This paper attempts to identify the high-risk areas for potential runoff of pyrethroid pesticides in the San Joaquin River Watershed. Pyrethroid pesticides have been detected in water and fluvial sediments in this watershed, creating concerns about potential negative impacts on water quality. However, little documentation exists regarding the distributions or the extent of the adverse effects caused by the use of pyrethroids. This study developed a geographic information systems (GIS) model to identify areas with high potential for pyrethroid runoff during the rainy season. The model was then validated using field-monitoring data. Nine factors were identified for the runoff risk assessment: amount of active ingredient used, soil erodibility factor, hydrologic group, surface layer depth, seasonal rainfall, seasonal number of rainy days, seasonal number of storm events, stream density, and land cover. The results indicated that high pyrethroid runoff risks were associated with basins such as the Stanislaus River Sub-basin, Newman Gustine Sub-basin and South Merced Sub-basin. This study demonstrated that the GIS model is capable of predicting high-risk areas of pyrethroid runoff at sub-basin scale. The model can be used to prioritize sites for water quality monitoring and guide implementations of best management practices.