An isotope and solute evaluation was applied to identify the origin and mechanisms of groundwater salinization in three major Tertiary aquifers in the Rub’ al Khali topographic basin. We demonstrate that the groundwater chemistry evolved from a low- (1800 ppm) to high- (>120,000 ppm) salinity Na–Cl water type, regardless of the aquifer. The similarity in water types between the groundwater from the different formations suggests that the same origin and geochemical processes may be controlling the salinity and major ion chemistry in these aquifers. The suite of hydrogeological, hydrochemical (Cl vs. Br), and isotopic (Cl vs δ18O and Br vs δ81Br) data indicates that the source of solutes is associated with the entrapment of evaporated paleo-seawater (connate water) in nearshore and lagoonal environments during the time of deposition. Moreover, the results from the 87Sr/86Sr ratios show no evidence of significant vertical connectivity between the three Tertiary aquifers. Instead, the data support that evaporated paleo-seawater was trapped in each aquifer individually during the time of deposition, and that each has evolved similarly through water-rock and redox reactions. The stable isotopic compositions of δ18O, δ2H, and 14C show that the entrapped paleo-seawater was partially flushed out by fresh meteoric water during the Late Pleistocene and Early Holocene periods.