This article contains data on the concentration of heavy metals and metalloids in the water of seven rivers in the Mantaro river watershed in the central Andes of Peru, collected during the autumn of 2019. The concentrations of Cu, Fe, Pb, Zn and As were determined by flame atomic absorption spectrophotometry to assess human risk. The concentration of heavy metals and arsenic varied according to the sector of the rivers evaluated. The cluster analysis identified four different groups among the observation sectors. The risk assessment for humans was conducted on the basis of exposure doses to heavy metals and arsenic in water by ingestion and dermal pathways, using standard methods established by USEPA. These data can be reused as a basis for estimating the cancer risk or as a comparison group for future risk studies. They can also be useful to public health policy makers when proposing surveillance and control programmes using remedial technologies.