A coalition of conservation groups has welcomed a federal judge’s ruling on Thursday that halts construction work on the controversial immigration jail in the Florida Everglades known as Alligator Alcatraz.

US district judge Kathleen Williams ordered workers to stop adding any new paving, infrastructure or ground filling at the remote tented detention camp that the Trump administration intends to eventually hold 3,000 migrants awaiting deportation.

Her verbal ruling, which she said would be reinforced by a written restraining order later on Thursday, will be in effect for two weeks while attorneys argue whether the construction of the camp broke environmental rules.

US Immigration and Customs Enforcement (Ice) can continue to operate the camp and hold detainees there, Williams said, pending the resolution of the lawsuit’s claims that the project threatens fragile wetlands that are home to protected plants and animals, and will reverse billions of dollars’ worth of environmental restoration.

“It’s a relief that the court has stepped in to protect the Everglades’ sensitive waters, starry skies and vulnerable creatures from further harm while we continue our case,” said Elise Bennett, attorney at the Center for Biological Diversity.

“We’re ready to press forward and put a stop to this despicable plan for good.”

The lawsuit, filed in Miami district court by an alliance including the Friends of the Everglades, Earthjustice and the Miccosukee Tribe of Indians of Florida, is challenging only the environmental impact of the jail, which opened last month after a high-visibility visit by Donald Trump.

A separate lawsuit brought by civil rights groups says detainees’ constitutional rights are being violated. They claim they are barred from meeting lawyers, are being held without charges, and that a federal immigration court has canceled bond hearings. A hearing in that case is scheduled for 18 August.

As well as the legal proceedings, the opening of Alligator Alcatraz has been greeted by a wave of outrage by Democrats, some of whom toured the facility last month and decried “inhumane” conditions inside, including detainees held in cages, flooding from heavy rain, non-functioning toilets, broken air conditioning and swarms of mosquitoes.

It was later also revealed that despite Trump’s assurances that the jail was reserved for “deranged psychopaths” and “some of the most vicious people on the planet”, hundreds of detainees had no criminal records or active charges against them.

The lawsuit claims the detention facility violates the National Environmental Policy Act (Nepa), which requires federal agencies to assess the environmental effects of major construction projects.

Jesse Panuccio, attorney for the state of Florida, said during the hearing that although the detention center would be holding federal detainees, the construction and operation of the facility was entirely under the state of Florida, meaning the Nepa review would not apply.

His argument appeared not to sway Williams, who said the project was at a minimum a joint partnership between the state and federal government, and that anything built at the site would probably remain there permanently, regardless of how the case was ultimately decided.

The plaintiffs presented witnesses on Wednesday and Thursday in support of the injunction, while attorneys for the state and federal government are scheduled to present their case next week.

Talbert Cypress, chairman of the Miccosukee Tribe of Indians of Florida, said he welcomed the decision to halt construction on and around the Big Cypress preserve, the group’s traditional tribal homelands.

“The detention facility threatens land that is not only environmentally sensitive but sacred to our people,” he said.

“While this order is temporary, it is an important step in asserting our rights and protecting our homeland. The Miccosukee Tribe will continue to stand for our culture, our sovereignty, and the Everglades.”

The Associated Press contributed to this article