A numerical model is presented in this study to investigate the wave transformation over a submerged permeable breakwater on a porous slope seabed. For this purpose, the time-dependent mild-slope equation is newly derived for waves propagating over two layers of porous medium. This new mild-slope equation involves the parameters of the porous medium, and it is a type of hyperbolic differential equation, therefore numerically efficient. The validity of the present model is verified based on the comparisons with the previous experiments. The effects of the permeable properties of both the porous seabed and the submerged permeable breakwater are discussed in detail. The geometry of the submerged permeable breakwater to the wave transformation is also investigated based on the numerical solutions.