HAMILTON, WASHINGTON

Karin Vail’s modest white house near Washington’s Skagit River seemed like a perfect choice when she bought it 22 years ago. She looked forward to raising her family on its spacious one-and-a-half acres. Now, however, she just wants out.

Vail, a resolute woman in her mid- 40s with long, curly red hair, stands on her shaggy lawn and gestures toward the Skagit, whose sandy banks lie about 1,000 feet away. On a mild day like today, the river slips peacefully by, but she knows all too well how menacing it can be.

“Every time it rains,” she says, “you’re stressing.” At least five times since she and her husband, Brian, moved here, heavy rains have sent the river raging over its banks. After a 1995 flood, they raised the house on a 9-foot-tall concrete foundation. Then a 2003 flood dumped enough mud in their basement to fill 60 wheelbarrows. “Goopy, gloppy, sticky stuff,” she says. “It’s horrible.”

Many of her neighbors’ houses are also perched on stacked foundations, and attempts have been made to barricade the river with levees. But the most effective flood-protection measures have proven to be strict rules on reconstruction and a ban on new building enacted by the state decades ago, restrictions that apply only to a handful of the state’s most flood-prone areas.

Now the National Wildlife Federation and other environmental groups want to see stronger development controls for more Western floodplains. It’s increasingly clear that construction in floodplains is not only dangerous for people, it also harms habitat for salmon and other animals protected by the Endangered Species Act, including orca, Mexican spotted owls, jaguar and two species of springsnails. And the anxiety over floodplain construction is likely to rise as climate change raises flood risks.

So in courtrooms from Washington state to New Mexico, environmentalists have filed lawsuits challenging the flood insurance offered by the Federal Emergency Management Agency and related FEMA programs, which has helped Vail and her neighbors rebuild in a place that  is fundamentally unsuited for it.

If the groups succeed with FEMA, that will give them greater leverage over countless state and local policies permitting floodplain construction. They see their work as a smart strategy that can protect river ecosystems, safeguard residents, and spare taxpayers the expense of repairing flood damage. But they’re up against strong opposition, including FEMA itself, as well as local governments and a building industry that want construction and the tax dollars that come with it.

The National Flood Insurance Program, the United States’ largest backer of flood insurance, was founded in 1968 in an attempt to save taxpayers money by paying for damage with insurance premiums rather than emptying federal coffers. Anyone seeking a loan from a federally backed bank to buy or build in a floodplain must have flood insurance. In turn, the insurance is available only in cities and counties that agree to limit the likelihood of damage by restricting development in hazardous areas and elevating structures above expected flood levels. Local regulations help reduce risks, but can harm the environment.

Rocky bulkheads and levees straitjacket rivers, making them flow more quickly and washing away the gravel where salmon deposit their eggs. The barriers meant to hold back floodwaters also bar fish from habitat for feeding and reproduction. Mounding fill elevates the land in floodplains, but provides less space for floodwaters to spill into.

Development can also flush pesticides, oil and grease, and metals such as copper from brake pads into rivers. It also means that less water soaks into the soil to replenish the groundwater that feeds and cools salmon-bearing streams in Northwestern summers.

Floodplains are a sanctuary for salmon in high water. The water flows shallowly across the land, providing a calm haven with easy swimming and fewer predators. Young finger-sized fish thrive, gorging on bugs among the flooded trees and shrubs. Because floodplains are so important to salmon, long-term plans to recover the fish emphasize curtailing new development and encourage restoration of damaged areas.

In the Puget Sound region alone, more than 103,000 properties valued at $28.7 billion sit in floodplains. Homeowners and businesses hold more than 47,000 government-backed flood insurance policies, and FEMA has paid out approximately $240 million in flood claims in the past 34 years.

Nearly $4 million of those have been made in Hamilton — an average of $33,700 per household. So many claims have been filed nationwide that FEMA has been forced to borrow from the U.S. Treasury. Before Hurricane Sandy struck this fall, the program was already about $17.8 billion in debt — an amount that will surely grow as Sandy-related claims are settled.

Yet the number of building permits for floodplains continues to grow. It’s difficult to predict how any single project might harm an ecosystem, but the fear is that each helps nudge sensitive species like salmon closer to extinction.

This has been the crux of the lawsuits filed against FEMA. In Washington, for example, the National Wildlife Federation is calling for better protection for salmon and orcas.

Development proponents are pushing back, arguing that not all construction in flood-prone areas is harmful. The suit, they claim, treats every floodplain in the Puget Sound region as if it’s a pristine area that provides tremendous habitat value.

“Most of them are in fairly poor condition,” says Molly Lawrence, an attorney for Property Owners for Sensible Floodplain Regulation. The alliance of industry groups and property owners has intervened in the case, saying that existing state and local laws already safeguard floodplains. “In terms of salmon habitat, they don’t provide a lot. … Fish don’t really want to end up in the parking lot of the REI office building in the Kent Valley.”

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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.

This article appeared in the print edition of the magazine with the headline The fight for floodplains.

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