The aim of the study is to evaluate the 3D dynamic response of a finite geological region containing two structures and rested on a semi-infinite elastic layered half-space with a dynamic source radiating transient waves. The hybrid modelling approach is applied. It is based on the decomposition of the whole domain under consideration into two sub-regions: a finite-sized near-field elastic isotropic zone with two containment structures and the open semi-infinite far-field layered region. The far-field zone is a semi-infinite elastic isotropic arbitrary layered medium where the near-field finite geological region is located on. The 3D hybrid computational tool is based on the boundary element method (BEM) for the far-field layered zone and the finite element method (FEM) for the finite near-field domain. The model for the semi-infinite layered zone is further extended by the incorporation of a new condensation algorithm which makes it possible to handle 3D wave propagation through arbitrary layered half-space. The condensation algorithm is developed to avoid high computational memory cost while retaining the compatibility with the hybrid FEM-hosted procedure which facilitates the useful solution for the practical three-dimensional engineering problems. The BEM model of the dynamically active far-field zone is inserted as a macro-finite element (MFE) in the FEM commercial program ABAQUS. The accuracy and convergence study of the hybrid numerical scheme is presented. Numerical simulations convincingly illustrate that the dynamic response of structure-soil-structure system depends on different key factors and their mutual interplay. These factors are arbitrary layering of the far-field geological zone, the characteristics of the dynamic source, the site effects phenomena, the structure-soil-structure dynamic interaction, the type and geometrical disposition of foundations and structures and the 3D features of the dynamic motion.