Seagrasses are vital components of estuaries that provide essential habitat to a range of species and support diverse ecological functions, yet they face growing pressure from stressors such as climate change and catchment-derived impacts. Between 2020 and 2022, La Niña conditions brought record-breaking rainfall to eastern Australia, triggering multiple major flood events across New South Wales. This study investigates the links between these flood disturbances and declines of the seagrass Zostera muelleri. Long-term distribution data have been augmented with high-resolution pre- and post-flood mapping across 10 estuaries spanning the NSW coastline. Results show substantial seagrass decline after the floods across all surveyed estuaries, with total losses exceeding 220 ha. Proportional losses ranged from 20% to an extreme of 99%, with seven of the ten estuaries losing more than half of their pre-flood seagrass extent. Limited recovery has been observed to date, likely reflecting the repeated nature of the floods reducing recovery pathways. Surveys of the seedbank in two estuaries are currently ongoing but initial findings suggest a limited number of viable seeds, which has implications for the recovery of Z. muelleri in affected estuaries.