Nitrate loadings to the French coastal waters of the Bay of Biscay and the English Channel have increased from 5 to 10 times during the four last decades, due to runoff on intensively fertilized agricultural watersheds. Eutrophication of this coastal zone is now a recurrent problem, with wellknown direct impacts (Ulva “green tides” on beaches, excessive phytoplanktonic blooms responsible for “coloured waters” and bottom hypoxia events offshore), but also indirect enhancement of the toxicity of some phytoplankton species, caused for instance by increased N:Si ratio in the coastal sea. In order to better guide the decision makers about nutrient loading reduction, Ifremer uses the so-called ECO-MARS3D biogeochemicalhydrodynamical model to simulate the present situation in terms of phytoplanktonic biomasses and oxygen concentrations, along with more specific information: concentrations of 3 harmful phytoplanktonic species (Pseudo-nitzschia, Karenia, Phaeocystis) and ASP toxin (domoic acid) in the sea water. The simulations of recent years have been compared favorably to satellite images and field measurements, and an operational version currently runs on the previmer.org site. An original tracking method of nitrogen (or phosphorus) coming from any source allows the assessment of the quantitative role of the 3 main rivers (Seine, Loire, Gironde) nitrogen loads in the phytoplankton blooms. The model points out the bay of Vilaine as very sensitive to bottom oxygen depletion in summer, and can be compared on-line to the automatic measurements coming from the MOLIT buoy. Through the appearance of too high N :Si ratio in the nutrients, the model also provides some explanation to the patchy location of ASP toxin recorded by the REPHY monitoring network.