Floating structures are sometimes deployed in shallow water areas close to reefs and islands as facilities serving tourists. In contrast to the open sea, the marine environment, such as wave and current, in the nearshore shallow water area will be affected by the non-uniform complex seabed bottom, and the hydrodynamic interaction between the floating structure and the seabed bathymetry should be investigated, instead of being ignored as the case when a uniform seabed is assumed. A hydroelastic analysis method for slowly varying water depths is proposed to calculate the hydroelastic responses of the floating structures, considering the seabed as a fixed boundary condition. This method was integrated into the software THAFTS (Three Dimension Hydroelastic Analysis of Floating and Translating, developed by China Ship Scientific Research Center). Based on the THAFTS software, the three-dimensional hydroelastic motion response analysis of a barge is carried out, in which the effects of different water depths and the complex bathymetry are investigated by comparing the results of the motion and structural responses of the barge. The stress distribution of the barge with the effect of the bathymetry taken into account is presented in this article as well as the modal stresses. The strength evaluation of the barge indicates that the effect of the inhomogeneous seabed plays a large role in the dynamic responses of the barge when it is deployed near reefs.