Chronic exposure to high fluoride (F-) levels in groundwater causes community fluorosis and non-carcinogenic health concerns in local people. This study described occurrence, dental fluorosis, and origin of high F-groundwater using δ2H and δ18O isotopes at semiarid Gilgit, Pakistan. Therefore, groundwater (n = 85) was collected and analyzed for F- concentrations using ion-chromatography. The lowest F- concentration was 0.4 mg/L and the highest 6.8 mg/L. F- enrichment is linked with higher pH, NaHCO3, NaCl, δ18O, Na+, HCO3-, and depleted Ca+2 aquifers. The depleted δ2H and δ18O values indicated precipitation and higher values represented the evaporation effect. Thermodynamic considerations of fluorite minerals showed undersaturation, revealing that other F-bearing minerals viz. biotite and muscovite were essential in F- enrichment in groundwater. Positive matrix factorization (PMF) and principal component analysis multilinear regression (PCAMLR) models were used to determine four-factor solutions for groundwater contamination. The PMF model results were accurate and reliable compared with those of the PCAMLR model, which compiled the overlapping results. Therefore, 28.3% exceeded the WHO permissible limit of 1.5 mg/L F-. Photomicrographs of granite rocks showed enriched F-bearing minerals that trigger F- in groundwater. The community fluorosis index values were recorded at > 0.6, revealing community fluorosis and unsuitability of groundwater for drinking.