The current study focuses on the application of a three-dimensional numerical model for the prediction of morphological bed changes. The sediment deposition in a reservoir during a 10-year-flood was investigated and the results of the simulation were validated with data derived from a physical model study. Because of the small grain sizes in the prototype, synthetic granulate was used in the physical model. The numerical computation domain was a reproduction of the physical model, including the grain sizes and the density of the particles, in order to ensure comparability. The CFD code SSIIM, which solves the RANS-equations in three-dimensions, was used for the simulations. The sediment transport in SSIIM is divided into suspended sediment transport, computed by solving the convection-diffusion equation, and bed-load transport, calculated by an empirical formula. The results of the numerical simulation correspond well to the results of the physical model study. The simulated location and the pattern of the sediment deposition in the reservoir are an accurate representation of the observed distribution in the physical model.