An elevated freeway that will slice up rare bushland in Melbourne’s suburban south-east risks polluting bodies of water that feed UN-protected wetlands, government documents reveal.

Environmental groups are sounding the alarm over the 9.7-kilometre Mordialloc Freeway, a road linking the Mornington Peninsula and Dingley Bypass that will cut through the area's green wedge.

The $375 million freeway set to carry 80,000 vehicles a day will soar above tranquil residential estates in Waterways and Aspendale Gardens and continue along the edge of Braeside Park, with a series of ramps connecting major arterial roads.

The area is renowned for its extensive park areas and wetlands, including the Edithvale-Seaford wetlands, which is recognised by the United Nations as an environmentally significant site.

But the health of the wetlands could be in jeopardy if the freeway is built, according to official documents that warn toxic chemicals underground could be disturbed during piling and excavation works.