FLOOD BOARD: Update on the San Joaquin River Restoration Program

Prior to the completion of Friant Dam in 1942, the San Joaquin River supported the southernmost populations of Central Valley spring-run Chinook salmon and fall-run Chinook salmon, where hundreds of thousands of Chinook used to return each year. After the construction of Friant Dam, parts of the San Joaquin River began to run dry as more water was diverted into canals for agricultural irrigation, which disconnected the salmon from their habitat.  Eventually they were eliminated from the upper San Joaquin River and while the tributaries of the lower San Joaquin River still support populations of fall-run Chinook salmon, spring-run Chinook salmon have been absent from the mainstem San Joaquin River for over 60 years.

In 1988, environmental groups sued the Bureau of Reclamation on the basis that the Federal government was in violation of California Fish and Game code 5937, because the dam did not direct enough water into the San Joaquin River to keep fish populations below the dam in good condition, resulting in the local extinction of the spring-run Chinook salmon. The trial went on for more than 18 years until a settlement was reached in 2006.  The settlement was approved by the federal court in 2006 and in 2009, the San Joaquin River Restoration Settlement Act was passed to implement the terms of the settlement.

At the October meeting of the Central Valley Flood Protection Board, Elizabeth Vasquez, Deputy Program Manager for the San Joaquin River Restoration Program for the Bureau of Reclamation and Paul Romero, Supervising Engineer with DWR’s South Central Region Office updated the board members on the ongoing implementation of the program.


The San Joaquin River Restoration Program (SJRRP) is a long-term collaborative program to restore flows in the San Joaquin River from Friant Dam to the confluence of the Merced River.

The two primary goals of the program are:

  1. To restore and maintain fish populations in “good condition” in the main stem of the San Joaquin River below Friant Dam to the confluence of the Merced River, including naturally reproducing and self-sustaining populations of salmon and other fish.
  2. To reduce or avoid adverse water supply impacts to all of the Friant Division long-term contractors that may result from the Interim Flows and Restoration Flows provided for in the Settlement.

The settling parties are a compilation of different agencies and private interests that included the NRDC, the federal government, and the Friant Water Authority.  There is an MOU with the Department of Water Resources and the Department of Fish and Wildlife regarding the implementation of the restoration program.

Over the past decade, the restoration program has been working to reconnect the river and have consistent flow in the section that went dry annually and to bring back a race of spring-run chinook salmon. 

Ms. Vasquez noted the substantial progress.  “We have fish populations that have returned for the last three years,” she said.  “We have had spawning and we have had emergence of juvenile fish in the river that have made their way to the ocean and come back.  We have also have been working with the stakeholders and with our own agencies to get the channel capacity that we need to maintain flow in this river year around and so we do have flow connectivity 365 days a year at this point.”


In 2018, the program took a hard look at the work remaining to be done and the likely funding sources for that work and developed the funding-constrained framework implementation plan.

The goal set for Stage 1 of the funding-constrained framework is to begin the reestablishment of spring-run and fall-run Chinook salmon through the establishment of volitional fish passage, sufficient flows to manage temperatures, and provide for the basic habitat needs of the species.

So much of the work being done is to create sufficient fish passage at key large barriers in the system.  This involves passage around Mendota Dam and Sack Dam, as well as in the East Side Bypass.  They are also working towards building the channel capacity to be able to have consistent flows in the river of 2500 cfs.  Ms. Vasquez acknowledged they were currently in the 200 cfs range, so definitely more work needs to be done there.

The map on the slide shows the restoration area.  Friant is on the far lower right of the map and the confluence of the San Joaquin and Merced Rivers is in the upper left corner.  The river miles in the restoration area has been divided into five reaches with Reach 1 beginning at Friant Dam and Reach 5 ending at the confluence of the Merced River.

Currently, Reclamation’s work is focused on a large fish passage bypass and fish screen project at the Mendota Pool, and another at Sack Dam and Arroyo Canal which is the last big diversion for the state contractors on the system.  The areas shaded in purple are where they are working to get the 2500 cfs capacity through the enitre system.


Ms. Vasquez then presented a slide showing the numbers for salmon at various points in their life cycle.  From August to September, they are doing redd surveys; the lower-left corner shows the numbers for the last three years.  When the powerpoint was turned in for the meeting two weeks ago, there were 17 redds, but that number has grown to 53 and is ultimately expected to be over 100.  She explained the variation in numbers of redds each year is due to the water conditions; it was drier in 2019 than in 2018. 

In the winter and spring, the fish emerge from the redds, and as they outmigrate to the ocean, they are caught and counted as they go through the screw traps.  They then return as adults to spawn in the river and start the cycle anew.  Many of those adults are trucked back to reach 1 where the spawning habitat is due to fish barriers, so that has been a focus with the constrained framework.


One of the projects in the planning stages is at Arroyo Canal and Sack Dam.  Arroyo Canal is the diversion canal and Sack Dam is a small low-head dam that pushes the water into the irrigation canal.  The slide shows the proposed nature-like fish bypass for the fish to swim around Sack Dam and a “V” screen to keep fish from being diverted into the Arroyo Canal itself.


The Mendota Pool and Reach 2B Improvements Project is similar to the Sack Dam project, but the fish bypass is larger.  The project involves building ¾ mile bypass that would connect Reach 2B to the portion of river downstream of Mendota Dam, and then a double “V” screen that can pass almost 2000 cfs of flow into Mendota Pool when needed.

Ms. Vasquez noted that this is the program’s biggest project and they have spent quite a bit of time on engineering, which included building a physical model of the headworks for the bypass itself.  The program has purchased land in the area to construct all the features. 

We needed to work with our engineering firms keep the engineering coming together in a way that’s incremental and will have a durable, a good project that will ultimately be able to be a part of a good operation at Mendota Pool,” she said.  “First and foremost, this facility cannot damage our contractual relationship to deliver water and it’s a big part of this project is to make sure we bring this project together in a way that won’t affect our water users.”

She also noted that the City of Mendota is working on the Mowry Bridge which will ultimately be the main entrance and haul route for much of the levee setback project.


Next, Paul Romero, Supervising Engineer with DWR’s Fresno Office discussed the work to achieve fish passage and capacity for restoration flows of 2500 cfs on the East Side Bypass.

The East Side Bypass Improvement Project has two fish passage elements and a levee improvement element to a stretch of the bypass in Merced County.  The project is a joint effort between the Bureau of Reclamation and the Department of Water Resources.

Merced Refuge Weir Project

The first project is a Bureau of Reclamation Project to remove two refuge weirs that are in the East Side Bypass.  In 2019, the lower weir was removed.  The upper weir will be removed in 2021.

Reach O Levee Improvement

The Reach O Levee Improvement Project is a Department of Resources project to install a two-mile slurry wall to improve seepage and stability issues in probably one of the weakest levees in the East Side Bypass.  Construction started in the spring of 2020.  Another element of the project was to construct six drainage culverts in to improve interior drainage.  The project is essentially completed at this point, with the exception of a special gate that had to be fabricated and will be installed next month.

This is just a great project not only because it’s going to allow the restoration program to increase restoration flows in the area but it also really strengthens a levee that was probably the weakest in the system that will now perform much better during flood conditions,” said Mr. Romero.

East Side Bypass Control Structure

The East Side Bypass Control Structure is a barrier for fish passage for three reasons:

  • There is a sill at the end of the structure that requires fish to jump over it and during low flows, the fish can’t make it over the sill.
  • Baffle blocks cause issues when the fish do get into the structure.
  • The flashboards at the upstream side of the structure are another barrier that fish are required to jump, which is they can’t do during low flows.

The Department of Water Resources has designed s rock ramp downstream of the structure that will allow salmon and other fish to swim the structure and not have to jump over the barriers.

There are also modifications to the control structure itself; the Department has been working through several iterations of the design to address the concerns of the Local Maintaining Agency.  Since the last briefing, they have reduced the changes to the downstream sill as well as leaving some of the baffle blocks on the outer bays to provide better hydraulics during a flood event.

We’re just waiting for comments back from the LMA and we’re hoping to get those soon so we can further our project to get it into construction,” said Mr. Romero.  “Unfortunately, we’ve missed our window of opportunity for constructing in 2021.  We had a very narrow window and it doesn’t look like we’re going to be able to meet that so we’re pushing our construction back to 2022.  We’re hoping by the end of this year to finalize our design, finish our permitting early 2021, and then advertise, start, and complete construction of the fish passage project by the end of 2022.”


The San Joaquin River Control Structure is on the San Joaquin River about 50 miles downstream of Friant Dam that they are working to improve fish passage.  This structure is a smaller structure than the East Side Bypass Control Structure with only four bays rather than six.  It also has a trash rack. 

Mr. Romero said the main issue is how the structure is operated.  The San Joaquin River control structure is a part of the Chowchilla Bifurcation, so the flows come out of Friant on the bottom right of the picture, and then they hit this bifurcation.  During restoration flows when there is no flood flows in the system, the Chowchilla Bifurcation Structure, which is in the middle of the picture, are closed and all the restoration flows stay in the San Joaquin River through the San Joaquin River control structure. 

However, during flood events, he pointed out that it’s totally opposite.  Most of the flows continue up to the right part of the picture into the Chowchilla Bypass, and in that case, the Chowchilla Bypass Structure is open and the San Joaquin River control structure, those gates are operated closed partially and in most cases, mostly closed. 

This impacts fish passage, but they can’t just build a rock ramp downstream and allow the fish to swim through it because these gates are operated pretty much every flood, said Mr. Romero.

Unlike the East Side Bypass control structure where those gates are only operated in emergency situations, it’s our understanding that structure has only been operated once in 50 years of operation, so we were pretty comfortable providing passage through the structure,” said Mr. Romero.  “But in this situation, we’re going to have to bypass the structure with either a ladder or a natural fishway to get the fish around the structure which is going to a much more complex and costly project.”


Mr. Romero than updated the board on the ongoing work that the Department of Water Resources and the Bureau of Reclamation are doing concerning the maintenance of the flood system.  With restoration flows in the system all year round, there are issues with the ability of the Local Maintaining Agency to maintain the system.  In the past, they have maintained the system when it was dry which was possible because flood flows only occur on the system every 4 to 5 years.  But now the system wet continually so it is preventing them from performing some of the maintenance as well as increases the cost and changes the types of methods they would need to do.

The Department has been working with the LMA to understand different methods to maintain the system and to understand the additional costs of maintaining the system in a wet system.  They have been focused on four types of maintenance: the trash rack, the control structures, the flap gates, and channel vegetation.  Mr. Romero said they potentially have a path forward. 

Reclamation, the Department, Flood Board staff, and the Local Maintaining Agency have met to understand how to fund the additional costs of maintenance to the flood system.  So far, a funding source has not been identified, but the first aspect is to understand what those costs are.  Mr. Romero said that hopefully, future meetings will be productive to understand how to fund these increased costs in maintenance.

Mr. Romero noted there have been some small successes:  The trash racks that were full of debris and causing fish passage issues for outmigrating juvenile salmon have now been cleaned by the Reclamation, and modifications were made to a flap gate on a culvert to make it easier for the LMA to maintain and operate the gate. 

These are small steps but progress and hopefully the next time we’ll have even more progress to report on this issue,” he said.  “It’s important not only to the restoration program but also to the flood system in making sure it can be maintained and operated as it was designed to.”

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