Illegal immigrant families are furious at the treatment they received after being detained at the border, complaining of bad burritos, cold soups, being forced to drink water out of toilets and contagious disease outbreaks that have swept through the facilities.

The complaints are detailed in a massive court filing on behalf of illegal immigrant children that claims the government is breaking its promise to provide quality care for juveniles who end up in the custody of the Homeland Security Department.

“We had to drink the water from the toilet to keep hydrated,” said one mother, identified only by her first name, Yojana, who was nabbed in Texas.

Several parents said their children contracted chickenpox from others in detention, the chill of the facilities was a universal complaint, and a number of families objected to the food situation.

“We received soup when we arrived, but it was cold,” complained two brothers who were nabbed in Arizona.

“They feed us two burritos per day, but it isn’t enough,” said one mother, identified only by her first name, Denia, who is still breastfeeding her young daughter. “I have an allergy to gluten, so I’m afraid to eat the burrito because it might make me sick.”

She went on to say that the conditions are causing her breast milk to dry up, leaving her daughter hungry as well.

The reports stem from the first stage of immigration detention, when migrants are nabbed immediately after crossing into the U.S.

Migrants are supposed to be processed and then either immediately returned home if possible, or else released into the interior of the U.S., put into longer-term detention by U.S. Immigration and Customs Enforcement or, in the case of juveniles, turned over to social workers at the Health and Human Services Department.

But in the first hours or days after they are caught, the migrants are still in the custody of U.S. Customs and Border Protection, and the families say that is where the treatment is its worst.

A number of parents said in court documents that guards yelled at both them and their children, made fun of their home countries and threatened to deport them. Children, meanwhile, reported that guards would kick them to prevent them from sleeping.

“They made us wake up three times in the night to make us line up and go through a list. In the middle of the night, they would kick us to wake us up,” one detainee, identified only as Leydi, said in her sworn declaration. “There were women who asked the officials not to be rude, but the officials said that it wasn’t their problem. The only thing the officials said was that it wasn’t their fault that we came to this country illegally.

The government disputes the accounts, pointing to its own inspectors, who say conditions are up to standards.

One of those inspectors visited a half-dozen Border Patrol stations and found everything in order: toilets and sinks worked, plenty of food was available, the facilities were regularly cleaned, and water, juice and baby formula were available. The monitor said the children he spoke with had been able to talk to their parents and were in touch with consular officials from their home countries.

Henry A. Moak Jr., the chief accountability officer for CBP, said migrants who complained about the water appeared not to know how to use a water fountain. Those who complained about the food said it was different from what they were used to, but he never heard reports of rotten or spoiled food.

In the case of those who complained about the temperature, “many of the minors and or parents I spoke to were not used to air conditioning,” Mr. Moak concluded.

A federal judge, fed up with the bickering and unsure which side to believe, late last week stepped in and said she would order an independent monitor to review the border facilities and report back to her.

“It seems like there continue to be persistent problems,” Judge Dolly M. Gee said. “I need to appoint an independent monitor to give me an objective viewpoint about what is going on at the facilities.”

Judge Gee’s case, known in legal circles as the Flores settlement, has been going on for years. It’s separate from, but in many ways is responsible for initiating, the recent border separations that have sparked their own legal battle.

The 1997 Flores agreement controls the way illegal immigrant juveniles are treated in immigration custody. For nearly two decades, it was deemed to apply only to children who jumped the border without a parent or guardian, but Judge Gee ruled in 2015 that it would, for the first time, also cover children who arrived with parents.

Her ruling meant the juveniles had to be quickly released — and since they were supposed to be released to their parents, that meant releasing the families.

Both the Obama and Trump administrations say that ruling sparked a surge of illegal immigrant families — and even abductions of young children so illegal immigrant adults could pretend to be families — hoping to take advantage of the policy and earn a speedy release into the U.S., where they could disappear into the shadows.

Despite the surge that followed her ruling, Judge Gee has rejected the suggested that she is responsible.

She has inserted herself ever deeper into the decision-making on detention, regularly overruling the government to set standards for care and conditions for quick release.

CBP declined to comment on the complaints, citing the ongoing litigation.

But Commissioner Kevin McAleenan, speaking at the Bipartisan Policy Center last week, acknowledged there have been struggles. He said most of the facilities were designed decades ago, when almost all of the illegal immigrants crossing the border were adult men from Mexico.

They were usually kept in custody for hours — long enough to be processed — then quickly returned to Mexico without a formal deportation. It was so quick that Border Patrol agents said it wasn’t uncommon to catch the same guy twice in a nighttime shift.

Beginning late in the Bush administration, the government began to move away from returns and toward removals, or a formal deportation, that required a longer process in the U.S.

But the bigger change was in the flow of people. More than 50 percent of the flow of illegal immigrants across the southwestern border now are from Central America and other non-Mexican nations — and a huge percentage of them are either families or juveniles traveling solo.

Processing takes much longer, particularly with myriad levels of protection built into the system for refugees and others fleeing real dangers. Holding families for several days is a far bigger challenge than holding Mexican men for a few hours.

“We have to have a better arrival point for children and families,” Mr. McAleenan conceded at the Bipartisan Policy Center.

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