Extreme precipitation events and multi-annual droughts, especially in arid to semi-arid subtropical regions, are among the most critical El Niño Southern Oscillation (ENSO) and global climate change impacts. Here, we assess the variability of torrential rainfall during the Late Holocene and its projection into the 21st century at the southern edge of the hyperarid Atacama Desert. The analysis of historical data since the beginning of the 20th century reveals that most (76.5%) alluvial disasters in the southern Atacama Desert (26–30°S) have resulted from extreme rainfall events occurring between March and September under El Niño conditions, and more frequently during the warm phase of the Pacific Decadal Oscillation. Particular rainfall events under these ocean-climate conditions are associated with the convective phase of the Madden-Julian Oscillation (MJO) near the central-equatorial Pacific, resulting in warmer sea surface temperature (SST) there and in the triggering of persistent/intense Pacific South America (PSA) tropical-extratropical teleconnection patterns which result in blocking of the westerly flow at high latitudes and the subsequent deviation of storm tracks towards central-northern Chile. On a longer timescale, marine sediments from Tongoy Bay (30°S) reveal an increasing trend of stronger runoff by torrential coastal rain since ca. 3500 cal yr BP and even stronger heavy rainfall since ca. 1700 cal yr BP. Highly variable coastal sea surface temperatures in the same time span deduced from the sedimentary record can be explained by intensified southerly winds in connection with stronger alongshore pressure gradients and reduced coastal low-cloud cover. Both storm intensification and increased intensity of upwelling-favorable winds point to a variable climate conditioned by strengthened interannual ENSO and interdecadal ENSO-like variability during the Late Holocene. Climate projections from the Coupled Model Intercomparison Project Phase 5 (CMIP5) indicate a reduction in annual precipitation of 15–30% during the current century, together with an intensification of the storms, such as the alluvial disaster on March 25, 2015 in Atacama. •PSA teleconnection pattern is a conditioning factor for most alluvial disaster in Atacama.•ENSO and ENSO-like conditions modulate the frequency of extreme rainfall events.•Marine sedimentary proxies point to the intensification of torrential rainfall since 3500 cal yr BP.•During the current century we expect increased aridification and heavier rainfall events.