Eutrophication of the Seine estuary and the Bay of the Seine is a crucial environmental issue for the management of ecosystems and economic activities related to fisheries and tourism. A large quantity of nutrients, especially nitrogen, is brought to the coastal zone by the Seine River, the main input of that area, but also by smaller rivers along the Normandy coast. This large delivery of nitrogen leads to an imbalance between nitrogen (N), phosphorus (P) and silica (Si), which affects the growth of planktonic organisms and can exacerbate the occurrence of harmful algal blooms (HABs). These events can be damaging for shellfish fisheries, an important economic resource for the region. The study describes a new modelling chain coupling a riverine and a marine model (the Seneque/Riverstrahler and the ECOMARS-3D, respectively), which allows us to explore the effects on the coast of two scenarios of watershed management. The first one, focused on an upgrade of wastewater treatment plants, decreases the P fluxes by 5–35 kgP km-2 yr-1 on average over the 2000–2006 period, depending on the watershed, and would reduce about three fold the concentration of dinoflagellates in the adjacent coastal zone. The second one explores a hypothetical scenario of generalisation of organic farming on all agricultural areas of the basin. Although this is not realistic, it shows the best theoretical results we can achieve. With this scenario the N fluxes decrease by almost 50%, and the dinoflagellate blooms and thus possibly the Dinophysis sp. blooms are drastically reduced by a factor of 20–40. Nevertheless, diatoms, which are the main primary producers in the bay and sustain the marine food web, are not significantly affected by this drastic scenario.