This study sought to clarify the relationship between stream structure and waterbird community composition in the Jungnangcheon stream, Seoul metropolitan district, South Korea from February 2018 to November 2020. Stream structure was assessed along the stream corridor. There were diferences in water width, depth, transparency, flow, bed materials, form of levee, and number of bends. The major waterbirds were cormorants, large wading birds, dabbling ducks, diving ducks, gulls, and small wading birds. The multiple linear regression analysis revealed close relationships between stream structure variables and major waterbirds. Waterbird community conservation requires wetland-based management programs that are applied to habitat complexes at the landscape scale to support the needs of waterbirds. The results of this study can help with the conservation of habitats and landscapes in urban streams. Further research should be conducted on the conservation of waterbirds and their habitat in the future.