High levels of sub-speciation in Australian mesic zone taxa have been attributed to the creation of biogeographic barriers by Pleistocene expansion of the arid zone. However, several of these barriers also align with major floodplains. The Carpentarian Barrier in the Gulf Plains (GUP) – one of Australia's most significant biogeographic barriers – experiences extreme floods on a sub-decadal timescale. These floods rise suddenly, cover thousands of square kilometres to a depth of several metres and can take weeks to subside. We investigated whether these floods have shaped community composition. If this is the case, species that are particularly vulnerable to extreme flooding – understorey animals and woody plants, particularly shrubs – should be under-represented, and grasslands should be over-represented on GUP floodplains. We used Akaike selection of logistic models to assess influence of floodplains and other potential drivers on grassland distribution and shrub abundance, and on representation of understorey fauna. We also compared post-flood faunal records with the bioregional data set to assess influence of the 2009 flood on representation of understorey reptiles. Grasslands and shrub-free vegetation were significantly over-represented and understorey fauna significantly under-represented on floodplains, even when the influences of other factors were taken into account. Understorey Gekkota were absent from – and understorey skinks under-represented in – recently flooded areas. Hence, floods appear to have shaped community composition on GUP floodplains by selectively displacing and/or destroying woody plants – particularly shrubs – and understorey animals. Our findings demonstrate association rather than causality, but show that further examination of the ecological and biogeographic impacts of extreme flooding is warranted. Influence of floods on the Australian biota should be considered an ongoing ecological and evolutionary driver, and one that is likely to intensify as extreme floods are expected to become more frequent under climate change.