Some staging regions support multiple groups of the same migratory species, each of which may use the region differently. Characterizing the ways, in which separate groups use such regions can therefore help to identify vulnerabilities during this sensitive period of the annual cycle. The Prairie Pothole Region (PPR) is a massive wetland complex in the northern Great Plains of North America used by ∼11 million shorebirds during migration. The PPR has been heavily modified by agriculture and is experiencing varied effects of global climate change, threatening the health of the shorebirds that rely on it. Here, we used 6 seasons of southbound tracking data of Tringa flavipes (Lesser Yellowlegs)—a long-distance migratory shorebird species with an estimated population decline of 63% over the last 4 decades—from 9 sites across their breeding range to explore differences in migratory behavior within this important staging region. We found that 75% of tracked individuals used the region during southbound migration, and T. flavipes from different breeding sites detoured 110–875 km from their most direct migratory route to access the PPR. Individuals that arrived later stayed longer and made more stops within the region than those that arrived early. Individuals originating from different breeding sites also displayed spatial and temporal segregation within the region: T. flavipes from southwest and central Alaska relied heavily on the northwestern PPR, while those from Canada used the central and southeastern portions of the PPR. Finally, timing of use varied among groups, but the southeastern PPR became increasingly important over the course of the southbound migratory window, as other wetlands likely dried out. Our study highlights the portions of the PPR of critical importance to migrating T. flavipes and the diversity of ways, in which different groups from within the same species can use a single staging region.