METROPOLITAN’S SPECIAL COMMITTEE ON THE BAY-DELTA: Longfin smelt science efforts, California Water Fix update

Committee members also discuss cost allocation

At the June 27th meeting of Metropolitan’s Bay Delta Committee, committee members heard about Metropolitan’s science efforts with regards to longfin smelt, and an update on the schedule for the decision process for the California Water Fix project.  Lastly, the directors discussed the cost allocation process for the California Water Fix.


Dr. Shawn Acuna is a research specialist that works out of Metropolitan’s Sacramento office; he does a lot of work on multiple stressor issues in the Delta, as well as Delta smelt and longfin smelt.  He gave this briefing to the committee on the science efforts being done for longfin smelt.

He began with the longfin smelt’s life history.  Longfin smelt have a wide distribution from Alaska all the way down to California.  They can live in the ocean along the shoreline; the arrows on the map show the estuaries where they can be found.  The southernmost population can be found in the San Francisco Bay Delta.  They’re known to be able to breed in both fresh and brackish water.


The longfin smelt were listed as endangered by the state of California in 2009.  They are currently in a ‘holding pattern’ for federal listing, meaning that listing is warranted but precluded because there is a backlog, but they are set up to be listed in the federal Endangered Species Act.

Some of the actions that have been promoted to help with the longfin smelt are outflow management so it’s from the Delta upstream flows; reducing entrainment through the diversion; and habitat restoration,” Dr. Acuna said.  “The dominant flow action has been promoted for the most part has been outflow.”

Annual surveys have been done for longfin smelt in the Bay Delta.  He presented a map compiled from the data for 1994-2008.  The circles indicate the percent of catch in the trawl data.  “The trawl data showing that they are widely distributed throughout the habitat; they can also be found in the ocean as well,” he said.

Delta outflow refers to all the flow that’s coming mostly from the Sacramento and San Joaquin Rivers.  “As you go from east to west, that effect will be lower, and then there are the other tributaries,” he said.  “The current status of longfin slow is pretty low, based on a lot of these surveys that we have out there where there’s an initial high periods with more recently very low numbers which has given us a lot of concern.  A lot of fisheries biologists are very concerned about it, so that’s why the management and listings have been promoted.”

Dr. Acuna said there is a flow-abundance relationship with longfin smelt, presenting a graph with flow on the x axis and abundance on the y axis.  “We can see, such as in this pattern, that as we increase the flow, there’s a positive relationship with abundance,” he said.  He explained that the blue line is the pre-clam era as the 1998 invasion of the clams has actually caused a step decline.  The white line is the post-clam pattern which shows a lower response with abundance.   The more recent period shown in green is the Pelagic Organism Decline, where a number of fish that are in the pelagic regions or the upper water column of the area also has this sort of step decline where the relationship is flow again.

So for the same amount of water, 20,000 cfs of water, we go up there to the preclam times, you get roughly about 3000 for the index; more recently, you get about 100, so a many-fold decrease in that relationship,” he said.  “So what are we really interested in when it comes to this relationship is why are we seeing that step change, what is the relationship governing abundance and flow relationship, and what factors may be contributing to that decline?”

Dr. Acuna then presented a heat map of salinity from 2008 (a dry year) and 1990 (a wet year) which shows the difference in the salinity field when there is more fresh water; he noted that there is a lot more blue in the higher flow years than in the low flow years.

Although we do have these really strong relatively higher flows from the Delta, there’s all these other in points that we get flow from.  Even in dry years, we still get a modest flow within some of the other areas as well, and you can see that in these sort of contour, there’s flow influences from Petaluma, from Sonoma and Napa also affecting the salinity field, not just Delta outflow.”

There are a number of surveys.  Dr. Lenny Grimaldo has done a lot of sampling out in Suisun Bay; the California Department of Fish and Wildlife does routine monitoring looking for larvae, as well as another researcher, Dr. Jim Hobbs at UC Davis.  “What we’ve been seeing over the years in sampling from 2013, 2014, as well as in 2017, spawning seems to be happening in brackish water.  This is important because a large portion we believed was happening in freshwater, so upstream areas directly influenced by Delta outflow.  The more brackish water is more westward; that influence is much lower.  There’s still going to be the influence, but it’s much lower.”

Dr. Acuna noted that the entire San Francisco Bay is not covered by the survey, so with additional work from Jim Hobbs and Lenny Grimaldo, they were able to cover the areas in the south Bay where sampling had not occurred and found that they were spawning there as well.  “In fact, this year, they found spawning out in the South Bay which was believed to be highly unlikely, but there was definitely spawning happening down in the South Bay,” he said.

What are the potential flow abundance mechanisms for longfin smelt?  “It could be habitat,” Dr. Acuna said.  “We believe it is habitat that is sort of like sweetening up where the saltier water has become a little bit fresher, allowing for longfin to be able to occupy those areas.  One of those areas are some of our investments in restoration such as Tule Red, and habitat in San Francisco Bay.  Restoration in San Francisco Bay is ongoing, but we feel that there’s a lot more influence of local tributaries that are affecting those habitats.  That’s habitat that’s not being assessed as well as estuarine habitat for longfin smelt.  So it needs to be highlighted and elevated in the San Francisco Bay.  Longfin smelt are using that habitat very extensively, and it’s very important.  Most of that habitat is being managed for more salt water species and those kinds of things, well longfin is more of an estuarine.

Dr. Acuna then turned to abundance trends, presenting a graph showing the decline in abundance.  “What is explaining a lot of this decline?” he said.  “For starters, there are a lot less fish out there, that’s for sure.  We’re seeing this trend that seems to be affecting that abundance, so there definitely seems to be less, but that makes sense, because more recently, there’s been a lot of dry years and therefore we would expect to see lower numbers of fish in the Delta.  I did mention that they are also in the ocean, so it doesn’t mean the overall abundance has reduced; it just means at least the abundance in the overall San Francisco estuary has reduced.  They could have gone out to the ocean; that is possible.”

Dr. Acuna explained that there are two trawls that are conducted from the San Francisco Bay all the way into the lower confluence of the Sacramento and San-Joaquin Rivers: The otter trawl and the midwater trawl.  He noted that the decline is much greater in the midwater trawl.  The difference between the two trawls is that the otter trawl is along the bottom while the midwater trawl is diagonally along the water column.

The midwater trawl is an important trawl to have because you want to know what the fish are doing along that gradient of the different layers of the water,” he said.  “But what happens is if the longfin smelt are more bottom oriented, that midwater trawl tends to only see them at a lower point.  There are also water clarity issues.  If it’s clear water, it’s been shown that in other estuaries and other fishery surveys that if the water is clearer, fish can detect the trawls and avoid them.  So it’s actually been found that there’s an increased clarity in the San Francisco Bay area that’s been ongoing; it may be considered a more increasing problem as sediment loads are reducing.”

Depth has also been increasing at some of the stations, he noted.  “The reason why the midwater trawl and the otter trawl are diverging and how bad their showing the decline, is that it’s likely that it could be correlated with this water clarity and depth, and so we want to do a study to look at that.”

So what explains the catch?  “Obviously the decreasing abundance,” Dr. Acuna said.  “For the benthic trawl itself, there are decreasing abundance and maybe a shift in distribution.  For the benthic trawl, it looks like water clarity and station depth has had a significant effect, so we’re going to be taking a look at that.”

Next steps

Our next steps in our research will be working with a lot of different research partners, state and federal, as well as our consultants and research institutes such as San Francisco State University and UC Davis,” Dr. Acuna said.  “We’re using genetic analysis to understand the population of the longfin smelt, are they exchanging with those upper populations or are they a distinct population?  Life histories will be examined, using a lot of fancy chemistry to try to figure out exactly where they are, and that if we can figure out where they are coming from – if they’re coming from the Napa or upstream in Suisun Bay, habitat restoration can be localized to those areas.”

We’re going to be looking with our partners on distribution as well, looking at the trawl data and looking at why that trawl data seems to correlate with depth and water clarity.  That’s just correlation data, it doesn’t mean that it’s actually happening, so we want to go out and see if we can prove it by looking at some trawls.”

They have received a Prop 1 grant to do a longfin smelt distribution study.   “That’s going to help us work with our partners and collaborators out there in the Delta, especially this year, as it’s a very wet year and we want to be able to take advantage of what we’re seeing here.  Especially since the wet years tend to correlate with higher abundance, we’re going to get a lot bigger signal, understand the distribution in the water column a lot better, so we’ll be doing trawls that allow us to understand at what depths these longfin are at.”

They’ve been investing in the “smelt cam”, which is attached to the trawl, and as the fish travel through the apparatus, a photo is taken.  “With that information, we can actually gather where they were in the water column and help us understand those correlations we’re looking at.  That will help us understand and interpret the survey data; that’s very key to understanding what is happening to these fish.”

He noted that the smelt cam helps with take, as most trawls are fatal to the fish caught in them.   “With this apparatus, it’s much better.  A lot of the fish tend to freely and more safely pass through it with much less harm, so it’s a lot safer and a lot more environmentally friendly for the fish.”

They are also investing in modeling to help predict where the fish can be located and how they respond to management.  “Modeling is key in that to make those kinds of predictions, and we’re going to be calibrating those models using a lot of remote sensing data as well as other long-term data.  For example, we are working with Jet Propulsion Lab, trying to use their remote sensing data. … And it can be used for adaptive management because this data can be fed into models, allow us to do these predictions, run the study, implement it, and do it again, and that will help us further our efforts along the way.”

In summary …

The importance of our research is that our findings have found that a lot of the longfin smelt are spawning in brackish water, a lot more than had been previously thought,” Dr. Acuna said.  “We’re seeing a lot more local production in the brackish water and that’s important because restoration can be targeted there.  It does have more dependence on more local flows; Delta outflow will have an effect, but more local flows will also be key.”

How the fish behave in the water and where are they are in that water column is going to be important for understanding that survey data.  If they are too low in the water column, such as the midwater trawl, the station is just too deep, that midwater trawl can just pass right over them and not know they are there.  Also if the water is too clear, it could pass right by them as the fish avoid the trawl, and they could have been there the whole time.

This research has been very helpful for our collaborative efforts, working with state and federal agencies, as well as research institutes and our consultants, and we hope to be able to use this for adaptive management purposes, for flow management, and restoration,” concluded Dr. Acuna.


Director de Jesus noted that on Slide 8, there was information regarding some issues that have reduced the population since 1989, and yet the study shows how well they can grow and also where they do their best spawning.  “You also told us that there was a location that you found them to be growing in that previously you indicated that that was improbable, so what I gather from this is they are adapting, they are moving.  They are willing to survive elsewhere, so either they are going to relocate along the coast then in the Delta, or they are just going to go extinct.  And so I’m trying to grapple with what is it that we can really do other than put a lot of money into this and still have these a clamfest, if you will.”

As for the south Delta, it’s more a case of unlikely,” Dr. Acuna said.  “It’s been understood in US FWS documents that spawning down there is possible, it’s just highly unlikely.  It doesn’t mean that it won’t happen, it’s just under these really high flow years, it’s possible.  We’re still surprised by how much spawning had occurred there.  It was sort of a marginal habitat that seems to be a lot more important in these high flow years like this year.”

“The distribution was something that I didn’t really key on too much,” Dr. Acuna continued.  “There’s abundance and distribution.  Abundance is the number of fish out there, and distribution is how far into the SF Bay estuary are they.  Are they all the way in up to the San Joaquin and the Sacramento, or are they just occupying more ocean-like area?  Where are they exactly?  We know that they like to spawn in lower salinity water so we’re going to be dependent on these estuaries.  Where else they can be found is in the ocean, so they can be distributed there.  It’s believed that they are sort of opportunistic whereas the salmon needs to spawn at a certain spot, it’s possible these fish that like areas that, if the opportunity arises, say in San Pablo Bay, the habitat becomes fresher because of increased flows out of the Petaluma.  Now that presents an opportunity for longfin smelt to spawn, and that allows for that.  For increasing salinities in the SF estuary, that would start beginning to exclude them unless that kind of management can happen.”

Not only do we need those flows, we actually need the habitat to exist,” Dr. Acuna said. “Let’s say you have increased flow out of Gallinas Creek or something more westward, but the habitat there just wasn’t going to work for longfin smelt, so you can have increased flows, lower salinity, but it just isn’t going to work, so you need both.  That lower salinity area plus the habitat.

Director De Jesus asked if we should be more concerned about salinity and flows or the clams and organisms?

The clams really cause a huge step change in their distribution, so they don’t seem to be out there in Suisun Bay as much as they used to be,” Dr. Acuna said.  “I haven’t seen any successful implementation for the clams, so the investment we’re going to have to carry out is we’re going to be forced to into salinity management and restoration management because the clams .  It doesn’t mean we can’t try, it’s just that clam management has not been successful.”

So you’re really saying is in order to deal with the clams, which we can’t, is to dump more water and control salinity?” asked Director de Jesus.

I think we need to have more of a broad plan, looking at salinity both in local tributaries and restoration,” Dr. Acuna said.  “You put flow into the system, but if there’s no habitat for them, it’s not going to help.  And it just can’t just be Delta outflow; it has to be local tributaries as well.”


Steve Arakawa, Manager of Bay Delta Initiatives Program, then updated Committee members on the decision process for the California Water Fix project.

Last week, the California Water Fix announced a key milestone, which was the issuance of the biological opinions to support Cal Water Fix for both the Delta smelt and the salmon.  “The biological opinions provided a no jeopardy opinion, which means that the proposed action would not negatively affect the future viability of the species or the future existence of the species, nor adversely modify its habitat,” he said.  “That’s important to move forward with the project and understand how the project would need to be managed. “

The next key decision point is the Environmental Impact Report and Environmental Impact Statement.  “Under the California Environmental Quality Act, the state would make a decision regarding the environmental impact report for Cal Water Fix,” he said.  “It would certify that it complies with the CEQA; it would adopt a mitigation, monitoring, and reporting program; and it would adopt other findings regarding the impacts of the project.  Once the state takes that action, it would then issue a project order that approves the project as a component of the State Water Project, so that’s a decision that’s related to the state’s Environmental Impact Report and the California Environmental Quality Act.”

After the environmental impact report is approved, there is a water code section 2081 permit that is issued by the Department of Fish and Wildlife that covers the state listed species: salmon, longfin smelt, Delta smelt.  There also is the Environmental Impact Statement as required by the National Environmental Policy Act, and there would be a separate action with the Department of the Interior and the Bureau of Reclamation.

Another regulatory process is providing that certification to the Delta Stewardship Council that the California Water Fix is consistent with the Delta Plan.  Mr. Arakawa said he has tentatively set summer 2017, but it could happen sooner rather than later.  It’s a little unclear when the state plans to move forward on that.  It would then be up to the Stewardship Council to identify any appeals to that certification of consistency and if there are any appeals, that would trigger an appeal process within the Stewardship Council’s procedures.

Moving into the fall, the Army Corps permit might be issued by the end of the year or perhaps early 2018.

Regarding the Cal Water Fix petition at the State Water Board for the additional points of diversion on the Sacramento River, that process has been divided into two parts.  Part 1 deals with potential injury to other legal water users, impacts such as water quality, water levels, and water supply in the system; part 2 deals with potential impacts to fish and wildlife and consideration of flow requirements.  The species protected through this decision include Delta smelt, longfin smelt, green sturgeon, and different runs of chinook salmon.

The State Water Board began the hearing process in July of 2016; they are close to the close of Part 1.   The parties put on direct testimony; there’s rebuttal, and then sur rebuttal that allows for parties to come back in and clarify things identified in rebuttal.  “We expect that day to happen in the middle of July, and then once that happens, then the State Water Board would determine how closing briefs would be filed,” he said.  “Then following approval of the EIR/EIS, the State Water Board would have the decision on when to initiate Part 2 because the biological opinions and the EIR are part of what they were waiting for in order to initiate Part 2 of the proceedings at the State Water Board.”

Regarding allocation of costs, Mr. Arakawa said discussions and efforts continue on that, both in terms of how costs would be allocated between the state and the federal water project contractors, and then also how those costs for each of those would be allocated within that group.  The costs would be divided up with 45% allocated to the Central Valley Project and 55% to the State Water Project.   On the State Water Project side, costs would be based proportionately on their Table A contract amount.

The cost of Cal Water Fix would be based on those terms in the contract, essentially the water benefits would be tied to the costs, so you would be paying for the investment based on the water supply and the benefits that are provided, consistent with the State Water Project contract, so that is still the approach that’s being pursued,” he said.  “A lot of the recent work has been on the finer details of how all of that would work, including how contractors could have the opportunity to manage their supply with other contractors through exchanges or transfers, and so that kind of detail is being worked out.

On the CVP side, similarly they are having conversations between themselves and determining how the investors and those that are not part of the export area that counts on the project or will not count on the project, how they will deal with that.


Director Steiner asked with the biological opinions are completed, are the conversations speeding up so that the white paper on Cal Water Fix financing will cover it?

Roger Patterson said they are planning to have the term sheets for the cost allocation.  “We won’t know who is participating on the CVP side as their decision on participation will come in September, but we’ll have the term sheets … ”

Director Steiner asks, “Regarding the CVP, there was an article about a letter that was sent by various northern and central California agencies to the Bureau saying that – and I may be incorrectly paraphrasing it – they are not interested in paying for the tunnels and they don’t want to lose any water and they are seeking assurances as one might expect that they in fact would not be paying for anything or having any diminishment of their water, and so is that part of what you’re talking about the CVP … ?

I don’t think that it is,” said Roger.  “I think Reclamation has essentially said, from what I’ve heard, that this is the way it needs to be, if you’re not getting benefits you shouldn’t pay.  There are mitigation measures for the entire project that we’re dealing with now under the biological opinions which they do distribute out to the entirety of the contractors, so that’s not what I’m talking about.  What I’m talking about having them on the CVP side describe the methodology for participation by CVP contractors in Cal Water Fix and how that will work and under what terms.”

Director Steiner asks, “If we have an agency or participant in the state contractors who is not interested in this and is going to assert that they have dual conveyance rights, that discussion is still going on as to what their rights might be to water if they choose not to participate.  Would that be correct?

I would describe it this way,” said Roger Patterson.  “DWR is working with the state contractors; we envision taking our share of the project and distributing that out proportionate to all of the contractors, except north of the Delta.  All of the contracts proportionate to Table A.  And then it will have the mechanisms that are provided in the contracts if someone wants to reduce their costs and is willing to accept less reliability, they find an arrangement with another contractors, which is what happens now, so that is the model that we are using on the state side, which doesn’t take a contract amendment to do that.”

One caveat on that is in the white paper, what the contractors have discussed amongst themselves and proposed arrangements, and that would be what we would be bringing to the board, with recommendations from GMs of all the agencies,” said General Manager Jeff Kightlinger.  “None of us can entirely predict how the board will react to those recommendations and the results may be different than the recommendations, but all we can do is bring to you what the plan is and then we’ll have to see how every agency votes.  We’ll be reporting back to the board how people reacted to that proposal.”

We’ve envisioned the project always being dual conveyance, so are we thinking that the part that’s going to come through the tunnels is what people are either going to opt in or opt out of, but to the extent that somebody didn’t participate in the tunnels, that what they get across the Delta is still going to be divided by Table A?” asked Director Morris.

On the state side we’re not looking at an opt in or and opt out approach,” said Mr. Patterson. “The approach is everybody is going to be allocated their share and then if you want to change the distribution of that because of economic impacts and you’re willing to accept less reliability, you can do a Table A transfer or some other kind of arrangement with someone else.  So all of the state contractors would be involved and their entitlement to the total water supply would be proportionate to their Table A.”

But then everybody has to pay their share for that deal … “ said Director Morris.

You could have someone say, ‘I don’t want to take on a certain amount of this additional cost; I’m willing to give up a certain amount of reliability proportionate to that, so is there another state contractor willing to pick up the extra cost and increase their reliability further?,” said Mr. Patterson.  “So that’s the transfer mechanism.”

I’ll provide a concrete example,” said Jeffrey Kightlinger.  “You’re probably aware Metropolitan has an arrangement with the Coachella Valley Water District, where we have transferred 100,000 acre-feet of Table A to them.  They pay for it, we have a callback right, when we need water and want to put it in storage, we call it back and then we pay for it, so that’s a way they get more water reliability, we get cost relief, and we’ve made that arrangement.  There are other such arrangements like that.

Director Morris said, “I just want to make sure we’re not going to get into a situation where a bunch of people say we’re going to pay for these tunnels because it improves our reliability, and somebody in the group says, I don’t’ want to pay for that, but you guys get your water through the tunnel, and then the water that comes across the Delta, I’ll get that because you already got yours, and I’ll get mine without paying for the tunnels.  I want to make sure that doesn’t happen.”

To take that last thought, you’re going to have your Table A, and you’re going to decide how much of it you want, and it’s either going to come through the dual conveyance or the tunnels, but that’s all you’re going to get if you choose not to pay for your share of the tunnel,” said Director Steiner.  “In that sense, wherever that water comes from, you’re just going to get that percentage.  Would that be right?  Because you can’t have it so that ‘I only get water through the dual conveyance and I’m not going to get water through the tunnel’; I just don’t envision how that’s going to work.”

Steve Arakawa said, “The way the contractors have been talking about Cal Water Fix is that it’s an integral part of the existing State Water Project, so it would be an added facility to the State Water Project and it would be up to DWR to operate that whole system, so there’s not Cal Water Fix water and then State Water Project water.”


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