Sediments and sediment transport influence the physical habitat and the ecology of the San Francisco Bay estuary. Bed sediments provide habitat for benthic organisms and the transport of sediment transports nutrients and contaminants throughout the San Francisco Bay. As part of the SF Bay-Delta Priority Ecosystems Science Program project: Biophysical Controls on Erosion and Near-Bed Turbulence: Strengthening Sediment Transport Modeling in San Francisco Bay, this data release represents data that can be used to examine the benthic biota influence on bed sediment properties.