Hydrodynamic and sediment transport time-series data, including water depth, velocity, turbidity, conductivity, and temperature, were collected by the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center within two embayments of San Francisco Bay. Data were collected in San Pablo Bay and Grizzly Bay from January to June 2020 at seven locations. Data files are grouped by area (shallows of San Pablo Bay, channel of San Pablo Bay, and shallows of Grizzly Bay). Each shallow site contained a variety of sensors located on two tripods, while the channel site consisted of one tripod. Users are advised to assess data quality carefully, and to check metadata for instrument information, as platform deployment times and data-processing methods varied.