Climate change and the extreme weather associated with it can be a major challenge to natural resource managers charged with the protection, restoration, recovery, and management of wetlands and wildlife habitats. Forecasting the potential impacts of climate changes will be important for decision-makers and land managers seeking to minimize impacts to habitats, infrastructure, and wildlife populations and prepare for the future. In collaboration with U.S. Fish and Wildlife Service (FWS) managers, we developed a climate change vulnerability assessment to spatially evaluate climate vulnerabilities across the Midwest region. To create the vulnerability assessment, we convened resource managers and scientists working across the region to determine the components and scope of the vulnerability assessment. The vulnerability assessment was watershed-based and composed of 15 indicators of climate change and five indicators that reflect the capacity of a watershed to buffer against the effects of climate change. The indicators were selected by FWS managers to have broad applicability across systems and programs in the FWS. To facilitate usability, we created an online application that allows users to generate customizable vulnerability assessments. We then integrated the assessment into a process for engaging in climate change adaptation thinking as a precursor to formal planning, implementation, and monitoring of adaptation actions. The process we designed focused on understanding the components of the system, assessing climate change vulnerabilities, creating and describing possible climate change scenarios, and identifying impacts and adaptation options for each scenario. We piloted this process in a virtual workshop setting with FWS managers and biologists on the topic of managed wetland systems. This work is currently being used by the FWS to better understand regional vulnerabilities and adaptation strategies and to advance integration of climate science into formal planning processes.