Floodplain rivers comprise three major ecological subsystems: the mainstream, the terrestrial floodplain, and floodplain waters – notably billabongs.Typically, the physicochemical environments of billabongs are extremely variable in space and time. This is reflected in a biota adapted to a highly variable and somewhat unpredictable lentic environment. As such, the billabong community is often taxonomically quite distinct from that of the associated mainstream ecosystem. Considerable ecological differences are also observed between quite proximate billabongs. Trophic structure and function are assumed to contribute to this distinction but limited existing data do not permit detailed analysis at this level.Human intervention, particularly flow regulation and floodplain land management, affect the ecology of existing billabongs and the ‘recruitment’ of new ones. Future research should aim to provide a basis for the development of ecologically optimized management regimes.