The delicate balance between human utilization and sustaining its pristine biodiversity in the Mara River basin (MRB) is being threatened because of the expansion of agriculture, deforestation, human settlement, erosion and sedimentation and extreme flow events. This study assessed the applicability of the Soil and Water Assessment Tool (SWAT) model for long-term rainfall–runoff simulation in MRB. The possibilities of combining/extending gage rainfall data with satellite rainfall estimates were investigated. Monthly satellite rainfall estimates not only overestimated but also lacked the variability of observed rainfall to substitute gage rainfall in model simulation. Uncertainties related to the quality and availability of input data were addressed. Sensitivity and uncertainty analysis was reported for alternative model components and hydrologic parameters used in SWAT. Mean sensitivity indices of SWAT parameters in MRB varied with and without observed discharge data. The manual assessment of individual parameters indicated heterogeneous response among sub-basins of MRB. SWAT was calibrated and validated with 10 years of discharge data at Bomet (Nyangores River), Mulot (Amala River) and Mara Mines (Mara River) stations. Model performance varied from satisfactory at Mara Mines to fair at Bomet and weak at Mulot. The (Nash–Sutcliff efficiency, coefficient of determination) results of calibration and validation at Mara Mines were (0.68, 0.69) and (0.43, 0.44), respectively. Two years of moving time window and flow frequency analysis showed that SWAT performance in MRB heavily relied on quality and abundance of discharge data. Given the 5.5% area contribution of Amala sub-basin as well as uncertainty and scarcity of input data, SWAT has the potential to simulate the rainfall runoff process in the MRB. Copyright © 2012 John Wiley & Sons, Ltd.