Climate induced changes of temperature, discharge and nitrogen concentration may change natural denitrification processes in river systems. Until now seasonal variation of N-retention by denitrification under different climate scenarios and the impact of river morphology on denitrification have not been thoroughly investigated. In this study climate scenarios (dry, medium and wet) have been used to characterize changing climatic and flow conditions for the period 2050–2054 in the 4th order stream Weiße Elster, Germany. Present and future periods of nitrogen turnover were simulated with the WASP5 river water quality model. Results revealed that, for a dry climate scenario, the mean denitrification rate was 71% higher in summer (low flow period between 2050 and 2054) and 51% higher in winter (high flow period) compared to the reference period. For the medium and wet climate scenarios, denitrification was slightly higher in summer (3% and 4%) and lower in winter (9% and 3% for medium and wet scenarios, respectively). Additionally, the variability of denitrification rates was higher in summer compared to winter conditions. For a natural river section, denitrification was a factor of 1.22 higher than for a canalized river reach. Besides, weirs along the river decrease the denitrification rate by 16% in July for dry scenario conditions. In the 42 km study reach, N-retention through denitrification amounted to 5.1% of the upper boundary N load during summer low flow conditions in the reference period. For the future dry climate scenario this value increased up to 10.2% and for the medium climate scenario up to 5.4%. In our case study the investigated climate scenarios showed that future discharge changes may have a larger impact on denitrification rates than future temperature changes. Overall results of the study revealed the significance of climate change in regulating the magnitude, seasonal pattern and variability of nitrogen retention. The results provide guidance for managing nitrogen related environmental problems for present and future climate conditions.