The present study is to estimate the effect of wave height affecting at the front face of breakwater systems due to specification of submarine trench such as distance from breakwater to dredged area and width of dredge. The wave diffraction field, which is important hydraulic factor in the ocean, is considered to be two dimensional(2D) plane and the configuration of the submarine dredge on the sea bed designated by single horizontal long-rectangular pit system according to the various specific conditions of dredged locations. The numerical simulation is performed by using Green function based on the boundary integral equation and meshed at moving boundary conditions. The results of present numerical simulations are illustrated by applying the normal incidence. It is shown that the ratios of wave height at the front face of breakwater was varied by dependance of distant from breakwater to dredged area and width of dredge. It means that, when the navigation channel or pit breakwater is dredged on seabed, engineers have to consider the specification of dredge. This study can effectively be utilized for safety assessment to various breakwater systems in the ocean field and provided for safety construction of offshore structure.