METROPOLITAN BAY-DELTA COMMITTEE: SWP contract amendment for Delta conveyance; Activities of the Delta conveyance JPAs; Delta Smelt Resiliency Strategy

At the September meeting of Metropolitan’s Special Committee on the Bay Delta, Steve Arakawa, Metropolitan’s Bay Delta Initiatives Manager, updated the committee members on the negotiations between the State Water Project contractors and the Department of Water Resources regarding the Delta conveyance project, and the activities of the Delta Conveyance Design and Construction Authority and the Delta Conveyance Finance JPA.  Then Dr. Shawn Acuña, a research specialist with Metropolitan, gave an update on the Delta Smelt Resiliency Strategy and other efforts to help the struggling Delta smelt.


With the demise of the California Water Fix, there have been some adjustments and further negotiations with the Department of Water Resources regarding cost allocation.  The negotiating parties are the Department of Water Resources and the State Water Project contractors, which are the 29 public agencies that have contracts for water.  Those contractors are located in the Bay Area, Southern San Joaquin Valley, Central Coast, and Southern California, as well as some in Butte County.

The negotiations are underway because in moving forward with Delta conveyance, the Department of Water Resources wants to identify how the cost allocation will work to pay for the planning, construction, and operation of the project.  There were similar negotiations that occurred with the California Water Fix in the first half of 2018; however, further negotiations are needed now that it’s a new formulation of the project.

The Agreement in Principle that emerged from the 2018 negotiations addressed how the California Water Fix project would be funded, as well as water management provisions for transfers and exchanges.

The water transfer and exchange provisions provided a means for individual contractors to manage their costs and the benefits that they are looking to receive from the State Water Project and in the end, provide a means for affording the project,” Mr. Arakawa said.  “During that time, all contractors would be paying but contractors would have the ability to transfer a portion of their water or to exchange their water through water management transactions to manage their costs and benefits.  However, with the Cal Water Fix no longer being the proposed project and moving to Delta conveyance, the discussion is now centered on a proposal for how individual contractors would opt in.”

He noted there was a negotiation session earlier this year to take out the portions of the Agreement in Principle that dealt with the California Water Fix and move forward with the water transfer and exchange provisions as a proposed contract amendment.  There was an environmental analysis done for the prior amendment, so the Department of Water Resources is in the process of preparing a recirculated document to reflect the changes.

Now with the new Delta conveyance project, the negotiations are centered around the allocation of costs and benefits for the reformulated project.  The negotiations began on July 5th and there have been a handful of negotiating meetings since.  The negotiations are conducted in public as per the settlement agreement for the litigation over the Monterey Amendments; members of the public are not directly involved in the negotiations, but they can observe and provide public input.

The scope of this round of negotiations is what kind of amendments to the contract are necessary to allocate both capital and operating costs among contractors, what arrangements are needed with the Department, and how the accounting will be done to assure that the benefits are being provided for those contractors who opt in and pay for the project to assure that the benefits go to the parties that are investing.

The State Water Project contractors are looking to come to an agreement with the Department of Water Resources on how an opt-in process would work for contractors who decide to participate and determining a methodology for cost and benefit allocation; that would then be brought to various boards for the State Water Project contractor agencies.  It would also include how the planning activities will be funded.

All of that would go through an environmental process and a permitting process, and the state would be the one responsible for deciding which is the proposed project based on all of the alternatives analysis,” he said.  “That would be a future action.  So there would be an environmental impact report and a contract amendment that would both come from all of this work.”

Mr. Arakawa then presented the estimated timeline.  It is expected to take two to three years to get to a final environmental impact report and permitting decisions, and concurrent with the environmental process, there will be engineering work to inform the environmental process.

The state has an interest in making sure that the water contractors have an interest in funding the project, and so the purpose of the negotiations is to indicate to the state that there is an approach for State Water Project funding and there is a methodology that’s agreed upon that would become contract language for allocating those costs and benefits,” he said.  “So on this chart, we’re showing those negotiations occurring sometime through October … that’s our targeted time frame for trying to get the public negotiations done for an Agreement in Principle.  That would allow for public water agencies to go back to their boards and review the Agreement in Principle with their boards and to talk about what necessary going forward in the planning process for these three years in order to move the project planning forward.”

The Notice of Preparation will begin the environmental review process.  The state has an interest in understanding how things are going with the water contractors and their boards of directors, and that Agreement in Principle would help inform the environmental review process and all of the preliminary engineering design work.  That is currently targeted to begin in earnest in January, but Mr. Arakawa emphasized that this is only the targeted timeline at this point and subject to change as they work through the process.  He said he would keep the committee informed on how the process is going.


Mr. Arakawa then turned to the activities of the Delta Conveyance Design and Construction Authority and the Delta Conveyance Finance Authority.

The September meeting of the Delta Conveyance Design and Construction Authority was focused on preliminary activities, such as working with the contractors on preparations for the environmental process, making sure the right engineering work is being done to help inform the environmental document, and understanding what the potential impacts and mitigation issues might be so that the environmental review process is as strong as possible, he said.

He also noted that the Design and Construction Authority will be moving into its own offices at the beginning of 2020, so a lot of the actions taken at the September meeting were in preparation for that.

Mr. Arakawa said that the Board of the Design and Construction Authority approved moving forward with a stakeholder engagement committee which would be an advisory committee to the board.  The purpose of the stakeholder engagement committee is to help inform the environmental review process and the project design to inform the environmental process as well as the design considerations for the project, such as construction effects.

This advisory committee would solicit the input of parties and stakeholders in the area and then the stakeholder advisory committee would provide that information to the board,” he said.  “It’s not a committee that takes any action; it’s a committee that is interacting with stakeholders and trying to understand the issues in helping to inform what kind of considerations need to be developed or could be developed.”

The stakeholder committee would have sixteen members; the board of the JPA would be involved in identifying who would be part of this advisory committee.  There committee will also include some ex-officio members from state agencies that would help provide information, but not necessarily be one of the formal stakeholder committee members.  The committee will meet up to two times per month so that a strong input and interaction can occur with the communities leading up to that point.  The committee would be chaired by one of the members of the JPA board.

During the public comment period, the comments were more around understanding how this process was different than other processes, such as the Governor’s water resilience portfolio.  “The Governor’s administration has a roundtable process with Delta interests to talk about what issues are important to them, including levees, water quality, land use, flood control, and things like that,” he said.  “This is different than that.  This is focused on how do we inform the environmental process and the design work for Delta conveyance talking with stakeholders.  This is not the environmental CEQA process that the state will go through for soliciting input on the alternatives in analyzing Delta conveyance.  This is more focused on how do we inform the design and the environmental document as far as what kind of effects that Delta conveyance might have in the Delta.”

The Delta Conveyance Finance Authority is only meeting when needed rather than having monthly meetings.  At their last meeting, they started discussing what kinds of potential changes are necessary to move from California Water Fix to the new Delta conveyance project and what role the Finance Authority would play.  There will be further discussions at a later point when more project details are known.


Director John Murray (Los Angeles) asked if there would be Delta advocacy or NGOs represented in the stakeholder engagement committee?

Mr. Arakawa said the intent is for interested people to submit their applications, and that would include those interests.  “The board would be considering what the makeup of the 16 member advisory committee would be, but it would include those kinds of stakeholders.

Director Russell Lefevre (Torrance) asked how the board was going to work through the committee selection process.

The stakeholders that have an interest would submit an application and then the board working with the Executive Director of the JPA, they would go through some kind of process to determine what the makeup of the 16 member committee would be, and then those selections would be made with board input from the JPA,” said Mr. Arakawa.  “There are 16 spots.  We don’t know how many applications will actually be submitted, but conceivably there could be more applications then there are spots and so the JPA board would have to decide.  There has been an interaction process to reach out and talk to parties about this process so that has been ongoing by Kathryn Mallon, the Executive Director, and others, so that the community is aware of this.  In the end, they would have to have an interest in submitting an application.”

Director Michael Hogan (San Diego) asked if state water project contractors had concerns about participating in the financial negotiations prior to determining what the capacity of the tunnel is.

The conversations have been around recognizing that the state can’t predetermine everything,” said Mr. Arakawa.  “They have to go through a CEQA process, but what the contractors have an interest in doing is providing valuable input in terms of what kind of facility sizing are they interested in investing in.  The hope of the contractors is that we’re able to converge on what the contractors feel they are able to or support funding and the state obviously is going to have to look at a range of options, but hopefully there’s some kind of convergence on how the state sees the state water project portion moving forward as a proposed project that would get evaluated in the environmental process, so it’s finding a way to do that.”

Director Hogan asked if the contract amendment revisions to the transfer and exchange agreement would create more flexibility and opportunity for the state contractors from previous agreements.

Mr. Arakawa noted that the 2018 negotiations included both how the Water Fix would be funded but also transfers and exchanges; the Water Fix portion has been removed, and so now the intent is that those transfers and exchanges provisions that were proposed to be included in the contract would complete its environmental process and then there would be a contract amendment for that separately.

I think the intent is two-fold,” said Mr. Arakawa.  “Hopefully it’s a way for contractors to see how their participation in Delta conveyance can work for them so that they can manage their costs and their benefits so that they are able to get the reliability that they need so being able to manage their water with more tools and flexibility.  It’s also building upon water management provisions that are in the existing contract, so it’s adding to those.”

Director Barry Pressman (Beverly Hills) notes that not every state contractor is going to opt in and therefore there will be some kind of tension between Table A and Article 21 and north of the Delta water.  Has that come up yet?  Do you have any feeling for where that is going?

The two main parts of the negotiation are who is opting in and how are they going to divide the costs and how are they going to allocate it,” said Mr. Arakawa.  “The second part is what you’re referring to which is what is the mechanism, what is the system that we can all rely on to ensure that the benefits that we’re paying for will go to the right parties.  It would deal with things like, when is it Table A water, when is it Delta conveyance water, when is the unscheduled water that we talk about as Article 21, when is it really being produced by Delta conveyance and not the existing project so it’s dealing with all of that.

To my mind, there’s two key things here,” added General Manager Jeff Kightlinger.  “One is that there has to be a clear definition of what are the benefits associated with investing in Delta conveyance, and those have to be fully allocated to those who opt in, and those who do not, it has to be clear that they do not receive those benefits.  So therefore there is no free ridership.  That’s one aspect.”

The second aspect is if you’re correct that there are a number of people that don’t end up opting in, and there is some excess capacity, what is the process for divvying up that excess capacity, people paying extra and insuring that they receive those extra benefits,” continued Mr. Kightlinger.  “So those two things have to be made very clear through this contract amendment process.  The parties have all thought about that, they are proposing ideas.  DWR has to agree to them, and then we would have to bring that back to our board and say, are we satisfied that we’ve correctly defined and demarked where the benefits go and do they correctly follow the money.”


Dr. Shawn Acuña is a research specialist that works out of Metropolitan’s Sacramento office, working on multiple stressor issues in the Delta, as well as Delta smelt and longfin smelt. For the second half of the meeting, Dr. Shawn Acuna gave an update on the Delta Smelt Resiliency Strategy and ongoing research that Metropolitan is involved with.

The Delta smelt is a listed species; it’s listed as either threatened or endangered, depending on the whether the regulations are state or federal.  The population continues to be at a very low level, despite the high abundance in 2012.  Even more advanced surveys are showing low population numbers.

This is a troubling trend that we are trying to deal with,” said Dr. Acuña .  “As a species in the Delta, this species is very important for water conveyance and a lot of the ecosystem services of the Delta.”

The Delta Smelt Resiliency Strategy was developed in 2016 by the Natural Resources Agency.  The strategy was designed to promote near-term actions to promote the resiliency of Delta smelt during drought conditions, and potentially to stave off the trend of negative abundance and achieve some recovery.  They are also hoping to gain a better understanding on the effectiveness of the management actions that have been promoted.

The resiliency strategy collaborators include the Interagency Ecological Program, state agencies, water contractors, and other public agencies.

Dr. Acuña then discussed some of the actions.

Aquatic weed control

Aquatic weeds are a pervasive problem in the Delta.  Aquatic weeds are impacting both navigation for commercial and private use; they are also impacting water diversions, both small diversions and ag diversions as well as large diversions.  The hypothesis for this action is that the weeds are believed to be impacting Delta smelt negatively by taking away their habitat.

What we can do is remove the weed by the actions that are already planned out and methods that have already been permitted out in the Delta and see if we can improve the environment and get a better handle on Delta smelt,” said Dr. Acuña.  “Unfortunately, the last two studies have shown that the treatments weren’t as effective as advertised.  There are some mitigating circumstances Some of the application methods need to be done differently, so they are going to explore alternative methods and try and reengage on this topic.  But this is a serious problem.  These weeds are impacting both commercial and private interests all over the Delta.  They are just taking over and it’s just getting worse.”

North Delta Food Web AMP

The North Delta Food Web action was more successful.  The action involved a number of state agencies, local reclamation districts, upstream diverters, and water districts.  The Delta has low productivity (meaning not a lot of fish food) and so one way to increase productivity is to run some water across the floodplain.

Floodplains are sort of like reactors; they produce a lot of nutrients, a lot of food, a lot of productivity for fish,” Dr. Acuña said.  “If instead of going down the mainsteam, the water instead flows into the bypass/flood area, we’d be able to make more efficient use of the water and produce a lot more food this way.”

The action was conducted in 2016 and 2018; 2017 was a high water year so the action was deemed unnecessary because it was already sort of happening.  In 2016, they were able to send water down through the Colusa Basin drain and through the Yolo Bypass.  Blooms were formed and a lot of food was produced.  In 2018, the results were a little bit more mixed.  Instead of diverting water from the Sacramento, they took agriculture return water, sent it through the bypass; this time, a bloom didn’t form, but they did see an elevation in food, so there was potentially a benefit.

The action was done again this year; it’s just now wrapping up so the results are not yet in, he said.  It’s basically a repeat of the 2018 action sending ag return water down through the Colusa Basin drain.  They are hoping to have similar benefits: more food for fish, better for growth and survival.

Reoperation of the Suisun Marsh Salinity Control Gate

The reoperation of the Suisun Marsh Salinity Control Gate was an action to manipulate salinities with the tidal gate in Suisun Marsh to create more habitat for Delta smelt.  Along Montezuma Slough, there is a tidal gate that can be opened or closed to help freshen up the water.

This is believed to reduce salinity stressors on Delta smelt and the hypothesis is if we reduce the stressors, the fish will then move into the system where there is a lot of food and productivity,” Dr. Acuña said.  “It is another food action where the fish would benefit by growing more, thriving more, and getting bigger.

In 2018, the action was implemented, and they did see a corresponding increase in presence of Delta smelt in Suisun Marsh, so it seemed somewhat successful, he said.  They are going to try and do it again during above normal and below normal water years.  During wet years, the area is already pretty fresh, so the tidal gate would have almost no real impact.  This will be an action conducted generally around the end of August and September which is when they think is the most critical period for Delta smelt to have access to Suisun Marsh.


Although restoration isn’t necessarily a near-term action, there are numerous restoration projects that are reaching completion and opening up land to natural processes.  Several restoration projects were identified as part of the Delta Smelt Resiliency Strategy and are shown in orange on the map; there are other restorations underway as part of the Eco Restore and Fish Restoration Project Agreement (FRPA).  The restoration on Decker Island, an area thought that Delta smelt tend to occupy, has been implemented and breached.  The Tule Red and Winters Island projects are nearing completion.

We have a lot of high hopes that these restoration projects will open up a lot more habitat for Delta smelt,” said Dr. Acuña.  “Not only do they need more food, they need more space.  So this allows for that space for Delta smelt for potential to thrive.”

Outflow augmentation

Outflow augmentation is an action that’s been discussed for a long time.   “In the summer, the idea is to use the water to help manipulate the system and perhaps make it a bit more turbid, perhaps do a number of different mechanisms that are involved here that would promote benefits and reduce the stressors,” said Dr. Acuña.  “This is a broad action as opposed to the targeted actions like the North Delta Food Web or the Salinity Control Gate.  Those are targeted; this one is a bit more broad where it’s adding water to the system through the mainstem.”

While they haven’t done any outflow augmentation specifically for the Delta Smelt Resiliency Strategy, there have been high outflow years which has required a manipulation of the system to add more water, he said.  One such year was in 2017, a wet year, where under the biological opinion, water would be used to push salinity out during the September, October, and November; this is known as the Fall X2 Action.

Under that action, there were a number of different projects,” he said.  “A flow synthesis was conducted on 2017 to evaluate the effects of the flow action and to see what benefits could be determined that might be helpful for Delta smelt as well as to test the hypothesis that augmented flows would actually help Delta smelt.  Those analyses were conducted.  The directed outflow project is still ongoing, it is designed to both look at high flow and low flow so it’s a comparative; so the 2017 high flow year and also much drier years such as 2018.  It’s continuing on right now and we are involved in that project.  The flow synthesis is basically an analysis of 2017 data from that year and then prior years and then a comparison analysis to see what other benefits or mechanisms that could be useful and then plan for future actions.

Dr. Acuña pointed out that one important finding was that temperature is playing a very significant role.  “2017 was a warm and wet year, and that warm part was actually a lot more key than we had anticipated,” he said.  “In general, there are a lot of researchers that called out temperature as an important factor and this really supported their arguments that these temperatures are really driving the system.  2017, being a high water year, it was proposed there would be better conditions and more smelt, but there weren’t more smelt.  What happened?  One of the things that is being attributed to is temperature.  Temperature seems to be a mitigating effect, at least, if not a dominating effect.”

Other ongoing studies not part of the Delta Smelt Resiliency Strategy

Dr. Acuña then discussed some of the research that Metropolitan and other agencies are working on.

Genome study:  There are some Delta smelt that are being kept in a hatchery; the population has been meticulously managed genetically to be as close to the wild population as possible.  “The genome study will be useful for understanding population management in the wild, as well as field studies, such as perhaps propagation where you would release the fish out into the wild, or using cage studies, putting them in cages and testing management actions in that way.”

Cage studies:  Earlier this year, they did some cage studies with the hatchery Delta smelt to see how they would do; it had been previously thought the fish were too fragile to survive a cage study.  However, they tried it earlier this spring and the fish did pretty well.  The results were more mixed with cage studies performed later in the year.  The cages were placed in the Yolo Bypass and also the ship channel.

The results of the cage studies were surprising.  “We expected to have high mortalities, they’d be really stressed, but they lived, they actually grew a little bit which means they were eating,” said Dr. Acuña .  “So potentially that we can start using these as sentinels.  We can put them out in the wild, do a flow action potentially or a habitat restoration action, see what the benefits are, add more food, or remove food or look at contaminants, perhaps manipulate other things such as aquatic weeds, and see if there is a response in the Delta smelt.”

eDNA tool development:  Just as humans shed skin cells with DNA, so do animals; this can be tested to see what species are present.  Metropolitan is helping to develop the eDNA tool.  One benefit is it’s a non-lethal tool; you can take a bucket of water, filter it, and test to see if the species you’re looking for is there or not.

eDNA has been used in a number of different areas, such as the Great Lakes or the Chesapeake Bay.  They have been working on applying it in the Delta, although there is a bit of an issue because of the tidal action.  Most of these deployments of eDNA have been along rivers which are one-directional; but in the Delta which has interconnected islands and being a tidal system, it’s hard to tell exactly where that water is coming from.  You can have water at the confluence and it could be coming down from the San Joaquin or it could be coming from the Sacramento or it could be coming from downstream and Suisun Bay, he pointed out.

There are a number of educational institutions and other collaborators who are working on developing the tool.  There will be a symposium in January to bring together experts to work on trying to achieve consensus for best eDNA practices.

Standardizing the method in the environment is really key,” Dr. Acuña said.  “Just because you found an eDNA signal, doesn’t mean anybody is going to trust that you actually found it, because they want to know your methods and whether you are truly finding it.  There have been a lot of contamination-false positive issues in other environments so we want to take care of that.  So with UC Davis and the Delta Science Program and a number of other different agencies, we’re helping support this workshop.  This workshop will bring both national and international scholars in to try and create a consensus on how to do the method.”

In summary …

The Delta Smelt Resiliency Strategy was developed in 2016 during a drought when there were critical issues and it looked like Delta smelt were on the verge of extinction.

A lot of actions were implemented and we’ve gotten some mixed results,” Dr. Acuña said.  “There is still more that needs to be done, but their status is still pretty low.  So we need to continue on with the strategy as well as other research efforts that we are working on, such as tool development and other food manipulation actions.  What we have found is we do have the potential to help with food and that might be beneficial for Delta smelt.  The cage studies will help test that.  Temperature is a really big issue, and with climate change, it’s just going to get bigger.

As for next steps, they are developing a structured decision making process, and they are developing an overall Delta science plan to help integrate the actions.  “Instead of all these actions being done by one predominant agency like DWR, and some other people helping out, there’s going to be a more systematic way of implementing these actions using directed decision making to understand the cost-benefits of these actions, because some of these actions still require some water, so you need to know which is the one that’s going to give us the best benefit for what we’re going to do.  There are several flow actions that are being implemented in 2019 – the North Delta Food Web and Fall X2.”


Director Michael Hogan asks what the benefit of eDNA is for Delta smelt management.

Dr. Acuña noted that not only can eDNA be used for Delta smelt, but it can be used for a variety of different species.  “But specifically for Delta smelt, why is it useful, why would a bucket of water be better than a trawl?  There’s a couple of issues.  One, trawls usually have take permits.  They are difficult to implement and they have their own limitations.  And also, as a take limit effort, there’s a potential for the species you’re collecting to die.  With the bucket, it’s a non-lethal take, so you’re taking the water and you can get the presence or absence of Delta smelt in that way.  You can look in areas that are hard for trawls to go in, such as really shallow areas, and that’s a pretty big benefit.  Also, traditional trawls have a standard methodologies; it’s really hard to adjust them without compromising the integrity of their survey, so this is an addition.  They wouldn’t replace standard surveys, but used in conjunction with them.”

Director Barry Pressman noted that based on the charts in the presentation, the actions being taken are not having a tremendous effect.  What are the negative effects on the Delta ecosystem from the absence of smelt?  What are we seeing empirically?

There’s not a lot of empirical data on that specifically, but generally Delta smelt is an indicator species,” said Dr. Acuña.  “You’re thinking of it as ‘I’m in the middle of the food web so everything is around me.’  Generally what Delta smelt is considered is more like the canary; if they are not doing well, then chances are other species are also not doing well, so that’s generally how Delta smelt is being managed, as opposed to being a critical part of the ecology.”

What the research agencies and fishery agencies are looking for is an ecosystem that is somewhat similar to predevelopment where there was a lot of open water habitat, emergent vegetation, and that kind of habitat would be beneficial for open water fish, such as Delta smelt,” he continued.  “If you see that fish not doing well, then chances are, the open water habitat you’re trying to promote is impaired, and so we’re using it more like the canary in the coal mine.”


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