Global warming is dramatically changing diverse coral reef ecosystems through an increasing frequency and magnitude of mass bleaching events. How local impacts scale up over affected regions depends on numerous factors, including patchiness in coral mortality, metabolic effects of extreme temperatures on populations of reef-dwelling species, and interactions between taxa. Here we use ‘before and after’ data to evaluate ecological change in corals, algae, fishes and mobile invertebrates at 186 sites along the full latitudinal span of the Great Barrier Reef and western Coral Sea following the 2016 mass bleaching event. One year post-bleaching, reductions in live coral cover of up to 51% were observed on surveyed reefs that experienced extreme temperatures, but regional patterns of coral mortality were patchy. Consistent declines of coral-feeding fishes were evident at the most heavily impacted reefs, whereas few other short-term responses of reef fishes and invertebrates could be attributed directly to changes in coral cover. Nevertheless, substantial region-wide ecological changes occurred that were largely independent of coral loss, and instead appeared directly linked to sea temperatures. Community-wide trophic restructuring was evident, with weakening of strong pre-existing latitudinal gradients in the diversity of fishes, invertebrates and their functional groups. In particular, fishes that scrape algae from reef surfaces, considered important for recovery following bleaching, declined on northern reefs, whereas other herbivorous groups increased on southern reefs. The full impact of the 2016 bleaching event may not be realised until dead corals erode through the next decade, but our short-term observations suggest that recovery processes, and the ultimate scale of impact, are affected by functional changes in communities, which in turn depend on the thermal affinities of local reef-associated fauna. Such change will vary geographically, and may be particularly acute at locations where many fishes and invertebrates are close to their thermal distribution limits.