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In groundwater environments, the interaction between microbial communities and the hydrogeochemical parameters have been investigated extensively in the past years. However, little is known whether the maximum contamination level (MCL) is a threshold value that dictates the microbial composition. In this study, we analyzed 10 groundwater samples for their nitrate, nitrite, COD and sulfate concentrations, and characterized their microbial compositions using 16 S rRNA based high-throughput sequencing methods. All the 10 samples had oxygen demands higher than the corresponding MCL of China (10 mg L−1); moreover, 4 out of 10 samples also had nitrate concentrations higher than the corresponding MCL, which indicated that the groundwater quality was negatively impacted by anthropogenic activities. Comparing the microbial composition of groundwater that had higher-than-MCL nitrate concentrations to those that had lower-than-MCL nitrate concentrations, no significant differences were detected in communities' richness and diversity. However, the non-metric multi-dimensional analysis suggested that the 4 groundwater samples whose nitrate concentration exceed MCL are distinctly different from those of the rest 6 samples, indicating that MCL does have a significant impact on microbial structures. Pearson's correlation analysis suggested that none of the four analyzed hydrochemical parameters had significant impact on microbial communities' richness and diversity; however, at the genus level, the correlation results suggested that JG3 0-KM -CM45 , Sphingomonas and Rhodococcus are closely correlated with nitrate concentration. The findings of this study deepened our understanding with respect to the relationships between the environmental quality indices and the microbial compositions of groundwater. • Impact of higher-than-MCL nitrate on microbial communities' structure were examined • No significant differences were found in richness and diversity • NMDS revealed higher-than-MCL NO3 led to distinct groundwater microbial community • JG-30-KM-CM45, Sphingomonas and Rhodococcus closely related with NO3 concentration [ABSTRACT FROM AUTHOR]