The federal government is required to “expeditiously” house migrant children who cross into the United States unlawfully, rather than allow them to remain in unsafe open-air sites along the border, a Federal District Court judge ruled Wednesday night.

The decision, handed down by Judge Dolly M. Gee of the United States District Court of Central California, sided mostly with the lawyers representing the children in a class-action lawsuit. It established that minors at the sites were in legal custody of the Department of Homeland Security and thus were entitled to certain rights and protections, such as a safe and sanitary environment, even if they had not yet been formally processed.

The court order, which takes effect immediately, is expected to impact thousands of children and potentially many more. It will likely force U.S. Customs and Border Protection to devote additional resources to keeping up with the flow of migrants. The agency said that it had already more than tripled the capacity at processing centers in San Diego and that it had increased the number of transport buses and personnel in order to expedite apprehensions.

The ruling comes amid a fierce political and cultural debate over the rights of migrants — including children — who enter the United States without permission. Because of an influx in crossings at the U.S.-Mexico border, immigration processing centers in southern San Diego County are strained, and migrants have waited for hours or sometimes days at makeshift camps to be taken into custody.

So far the open air encampments are only in California but the language in the order was not limited to the state, so if similar camps arise in other border states, the ruling would likely apply.

The outdoor areas lack shelter, food and sanitation, which has given way to an array of public health concerns for the most vulnerable. Unaccompanied children and young families sometimes arrive in poor health, according to aid workers and medical volunteers at the sites, suffering from traumatic injuries or chronic health conditions that require medications that have long since run out.

During the hot desert days, dehydration and heat stroke have become common problems, according to aid groups, and nighttime temperatures, wind and rain are creating conditions ripe for hypothermia. Doctors are particularly concerned about those elements for children, since many have lower body fat than adults and may be malnourished from their journeys.

The government had argued that the children were not yet in U.S. custody so it had no obligation to provide services. The judge cited Border Patrol agents’ control over the minors’ ability to leave the sites — and their power to affect whether the children have access to aid and medical treatment — as the rationale for her ruling.

“The ability to exercise discretion over, and make decisions affecting, a child’s health and welfare is indicative of maintaining legal custody of the child, regardless of whether that decision is to provide or withhold care,” the 12-page order read. “Juveniles, unlike adults, are always in some form of custody.”

Judge Gee denied the lawyers’ request for a specific time limit for how long minors could be held at the sites, but said the Department of Homeland Security needed to process all children “expeditiously” and place them in facilities that are safe, sanitary and “consistent with D.H.S.’s concern for the particular vulnerability of minors.”

She said that Border Patrol officers must stop directing minors to the sites or holding them in the sites “except for the amount of time D.H.S. reasonably requires to prepare the minor and/or actively arrange for transport of the minor to a more suitable facility.”

The lawyers who represented the children had argued that they should be given housing and services under a 1997 consent decree known as the Flores settlement agreement. That agreement established the standards of treatment for immigrant children in government custody, requiring that they be given access to basic provisions like toilets, food and drinking water, and that they generally be held in facilities that are licensed by the state to care for children in the child welfare system. The lawyers filed a motion in February seeking to enforce those terms for children at open-air sites.

The issue was whether children who crossed the southern border, alone or with their families, were the responsibility of the federal government while they remained in the outdoor areas waiting to surrender to U.S. border authorities.

In the motion, the lawyers argued that children who have not yet been formally apprehended deserve the same safe and sanitary housing as those already in official custody, since they are forbidden from moving from the camps and have no way of going back over the border.

In response, lawyers for the Department of Justice argued that because the children had not yet been formally taken into custody by American customs officials, they were not obligated to provide such service. They did not dispute that the conditions in the encampments were poor.

“C.B.P. has been apprehending and transporting minors to safe and sanitary U.S. Border Patrol facilities in a prompt manner,” the defense lawyers wrote. “But until that occurs, plaintiffs are not in D.H.S. custody,” they said.

A senior official at U.S. Customs and Border Protection said he could not comment on the legal matter, but emphasized that the current immigration system was not equipped to handle the influx of migrants arriving at the border. He noted that court rulings did not come with additional resources to make the orders more achievable.

The latest ruling from the court acknowledged those “practical difficulties” but said the agency “has not been processing class members as expeditiously as possible,” citing evidence that it “finds the ability to process children more efficiently in times of scrutiny.”