Microbial water quality, measured as Escherichia coli (E. coli) concentration, at beaches along the southern shore of Lake St. Clair in Canada, often exceeds public safety guidelines. Belle River, located near a public beach and a drinking water intake, is one of the several smaller tributaries of the lake whose contribution to nearshore microbial water quality is currently unknown. A flexible mesh 3D coupled TUFLOW-FV and Aquatic Ecodynamic (AED2+) model was used to simulate the hydrodynamics and microbial water quality in Lake St. Clair. A higher resolution nested model was developed within the lake-wide TUFLOW-FV model for better spatial and temporal resolution in the local region surrounding Belle River. Regular and up to a factor of four difference in predicted E. coli concentrations were observed with the nested and lake-wide models at the public beach next to Belle River, whereas the difference was marginal at the drinking water intake about a kilometre away from the shore. While the E. coli loading to Lake St. Clair from Belle River is considered negligible, >90% of the predicted daily E. coli concentration at the beach and > 50 % at the water intake were attributed to Belle River from amongst all watershed sources to Lake St. Clair considered in the model. The model results also show that the construction of a new 150 m jetty in 2018, replacing the older 25 m jetty separating Belle River from the public beach, is expected to significantly reduce E. coli concentrations observed at the beach.