3D geological models increase our understanding of the subsurface structures and the spatial distribution of sediment’s properties. The models can be applied in different aspects of geology and assist in reaching to more robust conclusions. In this study, a methodology for constructing a 3D geological model of the Tymbakion basin, Crete, Greece, is presented. The model is based on a dense array of newly acquired Transient Electromagnetics measurements (TEM), legacy Vertical Electrical Soundings (VES), and well data that cover an area of approximately 35 km2 and 500 m in depth. The model is representative of the Plio-Quaternary section, which hosts the Tymbakion shallow aquifer. The study area is one of the main agricultural sites of Greece with touristic activity. The model reveals the existence of 12 faults, which are not observed on the surface, and provides the lithological and resistivity distribution on the subsurface. The importance of the model relies in the fact that it gives a better insight into the hydrogeological setting of the shallow aquifer and the problems related to the intensive water exploitation during the last decades.