Riparian ecosystems, vital interfaces for soil-atmosphere greenhouse gases (GHG) exchange, are increasingly subject to perturbations from extreme flooding events and artificial hydrological alterations. The resultant effects on soil microbiomes and GHG emissions, particularly under varying flooding regimes, remain poorly elucidated. Here, we conducted an in-situ flooding manipulation experiment across three elevation gradients in a reservoir drawdown area, applying continuous flooding (Extreme), 3-day flooding alternating with 3-day drainage (Moderate), and no flooding (Control) to evaluate responses of CH4, CO2, and N2O emissions and associated microbiomes. Flooding exerted stronger control than elevation on GHG fluxes. CH4 emissions increased dramatically under both extreme and moderate flooding (24-fold and 25-fold, respectively), whereas CO2 and N2O emissions decreased: extreme flooding reducing CO2 by 51 % and N2O by 108 %, and moderate flooding reducing N2O by 67 % with minimal effect on CO2 emissions. CH4 emissions increased primarily due to elevated water tables and enhanced soil anaerobic conditions, stimulating methanogenic activity via methylotrophic pathways (up-regulated mtaC gene) and greater availability of labile plant litter. CO2 emissions declined as flooding reduced aboveground plant biomass, thereby lowering plant respiration. N2O emissions decreased because higher soil moisture promoted complete denitrification, converting N2O to N2. Using co-occurrence network analysis, the bacterial order Xanthomonadales emerged as keystone taxa, showing strong associations with microbial functional groups involved in GHG-related metabolic pathways. Overall, our findings indicate that riparian ecosystems may become CH4 emission hotspots under future climatic extremes and highlight the critical role of hydrological dynamics–microbiome interactions in shaping riparian carbon and nitrogen cycles.