Abstract: Based on the potential flow theory, the influence of water on the natural vibration characteristics of a typical rectangular entity pier as the prototype was analyzed at different water depths. As the same time, the distribution of hydrodynamic pressure acting on the pier, the action spot of hydrodynamic force and the effect of water on the seismic response of the pier were analyzed under the condition of different water depths and types of seismic loads. The results show the natural vibration period, the peak values of bending moment and shear force at the bottom of the pier increase with the rise of water depth. The bending moment and shear force increase by 31% and 50% at most respectively, which indicate that the effect of water on the dynamic response of the pier should not be ignored. The influence of different seismic waves on the distribution of hydrodynamic pressure acting on the pier is not identical. The results of hydrodynamic force acting on the pier according to the Japanese specification are closer to data in this paper.