Migratory wader populations face global threats, mainly related to increasing rates of habitat loss and disturbance driven by human activities. To a large extent, the long-term survival of these populations requires the conservation of networks of sites along their migratory flyways. The Tagus estuary, Portugal, is among the most important wetlands for waders in the East Atlantic Flyway. Annual winter wader counts have been carried in this wetland since 1975 and a monthly roost-monitoring programme was implemented in 2007. Wintering populations of three out of the five most abundant species, Dunlin Calidris alpina, Grey Plover Pluvialis squatarola and Redshank Tringa totanus, showed significant population declines over the past three decades, which are most likely due to the loss and degradation of roost sites as a result of increasing human activity. The situation is unlikely to improve, as a high proportion of the wintering waders use roost sites that are situated in highly urbanised areas with no legal protection. The use of different roost sites by waders is highly variable both temporally and spatially, thus emphasizing the need for a network of good quality roost sites. Additionally, during migration, 60–80% of all the waders of the Tagus estuary concentrate at a single refuge, thus increasing the risk for wader populations during these periods.