Sedimentary materials enclosed in basins modify the ground motion by energy trapping, resonance and surface wave generation at the basin edge. In general, the effects of basin presence are approximated by amplification factors (AF), focusing directly on the horizontal components of ground motion. The current study presents a coupled framework to assess the impact of basin effects on the seismic damage of a nonlinear structure. Using the Domain Reduction Method (DRM), a complete time-analysis from the earthquake source, at a regional scale, to an infrastructure, at a local scale is performed. The numerical wave propagation simulation uses a coupled 3D SEM-FEM approach including non-linearities and soil-structure interaction. With the results is possible to correlate the amplification factors obtained from ground motions and the associated damage of the structure. The findings indicate that basins' effect on structural damage may be estimated in a simplified form using a combination of a structural behavior predictor and AFs derived from the free-field ground motions. However, these factors should be correctly predicted, including both basin and source variability.