Bird species (BS) of the Nakdong River estuary (NRE) were selected to suggest conservation and management strategies, taking habitats and major threats into consideration. Five BS (Cygnus spp., Calidris alpina, Sterna albifrons, Fulica atra, and Anser fabalis) were selected following analysis of their dominance, national importance, seasonality, taxonomic group, and distribution within the NRE. The BS comprise two winter birds, one summer, one passage bird, and one resident bird. They can also be classified into four taxonomic groups: two under ducks and geese (Anatidae), and one each under gulls (Laridae), shorebirds (Scolopacidae), and diving birds (Rallidae). The results show that BS could be a useful tool in guiding estuary management because their habitats are clearly distinct, and include important areas of the NRE. A reduction of feeding and resting places—such as tidal flats, Scirpus planiculmis habitat, and agricultural farmland—and climate change are major threats to BS, therefore countermeasures to such threats should be considered in future estuary management plans.