It provides special habitats along major migration routes and is situated between international important wintering areas. The coast also harbours important breeding grounds for several coastal species. The ecosystem of the Fehmarnbelt is currently undergoing changes which affect bird habitats, not least due to global warming processes.

Due to the international importance of several shallow offshore areas to wintering water birds, several sites are enjoying protection both in Germany and Denmark, including the NATURA 2000 sites such as the eastern Kiel Bight, the Baltic Sea east of Wagrien and Rødsand. Several areas along the coast of Schleswig-Holstein and in the Rødsand lagoon south of Lolland harbour important breeding stocks of coastal birds, in particular terns and gulls.

Water birds
The Fehmarnbelt (and the Belt Sea) is characterized by permanent salinity gradients, which in connection with extensive areas of shallow waters give rise to rich food supplies for carnivorous, herbivorous and piscivorous water birds. The abundance of water birds is clustered within areas shallower than 25 m.

The Fehmarnbelt is a region of relatively high abundance of several water bird species of all three ecotypes, with species such as Great-crested grebe, Eider, Common scoter, Long-tailed duck, Tufted duck and Red-breasted merganser, occurring regularly in numbers of international significance. The breeding water bird fauna is profoundly less important, yet nationally important colonies of terns and gulls are found in the enclosed areas near Fehmarn and in the Rødsand Lagoon. 

Not only the abundance but also the structure of the non-breeding water bird community is highly dependent on the function of the ecosystems of the Fehmarnbelt. The salinity gradient seen in the Belt Sea is particularly important for the structure of the non-breeding water bird community, showing a decrease in the proportion of eiders and an increase in the proportion of long-tailed ducks with decreasing salinity. This is a direct function of the seasonal oxygen deficiency, which provides another stress factor affecting the available supply of mussels to water birds.

Migrating birds
Fehmarnbelt is considered a hotspot for bird migration, linking both Scandinavia with the European continent as well as the Baltic Sea with the North Sea. The Fehmarnbelt forms the shortest distance to cross the Baltic Sea between Scandinavia and continental Europe and thus forms a bottleneck where land bird migration concentrates and a high proportion of Scandinavian breeding population passes through.

A large variety of common and protected species migrates through the area. As most water bird and sea bird migration between the Baltic Sea and the North Sea crosses Jutland via Kiel Bay and Eckernförder Bay, almost all of this migration actually passes Fehmarnbelt. A very high proportion of the total flyway populations of Brent geese and Barnacle geese as well as substantial proportions of the flyway populations of Eider and Common scoter pass Fehmarnbelt. The fixed link will be orientated parallel to the main flight direction of land bird migration, but transverse to the flight directions of water birds and seabirds.

Terrestrial birds
Breeding grounds in the land approach areas to the fixed link are chiefly dominated by farmland birds, - species which are found throughout the general agricultural landscape in northern Schleswig as well as in southern Denmark. Species like Skylark, Yellowhammer and Lapwing breed commonly on Fehmarn and Lolland, including in the land approach areas. Outside the breeding season flocks of geese like Greylag and Bean goose are seen regularly resting and foraging in the fields.