Water wave-structure dynamic interaction problems are treated as eigenvalue problems of the coupled system by means of the boundary element method. The coupled system for a large-sized ocean structure is modelized generally with the three-dimensional continuum mechanics. The boundary integral equations of the coupled system are derived by the weighted residual method and related fundamental solutions. The solving scheme for the discretized equations is discussed in detail. Numerical examples of the three-dimensional problem are given to show the validity of the present method through the comparison with other results.