The management of water resources in hyper-arid coastal regions is a challenging task because proper information regarding groundwater recharge and water budget is needed for maintaining the hydraulic balance in optimal conditions, avoiding salinization and seawater intrusion. Thus, this article deals with the estimation of the hydraulic recharge and the study of the effects of salinization on the dynamics of major and trace elements in an alluvial aquifer located in the world's driest zone, the northern Atacama Desert. The result of stable water isotopes (δD and δ18O) and tritium (3H) indicated that groundwater in the area is not recent, whereas 14C results estimated a groundwater residence time ranging between 11,628 and 16,067 yBP. The estimation of the artificial recharge coming from the urban water-supply-system leaks and wastewater/river-water/groundwater infiltration during irrigation was about 19.84 hm3/year, which represents an annual negative water balance of 177 hm3/year for the aquifer. The groundwater salinization triggered by seawater intrusion (up to 32.6 %) has caused the enrichment of Li, Rb, Ca, Ba, and Sr in groundwater by cationic exchange, where the excess of aqueous Na is exchanged by these elements in the aquifer sediments. Other elements such as B, Se, Si, and Sb are enriched in groundwater by ionic strength and/or anionic exchange during salinization. The heightened B concentrations derived from the B-rich alluvial sediments were higher than the limit suggested by international guidelines, representing a risk to consumers. Vanadium seems to be unaffected by salinization, whereas Pb, Mo, As, U, and Zr did not show a clear behavior during saline intrusion. Finally, this article highlights the consequences of conducting improper water management in coastal hyper-arid regions with exacerbated agriculture.