Summary of Suspended-Sediment 

Concentration Data, San Francisco Bay, 

California, Water Year 2003

By Paul A. Buchanan and Neil K. Ganju

Data Series 113

U.S. Department of the Interior

U.S. Geological Survey

In cooperation with the CALFED Bay-Delta Program, and the U.S. Army Corps of

Engineers, San Francisco District
U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

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

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

Box 25286, Denver Federal Center

Denver, CO 80225

For more information about the USGS and its products:

Telephone: 1-888-ASK-USGS

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

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

endorsement by the U.S. Government.

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

reproduce any copyrighted materials contained within this report.

Suggested citation:

Buchanan, P.A., and Ganju, N.K., 2005, Summary of Suspended-Sediment Concentration Data, San Francisco Bay, 

California, Water Year 2003: U.S. Geological Survey Data Series 113, 46 p.
iii

Contents

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

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

Purpose and Scope ................................................................................. 1

Study Area .......................................................................................... 2

Acknowledgments ................................................................................. 2

Methods ................................................................................................... 4

Instrument Description and Operation ......................................................... 4

Monitoring Sites .................................................................................... 7

Suisun Bay Installations ..................................................................... 7

San Pablo Bay Installations .................................................................. 7

Central San Francisco Bay Installations ................................................... 7

South San Francisco Bay Installations ................................................... 7

Water-Sample Collection ........................................................................... 7

Data Processing .................................................................................... 8

Sensor Calibration and Suspended-Sediment Concentration Data ................................. 8

Suisun Bay .......................................................................................... 12

Mallard Island ................................................................................. 12

Benicia Bridge ................................................................................. 16

San Pablo Bay ....................................................................................... 20

Carquinez Bridge .............................................................................. 20

Mare Island Causeway ..................................................................... 24

Channel Marker 9 ........................................................................... 28

Central San Francisco Bay ........................................................................ 31

Point San Pablo .............................................................................. 31

South San Francisco Bay ........................................................................ 35

San Mateo Bridge ........................................................................... 35

Dumbarton Bridge ........................................................................... 38

Channel Marker 17 ........................................................................... 41

Summary ................................................................................................... 44

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

Figures

Figure 1. Map showing San Francisco Bay study area, California ................................. 3

Figure 2. Diagram showing typical monitoring installation, San Francisco Bay study ............ 5

Figure 3. Graphs showing example of raw and edited optical data, near-bottom 

sensor, Mare Island Causeway, San Pablo Bay, California, water year 2003 ......... 9

Figure 4. Graph showing calibration of near-surface optical sensor at Mallard Island, 

Suisun Bay, California, water year 2003 ................................................... 13

Figure 5. Graphs showing calibration of near-bottom optical sensors,

October 1–February 5 and February 5–September 30 at Mallard Island, 

Suisun Bay, California, water year 2003 ................................................... 14

Figure 6. Graphs showing time series of near-surface and near-bottom suspendedsediment concentrations calculated from sensor readings at Mallard Island, 

Suisun Bay, California, water year 2003 ................................................... 15

Figure 7. Graphs showing calibration of near-surface optical sensors, 

October 1–May 20, July 23–August 28 and May 20–July 2 at Benicia Bridge, 

Suisun Bay, California, water year 2003 ................................................... 17

Figure 8. Graph showing calibration of near-bottom optical sensor at Benicia Bridge, 

Suisun Bay, California, water year 2003 ................................................... 18

Figure 9. Graphs showing time series of near-surface and near-bottom suspendedsediment concentrations calculated from sensor readings at Benicia Bridge, 

Suisun Bay, California, water year 2003 ................................................... 19

Figure 10. Graph showing calibration of mid-depth optical sensor at Carquinez 

 Bridge, San Pablo Bay, California, water year 2003 .................................... 21

Figure 11. Graphs showing calibration of near-bottom optical sensors, 

 October 1–November 12 and January 29–September 30 at Carquinez Bridge, 

 San Pablo Bay, California, water year 2003 ............................................. 22

Figure 12. Graphs showing time series of mid-depth and near-bottom suspended-

 sediment concentrations calculated from sensor readings at Carquinez 

 Bridge, San Pablo Bay, California, water year 2003 .................................... 23

Figure 13. Graphs showing calibration of mid-depth optical sensors, 

 October 1–January 7 and February 4–September 30 at Mare Island 

 Causeway, San Pablo Bay, California, water year 2003 ................................. 25

Figure 14. Graphs showing calibration of near-bottom optical sensors,

 October 1–April 14 and April 14–September 30 at Mare Island Causeway, 

 San Pablo Bay, California, water year 2003 ............................................. 26

Figure 15. Graphs showing time series of mid-depth and near-bottom suspended-

 sediment concentrations calculated from sensor readings at Mare Island 

 Causeway, San Pablo Bay, California, water year 2003 ................................. 27

Figure 16. Graph showing calibration of near-bottom optical sensor at Channel 

 Marker 9, San Pablo Bay, California, water year 2003 ................................. 29

Figure 17. Graph showing time series of near-bottom suspended-sediment concentrations 

 calculated from sensor readings at Channel Marker 9, San Pablo Bay, 

 California, water year 2003 .................................................................. 30

Figure 18. Graphs showing calibration of mid-depth optical sensors, 

 October 1–February 5, April 30–September 30, and February 5–April 3 

 at Point San Pablo, Central San Francisco Bay, California, water year 2003 ......... 32
v

Figure 19. Graph showing calibration of near-bottom optical sensor at 

 Point San Pablo, Central San Francisco Bay, California, water year 2003 ............ 33

Figure 20. Graphs showing time series of mid-depth and near-bottom suspended-

 sediment concentrations calculated from sensor readings at Point San Pablo, 

 Central San Francisco Bay, California, water year 2003 ................................. 34

Figure 21. Graphs showing calibration of mid-depth and near-bottom optical sensors 

 at San Mateo Bridge, South San Francisco Bay, California, water year 2003 ...... 36

Figure 22. Graphs showing time series of mid-depth and near-bottom suspended-

 sediment concentrations calculated from sensor readings at San Mateo 

 Bridge, South San Francisco Bay, California, water year 2003 ........................ 37

Figure 23. Graphs showing calibration of mid-depth and near-bottom optical sensors

 at Dumbarton Bridge, South San Francisco Bay, California, water year 2003 ...... 39

Figure 24. Graphs showing time series of mid-depth and near-bottom suspended-

 sediment concentrations calculated from sensor readings at Dumbarton 

 Bridge, South San Francisco Bay, California, water year 2003 ........................ 40

Figure 25. Graphs showing calibration of mid-depth and near-bottom optical sensors 

 at Channel Marker 17, South San Francisco Bay, California, water year 2003 ...... 42

Figure 26. Graphs showing time series of mid-depth and near-bottom suspended-

 sediment concentrations calculated from sensor readings at Channel 

 Marker 17, South San Francisco Bay, California, water year 2003 .................. 43

Tables

Table 1. Optical sensor depths (in feet) below mean lower low water (MLLW), 

Suisun Bay, San Pablo Bay, and Central and South San Francisco Bays, 

California, water year 2003 .................................................................. 6

Table 2. Statistical summary of calculated suspended-sediment concentration 

data and usable percentage of a complete year of valid data (96 data 

points per day x 365 days) collected using optical sensors, Suisun Bay, 

San Pablo Bay, and Central and South San Francisco Bays, California, 

water year 2003 .............................................................................. 11
vi

Conversion Factors, Datum, Abbreviations,

and Acronyms

Multiply By To obtain

inch (in.) 25.40 millimeter

foot (ft) .3048 meter

foot per second (ft/s) .3048 meter per second

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

(NAVD 88); horizontal coordinate information is referenced to the North American Datum 

of 1927 (NAD 27).

Mean lower low water (MLLW): The average of the lower low water height above the bottom, 

in feet, of each tidal day observed during the National Tidal Datum Epoch. The National Tidal 

Datum Epoch is the specific 19-year period (1960–78 for values given in this report) adopted 

by the National Ocean Service as the official time segment during which tide observations are 

taken and reduced to obtain mean values.

Abbreviations and Acronyms

 ADAPS automated data-processing system

 DWR California Department of Water Resources

 mg/L milligram per liter

 mV millivolt

 NTU nephelometric turbidity units

 PInp nonparametric prediction interval

 RMS root-mean-squared (error)

 SSC suspended-sediment concentration

 USCG U.S. Coast Guard

 USGS U.S. Geological Survey

 WY water year (October 1–September 30) 
Summary of Suspended-Sediment Concentration Data, 

San Francisco Bay, California, Water Year 2003

By Paul A. Buchanan and Neil K. Ganju

Abstract

Suspended-sediment concentration data were collected in San Francisco Bay during water year 2003 (October 1, 2002–

September 30, 2003). Optical sensors and water samples were used to monitor suspended-sediment concentration at two sites 

in Suisun Bay, three sites in San Pablo Bay, one site in Central San Francisco Bay, and three sites in South San Francisco Bay. 

Sensors were positioned at two depths at most sites. Water samples were collected periodically and analyzed for concentrations 

of suspended sediment. The results of the analyses were used to calibrate the output of the optical sensors so that a record of 

suspended-sediment concentrations could be derived. This report presents the data-collection methods used and summarizes the 

suspended-sediment concentration data collected from October 2002 through September 2003. Calibration curves and plots of 

edited data for each sensor also are presented.

Introduction

Sediments are an important component of the San Francisco Bay estuarine system. Bottom sediments provide habitat 

for benthic organisms and are a reservoir for nutrients that contribute to estuarine productivity (Hammond and others, 

1985). Potentially toxic substances, such as metals and pesticides, adsorb to sediment particles (Kuwabara and others, 1989; 

Domagalski and Kuivila, 1993; Flegal and others, 1996). Benthic organisms can ingest these substances and introduce them into 

the food web (Luoma and others, 1985; Brown and Luoma, 1995; Luoma, 1996). Large tidal-induced velocities and wind waves 

in shallow water are capable of resuspending bottom sediments (Powell and others, 1989; Schoellhamer, 1996). 

The transport and fate of suspended sediments are important factors in determining the transport and fate of sedimentassociated contaminants. In Suisun Bay, the maximum suspended-sediment concentration (SSC) usually marks the position of 

the turbidity maximum—a crucial ecological zone where suspended sediments, nutrients, phytoplankton, zooplankton, larvae, 

and juvenile fish accumulate (Peterson and others, 1975; Arthur and Ball, 1979; Kimmerer, 1992; Jassby and Powell, 1994; 

Schoellhamer and Burau, 1998; Schoellhamer, 2001). 

Suspended sediments limit the penetration of light into San Francisco Bay, which affects photosynthesis and primary 

phytosynthetic carbon production (Cole and Cloern, 1987; Cloern, 1987, 1996). Sediments also deposit in ports and shipping 

channels, which then require dredging to maintain navigation (U.S. Environmental Protection Agency, 1992). The U.S. 

Geological Survey (USGS), in cooperation with the CALFED Bay-Delta Program, and the U.S. Army Corps of Engineers, is 

studying the factors that affect SSC in San Francisco Bay.

Purpose and Scope

This report summarizes SSC data collected by the USGS in San Francisco Bay during water year (WY) 2003 and is 

the latest in a series based on data collected beginning in WY 1992 (Buchanan and Schoellhamer, 1995, 1996, 1998, 1999; 

Buchanan and others, 1996; Buchanan and Ruhl, 2000, 2001; and Buchanan and Ganju, 2002, 2003, 2004). Collection of SSC 

data in San Francisco Bay required development of monitoring methods and calibration techniques which are presented in this 

report. SSC were monitored at two sites in Suisun Bay, three sites in San Pablo Bay, one site in Central San Francisco Bay, and 

three sites in South San Francisco Bay. These data were used to help determine the factors that affect SSC in San Francisco Bay 

(U.S. Geological Survey, accessed July 14, 2004). SSC data for WY 1992 through 2003 are available from the U.S. Geological 

Survey (accessed July 15, 2004). 

Introduction 1
Study Area

San Francisco Bay (fig. 1) comprises several major subembayments; Suisun Bay, San Pablo Bay, Central San Francisco 

Bay (Central Bay), and South San Francisco Bay (South Bay). In San Francisco Bay, tides are semidiurnal (two high and two 

low tides per day) with a range of about 5.5 feet (ft) in Suisun Bay, 6.5 ft at the Golden Gate and Central Bay, and about 10 ft 

in South Bay. The tides also follow a 14-day spring-neap cycle. Typical tidal currents range from 0.6 feet per second (ft/s) in 

shallow water to more than 3 ft/s in deep channels (Cheng and Gartner, 1984; Smith, 1987). Winds typically are strongest in 

summer during afternoon, onshore sea breezes. Most precipitation occurs from late autumn to early spring, and freshwater 

discharge into San Francisco Bay is greatest in the spring due to runoff from snowmelt. About 90 percent of the discharge into 

the Bay is from the Sacramento-San Joaquin River Delta, which drains the Central Valley of California (Smith, 1987).

Typically, discharge from the Delta contains over 60 percent of the fluvial sediments that enter the Bay (McKee and 

others, 2002), though this percentage varies from year to year. During wet winters, turbid plumes of water from the Delta have 

extended into South Bay (Carlson and McCulloch, 1974). The bottom sediments in South Bay and in the shallow water areas 

(about 12 ft or less) of Central, San Pablo, and Suisun Bays are composed mostly of silts and clays. Silts and sands are present in 

the deeper parts of Central, San Pablo, and Suisun Bays and in Carquinez Strait (Conomos and Peterson, 1977). 

Acknowledgments

The authors gratefully acknowledge the U.S. Coast Guard (USCG), California Department of Transportation, California 

Department of Water Resources (DWR), EAI International, and the City of Vallejo for their permission and assistance in 

establishing the monitoring sites used in this study. 

The CALFED Bay/Delta Program, USGS Priority Ecosystem Science Program, and the U.S. Army Corps of Engineers, 

as part of the San Francisco Estuary Regional Monitoring Program for Trace Substances, supported collection of these data.

2 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 1. San Francisco Bay study area, California.

Introduction 3
Methods

Instrument Description and Operation

Three different types of optical sensors were used to monitor SSC during WY 2003. The first type of sensor is 

manufactured by D & A Instrument Company and is a cylinder approximately 7 inches (in.) long and 1 in. in diameter with an 

optical window at one end, a cable connection at the other end, and an encased circuit board. A high-intensity infrared emitting 

diode produces a beam through the optical window that is scattered, or reflected, by particles that are about 0.2–12 in. in front of 

the window. A detector (four photodiodes) receives backscatter from a field of 140–165 degrees which is converted to a voltage 

output and recorded on a separate data logger. The second type of sensor, manufactured by BTG, is self-cleaning and differs 

from the D & A Instrument Company sensor in that it measures the intensity of light scattered at 90 degrees between a lightemitting diode and a high-sensitivity photodiode detector. The BTG sensor has a separate electronic unit that sets the resolution 

and maximum reading, expressed in nephelometric turbidity units (NTU). The output from the electronic unit is recorded on 

a separate data logger. The third type of sensor, versions of which are used by both Hydrolab and YSI instruments, measures 

the intensity of light scattered at 90 degrees between a light-emitting diode and a high-sensitivity photodiode detector, and the 

output is processed by internal software to read in NTU. The Hydrolab and YSI instruments are self-contained, including a 

power source and data logger.

Optical sensors were positioned in the water column using polyvinyl chloride (PVC) pipe carriages coated with an 

antifoulant paint to impede biological growth. Carriages were designed to align with the direction of flow and to ride along a 

stainless steel or Kevlar-reinforced nylon suspension line attached to an anchor weight, which allowed sensors to be easily raised 

and lowered for servicing (fig. 2). The plane of the optical window maintained a position parallel to the direction of flow as 

the carriage and sensor aligned itself with the changing direction of flow. Optical sensor depths in the water column are listed 

in table 1.Data acquisition was controlled by electronic data loggers. The loggers used with the D & A Instrument Company 

and BTG sensors were programmed to power the optical sensor every 15 minutes, collect data each second for 1 minute, then 

average and store the output voltage for that 1-minute period. The Hydrolab and YSI internal data loggers collect instantaneous 

values every 15 minutes. Power was supplied by 12-volt batteries.

Biological growth (fouling) interferes with the collection of accurate optical sensor data. Fouling generally was greatest 

on the sensor closest to the water surface. However, at shallower sites where the upper sensor was set 10 ft above the lower 

sensor, fouling was similar on both sensors. Self-cleaning optical sensors were used where conditions allowed. Due to the 

difficulty in servicing some of the monitoring stations, sensors were cleaned manually every 1–5 (usually 3) weeks. Fouling 

would begin to affect sensor output from 2 days to several weeks after cleaning, depending on the level of biological activity in 

the Bay. Generally, biological fouling was greatest during spring and summer.

On-site checks of sensor accuracy were performed using turbidity solutions prepared from a 4,000-nephelometric 

turbidity unit formazin standard. Formazin is an aqueous suspension of an insoluble polymer and is the primary turbidity 

standard (Greenberg and others, 1992). The turbidity solutions were prepared by diluting a 4,000-nephelometric turbidity unit 

stock standard with de-ionized water in a clean, sealable bucket. Prepared solutions ranged from 50 to 200 NTU. At the field 

site, the cleaned sensors were immersed in the solution and the output was recorded on the station log. Monitoring a period of 

sensor performance in a known standard helps to identify output drift or sensor malfunction.

4 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 2. Typical monitoring installation, San Francisco Bay study.

Methods 5
Table 1. Optical sensor depths (in feet) below mean lower low water (MLLW), Suisun Bay, San Pablo Bay, and Central and South San 

Francisco Bays, California, water year 2003 

[For definition of MLLW, see Conversion Factors, Datum, Abbreviations, and Acronyms entry at front of this report]

Site Station No. Latitude Longitude Sensor

depth

Depth below

MLLW

Water depth at 

MLLW

Mallard Island 11185185 38°02’34” 121°55’09” Near-surface

Near-bottom

3.31

20

25

Benicia Bridge 11455780 38°02’42” 122°07’32” Near-surface

Near-bottom

6

55

80

Carquinez Bridge 11455820 38°03’41” 122°13’23” Mid-depth

Near-bottom

40

83

88

Mare Island Causeway 11458370 38°06’40” 122°16’25” Mid-depth

Near-bottom

15

25

30

Channel Marker 9 380519122262901 38°05’19” 122°26’29” Near-bottom 4 6

Point San Pablo 11181360 37°57’53” 122°25’42” Mid-depth

Near-bottom

13

23

26

San Mateo Bridge 11162765 37°35’04” 122°14’59” Mid-depth

Near-bottom

19

40

48

Dumbarton Bridge 373015122071000 37°30’15” 122°07’10” Mid-depth

Near-bottom

22

41

45

Channel Marker 17 372844122043800 37°28’44” 122°04’38” Mid-depth

Near-bottom

12

22

25

1

Depth below water surface.

6 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
Monitoring Sites

Suisun Bay Installations

SSC data were collected in Suisun Bay at Mallard Island and Benicia Bridge (fig. 1, table 1). Optical sensors were 

installed at the DWR Mallard Island Compliance Monitoring Station on February 8, 1994. Optical sensors were positioned to 

coincide with DWR near-bottom electrical conductance and temperature sensors and near-surface pump intake. The pump intake 

is attached to a float and draws water from about 3 ft below the surface. The near-surface optical sensor is attached to a separate 

float and positioned at the same depth as the pump intake.

Optical sensors were deployed off of Pier 7 on the Benicia Bridge on March 15, 1996. The Benicia Bridge site was shut 

down in WY 1998 for seismic retrofitting of the bridge and was reestablished with sondes equiped with optical, conductance, 

and temperature sensors on May 1, 2001. A monitoring site at the Martinez Marina fishing pier was discontinued in WY 1996 

because data from the Benicia Bridge site were considered more representative of SSC in the Carquinez Strait area of Suisun 

Bay (Buchanan and Schoellhamer, 1998).

San Pablo Bay Installations

SSC data were collected in Carquinez Strait at Carquinez Bridge, Napa River at Mare Island Causeway, and San Pablo 

Bay at Channel Marker 9 (fig. 1, table 1). Sondes with optical, conductance, and temperature sensors were deployed off the 

center pier structure at Carquinez Bridge on April 21, 1998. Optical sensors were deployed off a catwalk beneath Mare Island 

Causeway on October 1, 1998. A sonde with optical, conductance, and temperature sensors was deployed off of USCG Channel 

Marker 9 on November 12, 1998. 

Central San Francisco Bay Installations

SSC data were collected in San Pablo Strait at Point San Pablo (fig.1, table 1). Optical sensors were deployed at San 

Pablo Strait on the northern end of the Richmond Terminal no. 4 pier on the western side of Point San Pablo on 

December 1, 1992. The station at Point San Pablo was shut down on January 2, 2001, and reestablished on December 11, 2001, 

off a pier-adjacent structure approximately 25 ft from the previous deployment site. A monitoring station at San Francisco Bay 

at Pier 24 was discontinued on January 3, 2002. The USGS assumed operation of these stations from DWR in October 1989 

(collection of conductivity and temperature data was cooperatively funded by DWR and the USGS). A monitoring station at the 

south tower of the Golden Gate Bridge was operational during water years 1996 and 1997. Conductivity and temperature data 

collected at Point San Pablo and Pier 24 prior to October 1, 1989, can be obtained from DWR. 

South San Francisco Bay Installations

SSC data were collected in South San Francisco Bay at San Mateo Bridge, Dumbarton Bridge, and USCG Channel 

Marker 17 (fig. 1, table 1). Optical sensors were deployed off of Pier 20 on the San Mateo Bridge, on the east side of the ship 

channel, on December 23, 1991. In addition to SSC, specific conductance and temperature (cooperatively funded by DWR and 

the USGS) were monitored at near-bottom and near-surface depths at San Mateo Bridge. The USGS assumed operation of this 

station from DWR in October 1989. Conductivity and temperature data collected at San Mateo Bridge prior to October 1, 1989, 

can be obtained from DWR. Optical sensors were deployed off of Pier 23 on the Dumbarton Bridge on the west side of the ship 

channel on October 21, 1992. Optical sensors were deployed at USCG Channel Marker 17 on February 26, 1992. 

Water-Sample Collection

Water samples, used to calibrate the voltage output of the optical sensors to SSC, were collected using a horizontally 

positioned modified Van Dorn sampler before and after the sensors were cleaned. The Van Dorn sampler is a plastic tube with 

rubber stoppers at each end that snap shut when triggered by a small weight dropped down a suspension cable. The Van Dorn 

sampler was lowered to the depth of the sensor by a reel and crane assembly and triggered while the sensor was collecting 

data. After collection, the water sample was marked for identification and placed in a container for transport. The SSC of water 

samples collected with a modified Van Dorn sampler and a P-72 point sampler, used until WY 1994, were virtually identical 

(Buchanan and others, 1996).

Methods 7
Samples were sent to the USGS Sediment Laboratory in Marina, California, for analysis of SSC. Suspended sediment 

includes all particles in the sample that do not pass through a 0.45-micrometer membrane filter. Suspended-sediment 

concentrations were referred to as suspended-solids concentration in previous reports (Buchanan and Schoellhamer, 1995, 

1996, 1998, 1999; Buchanan and others, 1996; and Buchanan and Ruhl, 2000, 2001). The analytical method used to quantify 

concentrations of suspended solid-phase material did not change but the nomenclature used to describe sediment data did change 

(Gray and others, 2000). Water samples collected for this study were analyzed for suspended-sediment concentration by filtering 

samples through a pretared 0.45-micrometer membrane filter. The filtrate was rinsed with de-ionized water to remove salts, and 

the insoluble material and filter were dried at 103°C and weighed (Fishman and Friedman, 1989). 

Data Processing

Data loggers stored the voltage outputs from the optical sensors at 15-minute intervals (96 data points per day). Recorded 

data were downloaded from the data loggers onto either a storage module or laptop computer during site visits. Raw data from 

the storage modules or laptop computer were loaded into the USGS automated data-processing system (ADAPS).

The time-series data were retrieved from ADAPS and edited using MATLAB software to remove invalid data. Invalid 

data included rapidly increasing voltage outputs and unusually high voltage outputs of short duration. As biological growth 

accumulated on the optical sensors, the voltage output of the sensors increased (except for the Hydrolab’s optical sensor output, which decreased). An example time series of raw and edited optical sensor data is presented in figure 3. After sensors 

were cleaned, sensor output immediately decreased (fig. 3A: May 6, 30, June 17, and July 8). Efforts to correct for biofouling 

proved to be unsuccessful because the signal often was highly variable. Thus, data affected by biofouling often were unusable 

and were removed from the record (fig. 3B). Identifying the point at which fouling begins to affect optical sensor data is somewhat subjective. Indicators are used to help define the point at which fouling begins to take place such as an elevated baseline, 

increasingly variable signal, and comparisons with the other sensor at the site. Spikes in the data, which are anomalously high 

voltages probably caused by debris temporarily wrapped around the sensor or by large marine organisms (fish, crabs) on or near 

the sensor, also were removed from the raw data record (fig. 3B). Sometimes, incomplete cleaning of a sensor would cause a 

small, constant shift in sensor output that could be corrected using water-sample data.

Sensor Calibration and Suspended-Sediment Concentration Data

 The output for the three types of sensors used for this study are proportional to the SSC in the water column at the 

depth of the sensor. SSC calculated from the output of side-by-side sensors with different instrument designs (BTG and 

D & A Instrument Company) were virtually identical (Buchanan and Schoellhamer, 1998). Calibration of the sensor output to 

SSC will vary according to the size and optical properties of the suspended sediment; therefore, the sensors must be calibrated 

using suspended material from the field (Levesque and Schoellhamer, 1995).

The output from the optical sensors was converted to SSC by linear regression using the robust, nonparametric, repeated 

median method (Siegel, 1982). In addition, the prediction interval and the 95-percent confidence interval were calculated and 

presented for each calibration equation.

 The repeated median method calculates the slope in a two-part process. First, for each point (X,Y), the median of all 

possible “point i” to “point j” slopes was calculated

(1)

The calibration slope was calculated as the median of i

 (2) 

Finally, the calibration intercept was calculated as the median of all possible intercepts using the slope calculated above

 (3)

8 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003

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Figure 3. Example of (A) raw and (B) edited optical data, near-bottom sensor, Mare Island Causeway, San Pablo Bay, 

California, water year 2003.

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Sensor Calibration and Suspended-Sediment Concentration Data 9
The final linear calibration equation is

 (4)

The nonparametric prediction interval (PInp) (Helsel and Hirsch, 1992, p. 76) is a constant-width error band that contains 

about 68 percent, or one standard deviation, of the calibration data set. The 68-percent value was selected because essentially it 

has the same error prediction limits as the root-mean-squared (RMS) error of prediction in ordinary least squared regression; the 

latter was used in previous data reports (Buchanan and Schoellhamer, 1995, 1996, 1998, 1999; Buchanan and others, 1996) to 

analyze random sets of normally distributed data. The prediction interval describes the likelihood that a new observation comes 

from the same distribution as the previously collected data set.

The PInp, unlike the RMS error of prediction, frequently is not symmetrical about the regression line. For example, the 

PInp may be reported as +10 milligrams per liter (mg/L) and −7 mg/L. This asymmetry about the regression line is a result of the 

distribution of the data set. The PInp is calculated by computing and sorting, from least to greatest, the residuals for each point. 

Then, based on the sorted list of residuals:

 (5)

where

Y is the residual value,

n is the number of data points, and

α is the confidence level of 0.68.

To calculate the confidence interval, all possible point-to-point slopes must be sorted in ascending order. Based on the 

confidence interval desired, 95-percent for the purposes of this report, the ranks of the upper and lower bounds are calculated as 

follows:

(6)

(7)

where 

Ru is the rank of the upper bound slope,

Rl is the rank of the lower bound slope, and

n is the number of samples.

To establish the 95-percent confidence interval, the ranks calculated above are rounded to the nearest integer and the slope 

associated with each rank in the sorted list is identified. This is a large-sample approximation and was used for each of the confidence intervals presented in this report. However, in the event that fewer than 10 samples had been collected, a direct calculation 

could be performed using the methodology presented in Helsel and Hirsch (1992, p. 273–274).

A statistical summary of the SSC, calculated from optical sensor data, is presented in table 2. The usable percentage of a 

complete year of valid data (96 data points per day × 365 days) for each site is presented in table 2. 

This section of the report also includes the robust regression (calibration) figures for optical sensor output versus SSC 

(in milligrams per liter). The calibration figures include the number of water samples (all water samples used to develop calibration, including those from previous water years), the calculated linear correlation equation, the nonparametric prediction 

interval (shown on the calibration figures as a grey band), and the 95-percent confidence interval (shown on the calibration 

figures as a dash-dot line). In addition, the time-series plots of calculated SSC data are shown for each site.

, and

10 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003

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Table 2. Statistical summary of calculated suspended-sediment concentration data and usable percentage of a complete year of valid 

data (96 data points per day x 365 days) collected using optical sensors, Suisun Bay, San Pablo Bay, and Central and South San Francisco Bays, California, water year 2003

[All values are in milligrams per liter except percent valid data. Lower quartile is 25th percentile; upper quartile is 75th percentile]

Site Depth Mean Median Lower 

quartile

Upper 

quartile

Percent valid data

Mallard Island Near-surface

Near-bottom

 38

 48

 33

 41

 28

 31

 42

 56

56

58

Benicia Bridge Near-surface

Near-bottom

 40

 86

 29

 74

 17

 46

 52

 112

60

61

Carquinez Bridge Mid-depth

Near-bottom

 31

 81

 21

 59

 13

 29

 38

 107

86

62

Mare Island Causeway Mid-depth

Near-bottom

 70

 114

 53

 86

 29

 52

 89

 147

59

71

Channel Marker 9 Near-bottom 132 63 32 160 73

Point San Pablo Mid-depth

Near-bottom

 27

 62

 20

 44

 14

 30

 31

 74

40

52

San Mateo Bridge Mid-depth

Near-bottom

 44

 51

 36

 40

 27

 28

 50

 62

26

31

Dumbarton Bridge Mid-depth

Near-bottom

 56

 76

 45

 59

 31

 36

 64

 91

33

47

Channel Marker 17 Mid-depth

Near-bottom

 72

 83

 53

 55

 29

 31

 91

 102

32

32

Sensor Calibration and Suspended-Sediment Concentration Data 11
Suisun Bay

Mallard Island

PERIOD OF CALIBRATION.—

 NEAR-SURFACE SENSOR: WY 2003 (fig. 4).

 NEAR-BOTTOM SENSOR (A): October 1, 2002, to February 5, 2003 (fig. 5A).

 NEAR-BOTTOM SENSOR (B): February 5, 2003, through WY 2003 (fig. 5B).

NUMBER OF DATA POINTS (WATER SAMPLES) USED FOR CALIBRATION.— 

 NEAR-SURFACE SENSOR: 18 (18 from WY 2003).

 NEAR-BOTTOM SENSOR(A): 181 (5 from WY 2003).

 NEAR-BOTTOM SENSOR(B): 7 (5 from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 NEAR-SURFACE SENSOR: SSC = 0.317 × millivolt (mV) + 5.2.

 NEAR-BOTTOM SENSOR(A): SSC = 0.499 × mV − 8.6.

 NEAR-BOTTOM SENSOR(B): SSC = 0.423 × mV + 51.1.

NONPARAMETRIC PREDICTION INTERVAL.—

 NEAR-SURFACE SENSOR: +10 to −4 mg/L.

 NEAR-BOTTOM SENSOR(A): +9 to −8 mg/L.

 NEAR-BOTTOM SENSOR(B): +24 to −14 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. Sensors were positioned at near-surface (attached to float assembly) and near-bottom depths to coincide with 

DWR near-surface pump intake and the near-bottom electrical conductance and temperature sensors. The near-bottom sensor 

malfunctioned and was replaced on February 5, 2003. The calibration developed for the replacement sensor included two 

water samples collected in WY 2004 to help define the calibration. A −90-millivolt shift to the near-bottom sensor calibration, 

calculated from five water samples not shown on figure 5B (not used to develop calibration), was applied from February 5, 2003, 

through May 8, 2003, when the gain setting on the sensor was changed. The calculated SSC time-series data collected during 

WY 2003 are presented in figure 6. 

12 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
Figure 4. Calibration of near-surface optical sensor at Mallard Island, Suisun Bay, California, water year 2003.

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Sensor Calibration and Suspended-Sediment Concentration Data 13
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Figure 5. Calibration of near-bottom optical sensors, (A) October 1–February 5 and (B) February 5–September 30 at Mallard Island, 

Suisun Bay, California, water year 2003.

14 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 6. Time series of (A) near-surface and (B) near-bottom suspended-sediment concentrations calculated from sensor

readings at Mallard Island, Suisun Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 15
Benicia Bridge

PERIOD OF CALIBRATION.—

 NEAR-SURFACE SENSOR (A): October 1, 2002, to May 20, 2003, and July 23, 2003, to August 28, 2003 (fig. 7A).

 NEAR-SURFACE SENSOR (B): May 20, 2003, to July 2, 2003 (fig. 7B).

 NEAR-BOTTOM SENSOR: WY 2003 (fig. 8).

NUMBER OF DATA POINTS.— 

 NEAR-SURFACE SENSOR (A): 31 (9 from WY 2003).

 NEAR-SURFACE SENSOR (B): 4 (4 from WY 2003).

 NEAR-BOTTOM SENSOR: 45 (16 from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 NEAR-SURFACE SENSOR (A): SSC = 0.939 × NTU + 2.2.

 NEAR-SURFACE SENSOR (B): SSC = 1.410 × NTU + 6.0.

 NEAR-BOTTOM SENSOR: SSC = 1.204 × NTU + 1.9.

NONPARAMETRIC PREDICTION INTERVAL.—

 NEAR-SURFACE SENSOR: +12 to −5 mg/L.

 NEAR-SURFACE SENSOR: undeterminable with 4 samples.

 NEAR-BOTTOM SENSOR: +10 to −18 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. MLLW was approximately 80 ft at the site but approximately 60 ft immediately adjacent, therefore, the near-bottom 

sonde was set approximately 25 ft above the bottom so that the data are representative of the surrounding area. The calibration 

used for data collected at the near-surface location from October 1, 2002, to May 20, 2003, and July 23, 2003, to 

August 28, 2003, was developed from samples collected during the deployment of two Hydrolab sensors. A +10.1-

nephelometric turbidity unit shift to the near-surface sensor calibration, calculated from water samples collected during the 

deployment of a third Hydrolab sensor with a different response and not shown on figure 7A (not used to develop calibration), 

was applied from July 23, 2003, to August 28, 2003. The second calibration used for data collected at the near-surface location 

was developed from water samples collected during the deployment of a YSI sensor from May 20, 2003, to July 2, 2003. The 

four water samples collected for the YSI sensor were insufficient for determining a nonparametric prediction interval. Several 

different sensors were used in the near-bottom location. Because the different sensors (all Hydrolabs) responded similarly to the 

uniform sediment characteristics found in San Francisco Bay (Schoellhamer and others, 2003), the calibration was developed by 

combining water samples collected during each sensor deployment. The calculated SSC time-series data collected during WY 

2003 are presented in figure 9.

16 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 7. Calibration of near-surface optical sensors, (A) October 1–May 20, July 23–August 28 and (B) May 20–July 2 at Benicia 

Bridge, Suisun Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 17
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Figure 8. Calibration of near-bottom optical sensor at Benicia Bridge, Suisun Bay, California, water year 2003.

18 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 9. Time series of (A) near-surface and (B) near-bottom suspended-sediment concentrations calculated from sensor 

readings at Benicia Bridge, Suisun Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 19
San Pablo Bay

Carquinez Bridge

PERIOD OF CALIBRATION.—

 MID-DEPTH SENSOR: WY 2003 (fig. 10).

 NEAR-BOTTOM SENSOR (A): October 1, 2002, to November 12, 2002 (fig.11A).

 NEAR-BOTTOM SENSOR (B): January 29, 2003, through WY 2003 (fig. 11B).

NUMBER OF DATA POINTS.— 

 MID-DEPTH SENSOR: 54 (20 from WY 2003).

 NEAR-BOTTOM SENSOR (A): 60 (2 from WY 2003).

 NEAR-BOTTOM SENSOR (B): 10 (9 from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 MID-DEPTH SENSOR: SSC = 0.978 × NTU + 4.5.

 NEAR-BOTTOM SENSOR (A): SSC = 0.985 × NTU + 5.3.

 NEAR-BOTTOM SENSOR (B): SSC = 1.404 × NTU + 9.6. 

NONPARAMETRIC PREDICTION INTERVAL.—

 MID-DEPTH SENSOR: +13 to −6 mg/L.

 NEAR-BOTTOM SENSOR (A): +19 to −13 mg/L.

 NEAR-BOTTOM SENSOR (B): +22 to −22 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. The near-bottom sensor malfunctioned and was pulled on November 12, 2002, and a replacement sensor was 

deployed on January 29, 2003. The near-bottom replacement sensor was calibrated on March 11, 2003, and recalibrated on 

April 2, 2003, resulting in a +56.8-nephelometric turbidity unit shift being applied during this period. The calculated SSC

time-series data collected during water year 2003 are presented in figure 12.

20 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 10. Calibration of mid-depth optical sensor at Carquinez Bridge, San Pablo Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 21
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Figure 11. Calibration of near-bottom optical sensors, (A) October 1–November 12 and (B) January 29–September 30 at Carquinez 

Bridge, San Pablo Bay, California, water year 2003.

22 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 12. Time series of (A) mid-depth and (B) near-bottom suspended-sediment concentrations calculated from sensor readings 

at Carquinez Bridge, San Pablo Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 23
Mare Island Causeway

PERIOD OF CALIBRATION.—

 MID-DEPTH SENSOR (A): October 1, 2002, to January 7, 2003 (fig. 13A).

 MID-DEPTH SENSOR (B): February 4, 2003, through WY 2003 (fig. 13B).

 NEAR-BOTTOM SENSOR (A): October 1, 2002, to April 14, 2003 (fig. 14A).

 NEAR-BOTTOM SENSOR (B): April 14, 2003, through WY 2003 (fig. 14B).

NUMBER OF DATA POINTS.— 

 MID-DEPTH SENSOR (A): 47 (4 from WY 2003).

 MID-DEPTH SENSOR (B): 7 (7 from WY 2003).

 NEAR-BOTTOM SENSOR (A): 101 (9 from WY 2003).

 NEAR-BOTTOM SENSOR (B): 15 (8 from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 MID-DEPTH SENSOR (A): SSC = 0.527 × mV − 14.8.

 MID-DEPTH SENSOR (B): SSC = 0.589 × mV + 22.7.

 NEAR-BOTTOM SENSOR (A): SSC = 0.686 × mV − 10.5.

 NEAR-BOTTOM SENSOR (B): SSC = 1.026 × mV − 0.5.

NONPARAMETRIC PREDICTION INTERVAL.—

 MID-DEPTH SENSOR (A): +9 to −11 mg/L.

 MID-DEPTH SENSOR (B): +12 to −15 mg/L.

 NEAR-BOTTOM SENSOR (A): +29 to −26 mg/L.

 NEAR-BOTTOM SENSOR (B): +77 to −15 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. The mid-depth sensor was replaced on January 7, 2003, because the output had drifted. The mid-depth replacement 

sensor was removed on February 4, 2003, because the instrument gain was found to be set incorrectly resulting in lost data 

during this period. The calibration of the near-bottom sensor changed after the site visit on April 14, 2003, possibly due to the 

optical window being scratched during cleaning. The calibration developed after April 14, 2003, for the near-bottom sensor 

included seven water samples collected in WY 2004 to help define the calibration. The calculated SSC time-series data collected 

during WY 2003 are presented in figure 15.

24 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 13. Calibration of mid-depth optical sensors, (A) October 1–January 7 and (B) February 4–September 30 at Mare Island 

Causeway, San Pablo Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 25
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Figure 14. Calibration of near-bottom optical sensors, (A) October 1–April 14 and (B) April 14–September 30 at Mare Island Causeway, 

San Pablo Bay, California, water year 2003.

26 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 15. Time series of (A) mid-depth and (B) near-bottom suspended-sediment concentrations calculated from sensor readings 

at Mare Island Causeway, San Pablo Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 27
Channel Marker 9

PERIOD OF CALIBRATION.—

 NEAR-BOTTOM SENSOR: WY 2003 (fig. 16).

NUMBER OF DATA POINTS.— 

 NEAR-BOTTOM SENSOR: 30 (22 from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 NEAR-BOTTOM SENSOR: SSC = 1.699 × NTU + 0.5.

NONPARAMETRIC PREDICTION INTERVAL.—

 NEAR-BOTTOM SENSOR: +27 to −12 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. The calculated SSC time-series data collected during WY 2003 are presented in figure 17. 

28 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 16. Calibration of near-bottom optical sensor at Channel Marker 9, San Pablo Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 29
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Figure 17. Time series of near-bottom suspended-sediment concentrations calculated from sensor readings at Channel 

Marker 9, San Pablo Bay, California, water year 2003.

30 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
Central San Francisco Bay

Point San Pablo

PERIOD OF CALIBRATION.—

 MID-DEPTH SENSOR (A): October 1, 2002, to February 5, 2003, and April 30, 2003, through WY 2003 (fig. 18A).

 MID-DEPTH SENSOR (B): February 5, 2003, to April 3, 2003 (fig. 18B).

 NEAR-BOTTOM SENSOR: WY 2003 (fig. 19).

NUMBER OF DATA POINTS.— 

 MID-DEPTH SENSOR (A): 16 (6 from WY 2003).

 MID-DEPTH SENSOR (B): 8 (1 from WY 2003).

 NEAR-BOTTOM SENSOR: 9 (all from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 MID-DEPTH SENSOR (A): SSC = 1.940 × NTU – 0.8.

 MID-DEPTH SENSOR (B): SSC = 1.008 × NTU + 6.7.

 NEAR-BOTTOM SENSOR: SSC = 2.170 × NTU + 7.2.

NONPARAMETRIC PREDICTION INTERVAL.—

 MID-DEPTH SENSOR (A): +15 to −5 mg/L.

 MID-DEPTH SENSOR (B): +4 to −14 mg/L.

 NEAR-BOTTOM SENSOR: +5 to −7 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. The mid-depth calibration (fig. 18A) was developed from water samples collected during the deployment of 

two Hydrolab sensors. The third Hydrolab sensor used at the mid-depth location from February 5, 2003, to April 3, 2003, 

had a much different signal response and a separate calibration was developed (fig. 18B). Three Hydrolab sensors were used 

at the near-bottom position which responded similarly to the uniform sediment characteristics found in San Francisco Bay 

(Schoellhamer and others, 2003), and the calibration was developed by combining water samples collected during each sensor 

deployment. The calculated SSC time-series data collected during WY 2003 are presented in figure 20.

Sensor Calibration and Suspended-Sediment Concentration Data 31
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Figure 18. Calibration of mid-depth optical sensors, (A) October 1–February 5, April 30–September 30, and (B) February 5–April 3 at 

Point San Pablo, Central San Francisco Bay, California, water year 2003.

32 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 19. Calibration of near-bottom optical sensor at Point San Pablo, Central San Francisco Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 33
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Figure 20. Time series of (A) mid-depth and (B) near-bottom suspended-sediment concentrations calculated from sensor readings 

at Point San Pablo, Central San Francisco Bay, California, water year 2003.

34 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
South San Francisco Bay

San Mateo Bridge

PERIOD OF CALIBRATION.—

 MID-DEPTH SENSOR: WY 2003 (fig. 21A).

 NEAR-BOTTOM SENSOR: WY 2003 (fig. 21B).

NUMBER OF DATA POINTS.— 

 MID-DEPTH SENSOR: 39 (16 from WY 2003).

 NEAR-BOTTOM SENSOR: 32 (16 from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 MID-DEPTH SENSOR: SSC = 0.592 × mV + 2.2.

 NEAR-BOTTOM SENSOR: SSC = 0.596 × mV + 1.7.

NONPARAMETRIC PREDICTION INTERVAL.—

 MID-DEPTH SENSOR: +6 to −12 mg/L.

 NEAR-BOTTOM SENSOR: +9 to −9 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. A +8.2-millivolt shift to the near-bottom sensor calibration, calculated from a water sample not shown on 

figure 21B (not used to develop calibration), was applied from August 20, 2003, to September 9, 2003. The calculated SSC 

time-series data collected during WY 2003 are presented in figure 22.

Sensor Calibration and Suspended-Sediment Concentration Data 35
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Figure 21. Calibration of (A) mid-depth and (B) near-bottom optical sensors at San Mateo Bridge, South San Francisco Bay, 

California, water year 2003.

36 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 22. Time series of (A) mid-depth and (B) near-bottom suspended-sediment concentrations calculated from sensor

readings at San Mateo Bridge, South San Francisco Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 37
Dumbarton Bridge

PERIOD OF CALIBRATION.—

 MID-DEPTH SENSOR: WY 2003 (fig. 23A).

 NEAR-BOTTOM SENSOR: WY 2003 (fig. 23B).

NUMBER OF DATA POINTS.— 

 MID-DEPTH SENSOR: 24 (14 from WY 2003).

 NEAR-BOTTOM SENSOR: 79 (16 from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 MID-DEPTH SENSOR: SSC = 0.725 × mV − 4.8.

 NEAR-BOTTOM SENSOR: SSC = 0.602 × mV − 11.0.

NONPARAMETRIC PREDICTION INTERVAL.—

 MID-DEPTH SENSOR: +9 to -12 mg/L.

 NEAR-BOTTOM SENSOR: +12 to −10 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. The calculated SSC time-series data collected during WY 2003 are presented in figure 24.

38 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 23. Calibration of (A) mid-depth and (B) near-bottom optical sensors at Dumbarton Bridge, South San Francisco Bay, 

California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 39
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Figure 24. Time series of (A) mid-depth and (B) near-bottom suspended-sediment concentrations calculated from sensor

readings at Dumbarton Bridge, South San Francisco Bay, California, water year 2003.

40 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
Channel Marker 17

PERIOD OF CALIBRATION.—

 MID-DEPTH SENSOR: WY 2003 (fig. 25A).

 NEAR-BOTTOM SENSOR: WY 2003 (fig. 25B).

NUMBER OF DATA POINTS.— 

 MID-DEPTH SENSOR: 115 (15 from WY 2003).

 NEAR-BOTTOM SENSOR: 90 (16 from WY 2003).

CALCULATED LINEAR CORRELATION EQUATION.—

 MID-DEPTH SENSOR: SSC = 0.633 × mV − 15.1.

 NEAR-BOTTOM SENSOR: SSC = 0.574 × mV − 2.8.

NONPARAMETRIC PREDICTION INTERVAL.—

 MID-DEPTH SENSOR: +13 to −13 mg/L.

 NEAR-BOTTOM SENSOR: +20 to −12 mg/L.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and(or) recording 

instruments. The calculated SSC time-series data collected during WY 2003 are presented in figure 26.

Sensor Calibration and Suspended-Sediment Concentration Data 41
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Figure 25. Calibration of (A) mid-depth and (B) near-bottom optical sensors at Channel Marker 17, South San Francisco Bay, 

California, water year 2003.

42 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
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Figure 26. Time series of (A) mid-depth and (B) near-bottom suspended-sediment concentrations calculated from sensor readings at 

Channel Marker 17, South San Francisco Bay, California, water year 2003.

Sensor Calibration and Suspended-Sediment Concentration Data 43
Summary

Suspended-sediment concentration (SSC) data were collected by the U.S. Geological Survey (USGS) at two sites in 

Suisun Bay, three sites in San Pablo Bay, one site in Central San Francisco Bay, and three sites in South San Francisco Bay 

during water year 2003. Three types of optical sensors, each controlled by electronic data loggers, were used to monitor 

suspended sediment. Water samples were collected to calibrate the output of the optical sensors to SSC, and the recorded data 

were recovered and edited. Water-sample sediment concentration data are available in the USGS sediment database. Time-series 

data are available in the USGS automated data-processing system database. The calculated SSC data are available from the 

USGS (accessed July 15, 2004).

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trace metal contamination in San Francisco Bay: Marine Ecology Progress Series, v. 124, p. 129–142.

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California, water year 1997: U.S. Geological Survey Open-File Report 99-189, 52 p.

Buchanan, P.A., Schoellhamer, D.H., and Sheipline, R.C., 1996, Summary of suspended- solids concentration data, San 

Francisco Bay, California, water year 1994: U.S. Geological Survey Open-File Report 95-776, 48 p.

Carlson, P.R., and McCulloch, D.S., 1974, Aerial observations of suspended-sediment plumes in San Francisco Bay and adjacent 

Pacific Ocean: U.S. Geological Survey Water-Resources Research, v. 2, no. 5, p. 519–526.

Cheng, R.T., and Gartner, J.W., 1984, Tides, tidal and residual currents in San Francisco Bay, California—Results of 

measurements, 1979–1980: U.S. Geological Survey Water-Resources Investigations Report 84-4339, 72 p.

Cloern, J.E., 1987, Turbidity as a control on phytoplankton biomass and productivity in estuaries: Continental Shelf Research, 

v. 7, no. 11/12, p. 1367–1381.

44 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2003
Cloern, J.E., 1996, Phytoplankton bloom dynamics in coastal ecosystems: a review with some general lessons from sustained 

investigation of San Francisco Bay, California: Reviews of Geophysics, v. 34, no. 2, p. 127–168. 

Cole, B.E., and Cloern, J.E., 1987, An empirical model for estimating phytoplankton productivity in estuaries: Marine Ecology 

Progress Series, v. 36, p. 299–305.

Conomos, T.J., and Peterson, D.H., 1977, Suspended-particle transport and circulation in San Francisco Bay, an overview: New 

York, Academic Press. Estuarine Processes, v. 2, p. 82–97.

Domagalski, J.L., and Kuivila, K.M., 1993, Distributions of pesticides and organic contaminants between water and suspended 

sediment, San Francisco Bay, California: Estuaries, v. 16, no. 3A, p. 416–426.

Fishman, M.J., and Friedman, L.C., 1989, Methods for determination of inorganic substances in water and fluvial sediments: 

U.S. Geological Survey Techniques of Water-Resources Investigations, book 5, chap. A1, 545 p.

Flegal, A.R., Rivera-Duarte, I., Ritson, P.I., Scelfo, G.M., Smith, G.J., Gordon, M.R., and Sanudo-Wilhelmy, S.A., 1996, Metal 

contamination in San Francisco Bay waters: Historic perturbations, contemporary concentrations, and future considerations: 

San Francisco Bay: The Ecosystem, Hollibaugh, J.T. (ed.), Pacific Division of the American Association for the Advancement 

of Science, San Francisco, p. 173–188.

Gray, J.R., Glysson, G.D., Turcios, L.M., Schwarz, G.E., 2000, Comparability of suspended-sediment concentration and total 

suspended-solids data: U.S. Geological Survey Water-Resources Investigations Report 00-4191, p. 14.

Greenberg, A.E., Clesceri, L.S., Eaton, A.D., 1992, Standard methods for the examination of water and wastewater: American 

Public Health Association, 18th ed., variously paged.

Hammond, D.E., Fuller, C., Harmon, D., Hartman, B., Korosec, M., Miller, L.G., Rea, R., Warren, S., Berelson, W., and Hager, 

S.W., 1985, Benthic fluxes in San Francisco Bay: Hydrobiologia, v. 129, p. 69–90.

Helsel, D.R., and Hirsch, R.M., 1992, Statistical methods in water resources: Studies in Environmental Science, v. 49, Elsevier, 

New York, 522 p.

Jassby, A.D., and Powell, T.M., 1994, Hydrodynamic influences on interannual chlorophyll variability in an estuary: Upper San 

Francisco Bay–Delta (California, U.S.A.): Estuarine, Coastal and Shelf Science, v. 39, p. 595–618.

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