The salmon-boat cemetery in Fort Bragg, a fishing port tucked into shaggy pines about 150 miles north of San Francisco, is full of bleached and peeling hulls. Over the years many California vessels have landed in Bruce Abernathy's front yard, pitched at steep angles among the weeds, some still rigged with trolling poles. The Anita II, the Dag. Eventually Abernathy's son David takes them apart with a tractor and chain saw and sells what he can for parts. Sometimes all that's left is a scrap with a painted-on name: My Pet.

Bruce Abernathy himself doesn't watch the demolitions. He finds somewhere else to be, or he stays inside his house, with its many framed prints of trim little ships atop frisky seas. The fisherman turned resale man, and lately junk dealer, has "a lot of remorse" about what's happening outside his window beyond the hot pink rhododendron bush. "I know almost everybody who owned these boats," he said. "Boats become part of you, like a wife."

Thirty years ago there were several thousand salmon boats in California. More recently, as the fish became scarce, only a few hundred worked the coast. Then salmon populations crashed, and this year for the first time U.S. officials canceled all ocean salmon fishing off California and most of Oregon, and curtailed it off Washington, a $300 million loss. When I visited Fort Bragg, in late May, the harbor felt about as cheerful as a junkyard. The docks should have quaked with activity, but the mooring basin was quiet except for the hoarse bark of sea lions. The fishermen with the biggest boats hoped to go way out after tuna later in the season; others had already joined roadwork crews or cobbled together odd jobs. Disaster relief money would be on the way, but to many second- and third-generation fishermen, a summer without salmon felt like the end of the line. For the better part of a century the fish supported Fort Bragg, home of the World's Largest Salmon Barbeque, at which local politicians flip fillets on the grill and tourists come from far and wide to taste one of the most sought-after fish in the sea, the chinook salmon, a.k.a. the king.

The sudden decline of California's chinooks, most of which originate in the Sacramento River, has shaken scientists as well as fishermen. Typically several hundred thousand adult fish return from the sea to the river in the fall. Last autumn, only about 90,000 made it back, and fewer than 60,000 are expected this year, which would be the lowest number on record. "Usually when something like that happens, you can point to something dramatic, an oil spill, closing of hatcheries, an earthquake," said Donald McIsaac, executive director of the Pacific Fishery Management Council, the regulatory group that advised U.S. officials to halt this year's salmon fishing. But no such catastrophe has been definitively linked to the shortage.

Salmon is the third most popular seafood in the United States, after shrimp and canned tuna, with about 600 million pounds consumed annually. Most of the fresh meat is Atlantic salmon raised in fish farms. California fishermen bring in about five million pounds of chinook meat in a good year. That's not terribly much, considering the national appetite, but king salmon is the largest and perhaps the choicest variety, owing to its deep reddish pink color (a result of its krill-heavy diet), high omega-3 fatty acid content and rich flavor. It is the stuff of white tablecloth restaurants and fancy markets, not salmon burgers. ("You would never put king salmon in a can," one fish market analyst told me.)

What's more, local chinook, chrome-colored and strong enough to charge up waterfalls, are revered as a symbol. We savor the salmon's story almost as much as its flesh—its epic slog from birth stream to sea and back again, its significance to Native Americans, who saw the fish as a dietary staple and a religious talisman. Salmon still retain something of that spiritual power. Called the "soul food of the North Pacific," king salmon is the flavor of healthy rivers and thriving coastlines. It is a pepper-crusted or pesto-smeared communion with nature, gustatory proof that in a region where cities are sprawling, wildness still waits below the surface—if you will only cast your fly and find it.

There are about a half-dozen salmon species worldwide, and populations are further defined by their rivers of origin and migration seasons. Chinook (Oncorhynchus tshawytscha) are found from California's Ventura River to Kotzebue Sound in Alaska to Russia's Andyr River and northern Japan. The species whose sudden disappearance has been in the news, prompting Congressional hearings this past spring, is the fall-run Sacramento River chinook, named for the river to which mature fish return to spawn and the season in which they do so. (The Sacramento River also supports much smaller winter and spring runs, which are classified as endangered and threatened, respectively, and a late-fall run.) After eggs are laid in autumn, young salmon emerge from their gravel nests as early as Christmastime, swimming south a few weeks later. They slink seaward mostly at night to avoid predators, lingering in brackish estuaries to gather strength. As they near the ocean, their bodies change. Their renal systems adapt to salt water. They lose black bars on their sides and gradually assume the silvery color—with a scattering of black spots—that thrills fishermen. "God, they're beautiful," exulted Dave Bitts, of McKinleyville, California, a commercial fisherman for more than 30 years. "That's what a fish is supposed to look like—the whole shape of them, the power of the back, the thickness of the tail."

The fish typically stay at sea three years, ranging thousands of miles in the Pacific and gaining 90 percent of their body mass (between 10 to 50 pounds, though the largest weigh more than 100). Then they head for home, tracing the smell of minerals and organic materials to find their natal streams. It is a brutal journey. The fish stop eating once they hit fresh water, and their bodies begin to deteriorate even as they ascend rapids (the word "salmon" comes from the Latin salir, to leap). Ready-to-mate males flush crimson and grow tough-guy hooked jaws for fighting; females search for gravel for a nest. Soon after laying and fertilizing eggs, the exhausted adults die. But the life cycle doesn't stop there. The kings' spawned-out carcasses nourish not only the baby salmon that will take their place but also living things up and down the food chain, stimulating whole ecosystems. Salmon-rich streams support faster-growing trees and attract apex predators like bears and eagles. In certain California vineyards, compounds traceable to salmon can be found in zinfandel grapes.

This is the elegant narrative that people in the West are fighting to preserve, a tale of determination and natural destiny that somehow touches even those of us who don't live there. And yet this ideal of wild salmon is increasingly an illusion.

Coleman National Fish Hatchery, Anderson, California, 4 a.m.: Had it been light, I could have seen the edge of the Cascade Range, which includes Mount Shasta, the Sacramento River's source. But I couldn't make out the hatchery's outbuildings, or anything much beyond a series of long concrete pools, or raceways, illuminated by floodlights.

It dawned on me that the gray current shifting and flickering below the surface of Raceway 5 was actually hundreds of thousands of three-inch-long fall-run chinooks. A hatchery worker scooped up a couple: squiggles with woeful expressions, they were barely princelings, never mind kings. But every so often one would snap itself suddenly out of the big pond, a hint of the athleticism that would one day launch it upstream.

We were there because the hatchery was taking a historic step. Usually, the federal facility—at the northern end of California's Central Valley—releases the juveniles out its back door into Battle Creek, which feeds into the Sacramento River six miles downstream. This year, though, natural resource managers had decided to load 1.4 million fish, about a tenth of Coleman's total stock, into trucks and drive them roughly 200 miles south to San Pablo Bay, above San Francisco Bay, bypassing the entire river, a tactic that state hatcheries have been using for years. I had already been startled to learn that between 50 percent and 90 percent of the Sacramento River's "wild" fall-run chinooks are actually born in hatcheries, which were created to compensate for the loss of spawning grounds to dams. Every autumn, hatchery workers trap returning adults before they spawn and strip them of sperm and eggs. The offspring are incubated in trays and fed pellets. Now this latest batch would not even have to swim down the river.

The shipment was an effort to rekindle future fishing seasons, Scott Hamelberg, the hatchery manager, said: "If you truck a fish from Coleman and bypass certain areas where mortality can happen, you may improve survival. You take out hundreds of miles of avoiding predators, water diversions, pollution, any number of things."

We spoke in his office, which held a shrine to Popeye, a cat who must have enjoyed an extremely happy tenure at the hatchery. Despite the low numbers of returning Sacramento salmon this year, Coleman planned to go ahead with its annual Return of the Salmon Festival in the third week of October, where in years past schoolchildren have shrieked over the chinooks jamming the creek.

Outside, a worker standing waist-deep in the raceway crowded the fish toward a hydraulic pump, using a broom to goad stragglers. Their shadowy forms shot up a transparent tube and into a tank on a waiting truck. In a few hours they would be piped into net pens in the bay, then hauled by boat farther out and released to swim out to sea. Some scientists say the hatchery fish are less physically fit than their wild brethren, with a swimming-pool mentality that does not serve them well in the ocean. And yet in years past, many survived to maturity simply because they were introduced in such overwhelming numbers. Some wildlife experts speculate that the hatchery-born fish may even be weakening wild populations they were meant to bolster by competing with the river-born fish for food and space, and heading home with them to breed, altering the gene pool.

The trucked fish won't know where home is, exactly. Many will likely never find their way back to Battle Creek, not having swum down the river in the first place. These strays might spawn successfully elsewhere, but without that initial migration it might seem that some essential quality of salmon-ness is lost.

If this is the price of keeping the species going, so be it, said Hamelberg, who wears a wedding band etched with tiny salmon. "There's a greater public good here," he told me. "We're providing fish to the American public to eat, and also for aesthetic reasons—just for people to know they're in the system, that they returned. Our obligation is to keep these runs as sound as possible."

The hatchery workers looked weary as the trucks pulled away. As it turns out, chauffeuring tons of pinkie-length fish hundreds of miles is trickier than it sounds. During shipping the day before, the circulation system in one of the trucks stopped working, and 75,000 chinooks died.

Native peoples of the Pacific Northwest used to think salmon were immortal, and it's easy to see why. Even though the rivers hosted spectacular mass death scenes every year and were filled for weeks with rotting bodies, the next season's fish always mobbed the gravel beds. To safeguard this cycle, tribes were careful to place the bones of the season's first catch back in the river.

But the California and Pacific Northwest salmon populations have been declining for more than a century and a half. Gold miners washed the gravel out of streams and loggers dismembered river habitats. Fishermen caught so many salmon that the canneries couldn't keep up; barge loads were dumped back into the sea, and salmon carcasses were used to feed hogs and fertilize fields. Today, the Columbia River supports at most 3 percent of the salmon it boasted when Lewis and Clark passed through. The Klamath River, which starts in southern Oregon, has suffered major salmon kills. Some Pacific salmon varieties may share the fate of their East Coast cousins, the wild Atlantic salmon, which were killed off in huge numbers in the 19th century by overfishing, pollution and dams and are today nearly extinct in the wild.

By now, Sacramento chinooks have lost an estimated 70 percent of their original spawning habitat in central California. Dams did the most damage, drying up riverbeds and cutting off access to mountain spawning streams. Shasta Dam, completed in 1945, is the nation's second largest, far too big for the fish ladders that in some places help salmon reach their spawning grounds. Some populations barely survived. There are plenty of complaints against hatcheries—the main one is that artificially producing millions of fish masks deep ecological problems—but without the hatcheries, the Sacramento run could hardly have rebounded from industrialization the way it did. The fall run, probably numbering about a million at its peak, was until very recently holding steady at a quarter or more of that level, enough to keep the West Coast salmon industry afloat.

Then came this summer's calamity. The official list of possible causes is more than 40 items long, ranging from bridge construction in migration areas to a surging population of Humboldt squid, grabby predators that may or may not have a taste for chinook. Scientists are looking back to 2005, when the fish that should be returning to the river now would have been sea-bound juveniles, small and vulnerable. There were poor ocean conditions off the West Coast that spring. A shift in weather patterns—possibly related to global warming—delayed the seasonal upwelling of cold, nutrient-rich water that supports the base of the marine food chain. As a result, "everything that was expecting something to eat in May died," including juvenile salmon, said Bill Peterson, a fisheries oceanographer with the National Oceanic and Atmospheric Administration.

Other experts cite freshwater dangers, since fish weakened by a stressful trip downstream are less likely to survive in a hostile ocean. This is a politically loaded argument: many of those stresses, from pollution to introduced species, are man-made. "Protecting this icon means protecting the watershed, from where these things spawn in the mountains down to the ocean," said Jon Rosenfield, an aquatic conservation ecologist based in Berkeley, California. "If you operate the rivers in the way that's best for agriculture, that's not necessarily how the water would be operating on its own."

In addition to being the most populous state, California is the most productive agriculturally. But much of its farmland, and more than 75 percent of its population, lie south of Sacramento, while three-quarters of the precipitation falls north of it. Huge dams, the Shasta chief among them, hoard water that's released downstream on demand and pumped to the Central Valley and Los Angeles. The arrangement works out for millions of people but not always for the fish, which can get disoriented in artificial flows created by water diversions and never make it to the sea.

Such problems are expensive to fix and the solutions can mean water shortages, especially for farmers, which heighten the conflict between interest groups. "The environmental community exploits the problems in nature and ignores human problems," said Jason Peltier, deputy manager of the sprawling Westlands Water District, which supplies hundreds of farms in the Central Valley. "That's their agenda. I can't understand how they get away with it. I can't understand how [the groups] push a fish-and-nature-first agenda at the expense of human socioeconomic conditions."

Over the past decade or so changes have been made to California's intricate plumbing to give salmon safer passage. Shasta Dam was retrofitted, at a cost of roughly $80 million, with a device that draws from the very bottom of its reservoir, supplying downstream areas with more of the cool water that spawning salmon require. In addition, hundreds of millions of dollars have been spent otherwise improving Sacramento River habitat.

But it's doubtful that any amount of effort or money can restore the salmon's world. I didn't fully understand this until I visited the most altered ecosystem of all, the one environmentalists are most likely to lament when discussing the king. It's where ocean and river meet: the vast and troubled estuary at the Sacramento's mouth, through which almost all the river's wild-born salmon pass en route to the Pacific. The former 400,000-acre tidal marsh is California's main water hub, a place both tamed beyond recognition and perilous for salmon in new ways, full of obstacles far more challenging than mere rapids.

Just east of San Francisco Bay, the Sacramento-San Joaquin Delta stretches 50 miles south of Sacramento and some 25 miles west. Part of the largest estuary on North America's Pacific Coast, the delta was once a marshy haven of cattails and bulrushes. Juvenile salmon from both the Sacramento and San Joaquin rivers (which converge in the delta) used it as a kind of staging ground, tarrying in its shallows before going out to sea.

But 150 years and 1,100 miles of man-made levees later, the wetlands have been transformed. During the gold rush, they were drained and converted into a web of farming islands with winding channels in between. Ninety-five percent of the original marsh is gone, and what remains is the epitome of an artificial landscape, so squarely under civilization's thumb that it's almost impossible to imagine it otherwise. The islands—many of them ten feet or more below sea level due to soil decomposition—are a patchwork of crops and alien species: palm trees, European sycamores, Himalayan blackberry bushes, spindly grapevines propped up on sticks, extensive plantings of Bartlett pear trees and fields of lawn turf as green and smooth as a pool table. At times the air suddenly smells of licorice—wild fennel, another invasive species. Go around a levy bend and there might be a beached World War II landing craft used by a local duck-hunting club, a sign for brand-new mansion developments "Coming Soon" or the pink explosion of a garden-variety rosebush.

The waterways surrounding these islands are about as hospitable to salmon as drainage ditches. The remaining marshland teems with nonnative species, many of them ravenous stowaways from the cargo ships of nearby San Francisco Bay. Brazilian waterweed, an aquarium favorite, clogs the sloughs and retains sediments, making the water clearer and juvenile fish easier to spot: predators like largemouth bass—introduced as a sport fish more than a century ago—lie in wait. Upriver farms release potentially poisonous pesticides and herbicides. Wastewater from the Sacramento area, with its ballooning population, also seeps into the delta, and scientists are increasingly suspicious that ammonia from human sewage interrupts the seasonal cycle of phytoplankton blooms at the base of the food chain.

And then there are the pumps. Naturally brackish, the delta is now managed as a freshwater system, because fresh water is what's needed to fill bathtubs and irrigate fields and quench the thirst of Californians, about 25 million of whom rely on the delta for at least some of their water. Mammoth federal and state pumps in the delta's southern end, near the city of Tracy, slurp up roughly half of the Sacramento's flow and send it to Silicon Valley, Los Angeles and beyond. When the federal pumps are going full blast, six 22,500-horsepower motors pull water through pipes 15 feet in diameter, raising the flow into a canal that helps irrigate the middle of California's Central Valley. (The state pumps are even bigger.)

The pumps are powerful enough to alter the currents miles away, confusing migrating salmon. Often, salmon are siphoned along with the water. More than half of these are salvaged near the pumps at fish-collection facilities, where the buckets are checked every two hours, the operators pawing through seaweed to find the tiny fish, which are then loaded into trucks and driven back to the delta. But the smallest chinooks can slip through; in past years tens of thousands have died. In 2005, that fateful year for this season's salmon, the pumps exported record amounts of water from the delta.

"The higher the export rate, the more fish are lost," said Tina Swanson, a biologist and head of the Bay Institute, an advocacy group that monitors San Francisco Bay and the delta. "Even small increases can lead to disproportionately high losses."

Constructed mostly in the middle of the last century, the pumps are relics of a time when fish populations were not much valued or understood. Lately California's attitude has changed. When I visited the federal pumps, they were churning much more slowly than usual because of a court order to protect a threatened fish called the delta smelt. Already, farmers to the south were not getting water they'd asked for. They were also nervous about another lawsuit, filed by a coalition of environmentalists, fishing associations and Native Americans on behalf of the Sacramento's winter-run chinook and other salmon species. Among other things, the plaintiffs want more reliable cold releases from the Shasta reservoir, which could limit flows to the pumps.

"I can't be without [that] water," said Daniel Errotabere, co-owner of Errotabere Ranch, which grows some 5,600 acres of almonds, lettuce and other crops with the help of delta flows. This summer the farm got just 40 percent of the water it had ordered from the pumps. "We're not wasting anything. All our crops are pretty much spoonfed. I can't do any more than I'm doing, unless there's a way to find a crop that doesn't need water."

My guide to the fantastical Sacramento-San Joaquin Delta was Peter Moyle, of the University of California at Davis, an estuary and fish expert who made room on his research boat to show me a bit of what the delta is and used to be. I wanted to see some wild baby salmon, which he said was not likely, since it was late in a dry spring. I felt sure he would be relieved to see some too. When I picked him up in Davis, there were salmon prayer flags fluttering in front of his house.

Moyle has spent much of the past 30 years in the grayish-brown marsh mud on the outskirts of the delta, and he's the authority on local fish—the California roach, the Sacramento sucker, the tule perch—much less glamorous than salmon. He's the go-to person on the delta smelt, a homely little fish that smells like cucumber and faces many of the same challenges as the chinook.

Moyle's rickety aluminum research vessel, The Marsh Boat, was crewed by two graduate students. We pulled on waders and life vests and then bounced off into a stiff north wind, which made the tall grasses on the shore roll like waves. We were surveying fish populations on the outskirts of the delta in the Suisun Marsh, which has not been tampered with as much as adjoining areas and is reminiscent of what the whole place might have looked like before the gold rush: an expanse of bulrushes and brownish water, with snowy egrets stalking the perimeter and white pelicans flapping overhead. It was almost possible to ignore the bellow of an Amtrak train bound for San Francisco and the jets landing at nearby Travis Air Force Base.

The boat stopped by a muddy beach, depositing Moyle, me and a graduate student studying invasive jellyfish from the Caspian Sea. The other student roared off in hot pursuit of zooplankton. We walked the shore, with the professor periodically plunging into the water to drag a net. "If you were a baby salmon, this is exactly where you'd want to be," said Moyle, his bifocal sunglasses glinting as he eyed a particularly inviting stand of bulrushes. "This would have been full of food, full of cover. You could have escaped your predators and there were strong enough currents that you could find your way out to sea."

Nearly everyone's unhappy with the delta as it is today. Some say that rising sea levels and earthquakes threaten its structure, and since Hurricane Katrina there have been calls to armor the levees to maintain the delta as a freshwater system. Others advocate reducing water exports from the delta, doing away with the levees and unleashing the river to become brackish again in places and flow where it will.

The plan that has lately gained the backing of Gov. Arnold Schwarzenegger involves digging a canal upstream of the delta that would send fresh Sacramento water straight to the pumps. With the help of fish screens, the salmon would stay in the main river and continue their migration without the threat of artificial currents. "Separate the water for people from the water for fish," said Timothy Quinn, executive director of the Association of California Water Agencies. "Manage each for their own purposes." Quinn says healthy fish populations and a reliable water supply aren't mutually exclusive. In fact, he takes his grandkids every year to see the spawning in Butte Creek, a Sacramento River tributary. "I don't want them growing up in a state where they'll sacrifice fish to get cheap water," he said.

But the peripheral canal, as it's called, is so controversial it's known as the "third rail" of California politics, and voters have nixed it before. Building it would take more than a decade and cost billions, and California will need to figure out how to accommodate another eight million thirsty residents by 2025. Still, academics from different disciplines have begun to agree that the canal may be the only way. "The devil's in the details, though," Moyle said. "No matter what you do, it's going to be complicated—and expensive."

Our nets yielded plenty of fish that morning on the marsh, many of them nonnative: baby carp, yellowfin goby and inland silversides, transparent little fish with a stripe like thermometer mercury. Moyle held flapping palmfuls as he measured them one by one, then tossed them back into the water. He had been right: we saw no young salmon.

To fishermen, the chinook is known as a fighter, and likewise its advocates won't let the fish die out without a struggle. People desperately want to save wild salmon. "DEMAND Wild Californian King Salmon" stickers adorn car bumpers, and products like Butte Creek Brewing's Spring Run Organic Pale Ale benefit the kings. A SalmonAid concert stirred up support in Oakland this past spring, and an advocacy group for Columbia and Snake River salmon hauled a 25-foot fiberglass chinook from Seattle to Washington, D.C., stopping at schools and farmer's markets along the way. Another lawsuit to ensure the wild salmon's safe passage continues to wind its way through the courts.

Even as the crisis deepens, the nation's appetite for salmon grows, thanks largely to the farmed variety. In 1980, almost none of our fresh salmon meat came from fish farms; now three-quarters of it does. Corporations in Norway, Canada and Chile run many of the farms, and most of the fish are Atlantic salmon. Raised in offshore pens, removed entirely from rivers, they eat formulated pellets instead of krill, so their flesh is naturally gray. Aquaculturists feed the fish color additives to make the flesh pink, fine-tuning the hue with the help of a color wheel called the SalmoFan. As a result inexpensive salmon meat is now sold practically everywhere, including Wal-Mart—an abundance that obscures the wild salmon's plight.

Salmon fishing in California and Oregon will probably have to be limited for a few years, to allow stocks to recover. Among those who continue to have faith in the king's return is 26-year-old Cyrus Maahs, a fourth-generation Fort Bragg salmon fisherman. He grew up trolling with his grandfather, Sonny Maahs, who helped found the town's annual salmon cook-off 37 years ago, when the rivers still thrashed with fish and the sea was full of them. Cyrus' father, Mike, put himself through college on salmon money and died at sea in a storm; his name is on the fishermen's memorial in the harbor, beside the charred concrete barbecue pits.

Cyrus believes he has inherited the family instinct to clear the jetty in a thick fog, to pick the perfect psychedelic-colored salmon lure. I asked him if he ever considered a more stable line of work—serving Fort Bragg's burgeoning tourist trade, perhaps, or leading whale-watching trips. "I'd much rather be out there fishing, and have a job with freedom to it," he said. "Once you get a taste of that, it's hard to give up."

The family boat, Kromoli, spent most of the summer at anchor with much of the rest of the town's fleet. Some fishermen contemplated putting their boats up for sale, on the off chance someone would buy them. And yet, even in Fort Bragg, the myth of a bountiful fishery persists. Visitors to this July's World's Largest Salmon Barbeque did not go hungry, for instance. They were served coho salmon flown in from Alaska.

Abigail Tucker is the magazine's staff writer.
Freelance photographer Ryan Anson is based in San Francisco.