Numerical simulations of the transport and fate of Escherichia coli were conducted at Chicago's 63rd Street Beach, an embayed beach that had the highest mean E. coli concentration among 23 similar Lake Michigan beaches during summer months of [2000][2001][2002][2003][2004][2005], in order to find the cause for the high bacterial contamination. The numerical model was based on the transport of E. coli by current circulation patterns in the embayment driven by longshore main currents and the loss of E. coli in the water column, taking settling as well as bacterial dark-and solar-related decay into account. Two E. coli loading scenarios were considered: one from the open boundary north of the embayment and the other from the shallow water near the beachfront. Simulations showed that the embayed beach behaves as a sink for E. coli in that it generally receives E. coli more efficiently than it releases them. This is a result of the significantly different hydrodynamic forcing factors between the inside of the embayment and the main coastal flow outside. The settled E. coli inside the embayment can be a potential source of contamination during subsequent sediment resuspension events, suggesting that deposition-resuspension cycles of E. coli have resulted in excessive bacterial contamination of beach water. A further hypothetical case with a breakwater shortened to half its original length, which was anticipated to enhance the current circulation in the embayment, showed a reduction in E. coli concentrations of nearly 20%.Beach water, as the interface between the land and coastal waters, is a dynamic physical and ecological system. The transport and fate of fecal indicator bacteria (FIB) in beach water not only have direct implications for human health in coastal areas (Nevers and Whitman 2005;Frick et al. 2008) but also constitute an integral influence on the coastal ecosystem. Recently, computational models allowing for a simulation of temporal and spatial variations of model variables have been developed to understand microbial water quality in open beach waters of Lake Michigan (Liu et al. 2006;Thupaki et al. 2010). Embayed (i.e., partially enclosed) beach waters have been of particular interest because of their significantly more complex hydrodynamic properties and the tendency to accumulate FIB and other contaminants (Grant and Sanders 2010).The 63rd Street Beach of Chicago, a frequently closed beach, had by far the highest Escherichia coli concentration (geometric mean 140 MPN [most probable number], 100 mL 21 ) among 23 recreational beaches along Chicago's 37-km Lake Michigan shoreline during 2000-2005. In comparison, the site with the second-highest E. coli concentration was Montrose Beach, with a geometric mean of only 77 MPN 100 mL 21 (Whitman and Nevers 2008). Since typical meteorological (e.g., rainfall) and hydrodynamic (e.g., current and wave) events usually have spatial scales larger than 37 km, the unique situation of microbial contamination at 63rd Street Beach likely resulted from local facto...