Boreal peatlands contain a large portion of the Earth's terrestrial organic carbon and may be particularly vulnerable to changes in climate. Temperatures in boreal regions are predicted to increase during the twenty-first century which may accelerate changes in soil microbial processes and plant community dynamics. In particular, climate-driven changes in plant community composition might affect the pathways and rates of methanogenesis, the plant-mediated emission of methane, and the scavenging of methane by methanotrophic bacteria. Climate change may also affect methane cycling through changes in pore water chemistry. To date, these feedbacks have not been incorporated into the carbon cycling components of climate models. We investigated the effects of soil warming and water table manipulations on methane cycling in a field mesocosm experiment in northern Minnesota, USA. Large intact soil monoliths removed from a bog and fen received infrared warming treatments crossed with water table treatments for 6 years. In years 5 and 6, concentrations, fluxes, and isotopic compositions of methane were measured along with aboveground and belowground net primary productivity and pore water concentrations of acetate, sulfate, ammonium, nitrate, and dissolved organic carbon. Water table level was the dominant control over methane flux in the fen mesocosms, likely through its effect on methane oxidation rates. However, pore water chemistry and plant productivity were important secondary factors in explaining methane flux in the fen mesocosms, and these factors appeared to be the predominant controls over methane flux in the bog mesocosms. The water table and IR treatments had large effects on pore water chemistry and plant productivity, so the indirect effects of climate change appear to be just as important as the direct effects of changing temperature and water table level in controlling future methane fluxes from northern peatlands. Pore water sulfate, ammonium, nitrate, and acetate had a relatively consistent negative relationship with methane emissions, pore water DOC had a positive relationship with methane emissions, and BNPP had mixed effects. The bog mesocosms had much higher methane emissions and pore water methane concentrations than the fen mesocosms, despite a much lower average water table level and peat that is a poor substrate for methanogenesis. We suggest that the relatively high methane fluxes in the bog mesocosms can be explained through their low concentrations of inhibitory pore water compounds, high concentrations of DOC, and high plant productivity. Stable isotopic data from pore water support acetate fermentation as the principal pathway of methanogenesis in bog mesocosms (mean δ13CH4 = -41.0‰, mean δD-CH4 = -190‰ ). Fen mesocosms had lower pore water concentrations and emissions of methane than bog mesocosms, despite much higher methane production potentials in fen peat. The methane from the fen mesocosms was isotopically heavy (mean δ13CH 4 = -28.9‰, mean δD-CH4 = -140‰), suggesting a strong oxidative sink. This is likely related to the dominance of graminoid vegetation and the associated oxygen transport into the rhizosphere. Our results illustrate the need for a more robust understanding of the multiple feedbacks between climate forcing and plant and microbial feedbacks in the response of northern peatlands to climate change.