Hydrodynamic and sediment transport time-series data, including water depth, velocity, turbidity, suspended particle size, conductivity, and temperature, were collected by the U.S. Geological Survey (USGS) Pacific Coastal and Marine Science Center at two locations in south San Francisco Bay. Data were collected in the channel (one platform) and in the shallows (three co-located platforms) for 2 weeks in July 2020. Data files are grouped by site (channel or shallows). Each site contained instrumentation to collect the data listed, with slight instrument and setup variations between the two sites due to logistics. Users are advised to assess data quality carefully, and to check metadata for instrument information, as platform deployment times and data-processing methods varied.