This data release documents the spatial and temporal variability of nutrients and related water quality parameters at high spatial resolution in Suisun Marsh and Suisun Bay in the San Francisco Estuary of California, USA. The data set includes nitrate, ammonium, phosphate, dissolved organic carbon, temperature, conductivity, dissolved oxygen, turbidity, chlorophyll, blue-green algal pigments, and phytoplankton community structure. Data-collection cruises were conducted under three different environmental/flow conditions between July - September 2018 that coincided with conditions prior to, during, and following the Suisun Marsh Salinity Control Gates Summer Action. The action is part of the Delta Smelt Resiliency Strategy and organized by the California Department of Water Resources and California Natural Resources Agency.