The East Asian–Australasian flyway contains some of the most threatened habitats in the world, with at least 155 waterbird species reliant on the tidal habitats it comprises. The black-faced spoonbill (Platalea minor) is an iconic endangered species distributed across the coast of East Asia. Its population suffered a severe decline into the 1990s, but extensive monitoring and conservation interventions have aided a substantial recovery of the species. We used a population viability analysis based on data collected over the past two decades in conjunction with species distribution models to project spatially explicit models of population change for the next 35 years. Over nearly all scenarios of habitat loss and climate change, the global spoonbill population was projected to increase in the short-term due to low population numbers likely well below current population carrying capacities. However, climate change and habitat loss together threaten the recovery of the spoonbill population such that, by 2050, population declines are apparent as a consequence of these cumulative impacts. These threats are also cryptic and represent a challenge to the conservation of species recovering from anthropogenic impacts; observed population increases can hide large reductions in habitat suitability that threaten the long-term viability of species.