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During the third global coral bleaching event in 2016, the Maldives experienced elevated water temperatures, inducing coral bleaching. We recorded the bleaching intensity and mortality of coral communities in different habitats, depths and wave exposure conditions around North Ari Atoll in the central Maldives to investigate the effect of physical and biological factors that may contribute to bleaching avoidance, resistance and recovery. Approximately 50% of coral cover bleached and similar to 20% died, with significant variation with wave exposure and depth. Deeper wave-exposed reefs were dominated by bleaching resistant massive and encrusting growth forms and experienced less thermal stress than shallow sheltered reefs. Shallow sheltered reefs showed rapid recovery from the previous mass-bleaching event in 1998, regaining high coral cover dominated by branching and tabular growth forms by 2015. However, these bleaching-sensitive growth forms experienced high bleaching and mortality in 2016, causing greater coral loss. Several of the reefs in central Ari Atoll simultaneously experienced a crown-of-thorn starfish (COTS) outbreak, resulting in very degraded reefs that lacked any apparent resilience in 2017. Our findings demonstrate the complex interactions between different components of resilience. In this case, wave exposure and depth appeared to promote avoidance and resistance of corals to bleaching, but reduced their recovery potential, while the reverse was true for shallow sheltered reefs. The resilience of reefs in the Maldives to date appears to be the result of low thermal and anthropogenic stress; therefore, their future condition will depend on the frequency and intensity of bleaching events and the level of human pressures such as construction and fishing.