The volume of sediment accumulations in the upstream reach of the dam and the selection of an efficient flushing measurse are determined by the accurate hydrological regime assessment that is made when designing run-of-river structures. In the Tartar River's water intake head sedimentation regime was investigated, the potential accumulation volumes on the dam's upper side were calculated, and a functional design for the deposited sediment flushing unit’s operation scheme was developed. Due to the lack of necessary data, the flow rate in the Tartar River water receiving head was measured using three parallel methods that were discovered through research on local watercourses. A comparative analysis of three sediment flow values was done and its calculated value is defined, on the basis of which the annual volume of sediment subject to accumulation in front of the dam of the head and the possible infilling size of the sediment in the upstream reach was determined. The rational placement of the outlets for flushing deposited sediment is shown while taking into account the volume of deposits, the geometric properties of the head, and its upstream reach.