Understanding species distribution patterns and what determines them is critical for effective conservation planning and management. In the case of shorebirds migrating along the East Asian-Australasian Flyway (EAAF), the loss of stopover habitat in the Yellow Sea region is thought to be the primary reason for alarming declines in shorebird populations. However, the rates of decline vary considerably among species, and it remains unclear how such differences could arise within a group of closely related species using apparently similar habitats at the same locales. We sampled and mapped the spatial distributions of both biotic (benthic invertebrates consumed by migrating shorebirds) and abiotic (sediment characteristics) environmental factors at a key stopover site in eastern China. We found that both benthic invertebrates and sediment characteristics demonstrated considerable spatial heterogeneity across the same tidal flat, with most benthic invertebrates concentrated on the upper and/or middle zones of the tidal flat, the area with finer-grained sediments. Moreover, the distribution patterns of focal shorebird species on the tidal flat were best explained jointly by these biotic and abiotic environmental factors. We show that the same stretch of tidal flat can exhibit considerable heterogeneity with respect to the distributions of both shorebirds and environmental factors. The loss of tidal flats along the Yellow Sea is typically concentrated at the upper and middle zones, which not only reduces the overall amount of staging habitat, but also disproportionately affects the most resource-rich portions for the birds. Effective conservation measures for shorebird staging areas along the EAAF and likely elsewhere must take into account the subtle habitat heterogeneity that characterizes these tidal flats, prioritizing the protection of those portions of the tidal flat that are richest in food resources, most frequently used by focal bird species, and most vulnerable to anthropogenic threats. This article is protected by copyright. All rights reserved.