Blue carbon (C) ecosystems are among the most effective C sinks of the biosphere, but methane (CH4) emissions can offset their climate cooling effect. Drivers of CH4 emissions from blue C ecosystems and effects of global change are poorly understood. Here we test for the effects of sea level rise (SLR) and its interactions with elevated atmospheric CO2, eutrophication, and plant community composition on CH4 emissions from an estuarine tidal wetland. Changes in CH4 emissions with SLR are primarily mediated by shifts in plant community composition and associated plant traits that determine both the direction and magnitude of SLR effects on CH4 emissions. We furthermore show strong stimulation of CH4 emissions by elevated atmospheric CO2, whereas effects of eutrophication are not significant. Overall, our findings demonstrate a high sensitivity of CH4 emissions to global change with important implications for modeling greenhouse-gas dynamics of blue C ecosystems.