Perhaps you've seen this place from above. Banking north toward San Francisco International Airport's tarmacs -- themselves built on former wetland -- the mosaic of rectangular and irregular ponds ringed by the South Bay's sprawl look like puzzle pieces, or strange agricultural fields. The more startling the color, the saltier the water: With evaporation, those blue-green with algae become saturated with orange brine shrimp, and later, red blooms of bacteria. Many ponds show the sinuous traces of former marsh channels.

The ponds exist because the South Bay is especially windy, which accelerates evaporation. Native Americans, the Ohlone, gathered salt for trade long before others sold it to Sierra Nevada silver mines to process ore. The first salt ponds were constructed around 1860. When all was said and dug, about 85 percent of the Bay Area's leg-swallowing wetlands were gone: filled and built upon, or in the case of the salt ponds, diked off from the tides. Just as the pond systems were designed so that increasingly saline water could be ushered toward central "crystallizer beds," ponds once owned by more than 100 small companies were eventually bought up by just one. The agribusiness giant Cargill still operates 11,000 acres here, producing 650,000 tons of salt annually -- 4 billion shakers' worth.

For decades, scientists and conservationists recognized the value of restoring tidal marsh, but only recently did a big opportunity present itself, when Cargill decided to scale back its holdings. Encouraged by local environmental groups  such as Save the Bay, Sen. Dianne Feinstein, D, stepped forward to finesse a deal. In 2003, the state, with support from federal agencies and local foundations, paid Cargill $100 million for land that included 15,100 acres of salt pond.

With that, the West's largest, most ambitious wetland restoration was born, spanning a triangle of South Bay pond complexes: the A and R ponds, owned and managed by the U.S. Fish and Wildlife Service; and the E ponds, belonging to the California Department of Fish and Game (see map below). The California Coastal Conservancy leads an impressive coalition that includes these agencies, the U.S. Army Corps of Engineers, local water and flood control districts, and supporting science organizations like the U.S. Geological Survey and the bird observatory.

The goal is to return salt pond to marsh, providing habitat for species like the endangered California clapper rail and salt marsh harvest mouse, while improving the Bay's water quality and protecting Silicon Valley's high-flown but low-lying real estate from flooding. California sea levels are predicted to lift as much as five-and-a-half feet by 2100 due to climate change, and tidal marsh is the first defense, a sponge that absorbs storm surges and slowly wrings them out.

Once rooted, marsh filters runoff and captures sediment, so to a degree, it's self-preserving, rising and falling with the ocean. But the Bay Area's severely fragmented marsh and dependent animals may not be able to keep up with rapid sea level change. Thus, the biggest restoration -- on par, in size, with the largest in the Everglades and Chesapeake Bay -- is a race against rising tides. The estimated $1 billion public-private endeavor aims to restore 5 to 10 percent of the Bay Area's wetlands in 50 years, as part of a larger push to reclaim a quarter overall. (About $600,000 of that money, though, is slated for flood control levees.)

A6 was one of the first ponds returned to the tides. Dubbed "the Duck's Head" because of its shape, the pond lacked a "water control structure" (a fancy name for a gate), and after the winter's rains, it dried to a hard, crusty pan. Protected from raccoons and coyotes by a moat-like ditch, the 23,000 nesting gulls gradually sprawled like tract housing across its salty flat. But when Robinson-Nilsen and I arrived, A6 looked like ocean. Power lines crisscrossed the horizon and the hangars of NASA's Moffett Field loomed to the west. But in the breeze, you could smell the Bay's fecundity, its ability to heal itself.

When A6 will become marsh again is anyone's guess. Once, its bottom was at sea level; now, it's six feet below. The land subsided as agriculture drew down the water table, causing deep alluvial layers to dry up and settle -- forever increasing flood risks. Alviso is especially vulnerable: Some areas are 13 feet below sea level. A devastating flood in 1983 left neighborhoods 10 feet underwater.

"A6 is an experiment," says Cheryl Strong, a wildlife biologist for the Don Edwards San Francisco Bay National Wildlife Refuge, which encompasses the A and R ponds. "It's going to take awhile before we've got enough sediment for the pond to be above the tide line. I mean, it's going to be aaawhillllle." In 2011, the breached pond collected nine inches of fresh sediment, but it may take 50 years or more for mature marsh to appear.

Robinson-Nilsen panned her Swarovski scope down a former A6 levee that the restoration project had broken apart and mounded into a dashed line of islets. In the long run, they'll provide dry, vegetative shelter for creatures during high tides. But until enough sediment settles, they'll be submerged periodically. Through the scope, they seemed bare mud, except for the marsh seeds and propagules we couldn't see -- and the thousands of gulls we could.

"There's a lot of copulating going on," Robinson-Nilsen casually reported. A gull flew overhead, hauling a stick for a nest probably destined to be flooded. By counting the birds in a single scope view, and counting the views, she estimated 3,000 gulls, just a fraction of A6's former colony. Robinson-Nilsen was glad to see them sticking it out, well clear of the snowiest spots.