Large rivers and their floodplains support a significant proportion of the world’s biodiversity and provide important goods and ecological services to society, including fisheries. Riverine ecosystems and fisheries are subject to intense pressure from a wide range of anthropogenic disturbances, the main ones being impacts from altered land use, modifications to river flow regimes, riparian and physical habitat loss, water pollution, exotic species invasions and intensive exploitation of fish stocks. As a consequence, a far greater proportion of freshwater species are threatened or endangered than terrestrial or marine species in the same taxonomic groups. In this paper we review ecological processes sustaining river and floodplain biodiversity and productivity. We also outline the status of knowledge of fundamental issues in fish ecology, including fish habitat requirements, trophic ecology, life history strategies, migration, the population biology of riverine fish and modelling of fish populations and assemblages.