Water bodies have suffered degradation due to the discharge of pollutants, including potentially toxic elements (PTEs), primarily from mining operations. One such instance is the extraction of metallic elements in Taxco de Alarcón, Mexico. In this study, elements were analysed by Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) in 11 points of Acamixtla, Taxco, and San Juan Rivers. The data analysis included principal components analysis (PCA) and determination of Heavy-Metals and Metalloids Pollution Index (HMPI), as well as their Health Risk Assessment. Additionally, solid samples from RSJMG S2.3 were characterized by Fourier Transform-Infrared Spectroscopy (FT-IR) and Scanning Electron Microscopy (SEM). The elements (As, Cr, Ni, Zn, Fe, Mn, Cu, Cd, Pb, Se, and Li) were identified in the water samples. PCA revealed that component one, accounted for 82.8% of the variability data, and Pearson correlation analysis showed a significant (p < 0.05) correlation of Fe with As, Cu, Pb, and Zn. The highest HMPI (8491.52) was detected at RSJMG S2.3 point. Other points exhibited a 96.45 % to 100% lower exposure than RSJMG S2.3 point, that could be due to metal complexation with naturally occurring mineral ferrihydrite (Fe10 O14(OH)2), that was identified by SEM and FTIR in solids collected at the RSJMG S2.3 point. For Health Risk Assessment, the chronic oral daily intake and dermal exposure were predominant in all points impacted by leachates downstream of the San Juan River. Likewise, for the elements Cd, As and Zn were highest values and all sites presented high hazard index.