A geophysical survey was performed at selected locations of Mt. Oiti and Mt. Kallidromon characterized by the hosting of priority habits of Mediterranean temporary ponds and the threatened plant species of Veronica oetaea, in order to understand the geoenvironment and contribute to the conservation of biodiversity. Primarily, the formation of these seasonal ponds, where Veronica oetaea occurs, seems to depend exclusively on the local hydrogeological regime. Thus, we investigated the subsurface structure of "Livadies" and "Nevropolis" ponds with the application of Electrical Resistivity Tomography for high accuracy information and Vertical Electrical Sounding for deeper data acquisition. Four ERT sections and 15 geoelectrical soundings in total were carried out. The combined results of their processing revealed differences at the geological structure beneath the ponds locations. At "Livadies" pond (Mt. Oiti), two geoelectrical layers were distinguished both corresponding to a folded flysch succession, contributing to the formation of this pond. On the contrary, at "Nevropolis" pond two geoelectrical layers were identified and interpreted as a surficial soil deposit stratum covering the geomorphological karst structure of a polje, created on the underlying limestones. The combined geophysical research offered significant data for the formation and the hydrogeological status of the priority habitats.