The Karamoja subregion of Uganda is in a state of flux. Rapid change to the livelihoods and economic integration of people living in the region is accompanied by prevailing uncertainties over future climate impacts, with implications for the future management and availability of water and grazing resources. These implications are important for a wider system within this corner of East Africa which we call the Karamoja-Turkana Complex. Neighboring groups in Kenya are part of this system and use resources of Karamoja as part of their livelihood strategies, sometimes bringing them into conflict with local populations. New water management investments aim to enhance the availability of surface water for livestock, to help protect against potential competition, particularly in water-scarce years. However, the location and management of these structures – part of wider efforts in implementing Integrated Water Resources Management (IWRM) – rarely take into account these wider system dynamics. We argue in this paper for a more comprehensive and system-wide perspective on water management in Karamoja and suggest an approach to do so. The paper will be of particular use to planners and agencies responding to the water development challenges in Karamoja in the context of rapid changes in livelihood systems.