New state water regs cause angst on all sides

April 9, 2020
by Lois Henry
Lois Henry


The Sacramento-San Joaquin Delta is an estuary where both the state Department of Water Resources and the federal Bureau of Reclamation pump water south to farms and cities through separate projects.

The DWR operates the State Water Project (SWP), which moves water through the California Aqueduct along the western edge of the Central Valley.

The Bureau operates the Central Valley Project (CVP), which moves water south through the Delta-Mendota Canal to the Los Banos area. It also moves water out of the San Joaquin River from Millerton Lake to farms and cities via the Friant-Kern Canal on the eastern flank of the valley.

While each entity has its own reservoirs throughout the state, they share space in the San Luis Reservoir just south of their pumping stations at Tracy. They also share responsibilities to keep enough water moving through the delta to keep back salt from the San Francisco Bay and to ensure the survival of native fish populations.

Those operations had been governed by federal biological opinions. The last set of opinions had been issued in 2008. Those were recently updated in fall 2019.

The state disagreed with some of the guidelines in those opinions and sued. It issued its own operating permit on Tuesday.


The 143-page highly technical incidental take permit issued to the Department of Water Resources (DWR) by the Department of Fish and Wildlife (DFW) for operation of the State Water Project is loaded with details that will either make or break water users, depending on the view point.

San Joaquin River flow

The 2008 federal biological opinions included a push-pull regulation that governed pumping exports depending on flow coming into the delta from the San Joaquin River.

In dryer years, when the river flow was less, exports were curtailed. Higher flows allowed for increased exports.

The object was to make sure pumping didn’t counteract the natural flow and suck endangered fish into dead-end portions of the delta or into the pumps themselves.

The inflow-export ratio was set by a strict calculation, according to Brent Walthal, Assistant General Manager for the Kern County Water Agency, the second largest contractor on the SWP.

Depending on the type of year, the inflow-export regulation could reduce the amount of water available to contractors by up to 100,000 acre feet, Walthal said.

The regulation was studied for years to see what effect it had on endangered fish.

“The studies found there was no correlation, at all, on fish takes at the pumps,” Walthal said.

The 2019 federal biological opinions eliminated the inflow-export pumping regulation based on those findings.

The state’s incidental take permit reestablishes an inflow-export regulation.

Not exactly, said Chuck Bonham, Director of the DFW, which wrote the permit based on the California Endangered Species Act (CESA).

The 2008 biological opinions regulated San Joaquin River inflow-exports for steelhead, which isn’t listed in the CESA.

This new regulation is for longfin smelt, which DFW believes needs a strong slug of spring flow water for better survival.

The ratio formula was the best means DFW had to make sure the longfin smelt got that water.

“If there’s a better formula or way of doing that, it says in the permit that we are expressly open to hearing that,” Bonham said. “I would love it if the State Water Contractors could help us find an alternative.”

Environmental blocks

Walthal pointed to two other water “hits” he believes the new permit will take on contractor supplies.

“In a wet year, it says we can pump 150,000 acre feet of extra water, but it has to be stored in Lake Oroville for possible use that year or the next for environmental purposes.”

Another 30,000 acre feet would be set aside for Suisuin Marsh habitat, he added.

“So, it’s not OK for us to pump that water to benefit farms or cities but it’s OK for DFW to pump it for environmental storage,” Walthal said.

Bonham countered that this kind of environmental water set aside is exactly what water contractors have called for over the years.

“It provides certainty. It’s a way to have a block of water that we capture in wet years and is  available in dry years for the environment,” he said. “The other thing in the permit is we included collaboration so each year the departments sit down and consult with Kern and other water users to plan the upcoming year and how we might use that block of water. That’s pretty progressive stuff.”

Coordination, or not

Water users are also concerned the state permit will be used to block the Bureau from moving federal water through state facilities.

The permit states that if the Bureau doesn’t comply with state law, the Delta-Mendota intertie into the California Aqueduct will be off limits.

That’s a key facility that moves delta water to a group of water districts in the Central Valley known as the Exchange Contractors.

Decades ago, those districts exchanged their San Joaquin River rights for delta water from the Bureau. Their river water is now taken to cities and farms in the southern valley via the Friant-Kern Canal.

If the Exchange Contractors can’t get water from the delta, as happened in 2014 and 2015 during the height of the last drought, they call on San Joaquin River water, which leaves Friant contractors dry.

“If the state wants to add additional mischief, which they apparently do, they could say all their facilities can’t be used by the Bureau, including the California Aqueduct and storage space in San Luis Reservoir,” said Jason Phillips, General Manager of the Friant Water Authority. “This permit could really affect water movement throughout the state.”

This isn’t a new issue, said DWR Director Karla Nemeth.

It came up after the WIIN Act (Water Infrastructure Improvements for the Nation) was passed by Congress in 2016.

The act allowed the Bureau to capture and move more water during storms, “Which was a good thing,” Nemeth said.

“The challenge was we had no way to determine of those actions complied with state law because we didn’t have a stand-alone CESA permit. Now, we can say, ‘Yes, you can use the intertie as long as you’re doing XY and Z to comply with state law.’”


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A new set of water regulations aimed at protecting California’s native fish came down from the state earlier this week to near universal condemnation from both agricultural and environmental water folks.

The regulations are contained in a 143-page “incidental take permit” issued by the Department of Fish and Wildlife that lays out when  — and how much —  water can be pumped out of the Sacramento-San Joaquin Delta by the State Water Project.

Agricultural contractors who get water from the project fear they could lose up to 300,000 acre feet a year under the new permit.

Environmentalists say the permit gives a “free pass” to pumpers and is a path to extinction for native fish.

For Central Valley water users, the new regulations come as they’re already struggling to reconcile excessive groundwater pumping with dwindling surface supplies.

“Our concern is, if (state and federal water users) are, collectively not meeting delta requirements under this permit, the State Water Contractors will have to make up for the federal side, making our deliveries worse,” said Jason Gianquinto, General Manager of the Semitropic Water Storage District in northwestern Kern County.

Semitropic, alone, has a 165,000 acre-foot groundwater overdraft that it’s trying to fill.

Karla Nemeth, Director of the Department of Water Resources which runs the State Water Project, sympathized with the challenges faced by ag water users, but felt concerns about the new permit are overblown.

“What’s happening with some State Water Contractors (being upset) is they are looking at the federal biological opinions that would have enabled them to export more water,” Nemeth said. “This permit doesn’t allow for that water to be exported. It reallocates it to environmental uses.”

She referred to biological opinions released by the Trump administration last fall and enacted after a campaign-style rally by President Trump himself in Bakersfield on February 19.

Those biological opinions relaxed some guidelines for how much water could be pumped out of the Sacramento-San Joaquin Delta.

In past years, the biological opinions have acted as the main governing documents for how the state and federal Bureau of Reclamation jointly operate the delta.

The state sued over the biological opinions and, for the first time, issued its own permit for delta operations.

Now there are two delta operation manuals, so to speak.

Brent Walthal, Assistant General Manager for the Kern County Water Agency, wasn’t surprised by the new permit, which has been in the works since last May. The Kern County Water Agency administers state water contracts that account for about a million acre feet on behalf of 13 agricultural water districts and is the second largest contractor on the State Water Project.

He anticipated the new permit would reinstate guidelines from the 2008 federal biological opinions, which, in some cases it does.

That includes reestablishing flow requirements on the San Joaquin River, which he said could reduce exports to State Water Contractors by up to 150,000 acre feet a year.

Add to that two new environmental water set asides of close to 130,000 acre feet a year and the total potential reduction could be 300,000 acre feet a year, he said.

“Modelers are still poring over this to try and understand exactly what it will mean to us,” Walthal said.

Nemeth described the permit as “export neutral,” when looking at it through the 2008 biological opinions.

She and Department of Fish and Wildlife Director Chuck Bonham both pointed to the permit’s advantages to water contractors, especially in wet years.

Such as, a cap on environmental outflows and moving the Fall X2 line closer to the delta.

The Fall X2 line is where salty water from the San Francisco Bay meets fresh water from the delta. That line had been required to be held at 70 kilometers away from the Golden Gate Bridge, which required heavier flows coming out of the delta.

The permit now allows it to be 80 kilometers from the bridge, Bonham said.

“That’s huge,” he said. “That alone, in wet years, will result in higher exports.”

He joked that he would love to see a letter to the editor in The Bakersfield Californian thanking the state for finally moving the Fall X2 line, something water contractors have lobbied for for years.

Those and other parts of the permit were roundly criticized by multiple environmental groups, according to a March 31 blog post by Doug Obegi, a lead attorney for the Natural Resources Defense Council.

“While the State’s permits are not identical to the Trump Administration’s plan for extinction, they share many of the same problematic elements,” he writes.

He predicts multiple groups will sue over the permit.

Indeed, the Metropolitan Water District, the State Water Project’s largest contractor, already has an agenda item on its April 14 meeting to discuss moving ahead with a lawsuit over the permit.

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Several observers speculated about the effect the new state permit would have on another ongoing water drama known as the “voluntary agreements.”

Some felt the permit was a political gambit to “gain leverage” in that process.

Others felt issuing the permit would cut the legs out from those discussions.

In 2018, the State Water Resources Control board required increases flows into the Sacramento-San Joaquin Delta from tributaries to the San Joaquin and Sacramento rivers to help native fish populations.

Chuck Bonham, Director of California Department of Fish and Wildlife

The edict requires 40 percent of those waterways’ unimpaired flows (meaning the amount of water that would flow down the channels if there hadn’t been dams and other diversions built).

That’s a significant water bite to the towns and farms that had been using the water.

In recognition of that, the Water Board, allowed time for the water users to develop voluntary agreements to find other ways to improve fish populations.

DWR Director Karla Nemeth and DFW Director Chuck Bonham both denied the new state permit would quash the voluntary agreements talks.

In fact, they noted that the permit holds out space to include actions under those agreements.

Karla Nemeth, Director of California Department of Water Resources

“If (the agreements) include commitments that are consistent with the requirements of the permit, the permit can be held in abeyance,” Bonham said. “The permit won’t run over those voluntary agreements.”

Brent Walthal, Assistant General Manager for the Kern County Water Agency, disagreed that the new state permit wouldn’t interfere with the voluntary agreements.

“It creates greater uncertainty,” he said.

The permit, on top of the state’s lawsuit over new federal biological opinions, makes the water portion of the equation too iffy for water users.

The federal biological opinions, issued last fall by the Trump administration are governing documents for the delta letting water users know, generally, how much they can pump water and when.

“All those federal water districts, especially on the Sacramento river, that had been offering certain amounts of water in the voluntary agreements were using the biological opinions as their base to calculate their overall water. The state’s lawsuit takes away that foundation,” Walthal said. “This permit makes that process even messier.”

SJV Water is an independent, nonprofit news site dedicated to covering water in the San Joaquin Valley. Get inside access to SJV Water by becoming a member.


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