Urban-use pesticides are of increasing concern as they are widely used and have been linked to toxicity of aquatic organisms. To assess the occurrence and treatment of these pesticides in stormwater runoff, an approach combining field sampling and watershed-scale modeling was employed. Stormwater samples were collected at four locations in the lower San Diego River watershed during a storm event and analyzed for fipronil, three of its degradation products, and eight pyrethroids. All 12 compounds were detected with frequency ranging from 50 to 100%. Field results indicate pesticide pollution is ubiquitous at levels above toxicity benchmarks and that runoff may be a major pollutant source to urban surface waters. A watershed-scale stormwater model was developed, calibrated using collected data, and evaluated for pesticide storm load and concentrations under several management scenarios. Modeling results show that enhanced stormwater control measures, such as biochar-amended biofilters, reduce both pesticide storm load and toxicity benchmark exceedances, while conventional biofilters reduce the storm load but provide minimal toxicity benchmark exceedance reduction. Consequently, biochar amendment has the potential to broadly improve water quality at the watershed scale, particularly when meeting concentration-based metrics such as toxicity benchmarks. This research motivates future work to demonstrate the reliability of full-scale enhanced stormwater control measures to treat pollutants of emerging concern.