The tropical rivers of northern Australia have received international and national recognition for their high ecological and cultural values. Unlike many tropical systems elsewhere in the world and their temperate Australian counterparts, they have largely unmodified flow regimes and are comparatively free from the impacts associated with intensive land use. However, there is growing demand for agricultural development and existing pressures, such as invasive plants and feral animals, threaten their ecological integrity. Using the international literature to provide a conceptual framework and drawing on limited published and unpublished data on rivers in northern Australia, we have derived five general principles about food webs and related ecosystem processes that both characterise tropical rivers of northern Australia and have important implications for their management. These are: (1) the seasonal hydrology is a strong driver of ecosystem processes and food-web structure; (2) hydrological connectivity is largely intact and underpins important terrestrial–aquatic food-web subsidies; (3) river and wetland food webs are strongly dependent on algal production; (4) a few common macroconsumer species have a strong influence on benthic food webs; and (5) omnivory is widespread and food chains are short. The implications of these ecosystem attributes for the management and protection of tropical rivers and wetlands of northern Australian are discussed in relation to known threats. These principles provide a framework for the formation of testable hypotheses in future research programmes.