In the future, climate change may severely alter flood patterns over large regional scales. Consequently, besides other anthropogenic factors, climate change represents a potential threat to river ecosystems. The aim of this study is to evaluate the effect of climate change on floodplain inundation for important floodplain wetlands in Europe and to place these results in an ecological context. This work is performed within the Water Scenarios for Europe and Neighbouring States (SCENES) project considering three different climate change projections for the 2050s. The global scale hydrological model WaterGAP is applied to simulate current and future river discharges that are then used to: (i) estimate bankfull flow conditions, (ii) determine three different inundation parameters, and (iii) evaluate the hydrological consequences and their relation to ecology. Results of this study indicate that in snow-affected catchments (e.g. in Central and Eastern Europe) inundation may appear earlier in the year. Duration and volume of inundation are expected to decrease. This will lead to a reduction in habitat for fish, vertebrates, water birds and floodplain-specific vegetation causing a loss in biodiversity, floodplain productivity and fish production. Contradictory results occur in Spain, France, Southern England and the Benelux countries. This reflects the uncertainties of current climate modelling for specific seasons.