Seagrasses found in estuaries tend to be of the colonising type, with rapid turnover and the ability to reproduce quickly and create seedbanks. We might expect this evolutionary strategy enables estuarine seagrasses to recover promptly after disturbances, however our data suggest natural recovery can still be extremely slow. Significant seagrass was lost between 2009 and 2015 in the Leschenault Estuary, south-western Australia (loss of >50% of seagrass area, equivalent to ~840 ha). The loss was likely due to a combination of anthropogenic and climate impacts (several years of major nuisance macroalgal blooms, a marine heat wave and extremely low rainfall). Signs of recovery were first seen at the plant-scale, with almost no flowering in 2014, increased flowering in 2015 and high flowering density and successful fruit production in 2016. These data suggested that the recovery potential of the seagrass was improving, however, it was not until the summer of 2018 that estuary-wide improvements in seagrass coverage were observed. Recovery since has still been extremely slow, with poor seagrass coverage observed in summer 2022 in the areas of historic loss. These findings indicate a bottleneck in recovery processes and suggest that active seagrass restoration might be required for this system.