Context: Migratory species’ resilience to landscape changes depends on spatial patterns of habitat degradation in relation to their migratory movements, such as the distance between breeding and non-breeding areas, and the location and width of migration corridors. Objectives: We investigated to what extent the impact of habitat degradation depended on the seasonal distributions of migratory waterfowl. Methods: Using logistic regression, we selected wetland sites for eight waterfowl species in the East Asian–Australasian Flyway (EAAF) by calculating the probabilities of species occurrence per wetland site in relation to environmental factors. We quantified landscape metrics related to habitat degradation within these wetland sites. We used general linear models to test for differences in the effects of habitat degradation on waterfowl species with different migration extents and at different latitudes. Results: The patterns of habitat degradation differed spatially across the EAAF and affected species to a different degree. Species with shorter and broader migration corridors (Anser cygnoid and A. anser) could benefit from improved habitat conditions in the west of the EAAF. Species with longer and narrower migration corridors (Cygnus columbianus, A. fabalis, A. albifrons, A. erythropus, Anas crecca, and Anas acuta) were under higher risk of habitat degradation in the coastal regions of China and Japan. Conclusions: Migratory species with longer and narrower migration corridors are more affected by habitat degradation, because they might have fewer alternative stopover sites at similar latitude. Our findings improve the understanding of species-specific effects of environmental changes on migratory species, and defines critical and endangered wetland sites, and vulnerable species.