The presence of live and dead emergent vegetation alters the microbial metabolism of communities within the water column of prairie pothole wetlands. To demonstrate the effects, dissolved CH₄, dissolved O₂, plant densities, and litter densities were measured in transects from emergent vegetation to open water zones. O₂ concentrations were consistently lower and CH₄ concentrations consistently higher in emergent zones. Plant surface cover most likely interferes with gas flux across the air-water interface in the emergent zone, impeding O₂ transport into the water column and impeding CH₄ transport out of the water column. Either directly or indirectly, the presence of emergent vegetation may alter aerobic and anaerobic metabolism; since wet and dry cycles can result in emergent plant cover from nearly absent to nearly 100%, understanding these dynamics over the long-term will require studies over a range of wetland stages.