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The impact and uncertainty of climate change on the hydrology of the Mara River basin (MRB) was assessed. Sixteen global circulation models (GCMs) were evaluated, and five were selected for the assessment of future climate scenarios in the basin. Observed rainfall and temperature data for the control period (1961–1990) were combined with expected GCMs output using the delta and direct statistical downscaling methods and three greenhouse gas emission scenarios (A1B, A2 and B1). Uncertainties of climate change were addressed through compare and contrast of results across diverse GCMs, future climate scenarios and the two downscaling methods. Both methods produced a relatively similar annual rainfall amount, but their monthly and daily pattern showed considerable differences. The relative advantages and disadvantages of implementing one method over the other were also explored. The hydrologic impact of climate change in the basin was assessed using Soil and Water Assessment Tool. The model was calibrated and validated with observed data in the control period with (Nash–Sutcliff efficiency, coefficient of determination) results of (calibration: 0.68, 0.69) and (validation: 0.43, 0.44) at Mara Mines. Results have shown a statistically significant increase in flow volume of the Mara River flow at Mara Mines for the year 2046–2065 and 2081–2100. With due attention to the limitations, findings of this study have a wider application for water resources sustainability analysis in the MRB in the face of uncertainties due to climate change.