The population changes in waterbirds are recognised as a global issue. Many waterbird species, especially migratory ones, are undergoing population changes. Monitoring these changes is crucial for waterbird conservation. However, the lack of data to quantify these populations hinders comprehension of the factors responsible for these changes. Although a few studies have investigated the long-term trends of waterbirds in the Republic of Korea (ROK), most have concentrated on a limited number of species and groups. Understanding these changes enables us to identify which species are vulnerable and develop more effective conservation measures accordingly. This study aimed to investigate the population dynamics of waterbirds in the ROK from 2000 to 2024. Data from the Winter Waterbird Census of Korea were used to analyse trends across various waterbird groups and species. The results showed diverse population trajectories, with some species experiencing notable increases while others underwent severe declines. Among the observed trends, several globally threatened species, such as the White-naped Crane Grus vipio and Oriental Stork Ciconia boyciana, exhibited significant population growth. This is largely a testament to the effectiveness of conservation interventions aimed at these species. However, the study also identified population declines of some species, such as the Tundra Swan Cygnus columbianus and Common Pochard Aythya ferina, indicating pervasive threats due to habitat loss and degradation. Lastly, several recommendations are made regarding the identified population trends that should be used to guide future conservation efforts in the East Asian–Australasian Flyway. This study, with its comprehensive and detailed findings, reiterates the importance of long-term monitoring data for developing effective conservation measures.