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Summary There is increasing concern about the world's animal migrations. With many land‐use and climatological changes occurring simultaneously, pinning down the causes of large‐scale conservation problems requires sophisticated and data‐intensive approaches. Declining shorebird numbers along the East Asian–Australasian Flyway, in combination with data on habitat loss along the Yellow Sea (where these birds refuel during long‐distance migrations), indicate a flyway under threat. If habitat loss at staging areas indeed leads to flyway‐wide bird losses, we would predict that: (i) decreases in survival only occur during the season that birds use the Yellow Sea, and (ii) decreases in survival occur in migrants that share a reliance on the vanishing intertidal flats along the Yellow Sea, even if ecologically distinct and using different breeding grounds. Monitored from 2006–2013, we analysed seasonal apparent survival patterns of three shorebird species with non‐overlapping Arctic breeding areas and considerable differences in foraging ecology, but a shared use of both north‐west Australian non‐breeding grounds and the Yellow Sea coasts to refuel during northward and southward migrations (red knot Calidris canutus piersmai , great knot Calidris tenuirostris, bar‐tailed godwit Limosa lapponica menzbieri ). Distinguishing two three‐month non‐breeding periods and a six‐month migration and breeding period, and analysing survival of the three species and the three seasons in a single model, we statistically evaluated differences at both the species and season levels. Whereas apparent survival remained high in north‐west Australia, during the time away from the non‐breeding grounds survival in all three species began to decline in 2011, having lost 20 percentage points by 2012. By 2012 annual apparent survival had become as low as 0·71 in bar‐tailed godwits, 0·68 in great knots and 0·67 in red knots. In a separate analysis for red knots, no mortality occurred during the migration from Australia to China. In the summers of low summer survival, weather conditions were benign in the Arctic breeding areas. We argue that rapid seashore habitat loss in the Yellow Sea is the most likely explanation of reduced summer survival, with dire (but uncertain) forecasts for the future of these flyway populations. This interpretation is consistent with recent findings of declining shorebird numbers at seemingly intact southern non‐breeding sites. Policy implications . Due to established economic interests, governments are usually reluctant to act for conservation, unless unambiguous evidence for particular cause–effect chains is apparent. This study adds to an increasing body of evidence that habitat loss along the Yellow Sea shores explains the widespread declines in shorebird numbers along the East Asian–Australasian Flyway and threatens the long‐term prospects of several long‐distance migrating species. To halt further losses, the clearance of coastal intertidal habitat must stop now.