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Abstract The Mara River is the lifeline of the transboundary Mara basin across Kenya and Tanzania. The basin is considered one of the more serene subcatchments of the Lake Victoria Basin and ultimately the Nile Basin, and traverses the famous Maasai Mara and Serengeti National Parks. The basin also contains forests, large-scale farms, smallholder farms, pastoral grazing lands, as well as hunter gatherers and fishers. There is growing concern, however, regarding land degradation in the basin, particularly deforestation in the headwaters, that is affecting the natural resource base and the river flows. Accurate scientific data are required to advise policy, and to plan appropriate mitigation measures. This study utilizes remote sensing and geographical information system (GIS) tools, and hydrological and ground-truth studies to determine the magnitude of the land-use/cover changes in the Mara River Basin, and the effects of these changes on the river flows over the last 30 years. The study results indicate that land-use/cover changes have occurred. In 1973, for example, rangelands (savannah, grasslands and shrublands) covered 10 989 km2 (79%) of the total basin area. The rangelands had been reduced to 7245 km2 (52%) by 2000, however, while the forest areas were reduced by 32% over the same period. These changes have been attributed to the encroachment of agriculture, which has more than doubled (203%) its land area over the same period. The hydrology of the Mara River also has changed, with sharp increases in flood peak flows by 7%, and an earlier occurrence of these peaks by 4 days between 1973 and 2000. There is evidence of increased soil erosion in the upper catchments, with silt build-up in the downstream floodplains. This has caused the Mara wetland to expand by 387%, adversely affecting riparian agriculture. There is need for urgent action to stem the land degradation of the Mara River Basin, including planning and implementing appropriate mitigation measures.