The response spectra of multidimensional analyses are compared with the one-dimensional (1D) local models to couple the irregular soil stratification effect in a site. In recent studies, the surface motion spectra ratios of 2D/1D or 3D/1D are defined as spectral aggravation factors for each region in a site. Particularly in alluvial basins, where the soil media is typically formed by fault ruptures or topographic depressions filled with sediments, the inclination of the rock outcrop in the edge of the basin has a considerable effect on the site response, and such effect has not yet been taken into consideration of recent seismic building codes and general engineering applications. In this study, the natural alluvial basin near the North Anatolian Fault in Gemlik, Maramara Region, Turkey, was investigated by 40 seismic site tests and 4 validation borings. The 2D and 1D nonlinear response history analyses in north-south and east-west directions of the Gemlik basin were performed by numerical model on finite difference scheme considering nonlinear elasto-plastic material behaviors and geometric discontinuities. 22 strong ground motions recorded on rock site are excited vertically as SH waves. The numerical results exhibited the narrow basin effects are derived not only by reflection, refraction, and shifting behavior but also by focusing and superposition of the seismic waves propagating from both opposite basin edges. As a result, the site-specific spectral aggravation factors, SAF2D/1D defined by the ratio between the 2D and 1D acceleration response spectra for each period and any location on the site, were proposed for the Gemlik basin. The variations of the aggravation factors were observed as increasing values to 1.2–2.2 on the near edge and basin center.