Groundwater is essential for water resources, serving as a key drinking source in China. It supports daily needs for urban and rural residents, aids development, and maintains ecological balance. This study conducted a sampling survey of groundwater in the Wen River basin (WRB), assessing hydrochemical features, genesis mechanisms, water quality, and health risks. The findings reveal that groundwater in the WRB is weakly alkaline, with an average total dissolved solids (TDS) concentration of 755.24 mg/L. Freshwater constitutes approximately 81.48% of the groundwater, with the following order of concentration for cations: Ca2+ > Na+ > Mg2+ > K+, and for anions: HCO3− > SO42− > NO3− > Cl−. The predominant hydrochemical types are SO4·Cl-Ca·Mg and HCO3-Ca·Mg. The chemical composition of the groundwater is primarily influenced by silicate rock weathering, dissolution processes, cation exchange, and human activities. The average Environmental Water Quality Index (EWQI) value of 74.65 for the WRB signifies that the overall quality of the groundwater is quite good, indicating that the majority of the groundwater is suitable for drinking purposes. Notably, the inferior quality water is predominantly found downstream of the Wen River. Calculations of the sodium adsorption ratio (SAR), residual sodium carbonate (RSC), and percentage of sodium (%Na) indicate that groundwater at most sampling points is suitable for irrigation. Furthermore, the human health risk assessment (HRA) reveals that oral intake presents a greater health risk to individuals than dermal contact. The mean Hazard Index (HI) for children is 3.24, with a staggering 79.89% of non-carcinogenic health risk (NHR) values surpassing the acceptable standards. For adults, the mean HI is 1.39, with 53.44% of NHR values exceeding the standards. These data indicate that children are more susceptible to health risks than adults and that the midstream and downstream of the river exhibit higher health risks compared to the upper reaches. These findings can provide critical data for groundwater quality assessment and risk management in the WRB and offer guidance for future groundwater resource management and pollution control efforts.