Declining natural resources have contributed to a cultural renaissance across the Pacific that seeks to revive customary ridge-to-reef management approaches to protect freshwater and restore abundant coral reef fisheries. We applied a linked land–sea modeling framework based on remote sensing and empirical data, which couples groundwater nutrient export and coral reef models at fine spatial resolution. This spatially explicit framework simultaneously tracks changes in multiple benthic and fish indicators as a function of community-led marine closures, land-use and climate change scenarios. We applied this framework in Hā‘ena and Ka‘ūpūlehu, located at opposite ends of the Hawaiian Archipelago to investigate the effects of coastal development and marine closures on coral reefs in the face of climate change.