Freshwater wetland systems can often display a mosaic of different vegetation types across the landscape. These “patches” are often characterized by functionally distinct vegetative groups that tend to display unique methane (CH4) flux signatures. However, it is unclear whether these unique signatures are due to the differences in the vegetation present or some other variable in the system (like hydrology). Natural field conditions limit our ability to isolate the individual effects of cooccurring factors on the stages of CH4 cycling as many of these factors interact. For example, vegetation and hydrology both have the potential to alter the redox state in soil, which will directly affect microbial activity levels. However, a wetland’s hydroperiod will also affect the location and growth of plant species. To investigate the relative impact of hydrologic stage vs. plant species type on CH4 fluxes, we designed a mesocosm experiment using various combinations of hydrologic stage (standing water, saturated, and low saturation) and vegetative states [emergent sedges (Carex striata), emergent grass (Panicum hemitomon), low growing forbs (Persicaria hydropiperoides/Proserpinica pectinata), submerged vegetation (Juncus repens/ Proserpinica pectinata), and no vegetation] across 60 mesocosms. In the standing water treatments, we found significant differences in the CH4 fluxes between vegetation treatments, which matched CH4 fluxes in field conditions with comparable water levels. We also found that there was a definitive interactive effect between vegetation and hydrology on CH4 fluxes, and that fluxes from emergent types of vegetation displayed an opposite pattern of response to changing water level compared to submerged groups. Whether these results are due to differences in how vegetation affects CH4 transport, production, or oxidation will require extended study.