A plan promoted as the way to balance environmental protection with the state's water needs is more likely to drive at least one native species to extinction than to help it recover, federal biologists have found.

The Bay Delta Conservation Plan, which has racked up nearly $140 million in study costs, would reduce the flow of water through the Delta and send more to farms and cities, according to a review obtained by Bay Area News Group.

The waning flow would draw brackish Bay water deeper into the estuary and reduce freshwater flushing, spreading habitat changes that have degraded the estuary and harmed native species.

Water weeds, toxic algae and undesirable bass would likely spread, the biologists found.

"Therefore, overall habitat conditions under the proposed project are likely to be worse than present day conditions or future conditions (if the project is not built)," the biologists concluded.

The water agencies that are counting on the plan to increase their water supplies reject that conclusion, documents show.

Their consultants contend the water flows are not as big a deal and that other elements of the plan would more than offset any problems caused by the flow changes.

The 50-year water supply and environmental protection plan, trumpeted for four years by the Schwarzenegger administration and the state's biggest water agencies, will not be completed this month as planned.


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Instead, an incomplete draft is scheduled to be released in the coming weeks.

Top water officials in state and federal government, local water agencies and environmental groups are meeting privately, trying to resolve a host of thorny questions in advance of the report.

The plan's fate remains uncertain.

Regulators are unlikely to approve it if it cannot make good on the promise of Delta restoration.

And if it cannot deliver an ample, secure supply of water, water agencies that rely on the Delta may be unwilling to pay for it.

On top of the biologists' review, an independent consultant hired to assess the plan also questions its progress and the emphasis on increasing water supplies.

That critique brought a sharp reaction from water users, who called the assessment "rife with inappropriate and inaccurate" statements.

Acknowledging that the point of the plan is to increase water supplies, they noted that it made little sense for them to invest in an expensive project if the result would be less water.

"(Water) Exports can be reduced without the investment of tens of billions of dollars and, in fact, have been significantly reduced over the last decade with little environmental benefit to show for it," states a recent letter from water contractors to the Delta Stewardship Council.

Ideas for more water

Central to the plan is a tunnel system capable of carrying 15,000 cubic feet per second -- big enough to carry the entire Sacramento River most of the time.

By taking water from the proposed tunnels rather than Delta pumps, fewer fish would be killed at the pumping stations near Tracy. And investing billions of dollars in wetlands restoration and other ecosystem improvements will justify the water diversions, supporters say.

But a number of recent studies suggest too much water is taken out of the Delta watershed to sustain a healthy ecosystem, and a high-cost construction project is not likely to change that basic imbalance.

"Four years ago, a lot of people thought this project would consist of a $3.5 billion ditch that would get a lot more water supply with big benefits to fish, but it is not working out that way at all," said Greg Gartrell, assistant general manager of the Contra Costa Water District.

"They need to step back and rethink this project using this new information that has replaced all the old assumptions."

The $12 billion tunnel option would deliver just 3 percent more water than a much smaller tunnel that would cost half as much, Gartrell said.

The Concord-based water district has a lot at stake because the state and federal water projects affect the water quality around its Delta intake pipes.

A top federal official cautioned that a final plan will not be adopted without public review. The ultimate decisions are months away, Deputy Interior Secretary David Hayes said in an interview.

Hayes said he had not seen the paper by his department's biologists, who concluded that the proposal was likely to cause more environmental harm than good, but he said the federal scientists' findings would weigh heavily.

"This is going to be a science-driven process. We feel very strongly about that," Hayes said.

"The environment needs to get better under the BDCP (Bay Delta Conservation Plan). That's going to be the bottom line, in addition to the water reliability," Hayes said.

Who pays for it?

Water districts across the state will have to decide whether to commit billions of dollars to the plan, but there is a more immediate decision.

To complete the studies, water districts will have to pay another $100 million. One already balked but later got back on board.

Others are wary.

"We're not at the point where push comes to shove, but there is going to be a point in time in the near future where everybody is going to have to put their cards on the table," said Dennis Cushman, a manager with the San Diego Water Authority.

Project costs and benefit questions loom large.

One farm district in Kings County that primarily serves two wealthy landowners had opted out as of April 2009, documents show.

More than 80 percent of the irrigated acreage in the Dudley Ridge Water District is owned by Sunnyvale-based Sandridge Partners and Paramount Farming, which is owned by Stewart and Lynda Resnick, one of the richest couples in Los Angeles.

"The primary reason was financial," Dudley Ridge general manager Dale Melville said in an e-mail. The district's board of directors preferred to keep money to buy supplemental water. Melville said the district still could choose to participate.

But the costs keep climbing.

Southern California water officials were told this year that the aqueduct would cost about $8 billion, but the latest figure is $13 billion, Cushman said.

The decisions will be relatively simple once water agencies know two things: how much water they will get, and how much they will have to pay. And there's a third variable: the nature of guarantees, or assurances, that the water will be there even if the ecosystem does not improve.

Generally speaking, urban water agencies like those in the Bay Area and Southern California can afford to pay more than agricultural districts in the San Joaquin Valley, because cities have no choice, but farmers do. They could choose not to plant such crops as cotton, lettuce, almonds or pomegranates if water costs exceeded the crop value.

"All of us are working with our growers to make sure they understand what the costs are," said Brent Walthall, an assistant general manager at the Kern County Water Agency. "I think they will (support the plan), but they want to know there are going to be assurances."

"Everybody is in a mode of getting as much information as possible before we make a decision (to fund the studies)," said Dan Nelson, executive director of the San Luis & Delta-Mendota Water Authority, an association that comprises mostly west San Joaquin Valley farm districts.

If any water agency drops out, the price for everyone else will rise.

But even urban districts will look carefully at the project's economics before committing their customers to paying higher rates.

Water rates have been climbing sharply and water usage in the declining economy is way down in San Diego, Cushman said.

"The biggest (unresolved question) of all is: Who is going to pay for it? Those tough conversations have not been had," Cushman said.

Balancing act

The plan being drafted came in response to the environmental collapse in the Delta that became apparent in 2005 and the water supply cuts that followed as regulators and judges tried to reduce the number of fish killed by the pumps.

The strategy was for water users to commit to a "habitat conservation plan," using alternative provisions of endangered species laws to escape the close supervision regulators normally exercise.

In exchange for a relatively stable water supply permit, good for 50 years, water users would have to set up a comprehensive plan to protect a host of fish and wildlife species, and not just prevent their extinction. Among the targeted species are Delta smelt, longfin smelt, several salmon runs, green sturgeon and even terrestrial species.

Water agencies are expected to pay for the tunnels, but ecosystem-restoration projects, which could cost billions of dollars, would mostly be charged to taxpayers.

The conservation plan has been described as the most complex such plan ever undertaken because of its focus on fish (not just land animals), its location in a highly altered and complex estuary, its broad scope, and the number of overlapping and competing demands on the Delta.

Schwarzenegger's team also tried to get it done in record time: four years. By contrast, a comparatively simple habitat conservation plan that most affects East Contra Costa County housing took about 10 years to complete.

"The BDCP is on a collision course with reality," said Assemblyman Jared Huffman, D-San Rafael, one of the authors of water reforms passed last year.

Under new law, the plan must be approved if it meets certain standards.

But the new laws also require the state to reduce its dependence on the Delta, treat the environment and economy as "co-equal" goals and increase regional self-sufficiency in water supply around the state.

Huffman, a former environmental lawyer and chairman of the Assembly's water committee, said the plan taking shape does not appear to strike the balance required by the new laws.

"The Legislature was very clear in laying out a policy of reduced dependence on the Delta," Huffman said. "One cannot credibly reconcile these new policies with an attempt to return to (pre-Delta crisis) exports for the next 50 years."

Of course, conservation plan supporters don't exactly see it that way.

They see the goal to reduce dependence on the Delta as a statewide responsibility and are emphatic that it is the plan, and not recent contrary studies, that is consistent with the balancing act required by the new "coequal" goals.

"If those flow criteria had any regulatory effect, it's 'game over' for the Delta," said Cushman, the San Diego water official.

Mike Taugher covers the environment. Contact him at 925-943-8257.