Natural flood plains are among the most biologically productive and diverse ecosystems on earth. Globally, riverine flood plains cover > 2 × 106 km2, however, they are among the most threatened ecosystems. Floodplain degradation is closely linked to the rapid decline in freshwater biodiversity; the main reasons for the latter being habitat alteration, flow and flood control, species invasion and pollution. In Europe and North America, up to 90% of flood plains are already ‘cultivated’ and therefore functionally extinct. In the developing world, the remaining natural flood plains are disappearing at an accelerating rate, primarily as a result of changing hydrology. Up to the 2025 time horizon, the future increase of human population will lead to further degradation of riparian areas, intensification of the hydrological cycle, increase in the discharge of pollutants, and further proliferation of species invasions. In the near future, the most threatened flood plains will be those in south-east Asia, Sahelian Africa and North America. There is an urgent need to preserve existing, intact flood plain rivers as strategic global resources and to begin to restore hydrologic dynamics, sediment transport and riparian vegetation to those rivers that retain some level of ecological integrity. Otherwise, dramatic extinctions of aquatic and riparian species and of ecosystem services are faced within the next few decades.