Montes was twice granted deportation protections under the Deferred Action for Childhood Arrivals (DACA) program created by President Barack Obama and left intact by President Trump.
Montes was brought to the United States at age 9, and his DACA status had prevented him from being deported twice in the past, USA Today reported.
The Montes case comes amid growing anxiety among DACA recipients.
On the night of February 17, Montes was walking to a taxi station in the border town of Calexico when a Border Patrol agent on a bicycle stopped him and asked for an identification, the suit says. Montes was not carrying his ID, which would have proved his DACA status, and agents refused to let Montes retrieve it, according to the report.
Those convictions are not serious enough to disqualify him from DACA protections, according to U.S. Citizenship and Immigration Services, the federal agency that approves DACA applications.
"Not a single piece of documentation or verbal explanation of what happened to him [was provided]", said attorney Nora Preciado of the National Immigration Law Center, which is representing Montes.
But the Department of Homeland Security claims that it has no record of Montes' renewal, and that his status expired in 2015.
On Feb. 17, Juan Manuel Montes, 23, who had lived in the United States since he was 9, was deported from the border city of Calexico, California, after being questioned by a U.S. Customs and Border Protection (CBP) officer, the newspaper said.
When he was detained in February, Montes did not have his identification on him, was not given an opportunity to see an immigration judge or ask for help from an attorney, and was escorted across the border into Mexicali without copies of the papers he signed that gave reason for his removal, his attorneys said in the lawsuit.
GOP strategist Ana Navarro on Tuesday blasted Rep. Steve King (R-Iowa) for celebrating the first deportation of a "Dreamer" during President Trump's tenure.
One supporter of the move, though, was hardliner Rep. Steve King, a Republican from Iowa who supports vastly restricting the flow of immigration into the United States and has a history of controversial statements about immigrants.
Ralph DeSio, a spokesperson for U.S. Customs and Border Protection, seemingly disputes Montes's account of what happened.
"His DACA status expired in August 2015 and he was notified at that time", DeSio added. He asked that the exact location of their home be withheld. "We will be talking to the attorney general", Trump said.
But DACA recipients haven't escaped the new administration's crackdown on illegal immigration. According to advocacy group United We Dream, at least 10 DACA enrollees are now in federal custody.
Montes has a record: three traffic violations and a shoplifting charge.
A young Seattle man was detained in March after the government said he admitted to gang ties, while an Argentinian woman was detained and later released after she spoke out about Trump's immigration policies at a news conference in Mississippi.