Groundwater is subjected to contamination threats from human activities, such as agriculture, especially long-term farming in the Sanjiang Plain, China. Identifying the sources and distribution of pollution is essential for its reasonable prevention and control. In this study, we analysed the chemical characteristics of 389 samples at 60 shallow groundwater monitoring points from 2011 to 2015 in the Sanjiang Plain using traditional hydrochemical methods, water quality assessment, Pearson’s correlation, and principal component analysis (PCA). Although groundwater type in this area was predominantly HCO3-Ca·Mg, three forms of nitrogen pollution (ammonia, nitrate, and nitrite) were all detected in this area. The interaction of natural geochemical and anthropogenic factors during hydrochemical formation is confirmed by the high coefficients of variation and Gibbs plots of the main ions in the water. The overall shallow groundwater situation was described as good, with more than 40% and 90% of groundwater samples suitable for drinking and irrigation according to the quality assessment, respectively. The proportion of poor water quality in the wet season was higher than that in the dry season. NO3-N and NH3-N were identified as the major anthropogenic pollutants in the study area. Results from Pearson’s correlation and principal component analysis shows two main pollutants fall into two chemical controlling factors together with natural chemical parameters, which implies that the migration and transformation of pollutants may have affected the overall hydrochemical characteristics of the regional groundwater. Therefore, findings from this paper can provide insight into the chemical evolution of groundwater in response to long-term agricultural activities and can help contribute to better management of groundwater resources and agricultural sustainable development.