Judge Ralph Erickson of the District Court for the District of North Dakota found that the 13 states suing to block the rule met the conditions necessary for a preliminary injunction, including that they would likely be harmed if courts didn't act and that they are likely to succeed when their underlying lawsuit against the rule is decided.

The decision is a major roadblock for the Environmental Protection Agency (EPA) and the Army Corps of Engineers, who were planning on Friday to begin enforcing the Waters of the United States rule, expanding federal jurisdiction over small waterways, like streams and wetlands.

But the Obama administration says it will largely enforce the regulation as planned, arguing that the Thursday decision only applies to the 13 states that requested the injunction.

"Once the rule takes effect, the states will lose their sovereignty over intrastate waters that will then be subject to the scope of the Clean Water Act," Erickson wrote in his order.

"While the exact amount of land that would be subject to the increase is hotly disputed, the agencies admit to an increase in control over those traditional state-regulated waters of between 2.84 to 4.65 percent. Immediately upon the rule taking effect, the rule will irreparably diminish the states' power over their waters," he continued, calling the Obama administration's interpretation of its jurisdiction "exceptionally expansive."