This paper presents a novel numerical modelling approach to physicochemical evolution of water – rock interactions in Upper Jurassic sediments in the Nadym–Taz interfluve (Arctic regions of Western Siberia). The results show that the authigenic mineral formation proceeds continuously and strictly successively (kaolinite – montmorillonite – illite – mica – chlorite – albite – microcline), involving definite geochemical parameters of the medium (pH, concentrations of SiO2, Al, Na, K, Ca, Mg in solution). For example, the widely spread kaolinite cement forms in the medium with near neutral pH (on average, рH = 7.2) with silica concentration in solution 15–20 mg/dm3, while the formation of authigenic illite begins at silica concentration of 25–40 mg/dm3 and pH about 7.3–7.4. Despite rather low salinity (up to 63 g/dm3) of the investigated groundwater and long-term interaction of water with the rocks (spanning ca. 165 Ma), the equilibrium with primary (endogenous) minerals such as albite, anorthite, microcline is practically unobserved. At the same time, the groundwater is in equilibrium with mica, illite, Ca–, Na– and Mg–montmorillonites, kaolinite, more rarely with Mg–chlorite. The state of groundwater equilibrium with primary aluminosilicate minerals is always challenged by a carbonate barrier, so rocks carbonatization in various degree is observed almost everywhere.