SAN DIEGO — Migrants who are allowed to remain in the United States to pursue asylum are usually given a choice when they are released from detention in San Diego: Go to the Greyhound bus station and fend for themselves, or try to find a cot and a shower at a local shelter.

One way or another, once the migrants have been dropped off by discreet white Immigration and Customs Enforcement vans in border towns across the Southwest, they are no longer the federal government’s problem.

President Trump has tried and failed to end a practice he derisively calls “catch and release,” and thousands of undocumented migrants apprehended at the border every month are still being granted routine entry to the United States while their cases are processed by immigration courts.

But as the number of migrant families in recent months has overwhelmed the government’s detention facilities, the Trump administration has drastically reduced its efforts to ensure the migrants’ safety after they are released. People working along the border say an ever larger number of families are being released with nowhere to stay, no money, no food and no means of getting to friends and relatives who may be hundreds or thousands of miles away.

Federal officials say they are unable to do more to help the migrants, and local governments have often been hesitant to get involved because of cost and potential liability.

Stepping into the void has been a growing network of charities, expanding along the border from California to Texas. Dating back well into the Obama administration, when the surge in migrant families began, these churches and other nongovernmental organizations have strung together millions of dollars worth of assistance to help keep migrants off the streets and speed their reunion with family members in the United States.

“The government isn’t doing anything — it’s been a total make-it-up-as-we-go thing,” said Kevin Malone, one of the founders of the San Diego Rapid Response Network, a consortium of faith-based nonprofits in the area. “People are working 24 hours a day trying to make this happen. Everyone is strapped.”

While there has never been a good solution to the issue of what to do with migrants after they are released by immigration agents, recent steps by the Trump administration have exacerbated the situation.

Undocumented migrants are held initially at Border Patrol and ICE facilities as their claims for asylum are registered. Previously, government agents would help coordinate plans for their release, contacting family members in American cities and helping secure transportation, even sometimes paying for bus tickets. When charity-operated shelters were full, government agencies sometimes held them a little longer, until they could be transferred.

Those practices, known collectively as “safe release,” ended in October, according to a statement from ICE, because the agency has become overwhelmed by the number of migrants it has to process.

Part of the problem, government officials say, is that the courts have established a limit of 20 days for holding migrant children in detention, and the government has a very limited number of detention facilities that can handle both adults and children. An earlier attempt to detain them separately was struck down by the courts and rescinded. Waiting to coordinate releases with charity shelters can result in migrant families being held in detention for too long, officials say.

“After decades of inaction by Congress, the government remains severely constrained in its ability to detain and promptly remove families with no legal basis to remain in the U.S.,” the agency said. “To mitigate the risk of holding family units past the time frame allotted to the government, ICE has curtailed reviews of post-release plans from families apprehended along the southwest border.”

Yet those now trying to help the migrants say the government has abandoned its moral responsibility to make sure they are released safely.

Even under President Obama, the government had no infrastructure to provide services to newly released migrants; instead it relied on a cooperative relationship with private shelter operators. Now, the shelter operators say, that cooperation has become fraught.

Some charity networks have had to quickly become experts in refugee aid in American border towns. They provide showers, nutrition and clean clothes. Many “guests,” as the volunteers call the migrants, arrive hungry, sick or traumatized. They need fresh diapers for their infants and clean clothes for their older children.

The sole shelter in San Diego, run by Jewish Family Service of San Diego, has processed nearly 5,000 asylum applicants since it began operating two months ago. It was built “on a wing and a prayer,” according to Mr. Malone, and has had to move five times to find adequate space. Newly arrived migrants are provided with austere blue cots, portable showers and donated bread and fruit. They are also screened for illnesses.

Kate Clark, the director of immigration services at Jewish Family Service, said the organization stepped in nine weeks ago when it learned migrants were being “dumped at the border.” But despite California’s political leaders talking about being receptive to migrants, “every single night, our ability to ensure that none of the migrants are sleeping on the street is questionable, because of the capacity of our shelters,” Ms. Clark said.

Their operating costs run between $350,000 and $400,000 a month, largely raised by faith organizations and a GoFundMe account. Still, on days when 100 or more refugees are dropped off, they have little option, because of capacity constraints, other than to turn away families and leave them homeless.

“It’s been a difficult couple of years, but there’s never been anything like this,” said Etleva Bejko, the director of refugee services at the organization.

The charities have also had to learn how to cope with the illnesses that migrants can develop during the difficult journey from Central America, which many make on buses and on foot.

Marcela Wash, a registered nurse who has helped treat migrants in San Diego, said that many arrive dehydrated and in various states of medical distress. Rashes, scabies, and respiratory infections have been extremely common, she said. She estimated that 80 percent of the women she saw had lice.

“Their journeys were hard, of course, but many of these things they caught either at a shelter in Tijuana or in detention,” she said.

Once migrants are healthy enough to travel, the shelter pays to transport them to join relatives wherever they are in the country, while their cases proceed in court.

Some border towns have a more established base of nonprofit assistance for migrants, but they too have seen demands grow in recent months.

In El Paso, the Annunciation House has coordinated migrant releases with ICE for years. The migrants typically stay for a few days at the charity’s main building or at one of nearly two dozen churches, hotels and other sites that are part of its shelter network. In recent months, the charity has been assisting about 2,200 migrants a week in El Paso.

On a recent afternoon, the shelter’s headquarters, a red brick building about a mile from the border, bustled with activity, part migrant dormitory, part cafeteria and part triage center. Upstairs, a worker holding bundles of laundry walked past family dorm rooms with bunk beds, as the aroma of a dinner being prepared filled the halls. Downstairs, migrant families waiting for a ride to the bus station kept busy by helping to unload a UPS truck parked outside. A new batch of donations had arrived, to add to the towers of Amazon boxes full of clothing and other goods that people around the country had donated.

The cost of these operations can be crushing. In just two Texas border regions — the El Paso and McAllen areas — several Catholic groups, charities and local governments have spent roughly $2 million in recent years on migrant relief efforts.

On Friday, Ruben Garcia, the director of Annunciation House, was preparing to pay for several rooms at a hotel for the next seven days to handle an overflow of migrants from their shelter. The tab came to about $14,000. Depending on the number of migrants ICE releases, the shelter’s hotel expenses can climb as high as $150,000 a month.

Bureaucracy and politics can tie up more significant investments at the local level. Mr. Malone, the executive director of the San Diego Organizing Project, said San Diego municipal and county officials have suggested to him they have been waiting for the state to officially declare a crisis to lend a hand. He presumed that had to do with the bottom line.

“It became just a bunch of people pointing fingers,” said Mr. Malone. “And at the end of the day, the other question was, ‘Who is going to pay the check?’ That’s the real reason that no one talked about.”

The California Department of Social Services gave the shelter $500,000, but the money could only be used for “case management,” including intake, registration and “know your rights” orientations. It could not be used for most of the shelter’s operating costs, or for transportation costs for the migrants, one of the primary needs. San Diego County has provided medical guidance and nursing and support staff.

“We want to help prevent a crisis,” Mr. Malone said. “It’s been our crisis, and I’ve been telling them, soon it’s going to be yours.”

Gov. Gavin Newsom’s office did not immediately respond to requests for comment.

The city of McAllen, Tex., which has seen the largest number of migrant families during the recent surge, has contributed $517,000 since 2014 toward a relief effort run largely by Catholic Charities.

In El Paso, city leaders were forced to act after federal officials made a series of unannounced nighttime releases of hundreds of migrants during Christmas week. The city officials put migrants on municipal buses to keep them warm, took them to shelter sites and coordinated the response with the local Office of Emergency Management. El Paso officials were told that none of the cost would be reimbursed by the federal government.

“It’s kind of hard to ask the federal government for emergency relief when they’re creating the problem to begin with,” Dee Margo, the mayor of El Paso, said at a recent City Council meeting.

Mr. Garcia, who runs Annunciation House, said that in October, for the first time since 2014 that he could remember, there were several releases of migrants onto the streets of El Paso without any coordination.

“I started getting calls from the police department, and everybody and their grandmother was calling me to figure out what was going on,” he said. “I wish to God you could get into one of their offices to ask them, ‘What in the world were you thinking when you did that? What was the objective?’”

Jose Del Real reported from San Diego and Manny Fernandez reported from El Paso. Mitchell Ferman contributed reporting from McAllen, Tex.

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