Key State Report to Show How Water Tunnels Will Impact Endangered Fish

This month, new details have emerged about Gov. Jerry Brown’s $23 billion plan to build new plumbing in the Sacramento-San Joaquin Delta. It could be the state’s largest water project in a generation, consisting of two massive, 40-foot-wide tunnels and thousands of acres of habitat restoration.

On Wednesday, state water officials will release new studies with environmental details that could determine its fate.

The analysis is part of a massive document that spells out Brown's Delta plan. Known as the Bay Delta Conservation Plan (BDCP), it is being released in parts during March and April. The sections released Wednesday outline the Brown administration's predictions about how salmon, smelt and other endangered fish and wildlife in the Delta would be affected if the two massive tunnels are built.

The new infrastructure is needed, state officials say, because in the current system, water pumping must be slowed down to protect the Delta's wildlife, affecting the water supply for millions of Californians from the Bay Area to San Diego and for millions of acres of Central Valley farmland, based on the impact on endangered fish.

A year ago, the administration’s first draft of the Bay Delta Conservation Plan was in trouble, after it showed the tunnels might harm populations of fish. “It did not get a good reception,” said Leo Winternitz of the Nature Conservancy.

Federal and state wildlife agencies pointed to harmful impacts the project would have on endangered Chinook salmon and Delta smelt. Those agencies – California’s Department of Fish and Wildlife, the US Fish and Wildlife Service and the National Marine Fisheries Service – are responsible for permitting the plan. In a document known as the “Red Flag Comments,” they spelled out the problems that could have led to a veto.

Unless the Brown administration can show that the tunnels would help restore the crashing fish populations, the project is very likely doomed.

“We need to be able to make a finding that the project as a whole is going to contribute to the recovery of the species,” said Carl Wilcox of the Department of Fish and Wildlife at the time. “If the analysis says, well, they’re going to do worse under the plan, we’re not going to be able to permit it.”

Since then, officials at the Department of Water Resources say they’ve been working hand in hand with wildlife agencies about the concerns.

“We’ve got a plan here that we believe will enjoy a lot of consensus from all of the agencies that worked on it,” said Mark Cowin, director of the Department of Water Resources, at the release of the first four chapters of the plan in early March. “It was very difficult to come by and frankly we’re pretty proud of it.”

In a first step, Gov. Jerry Brown announced last summer that the size of the proposed tunnels would shrink. The 35-mile tunnels would withdraw water at the north end of the Delta and deliver it south, where it feeds into hundreds of miles of canals that carry water to Southern California, the Central Valley and the Bay Area.

The original tunnels had the capacity to carry 10 billion gallons of water over a 24-hour period and had five intake points. The new proposal would have three intakes and could hold close to six billion gallons a day.

But as much as the size of the tunnels has been debated, the amount of water that they’ll carry has been the focus of the environmental community and the water contractors who will pay the construction costs.

It’s All about Freshwater

In some years, more that 50 percent of the Delta’s water is pumped out before it reaches San Francisco Bay, diverted for use in cities and on farms. Many scientists say this has been a major factor causing the decline of Delta smelt.

In 2008, federal wildlife agencies put new rules in place to protect the three-inch fish, found only in the Sacramento-San Joaquin Delta. Those rules were quickly the topic of a lawsuit from water agencies.

Delta smelt prefer low-salinity water, the mixing zone between freshwater from the rivers and brackish water of San Francisco Bay. This zone, known as X2, shifts back and forth depending on tides, runoff and water diversions. The more freshwater flowing out of the Delta, the farther this zone is pushed toward the bay. Federal scientists specified that in wet years, the low-salinity zone should be closer to Suisun Bay to create as much habitat as possible for young Delta smelt.

Another imperiled fish, longfin smelt, also depends on freshwater flows in the spring. “There’s a relationship and it’s a long-established relationship between outflow and longfin smelt abundance,” said Carl Wilcox.

Wildlife agencies pointed out the first BDCP draft didn’t include these freshwater flow protections. In the plan’s own analysis, smelt species either showed no improvement or even showed a decline.

The Decision Tree

The new proposal now includes freshwater flow requirements in the spring and fall for fish, but they’re part of what’s being called “the decision tree.”

Officials say that 30,000 acres of tidal marsh habitat will be restored before the new tunnels begin operation – an unprecedented amount for the Delta. “30,000 is a big number,” says Winternitz. “But look at it in context. It used to be 700,000 acres of tidal marsh. We’ve lost 90 percent of that, so 30,000 is a drop in the bucket.”

That habitat restoration could help Delta smelt and other fish populations come back, something that would be considered in a decade or so as part of the decision tree. If they show substantial improvement, spring and fall flow rules may not be required. If not, they’d be put into place.

“This postpones the final decision until theoretically we know more about those actions,” said Carl Wilcox, “keeping in mind that for Fall X2, it’s only happened once and there’s an ongoing research program to look at the benefits.”

State officials say this will allow them to adaptively manage the ecosystem, while others worry that they’re punting on unpopular decisions.

“The current proposal for outflow isn’t necessarily woeful deficient, but it’s very deficient,” said Doug Obegi, staff attorney with the Natural Resources Defense Council. “On spring outflow, the current proposal looks at everything from things being a lot worse than they are today to some relatively minor improvements. It’s really far below what’s needed to restore native fish populations.”

“I don't have any confusion,” said Chuck Bonham, director of the Department of Fish and Wildlife. “Fish need enough water of the right quality at the right time of year, period. And I think this plan reflects that concept. Where there’s still remaining discussion: just precisely how much and when.”

The decision tree will ultimately affect how much water is delivered to users around the state. Early numbers show that between 4.8 million and 5.6 million acre-feet of water would be exported, close the average for the last 20 years.

“The low end of the range would be the status quo and the high end of the range would dramatically higher exports than today,” says Obegi. “So they’re not even contemplating meaningful reductions in exports that would allow for greater flows into San Francisco Bay.”

The state will release the final chapters of the draft plan in April, which will include the estimated costs. Another full public draft will be released in the summer.