Setup, calibration and validation is described for a 3D water quality and primary production model in the Schelde. The area of interest is the Westerscheide. Target variables primary production and dissolved oxygen concentration were reproduced well. Primary production in this area is limited by light which is caused by the high turbidity in this area. The model is going to be used to estimate the effect of changes in suspended sediment by human activities (such as dredging) or natural processes (changing run-off) on primary production. An additional research application will be to disentangle the different processes contributing to the daily variation in dissolved oxygen, to improve measurements of primary production.