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The hyperarid core of the Atacama Desert possesses important reserves of "fossil" or ancient groundwater, yet the extent and timing of past hydrologic change during the late Quaternary is largely unknown. In situ and/or short-distance transported leaf-litter deposits abound along relict fluvial terraces inserted within four dry and unvegetated valleys that drain into the endorheic basin of Pampa del Tamarugal (PDT, 21 degrees S, 900-1000 m), one of the largest and economically important aquifers in northern Chile. Our exceptional archive offers the opportunity to evaluate the response of low-elevation desert ecological and hydrological systems to late Quaternary climate variability. Three repeated expansions of riparian/wetland ecosystems, and perennial rivers occurred along the southernmost PDT basin between 17.6-14.2 ka, 12.1-11.4 ka and from 1.01-0.71 ka. Both early and late archaic archaeological artefact are present in clear association with our fossil riparian/wetland assemblages, which suggests that these palaeoenvironmental changes facilitated past human occupations in the hyperarid core of the Atacama Desert. Using modern analogues, we estimate that these ecological and hydrological changes were triggered by a threefold increase in rainfall along the headwaters of what are presently inactive canyons. Comparisons with other regional palaeoclimatic records from the central Andes indicate that these changes were synchronous with the widespread pluvial stages now termed the Central Andean Pluvial Event (CAPE- 17.5-14.2 ka and 13.8-9.7 ka). In addition, we summarize new evidence for perennial runoff, riparian ecosystems and a major human settlement during the latest Holocene. Our findings clearly show that local hydrological changes in the PDT were coupled with precipitation variability in the adjacent eastern highlands during the late Quaternary. The long-term dynamics of low-elevation desert ecological and hydrological systems are likely driven by changes in moisture sources, with one source tied to the Amazon region (N-NE mode) and the other to the Gran Chaco region (SE mode). We conclude by linking ENSO-like variability and moisture variations over the Gran Chaco to the three major regional-scale recharge events over the last 18 ka in the PDT basin. We conclude by asserting that an important portion of the groundwater resources in the PDT is indeed fossil, inherited from past pluvial events. We recommend that the relationship between ancient recharge, together with palaeoclimate records of past headwater rainfall fluctuations should be incorporated into future water-balance models and evaluation of groundwater potential in northern Chile. (C) 2012 Elsevier B.V. All rights reserved.