Our study aims at making progress the estimate of herbicide and nutrient inputs to the Marennes-Oleron bay which could influence summer oysters mortalities, and to bring, a better understanding of the impact on coastal ecosystems by modelling the dynamics of these compounds in the shellfish-farming area. The development of a strategy adapted to the river Charente and its estuary reveals that agricultural activity on the watershed area is omnipresent, as well on the level of the nitrogen as on the one of herbicides contributions. It is thus necessary to specify Charente fluxes, which is the main tributary of the Marennes-Oleron bay, in order to better characterize its impact on shell fish-farming activity. Hydrodynamic modelling will constitute an invaluable help in the risk assessment with respect to pesticides, by specifying the periods of the high and low concentrations of these molecules and the biotope exposure durations.