The Warren Bioregion, in the extreme south-west of Western Australia, has a unique assemblage of aquatic invertebrates, fish and amphibians. Current literature indicates that 192 fully described species have been collected, of which 10 invertebrate, 1 fish and 6 frog species could be considered locally endemic. We estimate that secure nature reserves (A-Class and National Parks) in the Warren Bioregion provide a refuge for 86% of the aquatic faunal elements. Reservation alone, however, may not be sufficient to protect certain of the aquatic fauna. Adverse impacts occurring within catchments, including erosion and deposition of sediment, salinization, fire, land clearing, the presence of dams and the introduction of exotic fish, may adversely affect the aquatic fauna within a reserve. Management of protected habitats must ensure that only anthropogenic activities which are sympathetic to the long term persistence of all elements of the biota occur within, and adjacent to, the reserve system