The impact of global land use and land cover changes in relation to climate change and declining biodiversity has been a subject of interest in the recent years. Nonetheless, there is limited data capturing trends in land use and land cover changes in the Tanganyika catchment. This study characterized the trend in land use/ cover changes and examined the change in sediment and nutrients hotspot areas in the Kalimabenge microcatchment, for the last 40 years. Land use/cover change was quantified and reconstructed by analyzing a series of Landsat images taken in 1973, 1986, and 2010 using the Integrated Land and Water Information System (ILWIS) 3.3 software and field observations. Both supervised and non-supervised classifications were used in the classification of the Landsat images in order to obtain the land use/cover change map. Sediment and nutrient loading into the Kalimabenge micro-catchment were modeled using ArcSWAT software integrated in ArcGIS 9.3. ArcSWAT was calibrated using two years field observations at the river outlet into Lake Tanganyika. Results showed that the dominant land use/covers in the micro-catchment are cultivated land, followed by forest/tree plantations, grassland and built-up area. Grassland/savannah has declined gradually over time, forest/woodlot land increased gradually, built up areas acreage remained quasi similar, cultivated land followed a quadratic trend. The partial sources of sediments, runoff and phosphorous changed for the last 4 decades. These sources areas first decreased in 1986 and then increased in 2010.