Yialova Lagoon is an area of great ecological importance. The entire region, including the Bay of Navarino and the island of Sfaktiria is part of the Natura 2000 network and has been designated as a Special Protection Area (SPA) and a Site of Community Importance.

Yialova Lagoon is also a designated wildlife sanctuary, particularly for migratory birds, which make their first stop there en route from Africa to northern Europe. The 254 species of birds that seek shelter at the lagoon or rest in the area for a few hours include herons, cormorants, kestrels, flamingos, various species of eagles, stilts, kingfishers, swans, glossy ibis, peregrine falcons, griffon vultures, owls, blackbirds, European goldfinches and greenfinches, hoopoes and many, many more.

Moreover, many mammals, reptiles, amphibians and fish make their habitat at the lagoon. One of the most notable is the African chameleon, which is extremely rare in Europe and is considered an endangered species.