This study proposes a numerical, nonlinear wave model for a 3-dimensional wave field, which can evaluate Lagrangian and Eulerian wave-induced flows and wave deformations around and inside a permeable structure. To achieve stable computations, the model combines a VOF method with a nonreflective wave generator, in addition to the open-boundary treatment based on an added dissipation zone. Also, a numerical scheme is developed to convert the Eulerian velocity into Lagrangian velocity. A laboratory measurement for a rectangular offshore structure including wave-induced How and wave height distribution was also conducted to investigate the validity of the numerical model. It has been found that the numerical model predicts the wave deformation well, providing a reasonable estimate of the wave-induced flow around the porous media. Also studied further are the effects of media properties, wave specifications and structure length on wave-induced flow, water particle movement and wave deformation. It is concluded that wave period and porosity of structure affect the characteristics of wave-induced flow more than other parameters. Also, a return flow can be seen inside the structure depending on the ratio of structure width to wavelength.