U.S. GEOLOGICAL SURVEY

Open-File Report 

Summary of Suspended-Sediment 

Concentration Data, San Francisco Bay, 

California, Water Year 1999

By Paul A. Buchanan and Catherine A. Ruhl

Sacramento, California 

2001

01-100

Prepared in cooperation with the

CALFED BAY-DELTA PROGRAM, the

SAN FRANCISCO REGIONAL WATER QUALITY CONTROL BOARD, and the

U.S. ARMY CORPS OF ENGINEERS, SAN FRANCISCO DISTRICT 3009-36
U.S. DEPARTMENT OF THE INTERIOR

GALE A. NORTON, Secretary

U.S. GEOLOGICAL SURVEY

Charles G. Groat, Director

The use of firm, trade, and brand names in this report is for identification purposes only and does

not constitute endorsement by the U.S. Geological Survey.

For additional information write to: Copies of this report can be purchased

U.S. Geological Survey

Information Services

Box 25286

Federal Center

Denver, CO 80225

from:

District Chief

U.S. Geological Survey

Placer Hall, Suite 2012

6000 J Street

Sacramento, CA 95819-6129
Abstract.................................................................................................................................................................................. 1

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

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

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

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

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

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

Suisun Bay Installations .................................................................................................................................... 6

Mallard Island.......................................................................................................................................... 6

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

Carquinez Bridge..................................................................................................................................... 7

Mare Island Causeway............................................................................................................................. 7

Channel Marker 9 .................................................................................................................................... 7

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

Point San Pablo........................................................................................................................................ 8

Pier 24...................................................................................................................................................... 8

South San Francisco Bay Installations .............................................................................................................. 8

Channel Marker 17 .................................................................................................................................. 8

Dumbarton Bridge ................................................................................................................................... 9

San Mateo Bridge .................................................................................................................................... 9

Water-Sample Collection............................................................................................................................................. 9

Data Processing ........................................................................................................................................................... 10

Sensor Calibration and Suspended-Sediment Concentration Data........................................................................................ 11

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

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

San Pablo Bay.............................................................................................................................................................. 17

Carquinez Bridge............................................................................................................................................... 17

Mare Island Causeway....................................................................................................................................... 19

Channel Marker 9 .............................................................................................................................................. 22

Central San Francisco Bay .......................................................................................................................................... 24

Point San Pablo.................................................................................................................................................. 24

Pier 24................................................................................................................................................................ 27

South San Francisco Bay............................................................................................................................................. 30

Channel Marker 17 ............................................................................................................................................ 30

Dumbarton Bridge ............................................................................................................................................. 33

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

Summary................................................................................................................................................................................ 38

References Cited.................................................................................................................................................................... 38

FIGURES

1. Map showing San Francisco Bay study area........................................................................................................... 3

2. Schematic of monitoring installation ...................................................................................................................... 5

3–39. Graphs showing:

3. Example of raw and edited optical backscatterance data, mid-depth sensor, Point San Pablo, Central

San Francisco Bay, water year 1994................................................................................................................... 10

4. Calibration of near-surface optical backscatterance sensors, October 1–May 24 and June 29–

September 30, Mallard Island, Suisun Bay, water year 1999............................................................................. 14

CONTENTS

Contents III
 5. Calibration of near-bottom optical backscatterance sensor at Mallard Island, 

 Suisun Bay, water year 1999............................................................................................................................. 15

6. Time series of near-surface and near-bottom suspended-sediment concentrations calculated from 

sensor readings at Mallard Island, Suisun Bay, water year 1999....................................................................... 16

7. Calibration of mid-depth and near-bottom optical backscatterance sensors at Carquinez Bridge, 

 San Pablo Bay, water year 1999........................................................................................................................ 17

8. Time series of mid-depth and near-bottom suspended-sediment concentrations calculated from 

sensor readings at Carquinez Bridge, San Pablo Bay, water year 1999............................................................. 18

9. Calibration of mid-depth and near-bottom optical backscatterance sensors at Mare Island 

Causeway, San Pablo Bay, water year 1999....................................................................................................... 20

10. Time series of mid-depth and near-bottom suspended-sediment concentrations calculated from 

sensor readings at Mare Island Causeway, San Pablo Bay, water year 1999..................................................... 21

11. Calibration of near-bottom optical backscatterance sensor and near-bottom suspended-sediment

concentration calculated from sensor readings at Channel Marker 9, San Pablo Bay, water year 1999 ........... 23

12. Calibration of mid-depth and near-bottom optical backscatterance sensors at Point San Pablo, 

Central San Francisco Bay, water year 1999 ..................................................................................................... 25

13. Time series of mid-depth and near-bottom suspended-sediment concentrations calculated from 

sensor readings at Point San Pablo, Central San Francisco Bay, water year 1999 ............................................ 26

14. Calibration of mid-depth and near-bottom optical backscatterance sensors at Pier 24, 

Central San Francisco Bay, water year 1999 ..................................................................................................... 28

15. Time series of mid-depth and near-bottom suspended-sediment concentrations calculated from 

sensor readings at Pier 24, Central San Francisco Bay, water year 1999 .......................................................... 29

16. Calibration of mid-depth and near-bottom optical backscatterance sensors at Channel Marker 17,

South San Francisco Bay, water year 1999........................................................................................................ 31

17. Time series of mid-depth and near-bottom suspended-sediment concentrations calculated from 

sensor readings at Channel Marker 17, South San Francisco Bay, water year 1999 ......................................... 32

18. Calibration of mid-depth and near-bottom optical backscatterance sensors at Dumbarton Bridge, 

South San Francisco Bay, water year 1999........................................................................................................ 34

19. Time series of mid-depth and near-bottom suspended-sediment concentrations calculated from 

sensor readings at Dumbarton Bridge, South San Francisco Bay, water year 1999.......................................... 35

20. Calibration of mid-depth optical backscatterance sensor and mid-depth suspended-sediment concentration 

calculated from sensor readings at San Mateo Bridge, South Francisco Bay, water year 1999........................ 37

TABLES

1. Statistical summary of suspended-sediment concentration data, Suisun Bay, San Pablo Bay,

and Central and South San Francisco Bays, water year 1999 ................................................................................ 13

2. Usable percentage of a complete year of data (96 data points per day) collected by optical

backscatterance sensors, Suisun Bay, San Pablo Bay, and Central and South San Francisco 

Bays, California, water year 1999 .......................................................................................................................... 13

IV Contents
CONVERSION FACTORS, VERTICAL DATUM, ABBREVIATIONS, AND ACRONYMS

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

 ̊F = 1.8 ( ̊C) + 32.

Vertical Datum

Sea level: In this report, "sea level" refers to the National Geodetic Vertical Datum of 1929 (NGVD of 1929)—a geodetic datum derived from a general adjustment of the first-order level nets of both the United States and Canada, formerly 

called Sea Level Datum of 1929.

Mean lower low water (MLLW): The average of the lower low water height of each tidal day observed over 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 over which tide observations are taken and 

reduced to obtain mean values.

Abbreviations

Αh ampere hour

mg/L milligram per liter

mV millivolt

V volt

Acronyms

AC ...........alternating current

ADAPS.....automated data-processing system

DC ............direct current

DWR.........California Department of Water Resources

NTU..........Nephelometric Turbidity Units

PInp...........non-parametric prediction interval

PVC ..........polyvinyl chloride

RMS .........root mean squared

USCG .......U.S. Coast Guard

USGS........U.S. Geological Survey

Multiply By To obtain

inch (in.) 25.40 millimeter

foot (ft) .3048 meter

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

mile (mi) 1.609 kilometer

pound (lb) .4536 kilogram

Contents V
Introduction 1

Summary of Suspended-Sediment Concentration Data, 

San Francisco Bay, California, Water Year 1999

By Paul A. Buchanan and Catherine A. Ruhl

ABSTRACT

Suspended-sediment concentration data were collected in San Francisco Bay during water 

year 1999 (October 1, 1998–September 30, 1999). Optical backscatterance sensors and water 

samples were used to monitor suspended sediment at one site 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 were analyzed for concentrations of suspended sediment. The results of the analyses were 

used to calibrate the electrical output of the optical backscatterance sensors. This report presents 

the data-collection methods used and summarizes the suspended-sediment concentration data 

collected from October 1998 through September 1999. Calibration plots 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 of nutrients that contribute to the 

maintenance of 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). 

The transport and fate of suspended sediments are important factors in determining the transport 

and fate of constituents adsorbed on the sediments. In Suisun Bay, the maximum concentration of suspended sediment usually marks the position of the turbidity maximum, which is a crucial ecological 

region in which 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). 

Suspended sediments limit the availability of light in San Francisco Bay, which, in turn, limits 

photosynthesis and primary phytosynthetic carbon production (Cole and Cloern, 1987; Cloern, 1987, 

1996). Suspended sediments also deposit in ports and shipping channels, which then must be dredged to 

maintain navigation (U.S. Environmental Protection Agency, 1992). Large tidal velocities, spring tides, 

and wind waves in shallow water all are capable of resuspending bottom sediments (Powell and others, 

1989; Schoellhamer, 1996). The U.S. Geological Survey (USGS), in cooperation with the CALFED BayDelta Program, the San Francisco Regional Water Quality Control Board, and the U.S. Army Corps of 

Engineers, San Francisco District, is studying the factors that affect suspended-sediment concentrations 

in San Francisco Bay.
2 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

Purpose and Scope

This report summarizes suspended-sediment concentration data collected by the USGS in San 

Francisco Bay during water year 1999 (October 1, 1998–September 30, 1999) and is the latest in a series 

based on data collected beginning in water year 1992 (Buchanan and Schoellhamer, 1995, 1996, 1998, 

1999; Buchanan and others; 1996; Buchanan and Ruhl, 2000). Suspended-sediment concentrations were 

monitored at one site in Suisun Bay, three sites in San Pablo Bay, two sites in Central San Francisco Bay, 

and three sites in South San Francisco Bay. These data are used to determine the factors that affect 

suspended-sediment concentrations in San Francisco Bay (U.S. Geological Survey, accessed January 19, 

2001). Suspended-sediment concentration data for water years 1992 through 1999 are available from the 

files of the USGS California District Office in Sacramento, California. 

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 have 

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 (Smith, 1987; Cheng and Gartner, 1984). Winds typically are strongest in summer during afternoon onshore, coastal sea breeze. Most precipitation occurs from late autumn 

to early spring, and freshwater discharge into the 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 83–86 percent of the fluvial sediments that enter the 

Bay (Porterfield, 1980). 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 

(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), the San Francisco Port Authority, the 

PakTank Corporation, and the City of Vallejo for their permission and assistance in establishing the 

monitoring sites used in this study. 

METHODS

Instrument Description and Operation

Three different types of optical backscatterance sensors were used to monitor concentrations of 

suspended sediment during water year 1999. 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 
Methods 3

Suisun Bay

Carquinez Strait

San Pablo Bay

 Central

 San Francisco

 Bay

Pacific Ocean

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' 122°15' 122°00'

38°00'

37°45'

37°30'

Napa

Riv

er

Richmond/San Rafael

 Bridge

CENTRAL

VALLEY

C

A

L

I

F

O

R

N

I

A

San Francisco Bay/

Sacramento-San Joaquin

River Delta

STUDY

 AREA

Petaluma

River

Dumbarton Bridge

Channel Marker 17

Mallard Island

Point San Pablo

Pier 24

Honker Bay

 Benicia

Carquinez Bridge

 Bridge

Mare Island

 Causeway

Channel

Marker 9

South

San Francisco

Bay

Martinez

Figure 1. San Francisco Bay study area, California.
4 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

window at one end, a cable connection at the other end, and an encased circuit board (Downing and 

others, 1981; Downing, 1983). 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° (D & A Instrument Company, 1991) 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 similar in size and function to the other optical 

sensors used in the study, but each self-cleaning probe has a separate electronic unit that sets the resolution and maximum reading, expressed in Nephelometric Turbidity Units (NTU). The voltage output from 

the electronic unit is recorded on a separate data logger. The third type of sensor, manufactured by 

Hydrolab, is part of a multiprobe that also measures specific conductance, temperature, and depth. The 

Hydrolab optical backscatterance sensor measures the intensity of light scattered at 90° from two lightemitting diodes and is expressed in NTU. The multiprobe (or sonde) is self contained with its own power 

source and data logger. The voltage output for all three types of sensors is proportional to the concentration of suspended sediment in the water column at the depth of the sensor. Suspended-sediment concentrations calculated from the output of side-by-side sensors with and without the self-cleaning function 

(BTG and D&A Instrument Company), are virtually identical (Buchanan and Schoellhamer, 1998, 

fig. 4). Calibration of the sensor voltage output to concentrations of suspended sediment 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).

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 its position parallel to the direction of flow as the carriage 

and sensor aligned itself with the changing direction of flow.

Data acquisition, data storage, and sensor timing were controlled by an electronic data logger. The 

logger 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. Power was supplied by 

12-volt (V) direct current (DC), 12-ampere hour (Ah), gel-cell batteries, except for the sonde, which used 

eight size-C alkaline batteries.

Self-cleaning optical sensors with wipers were deployed at four sites during water year 1994 to 

reduce biological growth, which interferes with the collection of accurate optical backscatterance data. 

Because the self-cleaning sensor requires 95–130-V alternating current (AC), installation was limited to 

sites with AC power. The self-cleaning probes and electronic units were installed at two sites in Suisun 

Bay and at two sites in South Bay. Fouling in Suisun Bay was minor compared with that in South and 

Central Bays, and the self-cleaning probes were effective in keeping the optical ports clean. However, 

fouling at the two sites in South Bay during summer was so extreme that the self-cleaning probes often 

were rendered ineffective by biological growth on the carriage and wiper mechanism. During water year 

1995, all self-cleaning probes deployed in South Bay failed due to salt crystals forming on an O-ring, 

which resulted in water leakage. To address the leakage problem, the design was modified by the manufacturer. In water year 1996, an updated version of the self-cleaning probe was deployed at the 

Dumbarton Bridge site in South Bay, but it failed within the first month of operation. Thereafter, the selfcleaning probes were used only at the less saline Mallard Island site in Suisun Bay.

Fouling generally was greatest on the sensor closest to the water surface. However, fouling at 

shallower sites was similar on both sensors where the upper sensor was set 10 ft above the lower sensor. 

Optical sensors required frequent cleaning but, due to the difficulty in servicing some of the monitoring 

stations, they were cleaned 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.
Methods 5

Instrument

Shelter Davit

Sensor cable

Suspension line

Mid-depth sensor

and carriage

Near-bottom sensor

and carriage

Weight

Sensor

Head

SENSOR CARRIAGE

(Schematic not to scale) 

(Not to scale)

Figure 2. Monitoring installation.
6 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

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 specified as the primary turbidity standard by the United States Environmental Protection Agency (1992). The 

turbidity solutions are prepared by diluting a 4,000-NTU stock standard with high-purity water in a 

clean, sealable bucket. Prepared solutions ranged from 50 to 200 NTU. At the field site, the cleaned sensors are immersed in the solution and the voltage output is recorded on the station log. Monitoring a 

period of sensor performance in a known standard aids in identifying output drift or sensor malfunction.

Suisun Bay Installations

Suspended-sediment concentration data were collected at Mallard Island in Suisun Bay (fig. 1). A 

monitoring site at Carquinez Strait at Benicia Bridge was shut down in August 1998 for seismic retrofitting of the bridge and will be reestablished at a future date. Monitoring equipment was installed at the 

Mallard Island site during water year 1994, and the Benicia Bridge site was established during water year 

1996. The monitoring site at the Martinez Marina fishing pier was discontinued in water year 1996 

because data from the Benicia Bridge were considered more representative of suspended-sediment concentration in the Carquinez Strait area of Suisun Bay (Buchanan and Schoellhamer, 1998).

Mallard Island

Self-cleaning optical sensors were installed at the DWR Mallard Island Compliance Monitoring 

Station on February 8, 1994. This site is about 5 miles (mi) downstream from the confluence of the 

Sacramento and San Joaquin Rivers and is at the north shore of Mallard Island near the eastern boundary 

of Honker Bay, a subembayment of Suisun Bay (fig. 1). The station was constructed in the early 1980’s 

by DWR on Pacific Gas and Electric Company property, and water-quality data were first recorded at the 

station in January 1984. A 1/4-mi wooden walkway crosses the sometimes submerged reedbeds of 

Mallard Island and connects the concrete-block instrument shelter to the levee road.

Sensors were positioned at near-bottom (5 ft above the bottom) and near-surface (3.3 ft below the 

surface) depths to coincide with DWR near-bottom depth electrical conductance and temperature sensors 

and the near-surface pump intake. The pump intake was attached to a float that is housed inside a 12-in. 

PVC pipe, and the intake drew water from about 3 ft below the surface. Mean lower low water depth at 

this site was about 25 ft. DWR near-surface parameters were measured by sensors that are submerged in 

flow-through chambers inside the instrument shelter. This configuration saved the cost of installing 

duplicate sets of sensors and enabled the USGS to use DWR instruments for data, such as stage, pH, 

chlorophyll concentration, and meteorological parameters. 

Data storage is controlled by a data logger connected to a cellular phone and modem. AC power 

operated both optical sensors and charged a 12-V, 12-Ah battery that powered the data logger and 

modem. The data logger and peripheral equipment are housed in the instrument shelter. The sensors were 

suspended from a galvanized support stand that was attached to a metal railing on the station’s northwest 

concrete deck. The support stand has two stainless-steel lines attached to separate concrete weights; one 

line for the near-bottom sensor and one line for the near-surface sensor. The near-bottom sensor was 

attached to a PVC carriage suspended from the stainless-steel line by a nylon rope. The near-surface sensor was attached to a PVC carriage that was built onto a float. This float assembly moved up and down 

the suspension line during tidal cycles, which maintained the near-surface sensor at the same depth as 

the DWR pump intake. A pressure transducer was positioned on the float assembly at the same level as 

the sensor and provided data to verify the depth of the near-surface sensor. To prevent sensor cables from 

being snagged by debris, a counterweight was installed to keep slack cables out of the water.
Methods 7

San Pablo Bay Installations

Suspended-sediment concentration data were collected at three sites in San Pablo Bay; Carquinez 

Bridge, Mare Island Causeway, and Channel Marker 9 (fig. 1).

Carquinez Bridge

Suspended-sediment monitoring equipment was installed April 21, 1998, at the Carquinez Bridge. 

This site is located on the north side of the center pier structure of the Carquinez Bridge (fig. 1). Sondes 

with optical, specific conductance, temperature, and depth sensors were deployed at near-bottom and 

mid-depths (5 ft and 48 ft, respectively, from the bottom). Mean lower low water depth at this site was 

about 88 ft. The sensors were suspended between the concrete pier superstructure and the fender boards, 

which were approximately 1 ft apart. PVC carriages attached to 1/4-in. stainless-steel line were anchored 

to a 250-pound (lb) weight and used to suspend the sensors at the desired depth. Sensor timing and data 

storage were controlled by an internal data logger powered by eight size-C alkaline batteries that were 

replaced during site visits. No instrument shelter was needed at this site.

Mare Island Causeway

The USGS maintains a monitoring site on the Napa River at Mare Island Causeway near Vallejo 

(fig. 1). The USGS established this site in cooperation with the California Coastal Conservancy in water 

year 1998. The USGS assumed full operation of this site in water year 1999.

Optical sensors were installed at Mare Island Causeway on October 1, 1998, and were positioned 

at near-bottom and mid-depth (5 ft and 15 ft, respectively, from the bottom). Mean lower low water depth 

at this site was about 30 ft. Specific conductance and temperature data were collected at near-bottom and 

near-surface points in the water column (near-bottom and near-surface depths were sampled to define the 

vertical stratification). Sensor timing and data storage were controlled by a data logger. PVC carriages 

attached to 1/4-in. stainless-steel line were anchored to a 125-lb weight and were used to suspend the 

sensors at the desired depth. AC power charged a 12-V, 12-Ah battery that powered the data logger and 

sensors. The data logger and peripheral equipment were housed in a 3 × 2 × 1-ft plastic weather-proof 

shelter mounted on a catwalk underneath the causeway. 

Channel Marker 9

Suspended-sediment monitoring equipment was installed November 12, 1998, at USCG Channel 

Marker 9. This site was located in the navigation channel leading to the Petaluma River in the northwest 

corner of San Pablo Bay (fig. 1). A sonde with optical, specific conductance, temperature, and depth sensors was deployed at near-bottom depth (2 ft above the bottom). Mean lower low water depth at this site 

was about 6 ft. The sensor was suspended from the channel marker platform using a PVC carriage 

attached to 1/4-in. stainless-steel line anchored to a 125-lb weight. Sensor timing and data storage were 

controlled by an internal data logger powered by eight size-C alkaline batteries that were replaced during 

site visits. No instrument shelter was needed at this site.

Central San Francisco Bay Installations

Suspended-sediment concentration data were collected at two sites in Central Bay: Point San Pablo 

and Pier 24 (fig. 1). 
8 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

Point San Pablo

The USGS maintains a monitoring site at San Pablo Strait on the northern end of the Richmond 

Terminal No. 4 pier on the western side of Point San Pablo (fig. 1). The USGS assumed operation of this 

site from DWR in October 1989. Data collected prior to October 1, 1989, can be obtained from DWR.

Optical sensors were installed at Point San Pablo on December 1, 1992, and were positioned at 

near-bottom and middle depths (3 ft and 13 ft, respectively, from the bottom). Mean lower low water 

depth at this site was about 26 ft. Specific conductance and temperature data (cooperatively funded by 

DWR and the USGS) were collected at near-bottom and near-surface depths in the water column (nearbottom and near-surface depths were sampled to define vertical stratification). Sensor timing and data 

storage were controlled by a data logger connected to a phone line and modem. PVC carriages attached 

to 1/4-in. stainless-steel line were anchored to a 125-lb weight and were used to suspend the sensors at 

the desired depth. Water level was recorded using a float-driven incremental encoder wired into the data 

logger; outside water levels were read during site visits using a wire-weight gage. AC power charged a 

12-V, 60-Ah battery that powered the data logger and sensors. The data logger and peripheral equipment 

were housed in a 5×8×8-ft wooden shelter.

Pier 24

The monitoring station at Pier 24 is on the western end of the San Francisco–Oakland Bay Bridge 

(fig. 1). The USGS assumed operation of this station from DWR in October 1989. Data collected prior 

to October 1, 1989, can be obtained from DWR.

Optical sensors were installed at the Pier 24 site on May 25, 1993, and were positioned at nearbottom and middle depths (3 ft and 23 ft, respectively, from the bottom). Mean lower low water depth at 

this site was about 41 ft. As at the Point San Pablo station, specific conductance and temperature data 

(cooperatively funded by DWR and the USGS) were collected at near-bottom and near-surface depths in 

the water column. PVC carriages attached to 1/4-in. stainless-steel line were anchored to a 125-lb weight 

and used to suspend the sensors at the desired depth. Sensor timing and data storage were controlled by 

a data logger connected to a cellular phone and modem. AC power charged two 12-V, 12-Ah batteries 

that powered the instrumentation. The data logger and peripheral equipment were housed in a corrugated 

steel shelter.

South San Francisco Bay Installations

Suspended-sediment concentration data were collected at three sites in South Bay (fig. 1). 

Monitoring sites were installed during water year 1992 at two sites in South Bay; Channel Marker 17 

and San Mateo Bridge. The Dumbarton Bridge site was installed during water year 1993. 

Channel Marker 17

The southernmost monitoring site in South Bay is at the USCG Channel Marker 17 (fig. 1). 

Instrumentation was installed on February 26, 1992, and the optical sensors were positioned at nearbottom and middle depths (3 ft and 13 ft, respectively, from the bottom). Mean lower low water depth at 

this site was about 25 ft. Sensor cables were protected by a 10-ft PVC pipe suspended from the channel 

marker platform. Sensor timing and data storage were controlled by a data logger. PVC carriages 

attached to 1/4-in. Kevlar-reinforced nylon line were anchored to a 100-lb weight and used to suspend 

the sensors at the desired depth. The data logger and 12-V, 12-Ah batteries were housed in a 2 × 2 × 1-ft 

plastic weather-proof shelter mounted on the channel marker platform. 
Methods 9

Dumbarton Bridge

Suspended-sediment concentration monitoring equipment was installed on October 21, 1992, at 

Pier 23 of the Dumbarton Bridge on the west side of the ship channel (fig. 1). Optical sensors were 

deployed at near-bottom and middle depth (4 ft and 23 ft, respectively, from the bottom). Mean lower 

low water depth was about 45 ft. The sensors were suspended between the concrete pier superstructure 

and its surrounding protective fender boards, a space approximately 3 ft wide. Sensor timing and data 

storage were controlled by a data logger. PVC carriages attached to 1/4-in. stainless-steel line were 

anchored to a 125-lb weight and suspended the sensors at the desired depth. AC power charged a 12-V, 

12-Ah battery that powered the instrumentation. The data logger and peripheral equipment were housed 

in a 3×2×1-ft plastic weather-proof shelter mounted on the pier. 

San Mateo Bridge

The monitoring site on the San Mateo Bridge is at Pier 20 on the east side of the ship channel 

(fig. 1). This station was operated by DWR, but the USGS assumed operations in October 1989. Data 

collected prior to October 1, 1989, can be obtained from DWR. 

The optical sensors were installed on December 23, 1991, and were positioned at near-bottom and 

middle depths (8 ft and 29 ft, respectively, above the bottom). Mean lower low water depth at this site 

was about 48 ft. The sensors were deployed between the pier and a protective fender structure composed 

of multiple piles; flow past the sensors was significantly affected by the pilings and the concrete superstructure. PVC carriages attached to 1/4-in. stainless-steel line were anchored to a 200-lb weight and suspended the sensors at the desired depth. Sensor timing and data storage were controlled by a data logger. 

In addition to suspended-sediment concentrations, specific conductance and temperature (cooperatively 

funded by DWR and the USGS) were monitored at near-bottom and near-surface depths. AC power 

charged a 12-V, 60-Ah battery that powered the data logger and sensors. The data logger and peripheral 

equipment were housed in an 8×6×8-ft wooden shelter on the pier. 

Water-Sample Collection

Water samples, used to calibrate optical sensors, 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. Then, the water sample was removed from the sampler, 

marked for identification, and placed in an ice chest to limit biological growth. The suspended-sediment 

concentration of water samples collected with a Van Dorn sampler and a P-72 point sampler, used until 

water year 1994, were compared and found to be virtually identical (Buchanan and others, 1996, fig. 2).

An auto-sampler was used during water year 1999 to help calibrate the near-surface sensor at 

Mallard Island. The auto-sampler is a programmable peristaltic pump with 1/4-in. plastic tubing capable 

of collecting 24 separate samples. The auto-sampler tubing was deployed at the depth of the sensor by 

strapping the tubing to the sensor cables. The auto-sampler was programmed to collect samples hourly 

while the sensor was collecting data. 

Samples were sent to the USGS Sediment Laboratory in Salinas, California, for analysis of 

suspended-sediment concentration. Suspended sediment include all particles in the sample; the suspended sediment (material that settles to the bottom of the sample bottle) and buoyant particles that do 

not settle. Suspended-sediment concentration were previously referred to as suspended-solids concentration in previous reports (Buchanan and Schoellhamer, 1995, 1996, 1998, 1999; Buchanan and others, 

1996, Buchanan and Ruhl, 2000). The analytical method used to quantify concentrations of suspended 
10 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

SENSOR OUTPUT

CLEANING 

0

500

1,000

1,500

2,000

0

500

1,000

1,500

2,000

RAW DATA, IN MILLIVOLTS

EDITED RAW DATA, 

IN MILLIVOLTS

15 25 5 15 25 4 14 24 4

APRIL MAY JUNE

solid-phase material define the nomenclature used to describe sediment data (Gray and others, 2000). 

Water samples used in this and preceding reports were analyzed as suspended-sediment concentration 

(total water-sediment mass and all sediment were measured). Each sample was filtered through a 

0.45-micrometer membrane filter, the filter was rinsed to remove salts, and the insoluble material was 

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 logger onto a storage module during site 

visits. Raw data from the storage modules 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 sonde’s optical sensor output, which decreased). An example time series 

of raw and edited optical backscatterance data from water year 1994 is presented in figure 3. After sensors were cleaned, sensor output immediately decreased (fig. 3, April 19, June 8, and June 28). Efforts 

to correct the invalid data proved to be unsuccessful because the desired signal was sometimes highly 

Figure 3. Example of raw and edited optical backscatterance data, mid-depth sensor, Point San Pablo, Central San Francisco 

Bay, California, water year 1994 (Buchanan and others, 1996).
Sensor Calibration and Suspended-Sediment Concentration Data 11

variable. Thus, data collected during the period prior to sensor cleaning often were unusable and were 

removed from the record (fig. 3). 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. 3). 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 from the optical sensors was converted to suspended-sediment concentration using the 

robust, non-parametric, repeated median method (Siegel, 1982). In addition, the prediction interval and 

the 95 percent confidence interval were calculated and presented for each calibration relation.

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

.

The calibration slope was calculated as the median of βi

.

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

slope calculated above

.

The final linear calibration equation is

.

The non-parametric prediction interval (PInp) (Helsel and Hirsch, 1992, p. 76) is a constant-width 

error band that contains 68.26 percent, or one standard deviation, of the calibration data set. The 

68.26-percent value was selected because it has essentially the same error prediction limits as the rootmean-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.

It is important to note that 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 non-normal 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

,

where

is the residual value,

n is the number of data points, and

α is the confidence level of 0.6826.

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:

βi median Yj Yi ( ) –

Xj Xi ( ) – = ---------------------- for all j i ≠

slope = β

ˆ 1 median βi = ( )

intercept = β

ˆ 0 median Yi β

ˆ 1Xi = ( ) –

Y β

ˆ 1X β

ˆ = + 0

non-parametric prediction interval = PInp Yˆ α

2

---  

 ( ) n + 1

 to Yˆ

1 α

2 – ---  

 ( ) n + 1 =

Yˆ
12 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

, and

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 largesample 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 can be performed 

based on the methodology presented in Helsel and Hirsh (1992, p. 273–274).

A statistical summary of the calculated suspended-sediment concentrations is presented in table 1. 

The usable percent of a complete year of data (96 data points per day) collected by optical backscatterance sensors at each site is presented in table 2. 

This section of the report also includes the robust regression (calibration) plots for optical sensor 

output versus suspended-sediment concentration (in milligrams per liter). The repeated median regression plots include the number of water samples, the calculated linear correlation equation, the nonparametric prediction interval (shown on the plots as a grey band), and the 95-percent confidence interval 

(shown on the plots as a dash-dot line). Finally, the time-series plots of suspended-sediment concentration data are shown for each site.

Suisun Bay

Mallard Island

The calibration of the near-surface, self-cleaning probe (fig. 4A) was developed from 102 water 

samples collected from December 9, 1994, through May 24, 1999; flood samples collected from January 

through March 1995, January through February 1997, and February through March 1998 were excluded 

(flood conditions, which can cause a change in sensor calibration, did not occur in water year 1999). The 

near-surface probe malfunctioned after the site visit on May 24 and was replaced on June 29, 1999. The 

calibration of the near-surface replacement probe (fig. 4B) was developed from 14 water samples collected from June 29, 1999, through February 8, 2000. An auto-sampler was installed on September 23, 

1999, at the near-surface position that collected hourly water samples during a 24-hour period. Analysis 

of the 24 water samples collected by the auto-sampler indicated a shift in the calibration of the nearsurface probe, which was not verified by previous or subsequent water samples. All water samples collected by the auto-sampler were eliminated from the analysis due to the inability to ensure that the autosampler was not causing a bias to the data. The calibration of the near-bottom self-cleaning probe (fig. 5) 

was developed from 121 water samples collected from April 20, 1995, through water year 1999; flood 

samples collected from January through February 1997 and February through March 1998 were 

excluded. The data collected by the near-bottom probe from June 29 through July 28, 1999, was deleted 

from the record due to erratic data patterns and inability to correlate the voltages with water-sample data. 

Suspended-sediment concentration data collected during water year 1999 are presented in figure 6.

Ru

n n( ) – 1

2 ------------------- 1.96 n n( ) – 1 ( ) 2n + 518 ----------------------------------------  

  +

2 ---------------------------------------------------------------------------------------- 1 +

 

 

 

=

Rl

n n( ) – 1

2 ------------------- 1.96 n n( ) – 1 ( ) 2n + 518 ----------------------------------------  

  –

2 = ---------------------------------------------------------------------------------------
Sensor Calibration and Suspended-Sediment Concentration Data 13

Table 1. Statistical summary of suspended-sediment concentration data, Suisun Bay, San Pablo Bay, and Central and South 

San Francisco Bays, California, water year 1999

[All measurements are in milligrams per liter. Lower quartile is 25th percentile; upper quartile is 75th percentile; NA, not applicable]

Site Latitude Longitude Depth Mean Median Lower 

quartile

Upper 

quartile

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

Near-bottom

42

46

39

38

31

23

49

58

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

Near-bottom

66

203

46

151

22

52

78

297

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

Near-bottom

80

186

61

144

39

89

101

235

Channel Marker 9 38°05’19” 122°26’29” Near-bottom 213 142 81 263

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

Near-bottom

48

81

40

62

28

40

59

99

Pier 24 37°47’27” 122°23’05” Mid-depth

Near-bottom

25

33

22

28

18

22

29

38

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

Near-bottom

132

171

96

112

56

64

170

215

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

Near-bottom

95

150

76

127

52

80

117

190

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

Near-bottom

60

N/A

47

N/A

30

N/A

73

N/A

Table 2. Usable percentage of a complete year of data (96 data points 

per day) collected by optical backscatterance sensors, Suisun Bay, 

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

water year 1999

Site Depth Percent valid data

Mallard Island Near-surface

Near-bottom

81

70

Carquinez Bridge Mid-depth

Near-bottom

52

41

Mare Island Causeway Mid-depth

Near-bottom

91

89

Channel Marker 9 Near-bottom 62

Point San Pablo Mid-depth

Near-bottom

73

94

Pier 24 Mid-depth

Near-bottom

52

56

Channel Marker 17 Mid-depth

Near-bottom

74

75

Dumbarton Bridge Mid-depth

Near-bottom

55

59

San Mateo Bridge Mid-depth

Near-bottom

30

0
14 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

0 50 100 150 200 250 300 350 0

20

40

60

80

100

120

140

Number of data points = 102

y = 0.284 *x + 12.4

Non-parametric prediction interval: + 4 to -7

95 percent confidence bound on slope calculation: 0.355 to 0.276

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

60 80 100 120 140 160 180 200 220 0

10

20

30

40

50

60

70

80

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of data points = 14

y = 0.285 *x + 4.6

Non-parametric prediction interval: + 5 to -4

95 percent confidence bound on slope calculation: 0.334 to 0.224

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

A

B

Figure 4. Calibration of near-surface optical backscatterance sensor October 1–May 24 (A) and June 29–September 30 (B) at Mallard Island, 

Suisun Bay, California, water year 1999. 
Sensor Calibration and Suspended-Sediment Concentration Data 15

0 50 100 150 200 250 300 350 0

20

40

60

80

100

120

140

160

180

200

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS,

IN MILLIGRAMS PER LITER

Number of data points = 121

y = 0.545 *x 12.7

Non-parametric prediction interval: + 9 to -5

95 percent confidence bound on slope calculation: 0.595 to 0.519

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

Figure 5. Calibration of near-bottom optical backscatterance sensor at Mallard Island, Suisun Bay, California, water year 1999.
16 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

Figure 6. Time series of near-surface (A) and near-bottom (B) suspended-sediment concentrations calculated from sensor readings at 

Mallard Island, Suisun Bay, California, water year 1999. 

0

50

100

150

200

250

300

350

0

50

100

150

200

250

300

350

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

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

1998 1999

A

B
Sensor Calibration and Suspended-Sediment Concentration Data 17

0 50 100 150 200 250 300 350 400 0

100

200

300

400

500

600

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS,

IN MILLIGRAMS PER LITER

Number of data points = 33

y = 1.284 *x + 0.7

Non-parametric prediction interval: + 19 to -36

95 percent confidence bound on slope calculation: 1.468 to 1.064

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

San Pablo Bay

Carquinez Bridge

The suspension line for the sensors was found broken on October 1, 1998, and was replaced on 

October 15, 1998. A single calibration was used for the mid-depth and near-bottom sensors and was 

developed from 33 water samples (20 water samples collected from the upper position and 13 collected 

from the lower position) collected from June 23, 1998, through water year 1999 (fig. 7). Using a single 

calibration for both sensors was possible because the sensors were factory calibrated using the same NTU 

standard and were verified by on-site field checks during the period of deployment using NTU standards 

of varying concentrations. The mid-depth sonde was replaced due to failure of the instrument on April 7, 

1999, and June 10, 1999. The near-bottom sonde’s data logger did not store data from October 15, 1998, 

through March 17, 1999. The male pins on the near-bottom sonde’s communication port were found to 

be corroded on September 7, 1999, and the sonde was replaced. The near-bottom data file from 

August 11 through September 7, 1999, was lost when the unit was sent for repairs. Suspended-sediment 

concentration data collected during water year 1999 are presented in figure 8.

Figure 7. Calibration of mid-depth and near-bottom optical backscatterance sensors at Carquinez Bridge, San Pablo Bay, California, water year 

1999.
18 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

0

200

400

600

800

1,000

1,200

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

0

200

400

600

800

1,000

1,200

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

1998 1999

A

B

Figure 8. Time series of mid-depth (A) and near-bottom (B) suspended-sediment concentrations calculated from sensor readings at 

Carquinez Bridge, San Pablo Bay, California, water year 1999. 
Sensor Calibration and Suspended-Sediment Concentration Data 19

Mare Island Causeway

The calibration of the mid-depth sensor was developed from 30 water samples collected from 

October 6, 1998, through water year 1999 (fig. 9A). The calibration of the near-bottom sensor was developed from 30 water samples collected from October 6, 1998, through water year 1999 (fig. 9B). The station was shut down from December 29, 1998, through January 4, 1999, when the conductivity and 

temperature sensors were replaced. Suspended-sediment concentration data collected during water year 

1999 are presented in figure 10.
20 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

0 50 100 150 200 250 300 350 0

50

100

150

200

250

Number of data points = 30

y = 0.529 *x 5.4

Non-parametric prediction interval: + 15 to -10

95 percent confidence bound on slope calculation: 0.646 to 0.494

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

0 200 400 600 800 1,000 1,200 0

100

200

300

400

500

600

700

800

900

1,000

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of data points = 30

y = 0.613 *x 1.1

Non-parametric prediction interval: + 23 to -16

95 percent confidence bound on slope calculation: 0.713 to 0.583

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

A

B

Figure 9. Calibration of mid-depth (A) and near-bottom (B) optical backscatterance sensors at Mare Island Causeway, San Pablo Bay, 

California, water year 1999.
Sensor Calibration and Suspended-Sediment Concentration Data 21

0

200

400

600

800

1,000

1,200

1,400

1,600

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

0

200

400

600

800

1,000

1,200

1,400

1,600

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

1998 1999

A

B

Figure 10. Time series of mid-depth (A) and near-bottom (B) suspended-sediment concentrations calculated from sensor readings at Mare 

Island Causeway, San Pablo Bay, California, water year 1999. 
22 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

Channel Marker 9

A time shift (+9 hours) was applied to the record from November 12, 1998, through June 26, 1999, 

to correct a time lag in the sonde’s internal clock. The 9-hour discrepancy between the sonde’s internal 

clock and Pacific Standard Time (to which the data files were programmed) resulted in all after-cleaning 

water samples collected during this period to be unusable. The calibration of the near-bottom sensor was 

developed from 11 water samples collected from November 12, 1998, through water year 1999 

(fig. 11A). The optical sensor on the sonde can measure a maximum of 1,000 NTU, which was exceeded 

on February 17 and 18, 1999, at maximum ebb during a strong spring tide. Suspended-sediment 

concentration data collected during water year 1999 are presented in figure 11B.
Sensor Calibration and Suspended-Sediment Concentration Data 23

0 50 100 150 200 250 300 350 400 450 500 0

100

200

300

400

500

600

700

SENSOR OUTPUT, IN NEPHELOMETRIC TURBIDITY UNITS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of data points = 11

y = 0.911 *x + 45.4

Non-parametric prediction interval: + 43 to -26

95 percent confidence bound on slope calculation: 1.234 to 0.622

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

0

100

200

300

400

500

600

700

800

900

1,000

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

1998 1999

A

B

Figure 11. Calibration of near-bottom optical backscatterance sensor (A) and near-bottom suspended-sediment concentration (B) calculated 

from sensor readings at Channel Marker 9, San Pablo Bay, California, water year 1999.
24 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

Central San Francisco Bay

Point San Pablo

The calibration of the mid-depth sensor was developed using 85 water samples collected from 

August 15, 1995, through water year 1999 (fig. 12A). Shifts to the mid-depth record, calculated from 

water-sample data not shown on figure 12A, were applied from October 5 to November 17, 1998, 

(−29.5 mV), and September 21 to September 30, 1999, (−42.2 mV), to correct for shifts in sensor output. 

The calibration of the near-bottom sensor was developed using 108 water samples collected from 

August 15, 1995, through water year 1999 (fig. 12B). A −87 mV shift to the near-bottom record, calculated from water-sample data not shown on figure 12B, was applied from July 6 to July 26, 1999, to correct for a shift in sensor output. The data logger malfunctioned from July 26 through September 13, 

1999, and data were recorded at 30-minute intervals instead of 15-minute intervals. From mid-July to 

mid-September 1999, the near-bottom sensor was operating erratically, probably due to a problem with 

the data logger, and many spikes were edited from the data set. Suspended-sediment concentration data 

collected during water year 1999 are presented in figure 13 (30-minute data are shown as dots).
Sensor Calibration and Suspended-Sediment Concentration Data 25

0 100 200 300 400 500 600 700 800 0

100

200

300

400

500

600

SENSOR OUTPUT, IN MILLIVOLTS

Number of data points = 85

y = 0.529 *x 0.9

Non-parametric prediction interval: + 30 to -15

95 percent confidence bound on slope calculation: 0.630 to 0.502

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

0 200 400 600 800 1,000 1,200 1,400 0

100

200

300

400

500

600

700

800

900

1,000

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of data points = 108

y = 0.624 *x 2.8

Non-parametric prediction interval: + 42 to -25

95 percent confidence bound on slope calculation: 0.706 to 0.586

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

A

B

Figure 12. Calibration of mid-depth (A) and near-bottom (B) optical backscatterance sensors at Point San Pablo, Central San Francisco Bay, 

California, water year 1999. 
26 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

0

100

200

300

400

500

600

700

0

100

200

300

400

500

600

700

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

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

1998 1999

A

B

Figure 13. Time series of mid-depth (A) and near-bottom (B) suspended-sediment concentrations calculated from sensor readings at Point 

San Pablo, Central San Francisco Bay, California, water year 1999.
Sensor Calibration and Suspended-Sediment Concentration Data 27

Pier 24

The station was shut down due to seismic retrofitting of the bridge from August 14 through 

October 6, 1998. Calibration of the mid-depth sensor was developed from 20 water samples collected 

from May 20, 1998, through January 1, 2000 (fig. 14A). Calibration of the near-bottom sensor was developed from 77 water samples collected from June 22, 1995, through water year 1999 (fig. 14B). Data logger malfunction caused a loss of data from October 15 through November 1, 1998. The station lost power 

from November 29 through December 16, 1998, and June 7 through June 16, 1999. Suspended-sediment 

concentration data collected during water year 1999 are presented in figure 15.
28 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

0 20 40 60 80 100 120 140 160 180 0

20

40

60

80

100

120

140

Number of data points = 20

y = 0.337 *x + 4.1

Non-parametric prediction interval: + 13 to -8

95 percent confidence bound on slope calculation: 0.674 to 0.195

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

0 50 100 150 200 250 300 350 400 450 500 0

50

100

150

200

250

300

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of data points = 77

y = 0.428 *x + 5.8

Non-parametric prediction interval: + 13 to -15

95 percent confidence bound on slope calculation: 0.521 to 0.370

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

A

B

Figure 14. Calibration of mid-depth (A) and near-bottom (B) optical backscatterance sensors at Pier 24, Central San Francisco Bay, California, 

water year 1999. 
Sensor Calibration and Suspended-Sediment Concentration Data 29

0

50

100

150

200

250

300

0

50

100

150

200

250

300

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

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

1998 1999

A

B

Figure 15. Time series of mid-depth (A) and near-bottom (B) suspended-sediment concentrations calculated from sensor readings at Pier 

24, Central San Francisco Bay, California, water year 1999.
30 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

South San Francisco Bay

Channel Marker 17

The calibration of the mid-depth sensor was developed from 47 water samples collected from 

February 26, 1997, through water year 1999 (fig. 16A). The calibration of the near-bottom sensor was 

developed from 24 water samples collected from July 30, 1998, through water year 1999 (fig. 16B). 

Suspended-sediment concentration data collected during water year 1999 are presented in figure 17.
Sensor Calibration and Suspended-Sediment Concentration Data 31

0

100

200

300

400

500

600

700

800

Number of data points = 47

y = 0.641 *x 12.2

Non-parametric prediction interval: + 14 to -10

95 percent confidence bound on slope calculation: 0.660 to 0.618

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

0 200 400 600 800 1,000 1,200 0

100

200

300

400

500

600

700

800

900

1,000

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of data points = 24

y = 0.654 *x 6.9

Non-parametric prediction interval: + 61 to -15

95 percent confidence bound on slope calculation: 0.809 to 0.537

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

A

B

Figure 16. Calibration of mid-depth (A) and near-bottom (B) optical backscatterance sensors at Channel Marker 17, South San Francisco Bay, 

California, water year 1999.
32 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

0

200

400

600

800

1,000

1,200

1,400

1,600

1,800

0

200

400

600

800

1,000

1,200

1,400

1,600

1,800

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

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

1998 1999

A

B

Figure 17. Time series of mid-depth (A) and near-bottom (B) suspended-sediment concentrations calculated from sensor readings at 

Channel Marker 17, South San Francisco Bay, California, water year 1999.
Sensor Calibration and Suspended-Sediment Concentration Data 33

Dumbarton Bridge

The calibration of the mid-depth sensor was developed from 81 water samples collected from 

June 18, 1996, through water year 1999 (fig. 18A). A −48.5 mV shift to the record, calculated from water 

sample data not shown on figure 18A, was applied from October 7 through October 28, 1998. The calibration of the near-bottom sensor was developed from 16 water samples collected from October 7, 1998, 

through water year 1999 (fig. 18B). The station lost power from November 19 through December 15, 

1998, resulting in a loss of data. Suspended-sediment concentration data collected during water year 

1999 are presented in figure 19. 
34 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

0 100 200 300 400 500 600 0

50

100

150

200

250

300

350

400

Number of data points = 81

y = 0.564 *x 10.4



Non-parametric prediction interval: + 22 to -28

95 percent confidence bound on slope calculation: 0.622 to 0.457

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

0 50 100 150 200 250 300 350 400 450 500 0

50

100

150

200

250

300

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of data points = 16

y = 0.600 *x 2.6

Non-parametric prediction interval: + 11 to -13

95 percent confidence bound on slope calculation: 0.645 to 0.496

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

A

B

Figure 18. Calibration of mid-depth (A) and near-bottom (B) optical backscatterance sensors at Dumbarton Bridge, South San Francisco Bay, 

California, water year 1999.
Sensor Calibration and Suspended-Sediment Concentration Data 35

0

200

400

600

800

1,000

1,200

1,400

1,600

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

0

200

400

600

800

1,000

1,200

1,400

1,600

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

1998 1999

A

B

Figure 19. Time series of mid-depth (A) and near-bottom (B) suspended-sediment concentrations calculated from sensor readings at 

Dumbarton Bridge, South San Francisco Bay, California, water year 1999.
36 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

San Mateo Bridge

The calibration of the mid-depth sensor was developed from 34 water samples collected from 

March 13, 1997, through January 12, 1999 (fig. 20A). There were no valid data collected at the nearbottom depth due to a large mass of biological fouling (hydroids) that had accumulated at the bottom of 

the suspension cable and interfered with the optical sensor readings. The clump of fouling was removed 

on January 12, 1999, and data were successfully collected until March 4, 1999, when the station was shut 

down due to seismic retrofitting of the bridge. Insufficient samples were collected to establish a reliable 

calibration due to the near-bottom sensor (two samples of low concentration) and the data from 

January 12 through March 4, 1999, were not used. Suspended-sediment concentration data collected 

during water year 1999 are presented in figure 20B.
Sensor Calibration and Suspended-Sediment Concentration Data 37

0 20 40 60 80 100 120 140 160 180 200 0

50

100

150

SENSOR OUTPUT, IN MILLIVOLTS

SUSPENDED-SEDIMENT CONCENTRATIONS, IN MILLIGRAMS PER LITER

Number of data points = 34

y = 0.650 *x 11.1

Non-parametric prediction interval: + 10 to -12

95 percent confidence bound on slope calculation: 0.802 to 0.530

Non-parametric prediction interval 

95 percent confidence bound on slope calculation

0

50

100

150

200

250

300

350

400

450

500

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

1998 1999

A

B

Figure 20. Calibration of mid-depth optical backscatterance sensor (A) and mid-depth suspended-sediment concentration (B) calculated 

from sensor readings at San Mateo Bridge, South San Francisco Bay, California, water year 1999.
38 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

SUMMARY

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

one site 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 1999. Three types of optical backscatterance sensors, 

controlled by an electronic data logger, were used to monitor suspended sediment. Water samples were 

collected to calibrate the electrical output of the optical sensors to suspended-sediment concentration, 

and the recorded data were recovered and edited. Suspended-sediment concentration data are available 

from the files of the USGS in Sacramento, California.

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 Ruhl, C.A., 2000, Summary of suspended-solids concentration data, San Francisco 

Bays, California, water year 1998: U.S. Geological Survey Open-File Report 00-88, 41 p.

Buchanan, P.A., and Schoellhamer, D.H., 1995, Summary of suspended-solids concentration data, 

Central and South San Francisco Bays, California, water years 1992 and 1993: U.S. Geological 

Survey Open-File Report 94-543, 15 p.

———, 1996, Summary of suspended-solids concentration data, San Francisco Bay, California, water 

year 1995: U.S. Geological Survey Open-File Report 96-591, 40 p.

———,1998, Summary of suspended-solids concentration data, San Francisco Bay, California, water 

year 1996: U.S. Geological Survey Open-File Report 98-175, 59 p.

———, 1999, Summary of suspended-solids concentration data, San Francisco Bay, 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.

———, 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.

D & A Instrument Company, 1991, OBS-1 & 3: Suspended sediment and turbidity monitor (rev. 3/91): 

Port Townsend, WA, D & A Instrument Company Instruction Manual, Part No. OBS-1/3 man, 41 p.
References Cited 39

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.

Downing, J.P., 1983, An optical instrument for monitoring suspended particulates in ocean and 

laboratory: in OCEANS 1983, San Francisco, California, August 29–September 1, 1983, 

Proceedings: p. 199–202.

Downing, J.P., Sternburg, R.W., and Lister, C.R.B., 1981, New instrumentation for the investigation of 

sediment suspension processes in the shallow marine environment: Marine Geology, v. 42, p. 19–34.

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 SanudoWilhelmy, 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.

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: Elsevier, New York, v. 49, 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.

Kimmerer, Wim, 1992, An evaluation of existing data in the entrapment zone of the San Francisco Bay 

Estuary: Tiburon, California, Biosystems Analysis, Inc., Technical Report 33, 49 p.

Kuwabara, J.S., Chang, C.C.Y., Cloern, J.E., Fries, T.L., Davis, J.A., and Luoma, S.N., 1989, Trace metal 

associations in the water column of South San Francisco Bay, California: Estuarine, Coastal and 

Shelf Science, v. 28, p. 307–325.

Levesque, V.A., and Schoellhamer, D.H., 1995, Summary of sediment resuspension monitoring, Old 

Tampa Bay and Hillsborough Bay, Florida, 1988–91: U.S. Geological Survey Water-Resources 

Investigations Report 94-4081, 31 p.

Luoma, S.N., 1996, The developing framework of marine ecotoxicology: Pollutants as a variable in 

marine ecosystems?: Journal of experimental marine biology and ecology, v. 200, p. 29–55.

Luoma, S.N., Cain, D., and Johansson, C., 1985, Temporal fluctuations of silver, copper, and zinc in the 

bivalve Macoma balthica at five stations in South San Francisco Bay: Hydrobiologia, v. 129, 

p. 109–120.

Peterson, D.H., Conomos, T.J., Broenkow, W.W., and Doherty, P.C., 1975, Location of the non-tidal current null zone in northern San Francisco Bay: Estuarine and Coastal Marine Science, v. 3, p. 1–11.

Porterfield, George, 1980, Sediment transport of streams tributary to San Francisco, San Pablo, and 

Suisun Bays, California, 1909–1966: U.S. Geological Survey Water-Resources Investigations 

Report 80-64, 91 p.

Powell, T.M., Cloern, J.E., and Huzzey, L.M., 1989, Spatial and temporal variability in South San

Francisco Bay (U.S.A.). I. Horizontal distributions of salinity, suspended sediments, and 

phytoplankton biomass and productivity: Estuarine, Coastal and Shelf Science, v. 28, p. 583–597.

Schoellhamer, D.H., 1996, Factors affecting suspended-sediment concentrations in South San Francisco 

Bay, California: Journal of Geophysical Research, v. 101, no. C5, p. 12087–12095.
40 Summary of Suspended-Sediment Concentration Data, San Fancisco Bay, California, Water Year 1999

Schoellhamer, D.H., and Burau, J.R., 1998, Summary of findings about circulation and the estuarine turbidity maximum in Suisun Bay, California: U.S. Geological Survey Fact Sheet FS-047-98, 6 p.

Siegel, A.R., 1982, Robust regression using repeated medians: Biometrika, v. ‘69, p. 242–244.

Smith, L.H., 1987, A review of circulation and mixing studies of San Francisco Bay, California: U.S. 

Geological Survey Circular 1015, 38 p.

U.S. Environmental Protection Agency, 1992, State of the estuary: Dredging and waterway modification: 

U.S. Environmental Protection Agency San Francisco Estuary Project, chap. 8, p. 191–215.

U.S. Geological Survey, USGS Publications Related to Continuous Monitoring of San Francisco Bay: 

accessed January 19, 2001, at URL http://ca.water.usgs.gov/abstract/sfbay/sfbaycontbib.html/
USGS - Suspended-Solids Concentrations in SF Bay, CA

Water Resources of California

USGS Publications Related to Continuous 

Monitoring of San Francisco Bay

2001

Ruhl, C.A., and Schoellhamer, D.H., 2001, Time series of SSC, salinity, temperature, and total mercury 

concentration in San Francisco Bay during water year 1998: Regional Monitoring Program for Trace 

Substances contribution number 44, San Francisco Estuary Institute, Richmond, California. URL 

http://www.sfei.org/rmp/reports/time_series/timeseries_cont43.pdf (947 KB PDF) 

Schoellhamer, D.H., 2001, Continiuous monitoring of suspended sediment in rivers by use of optical 

sensors: Proceedings of the Seventh Federal Interagency Sedimentation Conference, Reno Nevada, March 

25-29, 2001, p. III-160 - III-167. URL: http://ca.water.usgs.gov/abstract/sfbay/Schoellhamer.pdf (293 KB 

PDF) 

Schoellhamer, D.H., 2001, Influence of salinity, bottom topography, and tides on locations of estuarine 

turbidity maxima in northern San Francisco Bay, in McAnally, W.H. and Mehta, A.J., ed., Coastal and 

Estuarine Fine Sediment Transport Processes: Elsevier Science B.V., p. 343-357. URL: 

http://ca.water.usgs.gov/abstract/sfbay/elsevier0102.pdf (160 KB PDF) 

2000

Brennan, M.L., Monismith, S.G., Schoellhamer, D.H., and Burau, J.R., 2000, Tidal asymmetry of 

erodibility at a site in San Francisco Bay, USA: Proceedings of the Sixth International Conference on 

Nearshore and Estuarine Cohesive Sediment Transport Processes, Delft, The Netherlands, September 4-8, 

2000, p. 6-7. 

Buchanan, P.A., 2000, Specific conductance, water temperature, and water level data from San Francisco 

Bay, California, in water year 1999: IEP Newsletter, v. 13, no. 3, p. 17-20. URL 

http://www.iep.ca.gov/report/newsletter/2000summer/

Buchanan, P.A., and Ruhl, C.A., 2000, Summary of suspended-solids concentration data, San Francisco 

Bay, California, water year 1998: U.S. Geological Survey Open File Report 00-88, 41 p. 

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Moon, G.E., Kuivila, K., Ruhl, C., and Schoellhamer, D., 2000, Exposure of Delta Smelt to dissolved 

pesticides in 1998 and 1999: Interagency Ecological Program Newsletter, v. 13, no. 4, p. 27-33. 

Ruhl, C.A., and Schoellhamer, D.H., Spatial and seasonal variability of suspended-sediment 

concentrations in Honker Bay, a shallow subembayment of San Francisco Bay: Proceedings of the 

CALFED Science Conference, Sacramento, California, October 3-5, 2000, p. 218. 

Schoellhamer, D.H., Burau, J.R., Brennan, M.L., and Monismith, S.G., 2000, Transfer of cohesive 

sediment between the bed and water column at a site in San Francisco Bay, USA: Proceedings of the 

Sixth International Conference on Nearshore and Estuarine Cohesive Sediment Transport Processes, 

Delft, The Netherlands, September 4-8, 2000, p. 8-9. 

Schoellhamer, D.H., and Dinehart, R.L., 2000, Suspended-sediment supply to the Delta from the 

Sacramento River: Proceedings of the CALFED Science Conference, Sacramento, California, October 3-

5, 2000, p. 124. URL http://ca.water.usgs.gov/program/sfbay/calfedsed/SedimentSupply.html

Takekawa, J.Y., Martinelli, G.M., Miles, A.K., Fregien, S., Schoellhamer, D.H., Duffy, W.G., and Saiki, 

M.K., 2000, Salt ponds and avian communities: Will benefits of tidal wetland restoration exceed costs to 

waterbirds?: Proceedings of the CALFED Science Conference, Sacramento, California, October 3-5, 

2000, p. 135. 

Warner, J.C., Schoellhamer, D.H., Burau, J.R., and Schladow, S.G., 2000, Effects of Tidal Current Phase 

at the Junction of Two Straits: Proceedings of the Fall meeting of the American Geophysical Union, San 

Francisco, California, December 15-19, 2000. AGU Citation

1999

Buchanan, P.A., 1999, Specific conductance, water temperature, and water level data, San Francisco Bay, 

California, water year 1998: Interagency Ecological Program Newsletter (PDF), v. 12, no. 4, p. 46-51. 

Buchanan, P.A., and Schoellhamer, D.H., 1999, Summary of suspended-solids concentration data in San 

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

http://ca.water.usgs.gov/rep/ofr99189/

Dinehart, R.L., and Schoellhamer, D.H., 1999, Sedimentation in the Delta of the Sacramento and San 

Joaquin Rivers: Proceedings of the 4th biennial State of the Estuary Conference, San Francisco, Calif., 

March 17-19, 1999, p. 75. 

Friebel, M.F., Freeman, L.A., Webster, M.D., and Anderson, S.W., 1999, Water resources data, 

California, water year 1998: U.S. Geological Survey Wataer-Data Report CA-98-2, v. 2, 360 p. URL 

http://ca.water.usgs.gov/data/

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Oltmann, R.N., Schoellhamer, D.H., and Dinehart, R.L., 1999, Sediment inflow to the Sacramento-San 

Joaquin Delta and the San Francisco Bay: Interagency Ecological Program newsletter, v. 12, no. 1, pp. 30-

33. 

Ruhl, C.A., and Schoellhamer, D.H., 1999, Time series of suspended-solids concentration in Honker Bay 

during water year 1997: 1997 Annual Report of the Regional Monitoring Program for Trace Substances, 

p. 82-92, URL http://www.sfei.org/rmp/1997/c0304.htm

Ruhl, C.A., Schoellhamer, D.H., Stumpf, R.P., and Lindsay, C.L., 1999, Remote sensing: Visual cues to 

suspended-solids transport in San Francisco Bay, California: Proceedings of the 4th biennial State of the 

Estuary Conference, San Francisco, Calif., March 17-19, 1999, p. 74. 

Warner, J.C., Schladow, S.G., and Schoellhamer, D.H., 1999, Summary and analysis, hydrodynamic and 

water-quality data for the Napa/Sonoma Marsh complex, Final Report: University of California, Davis, 

Department of Civil and Environmental Engineering. 

Warner, J.C., Schoellhamer, D.H., Schladow, S.G., and Burau, J.R., 1999, Napa/Sonoma Marsh 

Hydrodynamic and Water-Quality Study: Proceedings of the 4th biennial State of the Estuary Conference, 

San Francisco, Calif., March 17-19, 1999, p. 126. 

1998

Buchanan, P.A., and Schoellhamer, D.H., 1998, Summary of suspended-solids concentration data in San 

Francisco Bay, California, water year 1996: U.S. Geological Survey Open File Report 98-175, 59 p. 

Schoellhamer, D.H., 1998, The weak influence of flocculation at low salinities on the distribution of 

suspended-solids concentration in the San Francisco Bay estuary, California, USA: Proceedings of the 

Fifth International Conference on Cohesive Sediment Transport, Seoul, Korea, May 25-29, 1998, p. 1. 

Schoellhamer, D.H., and Buchanan, P.A., 1998, Measuring suspended-solids concentration with optical 

backscatterance sensors: Proceedings of the Federal Interagency Workshop on Sediment Transport 

Technology for the 21st Century, St. Petersburg, Florida, February 17-19, 1998, URL 

http://water.usgs.gov/osw/techniques/sedtech21/schoellhamer.html

Schoellhamer, D.H., and Burau, J.R., 1998, Summary of findings about circulation and the estuarine 

turbidity maximum in Suisun Bay, California, U.S. Geological Survey Fact Sheet FS-047-98, 6 p. URL: 

http://sfbay.wr.usgs.gov/access/suisunbay/dschoell/

Schoellhamer, D.H., Cacchione, D.A., Rubin, D.M., Cheng, R.T., Dingler, J.R., Jaffe, B.E., and Stumpf, 

R.P., 1997, Sediment-Transport Research in San Francisco Bay: Proceedings of USGS Sediment 

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Workshop, Harpers Ferry, West Virginia, February 4-7, 1997, URL 

http://wwwrvares.er.usgs.gov/osw/workshop/schoellhamer.html

Webster, M.D., Friebel, M.F., and Freeman, L.A., 1998, Water resources data, California, water year 

1997: U.S. Geological Survey Water-Data Report CA-97-2, v. 2, 322 p. 

1997

Freeman, L.A., Webster, M.D., and Friebel, M.F., 1997, Water resources data, California, water year 

1996: U.S. Geological Survey Water-Data Report CA-96-2, v. 2, 356 p. 

Jennings, B., Schoellhamer, D.H., and Kuivila, K.M., 1997, Optimum sampling strategy for sedimentassociated pesticides in Suisun Bay: Interagency Ecological Program newsletter, v. 10, no. 4, p. 16-20. 

Schoellhamer, D.H., 1997, Time Series of Trace Element Concentrations Calculated from Time Series of 

Suspended-Solids Concentrations and RMP Water Samples: 1995 Annual Report of the Regional 

Monitoring Program for Trace Substances, p. 53-55. 

Schoellhamer, D.H., 1997, Time series of SSC, salinity, temperature, and total mercury concentration in 

San Francisco Bay during water year 1996: 1996 Annual Report of the Regional Monitoring Program for 

Trace Substances, p. 65-77. 

Schoellhamer, D.H., Cacchione, D.A., Rubin, D.M., Cheng, R.T., Dingler, J.R., Jaffe, B.E., and Stumpf, 

R.P., 1997, Sediment-Transport Research in San Francisco Bay: Proceedings of USGS Sediment 

Workshop, Harpers Ferry, West Virginia, February 4-7, 1997. URL: 

http://water.usgs.gov/osw/techniques/workshop/schoellhamer.html

Warner, J.C., Schoellhamer, D.H., and Burau, J.R., 1997, A sediment transport pathway in the back of a 

nearly semienclosed subembayment of San Francisco Bay, California: Proceedings of the XXVII 

International Association of Hydraulic Research Congress, August 10-15, 1997, San Francisco, 

California, v. 2, p. 1096-1101. 

1996

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

Francisco Bay, California, water year 1995: U.S. Geological Survey Open-File Report 96-591, 40 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. 

Burau, J.R., and Schoellhamer, D.H., 1996, Residual Transport in Suisun Cutoff, San Francisco Bay, 

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California, During Summer 1995: Part 1, Salt Transport: abstract for the 1996 Fall AGU meeting, San 

Francisco, California, December 15-19, 1996. 

Friebel, M. F., Trujillo, L. F., and Markham, K. L., 1996, Water resources data, California, water year 

1995, vol. 2, Pacific slope basins from Arroyo Grande to Oregon state line except Central Valley: U.S. 

Geological Survey Water-Data Report CA-95-2, 339 pp. 

Lacy, J.R., Schoellhamer, D.H., and Burau, J.R., 1996, Suspended-solids flux at a shallow-water site in 

South San Francisco Bay, California: Proceedings of the North American Water and Environment 

Congress, Anaheim, California, June 24-28, 1996. 

Schoellhamer, D.H., 1996, Central San Francisco Bay suspended-sediment transport processes and 

comparison of continuous and discrete measurements of suspended-solids concentrations: San Francisco 

Estuary Regional Monitoring Program for Trace Substances, 1994 Annual Report, p. 198-206. 

Schoellhamer, D.H., 1996, Factors affecting suspended-solids concentrations in South San Francisco Bay, 

California: Journal of Geophysical Research, v. 101, no. C5, p. 12087-12095. 

Schoellhamer, D.H., 1996, Suspended-solids concentrations in San Francisco Bay, California: 

Proceedings of the Third Biennial State of the Estuary Conference, San Francisco, California, October 10-

12, 1996, p. 54. 

Schoellhamer, D.H., and Burau, J.R., 1996, Residual Transport in Suisun Cutoff, San Francisco Bay, 

California, During Summer 1995: Part 2, Sediment Transport: abstract for the 1996 Fall AGU meeting, 

San Francisco, California, December 15-19, 1996. 

Schoellhamer, D.H., Oltmann, R.N., Jaffe, B.E., and Smith, R.E., 1996, Sediment supply and wetlands in 

San Francisco Bay: Proceedings of the Third Biennial State of the Estuary Conference, San Francisco, 

California, October 10-12, 1996. p. 23. 

1995

Ayers, W., and others, 1995, Water resources data, California, water year 1994, vol. 2, Pacific slope 

basins from Arroyo Grande to Oregon state line except Central Valley: U.S. Geological Survey WaterData Report CA-94-2, 357 pp. 

Buchanan, P.A., and Schoellhamer, D.H., 1995, Summary of suspended-solids concentration data, Central 

and South San Francisco Bays, California, water years 1992 and 1993: U.S. Geological Survey Open-File 

Report 94-543, 15 p. 

Tobin, A., Schoellhamer, D.H., and Burau, J.R., 1995, Suspended-solids flux in Suisun Bay, California: 

Proceedings of the First International Conference on Water Resources Engineering, San Antonio, Texas, 

http://ca.water.usgs.gov/abstract/sfbay/sfbaycontbib.html (5 of 6) [8/20/2001 12:35:30 PM]
USGS - Suspended-Solids Concentrations in SF Bay, CA

August 14-18, 1995, v. 2, p. 1511-1515. 

1994

Palmer, J. R., Friebel, M. F., Trujillo, L. F., and Markham, K. L., 1994, Water resources data, California, 

water year 1993, vol. 2, Pacific slope basins from Arroyo Grande to Oregon state line except Central 

Valley: U.S. Geological Survey Water-Data Report CA-93-2, 412 pp. 

Schoellhamer, D.H., 1994, Central San Francisco Bay suspended-sediment processes study and 

comparison of continuous and discrete measurements of suspended-solids concentrations: San Francisco 

Estuary Regional Monitoring Program for Trace Substances, 1993 Annual Report, p. 129-134. 

Schoellhamer, D.H., 1994, Suspended-solids concentrations in central San Francisco Bay during 1993 

winter runoff: Eos, v. 75, no. 3, p. 122. (1994 AGU Ocean Sciences meeting, San Diego, California) 

1993

Markham, K. L., Palmer, J. R., Friebel, M. F., and Trujillo, L. F., 1993, Water resources data, California, 

water year 1992, vol. 2, Pacific slope basins from Arroyo Grande to Oregon state line except Central 

Valley: U.S. Geological Survey Water-Data Report CA-92-2, 405 pp. 

1992

Trujillo, L.F., Markham, K.L., Palmer, J.R., and Friebel, M.F., 1992, Water resources data--California, 

water year 1991. Volume 2, Pacific slope basins from Arroyo Grande to Oregon State line except Central 

Valley: U.S. Geological Survey Water-Data Report CA-91-2, 336 p. 

1991

Shelton, W.F., Trujillo, L.F., Markham, K.L., and Palmer, J.R., 1991, Water resources data--California, 

water year 1990. Volume 2. Pacific slope basins from Arroyo Grande to Oregon State line except Central 

Valley: U.S. Geological Survey Water-Data Report CA-90-2, 333 p. 

URL: http://ca.water.usgs.gov/abstract/sfbay/sfbaycontbib.html

Contact: David H. Schoellhamer

Maintained: webmaster@maildcascr.wr.usgs.gov

Last modified: Wed Jul 11 09:45:05 2001 

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