This paper introduces a combined modelling approach using a simple water budget model (THC-model) and a 3D reservoir sedimentation model (MOHID Water) to adapt reservoir operation and visualise their effects on the sediment deposition. By this, an effective combined sediment-water management can be identified under semi-arid conditions for dry, median and wet years. Results are presented for the reservoirs of the Tuyamuyun Hydro-Complex (THC), which is located in the lower Amu Darya River. The determination of the actual and usable reservoir storage volume shows that siltation will significantly adversely affect the ability of the in-stream Channel Reservoir to regulate seasonal demand for both irrigation and municipal water supply. However, modelling scenarios results confirm the effectiveness of adapted operation rules for the THC reservoirs and show that the operation of large dams could be modified according to a combined sediment-water management. The experience gained during this study emphasizes the fact that the concept of a combined reservoir management of sediments as well as water can be an efficient measure to improve the sustainable long-term use of reservoirs and to contribute towards a safe water supply in water crisis regions.