Pollution inputs in surface waters have resulted in extensive impairments to water resources; however, the effectiveness of stormwater best management practices (BMPs) in reducing pollution inputs related to harmful algal blooms (HABs) in headwater streams has not been widely reported. Skypark, Santa’s Village, is an outdoor recreation area in the semiarid San Bernardino National Forest, California. Recreational activities and impervious surfaces at the site contribute pollution to Hooks Creek, a first-order headwater tributary of the Mojave River. The Natural Resources Conservation Service designed and constructed a stormwater sediment erosion control basin system to reduce site gully erosion and improve surface water quality in situ and downstream. Basin water quality was tested biweekly for parameters associated with HABs including temperature, dissolved oxygen, pH, turbidity, conductivity, nitrate (NO 3 − ), and ammonium (NH 4 + ) in situ during wet and dry seasons, with periodic testing for total suspended solids (TSS), total dissolved solids (TDS), total coliform (TC), and Escherichia coli (EC). The BMP structure was effective in lowering temperature and pH and reducing NO 3 − , TDS, and turbidity during precipitation events, and increased pH levels and lower concentrations of TSS, TC, and EC were present during the dry season. Despite these advantages, the BMP was ineffective in reducing (NH 4 + ) concentrations, a primary contributor to HABs, with 100% of the samples exceeding regulatory criteria throughout the study period. Results highlight the benefits and limitations of stormwater BMPs in protecting water resources from downstream HABs to ensure water resources are protected for current and future generations.