Hydrological extremes can affect nutrient export from catchments to streams, posing a threat to aquatic ecosystems. In this study, we investigated the effects of hydrological drought on nitrate concentrations in the streamflow of 182 German catchments from 1980 to 2020. We found that across all seasons, 40% and 25% of the catchments showed significantly lower nitrate concentrations during drought and post-droughts, respectively, when compared to non-drought conditions. However, we observed pronounced spatial variability in the responses, particularly during winter droughts and post-droughts, with more catchments exhibiting higher nitrate concentrations. Specifically, nitrate concentrations were significantly higher in 25% of the study catchments during winter droughts, particularly in wetter catchments with low nitrogen retention. During winter post-droughts, nitrate concentrations are significantly higher in 19% of the catchments, especially in wetter catchments with more nitrogen surplus. Moreover, the likelihood of nitrate seasonal extremes increased by 6% during winter post-drought in our study catchments. Considering the projected increase in the frequency of droughts in Germany, the increase in nitrate concentrations during the corresponding post-drought periods poses a potential threat to aquatic ecosystem health.