The only globally important wetland in suburban Melbourne is at "significant" risk of major and long-term environmental damage from the removal of two level crossings on the Frankston line, a report for the Andrews government has warned.

The Edithvale-Seaford wetlands in Melbourne's south-east are a refuge for about 100 threatened or migratory bird species from Siberia, Japan and Alaska. Surrounded by suburban houses, they are the last remnant of a large swamp that once stretched from Frankston to Mordialloc.

Robin Clarey, vice president of Friends of Edithvale-Seaford Wetlands, and Ian Williams. Credit:Simon Schluter

Though small and heavily marked by urban encroachment, the Edithvale-Seaford wetlands have been classified as one of the world's significant wetlands for the richness and diversity of the wildlife they support, and are protected under an international treaty.

Threatened species found at the wetlands include the Australasian bittern, curlew sandpiper and swift parrot.