The first systematic study on high fluoride contaminated fractured rock aquifer in South Africa using geochemical and chemometric approach is presented. Groundwater samples were collected from 49 boreholes and analysed for EC, pH, major and minor ions. The groundwater with high fluoride is associated with NaCl water types. The groundwater chemistry is governed by mineral weathering, evaporation and wastewater infiltration. PHREEQC modelling indicates that carbonate mineral saturation is decreasing with increasing salinity due to evaporation whereas fluorite saturation increases with increasing F being one of the prime controlling factors. Silicate minerals namely chalcedony, quartz and talc express saturation and over-saturation while chrysotile and sepiolite are undersaturated in most of the samples. PCA provided four factors and justified the role of mineral weathering, evaporation, ion exchange, longer residence time and anthropogenic impacts on water chemistry. R-mode and Q-mode cluster analysis resulted in four clusters. In cluster 1, (29%) of groundwater is less mineralized due to recent recharge. In cluster 2 (45%), groundwater chemistry is governed by weathering of silicates and fluorite minerals. Cluster 3 (20%) reveals the impact of anthropogenic activities and induced mineral weathering. Cluster 4 shows high EC, TDS, major ions, F and low HCO implying that groundwater is affected by evaporation and longer residence time promoting mineral-water interaction and precipitation of carbonate minerals. More than 50% of the study area is degraded due to fluoride contamination which requires proper remedial actions and further investigations on human health risk due to impact of fluoride contamination in groundwater is recommended.