In late December 2019, the emerging disease COVID-19 was identified as a global pandemic. Countries around the world have implemented various types of blockades to stop this infection. These health measures have led to a significant reduction in air pollution. However, the impact of these measures on aquatic environments has been little analyzed. In this context, the water quality of rivers in the Mantaro River basin was evaluated using multivariate statistical methods and heavy metal contamination indices during the health crisis of the COVID-19 pandemic. Surface water samples were collected in triplicate from 15 sampling sectors at the end of the rainy season, between March and April. Concentrations of Cu, Fe, Pb, Zn and As were determined by the method of atomic absorption flame spectrophotometry. The average concentrations of heavy metals and arsenic in the rivers evaluated did not exceed the environmental quality standards for drinking water of the Peruvian, WHO and US EPA regulations, except for Pb, Fe and As in the Mantaro River and As in the Chia River. PCA presented a total variation percentage of 83.8%. The results showed a clear positive relationship between the five heavy metals and metalloids. The hierarchical cluster analysis according to Spearman’s correlation generated a dendrogram where the five chemical elements were grouped in two statistically significant groups, one group conglomerating to Cu, Pb, Zn and Fe and the other group to As. PERMANOVA partition shows that the spatial effects of the sectors are strong and significant. The HPI revealed that 13.33% of the sampling sectors exceeded the critical contamination value (150). The C_d revealed low degree of contamination (<1) in 86.67% of the sampling sectors