CLINT, Tex. — Since the Border Patrol opened its station in Clint, Tex., in 2013, it was a fixture in this West Texas farm town. Separated from the surrounding cotton fields and cattle pastures by a razor-wire fence, the station stood on the town’s main road, near a feed store, the Good News Apostolic Church and La Indita Tortillería. Most people around Clint had little idea of what went on inside. Agents came and went in pickup trucks; buses pulled into the gates with the occasional load of children apprehended at the border, four miles south.

But inside the secretive site that is now on the front lines of the southwest border crisis, the men and women who work there were grappling with the stuff of nightmares.

Outbreaks of scabies, shingles and chickenpox were spreading among the hundreds of children who were being held in cramped cells, agents said. The stench of the children’s dirty clothing was so strong it spread to the agents’ own clothing — people in town would scrunch their noses when they left work. The children cried constantly. One girl seemed likely enough to try to kill herself that the agents made her sleep on a cot in front of them, so they could watch her as they were processing new arrivals.

“It gets to a point where you start to become a robot,” said a veteran Border Patrol agent who has worked at the Clint station since it was built. He described following orders to take beds away from children to make more space in holding cells, part of a daily routine that he said had become “heartbreaking.”

The little-known Border Patrol facility at Clint has suddenly become the public face of the chaos on America’s southern border, after immigration lawyers began reporting on the children they saw — some of them as young as 5 months old — and the filthy, overcrowded conditions in which they were being held.

Border Patrol leaders, including Aaron Hull, the outspoken chief patrol agent of the agency’s El Paso Sector, have disputed descriptions of degrading conditions inside Clint and other migrant detention sites around El Paso, claiming that their facilities were rigorously and humanely managed even after a spate of deaths of migrant children in federal custody.

But a review of the operations of the Clint station, near El Paso’s eastern edge, shows that the agency’s leadership knew for months that some children had no beds to sleep on, no way to clean themselves and sometimes went hungry. Its own agents had raised the alarm, and found themselves having to accommodate even more new arrivals.

The accounts of what happened at Clint and at nearby border facilities are based on dozens of interviews by The New York Times and The El Paso Times of current and former Border Patrol agents and supervisors; lawyers, lawmakers and aides who visited the facility; and an immigrant father whose children were held there. The review also included sworn statements from those who spent time at El Paso border facilities, inspection reports and accounts from neighbors in Clint.

The conditions at Clint represent a conundrum not just for local officials, but for Congress, where lawmakers spent weeks battling over the terms of a $4.6 billion humanitarian aid package for facilities at the border. The lack of federal investment, some argue, is why the sites have been so strained. But the reports of squalor prompted several Democratic lawmakers to vote against the final bill, which did not have oversight and enforcement provisions.

By all accounts, the Border Patrol’s attempt to continue making room for new children at Clint even as it was unable to find space to send them to better-equipped facilities was a source of concern for many people who worked there.

“I can’t tell you the number of times I would talk to agents and they would get teary-eyed,” said one agent, a veteran of 13 years with Border Patrol who worked at Clint.

Mary E. González, a Democratic state lawmaker who toured the Clint station last week, said that Border Patrol agents told her they had repeatedly warned their superiors about the overcrowded facility, but that federal officials had taken no action.

“They said, ‘We were ringing the alarms, we were ringing the alarms, and nobody was listening to us’ — agents told me that,” Ms. González said. “I genuinely believe that the higher-ups made the Clint situation happen.”

A Forward Operating Base

Architects designed the Clint station as a type of forward base — replete with fueling stations, garages for all-terrain vehicles and horse stables — from which agents could go on forays along the border.

The station was never intended to hold more than about a hundred adult men, and it was designed with the idea that migrants would be detained for only a few hours of processing before being transferred to other locations.

Officials have allowed reporters and members of Congress on controlled tours of Clint, but prohibited them from bringing phones or cameras inside, and from entering certain areas. But through interviews with dozens of people with knowledge of the station — including lawyers, former detainees and staff members — The Times was able to model the main areas where children were held: the station’s central processing area, with its cinder-block cells; a converted loading area and yard; and a warehouse on the property.

Parts of the site resemble what might be seen at many government buildings. Photographs in the hallway celebrate the work of the Border Patrol, showing agents on horseback and in all-terrain vehicles. A conference room features high-backed chairs upholstered with faux leather.

But the sense of normalcy fades away the deeper one goes into the station. A detachment of Coast Guard personnel, sent to assist overworked agents, stock an ad hoc pantry with items like oatmeal and instant noodles. Monitors in blue shirts roam the station, hired through an outside contractor to supervise the detained children.

Beyond the pantry, a door leads to the site’s processing center, equipped with about 10 cells. One day this month, about 20 girls were crowded into one cell, so packed that some were sprawled on the floor. Toddlers could be seen in some cells, cared for by older children.

One of the cells functioned as a quarantine unit or “flu cell” for children with contagious diseases; employees have at times worn medical masks and gloves to protect themselves.

A part of the processing area was set aside for detained children to make phone calls to family members. Many broke into tears upon hearing the voices of loved ones, episodes so common that some agents merely shrugged in response.

Clint is known for holding what agents call U.A.C.s, or unaccompanied alien children — children who cross the border alone or with relatives who are not their parents.

Three agents who work at Clint said they had seen unaccompanied children as young as 3 enter the facility, and lawyers who recently inspected the site as part of a lawsuit on migrant children’s rights said they saw children as young as 5 months old. An agent who has worked for Border Patrol for 13 years — and who, like others interviewed for this story, spoke on condition of anonymity because he was not authorized to discuss the situation — confirmed reports by immigration lawyers that agents have asked migrants who are teenagers to help care for the younger children.

“We have nine agents processing, two agents in charge of U.A.C. care and we have little ones that need their diapers changed, and we can’t do that,” the agent said. “We can’t carry them or change diapers. We do ask the older juveniles, the 16-year-olds or 17-year-olds, to help us out with that.”

As immigration flows change, the scene inside Clint has shifted as well. The number of children in the site is thought to have peaked at more than 700 around April and May, and stood at nearly 250 two weeks ago. In an attempt to relieve overcrowding, agents took all the children out of Clint but then moved more than 100 back into the station just days later.

Unaccompanied boys are kept in a converted loading area that holds about 50 people. Until a few weeks ago, older boys were kept in a tent encampment outside.

Families, including adult parents, were also sent to Clint earlier this year, and Representative Will Hurd, a Republican whose Texas district includes Clint, said that 11 adult males “apprehended that morning” were also being held at the site when he visited on June 29.

Before the influx of migrants began to wane in recent weeks, the agents said they had kept the families in a warehouse normally used to house A.T.V.s. It was converted into two holding areas initially intended to house 50 people each.

A Chief Agent Under Fire

At least two Border Patrol agents at Clint said they had expressed concern about the conditions in the station to their superiors months ago. Even before that, senior Homeland Security officials in Washington had significant concerns about the El Paso Sector’s brash chief patrol agent and his oversight of the facility over the past year, when tighter security along other sections of the border prompted a steep rise in migrant crossings along the section that runs from New Mexico through West Texas.

The situation became so severe that in January, officials at Customs and Border Protection, the agency that oversees the Border Patrol, took the unusual move of ordering the sector chief, Mr. Hull, to come to headquarters in Washington for a face-to-face meeting. The officials were concerned that Mr. Hull, an agency veteran who speaks with a pronounced Texas twang, had moved too slowly to put safety measures in place after the deaths of migrant children, according to a Homeland Security official. After the meeting, Mr. Hull moved forward with the new procedures.

But tension has persisted between Mr. Hull and officials in Washington, particularly in recent months, as the number of migrants continued to increase at his facilities. The officials believe that Mr. Hull and Matthew Harris, the chief of the Clint station, have been slow to follow directives and communicate developments at the facilities in their sector, according to two Homeland Security officials.

Mr. Hull is seen as a hard-liner on immigration issues. He has often been heard saying that migrants exaggerate the problems they face in their home countries.

Officials at the border agency declined multiple interview requests.

Last month, the acting head of C.B.P., John Sanders, ordered an internal investigation into the Clint facility. The investigation — which is being conducted by the agency’s Office of Professional Responsibility and the department’s inspector general — has examined allegations of misconduct.

As part of the review, investigators have conducted interviews and watched hours of video footage to see how agents treated detainees. So far, investigators have found little evidence to substantiate allegations of misconduct. But they have found that the facility is several times over capacity and has horrendous conditions.

The uproar over the site is drawing scrutiny on Border Patrol facilities that are some of the least-regulated migrant detention centers in the United States.

That is in part because they are intended in most cases to hold migrants for no more than 72 hours, before they are turned over to better-equipped facilities operated by other government agencies with stricter regulations on, say, the number of toilets and showers required. But the 72-hour limit has been frequently breached during the current migrant surge; some children have been housed at Clint for weeks on end.

Lawyers who visited the Clint station described children in filthy clothes, often lacking diapers and with no access to toothbrushes, toothpaste or soap, prompting people around the country to donate supplies that the Border Patrol turned away.

But Mr. Hull painted a far different picture of his need for supplies in April, when the numbers of children held in Clint were soaring. Mr. Hull told commissioners in Doña Ana County in Las Cruces, N.M., in April that his stations had more than enough supplies.

“Twenty years ago, we were lucky if we had juice and crackers for those in custody,” Mr. Hull said, as quoted in The Las Cruces Sun-News. “Now, our stations are looking more like Walmarts — with diapers and baby formula and all kinds of things, like food and snacks, that we aren’t resourced or staffed for and don’t have the space to hold.”

An Inspector Arrives

One day in April, a man from Washington arrived unannounced around midday at the Clint station. He introduced himself as Henry Moak, and told the agents inside that he was there to inspect the site in his role as Customs and Border Protection’s chief accountability officer.

The Clint station was far over capacity on the day of Mr. Moak’s visit, bulging with 291 children. Mr. Moak found evidence of a lice infestation; children also told him about going hungry and being forced to sleep on the floors.

One girl, a 14-year-old from El Salvador, had been in custody for 14 days in Clint, including a nine-day stretch in a nearby hospital during which Border Patrol agents accompanied her and kept her under surveillance. Mr. Moak did not specify in his report why the girl had been rushed to the hospital. When the girl returned to Clint, another child had taken her bed so she had to sleep on the floor.

Two sisters from Honduras, one 11 and the other 7, told Mr. Moak that they had to sleep on benches in the facility’s hold room, getting their own cot only when other children were transferred out. “The sisters told me they had not showered or brushed their teeth since arriving at Clint station,” Mr. Moak said in his report. Showers had been offered twice during the girls’ time in custody, but the girls were asleep each time, his review showed.

Mr. Moak in the end stated that Clint was in compliance with standards.

One of a team of lawyers who inspected the station in June, Warren Binford, director of the clinical law program at Willamette University in Oregon, said that in all her years of visiting detention and shelter facilities, she had never encountered conditions so bad — 351 children crammed into what she described as a prisonlike environment.

She looked at the roster, and was shocked to see more than 100 very young children listed. “My God, these are babies, I realized. They are keeping babies here,” she recalled.

One teenage mother from El Salvador said Border Patrol agents at the border had taken her medicine for her infant son, who had a fever.

“Did they throw away anything else?” Ms. Binford said she had asked her.

“Everything,” she replied. “They threw away my baby’s diapers, formula, bottle, baby food and clothes. They threw away everything.”

Once at Clint, she told Ms. Binford, the baby’s fever came back and she begged the agents for more medicine. “Who told you to come to America with your baby, anyway?” one of the agents told her, according to the young woman’s account to Ms. Binford.

Border Patrol agents have said they have adequate supplies at Clint for most of the migrants’ needs. The facility lacks a kitchen, they said, so the ramen, granola bars, instant oatmeal and burritos that serve as most of the sustenance for migrants has been the best they could do.

Children sometimes could be seen crying, said one Border Patrol agent, who has worked for seven years at the Clint facility, but it most often seemed to be because they missed their parents. “It’s never because they’re mistreated; it’s because they’re homesick,” she said.

A Father Finds His Sons

Not long after Mr. Moak signed off on the conditions inside Clint, a man named Ruben was desperately trying to find his sons, 11-year-old twins who both have epilepsy.

The boys had crossed the border together in early June with their adult sister. They were hoping to reunite with their parents who had come to the United States earlier from El Salvador in order to earn enough money to pay for the boys’ epilepsy medications. They require daily injections and a strict regimen of care to prevent the seizures they began having at age 5.

But the twins were separated at the border from their sister and sent to Clint.

The first time they spoke to Ruben on the phone, the two boys sobbed intensely and asked when they would be able to see their parents again.

“We don’t want to be here,” they told him.

Ruben asked that his last name and the names of his sons be withheld for fear of retaliation by the American government.

Only later did Ruben learn that the boys had been given at least some of their epilepsy medication, and neither one had had a seizure. But one boy reported breaking out in a skin rash, his face and arms turning red and flaky. Both had come down with fevers and said they had been sent temporarily to the “flu cell.”

“There is no one to take care of you there,” one told his father.

It took 13 days after the boys were detained to speak to their father over the phone. A lawyer who had entered the facility, Clara Long of Human Rights Watch, met the boys, tracked down their parents, and helped them make a call. The boys were stoic and quiet, she said, and shook her hand as if “trying to act like little adults” — until they spoke to their father. Then, they could answer only with one- or two-word answers, Ms. Long said, and were wiping tears from their faces.

Much of the overcrowding appears to have been relieved at Clint, and overall arrivals at the border are slowing, as new policies make migrants, mainly from Central America, return to Mexico after they request asylum, as the summer heat deters travelers and as Mexico’s crackdown on its southern border prevents many from entering.

A Border Patrol agent who has long worked in the El Paso area said agents had tried to make things as easy as possible for the children; some bought toys and sports equipment on their own to bring in. “Agents play board games and sports with them,” he said.

But the Border Patrol long “took great pride” in quickly processing migrant families, and making sure children did not remain in their rudimentary stations for longer than 72 hours, the agent said. Clint, he said, “is not a place for kids.”

In the surrounding town, many residents were puzzled and sad at the news of what was happening to children in the station on Alameda Avenue.

“I don’t know what the hell happened, but they’ve diverted from their original mission,” said Julián Molinar, 66, a retired postal deliveryman who lives in a house facing the station. He served in the Army in Europe as the Berlin Wall came down, he said, and was dismayed that there was now talk of building a border wall near his home. As for the Clint facility, he said, “children should not be held here.”

Dora H. Aguirre, Clint’s mayor, expressed sympathy for the agents, who are part of the community in Clint and neighboring El Paso. “They’re just trying to do their job as a federal agency,” she said. “They are trying to do the best they can.”