Sea level rise was greatly concerned by society with its effects on saltwater intrusion and material transport in estuaries, which threaten drinking water supplies. In order to study the response of drinking water source to sea level rise, and prevent potential disasters in the future, a 3D numerical model for tidal flow and salinity was built based on the unstructured model FVCOM, and then applied to assess the impact of future sea level rise (SLR) on saltwater intrusion in the Qiantang Estuary through a series of numerical simulation. The results indicated that the sea level rise can cause substantial increase of salinity and the magnitude was higher during neap tide than during spring tide. The salinity intrusion moved farther upstream by 1.1, 2.2 and 6.0km, respectively, for the SLRs of 0.3, 0.6 and 1.0m during spring tide, while 2.8, 5.9 and 9.8km during neap tide. The maximum increase of salinity rised near Qibao station, and the values reached 0.17, 0.32 and 0.49respectively during spring tide, while, the maximum increase of salinity occurred near Yanguan station, and the magnitude reached 0.38, 0.80 and 1.22 during neap tide. When the relative sea level rise was in 0.3~1.0m, the increase of average salinity at three water intakes from Nanxingqiao to Shanhusha were 0.1~0.3, 0.1~0.3 and 0.1~0.2, the increase of maximum excessive salinity time were 1.0~4.1, 0.5~1.6 and 0.1~0.2 d respectively.