FEATURE: The state of the salmonids in California

Webinar takes a deep dive into the state of salmon and steelhead, and provides recommendations for resiliency

In 2005, the California Legislature passed SB 857 requiring CalTrans to locate, assess, and remediate fish passage barriers on the State Highway System and to report progress annually to the legislature.  In the October 2019 annual report, Cal Trans reported remediating 47 barriers, opening up an estimated 792 miles of improved access to salmon and steelhead habitat with five of those projects completed in 2018.  CalTrans is currently developing projects to remediate 27 active fish passage barriers, which are estimated to improve access to an estimated additional 166 miles of salmon and steelhead habitat.

Improving fish passage on the State Highway System requires a comprehensive approach using science and data, engineering, training, permitting, research, funding, multi-species benefits, and partnerships, because of complex considerations associated with successful barrier remediation.  To facilitate that, the California Fish Passage Advisory Committee (Cal Fish PAC) was formed between the California Department of Transportation, California Department of Fish and Wildlife, National Marine Fisheries Service, US Fish and Wildlife Service, and other interested stakeholders to share science and data related to known fish barriers and develop cost efficient and effective methods to prioritize both assessments and biological priorities for remediation.  They currently have about 200 members.

The science and data collected by Fish PAC members is entered into the Fish Passage Assessment Database, which informs strategic investments in barrier remediation.  The outcomes of Fish PAC efforts, many of which are full-span solutions that minimize interference between infrastructure and channel processes, enhance connectivity for all native species, including anadromous species and threatened and endangered wildlife.

NOTE:  There is a wealth of information regarding bridges, road crossings, and culverts in the training section on the Cal Fish PAC website.

In the spring of 2020, Cal Fish PAC sponsored a webinar covering the 2017 State of the Salmonids report reviewing the findings and discussing how to improve resiliency in salmonids moving forward.

The webinar presenters were Patrick Samuel, California Trout’s Bay Area Program Manager, and Dr. Rob Lusardi, California Trout-UC Davis Wild and Coldwater Fish Scientist and aquatic research scientist at UC Davis Center for Watershed Sciences.  Both presenters were co-authors of the report; Dr. Peter Moyle was the lead author.

The State of the Salmonids came out in two versions: The summary report is pictured above on the left and is the ‘coffee table’ version with beautiful illustrations of California’s native salmonids by Paul Waters.  The larger report upon which this presentation is based today reviewed the status of 32 different native species, subspecies, or ESUs of salmonids statewide.


The 2017 report is about 600 pages long and was peer reviewed by over 70 different scientists, including academia, federal and state agencies, and non-profits.  The report considered seven primary metrics along with a confidence rating which reflects the data and information that is available to make a determination on the status of the species.

There are often species experts that know a lot more about these species than we do that are located across the state, so when we would draft a review, a status review of an individual fish, we would then send that off to species experts throughout the state to make sure we got things right, take their comments into consideration and make the appropriate edits,” said Dr. Lusardi.

The 2017 report updates the first edition of the report which was published in 2008.  The biggest difference between the 2017 report and the 2008 report is that the 2017 report incorporated a climate change vulnerability score, which is based on a 2013 paper by Moyle et al that studied the vulnerabilities to all native fish in California.  The other impetus for updating the report was the 2012-2016 drought, so there was a push to figure out how the fish were impacted by the drought.

The report focuses on three questions that they addressed with each species, subspecies, or ESU: What is the status of California salmonids? What factors cause declines? And how can the species be conserved or recovered?

There are seven scoring metrics: area occupied, adult abundance, intervention dependence, physiological tolerance, genetic risk to the species or ESU, the climate change vulnerability, and manmade threats, which are things such as disconnections from habitat by culverts or large dams.

Each species was assessed based mostly on literature review, but also considerable professional judgement, said Mr. Samuel.  They read through the five-year status review updates that federal agencies are tasked with creating, every peer-reviewed or long-term monitoring plan they could find, as well as interviews with over 75 biologists across the state.  Each species was assigned a score between 1 and 5; the lower the score, the worse the status.

One of the most challenges portions of this effort which took about 16 months of work was actually gathering the necessary information to make these determinations,” he said.  “And in a lot of cases, we had significantly less data coming from long-term monitoring or peer-reviewed literature to help inform these assessments, so there was considerable professional judgement incorporated into this.  And that’s why we incorporated a confidence scoring rating.”

Mr. Samuel noted that it was important that their methods be transparent, so they laid out all of their methods clearly so the results would be repeatable – that others could come back, use the same methods, and come up with the same results.


Mr. Samuel then summarized some of the findings.  Most species have declined since the original 2008 report, which is probably not surprising, considering that five years of critical drought had occurred since the first report.  Three quarters of species are likely to become extirpated if current trends continue by 2100, so if current trends persist which is an important caveat, he noted.  Nearly half are likely to become extirpated in the next 50 years in California.

The slide on the upper left shows the 2017 status scores; the different colors represent anadromous and inland species.  The focus of the webinar is more on the anadromous species, which are represented by the blue bars.  A score of 0 means the species is extinct; a score of 4-5 means the species is of low concern.

The first thing that jumps out as you look at the chart is that most of the state’s anadromous species are in that critical species scoring – that score of 1 or 2,” Mr. Samuel said.  “What that means is those species are likely to become extirpated in California in the next 50 years.”

For anadromous species, the next most common scoring was moderate concern; there are no anadromous species in the low concern category nor have any become extinct.

Mr. Samuel then presented another slide comparing the 2008 status scores to those in 2017, noting that during the time period between the two reports, half of the species changed in status.

In 2017, the majority of our species were in the critical category, whereas in 2008 shown with the gray bars, most species were only of high concern, so there was a shift there,” he said.  “In 2008 there was more of a bell curve distribution of different scoring for species across the state, here in 2017, really there’s a strong preference over to the critical concern level.  So these species in general fared quite a lot worse than they had a decade ago.”

He said there are multiple causes for this, which was reflected in the literature review and in the interviews with the biologists.  The chart to the right lists all the manmade threats which make up the anthropogenic scoring metric, which is one of the seven metrics.

The blue bars represent the anadromous species; the highest threats are agriculture, estuary alteration, major dams, and transportation, which includes things such as proximity to roads or railroads, which is a specific threat that can not only affect the geomorphology and the ability of the stream of river system to move and migrate and be active over time, but also significantly changes how sediment through the system.

We know fish need access to cold water as salmonids are cold water fishes, so any old water just won’t do,” Mr. Samuel said.  “They need access to cold water year-round, especially in the warm, dry summer and fall months when it’s been the longest since there was any precipitation.  By restoring access to those areas with things like improving culverts, replacing culverts, or getting barriers out of their way is one potential approach to address this issue.”

Also when we have these impervious surfaces so close to a river system, that significantly increases the runoff and also can change the hydrograph, or what flows look like coming down and what is the quality of that water and the sediment and the habitat that’s left behind,” he said.  “So transportation incorporates both railroads and proximity to roads and stream systems in California, and that is one of our highest threats to anadromous species.”

The overarching threat as of the 2017 assessment was climate change, and maybe not surprisingly,” he said, noting that for over 60% of California’s salmonids, climate change was a critical threat and a high threat for 26%.  “We had a hot drought, so there was not a lot of precipitation falling, and where it was falling, it was as rain rather than snow,” said Mr. Samuel.  “In addition to that, the temperatures were some of the highest ever recorded.  What water did exist was not snowmelt, but precipitation or runoff, and that water was warmer than it had been in the past.  And that really was a double whammy for these salmonids in California.”

SPECIES EXAMPLE: Central California Coast coho salmon

Mr. Samuel presented a chart of the overall summary scoring table for Central California Coast coho salmon, noting that the template is the same for each species to allow for easier comparison.

For each species, there is a metric, a score, and a justification; he said that they tried to keep it as simple as possible, but sometimes there are up to 30 pages per species of description with literature cited with the best information they could find along with personal communication and professional judgment of biologists.  He reminded that the lower the score, the worse the species’ status.

The 1.3 score for Central California Coast coho is one of the lowest scores that we have for any of our salmonids,” said Mr. Samuel.  “These fish are critically endangered, and without critical improvement and management, this fish is likely to become extirpated in California in the next 50 years.”

The certainty score is from 1 to 4; it is based on the information available, so where there wasn’t good information, there are notes and a description of what information was available.  A score of 1 would be purely anecdotal information whereas a score of 4 is multiple peer-reviewed long-term datasets and monitoring in place to help determine the status for a species.

As for major threats, the first is water diversions, generally for agriculture and specifically for vineyards and cannabis cultivation,” Mr. Samuel said.  “Major dams, logging legacy, estuary alteration – this is a species that can and likes to spend significant time in the estuary.  Then climate change – they are cold water fishes; they over summer in all of our freshwater streams so we need to make sure they have access to cold water year round.”

Mr. Samuel then gave his recommendations for recovering the species:

Focus on high intrinsic potential habitats: “The recovery plans are part of the road map here.”

Conservation hatcheries:   There’s a conservation hatchery operated in partnership with NOAA fisheries and with Monterey Bay Salmon and Trout Project in Scott Creek that is basically to keep the population going until habitat can be restored to a point that can actually sustain this fish again.  “The conservation hatchery is providing an really important benefit and plays an important role down here in coho recovery,” he said.

Lagunitas Creek:This is a place where something about that system is working well.  There are still coho there – maybe not as many as there used to be, but starting with where you have fish is a good approach to try and bring back more fish and spread out those fish to other systems.”

Work with vineyards and cannabis cultivators:  “We need to work with some of these water users, especially the ones that need the water when the fish need the water the most.  That’s generally late summer and early fall when temperatures are highest, so that’s the time when the crops are the most thirsty, but the fish are too.”

Special status of Santa Cruz County CCC Coho: “We should explore creative solutions like potentially providing special status for Santa Cruz County CCC coho to try to allow us the flexibility to do different things to boost their survival, which gets back to the hatchery point earlier.”

He noted that the recommendations have been peer reviewed and were developed in partnership with biologists and folks on the ground which is available in the full report.

SPECIES EXAMPLE: North Coast summer steelhead

The Northern California summer steelhead has a score of 1.9, which is still in the critical category.  Similar to coho salmon, they need access to cold water and they need it year round.  These fish swim upstream during the big pulse spring flows into remote canyon reaches where they hang out in deep pools for the summer-fall months waiting for the winter rains to get up even higher in the watersheds and elevations than other steelhead.

They get the first shot at that habitat but there aren’t that many left in the areas where they live,” he said.  “While they are in these remote canyon reaches and deep pools, they are highly susceptible to things like harassment or poaching or water withdrawals that could potentially reduce stream flows to the point where you get disconnected pool habitats.”

The threats are similar to the Central California Coast coho: dams, agriculture, climate change, and estuary alteration.  “But Northern California summer steelhead are a species that really do need access to those higher reaches because those higher elevation tributaries and those deep pools are the places where the cold water persists year round,” he said.  “That’s their life history.  They’ve adapted to take advantage of those so that they could be the first in these really high elevation spawning grounds, once the rains do return in winter.”

Mr. Samuel then gave the recommendations from the report for how to recover Northern California summer steelhead:

Prioritize protection of the summer-run life history:  There is a scoring metric for genetic risk; the genetic information and quality of that information for salmonids in particular has greatly improved since the 2008 report.  “We know now that there is a genetic component to some of these life histories, especially steelhead, and a lot of that research is coming from the Southwest Fisheries Science Center and our partners, as well as academics across California,” he said.  “There is an effort currently at CDFW to list Northern California summer steelhead to protect that specific summer run life history and the genetics of those fish that could still express that life history diversity.”

Restore the Eel River:  “This is a place that provides the most habitat for this specific ecotype, this life history component of steelhead and getting those fish access to those high gradient, high elevation habitats is critical to help recover these species.”

Reduce hatchery and wild fish interactions:  “These fish should be spawning with wild fish, and the more hatchery fish that are out there on the spawning grounds that they come in contact with and have to compete with, the less of a chance we’re going to be able to maintain the genetic integrity that underpins their summer run life history.”


Dr. Lusardi then reviewed the most imperiled species – those with a score of 1.9 or lower.

It probably comes as no surprise, the Central Valley winter-chinook and spring run-chinook, the Central Valley coho, Southern Oregon, and Northern California Coast coho are in pretty bad condition,” he said.  “Upper Klamath spring run chinook, and both upper Klamath and Northern California summer steelhead – we think those are important really for diversity for the species as a whole, and maintaining that diversity will be key to their recovery.  Also South Central Coast steelhead and Southern steelhead.  Those were the species that we found to be the most imperiled through these status reviews.”

He also noted that three resident species are also imperiled: the California golden trout, the Kern River rainbow trout, and the McCloud River rainbow trout; the Little Kern golden trout was also very close to that imperiled score.


Dr. Lusardi presented a picture of a fossil of the oldest known salmonid that was found in British Columbia; it has been aged to 50 million years old.

Salmonids been around for 50 million years; they’ve dealt with incredible environmental perturbations and they’ve always successfully come out on the other end,” he said.  “So they’ve gone through volcanic eruptions, megadroughts lasting 100 years or more, landslides, disconnections from habitat, disconnections between populations, glaciation and glacial retreat as well.  So we really feel these are the keys to recovery moving forward.”

Dr. Lusardi presented a map of California, noting that the yellow dots represent populations.  “There may have been many, many populations throughout California of different anadromous species historically occurring,” he said.  “Then perhaps there’s a megadrought that eliminates several if not numerous of the populations throughout the state.   But those populations were so diverse, from their life history experience, their environment, their habitat diversity they’ve experienced, but also the genetic diversity.  So they were able to rapidly colonize these new habitats that if access was available, and ultimately, it would mean in the long-term they could persist.  Their persistence as a species as a whole is because of that diversity between populations and their ability to recolonize and repopulate watersheds.”

A lot of the habitat diversity has been extremely limited due to barriers to fish passage, such as disconnections from habitat vertically with road culverts and the high head dams and small dams throughout the state the block access to historical spawning and rearing habitat.

I mentioned earlier we have fundamentally changed in the way water is moved throughout California,” said Dr. Lusardi.  “In the Central Valley particularly, we have channelized systems with levee setbacks.  These levees are meant to prevent floods and so do not allow floodplain access for native fish, so we have limits in both the vertical but also lateral.  The habitat is really fundamentally changed.”

Add to that the numerous introduced and invasive species such as striped bass, brook trout, and many others, which because of competition and predation, non-native species are a contributing factor to the decline in native salmonids.

Production hatcheries are also an issue.  While production hatcheries play an important role, particularly for commercial fisheries, they can also potentially cause genetic homogenization of populations, particularly for ESUs like fall run chinook in the Central Valley but others as well.

All these factors have really come down to reducing population diversity within these species, and to us, restoring that habitat diversity and restoring that genetic diversity is key to their resilience in the future in California,” said Dr. Lusardi.  “It’s not going to be easy but we feel it is possible.”

The map shows how much spawning and rearing habitat has been eliminated for anadromous salmonids throughout the state.

These are habitats where historically chinook and steelhead would move into and would spawn and rear on their way out of the system that are no longer available to these species,” he said.  “This can be said for a lot of different things, particularly lateral connectivity between the river and its floodplain.  A lot has been eliminated, and for good reason – it’s to protect human populations in cities from flooding.  But where we can change that and provide access to these habitats, we think would be really important moving forward.”


Restore the population resiliency of salmonids comes down to two types of actions: places and strategies, said Dr. Lusardi.  He then discussed each in turn.


It’s important to protect the best of the habitat that is left, because these systems can continue to contribute to abundant, healthy, and diverse populations.  These places include Blue Creek, the Eel River, the Smith River, and Butte Creek.

These are important watersheds moving forward,” he said.  “They show natural habitat variability that is that is also part of the fish’s life history and provides diversity in those fish and so really protecting those strongholds moving forward, particularly places like Blue Creek and the Smith River would be really important.

Source waters are also very important, such as headwaters and the meadows in the high Sierra.  “Restoring hydrologic connectivity between these headwater streams and lower streams downstream would be important as well,” he said.  “Restoring those meadows so they can properly function from a hydrologic perspective and store water during wet winters, hold that water, and then slowly release it would be key.”

Spring-fed systems are also important from both a source water perspective and a rare habitat perspective.  “Spring fed systems and groundwater fed systems will be very important moving forward because the water is colder and often has high geologically-derived nutrients as well, so they are important from a productivity standpoint.”

The seasonal lagoons and estuaries along the coast are extremely productive and diverse habitats that are also important.

Spring-fed systems, such as Big Streams Creek, Fall River, Hat Creek, and Rising River are important and rare habitats. In Oregon, the Sprague, the Williamson, and the Wood Rivers are important because they provide cold water throughout the year, especially during the hotter months.  These cold water systems will be important for the fish that require an oversummering period for their life history.  These systems also have high geologically-derived nutrients, such as nitrate and phosphorous, act as fertilizer in the river.

Then we have prolific macrophyte growth, and the macrophytes are so important to the ecology of these systems,” said Dr. Lusardi. “They provide refuge and cover and they also provide extremely high densities of food for rearing fish, so we think these spring-fed systems will be really important to protect for the future, one reason being is because they are so rare, they can contribute to that life history diversity for these fish across the landscape.”


We live in a human dominated ecosystem and it’s important to incorporate conservation into these dominated ecosystems, so using a strategy of reconciliation ecology moving forward will really be important,” said Dr. Lusardi.

He noted the work being done by Cal Trout and UC Davis on flooding rice fields as surrogates for floodplain habitat; flooding the fields which increases productivity of zooplankton (or fish food) which helps the fish grow larger as shown in the picture.

You can see massive differences and that’s the diversity that we’re after here,” he said.  “We don’t think the river fish are bad by any means because of their size, but it’s that diversity in size and in the outmigration timing of these fish that’s going to be key to the recovery of these fish, so really adopting that reconciliation ecology, particularly in human-dominated landscapes like the Central Valley, will be important moving forward.”

Improving habitat connectivity and passage between spawning and rearing habitat and ensuring fish can access those places is also important.  This means focusing on the culverts that limit connectivity, as well as the large dams.

The Klamath Dams are anticipated to be removed in 2022; this will be a huge coup for fish because they will be able to access hundreds of miles of historical habitat,” he said.  “Huge dam removals are of course a big deal, but there is plenty of small dam removals, check dams and whatnot that block migration of fish to historically important habitats.  Opening those habitats will be key moving forward, especially to improve the habitat diversity of the fish and what they experience, and that in turn will improve their life history diversity which in turn will improve their resilience overall as a species.”

Lastly, Dr. Lusardi turned to hatcheries.  “It’s important to separate production hatcheries from conservation hatcheries,” he said.  “Conservation hatcheries have a history in California of saving and helping to recover species, such as winter run chinook.  But production hatcheries can be a little bit different, and so we think it’s really important to improve genetic management of these production hatcheries; this means reducing hatchery straying.  We know that when hatchery fish interact with wild fish, the wild fish are usually on the losing end of that.  We think that marking all hatchery fish is really important, but also using strict mating protocols to discourage in-breeding and what I would term fitness reductions in wild fish as well is really important moving forward.”

One action to consider would be to move the production hatcheries downstream where they could still contribute to commercial fisheries, but promote reproductive isolation in the headwaters and high water habitats for those wild fish and they are not interacting with the hatchery fish.  Doing this would continue to improve commercial fisheries, but also allow wild fish to thrive, he said.

Dr. Lusardi the concluded by thanking all the folks that worked on the State of the Salmonids report.  “This could not have been done without numerous people.  Foremost is the California Department of Fish and Wildlife.  They were really wonderful and provide access and helping and providing review of species and assessments that we provided, but there are numerous others such as such as NOAA Fisheries and NMFS, so many people helped review the assessment of these species.”


QUESTION: Regarding the prominence of climate change as the overarching threat, is that true equally for species and populations in all regions, including coastal watersheds where snowpack is not part of the hydrologic regime?

Patrick Samuel:  “I think what the question asked is getting at is, is it hitting fish the same way across the state? I think the answer to that is no, but being really specific from fish that rely on snowmelts versus fish that are more coastal, it’s hard to say.  It depends, that’s the short answer.”

Coastal salmonids don’t rely on snowmelt at all, but one of the ways the coastal salmonids are impacted is these fishes generally have offspring, steelhead or coho, that at least some proportion of the population is trying to oversummer.  When we have significant dry stretches, like this past February had almost no rain, some of these coastal systems were not even open to allow fish to come in and spawn at all.  And so who knows if those steelhead go back out to sea and try again later or wait it out near the coast and hope for rain, but there are significant impacts that relate to stream flow and temperature of that water.”

Dr. Rob Lusardi:I would agree with that 100%.  I think that there is variability across the state in terms of what population species would be affected by climate change and how.  But just because the coast range is not dependent on snow, there are still fundamental changes going on to the hydrology in those systems, such as changes in earlier summer base flow and longer periods during the summer that the fish, particularly those that have a life history where they have to oversummer, will become more critical.  I think there is definitely variability across the landscape but those coastal populations and streams are ultra-vulnerable, their hydrology in particular, as we see changes.”

QUESTION:  Can you touch on why or how hatcheries are the fifth highest threat to anadromous salmonids?

Patrick Samuel noted that Rob had mentioned some of the reasons.  “Remember we can’t just write all hatcheries off with a broad brush.  There are many different types of hatcheries that provide different services and are established for different purposes.  Rob had made the distinction between the conservation hatcheries versus production hatcheries.”

Dr. Rob Lusardi:We certainly feel like where genetic protocols are used, particularly for animals like winter-run chinook, they are important.  If you look back at the drought from 2012 to 2015-16 and think about what would have happened to winter-run chinook if there was not a conservation hatchery working there … those fish would largely be gone, there’s no doubt in my mind, so I just want to make sure we separate conservation hatcheries from production hatcheries.”

I think the question is aimed at why are hatcheries so low on the list, would be my guess?  I agree with that, but I would also mention that production hatcheries are one of the largest threats if they aren’t managed properly.  CDFW has made strong strides working on this, and thinking about this into the future for how these hatcheries can be better managed.  The key there is of course reproductive isolation and so we think the separation of these wild fish and these hatchery fish will be really important moving forward.  There’s a long history and a ton of literature on the effects of hatchery fish on wild fish and it’s not good, and so I don’t think we think of hatcheries as the fifth largest threat to anadromous species, at least I don’t.  We think of it as one of the major threats to native wild fish in California.

QUESTION: So the Fish PACs collect science and data and information that goes into informing strategic investments in fish passage barrier remediation, so they are always looking at habitat upstream of the barrier and all kinds of other factors.  This question is, what locations are considered priority for fish passage improvements particularly in the Bay Area?

Patrick Samuel: I’m a member of the Bay Area Fish PAC.  We had a chance to pull out the big maps in Santa Rosa with the rest of the group and really look at what habitats are available.  One of the things that I want to throw out to this group – it’s not just miles on a map, but it’s what that habitat availability is and what the habitat upstream that could be reconnected is, and putting that in context.  If that’s adjacent to an area where there’s significant restoration, or if that’s opening up a habitat that’s diverse because it has groundwater flows or something that’s rare or that’s connected to an estuary or there’s something that makes that diverse or rare or makes it likely that a fish either a natal fish from that watershed or non-natal fish might poke in and use that habitat even for some portion of time, I think that makes the habitat especially valuable, and those are some of the considerations that we took into account when we looked at the Bay Area map and made our priority list.”

In general, it’s not just, ‘this is x miles on map,’; it’s putting that in context and thinking how a fish may utilize that habitat.  It’s elevation, is there access to reliable flows, is this habitat different or maybe in better shape than some habitats around it?  Is it connected to other habitats that fish we know are using, so it’s not necessarily who is there now but who could be there in the future.  All those different facets come into play.  Some habitats might be used differently and at different times by these species and that whole mosaic of different diverse habitats coming online at different times or at least being accessible to fish that want to go up and use them is going to be key moving forward.”

Dr. Rob Lusardi:It’s not just saying we’re opening up habitat, but which habitats and at what times, etc, and so really thinking that not all habitats are equal.  I run into this a ton with my spring-fed research.  There are some habitats that may indeed be more valuable from a salmonid perspective, so it’s not just about the amount of miles that we’re opening but what’s in terms of the potential of that habitat and how will it contribute to these fish and these populations.  So having a plan and a strategy is really vital moving forward.”

Big Spring Ranch; photo courtesy WalMart


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