A fully transient, 2-dimensional physical and biological model has been developed to quantify the seasonal cycle of silica in the estuaries-coastal zone continuum of the Bay of Brest (France). The numerical model includes an explicit representation of the benthic-pelagic coupling, which is stimulated by the increasing density of an invasive megabenthic filter feeder, the slipper limpet Crepidula fornicata. The selected spatial resolution allows resolution of the heterogeneous density distribution of these organisms in the bay. Results show that the benthic nutrient dynamics are highly variable and strongly depend on the local conditions. This heterogeneity is not reflected in the pelagic phytoplankton Population dynamics because transport and mixing homogenize the distribution of nutrients and biomass. A seasonally resolved silica budget over the entire bay and estuaries emphasizes the important contribution of the benthic recycling fluxes to the supply of dissolved silica (dSi) during the productive period (similar to 50%, from 1 April to 1 September). In a prognostic scenario which forecasts the impact of removing the invasive benthic filter feeders, the dSi efflux is reduced by 63% and a pronounced harmful algal bloom of dinoflagellates develops in late summer.