Abstract: The mathematical models of the east china sea, the Yangtze River Estuary and the Huangpu River are established. On the basis of the calibration and validation of these models, the effect of the submarine tunnel under the Huangpu River is studied numerically, and the changes of the water level and the velocity field within the adjacent water area are analyzed. Results show that raising the pipeline segment in the deep pool has little influence on the flood control installations and on the boat sailing safety both after the completion of the submarine tunnel and at the construction stage. The influence sphere of the change of the velocity lies from the point 300m upstream to the point 400m downstream of the project axis.