When ships navigate in the inland waterway with limited water depth, which affects their hydrodynamic performance due to interaction between the ship and river-bottom, which leads to the ship squat and resistance will increase compared to sailing in deep water condition. This paper conducted study the impact of different water depths on ship resistance at various ship speeds using CFD method. Predicted the ship squat, resistance and the flow field pattern are compared to those in unlimited water depth to elucidate the shallow water effect. The numerical results indicated that the influence of water depth on resistance and squat is closely related to the depth Froude number. All numerical results are of great consistency with the theoretical prediction. A cargo ship of 4600DWT operating on Vietnam’s river-sea routes is chosen as a study object.