—The paper presents results of the pioneering study of equilibria in the water–gas system by the example of Jurassic–Cretaceous deposits of the Yamal–Kara depression located within northern West Siberia and its Arctic regions. Numerical modeling of physicochemical equilibria and evasion–invasion processes in the water–gas system allowed determination of the degree of groundwater saturation with gases and the nature of diffusive redistribution of gases in the media that form at the hydrocarbon deposit–groundwater contact. According to the degree of water saturation with gases (Kg), aquifers with poorly (<0.2) to ultimately (0.8–1.0) gas-saturated waters have been established. The revealed increase in the degree of groundwater saturation with gases in sinking producing reservoirs reflects its dependence on their total gas saturation. All waters with a total gas saturation of more than 1.8 L/L become ultimately saturated with gases (Kg = 1.0), thus theoretically predetermining the formation of hydrocarbon accumulations. Major gas condensate deposits are confined to the zone of gas-saturated waters with Kg from 0.8 to 1.0, while oil accumulations, to waters with lower gas saturation. Based on the established nature of water–gas, we can argue that oil and gas accumulations in Jurassic–Cretaceous reservoirs act as a conservative element of the lithosphere, i.e., its geologic and geochemical “relics”. The surrounding subsurface waters, as a more active constituent of the system, have largely anticipated its geochemical development, which is manifested in the differentiation of the fugacity ratios of individual gases in groundwater and hydrocarbon accumulations. The composition of the latter is therefore subjected to slow directional changes while the equilibrium is established, to usher in the qualitatively new state of the geochemical water–gas system.