Construction of the Włocławek Barrage on the Vistula River in 1970 became an important source of energy; however, it discontinued sediment transport in the Vistula River. This phenomenon resulted in accumulation before and erosion below the barrage; a similar problem can be expected due to the planned construction of the Lower Vistula Cascade. This study is dedicated to finding an effective and feasible solution to sediment transport management, acceptable to a wide group of users (e.g., navigation, energy producers, and ecologists). A numerical 1D model was applied to carry out analysis of hydrodynamics and sediment transport in the river section from Włocławek Barrage to the Vistula River mouth in the Baltic Sea. For calibration, historical data describing the accumulation and erosion created by the Włocławek Barrage were used. The proposed model allowed incorporation of new barrages chronologically, in accordance with the proposed time schedules. Analysis was carried out in a 50-year horizon, using a set of historical flow data. For sediment flushing, it was proposed to use natural flooding events exceeding Q10% discharge and to control sediment management of the adjacent barrages. To use this method in practice requires verification.