Coastal ecosystems, composed of corals, macroalgae, and seagrasses, provide numerous benefits to human life. These ecosystems are found along Japan’s coasts, but their distribution and health have been impacted by global and regional environmental stresses. With rising sea temperatures expected to bring significant changes to coastal ecosystems, it is essential to base the use and conservation of these species on their specific regional conditions. This study examined how these biological communities are addressed in the climate change adaptation plans of Japanese prefectures. The current distribution of corals, macroalgae, and seagrasses varies by prefecture, and there have been observable changes in the past, with potential shifts anticipated in the future. The extent to which these species are addressed in administrative documents also varies widely by species and region. Corals, in particular, were often found to lack specific conservation and adaptation measures, compared to macroalgae and seagrasses. As scientific understanding of future projections and adaptation strategies continues to grow, it is critical to incorporate this knowledge into administrative documents to support the sustainable use and conservation of these vital ecosystems.