AbstractBlue mussels are among the most abundant bivalves in shallow water along the German coasts. As filter feeders, a major ecosystem service they provide is water filtration and the vertical transfer of suspended organic and attached inorganic material to the sea floor. Laboratory and field studies previously demonstrated that blue mussels can remove large quantities of plankton from the surrounding water. I here perform numerical experiments that investigate the effect of filtration at the scale of an entire coastal sea—the southern North Sea. These experiments were performed with a state-of-the-art bentho-pelagic coupled hydrodynamic and ecosystem model and used a novel reconstruction of the benthic biomass distribution of blue mussels. The filtration effect was assessed as the simulated change in net primary productivity caused by blue mussels. In shallow water, filtration takes out up to half of the entire annual primary productivity; it is negligible in offshore waters. For the entire basin, the filtration effect is 10%. While many ecosystem models have a global parameterization for filter feeders, the coastal gradient in the filtration effect is usually not considered; our research demonstrates the importance of including spatially heterogeneous filtration in coupled bentho-pelagic ecosystem models if we want to better understand the spatial patterns in shallow water coastal systems.