Sea-level rise is a major threat facing the Coral Triangle countries in the twenty-first century. Assessments of vulnerability and adaptation that consider the interactions among natural and social systems are critical to identifying habitats and communities vulnerable to sea-level rise and for supporting the development of adaptation strategies. This paper presents such an assessment using the DIVA model and identifies vulnerable coastal regions and habitats in Coral Triangle countries at national and sub-national levels (administrative provinces). The following four main sea-level rise impacts are assessed in ecological, social and economic terms over the twenty-first century: (1) coastal wetland change, (2) increased coastal flooding, (3) increased coastal erosion, and (4) saltwater intrusion into estuaries and deltas. The results suggest that sea-level rise will significantly affect coastal regions and habitats in the Coral Triangle countries, but the impacts will differ across the region in terms of people flooded annually, coastal wetland change and loss, and damage and adaptation costs. Indonesia is projected to be most affected by coastal flooding, with nearly 5.9 million people expected to experience flooding annually in 2100 assuming no adaptation. However, if adaptation is considered, this number is significantly reduced. By the end of the century, coastal wetland loss is most significant for Indonesia in terms of total area lost, but the Solomon Islands are projected to experience the greatest relative loss of coastal wetlands. Damage costs associated with sea-level rise are highest in the Philippines (US $6.5 billion/year) and lowest in the Solomon Islands (US $70,000/year). Adaptation is estimated to reduce damage costs significantly, in particular for the Philippines, Indonesia, and Malaysia (between 68 and 99%). These results suggest that the impacts of sea-level rise are likely to be widespread in the region and adaptation measures must be broadly applied.