Profiles of salinity, temperature, turbidity, and particle size distribution 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 at depth intervals ranging between 0.5 and 2 m (depending on total water depth); sensors remained at each depth for 1 minute. Each profile was collected from surface to bed, and the near-surface region was sampled again at the end of the profile to check steady-state conditions. Profiles were collected for 4 days, for about 7.75 hours each day: Jul 21, 22, 24, and 28, 2020. Data files are grouped by site (channel or shallows) and by instrument (CTD or LISST). Users are advised to assess data quality carefully, and to check metadata for instrument information.