The prairie pothole region (PPR) in the north-central United States and south-central Canada constitutes the most important waterfowl breeding area in North America. Projected long-term changes in precipitation and temperature may alter the drivers of waterfowl abundance: wetland availability and emergent vegetation cover. Previous studies have focused on isolated wetland dynamics, but the implications of changing precipitation on managed, river-fed wetlands have not been addressed. Using a structured decision making (SDM) approach, we derived optimal water management actions for 20 years at four river-fed National Wildlife Refuges (NWRs) in North and South Dakota under contrasting increasing/decreasing (+/−0.4 %/year) inflow scenarios derived from empirical trends. Refuge pool depth is manipulated by control structures. Optimal management involves setting control structure heights that have the highest probability of providing a desired mix of waterfowl habitat, given refuge capacities and inflows. We found optimal seasonal control structure heights for each refuge were essentially the same under increasing and decreasing inflow trends of 0.4 %/year over the next 20 years. Results suggest managed pools in the NWRs receive large inflows relative to their capacities. Hence, water availability does not constrain management; pool bathymetry and management tactics can be greater constraints on attaining management objectives than climate-mediated inflow. We present time-dependent optimal seasonal control structure heights for each refuge, which are resilient to the non-stationary precipitation scenarios we examined. Managers can use this information to provide a desired mixture of wildlife habitats, and to re-assess management objectives in reserves where pool bathymetry prevents attaining the currently stated objectives.