Eutrophication of the Seine river/estuary/bay continuum of the French coast of the English Channel is a subject of growing concern. Because of huge nutrient inputs from the Seine river, with an excess of nitrogen over phosphorus and silica, chlorophyll concentrations reach very high level and episodic blooms of toxic dinoflagellates are regularly observed. In order to better understand the relationship between these ecological processes and the human activities in the Seine watershed, two models have been developed and used in connection : 1/ a model describing nutrient (N, P, Si) transfer processes at the scale of the whole Seine Basin (SENEQUE/RIVERSTRAHLER, Thieu et al, 2009), allowing human activity (agricultural practices, waterscape management, urban wastewater treatment, etc.) to be related to fluxes delivered to the sea, 2/ a 3D hydrodynamic (MARS model, Lazure & Dumas, 2008) and ecological model of the Seine Bight (Cugier et al. 2005) reproducing the spatio-temporal variations of sediment transport, thermo-haline stratification and phytoplanktonic development in the plume of the Seine river. Various scenarios of human activity in the watershed and the impacts at the coastal zone are simulated by these coupled models and analysed in terms of nutrients and phytoplankton dynamics. Such a modelling chain, describing an aquatic continuum from head waters to coastal zone represents a powerful tool to study several hypotheses of river basin management and their impact on the marine ecosystem. We show that the measures taken in the European Water Framework Directive would not restore the nutrient Redfield ratio (N:P:Si) required for an equilibrated algal development and seasonal succession. Such an approach therefore provides a better understanding of how human activities in the watershed govern the functioning of the river–estuary-coastal sea continuum.