BAY-DELTA SCIENCE CONFERENCE: Problems and promise of restoring tidal marsh to benefit native fishes

Suisun Marsh; photo by Wendy Hsieh

Dr. John Durand discusses the effectiveness of existing and proposed tidal marsh restoration sites in the Suisun Marsh and the Delta

Implementing aquatic restoration projects that scale appropriately with seasonal flows, tidal energy, and food production remains a challenge in the highly disturbed Sacramento-San Joaquin Delta and Suisun Bay. Many restoration projects may achieve aesthetically pleasing results that will offer some benefits to recreationists, terrestrial animals and plants without improving aquatic habitat for native fishes.

In this presentation from the Bay Delta Science Conference, Dr. John Durand, a researcher with UC Davis with over 10 years experience conducting research in the Delta and Suisun Bay, he discusses existing and proposed restoration sites, evaluates their design, determines how well they will support the stated aims or the project, and provide alternatives or design modifications that could improve their function.

Dr. John Durand began by noting that his and Dr. Peter Moyle’s research group has been examining regions of the Delta, including Suisun Marsh.  A lot of the work that they do overlaps with planned, preexisting, or nonexistent restoration sites.  The work spans a giant swath of habitat in the northern estuary that they refer to as the “Northern Arc of Native Fishes.’

Dr. Durand said the reason they have been pitching the northern Delta for habitat restoration is because they think it has a lot of the right elements to maximize the potential of restoration.  “There are other sites in the Delta that have potential, but we think that the northern arc has the fundamental things that are required to make it successful,” he said.  “That includes water, energy, and flow.  Water and energy equals flow energy across the landscape.”

He presented a map of the north Delta, noting that the map has been turned on its side.  The arc stretches from the Yolo Bypass to the Suisun Bay; it’s connected by flows off of the Yolo Bypass floodplain, the Sacramento River corridor, and the Toe Drain, which connects it via Montezuma Slough to Suisun Marsh.

There are substantial differences between these regions to be sure,” he said.  “Suisun Marsh, for instance, is a landscape that is aquatic but highly managed.  It’s managed for duck clubs and duck hunting for 150 years, and the reason that it is a marsh in any sense is because of the nature of that practice, which incorporates water and land use for environmental purposes.  It differs greatly from the management regime in the north Delta, which has been largely pasture land that’s been punctuated by access, by water channels which provided irrigation for grazing and for pasture management.

There’s more tidal energy in the Suisun Marsh as well as periodic fluvial energy that activates the aquatic landscape in the north Delta; the water ranges from brackish to fresh water so there’s a gradient of habitat that provides heterogeneity across the landscape that provides different opportunities for organisms to access aspects of the environment, including refuge and food resources at different times of the year and different years, he said.

He began with two restoration sites in Suisun Marsh: the Luco Pond or Potrero Club which has been recently acquired by Westervelt, and the Blacklock restoration site, which was breached a few years ago.  They have had the opportunity to survey both these sites for a number of years.

Among the things surveyed on the site include water quality, chlorophyll A concentration, zooplankton, fish abundance.  The map is a heat map of chlorophyll A, so where the colors are leaning towards red, the concentration of chlorophyll A is higher; where the colors are cold such as blue, chlorophyll A is less abundant.

One of the things that we found that was very interesting was that the chlorophyll concentration increased as one moves up slough,” Dr. Durand said.  “As one moves from Nurse Slough through Denverton and Luko Slough, the chlorophyll concentration increases; in other areas, the chlorophyll concentration is quite low.”

Dr. Durand noted that one of the things observed through monitoring was that the management practices of Luco Pond promoted phytoplankton concentration.   “We’re not sure yet whether it actually increased the rate of productivity, but we think it did,” he said.  “In the next couple years, we’ll be figuring it out, but we do know that we have an accumulation of phytoplankton in that site, and that accumulation of phytoplankton has corresponding abundance that we see in zooplankton.”

On the slide, the plots show the different species, and what’s important to note is the Luco Pond has the highest concentrations of zooplankton; the adjacent site, Luco Slough, has an intermediate abundance of zooplankton, and then Blacklock itself is quite low in zooplankton, which Dr. Durand attributed to management practices that differ across the sites.

Dr. Durand pointed out that the Blacklock site is underperforming in a number of ways. Besides low in production, it is dominated by an alien invasive species, Mississippi silversides, which are not desirable for a number of reasons.  “I’m not going to get into it as they are not the prime object of restoration in the system, but it is dominated by those species.  On the other hand, Luco Pond is dominated by a native species, threespine stickelback.  In some ways they both serve the same purpose as being forage fish for larger fish, but we would like to promote native species, and we also like to promote a diversity of organisms in our suite of species that we’re trying to restore for.

He then explained the differences between the two sites.  Luco Pond is being managed as a duck club; it has two flap gates that allow water in and out.  The gates are directional, so one only allows water in and one only allows water out; this means that on the flood tide, water is pumped on to the site, and on the ebb tide, water is removed from the site.

We believe that water works its way across the site, it has a residence time of between two days to two weeks, depending on how open or closed the gates are, and that slow moving water allows an incubation period to occur that promotes the growth of primary and secondary productivity,” said Dr. Durand.  “That’s the zooplankton that benefit not only organisms like Delta smelt or longfin smelt, which are rare in this region, but also juvenile fishes, which rely upon those resources to be able to transform into adults.”

So that seems to be the power of Luco Pond, but what we don’t know is how to calibrate it, he said.  “We don’t know how to adjust it or how to tweak it to maximize it, but with the acquisition of this property, we hope to work on it and figure that out over the next couple of years.”

In contrast, Blacklock is a restoration site that has two open breaches.  It represents the ideal of being able to open up a restoration site and walk away from it.  “I’m going to argue that you probably can’t do that in most cases,” said Dr. Durand.  “Most restorations in this really altered ecosystem are going to require long term maintenance or active management – not into perpetuity, but maybe 100 years, maybe for 200 years.  That may seem crazy but really, that’s what we’re doing here.  We’re planting seeds in this garden.  We’re not going to harvest it, but we want to set it on its course.  There are ways to make that happen using public and private partnerships that allow that relationship to continue into perpetuity.”

At the Blacklock site, it’s open to tidal action on both sides so there is water fluxing on and off the site with every tide, and there’s very little residence time.  There aren’t any directional flows and not a lot of residence time, even in the channel.  There is a large shallow area that gets really warm and it’s perfect habitat for silversides, he said.

There are a few things that can be done to modify the Blacklock site, Dr. Durand said.  They include things like putting a directional gate on one side, and maybe a subtidal berm on the other breach that would slow the passage of water across the site.  The shallow area could be mitigated by putting sediment to raise the elevation or plant it, or both.  A levee part way across the center of the island would facilitate a directional circulation of water.  “Directional circulation of water promotes a water residence time on the island, and a non-directional flow just means its sloshing back and forth a lot,” he said.

That same principle of intensely managing the ponds can apply to a number of sites across the landscape.  Meins Landing was a site acquired by DWR years ago; there were plans to make a naturalistic restoration but those were scrapped due to logistics and a PG&E pipeline running through the site.  Nonetheless, it’s a very valuable site, said Dr. Durand.

It’s adjacent to Montezuma Slough, and if we manage it intensively, not unlike one would manage a duck club with gates on it and water flowing across the surface, we could maximize the amount of productivity across the landscape and pump it in to Montezuma Slough,” he said.  “Montezuma at one time was a hot spot for Delta smelt and longfin smelt.  We haven’t seen them there for awhile.  But if they come back, this would be an ideal location to create a direct food source for smelt.  It’s not unlike what is planned on the Tule Red site, but this one would be more actively managed.  You need a person out here monitoring it, you need somebody thinking about it.

We manage water in the system with people thinking about it all the time,” said Dr. Durand.  “We should be able to manage water for the organisms that we care about as a function of mitigation.”

This is not the only site where this can be done.  “I think this practice can be extended to innumerable sites, including private clubs,” he said.  “The folks that are running the clubs that I have spoken with have expressed a desire to be part of this, so that they are managing them not just for waterfowl, but for aquatic benefits as well.  There’s a lot of desire for both hunters and fishermen in a lot of cases, to cooperate and work with us on this, so we see a lot of ways going forward in the next ten years.”

Dr. Durand then turned to the Liberty Island Conservation Bank and Preserve in the northern end of the arc.  “We call it the baby marsh because it’s just such a beautiful place,” he said.  “It’s like a garden.  It was sort of beautifully and pristinely manicured; the sculpting of the channels is really exquisite.  There’s something about me that’s a skeptic, it looked too good to be true.  I didn’t imagine that such a beautiful place would also be so productive, but as it turns out, the plan to sculpt in these dendritic channels and these sinuosity and the fact that it’s very long – it’s almost a mile long, it seems to have been very beneficial for fishes.”

There’s also a design element that was I think it was accidentally incorporated,” he continued.  “There’s an underwater berm at the mouth of it, and I think that berm slows down the flux of water in the system, so while there is still a lot of tidal energy, there is this reservoir of subsurface water that hangs out, and collects detritus and other invertebrates and provides a lot of food for fishes.  That’s speculation – we haven’t quite figured that out, but we’re working on it.

He then presented fish data for the site, noting that it is catch per unit effort for otter trawls conducted in 2015 and 2016.  The green bars indicate native species, the blue bars indicate alien species.  Dr. Durand reminded that although the proportion of alien species to native species is depressing, the proportion is the same as what you would see anywhere in the estuary.

The exciting thing is that the baby marsh has a lot of fish in it, both natives and aliens, whereas adjacent sloughs lack that, so this site is really performing really well,” Dr. Durand said.  “Shag Slough has almost nothing going on in it and that’s just around the corner from where this site is, so this site is very attractive to fish and is promoting fish somehow.  There is some mechanism, fish are finding it, they are using the habitat, and they are largely what we would call desirable species.  Hitch, the native minnow, we find a lot of shad which aren’t native but they are desirable, we found pikeminnow, we found salmon, we even found a Delta smelt there once by accident.”

So what is about this site?  Dr. Durand explained that even though it is located far up in the north Delta, there’s a lot of tidal energy in the system and this site is very well scaled to the amount of tidal energy in the region, such that the original channels that were put it have been expanding.  “You can see very faintly here that these little tiny sloughlets and side channels that are coming off of it, and those were not intended.  Those weren’t dug out; they’ve been developing and this is the way restoration should work.  It should be scaled and on and on, and they did it with this site.  Again, I don’t know if it was on purpose, but they managed to pull it off.”

We know that those side channels are very because of studies, said Dr. Durand.  “Denise DiCarrion did a study in Suisun Marsh in First Mallard slough.  She set up an array of pit tags which can detect the presence and the direction fish are moving as they pass the pit tag antenna here; she did that for striped bass, for tule perch, and for splittail, and the results she got were really encouraging.  … All three species were actively using that site, and it increased as the tide ascended.  There were varying patterns with time of day and the direction of the tide, but the general story is that fish, native and also desirable fishes are using those sloughlets, those branches.  Fish are moving up onto that habitat and using it as the tide goes up, so those little tiny branches that are being created off the side create ideal habitat.

Dr. Durand then turned to the Calhoun Cut Ecological Reserve, a younger restoration site in the same region as the Baby Marsh.  Calhoun Cut was dug around the turn of the 20th century by a guy named Calhoun who wanted to start a town; the town didn’t happen but the cut stayed.  “It’s a huge reservoir of water that kind of sits there,” he said.  “It’s beautiful in its own way, because it’s surrounded by overhanging riparian vegetation, but as an aquatic habitat, it’s not so functional.”

Barker Slough has been channelized and dug out to support the North Bay Aqueduct, which pulls water out to go to the north Bay Area.  The restoration called for redigging the channel, taking the sediments and creating berms to create some upslope habitat and some channel complexity.

The site has been doing okay but it appears to be declining rather than improving in performance; it underperforms adjacent sites in Calhoun Cut, which is surprising, and it underperforms Linsdsay Slough as well,” said Dr. Durand.  “This could be a function of the fact that it’s not very old and it needs time to develop, but I don’t think so.  I think there are some problems with it, chief among which the channel itself is very narrow, it’s sinuous, but it lacks dendrosity, and it lacks heterogeneity.  There’s not an opportunity for fishes to get up there and access the productivity of the intertidal marsh, and there’s not an opportunity for bugs and whatnot that are produced in the marsh to fall into the channel, so it doesn’t provide a lot of opportunities for native fish to get in there and find forage or refuge.”

The other problem is that Lindsay Slough is a funnel shaped system, he said.  The yellow lines represent levees, which are very constrained at the bottom; then they open up into intertidal habitat on the west side, and that creates a dispersion of tidal energy.  “There’s not a lot of energy to activate the system and as a result, we get a very pondlike environment up here.  Nothing is moving and we get a tremendous growth of hyacinth, of Egeria, of coontail and [algae] that makes it almost impassable for our native species.  Largemouth bass like it, blue gill like it, but not organisms that we care about.

Dr. Durand had some recommendations for this site as well.  “I’d like to reverse the North Bay Aqueduct; right now it takes water out of the system, I want to turn it around and put water into the system, and I’ve already started talks with people who think it’s a possibility,” he said.  “The North Bay Aqueduct is slated to pull their drinking water out of the Sacramento River directly.  No one in their right mind would want to drink this water, but for returning water into the system and flushing it out, it could serve a powerful reset to activate the system.”

I’d also like to cutoff Calhoun Cut which is a huge reservoir that blocks and mutes tidal energy in the system, and I’d like to allow that energy to go up through Lindsay Slough,” he continued.  “I also have some wild plans to reconnect these sloughs to upslope habitat, to reconnect things to seasonal watersheds that capture water and flush out the system.”

Dr. Durand then finished with his hot tips for restoration.  “Geomorphic complexity, upland gradient, you have to have water, some restorations don’t have water, you have to have energy coming with it, private public partnerships, reward novel approaches which we haven’t quite got around to, it’s got to be reversible, it’s got to be cheap, you got to experiment and study it and be willing to change it, and it has to be connected to the whole arc.”

For more from the Bay Delta Science Conference …

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