<p>Groundwater quality in arid and semi-arid regions has progressively declined, raising significant environmental and public health concerns. Groundwater pollution by fluoride and nitrate poses significant public health risks. This study assesses the health risks associated with fluoride and nitrate toxicity in the southern part of Jaipur district, Rajasthan, India, where rural residents totally depend on groundwater for consumption and irrigation purposes. Sixty-one samples were taken from bore wells and tested for physicochemical parameters to determine the fluoride and nitrate toxicity. Hydro-geochemical processes influence groundwater chemistry, revealing that ion exchange, oxidation–reduction, and precipitation-dissolution play crucial roles. The hydrochemical facies analysis indicated that most samples fall under Na⁺–K⁺–Cl⁻–SO₄²⁻ and Na⁺–K⁺–HCO₃⁻ categories. The Water Quality Index classified 31.25% of samples as good, 40.63% as poor, and 12.50% as very poor to unsuitable. Fluoride contamination, primarily due to silicate and carbonate dissolution, exceeded permissible limits in 42.18% of the samples, indicating a geogenic origin. Nitrate pollution, largely driven by fertiliser use, was found in 34.43% of samples beyond the allowable limit of WHO. A health risk assessment revealed substantial non-carcinogenic risks for all age groups, with children (87%) exhibiting the highest vulnerability, subsequent to adolescents (86%) and adults (81%). Adverse effects such as fluorosis and nitrate-related diseases, including blue baby syndrome and intestinal cancer, were linked to groundwater contamination. The study underscores the urgent need for mitigation strategies to safeguard public health, especially among children, and recommends targeted interventions to manage fluoride and nitrate pollution.</p>