Migratory birds undertake regular seasonal movements between breeding and non-breeding grounds each year, often spanning intercontinental distances. Several migratory waterbirds are declining globally, owing to multiple threats from parts of annual migration. Therefore, understanding the spatial distribution and conservation challenges of migratory waterbirds is critical for effective flyway-scale conservation. In this study, we compiled a comprehensive dataset of 199 migratory waterbird species, mapped seasonal distribution, and identified population trends and threats along the East Asian–Australasian Flyway and Central Asian Flyway. Species richness exhibited latitudinal gradients along the two flyways, peaking at approximately 60° N in the breeding season and 15° N in the non-breeding season. Migration distance and geographic spread significantly varied among orders. More than half of the waterbird species (50.75%) showed decreasing population trends; however, no significant difference in the proportion of population decline was noticed across flyways or orders. A total of 31 species (15.58%) were listed as threatened, most of which were concentrated in the East Asian–Australasian Flyway and primarily affected by the use of biological resources, pollution, and agricultural expansion. Overall, this study provides a comparative assessment of migratory waterbirds in Asian flyways. Our findings highlight the importance of multinational conservation efforts targeting key breeding and non-breeding regions, specifically for threatened species, and underscore the need for coordinated strategies to mitigate multiple, overlapping threats across flyways. These further emphasize that conservation actions should prioritize transboundary habitat networks and policy integration among flyway countries to enhance the long-term resilience of migratory waterbird populations.