Summary of Suspended-Sediment 

Concentration Data, San Francisco Bay, 

California, Water Year 2004

By Paul A. Buchanan and Megan A. Lionberger

Prepared in cooperation with the CALFED Bay–Delta Authority and the 

U.S. Army Corps of Engineers, San Francisco District

Data Series 226

U.S. Department of the Interior

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

Dirk Kempthorne, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2006

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reproduce any copyrighted materials contained within this report.

Suggested reference:

Buchanan, P.A., and Lionberger, M.A., 2006, Summary of Suspended-Sediment Concentration Data, San Francisco 

Bay, California, Water Year 2004: U.S. Geological Survey Data Series 226, 49 p. 
iii

Contents

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

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

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

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

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

Methods...........................................................................................................................................................2

Instrument Description and Operation..............................................................................................2

Establishment of Monitoring Sites.....................................................................................................5

Suisun Bay Installations .............................................................................................................5

San Pablo Bay Installations .......................................................................................................6

Central San Francisco Bay Installations..................................................................................6

South San Francisco Bay Installations ....................................................................................6

Water-Sample Collection.....................................................................................................................6

Data Processing....................................................................................................................................7

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

Suisun Bay ...........................................................................................................................................11

Mallard Island.............................................................................................................................11

Benicia Bridge............................................................................................................................14

San Pablo Bay .....................................................................................................................................18

Carquinez Bridge .......................................................................................................................18

Mare Island Causeway.............................................................................................................22

Channel Marker 1.......................................................................................................................26

Central San Francisco Bay................................................................................................................29

Point San Pablo..........................................................................................................................29

Alcatraz Island............................................................................................................................33

South San Francisco Bay ..................................................................................................................36

San Mateo Bridge......................................................................................................................36

Dumbarton Bridge .....................................................................................................................39

Channel Marker 17.....................................................................................................................43

Summary........................................................................................................................................................47

References Cited..........................................................................................................................................47
iv

Figures

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

Figure 2. Schematic showing typical monitoring installation, San Francisco Bay study ...... 4

Figure 3. Graph showing example of (A) raw and (B) processed optical backscatterance 

data, near-bottom sensor, Mare Island Causeway, San Pablo Bay, California, 

water year 2004 .............................................................................. 7

Figure 4. Graphs showing calibration of near-surface optical backscatterance sensors, 

(A) October 1–December 10 and (B) December 10–September 30 at Mallard 

Island, Suisun Bay, California, water year 2004.......................................... 10

Figure 5. Graph showing calibration of near-bottom optical backscatterance sensor at 

Mallard Island, Suisun Bay, California, water year 2004 .............................. 12

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

Suisun Bay, California, water year 2004 ................................................ 13

Figure 7. Graph showing calibration of near-surface optical backscatterance sensor at 

Benicia Bridge, Suisun Bay, California, water year 2004 .............................. 15

Figure 8. Graphs showing calibration of near-bottom optical backscatterance sensors,

(A) October 1–October 29, July 29–September 30 and (B) November 17–July 29 at 

Benicia Bridge, Suisun Bay, California, water year 2004 .............................. 16

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

Suisun Bay, California, water year 2004 ................................................ 17

Figure 10. Graphs showing calibration of mid-depth optical backscatterance sensors, 

(A) October 1–October 29, December 8–March 3 and (B) March 3–September 30 

at Carquinez Bridge, San Pablo Bay, California, water year 2004 ..................... 19

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

(A) October 1–October 29, May 13–June 14 and (B) November 18–May 4, 

June 14–September 30 at Carquinez Bridge, San Pablo Bay, California, 

water year 2004 .............................................................................. 20

Figure 12. Graphs showing time series of (A) mid-depth and (B) near-bottom suspendedsediment concentrations calculated from sensor readings at Carquinez Bridge, 

San Pablo Bay, California, water year 2004 ............................................. 21

Figure 13. Graph showing calibration of mid-depth optical backscatterance sensor at 

Mare Island Causeway, San Pablo Bay, California, water year 2004 ............... 23

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

(A) October 1–August 12 and (B) August 12–September 30 at Mare Island 

Causeway, San Pablo Bay, California, water year 2004................................. 24

Figure 15. Graphs showing time series of (A) mid-depth and (B) near-bottom suspendedsediment concentrations calculated from sensor readings at Mare Island 

Causeway, San Pablo Bay, California, water year 2004................................. 25

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

Channel Marker 1 at San Pablo Bay, California, water year 2004 ..................... 27

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

calculated from sensor readings at Channel Marker 1, San Pablo Bay, California, 

water year 2004 .............................................................................. 28

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

(A) October 1–October 30 and (B) November 19–September 30 at Point San 

Pablo, Central San Francisco Bay, California, water year 2004........................ 30
Figure 19. Graph showing calibration of near-bottom optical backscatterance sensor at 

Point San Pablo, Central San Francisco Bay, California, water year 2004............ 31

Figure 20. Graphs showing time series of (A) mid-depth and (B) near-bottom suspendedsediment concentrations calculated from sensor readings at Point San Pablo, 

Central San Francisco Bay, California, water year 2004 .............................. 32

Figure 21. Graphs showing calibration of mid-depth optical backscatterance sensors, 

(A) November 6–August 12 and (B) September 9–30, at Alcatraz Island, 

Central San Francisco Bay, California, water year 2004 .............................. 34

Figure 22. Graph showing time series of mid-depth suspended-sediment concentrations 

calculated from sensor readings at Alcatraz Island, Central San Francisco Bay, 

California, water year 2004 ............................................................... 35

Figure 23. Graphs showing calibration of (A) mid-depth and (B) near-bottom optical 

backscatterance sensors at San Mateo Bridge, South San Francisco Bay, 

California, water year 2004 ............................................................... 37

Figure 24. Graphs showing time series of (A) mid-depth and (B) near-bottom suspendedsediment concentrations calculated from sensor readings at San Mateo Bridge, 

South San Francisco Bay, California, water year 2004 ................................. 38

Figure 25. Graphs showing calibration of mid-depth optical backscatterance sensor at 

Dumbarton Bridge, South San Francisco Bay, California, water year 2004 ......... 40

Figure 26. Graphs showing calibration of near-bottom optical backscatterance sensors, 

(A) October 1–March 16 and (B) March 17–September 30 at Dumbarton Bridge, 

South San Francisco Bay, California, water year 2004 ................................. 41

Figure 27. Graphs showing time series of (A) mid-depth and (B) near-bottom suspendedsediment concentrations calculated from sensor readings at Dumbarton Bridge, 

South San Francisco Bay, California, water year 2004 ................................. 42

Figure 28. Graphs showing calibration of mid-depth optical backscatterance sensors, 

(A) October 1–June 9 and (B) June 9–September 30 at Channel Marker 17, 

South San Francisco Bay, California, water year 2004 ................................. 44

Figure 29. Graphs showing calibration of near-bottom optical backscatterance sensors, 

(A) October 1–June 9 and (B) July 1–September 30 at Channel Marker 17, South San 

Francisco Bay, California, water year 2004 ................................................... 45 

Figure 30. Graph showing 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 2004 .................................... 46

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 2004 ................................................................................. 5

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 2004 .............................. 9
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

quart 9.463 × 10–1 liter

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).

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

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 (1960–1978 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

mV millivolt

FTS Forest Technology Systems

NTU nephelometric turbidity units

PInp nonparametric prediction interval

PVC polyvinyl chloride

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) 
Abstract

Suspended-sediment concentration data were collected by the U.S. Geological Survey in San Francisco Bay during water 

year 2004 (October 1, 2003–September 30, 2004). Optical sensors and water samples were used to monitor suspended-sediment 

concentration at two sites in Suisun Bay, three sites in San Pablo Bay, two sites 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, in graphs, the suspended-sediment concentration data collected from October 2003 through September 

2004. Calibration curves and plots of the processed 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, can adsorb to sediment particles (Kuwabara and others, 1989; Domagalski 

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

food web (Luoma and others, 1985; Brown and Luoma, 1995; Luoma, 1996). Large tidal-induced current 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 sediment-associated 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) 2004 and is 

the latest in a series of reports 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, 2005). 

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 (a tidal estuary that drains into San Pablo Bay), three 

sites in San Pablo Bay (a northern extension of San Francisco Bay), two sites in Central San Francisco Bay, and three sites in 

South San Francisco Bay. SSC data from WY 1992 through WY 2004 were used to help determine the factors that affect SSC 

in San Francisco Bay (U.S. Geological Survey, 2006, accessed October 30, 2006). SSC data for WY 1992 through 2004 are 

available from the U.S. Geological Survey at http://sfbay.wr.usgs.gov/access/Fixed_sta/ (accessed October 30, 2006). 

Summary of Suspended-Sediment Concentration Data, 

San Francisco Bay, California, Water Year 2004

By Paul A. Buchanan and Megan A. Lionberger
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) and have 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 

the 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, as a result of 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 about 60 percent of the fluvial sediments that enter the Bay (McKee and 

others, 2006), 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), the National Park Service, 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 project was done in cooperation with the CALFED Bay–Delta Program, the 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.

Methods

Instrument Description and Operation

Three different types of optical sensors were used to monitor SSC during WY 2004. 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 Forest Technology Systems (FTS), 

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 laser diode and a high-sensitivity silicon photodiode detector. The output, in nephelometric turbidity units 

(NTU), 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 (NTU) is processed by internal software. 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.

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.

   Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Figure 1. San Francisco Bay study area, California.

Suisun Bay

Carquinez Strait

San Pablo Bay 

P a c i f i c O c e a n

0 5

0 5 10 MILES

10 KILOMETERS

EXPLANATION

Continuous suspended-sediment 

concentration monitoring site

San Mateo Discontinued monitoring site Bridge

Golden Gate

 Bridge Bay

 Bridge 

San Pablo Strait

122 30

38

37 45

37 30

122 15 122

Richmond/San Rafael

 Bridge

CENTRAL

VALLEY

San Francisco Bay/

Sacramento-San Joaquin

River Delta

STUDY

 AREA

Dumbarton Bridge

Channel Marker 17

Mallard Island

Point San Pablo

Pier 24

 Benicia

Carquinez Bridge

 Bridge

Mare Island

 Causeway

Channel

Marker 1

South

San Francisco

Bay

Central

San Francisco

Bay

Martinez

Alcatraz

Island

Channel

Marker 9

Napa River

Petaluma

River

C A L I F O R N I A

Methods 
Figure 2. Typical monitoring installation, San Francisco Bay study.

(Schematic not to scale)

SENSOR CARRIAGE

(Not to scale)

Weight

Near-bottom sensor

and carriage

Mid-depth sensor

and carriage Sensor head

Instrument

shelter

Suspension line

Sensor cable

Davit

   Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
On-site checks of sensor accuracy were performed using turbidity solutions prepared from a 4,000-NTU 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-NTU stock standard with de-ionized water in a clean, sealable bucket. 

Prepared solutions ranged from 50 to 200 NTU. Prepared solutions were checked with a Hach Drel 2000 Spectrophotometer 

for accuracy. At the field site, the cleaned sensors were immersed in the solution and the output was recorded on the station log. 

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

Data acquisition was controlled by electronic data loggers. The logger used with the D & A Instrument Company sensor 

was 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, YSI and FTS data loggers collect instantaneous values every 15 minutes. 

Power was supplied by 12-volt batteries.

Establishment of Monitoring Sites

Suisun Bay Installations

SSC data were collected in Suisun Bay at Mallard Island and at 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 the 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 August 7, 1998, for seismic retrofitting of the bridge and was reestablished with sondes equipped 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).

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 2004 . 

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

Abbreviated station name

Site identification 

number

Latitude Longitude

Sensor

position

Depth below

MLLW1

Water depth at

MLLW

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

Near-bottom

3.3

20

25

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

Near-bottom

9

61

80

Carquinez Bridge 11455820 38°03′41′′ 122°13′53′′ Mid-depth

Near-bottom

40

83

88

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

Near-bottom

3

25

30

Channel Marker 1 380240122255701 38°02′40′′ 122°25′57′′ Mid-depth 2 8

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

Near-bottom

8

23

26

Alcatraz Island 374938122251801 37°49′38′′ 122°25′18′′ Mid-depth 6 16

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

20

41

45

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

Near-bottom

11

21

25

1

Depth below water surface.

Methods 
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 1 (fig. 1, table 1). Sondes with optical, conductance, and temperature sensors were deployed off of the 

center pier structure at Carquinez Bridge on April 21, 1998. Optical sensors were deployed off of 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 1 on October 7, 2003. A monitoring site at USCG Channel Marker 9 was discontinued in WY 2003 because data from 

the USCG Channel Marker 1 site were considered less affected by the processes that occur at the mouth of the Petaluma River 

(Ganju and others, 2004).

 Central San Francisco Bay Installations

SSC data were collected in San Pablo Strait at Point San Pablo and San Francisco Bay at Alcatraz Island (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 sonde with 

optical, conductance, and temperature sensors was deployed off the northeast side of Alcatraz Island on November 6, 2003. 

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 funded cooperatively 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 output of the optical sensors to SSC, were collected using a horizontally positioned 

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 clean, 1-liter, plastic bottle for transport. The SSC of water samples 

collected with a Van Dorn sampler and a P-72 point sampler, used until WY 1994, were virtually identical (Buchanan and others, 1996).

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. The analytical method used 

to quantify concentrations of suspended solid-phase material was consistent from 1992 through the present study; however, 

the nomenclature used to describe sediment data was changed (Gray and others, 2000). Suspended-sediment concentrations

were referred to as suspended-solids concentrations in previous reports (Buchanan and Schoellhamer, 1995, 1996, 1998, 1999; 

Buchanan and others, 1996; Buchanan and Ruhl, 2000, 2001). Water samples collected for this study were analyzed for suspended-sediment concentration by filtering samples through a pre-weighed tared 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). 

 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Data Processing

Data loggers stored the optical sensor output 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 processed to remove invalid data. Invalid data included rapidly 

increasing sensor outputs and unusually high sensor outputs of short duration. As biological growth accumulated on the optical sensors, the sensor output increased (except for the Hydrolab’s optical sensor output, which decreased). An example timeseries of raw and processed 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 adjusted by applying a correction derived from water-sample data collected during the period of incomplete 

cleaning. 

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

Bay, California, water year 2004.

0

500

1,000

1,500

0

500

1,000

1,500

RAW DATA, IN MILLIVOLTS PROCESSED DATA, IN MILLIVOLTS

MAY JUNE JULY

2004

Sensor output

Cleaning

A

B

Methods 
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 some data sets, the variance of the residuals is not constant, as it increases with voltage. 

Constant variance of residuals is necessary when using ordinary least-squares to obtain the best linear unbiased estimator of 

suspended-sediment concentration (Helsel and Hirsch, 1992, p. 225). Therefore, robust regression is more appropriate than 

ordinary least squares for the calibration curves. In addition, the prediction interval and the 95-percent confidence interval were 

calculated and presented for each calibration equation. Whenever possible, water-sample data collected in previous water years 

are included in the calibrations to incorporate the largest range of observed concentrations. Previously collected water-sample 

data are discarded if a sensor’s calibration has drifted.

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

the median of all possible “point i” to “point j” slopes was calculated

βi

j i

j i

median

Y Y

X X = j i −− ≠

( )

( )

 for all 

 (1)

The calibration slope was calculated as the median of βi

slope = = ( ) βˆ

1 median βi (2)

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

intercept = = βˆ ( ) − βˆ o median Y X i 1 i (3)

The final linear calibration equation is

Y X = + o β β ˆ ˆ

1 (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:

 

nonparametric prediction interval = = 

















( ) +

PInp Y n

ˆα

2 1

to Yˆ

1 n 2 − 1 

















( ) + α

 (5) 

where

Yˆ is the residual value,

n is the number of data points, and

α is the confidence level of 0.68.

 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
To calculate the 95-percent confidence interval associated with the estimated calibration slope, all possible point-to-point 

slopes were sorted in ascending order, and the ranks of the upper and lower bounds were calculated as follows:

Ru

n n n n n

=

− +

 − +



















































 ( ) . 1 ( )( )

2

1 96 1 2 5

18

2





























 (6)

and

Rl

n n n n n

=

− −  − +























( ) . 1 ( )( )

2

1 96 1 2 5

18

2 (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 upper and lower ranks calculated above are rounded to the nearest 

integer and the slope associated with each rank 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 also is presented in table 2. 

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 2004.

[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

34

39

31

36

24

29

41

46

88

80

Benicia Bridge

Near-surface

Near-bottom

46

96

37

85

25

53

59

127

81

81

Carquinez Bridge Mid-depth

Near-bottom

49

77

41

65

28

42

62

95

77

70

Mare Island Causeway Mid-depth

Near-bottom

69

121

53

99

33

64

90

158

63

80

Channel Marker 1 Mid-depth 76 55 34 94 62

Point San Pablo Mid-depth

Near-bottom

46

61

36

49

23

33

58

76

70

79

Alcatraz Island Mid-depth 18 17 15 20 58

San Mateo Bridge Mid-depth

Near-bottom

41

40

37

33

27

24

49

48

47

47

Dumbarton Bridge Mid-depth

Near-bottom

44

48

35

35

26

25

52

54

33

39

Channel Marker 17 Mid-depth

Near-bottom

52

61

30

35

17

21

61

69

45

50

Sensor Calibration and Suspended-Sediment Concentration Data 
This section of the report also includes figures showing graphical results of the regression analysis (calibration) relating 

SSC (in milligrams per liter) to optical sensor output. The calibration figures (for example, fig. 4) include the number of water 

samples (all water samples used to develop calibration, including those from previous water years), the calculated linear regression equation, the nonparametric prediction interval (shown on the calibration figures as a grey band), and the 95-percent confidence interval for the regression line slope. In addition, the time-series plots of calculated SSC data are shown for each site.

Figure 4. Calibration of near-surface optical backscatterance sensors, (A) October 1–December 10 and (B) 

December 10–September 30 at Mallard Island, Suisun Bay, California, water year 2004.

0 50 100 150 200 250 300

0

50

100

150

200

SENSOR OUTPUT, IN MILLIVOLTS

Number of water samples  20

Calibration equation: y  0.388  mV  1.9

Non-parametric prediction interval: 7 to –10

95 percent confidence bound on equation slope (0.388): 0.276 to 0.556

0 20 40 60 80 100 120

0

50

100

150

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples  22

Calibration equation: y  0.711 NTU  8.4

Non-parametric prediction interval: 12 to –4

95 percent confidence bound on equation slope (0.711): 0.523 to 0.856

A

B

10 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Suisun Bay

Mallard Island

PERIOD OF CALIBRATION.—

NEAR-SURFACE SENSOR (A): October 1, 2003, to December 10, 2003 (fig. 4A).

NEAR-SURFACE SENSOR (B): December 10, 2003, through September 30, 2004 (fig. 4B).

NEAR-BOTTOM SENSOR: December 10, 2003 through September 30, 2004 (fig. 5).

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

NEAR-SURFACE SENSOR(A): 20 (3 from WY 2004).

NEAR-SURFACE SENSOR(B): 22 (22 from WY 2004).

NEAR-BOTTOM SENSOR: 22 (22 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

NEAR-SURFACE SENSOR(A): SSC = 0.388 × millivolt (mV) + 1.9.

NEAR-SURFACE SENSOR(B): SSC = 0.711 × mV + 8.4.

NEAR-BOTTOM SENSOR: SSC = 0.769 × mV + 7.2.

NONPARAMETRIC PREDICTION INTERVAL.—

NEAR-SURFACE SENSOR(A): +7 to -10 mg/L.

NEAR-SURFACE SENSOR(B): +12 to -4 mg/L.

NEAR-BOTTOM SENSOR: +9 to -5 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

NEAR-SURFACE SENSOR (A): 0.276 to 0.556.

NEAR-SURFACE SENSOR (B): 0.523 to 0.856.

NEAR-BOTTOM SENSOR: 0.643 to 1.108.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensor 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. Sensors with wipers (DTS-12’s) were 

deployed December 10, 2003. The wiper on the near-surface sensor malfunctioned and was replaced on June 22, 2004, with 

another DTS-12. Because the two sensors (DTS-12’s) 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 output from the near-bottom sensor (OBS) was highly irregular from October 1, 2003, through 

December 10, 2003, and these data were removed from the record. The calculated SSC time-series data for WY 2004 are presented in figure 6. 

Sensor Calibration and Suspended-Sediment Concentration Data 11
Figure 5. Calibration of near-bottom optical backscatterance sensor at Mallard Island, Suisun Bay, California, water year 2004.

0 20 40 60 80 100 120

0

50

100

150

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples  22

Calibration equation: y  0.769  mV  7.2

Non-parametric prediction interval: 9 to –5

95 percent confidence bound on equation slope (0.769): 0.643 to 1.108

12 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
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 2004.

0

50

100

150

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

0

50

100

150

OCT. NOV.

2003

DEC. JAN. FEB. MAR. APR. MAY JUNE JULY AUG. SEPT.

2004

A

B

Sensor Calibration and Suspended-Sediment Concentration Data 13
Benicia Bridge

PERIOD OF CALIBRATION.—

NEAR-SURFACE SENSOR: November 17, 2003, through September 30, 2004 (fig. 7).

NEAR-BOTTOM SENSOR (A): October 1, 2003, to October 29, 2003, and July 29, 2004, through September 30, 2004 

(fig. 8A).

NEAR-BOTTOM SENSOR (B): November 17, 2003, to July 29, 2004 (fig. 8B).

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

NEAR-SURFACE SENSOR: 18 (18 from WY 2004).

NEAR-BOTTOM SENSOR (A): 31 (7 from WY 2004).

NEAR-BOTTOM SENSOR (B): 12 (12 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

NEAR-SURFACE SENSOR: SSC = 1.010 × NTU + 0.4.

NEAR-BOTTOM SENSOR (A): SSC = 1.160 × NTU + 8.8.

NEAR-BOTTOM SENSOR (B): SSC = 1.123 × NTU + 18.7.

NONPARAMETRIC PREDICTION INTERVAL.—

NEAR-SURFACE SENSOR: +13 to -3 mg/L.

NEAR-BOTTOM SENSOR (A): +23 to -10 mg/L.

NEAR-BOTTOM SENSOR (B): +15 to -44 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

NEAR-SURFACE SENSOR: 0.824 to 1.146.

NEAR-BOTTOM SENSOR (A): 1.065 to 1.372.

NEAR-BOTTOM SENSOR (B): 0.838 to 1.457.

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

MLLW was approxi­mately 80 ft deep at the site but only approximately 60 ft deep immediately adjacent to the site, therefore, 

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

The near-surface Hydrolab sensor was replaced with a YSI sensor on October 29, 2003, but because of a faulty calibration reset, 

usable data were not collected until November 17, 2003. The calibration used for data collected at the near-bottom location 

from October 1, 2003, to October 29, 2003, and July 29, 2004, to September 30, 2004, was developed from samples collected 

during the deployment of two Hydrolab sensors. Because the two Hydrolab sensors 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 near-bottom Hydrolab sensor was replaced by a YSI sensor on October 

29, 2003, but because of a faulty calibration reset, usable data were not collected until November 17, 2003. The calculated SSC 

time-series data collected for WY 2004 are presented in figure 9.

14 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Figure 7. Calibration of near-surface optical backscatterance sensor at Benicia Bridge, Suisun Bay, California, water year 2004.

0 20 40 60 80 100 120 140 160

0

50

100

150

200

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples  18

Calibration equation: y  1.010  NTU  0.4

Non-parametric prediction interval: 13 to –3

95 percent confidence bound on equation slope (1.010): 0.824 to 1.146

Sensor Calibration and Suspended-Sediment Concentration Data 15
Figure 8. Calibration of near-bottom optical backscatterance sensors, (A) October 1–October 29, July 29–September 30 and 

(B) November 17–July 29 at Benicia Bridge, Suisun Bay, California, water year 2004.

0 20 40 60 80 100 120 140

0

50

100

150

200

250

SENSOR OUTPUT, IN MILLIVOLTS

0 20 40 60 80 100 120 140 160 180 200

0

50

100

150

200

250

300

350

400

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

A

B

Number of water samples  12

Calibration equation: y  1.123  NTU  18.7

Non-parametric prediction interval: 15 to –44

95 percent confidence bound on equation slope (1.123): 0.838 to 1.457

Number of data points  31

Calibration equation: y  1.160  mV  8.8

Non-parametric prediction interval: 23 to –10

95 percent confidence bound on equation slope (1.160): 1.065 to 1.372

16  Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
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 2004.

0

100

200

300

400

500

600

700

800

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

0

100

200

300

400

500

600

700

800

A

B

OCT. NOV.

2003

DEC. JAN. FEB. MAR. APR. MAY JUNE JULY AUG. SEPT.

2004

Sensor Calibration and Suspended-Sediment Concentration Data 17
San Pablo Bay

Carquinez Bridge

PERIOD OF CALIBRATION.—

MID-DEPTH SENSOR (A): October 1, 2003, to October 29, 2003, and December 8, 2003, to March 3, 2004 (fig. 10A).

MID-DEPTH SENSOR (B): November 18, 2003, to December 8, 2003, and March 3, 2004, through September 30, 2004 

(fig. 10B).

NEAR-BOTTOM SENSOR (A): October 1, 2003, to October 29, 2003, and May 13, 2004, to June 14, 2004 (fig.11A).

NEAR-BOTTOM SENSOR (B): November 18, 2003, to May 4, 2004, and June 14, 2004, through September 30, 2004 

(fig. 11B).

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

MID-DEPTH SENSOR (A): 17 (6 from WY 2004).

MID-DEPTH SENSOR (B): 11 (11 from WY 2004).

NEAR-BOTTOM SENSOR (A): 5 (5 from WY 2004).

NEAR-BOTTOM SENSOR (B): 14 (14 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

MID-DEPTH SENSOR (A): SSC = 0.762 × NTU + 24.0.

MID-DEPTH SENSOR (B): SSC = 0.921 × NTU + 3.8.

NEAR-BOTTOM SENSOR (A): SSC = 0.845 × NTU + 15.5.

NEAR-BOTTOM SENSOR (B): SSC = 1.116 × NTU +16.5. 

NONPARAMETRIC PREDICTION INTERVAL.—

MID-DEPTH SENSOR (A): +8 to -16 mg/L.

MID-DEPTH SENSOR (B): +11 to -10 mg/L.

NEAR-BOTTOM SENSOR (A): undeterminable with five samples.

NEAR-BOTTOM SENSOR (B): +17 to -18 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

MID-DEPTH SENSOR (A): 0.486 to 1.190.

MID-DEPTH SENSOR (B): 0.697 to 1.119.

NEAR-BOTTOM SENSOR (A): 0.608 to 1.092.

NEAR-BOTTOM SENSOR (B): 0.861 to 1.341.

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

The instruments were found out of position on October 6, 2003, and the data were deleted during this period. The mid-depth 

Hydrolab sensor was replaced with a YSI sensor on October 29, 2003, but because of a faulty calibration reset and a datalogger 

problem, usable data were not collected until December 8, 2003, when a Hydrolab was deployed. The calibration used for data 

collected at the mid-depth location from October 1, 2003, to October 29, 2003, and December 8, 2003, to March 3, 2004, was 

developed from samples collected during the deployment of two Hydrolab sensors. Because the two Hydrolab sensors 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 calibration used for data collected 

at the mid-depth location from March 3, 2004, through September 30, 2004, was developed from samples collected during the 

deployment of two YSI sensors. Because the two YSI sensors also responded similarly to the uniform sediment characteristics 

found in San Francisco Bay (Schoellhamer and others, 2003), the calibration for the second part of the water year was developed 

by combining water samples collected during each sensor deployment. 

The near-bottom Hydrolab sensor was replaced with a YSI sensor on October 29, 2003, but because of a faulty calibration 

reset, usable data were not collected until December 8, 2003. The YSI malfunctioned and was replaced with a Hydrolab on May 

13, 2004. The YSI was repaired and redeployed on June 14, 2004. The calibration used for data collected at the near-bottom 

location from October 1, 2003, to October 29, 2003, and May 13, 2004, to June 14, 2004, was developed from samples collected 

during the deployment of two Hydrolab sensors. Because the two Hydrolab sensors 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 for water year 2004 are 

presented in figure 12.

18  Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
0 10 20 30 40 50 60 70 80

0

50

100

150

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

0 50 100 150

0

50

100

150

200

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

A

B

Number of water samples  11

Calibration equation: y  0.921  NTU  3.8

Non-parametric prediction interval: 11 to –10

95 percent confidence bound on equation slope (0.921): 0.697 to 1.119

Number of water samples  17

Calibration equation: y  0.762  NTU  24.0

Non-parametric prediction interval: 8 to –16

95 percent confidence bound on equation slope (0.762): 0.486 to 1.190

Figure 10. Calibration of mid-depth optical backscatterance sensors, (A) October 1–October 29, December 8–March 3 and (B) March 

3–September 30 at Carquinez Bridge, San Pablo Bay, California, water year 2004.

Sensor Calibration and Suspended-Sediment Concentration Data 19
0 20 40 60 80 100 120 140

0

50

100

150

200

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

0 20 40 60 80 100 120 140

0

50

100

150

200

250

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

A

B

Number of water samples  5

Calibration equation: y  0.845  NTU  15.5

Non-parametric prediction interval undeterminable with only 5 samples

95 percent confidence bound on equation slope (0.845): 0.608 to 1.092

Kendall tau used for confidence bound calculation with small data set

Number of water samples  14

Calibration equation: y  1.116  NTU  16.5

Non-parametric prediction interval: 17 to –18

95 percent confidence bound on equation slope (1.116): 0.861 to 1.341

Figure 11. Calibration of near-bottom optical backscatterance sensors, (A) October 1–October 29, May 13–June 14 and 

(B) November 18–May 4, June 14–September 30 at Carquinez Bridge, San Pablo Bay, California, water year 2004.

20 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
0

50

100

150

200

250

300

350

400

450

500

SUSPNEDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

0

50

100

150

200

250

300

350

400

450

500

A

B

OCT. NOV.

2003

DEC. JAN. FEB. MAR. APR. MAY JUNE JULY AUG. SEPT.

2004

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 2004.

Sensor Calibration and Suspended-Sediment Concentration Data 21
Mare Island Causeway

PERIOD OF CALIBRATION.—

MID-DEPTH SENSOR: November 14, 2003, through September 30, 2004 (fig. 13).

NEAR-BOTTOM SENSOR (A): October 1, 2003, to August 12, 2004, (fig. 14A).

NEAR-BOTTOM SENSOR (B): August 12, 2003, through September 30, 2004, (fig. 14B).

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

MID-DEPTH SENSOR: 21 (21 from WY 2004).

NEAR-BOTTOM SENSOR (A): 27 (20 from WY 2004).

NEAR-BOTTOM SENSOR (B): 7 (3 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

MID-DEPTH SENSOR: SSC = 0.650 × mV – 10.9.

NEAR-BOTTOM SENSOR (A): SSC = 0.730 × mV + 8.2.

NEAR-BOTTOM SENSOR (B): SSC = 0.919 × mV – 39.6.

NONPARAMETRIC PREDICTION INTERVAL.—

MID-DEPTH SENSOR: +12 to -8 mg/L.

NEAR-BOTTOM SENSOR (A): +59 to -16 mg/L.

NEAR-BOTTOM SENSOR (B): +20 to -24 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

MID-DEPTH SENSOR: 0.583 to 0.701.

NEAR-BOTTOM SENSOR (A): 0.631 to 0.879.

NEAR-BOTTOM SENSOR (B): 0.811 to 1.657.

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

No valid data were collected from the mid-depth sensor prior to November 14, 2003. The mid-depth sensor first was replaced on 

October 2, 2003, because the output was highly irregular. The mid-depth replacement sensor also was replaced on November 14, 

2003, because the sensor was not functioning correctly. The near-bottom sensor was replaced on August 12, 2004, because the 

instrument was reading one fixed value even when the turbidity was changing. The calibration developed after August 12, 2004, 

for the near-bottom sensor, included four water samples collected in WY 2005 to help define the calibration. The calculated SSC 

time-series data collected for WY 2004 are presented in figure 15.

22 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
0 50 100 150 200 250 300

0

20

40

60

80

100

120

140

160

180

200

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples  21

Calibration equation: y  0.650  mV  10.9

Non-parametric prediction interval: 12 to –8

95 percent confidence bound on equation slope (0.650): 0.583 to 0.701

Figure 13. Calibration of mid-depth optical backscatterance sensor at Mare Island Causeway, San Pablo Bay, California, 

water year 2004. 

Sensor Calibration and Suspended-Sediment Concentration Data 23
0 50 100 150 200 250 300 350 400 450 500

0

50

100

150

200

250

300

350

400

450

500

SENSOR OUTPUT, IN MILLIVOLTS

0 50 100 150

0

50

100

150

200

250

300

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

A

B

Number of water samples  27

Calibration equation: y  0.730  mV  8.2

Non-parametric prediction interval: 59 to –16

95 percent confidence bound on equation slope (0.730): 0.631 to 0.879

Number of water samples  7

Calibration equation: y  0.919  mV – 39.6

Non-parametric prediction interval: 20 to –24

95 percent confidence bound on equation slope (0.919): –0.811 to 1.657

Kendall tau used for confidence bound calculation with small data set

Figure 14. Calibration of near-bottom optical backscatterance sensors, (A) October 1–August 12 and (B) August 12–September 

30 at Mare Island Causeway, San Pablo Bay, California, water year 2004.

24 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
0

100

200

300

400

500

600

700

800

900

1000

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

0

100

200

300

400

500

600

700

800

900

1000

OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEPT

2 0 0 3 2 0 0 4

A

B

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 2004.

Sensor Calibration and Suspended-Sediment Concentration Data 25
Channel Marker 1

PERIOD OF CALIBRATION.—

MID-DEPTH SENSOR: November 18, 2003, through September 30, 2004, (fig. 16).

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

MID-DEPTH SENSOR: 18 (18 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

MID-DEPTH SENSOR: SSC = 1.565 × NTU + 4.7.

NONPARAMETRIC PREDICTION INTERVAL.—

MID-DEPTH SENSOR: +13 to -21 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

MID-DEPTH SENSOR: 0.861 to 1.926.

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

Hydrolab sensor retrieved from the discontinued station at Channel Marker 9 could not be deployed on October 7, 2003, because 

it had malfunctioned. On October 28, 2003, a YSI sensor was deployed but because of a faulty calibration reset; usable data 

were not collected until November 18, 2003. During periods of heavy fouling, the sensor wiper was ineffective in keeping the 

optical ports clean because of biological growth on the wiper itself obscuring the optical ports. The calculated SSC time-series 

data collected for WY 2004 are presented in figure 17. 

26  Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
0 10 20 30 40 50 60 70 80 90

0

20

40

60

80

100

120

140

160

180

200

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples = 18

Calibration equation: y = 1.565 *x + 4.7

Non-parametric prediction interval: + 13 to -21

95 percent confidence bound on equation slope (1.565): 0.861 to 1.926

Figure 16. Calibration of near-bottom optical backscatterance sensor at Channel Marker 1 at San Pablo Bay, California, water year 

2004.

Sensor Calibration and Suspended-Sediment Concentration Data 27
0

200

400

600

800

1000

1200

1400

1600

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEPT

2 0 0 3 2 0 0 4

Figure 17. Time series of near-bottom suspended-sediment concentrations calculated from sensor readings at Channel Marker 1, 

San Pablo Bay, California, water year 2004.

28  Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Central San Francisco Bay

Point San Pablo

PERIOD OF CALIBRATION.—

MID-DEPTH SENSOR (A): October 1, 2003, to October 30, 2003 (fig. 18A).

MID-DEPTH SENSOR (B): November 19, 2003, through September 30, 2004 (fig. 18B).

NEAR-BOTTOM SENSOR: November 19, 2003, through September 30, 2004 (fig. 19).

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

MID-DEPTH SENSOR (A): 17 (1 from WY 2004).

MID-DEPTH SENSOR (B): 17 (17 from WY 2004).

NEAR-BOTTOM SENSOR: 20 (20 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

MID-DEPTH SENSOR (A): SSC = 1.975 × NTU – 1.2.

MID-DEPTH SENSOR (B): SSC = 1.746 × NTU – 1.3.

NEAR-BOTTOM SENSOR: SSC = 1.588 × NTU + 7.7.

NONPARAMETRIC PREDICTION INTERVAL.—

MID-DEPTH SENSOR (A): +17 to -5 mg/L.

MID-DEPTH SENSOR (B): +20 to -14 mg/L.

NEAR-BOTTOM SENSOR: +21 to -14 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

MID-DEPTH SENSOR (A): 1.270 to 2.727.

MID-DEPTH SENSOR (B): 1.095 to 2.538.

NEAR-BOTTOM SENSOR: 1.141 to 2.278.

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

The mid-depth calibration used from October 1, 2003, to October 30, 2003, (fig. 18A) was developed from water samples collected during the deployment of two Hydrolab sensors which responded similarly to the uniform sediment characteristics found 

in San Francisco Bay (Schoellhamer and others, 2003). The mid-depth Hydrolab sensor was replaced by a YSI sensor on October 30, 2003, but because of a faulty calibration reset, usable data were not collected until November 19, 2003. The near-bottom 

Hydrolab sensor malfunctioned, and no usable data were collected from October 1, 2003, to October 30, 2003. The near-bottom 

Hydrolab sensor was replaced by a YSI sensor on October 30, 2003, but because of a faulty calibration reset, usable data were 

not collected until November 19, 2003. The calculated SSC time-series data collected for WY 2004 are presented in figure 20.

Sensor Calibration and Suspended-Sediment Concentration Data 29
Figure 18. Calibration of mid-depth optical backscatterance sensors, (A) October 1–October 30 and (B) November 19–September 

30 at Point San Pablo, Central San Francisco Bay, California, water year 2004.

0 5 10 15 20 25 30 35 40

0

50

100

150

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

Number of water samples = 17

Calibration equation: y = 1.975 *x - 1.2

Non-parametric prediction interval: + 17 to -5

95 percent confidence bound on equation slope (1.975): 1.270 to 2.727

0 10 20 30 40 50 60 70

0

50

100

150

200

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples = 17

Calibration equation: y = 1.746 *x - 1.3

Non-parametric prediction interval: + 20 to -14

95 percent confidence bound on equation slope (1.746): 1.095 to 2.538

A

B

30 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Figure 19. Calibration of near-bottom optical backscatterance sensor at Point San Pablo, Central San Francisco Bay, 

California, water year 2004.

0 10 20 30 40 50 60 70

0

20

40

60

80

100

120

140

160

180

200

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples = 20

Calibration equation: y = 1.588 *x + 7.7

Non-parametric prediction interval: + 21 to -14

95 percent confidence bound on equation slope (1.588): 1.141 to 2.278

Sensor Calibration and Suspended-Sediment Concentration Data  31
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 2004.

32 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004

0

100

200

300

400

500

600

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

0

100

200

300

400

500

600

OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEPT

2 0 0 3 2 0 0 4

A

B
Alcatraz Island

PERIOD OF CALIBRATION.—

MID-DEPTH SENSOR (A): November 6, 2003, to August 12, 2004 (fig. 21A).

MID-DEPTH SENSOR (B): September 9, 2004, through September 30, 2004 (fig. 21B).

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

MID-DEPTH SENSOR (A): 34 (17 from WY 2004).

MID-DEPTH SENSOR (B): 17 (3 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

MID-DEPTH SENSOR (A): SSC = 11.028 × NTU + 9.5.

MID-DEPTH SENSOR (B): SSC = 2.357 × NTU + 8.4.

NONPARAMETRIC PREDICTION INTERVAL.—

MID-DEPTH SENSOR (A): +8 to -5 mg/L.

MID-DEPTH SENSOR (B): +9 to -4 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

MID-DEPTH SENSOR (A): 0.946 to 1.287.

MID-DEPTH SENSOR (B): 1.538 to 4.286.

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

YSI deployed on November 6, 2003, malfunctioned on August 12, 2004, and was replaced with a Hydrolab on August 18, 2004. 

The data collected by the Hydrolab were not used because one water sample was collected during the deployment and a calibration could not be developed. The Hydrolab was replaced with a second YSI on September 9, 2004. The calibration used for the 

YSI deployed from November 6, 2003, to August 12, 2004, (fig. 21A) was developed using 17 additional samples having high 

SSC collected from Carquinez Strait at Carquinez Bridge during WY 2005 to improve the calibration slope. Samples from both 

locations could be used to develop the calibration because the YSI responded similarly to the uniform sediment characteristics 

found in San Francisco Bay (Schoellhamer and others, 2003). The calibration used for the YSI deployed from September 9, 

2004, through the end of WY 2004 (fig. 21B) was developed using 14 additional water samples collected during WY 2005 to 

improve the calibration. The YSI wipers were ineffective during periods of heavy fouling because of biological growth on the 

wipers obscuring the optical ports. The calculated SSC time-series data collected for WY 2004 are presented in figure 22.

Sensor Calibration and Suspended-Sediment Concentration Data  33
0 20 40 60 80 100 120

0

50

100

150

200

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

0 2 4 6 8 10 12 14 16 18

0

20

40

60

80

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

Number of water samples = 34

Calibration equation: y = 1.028 *x + 9.5

Non-parametric prediction interval: + 8 to -5

95 percent confidence bound on equation slope (1.028): 0.946 to 1.287

Number of water samples = 17

Calibration equation: y = 2.357 *x - 8.4

Non-parametric prediction interval: + 9 to -4

95 percent confidence bound on equation slope (2.357): 1.538 to 4.286

A

B

Figure 21. Calibration of mid-depth optical backscatterance sensors, (A) November 6–August 12 and (B) September 9–30, at 

Alcatraz Island, Central San Francisco Bay, California, water year 2004.

34 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
0

10

20

30

40

50

60

70

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEPT

2 0 0 3 2 0 0 4

Figure 22. Time series of mid-depth suspended-sediment concentrations calculated from sensor readings at Alcatraz 

Island, Central San Francisco Bay, California, water year 2004.

Sensor Calibration and Suspended-Sediment Concentration Data  35
South San Francisco Bay

San Mateo Bridge

PERIOD OF CALIBRATION.—

MID-DEPTH SENSOR: WY 2004 (fig. 23A).

NEAR-BOTTOM SENSOR: WY 2004 (fig. 23B).

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

MID-DEPTH SENSOR: 55 (16 from WY 2004).

NEAR-BOTTOM SENSOR: 48 (20 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

MID-DEPTH SENSOR: SSC = 0.524 × mV +2.8.

NEAR-BOTTOM SENSOR: SSC = 0.522 × mV +4.5.

NONPARAMETRIC PREDICTION INTERVAL.—

MID-DEPTH SENSOR: +8 to -13 mg/L.

NEAR-BOTTOM SENSOR: +12 to -8 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

MID-DEPTH SENSOR: 0.452 to 0.674.

NEAR-BOTTOM SENSOR: 0.439 to 0.667.

REMARKS.—Interruptions in record were caused by fouling. Biological fouling in South San Francisco Bay 

is extreme, especially during the summer months, resulting in a fragmented data set. The calculated SSC time-series 

data collected for WY 2004 are presented in figure 24.

36  Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
0 50 100 150 200 250

0

50

100

150

200

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

0 50 100 150

0

50

100

150

SENSOR OUTPUT, IN MILLIVOLTS

Number of water samples = 55

Calibration equation: y = 0.524 *x + 2.8

Non-parametric prediction interval: + 8 to -13

95 percent confidence bound on equation slope (0.524): 0.452 to 0.674

Number of water samples = 48

Calibration equation: y = 0.522 *x + 4.5

Non-parametric prediction interval: + 12 to -8

95 percent confidence bound on equation slope (0.522): 0.439 to 0.667

A

B

Figure 23. Calibration of (A) mid-depth and (B) near-bottom optical backscatterance sensors at San Mateo Bridge, South San 

Francisco Bay, California, water year 2004.

Sensor Calibration and Suspended-Sediment Concentration Data  37
0

50

100

150

200

250

300

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

0

50

100

150

200

250

300

OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEPT

2 0 0 3 2 0 0 4

A

B

Figure 24. 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 2004.

38  Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Dumbarton Bridge

PERIOD OF CALIBRATION.—

MID-DEPTH SENSOR: WY 2004 (fig. 25).

NEAR-BOTTOM SENSOR (A): October 1, 2003, to March 16, 2004 (fig. 26A).

 NEAR-BOTTOM SENSOR (B): March 17, 2004, through September 30, 2004 (fig. 26B).

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

MID-DEPTH SENSOR: 41 (18 from WY 2004).

NEAR-BOTTOM SENSOR (A): 86 (8 from WY 2004).

NEAR-BOTTOM SENSOR (B): 17 (11 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

MID-DEPTH SENSOR: SSC = 0.666 × mV - 3.7.

NEAR-BOTTOM SENSOR (A): SSC = 0.606 × mV - 11.6.

NEAR-BOTTOM SENSOR (B): SSC = 0.666 × mV - 11.7.

NONPARAMETRIC PREDICTION INTERVAL.—

MID-DEPTH SENSOR: +9 to -10 mg/L.

NEAR-BOTTOM SENSOR (A): +12 to -11 mg/L.

NEAR-BOTTOM SENSOR (B): +14 to -10 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

MID-DEPTH SENSOR: 0.568 to 0.794.

NEAR-BOTTOM SENSOR (A): 0.553 to 0.637.

 NEAR-BOTTOM SENSOR (B): 0.487 to 0.837.

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

instruments. The near-bottom sensor was removed on March 16, 2004, because it was inoperable and replaced by a 

second OBS sensor on March 17, 2004. The calibration developed after March 17, 2004, for the near-bottom sensor, 

included six water samples collected in WY 2005, to help define the calibration. The calculated SSC time-series data 

collected for WY 2004 are presented in figure 27.

Sensor Calibration and Suspended-Sediment Concentration Data  39
Figure 25. Calibration of mid-depth optical backscatterance sensor at Dumbarton Bridge, South San Francisco Bay, California, 

water year 2004.

0 20 40 60 80 100 120 140 160

0

50

100

150

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples = 41

Calibration equation: y = 0.666 *x - 3.7

Non-parametric prediction interval: + 9 to -10

95 percent confidence bound on equation slope (0.666): 0.568 to 0.794

40 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Figure 26. Calibration of near-bottom optical backscatterance sensors, (A) October 1–March 16 and (B) March 17–September 30 at 

Dumbarton Bridge, South San Francisco Bay, California, water year 2004. 

0 100 200 300 400 500 600

0

100

200

300

400

SENSOR OUTPUT, IN MILLIVOLTS

Number of water samples = 86

Calibration equation: y = 0.606 *x - 11.6

Non-parametric prediction interval: + 12 to -11

95 percent confidence bound on equation slope (0.606): 0.553 to 0.637

0 50 100 150 200 250

0

20

40

60

80

100

120

140

160

180

200

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples = 17

Calibration equation: y = 0.666 *x - 11.7

Non-parametric prediction interval: + 14 to -10

95 percent confidence bound on equation slope (0.666): 0.487 to 0.837

A

B

Sensor Calibration and Suspended-Sediment Concentration Data 41
0

100

200

300

400

500

600

700

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

0

100

200

300

400

500

600

700

OCT NOV DEC JAN FEB MAR APR MAY JUNE JULY AUG SEPT

2 0 0 3 2 0 0 4

A

B

Figure 27. 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 2004.

42 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Channel Marker 17

PERIOD OF CALIBRATION.—

MID-DEPTH SENSOR (A): October 1, 2003, to June 9, 2004 (fig. 28A).

MID-DEPTH SENSOR (B): June 9, 2004, through September 30, 2004 (fig. 28B).

NEAR-BOTTOM SENSOR (A): October 1, 2003, to June 9, 2004 (fig. 29A).

NEAR-BOTTOM SENSOR (B): July 1, 2004, through September 30, 2004 (fig. 29B).

NUMBER OF DATA POINTS (WATER SAMPLES) USED FOR CALIBRATION.— MID-DEPTH SENSOR (A): 129 (15 

from WY 2004).

MID-DEPTH SENSOR (B): 5 (5 from WY 2004).

NEAR-BOTTOM SENSOR (A): 103 (14 from WY 2004).

NEAR-BOTTOM SENSOR (B): 8 (6 from WY 2004).

CALCULATED LINEAR CORRELATION EQUATION.—

MID-DEPTH SENSOR (A): SSC = 0.628 × mV - 14.5.

MID-DEPTH SENSOR (B): SSC = 1.023 × NTU + 10.8.

NEAR-BOTTOM SENSOR (A): SSC = 0.556 × mV - 1.2.

NEAR-BOTTOM SENSOR (B): SSC = 1.218 × NTU-NTU - 0.3.

NONPARAMETRIC PREDICTION INTERVAL.—

MID-DEPTH SENSOR (A): +13 to -12 mg/L.

MID-DEPTH SENSOR (B): undeterminable with five samples.

NEAR-BOTTOM SENSOR (A): +17 to -11 mg/L.

NEAR-BOTTOM SENSOR (B): +18 to -11 mg/L.

95-PERCENT CONFIDENCE BOUND ON SLOPE CALCULATION.—

MID-DEPTH SENSOR (A): 0.609 to 0.654.

MID-DEPTH SENSOR (B): 0.200 to 1.476.

NEAR-BOTTOM SENSOR (A): 0.539 to 0.635.

NEAR-BOTTOM SENSOR (B): 0.989 to 1.550.

REMARKS.—Interruptions in record were caused by fouling or malfunction of the sensing and (or) recording instruments. Hydrolab instruments, equipped with turbidity, specific-conductance and temperature sensors, replaced OBS sensors 

at near-surface and near-bottom depths on June 9, 2004. The sensor at mid-depth was replaced on August 11, 2004, because it 

was inoperable. Because the two sensors (Hydrolabs) responded similarly to the uniform sediment characteristics found in San 

Francisco Bay (Schoellhamer and others, 2003), a calibration was developed by combining water samples collected during each 

sensor deployment. The near-bottom sensor deployed on June 9, 2004, collected no data and was replaced on July 1, 2004. The 

calculated SSC time-series data collected for WY 2004 are presented in figure 30.

Sensor Calibration and Suspended-Sediment Concentration Data 43
0 200 400 600 800 1000 1200

0

100

200

300

400

500

600

700

800

SENSOR OUTPUT, IN MILLIVOLTS

Number of water samples = 129

Calibration equation: y = 0.628 *x - 14.5

Non-parametric prediction interval: + 13 to -12

95 percent confidence bound on equation slope (0.628): 0.609 to 0.654

0 50 100 150

0

50

100

150

200

250

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples = 5

Calibration equation: y = 1.023 *x + 10.8

Non-parametric prediction interval undeterminable with only 5 samples

95 percent confidence bound on equation slope (1.023): 0.200 to 1.476

Kendall tau used for confidence bound calculation with small data set

A

B

Figure 28. Calibration of mid-depth optical backscatterance sensors, (A) October 1–June 9 and (B) June 9–September 30 at 

Channel Marker 17, South San Francisco Bay, California, water year 2004.

44 Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
Figure 29. Calibration of near-bottom optical backscatterance sensors, (A) October 1–June 9 and (B) July 1–September 30 at Channel 

Marker 17, South San Francisco Bay, California, water year 2004.

0 200 400 600 800 1000 1200

0

200

400

600

800

SENSOR OUTPUT, IN MILLIVOLTS

Number of water samples = 103

Calibration equation: y = 0.556 *x - 1.2

Non-parametric prediction interval: + 17 to -11

95 percent confidence bound on equation slope (0.556): 0.539 to 0.635

0 20 40 60 80 100 120 140

0

50

100

150

200

250

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of water samples = 8

Calibration equation: y = 1.218 *x - 0.3

Non-parametric prediction interval: + 18 to -11

95 percent confidence bound on equation slope (1.218): 0.989 to 1.550

Kendall tau used for confidence bound calculation with small data set

A

B

Sensor Calibration and Suspended-Sediment Concentration Data 45
Figure 30. 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 2004.

0

100

200

300

400

500

600

700

800

900

1,000

SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER

0

100

200

300

400

500

600

700

800

900

1,000

B

A

OCT. NOV.

2003

DEC. JAN. FEB. MAR. APR. MAY JUNE JULY AUG. SEPT.

2004

46  Summary of Suspended-Sediment Concentration Data, San Francisco Bay, California, Water Year 2004
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, two sites in Central San Francisco Bay, and three sites in South San Francisco Bay during 

water year 2004. 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 processed. Water-sample sediment concentration data are available in the USGS sediment database. Time-series data 

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

data are available from the USGS at http://sfbay.wr.usgs.gov/access/Fixed_sta/ (accessed October 30, 2005).

References Cited

Arthur, J.F., and Ball, M.D., 1979, Factors influencing the entrapment of suspended material in the San Francisco Bay–Delta 

Estuary, in Conomos, T.J., (ed.), San Francisco Bay: The urbanized estuary: San Francisco, Pacific Division of the American 

Association for the Advancement of Science, p. 143–174.

Brown, C.L., and Luoma, S.N., 1995, Use of the euryhaline bivalve Potamocorbula amurensis as a biosentinal species to assess 

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

Buchanan, P.A., and Ganju, N.K., 2002, Summary of suspended-sediment concentration data, San Francisco Bay, California, 

water year 2000: U.S. Geological Survey Open-File Report 02-146, 42 p.

Buchanan, P.A., and Ganju, N.K., 2003, Summary of suspended-sediment concentration data, San Francisco Bay, California, 

water year 2001: U.S. Geological Survey Open-File Report 03-312, 47 p.

Buchanan, P.A., and Ganju, N.K., 2004, Summary of suspended-sediment concentration data, San Francisco Bay, California, 

water year 2002: U.S. Geological Survey Open-File Report 04-1219, 45 p.

Buchanan, P.A., and Ganju, N.K., 2005, Summary of suspended-sediment concentration data, San Francisco Bay, California, 

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