We studied the growing season (May to October) variability of NO₃-N across Swedish lakes and streams. We found that NO₃-N concentrations showed the highest growing season variability among all water chemical variables tested, both in lakes and in streams. However, the growing season variability of NO₃-N increased with increasing trophic status in lakes while it decreased in streams. We attributed the contrasting pattern between lakes and streams to the relative importance of biological uptake and denitrification with increasing trophic status. Our results highlight the relation between growing season NO₃-N variability and trophic status, which is positive in lakes but negative in streams. The findings of this study have important ramifications for ecosystem studies as well as water management. We suggest that the assessment of growing season variability of NO₃-N in aquatic systems can be improved by considering the effect of trophic status.