During its journey, the river water suffers natural or anthropic contamination, deteriorating its quality. This impact can be qualified by determining the pollution Indexes (IPO). The work aimed to evaluate the spatial and temporal variation of the IPOs in the water of the high Andean micro-basin of the Chumbao River. The study included the section from 13°46’38.4” S, 73°15’32.3” W at 4079 m of altitude up to 13°35’26.4” S, 73°27’00.8” W at 2572 m of altitude. Physical, chemical, and microbiological parameters of the water were determined in 8 points along the river. These were grouped to calculate the IPO by mineralization (IPOMI), organic matter (IPOMO), suspended solids (IPOSUS), and trophic (IPOTRO) in the dry and rainy seasons. The indexes were categorized from 0.0 (not polluted) to 1.0 (highly polluted). The data were collected in triplicate and valuated through ANOVA and Tukey’s test. It was found that IPOSUS, IPOMI, and IPOMO. The points near the head of the micro-basin reported no and low pollution, besides, they increased considerably in urban areas reaching highly polluted levels. In contrast, IPOTRO reported a eutrophic state, and that contamination levels were higher in the dry season. The waters of the Chumbao River above 2900 m of altitude and close to the head of the micro-basin do not show contamination, but in the urban area the index of pollution is high.