The Mokelumne River. Photo credit: EBMUD

FEATURE: The Magic of the Mokelumne: How such a small river produces so many salmon

Written by Robin Meadows for Maven’s Notebook

Salmon returns have risen dramatically in the Mokelumne River.

The Mokelumne River is on the modest side, running 95 miles from the Sierra Nevada and accounting for less than 3% of flows into the Sacramento-San Joaquin River Delta. But the river’s impact on salmon is outsized and the latest figures really made a splash. The California Department of Fish and Wildlife (CDFW) puts the Mokelumne’s contribution to the 2022 commercial ocean salmon fishery at a whopping 51% of the total for hatcheries.

“The Mokelumne is the single biggest contributor to the catch,” says John McManus, president of the Golden State Salmon Association. “It’s huge.”

The Mokelumne River Hatchery’s record is even more impressive given that it raises just a fraction of the young salmon—about 6 million of the 32 million total—produced by Central Valley hatcheries each year.

“It’s punching above its weight,” McManus says. “Why? What’s the magic with the Mokelumne?”

McManus credits the partnership between the CDFW hatchery and a dedicated team of biologists at the East Bay Municipal Utility District (EBMUD), which gets water from and manages part of the Mokelumne River.

Caring for hatchery fish

The Mokelumne River Hatchery was constructed in 1963 to mitigate for the spawning habitat lost when EBMUD built Camanche Dam, creating a second reservoir downstream of Pardee Reservoir in the Sierra Nevada foothills. A 2002 hatchery rebuild optimized conditions for raising salmon from eggs to three-inch smolts, adding water chillers, sediment filters, and UV to kill disease-causing microorganisms.

“Up to 96% of the eggs survive to the smolt stage,” says Michelle Workman, who leads EBMUD’s fish biology team. “That’s way higher than any other hatchery.”

Salmon eggs beginning to hatch. Photo: CDFW

The hatchery upgrades also help young salmon withstand the transition from what McManus describes as a life of relative luxury to the wild, where they suddenly face surviving on their own. The journey is stressful from the start: smolts are trucked to the Delta and shot out of a tube into net pens.

“It’s kind of traumatic,” Workman says.

Net pens keep smolts from being immediately snapped up by striped bass and other predators. And smolt survival after leaving the safety of these enclosures is also high, thanks to data-driven refinements. Net pens are placed where the Mokelumne meets the San Joaquin River, which is far enough into the Delta both to keep smolts from being sucked south by the pumps and to bypass the worst of the predators. In addition, net pen releases are staggered, with two days on and two days off, to keep predators from learning where to come for an easy meal.

“Striped bass are smart but we’re smarter,” Workman says. “They have a very short memory.”

Lower Mokelumne spawners

EBMUD biologists are also helping wild spawning salmon in the Mokelumne. The team spent the last couple of decades working with private landowners to restore gravel spawning grounds downstream of Camanche Dam. Landowners are often happy to grant river access for adding gravel because they love seeing the salmon, making it a relatively easy sell.

Now the team is working with landowners to restore the floodplains that make perfect nurseries for little fish. This is a harder sell because it entails a conservation easement on private land. However, floodplains can also benefit landowners by speeding groundwater replenishment.

EBMUD also works with private landowners to install screens that keep young ocean-bound salmon out of water diversion intakes. John Vink, a farmer in the Central Valley, signed up for a fish screen after chatting with biologists who came to check for juvenile salmon in the rotary screw trap—or fish counter, as he aptly calls it—he had allowed them to install on the property.

Vink uses Mokelumne water to irrigate nearly 300 acres of walnuts in Lockeford, a town just east of Lodi. “We’re right on the river,” he says, adding that he enjoys watching salmon coming upstream to spawn. The screen on his diversion intake, which is self cleaning, has been in place since 2021.

“We used to find little fish in the pump filters and now we don’t,” Vink says. “I like helping them out.” He also likes that the screens catch debris so he doesn’t have to clean the filters in front of the pumps anymore. “They’re helping us out too.”

Another key to the success of wild-born salmon is cool water, especially in the fall when the Mokelumne population returns to spawn. “For Chinook salmon, eggs need the coldest water  and it’s really hard to have enough in the summer in the Central Valley,” Workman says.

Salmon swimming up the Mokelumne River to spawn. Photo by EBMUD.

In the fall of 2015, deep into a severe drought, EBMUD came up with an out-of-the-box solution to supplying the cold water that salmon depend on. Regulations require Camanche Reservoir to maintain a store of cold water, but temperatures stay low much later into the year in Pardee Reservoir because it is much deeper.

So the team proposed drawing cold water from Camanche Reservoir through the summer and then replenishing it with large pulses from Pardee Reservoir in the fall. “Cold water is denser so it sinks and stays together as it flows through Camanche,” Workman says. “It’s about 1⁰C colder compared to similar years, which doesn’t sound like much but makes a difference in egg survival.”

She’s grateful for the trust of EBMUD’s resource agency partners. “They went out on a limb and tried it during drought because we were desperate.”

Upper Mokelumne spawning habitat

As good as the Mokelumne is for salmon, it could be even better. Workman hopes to restore these fish to their historical spawning grounds upstream of the reservoirs. This effort was initiated in 2011 by the Foothill Conservancy, an environmental nonprofit in Amador and Calaveras counties. The Conservancy then joined forces with EBMUD and other groups, including the California Sportfishing Protection Alliance, state and federal agencies, and local Miwok tribes, to form a salmon restoration working group.

“We wanted to get a key piece of the watershed ecology back,” recalls Katherine Evatt. She and her husband Pete Bell helped found the Foothill Conservancy and live near the Amador County town of Volcano. “Wildlife eat salmon carcasses, and forest plants get nutrients from carcasses that are dragged up from the river—everything in the watershed had salmon in it.”

Surveying the Upper Mokelumne for salmon spawning habitat. Photo by Foothill Conservancy.

In 2019 the restoration working group commissioned a survey that identified more than 13 miles of potential salmon spawning and rearing grounds in the Upper Mokelumne. “It was really exciting to find there was suitable salmon spawning habitat,” Evatt says. Next the group planned a small pilot reintroduction to test how well salmon would actually do once in the Upper Mokelumne.

The pilot required trucking adults from the lower to the upper part of the river, but this turned out to be a stumbling block. A pathology study showed that many salmon in the lower Mokelumne were infected with pathogens, and the state didn’t want to risk reintroducing diseases along with the fish.

“CDFW was really worried that the pathogens would get into the hatchery and said no,” Evatt says. “The project is in a limbo hold right now.”

Workman hasn’t given up on returning salmon to the Upper Mokelumne, however. She’s exploring the feasibility of disinfecting the hatchery’s water supply with ozone, which kills pathogens including viruses. While ozone treatment is quite costly, Workman sees it as a hedge against future warming. “We support moving fish above the reservoirs as a climate change strategy during drought,” she says.

This would be a dream come true for Evatt and her husband, who spent countless hours commuting—by car, Amtrak and Bay Area Rapid Transit—between their home and EBMUD’s offices in Oakland in hopes of seeing salmon in the Upper Mokelumne once again. “We love this project,” Evatt says. “We’re just waiting for the right time to bring it back.”

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