This data release provides a series of five bathymetric change grids generated from historical bathymetric surveys collected in south San Francisco Bay, CA from the 1858 to 2005. The National Ocean Service (NOS) and its predecessor, the United States Coast and Geodetic Survey, collected hydrographic surveys in 1858, 1898, 1931, 1956, and 1983 plus Sea Surveyor, Inc. collected a survey in 2005. Surface modeling software was used to generate bathymetric DEMs of each of these surveys. The bathymetric DEMs were then adjusted to account for gridding interpolation bias, changes in sea level through time, and ground subsidence that occurred in the Santa Clara Valley and lower South Bay from the 1930s to 1960s due to groundwater extraction. The adjusted DEMs for consecutive surveys were then differenced to reveal the amount of sediment erosion and deposition and changes from human activities (e.g., dredging and oyster shell mining) that occurred through time. These bathymetric change grids are provided here in GeoTIFF format with a horizontal resolution of 50 meters and can be used to quantify net sediment volume change and rates of change throughout the bay.