Numerous ephemeral rivers and thousands of natural pans characterize the transboundary Iishana-System of the Cuvelai Basin between Namibia and Angola. After the rainy season, surface water stored in pans is often the only affordable water source for many people in rural areas. High inter- and intra-annual rainfall variations in this semiarid environment provoke years of extreme flood events and long periods of droughts. Thus, the issue of water availability is playing an increasingly important role in one of the most densely populated and fastest growing regions in southwestern Africa. Currently, there is no transnational approach to quantifying the potential storage and supply functions of the Iishana-System. To bridge these knowledge gaps and to increase the resilience of the local people’s livelihood, suitable pans for expansion as intermediate storage were identified and their metrics determined. Therefore, a modified Blue Spot Analysis was performed, based on the high-resolution TanDEM-X digital elevation model. Further, surface area–volume ratio calculations were accomplished for finding suitable augmentation sites in a first step. The potential water storage volume of more than 190,000 pans was calculated at 1.9 km3. Over 2200 pans were identified for potential expansion to facilitate increased water supply and flood protection in the future.