Groundwater protection has become a vital issue due to the rapid development of agriculture. Clarifying hydrochemical characteristics and driving forces of groundwater systems is the key to protecting the groundwater environment. In this study, a total of 53 groundwater samples were collected from Chengdu Plain, an intensively agricultural area in southwest China. Hydrochemical analysis, principal component analysis (PCA), self-organizing mapping (SOM), and inverse geochemical modeling were employed to elucidate hydrochemical characteristics. Inverse geochemical modeling was applied to explore various groundwater flow paths and hydrochemical evolution across the study area. The results displayed that the groundwater was classified as HCO3-Ca type. The PCA and SOM results indicated that both natural processes and anthropogenic activities influenced hydrochemistry. Ion ratio analysis and mineral saturation indices identified natural processes such as silicate weathering, calcite dissolution, and positive cation exchange. Anthropogenic activities, particularly the use of agricultural fertilizers, were responsible for elevated nitrate concentration. An inverse geochemical model was utilized to investigate various water flow paths and to comprehend the hydrochemical evolution across different locations in the study area. Finally, the water quality index (WQI) revealed that 86.79% were classified as Excellent or Good rank, meeting drinking water standards. This study would offer valuable insights into the management and protection of groundwater resources in agricultural areas.