This paper develops in more detail the theory for a fully three‐dimensional version of an earlier boundary integral equation method (BIEM) formulation, for the computation of the scattering of underwater sound from compact deformations of an oceanic waveguide’s surfaces. The method allows for three‐dimensional sources and boundary deformations in an otherwise uniform waveguide. The technique involves only integrations over the compact surface of the waveguide deformation. The implementation is illustrated for a seamountlike deformation in an oceanic waveguide.