Factors controlling the abundance and distribution of species in the Bay-Delta system

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At a recent State Water Board meeting, Delta Lead Scientist Dr. Cliff Dahm summarizes four recent scientific reports on the fishes, flows, and other stressors in the Delta

The stated mission of the Delta Science Program is to provide the best possible scientific information to inform water and environmental decisions in the Bay Delta estuary.  This includes organizing peer reviews and sponsoring workshops on important issues in the Bay Delta system.

SWRCB logo water boardsIn recent years, the Delta Science Program has conducted multiple external peer reviews on factors believed to affect the abundance and distribution of fish species in the Sacramento-San Joaquin Bay Delta Estuary.  Two of the reviews, the peer reviews on the effect of interior Delta hydrodynamics and Delta outflow were conducted at the request of the State Water Resources Control Board (State Water Board).

In this presentation from the State Water Board’s April 5 meeting, Dr. Cliff Dahm, the Lead Scientist of the Delta Science Program, reviewed and synthesized key scientific findings, uncertainties, and recommendations on the biological resources in the Bay-Delta Estuary as summarized in four reports:

Dr. Dahm presented each of the reports in a similar manner, giving the background of the report, the key points and take home messages, key uncertainties and data gaps, and a specific look at the research going forward.


This report builds off some important papers published in the early 1990s that looked at the location of the interface between fresh water and brackish water.  Dahm at SWB_Page_03This interface is often referred to as X2, and it is the point where you have approximately 2 points per thousand salinity,” Dr. Dahm explained, noting that seawater salinity is 35 and freshwater is less than .5.  “These are locations that move in space and time.  The location does have some clear interactions with some of the physical dynamics and with some of the ecological players in the Bay and the Delta.  This report basically builds on some of this work that was done in the 90s that showed that there is zone of interaction that has some pretty important ecological and physical characteristics that are important to a lot of water quality issues and to a lot of fish species and food web relationships that go on within the Delta.”

Take home messages

The report had a number of take home messages.  One of them was that monthly and seasonal outflow objectives do not capture sufficient flow dynamics to protect species and ecosystem health.  Dahm at SWB_Page_04We often work at monthly and seasonally time steps to discuss the flow criteria, but most of the biological communities and most attributes of the food web work on a much shorter time frame – more of a daily or at most a weekly time step,” he said.  “There is a real need to get our time steps that we study, some of the dynamics of these systems, and the regulations we set to be more in tune with each other.  Daily is certainly the time step that the people that wrote this report were very much suggesting.”

He used the example of pulse flows that occur in the late winter or early spring.  “They affect a number of different factors,” he said.  “They cue a lot of behavior in some of the fishes and they provide certain types of water quality characteristics, so those are the kind of things that happen on more of a daily or short time period that doesn’t often capture well when you use a monthly time step in your decision making.

Dr. Dahm at SWBChair Felicia Marcus asked if there are tools existing today to do that now, compared to the 90s.  Dr. Dahm replied, “I think we do, certainly on the hydrodynamics side of it.  We probably still have a ways to go to be able to follow a lot of those short time step dynamics of some of the biological communities, but there’s some progress being made.”

Another take home message in the report was that the panel did not think that modest changes in fall Delta outflows were likely to result in increased abundance of the key pelagic fish species, Dr. Dahm Said.  “Fall outflow is a very controversial topic, and this was their conclusion.”

More significant changes, or doing it all … ?” queried Ms. Marcus.

“I think their focus was mostly that right now we’re probably not going to have much of an effect,” replied Dr. Dahm.  “You have two choices: you either go to a more dynamic fall outflow or you simply don’t continue to stress the need for the fall outflow.  Reading the report, from my perspective, I think they feel like the evidence for the fall outflow is moderately weak and spring is a much more important period of time, from the information that I got out of the report. Spring dynamics and spring flows.”

Another take home message was that variation in volume or area of physical habitat are unlikely to be the direct mechanism behind abundance-X2 relationships.  Dr. Dahm noted that the panel report discusses what’s causing interactions in the X2 area and how variable the location of X2 is.  “There’s been a tendency in recent years to have X2 be more static and not as dynamic as it’s been in the past, although wetter years still do produce some of the more dramatic changes of X2 moving further to the west,” Dr. Dahm said.  “That dynamic between X2 and habitat is one thing that there’s just not a lot of habitat in the area where X2 hangs out these days, compared to what it might have been historically.”

Key uncertainties and data gaps:

The panel recommends using tidally averaged values for X2.  “X2 is very much affected by tidal dynamics within the Delta, so it’s really important to use a tidally averaged X2, not an instantaneous X2, Dahm at SWB_Page_05because the tides are going to move this location and can move it fairly substantially, so use tidally averaged values,” he said.  “There are sensors and there is methodology available to do that.”

Another recommendation is to measure fish responses in space and time to outflow management. Our ability to put tags in smaller fish has improved; this latest generation of tags can be used on fish as small as 70 millimeters or about 3 inches long, said Dr. Dahm.  “This is a technology that will probably allow us to do better on measuring fish responses in space and time to various management actions,” he said.

Flow and salinity (X2) relationship changes with engineering changes, Delta levee failures, restoration activities, and sea-level rise.  “The report has some examples about how things like engineering changes to the Delta, levee failures, restoration activities that are being planned, and sea level rise are all going to affect the location of X2, and so X2 is in no way a static measure.  There are human and anthropogenic long term climate changes to be considered when you deal with the location of X2.”

Model predictions are relatively uncertain.  “There was a clear recommendation from the report that the capacity to model the Delta in three dimensions, not just 2D or 1D, is getting better and better,” he said.  “In fact, some of the 3D hydrodynamic models that are being utilized now are open source, so they are not proprietary like they used to be, and certainly there’s a suggestion that we move to the use of these kinds of open source models to do hydrodynamic modeling.  There are some really robust hydrodynamic models now available.”

Research needs moving forward

The panel did make a number of recommendations on research going forward, including improving the modeling capacity, but Dr. Dahm focused on the research studies needed.Dahm at SWB_Page_06

One of the areas they point out needs some attention is that the Delta is becoming clearer,” he said.  “The reason the Delta is becoming clearer is that a lot of that sediment that was mobilized during the mining days has moved through the system and the rim dams are holding back a fair amount of the sediment, so there’s been a distinct clearing of the water in the Delta.  That is a nice example of an interaction between flows and a parameter like turbidity, and the effects of that on the biological communities is something that deserves more attention.”

The panel also noted that invasive clams exist in high numbers in the sediments of the area affected by X2 and their effects on food webs and on food resources is an area that could be linked to hydrodynamic modeling.  “It is something that’s a real question about whether the food resources available to the fish communities is being limited by the tremendous amount of filter feeding that goes on by these two species of non-native clams.”

The panel report also notes that more focus is needed on the issue of primary production by the open water phytoplankton.  A couple of areas in particular are of interest, said Dr. Dahm.  “Since about 2000, the Delta has seen blooms of a harmful algal species.  It’s microcystis; it loves warm temperatures, it likes fairly stagnant flow, long residence times, clearer water and lots of nutrients, so you throw that mix together and you get blooms of microcystis.  Microcystis has become a problem particularly in the late summer or early fall months in the Delta.”

There are some other questions about growth characteristics and whether or not the form and concentration of the nutrients are having an effect on the kind of rates of production are occurring in the Delta, so those are some of the other research needs moving forward that this group highlighted,” he said.  “I think we can state with some confidence that there is certainly new research on all of these topics.


Dahm at SWB_Page_07Dr. Dahm noted that the issue of predation has really been raised recently by some important papers.  The paper by Nobriga and Feyrer published in 2007 really brought attention to predation within the Delta, particularly salmon smolts, he said.  “A few of the take home messages from some of this early work was that largemouth bass seem to be an important predator on the salmon smolts; a lot of the predators seem to be located in areas where submerged aquatic vegetation, particularly the egeria densa, the Brazilian waterweed, is doing well.  There’s also some interest in predation from striped bass and there’s a seasonality associated with that.”

This report and subsequent studies have tried then to focus more information on predation, using small acoustic sensors on the fish to gather more information, he said.

Take home messages, key uncertainties and data gaps

This report’s take home messages were that predator-prey dynamics in the Delta are quite complex, and they are quite variable spatially, Dr. Dahm said.  Dahm at SWB_Page_08They really need some information what proportion of the juvenile salmon mortality is predation; there are certainly some indication and some early data that it is quite high, particularly in the south Delta.  There are some information gaps that really need to be filled; we really need to know more about predation rates as a function of space and time.”

There is also a question about hydrologic features that are particularly conducive to high predation, he said.  “There are certain types of geometries and certain types of structures where predation is being focused.  If that’s true, that would certainly help if you wanted to design an effort to deal with predation in specific localities.  It is not the same at all places and in all times.”

Key uncertainties and data gaps include having more information on predation risks and exploitation risks.  Dahm at SWB_Page_09If you’re going to deal with predation, you need to know who the predator is, you need to know how many of the predators there are, and you need to know where they are hanging out; you also need to know how they are gathering their prey, what are the biomechanics of predation, and what kinds of environmental things help them, like for example, submerged aquatic vegetation or certain flow patterns around certain types of structures.”  While predator studies in the past have looked at striped bass and largemouth bass, a recent study found that channel catfish were another important predator, he noted.

Other things mentioned as key uncertainties and data gaps are identifying where to focus restoration and anti-predation efforts, and the issue of clarity and turbidity.  “This clarity issue is one where some of these fish do better under moderate but not high levels of turbidity, so that’s another covariate that seems to be important.”

With respect to the Delta’s habitat for diversity and variability, Dr. Dahm said: “A lot of the Delta basically has a channel to edge ratio of 2, in other words, they are straight channelized linear systems.  They are not very good places to hide, and they are not very good sources of high quality food, so these are issues that also play a role in the predation.  Habitat that is more complex has a greater ratio than 2 to 1; it has backwater sloughs, wetlands, tidal influenced habitat are places where we think fish will do better.”

Steve Moore SWBThat’s an important point, and yet one thing that’s puzzled me,” said Board member Steve Moore.  “The channelization of the Delta by and large was completed in the 30s and 40s, so those geomorphic conditions have been around for a long time and yet we haven’t necessarily had the poor numbers, the poor escapement, and everything else that we talk about, so while I hear loud and clear that structure is important in the Delta, it hasn’t been there for a really long time.”

Certainly it’s been a hundred years or longer where we’ve had those types of habitat conditions, so there are other questions,” said Dr. Dahm.  “That comes back to what you often hear, is that it’s multiple stressors interacting, it’s not a single issue that is affecting these fish population declines.”

Research needs

One of the things the report tries to highlight is the need to move away from correlation analysis – Dahm at SWB_Page_10that you have one variable going down and one variable going up and they are correlated; you actually really need to get an idea of what is going on with these individual organisms and their populations and that means using tagging studies,” he said.  “There’s a number of these that have been initiated recently and I know a number of others are going to be supported under Prop 1 funding, for example, so I think we’ll get quite a bit more information on some of the details that this report is asking for.  Studies are going to be in both the south Delta and in the Sacramento River so we’ll get an idea of the differences between those two habitat types.”


The third report is the Delta Interior Flows and Related Stressors.  One of the papers fundamental to this report was a 2011 paper by Monika Winder and Alan Jassby which studied shifts in the zooplankton community, a food resource for a lot the smaller fishes.  Dahm at SWB_Page_11A lot of the changes that you see in that left figure are due to invasive species of zooplankton establishing and doing well in the system, so again we have the same kind of introduced species problems that are found with the aquatic plants and that are found with the fish community are also found with some of the food resources for the fish community,” he said.  “In addition, there are some interesting questions about fish movement and some of the cues behind fish movement, and this report goes into some of the specific interactions that are important relevant to flows within the Delta and some of these related stressors.”

Dr. Dahm said from his perspective, this report is the most readable of the four.  “They looked at the flow regimes, and then they wrote sections on some of the things that flow interacts with and what we know about those interactions,” he said.  “They have a section on how flows interact with the geometry and hydrology of the system, a section on how flow interacts with turbidity or clarity in the system, a section on how flows interact with primary and secondary production, and a section on fish behavior and cues and how they interact with flow.  Invasive species and flows, food webs and flows, entrainment and salvage and flows, and population dynamics of the fish community and flows.”

Dorene D'Adamo SWBBoard member Dorene D’Adamo asked Dr. Dahm to talk about the concept of flow being a master variable.

There were some papers written in the 1990s that really focused very much on flow,” he replied.  “They were written particularly with a focus on riverine systems, and they really used the terminology you just used, that flow was the master variable in those kinds of systems.  I think there’s been a bit of a softening of that kind of single variable; it’s as I just said, multiple stressors interacting, and flow interacts with so many different things within the Delta, and I just listed seven or eight of those.  It’s really those interactions that I think would be the consensus that we need to examine more closely; it’s not just flow as an individual variables.  These interactions with flow and it needs to be in space and time, and it needs to be on a time step as I talked early about that is much smaller than the kind of monthly flow regimes that we often utilize for setting these standards.”

It’s not just add water and everything gets better; it’s being strategic with the addition with water,” said Chair Felicia Marcus.

Yes, timing and place,” agreed Dr. Dahm.  “Flows are more than just volumes; a lot of people fixate on volumes and volumes are certainly important, I’m not going to say they are not, but there’s also the timing, and there’s also the frequency and there’s also how rapidly it changes from one condition to another condition.  These are things that also have to be factored into the analysis of how flows affect an ecosystem.”

And in the Delta, you have to add in the tides.  “This is a tidally dominated system, and so with my training and working in river systems, I have found there are lots of things about the Delta, and if you don’t add the tidal dimension, you’re going to miss a lot of important aspects of physical, chemical and biological system.”

Take home messages, key uncertainties and data gaps

Dahm at SWB_Page_12This report really made the point that Delta flow is largely now decoupled from good habitat such as tidal marshes, floodplains, and riparian areas, Dr. Dahm said.  “Getting that connectivity back in the system would be an important step moving forward to having a healthier Delta; it’s getting things like connectivity in the Yolo Bypass improved, get some of the tidal marsh projects being planned completed, and also maintain better riparian habitat along some of the river channels.”

Dahm at SWB_Page_13Key uncertainties identified in the report include knowing more about the movement of Delta smelt.  “There are still some significant methodological challenges but certainly the movement characteristics of the smelt is a big unknown,” he said.  “There needs to be more studies as to what extent the fish use the tides to move about, basically surfing the tides when they are moving in one direction … that’s another thing that needs some further research.  Also the link between flows and particularly different parts of the food web, and again this gets into the availability of nutrients and clarity of water, and how much turbidity is in the water.”

Recommendations moving forward

Dahm at SWB_Page_14In terms of modeling, they pretty much agreed with the other report.  “The use of these three dimensional computational fluid dynamic models is giving us a much better ability to model the dynamics of water in the Delta, and they really have come a long way, they really are quite sophisticated now,” he said.  “But we need to link those to what the fish sense and what the fish do, so there’s this need to link people who are studying fish ecology and biology with these models that can give you accurate distributions of flow fields and movements.  Trying to do that is something that a lot of the science community is aware is an important next step, and there have been a number of efforts to get these people working together and they are actively working together.   So the process of linking what we know about the life history of the fishes with what we know about the three dimensional dynamics of the fluids is where I think the science is headed.”


The last report is from the Delta Independent Science Board on flows and fishes in the Delta.  The foundational research for this report include the workshops on Delta inflows and Delta outflows, as well as the reports from the National Research Council’s assessment of the Bay Delta.

The report had some clear take home messages, said Dr. Dahm.  Dahm at SWB_Page_16The first one is that moving forward, we really need to focus more on cause and effect relationships, not just correlations, because correlations can sometimes be spurious,” he said.  “If you actually have cause and effect, you can actually see things happening to these organisms, track their movement, get ideas of some of the pressures, predation rates, for example; those kinds of things are the way to move forward – move away from the correlation and get onto cause and effect.”

The second take-home message was to look at causal mechanisms on scales of space and time appropriate for the questions being asked.  “This is just another way of saying what I said earlier, which is that time dynamics needs to be built into a lot of our understanding.  Daily time steps are probably important for a lot of the things going on related to both the behavior of these organisms and the flow dynamics that occur within the system.  And the use of these three dimensional open source hydrodynamic models is another one of their take home messages.”

Dahm at SWB_Page_17The report acknowledges there are many ways that flows can interact with fish populations, but they said we need to know more about growth requirements, flow links to basic requirements for getting adequate food supply, measure vital rates such as reproduction success, mortality rates, and migration and transport movement, he said.

Another key point in their report is that we really spend a lot of our time focusing on our threatened and endangered species within the Delta, but a lot of the information going forward needs to focus on the non-native fishes that now make up a substantial part of the population within the Delta,” he said.  “One of their take home messages was that we need to have the same kind of information on diet, movement, mortality and predation on some of the non-native fishes that are in the system.”

The Independent Science Board had four things they thought would help make progress in the Delta.  Dahm at SWB_Page_18The first one is more on getting these various fields of scientific endeavor to talk to each other more effectively,” he said.  “The second one is one that here in California, a lot of our scientists have restrictions on abilities to travel out of state, to go to meetings, to access library materials, and to have the kind of tools that a lot of other scientists have, and moving forward, they were quite clear in that they would like to see improvements made in things such as access to the literature and the ability to go key conferences.”

They also pointed out that often, we spend most of our time in the data generating mode; but we don’t spend as much time in the data analysis and synthesis component, and we really need to invest more in synthesizing the information, both retrospective and current,” he said.  “And again, to improve coordination among disciplines and institutions.”

Read the report here: Flows and Fishes in the Sacramento-San Joaquin Delta (August 2015)

Upcoming workshops

Dahm at SWB_Page_19Dr. Dahm then concluded by noting there are five additional workshops or reviews in the works.  “One of them is a peer review on the regional instream flow ecological method manual that your staff is developing,” he said.  “The second one is peer review of the Delta flow estimation methods which is a tool being developed by DWR for your use.  We also have been asked to do a peer review on the Sacramento River Allocation Model, and then we are planning a training workshop provide an opportunity to learn more about the temperature modeling that goes on in the Sacramento River, and we’re planning a workshop that focuses in on some of these issues related to nutrients and their form and the effect they might be having on the food web.”

And with that …

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