The design of most current bridges across rivers still based on the consideration of the static environment in which the piers are located. The piers of wading bridges, especially the cross-sea bridges submerged in water, and many of them are still in earthquake-active areas, the analysis of dynamic effects of the piers is particularly important. Four models of piers were designed to research the influence of vibration frequency under different water levels by using model test and numerical computation method. The influence rule of seismic response of the model in the water was also discussed. The research results show that the first three frequencies of models decrease with the increase of water level. When the water depth exceeds three-quarters of the model height, the first-order frequency of the bridge pier model begins to decrease significantly. When the water depth exceeds one-quarter of the model height, the second-order frequency of the pier model begins to decrease noticeably. When the water depth exceeds one-eighth of the model height, the third-order frequency of the pier model begins to decrease remarkably. The shallow water condition has a small effect on the first-order frequency and a significant effect on the second and third-order frequencies. The deepwater condition has a significant effect on the first three frequencies of the pier model. The influences are more remarkable of flexible pier models. The seismic response of deep-water pier is increased by the action of fluid-structure interaction.