Distant swells generated by storms in the high latitudes (>40°) can impact islands and atolls of the Pacific Ocean far from their genesis locations. While common, they can also occasionally generate very high wave height (>5 m) at high period (>16 s) during several days. These rare mega-swells can damage distant human infrastructures in tropical islands by direct wave impacts, but also by the extreme elevation of the sea level in lagoons exposed to the incoming swell. The lagoon surge, and land flooding, resulting from these events can be catastrophic, especially for low-lying atolls. In July 2022, the hydrodynamic conditions during the third highest energy southern mega-swell of distant origin (55°S-150°W) impacting French Polynesia since 1996 could be monitored real time with an array of sensors (pressure, acoustic Doppler current profilers, temperature) previously deployed to study the physical environment of black pearl farms in Apataki Atoll (15.45°S, 146.35°W), a semi-open atoll of the Tuamotu Archipelago. This was a unique opportunity to characterize for the first time the hydrodynamics conditions before, during and after a mega-swell with measurements of lagoon and ocean water levels, incoming wave heights and periods on the oceanic forereef, current speeds and directions along the atoll rims and in the deep passes. The array of available sensors provided a real time spatial view of the transient conditions that the atoll experimented during the mega-swell event, that can complement the more traditional assessment carried out after similar events using sedimentologic and geomorphologic evidences. While the degree of protection offered by atolls in the south of Apataki have limited the impact, the significant wave height (up to 4.2 m), flows in the passes (with up to 6.4 knots outgoing currents) and a 0.5 m surge above the average lagoon level characterize a major event. Other atolls (e.g., Makemo) have experienced higher surges in similar events in 1996 and 2011, which confirms that assessment of risks induced by mega-swells should be specific to each atoll according to its position, exposure, geomorphology and the settlement of human infrastructures.