Environmentalists say it's exactly that kind of thinking that helped create the problem in the first place. "It's really important to save as much floodplain as we can," says DeeAnn Kirkpatrick, a retired biologist from the National Marine Fisheries Service. "Whatever (floodplain) is remaining, whether it is good habitat or not so good, really is important if we want these salmon to survive."

The Skagit is the largest of the western Washington rivers whose floodplains environmentalists want to protect. Its watershed boasts one of the Northwest's largest undammed river systems and is home to six populations of threatened chinook salmon. Historically, some of the returning chinook runs were 10 times larger than they are today. Chinook are the favorite food of the orcas that frequent Puget Sound, and their decline is one of the main causes for the decline of the iconic black-and-white whales.

In 2008, Kirkpatrick was the lead author of a federal biological opinion that concluded that FEMA's flood insurance program encouraged construction that damaged floodplains, harming salmon and orca. The report was the result of a 2003 NWF lawsuit against FEMA in Washington. In 2004, Seattle federal Judge Thomas Zilly ordered FEMA to consult with the National Marine Fisheries Service over how its program was affecting local imperiled species. The biological opinion provided the answer.

The federal biologists not only spelled out the harm caused by the insurance program, they also explained how to fix it. They called for taking climate change into consideration when drawing floodplain maps identifying at-risk areas, allowing only levees with salmon-friendly features such as vegetation and woody material, and banning new floodplain development unless damage was offset by creating fish habitat and flood storage elsewhere.

The insurance program changes affect 122 cities, counties and tribes in the Puget Sound region. But eight years after the ruling, builders are still getting permits for flood-plain projects that critics say are harming fish and orcas.

Last year alone, Puget Sound cities and counties approved more than 600 floodplain projects. The exact number is difficult to calculate. Despite a requirement to report all floodplain building permits, 48 of the 122 communities participating in the flood insurance program missed the deadline and weren't included in the 2011 report that FEMA provided to the Fisheries Service to demonstrate its compliance with the biological opinion.

An InvestigateWest review of submitted permits revealed that many are so short on details it is impossible to know their potential ecological impacts. Even though the permits include questions about the amount of hard surface being built, the number of trees removed and whether mitigation was required, these queries frequently remained unanswered.

Charging that FEMA has failed to make the fixes prescribed in the biological opinion, NWF sued the agency again in 2011. Fearing a halt to numerous development projects, 16 cities in the Puget Sound area joined a lawsuit opposing the environmentalists.

Last April, federal Judge Ricardo Martinez in Seattle denied NWF's request to immediately stop FEMA from issuing any new floodplain insurance near the most valuable salmon habitat.

The case remains in court. Similar lawsuits in Oregon, California, New Mexico, Arizona and Florida are either wending their way through court or have been settled, largely in favor of conservation groups, who argue that FEMA encourages cities and towns to reconfigure rivers and reshape floodplains in ways that have damaged habitat critical to salmon, sea turtles, deer and butterflies. (The graphic below lists the lawsuits.) The environmentalists' initial challenge to the program dates back nearly 20 years.

Even as battles are fought in courtrooms across the country, FEMA officials in the Northwest insist they are already making improvements to safeguard wild creatures. This region "is going to serve as a national model," says Mark Carey, director of mitigation for FEMA's Region 10 office.

The agency is also poised to make changes to the program nationwide. This summer, FEMA accepted public comment on a plan to prepare an environmental impact statement for the flood insurance program, which could include updates to better protect wildlife.

One of FEMA's key roles in floodplain management involves producing updated maps that incorporate climate change and other environmental information to better protect sensitive lands and prevent construction in risky areas. But with limited resources, many years can pass between updates. FEMA's regional office says one way the agency is helping endangered species locally is by prioritizing the updating of maps that include their habitat.

John Graves, senior National Flood Insurance Program specialist for the region, says his office is committed to making Puget Sound area communities comply with the requirements prescribed to protect wildlife. Change takes time, he says, but it's happening. "We're changing the culture of floodplain management. It used to be about armoring and keeping the water away. Now we're moving into a new culture of protecting natural, beneficial functions as well as protecting people and property. The battleship is turning.

The changes have come too late for Hamilton. With construction largely forbidden, the town's future is bleak. Buildings and residents alike are aging, and not being replaced. Some say their only hope for survival requires a drastic change: Move the entire town of 300 to higher ground. Local officials and residents have floated the idea before, but there's never been enough money and interest to make it happen.

Climate change could force the issue. A recent report from Washington's Department of Ecology predicts that the river-swelling runoff will increase by up to 21 percent by 2040, and "increased frequency and severity of floods will likely lead to greater taxpayer costs for cleanup and rebuilding as well as economic disruption."

That could also mean that more towns across the West will experience flooding similar to what Hamilton has suffered. "Instead of floodplains getting smaller, they're going to be getting bigger," says Kirkpatrick, the Fisheries scientist.

Vail, meanwhile, is waiting for the next flood -- making plans to move valuables in the basement to higher shelves and shift her rabbit hutches to the upstairs deck. She'll keep an eye on the levees and hope the water in town doesn't rise above nine feet.

She figures that, even if she tried to sell it, no one would want to buy her flood-prone property, and she doesn't have the down payment for another home anyway. She expects that over time, the once-thriving town of Hamilton will wither away.

And that, she believes, might be for the best. It's "probably a good idea," Vail says sadly, "to save future generations from the heartache we've been through."

Robert McClure of InvestigateWest contributed to this report. InvestigateWest is a nonprofit, reader-supported journalism studio in Seattle. Its website is www.invw.org.