Groundwater contamination by potentially harmful elements (PHEs) originating from the weathering of granitic and gneissic rock dissolution poses a public health concern worldwide. This study investigated physicochemical variables and PHEs in the groundwater system and mine water of the Adenzai flood plain region, in Pakistan, emphasizing the fate distribution, source provenance, chemical speciation, and health hazard using the human health risk assessment HHRA-model. The average concentrations of the PHEs, viz., Ni, Mn, Cr, Cu, Cd, Pb, Co, Fe, and Zn 0.23, were 0.27, 0.07, 0.30, 0.07, 0.06, 0.08, 0.68, and 0.23 mg/L, respectively. The average values of chemical species in the groundwater system, viz., H+, OH−, Ni2+, Mn2+, Mn3+, Cr3+, Cr6+, Cu+, Cu2+, Cd2+, Pb2+, Pb4+, Co2+, Co3+, Fe2+, Fe3+, and Zn2+, were 1.0 × 10−4 ± 1.0 × 10−6, 1.0 × 10−4 ± 9.0 × 10−7, 2.0 × 10−1 ± 1.0 × 10−3, 3.0 × 10−1 ± 1.0 × 10−3, 1.0 × 10−22 ± 1.0 × 10−23, 4.0 × 10−6 ± 2.0 × 10−6, 4.0 × 10−11 ± 2.0 × 10−11, 9.0 × 10−3 ± 1.0 × 10−2, 2.0 × 10−1 ± 2.0 × 10−3, 7.0 × 10−2 ± 6.0 × 10−2, 5.0 × 10−2 ± 5.0 × 10−2, 2.0 × 10−2 ± 1.5 × 10−2, 6.0 × 10−2 ± 4.0 × 10−2, 8.0 × 10−31 ± 6.0 × 10−31, 3.0 × 10−1 ± 2.0 × 10−4, 4.0 × 10−10 ± 3.0 × 10−10, and 2.0 × 10−1 ± 1.0 × 10−1. The mineral compositions of PHEs, viz. Ni, were bunsenite, Ni(OH)2, and trevorite; Mn viz., birnessite, bixbyite, hausmannite, manganite, manganosite, pyrolusite, and todorokite; Cr viz., chromite and eskolaite; Cu viz., CuCr2O4, cuprite, delafossite, ferrite-Cu, and tenorite; Cd viz., monteponite; Pb viz, crocoite, litharge, massicot, minium, plattnerite, Co viz., spinel-Co; Fe viz., goethite, hematite, magnetite, wustite, and ferrite-Zn; and Zn viz., zincite, and ZnCr2O4 demarcated undersaturation and supersaturation. However, EC, Ca2+, K+, Na+, HCO3−, Cr, Cd, Pb, Co, and Fe had exceeded the WHO guideline. The Nemerow’s pollution index (NPI) showed that EC, Ca2+, K+, Na+, HCO3−, Mn, Cd, Pb, Co, and Fe had worse water quality. Principal component analysis multilinear regression (PCAMLR) and cluster analysis (CA) revealed that 75% of the groundwater contamination originated from geogenic inputs and 18% mixed geogenic-anthropogenic and 7% anthropogenic sources. The HHRA-model suggested potential non-carcinogenic risks, except for Fe, and substantial carcinogenic risks for evaluated PHEs. The women and infants are extremely exposed to PHEs hazards. The non-carcinogenic and carcinogenic risks in children, males, and females had exceeded their desired level. The HHRA values of PHEs exhibited the following increasing pattern: Co > Cu > Mn > Zn > Fe, and Cd > Pb > Ni > Cr. The higher THI values of PHEs in children and adults suggested that the groundwater consumption in the entire region is unfit for drinking, domestic, and agricultural purposes. Thus, all groundwater sources need immediate remedial measures to secure health safety and public health concerns.