This paper presents new numerical results based on two-dimensional depth-integrated model equations developed by Hu et al. (2008) for describing nonlinear water waves propagating in a permeable sub-aerial structure with an uneven impermeable topography. The water waves travelling into the porous media can be described by Darcy's formula (e.g. Parlange et al., 1984; Liu & Wen, 1997; Artiles & Kraenkel, 2007) with the assumption of negligible inertial force. However, as the inertial force becomes significant, more sophisticated models that include inertial force and turbulent effects are required (e.g. Hsiao et al., 2002, 2005; Cruz & Chen, 2007; Hu et al., 2008). To validate the applicability of the present approach, mathematic equations are termed as a new numerical model and also be well-validated by comparing the linear wave theory. The nonlinear property of the proposed equation is calibrated against the weakly nonlinear theory of Liu & Wen. Good agreement suggests that the present model equations can be applied to simulate nonlinear waves propagating into a porous structure. A set of simulations was performed to explore the fundamental behavior of inertial force. The effect of wave nonlinearity is also addressed.