Beaches along the Great Lakes shorelines are important recreational and economic resources. However, contamination at the beaches can threaten their usage during the swimming season, potentially resulting in beach closures and/or advisories. Thus, understanding the dynamics that control nearshore water quality is integral to effective beach management. There have been significant improvements in this effort, including incorporating modeling (empirical, mechanistic) in recent years. Mechanistic modeling frameworks can contribute to this understanding of dynamics by determining sources and interactions that substantially impact fecal indicator bacteria concentrations, an index routinely used in water quality monitoring programs. To simulate E. coli concentrations at Jeorse Park beaches in southwest Lake Michigan, a coupled hydrodynamic and wave–current interaction model was developed that progressively added contaminant sources from river inputs, avian presence, bacteria–sediment interactions, and bacteria–sand–sediment interactions. Results indicated that riverine inputs affected E. coli concentrations at Jeorse Park beaches only marginally, while avian, shoreline sand, and sediment sources were much more substantial drivers of E. coli contamination at the beach. By including avian and riverine inputs, as well as bacteria–sand–sediment interactions at the beach, models can reasonably capture the variability in observed E. coli concentrations in nearshore water and bed sediments at Jeorse Park beaches. Consequently, it will be crucial to consider avian contamination sources and water-sand-sediment interactions in effective management of the beach for public health and as a recreational resource and to extend these findings to similar beaches affected by shoreline embayment.