The main objective of the present research was to examine the risk of fluoride-rich groundwater in the Shanmuganadhi River basin, south India on human health. The non-carcinogenic risks were estimated into two classes: (1) risks associated with oral intake of water and (2) risks associated with dermal contact. Hazard Quotient for oral intake and dermal contact was separately calculated for adult men, adult women and children from the geochemical results of 61 representative samples collected from the wells constructed in hard rock aquifers during the post- (January-2018) and pre-monsoon (May-2018) seasons. The collected samples were analyzed immediately after the field work for all the major ions and fluoride. Finally, total hazard index was calculated for adults (men and women) and children to evaluate the risk. It directed that 41%, 49% and 74% of post-monsoon samples and 30%, 43% and 62% of pre-monsoon samples possessed a non-carcinogenic risk for men, women and children, respectively. Because the basin falls in the drought-prone region, the water supply for drinking and cultivation are commonly based on groundwater resources. The study revealed that the minerals such as apatite, fluorite, biotite and pyroxene in the hornblende–biotite gneiss formation contribute fluoride ions to the groundwater system due to water–rock interaction mechanism. The Durov diagram depicted that dissolution of silicate minerals and cation exchange are the foremost hydrogeochemical activities, which decide the overall chemical composition of groundwater in this region. The ionic concentrations including fluoride increased with respect to depth of occurrence of groundwater. Escalation of the water table due to monsoon recharge and artificial recharge through a check dam decreased the total dissolved solids and fluoride ion concentration. The investigation conducted around the existing check dam at Kaldurai village highlighted that the fluoride concentration is below the allowable limit of 1.5 mg/l (WHO in World health statistics 2017: monitoring health for the SDGs, Sustainable Development Goals. World Health Organization, Geneva, 2017) in the wells closer to the check dam toward the downstream side. The concentration increased with distance, which lead the groundwater unsuitable for consumption. Therefore, it is recommended to implement the managed aquifer recharge using check dams in the other parts of the basin to enrich the quantity and applicability of groundwater.