Résumé : The freshwater (RIVE) and the marine (MIRO) biogeochemical models were coupled to a 1D hydro-sedimentary model to describe contemporary phytoplankton succession and nutrient transfers in the macrotidal Scheldt estuary (BE/NL) affected by anthropogenic nutrient loads. The 1D-RIVE-MIRO model simulations are performed between Ghent and Vlissingen and the longitudinal estuarine profiles are validated by visual and statistical comparison with physico-chemical and phytoplankton observations available for the year 2006. Results show the occurrence of two distinct spatial phytoplankton blooms in the upper and lower estuary, suggesting that neither the freshwater nor the marine phytoplankton gets over the maximum turbidity zone (MTZ) at the saline transition. Sensitivity tests performed to understand how changing conditions (salinity, turbidity and nutrients) along the estuary are controlling this bimodal spatial phytoplankton distribution identify salinity and light availability as the key drivers while the grazing pressure and nutrient limitation play a negligible role. Additional tests with varying salinity-resistant (euryhaline) species in the freshwater assemblage conclude that the presence (or absence) of euryhalines determines the magnitude and the spreading of freshwater and marine phytoplankton blooms in the estuary. Annual nutrient budgets estimated from 1D-RIVE-MIRO simulations show that biological activities have a negligible impact on nutrient export but modify the speciation of nutrients exported to the coastal zone towards inorganic forms, thus directly available to phytoplankton. The implementation of nutrient reduction options (upgrading of waste water treatment plants, conversion to organic farming) on the Scheldt watershed influences the whole estuary and affects both the magnitude and the speciation of nutrients exported to the coastal zone with expected impact on coastal phytoplankton dynamic. © 2012 Elsevier B.V.