During rainstorms, watersheds can introduce large amounts of faecal pollution into the rivers and sea, leading to shellfish contamination. In this study, we assessed Escherichia coli fluxes from a catchment, and their impact on estuarine water quality, using two assembled models. For the catchment, the agro-hydrological model SWAT was implemented integrating land uses, soil, topography, rainfall and other climatic data on Daoulas watershed (France). Initially, the SWAT model was calibrated and validated for river flow rates, and results were found satisfactory. Subsequently, different faecal contamination sources were integrated into the model: point sources (WWTP discharges into rivers) and non-point sources (manure spreading on fields). During rainfall events, the major source of contamination was manure spreading, due to the movement of faecal bacteria from fields to streams. For the estuary, the hydrodynamic model MARS-2D was set up, which takes into account realistic wind and tide values. E. coli concentrations in water were then calculated, and shellfish contamination derived using different values of bioaccumulation ratio. Results indicated a strong relationship between simulated and measured levels of shellfish contamination. To conclude, this application demonstrates the interest of using models to assess coastal contamination.