CENTRAL VALLEY FLOOD PROTECTION BOARD: Update on the San Joaquin River Restoration Program

Historically, the San Joaquin River has supported large chinook salmon populations. However, since the Bureau of Reclamation’s Friant Dam on the San Joaquin River became fully operational in the 1940s, much of the river’s water has been diverted from the river for agricultural uses.  This has resulted in about 60 miles of the river bed going dry in most years and the river no longer being able to support salmon populations.

In 1988, the Natural Resources Defense Council (NRDC) and other conservation and fishing groups sued the Bureau of Reclamation and the Friant Division contractors of the Central Valley Project (CVP) in the case, Natural Resources Defense Council v. Rodgers. The judge ruled that operation of Friant Dam violates state law because of its destruction of downstream fisheries.  Faced with mounting legal fees, uncertainty, and the possibility of dramatic cuts to water diversions, the parties reached a settlement in 2006 that called for releases of water from Friant Dam to restore fisheries, as well as efforts to mitigate those reductions in deliveries to water users that are a result of restoration flows.  Since that time, the San Joaquin River Restoration Project has been working towards achieving those objectives.

At the December meeting of the Central Valley Flood Protection Board, Elizabeth Vasquez from the Bureau of Reclamation and Paul Romero from the Department of Water Resources provided an update on the San Joaquin River Restoration Program.

Elizabeth Vasquez began with some background on the program’s recent progress.  In May of 2018, the program completed a Funding Constrained Framework, which focused on implementing the program, given a more limited future funding stream than previously anticipated.  The framework reset the goals for the near-term to align with the likely funding sources.

The main focus of the program are the barriers to fish passage for salmon from Friant Dam to the ocean and back again.  There are three key barriers:  the East Side Bypass Control Structure which is in the flood bypass; Sack Dam, which is the intake for Arroyo Canal for Henry Miller irrigation system; and Mendota Dam which controls Mendota Pool.

The program also needs to ensure enough habitat for the fish when they return to complete their life cycle, so they are also focusing on increasing safe channel capacity for fish and for the surrounding neighbors along the river, so they are working on seepage and levee stability projects to achieve up to 2,500 cfs capacity in all reaches.  Currently, they are working on levees in Reach O and Reach 2B which includes about 10 miles of levee right upstream of Mendota Pool.

There are other things called for in the Funding Constrained Framework, such as support for the conservation facility which is a research and hatchery facility to bring back the population as well as the water management work with Friant water users, but for this update, they will be focusing on the fish and the levee work as these are the two goals that are important to the work of the Central Valley Flood Protection Board.

Ms. Vasquez presented a map of the projects, noting that the fish have to move from the below Friant Dam on the far right of the map, past Mendota Pool, past Sack Dam, through the East Side bypass, and into Reach 5, which is the confluence of the Merced and the San Joaquin, on the far left of the map.

Thinking about channel capacity, we have to deal with the seepage with the potential water that could affect the nearby orchards as well as the levee stability in this full section as well to make sure that it safely passes 2500 cfs,” she said.  “Part of this river was dry for 60 years and so putting that water back has some real significant effects to the communities and the institutions that work in this part of the region.  So that’s why 2500 cfs doesn’t sound that big for most systems, but that’s why what’s such a big deal here.”


The San Joaquin Restoration Program had great success with reintroducing the salmon to the river.  Adult salmon came up the river and were captured beneath the East Side Bypass Control Structure; several fish made it past that structure and up to Sack Dam during the floods in late spring of last year.  Those fish were put in trucks and taken to Reach 1 so they could spawn, create redds, and complete their life cycle.

When Program staff went to count the redds, they were surprised to find more redds than fish that they put in the trucks.

Because of the significant flooding in the late part of last spring, we had more spring run up in Reach 1 than we had actually transported, so there were adult fish that had made it through the gauntlet of those fish barriers as well as the flood system to reach Reach 1 and naturally spawn,” said Ms. Vasquez.  “There were fish that made the full migration without our intervention.  We actually have documented 209 spring run redds at this point.”

They also counted carcasses as well, and there were 286 carcasses.   Now they’re counting the babies.

We are in the part of the season where we are looking at screw trap data and the juvenile fish that have made it out of the redds and into the river and are trying to then go back to the ocean,” she said.  “We are in the process of getting some of that data.  It’s not complete, but we have over 9000 juvenile fish counted at this point from the screw trap data.  We’ll see where we end at the end of the year, but we were definitely pleased with that.  It definitely proved up some of the science that had said that there could be naturally reproducing fish in the system.”


The keystone project in the funding constrained framework is the Mendota Pool Bypass and Reach 2B improvements project.  The top picture on the slide is of the physical model of the control structure of the compact bypass that will be the headworks of the bypass around Mendota Dam that was used in the development of the design.

The program has also been in active land acquisition around Mendota Pool, purchasing a piece of land on the shore of the Mendota Pool from the MLT Corporation.  When they took over the property, they realized there were some levees on the pool that had not been maintained at a level they would have expected and so there was a 30-foot patch that had to be fixed on the levee before they could proceed with the full project.  The MLT property will be the property that the physical project is constructed on.


There are three elements to the East Side Bypass Improvement Project:  Removing the weirs at the Merced National Wildlife Refuge, levee improvements to the East Side Bypass to help increase flows up to 2500 cfs, and a fish passage project at the East Side Bypass Control Structure.

Removal of weirs at the Merced National Wildlife Refuge: The Bureau of Reclamation has been working with the Merced National Wildlife Refuge who historically has had two weirs to bypass water from the river into the duck ponds.  Reclamation developed an alternative water supply for the refuge and removed the first of those weirs last year; they will be removing the second weir this summer when they get past flood season.

Levee improvements to the East Side Bypass:  There is about a two mile stretch of the bypass levees that need to be improved to handle the flows up to 2500 cfs.  They recently took potential contractors through the project and there was a lot of interest; they hope to have a contractor selected in February and be in construction late spring to early summer for this project.

This project has a two year construction window; it’s to be completed by the end of 2021, but if there are favorable conditions, they could potentially complete the project by the end of 2020.

Fish passage at the East Side Bypass Control Structure:  The control structure is barrier to chinook salmon as well as other native fish; most of the impact is during lower flows.  The photo on the upper right shows the significant jump at the upstream side of the structure, and the bottom left shows the significant jump at the sill at the bottom end of the structure, and then the spacing of the baffle boxes on the bottom right photo shows the small space that also causes migration problems for some of the larger fish.

DWR is designing a rock ramp fishway about 380 feet long with a low flow channel in it that will allow fish to swim through the structure itself without any significant jumps.  This project will also require some modifications to the control structure itself.

The modifications to the structure has caused some concern with the levee district, so DWR met with them with some initial designs.  Based on the levee district’s concerns, DWR made improvements to the design that are anticipated to address all of their concerns brought forward so far.   The levee district’s concern was mainly the stability of the structure from the proposed modifications, so one of the major improvements will be to install a sheet pile wall along the downstream end of the structure to reduce any erosion and potential undermining of the structure.  They will also only remove half of the baffle blocks, which is not ideal for fish but will continue to allow those blocks to dissipate energy from significant flood effects.  They also made changes to the engineered streambed material and other improvements to help the hydraulics as well as prevent any scour that would happen downstream that could potentially undermine the structure itself.

We do feel like have a good design that would address the levee district’s concern of structure stability,” said Mr. Romero.

One of the board members asked if subsidence was an issue or concern in this area.  Mr. Romero said that subsidence is not really an issue in this particular area, and if there was subsidence, it would make the flows deeper which would actually improve fish passage.  Most of the subsidence is significantly upstream in the Chowchilla Bypass and the upper end of the East Side Bypass.

DWR has done a lot of hydraulic modeling, and based on that analysis, they are confident they have a stable control structure.  Flows have been modeled up to 12,000 cfs which is 4,000 cfs more than the design flow for the structure, and considering how the gate would be operated, the analysis shows the rock structure would be stable under any flow under most potential gate operations.

There’s really a small window of gate operations that would actually move rock significantly, but we believe that those gate scenarios of probably unrealistic and it’s very likely that the levee district will not operate the gates in that manner,” said Mr. Romero.  “In fact, it’s our understanding that over the 50 years of operation of this structure, the gates have only been used one time in the 50 years, so we feel pretty comfortable that we’re going to have a very stable rock ramp without a lot of movement of the rock.  However, there is potential for rock movement so DWR is working with Reclamation right now to develop a long-term agreement for maintaining the rock ramp.”

Timeline is the challenge.  They are hoping to be in construction in 2020, but in order for that to happen, they would have to have all their permits by the end of January or February at the latest.  They have all of their permits in hand except for the Flood Board Encroachment Permit, so they will be working with flood board staff to get the application in promptly.

We need that to get an advertisement in March which will allow us to be in construction late April 2020, early summer of early 2020, to allow us to complete construction by the end of 2020,” Mr. Romero said.  “If we can’t get that done, then we’ll push our project out another year and be in construction in spring or summer of 2021.”

Mr. Romero said that DWR has been working closely with the levee district to understand the maintenance strategies for wet channels.  Previously, the levee district had done maintenance when the channel was dry, but as the restoration program gets underway, there will be a continuously wet channel all year long which will necessitate some changes to their maintenance procedures and possibly new types of maintenance equipment.  They are working to identify what the costs are, what types of maintenance activities are necessary, and to identify possible funding sources.

However, there is an immediate need to clean the trash rack on the San Joaquin River control structure as this debris could be a fish barrier to all the outmigrating juvenile salmon that are coming out of the system.  The restoration program is working closely with Board staff and the levee district to get this structure maintained prior to the salmon migration.

During the discussion period, a Board member asked , if the he San Joaquin River Restoration Project is to improve the San Joaquin River and restore flows along the San Joaquin River, why is this work being done on the East Side Bypass?  How does that relate to the restoration project?

Within the settlement is a routing decision section, which talks about where the restoration flows would ultimately be routed on the river,” answered Ms. Vasquez.  “Right now, the section of river that would connect Reach 5 to Reach 3, which is just upstream of the confluence between Sand Slough and the bypass system, has been closed for many, many years.  We had the advantage of being able to come back to channels that had been in flood situation and maintained to some degree, but the 4B channel had not been used in a very, very long time.  The headworks have been removed, there was no capacity at all for flow to move through there, and there are actually houses within the levees.  That project, the reopening of 4B, was looked to be about $1 billion in itself, and so the decision was made in the constrained framework that we would focus on the viable path for fish and flows, and right now, the only path for both flows and fish from the San Joaquin is through the East Side Bypass and down into the San Joaquin River, past the lower East Side Bypass.”

There’s no way for the river water to be completely taken off the bypass system because there’s no route,” she said.  “Ultimately, there’s still that routing decision to be made.  The settlement envisioned at least some of the river water going into the 4B reach, but there was a calculation made in the most recent funding constrained framework that there wasn’t the funding to support opening that channel right now.

There was some further discussion about how this is going to work.  One board member pointed out that we can route low flows pretty easily, but the high flows at some point are not going to be possible to be routed; they are going to route themselves.

That’s why the rock ramp isn’t stranded dollars,” said Mr. Romero.  “Because even if the program at some point chooses to put all restoration flows in the main stem of the San Joaquin, during a flood event, flows are going to be in both stretches so fish are going to have to pass both structures.”


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