Across the Pacific Islands, declining natural resources have contributed to a cultural renaissance of customary ridge-to-reef management approaches. These indigenous and community conserved areas (ICCA) are initiated by local communities to protect natural resources through customary laws. To support these efforts, managers require scientific tools that track land-sea linkages and evaluate how local management scenarios affect coral reefs. We established an interdisciplinary process and modeling framework to inform ridge-to-reef management in Hawai‘i, given increasing coastal development, fishing and climate change related impacts. We applied our framework at opposite ends of the Hawaiian Archipelago, in Hā‘ena and Ka‘ūpūlehu, where local communities have implemented customary resource management approaches through government-recognized processes to perpetuate traditional food systems and cultural practices. We identified coral reefs vulnerable to groundwater-based nutrients and linked them to areas on land, where appropriate management of human-derived nutrients could prevent increases in benthic algae and promote coral recovery from bleaching.