We present the results obtained from conventional and non-conventional analysis of 3D high-resolution seismic data acquired nearby the water spring line, which separates the upper from the lower Friuli–Venezia Giulia plain (Italy), in order to characterise an important multilayered confined aquifer. The main targets of this study were two shallow aquifers located at about 30 m and 180 m depth, respectively. The aquifer structures were reconstructed by adopting a technique consisting an iterative updating procedure, for refining and improving an initial model in depth. The method includes pre-stack depth migration, residual move-out analysis and seismic reflection tomography. In the final 3D migrated cubes, two high velocity layers were identified at about 270 m and 480 m respectively, which correspond to unknown deep aquifers, as confirmed by recent well data (stratigraphies and down-hole velocity measurements). Travel-time tomography and Amplitude Versus Offset analysis evidence that seasonal variation in the seismic response of the aquifers are not detectable. However, in this case, aquifers are well detectable by lithological changes.