Seagrass meadows are an ecologically important and economically valuable habitat in coastal and estuarine systems. Over the last century, these habitats have been declining due to coastal development, eutrophication and more recently extreme climate events such as floods, storms and heatwaves. For more than 20 years, our annual seagrass monitoring program has documented a catastrophic loss and slow recovery of tropical seagrass meadows in Cairns Harbour, far north Queensland. The seagrass loss was due to multiple years of climate events including above average rainfall and flooding during an intense La Nina system in 2009-10 accompanied by multiple cyclones that saw approximately 1000 hectares of meadows in the harbour almost disappear. The degraded seagrass habitat took 5 years for the extent of meadows to return to pre-disturbance levels, while biomass and species composition have taken over a decade to recover to near baseline levels. The long-term monitoring of these tropical seagrass meadows has been crucial to inform management decisions within the harbour regarding protection and restoration of these habitats and gives great insight into seagrass dynamics under future climate change scenarios when these climate events are forecast to be more intense.