Historical coliform measurements (n = 67,269; 32 years) in Newport Bay, a regionally important saltwater wetland and tidal embayment in southern California, have been compiled and analyzed. Coliform concentrations in Newport Bay decrease along an inland-to-ocean gradient, consistent with the hypothesis that this tidal embayment attenuates fecal pollution from inland sources. Nearly 70% of the variability in the coliform record can be attributed to seasonal and interannual variability in local rainfall, implying that stormwater runoff from the surrounding watershed is a primary source of coliform in Newport Bay. The storm loading rate of coliform from the San Diego Creek watershed--the largest watershed draining into Newport Bay--appears to be unaffected by the dramatic shift away from agricultural land-use that occurred in the watershed over the study period. Further, the peak loading of coliform during storms is larger than can be reasonably attributed to sources of human sewage, suggesting that nonhuman fecal pollution and/or bacterial regrowth contribute to the coliform load. Summer time measurements of coliform exhibit interannual trends, but these trends are site specific, apparently due to within-Bay variability in land-use, inputs of dry-weather runoff, and tidal mixing rates. Overall, these results suggest that efforts to improve water quality in Newport Bay will likely have greater efficacy during dry weather summer periods. Water quality during winter storms, on the other hand, appears to be dominated by factors outside of local management control; namely, virtually unlimited nonhuman sources of coliform in the watershed and global climate patterns, such as the El Nino Southern Oscillation, that modulate rainfall and stormwater runoff in southern California.