The global area and distribution of shallow water ecosystems (SWEs), and their projected responses to climate change, are fundamental for evaluating future changes in their ecosystem functions, including biodiversity and climate change mitigation and adaptation. Whereas previous studies have focused on a few SWEs, we modelled the global distribution of all major SWEs (seagrass meadows, macroalgal beds, tidal marshes, mangroves, and coral habitats) from current conditions (1986−2005) to 2100 under the RCP2.6 and RCP8.5 emission scenarios. Our projections show that global coral habitat shrank by as much as 75% by 2100 with warmer ocean temperatures, but macroalgal beds, tidal marshes, and mangroves remained about the same because photosynthetic active radiation (PAR) depth did not vary greatly (macroalgal beds) and the shrinkage caused by sea-level rise was offset by other areas of expansion (tidal marshes and mangroves). Seagrass meadows were projected to increase by up to 11 % by 2100 because of the increased PAR depth. If the landward shift of tidal marshes and mangroves relative to sea-level rise was restricted by assuming coastal development and land use, the SWEs shrank by 91.9% (tidal marshes) and 74.3% (mangroves) by 2100. Countermeasures may be necessary for coastal defense in the future; these include considering the best mix of SWEs and coastal hard infrastructure because the significant shrinkage in coral habitat could decrease wave energy. However, if appropriate coastal management is achieved, the other four SWEs, which relatively have high CO₂ absorption rates, can help mitigate the climate change influences.