Salmon population booms on state’s Mokelumne River as restoration efforts pay off

A salmon attempts to jump up the fish ladder to the Mokelumne River Hatchery in Clements. A salmon attempts to jump up the fish ladder to the Mokelumne River Hatchery in Clements. Photo: Mason Trinca, Special To The Chronicle Photo: Mason Trinca, Special To The Chronicle Image 1 of / 12 Caption Close Salmon population booms on state’s Mokelumne River as restoration efforts pay off 1 / 12 Back to Gallery

CLEMENTS, San Joaquin County — Salmon crowded in and around the Mokelumne River Fish Hatchery on Thursday, offering leaping and squiggling proof of what so far is a near-record return of the big pinkish delicacies after several years of low breeding numbers.

Schoolchildren watched as the fall-run chinook squirmed on conveyor belts into the “egg take” building, where, with help from about a dozen hatchery workers, they engaged in the decidedly unromantic process of spawning the next generation.

“It’s going to be one of the top three or four years that we’ve seen since 1940,” said Jose Setka, the manager of fisheries and wildlife for the East Bay Municipal Utility District, which supplies Mokelumne River water to 1.4 million East Bay customers. “We are getting more of our fish back where they belong.”

The large number of salmon, which are inspired by the first rains of the season to swim upriver and spawn, validate the effectiveness of a series of streambed, habitat and health improvements made over the years by the utility and the California Department of Fish and Wildlife.

As of Thursday, 13,799 chinook, each weighing as much as 31 pounds, had fought their way from the ocean up the Mokelumne into the Clements facility, compared with 4,129 at this time last year. With about a month left in the season, the record of 18,000 salmon, set in 2011, is within reach.

Steelhead numbers are also way up for the second consecutive year, with more than 350 fish having returned to the hatchery — and it is still early season for the wild cousins of rainbow trout, which usually spawn through early March. Last year, a record 600 steelhead returned.

“Before last year a good year would be about 100 steelhead, but we had over 600 last year, and we’re on track to beat that this year,” said Ed Rible, a fisheries biologist for the utility district.

The Mokelumne, one of California’s major salmon- producing rivers, flows from the Sierra foothills through the Central Valley. It ultimately meets the Sacramento-San Joaquin River Delta, a crossroads for the largest annual fish migration on the West Coast.

The salmon at the hatchery, which had returned to the Mokelumne after a three-year ocean voyage, were being pushed Thursday from a holding pen onto a conveyor belt, where workers beat them over their heads with mallets, cut them open for their eggs and squeezed out the milt. The precious life-giving fluids were mixed together in a bucket.

It is a less-than-noble end for a species that dies naturally in the wild after spawning, a system that also serves to provide bears and other wildlife with a meal.

“It is exciting to see, but at the same time the fish are being killed,” said one fourth-grade boy, speaking Thursday for many of his grossed-out classmates visiting the hatchery from Stockton’s Elkhorn Elementary School. “I don’t like seeing that.”

Chinook, otherwise known as king salmon, are historically most abundant in the Sacramento River and its tributaries, making up 90 percent of the salmon caught in California.

The fall run, so named because the chinook return to their native streams in the fall to breed and lay eggs, are the ones that commercial fishermen catch, that fish markets sell and that people eat. The other two runs of salmon — in the winter and spring — need colder water higher up in the mountains and became too scarce to be fished commercially after dams blocked their habitat.

The Mokelumne River facility releases several million of the 35 million hatchery-raised chinook that are placed in California river systems and the ocean every year in an effort by the state and federal governments to safeguard their future. About 25 percent of all the chinook that are released get wire tags with numeric codes inserted in their snouts so that biologists know where they came from when they die.

The system is required as mitigation for the construction of dams used by the East Bay Municipal Utility District, including at the Camanche Reservoir in Amador, Calaveras and San Joaquin counties and the Pardee Reservoir in Amador and Calaveras counties.

Photo: Mason Trinca, Special To The Chronicle Joshua Deanfipps of the California Department of Fish and Wildlife...

The number of fish returning to the Mokelumne is a strong indication that the river system is healthy, and Setka credited a partnership with the state and federal governments to put in place a series of habitat improvement projects.

He said some 70,000 cubic yards of gravel, or about 300 dump-truck loads every year, have been added to the river near the hatchery since the late 1990s to widen the channel and create more space and better conditions for spawning.

The district has also been releasing more cold water from Lake Camanche later in the season, what Setka called “pulse flows,” to inspire the salmon to swim upriver to spawn. Closing cross-channel gates near Walnut Grove in Sacramento County north of Stockton five days a week during spawning season has also prevented Mokelumne and Sacramento salmon from getting confused and going up the wrong river, he said.

Preventing such straying is important because biologists want fish to imprint on the rivers in which they were born, like their wild counterparts.

When salmon are released, Setka said, the fingerlings are now often barged down river in underwater tanks before being “planted,” a technique that helps them imprint on the river. A specialized diet has been developed to assist the freshwater-to-seawater transfer.

Heavy rains last winter certainly helped, but the moves appear to have worked given that returns on the Sacramento River and other tributaries have been average at best compared to the Mokelumne.

“We’re trying a lot of new things” that are improving the health of the river and optimizing conditions for spawning salmon, Setka said.

The Mokelumne work is critical because fisheries biologists in California are concerned that large numbers of hatchery fish are harming the health and fertility of wild chinook. Studies over the past decade have shown that hatchery-raised fish pass on genetic defects that hamper survival of their offspring, and can even reduce the fitness of their wild relatives when they interbreed.

Only about 20 percent of the Mokelumne fish were naturally born in the river this fall.

“Ideally,” Setka said, “we would like to see more spawning in the river itself.”

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