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Benthic invertebrate communities have been poorly studied in Andean streams apart from the Patagonian region. The primary objective of this work was to analyse the faunal composition at three different altitudes and to observe whether there were differences in aquatic insect community structure at spatial and temporal scales. Physicochemical variables were measured on a monthly basis. Sixteen families were found, the most frequent and abundant taxa being Massartellopsis (Ephemeroptera), Andesiops (Ephemeroptera), Metrichia neotropicalis (Trichoptera), Cailloma lucidula (Trichoptera), Austrelmis (Coleoptera), and the Chironomidae (Diptera). There was a change in benthic composition associated with land use and with the diminution of water quality from the headwaters to the mouth of the system. The middle reach was a transitional area where headwater species coexisted with species characteristic of the lower reach, with Austrelmis and the family Chironomidae being the most abundant elements.