The Duna-Tisza Interfluve, Hungary, is characterized by patchy surface salinization. However, in the Duna Valley, salinized wetlands appear in a N–S trending continuous zone (Lake Kelemenszék area). The source of the salts is reported to be the overpressured NaCl-type water of the Pre-Neogene basement and the NaHCO3-type water of the Neogene sediments. This “basement and basin origin of salts” concept is based on the strong correlation between the regional distribution of surface salinization and the basinal flow pattern. This study, applying integrated methods, presents hydrogeological evidence for this theory and creates a conceptual model for the salinization. The model reflects that the basement water rises near to the surface through conductive faults crosscutting an extensive aquitard and aquifer. These faults ensure “shortcut”-type water exchange between the basement and the uppermost aquifer. This hydraulic setting generates chemical anomalies in this aquifer up to the surface, producing Na–HCO3–Cl-type water. This water causes extensive surface salinization in those discharge areas where the infiltrating freshwater does not superimpose the upwelling saline water. Where a freshwater lens is located above the ascending saline water, this fresh gravity-driven flow controls the surface distribution of salts, which results in saline patches.