The battle, however, is not over.
Commissioners authorized Randy Kirkpatrick, executive director, to work out a deal with former New Mexico state engineer John R. D'Antonio, Jr.
The settlement would secure 6,300 acre-feet of water per year from an application the commission filed in 2001.
An acre-foot is roughly enough water to supply a suburban family for one year.
The water rights case, San Juan Water Commission vs. John R. D'Antonio, New Mexico State Engineer, is pending an appeal.
If the New Mexico Court of Appeals sides with the commission, Kirkpatrick will negotiate the settlement.
Farmington city officials disagree with stipulations in the commission's proposed settlement agreement, approved on Feb. 6.
The city's commission representative was directed not to vote to approve the deal based on issues related to who actually holds the water rights.
He abstained from voting.
Nonetheless, Mayor Tommy Roberts said Monday that the additional water will benefit all county residents.
"In my mind, that's a big plus," he said. "But we still have an issue -- whether the commission ultimately holds the water rights, or whether it is apportioned out to its member entities."
Kirkpatrick was traveling and could not be reached for comment on Monday.
The commission is made up of representatives of the cities of Aztec, Farmington and Bloomfield, and the San Juan County Rural Water Users Association.
Elected officials, however, are not directly represented, Councilwoman Mary Fischer said at a recent city council meeting.
That lack of representation is cause for concern, she said.
She feels the commission has little accountability to the public as a result.
"I have problems with how the commission operates," Fischer said on Monday. "These aren't new concerns. I was hoping they would take the information back to the governing bodies. That was the original intent for the commission when it was created."
Farmington City Council will go into a closed session Tuesday morning to discuss the settlement.
Commission representatives and state officials worked out the settlement deal in late January, according to a commission press release.
The settlement's origins go back more than a decade when the commission filed an application for the additional water rights in 2001.
The application requested water that was no longer needed for the Animas-La Plata Project but the office of the state engineer refused to publish the application. The commission appealed the decision.
The State District Court in San Juan County ruled in the commission's favor in August 2011 and ordered the state engineer to publish the application.
The San Juan Water Commission would withdraw its objections to a pending Navajo Nation Water Rights Settlement as part of the deal.
The commission has not voted on whether to support that settlement.
A trial to decide whether the Navajo Nation settlement should be approved is scheduled for June.