Most of the rivers in the Afrotropics emerge from forested uplands that are prime for human activities, including crop farming, grazing and settlement. However, streams draining these areas have a low diversity of fishes, which limits their use as indicators of water quality and ecological status. Here, we developed macroinvertebrate-and fish-based indices of biotic integrity and evaluated their responses to human activities in the Sondu-Miriu River, Kenya. Overall, water quality declined downstream because of the cumulative effects of human activities. The upper reaches had poor fish diversity with at most three species, but macroinvertebrate communities were diverse on the entire gradient of the river. Metrics that have been used to develop indices of biotic integrity in the Lake Victoria basin were selected and evaluated for responsiveness to various forms of human disturbance along the river. The poor diversity of fishes in the upper reaches limited the number of metrics that could be developed and evaluated. The fish index was only successfully applied in the middle and lower reaches where fish diversity was high. However, macroinvertebrates were diverse and sensitive to human activities on the entire gradient of the river. This study shows that for biomonitoring, macroinvertebrate communities offer a better alternative to fishes in high elevation Afromontane streams that harbour poor fish assemblages.