Biodiversity assessments have mainly focused on species richness but little is known about the diversity of species roles, i.e. functional diversity, while this is a key component to understanding the consequence of human impacts on ecosystems. We report Australian wide patterns of functional diversity among freshwater fishes at both the major drainages and individual river basin scale using four functonal metrics (functional richness, evenness, divergence and specialization). Fish functional groups were defined using a combination of morphological and life-history traits. The aim of this study is to assess the contribution of taxa to each of regional drainage’s functional diversity by measuring the functional uniqueness of each taxon within the drainage. The Timor Sea and the Northeast Coast drainages hosts more than 90% of the country’s functional diversity. Interestingly, the North Western plateau drainage presented higher functional specialization despite having the lower species richness, which may be explained by functional uniqueness of fishes adapted to living in harsh arid conditions. Finally, we quantified the functional vulnerability to species loss as the proportion of unique functional groups supported by species listed as threatened by the IUCN Red List or, if species were not assessed by the IUCN, other measures of extinction risk.