The river systems of east and southern Africa’s semi-arid areas are under severe stress due to several factors among which are climate change and variability as well as explosive population and urban growth. In these regions, water demand is outstripping supply, with water withdrawals being estimated to have increased six-folds during the twentieth century (IHE Delft 2002; Vörosmarty et al. 2005, Molden 2007). Widespread degradation of freshwater ecosystems has been reported in the region, with water quality declining due to increased pollution among other factors (Nel et al. 2011). This degradation of freshwater ecosystems inevitably compromises ecosystems service delivery and results in expensive management interventions and the ecosystems’ loss of resilience to the changing circumstances (Nel et al. 2011). In addition, increases in frequency and intensity of extreme weather events such as droughts and floods are complicating water resources management in the African continent and the southern African region in particular (Chigwada 2005; IPCC 2007, 2014, Darwall et al. 2009; Dube and Chimbari 2009; Mwendera 2010).