The unsteady, 2-d Navier-Stokes equations and the exact free surface boundary conditions were solved numerically to investigate the transformation of irregular waves propagating over a submerged breakwater. The deterministic spectral amplitude method performed by fast Fourier transform algorithm was applied to generate the incident irregular waves with the Goda-JONSWAP spectrum. Transformation of waves was discussed in terms of reflected energy and wave spectra. By providing the incident irregular waves with repeatable amplitude and phase for each wave component, effects of the height and width of the breakwater on the wave transformation were studied systematically. The numerical results show that propagation of irregular waves over a submerged breakwater produces not only the higher harmonics of the fundamentals waves, but also the subharmonic and superharmonic waves, due to the nonlinear interaction of different wave components in shallow water.