Migratory animals are crucial for global ecosystems, yet many species are threatened by human activities. Coastal shorebirds along the East Asian-Australasian Flyway have experienced precipitous declines over the past three decades, primarily due to the rapid development of the tidal flats, their major stopover habitat. However, populations of several species have declined must faster than the rate of habitat loss. To explain this discrepancy, we quantified the foraging distribution of 17 migratory shorebirds throughout the tidal cycle at two critical stopover sites. We found that shorebirds exhibit substantial interspecific and even site-specific differences in their foraging distributions. Notwithstanding these differences, however, the upper tidal flats prove to be especially important to most shorebirds by providing more than 70% of their cumulative foraging time, two-fold higher than its proportional area. Because coastal development typically starts near the high-tide line and proceeds outward, the upper tidal flats are also more prone to development, which may help to explain why shorebird populations have declined much faster than the overall rate of tidal flat loss. Our work highlights the importance of protecting upper tidal flats to conserve these migratory shorebirds, and demonstrates the need for detailed ecological understanding in effective conservation planning.