The Guangdong-Hong Kong-Macau Greater Bay Area (GHMGBA) has abundant wetland resource, and is regarded as important habitat for migratory waterbirds. Here, we use the Maxent model to explore the spatial pattern and hotspots of waterbirds diversity in the GHMGBA, based on the occurrence records of 55 waterbirds and 15 environmental variables. The results showed that precipitation seasonality, land cover, and distance to the nearest surface water were the main environmental factors affecting the potential distribution of waterbirds. In general, richness of waterbirds was highest in the southeast, and exhibited a trend of gradually declining to the inland area, which is consistent with the spatial patterns of local water resources. Waterbird hotspots are located in the southeast coastal area of the GHMGBA, especially in Zhuhai, Jiangmen, Shenzhen, and Zhongshan cities. Our results not only could provide a reference for conservation planning of waterbirds, but also are conducive to maintaining the safety and stability of the ecosystem in this region.