Two environmental problems affect the Venice area: subsidence, which has been increasing due to the intensive water abstraction after the Second World War, and contamination of the soil and shallow aquifers. In order to address these problems, which are decisive factors in the entire Venetian ecosystem, the aquifer structure must be known in detail. The lithologic data are abundant and of good quality up to a depth of 50 m, whereas boreholes beyond this depth are much rarer and more dispersed, making their associated lithological data unreliable. This work, which uses the available data together with fast and low cost passive seismic measurements, provides an improved understanding of the deeper hydrogeologic domain. For this purpose, a MATLAB package (Modalstrata) has been developed to improve the correlation of the stratigraphic succession for each selected homogeneous sub-area and applied to obtain a new, upgraded hydrostratigraphic model. The horizontal to vertical spectral ratio passive seismic surveys have confirmed the lateral correlations among the sample areas at least for the two main aquifer horizons. Analysis and comparisons of several previous studies performed on the data related to the only drilling continuous coring 951 m deep in the Tronchetto Island (Venice), have allowed a satisfactory validation of the proposed hydrogeological model.