The dominant plant species in many African wetlands is Cyperus papyrus. Its adaption 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 flow 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. The Indicators of Hydrologic Alteration (IHA) enable the evaluation of changes to flow regimes by examining hydrologic records and linking them to biologically-relevant hydrologic characteristics through the Environmental Flow Components (EFCs) approach. 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 EFCs (extreme low flows, base flow, high flow pulses, and small and large floods) on papyrus as a habitat. We find that agricultural water management considerably alters the magnitude, duration, timing and rate of change of EFCs for the irrigated area to catchment area ratio greater than 1:153, affecting both sexual and asexual reproduction in papyri plants. 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.