Busan and Gyeongsangnam-do region host numerous significant wetlands, including the Nakdong River Estuary, one of the largest migratory bird habitats in East Asia, making it an essential habitat for waterbirds. However, issues such as wetland area reduction have arisen due to accelerated industrialization and urbanization since the 1980s. This study analyzed annual and monthly changes in waterbird populations and examined habitat use patterns and interrelationships among four wetlands in Busan and Gyeongsangnam-do: the Nakdong River Estuary (NRE), Lower Nakdong River (LNR), Junam Reservoir (JUR), and Upo Wetland (UPO), using waterbird data collected from 1999 to 2024. The results showed a decreasing trend in waterbirds at the NRE and UPO, while an increasing trend was observed at the LNR and JUR. Notably, populations of Anatidae decreased at the NRE and UPO but increased at the LNR and JUR, indicating that changes in Anatidae significantly influenced waterbird population trends. Monthly population fluctuations were particularly pronounced at the NRE and LNR. While the population decreased at the NRE after November, it increased at the LNR. This suggests that waterbirds moved to the LNR due to habitat and food resource reductions in the NRE. In contrast, the JUR and UPO exhibited weaker associations with the other sites. This study aims to contribute to future wetland management and waterbird conservation strategies in the Busan and Gyeongsangnam-do region.