The assessment of natural background levels (NBLs) in groundwater is considered as an efficient way to distinguish the geogenic compound from anthropogenic pollution of groundwater—a basic issue in groundwater environmental management. At present, most studies only assess NBLs of single parameters in groundwater. Such method, however, ignored the complex components and interaction in the groundwater, which leads to the inaccuracy of the assessment. In this study, 51 groundwater samples were investigated in November 2018 in Pinggu basin—one of the most important emergency groundwater supply sources of Beijing. Hierarchical cluster analysis (HCA) was used firstly to divide the study area into four zones. By combining single-parameter NBLs assessment and comprehensive NBLs assessment, the possible anthropogenic impact on groundwater quality in different zones could be determined with the use of land use map. For single-parameter NBLs assessment, iterative Grubbs’ test was used to assess NBLs of the data following Gaussian distribution, and the median plus/minus twofold the median of the absolute deviations from the median (median ± 2MAD) method was used to assess NBLs of the data for the non-Gaussian distribution. For comprehensive NBLs assessment, Mahalanobis distances of scatters in scatter plots which express the hydrogeological evolution processes were involved. In addition, δ¹⁵N-NO₃⁻ and δ¹⁸O-NO₃⁻ were used to analyze the sources of nitrate in groundwater. The results showed that the groundwater was affected by industrial activities, agricultural activities, urban domestic sewage and landfills. And the groundwater quality in the east of the study area was better than that in the west. Nitrate in the groundwater of study area mainly came from nitrification, and denitrification occurred in the groundwater near the landfills. This study provides a way to assess the NBLs of groundwater quality, and to determine sources and transformation of nitrate in the groundwater, which contributes to the identification of anthropogenic pollution in groundwater.