Changes in global rainfall patterns and the construction of artificial dams have led to widespread alteration of hydrological processes in riparian ecosystems. Meanwhile, intensified agricultural activities have resulted in enhanced inputs of nitrogen (N) and phosphorus (P) into the riparian ecosystems associated with the Yangtze River. However, it remains unclear how the greenhouse gases (CO2, CH4, and N2O) respond to both the hydrological alterations and nutrient input in the riparian zone.