The study evaluated microbial and Potentially Toxic Elements—PTEs risks in high Andean river water in Peru using Monte Carlo simulation. A total of 144 water samples were collected from four rivers and evaluated for physicochemical parameters, PTEs and bacterial pathogens. The microbial risk analysis for exposure to pathogens present in the water was based on the probability of occurrence of diseases associated with Escherichia coli, Pseudomonas aeruginosa and enterococci. PTEs risk analysis was performed using a Monte Carlo simulation approach. The results showed that the highest microbial risk due to exposure to water contaminated by E. coli, P. aeruginosa and enterococci was recorded in the Miraflores and Chia rivers. Meanwhile, the analysis of carcinogenic and non-carcinogenic risk by PTEs in adults and children revealed that the Chia river presents a high risk of contamination by PTEs, especially the carcinogenic risk for children. The Monte Carlo simulation indicated a 56.16% and 94.85% probability of exceeding the limit value of 0.0001 for carcinogenic risk in adults and children, respectively. It can be concluded that children consuming the waters of the Chia river are potentially at risk of As toxicity.