Estuaries are dynamic systems constantly adapting to change. For the Wilson Inlet, a connection to the ocean has been created artificially almost every year for more than a century. Rainfall is one of the main factors determining sandbar openings, where the bar is opened once the water level of the estuary reaches a critical threshold. The reduced rainfall across the southwest of Australia associated with climate change makes sandbar openings in the Wilson Inlet less likely in the future. Indeed, water level thresholds for opening the bar have not been met four times in the last ten years. While organisms in estuaries are adapted to fluctuating conditions, the ecosystem of Wilson Inlet could be impacted by a shift in management of the sandbar. The seagrass in Wilson Inlet has been monitored periodically since the 1980s and seems to cope with irregular openings of the sandbar, but the effect of consecutive years without opening is unknown. Drawing upon knowledge of seagrass resilience and using historical and recent data, this work explores how seagrass habitats could be affected by changes to management of Wilson Inlet. Continued shifts in the climate may alter estuary ecosystems beyond the conditions to which they are adapted.