The chief U.S. District judge denied a motion for a stay on gay mariage following Walker's decision last week that Proposition 8 is unconstitutional.
But in his denial, Walker gave opponents of same-sex weddings until Aug. 18 at 5 p.m. to get a ruling from the 9th U.S. Circuit Court of Appeals on whether gay marriage should resume.
The group that had gathered on the steps outside of city hallcheered as they received word that Walker had ruled against a long-term stay.
One man carrying a rainbow flag crouched down and began to cry.
But the joyful reaction quickly turned to indignation a short time later as the couples learned that the stay would not be lifted immediately. Some couples had arrived at city hall early Thursday morning in anticipation of Walker's decision.
Charles J. Cooper, lead counsel for the initiative's proponents, said in a statement that they plan to appeal "promptly."
"On appeal we look forward with confidence to a decision vindicating the democratic process and the basic constitutional authority of the 7 million Californians who voted to retain the traditional definition of marriage," Cooper said.
One man who applauded the decision Thursday was Gov. Arnold Scwarzenegger.
"I am pleased to see Judge Walker lift his stay and provide all Californians the liberties I believe everyone deserves," he said. "Today's ruling continues to place California at the forefront in providing freedom and equality for all people."
Bay City News contributed to this report.