Denpasar City faces increasing flood risks due to rapid urbanization and population growth (0.12% per year; density 5,870 people/km²), which reduce infiltration areas, while Nusa Penida experiences chronic drought influenced by El Niño–Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD), threatening Bali’s tourism sector that contributes approximately 60% of regional GDP. This imbalance in water resources requires an integrated, adaptive approach to water conservation. This study aims to develop a sustainable rainwater harvesting (RWH) model by integrating geospatial analysis, hydrological assessment, and the local wisdom of Tri Hita Karana (THK). Rooftop rainwater harvesting systems were installed on Nusa Penida to address water scarcity in karst areas. In contrast, infiltration wells were installed in Denpasar to reduce surface runoff and enhance groundwater recharge. The results indicate that rainwater harvesting in Nusa Penida generates a surplus of approximately 184.9 million litres, covering about 16% of total domestic water demand. In Denpasar, infiltration well effectiveness ranges from 23.26% to 59.91%, with lower effectiveness observed in South Denpasar due to shallow groundwater levels (±1.5 m). These findings demonstrate that a GIS-based RWH system integrated with Tri Hita Karana values provides a practical, context-sensitive solution to address water inequality in Bali. The proposed model supports green economy-based water conservation policies and offers a replicable framework for sustainable water management in tropical island regions.