Structure-soil-structure interaction (SSSI) is investigated using a model of two shear walls supported by rigid foundations embedded in a soft layer over elastic bedrock. Solution is presented for the model response to incident plane SH-wave based on indirect boundary element method (IBEM). The analysis focuses on the effects of the soil layer. Although the dominant features in the response of flexible structures are those related to the structural resonances, the SSSI effects are not negligible. Further, the SSSI effect are enhanced by the soil layering, and are more pronounced for shallower layer and stiffer bedrock. It is shown that for closely spaced structures, reduction of the peak response occurs, which may reach 30–45%, while, for certain combinations of frequency and separation distance, amplification occurs, which may reach 45–50%, as compared to the stand-alone structure. For inclined wave incidence, the SSSI effects occur for larger separation distances than for vertical incidence. The results may be useful for interpretation of observed response in buildings and seismic response estimation in general.