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Natural riverbeds in arid regions of Central Asia play an important role in waterbird migration. However, agricultural irrigation in the Aral Sea basin, in combination with climate change, is leading to wetland habitat loss. In this study, we consider the importance of the 2 largest river systems in this region during postbreeding movements and compare waterbird assemblages in relation to habitat parameters between the Amu-Darya and Syr-Darya rivers. In the second half of August 2011, we counted waterbirds along 125 and 106 km of the Amu-Darya and Syr-Darya rivers, respectively. Both rivers showed a high similarity of richness indices. Analysis of waterbird occurrence in sections of river habitat showed no differences in the numbers of individuals, but the numbers of species on the Syr-Darya sections were significantly higher than on the Amu-Darya sections. A negative regression relationship between the number of species and the riverbed width could be explained by the greater attractiveness of small, shallow reservoirs compared with the flowing river with wide riverbeds. However, both rivers should be regarded as important places in the Palearctic for migratory waterbirds, despite negative changes in the habitat quality of wetlands in the arid zone of this region.