The controversial pipeline must be shut down and emptied within 30 days as officials review its environmental impact, a district court judge ruled.
DNA evidence led authorities to a Dakota Access Pipeline protester who was involved in the riots in 2016.
The Trump budget abandons community policing and boosts military spending.
The protest follows months of demonstrations in a remote part of North Dakota, where the Standing Rock Sioux tribe demonstrated in an attempt to stop the Dakota Access Pipeline.
Greenpeace argued in its letter that Exxon Mobil would "directly and predictably" benefit from the approval of Keystone XL because the firm has investments in Canadian oil sands.
About 50 police in riot gear, aided by National Guardsmen, moved slowly through the camp in Cannon Ball, North Dakota, checking structures for any of the several dozen protesters who had stayed beyond the Wednesday deadline to evacuate.
As freezing rain and snow fell, some demonstrators ceremonially burned tents and other structures at the camp in what they said was a tradition before leaving a dwelling place. But others said they were going nowhere.
Native Americans and environmental activists have lived at the Oceti Sakowin camp in North Dakota for months, fighting the construction of the pipeline that they say threatens the water resources of the Standing Rock Sioux tribe and sacred land.
Lawyers for the Cheyenne River Sioux and the Standing Rock Sioux wanted Judge Boasberg to block construction with a temporary restraining order.
The project had been put on hold under the administration of former Democratic President Barack Obama, but new President Donald Trump, a Republican, helped put it back on track.
Legal experts agreed the tribe faces long odds in convincing any court to halt the $3.8 billion project led by Energy Transfer Partners LP, which could now begin operation as soon as June.
Protesters were set to gather in a number of U.S. cities on Wednesday, a day after the U.S. Army said in a legal filing it planned to cancel an environmental study and grant the final easement needed to complete the Dakota pipeline.
Protesters have rallied for months against plans to route the Dakota Access pipeline under a lake near the Standing Rock Sioux reservation, saying it threatened water resources and sacred Native American sites.
While oil producers in Canada and North Dakota are expected to benefit from a quicker route for crude oil to U.S. Gulf Coast refiners, a revival of the projects would mark a bitter defeat for Native American tribes and climate activists.
Insulated tipis, yurts and ice cleats help prepare demonstrators for long winter with weather well below freezing.
Hundreds of veterans will be coordinating with protesters who have spent months rallying against the pipeline project.
Officials will not actively enforce an order for activists to vacate camp.
The Army Corps has insisted it has no plans to forcibly remove the anti-pipeline activists, many of them members of the Standing Rock Sioux Tribe.
Demonstrators held a prayer circle at a Bismarck mall and refused orders to leave.
Authorities say the protesters were aggressive, starting fires and hurling rocks.