The present paper discusses the nonlinear wave deformation due to a submerged coastal structure. Theory is based on the frequency-domain method using the third order perturbation and boundary integral method. Theoretical development to the second order perturbation and boundary integral method. Theoretical development to the second order Stokes wave for a bottom-seated submerged breakwater to the sea floor is newly expanded to the third order for a submerged coastal structure shown in Figure 1. Validity is demonstrated by comparing numerical results with the experimental ones of a rectangular air chamber structure, which has the same dimensions as that of this study. Nonlinear waves become larger and larger with wave propagation above the crown of the structure, and are transmitted to the onshore side of the structure. These characteristics are shown greatly as the increment of Ursell number on the structure. The total water profile depends largely on the phase lag among the first, second and third order component waves.