California floodplains and the fish that use them

Aerial view of the Yolo Bypass and the Vic Fazio Wildlife Area (DWR)

How restoring functional flows to floodplains could help restore native fish

Two centuries ago, the floor of the Central Valley was largely a marshy wetland.  In the springtime, the snowpack would melt, swelling the rivers beyond their banks and casting the young fish out onto the floodplains.  There they would stay for months, fattening up on the abundant zooplankton and invertebrates until the floodplains drained, signalling the time to migrate to the ocean.  However, the construction of levees to control flooding of cities and farmland also separated the rivers from their floodplains, denying access to native fish who have evolved to take advantage of the habitat.

In this brown bag seminar, Dr. Carson Jeffres discusses how historically California’s native fish have evolved to take advantage of floodplain habitats in the Central Valley, and how restoring the connection of the rivers to the floodplains can help restore struggling fish populations.

Dr. Jeffres began by noting that California is a diverse place from north to south.  In the far north, there are the spring-fed rivers and streams of the Sutter Cascades around Mt. Shasta and Mt. Lassen which have very stable hydrology, very cool water, and very unique assemblages.  The Central Valley has big floodplains where the Sierra Nevada drains down and coalesces into large rivers on the valley floors.  The Coast Range and the redwoods are fog-dominated and very cool.  The high Sierra has a very unique assemblage; Dr. Jeffres noted that in the high Sierra, the fish diversity is very low.  The Delta is this big mixing pot between what comes through the Central Valley and what comes in from the ocean.  And then there are the Southern California deserts.

Each of these regions has a unique assemblage of fish that have evolved to take advantage of the local hydrology and the climate,” he said.  “I’m going to talk about those fish and how they fit into the floodplain in the Central Valley, and how the floodplain used to function, how the floodplain functions now, how we’ve changed it, and what are our paths going forward.”

California has relatively few native fish, compared to other parts of the country, he said.   There are a lot of unique fish, but a lot of  diversity as compared to other places.  He explained that California is relative new on the evolutionary landscape; after the rise of the Sierra and the rise of Coast Range, California was isolated for about the last 20 to 70 million years.  The climate is rather harsh with dry summers and wet winters sometimes, so the fish that are here ultimately evolved under that climate regime in the diversity of geologic provinces that the state has.

Then humans came in and altered the landscape, making it drastically different than what the native fish evolved in.  It started in the 1850s with the hydraulic mining and the Gold Rush, followed by the construction of dams and levees.  “For the fish that evolved in that landscape, it’s hard for them to recognize lots of the physical processes that are happening right now,” he said.  “One of the reasons is that we’ve fundamentally changed the hydrology; we’ve put dams in, we’ve gotten rid of some of the high flows, and we’ve increased the low flows below most of the dams.  We’ve changed the sediment regimes in the system, originally with too much sediment coming down from the mining, and now we’ve put dams in and we’ve essentially curtailed the sediment moving through the system.”

Dr. Jeffres said considers levees just lateral dams, noting that there is emphasis on regulation of flows and sediment below dams (or the longitudinal habitats) but not a lot of regulation and managing for the lateral habitats.  “There is this fundamental dichotomy on how we think about those habitats,” he said.  “I think from an ecosystem perspective and even a geomorphic and a hydrologic perspective, they essentially function the same way as dams; they are just cutting off the habitats to the habitat to the lateral side of the river. We’ve changed how that system works.”

Competition among species has also been increased; non-native fish have been introduced and the habitat changes work well for those other fish. “Not only have we switched over the physical processes, but we’ve added the ecological competition with fish that are more adapted to dealing with the hydrology and the environment that we’ve created through our management, so for a lot of reasons, native fish in California have been struggling.”

Roughly 79% of California’s native fishes are endemic to our region, meaning they are found in California or neighboring states, but nowhere else in the world.  “That’s pretty unique, and I think a lot of it goes to our unique hydrology and our climate,” Dr. Jeffres said.

Recent reports have looked at the likelihood of some of these fish making it over the long term and it’s not very good, and that’s for reasons such as the habitat, the species, and the management, he said.  “So with that in mind, we’re thinking about how important and unique those fish are as well as the processes and how to keep them and understanding those physical processes are important.”

Out of the 131 native species found in California, half of them are relatively big fish – more than half of them at their adult stage are greater than 20 centimeters.  They are relatively long-lived, which makes them better able to deal with droughts.

One exception to that would be the Delta smelt, which is an annual fish.  “Without the long lives and high fecundity, you have a hard time dealing with these disturbances, whether it’d be introductions, droughts, or management,” he said.  “These larger fish that are fecund and able to live for a long period of time are able to kind of take advantage of the good conditions that do show up regardless of how we’re managing the system.”

In California, the water bodies in general are not very diverse – only between 1 to 7 fish per water body, as opposed to some places on the East Coast that have greater than 25 species per water body.  “We’re on a very fine edge,” he said.  “We don’t’ have a lot of species, they’ve adapted to a very specific regime, and there’s not a lot of room for failure in the system.”

California is a land of extremes, Dr. Jeffres reminded.  Most of the precipitation falls in the north, most of the people live in the south, and the state has developed an extensive plumbing system that allows all of us to be here, he said.  In any year, there is a wet period and a dry period, and every summer there is a drought where the rivers get low and warm.  Even under historic conditions, that’s part of how the system worked.

In addition to the seasonal drought, we have droughts and floods.  “There’s very little normal in here,” he said.  “If you actually put a straight line on the graph to show normal, there are very few years that would actually be close to it because we’re generally on one end or the other.  We’re constantly living between flood and drought, and the fish are here ultimately evolved to use that.”

This is the land of the hell and high water, and the fish that are here, this is what they experience,” he said, presenting two pictures (above, right) of the Cosumnes River just 5 weeks apart.  “Over that five week period, you go from a perfectly dry riverbed that’s dried out during the summer to a flood stage.”

To be able to take advantage of the rapidly changing conditions, fish have adapted in several ways.  They have physiological adaptations that enable them to tolerate high temperatures, high alkalinity, and low dissolved oxygen conditions; these help fish deal with conditions if they are stuck there.  The other way is behavioral:  the fish can move either within the watershed or leave the watershed and move out to the ocean.

For the anadromous fish, they leave fresh water and migrate out to the ocean where it stays wet all the time and conditions are fairly good; then they are coming back to finish their life history strategies,” he said.  “The fish that are utilizing both the rivers in the Central Valley are really using that migration time and they’re benefitting from floodplains.  Floodplains were a part of the historic migratory pathway for juvenile salmonids; other fish that were spawning in the floodplains, and it was a place where they were rearing and growing prior to their entry to either downstream into the Delta or in to the ocean.  So it was a habitat that was historically much more available than it is now.”

Floodplains are the land along the river that is subject to seasonal flooding; they also make great places for people to develop because it was flat and right next to the river, which were the historic pathways for transportation.  The Cosumnes River is unique as it only has a small number of diversion dams, so it is one of the last places in the Central Valley that actually sees a relatively natural flow regime, he said.

Floodplains are a great place for fish; at times, they are great places for cities, at times they are very terrible places for cities, and they are also very fertile agricultural land.  “We said, this is the land we want to put our footprint on, and so we’ve gone through it and we put in dams to help mitigate some of the flows coming down so we don’t have all the flood flows, we put the levees in, our lateral dams to keep the floods off of those lands, and then we’ve developed them.  We’ve gone through this process of reclaiming this land through control as opposed to integrating it into what we want from the ecosystem side and the flood protection side.”

Historically, much of the Central Valley was a big wetland; the Sacramento Valley was getting inundated basically on an annual basis, he said.   About 95% of those wetlands are now gone; they’ve been developed for agriculture or urban uses, and most of the remaining wetlands are either part of the reserve system or are duck clubs.

Dr. Jeffres presented two pictures, the left being a reconstruction of what California might have looked like in 1851, and the one on the right a recent satellite photo from 2017.  Pre-development, there was an immense amount of habitat throughout the Central Valley, but in the picture on the right, the Yolo Bypass and the Sutter Bypass are full and yet they can’t really be picked out on the landscape.

From a landscape perspective, the habitat that’s available even during our wettest year on record can’t hardly be seen from space without zooming in,” said Dr. Jeffres.  “So we’ve changed the system from the conceptualized picture to what is the reality now, and we’ve lost a lot of that habitat.  Now for a fish moving down the rivers, there isn’t a whole lot of habitat.  You’ve lost that extension of the river.”

A lot of the other habitats that are left aren’t great ecosystems, and we’re obviously not going to be taking people out of homes, so how can we work with what we have and what are our options for moving forward?

Dr. Jeffres said there are basically two types of floodplains: restored floodplains and managed floodplains.

The Cosumnes River is an example of a restored floodplain; it’s the only place that still has a relatively normal functioning hydrograph and there are geomorphic processes occurring, such as a lot of sediment that flows through the river, he noted.  On the Bear and the Merced rivers, the floodplains have been reconfigured and levees have been set back to create more floodplain habitat, but those rivers are still subject to upstream regulation.

You’ve fundamentally lost your geomorphic process in that you have a barrier that is stopping sediment coming down the system,” he said.  “You don’t have the same vegetation processes that are naturally recruiting and naturally distributing across the floodplain and allowing the river to move around.  I think those are really important; when you think about what a restored system looks like, it’s not just restoring the habitat; it’s restoring the processes that create and maintain that habitat over time.”

The other type of floodplains is the managed floodplains, such as the flood bypasses, such as the Yolo Bypass and the Sutter Bypass.  “They function seasonally as floodplains only when the water gets high enough to go over a crested weir,” he said.  “You still lose all of those smaller flow events, you’re still subject to upstream regulation as far as water being captured coming down, and you don’t have geomorphic processes happening out on these bypasses because if you did, then they wouldn’t function for the rest of the processes that they are doing, which is mainly flood conveyance and agriculture.

During the non flood season, some of the bypasses are being used as wetlands for ducks or waterfowl and some are used for agriculture although they still have to maintain flood conveyance, so they are truly a multi-use, multi-benefit system, he said.

In the Central Valley, fish use floodplains for either spawning or as rearing habitat.  “The splittail goes out and lays it eggs on submerged vegetation during floods, so it’s very tied into this flood regime,” he said.  “We see hitch, blackfish, a lot of other fish that utilize these floodplains as well, but then we also see fish like chinook, steelhead, sturgeon and suckers – we see lots of other fish that are using it during their outmigration or as a rearing habitat adjacent to the river.  And so there’s these two ways to use the floodplain.”

For floodplains to be useful to fish, there are three important factors: The first is timing, or when the flood happens; duration – how long the water stays on the floodplain; and then the magnitude, or how much water inundates the floodplain.  He then discussed each of these in turn.

With respect to the timing of floodplains, each of the species ultimately has a different timing for when they are using habitats, whether it be for outmigration, for spawning, for emergence of the invertebrates, or for recruitment for vegetation.  The dark blue line is the hydrograph for a rainfall system where rain falls and it moves through the system which is the Coast Range and some of the lower systems; the dashed blue line is a mixed rain-snow system such as the northern Sierra; and the red line is a snow dominated system, such as the San Joaquin.

These hydrographs are very conceptualized and averaged over time, but each individual year is what is important to the critters that are there during that year, whether they be frogs, fish, bugs, or plants,” he said.  “What is the recurrence interval of these events that you need to have benefit to the population over time?  If you’re a cottonwood, maybe you need a good event every 10 to 15 years.  If you are a salmon, you need it at least out of three or four years, and you can have some cohort mixing.  But not every year is going to be the perfect year and I think that is important when we think about how we control this system and how we manage for it.  And so, the different species have different life histories over time and different needs over time as well.”

Dr. Jeffres presented two graphs showing counts of splittail and juvenile salmon on the Cosumnes River from 2012 to 2016.  The splittail (top graph) use the floodplain from about February  through March – April.  The juvenile salmon (bottom graph) use the floodplain much later than the splittail.   He noted that the black dots for chinook outside the gray window are fish that have come into the Cosumnes from other rivers to use the habitat.

When we put windows on things such as the timing the windows that fish use, each watershed is a little different, but then it’s also species dependent,” he said.  “The Cosumnes is a natural system, and it is our living laboratory.  This is where we learn about processes that we then take to other places that we ultimately turns the knobs on and manage.  Thinking about these species, each has a different time frame that they need and how we get enough of those in a given amount of frequency that we maintain populations over time is really important.

The second important factor is duration, or how long the water stays on the floodplain.  Dr. Jeffres then presented a conceptual graph (below, left) for the current thinking on how the floodplain food web works.  About a week after the peak of the flood, chlorophyll A is high and there is primary production; next is secondary production of zooplankton and invertebrates who start grazing down the primary producers, and then there are the fish benefits.  “If you’re managing for fish, this is when we get into how long you have to have water on these habitats before you start to see benefits,” he said.

He presented a picture (above, right) with more details on how the process works.  “If you think about a river within a levee, this is more or less than the channel it’s going through,” he said.  “This is the solar panel as that water is moving through the levee.  It has a relatively low residence time … if you drive across the Yolo Bypass then drive across the Sacramento River during flood, you’ll get an idea of how big the solar panel is.  It fundamentally changes the system; not only did you make that solar panel really big, but you slowed it down and created some more diversity in it and so you increased the residence time for these processes to happen.  You increase the residence time for the algae in the water to develop.  You’ve increased the water substrate interactions so you have that decomp and you have that detrital food web that’s occurring, and all that funnels into the zooplankton population, and ultimately that is what drives your fish production and how quickly they are growing.”

He presented a slide with a picture of three samples of water from the Yolo Bypass, the Toe Drain, and the Sacramento River on the same day.  He noted there were about 250,000 invertebrates per meter in the water from the Yolo Bypass versus about 1300 in the water from the Sacramento River.  This demonstrates what happens when you spread that water out and slow it down, he said.

You end up getting what I call the zoop soup,” he said.  “This is where your production is coming from, this is where the food resources are coming from, and this is how you get the difference between the river and the floodplain habitats.

The third important factor is magnitude.  We have fundamentally changed the system; it is a system that we now manage, Dr. Jeffres said, presenting two graphs showing discharge of the Sacramento River at Red Bluff.

We’ve lost the big peaks that have come out of the system after the closure at Shasta Dam, and so we’ve lost those really large flood events.  Obviously we can’t have that happening because we live in the floodplains, so seeing 250,000 cfs at Red Bluff seems amazing.  It’s something that happened relatively frequently before the closure of Shasta Dam.  Then we’ve shrunk our peak flows coming down; we don’t have a recession any more as we’ve curtailed the recession.”

Another change that our management of the river has made is that summer flows are now higher, he noted.  “We’ve homogenized the system,” he said.  “We’ve gotten rid of the flood and drought, and we’ve knocked down the floods, increased the drought below the major reservoirs in the system, and so we’ve fundamentally altered the habitats that were here before.”

The average daily flows are actually higher post-Shasta Dam, due to water coming in from the Trinity River.  “We don’t have as much water coming down because we’ve gotten rid of the floods, but the mean daily flow is actually still higher if you incorporate the Trinity water coming over,” he said.  “I think it just highlights how different the system is now than it was before and how these fish who evolved through the hell and high water, now we just have Wonder Bread.  It’s kind of boring bread.  We still have a little bit of uncomfortability, but from a fish perspective, we don’t have nearly the uncomfortability that we had that allowed these fish to succeed in diverse and changing conditions on a relatively short scale.”

We ultimately control the system now,” Dr. Jeffres said.  “This is a heavily managed system and we’re not going back to what was here before.  This was a map from the early 1850s and it’s interesting thinking about what that looks like now versus what it looked like then, and how do we decide what we want to be in the system?

He noted that in a recent interview, he was asked, what is the future of salmon in California? “My answer was pretty simple,” he said.  “It is whatever we decide.  Because we’re ultimately turning knobs in the system, and we’re managing the floodways.  We’ve gone through a century of trying to control the system within its levees and behind the reservoirs, and there are other opportunities for reconciling both of these, putting them on the same landscape, whether it be through releases of water from reservoirs, is it through restoration of process?  Not just habitat, but process.  You can restore habitat, and if you don’t restore the process that maintains it and makes it useful, then it’s not necessarily beneficial.”

The flood bypasses have the potential to provide flood control benefits as well as ecosystem benefits.  There also need to be connectivity, much like a string of pearls.  “I look at this system, and there’s two big pearls on it,” he said.  “The idea is that ultimately, you need to have more pearls on this string; it’s not just having two big pearls on the bottom, that isn’t going to do it …  the idea is you need more of those pearls, and you have a lot of pearls, and they can be small and that’s okay, as long as they are connected and you ultimately increase that habitat and its functions over time.”

So I tried to end on happy note in that we’re not all doomed,” Dr. Jeffres said.  “We aren’t going back but I think there is a lot of opportunity to go forward within the system that we have.  It’s ultimately us that decides what we want for our future.  As much as we lose control occasionally, we ultimately control the system and I think that’s our job is to decide how we do want to control it.

And so, with that …


QUESTION: In places where there haven’t been floodplains a very long time, how do we encourage the fish to actually use those?  If we’re constructing new wetlands or floodplains, do they just have to wander into them?  Is there some kind of signal that can be given to encourage them to go that way where there’s favorable habitat or are we at the mercy of them stumbling upon these constructed facilities?

DR. JEFFRES: “Unlike the waterfowl, fish don’t have wings so they aren’t deciding as much. It has to be connected habitats that are adjacent to the river.  Also, the fish are migrating up the sides of rivers or down the sides of rivers and the likelihood of running into those habitats is higher when it’s connected.  The idea is you’re not going to get all the fish going by and utilizing one of those habitats.  The idea is that you have enough of them throughout the system that they aren’t reliant on hitting one of those on the way down, but if you have several of them throughout the system, and you have enough flow to get out there, then they have the opportunity to get out there.”

COMMENT FROM PARTICIPANT mentioned the Bullock Bend restoration site that was constructed on the Sacramento River last year.  As soon as it flooded even without any vegetation in it, we caught listed salmonids and steelhead in there, so as long it’s connected when it floods, they hit it.

DR. JEFFRES: “As long as there is slow water, the fish are going to use it on the side of the river. It’s really just getting out of that channel … I hate to say this so simply, but small fish are essentially particles in a big channelized river.  There is some ability to move around but as a 2” fry coming down the river, when you end up on a floodplain, you have the opportunity to choose where you’re going a little more.  We’ve seen this everywhere: as soon as you open something up and water is flowing out there, that we’ll see the fish out there as well.”

QUESTION:  One of my thoughts about residence time and also getting projects that get through permitting is that we see sometimes we want to create places that hold water on it, and yet some of the agencies say, ‘don’t create places that will strand fish.  Don’t create topography that will pond areas’.  But if you make it drain really nicely, than it doesn’t hold the water for long periods to get good and juicy.  Any thoughts on that?

DR. JEFFRES: “One of the first restorations out on the Cosumnes actually didn’t have draining topography, and so the main sites on the Cosumnes restoration where the levees were breached were ponds dug on the floodplain for waterfowl; the reason was that you could hold water long enough for waterfowl.  It was before the fish agencies were requiring drainage off.  We’ve been monitoring it for ten years now, and we almost never see native fish stranded in those ponds.  You see it as soon as the hydrograph turns over for the spring recession; you see this mass exodus of native fish.”

Now obviously, you’re not getting all of them; I think that would be crazy to think that you don’t have any native fish that get stuck out there.  You did get larval fish, you do get some bigger fish, but you get the vast majority of them out and having the benefits of having that residence time far outweigh losing a few fish.  For regulatory agencies, I get what their point is, you can’t have any winter run get stranded out here because we have so few left, but I think that the benefits so outweigh the negatives of losing a few individuals – and that’s what the landscape looks like over time and that’s what these fish are evolved to take advantage of.  We’ve seen that for years on the Cosumnes that as soon as that hydrograph turns over and gets close, we see this mass exodus of fish, and then as soon as it disconnects, if you throw a net out there, it is carp filled.  We’ve caught upwards of 80,000 juvenile carp in a net at a time, and its disgusting.  And then there will be 300 pelicans just sitting there … These fish have evolved to take advantage of this.


Take a virtual tour of California’s floodplains.

Note: This is the third in the series of three brown bag seminars focusing on flow targets and ecology.


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