Beach sand near the shoreline acts as a reservoir for fecal contaminants with fecal indicator bacteria (FIB) often orders of magnitude higher than in adjacent surface waters. Elevated FIB (Escherichia coli (E. coli), enterococci (ENT)) concentrations in the surface water can lead to beach water quality advisories. This study combines field measurements with numerical modelling to investigate the physical processes controlling the accumulation, distribution and release of FIB in beach sand. E. coli and ENT were measured in the pore water across two beaches on Lake Huron and Lake Ontario with samples collected up to 2.3 m depth below the water table. A numerical model simulating wave-induced groundwater flow recirculations coupled with microbial transport (using colloid filtration theory) reproduced the overall measured FIB distributions at the two beaches. The model was then applied to assess the impact of various factors including beach slope, sediment type and wave height on FIB accumulation. The infiltration zone width, average infiltration velocity and infiltration rate were shown to ultimately control the amount and spatial distribution of FIB in the sand. Study findings are important in identifying factors controlling the accumulation and release of FIB in beach sand at freshwater beaches and thus ultimately reducing health risk at beaches.