Abstract: The transboundary Mara River across Kenya and Tanzania and draining in to Lake Victoria has undergone major anthropogenic changes affecting its land cover over the past 50 years. However, these changes have not been quantified in a manner to allow wider scale understanding of the causative factors, their effects and show hot spots that required immediate intervention. To address these issues, a study of the land use/land cover change was done based on interpretation of digital LANDSAT TM and ETM images of 1986 and 2000 respectively with Idrisi Kilimanjaro software. In a separate addition, analyses of hydrological factors was done which involved comparing monthly mean flow hydrographs to assess changes in flow characteristics of the Mara river immediately after the basin forests. The results obtained showed 2.3 % deforestation, 0.7% reforestation, 20.9% of the basin was opened up for agriculture and 7.5% changed to wetlands. Hydrological investigations showed that river flow regimes have changed, with sharp increases in peaks, attenuation of the river hydrographs and reduction in base flows, factors that could not be linked to changes in rainfall amounts and characteristics but related to modifications of the land surface induced by artificial influences of the man in the basin.