The unsteady, 2-d Navier-Stokes equations and the fully-nonlinear free surface boundary conditions were solved numerically to investigate the interaction of irregular waves and submerged breakwaters. The deterministic spectral amplitude method performed by fast Fourier transform algorithm was applied to generate the incident irregular waves with the Goda-JONSWAP spectrum. After having verified the accuracy of the incident wave spectrum and the amplitude and phase for each wave component are repeatable, effect of the height and width of breakwater on the reflected wave energy, wave transformation, vorticity and vortex were studied systematically. The numerical results show that propagation of irregular waves over a submerged breakwater produces not only the second order bound waves (subharmonic and superharmonic waves) of the fundamentals waves, but also energy transferring, due to the nonlinear interaction of different wave components in shallow water.