Wisconsin wildlife officials are quietly considering a request from BNSF Railway to carry on construction in the La Crosse River marsh during the nesting season of an endangered species, prompting environmentalists to cry foul.

BNSF contractors began building a second line through the marsh last month after receiving a permit from the Army Corps of Engineers allowing them to fill 7.28 acres of wetlands.

The Wisconsin Department of Natural Resources had previously granted BNSF a permit that prohibited work during the May-July nesting period of the black tern, an endangered species in Wisconsin.

But the DNR this week amended that permit to allow construction during the nesting period if the department’s Bureau of National Heritage Conservation issues what’s called an incidental take permit, allowing “unintentional loss of individual endangered or threatened animals” so long as it doesn’t put the overall population at risk.

The incidental take permit could be issued as soon as May 18, at the conclusion of a public comment period.

Midwest Environmental Advocates, a Madison-based nonprofit organization that is suing the DNR over its issuance of the original wetland permit, is protesting that the DNR amended the permit without public notice.

“By changing permit conditions without public input,” said attorney Sarah Williams, the DNR “excluded the opportunity for natural resources experts to call attention to the environmental impacts of rail construction at this time and in this sensitive ecosystem.”

DNR water management specialist Carrie Olson referred questions about the permitting process to a department spokesman who in turn referred questions to the Department of Justice.

A DOJ spokesperson did not respond to a request for comment Wednesday. 

Notice of the incidental take permit was posted April 16 on a page within the department website and sent to La Crosse County media outlets. Conservation biologist Lisie Kitchel said the agency had received no public comments as of Tuesday.

“It took some digging for the petitioners to even discover that the incidental take permit was on public notice,” Williams said. “It’s a backdoor way to do something they could have done publicly and openly.”

Chuck Lee, president of the Friends of the La Crosse River Marsh, said he learned of the permit application from a friend who stumbled upon it weeks after it was posted. He assumed from the wording of the notice that the permit was already granted.

“The Department has concluded that the proposed project is not likely to appreciably reduce the likelihood of the survival or recovery of this species within the state, the whole plant-animal community of which it is a part or the habitat that is critical to its existence,” the notice stated.

A gull-like bird that feeds by diving into the water, the tern breeds in marshes, sloughs and other wetlands. The last survey documented just 169 pairs in the Great Lakes basin.

Its decline is attributed to loss of habitat, human disturbance, pesticide use and problems along the migration route.

“Loss of breeding habitat has undoubtedly been a major contributing factor in the decline,” according to the DNR.

Wildlife photographer Alan Stankevitz, one of the plaintiffs in the MEA suit, complains that the DNR is reversing a condition outlined in the original permit “without any justification” or study.

Stankevitz said the action contradicts the first line of the agency’s mission statement: “to protect and enhance our natural resources.”

“They should basically change the mission statement to ‘protect and enhance our industry,’” he said. “That’s basically what they’re doing.”

The DNR concluded that construction activity would likely discourage nesting, though it said the birds don’t typically nest near the busy track.

DNR spokesman Bill Cosh said Thursday that the agency has not conducted a survey of the area this year to determine how many terns are present. 

The marsh work is part of a controversial project to add about four miles of new tracks through the city of La Crosse between Farnam and Gillette streets. The entire project is expected to be complete by fall.

The railroad has said the upgrade should ease delays at each end of what is the area’s only section of single track. Because of the location of BNSF’s North Side rail yard and its crossing of the Canadian Pacific line and the constraints of the Mississippi River and bluffs, BNSF says finding an alternative route is unrealistic.

The project is one of 13 planned upgrades the railroad is making to its route along the Mississippi River between the Twin Cities and the Illinois border.

The U.S. Fish and Wildlife Service previously issued BNSF a similar permit for a bald eagle nest near the project.

Lee said the issuance of two such permits after the DNR’s initial permit was granted “call into question the extent of the environmental assessment that took place, which was minimal.”

MEA and a group of local citizens have sued the DNR and are asking the court to halt the project and require a more thorough environmental review. A hearing in that case is scheduled for Thursday.

Meanwhile, the organization says it’s most concerned about the lack of public input in the process.

This “is not what transparent and accountable government action is supposed to look like,” said spokeswoman Stacy Harbaugh. “This whole process has been a kind of a moving target and it can’t turn into the new normal.”

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