With prolonged and steady rain falling on Northern California for the first time in weeks, tensions are rising over how to manage the stormwater flows now streaming through the Sacramento-San Joaquin Delta.

Saying too much water is flowing out to sea, U.S. Sen. Dianne Feinstein on Friday called on operators of the federal and state water projects to pump more water south through the Delta to drought-stricken farms and cities in Central and Southern California.

The influential Democrat argued that federal regulators need to be more flexible in their approach to pumping in the Delta, the environmentally fragile estuary that serves as the hub of the state’s water delivery network. As it is, she said, they are being too cautious in their assessment of the dangers posed to endangered fish species.

Federal regulators painted a starkly different scenario, saying they are shipping as much water south as legally allowed under the environmental restrictions imposed by the Endangered Species Act. Fisheries officials cited recent surveys showing that smelt and the winter-run Chinook salmon are on the brink of extinction.

“We’re in the worst condition ever,” said Steve Martarano, spokesperson for the U.S. Fish and Wildlife Service. “Every (smelt) survey has pointed that out.”

The debate highlights the sharp divide that has come to define California’s water battles. On one side are the major agricultural interests who say they have borne the brunt of water cutbacks in the drought. On the other, the fisheries advocates who say fish have taken the biggest hit in California’s four-year drought. Now that El Niño is providing some measure of relief, both sides are hoping to benefit.

The argument centers on the Delta, the heart of California’s complex system of water conveyance. The California Department of Water Resources and U.S. Bureau of Reclamation operate water projects that rely on two giant pumping systems in the estuary, diverting river flows into canals that ship the water west to Silicon Valley and south as far as San Diego. The water not diverted flows to the Pacific.

Given the recent storms, there is 10 times as much water flowing out of the Delta to San Francisco Bay compared with a year ago, according to the Bureau of Reclamation. But flow alone doesn’t determine how much water gets pumped.

The bureau is subject to rulings issued by government biologists on how much water can be pumped and when. Those rulings are based on a variety of factors, including water quality, temperature, recent fish counts and where various fish species are in relation to the pumps. The decisions they make with regard to pumping are binding under Endangered Species Act rulings.

“We’re pumping as much as we legally can,” said bureau spokesperson Shane Hunt.

Feinstein said the pumping restrictions have allowed millions of gallons of water to escape into the Pacific, water that could have supplied 360,000 homes for a year. Advocates for increased pumping say Delta water could be filling groundwater banks and reservoirs that supply cities and farms throughout the south state.

“That water is now gone forever,” said Johnny Amaral, spokesperson for Westlands Water District, which supplies water to farmers on much of the west side of the San Joaquin Valley. Westlands farmers fallowed thousands of acres of land last year.

Feinstein, in a news release, noted that river flows more than doubled in the Delta this year compared with 2015, and yet less water has been pumped south.

“It’s inexcusable that pumping levels have been reduced without sufficient evidence of fish mortality,” she said in the release.

Fisheries officials, however, say there’s plenty of evidence that the fish are doing poorly. Endangered Delta smelt are at their lowest numbers in recorded history. The first two state trawling surveys for 2016 found only 13 of the finger-length fish.

Under environmental law, officials set a threshold of how many fish can get sucked into the Delta pumps in a given “water year,” which starts October 1. This year, the threshold is set at 56 smelt, the lowest ever. Since October, the pumps have sucked in 12, Martarano said.

The smelt aren’t the only fish at threat from pumping. Right now, tens of thousands of endangered juvenile winter-run Chinook salmon also are in the Delta.

In late February, federal officials released into the Sacramento River in Redding about 420,000 juvenile winter-run fish that were raised in a special hatchery, a stop-gap measure to prevent a complete die-off of the genetically distinct fish that spawn in summer along a stretch of river below Shasta Dam.

“They’re in the Delta right now, after carefully taking a few of the wild survivors and nurturing them in the hatchery and releasing them,” said Kate Poole, an attorney at the Natural Resources Defense Council. “So we’re going to wipe those out now? That’s an insane idea.”

The National Marine Fisheries Service said recently that only 3 percent of the wild juvenile salmon survived long enough to make it out to sea last year. It marked the second year in a row that the vast majority of juvenile winter-run Chinook got too hot and died in the Sacramento River.

Maria Rea, assistant regional manager for the National Marine Fisheries Service, said almost all the fish that did survive are in the Delta now, along with about 80 percent of the hatchery-released fish.

John McManus, executive director of the Golden Gate Salmon Association, said their best chance of survival in the Delta is as much fast-moving, cloudy water as possible to protect the Chinook from predators and push them quicker to sea. He said for all the complaining from farming interests about pumping curtailments, agriculture has fared far better in the drought than fish.

“There’s no existential threat to irrigated agriculture commensurate with the existential threat to salmon right now,” he said.

Salmon fishermen are facing a fishing season in peril. Fisheries officials warn there are so few salmon off the coast that they’ll likely have to curtail upcoming commercial and recreational fishing seasons.

Hunt, the Bureau of Reclamation spokesperson, said there’s simply not enough Delta water to make everyone happy. “Given the drought and where we’ve been,” he said, “we still don’t have enough in the right places to meet all of the demands.”

The good news is more water is on the way.

Sacramento has received 2.35 inches of rain so far this month; that’s more than two-thirds what it typically receives for all of March. The National Weather Service said Northern California can expect more precipitation Saturday and Sunday, with the chance of rain tapering off to 30 percent Monday.

For more coverage of the California drought and water issues, please visit the Sacramento Bee.

Top image: Second-graders from Colfax Elementary School release 50-day-old steelhead trout that they raised into the American River next to the Jibboon Street Bridge during a field trip to Sacramento on Friday, March 11, 2016 in Sacramento, Calif. (Randy Pench)