Crystalline aquifers are layered systems in which the hydrogeological path of waters extends from highly weathered, shallow and porous rocks to poorly weathered, deep and fissured rocks. This varying hydrogeological setting influences the water chemistry in different ways. The paper aims to reconstruct the water-rock interaction process in these various environments starting from a solid reactant represented by an average granite rock and several waters from the shallow aquifer. Afterwards, the water-rock interaction processes occurring in the deep environment are reconstructed, varying the geochemical conditions (primary reactants, secondary mineral phases allowed to precipitate, fO2 and fCO2), with a special focus on fluoride (F-). The evolution from the F-poor, Ca-HCO3 facies to the F-rich, Na-HCO3 water type of high pH was simulated using reaction path modelling. The obtained results show that the theoretical evolution trends well reproduce both shallow and deep water samples providing detailed information on the behavior of fluoride and other relevant constituents (i.e., Na, K, Ca, Mg, SiO2). The performed model represents a flexible and powerful tool for environmental research, applicable in other areas hosting F-rich groundwater.