Fluoride (F-), and arsenic (As) in the groundwater cause health problems in developing countries, including Pakistan. We evaluated the occurrence, distribution, sources apportionment, and health hazards of F-, and As in the groundwater of Mardan, Pakistan. Therefore, groundwater samples (n = 130) were collected and then analyzed for F-, and As by ion-chromatography (IC) and Inductively-coupled plasma mass-spectrometry (ICP-MS). The F-, and As concentrations in groundwater were 0.7–14.4 mg/L and 0.5–11.2 µg/L. Relatively elevated F-, and As coexists with higher pH, Na+, HCO3-, SO4−2, and depleted Ca+2 due to fluoride, sulfide-bearing minerals, and anthropogenic inputs. Both F-, and/or As are transported in subsurface water through adsorption and desorption processes. Groundwater samples 45%, and 14.2% exceeded the WHO guidelines of 1.5 mg/L and 10 µg/L. Water quality indexing (WQI-model) declared that 35.7% samples are unfit for household purposes. Saturation and undersaturation of minerals showed precipitation and mineral dissolution. Groundwater contamination by PCA-MLR and PMF-model interpreted five factors. The fitting results and R2 values of PMF (0.52–0.99)>PCA-MLR (0.50–0.95) showed high accuracy of PMF-model. Human health risk assessment (HHRA-model) revealed high non-carcinogenic and carcinogenic risk for children than adults. The percentile recovery of F- and As was recorded 98%, and 95% with reproducibility ± 5% error.