Changes in temperature and seasonality resulting from climate change are heterogeneous, potentially altering important sources of natural selection acting on species phenology. Some species have apparently adapted to climate change but the ability of most species to adapt remains unknown. The life history strategies of migratory animals are dictated by seasonal factors, which makes these species particularly vulnerable to heterogeneous changes in climate and phenology. Here, we examine the phenology of migratory shorebirds, their habitats, and primary food resources, and we hypothesize how climate change may affect migrants through predicted changes in phenology. Daily abundance of shorebirds at stopover sites was correlated with local phenology and peaked immediately prior to peaks in invertebrate food resources. A close relationship between migrant and invertebrate phenology indicates that shorebirds may be vulnerable to changes in seasonality driven by climate change. It is possible that shifts in migrant and invertebrate phenology will be congruent in magnitude and direction, but because migration phenology is dependent on a suite of ecological factors, any response is likely to occur at a larger temporal scale and may lag behind the response of invertebrate food resources. The resulting lack of sufficient access to food at stopover habitats may cause migrants to extend migration and have cascading effects throughout their life cycle. If the heterogeneous nature of climate change results in uneven changes in phenology between migrants and their prey, it may threaten the long-term viability of migratory populations.