Methane (CH4) dynamics in wetlands are spatially variable and difficult to estimate at ecosystem scales. Patches with different plant functional types (PFT) represent discrete units within wetlands that may help characterize patterns in CH4 variability. We investigate dissolved porewater CH4 concentrations, a representation of net CH4 production and potential source of atmospheric flux, in five wetland patches characterized by a dominant PFT or lack of plants. Using soil, porewater, and plant variables we hypothesized to influence CH4, we used three modeling approaches—Classification and regression tree, AIC model selection, and Structural Equation Modeling—to identify direct and indirect influences on porewater CH4 dynamics. Across all three models, dissolved porewater CO2 concentration was the dominant driver of CH4 concentrations, partly through the influence of PFT patches. Plants in each patch type likely had variable influence on CH4 via root exudates (a substrate for methanogens), capacity to transport gas (both O2 from and CH4 to the atmosphere), and plant litter quality which impacted soil respiration and production of CO2 in the porewater. We attribute the importance of CO2 to the dominant methanogenic pathway we identified, which uses CO2 as a terminal electron acceptor. We propose a mechanistic relationship between PFT patches and porewater CH4 dynamics which, when combined with sources of CH4 loss including methanotrophy, oxidation, or plant-mediated transport, can provide patch-scale estimates of CH4 flux. Combining these estimates with the distribution of PFTs can improve ecosystem CH4 flux estimates in heterogenous wetlands and improve global CH4 budgets.