The problem of housing affordability, long a concern in popular big cities, has moved to rural America.

Nearly one-fourth of the nation’s most rural counties have seen a sizeable increase this decade in the number of households spending at least half their income on housing, a category the federal government calls “severely cost-burdened.”

Those counties, none with towns of more than 10,000 residents, have experienced housing cost increases significant enough to force families to scrimp on other necessities.

Meanwhile, only two big-city counties – Bronx, New York; and Norfolk, Virginia – fell into the same category. Both had 2-point increases, according to a Stateline analysis of American Community Survey estimates from the U.S. Census. Stateline compared the early years of the Great Recession, 2006-2010, with the most recent economic recovery era, 2013-2017.

The share of severely cost-burdened households has fallen since the Great Recession in expensive destinations such as Cape Cod, Massachusetts; Key West, Florida; San Francisco; and Seattle. The share also has dipped slightly in Manhattan, New York, as the overall economy has recovered.

Losses of high-paying jobs have hit some rural regions, such as a cluster of coal-dependent counties in Kentucky, Tennessee, and Virginia, especially hard. Other places are struggling with affordable housing because new workers in economically revived areas are vying for rental housing, putting pressure on prices in a rental market with a limited supply.

“Sometimes all it takes is just one new facility in one of these communities,” said Corianne Scally, a research associate who studies affordable housing at the Urban Institute.

“All of a sudden you need more labor on hand to start up that plant, you’re stretching the ability of the rental housing base to accommodate new people and you see prices increase,” Ms. Scally said.

That’s the case in Irion County, Texas, population 1,516, where fracking and wind farms have been bringing new workers, said county clerk Shirley Miles. The county’s energy jobs tripled to 187 between 2010 and 2016, the latest federal data available, at average annual wages of more than $63,000.

Unemployment in the county dropped from 5.3 percent to 3.2 percent in that time, and typical monthly rents rose 44 percent to $858.

Another new wind farm is under construction now, and it’s already under contract to provide power to Mexico-based baker Grupo Bimbo and other customers. That’s bringing 300 temporary construction workers this year and a dozen more permanent jobs after the wind farm is operational.

“You think of these places like Irion County as ‘The Last Picture Show,’ all dusty and forgotten, and then you see that some of them are success stories. This isn’t all a dark story,” said Keith Wiley, senior research associate at the Housing Assistance Council in Washington, a nonprofit working to build more housing in rural communities.

Yet Irion County had one of the largest cost-burden increases, according to the Stateline analysis, with 13 percent of households severely cost-burdened in recent years, up from just 4 percent during the Great Recession.

There are similar situations in rural areas of Iowa and Georgia, where new meatpacking plants are stressing the local rental market and driving up prices, Mr. Wiley said.

One reason for the slow-moving crisis in rural rental housing is that federal incentives to include affordable units have all but disappeared, and those remaining are quietly expiring, allowing landlords to freely charge more when demand rises, according to a 2018 study by the Housing Assistance Council. More than 2,000 rental properties left the federal program, mostly in the Midwest, between 2006 and 2016, according to the study, as landlords paid off the loans.

Norton, Virginia, a town at the heart of Appalachian coal country with a population of 3,936, saw its cost-burdened population soar to 22 percent from 12 percent in Stateline’s analysis, one of the largest increases.

In Norton, people have lost good jobs and are struggling to make a living in a town that’s a commercial and health care center for surrounding rural counties. The area is having its own local recession after prospering during the nation’s Great Recession, officials there said, before the fracking boom made natural gas cheaper than coal. Median rent is unchanged at about $550 between 2010 and 2017, but household income dropped to about $27,000 from about $34,000.

“We never had a downturn here like other places. Our economic peak was probably around 2010,” said Norton City Manager Fred Ramey. “Then we lost a lot of coal jobs – probably a thousand in this area, and those were jobs paying $50,000 to $80,000, and the rest of the local economy was not able to absorb all those jobs.”

A similar thing is happening in Madison County, Idaho, 475 sprawling square miles of farmland and foothills with a population of about 40,000 people. The county seems an unlikely candidate to eclipse crowded hotspots such as Los Angeles and Key West in the number of residents struggling to pay rent. But 25 percent of Madison County households are severely cost-burdened, an increase of 6 percentage points, according to Stateline’s analysis.

That’s because Brigham Young University’s Idaho campus has expanded from a two-year to a four-year school, drawing thousands of new students from other states. Many of them are married with children, following a way of life common for members of The Church of Jesus Christ of Latter-day Saints, which is affiliated with the school.

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Eastern Idaho Public Health has expanded low-income family programs like immunizations and nutrition programs to serve the new residents.

This story was reported by Stateline, an initiative of the Pew Charitable Trusts. Interact with Stateline's housing affordability data here.