This data release provides a series of six bathymetric digital elevation models (DEMs) of San Pablo Bay, CA generated from single-beam hydrographic surveys collected from 1856 to 1983. The DEMs were constructed based upon historical United States Coast and Geodetic Survey and National Ocean Service (NOS) surveys collected in 1856, 1887, 1898, 1922, 1951, and 1983. Depth soundings from the pre-1930s surveys were manually digitized and georeferenced while the later surveys were obtained in digital format, and all information compiled into a geographic information system (GIS). Using surface modeling software, the soundings from each survey were supplemented with hand-drawn contours and shorelines obtained from topographic sheets to generate bathymetric DEMs at a horizontal resolution of 25 m. The bathymetric DEMs are provided in GeoTIFF format, vertically referenced to the Mean Lower Low Water (MLLW) tidal epoch referenced at the time of data collection.