In order to ensure that the chloride ions concentration of the water from a reservoir with high-salinity sediment reaches the standard(less than 250mg/L), the effects of high-salinity sediment, the main source of chloride ions, on the water quality of the reservoir were studied during the periods of layout design of reservoir gates and operation of the reservoir, using the Beitang Reservoir in Tianjin City as an example. To determine the optimal layout of gates from alternative schemes and to simulate the water salinization in the operation period of the reservoir, a three-dimensional hydrodynamic and water quality model was established, with the release of chloride ions from the high-salinity sediment considered. The results show that the water quality is directly influenced by the spatial layout of the inflow and outflow gates. It is put forward that the scheme with the inflow gate located in the southwestern corner and with the three outflow gates open at the same time is the optimal scheme, in which there is nearly no static region and the water quality will reach the standard after eight days. In the static period of the reservoir, the release rate of chloride ions from the sediment is positively correlated with the salt content in the sediment, and the concentration of chloride ions in the reservoir will exceed the standard at the 55th day after the release under the most unfavorable conditions.