The dominant plant species in many African wetlands is Cyperus papyrus. Its adaptation to saturated and low‐oxygen conditions and its dense structure and height provide breeding and feeding grounds for unique flora and fauna. As a keystone species adapted to local hydrology, the flooding regime of papyrus offers the full range of hydrologic conditions and events essential to ecosystem health. However, no study has attempted to link papyrus wetlands' flow regimes to their biologically relevant hydrologic attributes. This study assesses hydrologic alterations of a papyrus wetland's flow regime due to rice irrigation. We develop a conceptual ecological model linking papyrus to hydrologic attributes to determine the consequences of changed environmental flow components (EFCs) on papyrus as a habitat. We find that agricultural water management considerably alters the magnitude, duration, timing and rate of change of EFCs, which could affect productivity (seed dispersal, germination and establishment; rhizome spreading; papyrus distribution across transects; and dispersal of floating mats) in papyrus wetlands. However, the effect on the papyrus wetlands' natural pulsed regime is negligible when the ratio of irrigated area to catchment area is no greater than 1:150. Overall, a better understanding of the threats of water diversion for agriculture is made by linking papyrus' flow regimes to biologically relevant hydrologic attributes. Knowledge of the roles of the various EFCs could provide opportunities for conserving and protecting papyrus wetlands, especially for systems at risk of altered flows.