The preferred alignment of the proposed F6 Extension goes through the Rockdale Wetlands and the Royal National Park a site with some of the "richest concentrations of plant species in temperate Australia".
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The assessment, in a leaked Roads and Maritime Services report, also confirms that about 14 hectares of bushland, trees and wetlands will be cleared between Arncliffe and Loftus.
The first section of the $14.5 billion toll road, between WestConnex at Arncliffe and President Avenue, Brighton-Le-Sands, would be built primarily on land historically reserved for the freeway.
The "corridor of connecting natural and open space" forms part of the Rockdale Wetlands and Recreation Corridor.
"These areas provide foraging and roosting habitat for a range of migratory and non-migratory shorebirds and small bush birds. Wetlands include Eve Street, Marsh Street and Landing Lights wetlands which in combination form part of the only remaining migratory wading bird habitat on the western side of Botany Bay," the report says.
"Eve Street Wetland is listed on the Commonwealth government's directory of important wetlands in Australia. There are a number of environmental constraints within the wetland, protected under state and Commonwealth legislation."
The report warns the wetlands are "highly valued by the community".
Plans to build on them are "likely to be met with community opposition".
Parts of the Kogarah golf course will make way for a new M5 motorway operations complex.
The golf course provides key habitat areas for the Green and Golden Bell Frog, listed under the Environment Protection and Biodiversity Conservation Act. The report says plans are underway to creating a new "artificial Green and Golden Bell Frog habitat" as part of a biodiversity offset package.
The section between President Avenue and the Georges River includes a known habitat for the threatened plant species Magenta Lilly Pilly and important nursery and breeding areas for fish entering the wetlands corridor from Botany Bay.
The section that uses the Captain Cook Bridge will be upstream from an estuarine complex "comprising a mixture of spits, bars, mudflats, dunes and beaches".
The report says it is the largest wetland of its type in the Sydney Basin and includes vegetation types "now rare in the area".
The wetland system comprises 60 per cent of the remaining saltmarsh communities and 40 per cent of the remaining mangrove communities in Sydney and is an important area for migratory and native bird species.
The report says Roads and Maritime Services plans to expedite the project by getting it declared "critical state significant infrastructure" as were NorthConnex and WestConnex, ensuring local councils cannot frustrate the project and making it "entirely permissible without consent on land outside the Royal National Park".
Within the National Heritage-listed Royal National Park and adjacent Garawarra State Conservation Area, planners would need the approval of the Commonwealth government.
Asked whether the department acknowledged the risks identified in the report a spokesman for Roads and Maritime Services said the project was "in the early stages of planning with geotechnical investigations to help inform the future design, route and potential costs".
"As with any transport project of this scale, any future motorway proposal would be subject to a rigorous and comprehensive environmental assessment process, which would include detailed analysis of any potential impacts and extensive community consultation."
Design documents seen by Fairfax Media and the ABC specify the location of each of the six exhaust stacks and the preferred alignment, "immediately adjacent to and within the Royal National Park".
smh.com.au
