San Francisco Bay Bathymetry

Science Center Objects

Bathymetry of a dynamic tidal estuary, such as San Francisco Bay, provides the observable linkage between anthropogenic modifications of the landscape—such as evolving land use practices, flood control, and water diversions—and natural forces of climate-driven river flow, sea level change, tides, and wind. By examining our record of hydrographic surveys, spanning over 150 years, we can gain insights into the probable effect of future modification including efforts toward restoration.

In addition to historical change analysis, current bathymetry is critical for the calibration and interpretation of hydrodynamic and ecological models. Mass balance and sheer stress are driven by bathymetry—even ecological niches are influenced by bathymetry (depth, turbidity, particle size, light, turbulence, etc.).

Here, we provide information about the bathymetric data available for San Francisco Bay.

Methods

An illustration of a bay that shows water depth.

In the example sequence shown below, the first step in the preparation of regular grids displayed on this web site begins with irregular hydrographic survey data (soundings) that have been corrected to a common datum (1).

The National Oceanic and Atmospheric Administration (NOAA) is the primary resource for obtaining these original soundings. Other agencies, including the US Army Corps of Engineers, California Department of Water Resources, US Bureau of Reclamation, and the USGS, have contributed local studies. Once the soundings are in hand they are contoured, and shoreline and marsh perimeters are added and combined into a geographic information system (GIS) (2).

All data layers must be adjusted to a common horizontal and vertical datum and all depths must have the same orientation and units. At this point a grid can be generated.

Quality control is an iterative process, performed on the resulting grid by comparing it with the original soundings (34).

Errors are computed, plotted and repaired when appropriate. Errors are usually a result of incorrect unit tags on the source data or digitizing mistakes, but some are due to gradients in bathymetry that cannot be resolved by a single grid cell.

The final grid (5) can be adjusted to a different tidal datum using an adjustment grid.

This grid is produced by assigning tide levels observed at shore stations to co-tidal lines from the TRIM-2D model (67).

Schematics show the process and methods used to process and create maps from water depth data.

San Francisco Bay bathymetry methods

  1. Obtain the most recent published depth soundings and shoreline data
  2. Plot soundings and contour soundings. The South Bay figure here contains over 100,000 points and depth-colored contours.
  3. On closer examination we can see the individual points and identify inconsistencies. This figure shows depth contours with colored, labeled soundings.
  4. Check for errors. Here is an example where incorrect depth codes were assigned to shallow water soundings. A depth code for meters was assigned, the soundings were actually decimeters.
  5. Final grid produced using the ArcInfo command Topogrid.
  6. Datum adjustments for Mean Sea Level (MSL), Mean Higher-High Water (MHHW), National Geodetic Vertical Datum (NGVD). Since the adjustment for various tidal and non-tidal datums is not constant or is a simple function of distance, we use cotidal contours developed by the TRIM model. In this figure the cotidal contours are shown.
  7. Based on the tide records at stations around the perimeter of the Bay we can assign adjustment values to these cotidal contours and produce an adjustment grid. The example given here is the adjustment grid for Mean Lower-Low Water (MLLW) to MHHW.

Geostatistics

Using this 100m grid cell representation of the Bay we can compute some primary geomorphic features of the basin--such as surface area and volume--for a given tidal datum, and compare these and other statistical properties in the sub-basins of San Francisco Bay.

A graph showing depth versus cell count.

Map shows the separate basins of San Francisco Bay and their names.

Full Bay 

TIDAL DATUM VOLUME (Mm3) SURFACE AREA (Mm2) AVG. DEPTH
VOL/AREA (m)
MEDIAN DEPTH (m)
MLLW 7142 1138 6.3 2.8
MSL 8446 1219 6.9 3.6
MHHW 9570 1244 7.7 4.4

Properties based on the Mean Sea Level grid

PROPERTY SOUTH BAY CENTRAL BAY SAN PABLO BAY SUISUN BAY
Area (Mm2) 426.8 326.3 273.4 169.6
Volume (Mm3) 1971 4388 1016 990
Average depth (m) 4.6 13.4 3.7 5.8
Median depth (m) 3.2 10.9 2.5 3.6
% Area
< 5 m
69 32 82 57

 

Bathymetry Change

As described in our METHODS section, a continuous surface representation of each bathymetric survey was created using Topogrid, an Arc/Info module that utilizes sounding and contour information to create a hydrodynamically correct surface. Input data was a combination of point soundings and hand-drawn depth contours (see table below). Once a bathymetric surface has been created for each hydrographic survey, the surfaces are adjusted to a common datum and we compute change or difference grids. These new ‘change’ surfaces identify areas of erosion and deposition.

Here is an example difference map of San Pablo Bay (1856-1887). During this period there was massive sediment accumulation related to hydraulic gold mining.

The data supporting historical change analysis is quite extensive. The following tables summarize the survey dates, digitized soundings, and contours used to produce the bathymetric surfaces and difference maps for San Francisco Bay.

SUISUN BAY
SURVEY YEAR NUMBER OF SOUNDINGS CONTOUR INTERVALS (ft)
1867 18,202 -4, 0, 6, 12, 18, 30, 60, 90
1887 21,753 -4, 0, 6, 12, 18, 30, 60, 90
1922 17,303 -4, 0, 6, 12, 18, 30, 60, 90
1942 36,169 -4, 0, 6, 12, 18, 30, 60, 90
1990 93,393 -1, 2, 5, 10, 15, 20, 25, 30, 35, 45 (meters)
SAN PABLO BAY
SURVEY YEAR NUMBER OF SOUNDINGS CONTOUR INTERVALS (ft)
1856 4973 0, 2, 3, 4, 6, 12, 18, 24, 36, 42, 48, 60
1887 3679 -1, 0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 24, 30, 36, 48, 60
1898 1994 0, 3, 6, 12, 18, 24, 30, 36, 60
1922 42,764 -1, 0, 1, 2, 3, 4, 5, 6, 12, 18, 30, 60
1951 62,900 0, 6, 12, 30, 48
1983 65,739 0, 6, 12, 18, 30, 36, 60
CENTRAL BAY
SURVEY YEAR NUMBER OF SOUNDINGS CONTOUR INTERVALS (ft)
1855 21,052 0, 6, 12, 18, 30, 60, 90, 120, 180, 240, 300
1895 289,282 0, 6, 12, 18, 30, 60, 90, 120, 180, 240, 300, 360
1920 48,116 0, 6, 12, 18, 30, 60, 90, 120
1947 229,551 0, 6, 12, 18, 30, 60, 90, 120, 180, 240, 300
1979 177,144 0, 6, 12, 18, 30, 60, 90, 120, 180, 240, 300, 360
SOUTH BAY
SURVEY YEAR NUMBER OF SOUNDINGS CONTOUR INTERVALS (ft)
1858 20,036 0, 3, 6, 12, 18, 24, 30, 36, 50, 60, 70
1898 99,399 0, 3, 6, 12, 18, 24, 30, 36, 50, 60, 70, 80
1931 92,451 0, 3, 6, 12, 18, 24, 30, 36, 50, 60, 70, 80
1956 100,748 0, 3, 6, 12, 18, 24, 30, 36, 50, 60, 70, 80
1983 136,095 0, 3, 6, 12, 18, 24, 30, 36, 50, 60, 70, 80
2005 ~2.7 million 0, 3, 6, 12, 18, 24, 30, 36, 50, 60, 70, 80

 

Official Publications

 

Animations of change for North Bay

A series of illustrations showing water depth in a bay are shown in sequence to show how depth changed over time.

By linear interpolation, we can compute sedimentation maps for years between surveys and combine the maps to produce an animation of sedimentation for the North Bay. This animation gives an overall view of the system in time and space. We can see that, in the more active channels of Suisun Bay, surface sediment is deposited and erodes quickly in response to changing flows (floods/drought) and modifications (such as dredging the southern channel or long term mooring of the mothball fleet).

We assume:

  1. the sediment deposited in North San Francisco Bay between 1856 and 1887 was dominated by hydraulic mining debris;
  2. erosion observed in subsequent surveys was not re-deposited locally; and
  3. material deposited after 1887 was not mining debris.

Making these assumptions, we can predict the location and thickness of the original hydraulic mining debris. It is especially notable that the mercury employed in gold mining in the Sierra Nevada was refined liquid quicksilver or elemental mercury; this is a form of mercury much more likely to foster net methylation than is cinnabar, the form of mercury in most mercury mines. Approximately 10,000 tonnes of refined mercury were lost to the watershed during the Gold Rush mining era. Much of the mercury consumed by gold mining could have been incorporated into the 12 billion cubic meters of sediments extracted by the mining activities and released to the rivers of the Bay-Delta watershed. The mercury-laced hydraulic mining debris was ultimately transported to the bay-delta; it is known that large deposits of hydraulic mining debris remain in bay sediments. These wastes formed marshes, islands, or filled or diked marsh, or were deposited in shallow waters. Under the right circumstances this mercury contamination is transported through the food chain and concentrated in some commercial and sport fish. Human consumption of fish caught in the Bay is already restricted because of mercury contamination. Specifically, adults are advised to limit consumption of sport fish from the Bay to two times a month; pregnant or nursing women and children 6 or under should limit consumption to one time a month. Large shark and striped bass from the Bay should not be consumed at all. As we study the feasibility of restoration of marshes that were sinks for mining debris, the possibility of releasing mercury to the Bay must be considered.

Animations of mining debris deposition and subsequent erosion

A series of maps show how the bottom of a bay changes through time.

A series of illustrations of sediment coverage on a bay floor through time show how sediment depth changed.