The first part of this thesis describes a simulation model of the carbon flows in the Oosterschelde estuary, S.W. Netherlands. Aim of the model is to describe the availability of food for macrobenthic filterfeeders, and possible changes in this as a result of the construction of a half-open storm-surge barrier. Major aspects of the model are transport, primary production, zooplankton grazing, mineralization, microphytobenthos production and zoobenthos grazing.In the second part of the thesis the question how to asses uncertainty in model results of such a relatively complicated model is addressed. In a sensitivity analysis the parameters are classified into a limited number of groups with separate effects on model results. This classification is used to facilitate the calibration procedure. Calibration is treated as a method to reduce uncertainty in model output, and not as a procedure to test hypotheses concerning model formulations.The reduced uncertainty is used in the calculation of the effects of several scenarios. Despite the considerable physical changes as a result of the barrier the carbon flows in the Oosterschelde appear to remain near their old values. There is a limited possibility to extend the mussel culture in the seaward part of the Oosterschelde, but with a risk of causing overgrazing, with negative effects on mussel yields and the natural system. The risk of eutrophication of the Oosterschelde as a result of direct nutrient discharges is slight, but the impact on the Oosterschelde of further eutrophication of the adjacent North Sea would be larger.