Organophosphate and carbamate compounds are among the most widely used pesticides. Contamination of surface water by these compounds is of concern because of potential toxicity to aquatic organisms, especially those at lower trophic levels. In this study we evaluated the persistence of diazinon, chlorpyrifos, malathion, and carbaryl in waters from various sites in the Newport Bay-San Diego Creek watershed in southern California (USA). The persistence of diazinon and chlorpyrifos was much longer than that of malathion or carbaryl and was further prolonged in seawater. Microbial degradation contributed significantly to the dissipation of diazinon and chlorpyrifos in freshwater, but was inhibited in seawater, leading to increased persistence. In contrast, degradation of malathion and carbaryl was rapid and primarily abiotic. A greater temperature dependence was observed for carbaryl degradation in all waters and for diazinon degradation in freshwater. The interactions of pesticide persistence with water location, temperature, and type of pesticides suggest that site- and compound-specific information is needed when evaluating the overall ecotoxicological risks of pesticide pollution in a watershed. Because the persistence of diazinon and chlorpyrifos may increase significantly in seawater, mitigation should occur before the pesticides reach seawater. The relatively short persistence of these compounds in freshwater suggests that practices aimed at extending residence time (e.g., diversion to wetlands) may effectively reduce pesticide output to downstream water bodies.