Racine, Wisconsin, located on Lake Michigan, experiences frequent recreational water quality advisories in the absence of any identifiable point source of pollution. This research examines the environmental distribution of Escherichia coli in conjunction with the assessment of additional parameters (rainfall, turbidity, wave height, wind direction, wind speed and algal presence) in order to determine the most probable factors that influence E. coli levels in surface waters. Densities of E. coli were highest in core samples taken from foreshore sands, often exceeding an order of magnitude greater than those collected from submerged sands and water. Simple regression and multivariate analyses conducted on supplementary environmental data indicate that the previous day's E. coli concentration in conjunction with wave height is significantly predictive for present-time E. coli concentration. Genetic fingerprinting using repetitive element anchored PCR and cellular fatty acid analysis were employed to assess the presence of clonal isolates which indicate replication from a common parent cell. There were relatively few occurrences of clonal patterns in isolates collected from water, foreshore and submerged sands, suggesting that accumulation of E. coli, rather than environmental replication, was occurring in this system. Non-point source pollution, namely transport of accumulated E. coli from foreshore sands to surface waters via wave action, was found to be a major contributor to poor recreational water quality at the Lake Michigan beaches involved in this study.