A boundary element methodology is developed for studying the response of a system of two rigid, massless or massive, surface foundations of arbitrary planforms to various harmonic waves under three-dimensional conditions. The method employs the frequency domain Green's function for the surface of the elastic half-space, thereby restricting the discretization only to the soil-foundation interfaces, and isoparametric quadratic quadrilateral boundary elements for increased accuracy. Extensive comparison studies with other known numerical solutions confirm the high accuracy of the proposed method. Detailed parametric studies are conducted in order to study the harmonic wave response of two square foundations as a function of the kind of incident wave, the angles of wave incidence, the wave frequency, the separation distance between the foundations and the amount of mass in each foundation and compare it against that of a single foundation for assessing the through the soil coupling effect.