Fluvial systems are the most threatened ecosystems in the world by the development of anthropogenic activities. Advancing in the knowledge of the ecology of these systems is the basis for the creation of adequate management measures for the conservation of these systems. This study provides relevant background information on the structure of macroinvertebrate and fish assemblages in six tributary rivers of the Biobio River Basin, a basin characterised by high hydrological alteration and fragmentation index. Our results describe a good environmental condition in the rivers evaluated, with the Lirquen, Quilme and Mininco rivers standing out as water courses with a high richness and diversity of macroinvertebrate and fish species. Structurally, these rivers are a refuge for native fish species classified as Endangered (Nematogenys inermis, Bullockia maldonadoi, Percilia irwini, Diplomystes nahuelbutaensis). In this sense, the fundamental role of these as reservoirs of species and the importance at basin level of maintaining the connectivity of these tributaries with the main course, and not only the conservation of each river in a segregated way, is pointed out.