The phenomenon of mud volcanism has a connection with the processes of hydrocarbon generation, however, the genesis of sediments is not often taken into consideration. The study of mud volcanoes in the West Kuban marginal marine basin and the Junggar freshwater basin revealed significant isotope-geochemical differences due to various types of sedimentation. The waters from both basins exhibit three principal geochemical facies: Na-HCO
3, Na-Cl-HCO
3, and Na-Cl, of which the latter type of water is the dominant. The analysis of genetic coefficients (Cl/Br, Na/Br, and B/Cl) allowed us to distinguish different pathways of mud volcanic water evolution: evaporite dissolution, formation (sedimentation) waters, and waters formed by active water-rock interaction. Through statistical research, we were able to determine that noticeable variations in the behavior of chemical elements in waters from different areas can reflect discrepancies in the geological environment and the evolutionary stage of the diagenetic water transformation. Using thermodynamic modeling, the main directions of mass transfer were shown. It was established that the waters of the Junggar basin were at a relatively early stage of evolution and had reached equilibrium only with carbonates, while in the formation waters of the West Kuban basin, element concentrations were also controlled by silicate minerals. The correlations between δ
18O and δ
2H values and saturation indices of halides, aluminosilicates, sulfates, and borates confirm the enrichment of water with heavy isotopes during interactions with rocks without evaporation or thermal water partition. These reactions are characterized by clay dehydration and water enrichment with
18O and B. The data obtained made it possible to clarify the depths of formation of mud-volcanic fluids and their possible stratigraphic sources.