When the 2012 Waldo Canyon Fire was finally snuffed out, the residents of Manitou Springs, Colo., a small town on the Front Range of the Rocky Mountains, breathed a collective sigh of relief. The community had narrowly escaped what was then the most destructive fire in Colorado history. Not long afterward, Mayor Marc Snyder gave a tour to Carol Ekarius, the executive director of the Coalition for the Upper South Platte, a nonprofit that works to protect the watershed southwest of Denver. As the two walked through the picturesque town, with its eclectic historic buildings tucked between Pikes Peak and the Garden of the Gods, Ekarius pointed out structures she predicted would be damaged or destroyed when, inevitably, there would be flooding off the scorched slopes rising above them.

Snyder initially was appalled by this unsolicited warning. Ekarius, however, was persuasive: She had seen floods devastate her rural watershed in nearby Teller County after the 1996 Buffalo Creek Fire and again after the 2002 Hayman Fire, with catastrophic consequences for one of Denver’s main reservoirs.

“I wish I didn’t have a crystal ball, but I’ve seen it so many times after fires in the mountains,” Ekarius recalls. Snyder quickly recognized the danger his community faced, and he began trying to raise money to upgrade its drainage system — the best way, he thought, to avert impending disaster. “The consensus was it was coming, whether it came in Year 1 or Year 10,” he says. “It keeps you up at night, let me tell you.”

The town applied for funding from the Federal Emergency Management Agency, but the small amount Congress allocates to protect vulnerable communities before disaster was already depleted. Unable to upgrade the drainage system, town officials installed new emergency warning sirens, warned residents and steeled themselves for the calamity they knew was coming.

On Aug. 9, 2013, it arrived. Snyder spotted a heavy storm brewing over the mountains. “I’d been living under this shadow of doom for about a year,” he says. “I remember looking over and seeing that ominous dark cloud over the burn scar, and I thought: This is it.”

As rain pounded the charred slopes, a wall of muddy water carrying rocks, trees and other debris raced off them and raged through town, overwhelming the old drainage system. The torrent was so strong that it picked up cars on the highway and swept them downstream. Two people were killed nearby and dozens of homes and businesses were destroyed or damaged. So was the storm water system.

Afterward, FEMA’s largess flowed, helping to repair City Hall and paying for much of a new $6 million drainage system. But upgrading it before the flood would have cost far less, and much of the destruction could have been averted. So why wasn’t it?

FEMA says it receives requests for several times more funding than it has available each year for preventive projects.

“There’s a clear need there,” says Michael Grimm, director of the risk reduction division of the federal insurance and mitigation administration at FEMA. (In recent years, President Barack Obama has asked Congress for more funding for pre-disaster hazard mitigation, but Congress has allocated only $25 million. In his 2016 budget request, Obama is seeking eight times that much, $200 million — though the likelihood of getting that is small.)

But the shortage of pre-disaster funding is just one of the ways that FEMA is out of sync with community needs, now that climate change is impacting the West. A close examination by the New England Center for Investigative Reporting and High Country News reveals policies that discourage upgrades to help structures withstand larger floods; favor flood control using pipes and pumps, instead of systems that mimic nature; or provide aid to communities damaged by floods after wildfires only if each flood has been declared a national disaster.

Billions of dollars are at stake.

“Outside of defense spending, this is the biggest area where the feds are spending money to build things,” says Jeffrey Thomas, a Louisiana lawyer and former FEMA contractor. “Are they compatible with the high aims we are articulating for our cities to be more resilient to climate change?”

A White House task force recently called for reforms, and Obama responded with an executive order in January. He directed federal agencies to create a new standard, one that requires that projects constructed with federal funds be built on higher ground or elevated to withstand the floods expected with rising sea levels, greater deluges and other consequences of climate change. Obama also encouraged FEMA to support green infrastructure projects, such as moving buildings out of floodplains and planting trees and shrubs instead, to soak up floodwaters and make communities more resilient.

It’s too early to judge the effectiveness of the executive order, which FEMA has yet to implement. But it wouldn’t even address the dilemma faced by mountain communities like Manitou Springs. The necessary fixes, experts say, won’t come from FEMA or the White House alone. Lawmakers need to act, but, as Steve Adams, director of strategic initiatives for the Institute for Sustainable Communities, says: “Nobody thinks you could successfully amend statutes at this time because of the Congress.”

There are other possible sources of federal assistance for vulnerable communities. The Federal Agriculture Department’s Natural Resources Conservation Service can fund projects, even if the destruction doesn’t warrant a federal disaster declaration.

There’s not enough money, though, to do very much. For example, the program helped buy concrete Jersey barriers and sandbags to protect rural developments near Flagstaff, Ariz., against anticipated flooding after the 2010 Shultz Fire. But “what did come was orders of magnitude worse than anyone predicted” and quickly overwhelmed those barriers, says Dustin Woodman, engineering division manager for Coconino County, Ariz.. The torrential rain washed soil, trees and other debris down steep slopes into two rural neighborhoods, killing a 12-year-old girl and filling dozens of homes with several feet of mud.

Woodman has spent the last five years designing and funding $30 million in projects to handle floodwaters to protect the Timberline and Doney Park subdivisions outside Flagstaff. He quickly learned that FEMA would fund projects that used concrete or metal pipes to direct floodwaters, but not the green infrastructure favored by many scientists and communities. He sought funding elsewhere for such remedies, like meandering channels planted with grasses and shrubs to absorb and direct floodwaters. “FEMA is focused more on traditionally engineered flood-mitigation structures — levees and retention basins,” Woodman says. “Rather than fight that fight, we focused the FEMA funds we had on projects where we wanted to do more traditional projects.”

FEMA also resisted when Woodman wanted to use its money to replace a 2-by-4-foot roadside ditch with a channel 10 times larger.

“Those public assistance funds are only able to be used for replacement in-kind,” Woodman says. That makes it difficult for communities to upgrade drainage ditches, bridges or other structures when risks increase. But since the flooding had already carved a ditch the size Woodman wanted, he was eventually able to get a waiver for that project.

Other towns haven’t been as lucky. In Williamstown, near Vermont’s Green Mountains, for instance, FEMA paid to replace a pair of culverts four times — after they washed out — in 2004, 2007, 2011 and 2013. Each time, the agency refused to pay to upgrade the corrugated metal culverts, but it spent about $1 million to repeatedly repair the stretch of road destroyed by flooding. Town manager Jackie Higgins remembers telling a FEMA representative in 2013: “You’re still only going to put back what was there? You’re wasting money.” Late that year, Williamstown finally replaced one of the culverts with a much larger concrete structure. The project was funded by the state.

For years, counties have been asking FEMA and Congress to acknowledge that major fires often cause flooding and should be treated as one disaster. Currently, unless each flood is declared a federal disaster, victims likely won’t qualify for FEMA’s help.

Kayle Higinbotham, 68, lives in an 1880 Victorian ranch house five miles west of Manitou Springs, at the base of Pikes Peak. Her home flooded this spring when a 12-foot-deep gulch next to her house filled up with debris, and sediment washed down from the slopes. But even though three feet of muddy water filled her family room, her house isn’t in a mapped floodplain, so Higinbotham doesn’t qualify to have it bought out or moved to a safer location. Before the fire, her house and the 60 acres she inherited were valued at $1.7 million. Now, her real estate agent tells her she couldn’t find a buyer.

The risk of a dangerous flood is so great that the fire department advised her to leave home during the summer monsoon. When Higinbotham is home, she anxiously monitors the weather and listens for a flood warning on her radio. All this has left her with post-traumatic stress disorder.

“You get on your feet from the fire, and then comes the flood,” Higinbotham says. “And then you get on your feet from the flood, and here comes the next flood. There’s just no end in sight.”

The plight of people like Higinbotham has inspired community leaders to compete for federal grants, call for changes in federal policy and even levy new taxes. Other communities, however, have yet to awaken to their increased vulnerability to the bigger fires and bigger storms that are likely on the way.

Elizabeth Shogren is Washington, D.C., correspondent for High Country News; she can be reached at shogren@hcn.org or @ShogrenE. This story is part of a larger investigation by the New England Center for Investigative Reporting. The Fund for Investigative Journalism helped fund this report.