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This study is concerned with the problem of acoustic scattering by a three-dimensional obstacle in a shallow water waveguide. A method coupling of the finite-element and natural boundary-element is analyzed and presented for solving the acoustic scattering problem numerically based on the Galerkin variational principle and the DtN mapping theory. The proposed method has the advantage of avoiding the absorbing boundary condition of the conventional finite-element method. Numerical examples are given of successful computational results for several 3D obstacles of various shapes.