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Rapidly expanding water resource development in arid and semi-arid zones of Australia threatens the flow regime and ecological integrity of the few large dryland rivers and their immense floodplains. Efforts to manage and conserve the surface waters of these rivers are hampered by limited scientific data on the ecology of their flora and fauna and on their responses to the high natural variability of flow regime that typifies dryland rivers. Irregular floods connect channel and floodplain wetlands to differing degrees and for varying periods of time but the ecological significance of this connectivity is poorly understood. On Cooper Creek, a large dryland river in central Australia. we explored the degree to which assemblage composition varied with connectivity and hydrological regime. Shortly after protracted regional flooding, we sampled aquatic macroinvertebrate assemblages from the principal microhabitats in 12 channel and floodplain wetlands. Ephemeral and temporary lakes tended to have fewer taxa than semi-permanent channel or terminal lake habitats. Although hydrological connection had only recently been lost for some wetlands, there was already evidence of divergence in aquatic macroinvertebrate assemblage composition. Disruption of the natural variability in connectivity and hydrological regime by excessive water abstraction or river-flow regulation threatens the ecological integrity and aquatic macroinvertebrate biodiversity of dryland rivers. Preservation of the irregular flow regime and sporadic connectivity underpins conservation of the mosaic of floodplain wetlands that play such a crucial role in the ecosystem functioning of rivers such as Cooper Creek. (C) 2001 Elsevier Science Ltd. All rights reserved.