr.usgs.gov (Oblinger Childress and 

others, 1999). The LT-MDLs for constituents of interest in this 

study and their applicable time period are summarized in table 

3.

Table 2. Combination of water-quality sites and flow sites to create a long-term database for evaluating trends and loads for nitrate, 

ammonia, total nitrogen, orthophosphate, and total phosphorus.—Continued

[Abbreviations: RM, river mile; USGS, U.S. Geological Survey; STORET, STOrage and RETreival database; DWR, California Department of Water Resources; 

UCD, University of California at Davis; SRWP, Sacramento River Watershed Program; SRCSD, Sacramento Regional County Sanitation District]

Combined water-quality site name Water-quality sites included 

(site ID)

Flow site 

(site ID) Site agency Description of site

San Joaquin Basin—Continued

Tuolumne River at Shiloh Road 373612121080001 STORET at water-quality site

B0410500 DWR at water-quality site

Tuolumne R at Shiloh Rd UCD at water-quality site

11290000 11290000 USGS 12.6 RM upstream of water-quality 

site

Stanislaus River near Caswell 374200121101201 STORET at water-quality site

 State Park B0311500 DWR at water-quality site

A0147500 DWR at water-quality site

Stanislaus R at Caswell Park UCD at water-quality site

11303000 11303000 USGS 7.2 RM upstream of water-quality 

site

Santa Ana Basin

Santa Ana River at MWD Crossing 11066460 11066460 USGS

WB08Y6141000 STORET at USGS gage

T2SR5WSEC30 STORET at USGS gage

MWDCROSS STORET 0.4 RM upstream of USGS gage

Y6140000 STORET; DWR 1.1 RM downstream of USGS gage
24 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 Table 3. Changes in nutrient detection and reporting limits over time at the U.S. Geological Survey National Water Quality Laboratory.

[Abbreviations: NWIS, National Water Information System; mg/L, milligrams per liter; NA, not applicable; <, less than]

Combined 

parameter 

name

Combined 

parameter 

code

NWIS/STORET

parameter codes Dates Reporting level LT-MDL Description of NWIS/STORET parameter codes Equation for combining parameters

NITRATE NO3 71851 All NWIS NA Dissolved nitrate, in mg/L as NO3 NO3 = {71851, 0.2259, 1; 00618, 1.0, 

(mg/L as N) 00618 All NWIS NA Dissolved nitrate, in mg/L as N 2; 00631, 1.0, 3; 00620, 1.0, 4;

00631 Before 10-01-99 NWIS NA Dissolved nitrate + nitrite, in mg/L as N 71850, 0.2259, 5; 00630, 1.0, 6}

10-01-99 to 10-04-00 0.037 0.018

.050 NA

10-04-00 to 09-30-01 .037 .018

.047 .027.050 NA

10-01-01 to 09-30-02 .013 .009

.037 .018.047 .027.050 NA

10-01-02 to 09-30-03 .022 .011

.048 .024.060 .030

10-01-03 to 09-30-04 .016 .008

.040 .020.060 .030

00620 All NWIS NA Total nitrate, in mg/L as N

71850 All NWIS NA Total nitrate, in mg/L as NO3

00630 All NWIS NA Total nitrate + nitrite, in mg/L as N

AMMONIA NH3 00608 Before 10-01-94 NWIS NA Dissolved ammonia, in mg/L as N NH3 = {00608, 1.0, 1; 71846, 0.7765, 2}

(mg/L as N) 10-01-94 to 09-30-97 Values <0.02 .02

10-01-97 to 09-30-99 .02 NA

10-01-99 to 10-03-00 .002 NA

.020 NA.029 .014

10-04-00 to 09-30-01 .002 NA

.041 .021.049 .024

10-01-01 to 09-30-03 .015 .008

.041 .021.049 .024

10-01-03 to 09-30-04 .010 .005

.040 .020

71846 All NWIS NA Dissolved ammonia, in mg/L as NH4
Sources of Data for Nutrient Concentrations and Flow in Streams 25

Table 3. Changes in nutrient detection and reporting limits over time at the U.S. Geological Survey National Water Quality Laboratory.—Continued[Abbreviations: NWIS, National Water Information System; mg/L, milligrams per liter; NA, not applicable; <, less than]

Combined 

parameter 

name

Combined 

parameter 

code

NWIS/STORET

parameter codes Dates Reporting level LT-MDL Description of NWIS/STORET parameter codes Equation for combining parameters

TOTAL TKN 00625 Before 10-01-98 NWIS NA Total ammonia + organic nitrogen, TKN = {00625, 1.0, 1; 00635, 1.0, 2}

KJELDAHL 10-01-98 to 10-03-00 0.10 0.05 in mg/L as N

NITROGEN 10-04-00 to 09-30-01 .08 .04

(mg/L as N) 10-01-01 to 09-30-04 .10 .05

00635 All NWIS NA Total ammonia + organic nitrogen, in mg/L as N

TOTAL TN 62855 All NWIS NA Nitrogen, total, whole water, acidified, mg/L as N TN = {62855, 1.0, 1; [TKN + (00630, 1.0, 1;

NITROGEN 00625 Before 10-01-98 NWIS NA Total ammonia + organic nitrogen, in mg/L as N 00631, 1.0, 2;71851, 0.2259, 3;

(mg/L as N) 10-01-98 to 10-03-00 .10 .05 00618, 1.0, 4; 00620, 1.0, 5)]

10-04-00 to 09-30-01 .08 .0410-01-01 to 09-30-04 .10 .05

00635 All NWIS NA Total ammonia + organic nitrogen, in mg/L as N

00630 All NWIS NA Total nitrate + nitrite, in mg/L as N

00631 Before 10-01-99 NWIS NA Dissolved nitrate + nitrite, in mg/L as N

10-01-99 to 10-04-00 .037 .018

.050 NA

10-04-00 to 09-30-01 .037 .018

.047 .027.050 NA

10-01-01 to 09-30-02 .013 .009

.037 .018.047 .027.050 NA

10-01-02 to 09-30-03 .022 .011

.048 .024.060 .030

10-01-03 to 09-30-04 .016 .008

.040 .020.060 .030

71851 All NWIS NA Dissolved nitrate, in mg/L as NO3

00618 All NWIS NA Dissolved nitrate, in mg/L as N

00620 All NWIS NA Total nitrate, in mg/L as N

ORTHO- OP 00671 Before 10-04-00 NWIS NA Dissolved orthophosphate, in mg/L as P OP = {00671, 1.0, 1; 00660, 0.3261, 2;

PHOSPHATE 10-04-00 to 09-30-03 .018 .009 00666, 1.0, 3}

 (mg/L as P) .007 .004

10-01-03 to 09-30-04 .018 .009

.006 .003

00660 All NWIS NA Dissolved orthophosphate, in mg/L as PO4
26 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 Table 3. Changes in nutrient detection and reporting limits over time at the U.S. Geological Survey National Water Quality Laboratory.—Continued

[Abbreviations: NWIS, National Water Information System; mg/L, milligrams per liter; NA, not applicable; <, less than]

Combined 

parameter 

name

Combined 

parameter 

code

NWIS/STORET

parameter codes Dates Reporting level LT-MDL Description of NWIS/STORET parameter codes Equation for combining parameters

ORTHO- OP 00666 Before 10-01-91 NWIS NA Dissolved phosphorus, in mg/L as P

PHOSPHATE 10-01-91 to 09-30-98 Values 

<0.030

0.030

 (mg/L as P) 10-01-98 to 09-30-99 .05 .03

10-01-99 to 10-03-00 .05 .03

.007 .003.006 .003

10-04-00 to 09-30-01 .06 .03

.05 .03.0037 .0018.006 .003

10-01-01 to 09-30-02 .06 .03

.05 .03.0044 .0022.0037 .0018

10-01-02 to 09-30-003 .05 .03

.035 .018.0044 .0022.0037 .0018

10-01-03 to 09-30-04 .04 .02

.004 .002

TOTAL TP 00665 Before 10-01-91 NWIS NA Total phosphorus, in mg/L as P TP = {00665, 1.0, 1; 71886, 0.3261, 2}

PHOSPHORUS 10-01-91 to 09-30-98 Values 

<0.030

.030

(mg/L as P) 10-01-98 to 09-30-99 .05 .03

.004 NA

10-01-99 to 10-03-00 .05 .03

.008 .004

10-04/-00 to 09-30-02 .06 .03

.0037 .0019

10-01-02 to 09-30-03 .040 .020

.0037 .0019

10-01-03 to 09-30-04 .040 .020

.004 .002

71886 All NWIS NA Total phosphorus, in mg/L as PO4

Patton, 1997Foreman and others, 1998
Sources of Data for Nutrient Concentrations and Flow in Streams 27

Data Thinning

Because data were combined from several sources, this 

often required selecting subsets from the full time-series of 

available data to avoid placing disproportionate emphasis on 

certain time periods. Thus, a hierarchal process was used to 

reduce the database to a maximum frequency of one data value 

for every 5 days, except for the SJR near Vernalis site, which 

was allowed a maximum frequency of every 4 days because of 

the abundance of data collection. The first criteria for deleting 

too frequent data was the collecting agency. The agencies 

were ranked based on quality assurance, quality control, and 

detection limits of the data, with data prioritized by agency in 

the following order: NWIS, UCD, DWR, SRWP, STORET, 

RWQCB(CVR), and SRCSD. Secondary criteria used were 

the number of parameters included in the sample, the detection 

limits, the corresponding flow, and the timing of samples. 

More details are provided in the table CD-1 readme.doc file on 

the Data CD included in the report cover.

 There were many cases of multiple samples per day in 

the initial long-term database. In these cases, the samples were 

averaged and given the designation of the agency with the 

most parameters reported. In the final database on the Data 

CD, these averaged data are indicated by a yellow highlight on 

the DATES cell.

Influence of Sample Collection and Analytical 

Methods

The main sources of data for this study were NWIS, 

STORET, DWR, and UCD. Although it could not be verified 

for all data points, most of the STORET data reported in this 

study were collected by DWR. All NWIS data were collected 

and analyzed by the USGS. Thus, to evaluate the influence of 

different sample collection and analytical methods over the 

study period, information on the methods of USGS, DWR, 

and UCD was needed.

Samples collected by DWR and UCD primarily were 

midpoint surface-grab samples, whereas most USGS 

samples were cross-sectionally integrated samples (U.S. 

Geological Survey, 2008). For well-mixed sampling sites, this 

difference usually is not significant for dissolved constituents 

(ammonia, nitrate, and orthophosphate; Martin and others, 

1992). Suspended sediment and some sediment-associated 

constituents (such as TP) frequently have significantly lower 

concentrations in surface-grab samples compared to integrated 

samples (Martin and others, 1992). However, a comparison of 

STORET data (primarily surface-grab samples collected by 

DWR or the Bureau of Reclamation) to NWIS data (primarily 

integrated samples collected by USGS) for the SJR near 

Vernalis site using 1972–1990 data revealed no significant 

differences for the nutrient species considered in this study, 

only for suspended sediment (Kratzer and Shelton, 1998).

The samples collected by DWR primarily were analyzed 

at the DWR Bryte Laboratory in West Sacramento, California, 

using standard methods approved by USEPA at the time 

(Eaton and others, 1995; Eaton and others, 2005). The samples 

collected by USGS primarily were analyzed at the National 

Water Quality Laboratory in Denver, Colorado. The methods 

have changed over time, but the changes are well documented 

(Fishman and Friedman, 1989; Fishman and others, 1994). 

The samples collected by UCD were analyzed at the UCD 

Biogeochemistry Laboratory in Davis, California. Samples 

for ammonia and nitrate were filtered through a 0.45-μm 

Nucleopore membrane filter, and the dissolved concentrations 

were quantified simultaneously using an automated membrane 

diffusion and conductivity detection method (Carlson, 1978; 

1986). TN was determined by oxidizing a raw sample with 

a 1-percent persulfate oxidant solution and then using the 

same analytical method as for ammonia and nitrate (Yu and 

others, 1994). 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 Nucleopore membrane. 

TP was determined on a raw sample using the stannous 

chloride standard method following persulfate digestion as 

described for TN. A laboratory comparison performed during 

a collaborative study in the San Joaquin Basin between USGS 

and UCD in 2000–2001 revealed mean variability between 

the laboratories of less than 10 percent for nitrate and TN, and 

10–20 percent for orthophosphate and TP (Kratzer and others, 

2004).

Sites with Sufficient Data for Trends and Loads

The final database presented in table CD-1 on the Data 

CD includes data for 54 sites: 28 in the Sacramento Basin, 

20 in the San Joaquin Basin, and 6 in the Santa Ana Basin. 

These are all the sites evaluated in this report and in the Data 

CD. Many of these sites are mentioned in this report by a 

simplified name (see table 4 in this report and table CD-2d

on the Data CD). The primary geographic setting (for the 

subbasin upstream of each site) that impacts water quality 

also is listed in table 4. These settings are defined as mountain 

(Sierra Nevada, Coast Ranges, Cascades, or southern 

California mountains), valley (Central Valley), or basin (basin 

areas in the Santa Ana).

Sites with enough data for analyzing trends and (or) loads 

for any of the time periods of interest for the five water-quality 

parameters are shown in figure 7. The drainage subbasins for 

the sampling sites shown in figure 7 are shown in figure 8. For 

the Sacramento Basin and San Joaquin Basin sites, the outline 

of the valley floor is delineated clearly. For the Santa Ana 

Basin, the basin area is delineated clearly from the mountain 

area as well as the Inland, San Jacinto, and Coastal subbasins.
28 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 Table 4. Site names and primary geographic setting (mountain, valley, or basin) for all 54 sites in final database: official names and simplified names for use in this report.

[Primary geographic setting: Setting affecting water quality at site (for drainage basin upstream of site). Abbreviation: CA, California]

Official site name Site ID Latitude Longitude Site name in report figures and tables Site name in report text Primary geographic setting

Sacramento Basin Sites

Sacramento R at Delta, CA 11342000 405623 1222458 Sacramento River at Delta Sacramento River at Delta Mountain

McCloud R ab Shasta Lake, CA 11368000 405730 1221307 McCloud River above Shasta Lake McCloud River Mountain

Pit R nr Montgomery Creek, CA 11365000 405036 1220058 Pit River near Montgomery Creek Pit River Mountain

Sacramento R at Keswick, CA 11370500 403604 1222636 Sacramento River at Keswick1 Sacramento River at Keswick1 Mountain

Cottonwood Cr nr Cottonwood, CA 11376000 402314 1221415 Cottonwood Creek near Cottonwood1 Cottonwood Creek1 Mountain and valleySacramento R ab Bend Bridge nr Red Bluff, CA 11377100 401719 1221108 Sacramento River near Red Bluff1 Sacramento River near Red Bluff1 Mountain and valleyMill Cr nr Los Molinos, CA 11381500 400317 1220123 Mill Creek near Los Molinos1 Mill Creek1 MountainDeer Cr nr Vina, CA 11383500 400051 1215650 Deer Creek near Vina1 Deer Creek1 MountainSacramento R at Vina A0270000 395434 1220531 Sacramento River at Vina Sacramento River at Vina Mountain and valley

Sacramento R nr Hamilton City, CA 11383800 394506 1215940 Sacramento River near Hamilton City Sacramento River near Hamilton City Mountain and valley

Stony Cr bl Black Butte Dam nr Orland, CA 11388000 394907 1221926 Stony Creek below Black Butte Dam1 Stony Creek1 Mountain

Sacramento R at Colusa, CA 11389500 391251 1215957 Sacramento River at Colusa1 Sacramento River at Colusa1 Mountain and valleySacramento R ab Colusa Trib at Knights Landing, CA 11390650 384818 1214322 Sacramento River above Colusa Basin Drain1 Sacramento River above CBD1 Mountain and valleyColusa Basin Dr at Rd 99E nr Knights Landing, CA 11390890 384845 1214623 Colusa Basin Drain near Knights Landing1 Colusa Basin Drain1 ValleySacramento R at Fremont Weir (West End), CA 11391020 384536 1214000 Sacramento River at Fremont Weir1 Sacramento River at Fremont Weir1 Mountain and valleyButte Slough nr Meridian A0297200 391028 1215408 Butte Slough near Meridian Butte Slough Valley

Sutter Bypass ab RD1500 Pumping Plant A0292700 384706 1213912 Sutter Bypass Sutter Bypass Valley

Sacramento Slough nr Knights Landing, CA 11391100 384706 1213912 Sacramento Slough near Knights Landing1 Sacramento Slough1 Valley

Feather R at Oroville, CA 11407000 393113 1213248 Feather River at Oroville Feather River at Oroville Mountain

Yuba R nr Marysville, CA 11421000 391033 1213126 Yuba River near Marysville1 Yuba River1 Mountain

Bear R nr Wheatland, CA 11424000 390001 1212421 Bear River near Wheatland1 Bear River1 MountainFeather R nr Nicolaus, CA 11425000 385326 1213612 Feather River near Nicolaus1 Feather River near Nicolaus1 Mountain and valleySacramento R at Verona, CA 11425500 384628 1213550 Sacramento River at Verona1 Sacramento River at Verona1 Mountain and valleyArcade Cr nr Del Paso Heights, CA 11447360 383831 1212254 Arcade Creek near Del Paso Heights1 Arcade Creek1 ValleyAmerican R SF nr Kyburz A7455000 384549 1201939 American River South Fork near Kyburz American River SF near Kyburz Mountain

American R at Nimbus Dam, CA 11446400 383810 1211315 American River at Nimbus Dam American River at Nimbus Dam Mountain

American R at Sacramento, CA 11447000 383405 1212520 American River at Sacramento American River at Sacramento Mountain and valley

Sacramento R at Freeport, CA 11447650 382715 1212954 Sacramento River at Freeport Sacramento River at Freeport Mountain and valley

San Joaquin Basin Sites

Panoche Dr nr Dos Palos DPS3235 365524 1204118 Panoche Drain near Dos Palos Panoche Drain Valley

Camp 13 Slu at Head CTL4504 365630 1204518 Camp 13 Slough Camp 13 Slough Valley

San Joaquin R nr Stevinson, CA 11260815 371742 1205101 San Joaquin River near Stevinson San Joaquin River near Stevinson Mountain and valley

Salt Slough at Hwy 165 nr Stevinson, CA 11261100 371452 1205104 Salt Slough near Stevinson Salt Slough Valley

San Joaquin R at Fremont Ford Bridge, CA 11261500 371836 1205548 San Joaquin River at Fremont Ford San Joaquin River at Fremont Ford Mountain and valley

Mud Slough nr Gustine, CA 11262900 371545 1205420 Mud Slough near Gustine1 Mud Slough1 Valley

Merced R at Happy Isles Bridge nr Yosemite, CA 11264500 374354 1193328 Merced River at Happy Isles Merced River at Happy Isles Mountain

Merced R bl Merced Falls Dam nr Snelling, CA 11270900 373118 1201953 Merced River below Merced Falls Merced River below Merced Falls Mountain

Merced R nr Stevinson, CA 11272500 372104 1205739 Merced River near Stevinson1 Merced River near Stevinson1 Mountain and valley
Sources of Data for Nutrient Concentrations and Flow in Streams 29

Official site name Site ID Latitude Longitude Site name in report figures and tables Site name in report text Primary geographic setting

San Joaquin Basin Sites—Continued

Orestimba Cr at River Rd nr Crows Landing, CA 11274538 372449 1210054 Orestimba Creek at River Road1 Orestimba Creek1 Valley

San Joaquin R at Patterson Br nr Patterson, CA 11274570 372951 1210455 San Joaquin River near Patterson San Joaquin River near Patterson Mountain and valley

San Joaquin River near Grayson B0708000 373348 1210906 San Joaquin River near Grayson San Joaquin River near Grayson Mountain and valley

Tuolumne River at Tuolumne Meadows B4185010 375236 1192118 Tuolumne River at Tuolumne Meadows Tuolumne River at Tuolumne Meadows Mountain

Tuolumne River at LaGrange B0417500 374000 1202742 Tuolumne River at LaGrange Tuolumne River at LaGrange Mountain

Tuolumne River at Tuolumne City B0410500 373612 1210700 Tuolumne River at Shiloh Road1 Tuolumne River at Shiloh Road1 Mountain and valley

San Joaquin R at Maze Rd Bridge nr Modesto, CA 11290500 373824 1211342 San Joaquin River at Maze Road San Joaquin River at Maze Road Mountain and valley

Stanislaus R MF at Dardanelle B3348010 382030 1194924 Stanislaus River Middle Fork at Dardanelle Stanislaus River MF at Dardanelle Mountain

Stanislaus River below Goodwin Dam B3113000 375106 1203813 Stanislaus River below Goodwin Dam Stanislaus River below Goodwin Dam Mountain

Stanislaus River at Koetitz Ranch B0311500 374200 1211012 Stanislaus River near Caswell State Park1 Stanislaus River near Caswell SP1 Mountain and valley

San Joaquin R nr Vernalis, CA 11303500 374034 1211555 San Joaquin River near Vernalis San Joaquin River near Vernalis Mountain and valley

Santa Ana Basin Sites

Santa Ana R nr Mentone, CA 11051500 340630 1170559 Santa Ana River near Mentone Santa Ana River near Mentone Mountain

Santa Ana R at E St nr San Bernardino, CA 11059300 340354 1171758 Santa Ana River near San Bernardino Santa Ana River near San Bernardino Basin

Warm Cr nr San Bernardino, CA 11060400 340442 1171758 Warm Creek near San Bernardino Warm Creek Basin

Santa Ana R at MWD Crossing, CA 11066460 335807 1172651 Santa Ana River at MWD Crossing1 Santa Ana River at MWD Crossing1 Basin

Cucamonga Cr nr Mira Loma, CA 11073495 335858 1173555 Cucamonga Creek near Mira Loma Cucamonga Creek Mountain and basin

Santa Ana R bl Prado Dam, CA 11074000 335300 1173840 Santa Ana River below Prado Dam Santa Ana River below Prado Dam Mountain and basin

1 Sites have combined data from one or more sites (see table 2 for details).

Table 4. Site names and primary geographic setting (mountain, valley, or basin) for all 54 sites in final database: official names and simplified names for use in this report.—Continued[Primary geographic setting: Setting affecting water quality at site (for drainage basin upstream of site). Abbreviations: CA, California]
30 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

123°

122°

121°

39°

40°

41°

0 20 MILES

0 20 MILES

Nitrate

Ammonia

Total Nitrogen

Orthophosphate

Total Phosphorus

1

2

3

4

5

FAT Load

1

2

3

4

5

EXPLANATION

Flow-adjusted trends (FAT)

 and Load analytes

1

1

2

3

5

Bear River near Wheatland

American River South

Fork near Kyburz

1

American River at

Nimbus Dam

1

3

5

1

3

4

5

American River

at Sacramento

2

3 4

5 1

2

3 4

5 1

Arcade Creek near

Del Paso Heights

1

2

3 4

5 1 2

3

4

5

Sacramento River

at Freeport

1

2

3 4

5 1 2

3

4

5

Sacramento River at Verona

1

4 2

5 1

3

4

5

Sacramento River above

Colusa Basin Drain

1

2

3 4

5 1 2

3

4

5

Yuba River near Marysville

1

1

3

4

5

Sacramento River near 

Hamilton City

2

3 4

5 1

4

5

McCloud River above

Shasta Lake

1

4 2

5 1

2

3

4

5

Pit River near

Montgomery Creek

1

4 2

5

1

2

3

4

5

Sacramento River at Vina

1

4 2

5

1

2

3 4

5 1 2

3

4

5

Sacramento River

at Keswick

1

4 2

5 1

3

4

5

Sacramento River

at Delta

Feather River at Oroville

1

4 2

5

1

3

4

5

Cottonwood Creek

near Cottonwood

2

3 4

5 1

1

2

3 4

5 1 2

3

4

5

Sacramento River

near Red Bluff

1

4

5

1

3

4

5

Mill Creek

near Los Molinos

2

3 4

5 1

Deer Creek

near Vina

1

2

3 4

5 1

Stony Creek below 

Black Butte Dam

1

3

4

5

Sacramento River at Colusa

2

3 4

5 1

Butte Slough near Meridian

1

4

5

1

4

5

1

3

4

5

Feather River near Nicolaus

1

2

3

4

5

Colusa Basin Drain near 

Knights Landing 1

2

2

3

4

5

Sacramento Slough near

Knights Landing

2

3 4

5 1

A.

Figure 7. Sites in (A) Sacramento, (B) San Joaquin, and (C) Santa Ana Basins, California, with sufficient data for analyses of 

flow-adjusted trends and (or) loads of nitrate, ammonia, total nitrogen, orthophosphate, and total phosphorus, 1975–2004.
Sources of Data for Nutrient Concentrations and Flow in Streams 31

IP_002261_figure_07b

EXPLANATION

Flow-adjusted trends (FAT)

 and Load analytes

Nitrate

Ammonia

Total Nitrogen

Orthophosphate

Total Phosphorus

FAT Load

0 10 20 MILES 5

0 10 20 KILOMETERS 5

Stanislaus River Middle Fork

at Dardanelle

1

Stanislaus River below

Goodwin Dam

1

4

5

1

4

5

1

2

3

4

5 1 2

3

4

5

Tuolumne River at

Shiloh Road

1

2

3

4

5 1 2

3

4

5

San Joaquin River

near Vernalis

1

2

3

4

5 1 2

3

4

5

San Joaquin River

at Maze Road

1

2

3

4

5 1 2

3

4

5

San Joaquin River

near Patterson

1

2

3

4

5 1 3

4

5

Orestimba Creek

at River Road

1

2

3

4

5 1 2

3

4

5

Merced River

near Stevinson

1

2

3

4

5 1 2

3

4

5

Mud Slough

near Gustine

1

2

3

4

5 1 2

3

4

5

Salt Slough

near Stevinson

1

1

Panoche Drain near

Dos Palos

2

3

4

5 1 3

4

5

San Joaquin River

near Stevinson

1

2

3

4

5

1

2

3

4

5

Merced River at

Happy Isles

1

2

4

1

2

3

5

Merced River below

Merced Falls Dam

1

4

5

4

5

Tuolumne River

at LaGrange

1

4

5

1

5

1

2

3

4

5 1 2

3

4

5

Stanislaus River near

Caswell State Park

Grasslands

Drainage 

Project Area

121°

120°

37°

38°

B.

Figure 7.—Continued
32 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 7c

Warm Creek

Cucamonga Creek

Santa Ana River

San

Jacinto

River

Lake

Elsinore

Temescal Creek

118°

117°

34°

0 10 20 MILES

0 10 20 KILOMETER

Coastal

Basin

Inland

Basin

San Jacinto

Basin

San Gabriel

Mountains

San Bernardino

Mountains

San Jacinto

Mountains

Santa Ana

Mountains

Prado

Dam

Pacific Ocean

1

2 3 4

5

1

2 3 4

5

1 2

3

4

5

Santa Ana River

below Prado Dam

Cucamonga Creek

near Mira Loma

1

3 2

4

1

3

4

1

1

2

3

4

4

5

Santa Ana River

at MWD Crossing

1

Santa Ana River

near San Bernardino

Warm Creek near

San Bernardino Santa Ana River

near Mentone

1

3 2

4

1

1

4 3

5

4 1

1

2

3

4

5

1

2

3

4

5

EXPLANATION

Flow-adjusted trends (FAT)

 and Load analytes

Nitrate

Ammonia

Total Nitrogen

Orthophosphate

Total Phosphorus

FAT Load

C.

Figure 7.—Continued
Sources of Data for Nutrient Concentrations and Flow in Streams 33

IP-002261_fig 08a

A.

121°

122°

41°

40°

39°

0 20 40 MILES

0 20 40 KILOMETERS

Drainage Basins

Drainage Basin Outlet

EXPLANATION

McCloud River above

Shasta Lake

Sacramento River at

Delta

Pit River near

Montgomery Creek

Sacramento River at

Keswick

Sacramento River near

Red Bluff

Mill Creek

near Los Molinos

Deer Creek

near Vina

Cottonwood Creek near

Cottonwood

Stony Creek below Black

Butte Dam

Colusa Basin Drain near

Knights Landing

Butte Slough near

Meridian

Sacramento Slough near

Knights Landing

Feather River at

Oroville

Yuba River near

Marysville

Bear River near

Wheatland

Feather River near

Nicolaus

Arcade Creek near Del

Paso Heights

American River South 

Fork near Kyburz

American at Nimbus

Dam

American River at

Sacramento

Sacramento River at Vina

Sacramento River near

Hamilton City

Sacramento River at

Colusa

Sacramento River above

Colusa Basin Drain

Sacramento River at

Verona

Sacramento River at

Freeport

Figure 8. Drainage subbasins for sites in (A) Sacramento, (B) San Joaquin, and (C) Santa Ana Basins, California, with sufficient 

data for analyses of flow-adjusted trends and(or) loads of nitrate, ammonia, total nitrogen, orthophosphate, and total phosphorus, 

1975–2004. See figure 7 for respective basin site locations.
34 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

The number of samples in the final database (table CD-1

on the Data CD) for the five parameters are shown by 

data source for the three time periods in figure 9. For the 

Sacramento Basin, the parameter with the most data for 1975–

2004 was nitrate, followed by TP, orthophosphate, TN, and 

ammonia (fig. 9A). For all five parameters for 1975–2004, the 

data from DWR represented 27.8 percent of the total (21,262 

data points), followed by NWIS (26.4 percent), STORET (25.2 

percent), and UCD (19.0 percent). These percentages varied 

considerably through the three time periods (1975–1984, 

IP-002261_fig 08b

B.

120°

121°

38°

37°

0 10 20 MILES

0 10 20 KILOMETERS

EXPLANATION

San Joaquin River near Vernalis

San Joaquin River at Maze 

Road

San Joaquin River near 

Patterson

Stanislaus River near Caswell 

State Park

Stanislaus River below

Goodwin Dam

Stanislaus River Middle

Fork at Dardanelle

Tuolumne River at Shiloh Road 

Tuolumne River at LaGrange 

San Joaquin River near 

Stevinson

Merced River near Stevinson

Merced River below Merced 

Falls Dam 

Merced River at Happy Isles 

Mud Slough near Gustine

Salt Slough near Stevinson

Orestimba Creek at River

Road 

Drainage Basin Outlet

Drainage Basins

Figure 8.—Continued

1985–1992, and 1993–2004). For 1975–1984, STORET 

represented 63.1 percent of the database (7,426 data points), 

followed by NWIS (30.4 percent) and DWR (6.5 percent). For 

1985–1992, DWR represented 61.9 percent of the database 

(3,183 data points) followed by STORET (20.5 percent) and 

NWIS (17.5 percent). More recently (1993–2004), UCD 

represented the largest portion of the database (10,653 data 

points) with 37.9 percent followed by DWR (32.5 percent) and 

NWIS (26.3 percent). 
Sources of Data for Nutrient Concentrations and Flow in Streams 35

IP-002261_fig 008c

117°30'

118°

117°

34°

15'

34°

33°

45'

0 10 20 MILES

0 10 20 KILOMETERS

Santa Ana River below Prado Dam

Santa Ana River at MWD Crossing

Santa Ana River near San Bernardino

Santa Ana River near Mentone

Cucamonga Creek near Mira Loma

Warm Creek near San Bernardino

EXPLANATION

Drainage Basins

C. Drainage Basin Outlet

Figure 8.—Continued

For the San Joaquin Basin, the parameter with the 

most data for 1975–2004 was nitrate, followed by TP, 

orthophosphate, TN, and ammonia (fig. 9B). For all five 

parameters for 1975–2004, the data in NWIS represented 

39.2 percent of the total (19,023 data points), followed by 

UCD (28.0 percent), DWR (17.0 percent), and STORET 

(14.7 percent). These percentages varied considerably 

through the three time periods (1975–1984, 1985–1992, and 

1993–2004). For 1975–1984, STORET represented 63.8 

percent of the database (3,768 data points), followed by DWR 

(18.3 percent), and NWIS (17.9 percent). For 1985–1992, 

NWIS represented 70.9 percent of the database (4,593 data 

points), followed by DWR (20.3 percent), and STORET 

(8.8 percent). More recently (1993–2004), UCD represented 

50.0 percent of the database (10,662 data points), followed by 

NWIS (33.0 percent), and DWR (15.1 percent). 

For the Santa Ana Basin, the parameter with the most 

data for 1975–2004 was nitrate, followed by orthophosphate, 

ammonia, TP, and TN (fig. 9C). For all five parameters for 

1975–2004, the data in NWIS represented 70.5 percent 
36 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Figure 9. Number of samples in final database by data source for nitrate, ammonia, total 

nitrogen, orthophosphate, and total phosphorus for water years 1975–1984, 1985–1992, and 

1993–2004 for (A) Sacramento, (B) San Joaquin, and (C) Santa Ana Basins, California. IP-002261_fig 09abc

1,000

1,200

200

0

1,400

400

1,600

600

1,800

800

2,000

NWIS

DWR

STORET

UCD

SRWP

SRCSD

NWIS

DWR

STORET

UCD

SRCSD

SRWP

NWIS

DWR

STORET

UCD

SRCSD

SRWP

NWIS

DWR

STORET

UCD

SRCSD

SRWP

NWIS

DWR

STORET

UCD

SRCSD

SRWP

NWIS

DWR

STORET

UCD

CVRWQCB

NWIS

DWR

STORET

UCD

CVRWQCB

NWIS

DWR

STORET

UCD

CVRWQCB

NWIS

DWR

STORET

UCD

CVRWQCB

NWIS

DWR

STORET

UCD

CVRWQCB

NWIS

DWR

STORET

NWIS

DWR

STORET

NWIS

DWR

STORET

NWIS

DWR

STORET

NWIS

DWR

STORET

N U M B ER O F S AM P LES

1993–2004

Water years

1985–1992

1975–1984

1,200

1,000

800

600

400

200

0

1,400

1,600

1,800

100

0

200

300

400

500

600

NITRATE AMMONIA TOTAL

NITROGEN

ORTHOPHOSPHATE TOTAL

PHOSPHORUS

A

B

C
Sources of Ancillary Data 37

of the total (3,119 data points), followed by STORET 

(17.2 percent), and DWR (12.3 percent). These percentages 

varied considerably through the three time periods (1975–

1984, 1985–1992, and 1993–2004). For 1975–1984, NWIS 

represented 57.0 percent of the database (1,201 data points), 

followed by STORET (24.7 percent), and DWR (18.2 

percent). For 1985–1992, NWIS represented 40.5 percent of 

the total database (607 data points), followed by STORET 

(39.7 percent), and DWR (19.8 percent). More recently 

(1993–2004), NWIS represented virtually all of the database 

(1,311 data points) with 96.6 percent, with the rest from DWR.

The analytical results from different agencies and time 

periods created a final database with many censored values 

and MDLs. This was part of the reason for choosing the 

LOADEST model for analyzing loads and trends in this study. 

The AMLE component of the LOADEST model is able to 

work with censored data and MDLs (Cohn, 2005).

Sources of Ancillary Data

Ancillary data were evaluated in this study quantitatively 

and qualitatively to explore trends in water quality. The 

quantitative assessment involved relating average annual 

subbasin nutrient yields to average annual nutrient sources 

and subbasin characteristics for the Sacramento and San 

Joaquin Basins (including unmodeled load sources and(or) 

sinks between mainstem sites) using stepwise multiple linear 

regression. The types of ancillary data assembled in this study 

included information on point sources and nonpoint sources 

of nutrients. Much of the data was nonelectronic and involved 

synthesizing hard-copy data from various sources, especially 

for point sources, atmospheric deposition, and tile drainage.

With the exception of the Santa Ana Basin, ancillary data 

were assembled for 1985–2004. In many cases, the data for 

1975–1984 were either inaccessible or unreliable. Because 

of the importance of point sources in the Santa Ana Basin, 

wastewater inputs were evaluated for the entire 1975–2004 

time period.

Point Sources of Nutrients

A listing of all point-source discharges to surface 

waters was obtained from the SWRCB (California State 

Water Resources Control Board, 2006). These discharges are 

required to have National Pollutant Discharge Elimination 

System (NPDES) permits from USEPA. The number of permit 

listings was 260 for the Central Valley Region of the SWRCB 

(includes all of the Sacramento and San Joaquin Basins plus 

central Sierra and southern San Joaquin Valley drainages). The 

number of permit listings was 67 for the Santa Ana Region of 

the SWRCB (includes the entire Santa Ana Basin). In order 

to reduce these discharge data to a manageable number, only 

discharges greater than a certain magnitude were considered. 

This cutoff was based on the long-term mean daily flows at the 

basin outlet for each basin—23,750 ft3/s for the Sacramento 

Basin, 4,550 ft3/s for the San Joaquin Basin, and 206 ft3/s for 

the Santa Ana Basin. Based on these flows, the mean daily 

discharge cutoffs were set at 10 ft3/s in the Sacramento Basin, 

2 ft3/s in the San Joaquin Basin, and 0.5 ft3/s in the Santa Ana 

Basin. This reduced the number of point-source discharges 

in each basin to 10 in the Sacramento Basin, 10 in the San 

Joaquin Basin, and 20 in the Santa Ana Basin.

Sacramento Basin

The 10 discharges considered in the Sacramento Basin 

include 6 fish hatcheries, 3 wastewater treatment plants, and 

a heating and cooling facility. After a thorough review of the 

information available from the NPDES files at the Sacramento 

and Redding offices of the RWQCB(CVR), we determined 

that the only significant nutrient point-source discharges 

to the Sacramento River were from the three wastewater 

treatment plants. These three plants treat wastewaters from 

the cities of Redding, Chico, and Roseville (fig. 10). The city 

of Sacramento wastewater treatment plant discharges to the 

Sacramento River downstream of the Freeport site and is thus 

not considered in this study.

In December 1982, eight wastewater treatment plants in 

the Sacramento metropolitan area were consolidated into one 

discharge point at the present site of the Sacramento County 

Regional Wastewater Treatment Plant. This discharge point 

is about 300 ft downstream of the Sacramento River near 

Freeport site, and thus outside of the study area (Wendell 

Kido, former plant manager of Sacramento Regional 

Wastewater Treatment Plant, oral commun., Sept. 24, 2007). 

Three of the former discharges (about 39 ft3/s) were moved 

from the American River between the Nimbus Dam and 

Sacramento sites and one (about 15 ft3/s) from the American 

River downstream of the Sacramento site. One discharge 

(about 6 ft3/s) was moved from the Sacramento River between 

Verona and the American River confluence and two (about 

50 ft3/s) from the Sacramento River between the American 

River and Freeport. One discharge (about 15 ft3/s) had already 

been discharging at the consolidated site.

Nutrient data for the three most significant wastewater 

treatment-plant discharges in the Sacramento Basin upstream 

of Freeport (Redding, Chico, and Roseville) were obtained 

from the NPDES files at the RWQCB(CVR) offices. In 

general, there was an abundance of ammonia data and sparse 

data on nitrate, TN, orthophosphate, and TP.
38 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 10

1985 1993 2004

Discharge, in cubic feet per second 

EXPLANATION

< 10

10 – 30

> 30

IEUA

#1&4

IEUA

(Carbon Canyon)

IEUA #2

Western

Riverside Co.

Corona #1

Riverside

RIX

Rialto

Colton

San

Bernardino

117°

118°

34°

0 10 20 MILES

0 10 20 KILOMETERS

Modesto

Turlock

Roseville

(Dry Creek)

Chico

Redding

(Clear Creek)

0 50 100 MILES

0 50 100 KILOMETERS

Santa Ana River

San Joaquin River

Sacramento River

Figure 10. Locations of point sources of nutrients in Sacramento, San Joaquin, and Santa Ana Basins, California, with 

average discharge rates for 1985, 1993, and 2004.
Sources of Ancillary Data 39

San Joaquin Basin

The 10 discharges considered in the San Joaquin Basin 

include 4 wastewater treatment plants, 3 fish hatcheries, 

a worm farm, a chocolate factory, and a groundwater 

cleanup project. After a thorough review of the information 

available from the NPDES files at the Sacramento and 

Fresno offices of the RWQCB(CVR), we determined that 

the only significant nutrient point-source discharges to the 

SJR were from two wastewater treatment plants. These two 

plants treat wastes from the cities of Turlock and Modesto 

(fig. 10). The wastewater treatment plant discharges from the 

cities of Merced and Atwater generally end up being reused 

downstream and do not reach the SJR system, and thus were 

not relevant to this study.

Nutrient data for the two wastewater treatment plants 

were obtained from the NPDES files at the RWQCB(CVR) 

offices. The Modesto discharge to the SJR is only permitted 

during October through May when there is at least 20:1 

dilution available in the SJR receiving water. The rest of the 

time, the effluent is used to irrigate pasture and fodder crops. 

In general, there was an abundance of ammonia data and 

sparse data on nitrate, TN, orthophosphate, and TP.

Santa Ana Basin

The 20 discharges considered in the Santa Ana Basin 

include 17 wastewater treatment plants, 2 groundwater 

cleanup projects, and a facility for processing oranges. After 

reviewing information available from the NPDES files in the 

Riverside office of the RWQCB(SAR), we determined that the 

groundwater cleanup projects and the facility for processing 

oranges did not have significant discharges of nutrients to the 

SAR system. Although many wastewater treatment facilities 

have operated in the Inland Santa Ana Basin during the 

study period, most of the facilities are small, or discharge 

their effluent to receiving waters other than the SAR. Such 

receiving waters include holding ponds or reclamation 

facilities for local irrigation. The Santa Ana River Watermaster 

compiles annual hydrologic data reports identifying the 

major sources of streamflow in the SAR at Prado Dam. These 

annual reports are required as part of a stipulated judgment 

in the case of Orange County Water District vs. City of 

Chino et al entered by the court on April 17, 1969 (Case 

No. 117628-County of Orange). According to these reports, 

10 municipal wastewater-treatment plants have contributed 

significant discharges with hydraulic continuity to the SAR 

upstream of Prado Dam during the study period (Santa Ana 

River Watermaster, 2004). 

The 10 important plants are, or have been, operated 

by the following entities: Inland Empire Utility Agency, 

Western Riverside County Regional Wastewater Treatment, 

and the cities of Rialto, San Bernardino, Colton, Riverside, 

and Corona (fig. 10). Prior to 1996, the combined flows 

from the San Bernardino and Colton treatment plants 

were discharged to the SAR upstream of E Street in San 

Bernardino, constituting nearly the entire baseflow in the river 

at that location. Some early data on nutrient concentrations 

in this combined effluent were available from a few samples 

collected at a USGS stream-gaging site located there.

Treatment plant data for concentrations of inorganic 

nitrogen were widely available, but data for concentrations 

of organic nitrogen and for phosphorus were rarely available. 

Much of the data were available only as hard-copy NPDES 

compliance documents submitted to the RWQCB(SAR). A 

small amount of these compliance data also were obtained 

from the State Archives in Sacramento, where they were sent 

from the RWQCB(SAR). Such data generally were available 

only as far back as the early 1990s, because RWQCB(SAR) 

did not require long-term storage of historical data. In some 

cases, destruction of files was documented by RWQCB(SAR).

Effluent data also were provided electronically by 

personnel from municipalities and treatment facilities (Patrick 

Shields, Inland Empire Utilities Agency, written commun., 

2004; John Mellin, City of Corona, written commun., 

2004; Anicia Yambot, City of Riverside, written commun., 

2005; John Dahlke, Western Riverside County Regional 

Wastewater Treatment Plant, written commun., 2005; Greg 

Woodside, Orange County Water District, written commun., 

2005; Karen Connor, Riverside Regional Water Quality 

Control Plant, written commun., 2005). When hard-copy 

and electronic data were available for plant effluent quality, 

usually the two sources were in excellent agreement. In the 

few cases where the differences were significant, hard-copy 

NPDES compliance documents that had been submitted to 

RWQCB(SAR) were preferred over electronic data. 

The earliest estimates of typical effluent qualities for 

some of the important treatment plants were provided by 

the RWQCB(SAR) 1975 Basin Plan (California Regional 

Water Quality Control Board, Santa Ana Region, 1975). 

The 1985 Basin Plan provided updated estimates of typical 

nutrient concentrations in the effluent of these plants that 

discharge to the SAR or a major tributary (California 

Regional Water Quality Control Board, Santa Ana Region, 

1985). The following entities also provided electronic data 

on qualities and quantities of wastewater treatment-plant 

effluent in the Santa Ana Basin for this report: Santa Ana 

Watershed Project Authority (Mark Norton, Santa Ana 

Watershed Project Authority, written commun., 2004), 

Wildermuth Environmental, Inc. (Jeffrey Hwang, Wildermuth 

Environmental Inc., written commun., 2005), and the Santa 

Ana River Watermaster (Steven E. Mains, Santa Ana River 

Watermaster Support Services, written commun., 2005).
40 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

The earliest data on wastewater treatment effluent 

quality in the Santa Ana Basin were obtained from NPDES 

compliance reports submitted to the RWQCB(SAR) for 

effluent from the San Bernardino treatment plant during 

calendar years 1983–85. With regard to nutrients, only 

ammonia data were included in those reports. However, 

estimates of nutrient concentrations in effluent provided 

in the 1985 Basin Plan (California Regional Water Quality 

Control Board, Santa Ana Region, 1985), and a single 

data point for total inorganic nitrogen provided by the San 

Bernardino treatment plant for December 1986, indicate that 

virtually all inorganic nitrogen in effluent from this plant 

consisted of ammonia at that time. Data were summarized 

by month, so that if more than one value was available 

for a month (sometimes daily values were available), the 

stored data point was the mean of the available data for that 

month. Concentrations of the various species of nitrogen and 

phosphorus are reported herein as mg N or P per liter (L), 

respectively.

Nonpoint Sources of Nutrients

Nonpoint sources of nutrients are more difficult to relate 

to nutrient concentrations or loads in the rivers, because only 

a small percentage of these diffuse sources reach a surface 

water body through runoff or deposition. The nonpoint sources 

considered in this study include atmospheric deposition, 

fertilizer application, manure production, and tile drainage 

(San Joaquin Basin only). Unlike the other nonpoint sources, 

the tile drainage input to the SJR is more like a point source, 

as it directly discharges into the surface water. It is only 

considered a nonpoint source by definition because it is of 

agricultural origin and not municipal or industrial.

Atmospheric Deposition

The sources of atmospheric-deposition data for nutrients 

used in this study are the National Atmospheric Deposition 

Program (NADP), the California Acid Deposition Monitoring 

Program (CADMP), and the USEPA Clean Air Status 

and Trends Network (CASTNET) Program (California 

Air Resources Board, 1991; Takemoto and others, 1995; 

Blanchard and others, 1996; MACTEC Engineering and 

Consulting, Inc., 2006; National Atmospheric Deposition 

Program, 2005, 2007; U.S. Environmental Protection 

Agency, 2007). Samples at all sites included concentrations 

of ammonia and nitrate in rainfall and total rainfall volumes, 

which allowed for calculation of wet deposition amounts 

of ammonia and nitrate. Data on inorganic nitrogen are 

referred to as wet deposition of TN in this report. The 

CADMP and CASTNET programs also have collected 

dry-deposition data at some sites. The CADMP collected 

dry-deposition data for up to 10 sites in California during 

1988–94. The dry-deposition data collected at CADMP sites 

for nitrogen included nitric acid (HNO3), nitrite (NO2), and 

ammonia (NH3) in the gaseous form and nitrate (NO3) and 

ammonium (NH4

+) in the particulate form. The CASTNET 

program collected dry-deposition data for up to seven sites 

in California during 1996–2004. The dry-deposition data 

collected at CASTNET sites for nitrogen included only 

the gaseous form of nitric acid and the particulate forms of 

nitrate and ammonium. In both programs, dry deposition was 

calculated using atmospheric concentrations from samples 

pumped through filters along with meteorological data and 

information on land use, vegetation, and surface conditions. 

For consistency, only the gaseous form of nitric acid from the 

CADMP sites was used and not the gaseous forms of nitrite 

and ammonia.

For wet deposition, data from five NADP sites, six 

CADMP sites, and three CASTNET sites were used (fig. 11). 

For dry deposition, data from five CADMP sites and three 

CASTNET sites were used (fig. 11). Because only the NADP 

wet-deposition data were available for the entire 1985–2004 

period, wet and dry deposition were related for subbasins 

in the Sacramento, San Joaquin, and Santa Ana Basins to 

NADP wet deposition. For wet deposition, this was done by 

averaging wet-deposition sites and relating the average to a 

NADP wet-deposition site. For dry deposition, this was done 

by averaging the dry- to wet-deposition ratios for appropriate 

sites and relating the average to a NADP wet-deposition site. 

The total atmospheric deposition was then calculated as the 

sum of the factors for wet and dry deposition applied to a 

NADP wet-deposition site (table 5). Limited sampling for 

phosphorus deposition early in the NADP indicated that the 

atmosphere is not a significant source of phosphorus in most 

areas.

Sacramento Basin

There are three NADP sites in or nearly in the 

Sacramento Basin: Montague (CA76) is at an altitude of 

2,615 ft in the Siskiyou Mountains, Hopland (CA45) is at an 

altitude of 830 ft in the Coast Ranges, and Davis (CA88) is at 

an altitude of 59 ft in the Sacramento Valley. The Montague 

site is considered to be representative of atmospheric 

deposition for subbasins in the Sierra and Klamath Mountains, 

the Hopland site for subbasins in the Coast Ranges, and 

the Davis site for subbasins in the Sacramento Valley. The 

wet-deposition factors applied to these NADP sites range from 

0.58 for the upper Feather River Basin to 1.32 for the most 

northern subbasins (table 5). Dry-deposition factors applied 

to the NADP sites range from 0.33 for the most northern 

and upper Feather River subbasins to 2.11 for several valley 

subbasins (table 5).
Sources of Ancillary Data 41

IP-002261_fig 11

CADMP

CASTNET

CADMP

NADP

CASTNET

Dry deposition site 

Wet deposition site 

EXPLANATION

Azusa

Davis

Quincy

Gasquet

Hopland

Yosemite

Montague

Lassen NP

Sacramento

Bakersfield

Tanbark Flat Converse Station

0 50 100 MILES

0 50 100 KILOMETERS

Figure 11. Locations of sites in Sacramento, San Joaquin, and Santa Ana Basins, California, with atmosphericdeposition data. Data-source site acronyms are listed in front of report.
42 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 Table 5.

Wet and dry deposition factors applied to National Atmospheric Deposition Program data to estimate total atmospheric deposition of total nitrogen for subbasins in the 

Sacramento, San Joaquin, and Santa Ana Basins, 1985–2004.

NWIS

site ID Subbasin1 Effective subbasin area2 Sites used to calculate wet deposition3 (see fig. 11) Wet deposition factor applied to NADP site Sites used to calculate dry deposition4 (see fig. 11) Dry deposition factor applied to NADP site Ratio of dry to wet deposition Total atmospheric deposition, as factor of NADP site Average annual total atmospheric deposition [(tons/mi2)/yr]

Sacramento subbasins/sites

11342000 Sacramento River at Delta All CA76/CADMP(Montague);

CASTNET(Lassen NP)

1.32 CASTNET (Lassen NP) 0.75 0.57 2.07 * CA76 0.28

11368000 McCloud River above Shasta Lake All CA76/CADMP(Montague); 

CASTNET(Lassen NP)

1.32 CASTNET (Lassen NP) 0.75 0.57 2.07 * CA76 0.28

11365000 Pit River near Montgomery Creek All CA76/CADMP(Montague); 

CASTNET(Lassen NP)

1.32 CASTNET (Lassen NP) 0.75 0.57 2.07 * CA76 0.28

11370500 Sacramento River at Keswick All CA76/CADMP(Montague); 

CASTNET(Lassen NP)

1.32 CASTNET (Lassen NP) 0.75 0.57 2.07 * CA76 0.28

11376000 Cottonwood Creek near 

Cottonwood

All CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11377100 Sacramento River near Red Bluff Valley only CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11381500 Mill Creek near Los Molinos All CA88/CADMP(Sacramento); 

CADMP(Quincy)

0.87 CADMP(Sacramento)/

CASTNET(Lassen NP)

0.97 1.12 1.84 * CA88 1.20

11383800 Sacramento River near Hamilton 

City

Valley only CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11388000 Stony Creek below Black Butte 

Dam

All CA45 1.00 CADMP(Sacramento)/

CADMP(Gasquet)

1.00 1.00 2.00 * CA45 0.43

11389500 Sacramento River at Colusa Valley only CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11390650 Sacramento River above Colusa 

Basin Drain

Valley only CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11390890 Colusa Basin Drain near Knights 

Landing

All CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11391100 Sacramento Slough near Knights 

Landing

All CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11407000 Feather River at Oroville All CADMP(Quincy) 0.58 CASTNET(Lassen NP) 0.33 0.57 0.91 * CA88 0.59

11421000 Yuba River near Marysville All CA88/CADMP(Sacramento); 

CADMP(Quincy)

0.87 CADMP(Sacramento)/

CASTNET(Lassen NP)

0.97 1.12 1.84 * CA88 1.20

11424000 Bear River near Wheatland All CA88/CADMP(Sacramento); 

CADMP(Quincy)

0.87 CADMP(Sacramento)/

CASTNET(Lassen NP)

0.97 1.12 1.84 * CA88 1.20

11425000 Feather River near Nicolaus Valley only CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11425500 Sacramento River at Verona Valley only CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11447360 Arcade Creek near Del Paso 

Heights

All CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20

11447000 American River at Sacramento All CA88/CADMP(Sacramento); 

CADMP(Quincy)

0.87 CADMP(Sacramento)/

CASTNET(Lassen NP)

0.97 1.12 1.84 * CA88 1.20

11447650 Sacramento River at Freeport Valley only CA88/CADMP(Sacramento) 1.27 CADMP(Sacramento) 2.11 1.66 3.38 * CA88 2.20
Sources of Ancillary Data 43

NWIS

site ID Subbasin1 Effective subbasin area2 Sites used to calculate wet deposition3 (see fig. 11) Wet deposition factor applied to NADP site Sites used to calculate dry deposition4 (see fig. 11) Dry deposition factor applied to NADP site Ratio of dry to wet deposition Total atmospheric deposition, as factor of NADP site Average annual total atmospheric deposition [(tons/mi2)/yr]

San Joaquin subbasins/sites

11260815 San Joaquin River near Stevinson Valley only CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11261100 Salt Slough near Stevinson All CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11262900 Mud Slough near Gustine All CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11264500 Merced River at Happy Isles All CA99/CADMP(Yosemite)/

CASTNET(Yosemite)

0.96 CADMP(Yosemite)/

CASTNET(Yosemite)

0.36 0.38 1.32 * CA99 0.85

11273500 Merced River near Stevinson Valley only CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11274538 Orestimba Creek at River Road Valley only CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11274570 San Joaquin River near Patterson Valley only CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11290200 Tuolumne River at Shiloh Road Valley only CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11290500 San Joaquin River at Maze Road Valley only CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11302000 Stanislaus River below Goodwin 

Dam

All CA99/CADMP(Yosemite)/

CASTNET(Yosemite)

0.96 CADMP(Yosemite)/

CASTNET(Yosemite)

0.36 0.38 1.32 * CA99 0.85

11303300 Stanislaus River near Caswell State 

Park

Valley only CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

11303500 San Joaquin River near Vernalis Valley only CA88/CADMP(Sacramento); 

CADMP(Bakersfield)

0.89 CADMP(Sacramento)/

CADMP(Bakersfield)

2.49 2.80 3.38 * CA88 2.20

Santa Ana subbasins/sites

11051500 Santa Ana River near Mentone All CASTNET(Converse Station) 0.78 CASTNET(Converse 

Station)

2.09 2.68 2.87 * CA42 1.66

11059300 Santa Ana River near San 

Bernardino

Basin only CADMP(San Bernardino) 1.48 CADMP(Azusa) 14.49 9.79 15.97 * CA42 9.24

11060400 Warm Creek near San Bernardino Basin only CADMP(San Bernardino) 1.48 CADMP(Azusa) 14.49 9.79 15.97 * CA42 9.24

11066460 Santa Ana River at MWD Crossing Basin only CADMP(San Bernardino) 1.48 CADMP(Azusa) 14.49 9.79 15.97 * CA42 9.2411073495 Cucamonga Creek near Mira Loma Basin only CADMP(San Bernardino) 1.48 CADMP(Azusa) 14.49 9.79 15.97 * CA42 9.2411074000 Santa Ana River below Prado Dam Basin only CADMP(San Bernardino) 1.48 CADMP(Azusa) 14.49 9.79 15.97 * CA42 9.24

1 Subbasin: drainage basin upstream of the site.2 Effective Subbasin Area: portion of drainage basin area upstream of site as indicated (e.g., in the valley).3 Period of Data Availability for Wet Deposition sites: CA76 (Montague): 1986-2004 [use 1987 for 1985; as they are similar water years]; CA45 (Hopland): 1980-2004; CA88 (Davis): 1979-2004; 

CADMP (Montague): 1986-94; CADMP (Sacramento): 1985-94; CADMP (Quincy): 1986-87, 1990-94; CASTNET (Lassen NP): 1996-2004; CA99 (Yosemite): 1983-2004; CASTNET (Yosemite): 1996-2004; 

CADMP (Yosemite): 1985, 1987-89, 1991-94; CADMP (Bakersfield): 1985-94; CASTNET (Converse Station): 2003-04; CADMP (San Bernardino): 1985-94; CA42 (Tanbark Flat): 1982-2004.

4 Period of Data Availability for Dry Deposition sites: CADMP (Gasquet): 1988-94; CASTNET (Lassen NP): 1997-98, 2001-04; CADMP (Sacramento): 1988-94; CADMP (Yosemite): 1988-94; 

CASTNET (Yosemite): 1996-2004; CADMP (Bakersfield): 1988-94; CASTNET (Converse Station): 2004; CADMP (Azusa): 1988-94.

Table 5. Wet and dry deposition factors applied to National Atmospheric Deposition Program data to estimate total atmospheric deposition of total nitrogen for subbasins in the Sacramento, San Joaquin, and Santa Ana Basins, 1985–2004.—Continued
44 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

San Joaquin Basin

There are two NADP sites in or nearly in the San 

Joaquin Basin: Yosemite National Park (CA99) at an altitude 

of 4,620 ft and Sequoia National Park (CA75) at an altitude 

of 6,240 ft. The Sequoia site is about 90 mi southeast of the 

Yosemite site (fig. 11). Because the Yosemite site is in the 

San Joaquin Basin and the Sequoia site is in the Tulare Basin, 

the Yosemite site is considered to be more representative of 

atmospheric deposition in Sierran subbasins in the San Joaquin 

Basin. However, neither of these NADP sites is considered 

to be representative of subbasins in the San Joaquin Valley. 

For these subbasins, the atmospheric deposition for the Davis 

NADP site is considered to be more representative. The wetdeposition factors applied to the Yosemite and Davis NADP 

sites range from 0.89 to 0.96 (table 5). Dry-deposition factors 

range from 0.36 for Sierran subbasins to 2.49 for valley 

subbasins (table 5). 

Santa Ana Basin

The only NADP site nearly in the Santa Ana Basin is 

Tanbark Flat (CA42), just north of the Santa Ana Basin in the 

San Gabriel Mountains at an altitude of 2,799 ft. The wetdeposition factors applied to this NADP site range from 0.78 

for the mountain subbasin (SAR near Mentone) to 1.48 for the 

other subbasins (table 5). Dry-deposition factors range from 

2.09 for the SAR near Mentone subbasin to 14.49 for the other 

subbasins (table 5). Thus, dry deposition is a very important 

factor in the Santa Ana Basin with the NOX component of the 

Los Angeles Basin smog layer (Bytnerowicz and Fenn, 1996). 

Data on air quality, with regard to nitrogen species in the Santa 

Ana Basin, were obtained from a California Air Resources 

Board (ARB) website accessed November 10, 2005, at URL: 

http://www.arb.ca.gov/homepage.htm for a monitoring site 

at 5888 Mission Blvd. in Riverside (Riverside-Rubidoux). 

This site was chosen for trend analyses because it is centrally 

located in the Inland Basin, and abundant data were collected 

there for the oxides of nitrogen in gas and particle phases. 

Although air-quality data are not a direct measure of nitrogen 

being deposited in a watershed, trends in air quality would 

be expected to translate to trends in atmospheric loading of 

nitrogen to the landscape if we can assume a fairly constant 

atmospheric-deposition rate in the subbasin (Mark Nilles, 

Coordinator, USGS National Atmospheric Deposition 

Program, oral commun., May 2006). 

Fertilizer Application

Fertilizer sales can be used as a surrogate for 

fertilizer-application data. Distribution to the county level 

may not accurately reflect actual use, however, because 

fertilizer sales recorded in one county may not be used in 

that county. In addition, recorded sales include commercial 

landscape and other nonagricultural uses. Ruddy and others 

(2006) used Census of Agriculture fertilizer expenditures to 

allocate fertilizer use to the county level. These county-level 

fertilizer expenditures are based on the residence of the 

purchaser and thus are different from county-level fertilizer 

sales that are based on the location of the seller. Calendar-year 

fertilizer expenditures for each county in California were 

obtained from the Census of Agriculture for 1982, 1987, 

1992, 1997, and 2002 (Ruddy and others, 2006). Although the 

Census of Agriculture data are available only every 5 years, 

state-level fertilizer sales data were available annually from 

the Association of American Plant Food Control Officials 

(AAPFCO; Ruddy and others, 2006). Separate allocation 

methods were used for fertilizers applied on farms and those 

applied in nonfarm areas. State sales of nonfarm fertilizer 

were allocated to the county level based on population data. 

The county-level nutrients from nonfarm-fertilizer use were 

estimated to be in proportion to the “effective” population, 

defined as a function of population density (Ruddy and 

others, 2006). For farm-fertilizer use, county-level estimates 

were made in Ruddy and others (2006) using the relation in 

equation 6: 

= ( / ),

where

is the estimated nutrient input from farmfertilizer use in county of state , in

kilograms of N or P,

is total farm-fertilizer sales for state , in

kilograms 

ik i ik i

ik

i

FFCU FFSS FCE FSE

FFCU

k i

FFSS i

of N or P,

is fertilizer expenditures of county of

state , in dollars, and,

is total expenditures for state , in dollars.

ik

i

FCE k

i

FSE i

(6)

Because the fertilizer-expenditure data are available only 

from the Census of Agriculture every 5 years, the intervening 

years expenditures (FCEik and FSEi) were estimated by linear 

interpolation (Ruddy and others, 2006).

The fertilizer-use estimates from Ruddy and others 

(2006) are available at URL: http://pubs.usgs.gov/

sir/2006/5012/excel/Nutrient_Inputs_1982-2001jan06.xls. 

The data contain estimates of nitrogen (as N) and phosphorus 

(as P) inputs, expressed in kilograms, for each county in 

the conterminous United States. The fertilizer estimates 

are provided annually for 1987–2001 by farm and nonfarm 

use. For this report, data were extended to include 1985–86 

and 2002–04. The 1985–86 data were assumed to be the 

same as 1987. For 2002–04, the data are based on the above 

methodology with the annual state fertilizer sales from 

AAPFCO (JoAnn Gronberg, U.S. Geological Survey, written 

commun., 2006). For this report, the county-level inputs of 

fertilizer were distributed to specific land uses within each 

county based on the 1992 National Land Cover Data (Ruddy 

and others, 2006). This is a 30-meter resolution dataset 
Sources of Ancillary Data 45

classifying land cover of the conterminous United States in 

the early to mid-1990s (Vogelmann and others, 2001). For 

farm-fertilizer use, the inputs were distributed to orchards/

vineyards, pasture/hay, row crops, small grains, and fallow 

land-cover classifications. This distribution of fertilizer 

use allowed for a better estimate of nutrient inputs for each 

subbasin in this report.

Manure Production

Estimates of nutrient inputs from manure were based 

on county-level livestock population data collected by the 

Census of Agriculture for 1982, 1987, 1992, and 1997 (Ruddy 

and others, 2006). The method used to estimate the nitrogen 

and phosphorus content of manure produced by various types 

of livestock takes into account differences in the life cycles 

of farm animals and for nutrient losses in storage, handling, 

and application of manure (Goolsby and others, 1999). The 

estimates of nutrient input made for each livestock group 

were summed by county. Each county total was divided into 

the animals raised in confined feeding operations and those 

that were not confined (Ruddy and others, 2006). The ratio 

of manure produced from confined and unconfined livestock 

were determined on the basis of data reported by Kellogg and 

others (2000).

As for nutrient input data for fertilizer use, the dataset 

described in Ruddy and others (2006) for livestock manure 

estimates for 1982, 1987, 1992, and 1997 are provided at 

URL: http://pubs.usgs.gov/sir/2006/5012/excel/Nutrient_

Inputs_1982-2001jan06.xls. The data contains estimates of 

nitrogen (as N) and phosphorus (as P) inputs, expressed in 

kilograms, for each county in the conterminous United States. 

The manure estimates are provided annually for 1982, 1987, 

1992, and 1997 for confined and unconfined livestock. This 

dataset was extended for this report to include 2002 using the 

Census of Agriculture numbers for livestock populations and 

the methods in Ruddy and others (2006; JoAnn Gronberg, 

U.S. Geological Survey, written commun., 2006). As with 

the fertilizer use, the county-level estimates of nutrient inputs 

from manure was distributed to specific land uses within each 

county using the 1992 National Land Cover Data (Ruddy 

and others, 2006). For manure, the inputs were distributed to 

pasture/hay, row crops, small grains, and fallow land cover 

classifications. For unconfined livestock, the grasslands/

herbaceous land cover classification also was included (Ruddy 

and others, 2006). This distribution of manure allowed for 

a better estimate of nutrient inputs for each subbasin in this 

report.

Tile Drainage

The Grasslands area (see Grasslands Drainage Project 

Area, fig. 1B) of the San Joaquin Basin drains to the SJR 

through the Salt and Mud Sloughs (fig. 1B). Subsurface 

agricultural drains (tile drains) were installed in the Grasslands 

area between 1950 and 1991 to relieve areas with shallow, 

saline water tables to allow for continued agricultural 

productivity. By 1991, the total acreage drained by these 

subsurface drains was about 58,500 acres. Until 1985, much 

of this tile drainage was used to flood waterfowl areas in 

the Grasslands before being discharged to the SJR, and 

some nutrients were taken up by aquatic plants. Since 1985, 

virtually all this tile drainage has been discharged directly 

to the SJR due to concerns over the accumulation of trace 

elements (especially selenium) in the waterfowl areas. 

 About 10,000 acres of additional agricultural land 

downstream of the Grasslands area have tile drains that 

discharge drainage to the SJR (Kratzer and others, 1987). 

On the basis of estimates made by using a methodology 

described by Kratzer and Shelton (1998), the discharge from 

the Grasslands area tile drains in 1991 was about 56 ft3/s, with 

a nitrate (and TN) concentration of about 25 mg/L (as N), and 

orthophosphate and TP concentrations of about 0.05 mg/L and 

0.1 mg/L as P. The tile drains downstream of the Grasslands 

area were estimated to discharge about 10 ft3/s, by using 

the same methodology, and were assumed to have a TN 

concentration of 10 mg/L (as N) based on salinity as a proxy. 

The TP concentration was assumed to be the same as for the 

Grasslands area tile drains. These tile-drainage discharges 

and concentration values were considered to be representative 

annual averages for the 1985–2004 period for the MLR 

analysis.

Data for Stepwise Multiple Linear-Regression 

Analysis

The NAWQA Program compiled many types of ancillary 

data for a series of trends reports (Naomi Nakagaki, U.S. 

Geological Survey, written commun., 2008). The types of 

ancillary data included the general categories of drainage 

information, land use and land cover, population, climatic 

factors, soils and geology, agricultural pesticide use, nutrient 

inputs, agricultural management practices, hydrologic and 

physical parameters, landscape regions, roads and streams, 

and weighting factors. The data were compiled at the subbasin 

area scale, by using various techniques to convert from county 

or other level data to subbasin level (Nakagaki and Wolock, 

2005). Data used for the stepwise multiple linear-regression 

analysis included land use and land cover, precipitation, soil 

hydrologic groups, and a rainfall runoff factor.

The land-use and land-cover percentages used in the 

analysis came from the August 2005 enhanced version of the 

30-meter resolution grid of the 1992 National Land Cover 

Dataset (NLCDe; Naomi Nakagaki, U.S. Geological Survey, 

written commun., 2008). The percentage of land in orchards 

and vineyards and in row crops in the Sacramento and San 

Joaquin Basins ranged from 0 to 49 for valley subbasins and 

were less than 1 percent for all mountain subbasins. The 

percentage of land in pasture and rice ranged from 0 to 51 

for valley subbasins and from 0 to 6 for mountain subbasins. 
46 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

The percentage of urban land use ranged from 0 to 95 for 

valley subbasins and from 0 to 7 for mountain subbasins. The 

percentage of land covered by grasslands and shrublands was 

not too different between the valley and mountain subbasins, 

with a range from 4 to 58 in valley subbasins and from 7 to 

48 in mountain subbasins. The percentage of land covered by 

forest ranged from 0 to 30 in valley subbasins and from 40 to 

89 in mountain subbasins (see table CD-4 of Data CD for all 

data used in the MLR analysis).

The average annual precipitation (1980–97) data for 

subbasins came from DAYMET climate data (National Center 

for Atmospheric Research, 2003). The precipitation values 

for the Sacramento and San Joaquin Basins ranged from 10 to 

40 in. for valley subbasins and from 31 to 63 in. for mountain 

subbasins. The soil hydrologic groups were defined by the 

U.S. Natural Resource Conservation Service (Neitsch and 

others, 2005). They defined Soil Hydrologic Groups A through 

D, with runoff potential increasing from A to D. Group A 

consists mainly of sands and gravel with high infiltration 

rates and low runoff potential (Neitsch and others, 2005). 

Groups B and C have moderate infiltration rates (B higher) 

and runoff potentials (C higher). Group D consists mainly of 

clays with low infiltration rates and high runoff potential. The 

soils information used to define the groups are from weighted 

averages of STATSGO parameters by soil-map unit based on 

a 100-meter resolution representation of the soil-map units 

(Naomi Nakagaki, U.S. Geological Survey, written commun., 

2008). Thus, the Soil Hydrologic Groups C and D used in 

this analysis generally represent the percentage of the soils 

in a subbasin that are silts and clays. These values were not 

too different between valley and mountain subbasins in the 

Sacramento and San Joaquin Basins, ranging from 24 to 92 in 

valley subbasins and from 16 to 84 in mountain subbasins.

The rainfall-runoff factor (R factor) is from the Universal 

Soil Loss Equation (Wischmeier and Smith, 1978). It is 

a unitless value based on rainfall intensity, duration, and 

amount. The higher these factors are, the higher the R factor, 

and the higher the soil erosion potential from rainfall. R 

factors in the Sacramento and San Joaquin Basins ranged from 

12 to 60 in valley subbasins and from 56 to 188 in mountain 

subbasins. The R factor used in this study was estimated 

from a 1-kilometer resolution representation of a 2.5-minute 

resolution grid of mean (1971–2000) R-factor values, which 

were derived from R-factor values estimated by the Illinois 

State Water Survey (Naomi Nakagaki, U.S. Geological 

Survey, written commun., 2008).

Results

The results of analyzing the nutrient database assembled 

for this study, both concentrations and ancillary data on 

sources, are presented here. First, the ancillary data on sources 

are quantified for 1985–2004 for point and nonpoint sources, 

by subbasin. Then estimated stream loads are presented for 

the mainstem sites in the Sacramento, San Joaquin, and Santa 

Ana Basins for 1975–2004 for sites with enough data to run 

LOADEST. For selected reaches of the Sacramento, San 

Joaquin, and Santa Ana Rivers with load estimates for major 

tributaries, the unmodeled loads for sources and (or) sinks 

between mainstem sites are presented. The mainstem loads, 

tributary loads, and loads for unmodeled sources and (or) 

sinks between mainstem sites were combined to produce a 

map of TN and TP yields for the Sacramento and San Joaquin 

Basins. Using these yields for the Sacramento and San Joaquin 

Basins and data on sources and subbasin characteristics, a 

multiple linear-regression equation was developed for TN and 

TP yields. Finally, the trends in nutrient concentrations in the 

Sacramento, San Joaquin, and Santa Ana Basins are presented 

and evaluated using the information developed in this study.

Nutrient Sources, 1985–2004

Nutrient sources are given only in terms of TN and 

TP, and thus the discussion here will be limited to these 

constituents. Most of the data on nutrient sources is limited 

to the 1985–2004 period, so that will be the time period 

discussed here with the exception of point sources for the 

Santa Ana Basin, owing to the importance of point sources for 

that basin. 

Point Sources

The nutrient loads contributed by the significant point 

sources were discussed in the previous section, Sources of 

Ancillary Data, are estimated here. This includes 3 wastewater 

treatment plants in the Sacramento Basin, 2 in the San Joaquin 

Basin, and 10 in the Santa Ana Basin (fig. 10). The loads are 

presented here as the summation of all point sources for each 

basin. In the subsequent section, Relations between Nutrient 

Yields and Nutrient Sources and Subbasin Characteristics, the 

point-source loads are apportioned by the river reach for each 

of the discharge points. 
Results 47

Sacramento Basin

Mean annual discharges from the three most significant 

point sources in the Sacramento Basin upstream of Freeport 

together accounted for 25 ft3/s in 1985 and 43 ft3/s in 2004, 

only 0.1 and 0.2 percent, respectively, of the long-term mean 

daily flow at Freeport (23,750 ft3/s). Annual TN loads from 

these point sources ranged from 335 tons/yr in 1985 to 474 

tons/yr in 1997, with 422 tons/yr in 2004. Thus, TN loads 

increased by about 26 percent during 1985–2004 (fig. 12A). 

Annual point-source TP loads ranged from 61 tons/yr in 2000 

to 138 tons/yr in 1992, with 98 tons/yr in 1985 and 64 tons/yr 

in 2004. Thus, TP loads decreased by about 35 percent during 

1985–2004 (fig. 12A). 

San Joaquin Basin

Mean annual discharges from the two most significant 

point sources accounted for 38 ft3/s in 1985 and 31 ft3/s in 

2004, about 0.8 and 0.7 percent, respectively, of the long-term 

mean daily flow at Vernalis (4,550 ft3/s). Annual TN loads 

from these point sources ranged from 960 tons/yr in 1986 to 

274 tons/yr in 1992, with 941 tons/yr in 1985 and 378 tons/ yr 

in 2004 (fig. 12B). Thus, TN loads decreased by about 

60 percent during 1985–2004. Annual TP loads ranged from 

241 tons/yr in 1986 to 68 tons/yr in 2001, with 234 tons/ yr 

in 1985 and 78 tons/yr in 2004 (fig. 12B). Thus, TP loads 

decreased by about 67 percent during 1985–2004. Overall, 

point sources in the San Joaquin Basin were considerably 

more important than in the Sacramento Basin, but still 

accounted for a small portion of the average flow in the SJR.

Santa Ana Basin

Unlike the Sacramento and San Joaquin Basins, point 

sources of nutrients were substantial in the Santa Ana Basin 

(fig. 12C), accounting for close to 80 percent of the nonstorm 

flow in the SAR just upstream of Prado Dam (Mendez and 

Belitz, 2002). Although the amount of effluent discharged 

from wastewater treatment plants to the SAR has increased 

consistently during the study period, the proportions of 

wastewater discharged by each plant remained fairly constant 

throughout the study period (fig. 13). The most important 

wastewater treatment plants in the Santa Ana Basin were the 

Riverside Regional Water Quality Control Plant (Riverside), 

and the plants operated by the Inland Empire Utility Agency 

(IEUA; previously Chino Basin Water District). The plants 

operated by the cities of San Bernardino and Colton also were 

important dischargers. Since 1996, their combined effluent has 

been discharged to the Rapid Infiltration and Extraction (RIX) 

facility. 

Although the data record for wastewater effluent quality 

during the study period is incomplete, some generalizations 

on nutrient trends in the effluent are possible. During the first 

decade of the study period (1975–84), nitrate concentrations 

in plant effluents were low compared to concentrations later 

on in the study period. Nitrate concentrations averaged about 

2 mg/L in monthly samples collected for water years 1972–82 

from the SAR at E Street (the site receiving the combined 

flows from the San Bernardino and Colton treatment plants). 

The RWQCB(SAR) estimated nitrate concentrations of 1 mg/L 

in effluent from two IEUA treatment plants, and 1.7 mg/L 

in effluent from the Riverside treatment plant (California 

Regional Water Quality Control Board, Santa Ana Region, 

1975). Of the plants characterized by the RWQCB(SAR) in 

the 1975 Basin Plan, only the nitrate estimates for effluent 

from the Corona treatment plants were relatively high at 

4.5 mg/L (California Regional Water Quality Control Board, 

Santa Ana Region, 1975).

In contrast to the relatively low concentrations of nitrate 

in treatment-plant effluent to the SAR during the first decade 

of the study period, ammonia concentrations were relatively 

high during this time. Ammonia concentrations (as N) in 

treatment-plant effluent were estimated by RWQCB(SAR) in 

the 1975 Basin Plan to range from 14 mg/L for the Corona 

plants to 25 mg/L for IEUA Plant 2 (California Regional Water 

Quality Control Board, Santa Ana Region, 1975). Monthly 

samples from the SAR at E Street averaged 24 mg/L ammonia. 

Based on typical water temperatures and pH levels in Santa 

Ana Basin streams, ammonia concentrations near some 

treatment plant outfalls probably exceeded national chronic 

and maximum ammonia criteria for the protection of aquatic 

life at times during that period (U.S. Environmental Protection 

Agency, 1999). Sparse data for total Kjeldahl nitrogen (organic 

nitrogen plus ammonia) indicate concentrations only slightly 

higher than values for ammonia alone. This indicates that 

concentrations of organic nitrogen generally were low (mostly 

less than 2 mg/L) in treatment-plant effluent throughout the 

study period. 

During the first decade of the study period (1975–84), 

average dissolved orthophosphate concentrations ranged 

from 7 mg/L in samples collected from the SAR at E Street to 

14 mg/L in IEUA Plant 2. Dissolved orthophosphate was the 

dominant species of phosphorus in wastewater treatment-plant 

effluent of the Santa Ana Basin throughout the study period.

During the second decade of the study period (1985–94), 

wastewater treatment plants in the Santa Ana Basin began to 

upgrade treatment technologies to include nitrification of the 

effluent (Bachand and Horne, 1993). As a result, ammonia 

concentrations decreased, and nitrate concentrations were 

higher than in the first decade of the study period (fig. 14). 

Total inorganic nitrogen concentrations mostly remained 

about the same as for the previous decade and consisted of 

approximately equal proportions of nitrate and ammonia. 

Insufficient data were available on phosphorus concentrations 

in plant effluent during the second decade of the study period 

to determine whether these had changed since the first decade 

of the study period.
48 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 12abc

WATER YEAR

100

150

200

250

300

350

400

450

500

100

0

0

50

200

300

400

500

600

700

800

900

1,000

1,000

1,500

500

0

2,000

2,500

3,000

LOAD, IN TONS PER YEAR, 

AS NITROGEN OR PHOSPHORUS

LOAD, IN TONS PER YEAR, 

AS NITROGEN OR PHOSPHORUS

LOAD, IN TONS PER YEAR, 

AS NITROGEN OR PHOSPHORUS

TN load

TP load

1975197619771978197919801981198219831984198519861987198819891990199119921993199419951996199719981999

19851986198719881989199019911992199319941995199619971998199920002001200220032004

19851986198719881989199019911992199319941995199619971998199920002001200220032004

20002001200220032004

A

B

C

Figure 12. Total nitrogen and total phosphorus loads from point sources to (A) 

Sacramento River, 1985–2004, (B) San Joaquin River, 1985–2004, and (C) Santa Ana 

River, 1975–2004.
Results 49

IP-002261_fig 13abc

1975

Wastewater Discharged

(61,650 acre-feet)

100

0

200

300

400

500

600

FLOW, IN ACRE-FEET (X 1,000)

FLOW, IN ACRE-FEET (X 1,000)

1980

(75,740 acre-feet)

1985

(94,610 acre-feet)

0

100

200

300

400

500

600

FLOW, IN ACRE-FEET (X 1,000)

1990

(123,260 acre-feet)

100

0

200

300

400

500

600

FLOW, IN ACRE-FEET (X 1,000)

1995

(133,670 acre-feet)

0

100

200

300

400

500

600

FLOW, IN ACRE-FEET (X 1,000)

2000

(160,625 acre-feet)

100

0

200

300

400

500

600

FLOW, IN ACRE-FEET (X 1,000)

100

0

200

300

400

500

600

A B

C D

E F

IEUA Carbon Cyn

Western Riverside

Non-wastewater

Wastewater

Riverside

Corona (combined)

IEUA 1

IEUA 2

San Bernardino

Colton

RIX

Rialto

EXPLANATION

Wastewater Discharged

plus non-wastewater discharges

Wastewater Discharged

plus non-wastewater discharges

Figure 13. Contributions from wastewater treatment plants and non-wastewater discharges to flow in the Santa Ana 

River, 1975–2000.
50 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 14ab

A.

B.

0

5

10

15

20

25

30

35

40

1971 1974 1977 1980 1983 1986

CALENDAR YEAR

1989 1992 1995 1998 2001

AMMONIUM, MILLIGRAMS PER LITER AS NITROGEN

San Bernardino

Riverside

Corona 1A

Corona 2

IEUA 1

IEUA 2

0

5

10

15

20

25

30

NITRATE, MILLIGRAMS PER LITER AS NITROGEN

Figure 14. (A) Ammonium and (B) nitrate in the effluent of selected wastewater treatment plants of the Santa Ana 

Basin, October 1971–September 2003.
Results 51

IP-002261_fig 15

5

10

0

15

20

25

1993 1995 1998 2000 2003

TOTAL INORGANIC NITROGEN,

IN MILLIGRAMS PER LITER AS NITROGEN

In the early to mid-1990s, total inorganic nitrogen 

began to decrease in the effluent of most Santa Ana Basin 

wastewater treatment plants, as nitrate concentrations 

generally decreased and ammonia concentrations became 

negligible in the effluents. At the beginning of the 1990s, 

nitrate concentrations in the effluent were still often greater 

than 10 mg/L as N (the USEPA maximum contaminant level 

for nitrate as nitrogen). By 2000, nitrate concentrations in 

the effluents rarely exceeded 10 mg/L as N. This decrease is 

evident in the trend of total inorganic nitrogen concentrations 

in the Rialto (the most upstream outfall on the SAR) 

treatment-plant effluent (fig. 15). Improvements in wastewater 

treatment technology also may have resulted in decreased 

phosphorus concentrations in treatment-plant effluent toward 

the end of the study period. During the last few years of the 

study period, concentrations of dissolved orthophosphate (the 

dominant phosphorus species) mostly were less than 2 mg/L 

in the effluent from three treatment plants (RIX, IEUA Carbon 

Canyon, and Western Riverside), the only plants for which 

such data were available. Such concentrations represent a 

substantial decrease from orthophosphate concentrations 

observed during the first decade of the study period 

(7–14 mg/L).

Using the above information, the best estimates of 

TN and TP loads to the SAR for 1975–2004 are presented 

in figure 12C. Mean annual discharges from the 10 most 

significant point sources in the Santa Ana Basin together 

accounted for 86 ft3/s in 1975 and 239 ft3/s in 2004. Annual 

TN loads from these point sources ranged from 1,791 tons/yr 

in 1975 to 2,727 tons/yr in 1986, with 2,050 tons/yr in 2004. 

Thus, TN loads to the SAR increased by about 14 percent 

during 1975–2004. TN loads to the SAR decreased by about 

25 percent from 1985 to 2004 (fig. 12C). Annual TP loads 

from point sources ranged from 

842 tons/yr in 1975 to 289 tons/yr 

in 1996, with 339 tons/yr in 2004. 

Thus, TP loads to the SAR decreased 

by about 60 percent during 1975–

2004. This decrease in TP loads 

occurred prior to 1985 as the 1985 

and 2004 loads were about the same 

(fig. 12C).

Nonpoint Sources

As a result of data availability, 

the time periods of data for 

nonpoint sources varies. Estimates 

of atmospheric deposition and 

tile drainage are presented for 

1985–2004, fertilizer application for 

1987–2004, and manure production 

for 1982–2002.

Figure 15. Total inorganic nitrogen concentrations in 

effluent from the Rialto wastewater treatment plant, 

1993–2003.

2,000

0

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

20,000

NITROGEN LOAD, IN TONS PER YEAR AS NITROGEN

Sacramento Basin

San Joaquin Basin

Santa Ana Basin

CALENDAR YEAR

19851986198719881989199019911992199319941995199619971998199920002001200220032004

Figure 16. Estimated total nitrogen loads from atmospheric deposition in the 

Sacramento (valley only), San Joaquin (valley only), and Santa Ana (basin only) 

Basins, California, 1985–2004.

Sacramento Basin

The estimated total atmospheric deposition of TN in the 

valley portion of the Sacramento Basin was about 3.38 times 

the wet deposition at the Davis NADP site (table 5). Using 

this factor, the estimated rate of TN deposition in the valley 

portion of the Sacramento Basin for 1985–2004 ranged from 

1.18 (tons/mi2)/yr in 1987 to 3.55 (tons/mi2)/yr in 1998. 

When this rate of TN deposition was applied to the valley 

area (5,115 mi2), the total deposition estimates ranged from 

6,100 to 18,200 tons/yr (fig. 16). The estimated ratio of dry to 

wet deposition in the valley portion of the Sacramento Basin 

was about 1.7. No trend was apparent in the atmospheric 

deposition of TN in the Sacramento Valley, other than that 

caused by variation in precipitation (figs. 3 and 4).
52 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Fertilizer application of nitrogen in the Sacramento 

Basin ranged from 55,000 tons/yr in 1992 to 95,200 tons/ yr in 

2004, with 64,900 tons/yr in 1987 (fig. 17A). Thus, fertilizer 

application of nitrogen increased by about 47 percent during 

1987–2004. The fertilizer application of phosphorus in 

the Sacramento Basin ranged from 6,900 tons/yr in 1992 

to 15,100 tons/yr in 2002, with 8,300 tons/yr in 1987 and 

13,900 tons/yr in 2004 (fig. 17B). Thus, fertilizer application 

of phosphorus increased by about 67 percent during 

1987–2004.

The nitrogen content in manure production in the 

Sacramento Basin decreased steadily from 1982 (28,500 

tons/yr) to 2002 (21,000 tons/yr) (fig. 18A). Likewise, the 

phosphorus content in manure production in the Sacramento 

Basin decreased steadily from 1982 (7,900 tons/yr) to 2002 

(5,700 tons/yr) (fig. 18B). Thus, nitrogen and phosphorus 

contents of manure production in the Sacramento Basin 

decreased by 26 and 28 percent, respectively, during 

1982–2002.

San Joaquin Basin

Because the same NADP site was used to represent the 

valley portions of the Sacramento and San Joaquin Basins, 

the estimated total atmospheric deposition of TN in the 

valley portion of the San Joaquin Basin was considered to 

be the same as for the Sacramento Basin—about 3.38 times 

the wet deposition at the Davis NADP site (table 5). Using 

this factor, the estimated rate of TN deposition in the valley 

portion of the San Joaquin Basin for 1985–2004 ranged from 

1.18 (tons/ mi2)/ yr in 1987 to 3.55 (tons/mi2)/yr in 1998. 

When this rate of TN deposition was applied to the valley 

(2,263 mi2), the total deposition estimates ranged from 2,700 

to 8,100 tons/yr (fig. 16). The estimated ratio of dry to wet 

deposition in the valley portion of the San Joaquin Basin 

was considerably higher than in the Sacramento Basin; 2.8 

compared to 1.7. Because the same rate of TN deposition was 

used for the valley portion of the San Joaquin Basin as for the 

valley portion of the Sacramento Basin, the annual variations 

were the same (fig. 16).

Fertilizer application of nitrogen in the San Joaquin 

Basin ranged from 41,400 tons/yr in 1992 to 84,900 tons/

yr in 2004, with 48,400 tons/yr in 1987 (fig. 17A). Thus, 

fertilizer application of nitrogen increased by about 75 percent 

during 1987–2004. The fertilizer application of phosphorus 

in the San Joaquin Basin ranged from 5,200 tons/yr in 1992 

to 13,600 tons/yr in 2002, with 6,200 tons/yr in 1987 and 

12,400 tons/yr in 2004 (fig. 17B). Thus, fertilizer application 

of phosphorus increased by about 100 percent (doubled) 

during 1987–2004. The annual variations in fertilizer 

applications in the San Joaquin and Sacramento Basins were 

essentially the same for 1987–2004.

The nitrogen contents in manure production in the San 

Joaquin Basin increased steadily from 1982 (38,600 tons/ yr) 

to 2002 (57,500 tons/yr) (fig. 18A). Likewise, the phosphorus 

contents in manure production in the San Joaquin Basin 

increased steadily from 1982 (9,300 tons/yr) to 2002 

(13,000 tons/yr) (fig. 18B). Thus, nitrogen and phosphorus 

contents of manure production in the San Joaquin Basin 

increased by 49 and 40 percent, respectively, during 1982–

2002. The steady increase in manure production in the San 

Joaquin Basin is the opposite trend from the Sacramento 

Basin. This is a reflection of the increase in dairy production in 

the San Joaquin Basin.

The 68,500 acres of tile-drained agricultural land in the 

San Joaquin Basin contribute about 1,490 tons/yr of nitrogen 

to the SJR, based on a TN concentration of 25 mg/L as N 

for the drainage from the Grasslands Bypass Project (see 

Grasslands Drainage Project Area, fig. 1B) to Mud Slough and 

10 mg/L as N for tile drainage downstream of the Grasslands 

area (Kratzer and Shelton, 1998). The overall TP load from 

the tile drains is less than 10 tons/yr. These loads have not 

changed appreciably from 1985 to 2004, as the discharge of 

tile drainage from the Grasslands area reached its current level 

in 1991 and the concentration of nitrate in the tile drainage 

has not increased appreciably since 1985 (see Panoche Drain 

nitrate data in table CD-2b on the Data CD).

Santa Ana Basin

The estimated total atmospheric deposition of TN in the 

basin portion of the Santa Ana Basin was about 15.97 times 

the wet deposition at the Tanbark Flat NADP site (table 5). 

Using this factor, the estimated rate of TN deposition in the 

basin portion of the Santa Ana Basin for 1985–2004 ranged 

from 3.69 (tons/mi2)/yr in 2002 to 19.21 (tons/mi2)/yr in 1998. 

When this rate of TN deposition was applied to the basin 

area (902 mi2), the total deposition estimates ranged from 

3,300 to 17,400 tons/yr (fig. 16). The estimated ratio of dry 

to wet deposition in the basin portion of the Santa Ana Basin 

was about 9.8. No trend was apparent in the atmospheric 

deposition of TN in the basin portion of the Santa Ana Basin, 

other than the increased deposition during especially high 

precipitation years such as 1998 (fig. 3C). However, the use 

of dry-deposition data for the CADMP site at Azusa (fig. 11) 

from the early 1990s likely overestimated the actual dry 

deposition later in the study period, as air quality had steadily 

improved in the Santa Ana Basin during the study period 

with regards to oxides of nitrogen in gas and particulate 

phases (fig. 19; California Air Resources Board, 2005). The 

air samples for data in figure 19 were collected by ARB in 

Riverside by using high volume samplers. Concentrations of 

nitrate on total suspended-particulate (TSP in fig. 19) matter 

typically were greater than 25 μg/m3 in the basin in the late 

1970s. By the year 2000, concentrations typically were closer 

to 15 μg/m3 (fig. 19). Nitrogen oxide concentrations in air 

samples collected at this site indicated a peak of nearly 0.1 

parts per million in 1977, and showed a fairly consistent 

decline to 0.04 parts per million in 2004. Nevertheless, the 

rate of atmospheric deposition in the Santa Ana Basin greatly 

exceeded that in the Sacramento and San Joaquin Basins, and 

the overall amount of TN deposition usually exceeded that in 
Results 53

the San Joaquin Basin (2.5 times more area) and sometimes 

exceeded that in the Sacramento Basin (5.7 times more area) 

(fig. 19).

Fertilizer application of nitrogen in the Santa Ana 

Basin ranged from 2,900 tons/yr in 1990 to 6,100 tons/yr in 

2004, with 3,300 tons/yr in 1987 (fig. 17A). Thus, fertilizer 

application of nitrogen increased by about 85 percent during 

1987–2004. The fertilizer application of phosphorus in 

the Santa Ana Basin ranged from 380 tons/yr in 1992 to 

840 tons/ yr in 2004, with 440 tons/yr in 1987 (fig. 17B). 

Thus, fertilizer application of phosphorus increased by about 

91 percent during 1987–2004. On a mass basis, fertilizer 

application in the Santa Ana Basin is less than 10 percent of 

the application in the Sacramento or San Joaquin Basins.

The nitrogen content in manure production in the 

Santa Ana Basin ranged from 7,500 tons/yr in 2002 to 

12,100 tons/ yr in 1997, with 11,300 tons/yr in 1982 (fig. 

18A). Thus, nitrogen content in manure production in the 

Santa Ana Basin decreased by about 34 percent during 

1982–2002. Phosphorus content in manure production in the 

Santa Ana Basin ranged from 1,530 tons/yr in 2002 to 2,500 

tons/yr in 1997, with 2,400 tons/yr in 1982 (fig. 18B). Thus, 

phosphorus content in manure production in the Santa Ana 

Basin decreased by about 36 percent during 1987–2002. The IP-002261_fig 17ab

CALENDAR YEAR

1987

1988

1989

1990

1991

1992

1993

1994

1995

1996

1997

1998

1999

2000

2001200220032004

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

80,000

90,000

100,000

NITROGEN APPLIED, IN TONS PER YEAR AS NITROGEN

2,000

0

4,000

6,000

8,000

10,000

12,000

14,000

16,000

PHOSPHORUS APPLIED, IN TONS PER YEAR AS PHOSPHORUS

B

A Sacramento Basin

San Joaquin Basin

Santa Ana Basin

Figure 17. Fertilizer application in Sacramento, San Joaquin, and Santa Ana Basins, 

California, for (A) nitrogen, and (B) phosphorus, 1987–2004.
54 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

decrease in manure production in the Santa Ana Basin from 

1997 to 2002 was due largely to the movement of dairy cows 

out of the basin. During the study period, the Chino dairy 

area was the densest dairy production area in the United 

States; at one time with about 360,000 animals concentrated 

in about 15,000 acres. Dairy acreage in the Chino Dairy 

Preserve represented only about 2 percent of the Santa Ana 

Basin during the study period, and is currently in decline as 

residential housing expands in the area (Kenneth Manning, 

Chino Basin Watermaster, oral commun., February 6, 2006). 

Nevertheless, evidence indicates that dairies have been 

responsible for much of the nitrate (and presumably other 

IP-002261_fig 18ab

CALENDAR YEAR

10,000

0

20,000

30,000

40,000

50,000

60,000

70,000

NITROGEN PRODUCED, IN TONSPER YEAR AS NITROGEN

2,000

0

4,000

6,000

8,000

10,000

12,000

14,000

1982 1987 1992 1997 2002

PHOSPHORUS PRODUCED, IN TONS PER YEAR AS PHOSPHORUS

B

A

Sacramento Basin

San Joaquin Basin

Santa Ana Basin

Figure 18. Manure production in Sacramento, San Joaquin, and Santa Ana Basins, 

California, for (A) nitrogen, and (B) phosphorus, 1982–2002.

nutrients) entering the SAR. Nutrients from dairies have 

been known to enter the river when holding ponds containing 

manure-laden dairy wastewater occasionally spill into SAR 

tributaries (Vitko, 2005). An indirect, but probably more 

significant way that nutrients from dairies enter the SAR has 

resulted from long-term land applications of dairy manure and 

washwater in the area of the Chino Dairy Preserve. Although 

such land applications have been limited since the early 1970s, 

they have contributed salts and nutrients to the underlying 

groundwater, which discharges to the SAR upstream of Prado 

Dam (California Regional Water Quality Control Board, Santa 

Ana Region, 1990).
Results 55

Figure 19. Oxides of nitrogen in air samples collected from the Riverside-Rubidoux air sampling 

site, California, during the study period.

IP-002261_fig 19

0

5

10

15

20

25

30

1970 1975 1980 1985 1990 1995 2000 2005

PARTICULATE NITRATES, IN MICROGRAMS PER CUBIC METER

.0

.02

.04

.06

.08

.10

.12

OXIDES OF NITROGEN, IN PARTS PER MILLION

0

5

10

CALENDAR YEAR

PM10 Nitrates 

TSP Nitrates

N Oxides

 Other nonpoint sources of baseflow to the SAR include 

local runoff, supplemental releases of imported water (Burton 

and others, 1998), and rising groundwater levels. Most nonwastewater discharges to the SAR typically have nutrient 

concentrations less than those found in treated wastewater 

(Kent and Belitz, 2004). However, rising groundwater 

levels in gaining reaches of the SAR, such as around the 

Chino area, has had nitrate concentrations higher than those 

measured in treated wastewater (Wildermuth Environmental, 

Inc., 1999). These groundwater inputs vary daily (Troxel, 

1936) and seasonally (Wildermuth Environmental, Inc., 

2002), with inputs as much as 80 ft3/s in the winter and as 

low as 1 ft3/s in the summer. Although rising groundwater 

levels account for only 5–10 percent of SAR baseflow, it 

may contribute 30–40 percent of the nitrate in the river as it 

enters the Prado Wetlands (fig. 1C; California Regional Water 

Quality Control Board, Santa Ana Region, 1990). The long 

agricultural legacy of the Santa Ana Basin, including citrus, 

vineyards, and dairies, is the most likely explanation for the 

elevated nitrate concentrations found in rising groundwater 

(California Regional Water Quality Control Board, Santa 

Ana Region, 1995). Evidence of the agricultural source of 

nitrate was provided by the isotopic composition of N from 

nitrate samples collected from six wells in the Chino area 

(Wildermuth Environmental Inc., 1999). The nitrogen isotope 

signal in these samples indicated that the sources of nitrate 

in groundwater were predominantly nitrate fertilizer and 

animal waste. An additional contributing factor to the elevated 

nutrient concentrations found in Santa Ana Basin groundwater 

is that septic systems are still used in areas of the basin 

(California Regional Water Quality Control Board, Santa Ana 

Region, 2004).

Estimated Stream Nutrient Loads, 1975–2004

The monthly loads presented in this section for mainstem 

sites in the Sacramento, San Joaquin, and Santa Ana Basins 

include the monthly SEP and the timing of data collection 

(on a monthly basis). The standard criteria used for the loads 

shown in figures in this section was that there be acceptable 

LOADEST-estimated loads for at least one-half of the 

years from 1975 to 2004 and also from 1993 to 2004. All 

mainstem sites with loads shown met this standard criteria. 

Two mainstem sites (at Vina and at Colusa) in the Sacramento 

Basin are not shown although they met this criteria for 

certain constituents. These sites were not shown because they 

are near other mainstem sites that are shown (at Hamilton 

City and upstream of CBD). In addition, the SAR at MWD 

site met the standard criteria for nitrate, total nitrogen, and 

orthophosphate, but only is shown by difference (MWD to 

Prado) for nitrate. The main tributary between the MWD site 

and the downstream of Prado Dam site, Cucamonga Creek, 

did not meet the standard criteria for TN or orthophosphate 

loads. For good load calculations, the loads generally reflect 

the variations in runoff and major influences between 

mainstem sites (tributaries and diversions). In some cases, 

high SEP values, especially during high-flow periods, can 

give misleading information. A summary of load calculations 

(including SEPs and 95-percent confidence intervals) from 
56 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

the LOADEST program for sites with enough data to estimate 

loads with LOADEST is presented in table CD-3 of the Data 

CD. The sites presented on the Data CD needed only one 

acceptable year of LOADEST-estimated loads. Thus, there are 

many loads presented on the Data CD with SEP greater than 

50 percent.

Although LOADEST provides daily load estimates, they 

are not discussed in this report as they can have considerable 

error (see section, “Analysis Techniques”). The LOADEST 

results are better expressed as monthly or annual averages. 

Although LOADEST generally does a good job of estimating 

loads under the predominant flow conditions, estimated 

loads for extreme flow conditions had large errors (fig. 20). 

This is illustrated in figure 20 for the SJR near Vernalis, by 

plotting the LOADEST daily estimated nitrate loads and the 

instantaneous measured nitrate loads.

Sacramento Basin

Loads for sites on the mainstem of the Sacramento River 

are plotted from upstream to downstream for 1975–2004 

(figs. 21–25). Sites with at least 7 years of acceptable loads are 

plotted along with the SEP and the period of data collection 

for the appropriate constituent. These plots are available for 

other Sacramento Basin sites in table CD-3a on the Data 

CD. Three major features of the Sacramento Basin are useful 

for explaining variations in loads in the mainstem from the 

Sacramento River at Delta site (above Shasta Reservoir) to 

the Sacramento River at Freeport site: Shasta Dam, water 

diversions, and wastewater treatment in the Sacramento 

metropolitan area. The 4.5-million acre-ft Shasta Lake impacts 

the transport and timing of nutrient loads in the mainstem of 

the Sacramento River from Delta to Keswick. Agricultural 

diversions [especially Tehama-Colusa and Corning Canals 

and Glenn-Colusa Canal (fig. 5)] tend to impact the transport 

of nutrient loads from Bend Bridge to Hamilton City in the 

spring and summer months. Flood-control diversions into 

the Sutter Bypass and the Yolo Bypass (fig. 5) can affect the 

transport of nutrient loads in the mainstem from Hamilton 

City to Verona during winter and spring months. Starting in 

December 1982, about 110 ft3/s of wastewater effluent was 

diverted from the Sacramento Basin to a discharge point just 

downstream of the Freeport gaging station. 

Nitrate loads in the Sacramento River generally followed 

the seasonal pattern of flows, with maximums occurring 

in the winter/spring and minimums in the late summer/fall 

(fig. 21). This pattern was altered (loads were highest in the 

summer/fall) for the Sacramento River at Keswick site, as 

most of the flow at this site was the result of releases from 

the 4.5-million acre-ft Shasta Lake. The variations in annual 

nitrate loads in the Sacramento River generally followed the 

variations in annual runoff. From upstream to downstream, 

nitrate loads in the Sacramento River increased an average 

of about 120 tons/ mo from Delta to Red Bluff due to inputs 

from tributaries. From Red Bluff to upstream of CBD, the 

increases were smaller (about 30 tons/mo on average) as 

major diversions offset some of the inputs from tributaries 

(see fig. 5). Nitrate loads in the Sacramento River continued to 

increase from upstream of CBD to Verona (about 80 tons/ mo 

on average), although the increase was much less than would 

be expected because of the diversion of high flows into the 

Yolo Bypass at Fremont Weir in wet years. From Verona 

to Freeport, the average nitrate load in the Sacramento 

River increased by about 60 tons/mo due to inputs from the 

American River and the Sacramento metropolitan area.

The only two sites in the Sacramento Basin with enough 

data to calculate ammonia loads for 1975–2004 were the 

Verona and Freeport sites (fig. 22). Both sites had significant 

gaps in data collection that resulted in some SEPs exceeding 

the 50 percent criteria for usable loads. Like nitrate loads in 

the Sacramento River, the ammonia loads generally followed 

the seasonal pattern of flows, with maximums occurring in the 

winter/spring and minimums in the late summer/fall. Prior to 

1985, the ammonia loads in the Sacramento River increased 

greatly from Verona moving downstream to Freeport. Most of 

this increase was due to wastewater inputs in the Sacramento 

metropolitan area. Since 1985, most of this input was 

removed, as wastewater in the Sacramento metropolitan area 

was consolidated to a discharge location downstream of the 

Freeport site.

The TN loads in the Sacramento River at Keswick had 

a seasonal pattern representative of reservoir releases from 

Shasta Dam, with maximum loads occurring in the summer 

when releases were greatest for downstream agricultural uses 

and salinity control (fig. 23). Exceptions occurred during 

especially wet years when large reservoir releases were 

required for flood control in winter/spring. Tributary inputs 

between Keswick and Red Bluff displayed a more natural 

pattern of seasonal flows, with maximum flows in winter/

spring and minimum flows in summer/fall. The superimposed 

loads from these two flow regimes created a less variable 

IP-002261_fig 20

WATER YEAR

0.1

1.0

10.0

100.0

1975 1979 1983 1987 1991 1995 1999 2004

NITRATE LOAD, IN TONS PER DAY

LO A D E S T daily load estim ate, ton/d

M easured instantaneous load, ton/d

Figure 20. Estimated daily loads (from LOADEST) 

and measured instantaneous loads of nitrate for San 

Joaquin River near Vernalis, 1975–2004.
Results 57

IP_002261_fig 21abcdefg

0

0

10

20

30

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50

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1974197619781980198219841986198819901992199419961998200020022004

800

1,200

2,000

1,600

200

400

600

800

1,000

0

STANDARD ERROR OF PREDICTION, IN PERCENT

STANDARD ERROR OF PREDICTION, IN PERCENT

WATER YEAR

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

0

200

400

600

800

1,000

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2,000

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1,000

NITRATE LOADS, IN TONS PER MONTH

NITRATE LOADS, IN TONS PER MONTH

0

10

20

30

40

50

A B

C D

E

G

F

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

SEP = 50% 

 (Standard Error of Prediction)

Figure 21. Nitrate loads for mainstem sites in the Sacramento Basin: Sacramento River (A) at Delta, (B) at Keswick, (C) 

near Red Bluff, (D) near Hamilton City, (E) upstream of Colusa Basin Drain, (F) at Verona, and (G) at Freeport, 1975–2004, with 

standard error of prediction and timing of data collection.
58 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

load that varied less among seasons at Red Bluff, except for 

some exceptional periods of summer releases or winter-storm 

flows. The annual variation in TN loads in the Sacramento 

River followed the general pattern of wet and dry years 

(figs. 3 and 4). The particulate fraction of TN was important 

especially during high flows when more suspended sediment 

was transported. Thus, the TN loads in the Sacramento River 

at the Hamilton City and Freeport sites were especially high 

during winter storms due to their unregulated tributary inputs. 

As storm flows moved downstream, their magnitudes at Verona 

were reduced greatly by the diversion of high flows from the 

Sacramento River into the Sutter Bypass and the Yolo Bypass 

(fig. 5). Of all the stream reaches considered, the largest inputs 

of TN occurred between the Red Bluff and Hamilton City sites 

(average input of about 230 tons/mo) and between Verona and 

Freeport (average input of about 350 tons/mo).

Seasonal patterns for orthophosphate loads in the 

Sacramento River were similar to nitrate loads, with a natural 

pattern (unregulated) associated with runoff at the Delta site 

(fig. 24A), a pattern affected by releases from Shasta Dam 

dominating at the Keswick site (fig. 24B), and a mixture of 

these two patterns creating a less variable load pattern at 

Red Bluff (fig. 24C). Downstream of Red Bluff, the seasonal 

pattern was more reflective of the natural runoff pattern, with 

maximums in the winter/spring and minimums in the summer/

fall (figs. 24D–24G). Annual variations in orthophosphate 

loads in the Sacramento River generally followed the 

variations in annual flow, except for the Freeport site (fig. 24G).

At Freeport, as for ammonia, there was an overall decrease 

in loads after 1985 associated with the movement of treated 

wastewater out of the American and Sacramento Rivers in the 

Sacramento metropolitan area to a site downstream of Freeport. 

The largest increase in orthophosphate loads in the Sacramento 

River from upstream to downstream occurred downstream of 

CBD. From Delta to Keswick, the average load increased by 

11 tons/mo, from Keswick to upstream of CBD by 7 tons/mo, 

with an increase of 17 tons/mo from CBD to Verona and 32 

tons/mo from Verona to Freeport. Thus, close to one-half of the 

orthophosphate load at Freeport (average of 68 tons/mo) was 

contributed by the Sacramento metropolitan area.

The seasonal pattern of TP loads was similar to the TN 

loads, as they were both strongly influenced by high flows. The 

seasonal TP loads in the Sacramento River at Delta reflected 

the natural runoff pattern with maximums in winter/spring 

and minimums in summer/fall (fig. 25). The greatest monthly 

loads of TP in the Sacramento River (as much as 2,025 tons/

mo) occurred during high winter/spring flows at Hamilton 

City. Much of this TP load was contributed by storm inputs 

from tributaries, such as Cottonwood Creek, Mill Creek, and 

Deer Creek (figs. 1 and 7A). From upstream to downstream, 

the average load increased by about 19 tons/mo from Delta 

to Keswick, 72 tons/mo from Keswick to Hamilton City, 

35 tons/mo from Hamilton City to Verona, and 39 tons/mo 

from Verona to Freeport. Thus, unlike orthophosphate, the 

major input of TP was due to upstream tributary inputs rather 

than the Sacramento metropolitan area. This increase would 

IP_002261_fig 22abc

50

0

0

100

50

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50

0

100

40

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1974197619781980198219841986198819901992199419961998200020022004

STANDARD ERROR OF PREDICTION, IN PERCENT

WATER YEAR

AMMONIA LOADS, IN TONS PER MONTH

A

B

C Monthly Loads

Data Collection, by month

Std Error of Prediction, %

SEP = 50% 

 (Standard Error of Prediction)

Figure 22. Ammonia loads for mainstem sites 

in the Sacramento Basin: Sacramento River (A) 

at Keswick, (B) at Verona, and (C) at Freeport, 

1975–2004, with standard error of prediction and 

timing of data collection.
Results 59

IP_002261_fig 23abcde

STANDARD ERROR OF PREDICTION, IN PERCENT

STANDARD ERROR OF PREDICTION, IN PERCENT

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

TOTAL NITROGEN LOADS, IN TONS PER MONTH

TOTAL NITROGEN LOADS, IN TONS PER MONTH

0

10

20

30

40

50

0

10

20

30

40

50

2,500

2,000

1,500

1,000

500

0

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0

2,000

3,000

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0 0

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Figure 23. Total nitrogen loads for mainstem sites in the Sacramento Basin: Sacramento River (A) at Keswick, (B) near Red 

Bluff, (C) near Hamilton City, (D) at Verona, and (E) at Freeport, 1975–2004, with standard error of prediction and timing of data 

collection.
60 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP_002261_fig 24abcdefg

STANDARD ERROR OF PREDICTION, IN PERCENT

STANDARD ERROR OF PREDICTION, IN PERCENT

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

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ORTHOPHOSPHATE LOADS, IN TONS PER MONTHORTHOPHOSPHATE LOADS, IN TONS PER MONTH

0

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C D

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A B

Figure 24. Orthophosphate loads for mainstem sites in the Sacramento Basin: Sacramento River (A) at Delta, (B) at 

Keswick, (C) near Red Bluff, (D) near Hamilton City, (E) upstream of Colusa Basin Drain, (F) at Verona, and (G) at Freeport, 

1975–2004, with standard error of prediction and timing of data collection.
Results 61

have been even greater from Hamilton City to Verona if the 

upstream flood-control diversions had not been present. These 

diversions affected the transport of TN and TP loads more than 

the dissolved constituents because of the greater proportion of 

these constituents associated with sediment transport during 

high flows. As with orthophosphate, the TP loads at Freeport 

decreased since 1985 (fig. 25G).

For the quantitative analysis of loads (and yields) as a 

function of nutrient sources and subbasin characteristics, the 

unmodeled load sources and(or) sinks between mainstem 

sites also are of interest. Mathematically, these unmodeled 

load sources and(or) sinks are simply the leftover loads from 

a mass balance between mainstem sites (using LOADESTestimated loads). The unmodeled load sources and(or) sinks 

can be positive (source) or negative (sink). They represent 

the cumulative errors in load estimates, as well as sources 

and(or) sinks without LOADEST-load estimates. The best 

example of these unmodeled load sources and(or) sinks in 

the Sacramento Basin is the reach of Sacramento River from 

Verona to Freeport (fig. 26). The unmodeled load sources 

and(or) sinks in this case was the load at Freeport minus the 

combined load for Verona and the American River, plus the 

load diverted from the Sacramento River from Verona to 

Freeport. This diverted load ranges from 0 to 10 percent of 

river load, depending on month and year, except for 35 percent 

in February 1986 and 23 percent in January 1997 due to 

especially large releases from the Sacramento Weir to the Yolo 

Bypass (table CD-1a on the Data CD). 

For TN, there was an average of about 204 tons/

mo of unmodeled load source in this reach of Sacramento 

River (fig. 26A). This unmodeled load source ranged from 

about 100 to 200 tons/mo during the summer (only about 

50–100 tons/ mo since 2000) to about 200–1,000 tons/mo 

during winter/spring high flows (only about 100–300 tons/ mo 

since 2000). In January 1997, the unmodeled load source was 

greater than 1,800 tons. The other high-flow year (1986) with 

large diversions from the Sacramento Weir was not included 

in figure 26A due to high SEPs in LOADEST-load estimates. 

For TP, the unmodeled load sources and(or) sinks in this reach 

of the Sacramento River averaged only about 1 ton/ mo (fig. 

26B). This unmodeled load ranged from a source of about 

0 to 30 tons/mo in the fall and winter months to a sink of 

about 40 to 0 tons/mo in the spring months and a source of 

about 0 to 10 tons/mo in the summer months. This implies 

additional small inputs of TP in this reach during fall, winter, 

and summer months, and additional losses of TP in this reach 

during the spring. These losses might be a function of settling 

out of particulates in this reach of river, as diversions in this 

reach were accounted for in this analysis. The two high‐flow 

years (1986 and 1997) with large diversions to the Yolo 

Bypass were not included in this analysis due to high SEPs in 

LOADEST-load estimates.

Point sources of TN and TP (fig. 12A) were compared 

to LOADEST-estimated loads for the Sacramento River at 

Freeport (figs. 23E and 25G) by adjusting the point-source 

loads using loading factors (table CD-1a on the Data CD) to 

account for downstream diversions. Point sources accounted 

for about 4 percent of TN and 7 percent of TP loads in the 

Sacramento River at Freeport for 1985–2004. For TN, this 

contribution was fairly constant over the 20 years, but the 

TP contribution decreased from 10 percent during the first 

10 years (1985–94) to only 4 percent during the second 

10 years (1995–2004). For TN, the increase in point-source 

loads (fig. 12A) was offset by the higher flows during the later 

10 years (figs. 3 and 4). For TP, the decreased contribution 

from point sources between 1985–94 and 1995–2004 was 

attributable to a combination of the reduced point-source loads 

and the high flows.

San Joaquin Basin

Loads for the mainstem of the SJR are plotted from 

upstream to downstream for sites with many years of 

acceptable loads during 1975–2004, along with the SEP and 

the period of data collection (figs. 27–31). These plots are 

available for other San Joaquin Basin sites in table CD-3b on 

the Data CD. As generally was true for the Sacramento Basin 

(other than sites just downstream of Shasta Dam), the seasonal 

pattern for all five constituents was cyclical with maximums in 

winter/spring during high flow and minimums in summer/fall 

during low flow. For the extreme drought of 1977, the loads 

of all constituents decreased to near zero at all sites in the San 

Joaquin Basin during the summer/fall. Variations in annual 

loads generally followed the variations in annual flows (figs. 3

and 4). 

Nitrate loads in the SJR near Patterson include nitrate 

loads contributed by the upstream SJR near Stevinson plus 

Salt Slough, Mud Slough, Merced River, Turlock Wastewater 

Treatment Plant (WWTP), Orestimba Creek, and other inputs. 

SEPs were high for many of the nitrate LOADEST-load 

estimates for the SJR near Stevinson and, therefore, are not 

presented. The average load in the SJR near Patterson was 

175 tons/mo, and moving downstream, this increased by an 

average of 94 tons/mo between Patterson and Maze Road, 

and then by another 21 tons/mo from Maze Road to Vernalis. 

The increase from Patterson to Maze Road was the result of 

inputs from the Modesto WWTP and the Tuolumne River plus 

many smaller agricultural discharges, offset by the two largest 

diversions from the SJR plus several smaller diversions. The 

increase from Maze Road to Vernalis was due primarily to 

inputs from the Stanislaus River. 

As for nitrate, SEPs were high for many of the ammonia 

LOADEST-load estimates for the SJR near Stevinson, and, 

therefore, are not presented. Prior to 1984, SEPs were greater 

than 50 percent for most LOADEST-load estimates for the 

SJR near Patterson (fig. 28A). The average ammonia load for 

the SJR near Patterson was 24 tons/mo (for water years with 

SEPs less than 50 percent). Most of this load probably came 

from the Turlock WWTP (figs. 10 and 12B). Prior to 1981, 

SEPs were greater than 50 percent for most LOADEST-load 
62 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP_002261_fig 25abcdefg

STANDARD ERROR OF PREDICTION, IN PERCENT

STANDARD ERROR OF PREDICTION, IN PERCENT

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

100 200

160

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800

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800

1,000

20

40

60

80

100

TOTAL PHOSPHORUS, IN TONS PER MONTH

TOTAL PHOSPHORUS, IN TONS PER MONTH

A B

C D

E

G

F

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

SEP = 50% 

 (Standard Error of Prediction)

Figure 25. Total phosphorus loads for mainstem sites in the Sacramento Basin: Sacramento River (A) at Delta, (B) at 

Keswick, (C) near Red Bluff, (D) near Hamilton City, (E) upstream of Colusa Basin Drain, (F) at Verona, and (G) at Freeport, 

1975–2004, with standard error of prediction and timing of data collection.
Results 63

estimates for the SJR at Maze Road (fig. 28B). The average 

load for the SJR at Maze Road was 53 tons/mo (for water 

years with SEPs less than 50 percent). Most of this average 

increase of 29 tons/mo between Patterson and Maze Road 

probably came from the Modesto WWTP (figs. 10 and 12B). 

Continuing downstream, the average ammonia load decreased 

from Maze Road (53 tons/mo) to Vernalis (47 tons/mo). 

Much of this decrease could be either from uncertainties in 

LOADEST-load estimates or from the nitrification of ammonia 

to nitrate in this reach of river.

The LOADEST-load estimates for TN in the SJR near 

Stevinson usually were low except during large winter/spring 

storm flows. TN load estimates ranged from less than 1 to 

1,508 tons/mo, with an average of 87 tons/mo (fig. 29A). 

The average load increased from 87 to 336 tons/mo moving 

downstream from Stevinson to Patterson, then to 499 tons/mo 

at Maze Road. A small increase of 23 tons/mo then occurred 

moving downstream from Maze Road to Vernalis.

Prior to 1979, SEPs were greater than 50 percent for most 

of the LOADEST-load estimates for orthophosphate in the SJR 

near Stevinson (fig. 30A). For water years with SEPs less than 

50 percent, the average orthophosphate load for the SJR near 

Stevinson was 9 tons/mo. Moving downstream from SJR near 

Stevinson, the average load in the SJR increased to 22 tons/mo 

near Patterson, 29 tons/mo at Maze Road, and 33 tons/mo near 

Vernalis. Much of the increase from Stevinson to Maze Road 

probably was due to the Turlock and Modesto WWTP inputs 

(figs. 10 and 12B).

The average TP loads in the SJR increased moving 

downstream of Stevinson (13 tons/mo) to Patterson 

(41 tons/ mo) to Maze Road (62 tons/mo) to Vernalis 

(68 tons/ mo) (fig. 31). As for orthophosphate, the largest 

upstream-to-downstream increases were in the reaches with 

the two largest WWTP inputs (Stevinson to Maze Road).

For the quantitative analysis of loads (and yields) as a 

function of ancillary sources and subbasin characteristics, 

the unmodeled load sources and(or) sinks between mainstem 

sites also were of interest. The best examples of these 

unmodeled load sources and(or) sinks in the San Joaquin 

Basin were the reaches from the SJR near Stevinson to near 

Patterson (fig. 32), from the SJR near Patterson to Maze Road 

(fig. 33), and from Maze Road to near Vernalis (fig. 34). The 

unmodeled load sources and(or) sinks for the reach of SJR 

from near Stevinson downstream to near Patterson were the 

load near Patterson minus the combined load near Stevinson 

and Salt Slough, Mud Slough, Merced River, and Orestimba 

IP-002261_fig 26ab

WATER YEAR

198419851986198719881989199019911992199319941995199619971998199920002001200220032004

2,000

1,000

1,800

1,600

1,400

1,200

800

600

400

200

0

60

-60

-80

-100

40

-40

20

-20

0

TOTAL NITROGEN LOADS,

IN TONS PER MONTH

TOTAL PHOSPHORUS LOADS,

IN TONS PER MONTH

B

A

NA

Not applicable

(insufficient load estimates)

NA

NA

NA

Figure 26. Unmodeled load sources and (or) sinks for the Sacramento River from Verona to Freeport 

(adjusted by loading factors) for (A) total nitrogen, and (B) total phosphorus, 1985–2004.
64 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 28abc

STANDARD ERROR OF PREDICTION, IN PERCENT

AMMONIA LOADS, IN TONS PER MONTH

50

200

160

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40

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600

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600

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A1974

197619781980198219841986198819901992199419961998200020022004

WATER YEAR

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

SEP = 50% 

 (Standard Error of Prediction)

Figure 28. Ammonia loads for mainstem sites in 

the San Joaquin Basin: San Joaquin River (A) near 

Patterson, (B) at Maze Road, and (C) near Vernalis, 

1975–2004, with standard error of prediction and 

timing of data collection.

IP-002261_fig 27abc

STANDARD ERROR OF PREDICTION, IN PERCENT

NITRATE LOADS, IN TONS PER MONTH

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

50

40

30

20

10

0

50

40

30

20

10

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40

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600

800

1,000

20

40

60

80

100

A

B

C

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

Figure 27. Nitrate loads for mainstem sites in the 

San Joaquin Basin: San Joaquin River (A) near 

Patterson, (B) at Maze Road, and (C) near Vernalis, 

1975–2004, with standard error of prediction and 

timing of data collection.

Creek, plus the load diverted from the SJR from Stevinson to 

Patterson (this diversion ranged from 0 to 38 percent of river 

load, depending on month and year; see table CD-1b on the 

Data CD). For the reach from SJR near Patterson downstream 

to Maze Road, the unmodeled load sources and(or) sinks 

were the load at Maze Road minus the combined load near 

Patterson and the Tuolumne River, plus the load diverted from 

the SJR from Patterson to Maze Road (this diversion ranged 

from 0 to 80 percent of river load, depending on month and 

year; see table CD-1b). For the reach from SJR at Maze Road 

downstream to Vernalis, the unmodeled load sources and (or) 

sinks were the load at Vernalis minus the combined load at 

Maze Road and the Stanislaus River, plus the load diverted 

from the SJR from Maze Road to Vernalis (this diversion 

ranged from 0 to 36 percent of river load, depending on month 

and year; see table CD-1b).
Results 65

IP_002261_fig 29abcd 1974 1976 1978 1980 1982

19841986198819901992199419961998200020022004

STANDARD ERROR OF PREDICTION, IN PERCENT

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

WATER YEAR

0

400

400

800

1,200

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TOTAL NITROGEN LOADS, IN TONS PER MONTH

0

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IP_002261_fig 30abcd 1974 1976 1978 1980 1982

19841986198819901992199419961998200020022004

STANDARD ERROR OF PREDICTION, IN PERCENT

WATER YEAR

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

SEP = 50% 

 (Standard Error of Prediction)

250

150

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ORTHOPHOSPHATE LOADS, IN TONS PER MONTH

0

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20

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40

50

10

20

30

40

50

0

10

20

30

40

50

A

B

D

C

Figure 29. Total nitrogen loads for mainstem sites 

in the San Joaquin Basin: San Joaquin River (A) 

near Stevinson, (B) near Patterson, (C) at Maze 

Road, and (D) near Vernalis, 1975–2004, with 

standard error of prediction and timing of data 

collection.

Figure 30. Orthophosphate loads for mainstem 

sites in the San Joaquin Basin: San Joaquin River 

(A) near Stevinson, (B) near Patterson, (C) at 

Maze Road, and (D) near Vernalis, 1975–2004, with 

standard error of prediction and timing of data 

collection.
66 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP_002261_fig 31abcd 1974 1976 1978 1980 1982

19841986198819901992199419961998200020022004

STANDARD ERROR OF PREDICTION, IN PERCENT

WATER YEAR

Monthly Loads

Data Collection, by month

Std Error of Prediction, %

250

150

50

0

200

100

0

400

300

500

200

100

0

400

300

500

200

100

0

400

300

500

200

100

TOTAL PHOSPHORUS LOADS, IN TONS PER MONTH

0

10

0

20

30

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50

0

10

20

30

40

50

10

20

30

40

50

0

10

20

30

40

50

A

B

D

C

Figure 31. Total phosphorus loads for mainstem sites 

in the San Joaquin Basin: San Joaquin River (A) near 

Stevinson, (B) near Patterson, (C) at Maze Road, and 

(D) near Vernalis, 1975–2004, with standard error of 

prediction and timing of data collection.

IP_002261_fig 32ab 1985 1986 1987 1988

1989199019911992199319941995199619971998199920002001200220032004

WATER YEAR

1,500

-1,500

500

250

150

-150

50

-50

0

200

-200

100

-100

-500

0

1,000

-1,000

TOTAL PHOSPHORUS LOAD,

IN TONS PER MONTH

TOTAL NITROGEN LOAD,

IN TONS PER MONTH

A

B

NA

NA

Not applicable

(insufficient load estimates)

NA

Figure 32. Unmodeled load sources and(or) sinks 

in the San Joaquin River from Stevinson to Patterson 

(adjusted by loading factors) for (A) total nitrogen, 

and (B) total phosphorus, 1985–2004.

The unmodeled load sources and (or) sinks of TN and 

TP between the SJR near Stevinson and near Patterson was 

slightly positive (source) most of the time, except during 

several high winter/spring flows, including 1995, 1997, 

and 1998 (fig. 32). The unmodeled load sources of TN 

averaged about 100 tons/mo for water years 1988–91, 1993, 

and 1999–2004. In water years 1992, 1994, and 1996–97, 

the unmodeled load sources of TN was about 400 tons/mo 

(fig. 32A). Unmodeled sources of TN in this reach of San 

Joaquin River include the Turlock WWTP (figs. 10 and 12B) 

and several agricultural drains (Kratzer and Shelton, 1998). 

The unmodeled load sources of TP averaged about 20 tons/ mo 

for water years 1987–91, 1993, and 1999–2004. In water years 

1992, 1994, and 1996–97, the unmodeled load sources of 

TP was about 60 tons/mo (fig. 32B). The biggest unmodeled 

source of TP in this reach is the Turlock WWTP (figs. 10 and 

12B). Another unmodeled load source and(or) sink in this 

reach was the uncertainties associated with LOADEST-load 

estimates at each of the six sites that were summed for this 

calculation, especially during high flows.
Results 67

IP-002261_fig 33ab

-1,000

-500

0

500

1,000

1,500

-300

-200

-100

0

100

200

300

TOTAL NITROGEN LOADS,

IN TONS PER MONTH

TOTAL PHOSPHORUS LOADS,

IN TONS PER MONTH

B

A1985

1986198719881989199019911992199319941995199619971998199920002001200220032004

WATER YEAR

Figure 33. Unmodeled load sources and(or) sinks in 

the San Joaquin River from Patterson to Maze Road 

(adjusted by loading factors) for (A) total nitrogen, and 

(B) total phosphorus, 1985–2004.

Figure 34. Unmodeled load sources and(or) sinks 

in the San Joaquin River from Maze Road to Vernalis 

(adjusted by loading factors) for (A) total nitrogen, and 

(B) total phosphorus, 1985–2004.

TOTAL PHOSPHORUS LOAD, 

IN TONS PER MONTH

TOTAL NITROGEN LOADS, 

IN TONS PER MONTH

-700

-600

-500

-400

-300

-200

-100

0

100

200

-200

-100

100

-150

-50

0

50

19851986198719881989199019911992199319941995199619971998199920002001200220032004

WATER YEAR

For most of the 1985–2004 period, the unmodeled load 

sources and(or) sinks of TN and TP between the SJR near 

Patterson and at Maze Road were positive (sources) (fig. 33). 

However, significant negative (sinks) periods occurred during 

water years 1985, 1992, 1994, 1996–1997 for TN and TP. 

The average unmodeled load source for the 20-year period 

was about 200 tons/mo for TN and about 20 tons/mo for TP. 

Unmodeled sources of TN and TP in this reach of San Joaquin 

River include the Modesto WWTP (figs. 10 and 12B) and 

several agricultural drains (Kratzer and Shelton, 1998). The 

average unmodeled load sink for the 20-year period was about 

30 tons/mo for TN and 10 tons/mo for TP. Unmodeled sinks 

of TN and TP in this reach of SJR include the two largest 

diversions (fig. 5) and several smaller diversions (Kratzer and 

Shelton, 1998). As for the reach from Stevinson to Patterson, 

another unmodeled load source and(or) sink in this reach was 

the uncertainties associated with the load estimates at the three 

sites (SJR near Patterson, Tuolumne River, and SJR at Maze 

Road) that were summed for this reach.

According to the results of LOADEST-load estimates 

for the SJR at Maze Road, Stanislaus River, and SJR near 

Vernalis, there was an unmodeled sink of TN between Maze 

Road and Vernalis until 1998 (fig. 34A). The largest sinks 

were estimated for the high-flow periods of March 1995 and 

January 1997. These were periods of flooding near the Vernalis 

gage that could have resulted in low estimates of flow. Prior 

to 1998 (excluding March 1995 and January 1997), there was 

an average sink of TN of about 30 tons/mo between Maze 

Road and Vernalis. Uncertainties in LOADEST-load estimates, 

especially for Maze Road and the Stanislaus River, probably 

were responsible for much of this apparent loss. Besides the 

2 months of high flows, the unmodeled load source for TP 

averaged about 10 tons/mo (fig. 34B).

Point sources of TN and TP (fig. 12B) were compared 

to LOADEST-estimated loads for the SJR near Vernalis 

(figs. 29D and 31D) by adjusting the point-source loads using 

loading factors (table CD1b on Data CD) to account for 

downstream diversions. Point sources accounted for about 
68 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

8 percent of TN and 17 percent of TP loads in the SJR near 

Vernalis for 1985–2004. For TN and TP, this contribution 

decreased during the second 10 years (1995–2004). The 

TN contribution decreased from 11 to 6 percent and the TP 

contribution decreased from 24 to 11 percent. For TN and TP, 

the roughly twofold and threefold decreases in point-source 

loads, respectively (fig. 12B), along with increased flows 

contributed to the greatly reduced impact of point sources 

on SJR loads. The other direct input of TN and TP into the 

SJR is tile drainage, which contributed 22 percent of the TN 

and 1 percent of the TP during 1985–2004. The contribution 

of TN from tile drainage decreased from 25 to 18 percent 

during the second 10 years due to the increased SJR flows 

STANDARD ERROR OF PREDICTION, IN PERCENT

STANDARD ERROR OF PREDICTION, IN PERCENT

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

1974197619781980198219841986198819901992199419961998200020022004

WATER YEAR

 TOTAL NITROGEN LOADS, 

IN TONS PER MONTH

 TOTAL PHOSPHORUS LOADS, 

IN TONS PER MONTH NITRATE LOADS, IN TONS PER MONTH

AMMONIA LOADS, IN TONS PER MONTH

ORTHOPHOSPHATE LOADS,

IN TONS PER MONTH

0

10

20

30

40

50

0

500

400

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100

0

100

0

200

300

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Monthly Loads

Data Collection, by month

Std Error of Prediction, %

SEP = 50% 

 (Standard Error of Prediction)

A

C

E

D

B

0

10

20

30

40

50

0

0

10

20

30

40

50

10

20

30

40

50

Figure 35. Loads for the Santa Ana River downstream of Prado Dam for (A) nitrate, (B) ammonia, (C) total nitrogen, (D) 

orthophosphate, and (E) total phosphorus, 1975–2004, with standard error of prediction and timing of data collection.

(figs. 3 and 4). Thus, direct inputs of TN and TP to the SJR 

contributed about 30 and 18 percent of the loads, respectively, 

1985–2004. For TN, this contribution was about 36 percent 

for the first 10 years and 24 percent the later 10 years. For TP, 

this contribution was about 25 percent the first 10 years and 

12 percent the later 10 years.

Santa Ana Basin

The SAR downstream of Prado Dam site was the only 

site in the Santa Ana Basin with load calculations that met our 

standard criteria (fig. 35). Loads for other sites in the Santa 

Ana Basin along with the SEP and timing of data collection 
Results 69

are in table CD-3c on the Data CD. The loads downstream of 

Prado Dam were cyclical with annual maximums in winter/

spring and minimums in summer/fall. This annual cycle was 

overlain with magnified maximums in wet years (1980, 1983, 

1993, 1995, and 1998) with high storm loads.

The LOADEST-estimated loads of nitrate in the SAR 

downstream of Prado Dam increased from 1975 to 1999, then 

seemed to decrease (fig. 35A). The loads of other nutrient 

constituents had a similar pattern as nitrate (figs. 35B–35E). 

Because wastewater effluent represents close to 80 percent 

of nonstorm flow in the SAR at Prado Dam (Mendez and 

Belitz, 2002), these changes in loads over time likely were tied 

closely to changes in wastewater discharges (see section on 

point sources and figs. 10, 12C, and 13–15).

Figure 36. Unmodeled load sources and(or) sinks 

in the Santa Ana River from MWD Crossing to 

downstream of Prado Dam for nitrate, for 1985–2004.

0

50

100

150

200

250

300

350

NITRATE LOADS, IN TONS PER MONTH

Not applicable 

(insufficient load estimates)

NA

NA

19851986198719881989199019911992199319941995199619971998199920002001200220032004

WATER YEAR

For evaluating the unmodeled load sources and(or) sinks 

between mainstem sites, the only reach of the SAR where this 

calculation was possible for a reasonable number of years was 

the SAR from MWD Crossing to downstream of Prado Dam 

for nitrate only (fig. 36). This reach had acceptable estimates 

of the unmodeled load sources and(or) sinks for 1985–2002 

for nitrate. The unmodeled load source in this reach was the 

load downstream of Prado Dam minus the combined load at 

MWD Crossing and Cucamonga Creek. This unmodeled load 

source likely represents the load from wastewater effluent 

in the reach, storm runoff to the SAR that was not part of 

Cucamonga Creek, and groundwater accretions. As with the 

loads of nitrate downstream of Prado Dam, the unmodeled 

load sources in this reach decreased starting in 1999, 

indicating a decrease in wastewater-discharge sources.
70 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Average Annual Nutrient Yields for the 1985–

2004 Period by Subbasin

Mapping the average annual nutrient yields for 1985–

2004 by subbasin indicated where the highest input rates of 

nutrients occurred in the Sacramento and San Joaquin Basins 

(figs. 37 and 38). If best management practices were to be 

implemented to decrease nutrient loads to surface waters, the 

subbasins with the highest yields would be the best places 

to invest in such measures. The comparison of yields by 

subbasin did not include the Santa Ana Basin due to the lack 

of successful load calculations for 1985–2004. The analysis 

in the Sacramento and San Joaquin Basins generally was 

limited to subbasins where there were at least 7 years of 

successful (SEP<50 percent) LOADEST-load estimates during 

1985–2004. Exceptions to this were ungaged subbasins in the 

mountains of the Sacramento and San Joaquin Basins (Coast 

Ranges, Sierra Nevada, Klamath, or Cascade), and the CBD, 

Sacramento Slough, Cottonwood Creek (TP only), and Arcade 

Creek subbasins in the Sacramento Basin (fig. 8).

The average annual yield of TN and TP for subbasins that 

primarily drain the mountains generally were low compared 

to subbasins in the Central Valley. The average yields of TN 

and TP for 11 mountain subbasins (greater than 90 percent in 

the mountains) with LOADEST-estimated loads were 0.28 

and 0.03 (tons/mi2)/yr, respectively. The Sacramento River at 

Delta subbasin was not included because of the unusually high 

TN yield [(1.39 tons/mi2)/yr)] for a mountain subbasin. These 

average annual yield values [(0.28 and 0.03 (tons/ mi2)/ yr)] 

were used to estimate yields for mountain subbasins in 

the Sacramento and San Joaquin Basins that did not have 

LOADEST-estimated loads. Average annual yields for valley 

areas between mainstem sites on the Sacramento River and 

SJR were based on the unmodeled load sources.

Four areas in the Sacramento Basin were not filled in 

on the yield maps (figs. 37 and 38): (1) the mountainous area 

between Delta and Keswick (not including the McCloud and 

Pit River subbasins), (2) the valley area between Colusa and 

upstream of CBD, (3) the valley area between upstream of 

CBD and Verona that is not part of the CBD, Sacramento 

Slough, or lower Feather River subbasin, and (4) the valley 

area between the lower Feather River subbasin and Verona. 

The drainage area to the Sacramento River between Delta and 

Keswick that is not part of the McCloud or Pit subbasins is 

primarily drainage directly to Shasta Lake, and the unmodeled 

load sources and(or) sinks for this reach were negative (sinks) 

for TN and TP. Although these unmodeled load sinks make 

sense due to the long residence time of water in Shasta Lake, 

they were not useful for estimating yields for that area. The 

valley area between Colusa and upstream of CBD is only 

7 mi2 and this reach of the Sacramento River contains two 

large diversions (fig. 5), thus the uncertainty in the unmodeled 

load sources and(or) sinks was exacerbated when divided by 

such a small area. The last two valley areas (numbers 3 and 4 

above) could not be evaluated here as they were not included 

in any of the areas with estimated loads. All areas of the 

San Joaquin Basin were filled in using the above criteria for 

mountainous areas.

The criterion of at least 7 years of successful 

(SEP<50 percent) LOADEST-load estimates was relaxed 

for Cottonwood Creek (TP only) and Arcade Creek (TN 

and TP) in order to be able to fill these subbasins in on 

the yield maps (figs. 37 and 38). Cottonwood Creek had 

6 years of LOADEST-load estimates for TP with SEP 

less than 60 percent, although Arcade Creek had 6 years 

of LOADEST-load estimates for TN with SEP less than 

60 percent and 6 years of LOADEST-load estimates for TP 

with SEP less than 70 percent.

TN yields were low for the mountain subbasins of 

the Sacramento and San Joaquin Basins, except for the 

Sacramento River at Delta and the Mill Creek subbasins in the 

Sacramento Basin, based on either LOADEST-load estimates 

or assumption (fig. 37). There were more areas of subbasins 

with high TN yield [>2.45 (tons/mi2)/yr)] in the San Joaquin 

Basin than in the Sacramento Basin (fig. 37). TN yields were 

greater than 2.45 (tons/mi2)/yr in about 61 percent of the 

valley floor in the San Joaquin Basin (1,388 of 2,263 mi2) and 

in only about 12 percent of the valley floor in the Sacramento 

Basin (577 of 4,843 mi2). The highest yield areas in the San 

Joaquin Basin included Mud and Salt Sloughs, the valley area 

west of the SJR, the valley portion of the Tuolumne River, 

and the rest of the valley area east of the SJR between the 

Merced and Stanislaus Basins. The Merced River at Happy 

Isles Basin in Yosemite National Park was in a moderate 

category [0.57–1.51 (tons/mi2)/yr] for TN yields with a yield 

of 0.62 (tons/mi2)/yr (fig. 37). This is an area with some very 

popular hiking trails, which may be impacting the TN yields 

in the basin. The highest yield areas in the Sacramento Basin 

were the reaches of the Sacramento River from Hamilton City 

to Colusa and from Verona to Freeport. The Verona to Freeport 

reach was dominated by the Sacramento metropolitan area.

TP yields were low in all mountain subbasins of 

the Sacramento and San Joaquin Basins (fig. 38), many 

through LOADEST-load estimates and some by assumption. 

There were more areas of subbasins with high TP yield 

[>0.34 (tons/ mi2)/yr] in the San Joaquin Basin than in the 

Sacramento Basin (fig. 38). TP yields were greater than 0.34 

(tons/mi2)/yr in about 43 percent of the valley floor in the San 

Joaquin Basin (964 of 2,263 mi2) and in only about 5 percent 

of the valley floor in the Sacramento Basin (245 of 4,843 mi2). 

The highest yield areas in the San Joaquin Basin included 

the valley area west of the SJR, the valley portion of the 

Tuolumne River, and the rest of the valley area east of the SJR 

between the Merced and Stanislaus Basins. The highest yield 

area in the Sacramento Basin was the reach of the Sacramento 

River from Hamilton City to Colusa.

In the Santa Ana Basin, the yield of the entire SAR 

downstream of Prado Dam Basin was 1.4 (tons/mi2)/yr for TN 

and 0.3 (tons/mi2)/yr for TP. However, unlike the Sacramento 

and San Joaquin Basins, most of the nutrient loads in the Santa 

Ana Basin were contributed by point sources.
Results 71

Undefined

California Coast Ranges

California Trough

Great Basin

Klamath Mountains

Middle Cascade Mountains

Mexican Highlands

Salton Trough

Sierra Nevada

Sonoran Desert

Los Angeles Ranges

Physiographic Sections 

EXPLANATION

IP-002261_fig 37

Pacific

Ocean

California

Nevada

0 20 40 MILES

0 20 40 KILOMETERS

No value

<0.57

0.57-1.51

1.51-2.45

>2.45

Valley floor boundary

123° 122° 121° 120° 119°

41°

40°

39°

38°

37°

Average Yields for Total

Nitrogen, 1985 – 2004

(in tons/mi2-yr)

EXPLANATION

Sacramento

Basin

San Joaquin

Basin

Figure 37. Average yields of total nitrogen in subbasins of the Sacramento and San Joaquin Basins, California, for total 

nitrogen, 1985–2004.
72 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 38

Pacific

Ocean

California

Nevada

123° 122° 121° 120° 119°

41°

40°

39°

38°

37°

Sacramento

Basin

San Joaquin

Basin

0 20 40 MILES

0 20 40 KILOMETERS

No value

<0.08

0.08-0.21

0.21-0.34

>0.34

Valley floor boundary

Average Yields for Total

Phosphorus, 1985 – 2004

(in tons/mi2-yr)

EXPLANATION

Figure 38. Average yields for total phosphorus in subbasins of the Sacramento and San Joaquin Basins, 1985–2004.
Results 73

Relations Between Nutrient Yields and Nutrient 

Sources and Subbasin Characteristics

Using available ancillary data, attempts were made to 

relate the average annual yields (1985–2004) for subbasins in 

the Sacramento, San Joaquin, and Santa Ana Basins to various 

ancillary data types and subbasin characteristics. However, 

only three subbasins in the Santa Ana Basin (SAR at MWD 

Crossing, Cucamonga Creek, and SAR downstream of Prado 

Dam) met the load criteria (at least 7 years of acceptable 

loads for 1985–2004) for TN and two subbasins (SAR at 

MWD Crossing and SAR downstream of Prado Dam) for TP. 

Because of the low number of qualified subbasins in the Santa 

Ana Basin, the geographical and land-use differences between 

the Santa Ana Basin and the Sacramento and San Joaquin 

Basins, and the similarities between the Sacramento and San 

Joaquin Basins (see section, “Description of Study Area”), 

the subbasins in the Sacramento and San Joaquin Basins were 

combined in the multiple linear-regression (MLR) analysis 

and subbasins in the Santa Ana Basin were not included. 

For the Sacramento and San Joaquin Basins, 30 subbasins 

initially were included in the stepwise MLR analysis for TN 

and TP (17 in the Sacramento Basin and 13 in the San Joaquin 

Basin). The consideration of the Sacramento and San Joaquin 

Basins together improved the statistical power of the MLR 

analysis. Although the average annual yield for 1985–2004 

was used in the MLR analysis, several subbasins only had 

loads for the more recent time periods and if there were trends 

in explanatory variables, more recent data were used to better 

relate to the yields.

Point sources and tile drainage were not included as 

explanatory variables in the stepwise MLR analysis because 

of the low number of subbasins with these sources—5 and 3 

of the 30 subbasins, respectively. However, in order to include 

the effect of these direct discharges to the Sacramento and 

San Joaquin Rivers, appropriate amounts of these sources 

were subtracted from the subbasin loads before calculating 

the subbasin yields used in equation 7. This is different from 

the yield analysis done in the previous section, Average 

Annual Nutrient Yields for the 1985–2004 Period by Subbasin 

(figs. 37 and 38). For point sources, the average annual 

load for 1993–2004 was subtracted because of the trends in 

point-source loads noted in section, “Nutrient Sources, 1985–

2004.” Although all of this point-source load was subtracted, 

only a part of the average annual 1993–2004 tile-drainage 

load was subtracted. For tile drainage in the Salt and Mud 

Sloughs subbasin, only one-half of the load was subtracted, 

assuming that about one-half the tile drainage originated from 

anthropogenic factors (fertilizer and manure) and the other 

one-half was from native-soil nitrogen. For the tile drainage 

downstream of the sloughs, it was assumed that anthropogenic 

sources dominated and none of the tile-drainage load was 

subtracted.

Although the atmospheric deposition amounts in the 

Sacramento and San Joaquin Basins did not have apparent 

trends during 1985–2004, the fertilizer application amounts 

increased in both basins and manure production decreased in 

the Sacramento Basin and increased in the San Joaquin Basin. 

To remove the effects of these trends, just the average annual 

fertilizer-application amounts were used from 1993 to 2004 

and the average annual manure-production values from 1992 

to 2002 in the MLR analysis.

Thus, the MLR model used to explain the average annual 

1985 to 2004 yields for the 30 subbasins in the Sacramento 

and San Joaquin Basins was:

Yield (TN or TP)= + X + X +........+ X , 0 1 1 2 2 11 11

where

Yield is average annual yield of TN or TP for

1985 2004 (data used in figs. 37 and 38,

except as noted for subbasins with point

sources and(or) tile draina

ββ β β

−

0

1 11

1

ge), in

tons per square mile,

is intercept,

... is slope coefficient for respective 

explanatory variable,

X is fertilizer application of TN or TP 

(average annual for 1993 2004 (subbasin-specific dat

β

β

−

2

a used in fig. 17 per

subbasin area), in tons per square mile)

plus manure production (average annual

for 1992 2002 (subbasin-specific data

 used in fig. 18 per subbasin area), in tons

per square mile),

X i

−

3

s atmospheric deposition (TN only; average

 annual for 1985 2004 (see table 5), in

tons per square mile),

X is percent of subbasin in orchards and

vineyards (1992 National Land Cover

Dataset, August 2005 e

−

4

5

6

nhanced version

(NLCDe) codes 61 and 62),

X is percent of subbasin in row crops

(NLCDe code 82),

X is percent of subbasin in pasture and rice

 (NLCDe codes 81 and 83),

X is percent of subbasin in urban (NLC

7

8

9

De

codes 21, 22, 23, 25, 26, and 85),

X is percent of subbasin in grasslands and

shrublands (NLCDe codes 57 and 71),

X is percent of subbasin in forest (NCLDe

 codes 41, 42, and 43),

X is average annual pre

10

11

cipitation for 

1980 1997 f or each subbasin, in inches, 

X is Soil Hydrologic Group C and D (silts

and clays), in percent, and

X is subbasin R factor of Universal Soil Loss

Equation (rainfall and runoff f

−

actor),

unitless.

(7)
74 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Three outliers were removed from the stepwise MLR 

analysis for TN based on their Cook’s distance values (see 

section, “Analysis Techniques”)—Arcade Creek, the valley 

portion of the Sacramento River subbasin between Verona 

and Freeport, and the valley portion of the San Joaquin 

River subbasin between Maze Road and Vernalis. The first 

two subbasins were the only highly urbanized subbasins 

in the database, with urban land use (X6) values of 95 and 

44 percent, respectively. The next highest X6 value for a 

subbasin was only 17 percent. The third outlier is a relatively 

small valley area between mainstem SJR sites (Maze Road 

and Vernalis) with only one major input (Stanislaus River). 

It is very much influenced by the uncertainty in LOADEST 

estimates. TN yield was unusually low in this subbasin and 

could not be explained by the 11 variables.

Four outliers were removed from the stepwise MLR 

analysis for TP based on their Cook’s distance values—

the three removed for TN plus the valley portion of the 

Sacramento River subbasin between Hamilton City and 

Colusa. TP yields were unusually high from the valley 

portions of the SJR subbasin between Maze Road and Vernalis 

and the Sacramento River subbasin between Hamilton City 

and Colusa and could not be explained by the 11 variables.

For TN yields in the Sacramento and San Joaquin Basins, 

91 percent of the variance in the database was explained by 

the percentage of orchards and vineyards (X3), row crops (X4), 

pasture and rice (X5), urban (X6), grasslands and shrublands 

(X7), and the R factor (X11) (table 6). Using the standardized 

regression coefficient (see section, “Analysis Techniques”), the 

largest portion of this variance is explained by the percentage 

of land in orchards and vineyards, row crops, and urban.

For TP yields in the Sacramento and San Joaquin Basins, 

87 percent of the variance in the database was explained by 

the fertilizer application and manure production (X1), the 

percentage of urban land use (X6), and the precipitation in 

the subbasin (X9) (table 6). Using the standardized regression 

coefficients, the largest portion of this variance is explained 

by the fertilizer application and manure production in the 

subbasins.

Several of the most predictive explanatory variables for 

TN and TP yields were land use factors (table 6A). Some of 

this can be explained by the correlations between explanatory 

variables (table 6B). Fertilizer application and manure 

production (X1) was positively correlated with the atmospheric 

deposition (X2) (R = 0.74) and the percentage of land in 

orchards and vineyards (X3) and row crops (X4) (R = 0.77–

0.82), and negatively correlated with the percentage of land 

in forest (X8) (R = 0.77 to 0.78) and with precipitation in the 

subbasin (X9) (R = 0.70 to 0.71). The atmospheric deposition 

of nitrogen (X2) was positively correlated with the percentage 

of land in orchards and vineyards (X3) (R = 0.74) and pasture 

and rice (X5) (R = 0.79), and negatively correlated with the 

percentage of land in forest (X8) (R = 0.93). The percentage 

of land in forest (X8) also was negatively correlated with the 

percentage of land in orchards and vineyards (X3) (R = 0.76 

to 0.77) and pasture and rice (X5) (R = 0.81). Precipitation 

(X9) and the R factor (X11; Universal Soil Loss Equation) were 

correlated very positively (R = 0.92). Thus, several of these 

variables could be acting as surrogates for others in the MLR 

analysis. 

Trends in Nutrient Concentrations, 1975–2004

Trends in water quality in the Sacramento and San 

Joaquin Basins were tied closely to variations in flow from 

year to year (see figs. 3 and 4). Thus, the only quantitative 

trends evaluated for 1975–2004 for the Sacramento and San 

Joaquin Basins were flow-adjusted trends. Other than the 

completion of New Melones Reservoir on the Stanislaus River 

in 1979, there were no major changes in the hydrologic system 

of the Sacramento and San Joaquin Basins for the 1975–2004 

study period (Kratzer and Shelton, 1998). In the Santa Ana 

Basin, the constant growth in population resulted in a steady 

increase in the discharge of treated wastewater into the SAR. 

This increased the “baseflow” of the river by threefold over 

the 1975–2004 study period. Thus, for the Santa Ana Basin the 

quantitative nonflow-adjusted trends for the site downstream 

of Prado Dam were evaluated as well as the flow-adjusted 

trends. Results of the trend analyses (see fig. 7 for sites) are 

presented in table CD-5 of the Data CD.

Several important water-quality sampling sites did not 

have flow data for most or all of the 1975–2004 period. For 

these sites, time-series plots of nutrient concentrations are 

presented for 1975–2004. 

Trends in Flow-Adjusted Concentrations 

Trends in flow-adjusted concentrations (FACs) of nitrate, 

ammonia, TN, orthophosphate, and TP were evaluated for 

sites in the Sacramento, San Joaquin, and Santa Ana Basins for 

three time periods: 1975–2004, 1985–2004, and 1993–2004 

(table 7). Trend results with p-values less than 0.05 were 

considered to be significant. The slope of the trend indicates 

the magnitude of the trend, in terms of percent per year. The 

significant trends are separated into trends with slopes greater 

than or less than 5 percent/yr.

Sacramento Basin

The flow-adjusted concentrations that were calculated 

for the Sacramento River at Freeport are shown in figure 39

for 1975–2004. The LOESS trend lines visually represent 

the continuous trends for 1975–2004. The results in table 7

are just for the set time periods of 1975–2004, 1985–2004, 

and 1993–2004. These are essentially comparisons of the 

calculated flow-adjusted concentrations for the start and 

end periods and do not indicate the trends in concentrations 

between the periods, which are shown in figure 39. The trend 

lines indicate how the time period chosen can greatly influence 

the trend result.
Results 75

Table 6. (A) Results from stepwise multiple linear regression of basin yields versus basin nutrient sources and characteristics, and (B) correlation matrix for the 11 variables in 

the stepwise multiple linear regression.

[Abbreviations: MLR, multiple linear regression; AIC, Akaike’s Information Criteria; NA, not applicable]

Nutrient source or basin characteristic MLR variable Units

Yield (tons/mi2)

Total nitrogen

Standardized

regression

coefficient

Total phosphorus

Standardized

regression

coefficient

p-value

(all

variables)

Model p-value

(final 

MLR)

Model p-value

(all 

variables)

Model p-value

(final 

MLR)

Model

R2 AIC R2 AIC R2 AIC R2 AIC

Intercept unitless 1.00 0.92 5.29 1.00 0.91 4.13 0.00 1.00 0.90 6.07 1.00 0.87 4.65 0.00

Fertilizer application and manure production X1 tons/mi2 0.37 0.15 <0.001 0.99

Atmospheric deposition X2 tons/mi2 0.93 NA

Orchards and vineyards land use X3 percent 0.04 <0.001 0.51 0.62Row crops land use X4 percent 0.01 <0.001 0.93 0.22Pasture and rice land use X5 percent 0.98 0.001 -0.33 0.26Urban land use X6 percent 0.01 <0.001 0.47 0.03 0.010 0.25Grasslands and shrublands land use X7 percent 0.17 0.028 0.21 0.21Forest land use X8 percent 0.40 0.40

Precipitation X9 inches 0.57 0.46 0.011 0.31

Soil hydrologic groups C and D (silts and clays) X10 percent 0.77 0.36

R factor (Universal Soil Loss Equation) X11 unitless 0.17 0.010 0.30 0.99

TN X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 TP X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11

TN/TP 1.00 0.86 0.67 0.73 0.74 0.38 0.46 -0.38 -0.67 -0.62 -0.32 -0.54 1.00 0.88 0.73 0.65 0.65 0.58 -0.38 -0.77 -0.50 -0.33 -0.48

X1 1.00 0.74 0.77 0.81 0.63 0.46 -0.50 -0.78 -0.70 -0.30 -0.62 1.00 0.79 0.82 0.59 0.47 -0.49 -0.78 -0.71 -0.31 -0.64

X2 1.00 0.74 0.52 0.79 0.50 -0.08 -0.93 -0.47 -0.03 -0.54

X3 1.00 0.38 0.56 0.56 -0.31 -0.77 -0.51 -0.37 -0.50 1.00 0.42 0.56 0.55 -0.34 -0.76 -0.52 -0.37 -0.49

X4 1.00 0.42 0.01 -0.46 -0.56 -0.61 -0.16 -0.51 1.00 0.43 0.02 -0.46 -0.59 -0.62 -0.17 -0.52

X5 1.00 0.38 -0.26 -0.81 -0.26 -0.06 -0.30 1.00 0.37 -0.27 -0.81 -0.25 -0.06 -0.30

X6 1.00 -0.21 -0.46 -0.42 -0.01 -0.45 1.00 -0.22 -0.45 -0.42 0.00 -0.44

X7 1.00 0.01 0.23 0.54 0.02 1.00 0.02 0.23 0.54 0.02

X8 1.00 0.55 -0.01 0.61 1.00 0.55 -0.03 0.61

X9 1.00 -0.16 0.92 1.00 -0.16 0.92X10 1.00 -0.33 1.00 -0.34

X11 1.00 1.00

A

B
76 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Table 7. Summary of trends in flow-adjusted nutrient concentrations in the Sacramento, San Joaquin, and Santa Ana Basins, 

California, 1975–2004, 1985–2004, and 1993–2004.

[Significant trends; p<0.05. Trend in streamflow at Santa Ana River below Prado Dam: p-value = <0.001, slope = 2.79 %/yr. Abbreviations: NA, 

insufficient data (or too many censored) for trend analysis; <, less than; >, greater than; %/yr, percent per year]

Upward trend 

(slope > 5 %/yr)

Upward trend 

(slope < 5%/yr)

No significant trend 

(p>0.05)

Downward trend 

(slope < 5 %/yr)

Downward trend 

(slope > 5 %/yr)

Site NO3 NH3 TN OP TP

1975–2004

Sacramento Basin

Sacramento River at Delta 77-04 79-04 NA 77-04 77-04

McCloud River above Shasta Lake 77-04 79-04 NA 77-04 77-04

Pit River near Montgomery Creek 79-04 NA

Sacramento River at Keswick 79-04

Cottonwood Creek near Cottonwood NA NA

Sacramento River near Red Bluff NA NA NA

Mill Creek near Los Molinos NA NA

Deer Creek near Vina NA NA NA NA NA

Sacramento River at Vina NA NA NA NA NA

Sacramento River near Hamilton City 77-04 79-04 77-04 77-04 77-04

Stony Creek below Black Butte Dam 79-04 79-04 79-04

Sacramento River at Colusa NA NA NA NA NA

Sacramento River above Colusa Basin Drain NA NA

Butte Slough near Meridian NA NA

Feather River at Oroville NA NA NA

Yuba River near Marysville 77-04 79-04 77-04 77-04 77-04

Bear River near Wheatland NA NA NA NA NA

Feather River near Nicolaus

Sacramento River at Verona 79-04

Arcade Creek near Del Paso Heights NA NA NA NA NA

American River South Fork near Kyburz NA NA NA NA

American River at Nimbus Dam NA NA

American River at Sacramento

Sacramento River at Freeport 79-04 77-04

San Joaquin Basin

Panoche Drain near Dos Palos NA NA NA NA

San Joaquin River near Stevinson NA NA NA NA NA

Salt Slough near Stevinson NA

Mud Slough near Gustine NA NA NA NA NA

Merced River at Happy Isles 79-04 NA 77-04 NA

Merced River below Merced Falls NA NA

Merced River near Stevinson 79-04

Orestimba Creek at River Road NA NA NA NA NA

San Joaquin River near Patterson NA

Tuolumne River at LaGrange NA NA

Tuolumne River at Shiloh Road 79-04

San Joaquin River at Maze Road NA

Stanislaus River Middle Fork at Dardanelle NA NA NA NA

Stanislaus River below Goodwin Dam 77-04 NA NA NA NA

Stanislaus River near Caswell State Park 79-04

San Joaquin River near Vernalis
Results 77

Site NO3 NH3 TN OP TP

1975–2004—Continued

Santa Ana Basin

Santa Ana River near Mentone NA NA NA NA NA

Santa Ana River near San Bernardino 75-01 NA NA 75-01 NA

Warm Creek near San Bernardino NA NA NA NA NA

Santa Ana River at MWD Crossing NA NA NA 75-01 NA

Cucamonga Creek near Mira Loma NA NA NA NA NA

Santa Ana River below Prado Dam

Santa Ana River below Prado Dam (non-flow-adjusted)

Table 7. Summary of trends in flow-adjusted nutrient concentrations in the Sacramento, San Joaquin, and Santa Ana Basins, 

California, 1975–2004, 1985–2004, and 1993–2004.—Continued

[Significant trends; p<0.05. Trend in streamflow at Santa Ana River below Prado Dam: p-value = <0.001, slope = 2.79%/yr. Abbreviations: NA, 

insufficient data (or too many censored) for trend analysis; <, less than; >, greater than; %/yr, percent per year]

Upward trend 

(slope > 5 %/yr)

Upward trend 

(slope < 5 %/yr)

No significant trend 

(p>0.05)

Downward trend 

(slope < 5 %/yr)

Downward trend 

(slope > 5 %/yr)

1985–2004

Sacramento Basin

Sacramento River at Delta 88-04 NA

McCloud River above Shasta Lake 88-04 NA

Pit River near Montgomery Creek 88-04 NA

Sacramento River at Keswick

Cottonwood Creek near Cottonwood 88-04

Sacramento River near Red Bluff 88-04

Mill Creek near Los Molinos NA NA

Deer Creek near Vina 88-04

Sacramento River at Vina 88-04 NA

Sacramento River near Hamilton City NA

Stony Creek below Black Butte Dam 88-04

Sacramento River at Colusa 88-04

Sacramento River above Colusa Basin Drain 88-04 NA

Butte Slough near Meridian NA NA

Feather River at Oroville 88-04 88-04 NA NA 88-04

Yuba River near Marysville NA NA NA NA NA

Bear River near Wheatland NA NA NA NA

Feather River near Nicolaus

Sacramento River at Verona NA NA NA NA NA

Arcade Creek near Del Paso Heights NA NA NA NA NA

American River South Fork near Kyburz NA NA NA NA NA

American River at Nimbus Dam NA NA NA NA

American River at Sacramento NA NA NA NA

Sacramento River at Freeport
78 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Site NO3 NH3 TN OP TP

1985–2004—Continued

San Joaquin Basin

Panoche Drain near Dos Palos NA NA NA NA

San Joaquin River near Stevinson

Salt Slough near Stevinson

Mud Slough near Gustine

Merced River at Happy Isles NA NA

Merced River below Merced Falls NA NA

Merced River near Stevinson

Orestimba Creek at River Road 88-04 NA NA 88-04 88-04

San Joaquin River near Patterson

Tuolumne River at LaGrange NA NA

Tuolumne River at Shiloh Road

San Joaquin River at Maze Road

Stanislaus River Middle Fork at Dardanelle NA NA NA NA

Stanislaus River below Goodwin Dam NA NA

Stanislaus River near Caswell State Park NA NA

San Joaquin River near Vernalis

Santa Ana Basin

Santa Ana River near Mentone NA NA NA NA NA

Santa Ana River near San Bernardino 85-01 NA NA NA NA

Warm Creek near San Bernardino NA NA NA NA NA

Santa Ana River at MWD Crossing 86-01 89-01 86-01 86-01 NA

Cucamonga Creek near Mira Loma 89-01 89-01 89-01 89-01 NA

Santa Ana River below Prado Dam

Santa Ana River below Prado Dam (non-flow-adjusted)

Table 7. Summary of trends in flow-adjusted nutrient concentrations in the Sacramento, San Joaquin, and Santa Ana Basins, 

California, 1975–2004, 1985–2004, and 1993–2004.—Continued

[Significant trends; p<0.05. Trend in streamflow at Santa Ana River below Prado Dam: p-value = <0.001, slope = 2.10 %/yr. Abbreviations: NA, 

insufficient data (or too many censored) for trend analysis; <, less than; >, greater than; %/yr, percent per year]

Upward trend 

(slope > 5 %/yr)

Upward trend 

(slope < 5 %/yr)

No significant trend 

(p>0.05)

Downward trend 

(slope < 5 %/yr)

Downward trend 

(slope > 5 %/yr)

1993–2004

Sacramento Basin

Sacramento River at Delta NA

McCloud River above Shasta Lake NA NA

Pit River near Montgomery Creek NA

Sacramento River at Keswick

Cottonwood Creek near Cottonwood NA

Sacramento River near Red Bluff 96-04

Mill Creek near Los Molinos NA NA

Deer Creek near Vina NA

Sacramento River at Vina NA NA NA NA NA

Sacramento River near Hamilton City NA NA
Results 79

Site NO3 NH3 TN OP TP

1993–2004—Continued

Sacramento Basin—Continued

Stony Creek below Black Butte Dam NA

Sacramento River at Colusa 96-04

Sacramento River above Colusa Basin Drain NA

Butte Slough near Meridian NA NA NA NA NA

Feather River at Oroville NA NA

Yuba River near Marysville 96-04 96-04 96-04 96-04

Bear River near Wheatland NA NA NA NA

Feather River near Nicolaus NA NA

Sacramento River at Verona 96-04 96-04 96-04 96-04 96-04

Arcade Creek near Del Paso Heights 96-04 96-04 96-04 96-04 96-04

American River South Fork near Kyburz NA NA NA NA NA

American River at Nimbus Dam NA NA NA NA

American River at Sacramento 96-04 NA NA 96-04

Sacramento River at Freeport

San Joaquin Basin

Panoche Drain near Dos Palos NA NA NA NA

San Joaquin River near Stevinson NA NA

Salt Slough near Stevinson

Mud Slough near Gustine

Merced River at Happy Isles NA NA

Merced River below Merced Falls NA NA NA

Merced River near Stevinson

Orestimba Creek at River Road

San Joaquin River near Patterson

Tuolumne River at LaGrange NA NA NA NA

Tuolumne River at Shiloh Road

San Joaquin River at Maze Road NA NA

Stanislaus River Middle Fork at Dardanelle NA NA NA NA

Stanislaus River below Goodwin Dam NA NA NA

Stanislaus River near Caswell State Park

San Joaquin River near Vernalis

Santa Ana Basin

Santa Ana River near Mentone 99-04 NA 99-04 99-04 99-04

Santa Ana River near San Bernardino 93-01 NA NA NA NA

Warm Creek near San Bernardino 98-04 98-04 98-04 98-04 98-04

Santa Ana River at MWD Crossing NA NA NA NA NA

Cucamonga Creek near Mira Loma NA NA NA NA NA

Santa Ana River below Prado Dam

Santa Ana River below Prado Dam (non-flow-adjusted)

Table 7. Summary of trends in flow-adjusted nutrient concentrations in the Sacramento, San Joaquin, and Santa Ana Basins, 

California, 1975–2004, 1985–2004, and 1993–2004.—Continued

[Significant trends; p<0.05. Trend in streamflow at Santa Ana River below Prado Dam: p-value = 0.657, slope = -0.43 %/yr. Abbreviations: NA, insufficient 

data (or too many censored) for trend analysis; <, less than; >, greater than; %/yr, percent per year]

Upward trend 

(slope > 5 %/yr)

Upward trend 

(slope < 5 %/yr)

No significant trend 

(p>0.05)

Downward trend 

(slope < 5 %/yr)

Downward trend 

(slope > 5 %/yr)
80 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 39abcde

0

0

1

1

-1

-1

-2

-2

2

-3

3

0

1

-1

-2

-3

2

3

TOTAL NITROGEN, MG/L AS N NITRATE, MG/L AS N TOTAL PHOSPHORUS, MG/L AS P

ORTHOPHOSPHATE, MG/L AS P AMMONIA, MG/L AS N

1975 1980 1985 1990

WATER YEAR

WATER YEAR

1995 2000 2005

1975 1980 1985 1990 1995 2000 2005

2

1

1.50

0.75

0.00

-0.75

-1.50

-1

-3

-5

3

STORET

UCD

NWIS

A B

C

E

D

Figure 39. Flow-adjusted concentrations in the Sacramento River at Freeport, California, for (A) nitrate, (B) ammonia, (C) 

total nitrogen, (D) orthophosphate, and (E) total phosphorus, 1975–2004.
Results 81

Overall, there were 28 significant 

trends in FACs of nitrate at the 24 sites in 

the Sacramento Basin with enough data to 

calculate trends for the three time periods. 

All were downward trends except for the 

Feather River near Nicolaus (1975–2004 

and 1985–2004) (table 7, see fig. 7A for 

basemap of sites, fig. 40). Most of the 

decreasing trends occurred for the most 

recent time period (1993–2004), and 

slopes were greater than 5 percent per 

year for 10 of the 14 decreasing trends. 

The downward trend in the American 

River at Sacramento site likely was 

due to changes in wastewater treatment 

in the Sacramento metropolitan area. 

Nitrate concentrations in the wastewater 

discharges were fairly low in 1982, as 

most of the nitrogen was discharged as 

ammonia. However, even the relatively 

low concentrations of nitrate (and 

nitrification of some of the discharged 

ammonia to nitrate) were a significant 

source of nitrate in the American River, 

enough to cause a significant decrease 

in FACs during 1975–2004 when the 

wastewater discharges were routed out 

of the basin. FACs of nitrate decreased 

for several mainstem sites and major 

tributaries during the most recent time 

period, 1993–2004.

There were nine significant trends 

in FACs of ammonia in the Sacramento 

Basin, seven of these downward (table 7, 

fig. 41A). The only upward trends were 

in the Yuba River (1979–2004) and the 

Feather River near Nicolaus (1985–

2004). Many sites in the Sacramento 

Basin did not have enough ammonia 

data to calculate a trend, especially for 

1975–2004. The only trends in FACs of 

ammonia with greater than 5 percent per 

year slope were the downward trends 

at the Sacramento River at Colusa for 

1993–2004 and the American River at 

Sacramento for 1996–2004, and the 

upward trend at the Feather River near 

Nicolaus for 1985–2004. The significant 

downward trends in FACs of ammonia 

at the American River at Sacramento 

and Sacramento River at Freeport sites for 1975–2004 likely 

were due to the consolidation of wastewater in the Sacramento 

metropolitan area in December 1982. Unlike nitrate, the 

IP_002261_figure_40a

122° 121°

41°

40°

39°

0 10 20 MILES

0 10 20 KILOMETERS

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Flow Adjusted Trends for

Nitrate

Sample site

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

A. EXPLANATION

Figure 40. Trends in flow-adjusted concentrations of nitrate in the (A) Sacramento 

Basin and (B) San Joaquin Basin, California, 1975–2004, 1985–2004, and 1993–2004. 

See figures 7A and 7B for site names.

relatively high ammonia concentrations in the wastewater 

discharges in 1982 were a significant source in the Sacramento 

River, and their removal caused a significant downward trend.
82 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

_figure_40b

121°

120°

37°

38°

0 10 20 MILES 5

0 10 20 KILOMETERS 5

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Flow Adjusted Trends for

Nitrate

Sample site

EXPLANATION

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

B.

Figure 40.—Continued

For TN, most sites in the Sacramento Basin did not 

have enough data to calculate trends (table 7, fig. 42A). There 

were 11 significant trends reported for FACs of TN in the 

Sacramento Basin—9 of these were downward. The two 

upward trends were for 1993–2004 at the Sacramento River 

at Freeport (less than 5 percent per year) and the Yuba River 

(greater than 5 percent per year). Although FACs of TN at 

the Sacramento River at Freeport increased for 1993–2004 

(1997–2004 based on trend line, fig. 39C), they decreased for 

the entire 1975–2004 period. These decreases at the American 

River at Sacramento and Sacramento River at Freeport 

for 1975–2004 again likely were due to the consolidation 

of wastewater in the Sacramento metropolitan area in 

December 1982.

For orthophosphate 

in the Sacramento Basin, 

there were 19 significant 

trends in FACs, 11 for the 

1975–2004 period (table 7, 

fig. 43A). All except four of 

the trends were downward. 

The upward trends were for 

the Sacramento River near 

Hamilton City for 1977–

2004 (less than 5 percent 

per year) and for 1993–2004 

(greater than 5 percent per 

year), the Pit River for 

1993–2004 (greater than 

5 percent per year), and the 

Feather River near Nicolaus 

for 1993–2004 (greater than 

5 percent per year). The only 

downward trend in FACs 

of greater than 5 percent 

per year for orthophosphate 

was at the Yuba River for 

1996–2004. Decreasing 

trends for orthophosphate 

at the American River 

at Sacramento and the 

Sacramento River at Freeport 

for 1975–2004 were similar 

to the trends in ammonia 

and TN, and were likely 

due to the consolidation of 

wastewater discharges.

For TP, there were 11 

significant trends in FACs, 

with 8 downward (table 7, 

fig. 44A). The three upward 

trends were at the McCloud 

River for 1985–2004 (less 

than 5 percent per year), 

the Sacramento River at Colusa (greater than 5 percent per 

year) for 1993–2004, and the Sacramento River at Freeport 

(greater than 5 percent per year) for 1993–2004. As with TN 

(fig. 39C), the FACs of TP at the Sacramento River at Freeport 

increased for 1993–2004 (1997–2004, on the basis of the 

trend line, fig. 39E), but decreased for the entire 1975–2004 

period. These decreases at the American River at Sacramento 

and Sacramento River at Freeport for 1975–2004 were again 

likely due to the consolidation of wastewater discharges in 

the Sacramento metropolitan area in December 1982. The 

recent increase (1997–2004) in FACs of TN and TP, without 

corresponding increases in the dissolved forms (other than 

ammonia, see trend lines in fig. 39), suggests the possibility 

of increased stormwater runoff from the growing Sacramento 

metropolitan area.
Results 83

IP_002261_figure_41a

122° 121°

41°

40°

39°

0 10 20 MILES

0 10 20 KILOMETERS

EXPLANATION

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Ammonia

Sample site

1975-2004

1985-2004

1993-2004

Date Range for 

Trends

Flow Adjusted Trends for

A.

Figure 41. Trends in flow-adjusted concentrations of ammonia in the (A) 

Sacramento Basin and (B) San Joaquin Basin, California, 1975–2004, 1985–2004, 

and 1993–2004. See figures 7A and 7B for site names.
84 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP_002261_figure_41b

121°

120°

37°

38°

0 10 20 MILES 5

0 10 20 KILOMETERS 5

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Flow Adjusted Trends for

Ammonia

Sample site

EXPLANATION

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

B.

Figure 41.—Continued
Results 85

Figure 42. Trends in flow-adjusted concentrations of total nitrogen in the (A) 

Sacramento Basin and (B) San Joaquin Basin, California, 1975–2004, 1985–2004, 

and 1993–2004. See figures 7A and 7B for site names.

IP_002261_figure_42a

122° 121°

41°

40°

39°

0 10 20 MILES

0 10 20 KILOMETERS

EXPLANATION

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Flow Adjusted Trends for

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

Total Nitrogen

Sample site

A.
86 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP_002261_figure_42b

121°

120°

37°

38°

0 10 20 MILES 5

0 10 20 KILOMETERS 5

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Flow Adjusted Trends for

Total Nitrogen

Sample site

EXPLANATION

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

B.

Figure 42.—Continued
Results 87

IP_002261_figure_43a

0 10 20 MILES

0 10 20 KILOMETERS

122° 121°

41°

40°

39°

Sample site

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Flow Adjusted Trends for

Orthophosphate

Insufficient data for trend

analysis

A. EXPLANATION

Figure 43. Trends in flow-adjusted concentrations of orthophosphate in the (A) 

Sacramento Basin and (B) San Joaquin Basin, California, 1975–2004, 1985–2004, and 

1993–2004. See figures 7A and 7B for site names.
88 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP_002261_figure_43b

121°

120°

37°

38°

0 10 20 MILES 5

0 10 20 KILOMETERS 5

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Flow Adjusted Trends for

Orthophosphate

Sample site

EXPLANATION

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

B.

Figure 43.—Continued
Results 89

IP_002261_figure_44a

122° 121°

41°

40°

39°

0 10 20 MILES

0 10 20 KILOMETERS

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Flow Adjusted Trends for

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

Total Phosphorus

Sample site

A. EXPLANATION

Figure 44. Trends in flow-adjusted concentrations of total phosphorus in the (A) 

Sacramento Basin and (B) San Joaquin Basin, California, 1975–2004, 1985–2004, 

and 1993–2004. See figures 7A and 7B for site names.
90 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP_002261_figure_44b

121°

120°

37°

38°

0 10 20 MILES 5

0 10 20 KILOMETERS 5

Significant upward trend 

with slope > 5%/yr

Significant upward trend

 with slope < 5%/yr

No significant trend (p > 0.05)

Significant downward trend

 with slope < 5%/yr

Significant downward trend

 with slope > 5%/yr

Insufficient data for trend

analysis

Flow Adjusted Trends for

Total Phosphorus

Sample site

EXPLANATION

Date Range for 

Trends

1975-2004

1985-2004

1993-2004

B.

Figure 44.—Continued
Results 91

San Joaquin Basin

The calculated FACs for the SJR near Vernalis are shown 

in figure 45 for 1975–2004. The LOESS trend lines illustrate 

the continuous trends for 1975–2004, although the results of 

trends in FACs in table 7 are just for the set time periods of 

1975–2004, 1985–2004, and 1993–2004. The trend lines show 

how the time period chosen for trend analysis is critical to the 

resulting trends.

Overall, there were 22 significant trends in FACs of 

nitrate at the 16 sites in the San Joaquin Basin that have 

enough data to calculate trends for the three time periods 

(table 7, see fig. 7B for basemap of sites, fig. 40B). Unlike the 

Sacramento Basin, most (12) of the trends in FACs of nitrate 

in the San Joaquin Basin were upward. For 1975–2004, the 

FACs of nitrate decreased in Salt Slough and the Stanislaus 

River near Caswell SP, and increased at the Panoche Drain, 

Merced River near Stevinson, and the SJR sites near Patterson, 

at Maze Road, and near Vernalis. The Salt Slough site had 

decreasing FACs of nitrate for all time periods due to the 

re-routing of all tile drainage and most tailwater to Mud 

Slough in October 1996 with the Grasslands Bypass Project 

(California Regional Water Quality Control Board, Central 

Valley Region, 2000). This project was designed to remove 

selenium from Salt Slough so the water could be used safely 

to supply the wetlands. For 1993–2004 that spans this 

system change, the trend in FACs of nitrate in Salt Slough 

was -6.6 percent per year and in Mud Slough it was +493 

percent per year. The significant upward trends in FACs of 

nitrate in the Merced River near Stevinson and the SJR near 

Vernalis for 1975–2004 and 1985–2004 were not observed 

for 1993–2004 (see fig. 45 for Vernalis trend). The increase in 

FACs of nitrate at the Vernalis site was due to many factors, 

including tile drainage, fertilizer application, and manure 

production (Kratzer and Dahlgren, 2006). Upward trends were 

greater than 5 percent per year for 1985–2004 and 1993–2004 

at Tuolumne River at Shiloh Road. Downward trends were 

greater than 5 percent per year for 1993–2004 at all sites in the 

Sierra Nevada on the three major eastside tributaries (Merced, 

Tuolumne, and Stanislaus Rivers).

All 16 significant trends in FACs of ammonia were 

downward, except for an upward trend for the Stanislaus River 

near Caswell SP for 1979–2004 (table 7, fig. 41B). The SJR 

near Vernalis had downward trends for all three time periods, 

especially for the most recent, with a 5.3 percent per year trend 

for 1993–2004 (table 7, fig. 45B). Four other sites (Merced 

River at Happy Isles, Merced River near Stevinson, Orestimba 

Creek, and SJR near Patterson) also had a downward trends 

in FACs of ammonia of greater than 5 percent per year for 

1993–2004. The decreases in ammonia likely were due to 

improved nitrification at wastewater treatment plants (for the 

SJR near Patterson and SJR near Vernalis sites) and decreased 

surface runoff from agricultural activities (Orestimba Creek 

and mainstem SJR sites; Kratzer and Shelton, 1998). The 

decreases in nutrient concentrations at the Merced River at 

Happy Isles site could be the result of improved management 

practices by the National Park Service. Although this heavily 

visited subbasin in Yosemite National Park has relatively 

high TN yields for a Sierra Nevada subbasin (fig. 37), the 

concentrations have been decreasing over time.

The trends in FACs of TN generally reflected a 

combination of the trends in FACs of nitrate and ammonia 

for the San Joaquin Basin sites (table 7, fig. 42B). Of 16 

significant trends in FACs of TN, 10 were upward trends. 

The upward trend in FACs of nitrate combined with the 

downward trend in FACs of ammonia at the SJR near Vernalis 

produced an upward trend in FACs of TN for 1975–2004 

and no significant trend in FACs of TN for 1985–2004 and 

1993–2004 (table 7, fig. 45C). Trends with slopes greater than 

5 percent per year occurred at Salt Slough (-5.5 percent per 

year), Mud Slough (+38 percent per year), and the Tuolumne 

River at Shiloh Road (+10 percent per year) for 1993–2004. 

Of the 20 significant trends in FACs of orthophosphate, 

all but 3 were downward (table 7, fig. 43B). The upward 

trends were at Salt Slough for 1975–2004 and 1993–2004, 

and at SJR near Patterson for 1993–2004. The upward trends 

at Salt Slough likely were due to the diversion of tile drainage 

from Salt Slough to Mud Slough with the Grasslands Bypass 

Project in 1997. The low-phosphorus tile drainage was 

replaced with higher phosphorus water from the delta via 

the Delta-Mendota Canal (California Department of Water 

Resources, San Joaquin District, 1990; Kratzer and others, 

2004; California Department of Water Resources, 2007). The 

greatest downward trends in FACs of orthophosphate occurred 

in Mud Slough (-6.3 percent per year) and the Merced River 

near Stevinson (-5.7 percent per year) for 1993–2004. The 

Mud Slough decrease was the converse of the Salt Slough 

increase. The Merced River decrease and smaller decreases 

in the SJR for 1985–2004 likely were due to improved 

wastewater treatment and decreased surface runoff from 

agricultural activities (fertilizer and manure).

Of 17 significant trends in FACs of TP at the San Joaquin 

Basin sites, only 3 were upward (table 7, fig. 44B). The trends 

in TP generally agreed with the trends in orthophosphate. 

One exception to this was the trend for Salt Slough for 

1985–2004, as there was a downward trend in orthophosphate 

of 2.7 percent per year and an upward trend in TP of 

0.8 percent per year. The FAC of TP in the SJR near Vernalis 

decreased for 1975–2004 and 1985–2004 and did not change 

significantly for 1993–2004 (table 7, fig. 45E).
92 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Figure 45. Flow-adjusted concentrations in the San Joaquin River near Vernalis for (A) nitrate, (B) ammonia, (C) total 

nitrogen, (D) orthophosphate, and (E) total phosphorus, 1975–2004.

IP_002261_fig 45abcde

1975 1980 1985 1990 1995 2000 2005

WATER YEAR

1975 1980 1985 1990 1995 2000 2005

WATER YEAR

A

C

E

B

D

-2

-1

0

1

2

3

0

1

2

3

4

NITRATE, MG/L AS N TOTAL NITROGEN, MG/L AS N

NWIS

DWR

UCD

STORET

LOESS trend lines

-3

-2

-1

0

1

2

3

AMMONIA, MG/L AS N

-3

-2

-1

0

1

2

3

ORHOPHOSPHATE, MG/L AS P

-3

-2

-1

0

1

2

TOTAL PHOSPHORUS, MG/L AS P
Results 93

Santa Ana Basin

Because baseflows in the Santa Ana River increased 

almost threefold during 1975–2004, FACs and measured 

concentrations are shown for the SAR downstream of Prado 

Dam for 1975–2004 (fig. 46). In general, the flow adjustment 

reduced the variability in the data and made the determination 

of significance more sensitive to changes in slopes in the 

trend line. For nitrate, the trend results were the same for 

FACs and measured concentrations (table 7), although the 

slopes in the measured concentrations (fig. 46A2) seem greater 

than the slopes in FACs (fig. 46A1). For ammonia, the trend 

results were the same for FACs and measured concentrations 

(table 7, fig. 46B), except for the 1985–2004 period when the 

measured concentrations had a greater downward slope. For 

TN, the trend lines were very similar (fig. 46C), although the 

trend results for 1975–2004 were different, with a significant 

downward trend for the measured concentrations and no 

significant trend for the FACs. For orthophosphate and total 

phosphorus (figs. 46D and 46E), the trend results were the 

same for FACs and measured concentrations, although the 

slopes in the measured concentrations (figs. 46D2 and 46E2) 

seem greater than the slopes in FACs (figs. 46D1 and 46E1). 

However, as shown for nitrate, the trends for FACs were more 

sensitive to trend line slopes.

Overall, there were seven significant trends in FACs of 

nitrate at the six sites in the Santa Ana Basin that have enough 

data to calculate trends for the three time periods (table 7, 

see fig. 7C for basemap of sites). At the SAR downstream of 

Prado Dam site, the trend in FACs of nitrate was upward for 

1975–2004 and then downward for 1985–2004 and 1993–

2004 (table 7, fig. 46A1). The increase from 1975 to 1985 

likely was due to increased nitrification of ammonia to nitrate 

in secondarily treated wastewater (Bachand and Horne, 1993). 

The subsequent decrease in nitrate since 1985 likely was due 

to the increased use of tertiary treatment of wastewater in 

the Santa Ana Basin. The downward trend at SAR near San 

Bernardino for 1985–2004 was due to the opening of the 

RIX facility in 1996 (table 7). This facility replaced the San 

Bernardino and Colton wastewater treatment plants, which 

discharged to the SAR upstream of the San Bernardino site 

and moved the discharge point to downstream of the San 

Bernardino site. The upward trend at the San Bernardino site 

for 1975–2004 probably was due to the lack of nitrification in 

the wastewater treatment during the early years of the trend 

period.

There were six significant trends in FACs of ammonia 

in the Santa Ana Basin, all downward (table 7). For the SAR 

downstream of the Prado Dam site, the slope of this downward 

trend increased from 3.3 percent per year for 1975–2004 to 

4.9 percent per year for 1985–2004 to 7.9 percent per year for 

1993–2004. This downward trend in FACs of ammonia likely 

was due to changes in wastewater treatment as described in the 

previous paragraph, with increased nitrification and eventually 

increased tertiary treatment.

For TN, there were five significant trends in FACs in 

the Santa Ana Basin, all downward except for Warm Creek 

for 1993–2004 (table 7). For the SAR downstream of the 

Prado Dam site, the upward trend in FACs of nitrate and the 

downward trend in FACs of ammonia for 1975–2004 offset 

each other resulting in no significant trend in FACs of TN, 

although the trend line increased from 1975–85 and then 

decreased from 1985 to 2004 (fig. 46C1). The significant 

downward trends in FACs of TN for 1985–2004 and 1993–

2004 were due to the increased use of tertiary treatment.

All significant trends in FACs of orthophosphate (six) and 

TP (four) were downward except for Warm Creek for 1993–

2004 for TP (table 7). As with nitrate, the trend lines for FACs 

of phosphorus increased in SAR downstream of Prado Dam 

for 1975–85 and then decreased (figs. 46D1 and 46E1). These 

trends in FACs likely were due to the increase in wastewater 

effluent in the SAR during 1975–85 and then the increased use 

of tertiary treatment since 1985.

Figure 46. Flow-adjusted and measured 

concentrations in the Santa Ana River downstream 

of Prado Dam for (A) nitrate, (B) ammonia, (C) 

total nitrogen, (D) orthophosphate, and (E) total 

phosphorus, 1975–2004.

2.0

3.5

5.0

6.5

8.0

STORET

NWIS

Loess trend line

NITRATE, MG/L AS N

Measured Flow adjusted

0

3.5

7.0

10.5

14.0

1975 1980 1985 1990

WATER YEAR

1995 2000 2005

A
94 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Figure 46.—Continued

IP-002261_fig 46b1_2

-4

4

-2

2

0

AMMONIA, MG/L AS N

4.0

5.5

2.5

1.0

-0.5

STORET

NWIS

Loess trend line

B

1975 1980 1985 1990

WATER YEAR

1995 2000 2005

Measured Flow adjusted

10

9

8

7

6

TOTAL NITROGEN, MG/L AS N

10

15

20

25

5

0

STORET

NWIS

Loess trend line

C

1975 1980 1985 1990

WATER YEAR

1995 2000 2005

Measured Flow adjusted

IP-002261_fig 46d1_2 ORTHOPHOSPHATE, MG/L AS P

-2

2

3

4

-1

1

0

0

1

2

3

4

5

6

STORET

NWIS

Loess trend line

D

1975 1980 1985 1990

WATER YEAR

1995 2000 2005

Measured Flow adjusted

TOTAL PHOSPHORUS, MG/L AS P

0

1

2

3

4

0

2

4

6

8

E

STORET

NWIS

Loess trend line

1975 1980 1985 1990

WATER YEAR

1995 2000 2005

Measured Flow adjusted
Results 95

Trends in Measured Concentrations

For the Sacramento and San Joaquin Basins, this 

discussion of trends in measured concentrations is a qualitative 

analysis of sites that have a significant amount of nutrient data 

but insufficient flow data for flow adjusting the concentrations. 

For the Santa Ana Basin, a quantitative-trend analysis was 

done for the measured concentrations at the SAR downstream 

of the Prado Dam site for 1975–2004.

NITRATE, MG/L AS N TOTAL NITROGEN, MG/L AS N TOTAL PHOSPHORUS, MG/L AS P

AMMONIA, MG/L AS N ORTHOPHOSPHATE, MG/L AS P

1

2

3

4

5

0

0.1

0.2

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0.5

A

C

E

0

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0.5

B

D

0.2

0.4

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0.8

1

0

NWIS

<NWIS

DWR

<DWR

STORET

UCD

SRWP

0

0

1

2

3

4

5

1974 1979 1984 1989 1994 1999 2004

WATER YEAR

1974 1979 1984 1989 1994 1999 2004

WATER YEAR

Figure 47. Measured nutrient concentrations for Colusa 

Basin Drain in the Sacramento Basin for (A) nitrate, (B) 

ammonia, (C) total nitrogen, (D) orthophosphate, and (E) total 

phosphorus, 1975–2004.

Sacramento Basin

Time-series plots of measured nutrient concentrations 

for two important Sacramento Basin sites are presented in 

figures 47 and 48. These sites without flow data are (1) Colusa 

Basin Drain (fig. 47), a large agricultural drain on the west 

side of the Sacramento Valley, and (2) Sacramento River 

at Fremont Weir (fig. 48), a mainstem site downstream of 

Colusa Basin Drain and Sacramento Slough and at the largest 

diversion into the Yolo Bypass (see fig. 5). Time-series plots of 

measured nutrient concentrations for 1975–2004 are presented 

on the Data CD (fig. CD-1a) for an additional two sites in the 

Sacramento Basin (see fig. 5; Sutter Bypass and Sacramento 

Slough).
96 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 48abcde

0

0.05

0.1

0.15

0.2

0.25

AMMONIA, MG/L AS N

T O TAL N ITRO G EN , M G /L AS N

1974 1979 1984 1989 1994 1999 2004

WATER YEAR

1974 1979 1984 1989 1994 1999 2004

WATER YEAR

B

0

0.1

0.2

0.3

0.4

0.5

0.6

TOTAL PHOSPHORUS, MG/L AS P

0

0.05

0.1

0.15

0.2

0.25

0.3

ORTHOPHOSPHATE, MG/L AS P

0

0.5

1

1.5

2

2.5

0

0.5

1

1.5

2

2.5

NITRATE, MG/L AS N

A

C

E

D

NWIS

<NWIS

DWR

<DWR

STORET

<STORET

UCD

<UCD

Figure 48. Measured nutrient concentrations for Fremont Weir in the Sacramento Basin for nitrate, ammonia, total 

nitrogen, orthophosphate, and total phosphorus, 1975–2004.
Results 97

San Joaquin Basin

Time-series plots of measured nutrient concentrations 

for two San Joaquin Basin sites are presented in figures 49

and 50. These sites without flow data are (1) Camp 13 Slough 

(fig. 49), an agricultural drain in the Grasslands Bypass Project 

area, and (2) SJR at Fremont Ford (fig. 50), a mainstem site 

downstream of Salt Slough and upstream of Mud Slough (see 

fig. 1B). The water quality at both of these sites is affected 

by the Grasslands Bypass Project. The effect of re-routing 

high-nitrate tile drainage from Salt Slough (and its tributaries) 

DWR

STORET

NITRATE, MILLIGRAMS PER LITER AS NITROGEN

0

5

10

15

20

25

30

35

40

45

50

1975 1980 1985 1990 1995 2000 2005

WATER YEAR

Figure 49. Measured nitrate concentrations for 

Camp 13 Slough in the San Joaquin Basin, 1975–2004.

to Mud Slough in 1997 is illustrated in the Camp 13 Slough 

nitrate concentrations (fig. 49). Time-series plots of measured 

nutrient concentrations for 1975 to 2004 are presented on 

the Data CD (fig. CD-1b) for two additional sites in the San 

Joaquin Basin (SJR near Grayson and Tuolumne River at 

Tuolumne Meadows). The Grayson site is on the mainstem of 

the SJR about 5 river miles upstream of the confluence of the 

Tuolumne River, although the Tuolumne Meadows site is at an 

altitude of about 8,600 ft near the headwaters of the Tuolumne 

River in Yosemite National Park (see fig. 1B).
98 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 50abcde

0

2

4

6

8

10

12

TOTAL NITROGEN, MG/L AS N

0.1

0.2

0.3

0.4

0.5

ORTHOPHOSPHATE, MG/L AS P

0

0.3

0.6

0.9

1.2

1.5

TOTAL PHOSPHORUS, MG/L AS P

1974 1979 1984 1989 1994 1999 2004

WATER YEAR

1974 1979 1984 1989 1994 1999 2004

WATER YEAR

0

2

4

6

8

10

12

NITRATE, MG/L AS N

0

0

0.2

0.4

0.6

0.8

1

AMMONIA, MG/L AS N

NWIS

<NWIS

DWR

STORET

<STORET

CVRWQCB

<CVRWQCB

A B

C

E

D

Figure 50. Measured nutrient concentrations for San Joaquin River at Fremont Ford in the San Joaquin Basin for (A) 

nitrate, (B) ammonia, (C) total nitrogen, (D) orthophosphate, and (E) total phosphorus, 1975–2004.
Results 99

Santa Ana Basin

Flow data were sufficient for all Santa Ana Basin sites 

for 1975–2004. Thus, the only trend analysis on measured 

concentrations was for the SAR downstream of the Prado 

Dam site using the Mann Kendall test (see section, “Analysis 

Techniques”). The test estimated a significant (p<0.001) 

increase in flow from 1975 to 2004 of 2.8 percent per year. 

The 10 wastewater-treatment plants contributing significant 

flows to the SAR (see fig. 10) increased their discharges to 

the river by an average of 4.3 percent per year during this 

period (fig. 51; Santa Ana River Watermaster, 2004). During 

1985–2004, the flows in the SAR increased significantly 

(p<0.001) by an average of 2.1 percent per year. However, 

the combination of relatively wet years from 1993 to 1998 

and relatively dry years from 1999 to 2004 resulted in a slight 

(0.4 percent per year) nonsignificant (p = 0.66) decrease in 

flow from 1993 to 2004 (table 7). 

The trends in measured nutrient concentrations generally 

were in agreement with the trends in FACs. The disagreements 

were for ammonia for 1985–2004, and for TN for 1975–

2004 (table 7). Because there was a significant systematic 

change in flow over the trend period, the trends in measured 

concentrations are the more appropriate to use for this site.

Long-Term Nitrate Concentrations, 1905–2004

There are three sources of USGS nitrate data for selected 

sites in the Sacramento, San Joaquin, and Santa Ana Basins 

for 1905–07, 1908, and 1930 (Van Winkle and Eaton, 1910; 

Stabler, 1911; California Department of Public Works, 

Division of Water Resources, 1931). Any of the sites included 

in the final database (table 4) for this study that have long-term 

nitrate data (defined here as data from 1905–07, 1908, or 

1930) are discussed in this section. In some cases, additional 

sites were combined to fully utilize the pre-1975 data (table 2). 

As with the other site combinations in table 2, there is no 

clear reason to believe that these combined sites should not 

be comparable. Additional STORET and NWIS nitrate data 

for the 1931–74 period also are included for these sites. In 

addition, USGS data (not in NWIS) for the Feather River near 

Nicolaus site was obtained from a series of USGS WaterSupply Papers for 1951-58 (Love, 1954, 1955. 1957, 1958, 

1959, 1960, and 1961). 

Because there have been many important changes in the 

hydrologic systems of the Sacramento, San Joaquin, and Santa 

Ana Basins over this long-term period, only the measured 

nitrate concentrations (nonflow adjusted) are shown in this 

section. The USGS data sources do not include any data for 

the other N or P constituents evaluated in this report.

IP-002261_fig 51

0

100,000

200,000

300,000

400,000

500,000

600,000

1970 1975 1980 1985

EXPLANATION

1990

WATER YEAR

1995 2000 2005

ACRE-FEET PER YEAR

Total SAR flow

Storm flow

WWTP effluent

Figure 51. Wastewater and storm-flow 

components of flow in the Santa Ana River 

downstream of Prado Dam, 1975–2004.

Sacramento Basin

There are eight study sites in the Sacramento Basin with 

long-term nitrate data (fig. 52). The long-term data were in 

most cases inconclusive with regards to nitrate trends, due to 

the relative scarcity of data prior to 1960. However, there were 

relatively more frequent occurrences of high concentrations 

compared to other time periods at the Sacramento River near 

Red Bluff in the 1950s and 1960s, Sacramento River upstream 

of CBD in the 1950s, Feather River at Oroville in the 1960s 

and 1970s, and the Sacramento River at Freeport in the 1960s 

(figs. 52A, C, D, and 52H). Overall increases in concentrations 

are apparent between the few data points in 1930 compared 

with 1960–2004 data at the Sacramento River at Colusa 

(fig. 52B). The other sites do not indicate any changes in 

nitrate concentrations (figs. 52E–52G).

Major dam construction that spanned the long-term 

period for the Sacramento Basin sites includes: Shasta Lake 

(1945) on the mainstem of the Sacramento River, Lake 

Oroville (1968) on the Feather River, and Folsom Lake (1956) 

on the American River (fig. 1A; California Department of 

Water Resources, 2009). More details on these dams and the 

hydrology of the Sacramento Basin are available in section, 

“Water Resources.” 
100 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

IP-002261_fig 52abcdefgh

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

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0.9

1.0

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1.0

1.2

WATER YEAR WATER YEAR

NWIS

<NWIS

DWR

<DWR

STORET

<STORET

SRWP

<SRWP

UCD

SCRSD

<SCRSD

A B

C D

E F

G H

0.0

0.1

0.2

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0

0.2

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1

1.2

1.4

1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2004 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2004

NITRATE, MG/L AS NNITRATE, MG/L AS N

0.0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

Figure 52. Measured nitrate concentrations for Sacramento Basin sites with long-term data: (A) Sacramento River near Red 

Bluff, 1905–2004, (B) Sacramento River at Colusa, 1930–2004, (C) Sacramento River upstream of Colusa Basin Drain, 1930–2004, 

(D) Feather River at Oroville, 1905–2004, (E) Feather River near Nicolaus, 1930–2004, (F) Sacramento River at Verona, 1905–2004,

(G) American River at Nimbus, 1905–2004, and (H) Sacramento River at Freeport, 1930–2004. Open symbols represent values less 

than detection.
Results 101

San Joaquin Basin

There are four study sites in the San Joaquin Basin that 

have long-term nitrate data (fig. 53). For the three sites on the 

major eastside tributaries to the SJR—Merced, Tuolumne, 

and Stanislaus Rivers—virtually no data exist between 1930 

and the 1960s. Each of these sites is upstream of the valley, 

downstream of a present-day major reservoir. The lack of early 

data makes it impossible to interpret any possible trends at 

these sites (figs. 53A–53C). 

Major dam construction that spanned the long-term 

period for the San Joaquin Basin sites includes: Lake McClure 

(1967) on the Merced River, Don Pedro Reservoir (1923) 

and New Don Pedro Reservoir (1971) on the Tuolumne 

River, and New Melones Lake (1979) on the Stanislaus River 

(fig. 1B; California Department of Water Resources, 2009). 

The original Don Pedro Reservoir had a storage capacity 

of 290,400 acre-ft. It was replaced at the same site by the 

2.03 million acre-ft New Don Pedro Reservoir. More details 

on these dams and the hydrology of the San Joaquin Basin are 

available in the section, “Water Resources”.

The measured nitrate concentrations in the SJR near 

Vernalis in 1951 were similar to concentrations in samples 

collected in 1908 and 1930 (Van Winkle and Eaton, 1910; 

California Department of Public Works, Division of Water 

Resources, 1931), although 1908 and 1930 were relatively 

dry years (see fig. 4), which may have contributed to elevated 

nitrate concentrations. The measured nitrate concentrations in 

the SJR near Vernalis clearly increased since the early 1950s 

(fig. 53D; Kratzer and Shelton, 1998; Kratzer and others, 

2004; Kratzer and Dahlgren, 2006). With the completion of 

the Delta-Mendota Canal (fig. 1B) in 1951, most of the water 

in the SJR that originated in the upper San Joaquin Basin was 

replaced with water from the Sacramento–San Joaquin Delta. 

This water was enriched in nitrate compared with the Sierran 

water from the upper basin. Tile drains were first installed 

in the early 1950s in the Grasslands Drainage Project Area 

(fig. 1B) to relieve the damaging effects of high groundwater 

tables on crops. 

The tile drainage flowed to the SJR via Mud and Salt 

Sloughs. In addition to increases in nitrate from tile drainage, 

fertilizer applications and manure production in the San 

Joaquin Basin increased during 1950–75 (Kratzer and Shelton, 

1998). Nitrate concentrations in groundwater on the east side 

of the lower San Joaquin Basin also increased over this period 

(Burow and others, 2002). From 1950 to 1975, the nitrate 

increase in the SJR corresponded with the increases in tile 

drainage and fertilizer applications (Kratzer and Dahlgren, 

2006). Discharges of municipal wastewater also could have 

been a contributing factor, although probably relatively minor 

compared with the tile drainage and fertilizer applications 

(Kratzer and Shelton, 1998).

0.0

0.2

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1.2

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1.2

NWIS, MG/L AS N

0.0

0.1

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1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2004 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2004

0.0

0.5

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2.5

3.0

3.5

4.0

WATER YEAR WATER YEAR

NITRATE, MG/L AS N

NITRATE, MG/L AS N

NWIS

<NWIS

DWR

STORET

<STORET

UCD

A B

C D

Figure 53. Measured nitrate concentrations for San Joaquin Basin sites with long-term data: (A) Merced River below Merced Falls, 

1930–2004, (B) Tuolumne River at LaGrange, 1905–2004, (C) Stanislaus River below Goodwin Dam, 1930–2004, and (D) San Joaquin River 

near Vernalis, 1908–2004. Open symbols represent values less than detection.
102 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Santa Ana Basin

The Santa Ana Basin has four study sites that have 

long-term nitrate data (fig. 54). For the SAR near Mentone 

site, measured nitrate concentrations from 1997 to 2001 were 

similar to those measured in 1908 and 1930 (fig. 54A). Several 

high nitrate concentrations were measured at that site from 

the mid-1960s to the mid-1970s. The early data for Warm 

Creek consists of one data point in 1930, thus making any 

interpretation of changes impossible (fig. 54B). For the SAR 

at MWD Crossing site, nitrate concentrations have increased 

since 1930 and the 1950s, with a peak around 1970 (fig. 54C). 

For the SAR downstream of the Prado Dam site (fig. 54D), 

the measured nitrate concentrations increased from 1908 to 

about 1975–1985 and then decreased, as noted in table 7. The 

1908 data were collected near Corona, about 5.5 river miles 

upstream of the present site downstream of Prado Dam. This 

site is upstream of Cucamonga and Temescal Creeks (see 

fig. 1C). For comparison, on one occasion both sites were 

sampled on the same day, July 10, 1930, and the upstream site 

had a nitrate concentration of 1.13 mg/L as N, compared to 

0.95 mg/L as N at the downstream site. 

Major dam construction that spanned the long-term 

period for the Santa Ana Basin sites include: Prado Dam 

(1941) and Seven Oaks Dam (1999), both on the mainstem of 

the Santa Ana River (fig. 1C; California Department of Water 

Resources, 2009). The capacity of the impoundment behind 

Prado Dam is 314,400 acre-ft and the capacity behind Seven 

Oaks Dam is 145,600 acre-ft (California Department of Water 

Resources, 2009). The Seven Oaks Dam is just upstream of 

the sampling site near Mentone. More details on the hydrology 

of the Santa Ana Basin are available in the section, “Water 

Resources.”

0.0

0.5

1.0

1.5

2.0

2.5

3.0

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1.0

1.5

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4.0

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0

2

4

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14

16

18

1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010

0

2

4

6

8

10

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14

1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000 2010

WATER YEAR WATER YEAR

NITRATE, MG/L AS NNITRATE, MG/L AS N

NWIS

<NWIS

DWR

<DWR

STORET

NWIS

<NWIS

A B

C D

Figure 54. Measured nitrate concentrations for Santa Ana Basin sites that have long-term data: (A) Santa Ana River near 

Mentone, 1908–2001; (B) Warm Creek near San Bernardino, 1930–2004; (C) Santa Ana River at MWD Crossing, 1930–2001; and 

(D) Santa Ana River downstream of Prado Dam, 1908–2004.
Summary and Conclusions 103

Management Strategies Implemented 

in the Santa Ana Basin

The implementation of several management strategies in 

the Santa Ana Basin likely are responsible for the decreasing 

trends in nutrient concentrations in the SAR since 1975. 

The RWQCB(SAR) and other water-quality stakeholders in 

the Santa Ana Basin made intensive efforts to protect and 

enhance the quality of the river so that river water could 

meet water‐quality objectives for beneficial uses such as 

groundwater recharge (California Regional Water Quality 

Control Board, Santa Ana Region, 1990). The Santa Ana 

Regional Interceptor (SARI) pipeline is another example of 

water-quality protection efforts in the basin. SARI pipeline 

was built in the mid-1970s to convey wastewater having 

high concentrations of dissolved solids to the Orange County 

Sanitation District for treatment. In the year 2000, a few 

dairies in the Chino Basin Dairy Preserve (see fig. 1C) were 

connected to the SARI pipeline in response to the occasional 

but potentially devastating dairy spills of manure-laden dairy 

washwaters into the SAR (Vitko, 2005). Also starting in 

about 2000, some water purveyors began to pump and treat 

groundwater having high concentrations of dissolved solids 

and nutrients. As a result, less poor-quality groundwater 

reaches the SAR. Such hydraulic control is a strategy used in 

the area of the Chino Dairy Preserve to maximize groundwater 

yield and to minimize groundwater discharge into the SAR 

(Chino Basin Watermaster, 2005). It is believed that these 

controls prevent the discharge of about 1 billion ft3 of water 

with high concentrations of nitrate to the SAR (Wildermuth, 

2006).

Water treatment using soil-aquifer treatment and two 

constructed-wetland projects are additional strategies to lower 

concentrations of inorganic nitrogen in the SAR. The Rapid 

Infiltration and Extraction (RIX) facility in Colton, which 

opened in March 1996, removes inorganic nitrogen through 

nitrification-denitrification, and phosphorus through adsorption 

and precipitation in the soil. After rapid-infiltration land 

treatment, the system extracts the soil-matrix-treated water 

for additional treatment (disinfection) before it is discharged 

to the SAR (Quam, 2004). Wildermuth Environmental, Inc. 

(1998), calculated nitrogen removal rates at RIX facility of 

about 30 percent from the secondary effluent generated at the 

San Bernardino and Colton treatment plants. Quam (2004) 

reported removal rates at the facility of about 75 percent 

of inorganic nitrogen; with average ammonium-ammonia 

removal at 89–95 percent, nitrate removal at 17–59 percent, 

and nitrite removal at 14–97 percent. Nitrate removal 

averaged from 30 to 60 percent in one of the five constructed 

ponds in the Hidden Valley Wetlands Enhancement Program 

(in Riverside, fig. 1C) operated by the City of Riverside 

(Schneyer, 1998). The removal rates increased with increased 

retention time in the system. The Prado Wetlands (see fig. 1C), 

covering about 500 acres just upstream of the Prado Dam, are 

maintained to remove inorganic nitrogen from a portion of the 

SAR just before it combines with flows from Chino Creek, 

Cucamonga Creek, and Temescal Creek (see fig. 1C). Bachand 

and Horne (1993) reported inorganic nitrogen removal in the 

wetlands during the wet season at 26 percent, and 12 percent 

during the dry season. Reilly (1994) reported nitrate removal 

of almost 90 percent for river flow that passed through the 

marsh system.

Summary and Conclusions

A comprehensive database was assembled for the 

Sacramento, San Joaquin, and Santa Ana Basins on nutrient 

concentrations, flows, and point and nonpoint sources of 

nutrients for 1975–2004. Several parameters and sites were 

combined, as appropriate, to create the final database on 

nutrient concentrations and flows for nitrate, ammonia, 

TN, orthophosphate, and TP. Overall, the NWIS database 

represented 34.9 percent of the final database, followed by 

DWR (22.0 percent), UCD (21.7 percent), and STORET 

(20.2 percent).

A list of 327 NPDES permit sites for the Central Valley 

and Santa Ana regions was reduced to 15 significant pointsource-discharge sites of nutrients (3 in the Sacramento Basin, 

2 in the San Joaquin Basin, and 10 in the Santa Ana Basin). 

Point-source discharges account for a very small portion of 

river flows in the Sacramento and San Joaquin Basins (less 

than 1 percent), but close to 80 percent of the nonstorm 

flow in the Santa Ana River. The largest point sources in the 

Sacramento Basin, wastewater in the Sacramento metropolitan 

area, were removed from the basin in December 1982 when 

seven discharges in the basin were consolidated to a discharge 

point downstream of the basin. 

Nonpoint sources of nutrients quantified in this study 

included atmospheric deposition, fertilizer application, manure 

production, and tile drainage. Dry deposition of nitrogen was 

more significant than wet deposition in the Sacramento and 

San Joaquin Valleys and in the basin area of the Santa Ana 

Basin, with estimated ratios of dry to wet deposition of 1.7, 

2.8, and 9.8, respectively. Fertilizer application increased 

appreciably from 1987 to 2004 in all three California basins, 

although manure production increased in the San Joaquin 

Basin but decreased in the Sacramento and Santa Ana Basins 

from 1982 to 2002. 
104 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

Loads were calculated for 1975–2004 by using the loglinear multiple-regression model, LOADEST, for 20 sites in 

the Sacramento Basin, 15 sites in the San Joaquin Basin, and 

6 sites in the Santa Ana Basin. In addition, owing to gaps in 

the flow record, loads for two important agricultural sites in 

the Sacramento Basin (Colusa Basin Drain and Sacramento 

Slough) were estimated from average instantaneous loads. 

For loads calculated by LOADEST, plots of monthly loads 

included the standard error of prediction (SEP) and the timing 

of data collection. In general, only loads with SEPs less than 

50 percent were reported in this study. Major diversions in 

the Sacramento and San Joaquin Basins were included in the 

analysis of unmodeled load sources and(or) sinks between 

mainstem sites by the inclusion of loading factors. The most 

important findings from the loads were: (1) the greatest 

loads of TN and TP at Sacramento River sites occurred 

during storm flows at Hamilton City and Freeport, with the 

increased transport of suspended material in unregulated 

tributary inputs, (2) close to one-half the orthophosphate 

load in the Sacramento River at Freeport was contributed by 

the Sacramento metropolitan area, and (3) nutrient loads in 

the Santa Ana River downstream of Prado Dam generally 

increased from 1975 to 1999, then decreased.

Point sources accounted for 4 percent of the TN load 

and 7 percent of the TP load at Freeport for 1985–2004. Point 

sources accounted for 8 percent of TN and 17 percent of TP 

loads at Vernalis for 1985–2004. Average annual wastewater 

discharges in the Santa Ana Basin increased from 86 ft3/s 

in 1975 to 239 ft3/s in 2004. However, with improvements 

in wastewater treatment, moving from primary to tertiary 

treatment, overall nutrient loads to the Santa Ana River from 

point sources in 2004 were about the same as in 1975 for TN, 

but in 2004 they were less than in 1975 for TP. Tile drainage in 

the San Joaquin Basin contributed about 22 percent of the TN 

load at Vernalis for 1985–2004.

Average annual loads of TN and TP for 1985–2004 for 

subbasins in the Sacramento and San Joaquin Basins were 

divided by their drainage areas to calculate yields. About 

61 percent of the valley floor in the San Joaquin Basin had 

TN yields greater than 2.45 (tons/mi2)/yr compared with 

only about 12 percent of the valley floor in the Sacramento 

Basin. TP yields were greater than 0.34 (tons/mi2)/yr in 

about 43 percent of the valley floor in the San Joaquin Basin 

compared with only about 5 percent of the valley floor in the 

Sacramento Basin. The yields of TN and TP were low outside 

of the valley floor areas.

Yields of TN and TP for Sacramento and San Joaquin 

Basins were related to nutrient sources and subbasin 

characteristics by using a stepwise multiple linear-regression 

analysis. A total of 30 subbasins were included in the analysis 

(17 in the Sacramento Basin and 13 in the San Joaquin Basin). 

Loads from point sources and tile drainage were subtracted 

from the response variable (yield) before conducting the 

regression analysis for the small number of subbasins with 

these sources. Explanatory variables included fertilizer 

application and manure production, atmospheric deposition, 

six land-use categories, precipitation, and soils and runoff 

factors. For TN yields, the most important explanatory 

variables were the percentage of land use in (1) orchards 

and vineyards, (2) row crops, and (3) urban categories. For 

TP yields, the most important explanatory variable was the 

amount of fertilizer application and manure production.

Trends were evaluated in this study for three time 

periods: 1975–2004, 1985–2004, and 1993–2004. Trends 

in flow-adjusted concentrations (FAC) were calculated by 

using the decimal-time coefficients from the seven-parameter 

LOADEST model (or a five-parameter version for some sites 

with less data). Trends were considered significant if the 

p-value was less than 0.05, and their magnitude was reported 

as a slope in percent per year. Quantitative trends in measured 

concentrations were calculated for the Santa Ana River 

downstream of the Prado Dam site because of the significant 

upward trend in flow over the study period. FACs were plotted 

over time for the basin outlet sites (Sacramento River at 

Freeport, San Joaquin River near Vernalis, Santa Ana River 

downstream of Prado Dam) by adding the residuals from the 

LOESS trend line of the flow versus concentration relation to 

the mean measured concentration over time.

Most trends in nutrient FACs in the Sacramento Basin 

were downward for all three time periods—26 of 28 for 

nitrate, 7 of 9 for ammonia, 9 of 11 for TN, 15 of 19 for 

orthophosphate, and 8 of 11 for TP. Decreasing trends in 

nutrient FACs at the American River at Sacramento and the 

Sacramento River at Freeport sites for the 1975–2004 time 

period were attributed to the consolidation of wastewater 

treatment plant discharge in the Sacramento metropolitan 

area in December 1982 to a discharge point downstream 

of the basin. Unlike the Sacramento Basin, most trends 

in FACs of nitrate and TN in the San Joaquin Basin were 

upward, especially over the 1975–2004 time period. The 

increasing trend in nitrate and TN at the San Joaquin River 

near Vernalis site for 1975–2004 was due to many factors, 

including increases in tile drainage, fertilizer application, 

and manure production. Strong inverse trends in nitrate and 

TN for 1993–2004 at the Salt Slough (downward) and Mud 

Slough (upward) sites was due to the re-routing of all tile 

drainage to Mud Slough in October 1996 with the Grasslands 

Bypass Project. Most trends in FACs of ammonia (15 of 

16), orthophosphate (17 of 20), and TP (14 of 17) in the 

San Joaquin Basin were downward. All trends in measured 

nutrient concentrations at the Santa Ana River downstream 

of the Prado Dam site except for nitrate (1975–2004) were 

downward, explained by improvements in wastewater 

treatment.
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Acknowledgments

 The authors thank the following people who generously 

contributed their water-quality data to the combined database 

assembled for this study:

• Peter Coombe of California Department of Water 

Resources, Northern District,

• Michael Mosbacher of California Department of Water 

Resources, Central District,

• Michael McGinnis and David Lara of California 

Department of Water Resources, San Joaquin District,

• Randy Dahlgren of the University of California at 

Davis, and

• Claus Suverkropp of Larry Walker Associates 

(Sacramento River Watershed Program).

The authors also thank Naomi Nakagaki and JoAnn 

Gronberg of the NAWQA Program for assembling the 

ancillary database used in this study, including their 

willingness to include additional subbasins and the valley and 

basin-only portions of subbasins. A thank you also goes to 

Nehzat Motallebi of the California Air Resources Board for 

providing data on atmospheric deposition. The authors also 

thank Dave Lorenz of the U.S. Geological Survey, Minnesota 

Water Science Center for his helpful interpretations of some 

of the load and trend results from the LOADEST program. 

A special thank you goes to Bruce Agee of California 

Department of Water Resources for his overall persistent 

efforts in assembling historical DWR data and in pairing DWR 

parameter codes with NWIS parameter codes. 

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Data CD (in report cover) 111

Data CD (in report cover)

Data CD can be accessed and downloaded at URL http://pubs.usgs.gov/sir2010/5228/

Overview of Information on the Data CD (Data CD overview.doc)

Figure CD-1. Plots of Measured Nutrient Concentrations for 1975 to 2004

(a) Sacramento Basin

(Figure CD-1a(1-3).jpg) – Sutter Bypass (site id A0292700)

(Figure CD-1a(4-7).jpg) – Sacramento Slough near Knights Landing (site id 11391100)

(b) San Joaquin Basin

(Figure CD-1b(1-3).jpg) – San Joaquin River near Grayson (site id B0708000)

(Figure CD-1b(4).jpg) – Tuolumne River at Tuolumne Meadows (site id B4185010)

Table CD-1. Loading Factors used in Analysis of Loads and Yields (for loads shown in figures 26, 32-34)

(a) Sacramento Basin (Table CD-1a.xls; Table CD-1 readme.doc)

(b) San Joaquin Basin (Table CD-1b.xls)

Table CD-2. Final Database used in Report (for sites in figures 7, 47, 48, 50, 51, and CD-1)

(a) Sacramento Basin (Table CD-2a.xls; Table CD-2 readme.doc)

(b) San Joaquin Basin (Table CD-2b.xls)

(c) Santa Ana Basin (Table CD-2c.xls)

(d) Official Site Names (Table CD-2d.xls)

Table CD-3. Load Files (for sites in figure 7; from LOADEST program)

(a) Sacramento Basin (Table CD-3a(1-22).xls; Table CD-3 readme.doc)

(b) San Joaquin Basin (Table CD-3b(1-15).xls)

(c) Santa Ana Basin (Table CD-3c(1-6).xls)

Table CD-4. Data used in Stepwise Multiple Linear Regression Analysis for Sacramento and San Joaquin subbasins 

(see table 6 in report) (Table CD-4.xls; Table CD-4 readme.doc)

Table CD-5. Trends Files (for trends shown in table 7 of report)

(a) Sacramento Basin (Table CD-5a.xls; Table CD-5 readme.doc)

(b) San Joaquin Basin (Table CD-5b.xls)

(c) Santa Ana Basin (Table CD-5c.xls)

(d) All trends on one page (Table CD-5alltrends.xls)
112 Trends in Nutrient Concentration, Loads and Yields, Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004 

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http://ca.water.usgs.gov
Kratzer and others— Nutrient Concentrations, Loads, and Yields in Sacramento, San Joaquin, and Santa Ana Basins, California, 1975–2004—Scientific Investigations Report 2010–5228