The water resources of southern Africa have featured centrally in the global literature on water conflict and cooperation. This scholarship has appeared in two waves: (1) the post‐Cold War focus on resource scarcities and the possibility of 'water wars' and (2) the mid‐2000s rise of fears surrounding the impact of a changing climate on water resource regimes. The first wave, in the region, ironically resulted in a significant body of scholarship demonstrating the predominance of cooperation rather than conflict. The second wave has served primarily as a spur to better governance and management, and to better integration across the policy making landscape. Running as something of a countercurrent to these dominant trends, is critical scholarship that focuses primarily on water rights and regards conflict as a necessary means to more equitable resource access ends. A key challenge for scholars of water conflict and cooperation across the region is, therefore, to reconcile both theoretically and practically the macro studies of largely transboundary water politics with the micro studies of social struggles for water in urban and rural settings. The article concludes that for a third wave of studies to add value to questions of regional water security, scholars must (1) recognize the simultaneous presence of conflict and cooperation, (2) acknowledge that not all conflict is bad, neither is all cooperation good, (3) approach the analysis more systematically through hard data gathering, and (4) read beyond their disciplines in order to more fully understand the social dynamics of the region.