Along several migratory corridors in Europe, the Common Crane Grus grus exhibits a variety of migratory and roost site selection strategies. In this study we determined which environmental factors explained roost-site usage of Common Cranes in 64 fishponds and 25 marshes suitable for Crane roosting inside the Hortobágy National Park (HNP, Hungary) between 1995 and 2007. HNP has become the largest stop-over site of Cranes in Europe. Despite the relatively high number of potential roost sites, Cranes chose only 44% of suitable wetlands for roosting. Roost site selection of Common Cranes was primarily governed by conservation management measures, wetland type and size, as well as disturbance-related characteristics of the roost-site. Artificially flooded marshes, as well as large fishponds, actively managed through drainage, far from human settlements, are of critical importance for staging Common Cranes. The timing of controlled floods in marshes as well as the matching of drainage for fish-farming to migratory periods of Cranes, serve as suitable management measures for waterbird conservation. In summary, our study emphasizes the importance of managing large, undisturbed wetlands with species-specific management prescriptions in maintaining mass migrations of wetland birds.