MENLO PARK — The Ravenswood salt ponds do not look like a place where wildlife would thrive.

Decades of being cut off from the Bay by a tall levee has turned this national wildlife “refuge” into a lifeless expanse of mud flats, silent but for the hiss of nearby traffic climbing onto the Dumbarton Bridge, with former salt production ponds crusted in white and tinted the red-brown color of iodine.

Starting in January, this unlikeliest of places will become a staging ground for the biggest wildlife comeback in Bay Area history. Ravenswood will be the first major part of the Don Edwards San Francisco Bay National Wildlife Refuge to be transformed into tidal wetlands, a 50-year, $1 billion project that will boost habitat for endangered species at former salt ponds from Hayward and Menlo Park to San Jose.

The prospect of finally seeing the changes take place energized Mendel Stewart, refuge manager with the U.S. Fish and Wildlife Service, as he carted a series of brightly-colored maps along on a tour of Ravenswood in October.

“In the springtime, in the summer, there should be thousands of birds nesting out here,” said Stewart, his eyes sweeping the landscape.

Specifically, the South Bay Salt Pond Restoration Project will restore habitat for endangered species such as the California clapper rail and the salt marsh harvest mouse, which require varying degrees of salinity to survive, as well as American avocets, black-necked Stilts, and delicate western snowy plovers.

A handful of levees will be breached to allow the Bay tides to wash into certain salt ponds during the next 10 to 15 years, and these sites will act as test cases for the future success of the project on a wider scale.

By 2060, officials hope to open at least 50 percent and someday, hopefully, as much as 90 percent of the project’s 15,100 acres to tidal action.

“It will compensate for many of the things that have happened since people got here,” said Stewart. “If it’s successful and we can manage it, it shows that over time, we can bring it back.”

A new home on the flats

Bringing life back to the former Cargill salt ponds, acquired by the Fish and Wildlife Service for $100 million in taxpayer dollars in 2003, will not be as simple as poking a hole in a levee and watching the water rush in.

It took a long time to engineer the salt ponds into being — first by the Ohlone and then by Spanish padres who started solar saltworks projects near San Jose in the 1800s. Most of the South Bay had become a compartmentalized network of levees by the time the Leslie Salt Company came in and absorbed the competition in the 1930s.

Cargill bought Lesley Salt in the 1970s and perfected the five-year process of crystallizing and harvesting salt, a technique resembling a gigantic conveyor dumping water and collecting salt around the Bay.

Machines wrote the legacy of the salt ponds, and machines will be needed to restore them due to the fragility of wildlife the ponds will be put in place to protect.

Rather than fully breach the handful of levees designated as part of Phase 1, officials will allow a certain amount of water to enter particular ponds up to a specific level, depending on which birds they are trying to attract.

The ponds near Alameda Creek in Hayward at Eden Landing Ecological Reserve — 6,300 acres in all — will be divided into six mini-compartments of increasing salinity, with Bay water brought in and evaporated out of them in succession in an effort to lure species of shorebirds, including eared grebes, which prefer saltier environments and like to feed on super-salty brine shrimp.

At Ravenswood, a single large pond will be divided in two. One part will be transformed into a marsh filled with a foot of water and raised mounds of dirt to create a habitat coveted by black-necked Stilts. A rear open area closer to University Avenue will be retained as a dry mud flat for nesting Western snowy plovers, which Stewart said they will find reminiscent of the beaches where they usually like to lay their eggs.

“They like the blasted moonscapes, is what I call it,” he said.

That sinking feeling

If Cargill’s legacy made the salt ponds inhospitable for many forms of wildlife, the salt ponds had the opposite effect on promoting growth in Bayside communities. Millions of residents have settled into homes and offices on dry land protected from flooding hazards by a system of levees that are in some areas nearly a century old.

In the meantime, much of the land has sunk beneath them.

Parts of the South Bay near San Jose have subsided by as much as 14 feet because of groundwater extraction starting in the 1930s. Places such as the Google headquarters and Moffett Field in Mountain View only exist because of the levees protecting the shoreline from incoming tides, according to Stewart.

That’s why Phase 1 of the South Bay Salt Pond Restoration Project will only affect areas that don’t present flood control problems — all the crucial levees will stay in place until new ones are built closer to the shoreline to raise or replace them.

That also accounts for the $1 billion price. Planning, building, and maintaining levees is notoriously expensive. In 2007, taxpayers spent $2 million just to maintain levees around the Bay for habitat value and flood control.

The Army Corps of Engineers isn’t expected to present a new design for local flood protection for at least another decade. When they do, most of the cost will be borne by flood control districts that represent the Santa Clara Valley and Alameda County respectively.

San Mateo County, however, has yet to come up with a funding source for its levees at Ravenswood and elsewhere. That could eventually become a major problem, especially considering Ravenswood Point is the most exposed portion of all the salt ponds in the Bay Area. On a map, it sticks out like a fist into the Bay. Keeping those levees intact will cost a lot of money.

“It’s flat as a pancake out there. If those levees don’t hold up, the water could come in there and top Bayfront Expressway,” warned Steve Ritchie, executive program manager for the restoration project. “It’s a good reason to make sure we do something sooner than later.”

Facing down a flood

There’s another good reason to try to speed up the process: sea level rise. Scientists have predicted the oceans could rise by as much as one meter, or 3.3 feet, in the next 90 years. If the water comes in more quickly than that or in the form of a New Orleans-type epic flood event, it could overtop some levees and utterly thwart the benefits the wetlands officials are working so hard to create.

“If sea level rise starts to occur too fast, we will end up with large areas of mud flat and open water and we will have lost the opportunity for tidal marsh. By then we’ll be building flood walls as opposed to a levee-wetlands combination,” said Ritchie.

An area of transition between open water and dry land, tidal marsh has more hidden benefits than any inventor could have imagined. Its spongy surface, filled with plant life, actually absorbs storm surges and deflects the pressure of wave action, removing the need for levees the size of castle walls.

Tidal marshes are one of the most productive ecosystems on Earth, producing plant material to absorb carbon from the air at a rate scientists say rivals that of trees. Saltwater tidal zones, like the ones around the Bay, also do not emit high levels of methane (a potent greenhouse gas) like freshwater marshes — so there’s no risk of further polluting the atmosphere.

Wetlands solve water pollution by binding to pollutants, such as nitrogen, phosphorous, and even oil and heavy metals, and breaking them down over time before they are buried in the sediment.

“I had a friend who used to refer to (tidal marshes) as the lungs of the Bay, breathing in and out,” said Ritchie.

Walking along a levee at Ravenswood that will be closed to the public when construction begins next month, Stewart said locals have so far failed to grasp that this site and a handful of others will be part of “the next big thing” for the coming decade — an enterprise so ambitious in its proportions that other cities around the world with the potential for similar projects will be watching to see what happens.

More than anything, he would like to see locals begin to bridge the disconnect between their notion of nature and the rich diversity of life taking shape in the salt ponds they pass every day on their way to work.

“They go to Yosemite, they go to other parts of the Bay Area for nature,” said Stewart. “This project is all about changing that.”