Brunswick officials have been forced to delay replacing a culvert that was overwhelmed during a massive rainstorm last August, washing out part of the road, as they seek a federal permit and an assessment of potential effects on endangered Atlantic salmon.

City crews were preparing to install the replacement culvert on River Road this month when they learned that the project requires a permit from the U.S. Army Corps of Engineers. Additionally, that permitting process triggers a review by U.S. Fish and Wildlife Service biologists because the small stream flows into the Androscoggin River, a federally designated Atlantic salmon watershed.

As a result, the town could be required to go with a more fish-friendly but costlier design to avoid impacts on an iconic fish species teetering on extinction in the U.S. Just three Atlantic salmon were recorded passing through the fishway at the Brunswick dam this year.

Town Manager John Eldridge said the town was “surprised” to learn that the project required approval from the corps. Eldridge said he is concerned that the temporary fix – installed after more than six inches of rain fell on parts of southern Maine in a matter of hours – could fail in another large storm.

“They are talking about the window for working on this as sometime next summer, and that was my concern,” Eldridge said, referring to the timeframe often recommended to minimize impacts on salmon, brook trout and other wildlife. “Right now we have a culvert within a culvert . . . and last time when water came up, it washed out half of the road.”

Jay Clement, senior project manager at the corps’ Maine office, said the vast majority of the 25 to 30 municipal culvert permit applications his office receives each year qualify for a more general review that typically takes 60 to 90 days. The salmon watershed requires a more detailed look but Clement said the project could still qualify for an expedited review. The town plans to meet with corps representatives and federal biologists next week, Clement said.

“We are on track to help Brunswick navigate the process as quickly as we can so they can do the work,” he said.

The corps permit is required because the project would deposit fill, substrate or other materials into a waterway. The federal “critical habitat” designation for salmon does not prohibit development but does trigger an additional layer of review whenever a project requires a federal permit or is financed with federal funds.

In 2009, the U.S. Fish and Wildlife Service added Atlantic salmon populations in Maine’s three largest rivers – the Penobscot, the Kennebec and the Androscoggin – to the endangered species list, expanding a designation that already included salmon in more than a half-dozen Down East rivers.

Atlantic salmon once spawned by the hundreds of thousands in New England’s coastal rivers. But construction of dams that blocked upstream passage for spawning – combined with overfishing, pollution and habitat loss – have all but wiped out the species in the U.S. The Penobscot boasts the only sizable annual spawning run left in the nation, but even there only 255 adult salmon passed through the Milford fish lift last summer – less than 10 percent of returns just a few years earlier.

The Androscoggin’s three salmon were counted at the fishway at the Brunswick hydroelectric dam owned by Brookfield Renewable Energy Partners. The fishway allows sea-run fish such as salmon and alewives to bypass the first major barrier to a river that extends more than 161 miles through Maine and into New Hampshire.

Increasingly, landowners and municipalities within salmon watersheds are required to scrap plans for the traditional circular culverts that quickly funnel water underneath a roadway but create obstacles to fish swimming upstream. Instead, biologists often recommend open-bottom arches or box designs that maintain the full width of the stream and mimic the natural bottom of streams.

“Fish will hide behind one of those larger [rocks] to rest while they are moving upstream,” said Wende Mahaney, a biologist who reviews culvert permit requests for the U.S. Fish and Wildlife Service. “If you have a 75-foot culvert that is all sand, it is going to be more difficult for fish to move upstream, especially for smaller fish.”

On August 13, the culvert running under River Road at the bottom of Rocky Hill failed in a severe rainstorm that caused flooding throughout the greater Portland area. Brunswick officials are preparing to consult with the federal agencies but will also seek a waiver to allow the work to be complete before next summer.

“As soon as we can get at it we would like to take care of it,” Eldridge said. “Again, our concern is it is a public safety issue.”

The Brunswick Town Council appropriated $200,000 to replace the River Road culvert and several others damaged during the August storm. Eldridge said the town is still exploring options for the River Road crossing but said he expects the new design to cost more.

Mahaney said federal agencies take safety concerns into consideration as well as whether salmon inhabit the stream when deciding whether to offer more flexible construction dates. Although she had not yet visited the River Road site, Mahaney said she believes it is unlikely there are any salmon in the stream given the Androscoggin River’s low returns this year. But Mahaney said the wider, open-bottom designs, while costing more to install, often last longer and are better able to handle the large storm events that cause traditional culverts to fail.

Surveys have found that 40 percent of the tens of thousands of culverts across Maine create a “severe barrier” to fish passage while another 50 percent pose a barrier at least part of the year.

John Burrows, director of New England programs for the nonprofit Atlantic Salmon Federation, said large forest landowners have been leading the way in upgrading culverts that run under logging roads. Educating municipal officials within the salmon watershed in Maine’s more populous areas is an ongoing challenge, though.

“We are still seeing every year culverts that are being put in wrong or are sized improperly, so there is still a lot of work to be done,” said Burrows, whose office is on the banks of the Androscoggin in Brunswick.