The increasing pressure of anthropogenic development in areas with high natural value poses a huge challenge for wildlife conservation worldwide. The Tagus estuary in southern Portugal is among the most important wetlands for migratory shorebirds in the East Atlantic Flyway (EAF). However, in 2020 the Portuguese government approved the construction of the new Lisbon international airport at the heart of the Tagus estuary. Intense aircraft traffic, flying at low altitudes during both approach and take-off, is expected to cross the estuary, overlapping to a great extent the important intertidal foraging areas. Here, we aim to quantify the potential loss of conservation value of the intertidal areas of the Tagus estuary for shorebirds resulting from the disturbance (noise) caused by overflying aircraft. Using a comprehensive dataset of wintering shorebird abundance and distribution in the whole intertidal estuarine area we first identified priority areas for conservation using a spatial prioritization approach. We then performed a replacement cost analysis by excluding the areas likely to become unsuitable or severely underused by birds due to intense air traffic noise. Our results suggest that the implementation of the new Lisbon airport may lead to a loss of up to 30% of the conservation value of the Tagus estuary in terms of intertidal feeding areas of wintering birds alone. The global impact will likely be greater when effects on supratidal roosts, as well as on passage birds, are also considered. The Tagus estuary, which is internationally important for six of the 10 species included in our analysis, is just one of a network of already depleted sites along the EAF. Thus, negative impacts on bird populations on the Tagus estuary will have repercussions and undermine conservation efforts elsewhere. The plight of shorebirds at the Tagus estuary is thus a matter of international conservation concern.