The winter rains have caused the biggest surge of coho salmon in a dozen years in the celebrated spawning grounds of western Marin County, one of California’s last great strongholds for the embattled pink fish.

At least 648 coho this winter made their way against the current up meandering, forested Lagunitas Creek and its many tributaries on the northwestern side of Mount Tamalpais, according to a new census by biologists.

The coho run is the largest in the North Bay since the winter of 2006-07 and well above the long-term average of about 500 fish. It’s the sixth-largest run since systematic surveys began in 1996.

The surge of salmon is being credited to habitat restoration efforts for the endangered fish.

“Many organizations and individuals have worked tirelessly for years to improve fish habitat in the creeks of Marin County, and it’s gratifying to see so many salmon returning to those creeks,” said Eric Ettlinger, an aquatic ecologist for the Marin Municipal Water District, which conducted the count with Watershed Stewards Program, National Park Service and the Salmon Protection and Watershed Network.

“After looking at where the population was just a few years ago I’m actually quite happy that it’s grown so much,” he said.

The Lagunitas Creek migration is the largest run of wild coho between Humboldt and Monterey counties — most other river systems contain hatchery-raised fish — and one of the most remarkable. The fish swim 33 miles from the ocean into Tomales Bay and through the redwood- and oak-studded San Geronimo Valley, where half their spawning grounds are in developed areas, including the towns of Forest Knolls, Lagunitas, San Geronimo and Woodacre.

Now Playing:

The fish, which can reach lengths of 35 inches and weights up to 36 pounds, swim through people’s backyards, lay eggs and die. Their progeny migrate to the ocean to become adults, returning to the watershed — which includes Devil’s Gulch, Lagunitas, San Geronimo, Nicasio and Olema creeks — at age 3 to repeat the cycle.

The number of coho spawning this year is a 10 percent improvement over their parent’s generation three years ago and a 30 percent gain since their grandparents spawned, Ettlinger said. Generational improvements like this are what conservationists want to see, especially in a species that has long been in decline along the West Coast.

But the coho are far from being out of danger, as a half-eaten carcass in the gravel made clear to Ettlinger recently during a survey of Devil’s Gulch Creek. The bite marks were from a river otter, one of a half dozen that frequent the watershed.

“It looks like this otter ate the heart and internal organs and left the rest,” Ettlinger said, as he cut off the head with a knife and dug into the bone and tissues, which he would later send to a laboratory for analysis.

“River otters wouldn’t be a problem for a healthy population, but they can do real damage to a small population.”

Sea lions and other ocean predators are among the many obstacles facing coho, which are also known as silver salmon.

At least 10,000 coho once swam through the picturesque valley and bred in tributaries that snaked all the way up the side of Mount Tamalpais. Silvers, chinook and other salmonids were once so plentiful that, legend has it, old-timers living along the creek used to spear them from decks overlooking the creek.

The fish continued to thrive despite rampant logging and construction of five major dams, starting in 1873. The spectacular runs finally came to a halt when Seeger Dam, which formed the Nicasio Reservoir, was built in 1961, wiping out the salmon population in Nicasio Creek.

All together, the dams blocked 50 percent of the historic spawning habitat in the Lagunitas watershed.

Development, drought and habitat destruction have made things worse. In 2009, only 52 coho returned to spawn in Marin’s creeks and tributaries.

It’s not an isolated problem. Coho now make up only about 1 percent of their historic population along the coasts of California and Oregon. The species in California was listed in 2005 under the U.S. Endangered Species Act.

Biologists say a full coho recovery would require the return of 2,600 fish to the Lagunitas watershed. The best winter since biologists began keeping records in 1994 was 2004-05, when 1,342 coho were counted.

The Lagunitas surveys located a total of 324 egg clusters, known as redds, since the first big rains hit the Bay Area in late November. Since a male and female produce each egg cluster, the number of fish is calculated by doubling the number of redds.

A year ago, Ettlinger counted 110 redds, meaning there were 220 coho in the creek system, but to his astonishment 30,000 young fish, known as smolts, migrated out to the ocean.

“The number was far greater than what people thought this watershed could still produce, so that was very encouraging,” Ettlinger said. “We now know that tens of thousands of young fish can survive and go out to the ocean and that restoration efforts in the watershed are working.”

Chinook salmon also have been seen in the creek, and the steelhead trout run, which peaks in February, is on track to be one of the largest on record, he said.

He credited a community-wide habitat restoration program — including school work parties — and limits on creekside development. Future generations of coho will also benefit from a just completed project by the Salmon Protection and Watershed Network, or SPAWN, to build new floodplains on a mile-long stretch of land next to Samuel P. Taylor State Park where the community of Tocaloma once stood.

Still, only about 2 percent of the coho that left for the ocean over the past two years have returned to spawn, a well-below-average survival rate.

“This is still a critically endangered species,” Ettlinger said. “Salmon are going to be impacted by climate change and ongoing development, so the population could take a nose dive again if we are not very careful.”

Seeing coho salmon The best coho and steelhead viewing areas in the Lagunitas Creek watershed: Leo T. Cronin salmon viewing area: Just off Sir Francis Drake Boulevard where the Shafter Bridge goes over Lagunitas Creek near Samuel P. Taylor State Park. Fish can also be seen from the Shafter Bridge at the Inkwells, a series of small waterfalls along San Geronimo Creek. Roy's Pools: Salmon demonstrate their jumping skills in three pools below the former dam site, on San Geronimo Valley Drive, 5 miles west of Fairfax. Samuel P. Taylor State Park campground: Coho like to lay their eggs behind the park headquarters building, just off Sir Francis Drake Boulevard.

Read More

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com. Twitter: @pfimrite