Prolonged periods of floodplain drying are becoming increasingly common due to severe drought events and the effects of river regulation. Using long-term monitoring, we assessed changes in freshwater plant community structure and composition before (2000–2002) and after (2010–2013) an extended drying period that resulted in two formerly persistent and three seasonally inundated wetlands in south-eastern Australia remaining continuously dry for durations ranging from 4.7 to 9.4 years. Plant community composition and structure changed significantly between pre- and post-dry stages in all wetlands. These changes were characterised by significant reductions in the percentage cover of aquatic species and the loss of formerly dominant aquatic species—in particular, the herbaceous perennial species, Eleocharis acuta R.Br. and E. sphacelata R.Br., and the aquatic grass, Pseudoraphis spinescens (R.Br.) Vickery. Small areas of E. acuta began to re-establish in the second and third years of wetland refilling, whereas E. sphacelata and P. spinescens did not re-establish and the percentage cover of aquatic species overall remained significantly below 2000–2002 levels throughout the 2010–2013 period. These results lend empirical support to our understanding of floodplain dynamics and resilience, and in particular, the loss of dominant perennial aquatic species and establishment of opportunistic annual species following extended wetland drying.