Anthropogenic nitrogen (N) input has led to elevated levels of nitrate nitrogen (NO₃⁻-N) in the groundwater. However, insights into the responses of the microbial community and its N metabolic functionality to elevated NO₃⁻-N in suburban groundwater are still limited. Here, we explored the microbial taxonomy, N metabolic attributes, and their responses to NO₃⁻-N pollution in groundwaters from Chaobai River catchment (CR) and Huai River catchment (HR) in Beijing, China. Results showed that average NO₃⁻-N and NH₄⁺-N concentrations in CR groundwater were 1.7 and 3.0 folds of those in HR. NO₃⁻-N was the dominant nitrogen specie both in HR and CR groundwater (over 80 %). Significantly different structures and compositions of the microbial communities and N cycling gene profiles were found between CR groundwater and HR groundwater (p < 0.05), with CR groundwater harboring significantly lower microbial richness and abundance of N metabolic genes. However, denitrification was the dominant microbial N cycling process in both CR and HR groundwater. Strong associations among NO₃⁻-N, NH₄⁺-N, microbial taxonomic, and N functional attributes were found (p < 0.05), suggesting denitrifiers and Candidatus_Brocadia might serve as potential featured biomarkers for the elevated NO₃⁻-N and NH₄⁺-N concentration in groundwater. Path analysis further revealed the significant effect of NO₃⁻-N on the overall microbial N functionality and microbial denitrification (p < 0.05). Collectively, our results provide field evidence that elevated levels of NO₃⁻-N and NH₄⁺-N under different hydrogeologic conditions had a significant effect on the microbial taxonomic and N functional attributes in groundwater, with potential implications for improving sustainable N management and risk assessment of groundwater.