The Atacama Desert in Chile is known to be one of the driest deserts on Earth, with dominating hyperaridity at least since the Miocene. During recent times, however, especially the southern part of the Atacama repeatedly experienced exceptional precipitation events, like in 2015 and 2017. Locally, these events with high rainfall rates caused catastrophic floods with significant destruction and human fatalities. Although the meteorological drivers of these heavy rains are widely understood, only little is known about the frequency and amplitude of similar events on geological timescales. Here we present the results of a study on an endorheic clay pan at the southern edge of the hyperarid core of the Atacama, an area with a mean precipitation of ap-prox. 5 mm per year. A modern ground-truthing approach combining sediment data, remote-sensing and meteorological data as well as climate-modelling was applied. Our observations indicate that the clay pan reacted very sensitively to local precipitation during the past 30 years, with four events >20 mm total rain causing sufficient surface run-off in the catchment to partially flood the basin. Comparative analyses of the four events illustrate that the amount of run-off is dependent on the maximum rain rate during the events rather than the total rain sum. A 1.88-m long sediment core recovered from the centre of the clay pan records the local hydrological and -environmental history since the Late Pleistocene. Sedimentological, mineralogical, geochemical, and biological core analyses imply strong variations in the ampli-tude of the recorded rainfall, with a clear shift from enhanced alluvial activity caused by higher-amplitude rain events during the Late Pleistocene to lower-amplitude Holocene events. The Holocene background sedimentation is superimposed by seven severe “Millennial-scale rain events”, which imply precipitation maxima on sub-orbital timescales that are potentially driven by changes in the El Niño Southern Oscillation (ENSO). The results of the study shed new light on the glacial-interglacial but also the sub-orbital precipitation variability in the Coastal Cordil-lera of the Atacama Desert and its potential driving mechanisms, and provide perspectives of the future precipitation development in the region under progressive global warming.