Papyrus (Cyperus papyrus) wetlands support millions through food provisioning, which leads to loss of regulating ecosystem services. This study aimed at understanding the impact of changes in water regime and vegetation harvesting on nutrient retention in rooted papyrus wetlands. A simulation model (Papyrus Simulator), developed and calibrated with data from African wetlands, produced reasonable estimates of productivity and nutrient retention. Phosphorus retention was lower than nitrogen retention, leading to a nitrogen-limited environment by reducing the N:P ratio in the water. Absence of surface water during part of the year caused a reduction of biomass. Harvesting increased nitrogen retention from 7% to over 40%, and phosphorus retention from 4% to 40%. Sensitivity analysis revealed assimilation, mortality, decay, re-translocation, nutrient inflow and soil porosity as the most influential factors. Papyrus Simulator is suitable for studying nutrient retention and harvesting in wetlands, and contributes to quantification of ecosystem services and sustainable wetland management.