With increasing loss and degradation of natural wetlands on which waterbirds depend, artificial wetlands as alternative habitats for waterbirds receive more and more attention. Aquacultural ponds are one of the types of artificial wetlands. In this study, we investigated waterbirds and habitat properties of aquacultural ponds at Chongming Dongtan in the Yangtze River estuary. Our results indicated that large ponds supported a greater number of species and higher bird density than the small ones. More natatores were found in ponds before drawdown when the water level was high. In contrast, more grallatores were recorded in ponds after drawdown when the water level was low. Waterbird species number and individual density in ponds were higher during drawdown than those before and after drawdown. Importance of different habitat variables to waterbird communities varied among different phases of management. Before drawdown, area of water body and average water depth of the ponds had significant effects on the species number and abundance of all waterbirds; and the species number and abundance of natatores and grallatores were affected respectively by the area of water body and the average water depth. During drawdown, area of substrate and of reeds, human disturbance, average water depth and variation of water depth had significant effects on the species number and abundance of all waterbirds, natatores and grallatores. After drawdown, variation of water depth had significant effects on the species number and abundance of all waterbirds and grallatores, while natatores were greatly affected by the area of water body. Our results suggest that with effective management of these habitat variables, aquacultural ponds can not only provide economic benefits for the locals but also serve as the habitats for waterbirds.