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The origin of waters from small springs located at the hyper-arid northern coast of Chile, in the vicinity of Antofagasta, is discussed after hydrogeochemical and isotopic studies and supported by groundwater flow hydrodynamic considerations. Spring water is brackish to saline, with electrical conductivity ranging from 2 to 25 mS/cm. Chemical and water isotope data (O-18 and H-2) show that the rainfall events that produced part of the recharge could correspond to wetter conditions than at present. Their origin could be related to the emplacement of warm sea currents facing the coast of northern Chile, possibly associated to incursions of El Nino Southern Oscillation (ENSO). Radiocarbon dating and preliminary groundwater hydraulic calculations indicate that these spring waters could be remnants of a more significant recharge in the Cordillera de la Costa than that produced today during the less arid period about 5,000 to 3,000 years ago. The exception is Las Vertientes spring which is the only one that receives water transferred from the Central Depression. The springs are the visible discharge of a regional groundwater body in the very low permeability Cordillera de la Costa, whose hydraulic conductivity decreases downward and flow is dominantly though fissures and storage in the low porosity rock matrix.