Miles of Delta levees are at risk of floods; repairs could cost $3 billion

“It was way beyond our means, but we had to do it,” said Daniel Wilson, a farmer near the Delta town of Walnut Grove and trustee of the management agency responsible for the levee.

Because the region was declared a disaster zone, funding help was available through the Federal Emergency Management Agency. But two years later, the money still hasn’t arrived. Other districts in the region also are waiting for reimbursements.

The Sacramento-San Joaquin Delta is facing a funding crisis that has bogged down efforts to repair and maintain an aging network of about 1,100 miles of levees that protect the region from floods.

These protective ridges of dirt and rocks, mostly on private land, are at growing risk of rupturing, which would endanger half a million people, mostly in Stockton but also in smaller towns and farmsteads. Also threatened are thousands of acres of farmland, highways and water supply pumps that send water to much of the state.

The summer of 2004 saw a major failure when the privately owned levee surrounding a large parcel of farmers’ fields called Jones Tract, which mostly sits below sea level, burst. Water surged through the break, flooding 12,000 acres, which remained swamped for months. Dozens of barns and a few homes were submerged. The response and repair effort — including rebuilding hundreds of feet of levee and pumping out the water — cost $90 million in government and private funding.

More recently, last year, water seeped under a levee that rings Victoria Island west of Stockton, just a few miles north of pumping stations that send water to 30 million Californians and vast tracts of farmland. A breach would have created powerful suction, drawing in large volumes of brackish San Francisco Bay water and forcing the pumps to shut down for weeks. Crews drove sheet piles deep into the levee to stem the leak and stop the flow of water under the levee.

Without substantial improvements to Delta levees in the next 25 years, “more than $10 billion in agricultural, residential, commercial, and infrastructure assets and nearly $2 billion in annual economic activity would be exposed to flooding,” according to an estimate from the Delta Stewardship Council.

Jeffrey Mount, a geomorphologist and water infrastructure expert with the Public Policy Institute of California, said the recent near-miss at Victoria Island could be a harbinger of more dangerous levee breaks to come.

“That is considered one of the really good levees, and they nearly lost it,” Mount said. “So what about the other ones?”

With state and federal assistance programs falling behind on reimbursements or losing funding, landowners are struggling to keep pace with maintenance. Many are in debt from recent projects, and the backlog of upgrades and repairs is growing.

Billions of dollars are needed to upgrade the Delta’s levees to basic safety standards, but the estimated costs far exceed the funding metered out by state and federal agencies.

Repairing Delta levees could cost at least $3.2 billion by 2050, according to the Delta Stewardship Council. State water officials estimate that about $1.06 billion is needed for Delta levee upgrades in just the next five years.

Across the entire Central Valley, the problem balloons to $30 billion in overdue upgrades to protect against worst-case scenario flooding, which could cause $1 trillion in damage, according to the state’s 2022 Central Valley Flood Protection Plan.

“All the districts in the Central Valley have a list of projects that they would like to get accomplished,” said Meegan Nagy, general manager of the Sacramento River West Side Levee District, which manages levees upstream of the state capital.

A few miles southeast of Sacramento, a privately owned levee system beside the Cosumnes River ruptured on New Year’s Eve in 2022 during a powerful downpour. The flooding killed three people, swamped homes, shut down Highway 99 and washed away vehicles. The local levee management agency, funded by its landowners, was reportedly still waiting for federal emergency relief money two years later and, as of January, still owed the bank $7 million.

Stockton, on the eastern edge of the Delta, faces a constant risk of flooding. U.S. Rep. Josh Harder, a Democrat from Tracy, said the problem stems from inadequate federal funding for levee upkeep and red tape that hinders maintenance and repairs by local agencies. He has co-authored a bill, the Safeguarding Our Levees Act, that would address some of these issues.

“For too long we’ve been left behind in federal funding,” Harder said. “No family should have to watch floodwater pour into their living room while government stalls.”

Parts of the region are essentially on borrowed time, with levees facing a uniquely overbearing workload, said Steven Deverel, a hydrologist at HydroFocus, Inc., who has studied Delta levees.

Most levees, he explained, hold back water only during high flow events. But in the Delta, “levees are really more like dams in that they have to hold back water 24-7.” This unique arrangement makes much of the region particularly vulnerable to flooding.

“You basically have holes in the ground as much as 25 feet deep, and the only thing that holds back the water is levees,” Mount said.

Pumping the water out is increasingly expensive because of rising electricity rates, said engineer Gilbert Cosio with River Delta Consulting.

“The last few years have been a perfect storm for expenditures,” he said.

Since the 1970s, California has invested more than $700 million in Delta levee work. Just the last two budget cycles have dedicated $560 million to flood response and flood protection statewide, plus other investments, according to Laura Hollender, the California Department of Water Resources’ deputy director of flood management and dam safety.

Still, Delta locals worry that critical programs protecting their region are being sidelined. The state cut a key levee maintenance fund from the budget this year.

The sluggish state reimbursements on cost-shared projects through the Delta Levees Maintenance Subventions Program leaves local landowners — who must front the costs of repairs — accruing interest on loans they can’t pay back.

“It’s expensive and these districts go into debt to do these projects,” said Emily Pappalardo, an engineer with the local firm that designed and directed Wilson’s levee repair in 2023, DCC Engineering Co., in Walnut Grove. “Every dollar these districts spend should be on improving and maintaining their levees instead of chasing after the money to do it ... or paying interest on loans.”

Wilson said that the FEMA reimbursement would not cover the costs of borrowing money to pay for the repairs. “The whole time the interest clock is ticking,” he said. That means less money for further levee upkeep. “If we had an issue this winter or last winter, we’d have been in a world of hurt,” Wilson said.

Until several years ago, according to sources, levee upgrades completed in the fall were followed by state reimbursements in the spring. “By the end of June, everyone had their money” in time to start working on spring and summer levee projects, said Cosio, at River Delta Consulting. “Now, it’s not until the fall or later that we get the money.”

Farmer Harvey Correia, who has orchards near Isleton, said state claim filing requirements and slow processing mean that in some cases more than two years can pass before landowners are reimbursed.

“So we’re paying interest on loans while we’re waiting for money from the state,” Correia said.

Jason Ince, a spokesperson at the Department of Water Resources, said the agency strives to process payments “as quickly as possible” but said each request must be investigated and verified through site visits and coordination with other agencies.

Wilson, near Walnut Grove, said many local levee managers are financially swamped. “They’re in debt beyond their ability to pay it back.”

Pappalardo, who grew up in the Delta, wants to see more consistent funding of the levees subventions program.

However, the program relies on periodic bond funding. The current cash pool amounts to about $14 million and derives from bonds that voters approved in 2014 and 2006, Ince said.

Late last year, voters approved Proposition 4, a $10 billion water, wildlife and climate bond, directing $150 million to Delta flood protection, levee upgrades and climate resiliency work.

Sources said they expect it will provide more money for the program, but they emphasized that it, too, will run out.

“These levees aren’t going anywhere,” Pappalardo said. “This is infrastructure and these costs are always going to be here ... this is general maintenance.” Ideally, she said, money would come from the state’s general fund.

Also frustrated at the trickling pace of subventions funding for Delta levees is Stockton attorney Dante Nomellini, Jr., who has represented the Central Delta Water Agency and several Delta reclamation districts. He said the program is “well-oiled” but that its funding could be more reliable.

“The funding dries up every few years and we have to fight to get more,” he said.

Chris Neudeck, a levee engineer whose firm — Kjeldsen, Sinnock & Neudeck, Inc — repaired the Victoria Island breach this winter, believes the flagging funding for levees has a simple explanation:

“It’s called the flood memory half-life,” he said. “How long does a politician hold memory of a disaster? Many say it’s six months, others say nine months ... If we don’t have a flood event every year, we’re screwed.”

Levee upgrades come in different forms. Some are relatively quick and easy, involving basic materials — like riprap, the rocks and boulders that line many levees — to provide armoring against erosion.

Others are more sophisticated. One nearly finished project near the Delta town of Isleton, along Highway 160, builds in fish and bird habitat in the form of vegetated “benches” near the water line.

“The benches serve a double purpose,” said Pappalardo, whose firm designed the project. “While they provide habitat, they also reduce the velocity of the river.”

Because Pappalardo’s project provides multiple benefits, the upgrade qualified for a 94% funding reimbursement from the state. But the total cost was about $18 million for 1.4 miles of levee, and the 6% that the reclamation district must cover on its own “is still a heavy lift for them,” Pappalardo said.

Though costly and tangled in thickets of program and agency acronyms, most levee upgrade projects are not terribly complicated. They often involve dump trucks dropping material on top of or down a slope of a levee. Barges can help. The goal in most projects is to build the levee, vertically and horizontally, to dimensions defined by several distinct standards.

These federal and state standards call for a range of parameters in levee height, width and slope steepness. Among these standards is that of the U.S. Army Corps of Engineers known as Public Law 84-99. Certain levees built to this standard are eligible for support from the Army Corps should they leak or break.

Since 2019, the Flood Maintenance Assistance Program, enacted by the Department of Water Resources, has provided local levee maintenance agencies with $40 million to help their levees comply with the federal standard.

This has leveraged massive amounts of federal funding when levees damaged by high waters need to be repaired, said Nagy at the Sacramento River West Side Levee District.

“In my district alone, since 2017, we have had about $30 million worth of federal funding for post-flood repairs,” Nagy said. The program “is one of the most successful programs the department has executed.”

But the state’s Flood Maintenance Assistance Program was put “on hold” this year due to budget constraints, according to the Department of Water Resources. Nagy worries this could accelerate levee deterioration.

“If we have multiple years when that program is not funded, then every year we get closer to losing eligibility for federal funding post-flood,” she said.

In an assessment of Delta levee vulnerability in 2016, Deverel and several coauthors wrote that although general compliance with various standards is “encouraging,” fully protecting any given island in the Delta “requires 100% compliance.”

Nomellini thinks full protection is achievable. “This is not rocket science,” he said. “This is dirt and rock. If there was the political will, we could have the best levees west of the Mississippi.”

Mount said the amount of money needed to maintain the Delta’s levees may be the most insurmountable obstacle.

“What do you do if you don’t have the money?” he said. “What is the long-term vision for the Delta?”

At the Delta Stewardship Council, Jeff Henderson, deputy executive officer of planning and performance, said parts of the western Delta more exposed to the influence of tides and rising sea level may face an uncertain future.

“In such locations, reinforcing levees may become technically or financially unsustainable over time, prompting conversations about alternative strategies,” Henderson said.

Erosion and weathering are just two factors gnawing at levee integrity. Burrowing beavers cause occasional collapses. So have invasive nutria, semi-aquatic rodents native to South America and now a recognized nuisance to California’s wetlands and levees. Toppling trees, too, can tear out the flank of a levee, and earthquakes are considered a constant danger — though just how serious is debated.

Another matter that has progressively compromised the Delta’s levees is subsidence — the land is sinking, an outcome of when peat soil is exposed to oxygen and breaks down, emitting carbon dioxide.

More than 2 billion cubic meters of Delta soil volume has disappeared since the 1850s, according to Deverel’s 2016 paper. Today, much cropland and scattered residences lie a precarious 15 to 20 feet and more below sea level. All the while, the ocean is rising, though slowly, and winter flooding is growing more extreme.

“You have rising sea level, increasing winter storms and atmospheric rivers, and the longer it’s been since the last earthquake the closer we are to the next,” Mount said.

He predicts that lower-value land will eventually go underwater as levees wear out and the will to maintain them wanes.

“Will the Delta look like this forever?” he asked. “The answer is no.”