San Quintin Bay is a coastal lagoon influenced by the California Current System (CCS) coastal upwelling. Upwelling brings nutrient-rich waters near the bay mouth and tidal currents propagate those waters throughout the bay. Upwelling intensification and relaxation events occur with a period of ~2 weeks, possibly due to the variability of circulation of the CCS. Off San Quintin, the CCS has an offshore component of the flux, causing upwelling intensification events as strong as off Point Conception (34.5°N), with high phytoplankton productivity. At the lagoon's mouth, upwelling is the main cause of variability for all physicochemical properties except temperature. Semi-diurnal tides are the main cause of variability for temperature. Nutrient remineralization at the sediments and turbulence induced by tidal currents and wind waves increase nutrient concentrations in the lagoon. At the heads of the bay, phytoplankton abundance was tenfold lower, productivity and chlorophyll concentrations were threefold lower, chlorophyll content per cell was threefold higher, and turbidity was higher than at the mouth. The few available data suggest the hypothesis that the effect of ENSO events on phytoplankton biomass depends on the interdecadal regime shifts in the northeastern Pacific. At the lagoon's mouth and adjacent ocean, summer salinities as low as 32.4 suggest the arrival of water parcels that originate in the north, possibly the Columbia River estuarine plume.