Bathymetric survey data were collected in April 2009 just south of Dumbarton Bridge in south San Francisco Bay, California. Portions of the main channel and western shallows/intertidal mudflats were surveyed using an interferometric sidescan sonar system. The bathymetry is provided as a 1-m resolution raster in geoTIFF format, referenced to the vertical datum of mean lower low water (MLLW).