Migratory wader populations are declining across all major flyways, mostly due to habitat loss and human disturbance. Portuguese wetlands act as key wintering and stop-over sites for many waders due to their strategic location in the East Atlantic Flyway. Despite their importance, there are major knowledge gaps in some areas, such as the Sado Estuary. The main goal of this study was to identify the phenological patterns and wintering trends of the most abundant wader species in this wetland, and to compare the results with the population trends found at regional and flyway scales. A comprehensive dataset of count data collected monthly in high-tide roosts under a set monitoring programme (2010–2019) was used. The results revealed strong declines in the overall number of waders and of three of the most abundant species—Avocet (Recurvisostra avosetta), Dunlin (Calidris alpina), and Common Ringed Plover (Charadrius hiaticula)—associated with a 21% reduction of the suitable high-tide roosts across the study area. These trends are similar to those compiled from winter counts for the entire Sado Estuary, and at regional (Tagus Estuary) and flyway levels. Our results highlight the need to maintain suitable high-tide roosts to contribute towards reverting current declines in wader populations.