Water is critical to protecting wetlands in arid regions, especially in agriculture-dominated watersheds. This comparative case study analyzes three federal wildlife refuges in the Bear River Basin of the U.S. West where refuge managers secured water supplies by adapting to their local environmental context and their refuge’s relationship to agriculture in being either irrigation-dependent, reservoir-adjacent or diked-delta wetlands. We found that each refuge’s position confers different opportunities for securing a water supply and entails unique management challenges linked to agricultural water uses. Acquiring contextually-appropriate water rights portfolios was important for protecting these arid region wetlands and was accomplished through various strategies. Once acquired, water is managed to buffer wetlands against fluctuations caused by a dynamic climate and agricultural demands, especially during droughts. Management plans are responsive to needs of neighboring water users and values of the public at large. Such context-specific adaptations will be critical as the West faces climate change and population growth that threaten wetlands and agricultural systems to which they are linked.