Flows of the confluence of Yangtze River and Jialing River in the city of Chongqing are numerically simulated by using Delft3D Model with staggered grids and ADI integral method. The water level, flow velocity and drogue trace are studied. Comparing the numerical results with observed data shows good agreement. Therefore the computational model and the simplified parameters are of good accuracy and have practical meaning. The results show that the contamination will linger near the Caiyuanba area and drift to Chaotianmen and the right bank of Yangtze River upstream. The results can be used to forecast flood, inspect contamination and management of riverway in the city.