Water temperature and fecal indicator bacteria levels covary along the shoreline of Huntington and Newport Beach, California at interannual to tidal periods. During summer, cooler than average waters caused by interannual variability in sea surface temperature (SST), synoptic upwelling, and tidal-period cooling are coincident with elevated levels of microbial pollution in the surf zone. This relationship can be explained by the effects of weakening in stratification on the fate of a waste water plume and the prolonged persistence of fecal indicator bacteria in colder waters. During winter, warmer than average water caused by basin scale oscillations and atmospheric and oceanographic processes that contribute to the Multivariate El Nino Southern Oscillation Index are indicative of elevated total coliform levels in the surf zone. The elevated coliform levels can be ascribed to increased rainfall, and the resultant storm water inflow to the surf zone.