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Scientists and managers of natural resources have recognized an urgent need for improved methods and tools to enable effective adaptation of management measures in the face of climate change. This paper presents an Adaptation Design Tool that uses a structured approach to break down an otherwise overwhelming and complex process into tractable steps. The tool contains worksheets that guide users through a series of design considerations for adapting their planned management actions to be more climate-smart given changing environmental stressors. Also provided with other worksheets is a framework for brainstorming new adaptation options in response to climate threats not yet addressed in the current plan. Developed and tested in collaboration with practitioners in Hawai'i and Puerto Rico using coral reefs as a pilot ecosystem, the tool and associated reference materials consist of worksheets, instructions and lessons-learned from real-world examples. On the basis of stakeholder feedback from expert consultations during tool development, we present insights and recommendations regarding how to maximize tool efficiency, gain the greatest value from the thought process, and deal with issues of scale and uncertainty. We conclude by reflecting on how the tool advances the theory and practice of assessment and decision-making science, informs higher level strategic planning, and serves as a platform for a systematic, transparent and inclusive process to tackle the practical implications of climate change for management of natural resources.