The decision by U.S. District Judge Oliver Wanger means regulators will follow federal limits on the amount of water they can draw from the Sacramento-San Joaquin Delta, a delicate ecosystem that serves as the hub of California's water supply.
The restrictions were put in place to protect the smelt, a finger-sized fish considered a bellwether of the delta's health, as they swim downstream into the Pacific Ocean.
"This is good news for the smelt, and it's good news for the salmon," said Zeke Grader, executive director of the Pacific Coast Federation of Fishermen's Associations, whose members have had to dock their boats given the collapse of commercial salmon fisheries in the last two years. "It means that there will be a better chance that the fish will survive."
Farmers across the fertile San Joaquin Valley argued those same limits have caused hundreds of millions of dollars in crop losses as the shortages have forced them to fallow their fields and lay off thousands of farmworkers.
An attorney for the Westlands Water District, which gets its water from the delta, said water districts plan to appeal Wanger's decision next week.
"We can't plant any of our annual crops until we know what kind of water supply we're going to get this year," said Don Devine, a Fresno farmer who grows organic sweet corn and cantaloupes on the valley's dry west side. "It's a heartbreaker to have to lay people off, but we've had no choice because there's no water."
Both the state and federal government run massive pumps that siphon drinking and irrigation water from the delta to more than 25 million Californians and the farms that produce half the nation's fruits and vegetables.
Laura King Moon, whose organization represents districts that provide water to Los Angeles and Alameda counties, said the latest court order lay bare the need for a long-term solution to the delta's ills.
"This is clearly not the right way to manage water supply for millions of people, businesses and farms," said King Moon, assistant general manager of the State Water Contractors.
Last week, Judge Wanger agreed to temporarily lift a similar set of pumping limits aimed at safeguarding native, wild salmon.
The federal government began pumping at full capacity on Saturday, freeing up some water for farmers crippled by two years of limited deliveries.
But Tuesday, federal biologists announced they had found dead smelt near the pumps and said unrestricted pumping risked pushing the fish into extinction.
As a result, the U.S. Bureau of Reclamation plans to shut off one of its five pumps on Thursday. Those restrictions aim to protect both the smelt and salmon, and could last until June 30.