Coral reefs and lagoons worldwide are vulnerable environments. However, specific geomorphological reef types (fringing, barrier, atoll, bank for the main ones) can be vulnerable to specific disturbances that will not affect most other reefs. This has implications for local management and science priorities. Several geomorphologically closed atolls of the Pacific Ocean have experienced in recent decades mass benthic and pelagic lagoonal life mortalities, likely triggered by unusually calm weather conditions lasting for several weeks. These events, although poorly known, reported, and characterized, pose a major threat for resource sustainability. Based on a sample of eleven events on eight atolls from the central South Pacific occurring between 1993 and 2012, the conservative environmental thresholds required to trigger such events are identified using sea surface temperature, significant wave height and wind stress satellite data. Using these thresholds, spatial maps of potential risk are produced for the central South Pacific region, with the highest risk zone lying north of Tuamotu Archipelago. A regional climate model, which risk map compares well with observations over the recent period (r = 0.97), is then used to downscale the projected future climate. This allows us to estimate the potential change in risk by the end of the 21st century and highlights a relative risk increase of up to 60% for the eastern Tuamotu atolls. However, the small sample size used to train the analysis led to the identification of conservative thresholds that overestimated the observed risk. The results of this study suggest that long-term monitoring of the biophysical conditions of the lagoons at risk would enable more precise identification of the physical thresholds and better understanding of the biological processes involved in these rare, but consequential, mass mortality events.