To increase the life of small storage reservoir sediment flushing found very useful technique overall the world. A sediment flushing study of the Thakot D-3 hydropower project (THP) reservoir after construction of Dasu dam at 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 applicability and limitations. A Dasu reservoir sediment discharge data of 20 years were used to evaluate the sediment load with different transport function under no flushing (FSL 656 masl) and flushing conditions. Without flushing river bed would be raised 56.1 m at dam site and low-level spillway and power intake would be filled in 2–5 years' time. It was observed that reservoir sediment flushing economically realistic for this dam and HEC-RAS sediment simulation model encouraged for reservoir flushing modelling. If Thakot D-3 HPP is commissioned a number of years after Dasu a coarser sediment load will also be reached in the reservoir which can pose a serious challenge for Thakot D-3 reservoir life. It is recommended that without construction Bhasha-Diamer storage dam sedimentation is a complicated issue not only for Dasu HPP and Thakot D-3 HPP, it will also have drastic impact on other downstream run-of-river energy projects.