Abstract. The 2015–2016 El-Niño and related ocean warming has generated significant coral bleaching and mortality worldwide. In Indonesia, the first signs of bleaching were reported in April 2016. However, this El Niño has impacted Indonesian coral reefs since 2015 through a different process than temperature-induced bleaching. In September 2015, altimetry data show that sea level was at its lowest in the past 12 years, affecting corals living in the bathymetric range exposed to unusual emersion. In March 2016, Bunaken Island (North Sulawesi) displayed up to 85 % mortality on reef flats dominated by Porites, Heliopora and Goniastrea corals with differential mortality rates by coral genus. Almost all reef flats showed evidence of mortality, representing 30 % of Bunaken reefs. For reef flat communities which were living at a depth close to the pre-El Niño mean low sea level, the fall induced substantial mortality likely by higher daily aerial exposure, at least during low tide periods. Altimetry data were used to map sea level fall throughout Indonesia, suggesting that similar mortality could be widespread for shallow reef flat communities, which accounts for a vast percent of the total extent of coral reefs in Indonesia. The altimetry historical records also suggest that such an event was not unique in the past two decades, therefore rapid sea level fall could be more important in the dynamics and resilience of Indonesian reef flat communities than previously thought. The clear link between mortality and sea level fall also calls for a refinement of the hierarchy of El Niño impacts and their consequences on coral reefs.