In a series of studies along the Great Lakes, U.S. Geological Survey scientists are examining the physical processes that influence concentrations of fecal indicator bacteria and related pathogens at recreational beaches. These studies aim to estimate human health risk, improve management strategies, and understand the fate and transport of microbes in the nearshore area. It was determined that embayed beaches act as traps, accumulating Escherichia coli (E. coli) and other bacteria in the basin and even in beach sand. Further, shear stress and wave run-up could resuspend accumulated bacteria, leading to water-contamination events. These findings are being used to target beach design and circulation projects. In previous research, it was determined that E. coli followed a diurnal pattern, with concentrations decreasing throughout the day, largely owing to solar inactivation, but rebounding overnight. Studies at a Chicago beach identified the impact of wave-induced mass transport on this phenomenon, a finding that will extend our understanding of bacterial fate in the natural environment. In another series of studies, scientists examined the impact of river outfalls on bacteria concentrations, using mechanistic and empirical modeling. Through these studies, the models can indicate range and extent of impact, given E. coli concentration in the source water. These findings have been extended to extended lengths of coastlines and have been applied in beach management using empirical predictive modeling. Together, these studies are helping scientists identify and eliminate threats to human and coastal health.