The calculation modeling results of the nitric hydrotherms saturation in Baikal Rift Zone with calcite and dolomite are presented. The calcite and dolomite make the carbonate barrier to thermal waters equilibrium with primary minerals of igneous rocks. In the research territory, there are three main types of geochemical thermal waters which are characterized by the saturation degree with the calcite and dolomite and the proportion of precipitating minerals phases. It has been established that nitric thermal waters-rock system has equilibrium with these minerals, which leads to bonding migrated from the rocks calcium and magnesium by the secondary formed minerals - calcite and dolomite.