Highly productive papyrus (Cyperus papyrus L.) wetlands dominate many permanently flooded areas of tropical East Africa; however, the cycling of carbon and water within these ecosystems is poorly understood. The objective of this study was to utilise Eddy Covariance (EC) techniques to measure the fluxes of carbon dioxide and water vapour between papyrus vegetation and the atmosphere in a wetland located near Jinja, Uganda on the Northern shore of Lake Victoria. Peak, midday rates of photosynthetic CO₂ net assimilation were approximately 40 μmol CO₂ m⁻² s⁻¹, while night time losses through respiration ranged between 10 and 20 μmol CO₂ m⁻² s⁻¹. Numerical integration of the flux data suggests that papyrus wetlands have the potential to sequester approximately 0.48 kg C m⁻² y⁻¹. The average daily water vapour flux from the papyrus vegetation through canopy evapotranspiration was approximately 4.75 kg H₂O m⁻² d⁻¹, which is approximately 25% higher than water loss through evaporation from open water.