Microbial indicator organisms make up the greatest number of reported receiving water impairments, resulting in many questions on the fate of indicator bacteria passing through storm-water best management practices (BMPs). Storm-water BMPs are often considered effective tools to mitigate the effects of urbanization on receiving waters. The USEPA’s, Office of Research and Development investigated the processes occurring within two commonly used BMPs, constructed wetlands and retention ponds. This research focused on creating pilot-scale systems to determine the environmental mechanisms that affect effluent indicator bacteria concentrations and to provide better information for the prediction of bacterial indicators for models when developing and meeting total maximum daily loads. Research results indicate water temperature, light, and a combination of other environmental factors influence bacteria indicator concentrations. Results from this research suggest that both constructed wetlands and retention ponds lower microbial concentrations in urban storm-water runoff. Bacteria inactivation generally followed the first-order, KC* model, which includes irreducible or background concentrations of a stressor. Sediment analyses indicate bacteria accumulated in sediments which may maintain background concentrations could be reintroduced into the effluent of these BMPs by turbulent flow causing resuspension or by accumulation through lack of maintenance. First-order models that do not consider irreducible concentrations may underestimate actual bacterial concentrations. The relationship between turbidity and bacteria suggests storm-water management practices that substantially reduce turbidity may also provide the greatest improvement in reducing concentrations of bacteria in storm-water runoff.