Wave Energy Converter (WEC) development needs a thorough dynamic characterization of the device and tuning the design properties to harness the maximum power. This paper addresses this need by using experimentally validated numerical simulation for an array of flap-type WEC mounted on a surface of a breakwater as a coherent approach in sustainable coastal protection. The developed numerical model is combined with a parametric iteration procedure to find the optimized values of power take-off (PTO) coefficients, and the flap's distance from the breakwater. It is shown that tuning the design properties of flap-type WEC integrated into a coastal structure leads to high energy capture around 85 percent of the available power. It was found that the amplitude of oscillation is significantly affected by the presence of different frequencies resultant from standing waves, and the confined water between the flap and the breakwater. It turns out that by tuning the distance between the flap and the breakwater, the standing waves can be used for increasing the amplitude of oscillation and consequently power enhancement.