Nitrogen (N) deposition is globally considered as a major threat to ecosystem functioning with important consequences for biodiversity, carbon sequestration and N retention. Lowered N retention as manifested by elevated concentrations of inorganic N in surface waters indicates ecosystem N saturation. Nitrate (NO3) concentrations in runoff from semi-natural catchments typically show an annual cycle, with low concentrations during the summer and high concentrations during the winter. Process-oriented catchment-scale biogeochemical models provide tools for simulation and testing changes in surface water and soil chemistry in response to changes in sulphur (S) and N deposition and climate. Here we examine the ability of MAGIC to simulate the observed monthly as well as the long-term trends over 10–35 years of inorganic N concentrations in streamwaters from four monitored headwater catchments in Europe: Čertovo Lake in the Czech Republic, Afon Gwy at Plynlimon, UK, Storgama, Norway and G2 NITREX at Gårdsjön, Sweden. The balance between N inputs (mineralization + deposition) and microbial immobilization and plant uptake defined the seasonal pattern of NO3 leaching. N mineralization and N uptake were assumed to be governed by temperature, described by Q10 functions. Seasonality in NO3 concentration and fluxes were satisfactorily reproduced at three sites (R2 of predicted vs. modelled concentrations varied between 0.32 and 0.47 and for fluxes between 0.36 and 0.88). The model was less successful in reproducing the observed NO3 concentrations and fluxes at the experimental N addition site G2 NITREX (R2 = 0.01 and R2 = 0.19, respectively). In contrast to the three monitored sites, Gårdsjön is in a state of change from a N-limited to N-rich ecosystem due to 20 years of experimental N addition. At Gårdsjön the measured NO3 seasonal pattern did not follow typical annual cycle for reasons which are not well understood, and thus not simulated by the model.