Abstract The L ake E yre B asin, one of the world's last unregulated wild river basins, covers almost one sixth of the Australian continent, with large areas of connected wetlands (73 903 km 2 ), including floodplains, lakes, waterholes and river channels. Few data existed and so we used literature and government biotic and abiotic data and anthropogenic impacts to assess the conservation risk of the ecosystem as L east C oncern ( IUCN R ed L ist criteria for ecosystems, version 2.0). This was based on limited distributional change and low levels of degradation or anthropogenic threatening processes. The approach could be applied to ecosystem assessments of other large river basins around the world, given the L ake E yre B asin occupies one extreme (unmodified) while the A ral S ea (collapsed), previously assessed, occupies the other extreme (highly modified). River flow analysis with available biotic data is critical for risk assessment as well as identification and tracking of long‐term threats. Assessment was possible at this large basin scale and appropriate, given the critical importance of connectivity but could also occur at finer spatial scale. Increased diversions for irrigation, mining impacts on floodplains and projected increased temperatures threaten the current status ( L east C oncern) of the connected wetlands of the L ake E yre B asin ecosystem.