Among induced mass-mortality events on coral reef, extreme low tides may ultimately lead to considerable reef community deaths on intertidal reef flats due to unusually long and significant aerial exposure. Here, we report an extensive coral mortality event induced by a negative sea level anomaly (nSLA) that occurred across Reunion Island during the austral winter season between June and October 2015 preceding the 2015–2016 El Niño Southern Oscillation (ENSO) event. The nSLA was strong and long in duration with a rapid drop of 35 cm in the mean sea level over a one-month period. Surveys conducted over seven reef flat sites before and after the nSLA revealed that mean coral cover drastically decreased from 54.5 ± 12.7% in early 2015, to 27.4 ± 6.9% in November 2015, which is an equivalent cover loss of 50% following the 2015 nSLA event. The shallowest sites showed a greater decrease in coral cover while the deepest parts of the reef flat remained unaffected. We found a significant correlation between the bathymetry and the relative coral cover variation. Using this relationship between depth and coral cover changes, high-resolution hyperspectral imagery and Lidar bathymetric airborne data, we mapped the impacts of this event at the scale of the whole reef. Overall the modeled loss reached 13.0 ha, which represents a decrease of 45.5% of all live coral cover in this area during the 2015 nSLA event. The impact of a nSLA on emersion times is much greater than the regular variation in tide amplitude between neap and spring tides, reaching new bathymetric ranges that are usually stable in terms of water submersion. Temporal variation of coral cover on Reunion Island reef flat revealed regular decreases to be compared with mean low-water-level events among other sea and climatic related disturbances and stressors.