Stormwater runoff can transport high concentrations of pathogens to receiving waters. Bacteria indicator organisms, as surrogates for pathogens, are the most often reported cause of receiving water impairments. Stormwater best management practices (BMPs) are often considered effective tools to mitigate the effects of stormwater pollutants before they appear in receiving waters. However, BMP performance for pathogen removal is not well documented. Many questions remain on the transport and fate of indicator bacteria that enter and exit stormwater BMPs. The National Risk Management Research Laboratory (NRMRL), part of U.S. EPA's Office of Research and Development (ORD) investigated the fate of indicator organisms in the stormwater runoff entering and exiting two commonly used BMPs, constructed wetlands and retention ponds. This research used controlled-condition, pilot-scale systems that represent larger field-scale systems to determine the dominant mechanisms that influence the reduction of indicator organism concentrations. The pilot-scale work was supported by bench-scale laboratory experiments investigating the effects of single parameters such as temperature, sunlight, and salinity on indicator organism inactivation rates. Presented in this report are the results of developing techniques for creating bacterially enriched stormwater, bench-scale studies, and the pilot-scale BMP research. Bench-scale study results show that the temperature and sunlight affect the inactivation rates significantly. Results from the pilot-scale research suggest that constructed wetlands and retention ponds lower microbial concentrations in stormwater runoff. Bacteria inactivation generally followed the first-order, K-C* empirical model that acknowledges an irreducible concentration. Factors such as sunlight and temperature provide much of the inactivation in indicator bacteria, but other factors (e.g., predation, sedimentation, filtration, sorption, pH, and BOD) appear to also influence indicator bacteria concentrations. Future research validating results of the pilot-scale systems to field-scale systems should be done.