In this study, a frequency-domain finite element model is proposed to evaluate the seismic response of water-structure-sediment-foundation-backfill coupling system. It includes the seawater as a compressible fluid, seawall as viscoelastic solid, backfilled soil, sediment, and foundation as two-phase poroelastic domains with dynamic behavior described by u-p formulation of Biot’s equations. The dynamic interactions among various domains are fully considered and the PML is adopted as an absorbing boundary condition to truncate the computational domain, absorbing all out-going seismic waves. The dynamic responses in the structure, water and soil are assumed to be generated by the vertical propagating shear or compressional waves from the bedrock substrate under the foundation soil. Both the actions of horizontal and vertical seismic excitations at the bottom of foundation are respectively considered. After verifying the accuracy of PML and coupled model of soil-structure-water system, a series of parametric studies are conducted to investigate the effects of sediment thickness, water depth, foundation stiffness, foundation thickness, inclination of seawall, and properties of backfilled soil including soil permeability, shear modulus, and saturation degree, on the frequency response at the top of seawall.