When the hydropower station adopts the low-dam method for water intake, it is difficult to reduce sediment concentration in water flows into the hydropower station. It is necessary to develop a systematic technology to ensure that water intake and sediment management are handled safely within the power station. We established a numerical model for reservoir sedimentation and proposed a new method for calculating sediment removal efficiency to carry out a comprehensive study on sediment problems in the upper Marsyangdi-A Hydropower Station. Based on the study, some key indices were determined, including the flow rate for reservoir desilting, the threshold of sediment concentration to avoid damage to turbines, and the sediment removal efficiency of the sediment settling tank. The measured data after the operation of the power station showed that the results of sediment analysis and calculation are in good agreement with the observations. The water intake and sediment control measures adopted by the power station improved the sediment discharge efficiency of the reservoir and met the requirements for the continuous operation of the power station.