Migratory animals move in time with seasonal changes, occupying a sequence of geographically distinct habitats, typically at predictable times throughout the year. While the conservation of migratory animals has often focused on their long-term breeding and non-breeding sites, this dissertation focuses on the stops they make temporarily along the way. For birds, en route stopover events are often relatively brief, and many occur in unfamiliar landscapes under intense pressure. In Chapter 1, I break down emerging research into avian stopover events. Stopover patterns are generally assumed to arise from food availability along the migratory route, yet stopovers also fulfill other critical functions associated with physiological endurance, navigation, and survival. These functions also structure movement and should be considered in habitat conservation plans. In Chapter 2, I investigate the in-flight movements of Hudsonian Godwits — a shorebird species that is among the longest-distance migratory animals on Earth — during the marathon northward flights that precede their first stopovers. Godwits make flexible behavioral adjustments in relation to wind conditions during these flights, strategically alternating between compensation and drift in a way that indicates awareness of geospatially varying risks, even over the open waters of the Pacific Ocean. In Chapters 3 and 4, I focus on the Prairie Pothole Region of North America, a vast midcontinental wetland complex that is a core stopover area for shorebirds in the Western Hemisphere. Chapter 3 develops a shorebird habitat detection model for this complex that is among the first of its kind, separating shallowly inundated areas from deeper water in remote sensing imagery. Finally, in Chapter 4, I return to Hudsonian Godwits, investigating their stopover behaviors and the demographic consequences of climatic variability in the Prairie Pothole Region. For godwits, stopovers are opportunistic and involve wide-ranging, near-constant movements across a sequence of sites — a strategy that may contribute to their remarkable adaptive capacity. Together, these insights underscore the need for new approaches to wetland conservation at critical junctures along shorebird migratory routes.