Riverine pollution is an increasing threat to ecosystem integrity and economic development, thus a need for effective monitoring to guide the management of ecosystem health. Opportunely, aquatic macroinvertebrates have been proven to indicate the health status of the rivers. However, there is scanty information about their use in Rwanda. This study used macroinvertebrates to assess the water quality of the Nyabarongo and Akagera Rivers following the Tanzania River Scoring System (TARISS). The study was carried out between May 2023 and March 2024 and covered 13 sampling sites. Macroinvertebrates were collected using a kick sampling method while water samples were collected following standard methods for measuring water properties. Sites were clustered, and multivariate methods were used to assess dissimilarities in taxa distribution. Further, the Focal Principal Component Analysis (FPCA) was performed to assess the association of macroinvertebrates with water physico-chemical parameters. Collected macroinvertebrates belonged to 34 families dominated by Chironomidae, Baetidae, and Culicidae. The TARISS metrics (mean ± standard deviation) indicated a score of 44.53 (± 2.69), a taxa number of 11 (± 0.6), and an average scope per taxa (ASPT) of 4.07 (± 0.8). Dissolved oxygen had a significant positive influence on the distribution and abundance of the Libellulidae family. Conversely, dissolved oxygen and electric conductivity had a significant negative relationship with the Caenidae and Aeshnidae families, respectively. The low values of the TARISS metrics portend the poor water quality of the Nyabarongo and Akagera Rivers. Thus, management practices and regular biomonitoring are recommended to ensure that the ecosystem health of these rivers is maintained.