Tuolumne River salmon habitat enhanced

By Christine Souza 

Partnering with fisheries agencies, Central Valley irrigation districts, whose water users face flow reductions under the state’s Bay-Delta water quality plan, are enhancing habitat along the Tuolumne River to improve conditions for struggling fish.

“The overarching goal of this project is to restore the river channel to provide spawning and rearing habitat that increase the produc tivity of chinook salmon and rainbow trout,” said Michael Cooke, Turlock Irrigation District director of water resources and regulatory affairs. “We hope to see salmon spawning on the river this year.”

The $7.8 million habitat restoration project, happening down river from the La Grange Dam in Stanislaus County, includes a $5.5 million grant from the California Department of Fish and Wildlife and $2.3 million invested by TID, Modesto Irrigation District and the San Francisco Public Utilities Commission.

“The design of the project provides opportunities for spawning for adults but also ideal conditions for egg incubation and salmon rearing,” Cooke said. “There’s some additional flood plain that’s been created, which results in an increase in the food that juvenile salmon rely on, like aquatic insects and small invertebrates.”

The project unveiled in September adds 8 acres of main-stem restoration, 3 acres of flood-plain habitat and 50,000 cubic yards of spawning gravel. These actions, Cooke said, are expected to produce a five-fold increase in salmon habitat along the lower Tuolumne River.

As part of the project, crews have excavated more than 200,000 cubic yards of gravel from the flood plain, Cooke said. Gravel was washed and sorted. The process yielded 53,000 cubic yards of gravel for placement into the river. He said gravel was removed during the late 19th century and the early 20th century as the river was dredged during the Gold Rush.

“Even though most of that gravel was removed, this stretch of the river still remained the predominant spawning reach for salmonid species,” he said. “Over time, the number of opportunities for spawning has decreased as high-flow events washed that gravel downstream. We are augmenting it and putting it back.”

Pat Maloney, aquatic biologist for TID, compared the spot along the river where work is taking place to a shoebox, with vertical sides and a flat bottom, which he said are not conducive to spawning or juvenile rearing.

“For the most part, (salmon) are going to the coldest, hyper-oxygenated water, which is coming out of the dam, so the majority of adults that come here to spawn are moving past this location,” he said. “They’re headed upstream to find a gravel location where they can lay their eggs.”

With newly placed gravel, Maloney said, there are now many locations conducive for salmon to lay eggs.

“The transformation of the river from a shoebox to a riffle-run pool is just phenomenal,” he said. “The velocity increase just by the placement of alternating gravel bars means the river actually has more sinuosity, so more like a snake rather than a straight shot. It’s obvious to me that it’s going to work really well.”

The project also includes placing boulders and more than 60 almond trees and some cottonwoods and oaks into the river to add diversity and provide fish places to hide from predators. He said the partially submerged trees will provide refuge for juvenile fish and food for juvenile salmon and trout.

“A lot of this water was moving very slowly, which allows predators to just sit and wait for juvenile fish to come downstream, so by increasing the velocity and reducing the depth, we’ve reduced predator habitat significantly in this reach,” Maloney said.

Julie Vance, regional manager for the CDFW Central Region, said the Tuolumne River—the largest tributary to the San Joaquin River—and other San Joaquin River tributaries help support a diversity of species and habitats.

“Like many rivers in California, we’ve had an overall decline in salmon recently and a lot of fluctuations,” she said. “The Tuolumne (River) salmon escapement went from over 40,000 in the mid-1980s to as low as 186 in 2021.”

The Tuolumne River has the lowest salmon escapement rate of the San Joaquin River tributaries, she added.

While many factors affect the decline in the salmon population, Vance said the loss of spawning and rearing habitat is something that project partners seek to address.

“This project is in a part of the river that has the best water temperature for fall-run salmon and steelhead,” she said. “The project will greatly increase spawning and rearing habitats.”

The habitat restoration work is the first project developed under an agreement between the three utilities and the U.S. Fish and Wildlife Service and is part of the Healthy Rivers and Landscapes Program. The Healthy Rivers approach, also known as “voluntary agreements,” is included as an alternative implementation action in the state’s updated Bay-Delta plan.

Adopted in December 2018 by the California State Water Resources Control Board, the Bay-Delta plan requires affected water users to leave unimpaired flows of 30% to 50% in each of three San Joaquin River tributaries—the Tuolumne, Stanislaus and Merced rivers.

TID and MID, which jointly operate Don Pedro Reservoir on the Tuolumne River, signed an agreement in 2022 to work with the state to advance a voluntary agreement for the Tuolumne River.

MID General Manager Jimi Netniss said the districts are investing $80 million during the next eight years for many projects designed for the Tuolumne River and its flood plain from Don Pedro Reservoir downstream to the San Joaquin River to improve conditions for fish and other aquatic species.

“By 2030, the goal is to develop 77 acres of suitable salmon-rearing and flood plain habitat and add approximately 100,000 tons of gravel in specific areas of the river for optimal salmon spawning and rearing,” he said. “We continue to focus on habitat restoration, coupled with more water at the right times to improve the health and long-term recovery of the fishery.”

The effort, Netniss said, “builds on decades of collaborative stewardship along the Tuolumne River, with Tuolumne River-specific science.”

MID board member Larry Byrd, who for 40 years has raised cattle on property that borders a stretch of the Tuolumne River, said, “I have skin in the game too because I’m a rancher and a farmer, but I’m also an environmentalist.

“With this project, we’re optimistic that it is going to restore chinook salmon, and we’ll still have water availability for the farmers, the city of Modesto and the city of Turlock,” Byrd said, adding that the shared resource has to work for all uses. “We have to restore it, and I want to see the chinook salmon come back.”

Construction for the initial habitat restoration project began in June and is expected to be complete by summer of 2026.

(Christine Souza is an assistant editor of Ag Alert. She may be contacted at csouza@cfbf.com.)