One goal of the Salt Pond Restoration Project is to lower the salt content of the ponds, increasing the number of ducks, fish, plants and other freshwater species inhabiting the bay. (Susanna Frohman/Mercury News Archive) ( Susanna Frohman )

Nature will need a huge helping hand to restore the South Bay's system of salt ponds, says a long-awaited report on the future of the ambitious project.

In this unusual back-to-nature experiment, it will take more than $1 billion and 50 years of close supervision to roll back the clock to the Bay's pre-industrial conditions, concludes the draft environmental impact report on the Salt Ponds Restoration Project.

"We can't just throw it all back 100 years," said project manager Steve Ritchie of the California Coastal Conservancy, a state agency based in Oakland. "We've changed everything."

The project - the largest wetlands restoration ever conducted on the West Coast - would set aside habitat for endangered wildlife, while providing flood protection and places to play for South Bay residents.

Among new recreational sites would be a kayak launch in Hayward and 37 miles of new waterside trails in areas long off-limits to humans, including the edge of Moffett Field. The 2,400-page report offers the first formal public viewing of the project plans since the ponds were sold to the state and federal government for $100 million in 2003.

The public can respond to the report until April 23, and then a final report will be submitted and reviewed before the project can begin.

One option - doing nothing - is discouraged by the experts, who say that would not help either humans or wildlife. Also, they worry that ignored levees will breach, posing flood risks.

Fifty to 90 percent of the former Cargill ponds should be allowed to revert to wild freshwater marshland over the five-decade span of the project, the report recommends.

The new saltwater marshland would benefit harbor seals, estuarine fishes, salt marsh harvest mice, steelhead trout and "dabbling" ducks, which feed with their tails in the air.

But there will be no rush to freedom for these long-captive salt pond waters.

The restoration will be cautious and data-driven, as experts seek the best balance between artificial and wild environments for the creatures that depend on the bay.

Salt-dependent species

The challenge is that several types of birds, such as migratory shorebirds and ruddy ducks, have become reliant on the salt ponds over the past century. And many of these birds' original habitats have disappeared in the meantime.

"We can't just take it away," Ritchie said. "We can't just put it back like it was."

So some high-salinity ponds - an estimated 10 to 50 percent of the total acreage - may never be fully restored, due to the dependency of birds. They will be retained and "managed" to keep their walls and waters strong.

How much is enough? The final number of preserved ponds won't be known until the process is well under way. If salt-dependent bird populations show signs of stress, the conversion process will slow. "We'll stop and take a long breath," Ritchie said.

"None of the species have read the textbooks that we have. They will respond however nature intends them to," he said. "It is a huge adventure."

Measurements of species, salinities, water levels and the presence of mercury and other toxics will continue for 50 years. New islands will be built, and predators will be controlled.

The first phase of the formal project, opening tidal gates of four ponds, is expected in 2008 and 2009. A few ponds were opened last year in a preliminary step.

Huge undertaking

Although this report identifies sites for potential levees, it does not make any formal proposal for flood protection measures. It will, however, act as the foundation for detailed flood protection plans by the U.S. Army Corps of Engineers in the upcoming South Bay Shoreline Study, said Jim Fiedler of the Santa Clara Valley Water District.

"It is a significant milestone. It will help us move towards the goals of restoration, public access and tidal flood protection," said Fiedler, chief operating officer for watersheds with the water district.

The project is rivaled in size only by efforts to restore the Florida Everglades and Mississippi River Delta in Louisiana.

Project manager Ritchie estimated that the cost of construction for the first phase of the project will be $25 million to $30 million. The total cost of construction will be $600 million to $1 billion. The cost of monitoring ponds over the first decade will be $3 million a year.

The San Francisco Bay has lost almost all of its tidal marshes to ponds, development and hay fields. This effort will restore 10 percent of what's been lost, and most of it will be off-limits to human interference.

"The vision is very exciting, and is definitely something we support," said David Lewis, director of Save The Bay environmental organization.

Lewis also welcomed the creation of new places for people.

"These were shoreline communities - and will be, again."

IF YOU'RE INTERESTED

The South Bay Salt Pond Restoration Project's draft environmental impact statement can be read at some public libraries, government agencies and online at http://www.southbayrestoration.org/EIR/

Public hearings will be held from 6 to 8 p.m. in Mountain View on March 28 and in Hayward on March 29. The first meeting will be the NASA/Ames Research Center's Eagle Room, Room 943, Mountain View. The other will be at Centennial Hall, Room 1, 22292 Foothill Blvd., Hayward.

Contact Anna Schneider at the Coastal Conservancy at (510) 286-1015 or e-mail mailto:aschneiderscc.ca.gov