We investigate the hypothesis by Winterwerp and Wang (Ocean Dyn 63:1279–1292, 2013) that channel deepening in the Scheldt River Estuary could lead to a large increase in suspended sediment concentrations, with subsequent severe consequences to primary production and navigation. To this end, we use an idealised model to investigate the long-term development of the sediment concentration under the uncertainty of future changes in model parameter values and channel deepening. The water motion is calibrated to recent conditions after which the sediment concentration is validated against long-term observations and is subsequently tested for a wide range of parameter settings and deepening scenarios. We also investigate the effect of anthropogenic dumping of dredged sediments in the estuary on the sediment concentration. Deepening the channel, but keeping all other model parameters the same, we find lower long-term average sediment concentrations in most of the estuary. Thereby, our results suggest that deepening in the Scheldt alone cannot lead to high sediment concentrations, and we suggest to reject the investigated hypothesis. Further study of uncertain model parameters reveals that an increase of the erosion parameter by an order of magnitude allows for the development of high concentrations of several tens of grams per liter near the bed in narrow turbidity zones. It is unknown whether such an increase of the erosion parameter can happen in the future, which stresses the importance of further research into the factors that can lead to a change of this parameter.