Back, but not for good?

A fter years of going begging, Northern California is awash in salmon. Charter boats are booked up to two weeks in advance, and anglers claim to be bagging their limits before noon. The smell of gurry and the glimmer of scales are back at San Francisco’s Pier 45, where commercial fishermen unload their catch.

The return is also a boon to eager chefs, diners and fishmongers, who saw California salmon disappear from dinner plates when the fishery was closed for the 2008 and 2009 seasons and the fish was declared an endangered species.

“We’re making a living for the first time in a while,” said Larry Collins, who explained that he and his fellow commercial anglers barely survived when the fishery shut down.

Cooks are busy in the kitchen: “These fish are so fresh and delicious,” said Pam Mazzola, chef at San Francisco’s Prospect, whose summer menu features local wild chinook salmon with nasturtium pesto.

The 2010 fishing season lasted only 10 days, but a year later, 114,741 fish came in from the sea to spawn in the Sacramento River—nearly triple the number from two years before. And this year, fishery scientists expect 820,000 chinook to swim up the Sacramento River and even more to head to the Klamath River.

Based on new studies about the state of California’s waterways, however, it might be too soon to celebrate. A certain amount of fluctuation in the annual salmon yield is natural, but some scientists think that the collapse in ’08 and ’09 was part of a more dramatic—and unpredictable—boom-and-bust cycle, and that the fishery could be in for more of the same. The problem, they say, stems from the fact so much of the catch—a full 90 percent—originates in state hatcheries.

California’s eight salmon hatcheries were built in the 1950s and 1960s to make up for the loss of spawning grounds when the state’s major rivers were dammed for hydroelectric projects and for irrigating the Central Valley. In a typical hatchery, a wild population remains just below the river’s dams to spawn. Others swim up cement fish ladders that run around the dams and allow the fish to return to the hatchery.

Once there, the ladder-climbers are artificially inseminated, and their fry are raised for about six months. Then, they’re released back into the river, from which they migrate out to sea for three to four years and eventually return to the river where they were born. The fact that they live for all but six months in these natural habitats is what distinguishes them from farmed salmon, which spend their entire lives in crowded offshore net pens.

Hatcheries have been a lifesaver for the salmon population, which might otherwise have been ravaged or even wiped out, but they also are the source of certain weaknesses—both for the fish they produce (which most people still refer to as wild, despite their human matchmakers) and for the river population.

In the first case, hatcheries have a tough time mimicking nature: Salmon choose their mates based on evolutionary instinct, but the hatched fish are paired randomly. The result is a lot more fish but a lot less biodiversity, which makes the fish more fragile and more vulnerable to extreme changes in ocean conditions.

Those extreme conditions likely produced the last crash. Scientists believe that unusually warm water between 2004 and 2006 killed much of the zooplankton that young salmon eat, so by the time they would have reached maturity four to five years later, the population had been decimated. Since then, ocean conditions have improved—but there’s no telling when that could happen again, or whether some new disruption could occur.

“Look, this isn’t natural,” said William Cox, program manager at the Nimbus Fish Hatchery in the suburban neighborhood of Gold River, just outside of Sacramento. “But we can do a better job diversifying the hatchery fish. We’re increasing our genetic fitness program here and doing our best to raise fish as close to the wild salmon as possible.”

But even if such efforts succeed, another concern is that the fish produced in hatcheries can actually harm the river population. Hatchery salmon have a harder time surviving in the ocean than the diverse population of truly wild fish, but they have a distinct advantage when they’re first released into the river. Because they’re well-fed and cared for in the hatchery, they’re larger than their river-spawned counterparts, so they out-compete them for food, and, eventually, take over the habitat.

Studies are pouring in from around the Pacific Rim about the ecological risks of mixing hatchery and wild fish. California scientists contributed a report that describes the current salmon surge showing up on dinner plates as “the false appearance of positive natural population growth.”

Peter Moyle, a fish expert at UC Davis, has been sounding the alarm about California salmon for some time, and he points out that hatcheries are only part of the problem.

“Fixing this for a healthier fishery requires a two-pronged approach,” Moyle said.

Moyle wants to relocate the hatcheries, or at least release the hatchery fish downriver, so they don’t compete with river-spawning salmon. He also thinks the state needs to restore the rivers and estuaries so the wild fish can thrive.

The best possible scenario for salmon, environmentalists say, would be to remove major dams in California that block the salmon migration.

“There are some dams that have outlasted their usefulness,” said Curtis Knight, Mt. Shasta regional manager of the environmental group California Trout.

Knight points to dams on the Klamath River, four of which are scheduled to be removed in 2020 in California and Oregon if current plans get the green light. These dams don’t generate much hydroelectric power, irrigate many farms or help with flood control, he said. But they block more than 300 miles of salmon habitat. Independent scientific reviews show that the adult salmon population in the Klamath basin would rise by 80 percent once the dams were removed.

Dams also are being dismantled on Battle Creek, a tributary to the Sacramento River east of Red Bluff, and there are rumblings about removal of the Englebright Dam on the Yuba River, which runs into the Sacramento Valley. These dams are cited by environmental groups like California Trout as “low economic value/high environmental cost” dams.

Already, a dam removal project on the Elwha River on Washington’s Olympic Peninsula has shown early promise in restoring fish migrations. But until these measures are taken in California, scientists say, the boom-and-bust cycle from the hatchery-based system may be here to stay.