Corals are a major habitat-building life-form on tropical reefs that support a quarter of all species in the ocean and provide ecosystem services to millions of people. Marine heat waves continue to threaten and shape reef ecosystems by killing individual coral colonies and reducing their diversity. However, marine heat waves are spatially and temporally heterogeneous, and so too are the environmental and biological factors mediating coral resilience during and following thermal events. This combination results in highly variable outcomes at both the coral bleaching and mortality stages of every event. This, in turn, impedes the assessment of changing reef-scale patterns of thermal tolerance or places of resistance known as reef refugia. We developed a large-scale, high-resolution coral mortality monitoring capability based on airborne imaging spectroscopy and applied it to a major marine heat wave in the Hawaiian Islands. While water depth and thermal stress strongly mediated coral mortality, relative coral loss was also inversely correlated with preheat-wave coral cover, suggesting the existence of coral refugia. Subsequent mapping analyses indicated that potential reef refugia underwent up to 40% lower coral mortality compared with neighboring reefs, despite similar thermal stress. A combination of human and environmental factors, particularly coastal development and sedimentation levels, differentiated resilient reefs from other more vulnerable reefs. Our findings highlight the role that coral mortality mapping, rather than bleaching monitoring, can play for targeted conservation that protects more surviving corals in our changing climate.