Chinook salmon need freshwater flows for adults to migrate upstream to spawn, to keep their eggs cold, and for young fish to migrate downstream to the ocean. Photo by USFWS.

THE DELTA AND THE TRIBUTARIES, part 2: California’s salmon face challenges, but there are success stories, too

In the fall of every year, an incredible phenomenon takes place in the Central Valley: the fall salmon run.  Adult salmon travel many miles from the Pacific Ocean upstream to their spawning grounds, returning to the river where they were born, sometimes even to the same riffle, where they will spawn, laying their eggs in the gravels of the rivers and streams.  Once hatched, the young salmon will spend several months, sometimes longer, lingering in the freshwater until it is time for them to migrate down the rivers, through the Delta, and out the Golden Gate.  After a few years at sea, the adult salmon will begin their long and final journey upriver to return to their birthplace, and thus the cycle continues, a timeless dance in the circle of life.  It’s an event that has taken place in our local rivers for thousands of years.

Salmon have existed more than a million years and have evolved with California’s climate.  However in recent decades, populations of salmon and other native species have experienced significant declines which studies have attributed to several factors, including overuse of water resources, habitat loss and degradation, and overfishing.  The construction of dams across rivers has blocked access to the spawning grounds above them; the flood control provided by these dams and the development of cities and farms on the valley floor has eliminated much of the floodplains that historically, young salmon and other native fish utilized for rearing and feeding.

It would seem that California’s management of water for is not working for anyone, human or otherwise.  Environmental advocates argue that water quality and flow standards do not adequately protect fish and wildlife, and regulators have failed to enforce these requirements when they are most needed, while agriculture and urban interests say these regulations have been ineffective and expensive in both dollars and acre-feet.  However, if fish populations continue to decline, regulators may likely conclude that more water is needed to support struggling fish populations, further stressing already tenuous water supplies.

At the Mountain Counties Water Resources Association forum,The Sacramento-San Joaquin Delta and its Sierra Nevada Tributaries: The Stressors and the Fix, fish biologists discussed the status of salmon and other native fish in the tributaries.  First, Dr. Bruce Herbold, retired EPA and fisheries consultant, gave an overview of native fishes and talked about how the habitats have changed since humans have developed the landscape.  Next, Doug Demko, president of FishBio, then discussed the effects of predation and hatcheries on salmon.  Lastly, Jose Setka, Manager of the Fisheries and Wildife Division at East Bay Municipal Utilities District, discussed the factors behind the success of salmon on the Mokelumne River.

BRUCE HERBOLD: Strategies for survival with California’s inherent hydrologic variability

Dr. Bruce Herbold began by positing the question, how do you fix a problem?  You clearly define the problem; recognize limits, scope and uncertainties; set goals and establish acceptable costs, he said.  “This isn’t news. This is all obvious stuff.  We haven’t done it for California’s water problems because it’s too complex and since it’s too complex, we won’t do it in any logical fashion.”

Our grandparents had a problem, he said.  California has water at the times when we don’t need the water so much, and we have all this need for water in places where we don’t have it, so the problem our grandparents faced was how to cope with that.  The other problem is that it varies a lot from year to year.  “Some of our grandparents came out here during the dust bowl; there were lots of people, and they said, ‘We need to do something about this.  We need to move water south because people like living in Los Angeles where it doesn’t rain, and we need to stabilize water supplies.  We’ll build reservoirs.”

While our grandparents recognized the hydrologic variability, they didn’t understand to the degree to which California’s climate could vary.  “We do know by going back and looking at tree rings and sediment records, we see that there were huge floods,” he said.  “The 1862 flood was not the biggest one that seems to be on record.  We have about every 200 years, from various data sources, evidence of the enormous floods.  If we had half the flood that we had in 1862-63, that would be worse than any damage from earthquakes that the USGS has ever modeled for our state, because we have all these nice cities in floodplains, so what used to be an inland sea, if it becomes an inland sea again is according to the USGS, is much worse than anything we’ll see from earthquake impacts.  You’ll notice that we’re about 200 years from the last one.”

Salmon have a strategy for dealing with this problem, Dr. Herbold said.  There are four different runs of chinook salmon in the Central Valley that evolved to cope with the substantial variation in water supply and habitat conditions.  Two of the runs, the fall run and late-fall run come in and spawn almost immediately and as soon as the spawning is over, they start maturing and moving out.  “That’s the strategy, ‘let’s not take any risks because it may dry out,’” he said.  “They spawn mostly downstream in the valley, so their fear that it may dry out is reasonable.”

Winter run and spring run salmon are much more tied to where they can find reliable cold water.  The spring run would migrate all the way up to the headwaters of most of the tributaries where it was always cold; if there wasn’t snow, there was at least springs.  Winter-run went up to Shasta where there was always cold water for spawning.  The young can hang out for six months or more, sometimes as much as a year; if it was a bad year to migrate out on one year, they would go out the next year.  They were bigger and less likely to fit in predators mouths.  “It was a really good solution,” he said.  “This really works.

Steelhead take flexibility to an extreme; we can’t even be sure when we have a steelhead population or not, because they migrate out, they may not migrate out, or they will migrate out when it’s convenient, Dr. Herbold said.  The adults move up and spawn and they move back out, they don’t die, so they can come back and spawn later.  “They are as flexible as a fish can be which is really good in California,” he said.  “Being flexible is a really cool tool.”

Unfortunately, the construction of dams has blocked access of the spring run to those spawning areas, with Deer and Mill Creek being some of the few remaining spots for cold water, Dr. Herbold said.

The multiple ways in which salmon can adapt to variable conditions is called the portfolio effect.  “However, we have done everything we can to minimize that portfolio,” Dr. Herbold said.  “We have built hatcheries and we manage them the same way.  We have hatcheries on all these affected rivers, and we try to get them out at the same time – even coordinate water releases so that all the tributaries on the San Joaquin can have their young come out at the same time.  If that isn’t the right time, then they are all – the technical term is screwed.  There’s a little window of time when salmon entering the ocean is good, and it’s not really predictable if you’re a salmon, so if you come down at a variety of times, some of you are going to hit the good window, and some of you aren’t.  Restoring that portfolio, especially in the face of climate change when all of our abilities to stabilize everything are going to be perhaps in some ways overrun, is I think a suitable feature to focus on.  Right now, we’ve done everything we can to remove that portfolio effect, that’s not irreversible, because they are really flexible fish.”

California has native fish other than salmon, and they are very odd fish, Dr. Herbold said.  “Dr. Peter Moyle is holding a pike minnow.  It is a very large minnow; it grows 2 to 3 feet long and it’s predatory.  Like all minnows, it doesn’t have any teeth in its jaws so it has extensions on its gills that are knifelike and long and can grab into preyfish, and it makes it a very effective predator.  On the other hand, one of our other minnows, the splittail on the upper right, also grows to 2 feet or so, and is like a little freshwater shark.  Its tail is the shape of a shark tail and helps it move along the bottom.  If you look at it from underneath, it’s eyes are looking straight downward.  It’s great specialist on eating benthos, on finding and eating the bottom organisms.  The fish getting the kiss in the middle is a hitch is another minnow that grows to one foot or more, and is up in the open waters of ponds or rivers and eating plankton.  These are all minnows.”

On the other hand, we have Delta smelt that only lives for a year,” he continued. “How can a fish deal with California’s climate if it lives for only a year?  It finds one of the few habitats that is there every year; it lives in the low salinity zone where saltwater meets freshwater, and that tends to be a nice place to be.  It is a nursery zone in most estuaries, so it may move where it is depending on how wet it is, but it’s always there, it’s a habitat that can be relied on.”

The lower right is a tule perch, which is a live bearer.  “We have 13 species in the family, they all live on the Pacific Coast.  This is the only freshwater one; the female will give birth to about 80 little babies that come out of her and immediately start eating like the adults.  We also have the largest sturgeon in North America, and they solve the problem because they don’t have to spawn every year; they will happily wait until a pulse flow comes down and triggers that it’s a good wet year, and they will go up and spawn.  Both the green and white sturgeon can go years without spawning and then spawn nicely and recharge that.  Another perfectly good strategy.”

So what did our grandparents do to solve the problem?  “They stored and moved water,” he said.  “And they simplified the system.  They took Economics 101 and they got as much as they could out as fast as they could, and that’s the economics lesson that we continue to apply.  It may not be overall the best for the state, but it works for individuals very well.  And we hope and pray.”

During the CalFed days, there was a call for more storage which resulted in an intensive look for suitable sites to build reservoirs, and four sites were identified.  One was taken off the table; the other three are Los Vaqueros Reservoir Expansion, Sites Reservoir, and Temperance Flat.  “We have 1,594 dams in this state already,” Dr. Herbold pointed out.  “Our grandparents culminated their efforts to build dams between 1950 and 1969.  The dams came online, and then they didn’t build many more dams.  It wasn’t because of those harsh environmental regulations or the harsh permits of the 70s.  We just ran out of places to build dams.”

We have a lot of big dams: there are 278 dams greater than one hundred feet tall.  “Our grandparents were not dumb,” he said.  “They went and said, ‘that place right there needs a dam on it,’ and everywhere that they could say that, they built one.  And of course, those dams are why we lost the spring-run habitat, because you can’t get them over that.”

Our grandparents also simplified things,” Dr. Herbold said, presenting a map of the Central Valley pre-development.  He noted that the gray in the middle indicates the historic wetlands, almost all of which is gone now.  In the Delta, we refer to the lands as islands, but instead of sticking up out of the water, they are more like bowls in the water and the levees are more circular dams.

The Delta, pre-development, had channels built like tree branches which ended in dead-end channels.  “Those were lovely places to be a fish,” he said.  “They were really productive and there were lots of them.  If something bad happened in another channel, it has no effect on the one you happen to be in.”

The channels were simplified in order to make navigation easier.  “We simplified them all because the boat has to be able to get from one place to another so we’ll just dig a channel here,” he said.  “We need to do various things so we’ll dig a channel there – all those nice straight lines mean that now, as the tides move in and out, it’s a mix master and there’s no place that is not connected intimately to every other place in the Delta through those waters.  So if something bad happens in one place, it happens bad everywhere.

The picture on the bottom is the Sacramento River at Decker Island which doesn’t look anything like the wetlands that used to be in the Delta, he said.  “If you look at that aerial view of the Sacramento River, you can see there’s not much fish habitat than just the water, whereas if you go to a place like Suisun Marsh, that looks like fish habitat.  Salmon can survive there, salmon can thrive there, whether there are striped bass there or not.”

Today, the problems we face are changes in climate, invasive species, and aging infrastructure.  Dr. Herbold then discussed each of those in turn.

California is the perfect place to look for climate change impacts as we have really good records that go back a long time and it shows a really clear signal, he said, presenting a chart showing the deviation from the mean temperature from October to January.  “All of those positive deviations from average on the right hand side of the graph tell you what you already know – it’s getting warm,” he said.  “We’re getting pretty much no snow in some of those years.  Getting warmer, less snow.  It’s not disconnected.”

Invasive species are another problem.    The overbite clam arrived in the mid-1980s; in the Suisun Bay, there can be 10,000-30,000 clams per square meter, capable of turning over the water column of Suisun Bay twice a day.  “We don’t get algal blooms any more, and this has been a bad thing for zooplankton, but not such a bad thing for fish.  The fish still show the same patterns with flow that they used to, but sometimes not as well.  But for that part of the ecosystem, there seems to be some disconnect between the food for our fish and the fish themselves.”

In warm seasons, we’re now seeing a lot of microcystis blooms.  “It’s a bacterium with a behavior,” he said.  “They grow in colonies, and when they photosynthesize, they generate gas and they keep it in bubbles which floats them to the surface where there’s more light.  And then they used that oxygen up and sink down during the night, so you have got bacteria colonies that migrate on a daily basis.  They are really cool; they are also toxic and really nasty.”

There are a lot of other invasive species which bring in other problems.  “We’ve made the Delta into a very poor copy of the Mississippi and we’ve stocked it with Mississippi fish, and some of the Mississippi fish are doing really well,” he said.  “Because of climate change and California’s inborn climate, that’s probably not sustainable, so I like the idea of keeping our native fish around so that when it all goes to hell, we have some fish that can deal with it.”

He presented a graph of Central Valley runoff from 1906 to present day [below, left], pointing out that in 1976, they had a critically dry year, followed by the driest year on record (at the time), and Shasta Dam was drawn down so far that there was no cold water for the winter-run salmon.

Droughts and floods are part of California’s normal climate, so how do we respond?  “In 1976-77, we drained the reservoirs, we exported all that water.  That was an approach,” he said.  “Then we have very low exports the next year because we don’t have any water.  We did the same thing on a big scale with the eight-year drought; that seventh year was wet but the reservoirs we’re all empty, so it caught all the water so the fish didn’t see any benefit of that wet year, so for them it was an eight year drought.   How did we respond?   ‘OMG, a drought is starting.  Let’s increase reservoir releases and export more so that we can run out really hard.’  You can see that we continued to do that in the last two droughts there.  What are reservoirs for but to get us through dry periods.  Notice that dry periods are never one-year long.  So if you have full reservoirs and it hasn’t snowed this year, there’s a possibility we could manage things differently.  We could actually save something in the piggy bank, save some cold water for salmon and try to stretch that out until the drought is over instead of ‘OMG, we’re out of water.’”

Dr. Herbold then gave his conclusions.

The native fish that are adapted to California’s climate are at risk, Dr. Herbold said.  “California has really cool fish, not just salmon and they really have cool solutions to California’s climate and thereby they have cool solutions to the changes that California’s climate is likely to see.  I want them not to go extinct.

We can’t solve the problem with any single thing, Dr. Herbold said.  “Some sort of getting those thousands of water users on board with a statewide solution is the only solution that I see that has any hope of working,” he said.

We need to set goals, he said.   “Here we have choices to make, and it’s not either-or, but do you want your water supply to take as much as you can every year, or do you want to have a reliable average?  We can do reliable average really well, but you won’t get as much in the wet years because we’ll hold on to some of it.  That might be a strategy.”

We have contracts that say you’re entitled to so much water if it’s available, so how do we know when it’s available and how much does that weigh in?  and how much are we willing to pay for it?” he said.  “So with limited funds, how much do you want to keep what is working now, versus how much do you want to try and build something new to increase how much you can get?

One of my soapboxes is that we manage the estuary as the Bay but you can’t drink the water, and the Delta where you usually can, and we treat them as entirely separate bodies,” he said.  “Climate change is going to push that Bay right up into the Delta, so it would be nice to integrate at least the agencies dealing with that.”

Thank you.”

DOUG DEMKO: The effects of predation and hatcheries

Doug Demko started working with salmonid fisheries with his first job in 1989; most of his work has focused on evaluating the impacts of flows and hydropower on salmon populations. Mr. Demko’s company is FishBio; it’s a private company with about 75% of funding currently coming from industry and the remainder from NGOs and government contracts.

Mr. Demko noted that the construction of dams in California during the early and mid 20th century have blocked 85+% of the historical habitat for salmon and steelhead; however, habitat degradation and change dates back to California’s earliest history during the Gold Mining era when hydraulic mining was washing mountains away and the sediment was moving downstream into the lower rivers and the Delta, creating flooding problems. Add to that, railroads were being constructed along streams, trees were being cut down, water was being diverted, and so the problems California is dealing with today with declining native fish populations are deeply rooted, going back to the early days of the state’s history, he said.

He presented a slide showing the top 5 fish species, noting that the Delta smelt, steelhead, and salmon getting the majority of the funding.

Since the early 80s, we’ve spent hundreds of millions if not billions of dollars on restoration and physical projects to improve conditions for salmon, but what people outside of the industry don’t see is if you get to peek behind the curtain … the amount of work when you look at the consultants, the attorneys, and all of the other people that are involved with it – very little of the money actually seems to make it to on the ground projects, which I think is one of our challenges,” he said.

The life history of the salmon is complex. When salmon are in the ocean, they are bright silver; it is when they come back to spawn that they turn red and develop the big hook nose. The female will lay the eggs, the male fertilizes the eggs, and the juveniles remain in the gravel for anywhere from a month or two before they spend the next 6 months migrating downstream through the lower rivers and the Delta out to the ocean where they will spend a couple of years before they come back to spawn, usually in the same stream and sometimes even in the same riffle where they were born.

Why this is a challenge for them and for researchers is that they pass through a lot of environments,” he said. “When you have such a diverse life history, you’re exposed to a lot of different challenges along the way with a lot of potential for mortality, so if you’re a researcher trying to assess those causes of mortalities and rebuild the population structure, from a statistical standpoint, it can be a very challenging thing to do.”

He presented a picture of a natural landscape in the Delta [below, left], noting that this is good habitat for a fish. It’s shallow water, the vegetation provides food and good cover for baby fish. This is what the historical Delta or even some of the floodplains would have looked like, he said.

I’m reminded that every time I’m out on the Delta, we really don’t have a Delta anymore,” Mr. Demko said. “What we have is a water conveyance facility. We call it a Delta and we talk about managing the Delta, but it’s just been so drastically changed over the years.” Presenting a picture of a rip-rapped levee [above, right], he noted that raising the water in such an environment is much like raising the water in a swimming pool or in a bathtub; it’s not making nursery habitat for fish. “The estimates are greater than 95% of our tidal wetlands and marshlands have been eradicated or they are gone from the Delta now, so we need to recognize that as we move forward and as we plan.”

There are some programs in place to address habitat restoration in the Delta and the Central Valley, the main one being Eco Restore. Eco Restore is looking to restore over 30,000 acres of important Delta habitat and expected to cost $300 million, which is just a drop in the bucket, he said. “The only discouraging fact for Eco Restore for me is that it really doesn’t go far enough,” Mr. Demko said. “It doesn’t look at the south Delta and the lower San Joaquin where more extensive habitat is certainly needed.”

Back when he was in school, he said the foundation issues for California fisheries were the four Hs: hydropower, habitat, hatcheries, and harvest. “Hydropower is really flow,” he said. “I think certainly hydropower or flow and habitat were tightly linked, but because of the scope of our habitat change, that’s not necessarily the case anymore, and that’s a challenge that we have. I do think that hatcheries and harvest are tightly bound together. In-river harvest of salmonids is relatively low, usually less than 10% and probably averaging 5 or 6%; ocean harvest has probably been averaging about 50%, at least I think that’s the goal at this point in time. But if you go back a couple of decades, 80-84% of all the fish available for harvest in the ocean were being harvested, and that’s one of the challenges that we’re still facing today.”

A significant issue that has been realized in the last 25 years of his career is the impact of invasive aquatic species. “This is one for the next generation of biologists,” he said. “I hope to be long gone or at least retired by the time this one really gets the attention that it deserves, but at this point, this is a problem and a issue that is equal to the other four. It certainly is related to the other four.”

The increase in invasive species is tied to changes we’ve made in flows and the changes that we’ve made in habitat over time, and it starts at the food chain – with the phytoplankton and the zooplankton. He presented a graph showing how the Delta zooplankton has changed to predominantly non-native zooplankton species.

The red shows the native species of zooplankton, the food source for juvenile fish and for salmon,” Mr. Demko said. “Native species have been in decline, the non-native species are increasing and some people look at this and say, food is even more abundant than it ever was before. The problem with this is that we know that some species have food preferences, and some of the non-native species are certainly not as nutritious or not as available to juvenile fish. These are the types of issues that really, really are difficult to research.”

Mr. Demko said it will be key moving forward for researchers to determine the true impacts of these non-native food sources on fish populations. The even more difficult question is how to rectify it; there are challenges dealing with big animals that are easy to see and easier to research, but it’s much harder for phytoplankton and zooplankton, as well as submerged aquatic vegetation, he said.

He noted that people are often surprised to learn that the non-native fish populations here in California are largely a problem that we created by intentionally introducing desired species, such as striped bass or other big game fish.

We wanted gamefish, we wanted big fish that we could eat,” he said. “We introduced the big fish, and then we figured the big fish have to eat something, so what we do? We put the bait fish in. We didn’t know any better at the time. I think we’ve known better in more recent times, but unfortunately, even in the 1980s when largemouth bass were well established in the Central Valley, we planted the Florida strain of largemouth bass in the Delta, which are more aggressive, grow faster, and to a larger size, so as recently as the 1980s we were still taking actions to promote sport fisheries and to promote populations of predators in our Delta. We promote the Delta as a world-class bass fishery to get people to get tours to come into the area and fish for bass.”

Mr. Demko said that it has been estimated that over 95% of the fish biomass currently in the Delta currently is non-native. “It goes back to the factors, water and habitat,” he said. “When we look at centrarchids, you can see that centrarchid populations have roughly doubled, so the bass and some of the largest predators and competitors are the ones that seem to be winning out in the environment that we have today.” (lower, left)

While the abundance of striped bass has dipped at times, there are still well over 1 million striped bass over 18” in length, which doesn’t include the juveniles and the sub-adults, which are significant predators as well. “Others here may say differently, but I think with fish biologists and researchers, that at least in the last decade, everybody has recognizes the extent that predation causes mortality to the juvenile salmon and other fish species as they migrate out,” Mr. Demko said. “In 2009, the NMFS recovery plan to recover winter-run and spring-run salmon populations noted that significantly reducing non-native predatory fishes that inhabit the lower reaches of the Delta is critically important, and even going farther and saying that reducing abundance of striped bass and other non-native predators must be achieved to prevent extinction, or to prevent the species from declining irreversibly.”

Mr. Demko said at the time, he thought that was significant that NMFS had said that, but afterwards he didn’t really see it change the game. “There’s more research being done today on non-natives and on predators than there was in 2009 largely by UC Davis and other university groups, but I think by the state, it’s still not yet recognized yet as a priority issue.”

Whether one believes it is due to predation, lack of water, or lack of habitat, several studies have shown that survival of outmigrating juvenile salmon is just atrocious in the Central Valley right now, Mr. Demko said, presenting a chart showing survival rates for some of the tributaries and the Delta, many under 10% [above, right]. “For instance, when fish leave Battle Creek, only 4% live to make it to the ocean,” he said. “They still have to compete with or contend with predators. Everything eats everything else, and once they get to the ocean, they still have the chance of being eaten. On top of that, if they grow up and live to be an adult, they have a 50% chance of being harvested and ending up on one of our plates.”

Studies of survival of outmigrating salmon from Mill Creek found that out of 300 juvenile salmon, just one made it to the Golden Gate, which is less than 1% survival through the system. The lower Stanislaus River telemetry studies by the US FWS found average survival rates between 7 – 25%. Mr. Demko noted that he’s been working in the Stanislaus since 1991 where they operate rotary screw traps and do production estimates upstream and downstream every year.

Since about 2000, it seems like everything in the Delta and the tributaries is at its worst. It’s kind of flat lined, but we’re lucky to get 7 to 8% survival estimates through the reaches of the river we’re looking at, so these are all realistic numbers,” he said. “The Delta and at Vernallis, we’re talking less than 12% survival and more recent research even suggests it’s more like 5%. I would probably go more like the 5%, then the 12%.”

Mr. Demko did a study specifically looking at predation and survival in the Tuolumne River in 2012. It was a study with extensive stakeholder involvement, and what they found was that only 4% of the juvenile salmon were estimated to survive the 25 mile migration – and the study site ended at River Mile 6. “They still had to go six more miles down the Tuolumne River, then they had to make a right turn and go down San Joaquin River, and then they had to go down the Delta, so it’s with a straight face that I tell you that in some years, nothing – zero – nothing makes it out of our tributaries,” he said.

He acknowledged that after the study was completed, at least one of the agencies didn’t really agree with the findings, so they went back to the drawing board, added some university partners and more experts, turned the half million dollar study into a one million dollar study, and then were denied permits to do the study in 2014, so the 2012 study has to serve as the best available science for the Tuolumne River.

They have also been trying to do similar work on the Stanislaus River since 2009, and last year, one of the provisions in the WIIN Act was to allow the study of non-native fish and predators on the Stanislaus River. It’s a highly ambitious project they have started planning with field work to start in 2018. The project is being funded by the South San Joaquin Irrigation District and the Oakdale Irrigation District, and NMFS.

The idea is to bring in as many experts as you can, and you’re going to get the best study results, which is what we’re all looking for,” Mr. Demko said. “More importantly, when you develop those partnerships, you get better buy off on the science, and that’s really what we want to make sure that we have, that we’re doing the best quality science that we can and that when this is done, it’s recognized that the science is solid. The idea is to remove predators on an annual basis for ten years and evaluate every year salmon survival through the lower Stanislaus River, so we’ll be doing a pre and post comparison, as well as monitoring the response to all fish populations, both native and non-native fish. This is a very unique project along the west coast and nothing of this size and scope has been attempted before in the Central Valley, and we’re hoping that we receive state permits so that this work can continue in 2018.”

Salmon hatcheries are also really ingrained in our culture, Mr. Demko said. The first salmon hatchery in California was built in 1872 on the McCloud River because even by then, the impacts of mining and water diversions already had significant impacts on salmon populations. The first salmon cannery was also on the Sacramento River, so harvest rates of salmon coming back to the river were really high, he said. More recently, in the past four to six decades, as we’ve built dams, we’ve built hatcheries to mitigate for the loss of upstream habitat.

He presented a slide showing the number of fish produced in hatcheries and released by the state. “At least for the last 30 years, there are 30+ million juvenile fish every year going out into our system,” he said. “What’s more alarming is the red bar. It’s been well documented if you release a fish or a fish is born naturally in a stream, that fish will come back to that same stream, perhaps that same riffle, but what we’ve been doing for 30+ years is releasing a good portion of those fish off-site, so when they come back to spawn, they don’t go back to their natal stream, they go everywhere. The numbers are much more alarming in the last couple of years in response to the drought. The reason that we do this is efficiency. It’s been known we have mortality problems instream that are challenging to address and haven’t been addressed, so we take them down to the Bay, the Delta, and release them down there. There is better survival; they come back, but the problem is they come back everywhere.

In 2008-09, the state started the Constant Fraction Marking system, which is where they mark the same percent of the hatchery fish each year. The percent is 25%, so if you mark 1 of every 4 fish you release and three years later, your return of adult fish on the stream is one out of every four, you’d figure that’s 100% hatchery fish coming back, Mr. Demko explained. “When you look at the last 5 years on the Stanislaus River, what we see is four out of the last five years, we can roughly say we have all hatchery fish coming back to the Stanislaus River. The problem with that is we don’t have a hatchery on the Stanislaus River, and the water rights people would really rather have naturally produced rather than hatchery fish.”

So if your goal is abundance and you want to make fish, hatcheries are an easy and effective way to do it; it’s certainly much cheaper than fixing the habitat upstream,” he said. “The problem is we’re fixing the habitat upstream, spending hundreds of millions of dollars adding gravel, screening diversions, adding flow requirements, doing adaptive management, but if the fish aren’t surviving to make it to the ocean and come back, hatcheries are certainly a much cheaper, effective way of doing it.

Mr. Demko said that he’s a firm believer that the negative impacts outweigh the benefits. “Studies have shown that over 90% of our fall run Chinook are the result of hatchery fish, which has resulted in a loss of genetic diversity and overall reduced genetic fitness,” he said. “When you look historically at California, all of our watersheds and subwatersheds had nice locally adapted populations. There was a very diverse gene pool, and the worry now is that we’ve got one generic gene pool, and is that really a strategy that’s going to take us into the future? Are these fish going to be prepared to fight disease and adapt to climate change? Is it a better strategy to just have large numbers of fish coming back to our streams, or is it a better strategy to have fewer fish but have those fewer fish locally adapted, genetically diverse, and prepared to move forward into the future?

He then gave his conclusions. “Perhaps less is more; focus on healthy populations of wild fish, rather than hatchery fish,” he said. “Abundance goals should correspond to habitat capacity. For instance, when you look at our goals for the Stanislaus River, the government goal is to get 11,000 fish back to the river; we’re pretty confident that we have habitat to support 3 to 5000 fish, so why do we have a goal of 11,000 fish? Then in years we see 14,000 fish come back, and we know they are all hatchery fish, why can’t the public go out and fish for those fish? Why is angling closed to the public? We have a bunch of hatchery fish coming back to the system that weren’t born in the system, they exceed the carrying capacity of the system, and yet the public can’t get the benefit in a fishing form, which by the way, increases enthusiasm, gets support, and leads people to want to protect those fish and see those fish back in the system.”

We need to move away from single species management, he said. “Science is very trendy, whether it’s the problems that were trying to solve or the species we’re looking at. If the species is imperiled, we throw money at the problem, but perhaps it’s a better strategy to look at the overall ecosystem. If we focus on restoring large tracts of land and changing the way our system behaves on a large scale, then maybe a single species or two will remain imperiled or perhaps go extinct, but 50 years from now or 100 years from now, we may actually have a healthier environment.”

I think reducing non-natives has a role in future management,” Mr. Demko continued. “There are possible flow actions to help reduce non-natives or mechanical removal but again, I think this is the next trend in fisheries that needs to be properly addressed and more money needs to be spent here.”

A passion of mine is reducing redundant regulatory requirements for research and monitoring,” he said. “As somebody who has spent 25 years now researching monitoring, I can tell you we’ve spent $100,000 getting permits and taking over a year. One project we did, which was a unique project, I had to get 14 permits from the county, municipalities, all the way to the federal government. There were entities that I had never even heard of. And funding is limited, And I’ve seen money left on the table because the private side and the public side can’t get together and it’s often because political reasons, but government funding is limited. I suspect it’s going to become more limited in the next couple of years, so we really need to be looking for opportunities to build the relationships between the private parties and the resource agencies to get more done.”

JOSE SETKA: Mokelumne River Joint Settlement Agreement: From litigation to collaboration to success

Jose Setka, Manager of Fisheries & Wildlife Division for the East Bay Municipal Utilities District, then discussed the work EBMUD’s been doing on the Mokelumne River as a result of litigation back in the 1980s, work that he views as being largely successful.

Back in the late 1980s, conditions on the Mokelumne River were bad, Mr. Setka acknowledged; basically, if on January 1st, they felt there wasn’t enough water, they just shut the river down and went from 800 cfs to 100 cfs.  “Redds don’t do well in that kind of operating regime,” he said.  “Low dissolved oxygen, hydrogen sulfide, unscreened diversions, dead fish – the problems were on and on.”

As a result of lawsuits, the agencies and water district developed the first technical advisory committee, the MRTAC, which tackled a number of issues.  Some of those issues included the Delta Cross Channel, flow patterns, and export impacts to outmigrants.

There were a number of key issues that the technical advisory committee focused on finding solutions for.  One of them was a tenfold increase in water, which was important because at the time, they weren’t releasing a lot of water down the river.  However, it was the formal collaboration with resource agencies and stakeholders to optimize river management that Mr. Setka said that’s led to the most success.

Many organizations and groups wouldn’t work with them and were probably suing them back in the 80s, but today those groups are collaborating with the district.  The collaboration now includes the state and federal fisheries agencies, local stakeholders, universities, and NGOs.  “Collaboration is the most important issue in this whole process that has led to our moving forward on some successful outcomes,” he said.

EBMUD has worked cooperatively with the downstream Woodbridge Irrigation District to improve fish passage in the lower Mokelumne River, helping to increase survival.  One of the important things resulting from the collaboration was establishing a monitoring program on the river. There are a number of different types of monitoring they do, but one example is at Woodbridge Dam, they have a camera, a ladder, and they can count every single adult salmon that comes into the system, he said.

Suitably sized spawning gravel is needed to help maintain adequate water temperatures, velocity, and dissolved oxygen levels for incubating salmon embryos.  Since the 1990s, 65,432 tons of spawning gravel have been added to the river to improve spawning habitat for salmon and steelhead.  “Back in the early 90s, our idea of spawning restoration was to just build a berm across the river and we’d say we did such a good job,” he said.  “We got some partners involved, including UC Davis, and actually put a design to it and that system is continued to move downstream, but it has been extremely successful.”

Predation is a problem in some areas on the Mokelumne in locations where there are hard structures where predators and their food – in this case, the juvenile salmon moving down the system, he said.  “We worked with a couple of different researchers,” he said.  “What we do now is collect the fish and put them back out in the Delta.  It’s probably not the best solution but it fixes our problem.  Generally with stripers, once you hassle them, they don’t come back.  We’ve radio-tagged some of these fish to see if they are coming right back to the Mokelumne and they tend not to … so good for us, maybe not for others.”

The hatchery on the Mokelumne River was built in 1964 when Comanche Dam was completed.  They have taken actions to avoid or minimize straying of their fish, including release timing and location.  “For many years, all that work was done based on convenience of staff as it was easier for them to release the fish during these two weeks when they had the trucks, so that’s when it all got done,” Mr. Setka said.  “It had nothing to do with the biology of the fish or when the best time might to move those fish out.  That has changed over the last decade or so; we’ve gotten better, but there are still some issues to be resolved.”

They also took steps to improve the quality of the feed for the hatchery fish.  “Historically when DFW was in charge of making all the purchases for the facility, the lowest bid won, so poor feed quality which means you have poor fish quality going out, so we made some changes there and that has certainly improved,” he said.

Mr. Setka also noted that tagging the fish has cost them about a half million dollars a year to do, but it provides a lot of information that they then try to use to make management changes.  They have also done a lot of experimental releases to see where things might work better in terms of where the fish are released, the timing, and locations.

The Delta Cross Channel has been a significant problem for them in terms of fish migrating up and juveniles migrating out.  The forks of the Mokelumne River are used as conveyance for water from the Sacramento River down through the Central Delta to the pumps.

When our fish are coming up in the fall, we may be releasing anywhere from 40 cfs to a couple hundred cfs, but there’s 3000 cfs going through there, moving water down south that’s going to overwhelm the cue of the Mokelumne and our fish are going to go right past that through the Delta Cross Channel,” Mr. Setka said.  “So we worked with the Bureau and with NGOs, and came up with a few closure plans that have worked periodically over the last 7 years.  It’s a challenge because the water from those channels refreshes the water quality within the Central Delta, so it’s a balance – what might protect fish is certainly going to harm water quality, so that’s an issue that will continue on until next decade in terms of trying to solve it.”

Another problem with the Delta Cross Channel the juvenile fish get entrained with the flows moving south, so they have done a barging study.  “It’s an artificial concept; it’s not what we’d like to do, but if you look at as an example, that in-river recovery compared to the barge fish recovery,” said Mr. Setka.  “Of the 100,000 fish we planted in the river at the top of the Mokelumne forks, we got two of those back.  But the barged fish that we took from there to the Golden Gate and released, we got about 192 of those back to the Mokelumne and then some sporadic ones that strayed elsewhere.  Not the ideal way to have fish move through the system; however, we can’t get fish to survive coming out of the Mokelumne through those forks and out through Chipps Island and out the Golden Gate.  They don’t’ survive.”

After the 2008 stock collapse of Central Valley salmon, they started initiating pulse flows in 2010 in an effort to get attraction flows down the Mokelumne to see if fish can move up from the Delta in a more aggressive way and overcome some of the issues associated with the Delta Cross Channel.  Sometimes it’s the flood control water in that October-November period and instead of releasing it in a more regular pattern over the summer, they hold on to it and pulse it out late September, October, and November; sometimes it involves asking the State Board for an adaptive management action to shift water from one season to another by dropping below their minimum flows, collecting all the water up, and releasing it in the fall; and sometimes water becomes available through the Freeport project, he said.

During the drought, there were issues with the reservoir water temperature.  In 2015, there was very little water left in Camanche Reservoir, so the question before them was do they attempt to keep the water cold or store the water in the upstream reservoir to keep it colder and release it in one big slug in October?  The partnership decided to take the risk, even though it could have ended up killing steelhead in the hatchery, and although other hatcheries ended up moving their fish, they were successful and did not have any fish kills.  “In fact, that year we had some of the coldest water below Comanche that we’ve had in the last decade or so, so something to think about for future management,” Mr. Setka said.

He presented a slide showing the 2016 pulse flows, noting that the blue line are the pulse flows going past Woodbridge Dam and the bars represent the number of fish moving up on each of those pulses.

With almost an every single pulse, you see a spike of fish moving up through the ladder and into the system,” he said.  “The gray lines are Delta Cross Channel closures; there’s a number of different criteria that they use to close the Cross Channel, particularly down in November, it has to do with the Rio Vista flow standard as well as the winter-run captures at Knight’s Landing that can initiate a closure, so in that year, they started about November.  If we had our way, we’d like to see closures in October.”

Mr. Setka then reviewed the outcomes of the Joint Settlement Agreement, which was the result of the lawsuits in the late 80s.  “In the post-JSA period, the number of fish has more than doubled returning to the Mokelumne,” he said.  “If you take out that stock collapse in 2008, right now we’re running an average of about 9000 fish per year, post JSA.  Our AFP doubling goal which is that federal goal that was laid out by the CVPIA is about 9000 fish, so we’re kind of right on target with that.”  He noted that the graph does not include 2017 returns, which exceed 9000 fish.

Another important aspect is that they want there to be a successful commercial recreational fish for part of these fish.  “That’s what the hatchery was in part put there for,” he said.  “These fish are supposed to be caught.  San Joaquin River fall run which is primarily Mokelumne fish that are out there, you can see they make up 19% of the recreational and 16% of the commercial ocean fisheries, which is a pretty substantial chunk of that fishery.  From what I’ve heard, 2017 is going to be much higher than that.”

They are currently conducting a study started by the Foothill Conservancy to look at the habitat above Pardee Reservoir, considering climate change and the future.  “Right now we’re doing a habitat assessment to see what exactly the habitat is there, and as we roll into the future, our hope is that we’ll be able to move some fish up there, and do the proper tagging or not and see how they perform up there and what their survival is and have that ready to go as one of the options in the portfolio,” he said.

The partnership is also looking at improving conditions downstream in an effort to improve survival of outmigrating salmon.  The McCormack-Williamson tract project has been in the works for decades, but hopefully will soon have floodplain habitat available for young salmon as they migrate out to the ocean, he said.

In closing, the partnership continues to be pretty successful in terms of implementing the JSA and the things we started to do,” he said.  “The habitat conditions through the groundwater enhancement program and some of the other work we’ve done in terms of floodplain work has been very successful.  We’ve attained our AFRP doubling goal.”

Mr. Setka said as the collaborative effort has progressed, they have brought more stakeholders into the mix, and it has been incredibly beneficial.   “We’ve moved on to that broader scope in terms of looking at things we can do in the Delta, moving above Pardee Reservoir and looking at things we can do to bring that into the mix as far as protecting the resources, but challenges remain,” he said.  “The big one is the straying issue; how can we keep our fish returning to the Mokelumne and not going elsewhere.  If we get better survival, particularly for our natural production, that means we have to reproduce less fish in the hatchery.  The better we can do in terms of our natural systems, the less we’ll have to artificially prod it, but right now, we’re just not in a position where we can do that.”

The upcoming Bay Delta Water Quality Control Plan update is not a challenge from a negative perspective, he said.  “But we’re going to have to figure out how we balance the needs of the river with the needs of the Delta and how we can continue the successes we’ve had in terms of moving fish up in habitat and yet contribute to the overall Delta health that’s being looked for in this new plan.”

Permitting is an issue, Mt. Setka said.  “There are a lot of entities out there that want to do good work in these rivers, in the Delta, in terms of monitoring and quite frankly they are being obstructed from doing that by the permitting process,” he said.  “There’s no reason that an entity should have to get a congressional act to do a study in a river, that’s ridiculous.  So somehow we have to get these permit process moved more towards a panel type of approval rather than just having individuals being solely charged with approving some of these permits.  Because if not, it doesn’t matter if it’s a striped bass study or if we want to do monitoring to implement some new plan, it’s just not going to happen.  It’s too slow of a process, it’s not dynamic enough.”

And when some of the water users in this group pay into a program to improve habitat and half that money or more goes to administrative costs to in part obtain permits, you shouldn’t be happy,” he continued.  “That’s something that has to change.”

He closed by presenting a slide of the various entities that are working together on the Mokelumne.  “As we move forward, we’re working more and more with various different entities, and I think that has been the leading indicator of success in our rivers.  The more people we can put up here that aren’t suing us, the better we are, and I think we’ve come a long way.”

So with that …


  • Coverage of the Mountain Counties Water Resources Assocation’s Delta and the tributaries forum concludes with keynote speaker, Delta Watermaster Michael George, and a lively panel discussion moderated by Dr. Jeff Mount, senior fellow with the Public Policy Institute of California.


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