KNAPPA - It's been more than three years since a winter storm washed out the Portland and Western Railroad grade on Warren Slough in Knappa, flooded surrounding pastureland and threatened the nearby county road and bridge.

For three years, the tides have sent water washing through the breach, welcoming juvenile salmon to more than 60 acres of wetlands that experts say are now prime rearing habitat for young smolts.

As if this marathon repair project weren't complicated enough already - with private landowners, Clatsop County, multiple state agencies, federal permitting agencies and the railroad company struggling to find common ground - the newly enhanced habitat for threatened and endangered salmon adds yet another wrinkle.

Clatsop County, which applied for the permit to plug the breach because of the threat to Ziak-Gnat road and bridge, has slogged through a difficult permitting process complicated by confusion over jurisdiction. Now, though many of the ownership issues have been untangled, the permit application is still incomplete and repair work cannot begin.

The National Oceanic and Atmospheric Administration, the federal agency that looks out for protected salmon, is required to sign off on the permit to repair the damage. And, because of the valuable salmon habitat that has been created inside the breach, the agency is asking for a list of alternatives to plugging the hole in the dike, as well as a proposal for mitigating the impact the repair work will have on salmon habitat.

Conservationists who would like to see the salmon habitat protected have proposed an alternative to plugging the breach - repairing the railroad in a way that would allow water to continue flowing through the dike and paying the affected landowners for the loss of their property. But for that to work, all the affected landowners would have to agree to it.

After enduring years of false starts, landowners are frustrated by the slow-motion response from government agencies to repair the breach, and the Port of Astoria is anxious to see the rail line fixed to help attract tenants to the industrial land it's hoping to buy at North Tongue Point.

'Free' habitat restorationCathy Tortorici, chief of the lower Columbia River region for NOAA, said the 2006 breach in the railroad grade re-established a tidal connection to Warren Slough and created the kind of wetland environment the lower Columbia River is sorely lacking.

"In the lower river, thousands of acres over time have been lost to diking and ditching, and so this kind of wetland habitat is the exact type we like because it does provide rearing and resting habitat for juvenile fish," she said.

The fish habitat doesn't mean the railroad can't be repaired, she said, but it does mean the parties involved need to consider how the repairs will affect salmon.

"We've found the wetland area that's opened up contains 60 acres of high-quality rearing habitat for fall chinook," said Tortorici. "The habitat is functioning, and it's been there a couple years now."

Doug Ray, a natural resource consultant in Seaside who specializes in wetlands mitigation and ecological restoration, said during high tide, juvenile fish are swept into the slough and delivered to the insects they need to bulk up and survive in the ocean. When the tide pulls them back out, they're loaded with calories.

"It's like getting fast food at the McDonald's drive-through," he said.

Conservation organizations design costly restoration projects in the hopes of creating the kind of estuary habitat that developed on its own for free in Warren Slough, Ray said.

"This is the third-largest passive restoration in the lower Columbia River - put back by nature herself," he said.

Nadia Gardner, conservation lead for the Columbia Land Trust, said her organization focuses on reclaiming lost habitat as one avenue toward salmon recovery and would be interested in purchasing the inundated land inside the breach or paying for a conservation easement on the affected property.

Either option would allow the railroad to be repaired while preserving the fish habitat and compensating property owners for their losses, but all the landowners would have to agree to the plan.

"We only work with landowners who are willing to work with us," she said. "I think it could be a win-win if the landowners were open to it."

Frustrations mountAt one point, Lori Lilly, director of the North Coast Watershed Association, tried to gather all the stakeholders together to discuss the possibility of Columbia Land Trust purchasing the flooded property. One of the most affected landowners, 83-year-old Marjorie Leback, had expressed interest in the idea prior to her death in October.

But Lilly said she never got cooperation from the county or Floyd Holcom, who was the railroad's representative at the time.

"We've tried to get involved, but have not been able to be successful," Lilly said. "The county told us to stay out of it."

Gary Ziak, the second-most affected landowner next to Leback, said after several false starts on repairing the dike and countless un-returned phone calls to public officials, he's at wit's end. He said he wants to recall the Clatsop County commissioners who have failed him.

"It looks like nobody cares," he said. "I've gotten no help from anybody, right on down the line: the governor, (state Sen.) Betsy Johnson, the county, the division of state lands. Now all of a sudden NOAA's got something to do with it."

Ziak said he wants some water to flow into the slough for fish habitat - that's why there were fish-friendly tide gates installed on the dike. But right now, there is too much water, he said. It's killing some of the habitat he'd like to keep, and it's endangering cars and school buses on the county road. Plus, even though the land has been inundated for years, he's still paying property taxes for pastureland.

"If they want to work some kind of deal out, I'm willing to work with them," he said. "As long as they don't tell me they're kind of busy and they'll call me back. If you wait by the phone, you'll starve to death."

The Port of Astoria Commission passed a resolution at its February meeting calling for the repair of the railroad. Holcom, who is now a Port of Astoria commissioner, said the project should have been a quick emergency repair job, but has become the victim of "bureaucratic tyranny."

"With times the way they are, I think we need to be focusing our money on infrastructure repairs that create jobs and add to the economy - not the niceties we can work on later," he said. "The Port wants to see the line repaired as soon as possible to help bring in tenants at North Tongue Point."

Permitting still under wayKarla Ellis of the U.S. Army Corps of Engineers, who worked with the county on its application to repair the breach, said the initial application did not contain a complete list of alternatives or a mitigation plan.

"If the project goes forward as proposed with an entire fill of the breach, a large area needs to be mitigated," she said.

Ellis said her goal is to get the permit approved in time for the next in-water work period, which starts in November.

Ed Wegner, director of Clatsop County's Community Development Department, said one of the alternatives to plugging the breach will be a less-than-complete berm across the breach with culverts and fish-friendly tide gates built in to allow for water and fish passage.

John Speight, vice president of marketing for Portland and Western Railroad, says his company, which is no longer represented by Holcom, just wants to repair the railroad and doesn't care how.

"It is of no interest to us whatsoever whether it has one culvert, two culverts, three culverts, or more," he said.

Tortorici said ultimately the solution will involve balancing the economic value of the railroad, the needs of the landowners and the obligation to protect listed species and their habitat.

"The ideal outcome would be to have a fully functioning railroad and have that wetland and have the people involved coming together to have a consensus," said Tortorici. "We're hoping for the best."