Over the past four decades, Lake Victoria basin has experienced drastic environmental changes on account of both natural and anthropogenic factors. The natural factors include prolonged droughts and the recent emergence of water hyacith in the lake, while anthropogenic factors include the deforestation rates, poor agricultural practices, and destruction of critical wetlands. This study examines the potential impact of deforastation on rainfall over the lake basin. To assess the potential impact of deforestation on rainfall over the region, the General Circulation Model (GCM) ECHAM5 was applied. ECHAM5 was used to predict the possible impact of land cover and land use changes on rainfall using land cover and land use scenarios based on the integrated model to Assess Global Environment (IMAGE). The projected vegetation cover for 2050 was used to model the impact of deforestation, which indicated a general decrease in the canopy. The results from the model indicated a decrease in rainfall over many parts, although some areas showed increased rainfall. From the study we conclude that while deforestation has an impact on climate, there seem to be a complex interaction between forest and the rainfall generation mechanism.