Abstract: The polder reservoir,storing fresh water,is one of the measures to solve water-deficient problems in the coastal areas.How to accelerate water desalination process is the most important problem in a polder reservoir.Pumping out the saline water near the bottom in the deepwater areas is one of the effective measures to accelerate this process In this paper,the pumping locations and scales are determined based on the salinity distribution and the volume of deepwater,and the Delft 3D model is employed to calculate the salinity variation during the period of 2004 to 2006 under the designed hydrologic conditions.After three-year operation,draining out the saline water near the bottom in the deepwater,the total residual salinity in the reservoir is only 40% comparing with without pumping Numerical results indicate that it greatly accelerates water desalination process in the polder reservoir.