“What data we have suggests that the predation is a huge factor that will probably preclude any recovery of salmonids no matter what other management actions we take within this region.”
At last week’s ACWA Fall Conference, one of the sessions highlighted studies on predation and fish populations in the lower San Joaquin River and south Delta that the fisheries and environmental consulting firm FishBio has been conducting with funding and support from several San Joaquin Valley water districts.
“The reason we’re bringing this to you is even though this study is in a smaller geographic area, the results that you will hear about today infer that this is an issue of non-native species populations being so large that they’re impacting the native species and an issue greater than our focus area,” said David Weisenberger, General Manager of the Banta-Carbona Irrigation District.
The way we manage fisheries, particularly salmon, mainly revolves around providing additional flows for fish. “That means that the burden for this management is largely placed on water users,” said Dana Lee, a fisheries biologist with FishBio. “But we haven’t seen the benefits of that approach. In fact, most of the salmon species are in decline. This is the second year in a row, the second time in history, that we’ve had a multi-year closure of the salmon season. So I think the mechanisms behind providing that flow are not particularly well understood.”
Fish and water management in Central Valley is complicated; there are a lot of agencies, policies, plans, and laws. From a fisheries perspective, the three most impactful things are:
- The state and federal Endangered Species Acts.
- The biological opinions for the Central Valley and State Water Projects.
- The State Water Resources Control Board update of the Bay Delta Water Quality Control Plan.
“There are many different parameters for all these programs, but they are mainly focused on providing additional flows for fish,” said Mr. Lee. “However, this approach hasn’t resulted in much success. We’ve been trying the same thing for 20 years. The main species managed for in the Delta are green sturgeon, longfin smelt, Delta smelt, steelhead, and Chinook salmon. All of them are particularly in peril. All of them are probably doing as poorly as they ever have.”
Mr. Lee noted that this presentation focuses on salmon, but the results could apply to all of these species.
The salmon lifecycle
Chinook salmon have a complicated life history. It’s primarily an ocean species; they spend two to three years, most of their adult life, in the ocean. There isn’t much management once in the ocean outside of harvest management. It’s a black box; there’s not much we can do once they are there. So the management focus is on the freshwater life stages.
Most salmon come back in the fall; they spawn in rivers and their native tributaries, lay their eggs, and die soon after. The eggs then incubate over the winter.
“The critical stages of the salmon life history that we manage for are fry, parr, and smolt,” said Mr. Lee. “These are the juveniles that have hatched from the eggs in the spring and are making their way out to the ocean. These are the fish that we’re providing flows for. There is also some management for egg temperatures and other things, but this is the key limiting factor, as we see it.”
Salmon management is centered around harvest, hatcheries, habitat, and hydropower (or flow).
Harvest numbers have remained relatively consistent for the last 30 years; outside of the closures, 50-70% of fish are consistently taken from the ocean each year. Hatcheries are likewise consistent, producing about 30 million juveniles per year. Habitat has been an important focus in recent years through the CVPIA, EcoRestore, and now the Healthy Rivers and Landscapes Agreement; tens of thousands of acres of habitat have been restored; it is working, but more is needed, and it’s not the end all solution.
Flow is the number one management tool that is used; it’s the easiest knob to turn and has long been held as the number one management tool needed to increase populations. There is also a paradigm that more flow equals more fish. But what drives salmon abundance, and how does flow affect that?
More flow does not equal more fish anymore
This graph below shows fall chinook abundance in the San Joaquin Basin from 1950 – present. “There is a long term decline in population abundance since the 50s,” said Mr. Lee. “But these boom or bust cycles are largely driven by climatic events. So when we get good water years, we get bigger flows, and you see these booms in the populations. You’ll hit a drought period and see less returns and less abundance after that. But focusing on the last 20 years, we see a little bit of a breakdown, not only low abundance overall but a breakdown of that relationship and a pretty muted response to those high flows.”
“However, looking just since the year 2000, we see almost a complete breakdown of this relationship. If anything, now, when we get higher flow years, we see fewer adults returning. So that’s telling us something’s going on here. Something else is acting on the population. Increased flows are not getting us the same population response that we used to see.“
The graphs below depict mean spring flows in the San Joaquin basin; the x-axis shows the flows in the San Joaquin River as the fish were migrating to the ocean during the juvenile life stages, and the y-axis is the population of adults two years later. The graph on the left is from 1953-1999; the graph on the right is from 2000-2021.
“It’s looking at what happened during that flow – were those flows high or low when they left? And what happened when those adults came back after spending their time in the ocean. Did we see a response in those adults? Historically, we did. The graph on the left is from about 1950 to 2000 and shows more flow equals more fish. When we had bigger flow years, we tended to get higher adult returns. And that’s long been this management paradigm.”
“The main thing that seems to be going on is just very poor outmigration survival across the Central Valley,“ said Mr. Lee. “In all these different streams, we see poor survival. These studies are all from telemetry-tagged fish. We’re tracking their movements through the system to see how many survive to the Golden Gate.“
Mr. Lee acknowledged there is variation, and there are still some boosts and increased survival in wet years. “But overall, we’re talking about very, very poor survival – less than 1% in the Sacramento River in some years in what is some of our better habitats; 0% survival through the Delta in other years. That’s pretty abysmal. It’s pretty alarming, especially when you compare it to other Pacific or West Coast rivers. The Columbia River, for example, we see pretty consistently 50% survival in that basin. So California is doing very, very poorly despite the management actions and the habitat improvements we’ve been trying the last 20 years.“
Meanwhile, non-native species have proliferated in the South Delta
At the same time, there’s been a proliferation of non-native species, and the species are not responding to flow and habitat. This led to the studies of the impacts of non-native species on the native fish.
So, how did the non-native fish get here? Most were introduced by either the State Fish and Game Commission or the Department of Fish and Wildlife beginning in 1860. About two-thirds of all introductions resulted from state agencies trying to provide sportfishing opportunities or bringing forage fish to feed those sportfish. Any management of these species was intended to increase populations, thus bringing non-native predators into the system.
The impacts on the native fish community are clear. “We’re seeing these dramatic declines,“ said Mr. Lee. “These are three similar studies, all done electrofishing in the Delta, going back to about 1980, where they saw about 20% of all their catch was native fish species, and about a third were black bass and sunfish. Black bass, in this case, includes large mouth, small mouth, and spotted bass. So within 30 years of that, the study was redone by 2009, and found less than 5% native fish species and an explosion of black bass in the Delta. And in 2022, we see less than 1% native fish species in all of our sampling in the Delta. So we’ve seen pretty much a complete takeover of that community by non-native fish. You now have a world-class trophy bass fishery in the Delta.”
The pinch point is the Delta, the migratory corridor where all the juvenile salmon need to get through. So, these results led them to want to study this further.
2012 Tuolumne River predation study
So, in 2012, they started a predation study on the Tuolumne River to examine how many predators there were and what they ate. “We found only 4% of Chinook were estimated to have survived just the 25-mile migration route within the Tuolumne, and not only that, but the entirety of that loss could be explained by non-native predators and predation.“
These results were surprising, yet the state agencies didn’t like the results and took issue with some of the methods used. “So we revised this study to redo it the next year because we were thinking of repeating it ourselves. We’ve been continually denied permits for that study ever since. So we’re not able to get the permits to redo that work.”
Other predation studies
Mr. Lee pointed out that other groups have been studying predation. The National Marine Fisheries Service acknowledged as early as 2009 that striped bass were going to be an issue precluding the recovery of salmon. A study in the Delta looked at the caloric needs of striped bass, and they found that the estimated population of striped bass in the Delta could consume 55 million pounds of fish per year.
“So putting in that perspective, if you took the weight of every single juvenile salmon out-migrating in a given year, that would be 2% of the annual diet of striped bass,“ he said.
On the Mokelumne River, a researcher was looking at the site-specific predation just below Woodbridge Dam at a single location and found up to 30% of population-level impacts at just that location.
Stanislaus predation research
“So across the board, we’re starting to see evidence that there are some issues here,“ he said. “This led us to work that we implemented on the Stanislaus River. This study was first proposed by the districts prior to the Tuolumne work. We first proposed this in 2009 and were continually denied permits to do this work. It actually took an act of Congress through the WIIN Act in 2016, which required the state and federal agencies to work with the districts to implement this study.”
It is probably the largest and most comprehensive predation study in the Delta to date. They completed field work last year and are in the process of reporting right now. The goals of the study were to estimate the abundance of predators of each species of black bass or striped bass, what they’re eating, and the total impacts on salmonids.
The slide below shows the impacts on chinook salmon by year, broken out by species. “What we can see here are some pretty high impacts in some years, as high as 60%,“ said Mr. Lee. “What we also see are pretty consistent levels of predation. It fluctuates in some years, but even in really high water years in 2019 in 2023, we’re still seeing very big impacts of a large number of those chinook lost to fish predation under what should be some really good conditions.“
Predation is a natural feature of ecosystems, but the impact from non-native predators is significant: black bass, a non-native predator, has a significant impact, while the native predator in the system, the Sacramento pikeminnow, has minimal impact overall.
San Joaquin River and South Delta research
In 2020, they began electrofishing to collect data in the San Joaquin River and the south Delta. “This region is an unknown mortality sink for juvenile salmon for out-migrating salmon,“ he said. “We know from telemetry studies that these are the areas where we sometimes get 0% survival. We actually see the fish survive better that make it to the federal pumping facilities survive better because they then get trucked out to the bay.“
There’s a lot of active management in the study area for inflows and exports, but again, it hasn’t been working, and there’s very little data. So they partnered with the water districts to collect data to estimate the abundance of the non-native predators, look at their movement patterns and distribution and how that might change from year to year, and then assess the population level impacts.
“What we found was that bass are everywhere,“ he said. “We knew that. We expected that in almost all the units we go to, we would find bass. What we didn’t expect to find was less than ten salmon in five years of study. We’re out there monthly, sometimes twice a month, for more than half the year; we’ve only seen nine chinook in this entire region. There’s a hundred times more predators there than chinook, and just this year, for the first time, 2024, is the first evidence we have of a chinook being consumed by a predator in this region.”
The two region-wide studies made it possible to link up the data and figure out why we aren’t seeing salmon in the Delta.
The maps below show the San Joaquin River and the South Delta and the probability of an individual juvenile salmon getting consumed at any particular site along the reach.
“What we can see here when we link up this data against similar methods of collection is that almost the entirety of all of the consumption is occurring in the tributaries,“ he said. “So we’re not seeing [salmon] in the Delta because they are not surviving far enough for them to even get there to be within our study reach. However, we know if they did make it there, we know there’d be a problem. The density of predators is much higher. We know there are problems in Delta. We know that from telemetry and other studies. We know the survival will be extremely poor, but we have issues even getting fish out of the tributaries in what should be better habitat in the Delta to survive. So we have some big survival problems.“
Further research needed
They are currently working to publish the data, but here is what Mr. Lee says is needed to better understand predation in the Delta:
Information needs to be collected. We need data on predator abundance; since these are managed sportfish populations, abundance data should be available, but it isn’t.
Next, we need to look at what they’re eating and the consumption rates of the salmon, which tells us how many salmon those fish are possibly eating. Then we can take the number of salmon available through long term monitoring programs on the tributaries and in the Delta, and we can start to get at that predation impact across any given region.
“We’ve spent significant effort, and significant resources have been expended to start to collect this data over a large migratory corridor across the Stanislaus River in the south Delta,“ said Mr. Lee. “However, when you look at that on the scale of what we’re talking about here in the Central Valley, that’s a very, very small area in comparison. But what data we have suggests that the predation is a huge factor that will probably preclude any recovery of salmonids no matter what other management actions we take within this region.“
The studies should be expanded to the Sacramento River basin, as 90% of the salmon population is on the Sacramento River. There are two listed runs, the spring run and the winter run, in the Sacramento River Basin, and there isn’t this kind of information available.
“We do know the number of salmon, but everything else is kind of a black box at this point,“ he said. “So that’s the coordinated data collection effort we think would be very valuable.”
“I want to make the point here – we’re not talking about eradication,“ he said. “We’re not going to eradicate all these predators. It’s not possible, but for any species we’re going to manage, we’re talking about collecting just the basic data to begin to even think about implementing management actions and where those actions would be implemented.”
Take home messages
There are multiple factors influencing salmon abundance. It’s not just flows, it’s not just habitat, it’s not just non-native predators, it’s all of those things. It’s going to take a suite of actions. But the management actions to date have really focused primarily on flow and habitat to some extent. It doesn’t appear to be working.
Flow alone is not enough to recover listed species. The Central Valley has many issues: climate change, drought, and increased temperatures. Flow alone will not be able to recover these species, and the data suggests that non-native fish substantially impact native species’ survival.
Coordinated long-term data collection is needed across Central Valley. The study area is small, so we need this data collected and coordinated long-term across Central Valley to start making the case.
“The overall goal is the recovery of salmonids and other native fish,” said Mr. Lee. “We all want the recovery of salmonids. We want water supply reliability. We want abundant resources. That’s the goal. It’s looking like the management of non-native species is probably going to be one factor that is needed to prevent extinction. It’s going to need to be one tool in the toolkit, and to do that, we’re going to need to increase our data collection efforts.”
More coverage of predation on Maven’s Notebook …
NOTEBOOK FEATURE: The impacts of non-native fish on salmon populations in the San Joaquin River
“What data we have suggests that the predation is a huge factor that will probably preclude any recovery of salmonids no matter what other management actions we take within this region.” At last week’s ACWA Fall Conference, one of the sessions highlighted studies on predation and fish populations in the lower San Joaquin River and south Delta that the fisheries and environmental consulting firm FishBio has been conducting with funding and support from several San Joaquin Valley water districts. “The […]
PRESS RELEASE: The missing piece: Protecting California’s struggling native fish
New study reveals significant impact of predation on native fish populations Press release from the Banta-Carbona Irrigation District A groundbreaking five-year study conducted by FISHBIO and a coalition of Central Valley water agencies has uncovered a potential missing link in efforts to protect California’s declining native fish populations: predation by non-native species. A new video released by Banta-Carbona Irrigation District (Banta-Carbona), “A Startling Picture,” takes a closer look at the research that challenges many long-held beliefs about why California’s native […]
IEP ANNUAL MEETING: Understanding Predators to Better Understand Predation
Salmon populations in the Sacramento-San Joaquin Delta have significantly decreased over the past century, with most populations considered endangered, threatened, or species of concern. Non-native sport fishes, such as striped bass or black bass, are popular sportfish and economically important to the Delta; however, as predators, they create challenges for the recovery of salmon as predation during outmigration is a major factor contributing to the population decline. Balancing competing interests of non-native fisheries with the need to reduce predation pressure […]
DELTA LEAD SCIENTIST: The role of water quality in salmon predation
At the November meeting of the Delta Stewardship Council, Delta Lead Scientist Laurel Larsen spotlighted research funded by the Council that examined whether water quality is a factor in juvenile salmon mortality with a somewhat surprising result. She also updated the Council on the discovery of nutria on Lower Sherman Island and a workshop scheduled for the spring of 2023 on the development of a ‘collaboratory.’ Article spotlight: Are Habitat Variability Factors like Water Quality Important for Salmon Survival? Four […]
EXPLAINER: Delta fishes: Introduction to a dynamic fauna
Dr. Peter Moyle is a distinguished professor emeritus and Associate Director of the Center for Watershed Sciences at UC Davis. He has studied the ecology and conservation of fishes in freshwater and estuarine habitats in California for over 50 years. At the February meeting of the Delta Independent Science Board, Dr. Moyle provided an overview of Delta fish, explaining why some fishes have become overabundant and others are headed for extinction, all while being participants in a novel ecosystem. The […]
Click here for all coverage of predation on Maven’s Notebook.
