Short-term variability of a conservative quantity (salinity) and two nonconservative quantities (chlorophyll a, suspended particulate matter) was measured across a sampling grid in the South San Francisco Bay estuary. Surface measurements were made every 2 h at each of 29 (or 38) sites, on four different dates representing a range of tidal current regimes over the neap-spring cycle. From the distribution of phytoplankton biomass (chlorophyll a) and turbidity (SPM), we also estimated daily productivity and its variability at each site over the four tide cycles. As a general rule, both chlorophyll a and SPM concentrations varied about 50% from their tidal-means. However derived daily productivity varied less (about 15% from the mean) over a tidal cycle. Both chlorophyll a and SPM varied periodically with tidal stage (increasing on ebbing currents), suggesting that the short-term variability results simply from the tidal advection of spatial gradients. Calculation of the advective flux (current speed times spatial gradient) was used to test this hypothesis. For surface salinity, most (70–80%) of the observed intratidal variability was correlated with the tidal flux, both in the deep channel and over the lateral shoals. However the short-term variability of SPM concentration was only weakly correlated with the advective flux, indicating that local sources of SPM (resuspension) are important. Hourly changes in chlorophyll a were highly correlated with the advective flux in the deep channel (implying that phytoplankton biomass is conservative over short time scales there); however, chlorophyll a variability was only weakly correlated with the advective flux over the shoals, implying that local sources/sinks are important there. Hence, the magnitude and mechanisms of intratidal variability differ among constituents and among bathymetric regimes in this estuary.