EVERETT — Building near shorelines may get a lot more complicated this fall.

That’s when new rules are scheduled to take effect that further limit development in floodplains.

The rules, handed down by the Federal Emergency Management

Agency, are intended to protect vital fish habitat.

They also could severely limit building within 250 feet of waterways. That includes hundreds of acres slated for development or already developed now in local cities.

In Everett, these areas include the Port of Everett’s Riverside Business Park and part of the city’s multimillion-dollar planned riverfront development. Spencer Island, Smith Island and private home sites along Lowell-Larimer Road also fall under the FEMA rule.

More than 100 Puget Sound communities are expected to be affected by the rules, including Snohomish, Monroe, Sultan, Arlington, Granite Falls and county areas along waterways.

If communities can’t appease the federal agencies involved, they risk losing eligibility for federal flood insurance.

“It’s kind of scary when we look at the amount of land that would be affected,” said Allan Giffen, Everett’s Planning Community Development director.

The guidelines stem from an opinion issued by the National Marine Fisheries Service.

The agency found that the FEMA’s flood insurance program is so widely available in the Puget Sound region, it’s leading to rapid development in floodplains. That, in turn, harms habitat for fish protected under the Endangered Species Act.

“What we’ve tried to do with the biological opinion is change standards and activities that adversely affect fish in the floodplain,” said Tom Sibley, north Puget Sound branch chief for the National Marine Fisheries Service.

Floodplains play a vital role in the health of Puget Sound, he said. They store nutrients, filter pollutants and provide shelter for young salmon.

Floodplains also help protect people by slowing down millions of gallons of destructive floodwaters, he said.

In Everett, officials are concerned the new rules are designed for pristine habitat, not urban areas such as Everett that have been diked and developed for a century.

“We aren’t talking about pristine habitat,” Giffen said. “We are talking about already developed areas that are definitely not native.”

Everett already follows local and state rules for building near shorelines, he said. Those rules include a biological assessment to make sure there is “no net loss” to fish habitat.

The new rules are more restrictive, requiring “no adverse effects” to fish habitat — even in the short term. Giffen worries that means restoration projects, such as breaching dikes or pulling out creosote pilings, wouldn’t be allowed because they temporarily harm fish habitat by stirring up the water.

Development in floodplains has led to dozens of acres of habitat restoration in and around Everett. That’s because the city requires builders to pay for enhancement or restoration of habitat when they build in floodplains.

The new rules aren’t intended to return already developed areas to their pristine beginnings, Sibley said. The intention is to protect floodplains from losing any more fish habitat.

“We didn’t mean for urbanized areas to go back to 1820,” he said. “If you don’t have any fish functions, it’s hard to lose any.”

He also said restoration projects and utility work are still allowed under the new rules.

FEMA has held workshops for local public officials to help make sense of the rules, and more are planned.

Yet, officials from several local cities indicated there are still unanswered questions and widespread confusion about what the rules mean.

The city of Snohomish’s public operations yard is located in a floodplain, and it’s not clear if moving raw materials to and from that yard might violate the rules, said Snohomish City Manager Larry Bauman. He’s also not certain whether the trail by the Snohomish River that’s sometimes damaged during floods could be repaired.

“We are deeply concerned about these regulations and what they mean and how they might affect city operations,” he said.

In Sultan, public and private property — including a number of homes and one planned subdivision — could potentially be affected. That may mean the city has to change its plans for future growth, something all cities are required to do by the state.

County officials said they aren’t quite as concerned, since most of the land affected in unincorporated areas is agricultural.

But that’s not entirely true. The Election Day floods of November 2006 caused nearly $9 million in damage to homes and personal property countywide. A Herald investigation a few weeks later showed that between 1995 and 2003, more than 1,100 permits were issued for building and grading projects in the county’s flood-prone areas, including more than 300 single-family homes and nearly 100 double-wide mobile homes.

One week after the Election Day flood, county officials issued permits for a new home in one of the county’s hardest-hit neighborhoods.

Communities have a few options for complying, including convincing the federal agencies that rules already on the books are sufficient. That’s the route Everett is taking.

It’s not clear yet how that will pan out.

One thing is certain: The old way of doing things wasn’t working, Sibley said. The new rules should do more to save what fish habitat remains.

Reporter Noah Haglund contributed to this report.

Debra Smith: 425-339-3197 or dsmith@heraldnet.com