Excessive amounts of fluoride (F-) and nitrate (NO3-) in groundwater pose a significant threat to human health. However, a quantitative approach to assessing the human health risks caused by these harmful substances is lacking. To optimize the probabilistic assessment process for human health risk (HHR), this study introduced kernel density estimation (KDE) into the stochastic simulation of F- and NO3- content in groundwater samples. The potential HHRs caused by F- and NO3- in Songyuan City were summarized by combining the probabilistic and deterministic assessments. This study found that the concentrations of F- and NO3- did not follow common probability density functions (PDFs), but the KDE method passed the Kolmogorov-Smirnov test with the critical value of 0.067 and 0.062, showing high fitting accuracy. Monte Carlo simulation indicated that the probability of NO3- for children and adult exceeding the standard is 21.95% and 15.14%, respectively, which is comparable with the results of the deterministic assessment, but the probabilistic assessment emphasized lower probability of HHRs in children caused by excess F-(4.14%). Global sensitivity analysis revealed that excessive NO3- in groundwater has the highest sensitivity of the HHR (>0.1), followed by other factors representing water use habits (>0.01). This study presents a refined probabilistic assessment method for HHR and provides a scientific reference for understanding the state of groundwater environments.