The three-dimensional thin layer element method is formulated for the dynamic response analysis of an axi-symmetric structure in submerged soil. Biot's wave equation for fluid-filled porous medium is used in the formulation. The three-dimensional thin layer element method computes the wave numbers and their associated mode shapes, for both Rayleigh waves and Love waves in submerged soil, which define the characteristics of the waves. The submerged condition affects the characteristics of the Rayleigh waves in soil. As a result, it alters substantially the soil-structure interaction stresses if the permeability of the soil is relatively large and, to less extent, the response of the structure. The thin layer element method is far more efficient than the finite element method for analyzing the fluid-filled porous medium, yet capable of taking into account a multi-layered inhomogeneous soil.