At present, a high scientific interest is directed to the doctrine of the geological evolution of the interaction between groundwater and rocks. This is explained by the fact that the water-rock system is all-encompassing and its geological evolution leads to the formation of numerous geochemical types of natural waters and various secondary mineral formations, including weathering crusts, hydrothermally altered rocks, various mineral deposits, etc. The work purpose is to identify trends in the processes of interaction between groundwater and rocks in the framework of modeling the processes of secondary mineral formation for drinking groundwater. The aquifers of interstratal waters of the Lower Sarmatian, Middle Sarmatian and Upper Cretaceous deposits, which are widely and intensively used for centralized water supply of settlements and economic objects of the country, were chosen as representative objects for this research. The methodology of studying geochemical processes in the water-rock system is based on the methods of equilibrium thermodynamics of hydrogeochemical processes and the analysis of elementary reactions, the initial products of which are the main rock-forming minerals and water, the final products are secondary minerals, as well as ions and neutral molecules that have passed into the liquid phase. Calculations of ionic equilibria were carried out using the HydroGeo software package developed by M. Bukaty. To determine the degree of groundwater saturation with various minerals, we used the methodology of constructing mineral stability fields developed by R. Garrels and C. Christ. Having analyzed the equilibrium - non-equilibrium state of the system, it can be argued that the primary aluminosilicates (anorthite, analcime, K-feldspar, pyrophyllite, etc.) are not in equilibrium with the groundwater aquifers of Moldova and they are dissolved in these conditions with the formation of secondary minerals (gibbsite, kaolinite, montmorillonite, illite, calcite, etc.). Thus, a significant part of the chemical elements entering the solution due to the incongruent primary minerals dissolution is bound by secondary products, while the other part (mobile elements) is concentrated in the solution. Studies of this direction should be continued due to the wide distribution of soda groundwater and the formation of unique secondary mineral formations.