<p>Methane emissions from the nearshore zones of lakes are relatively large but can vary by several orders of magnitude. This variability may reflect differences in organic matter inputs, particularly the concentration of polyphenolics that alter the electrochemical favourability for methanogenesis and microbial composition and abundance. However, the importance of these different mechanisms relative to each other and to other explanations, such as variability in temperature, remains poorly understood. Here we tested how polyphenolic concentrations and reduction–oxidation potential influenced methane emissions in a comparative study of 19 littoral sites in the UK that varied in organic matter sources and microbial composition. Using path analysis, we compared multiple predictions to explain methane fluxes from polyphenolic concentrations both directly and indirectly via changes to reduction–oxidation conditions and microbial abundance and composition. We found that the prediction that organic matter composition, namely the concentration of polyphenolics, controls methane emissions by changing electrochemical conditions was better supported than predictions involving methanogen and methanotrophic bacteria abundances, methanogen diversity, or other physicochemical conditions. Electrochemical conditions had similarly supported direct and indirect effects mediated by changes in methanogen community composition. Diffusive CH₄ fluxes were estimated to increase by 2.3–10.8 times (95% confidence interval) with increasing polyphenolic concentrations, mostly because they lower reduction–oxidation potentials. Rather than strongly inhibiting methane-producing microorganisms, our results suggest polyphenolics change reduction–oxidation potentials to favour acetoclastic and methylotrophic methanogens. These results help explain conflicting evidence about the responses of methane to organic matter inputs and can improve future predictions of aquatic carbon cycling.</p>