The horizontal pattern of mesoscale (1–4 km) variability in salinity was a poor predictor of mesoscale patterns in chlorophyll a, suspended particulate matter, and daily primary productivity in the South San Francisco Bay estuary during spring 1987. The tidally-averaged salinity distribution varied over weekly time scales, reflecting inputs of freshwater as well as transport processes. Spatial distributions of the other quantities also varied weekly, but not in concert with the salt field. Spatial patterns of phytoplankton biomass (chlorophyll a) deviated from the salinity patterns, largely reflecting in situ production of phytoplankton biomass during the spring bloom. The tidally-averaged distribution of suspended particulate matter (SPM) was highly dynamic and responded to (1) the riverine input of suspended sediment during a freshet, (2) neap-spring variations in tidally-driven resuspension, and (3) resuspension in shallows following a period of wind mixing. Two-dimensional distributions of primary productivity P′, derived from maps of biomass and turbidity (SPM), also varied weekly, but the spatial variability of P′ was only about half that of SPM and chlorophyll. Since the magnitude and patterns of spatial variability differ among nonconservative quantities, at least in part because of local sources and sinks, we conclude that the spatial distributions of nonconservative quantities cannot be predicted from distributions of conservative tracers, such as salinity.