DELTA STEWARDSHIP COUNCIL: Update on the Delta smelt resiliency strategy

Hypomesus_transpacificus Delta smelt sliderbox

In July, the Natural Resources Agency released the Delta Smelt Resiliency Strategy, a set of immediate and near-term management actions intended to improve the status of the Delta smelt, in response to record low numbers of Delta smelt for two consecutive years.

delta-smelt-resiliency-strategy-final070816_page_01The strategy identifies 13 management actions intended to be implemented by the Department of Water Resources, Department of Fish and Wildlife, and Department of Boating and Waterways, with assistance from the Bureau of Reclamation in actions that involve flows.  The identified actions include habitat restoration actions, water quality improvements, food production increases, and flow alterations to expand the area of low salinity in the Delta.   The 2016-17 budget allocates funding for three of the proposed actions: aquatic weed control, North Delta food web projects, and a feasibility study for restoration at Frank’s Tract.

At the September 29 meeting of the Delta Stewardship Council, Kris Tjernell, Special Assistant for Water Policy at the California Natural Resources Agency; Cindy Messer, the Assistant Chief Deputy Director at the Department of Water Resources; and Carl Wilcox, Policy Advisor to the Director of the Delta coming from the Department of Fish and Wildlife, updated the Council on the status of the strategy.

KRIS TJERNELL, Special Assistant for Water Policy at the California Natural Resources Agency

Earlier this year, we were faced with a couple of really challenging facts,” Kris Tjernell began.  “One was we were at the beginning of what was likely to be the beginning of a fifth year of extreme and widespread drought, not just affecting the Delta region but statewide, and the other fact was that we were facing continuing declining trawling data and increasingly worse data from Delta smelt surveys.   The information that was coming back was so bad, it prompted to a large degree the Delta smelt symposium in late March of this year that was called, Delta and Longfin Smelt: Is extinction inevitable?  It became clear there was an opportunity and a tremendous need for a coordinated effort to do something about the situation.”

tjernellThe Natural Resources Agency worked closely with the Department of Water Resources, California Department of Fish and Wildlife, US Fish and Wildlife Service and other partners, and began crafting a strategy to start addressing these issues.  Using the Delta smelt lifecycle work and recommendations from the Delta smelt symposium, actions were identified that could be advanced in the next several years.  The CSAMP or the Collaborative Science and Adaptive Management Program is the forum for determining the research questions and the monitoring actions necessary to evaluate the success of the actions and implement adaptive management actions if not.  In July, the official Delta smelt resiliency strategy was released to the public.

The timing of all this realization and invigorated effort worked well with the budget process, so through the May revise process, we were able to insert $4+ million into the Governor’s 2016-17 budget to help seed some of the early efforts,” said Mr. Tjernell.

Mr. Tjernell likened the Delta smelt strategy to the California Water Action Plan, only focused on the Delta smelt.  “Similarly, the Delta smelt resiliency is an attempt to rise above the rhetorical fray, cut through the politics, and articulate an scientifically sound and doable three-ish year strategy for trying to flip this particular fish’s fortunes and see what we can get done over the short period of time and do it in a concerted coordinated fashion, and with everything going hopefully very well, we really will see a change in the population dynamic out there,” he said.

CINDY MESSER, the Assistant Chief Deputy Director at the Department of Water Resources

Cindy Messer then spoke about one of the early successes of the strategy that was implemented this summer.

item-9_page_1Delta smelt abundance is at an all-time low, and the low numbers from the long-term surveys are continuing.  “We took a look at what are the major causes of the low abundance numbers, and food limitation is one of those,” he said.  “This particular action is in the strategy because it helps to address not only the limitation on food quantity, but also the quality of food that Delta smelt and other key species in the Delta require.”

Ms. Messer noted there were other reasons for taking this particular action.  “There were past events that occurred naturally that led us to believe that we could successfully implement this action,” she said.  “Back in 2011 and 2012, there were higher than normal outflow or ag return flows coming out of the Yolo Bypass that spurred a plankton bloom in the Delta in the Rio Vista area.  Scientists detected that blip in the phytoplankton numbers and retraced it back to water that was coming out of the bypass, so we thought maybe we could recreate this event on an annual basis with very little or no cost to water users.”

Ms. Messer then addressed short-term and long-term goals of the strategy. “In the short run, what we wanted to do was get something implemented, get a pilot effort on the ground, adopt an adaptive management approach to this action as well as all of the actions in the resiliency strategy, and to learn what we could learn this year, apply it to the next several years, revise the work plan and the action itself, and continue to make this a very efficient and effective means to help Delta smelt out,” she said.  “That was our short term goal.  I think we met those, we got an action on the ground, we’re still analyzing all of the sampling that we did.  We have some lessons learned and we definitely worked through a lot of kinks that I think in the next several years are going to make this even more successful.  Our longer term goal is helping to address the food limitation issues.”

item-9_page_2For the food web action, water was redirected out of the Sacramento River through the Colusa Basin drain as indicated by the red dotted line on the map.  The water was redirected through the Knights Landing Ridge Cut slough, past the Wallace Weir, and through the bypass and into the Delta.  About 12,750 acre-feet of water was redirected through the bypass over a three-week period in July.  Monitoring was able to pick up signals from that pulse flow down by Rio Vista and other stations in the Delta.

Ms. Messer said one of the exciting things about implementing the action was that there were some current conditions they were able to work around.  “There’s quite a bit of activity in the Yolo Bypass on some other priority efforts, the construction of the Wallace Weir being one of those, and so we found ourselves meeting up against a construction schedule for the weir, so we had to quickly adjust our timing for this action,” she explained.  “We originally had thought about doing this later in August, maybe the first part of September, but that wasn’t going to work for this year, so we kind of rallied around an earlier date, looked at a source of water and quickly gathered our partners to figure out how to move that water through the system in the time that we had to do it.  It was an exciting four or five weeks of getting this together.”

In terms of monitoring, there was extensive monitoring of parameters to track the pulse flow as it moved through the system out into the Delta; there was also extensive monitoring of water quality parameters such as nitrogen, phosphorous, dissolved oxygen, pH, total dissolved solids, some organic carbon, and others, as well as phytoplankton and zooplankton samples.  There was also contaminant monitoring for pesticides and herbicides, and benthic monitoring, mostly around clams and any response they might have to the phytoplankton bloom.

Ms. Messer pointed out that the successful outcome was the result of a high degree of collaboration and coordination with the local entities, various state agencies, the federal agencies, and academic partners.

item-9_page_4She then presented a graph of chlorophyll A measurements at Rio Vista.  “You can see the big spike and the big bloom detected out at this location in the Delta,” she said.  “We did get a little nervous, as this was at the point of time when there was a lot of attention around harmful algal blooms going on, so we thought we better get out there and make sure we’re not creating more bad species.  So we did some additional grab samples and quickly did laboratory work to identify the species, and in fact, we found this bloom was made up of beneficial or good species of phytoplankton.”

We also did some backtracking with stations up the Sacramento River just to reassure ourselves that the bloom wasn’t coming down the river but in fact was coming through this pathway we created in the bypass and we were able to also detect that with the sampling and the monitoring we had in place,” she added.

messerMs. Messer said they are very sure they will be able to repeat this exercise in the next couple of years.  “We’re looking at possibly more than one event in the year, but obviously that requires us to take a look at sources of water,” she said.  “Ideally what we would do is maybe shoot for the late August, early September time frame when we would have ag return water as was our original goal, but having seen such a positive response even in July with a different water source, we’re going to be looking at what our options might be for the next couple years to repeat this exercise and enhance it.”

Ms. Messer noted that the funding in the Governor’s budget will carry the strategy through the next several fiscal years.  “Stay tuned as we definitely will have a fuller story of what happened when we start to get the other samples processed and we pull that together in some sort of a publication.”

CARL WILCOX, Policy Advisor to the Director of the Delta coming from the Department of Fish and Wildlife

Carl Wilcox then briefly ran through some of the other actions identified in the resiliency strategy.  “Nine of them are really things that based on the plight of the species this year as a result really of the last four years of drought and the really poor conditions that Delta smelt in particular have experienced in the Delta,” he said.  “Using the conceptual model that’s been developed through the Interagency Ecological Program for Delta smelt, we made a strong effort to identify actions that we could take in an adaptive management way that could potentially provide benefit. … Some of them are move developed than others.

wilcoxThe aquatic weed and the north Delta food web actions were things people were already thinking about, Mr. Wilcox said.  “The food web enhancement was something that Ted Sommer at DWR and his folks had been working on and looking to implement, and the Department was able within this year’s budget to get funding to support that.  The things is we needed to implement it sooner and on a revised schedule because of other things going on in the bypass, so we actually have spent some of that money in an emergency way and in an incredibly quick turnaround to support diversion of water by RD 108 and RD 2035 to help stimulate and actually make the food web experiment work this year.

In future years, they will be relying more on ag drainage and won’t necessarily have to work with cooperators to divert flows specifically for that purpose.  “I think that’s something we’ll be evaluating since we did see a benefit in July from that action, and that’s kind of a critical time, and that goes to the idea of a summer outflow action,” he said.  “This was a new thing that is an outgrowth of seeing relatively good conditions this year from a flow perspective and an outflow perspective for Delta smelt coming out of the last four years of really poor outflow conditions particularly in the spring.  The idea was that if water could be acquired to maintain outflow which is basically a surrogate for habitat quality within the rearing zone for Delta smelt, and trying to keep rearing habitat as far down the Delta and hopefully into Suisun Bay, which has been historically an important area, we can look at potentially overcoming a bottleneck that even in better years, poor summer conditions that result in basically poor juvenile survival, which results in lower adult survival in the fall and then going into the spawning season in the winter.”

Posterboards at media event in Yolo Bypass

Unfortunately, given the lateness of the action, the issues tied up with Shasta temperature management actions, and just the ability to acquire water on a short time basis, the summer outflow action wasn’t pursued, but we’re going to be moving forward this year,” Mr. Wilcox continued.  “We have six months to come up with a plan and associated monitoring program to evaluate an action if it can be implemented, to lay out when the water would be best applied, and the monitoring program which we’ll be looking to the CSAMP process to help us develop in a collaborative fashion, so we’ll be ready to implement that and to assess what the benefits coming out of the action would be.”

Mr. Wilcox acknowledged that much will depend on whether or not the water year is one that actually generates enough water to be able to buy, acquire, or have water for that kind of an action.  “There are a lot of unknowns, so we’ll be laying out some scenarios about how we would proceed and that would go into a water plan that would look at not just the summer action but how that fits together with the temperature management plan for Shasta and the overall operations plan within the requirements of the existing biological opinions and CESA authorizations for the state and federal projects, as well as meeting the water quality control standards and those kinds of things.  It’s not a simple process to get all those things lined up.  Any time we talk about flow and augmentation of flow as Delta outflow, it’s intimately tied to what you’re doing at particularly at Shasta to manage cold water pool, and so that’s a very delicate balance to work through.”

Flows were sent through the Yolo Bypass to stimulate the Delta’s food web. (Photo courtesy of DWR.)

There is funding for the aquatic weed control program which will be a multi-year effort and assessment program that will focus first on Franks Tract, but potentially in other places.  “There are issues to overcome relative to having the appropriate endangered species authorizations currently as they are somewhat limited on that program, particularly on the scale we want to pursue it,” he said.  “The underlying idea there is to improve places like Franks Tract, potentially Big Break, and Sherman Lake as suitable habitat.  They are heavily invaded by particularly Egeria, and other aquatic species that serve as great habitat for non-native predatory fish, particularly black bass and other centrarchids.  By reducing the habitat suitability for those species by removing the aquatic weeds, the idea is that we can potentially improve the habitat for Delta smelt, which would use those areas otherwise because it’s within their rearing habitat and the low salinity zone.  That will be ongoing over the next couple of years.  It will be implemented starting next year.”

One of the actions that requires more planning over the coming year is looking into how the salinity gates on Montezuma Slough to better manage habitat.  “There’s a tricky interaction that goes on between operation of those gates to keep salinities lower in Suisun March as opposed to what the effects of those are on salinity in Suisun Bay and in the confluence area, so a lot of work that’s going to have to happen,” he said.   “The underlying rationale is that if you could keep Montezuma Slough, Nurse Slough, and Suisun Marsh a little fresher, it is potentially better habitat for Delta smelt, and how you might be able to operate that to achieve that benefit.  Past studies have shown that this is an important refuge area for that species, and also the food supply tends to be a little better up there, potentially, so they are healthier and they are not as affected by contaminants as fish in Cache Slough or Suisun Bay in general are.  Whether or not we can make that work necessarily is something to be determined.”

There are some additional actions in Suisun, looking at taking managed wetland water from Roaring River and other managed wetlands and releasing it into Suisun Bay or Montezuma Slough to stimulate food web support for Delta smelt and other species.  “Basically the managed wetlands bring in water, they hold it,” he said.  “In the manner of holding it, you have longer residence time, it tends to grow lots of zooplankton and algae that when released, can provide a boost to the receiving waters.  Those are things that we’ll be working on and hopefully have ready to go next year as we manage into that season.”

Other actions are looking at augmenting turbidity and potential spawning habitat, but more planning is necessary.  “These actions will probably have regulatory consequences, particularly as it relates to water quality, because it’s going to involve putting sediment back into the system to create turbidity and stimulate that, and turbidity is an important factor, particularly for Delta smelt and their success,” he said.

As part of the strategy, they will be developing a conceptual plan and feasibility study for restoring Franks Tract and other flooded islands as habitat.  “Franks Tract is flooded; there are lots of aquatic weeds, highly dispersed tidal circulation, and very poor habitat, and whether or not we can modify that in a way that improves the habitat quality for Delta smelt and potentially provides resilience in the future for sea level rise accommodation within that area, as the low salinity zone moves up into the Delta, and by providing improved habitat there that can meet a number of the life history requirements and physical habitat characteristics that can be used by Delta smelt.

Construction underway at Wallace Weir to prevent salmon straying into the Colusa Basin
Construction underway at Wallace Weir to prevent salmon straying into the Colusa Basin (Photo courtesy of DWR)

The target is to have that feasibility study and a conceptual plan done by the spring so then we can move forward with further refinement if it proves to be something that’s doable,” he continued.  “That’s really looking at placing fill within Frank’s Tract to build up the elevations to intertidal and making it a little more like it was historically.”

Mr. Wilcox said that while Franks Tract is a potential area for improving conditions, there are issues.  “We’ll need to work with the County and the local communities on some issues, but hopefully balance the benefits for native species as well as the concerns of the local communities as well, because it’s going to have navigational issues probably and other kinds of things.  It’s probably going to have some effect on that booming black bass fishery and tournament fishing that goes on down there, so that’s all going to have to be taken into consideration as we go forward.”

Mr. Wilcox noted that the Department did receive $4.2 million this year in reprogrammed drought money, most of which is going to support the scientific work being done to support the food web augmentation and the invasive weed control program and assessment; a portion is going to go for developing this feasibility study for Franks Tract.

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fioriniI recently realized that nothing good happens in the Delta without a champion to move things forward,” said Chair Randy Fiorini.  “The evidence of that is Eco Restore, the Yolo partnership that we regularly receive reports on of successes that have been achieved and obstacles that have been overcome through cooperation.  So I count the smelt resiliency plan as another in the efforts of this administration to take some bold action.  I know that there’s some criticism that not everything that’s been proposed has been universally embraced, but I’m glad that you are taking steps to do something.”

piephoCouncilmember Mary Piepho asked if 12,750 acre-feet was the desired amount of supply or only what was available.

The original proposal anticipated something on the order of 24,000 acre-feet, and it was really intended to be driven off of ag drainage as the rice fields were drained for harvest and the water was run down the bypass,” replied Mr. Wilcox.  “In this case, since it was July, and the water that was available, it was a shortened time window, and it was also driven to a great degree by the willingness of particularly the Glenn Colusa Irrigation District to actually divert the water at no cost and forgo the use of that water since it was diverted under their rights, and run it through the system.  That was augmented by RD 108 pumping some additional water and then the Conaway RD 2035 provided additional water later in the flow period, because we were running into issues with actually being able to run water through the Colusa Basin drain because of the Wallace Weir reconstruction.  RD 2038 is downstream of that site, so their water came in later in the exercise, but it wasn’t as much, but we obviously saw a signal.  This goes to the issue of taking in adaptive management action, and we took a chance, it seems to have worked, and we had monitoring in place.”

weinbergCouncilmember Ken Weinberger asks, “How do you get timely action on dealing with these conflicts between what you’re trying to accomplish in a pretty expedited manner, given the abundance indices and dealing with water quality issues and those kinds of conflicts?

Let me start by describing our approach to each of these actions,” Ms. Messer replied.  “Some are further down the road than others.  I think we are fully embracing the adaptive management spirit in this.  We’re always looking for what are the potential tradeoffs or indirect impacts from these actions as we move through, and I think we have the flexibility to revise and craft these actions in ways that might minimize those other impacts.  There may be some actions as we go through and we start to peel away the layers … each one of these is kind of its own project, it has many layers and discussions that need to happen; we will just have to adjust in some ways to still try to carry out the actions, get the benefits that we’re aiming for and meeting the objectives. … I think we’re spending a lot of time this year in this feasibility planning mode to really lay out what are the challenges, what are the opportunities, and then where do we go with a work plan from there, but each one definitely has a full suite, ranging from very minor things to whether it’s regulatory hurdles or just physical limitations, and feasibility.”

I think a lot of the strategy is going to implicitly rely on being at the right place at the right time,” said Mr. Tjernell.  “I think there’s a lot of value in having a plan like this articulated in advance so we can be as ready as humanly possible, with the understanding that there may not be, for every one of these actions, a perfect right place at the right time.  The example that Cindy went through is a good example; we’re constructing Wallace Weir on an extraordinarily fast timeline.  They are about to go to 24 hour construction days, for primarily the benefit of winter-run chinook salmon.  But that construction schedule was right in the way of this action, so what did we have to do?  We still had to go for it, so we said, ok, we’re probably not going to be able to move all 20,000 acre-feet of water, but we can move less.  And maybe we can’t move it in August or September like we’d want to, but we can move it in July.  We decided we should still do it, because we have a little bit of history suggesting that at least in different parts of the year, we actually can see a response … We actually had this plan and said, it’s not perfect, but let’s go ahead and do it, and I think that’s where a lot of the value lies.”

dr-dahmDr. Cliff Dahm, Delta Lead Scientist, noted that there was a similar event that produced chlorophyll in the March-April timeframe.  “The big March flows that spilled into the Yolo Bypass which then over a period of time began to drain back into the Sacramento River, and a similar kind of response to the one that was generated by the July flows occurred and peaked at something like 30 micrograms of chlorophyll A and I think the values here were 10 to 15, so even stronger and that one is again a byproduct of what you’ve heard about a lot and that’s the importance of these spring pulse flows in connecting the river and the bypass and the floodplain and getting that water out onto the floodplains, and then as it comes back into the Delta, providing the stimulation to the base of the foodweb.  I think all of us are very interested in the question of whether this is going to cascade upward into an effect on fish and particularly an effect on native fishes, and I know that’s what the monitoring program is all about.”

We’re talking about doing this action in 2017 with augmentation in the late spring-summer, and in 2018,” continued Dr. Dahm.  “We’ve heard a lot of discussion about the amount of water it’s going to take …  Could you give me an update on where we are on the summer augmentation planning for 2017-18?

wilcox-discussionWhat has been discussed is something in the range of 250,000 acre-feet that would be used to augment outflow, depending on the water year type, either beginning in the spring or later in the summer,” said Mr. Wilcox.  “This would primarily be releases into the river system as opposed to in the bypass, so there’s a difference.  In the bypass, the volumes of water there were basically generated off of what could be run through the system using primarily drain water without adversely affecting ongoing agricultural activities within the bypass, so primarily keeping the flow within the Toe Drain and the Tule Canal as opposed to getting it outside, and really just focused on having a positive outflow from the bypass.  Normal conditions without input from upstream, it’s basically either a negative system or zero, so there’s not really any exchange downstream, and it’s tidally driven, so they are different in how they would operate.  The larger flow augmentation is basically targeted at affecting Delta outflow as opposed to what it might do in relationship to the bypass; one of the things is in doing this action in July, the water that basically put to it did contribute to outflow in a small way, so there are some synergies, depending on how those things can be timed and whether or not they fit with the upstream diverters ability, particularly in July or earlier in the year, to work with their agricultural operations and their water demand and their water issues.  We’re fortunate this year, particularly as it related to Glen Colusa that they were willing to do this and forego the use of that water and putting it through the system.

Then I assume these future year summer flow augmentations are more focused on changing the salinity field then stimulating the food web, or are the goals still both?,” asked Dr. Dahm.

The flow augmentation would be affecting the location of the low salinity zone and intended to keep it farther down the system, so the idea would be to keep X2 at Collinsville or below Collinsville and towards Chipps Island for as long as you could with the amount of water you have available,” he said.  “The idea there is to provide good conditions for rearing Delta smelt, so that they get to the point where they have the health conditions that they can make it through or habitat conditions later in the summer.

Dr. Dahm notes that Eco Restore has about 30,000 acres of restoration planned, 17,000 acres of that being floodplain connectivity projects.  “What have we learned from the pulses that are guiding you or assisting you in thinking about that part of Eco Restore?

tjernell-discussionThe timing for learning from these experiments and actions is perfect because we are planning on having ready for the larger Yolo Bypass salmonid restoration and floodplain habitat project EIR/EIS public draft in summer or late summer of next year,” said Mr. Tjernell.  “So to the extent that we can learn examples, that could ostensibly affect how we craft the specifics of the operation of essentially the notch in the Fremont Weir that’s going to be facilitating the increased frequency and duration of floodplain inundation.  Clearly the focus of that project right now is on sturgeon, salmon, and steelhead, but to continue down the path that is exclusively focused on the species that the biological opinion requires us to focus on at the expense of taking advantage of opportunities that might otherwise be there would certainly be a bad idea, so we’re going to be drawing in this type of data as it becomes available and trying to adjust as is possible.

One of the things that the reconstruction of the Wallace Weir allows us to do, it allows us to have significantly more flexibility when it comes to regulating flows from the Colusa Basin drain down to the Knight’s Landing Ridge Cut into the Yolo Bypass,” continued Mr. Tjernell.  “Just that construction project alone that is focused on keeping winter run chinook salmon out of the places they shouldn’t be itself will have an adaptive management program associated with it, has the potential to be extraordinarily beneficial for these smelt-focused projects as well.”

Dr. Dahm then asked about evaluating the effectiveness of these 13 actions.  “The difficulty of doing that when you have such limited take on Delta smelt, so how are you going to evaluate the effectiveness of these actions with some of the very serious constraints that exist now in the system?

The focus is not going to be so much on the fish, it’s going to be on let’s say as it relates to the food web augmentation, it’s going to be on did we generate food,” said Mr. Wilcox.  “We’ll find out what the fish benefit was potentially through the ongoing monitoring for fish, either through the Fall Midwater Trawl or the Summer Townet, but not adding more of that kind of sampling.  One of the issues that we’re confronting with the veg management stuff is being able to have any take at all, so how are you going to assess that and it’s probably going to be are we seeing a decrease in the footprint of vegetation and then can we sample for non-target fish that we’re concerned about as it relates to reducing habitat quality without getting into a situation where we might incur take, and what’s that going to look like.  This is a real struggle right now, with particularly Delta smelt being at such low population levels.  How do you authorize the ability to do that without jeopardizing its continued existence and how do you assess whether or not the benefits of your management actions are doing good things for them, but you have to do that by looking at surrogates which would be indicators of improved environmental quality that we know they would benefit from.”

For more information …

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