METROPOLITAN BAY-DELTA COMMITTEE: Briefing on the reconsultation for the operation of the state and federal water projects, Delta ecosystem restoration, and prepping for a major Cal Water Fix announcement

Briefing on the reconsulation process gives context for recent public meetings to maximize CVP deliveries

The January meeting of Metropolitan’s Special Committee on the Bay Delta featured a briefing on the process underway at the Bureau of Reclamation for the reconsultation on long-term operations of the state and federal water projects, an update on restoration projects underway in the Delta, and a preparatory briefing on the Cal Water Fix project in anticipation of an announcement by the state this week that would presumably be some sort of one-tunnel project.


Metropolitan attorney Becky Sheehan gave an update on the reinitiation of consultation with the federal fish agencies on the ongoing operations of the Central Valley Project and the State Water Project, which was in part what was behind a series of public meetings was held in Sacramento, Los Banos, and Chico by the Bureau of Reclamation in recent weeks.

The reconsultation is on the existing biological opinions under Section 7 of the Endangered Species Act, which requires all federal agencies to insure that their actions do not jeopardize listed species or adversely modify those species critical habitat.  The federal action in this case is the operation of the Central Valley Project; the State Water Project is involved as well because the projects are jointly operated through the Coordinated Operations Agreement.  The State Water Project is subject to the federal ESA through this process, and then related (although separate) is the consultation with the State under the CESA statute.

Ms. Sheehan presented a slide of several species in the Delta that are listed as endangered or threatened, noting that some of them are listed either by the state or by the federal agencies and some are by both.  The Delta smelt is listed by both state and federal agencies; at one time, there was a thought that perhaps they would warrant listing as endangered but it wasn’t high priority listing and so it was put on the list of potential future actions because they already were protected and they wouldn’t have received more protection if they were uplisted them, Ms. Sheehan explained.

Chinook salmon, winter run, and spring run are listed in the state and federal endangered species act; fall run is also addressed in the federal opinion only because they are a food source for the Orca whale.  Steelhead and green sturgeon are federally listed.  The longfin smelt is only state listed, although there was a decision on the federal side that they warranted listing under the federal ESA, but it was determined they were sufficiently protected at least now by the state, and so that listing was not a high priority, she said.

The current biological opinions have many requirements which fall into two categories:  non-operational and operational requirements.  Non-operational requirements are for things such as habitat restoration, monitoring, and studies.  Operational requirements include:

  • Old and Middle River (OMR) requirements which is a way to look at pumping rate and entrainment risk;
  • Inflow/export ratio on the San Joaquin which manages how much is being pumped based on inflow for certain months of the year for the protection of steelhead.
  • Cross channel gate operations which specify that they are to be closed at certain periods of time to protect outmigrating salmon on the main stem of the Sacramento.
  • Fall X2 requirement which is for low salinity habitat for Delta smelt in the fall of wet and above average water years;
  • Temperature management requirements below reservoirs, most notably at Shasta Dam because all winter run salmon spawn mainly downstream of the dam so temperature is a particular concern there.

Ms. Sheehan then gave a brief, partial history of the consultation, noting that consultations are contentious.  In 2004, a biological opinion was issued on joint operations of the Central Valley Project and State Water Project; various entities sued on that opinion.  Subsequently, there was some clarification on the critical habitat rules and another biological opinion was issued; those same entities sued on that biological opinion. Judge Wanger made a decision on that opinion in 2007; he did find some issues with the biological opinions, so the federal agencies went back and issued the current biological opinions, the 2008 fish and wildlife service biological opinion and the 2009 NMFS opinion.  Those biological opinions were also sued on but were ultimately upheld by the 9th circuit, and those are the opinions that are now going through the reconsultation process.

The Bureau of Reclamation and DWR requested the reinitiation of consultation in August of 2016.  Agencies request reinitiation when there’s a changed circumstance, and in this case it was the extended drought, the effect of some of the temperature control up near Shasta for winter run, and then some of the low abundance index numbers, Ms. Sheehan said. There was a bit of schedule lag during the switch in administrations, but the consultation really started to get going around the summer/fall of 2017.

The project has three tracks:

  • The first track is near-term environmental change, projects that can be evaluated in a year and that could potentially be implemented in the next year or two. (Ms. Sheehan noted that’s not necessarily directly related to the reconsultation; it’s more of an early phase.)
  • Track 2 is a programmatic document where Reclamation would evaluate a whole range of potential actions.
  • Track 3 is the project level consultation; this is where a project level NEPA document is generated, as well as the consultation and a biological opinion on ongoing operations.

Bureau of Reclamation recently issued Notice of Intent and held public meetings to begin the process for making revisions to the long-term operation of the CVP-SWP; this action is related to track 2 and track 3.

Reclamation has laid out a very broad description of all of the items that it may consider as a part of developing the proposed action to revise long-term operations; the list includes operations with new or proposed facilities to increase water supply deliveries and power generation; increasing storage north and south of the Delta, actions that increase supply or water recycling, modified operations including possible changes to environmental and regulatory requirements, and ecosystem restoration and modification to existing facilities to reduce impacts to listed species.

Metropolitan will provide comments through the State Water Contractors, and likely as well individually, Ms. Sheehan said.  “The type of comments we would expect to make would be certainly in favor of operational improvements to existing facilities,” she said.  “If there is a better way to protect the fish and optimize water supply, that would be great.  We have some of our technical folks working on that and we hope to have proposals that we can submit.  We’d also like a project that’s discrete enough and that you could actually complete the environmental documentation in the next two or three years.”

She noted that Reclamation has laid out some ambitious timelines they are hoping to meet, but if they were to really take a broad expanse of project description, it would probably difficult to meet that time frame.

Ms. Sheehan said they are looking for a ‘short-term’ biological opinion to bridge the gap between now and when Cal Water Fix comes online, noting that another consultation will occur and another biological opinion developed after Cal Water Fix comes online.

Of course we want the analysis to be based on best-available science as always, and we also want to reaffirm with Reclamation the importance of having the Department of Water Resources there at the table as a partner because these projects are jointly operated and they really have to jointly decide how they are going to do that and what that project is,” she said.  “We also have the state’s Endangered Species Act, so it’s important for us to have the California Department of Fish and Wildlife plugged in and supportive of what’s going on because we would really like to proceed with what our current structure is where we have a consistency determination, which means that the state says that as long as we comply with our federal biological opinion, we also comply with state law – that would be the most desirable approach but they really need to be on board and engaged to be able to get there.”

Ms. Sheehan concluded her presentation by saying that Metropolitan would be submitting comments by the February 1st deadline.  “We’ll continue to engage as the WIIN Act, the Water Infrastructure Improvement for the Nation Act, gave the contractors more clear role in the consultation process.  And so we look forward to engaging with the agencies and working together to come up with a solution that works for everyone.”


Randall Neudeck then gave an update on ecosystem restoration activities in the Delta.  He began by explaining the need for aquatic habitat restoration in the Delta.  Back in the early 1880s, the Delta looked much like the picture on the lower left: winding channels, with an overgrowth of vegetation on the side.  There were dendritic channels with all kinds of wildlife, not only fish but birds and the tule elk as well.

The picture on the upper right is what the Delta looks like today.  95% of the wetlands throughout the Suisun Marsh, Cache Slough, Yolo Bypass, and the Delta have been eliminated, mostly broken up into islands that were farmed.  The water has become channelized in levees with rip rap on the side.

Since the early 1990s, six species have become listed as endangered or threatened.  There have been two biological opinions put out by the USFS and the NMFS that are related to the operations of the state and federal projects.  Restoration components of those biological opinions include 8000 acres of tidal marsh in the Suisun Marsh, Delta, and the Lower Yolo Bypass area, and 17,000-20,000 acres of seasonally inundated floodplain mainly in the Yolo Bypass and Lower Sacramento River area.

The listing of fish and the restrictions as a result of the biological opinions have reduced the amount of water that can be exported from the south Delta (below, left).  In 2007, the Metropolitan Board of Directors approved a Delta action plan framework, and as part of that framework, two of the strategies were to implement mid-term and long-term ecosystem restoration projects, he said.

With respect to what habitat is needed, Mr. Neudeck noted that the biological opinions have set numbers of acreage for habitat restoration, but what the agencies are really looking for is more of a gradient or range of functions to restore the system.  “Not just acreage but how can we put the functions that are needed to restore the ecosystem from functions related to the shallow open water channel to tidal marshes, to riparian corridors, and to floodplains so these species can not only deal with the dry periods or the difference between dry and wet periods, but the other conditions that are out there …  so trying to restore all of those functions was important, not just acreage as well.”

In the summer of 2017, Chuck Bonham, the Director of the Department of Fish and Wildlife, spoke to the committee about the Eco Restore program and the 28 restoration projects they are working to implement, as well as the Delta smelt and salmon resiliency strategies.  “Those are strategies to add to the acres, add to what can we do,” Mr. Neudeck said.  “Not just habitat restoration but look at fish food improvement projects, screening, salmon migration, migration of fish through the system, how to improve that as well, so kind of an overall strategy that the state is looking at.”

Metropolitan is working with several different agencies and organizations on restoration in the Yolo Bypass, Suisun Marsh, Cache Slough area, and in the Delta; the list includes environmental organizations, state and federal agencies, local counties, and other interest groups, including local island owners.  The current approach is to restore the contiguous large scale ecosystem gradients and processes, not just for a single species like Delta smelt and salmon, but for a multitude of species that can take into account these dry and wet periods and other factors, he said.

Mr. Neudeck presented a map of the Delta, noting that there are 16 publicly owned islands in the Delta shown in lime green, and the four islands that Metropolitan purchased in 2016 shown in orange (below, left).  “This is just for illustrative purposes only, but it kind of creates a gradient of where we can do habitat restoration through those public islands, from the ocean up through the Delta through the Yolo Bypass and up to the watersheds as well,” he said.  “That’s the connectivity that the state is looking for.”

He then presented a map (above, right) showing some of the projects that the Cal Eco Restore program is working on.  The projects include fish passage projects, levee setback projects, and tidal restoration projects.

Tule Red Project

The Tule Red project is located in the Suisun Marsh; Metropolitan, Westlands Water District, and the Santa Clara Valley Water District provided early funding for this project.  This project is actually under construction right now, and it’s the first project that will be credited towards the 8000 acres of tidal marsh restoration required by the US FWS biological opinion, he said.

They are starting to reform some of the land; they are not having to do very much, he said. There was a groundbreaking ceremony in the spring of 2017; there will be another ceremony coming this spring or summer, he said.  They were waiting for the ground to settle and all those channels to get some vegetation and then they are going to open up the levee to Grizzly Bay and water will start coming in.

The Tule Red project has about 610 acres of creditable habitat; 400 acres of tidal wetlands, and about 200 acres of sub tidal habitat.

This land is at a good elevation right now,” Mr. Neudeck said.  “It’s suitable for this type of habitat as it allows for these critical water interfaces.  What happens in the Delta, if you can restore it this way, then water can come in through the tidal cycle, especially in the evening, and the breeze will cool down that water, the nutrients will go into that water, and then when the tide goes down, all those nutrients and cooler water will come back into the system and start the process of the phytoplankton and zooplankton producing the food.  All those functions have been lost in the Delta largely, so the more we create that, the better we can improve the fishery system.”

Fremont Weir/Yolo Bypass

The Sacramento River provides about 80% of the flow throughout the Delta, entering the Delta from the north.  As it flows into the Delta, there are two weirs; weirs are just low parts on the levee, Mr. Neudeck explained.  The weirs and the flood bypass system was built to protect Sacramento from flooding after the city was flooded a number of times in the early part of the 19th century.  He noted that during the 2017 water year, about 40 million acre-feet went through the system with about 2/3rds of that through the Yolo Bypass, so without the flood system in place, Sacramento would have endured serious flooding.

Most years, the flood bypasses aren’t needed, so what the fishery agencies are looking for is how to restore the area at the southern end that used to be a tidal marsh and the area at the northern end that used to be a seasonally inundated floodplain; how do we restore those functions more?  He noted that there are several projects in the area addressing this strategy, such as the Lower Yolo Restoration Project; the Knagg’s Ranch salmon project, and Wallace Weir.

Mr. Neudeck then focused on the work proposed for the Fremont Weir.  The Fremont Weir is at the north end of the Yolo Bypass, and is how most floodwaters enter the Yolo Bypass.  When the floodplains become inundated, they produce a lot of fish food.

He presented a picture from the Knagg’s Ranch to illustrate the density of fish food that was produced out in the floodplain versus the Sacramento River (above, left), and the difference it makes in the size of the fish (above, right).

The Fremont Weir is 2 miles long.  When the flows in the Sacramento River get high enough, the water flows over the weir, over the 6 foot wall, and flows down south to the Delta.  When those floodwaters recede, the migrating fish have to find the notch in the weir – just 4 feet wide and 6 feet tall – to get back into the river; many of them don’t.

There is a near-term project that the environmental documentation is being finalized that will enlarge the hole to 15-feet wide by 1- feet tall. The longer-term project is modify the weir for both migrating fish coming upstream and the small smolts coming downstream to get onto the floodplain.  The project alternatives range from 3000 cfs to 12,000 cfs and anywhere from 3 gates to 27 gates with multiple locations.  When the environmental documents are finalized, they will start the design.

So in summary, we just wanted to present you that ecosystem restoration not only affects our water supply operations, and fish enhancement, it also affects issues related to subsidence reversal, salinity impacts, and where you put the habitat can affect tidal range and salinity impacts, invasive species control, and other elements,” Mr. Neudeck concluded.


Steve Arakawa, manager of the Bay-Delta Initiatives Program, began by saying that there is an anticipated announcement by the state coming soon regarding how the Cal Water Fix project would move forward, so his briefing would be just a reminder of where things left off in the fall.  (Maven note to reader: Not a lot of new information here; really more of a review.)

In October, there were a series of joint meetings of the Special Committee on Bay Delta and the Water Planning and Stewardship Committee that focused on three white papers that covered in detail the infrastructure of the proposed facilities, the operation of those facilities, and the finance and cost allocation.  There was also a question and answer document prepared.  The Board voted to participate in the project on October 10, 2017.

The project parameters at the time were 2 tunnels and three intakes with a combined capacity of 9000 cfs.  The total cost of the project with mitigation was $16.7 billion to be allocated against all of the participants.  Estimated operating costs were about $65 million per year.  At that time, Metropolitan’s share was to be 29.5% of the total cost.

The cost impacts to Metropolitan’s water rates were evaluated at 4%, 6%, and 8% interest rates, and based on the $16.7 billion cost estimate and Metropolitan’s share of roughly 26%.  Staff also presented a business case or benefit-cost assessment that Metropolitan stands to gain a benefit of about 350,000 acre-feet of supply that was seen at risk when it is taken into account the kind of operating requirements being considered by the regulatory agencies.  “If you recall, we had a base condition without Water Fix and then what the project would provide with Water Fix, and the estimated benefit of that was 340,000 acre-feet to Metropolitan, so that was factored into what the cost would be on a marginal level.  That is, 340,000 acre-feet and a cost at that time of about $4.3 billion would be Metropolitan’s share.

So, in terms of supply and quality, Metropolitan staff’s analysis showed a range of supply benefit for the state and federal projects of 4.7 to 6.3 MAF; if there were no Water Fix and including the operating requirements projected to be implemented, the range of supply benefit would be 3.5 to 3.9 MAF.

You may recall that we were saying in total, the benefit of Water Fix was about 1.3 MAF, if you take the midpoint of each of those ranges,” Mr. Arakawa said.

There are water quality benefits because the ability to divert water on the Sacramento River rather than the South Delta means less total dissolved solids, bromides, total organic carbon and nitrates.  Staff also provided information on how Cal Water Fix could actually enhance water transfer capabilities and opportunities.  “Without the Water Fix, being constrained at the south end of the Delta with the needs to protect the fish with the reverse flow requirements and such, having the new proposed intakes at the north end of the Delta could enhance the opportunities to move water for water transfers,” he said.

Staff also provided costs per household for Cal Water Fix, as well as in comparison to other alternatives, including recycled water and desalination.   “Recognizing that Metropolitan’s regional water supply strategy is basically to have diversity in its supply so moving forward with local supply as a way of meeting our future demands but also securing our existing supply through the State Water Project,” he said.

The Board action on October 10 was to adopt the CEQA action and to express support for the project.  The action also included three agreements: the adaptive management program agreement which is what the water contractors would be agreeing to with the fishery agencies and the operating agencies, the design and construction JPA, and the finance JPA.  Then the Board adopted a resolution indicating that it would be participating based on its 25.9% share.

Mr. Arakawa said that if the forthcoming project announcement is that it is to be staged, staff will bring back the analysis of how that impacts Metropolitan in terms of adjustments to Metroplitan’s share, moving forward with bond financing, and proposed  water transfer agreements between contractors that would help support the investment strategies that each of the contractors are making as part of Cal Water Fix.

He then laid out the proposed schedule, based on the anticipation of the announcement from the state.  Once the announcement is made, staff would make a presentation at the next Water Planning and Stewardship Committee on the state’s direction, and what it means in terms of costs and benefits, and benefits to Metropolitan.  Then at the February 27 meeting of the Special Committee on Bay Delta, staff would bring back further information on costs and benefits, along with detail on the water transfer agreements.

This would be informational so the Board has an understanding in detail of the types of water transfers that are possible and what Metropolitan might want to consider, and then how all of that fits in with the integrated resources plan,” he said.  “If all of this schedule works, then there would potentially be a board action for the board to consider in March.  That would include what Met’s share of moving forward to be, the water transfer agreements, and then any kind of funding needs in the early term prior to any bond financing that would occur in the long term.”


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