In the tropical high mountains, human activities have strongly intensified in recent decades. Agricultural frontier movement toward higher elevations, river channel modifications, mining, and urban waste discharge threaten river ecosystem health, which is even more alarming when drinking water supply comes from surface water. The aim of the current study was to evaluate the ecological status of high mountain fluvial networks of tropical Andean catchments based on the definition of different river types. Physical–chemical variables and macroinvertebrate communities were sampled in 90 stations of seven tropical high mountain catchments. River habitat and riparian vegetation quality were further evaluated. K-means classification, using physical and hydro-morphological characteristics, identified six different river types. This classification was further refined to five river types by the analyses of macroinvertebrate communities through multidimensional scaling and analysis of similarity. The anthropogenic pressure gradients, present in the different river types, were inorganic (i.e., conductivity, turbidity), organic (i.e., fecal coliforms), river habitat, and riparian vegetation quality. Macroinvertebrate communities responded to different environmental variables in the páramo, mountain forest with humid shrub, urban, and Tarqui river types. Heterogeneous fluvial habitats and high altitude favored taxa such as Atanatolica, Mortoniella, Helicopsyche, Anacroneuria, Paltostoma, Helicopsyche, Paltostoma, Atopsyche, Pheneps, and Maruina. Chironomidae and Psychoda dipteran were associated with higher biochemical oxygen demand, lower oxygen concentration, high fecal coliforms, and total dissolved solids, while Haitia was linked to elevated nitrate concentrations. Integrated watershed management could benefit from a well-established biomonitoring network, considering different river types, which represents the natural variability of the ecosystems, as well as anthropogenic pressure gradients.