The Permian–Mesozoic cover of the Western European Platform includes numerous aquifers containing mineralized water. An attempt has been made to determine both the genesis of water from the Jurassic formations of the Marginal Trough (tectonic unit in the Zechstein–Mesozoic structural floor, located in central Poland) and the processes to which they were subjected. The results of archival chemical analysis of waters from deep boreholes located in the Marginal Trough have been studied. Hydrogeochemical ratios of Na/Cl, Cl/Br, (SO 4 × 100)/Cl, HCO 3 /Cl and Na/(Ca + Mg), together with their variability depending on water depth, were presented and discussed. The majority of waters from the Jurassic formations are Na–Cl waters, typical for areas isolated from hypergene zones. Their mineralization is closely related to the depths of the Jurassic formations. The analyses of hydrochemical parameters of the Jurassic waters have shown that the vast majority of these waters are brines or chloride waters, genetically related to seawater. The diversity in mineralization and hydrochemical parameters, together with their dependence on the depth of occurrence of the analysed waters, indicate that waters from the Lower Jurassic formations originate from isolated geological structures, while the Middle and Upper Jurassic waters are/or were affected by infiltration waters.