Equatorial rivers of East Africa exhibit unusually complex seasonal and inter-annual flow regimes, and aquatic and adjacent terrestrial organisms have adapted to cope with this flow variability. This study examined the annual flow regime over the past 40 years for three gauging stations on the Mara River in Kenya and Tanzania, which is of international importance because it is the only perennial river traversing the MaraSerengeti ecoregion. Select environmental flow components were quantified and converted to ecologically relevant hydraulic variables. Vegetation, macroinvertebrates, and fish were collected and identified at target study sites during low and high flows. The results were compared with available knowledge of the life histories and flow sensitivities of the riverine communities to infer flow–ecology relationships. Management implications are discussed, including the need to preserve a dynamic environmental flow regime to protect ecosystems in the region. The results for the Mara may serve as a useful model for river basins of the wider equatorial East Africa region.