The hydrological characterization of the vadose zone remains a major challenge considering the spatiotemporal variability of its properties and the limitations associated with hydrological measurements techniques. Geophysical methods, in particular the DC-resistivity and ground penetrating radar, can provide large scale images of hydrogeological structures and a non-invasive assessment of the subsurface dynamic processes. However, these approaches rely on the accuracy of the petrophysical relationships connecting the geophysical parameters to hydrogeological ones, where the site-specific determination of the associated petrophysical parameters is considered crucial. The first objective of this study was to investigate the relationship between the water content, geological properties, and geophysical attributes at the vadose zone of a vulnerable limestone aquifer. The second objective aimed to obtain the Archie’s and Complex Refractive Index Model (CRIM) petrophysical parameters by using borehole electrical resistivity and cross-hole ground penetrating radar data. For this purpose, we adopted a grid search inversion algorithm where the field geophysical data were integrated with water content profiles simulated by using HYDRUS-1D. The vadose zone profile was divided into three layers, and the inversion was carried out for the petrophysical parameters in each of the model layers. The electrical resistivity and relative dielectric permittivity data showed a very good correspondence with the simulated and experimental water content distributions along the vadose zone profile. The petrophysical parameters estimated by the inversion showed values that fall in the ranges reported in the literature. Similar values have been observed in the different model layers, with slight differences that were attributed to the vertical heterogeneities associated with the alteration and fracturation features of the limestone vadose zone. This study showed a very good correlation between geophysical, hydrogeological and geological data, and highlighted the presence of heterogeneities that can have profound effects on the vadose zone water dynamics.