The concentration of Cu, Fe, Pb, Zn and As in the surface water intended for human consumption and other uses in the Mantaro River basin were analysed using multivariate methods. The water samples were collected from seven water bodies in the Junín region in June 2019, in the low discharge period. In each body of water, a sector with six sampling sites was established. The Cu, Fe, Pb, Zn and As contents were determined by the flame atomic absorption spectrophotometry method. The correlation analysis revealed positive and significant correlations (P < 0.05) for the Zn/Pb, Pb/Fe and Zn/Fe pairs with a good association, higher than 0.80 and for the Pb/Cu, Fe/Cu, As/Pb and As/Zn pairs a weak degree of association (P < 0.05). The analysis of the main components showed three components with their own values > 1. The hierarchical grouping analysis classified the evaluated water bodies into three groups according to the concentration of the Cu, Fe, Pb, Zn and As. The high concentrations of heavy metals and arsenic recorded in the CIMIRM and MERIS irrigation channels reveal that the Mantaro River continues to be a sink for mine wastewater discharges and runoff from mining liabilities at the headwaters of the Mantaro basin. It is, therefore, necessary to implement urgent management policies to control and reduce the levels of contamination by potentially toxic metals and metalloids in the Mantaro River.