Secondary salinisation is recognised worldwide as a threat to aquatic biodiversity. Wetlands in the Wheatbelt Region of Western Australia are particularly affected as a result of clearing of deeprooted native vegetation for agriculture. Between 1996 and 2001, the Western Australian government nominated six natural diversity recovery catchments (NDRCs), being catchments with high value and diverse wetlands in need of protection. One, the BuntineMarchagee NDRC, supports approximately 1000 wetlands in varying states of salinisation. The challenge is to prioritise these wetlands for ongoing management. In this paper we propose an approach to prioritise representative wetlands using aquatic invertebrates. On the basis of hydrology, salinity and remnant vegetation, 20 wetlands covering a range of salinities were selected for sampling of water quality and aquatic invertebrates. Of the 202 taxa recorded, most endemic taxa occurred in fresh/brackish wetlands, while hypersaline wetlands supported predominantly cosmopolitan species. Taxa richness was greater in fresh/brackish than saline and hypersaline wetlands, with conductivity explaining 83 % of between-wetland variation in taxa richness. Classification using invertebrate assemblages separated fresh/brackish, saline and hypersaline wetlands, with greatest between-year variability within saline and hypersaline sites. Wetlands were ranked using taxa diversity, presence of conservation-significant taxa and temporal similarity. Mean rank across indices provided the final overall order of priority. Hypersaline wetlands were ordered separately to the fresher water wetlands (fresh/brackish and saline) so that priority for future management was detailed for both types of wetlands. The analysis indicated that although fresh/brackish sites support the highest biodiversity, naturally saline sites also supported wetland assemblages worthy of ongoing protection.