Neogene formations display complex structure, and host confined aquifers that are alternated, and very often interrupted by impermeable clay layers. In many cases, the lack of hydrogeological information and data on those aquifers hinders research and planning of exploitation projects. This study attempts to exploit the available information that can be derived from a sampling, and the corresponding chemical analyses, to reconstruct the hydrogeological image of such areas. Thus, the chemical composition is used as a tool for natural tracing of the groundwater origin and movement in a previously unknown environment such as that of Ilia region, which was selected as the application area. The distribution maps of certain hydrochemical parameters, combined with the appropriate hydrochemical and isotopic data, contributed to the classification of the groundwater samples by linking the hydrochemical processes with the samples' locations as well as the origin of the aquifers' recharge water. At the same time, the effectiveness of the used methodology was evaluated. The use of R-mode factor analysis led to the determination of the basic hydrochemical processes that shape the groundwater quality. The analysis showed that the reducing environment is the defining factor that regulates the presence of the various chemical compounds. Finally, the conceptual model of the aquifers emerged from the analysis of all the data. This analysis also pointed out that the recharge of the local aquifers takes place mainly through the river beds and laterally from their contact with the carbonate rocks.