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The geochemistry of surface water and groundwater from the Elqui River basin, North-Central Chile, was studied in spring 2007 and fall 2008 to obtain a general understanding of the factors and mechanisms controlling the water chemistry of steep rivers located in mineral-rich, arid to semi arid zones. Besides its uniform intermediate igneous lithology, this basin is known for acid drainage and high As contents in the El Indio Au-Cu-As district, in its Andean head. Abundant tailings deposits are present in the middle part of the basin, where agricultural activities are important. According to the results, the chemical and isotopic composition of the Elqui basin surface water and groundwater is related to uniform calc-alkaline lithology and the major polluting system of the chemically reactive, but closed El Indio mining district. The resulting compositional imprints in surface and ground-water are, (a) high SO4 levels, reaching about 1000 mg/L in the Toro River water, directly draining the mining area; (b) a major depletion of Fe and pollutant metals in surface water after the confluence of the Toro and La Laguna rivers; (c) similar chemical composition of surface and ground-waters that differ in H and O isotopic composition, reflecting the effect of differential evaporation processes downstream of the Puclaro dam; and (d) seasonal variations of Fe, Mn, Cu and Zn in surface water. In contrast, the groundwater chemistry exhibits moderate seasonal changes, mainly in HCO3- content. In spite of the acid drainage pollution, water quality is adequate for human consumption and irrigation. This is a consequence of both the dominant calc-alkaline lithology and the existing arid climate, resulting in neutral to moderately alkaline pH values that are responsible for the precipitation of metal hydroxides and As sorption by Fe(OH)(3). (C) 2013 Elsevier Ltd. All rights reserved.