Wetlands improve water quality through denitrification, but these ecosystems are also an important source of the greenhouse gas, methane. The objective of this research was to determine the effect of two common macrophyte species (Juncus effusus and Salix nigra) on denitrification and on the methane cycle. The research was conducted in a newly constructed wetland on the Columbus campus of The Ohio State University during two growing seasons. In the wetland, some plots were left unplanted, while others were planted with Salix or Juncus species (i.e., 3 treatments; n = 15 per treatment). For each treatment, we quantified concentrations of methane at two depths (15 and 25 cm) in the sediment, emissions of methane from the sediment and through the plants, and denitrification rates. During most of the second growing season, both species had a limited effect on denitrification and methanogenesis. The effects of the plants became evident by the end of the second growing season and during the third growing season. During the third growing season, Salix species enhanced the release of the greenhouse gas methane to the atmosphere, while Juncus limited the emission of methane. In comparison to the unplanted plots, the long-term removal of nitrate by denitrification was favored in the plots planted with Juncus and was not affected by Salix. Our study provides evidence that certain plants (such as Juncus) can be planted in constructed wetlands to favor denitrification, while buffering methane emission.