Telmatobius macrostomus and Telmatobius brachydactylus are two high Andean aquatic frogs categorized as “Endangered” by the Red List of the International Union for Conservation of Nature and by the Peruvian Legislation. With the aim of evaluating the water quality of their habitats, four bimonthly samplings in the field were carried out at 12 study sites located in the Junin and Pasco regions of Peru. Physicochemical, hydrological and microbiological variables were measured. Samples of aquatic macroinvertebrates were taken and the following water quality indices were applied: Andean Biotic Index (ABI) and Family Biotic Index (FBI). The results show that the environmental variables total dissolved solids (TDS) and total coliforms exceed the Environmental Quality Standards (ECA) for water according to Peruvian regulations. The aquatic macroinvertebrate community showed differences in its community structure between sampling stations and indicated moderate to good water quality according to the applied indices, except in the stations that would be being impacted by cattle farming and chuño production (ancestral activity whereby freeze-dried potatoes are fermented in cold, running stream water), both activities impact the water quality of the studied habitats and could influence the presence of frogs, because both species generally inhabit clean aquatic ecosystems.