Waterbird diversity as an indicator for identifying key habitats in the Yangtze River Basin

• We collected 26,429 observation records, 226 waterbirds in the Yangtze River Basin. • We established a spatially stratified key habitat identification framework. • Urban and non-urban area exhibited distinct environmental drivers for waterbird diversity. • We identified 29 key habitats (586,234 km 2 ) across the Yangtze River Basin. • There is a spatial mismatch between protected areas and key habitats. Large human-modified river basins require biologically meaningful yet operational indicators to locate key habitats and guide protection. The Yangtze River Basin (YRB), as the world’s third longest river and a core inland segment of the East Asian-Australasian Flyway, exemplifies a highly heterogeneous socio-ecological system where rapid, uneven urbanization intersects steep climatic and hydrological gradients. Drawing on 26,429 citizen‑science waterbird observation reports (2007–2021), we found a spatiotemporal divergence in environmental factors affecting waterbird diversity across urban versus non-urban areas and between breeding and wintering seasons. Specifically, waterbird diversity is driven mainly by disturbance and fine-scale site conditions in urban areas but by a broader environmental suite in non‑urban areas. We also found that currently designated protected areas (PAs) only covered most of the key habitats in non‑urban areas during breeding season. Thus, we proposed a spatially stratified framework to identify key habitats that distinguishes urban and non‑urban areas for waterbirds. Connectivity modeling based on these key habitats identified corridors bridging urban and non‑urban wetland complexes and highlighted unprotected linkage bottlenecks. Integrating the revealed spatial and seasonal driver contrasts with diversity hotspots, focal species distributions, and connectivity outputs, we propose a stratified multi‑indicator framework that operationalizes waterbird diversity as a habitat network design tool to guide targeted protected areas expansion and ecological corridor planning in large human‑modified river basins.