Australia's premier environment law, the Environment Protection and Biodiversity Conservation Act (EPBC Act) lists threatened species and ecological communities (ECs). Some 60 threatened ECs have now been listed at the national level, with nearly half listed since the Act was last amended in 2007. The first riverine threatened ecological community, the River Murray and associated wetlands, floodplains, and groundwater systems from the junction with the Darling River to the Sea, was listed in August 2013. Listing of threatened ECs under the EPBC Act represents an effective national approach to ‘whole of system’, landscape-scale, and multi-species conservation. It is also a valuable tool for increasing awareness of important ecosystems, habitats and native species under pressure, and of the related ecosystem services they provide. Listing can also provide leverage for conservation related funding and complements other protective measures, such as parks and reserves. Listing is based on a scientifically rigorous assessment, including analysis of criteria as set out in the EBPC Act Regulations, supported by indicative thresholds and interpretive guidance which are available in the Guidelines of the national Threatened Species Scientific Committee. Australia's approach to the assessment of threatened ecological communities (which can be likened to ecosystems in many cases) may be considered international best practice. The methodology and challenges associated with listing this iconic riverine/floodplain community will be discussed and an overview of the scientific assessment provided.