ABSTRACT Globally, climate and human‐induced environmental changes affect the populations and distributions of most organisms. This is particularly true for migratory birds, which change habitats throughout the annual cycle. Understanding how waterbirds adapt to environmental change is important for their conservation; however, this subject remains largely unexplored. Based on wintering waterbirds and environmental data from Dongting Lake and its surrounding lakes, we compared the changes in waterbird diversity in subregions with different habitat variations during four hydrological periods. This allowed us to identify key environmental factors affecting waterbird diversity and explore the potential mechanisms by which waterbirds adjust to these environmental changes using the waterbird‐habitat patch network method. The results indicated that waterbird distribution differed across Dongting Lake and the surrounding wetlands under varying hydrological conditions associated with habitat changes. Notably, the surrounding lakes with stable habitats served as refuges for waterbirds during extreme drought, with the percentage of waterbirds increasing from 9.3% (late recession) to 63.8% (extreme drought). Areas of habitat (i.e., water, mudflat, and vegetation) and human disturbance were key factors influencing waterbird diversity. As indicated by the β ‐diversity of the waterbird‐habitat patch network, the waterbird metacommunity remained relatively stable in terms of spatiotemporal differences across hydrological periods, while its components displayed distinct patterns. Specifically, the colonization component dominated during extreme drought, whereas the extinction component dominated during the late recession. Compared to normal recession, an earlier recession led to a higher proportion of colonization components. Waterbirds migrated between habitat patches to adapt to the various hydrological conditions. This study enriches the theory of community assembly by emphasizing the significance of extinction and colonization processes shaped by hydrological conditions. Furthermore, it provides valuable insights into the conservation and management of waterbird habitats, highlighting the importance of hydrological dynamics and their impact on waterbird populations.