In this study, the influence of the 3D local geology and seismic directivity on the synthetic earthquake ground motion prediction is assessed on a real site. The studied site is located at Kefalonia Island (Greece). This site is well characterized and instrumented by several sensors. The numerical model of the earthquake scenario of the affected area is built-up and three small point-wise are simulated, changing the relative source-site position. Broad-band (0-5 Hz) synthetic wave-forms are obtained considering the the presence of the 3D sedimentary basin of Koutavos. The different site amplification corresponding to three sources highlight the strong dependency on the wave direction. The impact of the sedimentary failures is also quantified at two different stations located inside and outside the basin.