For evaluation of wave heights and currents in shallow water area, the Boussinesq computation model has been widely applied. However, only the open sea and perfect reflection wall are applicable to computation boundary in the present Boussinesq model. A harbor is usually protected with some breakwaters and sea walls. The reflection coefficients of such prototype wave barriers vary from 0.0 to 1.0 according to the type of structure. Therefore, the wave height computation model in the harbor should include numerical techniques to consider the variable reflection coefficient.
　In the paper, the improvement of the Boussinesq equation is described. In the newly developed model, the wave absorbing boundary at the breakwater covered with wave energy dissipating blocks is computed as the porous layer. The newly developed porous layer is applicable as the partial reflection boundary in which the reflection coefficient Kr varies from 0.0 to 1.0.
　The parameters to determine the reflection coefficient Kr in the computation model are obtained by carrying out the experimental model test in a wave channel implemented a vertical sea wall covered with armor blocks.
　The reflected wave profiles numerically estimated in the model agree well with those obtained in the experiment. Therefore, the developed model is applied to simulate the partial reflection boundary and the phase of reflected waves in harbors.