Tropical wetlands contribute significantly to global carbon dioxide (CO2) and methane (CH4) emissions, however gaps exist in understanding emissions sources and drivers, especially in African peatlands. We captured plant mediated and diffusive CH4 and CO2 emissions from monthly chamber sampling from both plants and soils in an intact Cyperus papyrus wetland in Eastern Uganda. This wetland was a strong source of atmospheric CH4 in the rainy season, with monthly plant mediated CH4 fluxes averaging 3.6  0.8 nmol CH4 per stem s-1 ( SE), and monthly diffusive CH4 emissions averaging 918  96 nmol CH4 m-2 s-1. Heterotrophic CO2 emissions sampled from trenched plots were highest during the dry season with a mean of 3,410  212 nmol CO2 m-2 s-1 over this period. Stem measurements varied seasonally in stem count and biomass, with higher C. papyrus biomass in the dry season, averaging 1,888  130 g dry biomass m2. Linear models showed a significant effect of water levels on CH4 and CO2 emissions from soils and plants (p<0.1 to p<0.001). This study is the first to observe CH4 emissions directly from the C. papyrus plant, and contributes to the limited datasets on carbon cycling in these systems.