Climate change is increasingly leading to more extreme weather events, such as droughts, which pose significant threats to many water bird species. During the winter season of 2022-2023, Poyang Lake, China’s largest freshwater lake, faced its most severe drought on record. This unprecedented event prompted the local government to reaffirm and intensify their proposal for constructing a dam. To evaluate the ecological impact of the drought, we used the White-naped Crane (Antigone vipio) as a case study. By tracking 56 birds with GPS transmitters, we gathered 268,615 valid location data points recorded at hourly intervals. We then developed a model system known as Heterogeneous-Occurrence Species Distribution Models (HOSDMs), which allows for the prediction of habitat suitability while distinguishing between different individual occurrence patterns. This methodology was encapsulated in an R package named migrationR, designed for streamlined analysis. Our findings indicated that the habitat suitability for White-naped Cranes reached its lowest point during this exceptionally dry winter. Reduced water levels forced the cranes to seek alternative habitats, especially shallow water areas for overnight roosting. Regarding the debate on the dam construction, we strongly advocate against an economically driven approach to dam management and instead support an ecologically focused strategy. Ensuring the preservation of the annual flooding cycle should be a fundamental requirement for protecting the habitats of waterbirds.