River flows support productive freshwater, estuarine, and coastal fisheries around the world, and many tropical fisheries are reliant on a seasonally variable flow regime. Understanding the flow dependence of fisheries species and impacts of water resource development is an important consideration for fisheries and water management. Research conducted in free-flowing rivers is critical for understanding flow-dependence because the findings can be used to mitigate impacts of water resource development, which typically alters flow regimes. We synthesised research on flow-dependent fisheries species in the wet-dry tropics of northern Australia, an area where water resources are relatively undeveloped compared to many tropical regions. We included fish and crustacean species that are harvested by commercial, recreational, or Indigenous fishers and evaluated potential impacts of flow alteration, habitat fragmentation and degradation associated with water resource development. Overall, our research indicated that the impacts of water resource development are likely to vary with the mode of water extraction and among species with varying habitat use and life-history requirements in response to multiple factors including changes to flow, habitat connectivity and water quality. Among these impacts were reduced recruitment of species that rely on productive flood years to maintain stock biomass (via wet season water extraction), reduced movement opportunity and quality of freshwater dry season refuge habitat (via dry season/groundwater extraction), and entrapment or entrainment in water infrastructure (e.g. pumps, channels, storages). Knowledge regarding flow dependence and likely impacts learned from these free-flowing rivers may be applied in other regions to mitigate the environmental impacts of water developments.