CENTRAL VALLEY FLOOD PROTECTION BOARD: Yolo Bypass Salmonid Habitat Restoration and Fish Passage Project

Two centuries ago, the floor of the Central Valley was largely a marshy wetland.  In the springtime, the snowpack would melt, swelling the rivers beyond their banks and casting young fish out onto the floodplains where they would stay for months, fattening up on the abundant zooplankton and invertebrates until the floodplains drained, signaling the time to migrate to the ocean.  However, the construction of levees – needed to control flooding of homes and farmland – also separated the rivers from their floodplains, denying access to native fish who have evolved to take advantage of floodplain habitat. 

Recent studies have shown that juvenile fish reared on floodplains are larger, healthier and more robust than those that stay in the river; however, access to floodplain habitat in the Sacramento Valley is limited.  So the Bureau of Reclamation and the California Department of Water Resources are partnering on projects in the Yolo Bypass to reconnect floodplain habitat and improve fish passage for young salmon, as well as returning adults.  The Yolo Bypass Salmonid Habitat Restoration Program is composed of several smaller projects that will reconnect the floodplain for fish during the winter season and improve connectivity within the bypass and to the Sacramento River.

At the April meeting of the Central Valley Flood Protection Board, Board members heard an informational briefing on the Yolo Bypass Salmonid Habitat Restoration and Fish Passage Project being planned for the Fremont Weir.  Referred to as the Big Notch, this project will construct a gated notch at Fremont Weir that will allow a controlled flow from the Sacramento River into the Yolo Bypass to create seasonal floodplain habitat for juvenile fish as well as to improve migration for adult fish.

Maninder Bahia, Water Resource Engineer with the Department of Water Resources, gave the presentation.

A drone view of floodwaters from the Sacramento River overtopping the Fremont Weir in Yolo County, California. Photo taken March 1, 2019.


The project is located at the Fremont Weir in the Yolo Bypass, a key flood control facility that is about 40 miles long and 2 to 3 miles wide.  The Yolo Bypass receives excess Sacramento River flow at the Fremont Weir and the Sacramento Weir.  The Yolo Bypass also receives near year round flow from Knight’s Landing Ridge Cut, Cache Creek, Willow Slough, and Putah Creek.  The Fremont Weir is designed to receive 343,000 cfs from the Sacramento River and the Sutter Bypass, which is just upstream of the Fremont Weir and the Yolo Bypass.

The Fremont Weir is adjacent to the Sacramento River and is the northernmost feature of the Yolo Bypass.  The Fremont Weir, shown below on the right, is an approximately 2 mile long fixed crest weir about 6 feet long. 

In the picture, the Sacramento River is to the right and the Yolo Bypass is to the left.  When the water levels rise beyond the capacity of the river at that location, water flows south into the Yolo Bypass.  On average, the river runs high enough to flow over the weir about two out of every three years; however, in the last six years, the Fremont Weir has overtopped 5 times.

Juvenile fish often swim past the weir and don’t have the opportunity to enter the Yolo Bypass and get onto the floodplain as it takes a significant amount of flow in the river to overtop the weir.  Additionally, fish that enter the Yolo Bypass as its southern end near Rio Vista swim up the Bypass to this location and often cannot maneuver over the 6 foot tall weir to get back into the river.

The Bureau of Reclamation and DWR are implementing this project to comply with state and federal mandates for the State Water Project and the Central Valley Project operations as well as to comply with the Endangered Species Act and the California Endangered Species Act.  The objectives of the project are to create critical floodplain habitat for juvenile fish and to improve migration for adult fish.  The project is being funded by both the State Water Project and the Bureau of Reclamation.

Planning for the project began in 2012, with the environmental document preparation completed in 2019. 

This effort lasted 7 years and that’s mostly because DWR and Bureau of Reclamation implemented an extensive stakeholder outreach process,” said Mr. Bahia.  “There were numerous and regularly occurring stakeholder meetings in which the project teams listed the feedback in regards to the project alternatives and the scope.  In fact three of the six alternatives considered in the environmental document were developed by landowners and NGOs.

Fremont Weir; photo by Dan Brekke


The primary feature of the project is the primary headworks structure which will be located on the east side of the Fremont Weir; this is what is referred to as the ‘Big Notch”.  There will be an excavated channel that connects the river to the structure and control building to operate the structure, and a pedestrian bridge to maintain access from the west side to the east side of the structure.  There will also be a channel that connects this structure to the Yolo Bypass.

Mr. Bahia said that the current analysis is showing a cutoff wall may be needed in the east Yolo Bypass where they will be excavating adjacent to the Yolo Bypass levee.  Further analysis on this is being done and they are coordinating closely with Board staff and Army Corps on this matter.

There is also an agricultural diversion at the southern extent of the state Fremont Weir Wildlife Area which is delivers water to the landowners; this structure will be modified to be an inverted siphon which will improve fish passage upstream within the Yolo Bypass and maintain the water delivery components for the landowner.

The last component is a supplemental fish passage, which is on the west side of the Fremont Weir, and this will essentially function as a drain to empty out the water and fish that remain in the energy dissipation basin after an overtopping event.

The headworks structure will consist of three gates and three bays; the deepest bay will be 18 feet and 24 feet wide and the other two will be 14 feet deep and 27 feet wide.  The foundation of this structure will be built on 24 inch square precast concrete piles with an approximate depth of 75 feet, or 85 feet to an elevation of negative 75 feet.  The gate type that’s being considered right now are pneumatic air ladder gates.  The project team is working on 30% design and fine tuning that element.  The top of the headworks structure or the gates will be matching the existing elevation of the weir which is approximately 32 feet.

The project gates will be operated between November 1st and March 15th and when the river is high enough, flow will naturally enter the Yolo Bypass through the gated structure, Mr. Bahia said.  The peak flow through the structure would be 6,000 cfs prior to the Fremont Weir overtopping.  However, it all depends on the stage in the river, so as the river levels rise, the amount of flow going through the notch will increase.  The average flow during this period of time of November 1st and March 15th when Fremont Weir is not overtopping will be 1,000-2,000 cfs. 

The slide on the lower left further details how the structure will operate.  When the river level is low, there won’t be any flow coming through the structure.  As the river stages rise to 18 feet, there will be approximately 200 cfs coming through the structure.  As the river levels continue to rise to an elevation of 24 feet, approximate 2500 cfs will be coming through the structure.  Just prior to Fremont Weir overtopping, flow will be approximately 6500 cfs coming through the structure.

To evaluate the effects of inundation in the Yolo Bypass, a two-dimension hydraulic model was created and water years 1997 to 2012 were modeled.  The model results showed that the typical increase in wetted days would be 10 to 15 days and the typical increase in depth would be a half a foot.   

One thing to note here is when Fremont Weir overtops, the two year flow event which is approximately 60-80,000 cfs will inundate the Yolo Bypass from levee to levee, so these changes are on the front end of the overtopping event and on the tail end of an overtopping event,” said Mr. Bahia.


Print Friendly, PDF & Email