The Critically Endangered Spoon-billed Sandpiper Calidris pygmaeus is one of the most threatened migratory shorebirds in the world, breeding in Russia and wintering in Asia. The global population is declining rapidly and is projected to be extinct within a few decades without intervention. Here, we present the results of shorebird surveys in previously unrecognised site in Bangladesh along the Meghna Estuary, identified for the first time by using species distribution models. Counts and habitat preference of Spoon-billed Sandpipers and other endangered shorebirds are described here with notes on the global importance of the newly discovered site. The sum of the peak counts for each shorebird species across the two surveys was 25,993 including a minimum of 48 Spoon-billed Sandpipers. The majority of the Spoon-billed Sandpipers were observed during low tide while foraging (66.6%) and logistic regression testing for effects on the presence of foraging Spoon-billed Sandpiper indicate that they mainly preferred to forage on shallow mud. We summarise the threats to Spoon-billed Sandpipers and other birds in the new site that is currently not recognized as a Wetland of International Importance under the Ramsar Convention, although it fulfils several Ramsar Criteria. We also propose conservation and monitoring measures for long-term protection of the Spoon-billed Sandpiper and its habitat.