El Niño, the warm phase of the ENSO cycle, involves ocean-climate anomalies in the tropical Pacific Ocean and in the extratropics, which frequently result in heavy rainfall episodes along the equatorial and subtropical regions of western South America. Here, we investigate meteorological mechanisms producing heavy rains, floods and debris flows along the less-known hyperarid coasts of southern Peru and northern Chile, to evaluate the paleoclimate significance of Holocene debris flow deposits. Our results reveal that heavy rainfall over the coast of southernmost Peru occurs either during austral summer, at the mature stage of El Niño in connection with warmer sea surface temperatures and anomalous jet streams off northern Chile, or during the previous austral winter spring associated with equatorward-shifted Pacific South America (PSA) atmospheric teleconnection patterns. At Antofagasta, in northern Chile, such events occur almost exclusively in the latter season when deeper PSA-related anomaly poles extend their influence equatorwards beyond central Chile. During non-El Niño conditions short-lived heavy rainfall episodes in southernmost Peru can be associated with similar, albeit weaker or less persistent, circulation anomalies. In addition to that, a seasonally-enhanced low-level southerly flow provides orographic uplift (rainfall-favourable conditions) by the Andes at the 18 °S coastal bend. Ultimately, the trigger for rainfall events in all seasons and phases of the ENSO cycle was invariably connected with mid-troposphere wave disturbances from mid-latitudes. The chronostratigraphy of debris flow deposits from both areas and its comparison with other paleoclimate records at the western side of the Andes, suggests that the ENSO-related teleconnection patterns operated only during the second half of the Holocene, supporting an onset of modern El Niño manifestations at 5300 5500 cal BP and increased frequency of major events during recent times. We suggest that several debris flows dated between 12,900 and 8400 cal BP in southernmost Peru, previously interpreted as an indication of strong El Niño events, were associated with short and intense heavy rainfall episodes similar to those described here during the late winter spring season in non-El Niño conditions, concomitant with stronger low-level southerlies, strengthened South-Eastern Pacific Subtropical Anticyclone and intensified coastal upwelling.