To ensure sustainable uses of the coastal zone, an integrated ecosystemic approach and ecosystem models are required to frame ecological processes and evaluate environmental impacts. Here, a mass-balance trophic (Ecopath) model of the Mont Saint Michel Bay (MSMB) was developed, to analyze the bay's functioning as an ecosystem. This bay, intensively exploited by fishing and for shellfish farming, is also suffering from the proliferation of the gastropod Crepidula fornicata, an exotic species. The MSMB model has 18 compartments, from the primary producers to top predators, and emphasizes the large biomass of filter feeders. The model identified the MSMB as a highly productive ecosystem controlled largely from the bottom-up, and strongly impacted by huge biomasses of filter feeders. However, the low transfer efficiency rates imply that a large part of the primary production is not transferred upward to higher trophic levels, but is lost in high hydrodynamic exchanges and in the trophic impasse represented by a large biomass of Crepidula fornicata.