Coral reefs around the world are increasingly threatened by marine heatwaves causing widespread coral bleaching and mortality. Global analyses of projected heatwaves can inform decision-making, but forecasting the interactions between disturbance refugia, coral life histories and capacity to adapt is key for guiding strategic management of coral persistence. Here, we simulate coral eco-evolutionary dynamics across 3800 reefs of Australia’s Great Barrier Reef under current climate projections. We project a rapid coral decline by mid-century under all emission scenarios, with further decline under the most likely warming trajectory. However, recovery is possible this century if warming remains below 2 °C, allowing thermal adaptation to keep pace. Our simulations show that resilient reefs are primarily in bleaching refugia, which also support a greater diversity of thermal phenotypes. While cool-adapted corals disperse to warm spots, we found no evidence of ‘gene swamping’ undermining thermal adaptation. Our findings highlight that management opportunities exist to promote adaptation in thermal refugia and warm spots, but emphasize that curbing global warming by 2050 is crucial for coral persistence.

Novel tools and methods for monitoring marine environments can improve efficiency but must not compromise long-term data records. Quantitative comparisons between new and existing methods are therefore required to assess their compatibility for monitoring. Monitoring of shallow water coral reefs is typically conducted using diver-based collection of benthic images along transects. Diverless systems for obtaining underwater images (e.g. towed-cameras, remotely operated vehicles, autonomous underwater vehicles) are increasingly used for mapping coral reefs. Of these imaging platforms, towed-cameras offer a practical, low cost and efficient method for surveys but their utility for repeated measures in monitoring studies has not been tested. We quantitatively compare a towed-camera approach to repeated surveys of shallow water coral reef benthic assemblages on fixed transects, relative to benchmark data from diver photo-transects. Differences in the percent cover detected by the two methods was partly explained by differences in the morphology of benthic groups. The reef habitat and physical descriptors of the site—slope, depth and structural complexity—also influenced the comparability of data, with differences between the tow-camera and the diver data increasing with structural complexity and slope. Differences between the methods decreased when a greater number of images were collected per tow-camera transect. We attribute lower image quality (variable perspective, exposure and focal distance) and lower spatial accuracy and precision of the towed-camera transects as the key reasons for differences in the data from the two methods and suggest changes to the sampling design to improve the application of tow-cameras to monitoring.