The middle and lower reaches of the Yangtze River are critical habitats for waterbirds along the East Asian-Australasian Flyway. However, habitat degradation and fragmentation, driven by climate change and human activities, pose severe threats to waterbird diversity. This study utilized citizen science data and the MaxEnt model to predict the potential habitats for 123 waterbird species, and to identify biodiversity hotspots as ecological sources. By integrating circuit theory with ecological resistance surfaces, we delineated ecological corridors and identified “pinch points”. These critical habitats, including ecological sources and pinch points, were overlaid with the existing protected areas to assess conservation gaps. Our results showed that: (1) The total potential habitat area for key waterbird species in the middle and lower Yangtze River was 30322 km2, comprising 27669 km2 of ecological source areas and 2653 km2 of pinch points; (2) Although 26.85% of key habitats were protected, only 12.24% of ecological pinch points fell within protected area, indicating a substantial gap in the conservation of highly connected habitats; (3) The total area of conservation gaps was 9417.5 km2, including 44 sites partially protected and 19 entirely unprotected. Based on the spatial distribution of these conservation gaps, we propose four conservation strategies: establishing food resource corridors, optimizing multi-objective management within protected areas, restoring ecological connectivity in critical river sections, and prioritizing the inclusion of high-biodiversity zones in the protected area network. Incorporating flexible conservation approaches, such as other effective area-based conservation measures (OECMs), can fill gaps in traditional systems and provide practical pathways for enhancing waterbird diversity conservation.