Benthic macroinvertebrates, which serve as crucial bioindicators of aquatic ecosystem health, face growing threats from increasing anthropogenic pressures, yet long-term studies in Afrotropical regions remain scarce. This study examines temporal and spatial changes in macroinvertebrate communities along a longitudinal gradient from headwaters to the Kenya-Tanzania border in Kenya's Mara River over 15 years (2008–2009 to 2021–2023). We found significant temporal shifts in community composition. Biodiversity increased from 2008-2009 to 2021–2023, and we found significant heterogeneity at downstream sampling sites. We also found that elevation, velocity, temperature, and dissolved oxygen were crucial drivers of community composition.
Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa exhibited peak abundances at specific elevations of 1500 m, 1800 m, and 1600 m, respectively. The South African Scoring Systems (SASS) scores reflected a decline in ecological health, with most sites transitioning from "Natural" to "Good" conditions from 2008-2009 to 2021-2023. These findings underscore the need for continued monitoring and conservation to mitigate environmental impacts and preserve freshwater biodiversity in the Mara River. Documentation of temporal changes in tropical rivers is rare, highlighting the critical need for ongoing monitoring and conservation efforts to mitigate environmental change's impacts and preserve the Mara River's freshwater biodiversity. This study provides valuable insights for managing riverine ecosystems under increasing anthropogenic pressure.