In arid and semiarid coastal areas, freshwater resources are scarce and are frequently affected by salinization processes. The aim of this work is to evaluate the influence of Late Quaternary climatic events on the hydrogeologic characteristics conditioning the distribution of fresh, brackish, and saline ground water in the Holocene and Pleistocene beach ridges in coastal aquifers of northern Patagonia. To achieve this, geologic, geomorphological, geophysical, hydrochemical, and isotopic studies were carried out, which allowed the identification of the hydrolithologic characteristics controlling groundwater salinity in a context of Quaternary geologic–geomorphological–climatic evolution. In Pleistocene beach ridges, it was recognized that the formation of calcretes in an arid period after Marine Isotope Stage (MIS) 5e conditioned the permeability of superficial sediments, strongly decreasing infiltration rates. During the Holocene, beach ridges were deposited and sea water entered the Pleistocene ridges. Subsequently, with the sea-level drop and wetter climatic conditions, rainwater began to infiltrate, recharging the aquifers and displacing seawater, allowing development of freshwater lenses. However, freshwater lenses only developed in Holocene ridges due to the lower permeability of Pleistocene ridges, which determines that in these geoforms, sea water cannot be displaced by rainwater, and therefore groundwater is brackish to saline.