To protect salmon and orcas, federal fisheries managers are calling for a moratorium on development near rivers in the Puget Sound region.

In a potentially far-reaching decision for more than 270 municipalities, the National Marine Fisheries Service said the federal flood insurance program that protects homes and businesses built in flood plains is illegal. The reasoning: Flood insurance allows development that harms salmon and, consequently, the orcas that eat salmon. Both are protected under the Endangered Species Act.

“It’s a significant wake-up call to (municipalities) who might have begun to think the Endangered Species Act didn’t carry a lot of implications for local land use,” said Jan Hasselman, the Seattle lawyer who filed suit over the issue on behalf of the National Wildlife Federation, which led to the Fisheries Service decision.

“That’s back on the table.”

It’s now up to the Federal Emergency Management Agency, which administers the flood-insurance program, to outline steps it will take to make development more friendly to salmon and orcas. FEMA spokesman Mike Howard said agency officials are still studying the decision and plan to outline their plans within the next month.

Inside flood zones, it’s virtually impossible to develop without flood insurance and inability to obtain it “would effectively shut down new housing” in flood plains, the Washington Association of Realtors has said.

“We will continue working with local governments to ensure that FEMA floodplain mapping and related analysis doesn’t result in a net loss of buildable lands,” said Bill Riley, Washington Realtors’ vice president of government affairs, in an e-mail Monday.

The Fisheries Service decision also says that if towns do figure out a way to legally allow building near rivers, builders will have to use “low-impact” techniques to minimize polluted runoff that can stun or even kill salmon.

A state administrative court recently mandated such low-impact techniques in large cities such as Seattle. The Fisheries Service decision — issued last week — expands it to the flood plains of smaller cities and towns.

Redevelopment is affected, too. Any building that expands by more than 10 percent should kick in the new requirements, the Fisheries Service said. Currently that doesn’t happen until a building expands by at least 50 percent.

The moratorium on development in flood plains could be withdrawn, the agency suggested, after FEMA issues new rules and cities and towns revise their development regulations to make them more salmon- and orca-friendly.

But it’s unclear how long that will take, and what the effect will be.

Conceptually, local governments would have to make sure builders make up for any damage they do to salmon habitat.

One way to do that would be to create big chunks of salmon-friendly waterfront by planting streamside trees. Scientists say such trees keep the water cool and attract bugs that fall into the water, providing food for salmon.

Then, whoever builds such habitat for fish could sell credits to builders who develop in flood plains. So far, though, there has been little interest locally in a large-scale project like this, although the state’s Puget Sound Partnership is carefully eyeing such a system.

“There may be alternatives here that would quickly decrease the burden,” said Tom Sibley, the Fisheries Service’s branch chief for the habitat division. “We are a long way from having that in place.”

Around the Puget Sound region, every area where rivers support threatened Puget Sound chinook has drawn up a plan to help the fish recover. Actions outlined in those plans might be taken on by developers to balance the harm they do, he said.

The Fisheries Service’s 226- page decision cites one estimate that 10 percent or less of the land inside urban growth boundaries in Western Washington is in flood plains.

But the maps delineating those flood plains are being redrawn and in many cases expanded a great deal. An analysis for the Washington Realtors noted that this has “effectively frozen all development and redevelopment in the South Snohomish Urban Growth Area. Similarly, under FEMA’s new maps, large portions of the Kent industrial area will become part of the floodplain. …”

That trend is likely to continue as climate change throws stronger storms at the region, said John Kostyack, director of wildlife and global warming for the National Wildlife Federation. Coupled with a court ruling on the same point in the Florida Keys, he said, the Fisheries Service decision shows that FEMA has to consider endangered species — but that also might help protect people.

“Now we have the Endangered Species Act showing that the development FEMA has been funding … is leading to the extinction of species,” Kostyack said. “There’s no reason we should be putting people in harm’s way, especially with what we know is coming at us — it’s already begun — in terms of more intense storms and higher sea levels.

“We can restore these flood plains as habitat and those habitats actually provide buffers against powerful storms.”