Judge James Wechsler, who is overseeing the case in San Juan County, initially ruled in August that the settlement was fair and reasonable. But critics filed motions in an effort to block him from entering the decrees.
Wechsler denied those motions and entered the judgment Friday. The ruling is subject to appeal.
The settlement grants about 635,000 acre-feet of diversions and 335,000 acre-feet of depletions from the San Juan River to the Navajo Nation as well as additional rights for impoundments.
The settlement also authorized a pipeline to serve Gallup and Navajo communities in New Mexico and eastern Arizona.