Many streams and rivers outside conservation areas across the Afrotropics face multiple stressors from land use change, urbanization, and excessive water withdrawals. Thus, there is a need to develop cost-effective tools for assessing and monitoring ecological changes to inform management decisions. Studies utilizing macroinvertebrate communities as indicators of the ecological condition of streams and rivers in the Afrotropics use diverse methods, including diversity, richness, biotic and multimetric indices. However, some of these indices are region- or country-specific, which limits their general use across multiple regions or countries. In this study, we address this challenge by testing and comparing the performance of diversity and richness indices (e.g., Shannon-Wiener and Simpson), regional biotic indices (the African Scoring System Version 5 [SASS5], Tanzanian River Scoring System [TARISS] and a biotic index developed for the Ethiopian highlands [ETHbios]), and a macroinvertebrate-based index of biotic integrity (M-IBI) in assessing the ecological condition of Afrotropical rivers with the transboundary Mara River, Kenya and Tanzania, as a case study. In this study, we analyzed water and habitat quality degradation caused by multiple stressors such as land use change, organic pollution and flow alteration and the corresponding responses in macroinvertebrate communities. We utilized macroinvertebrates data collected from 143 sites covering the entire gradient of the river and its major tributaries in Kenya and Tanzania. To develop the M-IBI, we used 12 metrics that describe macroinvertebrate community richness, composition, tolerance to disturbances (indicator taxa), and the composition of functional feeding groups. Although all the biotic indices were sensitive to poor water quality and human disturbance of the river, the M-IBI performed better than biotic indices (SASS5, Tanzanian River Scoring System, and Ethiopian highlands), diversity and richness indices by having a higher discriminatory ability of site categories according to different levels and types of disturbance. Diversity and richness indices performed poorly and failed to discriminate between stressor gradients in the river. This study demonstrates a need for testing and evaluating indices or protocols before adoption and use in biomonitoring streams and rivers in other countries and regions. There is an even greater need to assess the tolerance of macroinvertebrate taxa before inclusion in biotic indices for improved performance as discriminators of multiple stressors.