Hydraulic–morphological river models are applied to design and evaluate measures for purposes such as safety against flooding. These numerical models are all based on a deterministic approach. However, the modeling of river processes involves numerous uncertainties. The aim of this study is to identify the sources of uncertainty that induce the largest uncertainties in the model outcomes and quantify this uncertainty using expert opinions. Experts have been selected based on a Pedigree matrix. The selected experts are asked to list and quantify the most important uncertainty sources for two situations: (1) the computation of design water levels (DWL) and (2) the computation of the hydraulic effect of a change in the river bed. The experts stated that the sources of uncertainty are different for the computation of the DWL and effect studies. The experts agreed that for DWL, the upstream discharge and the roughness predictor for the main channel have the largest uncertainty. For effect studies, no clear dominant source could be identified. The quantification of the uncertainty sources showed a significant effect on the predicted water levels under design discharge conditions.