The Beibu Gulf (Gulf of Tonkin, Vinh Bac Bo in Vietnamese), located midway along the East Asian-Australasian Flyway (EAAF), is a critical stopover and wintering region for migratory waterbirds. This transboundary coastal region, spanning between China and Vietnam, harbors diverse wetland habitats that provide refuge to waterbird species, including highly threatened species such as the spoon-billed sandpiper (CR) and the black-faced spoonbill (EN). However, the scarcity of comprehensive assessments regarding waterbird abundances, distribution, key wetland habitats, and regional threats hinders our understanding of its conservation significance at the flyway level. Further research is needed to address these knowledge gaps and facilitate effective conservation efforts in the Beibu Gulf. By synthesizing accessible citizen science datasets and published records from wetland sites in south China and northeast Vietnam, we concluded that at least 97 waterbird species used the Gulf’s wetlands during their annual cycle. Among surveys conducted from 2014 to 2022, 6 and 13 waterbird species were considered as first and second class protected species under the National Key Protected Wild Animal List in China; 2 species were listed as Critically Endangered on the IUCN Red List, 5 as Endangered and 2 as Vulnerable, underlying the critical importance of the Beibu Gulf for the survival of these species. Our study identified 25 sites in the Beibu Gulf that met the criteria for designation as internationally important wetlands. Alarmingly, less than a quarter (n = 6, or 24%) of these sites benefit from national or international protection. Localized threats, including aquatic resource harvesting, hunting, and aquaculture/fisheries, were widespread in the region. This study provides a crucial scientific baseline for continued waterbird monitoring, site prioritization, and the development of effective habitat management plans to conserve vital coastal wetland habitats in the Beibu Gulf in China and Vietnam.