Fluoride contamination in groundwaters of a rural region in semi-arid Western India has been studied using combination of geochemical-and-isotopic techniques, in conjunction with Health Quotient assessment approach. The objective of this study is to determine the sources and controls on fluoride content and to evaluate probabilistic non-carcinogenic risk associated with its long-term consumption. F− ranges from 0.3 to 12 mg L−1, shows high spatial variability, and ~ 35% of the samples have F− > 1.5 mg L−1 (WHO maximum limit for drinking). Two sources are identified: high F− results from water–rock interaction of F-bearing minerals in granites and gneisses, while phosphate fertilizers can contribute up to ~ 0.46 mg L−1 of groundwater F− that can be significant for low F− samples. High F− samples are characterized by high pH, Na and alkalinity, and low Ca. Calcite precipitation drives the solubility of F-bearing minerals. Kinetic fractionation of water isotopes (18O and 2H) demonstrates that evaporation plays role in enriching groundwater F−. Non-carcinogenic risk, estimated by Hazard Quotient (HQoralF\documentclass[12pt]{minimal}
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\begin{document}$$HQ_{{{\text{oral}}}}^{{\text{F}}}$$\end{document}), ranges from 0.13–5.72 to 0.26–11.86 for adult and children, respectively. Conservative estimate shows that ~ 0.467 million of adults and~0.073 million of children in four sub-districts are under the risk of fluorosis—while the residents of other five sub-districts remain safe from it. Finally, we suggest stakeholders to install F− treatment plants to ensure the health safety of local residents in the high-risk zones, create awareness in farmers for optimum use of fertilizers, and promote rainwater harvesting, for better management of groundwater resources and quality in the region.