The U.S. Geological Survey Pacific Coastal and Marine Science Center collected hydrodynamic and sediment-transport data at shallow water sites in San Pablo Bay and Grizzly Bay, in northern San Francisco Bay between June and November 2019. The data were collected to determine hydrodynamic forcing, bed roughness, suspended-sediment concentration, and physical properties of the sediment bed. This data release includes hydrodynamic and sediment transport time-series data spanning from June to August 2019, as well as sediment bed properties and water column suspended-sediment concentrations collected on eight days from June to November 2019. Details on station location, instrumentation, and measured variables are included on pages for each data type. These data were collected as part of a collaborative project with the USGS California Water Science Center and the USGS Water Mission Area who collected erodibility and benthic infauna data (published separately). The goal of the project was to determine physical and biological controls on sediment erodibility in San Francisco Bay. Funding was provided by the USGS Priority Ecosystems Studies Program for San Francisco Bay and Delta and the USGS Coastal and Marine Hazards and Resources Program.