Sediment Deposition and Erosion in South San 

Francisco Bay, California from 1956 to 2005 

By Bruce Jaffe and Amy Foxgrover 

Open-File Report 2006-1287 

U.S. Department of the Interior 

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

Dirk Kempthorne, Secretary 

U.S. Geological Survey 

P. Patrick Leahy, Acting Director 

U.S. Geological Survey, Reston, Virginia 2006 

Revised and reprinted: 2006 

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Suggested citation: 

Jaffe, B.E. and Foxgrover, A.C., 2006, Sediment Deposition and Erosion in South San Francisco 

Bay, California from 1956 to 2005: U.S. Geological Survey Open-File Report 2006-1287, 24 p. 

[URL: http://pubs.usgs.gov/of/2006/1287]

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

copyright owners to reproduce any copyrighted material contained within this report. 
 iii

Front Cover: 

Preliminary maps of bathymetry, intertidal flat, tidal marsh and deposition and erosion in South 

San Francisco Bay from 1956 to 2005.
 iv

Contents 

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

Background and Introduction ........................................................................................................1

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

Data Sources .............................................................................................................................2

1950s ......................................................................................................................................2

1980s ......................................................................................................................................3

2005 ........................................................................................................................................4

Creation of Grids........................................................................................................................5

Bathymetry Grids ....................................................................................................................5

Deposition and Erosion Grids..................................................................................................5

Determination of Geomorphic Zones .........................................................................................7

Error Analysis................................................................................................................................7

Deposition and Erosion from 1956 to 2005 ...................................................................................9

Discussion...................................................................................................................................17

Summary.....................................................................................................................................17

Acknowledgements .....................................................................................................................18

References..................................................................................................................................18

Contact Information.....................................................................................................................20
 1

Sediment Deposition and Erosion in South San 

Francisco Bay, California from 1956 to 2005 

By Bruce Jaffe and Amy Foxgrover 

Abstract 

Sediment deposition and erosion in South San Francisco Bay from 1956 to 2005 was studied by 

comparing bathymetric surveys made in 1956, 1983, and 2005. From 1956 to 1983, the region was 

erosional. In contrast, from 1983 to 2005, the region was depositional. Analysis of subregions defined by 

depth, morphology and location revealed similarities in behavior during both the erosional and 

depositional periods. During the entire period of the study, there was net erosion in the shallows (<1 m 

depth) on the eastern shore of the bay north of the Dumbarton Bridge and net deposition in the region 

south of Dumbarton Bridge. The rates, however, reflected the sediment regime of each time period. 

Erosional areas were less erosional during the period with net deposition and depositional zones were 

more depositional. The cause for the increase in deposition from 1983 to 2005 is unknown, but could be 

related to an increase in sediment supply from Central Bay. The patterns of deposition and erosion and 

the change in rates are consistent with an increase in sediment supply from the north, as would occur if the 

supply from Central Bay increased from1956-1983 to 1983-2005. Additional research is needed to fully 

understand why South San Francisco Bay became depositional from 1983 to 2005 and to determine the 

implications of this change to the planned salt pond restoration in the region.

Background and Introduction 

Key issues in the restoration of salt ponds in South San Francisco Bay are (1) whether there is 

enough sediment in the system to restore the salt ponds to tidal marsh and, (2) whether the increased 

sediment demand from restoration will result in detrimental impacts to other parts of the bay, such as loss 

of intertidal flats (Jaffe and Foxgrover, 2006). The history of sediment deposition and erosion within the 

bay can be analyzed to help answer these questions. This report presents the quantities and patterns of 

deposition and erosion in South San Francisco Bay from 1956 to 2005 (Fig. 1). The goal of this report is 

to document the historical temporal and spatial variability of deposition and erosion for specific 

geomorphic zones in South San Francisco Bay. These data serve as a basis for conceptual and quantitative 

models to predict the likelihood of successful restoration as well as potential detrimental effects resulting 

from the creation of sediment sinks when the ponds are opened to tidal influence. These data also provide 

information for evaluating the cause of deposition and erosion that has occurred during the last 49 years. 

During this time period numerous factors and forcings such as wind wave erosion, tidal current 

redistribution of sediment, changes in sediment supply from tributaries and Central Bay, and sea level rise, 

have altered the system. These factors and forcings will continue to alter the system as restoration 

proceeds. 
Figure 1. Location of study area showing pond complexes being considered for restoration as 

part of the South Bay Salt Ponds Restoration Project. 

Methods 

In order to quantify spatial and temporal variability of sediment distribution in South Bay over the 

past 49 years we modeled the surface of the bay floor for three time periods: 1956, 1983, and 2005. After 

the bathymetric models were adjusted to account for changing vertical datums and subsidence that 

occurred in the Santa Clara Valley from the 1930s to 1960s (Poland and Ireland, 1988), the grids were 

differenced to reveal patterns of sediment deposition and erosion. 

Data Sources 

Data used to create models of the bay floor, and subsequently to generate erosion and deposition 

grids, were collected by the National Ocean Service (NOS) branch of the National Oceanic and 

Atmospheric Administration (NOAA) and the California Coastal Conservancy. These data include depth 

soundings, shoreline location, and elevation data near the shoreline. The extent of tidal marsh was derived 

from topographic sheets (T-sheets) and has been displayed for visual reference. 

1950s 

Hydrographic survey data from the 1950s covers the bay and a select number of sloughs and 

creeks for the region extending south from Hunters Point, approximately 420 km2

 (Fig. 2). Depth 

soundings for the 1950s NOS surveys were collected from 1954 to 1956 and obtained digitally from the 

National Geophysical Data Center’s (NGDC) GEOphysical DAta System for Hydrographic Survey Data 

(GEODAS) database (1996) (Table 1). Contours were digitized from hydrographic smooth sheets 

(H-sheets) and supplemented by additional hand-drawn contours based upon depth soundings to maintain 

a consistent contour interval throughout all of the surveys (Fig. 2). Shorelines for the 1950s surveys were 

digitized from H-sheets. The marsh boundaries were digitized from scanned, georeferenced images of 

T-sheets obtained from the NOS Coastal Services Center. 

Some soundings on H-sheet H8025 (near Hunter’s Point) were missing from the GEODAS 

database; these soundings were manually digitized from the H-sheet and used in the surface modeling. 

 2
Table 1. Table of 1950s H-sheets of South San Francisco Bay. 

H-Sheet Year Scale Soundings

H8023 1954 1:5,000 7,651

H8024 1954 1:10,000 20,123

H8025 1954-55 1:10,000 13,137

H8026 1954-55 1:10,000 14, 174

H8027 1955 1:20,000 12,900

H8210 1956 1:10,000 4,683

H8275 1956 1:10,000 15,733

H8281 1956 1:10,000 9,429

H8282 1956 1:10,000 2,918

Total = 100,748

Figure 2. 1950s soundings and contours used for bay floor surface modeling.

1980s 

Hydrographic survey data from the 1980s covers the bay and a select number of sloughs, and 

creeks for the region extending south from Hunters Point, approximately 400 km2

 (Fig. 3). Depth 

soundings for the 1980s surveys were collected from 1979 to 1985 and obtained digitally from NGDC’s 

GEODAS database (National Geophysical Data Center, 1996) (Table 2). We drew contours based on 

depth soundings and digitized them for use in the surface modeling (Fig. 3). The shorelines as well as the 

marsh boundaries were obtained digitally from the San Francisco Estuary Institute (SFEI) EcoAtlas 

(1998). 

Soundings above Mean Lower Low Water (MLLW) (intertidal soundings) for H-sheet H10132 

were recorded in centimeters rather than decimeters in the GEODAS database. These points were 

converted from centimeters to decimeters to match the rest of the data. There was an additional cluster of 

approximately 30 soundings within H-sheet H10102 located near Redwood Creek whose values differed 

 3
from their surrounding soundings by over an order of magnitude. No logical correction was evident, so 

these points were removed. 

Table 2. Table of 1980s H-sheets of South San Francisco Bay. 

H-Sheet Year Scale Soundings

H9819 1979 1:5,000 19,645

H10102 1983-84 1:10,000 12,600

H10158 1984-85 1:10,000 5,819

H9869 1980 1:10,000 12,726

H9872 1980 1:20,000 21,356

H9952 1981-82 1:10,000 22,439

H9984 1981-83 1:10,000 11,413

H10070 1982-83 1:10,000 12,227

H10132 1984-85 1:10,000 17,870

Total = 136,095

Figure 3. Soundings and contours used for 1983 bay floor surface modeling.

2005 

Sea Surveyor Inc. conducted a hydrographic survey of South San Francisco Bay from January 10 

to April 5, 2005. The 2005 survey covers the bay and a select number of sloughs, and creeks for the region 

extending south from a line connecting Coyote Point on the west shore, to just south of the Oakland 

airport on the east shore, approximately 250 km2

 (Fig. 4). Soundings were collected at a nominal spacing 

of 0.15 m along 2,600 km of trackline resulting in a total of approximately 20 million data points. 

Soundings decimated to 1-m spacing (approximately 2.7 million data points) were used to model the 

surface of the bay floor. 

 4
Soundings were reduced to the National Tidal Datum Epoch (NTDE) 1983-2001 MLLW at 

Alameda using tidal zoning developed by the NOAA Center for Operational Oceanographic Products and 

Services (CO-OPS). For each tidal zone, the soundings were reduced to MLLW using Alameda as the 

control tide station and three temporary tide gauges (San Leandro Marina, west side of San Mateo Bridge, 

and east side of the Dumbarton Bridge) to apply phase and amplitude corrections. 

Sounding data was augmented by hand-drawn digitized depth contours drawn based upon depth 

soundings at an interval consistent with previous NOS surveys (Fig. 4) (Foxgrover et al., 2004). The 2005 

shoreline was based on EcoAtlas data (San Francisco Estuary Institute, 1998) adjusted using data from a 

May 2004 topographic lidar survey (Foxgrover and Jaffe, 2005). 

Figure 4. Soundings and contours used for 2005 bay floor surface modeling.

Creation of Grids 

Bathymetry Grids 

After inputting the data into a Geographic Information System (GIS), we used ArcInfo’s TopoGrid 

module to generate a continuous surface representation of each hydrographic survey (Foxgrover et al., 

2004). TopoGrid is a gridding algorithm designed to utilize both sounding and contour data to generate a 

hydrologically correct Digital Elevation Model (DEM). The use of contours in addition to soundings 

helps to better constrain the surface in areas where there is sparse data (between tracklines). TopoGrid 

uses an iterative finite difference interpolation technique in which the contours are initially used to build a 

generalized drainage model that is further refined using both soundings and contour values to determine 

elevation values at each cell. The 1956 and 1983 surfaces have a horizontal resolution of 50 m and the 

2005 surface has a resolution of 25 m. Each historical hydrographic survey is defined by more than 

160,000 grid cells. 

Deposition and Erosion Grids 

Prior to generating the deposition and erosion grids, all of the bathymetric grids were adjusted to a

common vertical datum to account for changing surveying datums accompanying fluctuations in sea level 

 5
over the 49-year span of the surveys. All soundings are relative to the MLLW datum, which is the mean 

of the lower-low water heights of each tidal day observed at a control tidal station (formerly called a 

primary tide station) over the NTDE in use during the survey (Swanson, 1974). The NTDE is a 19-year 

period (18.6 year tidal epoch rounded to a full year to minimize bias from seasonal variation) that is 

updated approximately every 20 years to incorporate changes in the mean of MLLW caused primarily by a 

combination of eustatic sea level rise and land elevation change at the control tidal station (National Ocean 

Service, 2006). The MLLW tidal datum, therefore, varies depending upon the NTDE and the control tidal 

station used for the survey. Assuming no change in the bathymetry, an increase in the height of the tidal 

datum between surveys would result in a sounding from the later survey appearing deeper than a sounding 

at the same location from the earlier survey. 

To determine the amount of sediment deposition and erosion, it was also necessary to account for 

land subsidence that occurred within the southern extent of South San Francisco Bay as a result of 

excessive ground water withdrawal from 1934 to 1967 (Poland and Ireland, 1988). Without correcting for 

subsidence, erosion would be erroneously overestimated during this time period. The degree and spatial 

extent of subsidence was documented in Poland and Ireland (1988). The majority of subsidence was 

concentrated near San Jose, approximately 16 km (10 mi) south of our study area, where subsidence 

reached a maximum of approximately 2.4 m (8 ft) from 1934 to 1967. Within our study area subsidence 

from 1934 to 1967 ranged from 0 in the north to 2.2 m (4 ft) in the south. 

Subsidence grids were created from a surface defined by contours of equal subsidence on Poland 

and Ireland’s (1988) 1934-1960 and 1960-1967 land subsidence maps (Figure 5) (Foxgrover et al., 2004). 

To define subsidence in the entire study area it was necessary to extrapolate the land subsidence contours 

of Poland and Ireland (1988) across the bay in the region north of the Dumbarton Bridge. Assuming 

linear rates for each map period, the proportion of subsidence that occurred from 1956 to 1967 was 

applied to the 1956 to 1983 grid of deposition and erosion. This subsidence correction accounted for 

approximately 9 × 106

 m3 of the sediment deposited from 1956 to 1983. We did not need to correct for 

subsidence for the 1983 to 2005 period because significant subsidence has not occurred within the area 

since about 1969 (Ingebritsen and Jones, 1999). 

Figure 5. Subsidence corrections applied to 1956 to 1983 grid of deposition and erosion. 

 6
 7

After all of the adjustments were made, grids of deposition and erosion were generated by 

differencing the corrected bathymetric grids and, for the period from 1956 to 1983, adding the subsidence 

grid. Sediment volume change was calculated by multiplying the grids of deposition and erosion by the 

surface area in each geomorphic zone. 

Determination of Geomorphic Zones 

We subdivided South San Francisco Bay into geomorphically similar zones to analyze the spatial 

and temporal patterns of sediment deposition and erosion. The ability to link observed changes with the 

forcing processes, a goal of this research, is enhanced by using geomophically similar zones. The 

boundaries of these zones were determined using depth, slope, and breaks in slope of the bay floor as well 

as distinct anthropogenic artifacts such as dredge areas or sediment borrow pits. Geomorphic zones were 

delineated based upon the earlier year’s morphology (e.g.; depths in the 1956 bathymetric model were 

used to determine zones for analyzing change from 1956 to 1983). The rational of using the 

characteristics of the earlier year to delineate zones is that it facilitates interpretation of the change (e.g.; 

was the shallow zone erosional or depositional). Coherent patterns of erosion or deposition and the 

distribution of hydrodynamic forcings, such as wind wave energy, were also used to guide the delineation 

of zones. The main channel system was defined as the region bounded by slopes greater than 0.3 degrees, 

which corresponds to the upper channel wall. Outside of the defined channel system, two breaks became 

apparent: one at approximately 1 m below MLLW and one at approximately 2 m below MLLW. Areas 

with depths less than 1 m (MLLW) were partitioned into shallow zones and areas with depths between 

1 m and 2 m were partitioned into mid-depth zones. 

Error Analysis 

Two types of error are associated with the deposition and erosion grids—random error and 

systematic biases (HQUSACE, 2002). Bias enters from inaccuracies in determining the relation of 

MLLW datums used for different survey periods, from differences in rounding schemes used for recording 

sounding values, from methods used in the construction of subsidence grids, and from the methods used in 

the interpolation of the bathymetry grids. Random error is associated with sounding inaccuracy (Adams, 

1942; Schallowitz, 1964; Sallenger et al., 1975). Sounding errors are assumed to be randomly distributed 

in space and independent of each other and therefore do not significantly affect our estimates of deposition 

or erosion. This assumption is supported by an analysis of the 2005 survey. The presence of non-random 

sounding errors was evaluated by comparing sounding values at the intersection of independent survey 

lines. Quality control survey lines (cross-check lines) running approximately perpendicular to the primary 

survey tracklines were collected as part of the 2005 hydrographic survey (Fig. 4). The mean difference of 

sounding values at the more than 600 survey line intersections analyzed is less than 0.01 m. 

Error in the bathymetry grids caused by the interpolation of values between soundings is a 

potential source of bias that is difficult to quantify. Additional factors that influence uncertainty in 

sediment volume change calculations derived from a series of bathymetric grids are sounding density, 

irregularity and relief of the terrain, and the orientation of survey tracklines relative to geomorphic 

features (HQUSACE 2002, from Byrnes 2002). Because the morphology of the majority of the terrain in 

South San Francisco Bay is relatively simple (e.g.; intertidal flats), the high sounding density, and the 

consistent method of grid construction, such biases are minimal. A value of 0.02 m of error was assigned 

for bias in the grids introduced by interpolation. This estimate was determined by comparing the value of 

individual depth soundings to the cell value of the bathymetric grid at that specific location. Differences 

between sounding values and grid cell values were -0.02 m and less than -0.01 m for the 1956 and 1983 

surveys, respectively (Foxgrover et al., 2004). This is, however, only a crude estimate of the bias 

introduced by interpolation and does not accurately estimate the influence of interpolation algorithms in 

areas where no sounding data exists. 
 8

Differences between the adopted MLLW datum for different NTDEs can introduce uncertainties 

when the primary control stations used to reduce soundings are unknown or if these stations change in 

between epochs. For the two most recent hydrographic surveys, 1983 and 2005, there is not an error 

associated with change in the MLLW datum because the offset in MLLW between the two epochs is 

known (calculated from data collected for the 1960-1978 and 1983-2001 tidal epochs at the long-term tide 

station at Alameda). For the 1956 hydrographic survey, soundings were reduced using the 1924-1942 

tidal epoch at the San Francisco tide station (pers. comm., James Hubbard, NOS, 2005). Because the 

change in MLLW for the 1960-1978 to the 1983-2001 tidal epochs differs by 0.046 m between the San 

Francisco and Alameda tide stations, and we do not know the effect of using different control stations for 

different surveys, we are assigning a value of 0.02 m to this bias error. 

Uncertainty in the subsidence correction derives primarily from the extrapolation of the land 

subsidence contours of Poland and Ireland (1988) across the bay in the region north of the Dumbarton 

Bridge. Our extrapolation scheme (Foxgrover et al., 2004) assumed subsidence in this region did not have 

strong spatial gradients (Fig. 5), which is consistent with groundwater withdrawal away from the bay and 

no strong structural controls in the aquifer. The lack of data in the bay only effected subsidence contours 

with values less than 0.15 m (0.5’). We assigned a uniform 0.02 m value for uncertainty in our subsidence 

correction. This bias is only an estimate. 

A bias towards erosion has been introduced to the 1956 to 1983 calculations as a result of sounding 

rounding conventions used in the 1950s hydrographic surveys that were not used in the 1980s surveys. 

For both surveys, soundings were originally recorded in feet and tenths, however, the majority of values 

plotted on the smooth sheets are rounded to integral feet using a shoal biased rounding scheme. The 

1950s GEODAS soundings were digitized off of the H-sheets and are therefore plotted sounding values 

(shoal biased rounding applied). In contrast, the 1980s GEODAS soundings are the reduced sounding 

values (no rounding applied). 

The rules for converting reduced soundings to integer values for plotting on smooth sheets are: 

“when rounding positive soundings to integral feet, decimals less than 0.8 ft are disregarded; decimals of 

0.8 to 0.9 ft are increased to the next whole unit. When rounding minus soundings, decimals less than 

-0.3 ft are disregarded and decimals from -0.8 to -0.9 ft are treated as -1.0 ft” (Umbach, 1976). South San 

Francisco Bay 1950s hydrographic smooth sheet soundings were plotted in whole feet except for areas 

where a higher degree of accuracy was desirable to define depth contours, such as near the mean lower 

low water line and standard 3 and 6 ft depth contours. In these regions soundings are shown to the nearest 

0.5 ft increments. Reduced decimal values from 0.3 to 0.7 ft are shown as 05 (representing 0.5 ft) for both 

positive and negative soundings (Umbach, 1976). As a result, the select soundings plotted in 0.5 ft 

increments do not create a systematic bias because values within ± 0.2 ft of the plotted value are rounded. 

To approximate the amount of bias introduced through rounding, we compared the 1980s reduced 

soundings (not rounded) to ones we generated using the above rounding conventions. For the 139,436 

soundings in the 1983 survey, rounded soundings on average were 0.07 m shallower than those not 

rounded. A complete analysis of the spatial variation of the rounding error is necessary to accurately 

correct this bias. Although the effect of rounding varies spatially throughout the study area, and our 

+0.07 m value is only a rough approximation, we have used this value as an estimate of error introduced 

by rounding soundings. This error only applies to the 1956-1983 deposition and erosion volumes because 

both the 1983 and 2005 soundings were not rounded and can be compared directly after correcting for 

vertical datum change. 

The total estimated error in our erosion and deposition volume calculations for 1956 to 1983 and 

1983 to 2005 are shown in Table 3. The bias errors for soundings, grid interpolation, datum correction, 

and subsidence correction are added in quadrature because they are not systematic (sign of each bias is not 

known) (Mikhail, 1976). The estimate of total error for deposition and erosion, which includes the total 

non-systematic error and the error introduced by rounding of 1956 and not 1983 soundings, is 
 9

+0.105/-0.035 m for calculations for 1956 to 1983 and ± 0.02 m for 1983 to 2005 (Table 3). This bias is 

treated as an error because it is spatially variable and cannot be corrected without further analyses. 

Table 3. Error estimates for erosion and deposition volume calculations for South San Francisco 

Bay. The total non-systematic error is calculated by adding individual errors in quadrature. 

Comparison of rounded soundings of the 1956 surveys with un-rounded soundings from the 

1980s survey introduces a bias towards erosion. This bias creates an asymmetry in the total 

error with positive (deposition) error being larger than negative (erosion) error, reflecting the 

greater likelihood that deposition is underestimated. 

Estimate of Error (m) 

1956-1983 1983-2005 

Sounding 0 0 

Deposition and Erosion 

Grid ± 0.02 ± 0.02 

Datum Correction ± 0.02 ± 0.00 

Subsidence Correction ± 0.02 ± 0.00 

Total non-systematic error ± 0.035 ± 0.020 

Rounding (shallow bias) +0.07 0 

TOTAL ERROR +0.105/-0.035 ± 0.020 

Deposition and Erosion from 1956 to 2005 

Bathymetry and deposition and erosion in South San Francisco Bay from 1956 to 2005 are shown 

in Figure 6. The period from 1956 to 1983 was more erosional than from 1983 to 2005, with much of the 

eastern part of the bay losing sediment. Borrow pits on the 1956-1983 deposition and erosion maps 

appear as dark blue (erosional) straight-walled regions north of San Mateo Bridge. 
 10
a) 

b) 

Figure 7. (a) Region for hypsometric curves shown in (b). Elevation is relative to MLLW for 

each survey. 

 11
During both periods channels filled with sediment. Channel filling in the region south of the 

Dumbarton Bridge is illustrated by lower cumulative area values for channel depths in the hypsometric 

curves for the 1956, 1983, and 2005 bathymetry (Fig. 7a,b). Growth of intertidal flat area from 1983 to 

2005, which increased by approximately 35% from 17.6 +2.5, -1.7 km2

 to 24.2 +1.8, -1.0 km2 (Jaffe and 

Foxgrover, 2006), is also shown in Figure 7b. 

The change from an erosional system from 1956 to 1983 to a stable or depositional system from 

1983 to 2005 is further illustrated by the location of the MLLW and 6 foot depth contours (Fig. 8). North 

of the Dumbarton Bridge, in general, the MLLW contour moves shoreward from 1956 to 1983, indicating 

erosion. From 1983 to 2005, in general, there was little change in the MLLW contour location, indicating 

only a small amount of erosion or deposition. The 6 foot depth contour exhibited similar temporal 

behavior as the MLLW contour. For both time periods, the region south of the Dumbarton Bridge was 

depositional (Figs. 6, 7b; Foxgrover et al., 2004). This pattern of greater erosion to the north and 

deposition to the south of the Dumbarton Bridge is consistent with net transport from north to south in the 

southern portion of South San Francisco Bay. The north to south transport pathway is supported by the 

history of intertidal flat change (Jaffe and Foxgrover, 2006). 

Figure 8. Change in 0 and 6 foot contour locations for 1956, 1983, and 2005 in South San 

Francisco Bay. 

 12
The net volumes of deposition and erosion were calculated in selected subregions of South San 

Francisco Bay to explore the temporal and spatial patterns of change. A total of 16 geomorphically 

similar zones were defined as 11 shallow zones (shallower than 1 m), 3 mid-depth zones (from 1 m to 2 m

up to the channel edge), and 2 channel zones (Fig. 9). Although the same criteria were used for 

determining the geomorphic zones, the boundaries of the 1956-1983 zones are different than those of 

1983-2005 because the morphology changed between the two time periods. 

From 1956 to 1983, only the zones south of the Dumbarton Bridge experienced net deposition 

(Table 4, Fig. 10). Approximately 12 +7.4/-2.5 × 106

 m3 of sediment was eroded from the shallows along 

the east shore of the bay north of the Dumbarton Bridge (E1 Shallow, E2 Shallow, E3 Shallow) at an 

average rate of 0.66 ± 0.13 cm/yr. Erosion of the east shore shallows slowed from 1983 to 2005 as 

approximately 4 ± 1.2 × 106 m3 of sediment was eroded at about half the rate, 0.32 ± 0.09 cm/yr, of the 

previous time period (Table 4, Fig. 11). 

Figure 9. Boundaries for geomorphic zones overlying 1983 bathymetry. 

 13
Figure 10. Boundaries for geomorphic zones overlying deposition and erosion from 1956 to 

1983. 

 14
Figure 11. Boundaries for geomorphic zones overlying deposition and erosion from 1983 to 

2005. 

 15
Table 4. Deposition and erosion from 1983 to 2005 in selected regions of South San Francisco Bay

calculated using +0.105/-0.035 m estimates for 1956-1983 and ±0.02 m for the 1983 to 2005 time pefor determining the error estimates is given in the Error Analysis section.

1956-1983 1983-2005

Net Sediment

Volume Change1

(mcm) 

Area 

(km2) 

Net 

Sedimentation 

Rate1

(cm/yr) 

Net Sediment

Volume Change2

(mcm) 

Area 

(km2) 

E1 Shallow -7.37 +3.91/-1.29 36.91 -0.74 +0.39/-0.13 -2.14 ± 0.56 28.24 E2 Shallow -1.02 +1.20/-0.40 11.35 -0.33 +0.39/-0.13 -0.84 ± 0.23 11.39 E3 Shallow -4.39 +2.53/-0.84 23.92 -0.68 +0.39/-0.13 -1.36 ± 0.43 21.28 E4 Shallow -0.01 +0.05/-0.02 0.47 -0.12 +0.39/-0.13 0.11 ± 0.01 0.50 E5 Shallow -0.01 +0.17/-0.05 1.57 -0.02 +0.39/-0.13 0.57 ± 0.04 1.77 E6 Shallow -0.12 +0.43/-0.14 4.05 -0.11 +0.39/-0.13 1.69 ± 0.09 4.50 E7 Shallow 1.31 +0.10/-0.03 0.97 5.01 +0.39/-0.13 1.12 ± 0.02 1.08 W1 Shallow -1.52 +1.18/-0.39 11.11 -0.51 +0.39/-0.13 -1.00 ± 0.23 11.50 W2 Shallow 0.52 +0.34/-0.11 3.22 0.60 +0.39/-0.13 0.50 ± 0.07 3.55 W3 Shallow 1.85 +1.27/-0.42 11.95 0.57 +0.39/-0.13 3.38 ± 0.25 12.65 W4 Shallow 0.08 +0.04/-0.01 0.35 0.82 +0.39/-0.13 0.28 ± 0.01 0.47 E1 Mid -4.98 +2.07/-0.68 19.57 -0.94 +0.39/-0.13 -1.86 ± 0.50 24.91 E2 Mid 0.09 +0.11/-0.04 1.00 0.35 +0.39/-0.13 -0.15 ± 0.02 1.13 E3 Mid -0.66 +0.33/-0.11 3.10 -0.79 +0.39/-0.13 -0.80 ± 0.11 5.53 Channel 1 0.00 +1.15/-0.38 10.84 0.00 +0.39/-0.13 6.05 ± 0.21 10.40 Channel 2 9.52 +1.61/-0.53 15.22 2.32 +0.39/-0.13 8.79 ± 0.26 13.15 11956 - 1983 values include a subsidence correction and a vertical datum adjustment of 4.9 cm based upon the San Francisco tide st21983 - 2005 values include a vertical datum adjustment of 1.8 cm based upon Alameda tide station

16
 17

In general, the 1983-2005 period was more depositional than the 1956-1983 period everywhere in 

the region of this geomorphic zone analysis (Table 4). The exceptions to this are two small zones, E2 Mid 

and E7 Shallows. The greatest increase in deposition rates were on the shallows south of the Dumbarton 

Bridge (E4 Shallow, E5 Shallow, E6 Shallow, W4 Shallow), with more than 1 cm/yr increased deposition, 

and the main channel north of Dumbarton (Channel 1) with more than 2.5 cm/yr increased deposition 

(Table 4; Figs. 10, 11). 

Discussion 

A key question that needs to be addressed to predict sediment erosion and deposition in the future 

in South San Francisco Bay is, “Why was the period from 1983 to 2005 more depositional than the period 

from 1956 to 1983?” The pattern of net erosion in the shallows on the eastern shore north of the 

Dumbarton Bridge and net deposition south of the Dumbarton Bridge may provide the answer. 

From 1983 to 2005, net sediment deposition for the entire region south of the Dumbarton Bridge 

was approximately 16 ± 1.2 × 106

 m3. Sediment input from local streams is difficult to determine because 

of limited data on stream sediment loads. Schoellhammer et al. (2006) estimated that the sediment load of 

streams discharging to the bay south of the Dumbarton Bridge is now approximately one-quarter of the 0.4 

× 106

 tons/yr calculated by Porterfield (1980). If a sediment bulk density of 33 lbs/ft3 (soft mud) is used to 

convert from tons/yr to m3/yr, the Schoellhammer et al. (2006) estimate equates to less than 0.1 × 106

m3

/yr. Even under the assumption that all the sediment from local streams was deposited South of the 

Dumbarton Bridge, deposition from these streams can only account for ~15% (~2 × 106 m3) of the total 

net sediment deposition observed from 1983 to 2005. Sediment must have been transported from the 

north into the region south of the Dumbarton Bridge. 

Part of the deposition south of the Dumbarton Bridge, 4 ± 1.2 × 106

 m3, could have been supplied 

by erosion of the shallows on the east shore to the north. Additional sediment from the north is needed to 

account for the amount of net deposition observed south of the Dumbarton Bridge. South San Francisco 

Bay tends to be more erosional progressing south to north (Foxgrover et al., 2004). The imbalance of net 

deposition and sediment supply from local streams, and the pattern of greater erosion towards the north 

support net transport of sediment from north to south in South San Francisco Bay. 

Summary 

South San Francisco Bay was more depositional from 1983 to 2005 than during the preceding 27 

years (from 1956 to 1983). Despite this change, three patterns were present during both periods: 

(1) Net erosion in the shallows (<1 m depth) on the eastern shore of the bay north of the 

Dumbarton Bridge

(2) Net deposition in the region south of the Dumbarton Bridge 

(3) Filling of channels 

The rates of change reflected the sediment regime of each of the time periods. During the net 

depositional period from 1983 to 2005, erosional areas were less erosional and depositional zones were 

more depositional. The cause for the increase in deposition from 1983 to 2005 is unknown. A possible 

explanation which is supported by the patterns of deposition and erosion and the change in rates is an 

increase in sediment supply from the north, as would occur if the supply from Central Bay increased from 

1956-1983 to 1983-2005.

It is clear that the sediment system of South San Francisco Bay changed from 1956 to 2005. 

Additional research is needed to fully understand the causes of these changes and to predict future changes 

and their effects on restoration of the South San Francisco Bay salt ponds. 
 18

Acknowledgements 

The California Coastal Conservancy, U.S. Geological Survey Priority Ecosystems Science 

program, and the San Francisco Bay Regional Water Quality Control Board supported this research. 

Melissa Ingraca digitized historical hydrographic and topographic surveys. Shawn Higgins contributed to 

georeferencing H-sheets and modeling of the bay surfaces. The NOAA Center for Operational 

Oceanographic Products and Services (James Hubbard, Manoj Samant, Gerald Hovis, Craig Martin and 

others) played a key role in the hydrographic survey by assisting in the selection of tide gauge type, 

loaning accurate acoustic tide gauges, determining optimum locations for tide gauges, aiding in 

installation of tide gauges, and in developing tidal zoning to reduce soundings to the National Tidal Datum 

Epoch (NTDE) 1983-2001 MLLW at Alameda. Steve Sullivan, Sea Surveyor, Inc., took great care to 

ensure that the 2005 bathymetric survey was as accurate as possible. This report was improved by reviews 

from David Finlayson and Ann Gibbs. 

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 20

Contact Information 

Bruce Jaffe: bjaffe@usgs.gov

Amy Foxgrover: afoxgrover@usgs.gov

For details on the South Bay Salt Pond Restoration Project visit: http://www.southbayrestoration.org