One of the major constraints on sustainable development in the semi-arid areas of Africa is the supply and access to a range of natural resources underpinned by water. Water is needed to support domestic use, agriculture and the preservation of wildlife. With increasing human populations and drive for development, pressure is exerted to harness water resources for higher economic uses instead of developing and adopting an integrated approach. In an integrated approach the various needs and provisions for sustainable livelihoods and ecosystem conservation are assessed and balanced. However, the linkages between water resource management, sustainable livelihoods and biodiversity conservation are poorly known. As a result river basin management programmes and policy initiatives in Africa have evolved independently, often with overlapping and/or conflicting goals and responsibilities. The outcomes from this have been persistent within-country and trans-boundary conflicts; leading to increased poverty and declines in biological diversity. Within this context the Mara River basin has been used as a case study to better understand the potential linkages, conflicts and complementarities amongst existing management programmes and policy initiatives. Many policy initiatives to manage different aspects of the ecosystem services provided by the transboundary river have evolved independently, often with overlapping, even conflicting objectives and responsibilities. To reap the desired improvements in human livelihoods, biodiversity conservation and water resources in the basin, a holistic systems approach to managing the Mara river and coordination amongst responsible authorities are required.