To increase the life of small storage reservoirs, sediment flushing is found to be a very useful technique throughout the world. A sediment flushing study of the Thakot D-3 Hydropower Project reservoir after construction of the Dasu dam on the Indus river is presented in this paper. HEC-RAS 5.0.6 numerical model has been employed to check the sediment removal during flushing and to assess the model's applicability and limitations. Dasu reservoir sediment discharge data of 20 years were used to evaluate the sediment load with different transport functions under no-flushing (FSL 656 m asl) and flushing conditions. Without flushing, the river bed would be raised 56.1 m at the dam site and the low-level spillway and power intake would be filled in 2–5 years' time. It was observed that reservoir sediment flushing is economically realistic for this dam and the HEC-RAS sediment simulation model is encouraged for reservoir flushing modeling. If the Thakot D-3 HPP is commissioned a number of years after Dasu, a coarser sediment load will also be reached in the reservoir which could pose a serious challenge for the Thakot D-3 reservoir life. It is recommended that without construction of the Bhasha-Diamer storage dam, sedimentation not only is a complicated issue for Dasu HPP and Thakot D-3 HPP, but will also have drastic impacts on other downstream run-of-river energy projects.