—Results of studies of soda waters of the Chulym–Yenisei artesian basin are presented. It is shown that these waters are ubiquitous within Cretaceous or Jurassic sediments at depths of ~100–300 m to 1.5–2.3 km. According to the formation conditions, mineralization, and pH, they are divided into three groups: Type I waters spread to a depth of 600 m and have pH = 7.4–8.4 and TDS ≤ 0.5 g/L, type II waters occur at depths of 0.6–2.3 km and are characterized by pH = 8.0–8.9 and TDS = 0.7–4.1 g/L, and type III waters (“Omega”) form a local segment among type II waters and have a unique composition: high alkalinity (pH = 9.0–10.3) and low mineralization (TDS = 0.2–0.6 g/L). We focus special attention on type III waters and present results of studies of their microcomponent, gas, and isotope compositions. The cause of their low salinity and high pH is explained for the first time. Taking into account the isotope data (δD, δ18O, and δ13C), we have established the infiltration origin of soda waters of the three types and the biogenic source of their carbon dioxide. Calculations of equilibria in the water–host-mineral system have shown that all soda waters are in disequilibrium with many primary aluminosilicate minerals but are in equilibrium with a wide range of carbonates and clays. In passing from type I to type III waters, the number of minerals in equilibrium with water continuously increases (albite, microcline, muscovite, and biotite). Taking into account the data obtained, we present schemes of formation of different types of soda waters in the studied basin at different stages of the evolution of the water–rock– gas–organic-matter system and estimate the time of each stage.