ADAPTIVE MANAGEMENT FORUM, Part 4: Case studies from the Bay Delta system

Presentations highlight the Montezuma Wetlands Project and the Nigiri Project

Adaptive management is widely regarded as an effective approach to environmental management in the face of uncertainty because the approach provides a way to build science and learning into management practices under changing conditions.  And while implementation of adaptive management is still challenging in the Delta, there are some examples of success.

At the Adaptive Management Forum, hosted by the Delta Science Program in 2019, the last set of presentations were two examples of how adaptive management is being applied in the Delta.  First, Cassie Pinnell discusses how the Montezuma Wetlands Project utilizes an adaptive management approach in two case studies from the project.  Then Dr. Carson Jeffres discussed how the Nigiri Project was adapted through the years to apply lessons learned and achieve successful outcomes.

CASSIE PINNELL: Adaptive management and the Montezuma Wetlands Project

Cassie Pinnell is a senior ecologist with Vollmar Natural Lands Consulting.  Over the last 15 years, her work has focused on the restoration and conservation of California wetland systems, including vernal pools, living shorelines, and tidal systems.  She has been conducting biological monitoring on the Montezuma Wetlands Project since 2006 and she has recently become the site project ecologist.

At the Adaptive Management Forum, Ms. Pinnell gave a presentation on the Montezuma Wetlands Project and how they have integrated adaptive management into their project over the last 30 years.

The Montezuma Wetlands Project is located in Solano County on the far eastern side of Suisun Bay and is outlined in red on the map on the lower left.  The four projects highlighted in yellow: Rush Ranch, Hill Slough, Nurse Slough, and Browns Island, are other sites that existed when the Montezuma Wetlands Project was under its initial design considerations in the 90s, so they were some of the most early reference sites.

The 2400-acre site was once about 1800 acres of tidal marsh that transitioned into bunch grass and large vernal pools.  In the 1870s, a levee was built around the perimeter of the site by Chinese labor crews who worked predominantly in this area. Livestock was introduced in the 1880s and remained the predominant use of the land, although there was a little bit of dry land grain farming and other things that have happened at the site.  The diked area subsided up to about 10 feet across the project site which is similar to a lot of other projects in the area.

The bunch grass and vernal pools are still mainly intact and those have been preserved as the upland component of the project which is host to a number of endangered species such as tadpole shrimp, a few different fairy shrimps, and several different plant species.

The Montezuma Wetlands Project was conceived of in the 1990s as a unique privately-funded project to restore 1800 acres of the parcel back to tidal marsh.  On the project map, the blue areas are planned to be low marsh, the green areas are planned to be high marsh, and the orange and yellows are seasonal wetlands and transition zones for the project to move up.

We’re very lucky on this site,” she said.  “Part of the reason it was chosen is because we’re not bounded by any hard infrastructure up here.  We do have our perimeter levees and there is a DWR Salinity Control Station, but other than that, we’re looking at mainly expansive, mildly rising topography bumping up here to the Montezuma Hills.”

This project is a privately-funded project that works with the Army Corps of Engineers, the Port of Oakland, and other dredging projects to accept sediment, both clean cover sediment and foundation settlement, which is sediment with higher levels of contaminants than what would otherwise be considered clean sediment.  The general design of this project to accept the foundation sediments and lay it down very low in the first layer of the marsh lift, then cover it with many, many feet of clean sediment, thereby locking the contaminated sediment down in an anoxic environment and keeping those sediments from reaching areas that would have tidal channel formation cutting through them as well as making it inaccessible to the wildlife and plants.

This project was developed in the early days of the Long Term Management Strategy, which is a collaboration of agency scientists trying to figure out how to have best beneficial reuse practices for the dredging sediment.  The current goal is to have about 40% of the dredged material coming out of the Bay to be beneficially reused.  The Montezuma Wetlands Project was one of the earliest beneficial reuse projects.

The project has an off-loader; barges full of sediment are brought up to the off-loader, the pipe goes down into the sediment, slurries it with water, and pushes it up to four miles across the project site, dumping it down into the cells that have been built up with levees around them.  The sediment is allowed to settle out, the clean water raises up and goes into the return water channels to be used again.

The construction and monitoring costs have been covered by the tipping fees associated with dumping the sediment at the project site, and so far, they have collected about 7 million cubic yards of sediment from regional dredging projects.  The project has been ranked as a highly cost-effective beneficial reuse project.  The 12-year initial permitting and design was covered by private investors until the project started receiving the tipping fees that would then cover the costs of construction and monitoring work.

Adaptive management was built into the project at an early level because a lot of science and oversight was necessary for the project.  The Technical Review Team is chaired by Josh Collins from the San Francisco Estuary Institute and includes specialists from all disciplines that the project relates to, such as water quality, vegetation, sediment, chemistry, etc.  The core project team meets at least weekly and has experts in sediment, engineering, biology, and chemistry.  There are a suite of technical specialists who do the actual monitoring for the very specific components of the project, such as salt marsh harvest mouse, or the California least tern.  There are also all of the project’s regulatory agency partners with their many permits that provide a lot of support and review for the project.

They developed an early mitigation and monitoring reporting plan that synthesized all of the permit requirements and identified 66 features or measures that needed to be tracked over time.  Each one of those measures is assigned performance criteria.

For example, native marsh vegetation, we need to have a low and high marsh percent cover for target species in phase 1 before we can begin the next phase of our project,” said Ms. Pinnell.  “These performance criteria are built into our project to keep us making sure that we’re actually doing what the project is supposed to be doing before we continue building the project out.

Each performance measure is then given monitoring details: how it will be monitored, when it will be monitored, what type of monitoring is to be done, how the results are reported, and who they are reported to.  The performance measures are then assigned contingency measures to take when the performance measure is not at the target levels, so for example, if the vegetation is not coming in at the target levels, they need to investigate why and then implement remediation measures such as revegetation or weed control.

The other key element of the project is the temporal and spatial phasing that’s required to ensure they are using the best available science in doing adaptive management.  All of the work done so far is in phase 1; they will be breaching the levee in the fall.  Before they can really move into the next phase, with the exception of minor prep work, there are performance criteria that need to be met.

So not only are these phases temporally isolated where we can’t start one until we finish and show success in the other, but they are also geographically isolated in that they are separated from each other by levees so that if something were to happen in one, it wouldn’t impact the next one,” she said.  “This also means that after we finish one phase, we need to essentially redesign what the next phase will be by incorporating all of our lessons learned from the phase previous and the new science that has come to light within the last 30 years, and then update all of our permits and plans as necessary.


There have been a lot of changes over the last 30 years.  For example, they started placing sediment on the site in 2002, and in 2005, California least terns, a state and federal listed endangered species, was observed on the site.  The following year, there was nesting and 110 individuals were observed.

It’s great news when endangered species decides to come to the party on your site,” said Ms. Pinnell.  “The bad news is that the areas that they really like on our site are right where the pipe is putting the sediment out, so we have a little coarse grain material falling out and there’s lack of vegetation – it’s not a sustainable place to be.  They really like the areas that are targeted for low marsh, which means that once we breach, the beautiful new nesting habitats will flood.

In response, they needed to establish goals and objectives for the least terns, so they engaged the technical review team, specialists, and agencies to figure out how to address the least terns.  They came to the conclusion that the goal would be to support the least tern habitat, but move it to an area of higher elevation to protect them from predators and to create an appealing nesting and rearing habitat for them.  They did not build a model for this; instead they relied on the experience from the best available science, the technical review team, least tern working group, and agency discussions.  Ms. Pinnell noted that sometimes modeling is not included in their process.

Next, they decided to create new peninsular-style habitats that were somewhat protected from predation but also not in the transition area above the high marsh and going up into the uplands.  To encourage the least terns into the new habitat, the put decoys strategically positioned to look like very available and interesting singles.

The shot on the slide on the far right shows one of the peninsular habitats; construction on the second one was finished a couple of months ago and hasn’t been captured by Google yet, she noted.

A reinitiation of the consultation with Fish and Wildlife Service was necessary because new species were on the site that weren’t included in the initial biological opinion; it also required a major modification of a number of their permits.  The result now is a smaller adaptive management plan that has been designed and implemented for the least tern that is within the larger monitoring and mitigation plan.  The least tern plan details exactly how they would be doing the nesting surveys, how they would track whether or not the habitat was sinking or subsiding, and how the vegetation was doing, and the steps that would be taken to correct anything and to make sure that they were keeping this very appealing for the least terns.

For analyzing, synthesizing, and evaluating the information, they conduct weekly to every two-week nesting surveys during the nesting period, they regularly monitor the vegetation levels on the site, and compare the information not only to past years of the project, but also to the other projects around the bay.  The graphs are showing the four largest San Francisco Bay area colonies of least terns, of which Montezuma Wetlands is one; the others are the Napa Sonoma Marshes, Hayward Regional Shoreline and Alameda Point.  They look to see if their trends are following the regional trends; they are also looking at available fish data from Montezuma Slough to see if there’s any correlation between fledgling success and food availability.

For communicating their current understanding, Ms. Pinnell says that there is a data and report review done every year for all of the features by the entire project team; this is submitted to the regulatory agencies.  In addition, the project data and information is put on EcoAtlas, which is a website that tracks restoration projects throughout the area and is a public access portal for all of their plans, survey reports, and other documents.  There’s also a lot of communication with least tern working groups at other sites, the specialists who do least tern monitoring on the project site, and with the site managers and crew so that they don’t have heavy equipment driving over their nesting habitats.

The project has adapted a bit, Ms. Pinnell said.  They are working on better ways to attract the birds, so besides decoys, they have a solar powered sound system that plays an iPod least tern call on a loop to try and lure them in to the preferred nesting habitat and away from the older nesting habitat that will hopefully be cleared out by the time they need to breach the levee.  They have experimented with different types of vegetation management such as leaving some protection in place for chicks to hide or using preemergent herbicides and other ways of clearing out the vegetation because the terns like fairly nice clean habitat.  They are also trying to figure out how to protect the least terns from predators including native species such as raptors, and they’ve modified their construction processes so they are working outside of the nesting area or very far away from the birds when they are there.


Oftentimes, projects have multiple different types and stages of adaptive management going at the same time, said Ms. Pinnell.  They have been working with the least terns long enough to make it through the loop, but with other features of the project, they are in the earlier stages, such as the part of the project working to revegetate the entire 1800 acres of the tidal marsh in a way that can be scaled up.

They have been working for many years with the Technical Review Team to plan a revegetation strategy.  At this point in their adaptive management process, they are planning and doing pilot projects and experiments.  They are salvaging pickleweed and transplanting them to the higher marsh where revegetation is a priority; Ms. Pinnell noted that they need to focus on this upper edge so that they can outcompete Russian thistle, as well as other invasive plants.  They are also working with the technical review team to experiment with how to restore the new ecotone levee which was added to the project but is potentially susceptible to weed invasions.

As the construction of phase one nears completion, they have been thinking about what they have learned from that phase to revise and improve the next phase of the project.  The original design is on the left and the current design is on the right.  “We were imagining initially that most of the site would be low marsh; we’ve since added a lot more high marsh because of sea level rise which is shown in green,” Ms. Pinnell said.  “We’ve also added more transition zone. … The upper areas will remain as high refugia upland transition areas and allow the marsh to move over time.

They’ve also revised the plans for the next phase to include removing a large levee that was planned for the middle of the low marsh and instead constructing it as larger cells to allow the sediment adequate room to settle out.  They are also switching to the bulk fill method which is a very specific way of filling the sediment into these cells that is based on practices done at the Hamilton restoration.  They are adding more transition zone and changing public access on the site to route people to the higher areas and away from the more sensitive features.  They are also updating their species management plans, so they are looking to other restoration sites to better understanding how to manage the species on their site.

They have also been updating their monitoring plan, as monitoring methods have improved grealy over the last 30 years.  “For example, instead of having target percentages of marsh, Josh Collins and SFEI are recommending that we look instead at habitat development curves and reference envelopes to sites around the bay that are similar, relying on things more like CRAM and site-wide assessments instead of just exact numbers of specific plants,” she said.

Ms. Pinnell then shared the critical components for implementing adaptive changes to their project.  “It comes down to funding as one of the top and foremost,” she said.  “Since this project is paid for by tipping fees predominantly, we are a little bit unique in that we have a slower, steady smaller stream of funding instead of a big burst of grant funding that then disappears later.  So because of that, we’ve been able to pay for 18 years of monitoring, and we also have money set aside for much longer-term monitoring, so we’re able to continue monitoring because we’re not tied to grant lines.”

We are able to make changes that are within our permitted actions as they are needed to be made, so we can make small revisions to the project as long as it’s okay with our permitting agencies,” she continued.  “That allows us to try a couple of things while we’re trying to get to the right answer.  And of course, communication.  We have regular communication with everybody within the project, communication with our technical review team partners and other sites.”

Without the spatial and temporal phasing built into our project, we wouldn’t be forced to make sure that everything is working how we wanted it to work before we start building the next, so I think this is a really important part of our project that has allowed us to try things before we go full out on the entire site.  Our agency partners have been incredibly supportive and we’re very lucky to have a number of project managers who are highly responsive to us and help us move through permit amendments or modifications quickly.”


DR. CARSON JEFFRES: The Nigiri Project: Learning by Trying Something Different

Dr. Carson Jeffres is a research ecologist with the UC Davis Center for Watershed Sciences, specializing in better understanding of physical processes and management actions that influence aquatic food webs and fish habitat.  He’s been studying the physical processes and ecology of floodplains in the California Central Valley for 16 years.  In addition to projects in the Central Valley, he’s also been studying spring-fed systems in the southern Cascades.  One of the themes of his research is using rigorous scientific research to help guide management questions.  At the Adaptive Management Forum, Dr. Jeffres discussed the multi-year Nigiri project that studied floodplains and the benefits for juvenile salmon.

Dr. Jeffres began by acknowledging he feels a bit like an imposter; he doesn’t do management and working at the University, he has the luxury of not having to make actual decisions.  However, they do have an iterative process where every year, they design a project, implement it, and see what worked and what didn’t work.  They then take that and change it for the following year, which ultimately starts sounding a lot like adaptive management, he said.

A lot of people worked on this project over the several years, too many people and agencies to name.   Putting the presentation together was a walk down memory lane, realizing that there was an iterative process:  “We started with a plan, but it didn’t always work,” he said.  “In fact, I think we learned more out of the things that didn’t work then the things that actually worked, because the things that worked, we had to question why they worked; but the things that didn’t work that we ended up focusing a lot of our efforts on for the following year and try to mitigate that.  So I think that process is something that is worthwhile.”

The project started out in the late 1990s with Ted Sommer realizing that fish moving through the Yolo Bypass were actually growing faster than fish that were moving through the river.

That was a big fundamental change in our thinking about how this lower part of the valley functioned for fish,” he said.  “So we went down to the Cosumnes River which is a much more natural system.  There were levees that were removed as part of management on the Cosumnes, and it led to this picture on the bottom.  Really if I were to define my career in one picture, it would be that picture.  And so we realized that floodplains were beneficial for salmon.”

The Cosumnes is but a postage stamp on the landscape; there are few natural floodplain systems that are inundated frequently enough to have ecosystem benefit over the landscape scale, he said.  And the Yolo Bypass doesn’t provide habitat at a scale or even frequently enough to have large-scale population benefits.

So the question was what was it about the bypasses in particular that were so beneficial for salmon?  The largest opportunity in the Central Valley are the flood bypasses and we know that they are beneficial during big years.  But what is it about the big years and can we make the flood bypasses beneficial during non-large years?  What are the modifications we can make in the system?

The group started the project in 2012 with their farming partner John Brennan, who provided them a 5-acre plot of land at Knagg’s Ranch in the Yolo Bypass.

We had this great idea of putting salmon out in what was essentially a mud puddle,” Dr. Jeffres said.  “I remember that day, because we were looking at the water and thinking, are we about to kill all these fish?  There was literally that thought in our minds.  If we put fish out there, are they going to survive?  If they do survive, will they grow?  That was the question we were asking that first year.

So they put 10,000 fish out there for six weeks; they collected the fish and found that the fish had grown rapidly.  “This was fundamentally the light bulb for us,” he said. “Seeing this on this habitat during a non-flood year, and this isn’t what you would normally consider to be a naturally looking habitat, and yet we saw these same type of results that we’ve seen through the large scale flooding on the Yolo Bypass as well as the Cosumnes work on a naturally flooded bypass.”

This led to a series of questions that drove their research for several years focusing on how the project could be scaled up and how management of tens of thousands of acres in the flood bypass system could be optimized for salmon rearing.

Next, they wanted to understand the substrate.  Is there something magical about rice or how the rise is treated?  They wanted to see if the fish have a preference for the substrates in the rice fields, and what the physical drivers were that lead to the ecological drivers that create the conditions where the fish can grow.  They wanted to see if the fish need refuge; if it’s just a wide open plain, they were thinking it would be a massacre of juvenile fish.  They wanted to study the actual survival numbers.

So they worked with their farming partner who provided nine replicated 2-acre fields, each with an individual water source.  “It was amazing the amount of effort that goes into taking these large rice fields and making them a science experiment for us,” he said.  “This is where you see who your real friends and real partners are and who is willing to come to the table the next week after you make these requests.”

That year, they had 9 two-acre fields with some were planted with rice, some were fallow.  Since rice these days is planted by airplane, the rice fields were planted with a different type of rice that could be planted by tractor.  Some of the fields were disced, some were stubble, and some were fallow, in a random order, and each had an independent water source.

One of the questions was how the different substrates would affect the outcome.  “When we went into this, in my mind, I was thinking fallow was going to be the best thing out there,” Dr. Jeffres said.  “If you don’t do any ag on this field, it’s probably going to be better than what you would expect to see in the stubble or disced fields.  But it turns out it’s not that much different.  The graph shows the zooplankton numbers in each of the different field types.  You can see there are some differences, but the point is, is that these numbers are outrageous, so even our lowest numbers are really outrageous, so it turns out that it doesn’t really matter whether you fallowed, disced, or stubbled.”

So they sampled the fish, measured and weighed them, and it turns out that the growth of the fish was also pretty amazing regardless of these habitats.

But we realized that 2013 was a little different in that the fish that did survive, they did really well,” he said.  “Then the question is, how did these fish survive and why is the context of those fish surviving important? … In 2013, roughly February through March, we did not get a lot of rain in the system, and that really made us the one wet spot in a lot of area on the bypass.  When it’s not raining, the bypass is a pretty dry place, and when you have the one wet spot in a large area, the birds showed up in mass, and we got a lot of mortality.  It was kind of scary.  That first year, we thought more fish should have left these fields.  The ones that were left did great, and that’s why there were a bunch of pelicans and happy egrets is they had these big fat fish, and so that led us down this next step in understanding this.”

So that year they learned that the fish grew, regardless of the habitat, but they had a predation issue, particularly in a dry year when the experimental fields are the only wet spot and that is attracting every bird within the area.  So they next asked their farming partner to build a channel for refuge, so they were curious to know if there was more depth and cover, would there be more survival of fish?

The other thing that they were curious about was volitional passage.  If the fish were no longer managed through the entire experiment, will the fish leave on their own and what does that look like?  And how much time do they spend in the fields before they see the real benefit?

Throughout the years, the growth was a constant factor.  They also realized that the fish themselves looked different, not only size but the depth, so they wanted to also put some wild fish out on the fields to see if they would get fat like the other fish.

The graph on the left is the condition factor, which is basically how fat a fish is for it’s length or its health.  “What you see here is that the wild fish ended up meeting and catching up to their friends that had been out there for awhile in about 20 days, which was pretty informative that this response happens really quick,” he said.  “We also saw that the fish with the little bit of refuge we dug down the fields did pretty well.  Part of that was we had more water in 2014 and the time that it arrived was actually more conducive to doing this.  I don’t think that we saw a benefit from the ditches but it was the context of what is happening in the rest of the system is important.”

So, we know that the fish grow, and providing a little bit of habitat and refuge for them helps them from predation as well as the water year type.  The next thing was how to get the fish out of the fields.  “We know that they do leave on their own, but there’s a certain point where you realize you have to get the fish off the fields and they aren’t necessarily going to leave on their own,” he said.  “If we’re going to manage this system on a large scale, there’s a point where you have to transition over to agricultural processes.  The farmers need the field to be dry by x date, which means the fish have to be out of the field by y date.  So we were curious, if we need to get these fish out of the fields, what are the protocols for doing that?”

So they tried three different treatments: A fast drain where they completely cut the water off, a slow drain with some inflow provided, and one that slowly drained with no inflow coming in. Dr. Jeffres said he expected the slow drain with inflow would be the most effective because it replicates what would be seen in a natural system.

Surprisingly, the field with the fast drain had the most survival, he said.  “We had about 43% of the fish made it through that six weeks on the floodplain under the fast drain; when we did the slow with flow which I expected to be the highest survival, it was about half of that survival; and on the slowly draining field, there was pretty low survival.  It was pretty grim.”

We’ve had predation, we’ve had drought, and now we have trying to get fish out of the fields where we failed pretty hard,” he said.  “We learned a lot from them, but only 11% of these fish made it out of this field when we did this treatment, and that’s not great.  If we put 1000 fish out there, getting this number isn’t what we’re looking for, so really managing this system for what we needed to get out of it isn’t mimicking natural processes, it’s more about managing the system.  That’s not a natural system … you shouldn’t necessarily replicate all the natural processes that are happening out there.”

So by 2016, they were feeling confident about how to manage the fields, so they wanted to know how it compared to other places.  “We know the habitats out there are good, but what’s it like compared to the Toe Drain or the Sacramento River,” Dr. Jeffres said.  “So the next logical step in managing this as a system is that we had to start comparing it to everything else out there, so we did a transect between the three habitats.”

One of the things that was really striking was the differences in the food web between the three habitats.   On the rice field, there is so much productivity – so much zooplankton, they called in ‘zoop soup’.  The Toe Drain had a little more, but the river was quite barren.

We were able to see that the relative difference between those habitats is also important, and if you’re looking at the growth rates in here, you can see that the floodplain is just in a whole different league than every place else.  So we know the fish grow out there well, but now we know how well they grow compared to the other habitats.”

He presented a slide showing the growth of the fish over time.  He noted that it’s the same fish for all of the pictures; they put PIT tags in them to identify them. “You can really see the difference between the habitats now.  Before we were really just showing this, these fish getting fat, and now we know how fat they get compared to the other habitats.”

So in conclusion, Dr. Jeffres said he thinks they followed a form of adaptive management.  “We’re not managing the system, we’re doing science,” he said.  “This is the scientific method more than adaptive management, but I think at the same time, adaptive management is fundamentally that scientific method in that you have hypotheses, you’re testing hypotheses, and you’re learning from your results; you put new hypotheses out there and you test them.  There was a lot of effort doing this and there were a lot of interesting discussions between people on a frequent basis.  The thing that I liked most about that, is that we didn’t always agree.  We would be in our weekly group meeting, and we wouldn’t always agree, but the discussions are what ultimately led to this path becoming more interesting and informative.  I think having different people with different voices and different opinions makes for much better information coming out of it.”

Being open to failure is fine,” he continued.  “At first, those results were super scary.  When we were getting 11% survival out of some of our field treatments, that’s not something you want to go tell somebody about.  But if you’re able to learn from it and make the next year better and make the overall program better.  I’ve become more comfortable with failure; we should all be comfortable with failure.  You don’t learn from the stuff you know is going to work, you really learn from the stuff that doesn’t necessarily work right.  It’s honestly been probably the most fun thing that I’ve done in my career at this point is going through that process with a group of people.  Misery loves company, and I think when it’s not working great is when you really need that company and it really makes it better going forward.”


  • For the forum agenda and video, click here.
  • To view documents on adaptive management at the California Water Library, click here.
  • To read more articles on adaptive management on Maven’s Notebook, click here.

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