“There is no evidence, or contention, that any of these plaintiffs satisfy the definition of a ‘known terrorist,’ ” wrote Trenga, adding that even harmless conduct could result in someone being labeled as a “suspected terrorist” on the watch list.

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“An individual’s placement into the [watch list] does not require any evidence that the person engaged in criminal activity, committed a crime, or will commit a crime in the future,” the judge wrote, “and individuals who have been acquitted of a terrorism-related crime may still be listed.”

The ruling could reshape the government’s process for a watch list that has long been criticized for inaccuracy and described by opponents as “a Muslim registry created in the wake of the widespread Islamophobia of the early 2000s.” Trenga ordered both the plaintiffs and defendants to submit arguments about how to fix the constitutional problems with the database, which encompasses nearly 1.2 million people, including about 4,600 U.S. citizens or residents, as of June 2017.

Trenga’s 32-page opinion was hailed as a significant win by the Council on American-Islamic Relations, the civil liberties organization that filed the lawsuit in 2016.

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“Innocent people should be beyond the reach of the watchlist system,” Gadeir Abbas, a CAIR attorney for the plaintiffs, said in a statement. “We think that’s what the Constitution requires.”

The watch list is a different, less restrictive database than the No Fly List, which bars people from boarding U.S. airplanes or flying through the nation’s airspace. In 2014, a federal judge in Oregon ruled the No Fly List was unconstitutional, forcing the Department of Homeland Security to modify its procedures. Abbas told the Associated Press that Wednesday’s ruling was the first to specifically target the watch list.

The FBI did not immediately respond to a request for comment late Wednesday. The AP reported that the FBI’s lawyers argued in court that the government’s efforts to combat terrorism outweighed the difficulties alleged by the nearly two dozen Muslim American citizens on the list.

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But the Muslim American citizens on the watch list told the court they suffered a wide range of abuse and harassment, according to the opinion.

Anas Elhady was returning to the United States after a brief trip to Canada in April 2015 when he was surrounded by Border Patrol before he was handcuffed and interrogated for more than 10 hours. During this time, he needed emergency medical attention. Elhady would be detained at least two other times at the border, and on one occasion an FBI agent told him his cellphone conversations were being monitored, according to the opinion.

“When Elhady attempted border crossings, [Customs and Border Protection] officers told him, ‘Are you serious? Someone like you should have stopped crossing the border by now,’ ” wrote Trenga, a 2008 appointee of President George W. Bush.

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Hassan Shibly, a plaintiff who works in CAIR’s Florida chapter, said he has been searched dozens of times because of his inclusion in the database. Once he was handcuffed by authorities in front of his grandmother near a border crossing in Detroit.

“It’s humiliating,” Shibly told the AP in April. “The government lawyers could never make the arguments they made ... if they had personally faced the same treatment we’ve faced.”

Another plaintiff, Hassan Fares, said the secrecy of the watch list had him questioning whether his struggle to open a bank account stemmed from his placement on the list.

“It’s difficult to determine whether it’s random or whether it’s [connected] to something else,” he said to the AP. “Suspicion just leads to paranoia.”

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Abbas also argued that the broadly disseminated database — which grew from 680,000 people in 2013 to 1.16 million in 2017 — was worthless in stopping terrorism.

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After noting that many who have actually committed acts of terrorism never had their names included on the list, Abbas pointed to the case of Omar Mateen, who killed 49 people in 2016 at the Pulse nightclub in Orlando. Though Mateen was on the FBI’s watch list and had been interviewed twice by authorities, he was eventually removed from the database in March 2014. James B. Comey, then director of the FBI, said federal agents had concluded he was not a threat, The Washington Post reported.

In his ruling, Trenga gave the parties in the lawsuit 45 days to submit their arguments and replies for how the watch list could be changed.