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Land use changes and mounting water demands reduce freshwater inflows into estuaries, impairing estuarine ecosystems and accelerating coastal seawater intrusion. However, determining minimum river inflows for management guidelines is hampered by a lack of ecosystem-flow link data. This study describes the development of freshwater inflow guidelines for the Wami Estuary, combining scarce river flow data, hydrological modeling, inferring natural salinity regime from vegetation zonation and investigating freshwater requirements of people/wildlife. By adopting the Building Blocks Methodology, a detailed Environmental Flows Assessment was performed to know the minimum water depth/quality seasonal requirements for vegetation, terrestrial/aquatic wildlife and human communities. Water depth requirements were assessed for drought and normal rainfall years; corresponding discharges were obtained by a hydrological model (HEC-RAS) developed for the river channel upstream of estuary. Recommended flows were well within historically occurring flows. However, given the rapidly increasing water demand coupled with reduction in basin water storage due to deforestation/wetland loss, it is critical to ensure these minimum flows are present, without which essential ecosystem services (fisheries, water quality, mangrove forest resources and wildlife/tourism) will be jeopardized. The EFA process is described in painstaking detail to provide a reference for undertaking similar studies in data-poor regions worldwide. [ABSTRACT FROM AUTHOR]