Shellfish cultures worldwide are often located in sheltered marine bays. The Oosterschelde is such a bay in the southwestern delta of the Netherlands, harboring extensive shellfish cultures, whose yield is partly driven by seston renewal from the North Sea. Tracer experiments performed with a three-dimensional hydrodynamic model were used to study the relative influences of benthic filtration and physical processes on seston replenishment. The model exhibited good skills in reproducing observed water level, temperature, salinity, and current velocity during 2009–2010. Turnover and residence times as indicators of water renewal showed substantial gradients from the mouth to head of the Oosterschelde. Surveyed bivalve biomass and empirical filtration rates were incorporated to estimate the effects of aquaculture on the seston concentration. The filtration created strong bio-deposition suppressing the eastward seston transport and causing <10% of external seston to be delivered to the head of the Oosterschelde. The effect of biological filtration on seston transport was comparable to that of physical forcing. This simple approach combining effects of physics and benthic communities can be applied more generally in food sustainability assessments of tidal bays.