Climate change presents a particularly complex challenge in the context of flyway-scale conservation of migratory bird species as it requires coordinated actions of several countries along their migratory routes. Coordinating conservation responses requires understanding the vulnerability of species and their habitats to climate change at the flyway scale throughout each species’ annual cycle. To contribute to such understanding, we used species distribution models to assess the exposure to climate change of waterbird species that are the focus of the Agreement on the Conservation of African-Eurasian Migratory Waterbirds (AEWA). The species with the smallest proportion of their current range projected to be climatically suitable by 2050 are dispersive species in the Afrotropical biogeographic realm (i.e. those whose distributions respond to changes in water availability but that do not perform synchronised migration), and migratory species in their breeding season, particularly Arctic breeding waders. These species also have the most limited availability of newly suitable areas. Projections for most other Palearctic migratory waterbird species suggest that losses of suitable areas in their current passage and wintering ranges may be largely offset by new areas becoming climatically suitable. The majority of migratory Palearctic waterbirds in the breeding season and Afrotropical waterbirds are widely dispersed with only a small proportion of their populations currently supported by Critical Sites (i.e. sites that are either important for Globally Threatened Species or support 1% of the bioregional population of a Least Concern species). This makes it unlikely that climate change adaptation measures focusing only on key sites will be sufficient to counter the predicted range losses. Therefore, climate change adaptation measures should be implemented also at the landscape scale for Afrotropical waterbirds and for breeding populations of Palearctic migrant waterbirds.