Understanding the impact of fluid–structure interaction during the entry of a marine vessel into water is crucial for its design. While numerous models have been proposed to investigate the penetration of symmetric elastic wedges into water, in this study, we propose a numerical model that combines the fully nonlinear boundary element method with a mode superposition method to analyze the penetration of symmetric and asymmetric elastic wedges into water. We derive the boundary conditions of the acceleration potential within the flow field for the problem of fluid–structure interaction and use auxiliary functions to decompose the acceleration potential and extract the instantaneous added mass. Following this, the differential equations of the modes of rigid motion and elastic deformation of the body are established and solved. This approach enables the simultaneous solution of the motion and vibrations of the wedge as well as the hydrodynamic pressure. The proposed model also accounts for flow separation while the wedge is submerged, thereby prolonging the simulation. We confirmed the validity of the model through comprehensive examinations based on semi-analytical, computational, and experimental data on the problem of the entry of a symmetric body into water. We then extended our study to encompass the free-falling entry of an asymmetric elastic wedge into water. The results revealed notable discrepancies in the evolution of deformation and jet flow between the right and left boundaries during the entry of the wedge into water.