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In most of Europe, an increase in average annual surface temperature of 0·8 °C is observed, and a further increase is projected. Precipitation tends to increase in northern Europe and decrease in southern Europe, with variable trends in central Europe. The climate scenarios for Germany suggest an increase in precipitation in western Germany and a decrease in eastern Germany, and a shift of precipitation from summer to winter. When investigating the effects of climate change, impacts on water resources are among the main concerns. In this study, the first German-wide impact assessment of water fluxes dynamics under climate change is presented in a spatially and temporally distributed manner using the state-of-the-art regional climate model, Statistical Regional (STAR) model and the semi-distributed process-based eco-hydrological model, soil and water integrated model (SWIM). All large river basins in Germany (lower Rhine, upper Danube, Elbe, Weser and Ems) are included. A special focus of the study was on data availability, homogeneity of data sets, related uncertainty propagation in the model results and scenario-related uncertainty. After the model calibration and validation (efficiency from 0·6 to 0·9 in 80% of cases) the water flow components were simulated at the hydrotope level, and the spatial distributions were compared with those in the Hydrological Atlas of Germany. The actual evapotransipration is likely to increase in most parts of Germany, while total runoff generation may decrease in south and east regions. The results for the second scenario period 2051–2060 show that water discharge in all six rivers would be 8–30% lower in summer and autumn compared with the reference period, and the strongest decline is expected for the Saale, Danube and Neckar. Higher winter flow is expected in all of these rivers, and the increase is most significant for the Ems (about 18%). However, the uncertainty of impacts, especially in winter and for high water flows, remains high. Copyright © 2010 John Wiley & Sons, Ltd.