More than a decade after government biologists first warned the Federal Emergency Management Agency (FEMA) that allowing development in floodplains is helping kill salmon and orcas, environmental groups on Wednesday turned to their most potent — and controversial — weapon:

They asked a federal judge in Seattle for an emergency injunction that would effectively halt a sizable chunk of the building in flood-prone areas until FEMA finds a way to make sure it won't harm endangered fish or whales.

U.S. District Judge Ricardo Martinez likely won't rule on the matter until next year, but environmental groups have consistently won in federal court when challenging how the agency deals with construction in Puget Sound river valleys. Federal fisheries biologists already determined in 2008 that FEMA's flood plain insurance program violates the Endangered Species Act.

And while it's impossible to know how much construction might be curtailed, the National Wildlife Federation says its review of FEMA data suggests 700 to 800 new structures have been built in floodplains in the three years since the biologists said the practice must change.

"Salmon are going over the edge, and we've waited years for it to change and it hasn't," said Jan Hasselman, an attorney with the environmental legal firm Earthjustice, which filed the motion in federal court. "As far as we can tell, not one project has been prevented, delayed, reconfigured or reconsidered" since 2008.

Mike Pattison, with the Master Builders Association of King and Snohomish Counties, called the move "unfortunate" and said an injunction could stop hundreds of projects around a region still struggling with an economic downturn.

"The effect would not be widespread, but those whom it does affect will be hit substantially," he said. "Will homebuilders as a unit get clobbered? Probably not. But those who do will lose all utility of their property, even for remodels or small changes."

A FEMA official Thursday wouldn't comment directly on the legal challenge, but said in the three years since hearing that the flood insurance program violated the Endangered Species Act, his agency has completely overhauled what kind of development in flood zones it will insure. Local communities, from King and Pierce counties to the small cities on the Kitsap Peninsula, must now show development won't adversely impact salmon.

At issue is what happens when streets, homes, businesses and parking lots are built near rivers that occasionally overflow their banks.

Scientists with the state Department of Ecology and the National Marine Fisheries Service have warned since the mid-1990s — before orcas and Puget Sound chinook were listed under the Endangered Species Act — that such building can destroy stream-side channels that fish use when trying to escape rushing floodwaters. It can also change stream hydrology and increase the pollution that drains into salmon-bearing streams after heavy rains.

In addition, the fisheries service determined that kind of development contributes to the decline of southern resident killer whales, which depend heavily on chinook.

While FEMA doesn't directly permit development — cities and counties do — it often only happens because FEMA provides insurance for builders in flood zones who meet minimum requirements to reduce risk.

But a federal judge in 2004 ruled the flood-insurance program had wrongly allowed tens of thousands of buildings to go up without considering the impact on Puget Sound's troubled marine species. Four years later, the fisheries service said the program also violated the Endangered Species Act.

After years of negotiating with federal fisheries biologists to tighten building rules, FEMA's program still lacks many strict requirements, environmentalists said. So far, most of the 120 or so communities affected by FEMA flood insurance plan to tackle new development on a "project-by-project" basis that doesn't address cumulative impacts.

Earlier this fall, FEMA didn't know which flood plain rules communities are following. In a letter to FEMA earlier this fall, Will Stelle, the head of the fisheries service in the Northwest, criticized the emergency-management agency's inability to gather such basic data.

"The bottom line, overall, is that not much has changed," said Dan Siemann with the National Wildlife Federation. "Salmon habitat is still being harmed or destroyed."

But Mark Carey, mitigation division director for FEMA's Northwest region, couldn't disagree more. He said his agency has spent hundreds of hours in meetings with cities and counties and tribes and dramatically changed the minimum requirements all those communities must follow before building in flood plains.

"As of today, we believe we are fully compliant" with the Endangered Species Act. He also said FEMA knows which rules each community is following.

While most are taking a "project-by-project" approach to review development rather than changing local ordinances to reflect new standards, Carey said that is a temporary solution. Many communities have longterm plans to update other building rules, and plan to fold in new flood-insurance rules at the same time.

Carey also disputed the notion that the very existence of flood insurance encourages people to build in dangerous places. In order for communities to be eligible for flood insurance they have to mitigate potential hazards, he said. And payouts to people whose properties are later damaged don't come from taxpayers — they come from premiums paid by other flood insurance recipients.

"This whole program is just a fundamental part of personal emergency preparedness," he said.

Meanwhile, Molly Lawrence, an attorney for a coalition of property owners and industry groups opposed to the filing by environmentalists, said the injunction request — and even the fisheries service's concern about floodplains in 2008 — doesn't take into account how the flood insurance program really works on the ground. It evaluated the program in isolation when it is actually just one of a number local government regulations that dictate how fish habitat is to be protected.

Still, not even environmentalists are suggesting that building in floodplains needs be banned. They argue that it should only be allowed if rules limit the density of development in sensitive areas, require stricter controls on management of stormwater, limit removal of vegetation and don't adversely impact salmon.

So far, Hasselman said, "it's clear to us that it's not going to happen without somebody else getting involved. That somebody else is the court."

Craig Welch: 206-464-2093 or cwelch@seattletimes.com. On Twitter @craigawelch.