The high degree of physical factors in intertidal estuarine ecosystem increases material processing between benthic and pelagic compartments. In these ecosystems, microphytobenthos resuspension is a major phenomenon since its contribution to higher trophic levels can be highly significant. Understanding the sediment and associated microphytobenthos resuspension and its fate in the water column is indispensable for measuring the food available to benthic and pelagic food webs. To identify and hierarchize the physical/biological factors potentially involved in MPB resuspension, the entire intertidal area and surrounding water column of an estuarine ecosystem, the Bay des Veys, was sampled during ebb tide. A wide range of physical parameters (hydrodynamic regime, grain size of the sediment, and suspended matter) and biological parameters (flora and fauna assemblages, chlorophyll) were analyzed to characterize benthic-pelagic coupling at the bay scale. Samples were collected in two contrasted periods, spring and late summer, to assess the impact of forcing variables on benthic-pelagic coupling. A mapping approach using kriging interpolation enabled us to overlay benthic and pelagic maps of physical and biological variables, for both hydrological conditions and trophic indicators. Pelagic Chl a concentration was the best predictor explaining the suspension-feeders spatial distribution. Our results also suggest a perennial spatio-temporal structure of both benthic and pelagic compartments in the ecosystem, at least when the system is not imposed to intense wind, with MPB distribution controlled by both grain size and bathymetry. The benthic component appeared to control the pelagic one via resuspension phenomena at the scale of the bay. Co-inertia analysis showed closer benthic-pelagic coupling between the variables in spring. The higher MPB biomass observed in summer suggests a higher contribution to filter-feeders diets, indicating a higher resuspension effect in summer than in spring, in turn suggesting an important role of macrofauna bioturbation and filter feeding (Cerastoderma edule).