Migration is a vital survival strategy for many species, but the increasing interruption of migratory routes by human activities has placed migratory shorebirds at high risk of extinction, particularly in Asia. Bangladesh, positioned at the crossroads of the Central Asian and East Asian-Australasian Flyways, is a critical region for shorebird migration and for understanding anthropogenic impacts on migratory populations. Here, we use 14 years of shorebird surveys and satellite tracking to investigate potential correlates of interspecific variation in shorebird population trends in Bangladesh. We find that 12 out of 20 shorebird species studied experienced population declines in 2009–2023. Coastal habitat obligates (e.g. spoon-billed sandpiper) showed the largest decreases. In contrast, several non-coastal obligate species (e.g. Tibetan sand plover) exhibited stable or increasing trends. Migration stopover habitat emerged as the primary factor predicting population trends. Our results emphasize the critical importance of previously overlooked inland stopover sites, particularly in the Qinghai–Tibet plateau, where 64% of sites used by tracked birds are unprotected. Conserving coastal wetlands is vital to the conservation of Asia’s shorebirds, but so too is the protection of stopover areas inland.