The lawsuit, announced on Friday, names as defendants Attorney General Jeff Sessions, the Immigration and Customs Enforcement, ICE, and the Department of Health and Human Services' Office of Refugee Resettlement, ORR.
The lawsuit was filed in San Francisco on behalf of three teenagers recently detained on Long Island, east of NY.
Yolo County spokeswomah Beth Gabor said Saturday that county officials have not yet seen the lawsuit and declined to comment.
Freeman said the children had previously been screened by the Office of Refugee Resettlement and placed with their parents on Long Island after entering the country illegally from Central America.
Police on Long Island have been sweeping up dozens of people suspected of being MS-13 gang members in the past year following the deaths of 17 people in possible gang violence in Suffolk County.
The organization also alleges that federal authorities are "embarking on a concerted effort to detain and deport children based on unreliable claims of gang affiliation and flawed reports of criminal history" under the guise of a "crackdown" on transnational street gangs.
The juvenile plaintiffs, all of whom are Latino, say they are being watched, targeted and profiled by local law enforcement.
One of the juvenile plaintiffs says he was arrested while "play-fighting" with a friend after a soccer game.
Devin O'Malley, a spokesman for the Department of Justice, defended the detentions. He is being held in ORR detention due to ICE's unsupported allegations of "gang affiliation", the ACLU said.
Due to this investigation and its findings, the department is now a party to an agreement that requires it to implement "significant changes in how it engages the Latino community". An ACLU lawyer says the lawsuit was filed there because the teenagers were taken to a government facility in northern California.
"They have dreams and legal claims to remain in the United States, but they've been swept up by an administration that prioritizes deportations over truth and justice", he said.
Children who enter the USA illegally unaccompanied by their parents are treated differently under US law.
According to the ACLU, the plaintiffs seek to be returned to their parents' custody and request a declaration that the government has violated their rights under the Constitution, federal immigration law, and a 1995 consent decree that sets national standards for the treatment of immigrant children.
In its lawsuit, the ACLU seeks the release of the illegals who are plaintiffs in the case and an injunction to prevent the administration from detaining any other immigrant children without cause.