Nonpoint source pollution is a global challenge affecting streams and rivers. Due to the highly dispersed nature of nonpoint sources, they are difficult to track and manage. The goal of this study was to assess the extent of bacterial pollution along Coyote Creek in Northern California and to provide insight on microwatershed characteristics and their potential correlation to bacteria loads. Samples were collected and analyzed for fecal indicator bacteria concentrations at 21 geographic locations from within the creek and its stormwater outfalls. E. coli levels within Coyote Creek and stormwater entering the creek exceeded recreational water quality standards. Stormwater outfall samples tended to have higher bacteria concentrations than creek samples. The average concentration for stormwater outfall samples was 439% higher than the average for creek samples. Increased bacterial concentrations were found in creek samples draining adjacent to industrial microwatersheds when compared to samples draining residential microwatersheds. Bacteria levels from creek samples showed weak positive correlations with the number of historical encampments upstream of each sample site. This study concludes that bacterial load mitigation efforts should focus on industrial land uses and prioritize stormwater retention and treatment. The effects of homeless encampments on bacterial load may be less of a concern than other sources. Recommendations include further investigation of sources contributing to elevated bacteria levels exiting stormwater outfalls using DNA tracking methods.