Sedimentation is a major problem for agricultural dams in Botswana, as it reduces the storage capacity and life span of the reservoirs. The process of sedimentation starts from day one of the impounding of water in any given reservoir. Even though a provision is made for every reservoir during planning for a certain storage capacity, specifically for sediment deposition, called dead storage, a major portion of the sediment gets deposited for many years of the reservoir’s life in areas other than the dead storage, and this trend cannot be reversed at easy cost. This study is aimed at the analysis of prevailing sedimentation processes in the nearby dozens of dams found in the Lotsane catchment located within the Limpopo Basin of Botswana, and focuses on assessment of annual sedimentation rate. A spatial analysis and modelling study was conducted based on the Revised Universal Soil Loss Equation and GIS to determine sediment yield and degree of impact of each reservoir for a given landscape, rainfall and catchment heterogeneity. Field observations and soil sampling were carried out in order to determine the factors that lead to reservoir sedimentation. Spatial data on the dams in Lotsane catchment were also collected from Ministry of Agriculture, which were used for ground-truthing, GIS-based calculations and model validation. The average sediment rate and sediment delivery ratio were found to be 1.74 t/ha/year and 81%, respectively. These are useful parameters to estimate service life of the dams and plan remedial measures related to sedimentation problems.