The bill to progress the section of HS2 to run from Birmingham to Crewe included in the speech will give legal powers to compulsorily purchase land, and to construct and operate the railway.
However the proposed route will run through the Meres and Mosses Nature Improvement Area and, the trust says, will destroy 69 ponds, 14 miles of hedgerows, and 11 hectares of native woodland.
Cheshire Wildlife Trust evidence and planning manager Rachel Giles said: "Although Cheshire Wildlife Trust is generally supportive of sustainable transport schemes, we believe this must not be achieved at the expense of the natural environment," she said.
"We have concerns that the proposed route, just south of Crewe, will cut through the Meres and Mosses Nature Improvement Area. This area was designated by the coalition government in 2012 in order to reconnect important wetland habitats, which had become isolated from each other. HS2 will effectively sever ecological connectivity with the eastern section, undermining the very reasons for its designation."
"We are particularly concerned about farmland birds, water voles, and globally endangered native crayfish - all of which are likely to be impacted by the route and its associated infrastructure."
Cheshire Wildlife Trust is a key member of the HS2 Phase 2 Ecology Technical Group. This group voluntarily provides expertise and data to inform the ecological principles and practices of HS2 Ltd to enable the best possible outcome for ecology.