Net phytoplankton productivity in the Westerschelde, a relatively deep, highly turbid and eutrophic estuary in the Southwest Netherlands, was examined by means of a 13-compartment dynamic simulation model. The description of the light-limited primary production was based on the model of Eilers and Peeters (1988, Ecol. Model., 42, 185–198). This light limitation was parameterized to the different model compartments by integrating the Eilers-Peeters model over a day and over depth, taking into account the morphology of the Westerschelde compartments, the daily fluctuating light regime and characteristics of the photosynthesis-light curves of the phytoplankton community. The availability of light to the phytoplankters limited primary production to on average ˜2% of maximal production. Basin morphology, the turbidity gradient and light emission were important in the light-limitation function. Nutrient limitation was almost non-existent, except for diatoms in the marine part in summer, where production decreased to ˜85% due to silicate limitation. A large fraction of algal biomass was respired by the algae in the model. From late fall to early spring, the entire estuary was a respiratory sink for modeled phytoplankton biomass. Viewed on a yearly scale, phytoplankton respiration exceeded gross production in three model compartments where turbidity and basin morphology were most limiting. Due to the high turbidity of the area and the relatively large mixing depth, net pelagic primary production in the model was relatively low: the global estuarine average was 41 g C m−2 year−1. It fluctuated from a negative production of −74 g C m−2 year−1 in the turbidity zone to a maximum net production of 60 g C m−2 year−1 near the sea. Salinity stress mortality was the main factor causing freshwater algal stocks to decline, while marine and brackish phytoplankton biomass was mainly controlled by grazing.