The aim of this paper is to clarify the extent of near-source effects and non-linear soil response that took place at the Japanese nuclear site of Kashiwazaki-Kariwa, during the MW 6.6 Niigata-Ken Chūetsu-Oki earthquake (July, 16th 2007). The interest of this case study stems from the relative small source-to-site distance and shallow hypocenter depth, coupled with the consistent seismic record database available from two down-hole arrays of strong motion accelerometers, installed within the nuclear site. Records were processed first to highlight those features related to near-source conditions, such as directivity and polarization, and, subsequently, to identify dependence of site response on the direction of motion and on the non-linear soil behaviour. Moreover, borehole interferometry was used to check the two available velocity profiles (estimated by in situ PS logging) used for 1D linear equivalent numerical simulations. In one case, an improved agreement with the empirical amplification functions was obtained using a smoothed profile. The main non-linear features highlighted by signal processing were globally reproduced by means of linear-equivalent analyses, that pointed out the strong influence of the input motion direction. Among the principal results of this research, it was found that the hanging-wall and directivity effects along with the non-linear site-effects dominate the ground response during the main shock, and that the site amplification features are strongly dependent on the rotation angle of the horizontal components.