Glaciers in the Vilcanota Range (Cusco, Peru) have shrunk by over 40% since 1990, leading to significant reductions in dry-season streamflow (22–35%) and growing risks to water security for Andean communities. This study combines remote sensing (Landsat, Sentinel-2), hydrological modeling (SWAT), and qualitative analysis of 50+ community interviews to assess coupled glacier–water–society dynamics. Findings reveal four key Quechua adaptation strategies: modernization of terraced irrigation systems, use of rain-fed ponds and spring management, community-based water governance, and native seed recovery programs. These practices reflect ancestral hydrological knowledge adapted to a changing climate. The research emphasizes the importance of integrating Indigenous knowledge with scientific data to support resilient water governance in glacier-fed mountain regions. Recommendations include formal recognition of Indigenous water frameworks, co-managed glacier monitoring systems, and reinvestment of ecotourism revenues into watershed restoration.