Australia’s tropical river systems are poorly understood in comparison with Australia’s temperate freshwater and tropical marine systems. Tropical rivers convey ~70% of the continent’s freshwater runoff, and are increasingly being targeted for development. However, existing knowledge is inadequate to support policy for tropical regions that avoids repeating the environmental problems of water use in southern Australia. This paper summarises existing knowledge on the hydrogeomorphic drivers of tropical catchments, fluxes of sediments and nutrients, flow requirements and wetlands. Key research issues include improved quantification of available water resources, hydrological, biogeochemical and ecological linkages at systems scales, understanding and valuing ecosystem processes and services, and projecting the effects of long-term climate change. Two special considerations for tropical Australia are the location of major centres of government and research capacity outside the tropical region, and the legal title of much of tropical Australia vesting in Aboriginal communities with different cultural values for rivers. Both issues will need to be addressed if tropical research is to be effective in supporting resource management needs into the future. Systems-scale thinking is needed to identify links between system components and coastal enterprises, and to protect the environmental, social, and economic values of Australia’s tropical river systems.