Comparisons of wave reflection,transmission and harmonics due to different types of submerged structures are investigated by a numerical method,the boundary-fitted coordinate(BFC) method.The types of submerged structures include a submerged horizontal plate,submerged breakwatern(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 transmitted 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 structures are investigated.