US President Donald Trump's executive order to allow this and other types of commercial fishing in part of the monument changed regulations without providing a process for public comment and stripped core protections from the monument, the groups argued in a lawsuit.
US District Judge Micah W. J. Smith granted a motion by the environmentalists.
The ruling means boats catching fish for sale will need to immediately cease fishing in waters between 93km to 370km around Johnston Atoll, Jarvis Island and Wake Island, said Earthjustice, an environmental law organisation representing the plaintiffs.
US Justice Department lawyer representing the government did not immediately return a request seeking comment.
Trump has said the US should be "the world's dominant seafood leader," and on the same day of his April executive order, he issued another one seeking to boost commercial fishing by peeling back regulations and opening up harvesting in previously protected areas.
President George W. Bush created the marine monument in 2009. It consists of about 500,000 1.3 million sq km in the remote central Pacific Ocean southwest of Hawaii. President Barack Obama expanded it in 2014.
Soon after Trump's executive order, the National Marine Fisheries Service sent a letter to fishing permit holders giving them the green light to fish commercially in the monument's boundaries, Earthjustice's lawsuit says. Fishing resumed within days, the group said.
Government lawyers say the fisheries service's letter merely notified commercial fishers of a change that had already taken place through Trump's authority to remove the prohibition on commercial fishing in certain areas.
Earthjustice challenged that letter, and by granting the motion in their favour, the judge found the US government had chosen not to defend its letter on the merits and forfeited that argument.
Smith also ruled against the government's other defences, that the plaintiffs lacked standing to challenge the letter and that the court lacked jurisdiction over the matter.
David Henkin, an Earthjustice lawyer, said Smith's ruling requires the government to go through a process to determine what kind of fishing, and under what conditions, can happen in monument waters in a way that wouldn't destroy the area.
The lawsuit says allowing commercial fishing in the monument expansion would also harm the "cultural, spiritual, religious, subsistence, educational, recreational, and aesthetic interests" of a group of Native Hawaiian plaintiffs who are connected genealogically to the Indigenous peoples of the Pacific.
