Seagrass meadows are among the most ecologically valuable yet vulnerable coastal ecosystems, but mechanisms by which flood disturbances influence their decline remain poorly understood. Here we document significant losses of Posidonia australis in Port Stephens, New South Wales, following a major flood event in 2021, and less severe flood events in 2022 and 2025. Shoot densities declined by up to 80% after the 2021 flood but recovered within 26 months. Remapping in 2025 revealed a 27% reduction in meadow extent across the estuary since 2017, with greatest losses near the Myall River mouth. During floods, salinity can drop below 5 ppt for approximately five days and remain below 10 ppt for over a week. We propose that this protracted hyposaline exposure was the primary driver of decline. To disentangle the effects of reduced salinity from flood-associated turbidity, we exposed mature P. australis shoots to controlled salinity-reduction and light-attenuation treatments. We also tested the salinity sensitivity of juvenile plants, providing insight into how flood events may compromise recruitment. Together, our findings highlight the compounding risks that increasingly frequent and intense floods pose to P. australis meadows.