You can't blame the gulls. In the web of ecology, there are many knots that are difficult to untangle. Right about when the gulls first appeared in the South Bay, something unusual happened at salty Mono Lake, clear across the state on the dry side of the Sierra Nevada. Since 1941, the city of Los Angeles had siphoned water from the lake's tributaries 350 miles south to faucets. The lake dropped 45 feet in 40 years, and in 1977, a land bridge formed between the sagebrush mainland and Mono's second largest island, Negit.

California gulls typically breed inland, from the Great Basin to Manitoba. (It's the Utah state bird, in fact, the "seagull" that saved Mormon settlers' crops from a katydid plague.) About 50,000 of them nested at Mono each year, two-thirds on Negit, feasting on brine shrimp and alkali flies before wintering on the coast. But suddenly, coyotes could stroll over to the island. The gulls abandoned ship in 1979, settling on surrounding islets, where many remain. Negit became an island again, but it's still gull-free.

Curiously, though, since then a decline of Mono's summer California gull numbers has correlated almost exactly with the rise of the South Bay colonies. In 1980, the first nests were spotted: 24 gulls, on a salt pond island. In 1982, less than 200. In 2010, 46,000. That's nearly exponential growth: the myth of the inexhaustible West played out by a bird. The population likely snowballed in the city for many reasons; you can't pin it on Negit's land bridge alone. But the parallels are striking.

Now, A6's displaced gulls also have to go somewhere. "We don't really want the gulls in the Bay," says Robinson-Nilsen, "but we don't want to force our problem on other people, like Alcatraz and the Farallones." The Farallones, a cluster of rugged islands 30 miles offshore, are known for seabird rookeries with their own slew of problems. They don't need a plague of rogue gulls. And surely researchers would haze them right back around.

If the gulls remain in the Bay, the restoration team would prefer they resettle near A6 or join another existing colony, where their impact on other species is at least known. Call it smart growth: No new sprawl, only infill. In fact, the restoration team decided not to evict one 10,000-gull colony near the plover's primary stronghold in the E ponds -- E for Eden Landing Ecological Reserve -- for fear of further upsetting the status quo. "At least they're not nesting in the middle of a plover pond," says Robinson-Nilsen.

We were now driving a nine-mile loop of levees open to joggers. In the distance, the white, upswept tents of Mountain View's Shoreline Amphitheatre -- a rock 'n' roll pavilion whose lawn seating is the flank of another landfill -- mirrored Cargill's towering salt stacks. We stopped to survey a boisterous colony of gulls that had cropped up beside A14, just east of A6 and a good distance from the "no gull zones." Robinson-Nilsen counted 4,500 gulls, up from last week's 3,000. Since there were no eggs yet, we strolled a short way into the colony. I wasn't sure if it was a wise decision. "Of course, I forgot my raincoat today, but this would be a pretty good place to wear it," said Robinson-Nilsen. The gulls rose like a handful of salt flung into the wind. They hovered in the airstream, white crosses barking down at us. We were surrounded.

At first, Robinson-Nilsen didn't care for the gulls, but now, she says, "I find them completely fascinating. They're beautiful, and very good parents. I respect that they dive-bomb us and poop on us, and hit us on the head." My jacket was Gore-Tex and hooded, but luckily it wasn't quite bombs away. The gulls were still building "nest bowls" in the humped dirt, lined with sticks, minor construction debris and decorative items from the Newby Island landfill and beyond: chicken bones, Barbie limbs, and once, said Robinson-Nilsen, a plastic French fry.

Years ago, 20,000 or 30,000 gulls were said to have gathered at Newby Island, when the winds were right. So many circled above the refuse that employees complained of vertigo. The landfills became to gulls what refrigerators are to teenage boys or the moon to tides: Of "over-riding importance (to their) movements," as Josh Ackerman, a U.S. Geological Survey biologist studying the South Bay's avocets, stilts, terns and gulls, wrote in a recent report. In 2008, Ackerman's team attached radio-transmitters to gulls, and discovered they reliably put in a long day at Newby Island, arriving fairly punctually at 6 a.m. to meet the first wave of trash, and punching the clock with the last truck at about 6 p.m.

"I'm sure it's not good for them," says Robinson-Nilsen, of the menu. "Most of it's not good for us." Good, of course, is a relative term: California gulls are one of the few birds able to raise a brood on garbage. Yet the landfills haven't taken pressure off the South Bay's waterbirds: They've established the gull's home range right where more than half of the South Bay's waterbirds nest. In 2008, gulls snatched up a gluttonous 61 percent of avocet chicks and eggs here. Of the 212 Forster's terns Ackerman's team recently radio-tagged, the gulls digested about half -- worrisome, considering the salt ponds hold a quarter of the Pacific Flyway's population

The gulls' toll on the plovers in the E ponds is unknown, but given a Bay Area population of fewer than 250, any consumption hurts. In the bird observatory's office in Milpitas, Robinson-Nilsen showed me evidence from a camera trained on plover nests: A hapless plover flushes. Ten awful seconds later, a gull lands and chokes down three supposedly camouflaged eggs so fast the footage looks accelerated.

In response, Newby Island has begun an ambitious abatement program, employing a falconer, and pyrotechnicians in fluorescent vests and hardhats who fire off "bird bombs" and "whistlers" that leave hanging spirals of smoke in the air. When I visited, hundreds of gulls landed sneakily on a ridge behind a sharpshooter. Eventually, he discovered them, turned and fired. They sprang off, like plastic shopping bags swept up in a gust.

Barriers between waste and wildlife are expensive to rebuild. This program costs several hundred thousand dollars annually. At least it works. Twice a month, Robinson-Nilsen surveys Newby Island. The flock has thinned dramatically. "If they stop eating at the landfill, then the population will decline or plateau," she says. "And if that means they turn to wild sources (of food), well, it's worth having a few tough years for our birds."

But the South Bay's avocets, stilts and snowy plovers may face an even bigger menace than California gulls: the restoration itself. Converting pond to marsh will make the ecosystem healthier overall, but reduce the birds' niches. In fact, before the salt ponds appeared with their vacant stretches, snowy plovers probably didn't nest around the Bay's rim. They were found on San Francisco's Ocean Beach, in Pacifica, and around Half-Moon Bay -- places they no longer breed because of increased human traffic. Nor were nesting avocets and terns as common bayside, since there were few sparsely vegetated islands. Forster's terns only colonized in 1948, on dredge spoil islands left in salt pond corners. Like the gulls, these birds are dependent on the mess we made.

Should we worry about gulls seizing plovers and other birds if those species didn't live here historically? "When it comes to this restoration, as far as what were baseline conditions, there really is no such thing," Josh Ackerman says. "Most people would argue that the baseline state is the present." We don't know, precisely, the ecological equation of old; even if we did, the conditions that created and sustained it are long gone, and there are responsibilities, now, to additional agencies. In other words, the very word "restoration" should be taken with a grain of salt. Those redesigning the ponds are juggling a vision of the past with today's reality -- and moving forward.

Two options have been proposed: In the minimum "50/50" scenario -- which would leave many ponds intact -- only half of the 15,100 acres would be reopened to the tides. Since 2011, 2,910 acres have been returned to the bay, about 39 percent of this goal. But restoration leaders are gunning for another vision, "90/10," wherein all but 10 percent of the salt ponds become marsh. The outcome will depend on scientific feedback -- the kind of data Ackerman and Robinson-Nilsen are collecting -- and, of course, on funding.

For the gulls, the breaching of A6 was an ecological disturbance on the order of the Mono Lake land bridge. For other waterbirds that have adopted the salt ponds as a surrogate for lost wetlands, the restoration -- without vigilant management -- could loosely resemble the disappearance of Mono's wetlands, which supported millions of birds. These events epitomize the changing times: The first of insatiable thirst, without any regard for ecology; the second of an awakened environmental consciousness, with tough choices to make. Going with 90/10 would likely end the stay of snowies in the Bay Area, says Strong, failing an official restoration goal: to "maintain current migratory bird species." Thus there are "marshistas and pondistas," Strong explains.

The arguments for more marsh are compelling, however, in terms of water quality and flood control over the long term, and from yet another avian perspective. The California clapper rail might benefit most from the 90/10 scenario. Shy, secretive and about ankle-height, it's arguably the Bay's highest-profile endemic creature, a subspecies listed as federally endangered in 1970. Its numbers climbed from a low of about 500 to a peak estimate of 1,400 in 2006. Invasive red fox control helped, and so did the spread of an East Coast cordgrass.

The U.S. Army Corps of Engineers first planted Spartina alterniflora in the '70s to stabilize Alameda flood-control channels. It hybridized with native cordgrass and infiltrated the lower marsh, where it grows so densely it shades out other flora. While native cordgrass sticks to channel edges on the Bay's upper marsh, the super-vigorous mongrel chokes waterways and flood-control channels. The invasive spreads across the mudflats, reducing the foraging grounds of many waterbirds, including the clapper rail. However, the birds used it for nesting and cover from predators.

Beginning in 2005, the San Francisco Estuary Invasive Spartina Project began using helicopters, hovercraft and spray-packs to make coordinated herbicide attacks. Once the grass is eradicated, native vegetation recolonizes quickly. But much as A6's breaching spelled change for gulls and plovers, there were unintended consequences: Over the next five years, the already slim rail population declined by about 15 percent.

Cory Overton, another USGS wildlife biologist, has been slipping through the marsh since 2007, tracking these solitary birds. They're highly territorial, he says, so their population is tied "one-to-one" to available habitat. Each bird defends about five acres. (A major league baseball field is about three.) "You can't necessarily cram more birds into smaller areas," says Overton. "The best bang for your buck is new marsh."

Contrast that with semi-colonial plovers, where you might find a nest scrape or two every few acres. "Because plover ecology and behavior is so different, you can probably do more with less land," Overton suggests, especially if you keep out predators -- and keep humans at a distance, on trails. Potentially, you can also make new habitat, just like the retired salt ponds. "But you just can't make a tidal marsh where it hasn't been before," says Overton. "It has to be at the right elevation, with the right wave action. We can do a lot of things, but we haven't figured out how to control the tides."

We can, however, provide clappers with a temporary place to escape to during the highest tides, when they can be exposed and easily picked off. Between the Oakland Airport and the A's Stadium, in a tract called Arrowhead Marsh, Overton's group has anchored a fleet of "floating islands": platforms with small tents made of woven-palm fronds. Clapper cams have shown they're much appreciated.

Still, says Overton, "Everybody prefers a natural alternative to an artificial one." That means more genuine marsh. "The San Francisco Bay is one of the most invaded ecosystems on the planet," he observes. That's no exaggeration -- the estuary was described as North America's most invaded aquatic ecosystem in a 1995 report for the Fish and Wildlife Service, primarily because so many foreign bilges have come to port and released their ballast water. What's changed? "From mussels and clams and tube worms that live in the bottom, to the fish that are swimming through the sloughs, to the plants," says Overton. "You can't make the bay a pristine natural system," he admits. "But you can make it a functioning tidal marsh. That's still restoration."