The state voluntarily shut down the Banks Pumping Plant north of Tracy on Thursday, a response to the dwindling number of Delta smelt in the rivers near the pumps.

Lester Snow, director of the Department of Water Resources, and Ryan Broddrick, director of the California Department of Fish and Game, said they will give the tiny fish at least seven to 10 days to migrate away from the pump intakes along Old River.

They did not expect that the water agencies that serve 25 million Californians would have to curtail their deliveries to customers, though the break in pumping from the Delta will reduce the level of the San Luis Reservoir near Santa Nella. Bay Area water agencies that rely on Delta water will also have to rely on their reservoir stores until the state can start to pump again.

Bill Jennings, executive director of the California Sportfishing Protection Alliance, said he’s not surprised that the state stopped the pumps. He planned to get an emergency order from an Alameda County Superior Court judge, who ruled two months ago that the pumps must shut down in order to protect the fish.

Only 25 smelt were found in a recent annual Delta survey by the Fish and Game Department. About 350 smelt, on average, were found during the same survey between 2000 and 2006.

Under the court order, the state had until the end of May to shut down the pumps or come up with a plan to save the fish. That deadline was extended indefinitely after the DWR appealed the ruling.

“We were expecting this weekend to see reverse flows in the south Delta, and that would have been a nightmare,” Jennings said.

“We’re delighted it has been curtailed, but we don’t think it will be long enough, and we don’t think it will be adequate if they don’t include the federal pumps.”

The federal pumps, which send water through the Delta-Mendota Canal to the western San Joaquin Valley, have been slowed but not shut down.

Jeff McCracken, spokesman for the U.S. Bureau of Reclamation Sacramento office, said the federal Tracy Pumping Plant has a single pump running now, sending 850 cubic feet per second into the Delta-Mendota Canal. Ordinarily at this time of year, it would be pumping more than four times that amount of water.

He said eight agencies, including the city of Tracy, still require water from the canal.

“We are looking to continue to provide the minimum flow possible to meet health and safety requirements for those customers,” he said.

Broderick said that as the Delta waters warm up, the fish will move to cooler water at the western end of the Delta. He and Snow said that operation of the pumps, despite recent reductions in the amount of water pumped, could still cause a reverse flow in Old River. That could either suck the fish into the pumps or keep them in warmer water where they would perish.

“The reality was, we’re having take (of fish in the pumps) in the year when we had the lowest numbers of smelt, so the smelt are driving the dynamic,” Broddrick said. “I don’t think they’re at the edge of extinction, but we are in a long-term 50-year decline.”

Snow said that, ordinarily, the state reduces pumping in April and May to protect water quality in the Delta but starts the pumps up again in June.