AbstractThe Zambezi‐Chobe wetlands in Namibia are of great international importance for trans‐boundary water management because of their remarkable ecological characteristics and the variety and magnitude of the ecosystem services provided. The main objective of this study is to establish the hydro‐ecological baseline for the application of environmental flow regimes (EFR). The specific objectives are: (i) the assessment of environmental flow components (EFC) in the current near‐natural hydrological conditions; (ii) the generation of future scenarios for climatic and socioeconomic changes; (iii) the estimation of the area–duration curves and estimated annual habitat during the inundation of the critical habitats for fisheries (mulapos), under the existing conditions and future scenarios; and (iv) to provide a framework for the future application of EFRs, based on hydrological and ecological processes. To make a sound analysis of the ecological implications, first we develop a conceptual framework of the linkages between the hydrological and biological processes concerning fish communities, because of the critical role of fisheries in the region. The EFCs in near‐natural hydrological conditions provide the basis for developing interim EFRs in the region, within the framework of an adaptive management of water resources. The future scenarios indicate a mitigation of the flow variability; and, in the worst‐case scenario, the reduction of the maximum flow and inundated area of themulaposwould result in a reduction of the estimated annual habitat of 22%. This means a reduction in the spawning habitats for quiet‐water species, in the food resources for fry and juvenile fish and a consequent reduction in fish stocks. Furthermore, the habitat loss during low events is similar and greater under both scenarios, at ca. 35%. Here we corroborate that the EFCs and their variability may become the building blocks of flow‐ecology models that lead to environmental flow recommendations, monitoring and research programmes and flow protection activities. Copyright © 2016 John Wiley & Sons, Ltd.