Climate change poses significant threats to wellbeing and livelihoods of people and the ecosystems in many Small Island Developing States (SIDS). Adaptation solutions must counteract these threats while also supporting development in vulnerable SIDS. Suitable options need to ensure that connections between the social, economic, and environmental dimensions of socio-economic systems are defined in a way that can support how decisions are made (and by whom) and how these can impact on other parts of these systems. This is particularly important in many Pacific SIDS, where communities practise customary natural resource management and continue to rely on local natural resources. In this study, we model the anticipated impacts of climate change and the benefits of the ecosystem-based adaptation (EbA) approaches on community wellbeing in Vanuatu. To do this, we applied participatory and expert elicitation methods to develop a Bayesian network model, which was designed to evaluate community wellbeing responses at four explicit spatial scales. The model includes both acute and chronic impacts of climate change, the impact of coral bleaching, and the potential loss of Vanuatu’s fringing coral reefs. The model predicts that all proposed EbA interventions will have a positive impact on wellbeing in all four locations to some degree, by either directly improving the integrity of Vanuatu’s ecosystems or by protecting these ecosystems as a positive spill-over of related actions. Significantly, it also predicts that if climate change exceeds 1.5 °C of warming, the costs of achieving the same level of wellbeing are increased.