Papyrus (Cyperus papyrus L.) is a C₄ sedge which forms highly productive monotypic stands over large areas of wetland in Africa. Carbon flux measurements made using Eddy covariance over a papyrus wetland at Lake Naivasha, Kenya, have been used to evaluate WIMOVAC (Windows Intuitive Model of Vegetation response to Atmosphere and Climate Change), which calculates canopy carbon uptake and loss from a process-based model of leaf photosynthetic characteristics and canopy microclimate. The model has been developed from a detailed experimental database at the leaf scale relating photosynthetic responses to the environment. Comparison of measured and modelled rates of bracteole (leaf) photosynthesis demonstrates the robustness of the model and modelled diurnal patterns of photosynthesis show a close conformity to experimental results. Papyrus canopy assimilation calculated using the model shows a small annual cycle and predicts a net canopy carbon gain of 3.16 kg C m^-2 yr^-1 when the rhizomes and roots are submerged. Measured soil and plant respiration rates combined with the canopy model produce realistic ecosystem fluxes and indicate a current net loss of 2.84 g C m^-2 day^-1 from the system at a time of hydrological drawdown when detritus is exposed to the atmosphere. Carbon flux measurements using eddy covariance indicate a current net loss of 2.88 g C m^-2 day^-1, a value close to that predicted by the model. The measurements show that papyrus wetlands are a large source of carbon dioxide during drawdown but have the potential to be very large carbon sinks when water inundates the detritus.