The Wintering Waterbird Census of Korea was started in 1999 and monitors 200 major migratory sites in South Korea. Waterfowl counts have been undertaken for more than 20 years since; however, a limited number of studies have analyzed the temporal patterns of waterfowl population. In this study, we analyzed population size changes of wintering whooper swan (Cygnus cygnus) at 112 monitoring sites from 2001 to 2018. The average number of whooper swans was 4,296±42.66 and there was a trend for an increase in population size across the survey period. We found that the population in the Nakdong River Estuary, one of the major wintering sites over 18 years (26.22% of the national population), had rapidly decreased (- 0.77% per year). Conversely, the whooper swan population in the Junam Reservoir and Sihwa Lake increased (+1.64%, +0.54% per year, respectively). Estuaries showed the highest dominance of whooper swans among the five different habitat types, accounting for 32.13% of the population. Reservoir/lakes had 30.60% of the total population and reclaimed lakes (18.24%), river (13.11%), and coast (5.93%) followed. The annual distribution of the whooper swan population in South Korea has been affected by various habitat conditions resulting from human activities and urbanization. To better understand the complex factors that can cause rapid changes in wintering waterfowl populations, it is necessary to integrate the data from the bird census program with environmental conditions to conduct in-depth pattern analyses over longer time periods.