The Mike 11–TRANS modelling system was applied to the lowland Gjern river basin in Denmark to assess climate-change impacts on hydrology and nitrogen retention processes in watercourses, lakes and riparian wetlands. Nutrient losses from land to surface waters were assessed using statistical models incorporating the effect of changed hydrology. Climate-change was predicted by the ECHAM4/OPYC General Circulation Model (IPCC A2 scenario) dynamically downscaled by the Danish HIRHAM regional climate model (25 km grid) for two time slices: 1961–1990 (control) and 2071–2100 (scenario). HIRHAM predicts an increase in mean annual precipitation of 47 mm (5%) and an increase in mean annual air temperature of 3.2 °C (43%). The HIRHAM predictions were used as external forcings to the rainfall-runoff model NAM, which was set up and run for 6 subcatchments within and for the entire, Gjern river basin. Mean annual runoff from the river basin increases 27 mm (7.5%, p < 0.05) when comparing the scenario to the control. Larger changes, however, were found regarding the extremes; runoff during the wettest year in the 30-year period increased by 58 mm (12.3%). The seasonal pattern is expected to change with significantly higher runoff during winter. Summer runoff is expected to increase in predominantly groundwater fed streams and decrease in streams with a low base-flow index. The modelled change in the seasonal hydrological pattern is most pronounced in first- or second-order streams draining loamy catchments, which currently have a low base-flow during the summer period. Reductions of 40–70% in summer runoff are predicted for this stream type. A statistical nutrient loss model was developed for simulating the impact of changed hydrology on diffuse nutrient losses (i.e. losses from land to surface waters) and applied to the river basin. The simulated mean annual changes in TN loads in a loamy and a sandy subcatchment were, respectively, + 2.3 kg N ha − 1 (8.5%) and + 1.6 kg N ha − 1 (6.9%). The rainfall-runoff model and the nutrient loss model were chained with Mike 11–TRANS to simulate the combined effects of climate-change on hydrology, nutrient losses and nitrogen retention processes at the scale of the river basin. The mean annual TN export from the river basin increased from the control to the scenario period by 7.7%. Even though an increase in nitrogen retention in the river system of 4.2% was simulated in the scenario period, an increased in-stream TN export resulted because of the simulated increase in the diffuse TN transfer from the land to the surface-waters.