Wetlands are often important carbon sinks, but their carbon storage efficacy may be offset by greenhouse gas (GHG) emissions, especially of methane (CH4), which may be altered by plant community structure. Floating plants such as duckweed (Lemna, Wolffia spp.) augment methanogenesis by inducing anoxia through rapid turnover of biomass and the creation of physical barriers to oxygen diffusion. Much of the CH4 in ponds can be retained by sediments and oxidized via methanotrophy. However, cattails (genus Typha), despite being effective at sequestering carbon dioxide (CO2), provide a conduit through their aerenchyma for CH4 to bypass methanotrophic bacteria in sediments and water. To determine whether the copresence of these two plants synergistically enhances CH4 emissions in small wetlands, we sampled CH4 and CO2 fluxes from ponds characterized by the presence or absence of duckweed or cattails in a 2 x 2 full factorial design. Fluxes of GHGs were analyzed with linear mixed effects models as a function of vegetation type and other environmental parameters, and model selection was performed with Akaike’s Information Criterion. The copresence of these two plants synergistically enhanced CH4 emissions, and cattail-dominated systems featured the greatest rates of carbon uptake. These results suggest that plant community assemblages are important in determining a wetland’s carbon source-sink status, that wetlands with emergent vegetation may be most effective for carbon capture, while also generating greater tradeoffs in CH4 emissions. These results provide context for considering plant community structure while managing wetlands as carbon sinks and nature-based solutions to climate change.