Within the frame of linear potential flow theory, the impact of a porous rectangular barrier on a seabed on the dynamic characteristics of gravity waves is investigated. The porous barrier can be regarded as an abstract representative such as a seabed plant, a wave breaker, inhomogeneous topography, and trussed supporting of ocean engineering platform, etc. In the process of mathematical modeling, the method of matched eigenfunction expansions is employed for analysis, where a newly defined form of inner product is introduced to improve the simplicity of derivation. Under this definition, the inner product is automatically orthogonal, which will provide great simplification to obtain the expansion coefficients. Once the wave numbers for the fluid region and the barrier region are obtained, the reflection and transmission coefficients of the wave motion can readily be calculated.