The Quaternary is characterized by the occurrence of significant climate oscillations that led to noticeable sea-level changes. On the basis of hydrochemical indicators, the origin of the water salinity in the semi-confined aquifer in the region of the middle Río de la Plata estuary, Argentina is determined. Exploration wells were drilled and sediments were sampled for mineralogical analysis alongside water samples collected to determine major and minor ions and environmental isotopes in the aquifer. The Plio-Pleistocene fluvial sands in which the aquifer occurs are mainly composed of grains of quartz, feldspar, and mafic minerals. The water chemistry shows Na-Cl facies with a marked increase in salinity towards the Río de la Plata. The δ 18O vs. δ 2H, Br− vs. Cl−, and δ 18O vs. Cl− ratios clearly trend towards seawater. Minor ions, such as Si, Sr, Li, Se, Br, and Rb, were the result of the prolonged interaction between the water that occurs in the aquifer and the mineral components of its matrix. The hydrogeochemical data show the marine origin of the saline water and that the hydrogeological evolution of the area during the Quaternary is as a result of sea-level oscillations.