Transboundary water relations in Southern Africa are governed by an elaborate and intricate policy framework. In spite of this framework, the future of sustained cooperation on water utilisation in the region is still precarious and uncertain. Some subtle and unresolved dilemmas that may constrain future cooperation need to be dealt with. Two of these underlying dilemmas, namely the importance attached to national sovereignty and the strategic nature of water in the region, are explored in this article. These dilemmas form critical undercurrents that steer nations away from cooperation, cause stagnation in policy implementation and hamper progress in facilitating sustained solutions in transboundary water issues. Stemming from this background, this article argues for (a) the importance of a stronger regional perspective on water to steer countries away from the need to protect sovereign interests and (b) addressing the nature of current power relations in the region where water is concerned.