Methane flux from freshwater mineral-soil (FWMS) wetlands and its variability among sites is largely modulated by plant-mediated transport. However, plant-mediated transport processes are rarely resolved in land surface models and are poorly parametrized for plants commonly found in FWMS wetlands. Here, relationships between methane flux and CO2 uptake, as well as plant conductance of methane were evaluated for three plant species and two characteristic functional types: emergent (narrow-leaved cattail) and floating-leaved (American lotus and water lily). We found significant but contrasting correlations between methane flux and CO2 uptake in cattails (r2 = 0.51, slope = −0.16, during morning) and water lily (r2 = 0.32, slope = 0.064, after midday). This relationship was not significant in American lotus, showing that stomata regulation of methane fluxes is species-specific and not generalizable across the floating-leaved plant functional type. Conductance of methane per leaf area showed distinct seasonal dynamics across species. Conductance was similar among the floating-leaved species (6.2 × 10−3md−1 in lotus and 7.2 × 10−3md−1 in water lily) and higher than conductance in the emergent species (2.7 × 10−3 m d−1). Our results provide direct observations of plant conductance rates and identify the vegetation parameters (leaf area, stomatal conductance) that modify them. Our results further suggest that models of methane emissions from FWMS should parameterize plant-mediated transport in different plant functional types, scaled by leaf area and with variable seasonal phenological dynamics, and consider possible species-specific mechanisms that control methane transport through plants.