In the Oosterschelde estuary, primary production has decreased by 50% in the last 15 years. Nutrient concentrations are low but primary production is nutrient limited only for short periods during the growing season. Dominant bivalve filter feeder stocks consist of mussels (Mytilus edulis), cockles (Cerastoderma edule) and the introduced Pacific oysters (Crassostrea gigas). The mussel stock, which is under control of the mussel farmers, has decreased due to shortage of mussel seed, cockle stocks have maintained and oysters have expanded. Total filtration capacity has increased, also due to the invasion of Ensis americanus. Bivalve growth and condition are food limited, as shown by a negative correlation between average mussel meat content and bivalve filter feeder stock size in a certain year. The annual growth of cockles has decreased, and the fraction picoplankton is now up to 30% of total phytoplankton. Food limitation, high filtration capacity, picoplankton abundance, and only short-term bottom-up control of primary production by nutrient limitation, point to overgrazing as a cause of primary production decline. Further expansion of shellfish stocks may induce the risk of overexploitation.