The influence of faults and different lithology in the evaluation of possible seismic energy amplification has been studied. The area of Augusta, located in the Hyblean Plateau (south-eastern Sicily), was selected as test site and several ambient noise measurements were carried out with the aim of investigating the local seismic response. Data were gathered both on the main lithotypes outcropping in the study area and along some profiles crossing the Mt Tauro fault, in order to estimate the site response connected to the different geo-lithological features and to investigate on the possible amplification effects caused by the presence of a tectonic structure. The horizontal to vertical (H/V) spectral ratios calculated for the sites located near the fault showed a rough tendency towards amplifications in the frequency band 1.5–2.0 Hz, disappearing with increasing distances from the fault. Significant amplifications were observed at about 0.7 Hz in the sites located on the clays and in all the lithotypes laying on them. Observed dominant spectral peaks have been explained as the resonance of a soft sedimentary sequence overlaying an “equivalent basement” located inside the clayey formation at a depth of 160–290 m, or at the stratigraphic interface separating the clays from the calcareous basement. Finally, the results of 1-D modelling allowed us to delimitate the trend of the Augusta graben at depth.