Yolo Bypass Adult Fish Passage Project

WATER COMMISSION: Update on State Water Project restoration efforts in the Delta

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One of the goals in the California Water Commission’s strategic plan directs the Commission to remain apprised of the operations and construction activities of the State Water Project, focusing on how the State Water Project adapts and responds to hydrological extremes expected with climate change, restores critical ecosystems, and addresses aging infrastructure. 

At the October meeting of the California Water Commission, Catherine McCalvin with the Department of Water Resources Office of Environmental Compliance discussed the status of projects that are underway to restore habitat for listed species associated with the State Water Project operations.

Environmental compliance drives restoration work

Ms. McCalvin began by noting that the Department of Water Resources does a lot of environmental work across the state, and the operations and maintenance of the State Water Project is one of the big drivers for that work.

The Office of Environmental Compliance is part of the Division of Environmental Services which is housed within the State Water Project and has about 200 staff including engineers, water quality specialists, scientists, ecologists, planners, and project managers.  The work done by the Office of Environmental Compliance is only part of the environmental work the Department undertakes.

The Department of Water Resources and Bureau of Reclamation coordinate operations of the State Water Project and the Central Valley Project to comply with the Endangered Species Act, which requires the agencies undertake restoration efforts to mitigate the effects of the long-term operations of the water projects on numerous federal and state protected fish species. 

There were new biological opinions issued from the National Marine Fisheries Service and the US Fish and Wildlife Service in October of 2019 which direct the actions to be taken within the Delta to mitigate the operations of both the State Water Project and the Central Valley Project, a joint responsibility between the Department and the Bureau of Reclamation.  Additionally, a new Incidental Take Permit from the California Department of Fish and Wildlife issued in March of 2020 directs the actions the Department must take to mitigate the effects of the State Water Project operations.

These regulatory documents are all very long and a little bit different; there are different requirements for DWR and for the Bureau of Reclamation, some of which they do together and some that they do separately.  The requirements are actions to minimize and mitigate effects to endangered species as well as monitor the operations and the effects on the endangered species.  Ms. McCalvin noted that this presentation will be focusing on the requirements for restoration.  She also noted that there’s a wide range of species covered that have different life histories and habitat needs so not one restoration project will necessarily work for all of them.

The Natural Resources Agency has the Eco Restore program which is an umbrella program for all the restoration work that the state is undertaking in the Delta.  She explained that the Department has other environmental restoration work that is outside of these requirements, so the work her office does is only part of the work being done under Eco Restore.

Overview of restoration requirements

Ms. McCalvin focused on the restoration programs that are intended to benefit salmon and Delta smelt:

Fish Restoration Program

The Fish Restoration Program is intended to help Delta smelt and longfin smelt by restoring 8000 acres of tidal habitat for the Delta smelt and a little over 1000 acres for long-fin smelt.  She noted that the longfin smelt is a state-listed species and is not federally protected. 

“What we’re trying to do is restore the functions and processes that promote export of nutrients and productivity to Delta food webs,” she said.  “We’re trying to create smelt food, essentially.  Thankfully, these projects can provide some floodplain habitat for salmon but that’s not the primary purpose of these, but there are some benefits for salmon.”

Yolo Bypass Program

The Yolo Bypass program is focusing on increasing floodplain habitat for the rearing of juvenile salmon as well as improving fish passage for salmon, sturgeon, and steelhead going up and down the Sacramento River.

Upper Sacramento Watershed Restoration Program

This is a new requirement from the Incidental Take Permit from the Department of Fish and Wildlife at the end of March.  The program intends to restore habitat for juvenile salmon rearing and adult fish passage.  The program will cost $20 million over the next ten years.  Ms. McCalvin said they are working out the details of the program with the Department of Fish and Wildlife so she wouldn’t be talking about this program today.

Fish restoration program

The Fish Restoration Program is to benefit the Delta smelt.  Prior to the development of the Delta for agricultural uses, the Delta was a mosaic of different wetland habitats, most of which have been lost.  The requirement is to restore about 8000 acres of tidal habitat. 

The areas shown in green are the tidal restoration projects.  There are eleven projects in various stages of development that when completed, will restore over 9000 acres of tidal marsh habitat for Delta smelt. 

Of the eleven projects, four projects totaling 1500 acres have completed construction: Tule Red in the Suisun Marsh, Flyway Farms in the Yolo Bypass, Decker Island down below Rio Vista, and Winter Island near Pittsburgh.

Currently under construction are Wings Landing in the Suisun Marsh below Fairfield, and Lower Yolo Ranch, which is next to Flyway Farms in the Yolo Bypass.

Several projects are still in the design and permitting process that are scheduled to be completed by 2023.

Ms. McCalvin described the restoration projects as ‘passive’; the construction involves changing the topography of the land so that it floods more and breaching the levees or even removing them to create an active tidal area.  There are no gates to be operated; it will be open tidal habitat.

For more information:

Yolo Bypass projects

The Yolo Bypass parallels the Sacramento River and operates as a flood bypass; when the flow in the Sacramento River gets up to about 55,000 cfs, it overtops the Fremont Weir and the floodwaters flow into the Yolo Bypass.  The bypass is about 41 miles long, three miles wide, spans almost 60,000 acres, and the capacity is about three times the flow of the Sacramento River.

Fish passage is important for both juvenile and adult salmonids.  Adult salmon and sturgeon are coming from the ocean and going up the Sacramento River to get to their spawning habitat, but instead of going up the river, they are pulled into the Yolo Bypass, and they may or may not be able to get back to the Sacramento River.  So the Department has been working on several projects to build or replace structures to improve fish passage and to create floodplain habitat for juvenile salmon.

A number of projects have already been completed: The Fremont Weir Adult Fish Passage Project, the Wallace Weir Fish Passage Rescue Facility, and some agricultural crossings have been improved.

Several projects are still in the planning phase.  One of those is the Yolo Bypass Salmonid Habitat and Fish Passage Project is more commonly known as the Big Notch project.  They are also working on another agricultural crossing improvement. The Lisbon Weir and Putah Creek projects are on hold until the Big Notch project has been completed.

Fremont Weir Adult Fish Passage Project

Prior to the construction of this project, the only fish passage through the Fremont Weir was a narrow opening in the near two-mile long structure.  It was problematic as it was hard for the fish to find and the amount of flow that went through it was often insufficient and it led to the frequent stranding of adult fish.  The new fish passage structure was constructed in 2017 and was operable in 2018; it did require some repair work in 2019. 

“This is amazing,” said Ms. McCalvin.  “There’s much more water going through it and it’s bigger and easier to find.  It’s working successfully.  We have underwater window chambers that were designed into the facility with sonar cameras that can record fish crossing through.  The sturgeon are very distinctive.  We reported quite a few sturgeon passing through that would have been otherwise trapped and would have had to be rescued, so this is functional and it’s allowed many fish to pass through wouldn’t’ have.”

Agricultural road crossing

They have several agricultural road crossing projects they have been working on.  The slide shows the Tule Canal; on the left was the prior earthen crossing that was built and rebuilt each year, and on the right is the new permanent structure.

Yolo Bypass Salmonid Habitat and Fish Passage Project (Big Notch)

The Yolo Bypass Salmonid Habitat and Fish Passage Project is a complicated project; they are in the middle of finishing permitting and completing the design work.  The final EIR/EIS has been completed.  The cost of $139 million will be shared with the Bureau of Reclamation. 

This project will construct a large gated notch in the Fremont Weir that would improve volitional passage for juvenile and adult salmon.  The project will also allow for more flows to get onto the bypass to create more floodplain habitat for juvenile salmon.  The gates will be operated at up to 6,000 cfs and between November and March.  The project will create about 140,000 acres of seasonal floodplain habitat for juvenile salmon and much more improved fish passage.

For more information:

Parting thoughts

Ms. McCalvin noted that the Department has had these projects underway since before 2010, and they are nearing the finish line.  “The big fish passage project in the Yolo Bypass, that should start construction next year and we finish our goals by the end of 2022,” she said.  “We are near the end of our marathon race which has everyone excited.  Already things are working better for the imperiled fish species and it’s so incredibly important for the recovery of these species as well as allowing for the ongoing operations of the state and federal water projects.”

There have been some challenges, she noted.  “The reason why all these projects take so long is that in part we have to get them permitted and we often have to do mitigation for these projects, so these are mitigation projects that we then have to do more mitigation for.  And also for endangered species like the garter snake and Swainson’s hawk, so the permitting can take a long time.  Designing them takes time.  There are real estate issues, we had to figure out land and access and easements and that sort of thing, and then there are local issues we have to address with respect to land use, agriculture, other concerns that can actually lead to opposition to some of these projects that we have to address.”

“So they take a little bit of time.  What’s next is that hopefully we will be done with these in a few years, and we’re hoping to apply our lessons learned to new projects, as well as we need to do that extra ten years’ worth of restoration.”

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