In tidal areas, natural land boundary is complex and underwater topography varies acutely due to influence of upstream runoff and outer tide. The simulation and forecast of water current and mass transportation play an important role in practical engineering. According to the situation of irregular natural boundaries in tidal region, unstructured triangular grid arrangement is applied to suit for complex condition. A finite difference method with alternating directional implicit scheme for triangular grid is established in this paper. The model has been applied in calculation of flow and concentration fields for Nantong reach of the Yangtze River. It is satisfied that the calculated values are in agreement with observed data.