To evaluate the relevance of a watershed modelling for assessing the contamination of coastal waters due to land-based sources and activities, a modelling approach, using SWAT (Soil and Water Assessment Tool) model, was implemented on the watersheds of Pen-Bé estuary and Le Croisic bay. For the past few years, various dysfunctions occurred in these shellfish farming areas located on the West coast of France. Therefore, it seemed critical to estimate the coastal watershed loadings in order to get a better understanding of the dysfunctions. In the same way, an empiric method based on water quality samplings was also carried out in order to evaluate the potential pollutant attenuation of the coastal wetlands. The results presented in this paper focus on simulated streamflows and phosphorus flows. Despite the limited existing data, which involved to integrate aggregated or averaged values for several aspects, according to the Nash and Sutcliffe efficiency criterion, the simulated flows seem close to the measurements. The simulated continuous flows appeared as a useful complement to intermittent water quality samplings and streamflow measures resulting from water monitoring networks. Moreover, by identifying the most contributory sub-watersheds, the simulations could be used to suggest priority areas of intervention for decreasing the coastal watershed loadings.