The most drenching storms in the past five years have soaked Northern California, sending billions of gallons of water pouring across the state after three years of severe drought.

But 94% of the water that has flowed since New Year’s Eve through the Sacramento-San Joaquin River Delta, a linchpin of California’s water system, has continued straight to the Pacific Ocean instead of being captured and stored in the state’s reservoirs.

Environmental regulations aimed at protecting a two-inch-long fish, the endangered Delta smelt, have required the massive state and federal pumps near Tracy to reduce pumping rates by nearly half of their full limit, sharply curbing the amount of water that can be saved for farms and cities to the south.

The move has angered Central Valley politicians of both parties along with agricultural leaders, who have been arguing for many months that someone must help farmers suffering terribly during the drought. Now they are frustrated that the state Department of Water Resources and the federal Bureau of Reclamation aren’t capturing more water amid the record rainfall.

“It’s like winning the lottery and blowing it all in Vegas,” said Jim Houston, administrator of the California Farm Bureau Federation. “You have nothing to show for it at the end of the day.”

The rules were put in place by the Trump administration in 2019 and reinforced by the Newsom administration in 2020. They also are affecting urban water supplies.

The Contra Costa Water District, which relies on Delta water, has been able to add almost no water to its largest reservoir, Los Vaqueros, in the past two weeks. Its level has gone from 48% full to 50% full. And less water has flowed into San Luis Reservoir, east of Gilroy, a major supply for the Santa Clara County Valley Water District, the Metropolitan Water District in Los Angeles, and others, than otherwise would have. San Luis Reservoir has gone from 34% full on Jan. 1 to 42% full on Thursday.

“This happens every time we have high flows in the winter,” said Cindy Kao, imported water manager for the Santa Clara Valley Water District in San Jose, which provides water to 2 million people in Silicon Valley. “We are able to capture very little of it because of regulations to protect species.”

Karla Nemeth, director of the California Department of Water Resources, said Friday that the state and federal governments do not have much flexibility under the law. She said the current pumping restrictions began Jan. 3 and are scheduled to end Monday.

She said the restrictions have reduced pumping by about 45,000 acre feet over the two weeks. That’s enough water for about 225,000 people a year or enough to fill Crystal Springs Reservoir south of San Francisco 80% full.

“We share the urgency to move as much water as we can during these storms,” Nemeth said. “No question. But we also have species that are hammered by the same drought conditions. And those protections are important so we can operate the system in a balanced way.”

Under the federal Endangered Species Act signed in 1973 by Richard Nixon and the state Endangered Species Act signed in 1970 by then-Gov. Ronald Reagan, it is illegal to kill fish or wildlife at risk of extinction.

The Delta, a vast area of marshes and sloughs between Sacramento and San Francisco Bay that is roughly the size of Yosemite National Park, is where some of California’s biggest political battles over endangered species have been fought in recent decades.

The Delta is the meeting point for the state’s two largest rivers, the Sacramento, which flows south, and the San Joaquin, which flows north. That water mixes and runs westward, eventually flowing into San Francisco Bay and out through the Golden Gate to the Pacific Ocean.

In the 1950s, the federal government built huge pumps near Tracy to send water south to farmers and cities through the Central Valley Project. In the 1960s, former California Gov. Pat Brown built even bigger pumps two miles west, near Byron, that pumps Delta water into the State Water Project, which serves 27 million people.

The pumps are enormous and over time have disrupted fish and wildlife in the Delta, including smelt and salmon, sometimes grinding them up, sometimes making sloughs run backward, and other times removing up to half the Delta’s fresh water. Once plentiful, smelt and salmon numbers crashed. This winter, only five smelt have been found in the Delta by scientists.

After Sacramento River winter-run Chinook salmon were listed as endangered in 1989 and Delta smelt were listed in 1993, state and federal wildlife agencies began limiting how and when the big pumps could operate. That sparked relentless lawsuits from environmental groups, farmers and urban water agencies that continue to this day.

The key rule that has limited pumping the last two weeks is called the “first flush” rule. It requires that the pumps be ratcheted down after the first big rain every winter so that migrating smelt can move westward away from the pumps. The rule was included in the Trump administration’s Delta permits in 2019, called biological opinions, and in the Newsom administration’s state rules in 2020, known as an incidental take permit.

Environmentalists say the fish are “canaries in the coal mine” that indicate the health of the Delta, the West Coast’s largest estuary. The solution, they say, is for farms and cities to use water more efficiently and develop local sources so they take less from the Delta.

“The notion that we should just let some species go extinct because they get in the way of corporate agribusiness profits, I don’t think that’s what Californians want,” said Doug Obegi, an attorney with the Natural Resources Defense Council in San Francisco, who noted that other reservoirs around the state are filling from the rains. “No one should have the right to kill the last Delta smelt, the last chinook salmon or the last bald eagle.”

But political leaders are angry and asking for relief.

“This is no time to be dialing back the pumps,” wrote State Sen. Melissa Hurtado and Assemblywoman Jasmeet Bains, both Democrats from Bakersfield, in a letter to Gov. Gavin Newsom on Tuesday. “After several years of drought and low reservoir levels, it only makes sense to capitalize on wet conditions”

Five Republican congressmen, led by Rep. David Valadao, R-Hanford, wrote to Newsom and President Biden this week. “We have a moral obligation to provide Californians any relief that is within our control,” they said. “Government regulations should not and must not deny our constituents critical water from these storms.”

An immense amount of water was moving through the Delta on Friday. The flow rate was so high that it surpassed the volume raging down the mighty Columbia River near Portland, Oregon.

At that rate, about 159,000 cubic feet per second, the Delta was carrying enough water — 316,500 acre feet a day or 1.2 million gallons every second — to fill an empty reservoir the size of Hetch Hetchy in Yosemite National Park to the top every 27 hours.

When the state and federal pumps are fully running, they can move roughly 10,800 cubic feet per second. That means they are unable to catch most of the current deluge even if maxed out. But since Jan. 1, they have averaged just 6,415 cfs per day — far less than their capacity.

Nemeth said the issue shows the need for Newsom’s $16 billion Delta tunnel project that is designed to catch more water during big storms. She said it also shows the need to construct more reservoirs to capture wet winter flows.

If rain and snow continue this winter, the current reduced pumping won’t make much difference, experts say. But if the rain stops, as it did last year, these past two weeks will loom larger.

“It’s incredibly frustrating,” said Jennifer Pierre, general manager of the State Water Contractors, who said the rules need to be rewritten to allow more flexibility as climate change makes droughts and storms more volatile. “The jury’s still out. In May we’ll know if it was a big deal or not.”

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