Salmonid Restoration: Executive Summary

Executive Summary

In 2011, the Foothill Conservancy began discussing a project to explore reintroducing salmon to the Upper Mokelumne River upstream of the East Bay Municipal Utility District’s Pardee Reservoir, southwest of Jackson. Recognizing the need for EBMUD to be fully engaged in the project, Conservancy leaders met with EBMUD staff to discuss the potential for partnership.

In 2014, adult fall-run Chinook salmon returning to the Mokelumne River numbered more than 11,000 fish. That led the Conservancy to invite EBMUD and other stakeholders to participate in a collaborative effort to explore Mokelumne salmon reintroduction. A team of diverse stakeholders, later named the Mokelumne Salmonid Restoration Team, assembled and began holding meetings. They included representatives from local, state, and federal agencies; nonprofit organizations; tribes; and local business.

Over the next six years, the team narrowed its focus to fall-run Chinook salmon, took field trips, reviewed literature, and developed a draft salmon reintroduction pilot study. It also commissioned a study of the available spawning habitat upstream of Pardee Reservoir and carried out fish sampling to analyze potential disease issues that might arise with reintroduction.

In 2020, the team put its efforts on hold after learning that the California Department of Fish and Wildlife was concerned that reintroduction of salmon had the potential to spread diseases that could affect the Mokelumne River Fish Hatchery and fish downstream. Recognizing that these obstacles may be overcome by technology or facility upgrades in the future, the team has documented and archived its work so that the knowledge gained and ideas generated can be used as a new starting point for restoring iconic native Mokelumne salmon to their historical spawning habitat if the opportunity for reintroduction arises in the future.


In late 2013, the Foothill Conservancy, in partnership with the East Bay Municipal Utility District (EBMUD) and the California Sportfishing Protection Alliance (CSPA), set out to restore a missing piece of the upper Mokelumne River ecosystem: to reestablish a successfully reproducing population of Chinook Salmon and/or Central Valley Steelhead in the upper Mokelumne River upstream of Pardee Reservoir. Doing so would restore marine nutrients lost when migration corridors were cut off by large rim dams, provide climate change resilience, and bring back a key cultural and economic resource that has been missing from the region for over 100 years. While historical records indicate that spring-run Chinook Salmon and Steelhead once navigated upstream beyond the current location of Pardee Dam, there are at present no viable spring-run Chinook Salmon and a very small Steelhead run on the Mokelumne. In addition, reintroduction of Endangered Species Act (ESA) listed species into reaches of the river where they are not currently present would add layers of complexity. The fall-run of Chinook Salmon on the Mokelumne River is fairly robust, with the annual average escapement since signing the Lower Mokelumne River Joint Settlement Agreement rising to over 10,000 fish in 2019, from a pre-JSA average of 3,636. For these reasons, the group chose to focus on fall-run Chinook Salmon.


A fish barrier assessment documented historic passage of fall-run Chinook Salmon was once achievable to Bald Rock Falls, upstream of Roaring Camp. Local historians and residents also confirm spawning to this location. In 1910, upstream migration was blocked by construction of the Woodbridge Dam in the town of Lodi. It was constructed with a fishway that had limited value, and only functioned at specific flows; it was replaced in the mid-40s with a ladder that was more efficient. Construction of a state of the art fish ladder on the Woodbridge Dam was completed in 2006, providing effective and efficient upstream migration.

In 1924, construction of EBMUD’s Pardee Reservoir completely cut off upstream passage for salmon. The most recent structure that blocks migration is Camanche Dam, completed in 1964. EBMUD, in partnership with the California Department of Fish and Wildlife (CDFW), maintains the Mokelumne River Fish Hatchery at the base of Camanche Dam as mitigation for the loss of salmon spawning habitat inundated by Camanche and Pardee Reservoirs.


In addition to Foothill Conservancy, EBMUD and CSPA, the stakeholders that assembled and formed the Salmonid Restoration Team (SRT) included the California Department of Fish and Wildlife, U.S. Forest Service, U.S. Fish and Wildlife Service, Bureau of Land Management, National Marine Fisheries Service, Roaring Camp, Amador Water Agency, Calaveras County Water District, Jackson Valley Irrigation District, Pacific Gas & Electric, Calaveras Public Utilities District, California Valley Miwok Tribe, Buenavista Rancheria, Trout Unlimited, CalTrout, Delta Flyfishers, Restore the Delta and several members of the public.

The team met regularly and developed a plan to conduct a pilot project to reintroduce a small number of adult fall-run Chinook Salmon into the upper watershed. As proof of concept, the objectives of the planned pilot project were to answer the following specific and measurable questions:

  • Can a project successfully transport adult fall-run Chinook Salmon with an expectation of high survival during transport?
  • Will transported fish spawn in available habitat?
  • Where will reproduction be successful, and can the project quantify juvenile production?

As an initial step, the team wanted to establish whether there was suitable salmon habitat upstream of Pardee Reservoir. The team contracted with Cramer Fish Sciences, funded by the Firedoll Foundation and the Lower Mokelumne River Partnership, to perform a Habitat Assessment to evaluate the suitability of spawning and rearing habitat in the Upper Mokelumne River. To determine suitability and extent of habitat available for Chinook salmon, the study analyzed the following:

  • Water quality
  • Spawning gravel
  • Rearing habitat
  • Existing barriers to migration

The Habitat Assessment found that there are about 17 miles of suitable habitat that salmon would be able to access in the Upper Mokelumne River, roughly from the Middle Bar Bridge to just upstream the confluence of the North and Middle forks of the Mokelumne. The Assessment provided a framework for further development of a pilot reintroduction project.

The team consulted with EBMUD about the possibility of using surplus Mokelumne River Fish Hatchery salmon for the reintroduction. The Mokelumne River Fish Hatchery is one of the most productive Chinook Salmon fish hatcheries in California, especially considering its relatively small size and watershed area. In good salmon years, the Hatchery may bring in more adult fish than are needed to meet its production goals. The pilot project planned to transport up to 100 excess adult fall-run Chinook Salmon at a 1:1 sex ratio to the Upper Mokelumne River at the Middle Bar Bridge. Additionally, up to 100,000 eyed eggs would be placed in the Upper River in experimental incubation chambers. Standard aquaculture transport methods would be used to minimize transport stress on adults and mortality in eggs.

Released adult fish would be tracked and their nests, known as redds, would be located and monitored. Biologists would place the eyed eggs obtained from the Hatchery in an artificial egg incubation tube near the natural redds. The natural redds would be capped with a net enclosure prior to emergence so that young salmon (alevin) could be counted, and condition evaluated prior to final disposition either in the river downstream of the major dams, or to continue rearing to release size in the hatchery. Spawning success, hatch rate, and condition would be evaluated relevant to location on the river and other environmental variables. At the appropriate time, the alevin would be removed from the upper watershed and released with hatchery stock through a coordinated effort.


Permits and Support

The public, local businesses, and agencies were supportive of the pilot project; however, any reintroduction effort would require permits and support from several state and federal agencies. Although fall-run Chinook Salmon are not listed on any state or federal Endangered Species list, many of the Salmonid Restoration Team members shared the vision that this non-agency driven reintroduction of salmon would have positive ecological, economic, and cultural benefits. If fall-run Chinook Salmon can successfully reproduce in the upper Mokelumne River, it will provide insight for the management of threatened species like Central Valley Steelhead and spring-run Chinook Salmon.

The team hosted discussions with the three primary fisheries agencies that have regulatory responsibility over anadromous fish and habitat in the Central Valley, the U.S. Fish and Wildlife Service, National Marine Fisheries Service, National Oceanic Atmospheric Administration, and California Department of Fish and Wildlife (CDFW).

In any reintroduction or translocation project, whether it is Bighorn Sheep or, in this case, salmon, it is important to determine if there is any risk of disease transmission between the reintroduced species and the wildlife in the habitat. The SRT consulted with the CDFW and USFWS pathologists and hosted a pathology risk assessment to determine if the risks were manageable. This risk assessment, identified two infectious diseases that create the majority of the risk associated with a reintroduction effort in the Mokelumne River.

Infectious Hematopoietic Necrosis Virus (IHN)

Infectious Hematopoietic Necrosis Virus (IHN) is the primary disease of concern. It currently exists in Chinook Salmon downstream of Camanche Dam. Any reintroduction of salmon upstream of Pardee Reservoir would potentially transport infected fish upstream of the dams, thereby introducing the disease into water upstream, where it currently does not exist. The Mokelumne River Fish Hatchery gets its water supply from upstream of Camanche Dam, and the water is filtered through sand filters and UV filtration before being used for hatchery operations. Only a portion of the water supply that is used in the incubation building is filtered. The raceway water supply is unfiltered. If infected fish upstream of the hatchery were to die or transmit the disease to another host, the disease could survive and persist in the water column and infect the water supply used for the hatchery. IHN can easily proliferate in a hatchery setting because of the density of the fish in the hatchery raceways.

Whirling Disease

Another pathology concern for the reintroduction project is Whirling Disease. Whirling Disease has been present in Rainbow Trout upstream of Pardee Reservoir. Chinook Salmon brought to the Upper Mokelumne River could encounter fish infected with Whirling Disease and other biota that are part of the disease’s life cycle. As salmon tend to want to move up and downstream, there is a possibility that an infected salmon from upstream could pass through the dams and into the lower river, introducing Whirling Disease below Pardee Dam. Steelhead and resident Rainbow Trout in the lower river would be particularly susceptible to mortality from Whirling Disease.

CDFW staff informed SRT representatives that a more robust water treatment facility at the Mokelumne River Fish Hatchery would be required before CDFW would consider support for a reintroduction program. An ozone treatment facility, which is very costly and requires a great deal of space, would be acceptable as mitigation.

Current Status

Due to the risk of disease transmission and the expense and space requirements of an appropriate filtration and treatment facility for the hatchery, the Salmonid Restoration Team has made the tough decision to place the pilot reintroduction project on hold until these significant concerns are worked out.

The relationships formed during the length of this project have created traction for a broader collaboration to address Mokelumne River related projects, issues, and coordination during semi-annual Mokelumne River symposia.

Foothill Conservancy and the SRT would like to extend thanks to the organizations and individuals who contributed to this effort:

  • Rick Breeze-Martin of Breeze-Martin Consulting
  • Marie Rainwater of Rainwater and Associates
  • The Hewlett Foundation for grant funding to the California Hydropower Reform Coalition
  • The Firedoll Foundation for its support of the Upper Mokelumne River Habitat Assessment
  • Tribes: California Valley Miwok Tribe, Buena Vista Rancheria of Mi-Wuk Indians
  • Nongovernmental organizations: Foothill Conservancy, California Sportfishing Protection Alliance, Trout Unlimited, Delta Fly Fishers, Restore the Delta, Amador Flyfishers, CalTrout
  • Water agencies and utilities: East Bay Municipal Utility District, PG&E, Calaveras Public Utility District, Amador Water Agency, Calaveras County Water District
  • State and federal agencies: U.S. Forest Service, Bureau of Land Management, U.S. Fish and Wildlife Service, California Department of Fish and Wildlife, National Marine Fisheries Service, State Water Resources Control Board

Reference Documents

2019 Lower Mokelumne River Federal Energy Regulatory Commision project report

Boyd Verifying Reported Historical Natural Barriers to the Upstream Migration of Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (Oncorhynchus mykiss) in the Mokelumne River Watershed

Cramer Fish Sciences Salmonid Habitat Analysis on the Upper Mokelumne River

Lower Mokelumne River EBMUD Joint Settlement Agreement

Yoshiyama et al. Historical and Present Distribution of Chinook Salmon in the Central Valley Drainage of California

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Leslie Smith, Sutter Creek, CA: Raised in Washington State, Leslie is a happy California transplant having moved to Sunny Sutter Creek full time in 2020. As a nascent fly fisher and lifelong skier, she is committed to the natural environment and brings extensive organizational and finance experience to the board from a nearly 40 year career in banking.