High arsenic (As), fluoride (F-), and microbial pathogens coexist in semiarid conditions afflicting > 240 million people worldwide including Pakistan. Groundwater quality has declined due to geogenic and manmade activities providing suitable ground for ubiquity, bioavailability, and toxicity of contaminants. We tested the health hazard, distribution, and apportionment of As, F-, and microbes in groundwater around coal mines in Quetta, Pakistan. The range of As, and F- concentrations in groundwater were 0.2–16.6 µg/L, 0.4–18.5 mg/L. Both, As and F- correlate with high HCO3-, pH, Na+, SO42-, Fe, and Mn, and negatively with Ca2+ water. The coalfield showed many folds higher As 15.8–28.5 µg/L, and F- 10.8–34.5 mg/L compared to groundwater-wells. Geochemical phases revealed saturation of groundwater with calcite, dolomite, fluorite, gypsum, and undersaturation with halite-mirabilite, and arsenopyrite minerals. The positive matrix factorization (PMF) model assessed five-factor solutions: geogenic, industrial, coal mining, sulfide & fluoride-bearing mineral-dissolution, and agriculture pollution delivered As, F-, and microbial contamination. About 24.6 % and 64.4 % of groundwater samples exceeded the WHO guidelines of As 10 µg/L, F- 1.5 mg/L. The carcinogenicity, and non-carcinogenicity of As, and F- were higher in children than adults. Therefore, health hazards in children are of great concern in achieving sustainable management goals.