Tules on Twitchell Island in the Delta. (Photo: Josh Cassidy/KQED)

With thousands of acres of rich farmland, the Delta has a long agricultural legacy. But farming there can be a risky business. Dozens of farms have been flooded over the past half century as aging levees have collapsed.

That became a reality for farmer Rudy Mussi on the morning of June 3, 2004. It was clear, sunny day. "You never expect a flood in the summer months," says Mussi.

Mussi was growing corn and asparagus on lower Jones Tract, an island in the Delta, 10 miles west of Stockton. That morning, he got a phone call. Water was flooding onto his farmland.

"Your heart stops for a second or two and then realism sets in. And you just start moving your equipment and get it to high ground," says Mussi.

How did a flood happen a on a sunny day? It's because of a basic rule of physics. Mussi farmed on an island below sea level, like a lot of the islands in the Delta. The Delta used to be a huge swath of wetlands, where two major rivers met San Francisco Bay. Today, earthen levees hold that water back – most of the time.

"Once a break occurs, you know, there's no way you're gonna stop that, not with 10 feet of water on the other side," Mussi says. Draining the island and repairing the levees around Jones Tract cost about $90 million.

The levee break on Jones Tract in 2004. (Photo: CA Department of Water Resources)

It wasn't an isolated incident. Over the last century, more than 150 levees have failed in the Delta.

Delta Infrastructure at Risk

"This is how we get ourselves in kind of an arms race between the water and the land," says Jeff Mount, professor with the Center for Watershed Sciences at the University of California-Davis.

Levee-building began in the 1850s, when settlers came to the Delta for the rich soil. More than a thousand miles of levees were built. "This network of levees through time had to get bigger and bigger for a very basic reason: the land has been steadily lowering," says Mount.

As farmers exposed the rich peat soil, it started decomposing. The land level dropped; "In some places they talked about four inches per year," says Mount. Today, it's less than an inch per year thanks to better farming practices.

Add up all those inches over the past century and some islands are now 30 feet below sea level. That puts a lot of stress on the levees. There are also other concerns: rising sea levels and extreme floods. "And then the big 800-pound gorilla in the room – we're due for a very large earthquake on the San Andreas system."

Add up all these risks and Mount says there's a two-thirds chance of a catastrophic levee failure in the next 50 years. That, of course, affects farmers and communities in the Delta, but it could also impact California's water supply.

"The raindrops that fall in Mount Shasta are consumed by people in San Diego. Water moves a great distance and this is one of the critical hubs in that system," says Mount.

Fixing the Delta's levees is estimated to cost billions. But on some islands, scientists are experimenting with a new fix.

Farming Carbon

Peat soil samples on Twitchell Island. (Photo: Josh Cassidy/KQED)

On a windy day on Twitchell Island in the Delta, ecologist Lisa Windham-Myers of the US Geological Survey pushes her way through a wetland filled with a tall, reed-like plant known as tule.

"The plant grows… some of these are 16 feet tall. They're just huge," she says. That growth is changing the ground we're standing on. Windham-Myers pulls out a sample of the dark peat soil.

The wetland produces soil at a rapid rate – four inches a year on average. That's huge, says USGS scientist Brian Bergamaschi, in a place where the land is sinking. "These islands are like bowls and the way we see projects like this is you want to fill up the middle of that bowl and help level out the whole island."

Planting wetlands like this one could raise the land level and water table on the inside of levees, relieving some of the pressure. But why would farmers want to replace cash crops with tule? Windham-Myers points to the soil.

"This is basically almost 100 percent carbon. These take up far more than a typical forest environment," she says. California is setting up a market for carbon, as part of the state's effort to cut global warming emissions. Early next year, companies that need to reduce their emissions could pay farmers to store carbon in wetlands like this.

USGS scientist Brian Bergamaschi talks with Delta farmer Al Medvitch. (Photo: Josh Cassidy/KQED)

Today, two farmers are here checking out the project: Steve Mello, a Delta farmer on Tyler Island and Al Medvitch, a farmer in the Montezuma Hills.

"The potential has been demonstrated well. You guys are standing in the middle of it. But in order to move from here to market, we need to develop a lot more techniques so people can come and verify that the carbon is stored," says Brian Bergamaschi, describing how wetland farming might work.

Both farmers seem open to the idea. But Mello says ultimately, it depends on the bottom line. "It would absolutely need to cash flow. While it could dovetail with levee stability, it would still need to generate enough to amortize your property value."

Still, Mello says assuming carbon prices are high enough, growing patches of wetlands could be a feasible way to improve the levees and to stay farming.

A map of the Delta created by the US Geological Survey in the 1910s.

As detective stories go, this sunny, spring day in the Delta isn't a typical backdrop. In the distance, tractors move slowly through dry fields of row crops.

"Once he got lost, they were wandering all over," says Alison Whipple of the San Francisco Estuary Institute, a non-profit research group based in Richmond. Her colleague, Robin Grossinger, agrees. "They were all over this place." The two are trying to piece together the path of William Wright, a man who got hopelessly lost somewhere nearby.

I should probably mention: it happened 160 years ago. Whipple and Grossinger are historical ecologists. They use sources like old photos, hand-drawn maps and early land surveys to sleuth out what this landscape looked like before it was dramatically remade by Californians.

The Delta's landscape has been dramatically remade over the last 200 years. Today, it's a crucial part of the state's water system, supplying 25 million people and irrigating millions of acres of farm land. But with this re-engineering, the Delta's ecosystem has collapsed, harming the fishing industry and putting water supplies at risk. Little is known about what it once looked like.

Lost in a Delta Marsh

Standing on a levee about 20 miles south of Sacramento, Whipple and Grossinger are discussing what they found a tattered, yellowing notebook uncovered in a state archive. It contains stories from William Wright, a duck hunter who spent a long, cold night lost in the Delta in 1850.

"On all sides stretched a vast wilderness of tules from ten to fifteen feet in height. The driving storm of sleet was bad, but the pitchy darkness was infinitely worse… Our situation was so miserable that no words can do justice to it."

It's not just the dramatic story they're interested in. It's passages this like one:

"The lakes proved to be from one hundred to three hundred yards in width, as near as we could judge. The water was very cold and often waist‐deep."

When Whipple and Grossinger read his account, they knew they’d found a Holy Grail source document. Its detail reveal a landscape that doesn't exist here today and hasn’t existed for some time.

"The Delta is probably one of the most intensively transformed parts of California and it was also changed really early on because of such fertile land," says Grossinger.

As California's Gold Rush boomed, farmers came to the Delta for its rich soil. Land went for a dollar an acre and settlers turned the wetlands into dry, agricultural land. 97% of the historic marshes were lost.

“We have here maybe one of the most important parts of the state's ecosystem and we don’t actually know how it used to work," Says Grossinger.

Alison Whipple and Robin Grossinger examine historic maps in the Delta.

He and Whipple have layered together thousands of historical sources that reveal an ecosystem of incredible complexity. “We would be in trees right here with a couple winding channels that were dry in the summer but had flowing water in the wintertime," explains Whipple.

Yearly floods from the Sacramento River inundated Delta marshes creating habitat for birds and young salmon. Closer to San Francisco Bay, hundreds of miles of small tidal channels branched out like capillaries in the wetlands. Today, most of those channels have been filled in.

Returning the Delta to this pristine state just isn’t possible, says Whipple, and that’s not the goal of the project. But knowing how the ecosystem once worked could improve the habitat restoration efforts that are happening.

Restoring Habitat

Liberty Island is one place in the Delta that looks as it might have 200 years ago. Not long ago, it was a low-lying expanse of farmland, protected by tall levees.

“The levees broke and it wasn’t financially worth reclaiming,” Says Carl Wilcox of with California’s Department of Fish and Game. The landowners gave up when the island flooded 15 years ago. After that, nature took over. Tules and cattails started sprouting and wildlife followed.

Returning vegetation at Liberty Island in the Delta.

Now, “some of the endangered native fishes, Delta smelt, longfin smelt are using this area,” says Wilcox. They're finding endangered Chinook salmon as well. "These are more productive areas for them, they’re more protected, they’re less prone to predators."

California Considers Ambitious Restoration Plans

California is using the Liberty Island project as a model for a proposal to restore 65,000 acres of Delta habitat. It's part of the Bay Delta Conservation Plan – a major overhaul of the Delta’s water infrastructure.

Leo Winternitz of the Nature Conservancy says bringing back habitat for declining wildlife could make the state’s water supply more reliable. Restrictions under the Endangered Species Act have limited how much water can be pumped from the Delta in recent years.

There is one big problem with restoration: most of the islands in the Delta are below sea level.

"Just south of here, some of the islands, they're in the 17 to 25 below sea level range. So if their levees broke, what you’d have is a large open body of water. You can’t create tidal marshes in those areas," says Winternitz.

That leaves only a few places where restoration is feasible. Winternitz says in those areas it’s crucial the state look to the past to create the same interconnected habitat that once was.

Governor Jerry Brown's administration is set to unveil the sweeping plan to restore the Delta later this year.

A canal in the Delta, heading to the Central Valley Project.

If you're not familiar with where the Sacramento-San Joaquin Delta is or why it's so important to the state, you're not alone. Polls show most Californians have never heard of it.

This relatively small part of California plays a crucial role in the state's water supply. And, as might be expected, it's become ground zero for a decades-long water war involving cities, farmers and fish. This year, the state is taking on an ambitious planning effort to break that deadlock.

Re-plumbing California

The reason the Delta has this starring role is thanks to a basic geography problem. Almost all of the state's water is found in the top third of the state. Most of the population lives in the bottom two-thirds of the state.

This issue was painfully obvious to state planners a century ago. The Central Valley promised rich soil for farmers, but had little rainfall. They knew for California to grow, they had to move water to drier parts of the state.

The Delta is where California's two largest rivers come together, carrying runoff from the Sierra Nevada Mountains. To water planners, it looked like the perfect place to tap into. California began building water infrastructure at a massive scale.

Water is exported out of the Delta primarily through two large pumping plants near Tracy, about 60 miles east of San Francisco. Each moves millions of gallons of water a minute. From there, the water rushes into concrete canals that reach Los Angeles, Silicon Valley and millions of acres of farmland.

This 700-mile system has made California the state it is today. But it's come with a cost…

An Ecosystem in Decline

On a boat in the western Delta, environmental scientist Julio Adib-Samii and team from California's Department of Fish and Game pull in a long fishing net.

A Delta smelt.

"Well, we have an adult Delta smelt," he says, holding a small, silver endangered fish that smells distinctly like a cucumber.

Fish and Game scientists have done these monthly fish surveys for decades. But starting in 2002, they noticed something strange. Where they once caught a lot of Delta smelt, now, they weren't catching any. The population had crashed, as well as populations of striped bass, threadfin shad, longfin smelt and Chinook salmon. In 2008, the commercial salmon fishery shut down completely for two years.

"Their decline is an indication of a changing environment and place they didn't evolve to be in," says Adib-Samii.

The Delta was once a massive tidal marsh, full of winding channels that spread out like capillaries. After the Gold Rush, settlers put up levees to create low-lying islands for farming. Ninety-seven percent of the historic wetlands were lost.

Multiple Stressors, One Big Question

"We've converted almost every scrap of habitat in the Delta to farmland and we need to return some of that to habitat," says Barry Nelson, senior policy analyst with the Natural Resources Defense Council. The ecosystem has also been hit by pollution, invasive species – and by the pumping plants.

"The pumps in the south Delta are so powerful that they literally reverse the direction of flow. It's very easy for those fish to follow that water and get sucked right into the pumps," says Nelson. A few years ago, federal wildlife agencies issued decisions requiring the pumping to slow down during certain times of year to protect fish.

This brings us to the central debate in the Delta: how much water should be pumped out and how much should be left for fish?

"There's a limit to the amount of water you can pump from the Delta ecosystem and in the last decade it's become incredibly clear that we've exceeded that, and we've exceeded it by a lot," says Nelson.

Not everyone agrees. "There is, you know, always going to be shortages. But there's also a lot of years when we have absolutely plenty of water in the system to meet the reasonable needs that are out there," says Jason Peltier with Westlands Water District, an agricultural area in the San Joaquin Valley that depends on Delta water. He says limits on pumping have hurt the district's farmers.

"You can't get a loan to farm unless you can show the banker what water you have. And they don't have a lot of confidence in going to their bankers," says Peltier.

The battle over the environmental rules went to the courts. "There was lawsuit after lawsuit," says John Laird, California's Secretary for Natural Resources. "It got to the point that it made much more sense to look at the entire Delta as a whole."

A New Attempt at Progress

Laird's agency is trying to reach a compromise with the Bay Delta Conservation Plan. The 10,000-page plan calls for a new way to pump water out of the Delta, through what's commonly known as the peripheral canal. Huge tunnels would take water from further upstream, bypassing the Delta, which supporters say would make the water supply more reliable.

This isn't a new idea. In 1982, California voters defeated a similar plan. "The real debate is not the tunnel itself. It's how much water and when can it flow through the tunnel," says Laird.

The massive project could harm the Delta's endangered species, but Laird says they'll restore thousands of acres of wetlands to compensate. California voters would be on the hook for that cost, while the $12 billion tunnel would be paid for by water users.

It's a tough sell but, according to Laird, a necessary one since climate change will make the state's water supply more unpredictable. The agency will release a full draft of the plan in July.

Reported by Alison Hawkes

As the sun comes up, lighting a ridge of windmills, I'm traipsing around the State Water Project grounds outside of Tracy trying to puzzle out this battle between farming and fish

The courts are packed with lawsuits on this issue. But one in particular caught my attention. It has to do with striped bass, a voracious predator in the system that was introduced in the 1870s and went on to become a popular sport fish.

Stripers are almost a naturalized citizen to the Delta, but farmers hope to blame the big fish for the plummeting numbers of endangered fish. If they win the case, which is now headed for trial, it could surely lessen the onus on water diversions from the Delta. That means the farmers could get more water, leaving the state to pay for costly mitigation measures to save the endangered fish species like Delta smelt and chinook salmon.

What is the evidence that stripers are wiping out these native species? At Clifton Court forebay, a large reservoir that feeds water to the pumps, stripers are a-plenty. Fishermen line the banks waiting for the gates to the forebay to rise so that the rushing water jostles the stripers out of their slumber. I met one fisherman down there who showed me a photo on his cellphone of a 15-incher he had recently caught. He brought it home for dinner.

It was also easy fishing for a team of state biologists who were on a motor boat in the forebay catching and tagging the stripers for further study. The big question the courts want answered is whether the stripers have a population level affect on the endangered fish species. Meaning, do stripers eat enough of these smaller fish to affect their numbers delta-wide. Here's where the science gets squishy.

In the lawsuit, the farmers and water users argue that stripers do have a population level effect.
They want to see fishing regulations on stripers lifted as a means to bring back endangered fish. But some biologists claim there's not enough research to show a population level impact. UC Davis fish biologist Peter Moyle says the best estimate done, involving a winter run chinook salmon, showed a 9 percent loss to stripers, which he says is “not a big number.” That was a National Marine Fisheries study. Remove the stripers, he says, and you could actually be upsetting a balance in the ecosystem. Stripers may be keeping other predators in check, like the tiny inland silverside, another non-native fish that has an appetite for delta smelt eggs.

Perhaps the best solution is to target striped bass fishing where we know they hang out – at places like Clifton Court Forebay and other structures created by the state and federal water projects. It's here where the endangered fish are most vulnerable, and where the stripers know they can find an easy meal.

Listen to Delta Predators radio story online.

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Every year, millions of fish make a strange and harrowing detour through the Skinner Fish Facility, part of the State Water Project's facilities in the Delta.

In my last post, I wrote about my visit to the Banks Pumping Plant, whose giant pumps slurp water from the Delta to help quench California's thirst. As the volumes of water are sucked up, both resident and migrating fish come along for the ride. The Skinner Facility, in operation since 1968, was built to protect fish from being killed at the pumps–an effort that sadly is not as successful as one would hope (more on that below).

I was amazed to learn there is a whole art and science to fish screens, which range from physical barriers–called positive barriers–like perforated plates or wire mesh, to behavioral barriers like sound, light, or other stimuli aimed at keeping fish away. Well-designed screens minimize both entrainment (fish being pulled into the pump or diversion) and impingement (fish being trapped or injured against the screen itself due to water velocity).

Both physical and behavioral barriers are used at the Skinner Facility. Fish being pulled toward the pumps first encounter a trash rack that diverts many bigger fish, along with floating debris. Next, fish encounter a large, v-shaped array of metal louvers. The louvers create turbulence that functions as a behavioral signal, encouraging the fish to swim away into bypass pipes that function, as our tour guide put it, like "a big vacuum system."

From the bypass pipes fish travel to another set of louvers and pipes, concentrating them into a smaller volume of water, and then into holding tanks in a nearby warehouse. Giant, suspended cone-shaped buckets are used to periodically sample the fish, which are identified, counted, and measured. Some 90 species turn up in the facility, including Chinook salmon, steelhead, white sturgeon, and delta smelt. (I asked our guide if delta smelt really do smell like cucumbers. He confirmed it. In fact, when a school of smelt comes through–an event that has become rare–the warehouse smells "like a salad.") When enough fish have been collected, they are loaded into trucks and driven back to the Delta.

Here's the rub. Many fish caught in the pull of the pumps are lost to predation before even reaching the screening facility. Then, the facility does not effectively screen fish smaller than about 1.5 inches, meaning that littler, less powerful species and juveniles are still vulnerable to the pumps. For the fish that make it to the holding tanks, the process is such a trauma–with big and little fish squashed together in the tanks, buckets, and trucks–it's no surprise there are casualties; in fact, the delicate delta smelt often do not survive. And even for fish that make it through the entire process and out the other end, there's a final, fatal hurdle: the trunks routinely dump salvaged fish at the same locations, where more predators have learned to cluster for a free lunch.

Scientists agree that the loss of fish at the huge state pumps–and other pumps and intake pipes throughout the Delta–is a major contributor to plummeting populations. How much water we use makes a difference: The higher the export rates, the more fish are entrained. There also is broad consensus that more state-of-the-art fish screening facilities are needed. That could come with a hefty price tag. But with our fish disappearing, can we afford not to invest in their survival?

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