Compartsons of wave reflection, transmission and harmonics due to different types of submerged structures are investigated by a ntmnerical method, the boundary-fitted coordinate (BFC) method. The types of submerged structures include a submerged horizontal plate, submerged breakwaters (rectangular and trapezoidal) and a step-type structure (topography). First, the BFC method is verified by comparing the computed results with the experimental data, including wave surface elevations, reflected and transmited wave heights, and amplitudes of higher harmonics, showing that the method is a reasonable one to predict wave deformations due to the submerged structures. Secondly, the wave surface elevations and the higher harmonics over different submerged structures are compared. Thirdly, reflected and transmitted waves due to different submerged structtmes are investigated.