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With winter rains arriving, the region’s rivers and streams are swelling. In Marin, the increased flow in streams like Lagunitas Creek allows one of the world’s most magnificent natural cycles — the return of the salmon — to unfold as it has for millennia.

Narrow streams are starting to be filled with improbably big, red fish, back in their home waters after three years at sea, fat and ready to breed. In the midst of our self-absorbed human world, wild nature can still find a way to hang on. Each year’s return of these fish is a sign of hope, but also a reminder of how close we are to irreversibly damaging the world around us.

“The most important lesson in ecology is: Everything’s connected,” says Todd Steiner, director of Salmon Protection and Watershed Network, an organization that works to protect salmon in the Lagunitas watershed, which comprises 103 square miles in West Marin, from Woodacre to Tomales Bay. “We’re trying to repair natural processes by taking a watershed approach.”

SPAWN employs a combination of research (Steiner is a wildlife biologist by training), habitat restoration, lobbying, education (including guided public salmon viewing) and litigation — a microcosm of the activity surrounding salmon from California to Alaska.

Salmon restoration requires such a multifaceted tool kit because the fish’s life cycle is so complex, linking land and sea. Each year, baby salmon hatch in freshwater streams throughout the West. They move downriver as they grow, before finally transforming themselves into ocean fish.

Several years later (the timing depends on the species), they return to the exact same stream they were born in and make the arduous journey up to the headwaters. There, they pair up and spawn in gravel nests before expiring, exhausted.

The oldest known salmon fossil, from British Columbia, is about 50 million years old, making this fish a vital part of ocean and terrestrial ecosystems.

“Through the evolutionary process they’re specific to the local conditions — water temperature, water chemistry, when rainfall happens and so on,” says Steiner. “They’re all adapted specifically to their location.”

While the thousand endangered coho salmon in Lagunitas Creek don’t go more than a few miles inland, the nearly two million chinook salmon that swim through the Golden Gate and into the Sacramento River go hundreds of miles, into the Sierra foothills and, before the Shasta Dam was completed in 1945, all the way to Shasta.

The Sacramento is the second-largest salmon-producing river in the lower 48 and is home to nine-tenths of California salmon, despite the loss of 90 percent of its salmon habitat by the 1970s. Salmon are a defining part of nature here.

“These fish have been important in both the nutritional and spiritual sustenance of people in the Northwest forever,” Steiner points out, “– as long as there have been people.”

And modern people in this place are no different: Salmon are of huge economic importance, which may be the only reason any are left. Salmon conservation efforts on the Klamath River go back at least to the 1890s.

Fifty years ago, salmon fishermen, seeing the decline of the salmon fishery in San Francisco Bay, organized and began to call for more comprehensive conservation measures.

“With salmon, you get involved with just about every possible environmental issue,” says Zeke Grader, the San Francisco-based executive director of the Pacific Coast Federation of Fishermen’s Associations.

“I never thought about that when I started doing this 30 years ago, but to try and protect those fish that our members rely on we’ve worked on everything from water diversions to dam operations to gravel mining to pesticides to genetically modified organisms — you name it. I thought, ‘Thank God, at least we don’t have to get involved in air quality issues,’ but now we’re finding that between mercury deposition in the ocean and carbon sequestration that we have to start paying attention to that too.”

Mercury released into the air by coal-fired power plants rains into the sea, where it can accumulate in fish. Eventually it makes its way into the bodies of people who eat the fish, where it can cause illness.

Grader, whose father was a salmon fisherman and who grew up working in salmon processing plants, says that salmon fishing is a threatened way of life. There’s been a decrease of 80 percent in the number of salmon fishing permits in the past two decades, with fewer than a thousand currently in California. Each one represents a local small business directly dependent on a healthy environment.

But now they’re up against agribusiness too. In the past decade, a handful of Scandinavian multinationals have been setting up salmon farming operations around the world. Originally a response to exterminated wild stocks in Norway, these cookie-cutter operations now churn out fish in British Columbia, Chile and elsewhere. (Salmon farms are not allowed in California, Oregon and Alaska.)

Farmed fish typically sell for half the price of wild salmon, seriously threatening the fishermen’s livelihoods. Worse, farmed salmon also threaten wild fish populations.

“It’s like industrial-scale beef or pig feedlots,” says Sophika Kostyniuk, the California markets campaigner at the Coastal Alliance for Aquaculture Reform. “There’s a tremendous concentration of animals being raised in a small area. They’re fed antibiotics and pesticides if there’s an outbreak of disease.”

The diseases fostered in these floating nets filled with fish can pass to nearby wild fish. Worse, farmed fish can escape.

Kostyniuk says that in July more than a million fish escaped during a single storm in Chile. “Chile didn’t even have an indigenous salmon population,” adds Kostyniuk, “but now they do.” The invasive Atlantic salmon threaten to disrupt Chilean river ecosystems, with unknown consequences for native species.

In places like British Columbia that do have native salmon, farm fugitives, which are mostly of Atlantic stock, displace the natives that are so finely tuned to local ecosystems. Juvenile Atlantic salmon have now been found in Alaskan streams, hundreds of miles from the nearest fish farms in Canada.

Because salmon farming is driven by consumer demand, says Kostyniuk, this is an area where consumer choice can have instant environmental benefit. “The most important thing consumers need to do,” she says, “is question why this fish is being offered to them so cheaply.”

Though CAAR is based in British Columbia, Kostyniuk is in San Francisco because California is that province’s major farmed-salmon market. More than 60 percent of the salmon sold in the United States was farmed in British Columbia or Chile.

“We always encourage people to ask questions to find out where their salmon is coming from,” says Kostyniuk in her sensible-sounding Canadian accent. “Just ask in your restaurant or grocery store if it’s wild or farmed. … I’ve been working on this issue for three years in the Bay Area, and I’ve just seen such a change in public consciousness of the issue.”

Most recently, the issue has been picked up by chefs around the country. “Just like vegetables are seasonal, so are fish,” says Chris Cosentino, chef at Noe Valley’s Incanto. “If it’s in season that’s when it’s at its best — it’s pretty logical.”

Cosentino notes with disgust that farmed fish are fed dyes to make their flesh pink. “We serve only local wild salmon,” he adds.

But this year has seen a double whammy for local salmon fishermen. On top of all their other woes, catches were severely restricted because of disastrously low salmon populations on the Klamath River three years ago. The fish were caught in a political battle in which the Bush administration overallocated the Klamath’s water to farmers, allowing the young fish in the river to die.

“We got really whacked on our salmon season,” says Grader, the Fishermen’s representative. “What should have been a very good salmon season was a bleak one. We figure the losses may have reached or exceeded $100 million, and it doesn’t look good for the next two years.”

“The tribes on the Klamath really got screwed,” he adds, his voice cracking slightly. “The pain up there was just tragic.”

In view of these kinds of challenges, every native salmon happily spawning in the place it was born is a small environmental victory, something that is not lost on Grader. “Actually things look good in a lot of ways, compared to the things we’ve been up against,” he says. “What needs to be done is known. It’s a matter of political will.”

Steiner has faced the same thing in Marin, and the rebounding coho stocks in the Lagunitas watershed give him hope. “We use the salmon as our totem species,” he says. “These endangered species are the canary in the coal mine. The things that we do to protect them protect my children who play in the creek, and protect the health of the community in general.”

Gregory Dicum, author of Window Seat: Reading the Landscape from the Air, writes about the natural world from San Francisco. A forester by training, Gregory has worked at the front lines of some of the world’s most urgent environmental crises. For more of his work, see www.dicum.com/list