Inter-basin water transfers (IBTs) are a major form of river basin manipulation. In southern Africa they are increasingly being used to reconcile the problems of water distribution within the region. Despite their high cost and ‘high profile’ in terms of the complex engineering and technical inputs that they require, the ecological and social implications of such schemes have been, and continue to be, inadequately addressed. Many rivers in southern Africa are shared resources, flowing through or between more than one province or country. The combined effect of climatic stochasticity, rapid population growth and inefficient water infrastructure is increasing the pressure on the river ecosystems of the region. As stresses on rivers continue to increase, re-distribution networks are rapidly assuming the status of a ‘growth industry’, but they have a disturbing and unaddressed potential for intra- and international conflict and for severe ecosystem perturbation. This paper examines inter-basin water transfer schemes at three levels in terms of spatial and temporal scales in southern Africa. Each scheme augments water supply to the industrial centre of South Africa, the Province of Gauteng. We have selected a temporary intra-basin scheme built for emergency supply within the Vaal River (the major tributary of the Orange River), an inter-provincial scheme involving transfer of water from the Tugela River in KwaZulu/Natal to the Vaal River, and an international transfer scheme centred in Lesotho (the Lesotho Highlands Water Project), which shortly will move water from the headwaters of the Orange River, again to the Vaal River. These schemes illustrate some of the extremely complex ecological, geomorphological, chemical, social and political ramifications that occur when river basins are manipulated for water supply. Although pleas for detailed ecological studies of the effects of IBTs have been made over the past decade, they have fallen on deaf ears in administrative, engineering and political circles. We again caution that IBTs can be highly problematic, and expand the plea for intelligent and integrated planning and management, and for strict adherence to Environmental Impact Assessment (EIA) and Integrated Environmental Management (IEM) procedures for both future and extant schemes in the region.