Hydrodynamic performance of a movable submerged breakwater was analyzed using energy dissipation model. Based on two-dimensional boundary element method the equation of motion including a viscous dissipation term proportional to velocity squared was solved by Newton-Raphson method. Energy dissipation coefficients as well as reflection and transmission coefficients of a submerged flat plate were calculated with various plate lengths and thickness. Both real and imaginary components of body displacement and forces were used to solve the motion of breakwater accurately. The effect of the magnitude of dissipation coefficient on the body displacement was evaluated. The results from the potential theory with no dissipation term were found to be an overestimate in resonance frequency.