When Roselins Sequera’s family of seven finally reached the U.S. from Venezuela, they spent weeks at a migrant shelter on the Texas border that gave them a place to sleep, meals and tips for finding work.

“We had a plan to go to Iowa” to join friends, said Sequera, who arrived at the Catholic Charities of the Rio Grande Valley in October. “But we didn’t know how.”

Dozens of shelters run by aid groups on the U.S. border with Mexico have welcomed large numbers of migrants, providing lifelines of support and relief to overwhelmed cities. They work closely with the Border Patrol to care for migrants released with notices to appear in immigration court, many of whom don’t know where they are or how to find the nearest airport or bus station.

But Republican scrutiny of the shelters is intensifying, and President-elect Donald Trump’s allies consider them a magnet for illegal immigration. Many are nonprofits that rely on federal funding, including $650 million under one program last year alone.

The incoming Trump administration has pledged to carry out an ambitious immigration agenda, including a campaign promise of mass deportations. The new White House’s potential playbook includes using the National Guard to arrest migrants and installing buoy barriers on the waters between the U.S. and Mexico.

As part of that agenda, Trump’s incoming border czar, Tom Homan, has vowed to review the role of nongovernmental organizations and whether they helped open “the doors to this humanitarian crisis.” Entrepreneur Vivek Ramaswamy, who along with Elon Musk was tapped by Trump to find ways to cut federal spending, has signaled that the groups are in his sights and called them “a waste of taxpayer dollars.”

“Americans deserve transparency on opaque foreign aid & nonprofit groups abetting our own border crisis,” Ramaswamy said on X.

The Trump administration did not respond to repeated requests for comment.

The developments have alarmed immigration advocates and some officials in border communities, including Republicans, who say those communities can collapse without shelter space or a budget to pay for humanitarian costs.

Aid groups deny that they are aiding illegal immigration. They say they are responding to emergencies foisted on border towns and performing humanitarian work.For the past year, Texas has launched investigations into six organizations that provide shelter, food and travel advice to migrants. Courts have so far largely rebuffed the state’s efforts, including rejecting a lawsuit to shut down El Paso’s Annunciation House, but several cases remain on appeal.

The Texas Civil Rights Project, which represents two organizations being probed by the state, says it has trained more than 100 migrant aid organizations in the weeks since Trump’s reelection on how to respond if investigators come knocking.

The Texas investigations began after Republican Gov. Greg Abbott alleged in 2022, without evidence, that border nonprofits were encouraging illegal crossings and transporting migrants.

The shelters have received help from U.S. Rep. Henry Cuellar, a Texas Democrat who since 2019 has steered federal funding to them through the Federal Emergency Management Agency. He beat back Republican opposition last year.

“Will they attack it again and try to eliminate it?” Cuellar said. “Yes.”