© 2019, The Author(s), under exclusive licence to Springer Nature Limited. Water resources worldwide are under severe stress from increasing climate variability and human pressures. In the tropical Andes, pre-Inca cultures developed nature-based water harvesting technologies to manage drought risks under natural climatic extremes. While these technologies have gained renewed attention as a potential strategy to increase water security, limited scientific evidence exists about their potential hydrological contributions at catchment scale. Here, we evaluate a 1,400-year-old indigenous infiltration enhancement system that diverts water from headwater streams onto mountain slopes during the wet season to enhance the yield and longevity of downslope natural springs. Infiltrated water is retained for an average of 45 d before resurfacing, confirming the system’s ability to contribute to dry-season flows. We estimate that upscaling the system to the source-water areas of the city of Lima can potentially delay 99 × 106 m3 yr−1 of streamflow and increase dry-season flows by 7.5% on average, which may provide a critical complement to conventional engineering solutions for water security.