Balancing the freshwater needs of humans and ecosystems is a fundamental challenge for the management of rivers worldwide. River regulation and water extraction can affect all components of the natural flow regime, yet few studies have investigated the effects on the low-flow end of the hydrograph. Low-flow periods are hydrologically distinctive and ecologically important, varying in nature among climatic zones. Tropical savannah rivers are characterized by highly seasonal and predictable flow regimes, but with high interannual variation in the magnitude, timing, and duration of low flows. Many tropical savannah rivers are relatively intact, especially in northern Australia, but many are now receiving increasing attention for water-resource development through surface- and groundwater extraction. We identified the hydroecological effects of water extraction on 3 phases of the seasonal flow regime: the wet-dry transition, dry season, and dry-wet season transition for perennial and intermittent rivers in tropical savannah climates. We propose a conceptual model and 7 predictions that describe the ecological implications of dry-season water extraction in tropical savannah river systems worldwide. The predictions address: 1) connectivity, 2) availability of in-stream habitat, 3) dry-season persistence of in-channel refugia, 4) water quality during dry-wet and wet-dry transition periods, 5) decoupling of wet- and dry-season flows, and the cumulative effects on 6) groundwater-dependent species and 7) whole-ecosystem shifts. We used northern Australia as a case study to review the current level of evidence in support of these predictions and their potential ecological consequences, and used this review to propose key priorities for future research that are globally applicable.