In the design of deepwater foundation for bridges, the interaction between water and the structure especially under earthquake motions should be addressed. This paper presents a practical simplified method to analyze deepwater pile group foundation to determine its dynamic characteristics by combining approximate analytical solutions with the finite element method. The applicability of this proposed method is shown in a case study of a nine-pile foundation. Compared with those from complete numerical method, the analysis results from this simplified method are in agreement when the pile cap is not submerged in water. Furthermore when ignoring the vertical hydrodynamic added mass of the pile cap, the vertical vibration mode results are greatly affected, but not for other non-vertical vibration modes. This simplified method is also used in the study of the influence of water on the dynamic characteristics. The deeper the water is, the more obvious the impact of water is, particularly for the pile cap lateral bending modes, and there appears no evident difference for the pile lateral bending modes, on which water effect is stronger than that on pile cap lateral bending mode.