Abstract: As a typical pollutant in aquatic environments, high concentrations of ammonia nitrogen have been widely detected in shallow groundwater. However, there is still no consensus on its sources. Identifying the sources of ammonia nitrogen in groundwater at national monitoring sites is a crucial foundation for implementing source control of groundwater pollution. This study comprehensively utilized field investigations, hydrochemical analysis, multi-isotope tracing and principal component analysis (PCA) methods to analyze the sources of ammonia nitrogen in groundwater at national monitoring sites. The results indicate that in the small regional aquatic environment where the target national monitoring site is located, ammonia nitrogen concentrations are generally high in both groundwater and surface water. The concentrations and isotopic compositions of ammonia nitrogen in groundwater and surface water exhibit fluctuating patterns influenced by multiple controlling factors. Hydrochemical evidence, along with isotopic data from ammonia nitrogen and nitrate nitrogen, suggests that the primary source of ammonia nitrogen in the groundwater at the target national monitoring site is domestic and industrial wastewater, while the use of agricultural nitrogen fertilizers is another significant source of ammonia nitrogen in the groundwater of the study area. The PCA results derived from water quality data corroborate the above findings. This research provides methodological guidance for source analysis of groundwater pollution in small regions of national monitoring sites and offers important scientific evidence for improving the groundwater environment at these sites.