Coastal ecosystems consist of diverse habitats, such as reed beds, salt marshes, mangrove swamps, tidal flats, river deltas, seagrass fields, coral reefs, sandy/rocky-shore beaches and other habitats that harbour biodiversity. The Great East Japan Earthquake of March 2011 caused severe damage to one-third of the fishing communities along the Pacific Ocean of NE Japan. Coastal species, such as seagrasses, function as nursery areas for commercially important species. Coastal ecosystems provide natural infrastructure for the prevention and reduction of hazardous events, a process known as ecosystem-based disaster risk reduction (Eco-DRR). The preparation of topographic and thematic maps of coastal marine environments is essential to establish and visualize the concept of Eco-DRR. Experience gained following the Japanese earthquake, as well as examples from Indonesia and Thailand in the wake of 2004 Indian Ocean tsunami, showed that Eco-DRR is an affordable and sustainable approach. Dissemination of habitat maps should be further promoted as a way to ‘Build Back Better’. To scale up and promote Eco-DRR, scientists must work in a transdisciplinary manner and engage with society by understanding the roles of ecosystems by monitoring and analysing, providing solutions and raising the awareness of community and policy makers, enabling them to better implement Eco-DRR.