This study mainly focused on fluoride contamination of groundwater in the semi-arid Nanganji River Basin of Southern India. We examined the geochemical concepts governing fluoride mobilization as well as the health risks associated with fluoride intake. Despite fluoride research in India, there are gaps in hydrogeochemical and health risk assessments (HRA) related to the hard rock aquifer. A total of 72 groundwater samples were analyzed, and over 52 % exceeded the World Health Organization (WHO) limits for total dissolved solids and hardness. Fluoride levels reached 2.4 mg/L due to processes like calcite and dolomite dissolution, silicate weathering, ion exchange, and evaporative concentration. Principal Component Analysis (PCA) identified three components explaining 91.34 % of the variance, linking fluoride to mineral dissolution, nitrate pollution, and pH-regulated solubility. Saturation index (SI) analysis confirmed the undersaturation of fluorite and gypsum, promoting further fluoride release in spatial mapping. Fluoride risk areas scatered in the study region (fluoride > 1.5 mg/L). Age-stratified health risk assessments (HRA) showed that 66 % of children, 50 % of women, and 44 % of men exceeded the non-carcinogenic hazard quotient (HQ > 1.0). This study outlines a novel integrative approach that combines hydrogeochemical modeling, geographic information system (GIS), principal component analysis (PCA), and health risk assessment (HRA). Fluoride contamination is targeted across a wide range of spatiotemporal scales in fractured aquifer. In study results contribute to reduce groundwater fluoride pollution and related health hazards in accordance with Sustainable Development Goals 3 and 6 (SDGs) of the United Nations Development Programme (UNDP) for a healthy community.