Non-directional re-flooding of the wetlands in southern Iraq, which were extensively drained during the 1990s, started in 2003. The change in species composition and abundance of rotifer and cladoceran communities together with their abiotic environment were studied for 15 months in the re-flooded wetlands. The re-flooded wetlands were characterized by higher salinity than typical freshwater inland marshes, and some rotifer and cladoceran species were characteristic of the saline, post-reflooding environment. The changes in species composition and abundance of rotifers were mostly seasonal, demonstrated by the cyclic changes in principal component analysis and their positive relationships to water temperature. Al-Huwaiza Marsh is distinguished from the other two marshes (Central and Al-Hammar Marshes) and is characterized by relatively lower and stable salinity, close to neutral pH, near or above saturation DO, and lower SO 4 À2 . These characteristics might explain the differences in recovery processes of zooplankton communities among the three marshes. The Jaccard's similarity index for Cladocera revealed similarity between the two stations of each marsh (in terms of maximum densities recorded); however, this was not mirrored by Rotifera. Al-Huwaiza Marsh stations were very similar to each other, whereas the Al-Hammar and Central Marshes had one station of each very similar to the other station of the other marsh. Cladocera and Rotifera are predominantly freshwater species; Rotifera is more sensitive to water quality changes, particularly salinity, than the Cladocera. The observed seasonal cycles of zooplankton communities might suggest that the system was stabilizing during the study period. However, water supply shortages since 2008 continue to threaten the wetlands.