Active revegetation (AR) and natural regeneration (NR) are two restoration approaches widely used to rehabilitate degraded riparian ecosystems, which are subjected to frequent hydrological fluctuations owing to climate change and human activities. Nevertheless, the impacts of restoration approaches and hydrological changes on the key processes of carbon and nitrogen cycling, particularly in degraded riparian ecosystems, remain unclear. In this study, we conducted hydrological experiments, which began in 2016, at three flooding zones (extreme flooding zone, severe flooding zone, and moderate flooding zone) of AR and NR areas in the Three Gorges Reservoir to investigate the effects of restoration approach and hydrological changes on soil properties, vegetation diversity, microbial characteristics, denitrification rates, and greenhouse gas fluxes. The results showed that compared with NR, AR did not change vegetation diversity, microbial diversity, and soil denitrification rates, but decreased soil ammonium and total carbon contents. The vegetation coverage of each flooding zone was more than 90%, and vegetation diversity was relatively high in the moderate flooding zone. Moreover, the maximum denitrification rates and CO₂ fluxes were observed in the extreme flooding zone along with a high soil nutrient content. Additionally, the effect of flooding zone superseded the impacts of restoration approaches since AR could only significantly increase the CO₂ flux (p < 0.05). Overall, this study elucidates the impacts of restoration approaches and hydrological changes on C and N cycling, and aids in developing restoration strategies for degraded riparian ecosystems.