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Water is vital for human survival and ecosystem health. In arid and semi-arid areas like the Limpopo River Basin (LRB) in Southern Africa, water is a precious commodity. The study of spatial and temporal distribution of freshwater components is an important step toward sustainable planning and management of water resources. This case study applied the Soil and Water Assessment Tool (SWAT) to characterize freshwater availability and scarcity in the LRB. SWAT predictions of hydrologic fluxes in the basin are generally satisfactory when compared to measured streamflow records, although uncertainties persist in model estimates. Estimates of streamflow, herein referred to as blue water, varied from 0.2 to 570 mm/year between 1984 and 2013 over the basin. The analysis revealed alternating cycles of one to two years of water surplus periods and three to five years of dry periods during the study period. The results also indicated that, considering the natural water yield, 20% of the basin (mostly east) has enough water, while the remaining 80% continues to experience dryness and water stress. (C) 2019 European Regional Centre for Ecohydrology of the Polish Academy of Sciences. Published by Elsevier B.V. All rights reserved.