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1. Riparian zones, an aquatic-terrestrial interface, can intercept more than half of nitrogen (N) exported from terrestrial ecosystems to adjacent rivers, primarily by denitrification processes. However, damming has disrupted natural patterns and processes of flooding and vegetation community assemblages, and yet little is known about how hydrological changes and ecosystem restoration affect the biogeochemical functioning in the riparian ecosystems.2. We conducted an in situ experiment to evaluate the effects of hydrological change (e.g. altering flooding intensity and frequency) and restoration approaches (e.g. natural regeneration and active revegetation) on denitrification rates and the abundance of denitrifier genes in the riparian zone of the Three Gorges Reservoir, China.3. Our results showed that active revegetation did not significantly increase denitrification rates compared to the natural regeneration, but their underlying mechanism was different. At the natural regeneration area, the denitrification rate was primarily regulated by soil properties and abundance of nosZ gene, while at the active revegetation area, it was controlled merely by the abundance of nosZ gene. In addition, vegetation types showed little effect on the soil denitrification process, and the denitrification rate decreased with flooding intensity by reducing denitrifier gene abundance.4. The periodic flooding treatment doubled the denitrification rate compared with the no flooding treatment, which might be attributed to the enhancement of soil carbon availability. Our results suggest that in terms of N removal via denitrification processes, natural regeneration is a priority approach to restoring degraded riparian ecosystems.