Sea-level rise, potential changes in the intensity and frequency of storms, and consequent shoreline erosion and flooding will have increasing impacts on the economy and culture of coastal regions. A growing body of evidence suggests that coastal ecosystems—natural infrastructure—can play an important role in reducing the vulnerability of people and property to these impacts. To effectively inform climate adaptation planning, experts often struggle to develop relevant local and regional information at a scale that is appropriate for decision-making. In addition, institutional capacity and resource constraints often limit planners’ ability to incorporate innovative, scientifically based approaches into planning. In this paper, we detail our collaborative process in two coastal California counties to account for the role of natural infrastructure in climate adaptation planning. We used an interdisciplinary team of scientists, economists, engineers, and law and policy experts and planners, and an iterative engagement process to (1) identify natural infrastructure that is geographically relevant to local jurisdictional planning units, (2) refine data and models to reflect regional processes, and (3) develop metrics likely to resonate within the local decision contexts. Using an open source decision-support tool, we demonstrated that protecting existing natural infrastructure—including coastal dunes and wetlands—could reduce the vulnerability of water resource-related structures, coastal populations, and farmland most exposed to coastal flooding and erosion. This information formed part of the rationale for priority climate adaptation projects the county governments are now pursuing. Our collaborative and iterative approach, as well as replicable use of an open source decision-support tool, facilitated inclusion of relevant natural infrastructure information into regional climate adaptation planning processes and products. This approach can be applied in diverse coastal climate adaptation planning contexts to locate and characterize the degree to which specific natural habitats can reduce vulnerability to sea-level rise and storms.