Chinook salmon, Feather River Hatchery, Oroville. Credit: Dan Brekke

After years of dire tidings, the news this year about California's chinook salmon all sounds good.

Federal fisheries biologists have predicted big numbers of Sacramento River fall run chinook–the state's biggest, most commercially important salmon fishery–and the biggest population of Klamath River fall-run fish in memory. The California Salmon Council, a commercial fishermen's group, forecasts a harvest of 3 million pounds this year. That's triple last year's take and represents a comeback from the Great Salmon Crash of '08-'09, when the sudden collapse of the Sacramento fall run forced state and federal officials to shut down salmon fishing two years in a row. Salmon fishermen who barely hung on through the crash, along with those who sell them gear and supplies and process and market their catch, can look forward to something like a prosperous season.

And for the rest of us, the civilian salmon lovers? Victor Gonella, who heads the Golden Gate Salmon Association, promised in March that "consumers can look forward to some of the best food on earth–wild salmon, coming to a dinner plate near them soon."

Yes, that all sounds good. But here's the rest of the story.

Feather River Hatchery

A declining catch

Let's start with that commercial harvest number. We won't really know until later this year how the season turns out, but that 3 million-pound catch is only impressive next to the recent string of disastrous salmon years. The forecast for this year is nearly one-third lower than the average yearly harvest for the decade before the crash. And National Marine Fisheries Service data shows the catch has been slowly dwindling since 1950, with a more rapid decline starting in the late 1980s.

But nothing prepared fishing communities, scientists, or interested onlookers for the population crash that took place in 2008. Everyone would still like to know why it happened. Scientists have studied factors from water pollution to a big bridge project in the Carquinez Strait–did construction noise harm out-migrating juvenile salmon?–without identifying a single factor. The consensus is that circumstances ranging from poor ocean feeding conditions to water diversions from the Delta played a role.

But this is a mystery with an answer hiding in plain sight.

From abundance to scarcity

Once, salmon returned by the millions each year to the Bay, the Delta, and the rivers and streams in the Central Valley. Napa Valley pioneer George C. Yount recalled the region between San Pablo Bay and Sutter's Fort (in present-day Sacramento) as one where "the Rivers were literally crouded [sic] with salmon." And there's plenty of pioneer testimony that echoes that description.

What changed? Just everything, starting with the Gold Rush, which brought forth fabulous wealth and wrought unimaginable environmental destruction to salmon streams. And then dams, cities, farms, and industry. In a word: Us.

Feather River Hatchery

Even some efforts to preserve commercial chinook salmon populations may be hurting rather than helping the fish. When the Sacramento River fall-run chinook population collapsed a few years ago, it happened despite a long and aggressive effort to use hatcheries to replace spawning streams destroyed by dams, logging, and development.

But the heroic effort to improve on nature—even trucking baby hatchery fish downriver so they can avoid predators, polluted water, and Delta pumps—could be exacting a toll on the long-term fate of the run. Some biologists believe that the combination of habitat loss and hatchery production has essentially wiped out the last truly wild Sacramento Valley fall-run chinook. Worse, the surviving hatchery stock lacks the genetic variety of wild fish and could be more vulnerable to changes in ocean conditions or disease–and thus more prone to collapses like the crash of '08-'09.

The outlook

Is there anything hopeful about the salmon's story in California? There is. Over the past twenty years, government and resource managers have taken the first steps to restoring both water and habitat for chinook salmon. One of the most publicized actions—a limit on pumping from the Delta at certain times of year to protect threatened salmon and other species. That action was prompted by an environmental lawsuit, and it prompted a wave of lawsuits from farm and city water users south of the Delta. Outside of court, both the state and federal governments are working on plans that are supposed to restore the Delta and its species while delivering the water that farms and cities expect. Doing that will take a lot of money and determination.

The chinook can't help with the cash, but they may provide a lesson about persistence. As a species, they are the product of millions of years of evolution. The few wild fish still out there have been doing what they do, sometimes climbing thousands of vertical feet out of the Central Valley to their home streams, for a very long time. They are engineered to deal with disasters on their home streams and famine at sea. Given half a chance, they not only survive, but thrive. Fortunately or unfortunately for them, they now depend on us for that chance.

Chinook salmon on the Lower Tuolumne River in California's Central Valley. Photo courtesy of the US Fish and Wildlife Service

At Fisherman's Wharf, in San Francisco, what brings in the crowds are crabs. There's the Crab House. Crab Station. Crab Shack.

Larry "Duck" Collins is president of the San Francisco Crab Boat Owners Association, based at the wharf. But even though he makes his living, or part of it, fishing crab, that's not because he likes doing it.

"Salmon fishing’s fun," says Collins. "Crabbing’s not."

Crabbing, he says, is like factory work. Pull up the traps, empty them out, drop them back down. Salmon? Now that's real fishing.

"We use single, barbless hooks, catch them one at a time," he says. "It’s pretty exciting when you get a 40-pound salmon on the end of a piece of 90-pound mono and you haul it in, gaff off the head. It’s a lot of fun."

This year, Collins is poised to do more salmon fishing than he’s done in years.

Biologists say more than 800,000 Sacramento chinook are off the coast right now. It’s the biggest number they've seen since 2005.

As a result, the Pacific Fishery Management Council, which sets guidelines for commercial and sport fisheries, announced earlier this month that it’s considering three options for a 2012 salmon season, all of which would give anglers a chance to catch more fish than they have in years. The final decision will be announced in early April.

A much-needed reprieve

The last few years have been brutal for commercial fishermen. Salmon is a $1.2 billion business in California, but habitat loss, water diversions, and pollution have taken their toll. Salmon populations dropped so low that no fishing was allowed in 2008 and 2009. For the last couple of years, salmon fishermen were allowed back onto the ocean for limited seasons.

Salmon, says Collins, are why people get into this business in the first place. When the industry collapsed, his friends started leaving, taking what he refers to as “land jobs.”

"When I started fishing there were 5,000 salmon boats” he says. "Last year, I'd say, 400 or 500 boats fished. So we're at ten percent of where we used to be as an industry here."

Great news, but will it last?

Given the big 2012 projections, it would seem that nature is on the mend, right? Well, not if you ask Jacob Katz, who studies salmon biology at UC Davis.

"Sometimes if you put all your fish in one basket," he says, "they all hatch."

Katz means this almost literally. He says one big reason there are so many returning salmon is that we humans have been producing tens of millions of the baby fish in breeding facilities called hatcheries. These aren’t GMO fish or farmed fish. They swim out to sea, grow in the ocean, return to spawn and are sold as wild salmon.

California's salmon hatcheries date back more than a hundred years and actually began as an attempt to transplant chinook to East Coast streams to save declining fisheries there (it didn't work). Later, dams on rivers up and down the Central Valley made it impossible for chinook to get to their spawning grounds, and the hatcheries were put to work maintaining native salmon runs. Adult salmon were artificially spawned, then young salmon were raised in tanks and released into rivers below the dams so they could migrate safely to the ocean.

"It was improving on the inefficiencies of nature," says Katz. "Look, we can do this in a bucket!"

But over time, researchers started noticing something else: In some parts of the state, hatchery fish had nearly replaced the native fish. A study released earlier this year found that only ten percent of the fall-run chinook salmon spawning in California's Mokelumne River had spawned naturally.

"The native salmon problem hasn’t been solved," says Katz. "It’s just been papered over."

"The fact that you can sometimes make a lot of fish in a bucket has masked the fact that we've almost completely driven our wild fish to extinction," he says.

Why the Boom and Bust?

The question you should be asking now is this: If hatcheries have been around for a century, why are we seeing this sudden influx of fish?

The short answer is: No one knows. It could have to do with good ocean conditions, or the fact that there was more rain in 2011, and a decrease in water diversions.

But some biologists, including Katz, say the influx has everything to do with the hatchery system. Because they're produced from a smaller stock, hatchery fish lack genetic diversity. They can’t adapt quickly.

So, when ocean conditions are good – with cooler temperatures and good upwelling, like last year — the fish thrive. But the pendulum can easily swing the other way.

Which brings us back to Larry Collins.

I ask Collins whether, if the salmon disappear again, he too could be forced to take a land job. He looks at me like I've just sprouted fins. He's been fishing for 29 years. There’s no going back.

“When we leave the dock and go out there it’s a straight deal,” he says. “You fill your boat up, you get paid. There’s no boss. It’s a freedom thing that you get used to pretty quick when you start doing it.”

Salmon season is expected to start in April and wrap up around October or November.