Coral reef ecosystems are being fundamentally restructured by local human impacts and climate-driven marine heatwaves that trigger mass coral bleaching and mortality. Reducing local impacts can increase reef resistance to and recovery from bleaching. However, resource managers lack clear advice on targeted actions that best support coral reefs under climate change and sector-based governance means most land- and sea-based management efforts remain siloed. Here we combine surveys of reef change with a unique 20-year time series of land–sea human impacts that encompassed an unprecedented marine heatwave in Hawai‘i. Reefs with increased herbivorous fish populations and reduced land-based impacts, such as wastewater pollution and urban runoff, had positive coral cover trajectories predisturbance. These reefs also experienced a modest reduction in coral mortality following severe heat stress compared to reefs with reduced fish populations and enhanced land-based impacts. Scenario modelling indicated that simultaneously reducing land–sea human impacts results in a three- to sixfold greater probability of a reef having high reef-builder cover four years postdisturbance than if either occurred in isolation. International efforts to protect 30% of Earth’s land and ocean ecosystems by 2030 are underway. Our results reveal that integrated land–sea management could help achieve coastal ocean conservation goals and provide coral reefs with the best opportunity to persist in our changing climate.