Salix variegate, a widely distributed species along the riverbank in Three Gorges Reservoir area, plays an important role in soil conservation and riverbank stabilization. Waterlogging from April to May was simulated in 2006 to test the adapting ability and mechanism of S. variegate seedlings to water environment change resulted from the construction of Three Gorges Project. The results showed that under waterlogging, all of the S. variegate seedlings could survive, but their maximum photosynthesis (Pmax), transpiration rate (Tr), water use efficiency (WUE), and stomatal conductance (Gs) decreased significantly with the prolongation of waterlogging. In the early period of waterlogging (20 days), these indices changed little, with the Pmax and Tr decreased by 18.5% and 2.2%, respectively, compared with the control. After 30 days, Pmax and Tr decreased by 53.4% and 23.7%, respectively, and then, kept stable. The contents of chlorophyll and carotenoid and their ratio decreased significantly with the prolongation of waterlogging, while the ratio of chlorophyll a to b increased significantly. The ratio of chlorophyll to carotenoid ranged in 4.873-6.883, and that of chlorophyll a to b ranged in 2.855-3.912. Adventitious roots were developed after waterlogging, which would benefit the oxygen supply for the plants. It was suggested that S. variegate had good adaptability to waterlogging, and could be used as a pioneer species in the restoration of degraded water-level fluctuation zone.