South coast rail, which is already facing questions about its nearly $2 billion cost, will also have to contend with environmental concerns about the impact of the rail line on endangered species and drinking water supplies.

South Coast Rail would run from Boston to Fall River and New Bedford.

Environmental groups so far have reserved judgment on the project itself, but only because state and federal officials have failed to provide much information on how they plan to reduce damage to wildlife and wetlands habitats as the line from Boston to New Bedford and Fall River follows the preferred Stoughton route through the Hockomock Swamp, the state’s largest fresh water wetland.

The swamp, which straddles portions of Easton, Norton, Raynham, Taunton, and West Bridgewater, has been designated by the state as an area of critical environmental concern. Thirteen rare and endangered state-listed species, such as the blue-spotted salamander, Blanding’s turtle, and eastern box turtle, live in the swamp. The area also supplies drinking water to towns in the region and provides billions of gallons of flood storage.

Priscilla Chapman of the Taunton River Watershed Association says she is disappointed that state officials have had so little to say publicly about the environmental impact of South Coast Rail. But she says she understands. “We know that this project is a high priority for the governor, and we know that state agencies work for the governor,” she says.

One idea that MassDOT has proposed to help minimize impacts to the habitat is to run commuter rail trains across the swamp on a 1.5-mile elevated trestle with “critter crossings.”

State officials will begin work on a comprehensive wetlands mitigation plan this year and the Army Corps of Engineers must review and accept that plan before federal permits can be pursued, according to a MassDOT statement. Late last year, Richard Sullivan, the state secretary of energy and environmental affairs, issued a Massachusetts Environmental Policy Act certificate to kick off the state permitting process. The Department of Environmental Protection will prepare a final comprehensive mitigation plan once all state and federal permits are finalized.

In 2011, the EPA informed the Army Corps that “the proposed project may have a substantial and unacceptable impact on aquatic resources of national importance, which include, among others, the Hockomock Swamp.” The EPA declined comment.

Trains ran through the swamp in the 1800s, but no one has done a study showing what the impact of those trains was on animals and plants, according to Chapman. “Nobody knew how many vernal pools were there before they built the railroad, what the populations of salamanders, turtles, and interior birds were,” she says.

Swamp is focus of concern. Trees have overgrown most of the old rail bed and a stream runs for about a half-mile where the tracks once were, according to Kyla Bennett, director of the Public Employees for Environmental Responsibility, a longtime opponent of the plan. Now it’s “just a path through the woods,” she says.

Tracts of Atlantic white cedar, globally rare trees that are sensitive to changes in water cycles, grow primarily on the west side of the old rail line now; for the most part, swamp red maple grows on the east side of the rail line. Chapman says the original rail line construction most likely disrupted water flows and the white cedars on the east side could not survive.

A Massachusetts Natural Heritage and Endangered Species Program fact sheet on Atlantic white cedar swamps notes that the two greatest threats to the wetlands are “land clearing” for development and disruptions to the water cycle caused by excavation and construction. “Due to the limited distribution of these unique [white cedar] communities,” the fact sheet says, “it is recommended that no clearing or filling of these wetlands be allowed.” About 12 acres of wetlands would be filled during the construction of the commuter rail project.