Elucidating the hydrogeochemical processes and quality assessment of groundwater holds significant importance for its sustainable development. In this paper, 53 groundwater samples were collected from a typical agricultural area in the northeastern Chongqing municipality in SW China. The integration of multivariate statistical analysis, ion ratio analysis, geomodelling analysis, the entropy water quality index, health risks assessment, and sensitivity analysis was carried out to explore the hydrochemical processes and quality assessment of groundwater in this study. The statistical results reveal that the cationic concentrations followed the order of Ca2+ > Mg2+ > Na+ > K+, while the anionic components were in the order of HCO3− > SO42− > NO3− > Cl−. Based on the Piper trilinear diagram, the hydrochemical types were shown as Ca-HCO3 and Ca-Mg-HCO3 types. Hierarchical cluster analysis indicated that the groundwater samples could be categorized into three groups. The hydrochemical compositions were primarily influenced by water–rock interactions (e.g., carbonate dissolution and silicate weathering). In terms of irrigation suitability, the sodium adsorption ratios (SARs) ranged from 0.05 to 1.82, and the electrical conductivity (EC) varied from 116 to 1094 μs/cm, indicating that most groundwater samples were suitable for irrigation. The entropy-weighted water quality index ranged from 15 to 94, suggesting that the groundwater samples were suitable for drinking purposes. Non-carcinogenic human health risks followed the order of children > adult females > adult males, within the average values of 0.30, 0.21, and 0.18, respectively. Sensitivity analysis showed that the parameters had the weight order of NO3 > body weight (BW) > ingestion rate (IR) > exposure frequency (EF). Hence, we recommend prioritizing the management of areas with high salinity levels, while avoiding the excessive use of nitrogen fertilizers, raising awareness among local residents about safe groundwater, and providing robust support for the sustainable development of groundwater in typical agricultural areas.