In many densely populated areas, riverine floodplains have been strongly impacted and degraded by river channelization and flood protection dikes. Floodplains act as buffers for flood water and as filters for nutrients and pollutants carried with river water and sediment from upstream source areas. Based on results of the EU-funded "AquaTerra" project (2004-2009), we analyze changes in the dynamics of European river-floodplain systems over different temporal scales and assess their effects on contaminant behaviour and ecosystem functioning. We find that human-induced changes in the hydrologic regime of rivers have direct and severe consequences on nutrient cycling and contaminant retention in adjacent floodplains. We point out the complex interactions of contaminants with nutrient availability and other physico-chemical characteristics (pH, organic matter) in determining ecotoxicity and habitat quality, and draw conclusions for improved floodplain management.