Riparian ecosystems are essential carbon dioxide (CO2) sources, which considerably promotes climate warming. However, the other greenhouse gas fluxes (GHGs), such as methane (CH4) and nitrous oxide (N2O), in the riparian ecosystems have not been well studied, and it remains unclear whether and how these GHG fluxes respond to extreme weather, fertilization and hydrological alterations associated with reservoir management. Here, we assessed the impacts of hydrological alterations (i.e., flooding frequency) and fertilization (nitrogen and/or phosphorus) induced by human activities (hydroengineering construction and agricultural activities) on GHG fluxes, and further investigated the underlying mechanisms in two contrasting years (normal vs. extreme rainfall years) in a reservoir riparian zone dominated by grasses. The significant combined effects of extreme rainfall events and human activities (hydrological alterations and fertilization) on the GHGs were observed. Continuous flooding reduced CO2 emissions by 24% but increased CH4 emissions by ∼4 times in a normal rainfall year. In addition, nitrogen fertilization promoted CO2 emissions by 37%. However, these phenomena were not observed in the year with extreme rainfall events, which made the flooding levels homogeneous across the treatments. Furthermore, we found that CO2 fluxes were driven by the soil moisture, nutrient content, aboveground biomass, and root carbon content, while CH4 and N2O fluxes were merely driven by the soil properties (pH, moisture, and nutrient content). This study provides valuable insights into the crucial role of extreme rainfall events, hydrological alteration, and fertilization in regulating GHG fluxes in riparian ecosystems, as well as supports the integration of these changes in GHG emission models.