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Supergene enrichment of Cu deposits in the Atacama Desert has played a critical role in making this the prime Cu-producing province of the world. Previously, this has been believed to have occurred exclusively over a long period from the middle Eocene to the late Miocene, which ended when climatic conditions changed from arid to hyperarid. Here, we report U-series disequilibrium ages in atacamite-bearing supergene assemblages that provide a new conceptualization on both the supergene enrichment process and the onset of extreme hyperaridity in the Atacama Desert. Th-230-U-234 ages of gypsum intergrown with atacamite in supergene veins from Cu deposits cluster at similar to 240 ka (Chuquicamata), 130 ka (Mantos Blancos, Spence), and 80 ka (Mantos de la Luna, Michilla). When coupled with previous data, these results indicate that supergene enrichment of Cu deposits did not cease after the onset of hyperaridity. We propose that supergene enrichment in the Atacama region developed in two main stages. The main phase, caused by downward circulation of meteoric waters in a semi-arid setting, was active from 45 until similar to 9 Ma, with a last pulse ca. 5 Ma in the southern Atacama Desert. During this phase, atacamite-bearing supergene assemblages were not preserved because atacamite requires saline water for its formation and rapidly dissolves when contacted by meteoric water. This was followed by a second stage starting at similar to 2-1.5 Ma and continuing until at least the late Pleistocene, when deep formation waters derived from the basement passed up through and modified the pre-existing supergene Cu oxide minerals. Atacamite has then been preserved in the prevailing hyperarid climate.