A three-step method for the identification of the main sources of fecal coliforms (FC) in urban waters and for the analysis of remedial actions is proposed. The method is based on (1) The statistical analysis of the relationship between rainfall and FC concentrations in urban rivers; (2) The simulation of hydrology and hydraulics; and (3) Scenario analysis. The proposed method was applied to the Beauport River watershed, in Canada, covering an area of 28.7 km2. FC loads and concentrations in the river, during and following rainfall events, were computed using the Storm Water Management Model (SWMM) hydrological/hydraulic simulation model combined with event mean concentrations. It was found that combined sewer overflows (CSOs) are the main FC sources, and that FC from stormwater runoff could still impair recreational activities in the Beauport River even if retention tanks were built to contain CSOs. Thus, intervention measures should be applied in order to reduce the concentration of FC in stormwater outfalls. The proposed method could be applied to water quality components other than FC, provided that they are present in stormwater runoff and/or CSOs, and that the time of concentration of the watershed is significantly lower than their persistence in urban waters.