<p>Deoxygenation events threaten coral reefs as they can result in biodiversity loss and are expected to occur more frequently with increasing sea temperatures and eutrophication. Multiple deoxygenation events have occurred at Bill’s Bay, a semi-enclosed lagoon within the UNESCO World Heritage-listed Ningaloo Marine Park, and have been associated with significant ecosystem impacts, including fish kills and coral mortality. Although these events are thought to be linked to the entrapment and decomposition of coral spawn, the physical mechanisms that trigger these events remain poorly understood, making it difficult to predict when these events may occur and to assess the capacity for reef recovery. Here, we identify the physical conditions associated with known deoxygenation events and develop thresholds to support the prediction of future events. We also examine the status of the coral communities and juvenile abundance in Bill’s Bay using a multi-decadal dataset. The results show that for recorded events, anomalous physical conditions shut down the typical water circulation patterns and trap coral spawn slicks close to shore for longer than usual. Coral cover and juvenile abundance in the inner and middle lagoon were the lowest on record following the 2022 event and were composed of just a few tolerant genera. Yet, coral cover and juvenile abundance remained relatively high in the outer lagoon, which importantly may promote future recovery. Bill’s Bay is located within a sanctuary zone and has minimal impacts from local anthropogenic pressures, yet our results suggest that it is predisposed to these naturally occurring deoxygenation events.</p>