The Smoothed Particle Finite Element Method (SPFEM) has emerged as a robust and efficient numerical approach for solving geotechnical problems. While previous studies have proposed two-phase single-layer frameworks for soil-water coupling problems [1,2], accurately modelling the dynamic interactions among free water, porous media, and pore water within a unified framework remains challenging. This study develops a novel two-phase two-layer coupled SPFEM formulation to address complex soil-water interaction problems. The proposed approach employs two overlapping meshes to independently represent the water and soil phases. Water is modelled as a weakly compressible fluid, whereas soil behaviour is captured using an elastoplastic constitutive model, with both phases solved within an explicit SPFEM framework. To enhance numerical stability, a pressure diffusion technique [3] is implemented to mitigate pressure oscillations in the weakly compressible fluid, and a porosity averaging scheme is adopted to smooth discontinuities at the soil-water interface. Additionally, a boundary correction algorithm adapted from SPH research [4] is incorporated for the solid mesh in submerged conditions. The proposed method is validated against Terzaghi's consolidation problem and gravitational loading of fully submerged soil. The framework is then applied to large deformation problems, including dam-break flow through a porous dam and submerged landslide-induced wave generation. The results demonstrate that the proposed method effectively captures the dynamic soil deformation, free water surface evolution, and pore water pressure development throughout the large-deformation soil-water coupling process. The numerical results confirm the accuracy and computational efficiency of the proposed method for analysing large deformation soil-water interaction problems. This framework offers significant potential for engineering applications in hydraulic and marine geotechnical engineering.