Sediment dynamics in the shallow water zone of lakes are affected by the properties of the surface wave and current field, the morphometry, and water level fluctuations. Empirical investigations on sediment dynamics, however, are mostly limited in their spatial and temporal scales. Within the framework of the ReWaM-joint project HyMoBioStrategie, a coupled, numerical model was developed that is able to simultaneously reproduce the spatiotemporal dynamics of the wave and current field, the sediment transport and the resultant morphodynamics within lakes. Effects of different wind directions and water levels on the wave and current field as well as the sediment transport were identified using model scenarios and the simulation of a storm period within the range of Kressbronn Bay (KB) of Lake Constance. The spatially and temporally high-resolution model domain was validated with field data. The results of the numerical simulations helped to identify among others the dynamics and conditions of the sediment transport as well as local hot spots of sediment erosion and accumulation. The sediment transport in the shallow water zone is usually in parallel to the shore. The highest magnitudes and dynamics in the sediment transport occur during strong wind events and especially during low water levels in the near-shore zone up to similar to 3 m water depth. The observed patterns in the sediment net transport result from the specific shore exposure, the interaction between the direction of the wave and current field, and small-scale changes in morphology. For the first time, the development of sand dunes in the shallow water zone of Lake Constance could be shown. The presented numerical sediment transport model can be used as a prognosis tool for future planning, e.g., shore restoration and erosion measures.