Science of an underdog: the improbable comeback of spring-run Chinook salmon in the San Joaquin River

By Andrew L. Rypel, Gabriel Singer, and Nann A. Fangue

Fig. 1. (Left) U.S. Fish and Wildlife Service biologists and partners prepare to release ~90,000 spring-run Chinook salmon into the San Joaquin River, 3/6/17. USFWS Photo/Steve Martarano, downloaded from (Right) Transferring juvenile spring-run Chinook salmon prior to release. Photo by Gabriel Singer.

“You can’t design a worse evolutionary strategy for the Anthropocene”

There are many variants on this quote, and we’ve heard them often in reference to the status of native fishes in California and other freshwater organisms worldwide. Indeed, the statement rings true for Pacific salmon, but especially spring-run Chinook salmon (Oncorhynchus tshawytscha) in California. And although the current situation certainly looks bleak overall for endangered salmon (Moyle et al. 2017), there are signs in a few corners that the arrow may finally be pointing up. For the last four years, our team at UC Davis has been conducting scientific studies on reintroduced spring-run Chinook salmon in the San Joaquin River and we wanted to take a minute to share some of what we’ve learned. Plus, everyone loves a good comeback story right?

Primer on the life-history of spring-run Chinook salmon

The complicated life-histories of Chinook salmon in the Pacific are well-known. Indeed they are a frequent topic of blog posts here! (examples, 1, 2, 3). Living as adults in the Pacific Ocean and migrating into freshwater tributaries, adults spawn and subsequently die leaving their carcasses to fertilize freshwater ecosystems with marine-derived nutrients. Young salmon must outmigrate from freshwater habitats to the ocean (and survive!) where they feed and live as adults. In California, we think of late summer and into fall, and maybe even into winter as prime time adult Chinook salmon migration time. But, spring-run Chinook salmon are different. These fish enter freshwater in spring months as sexually immature adults, and historically migrated long distances upriver to coldwater refuges in the mountains. Here, they “oversummer”, often congregating in deep coldwater plunge pools high in the landscape where they survived on their fat reserves, which dwindled as they continued to mature. When rains and flows increase in the late fall, barriers to movement suddenly become passable and fish would migrate further into the high California landscape to spawn in the fall. When you consider this life-history, and the current human-dominated landscape of California (think dams built without fish passage, climate change, landscape alterations), it is little wonder that this species (technically an “ESU, Evolutionarily Significant Unit”) has declined to where it is listed under the CA and US Endangered Species Act. Yet, spring-run Chinook salmon are full of surprises. Here’s some of them: 

Fig. 2. Long-term trends in adult abundances of spring-run Chinook salmon in the Sacramento Valley. Data are from CDFW Status Report (1998), and Grandtab (Azat 2019). Historical (pre-1900) abundance estimates are based on extrapolations from cannery records.

Surprise 1 – Spring-run Chinook salmon historically were co-dominant with the fall-run in the Central Valley and in some years may even have exceeded the fall-run in overall abundance. Today, we tend to consider fall-run Chinook salmon as the main run of salmon in California, but alas, it was the spring-run that originally predominated in the early commercial salmon fishery due to its great abundance, wide distribution and higher food quality. In one year alone (1883), at least 567,000 spring-run salmon were reported caught in the commercial fishery, not to mention all the fish that escaped the fishery and spawned in their home streams. Through the 1880s, total commercial harvests (composed primarily of spring-run fish) generally hovered around 5 million to 10 million pounds — which, at an average weight of 16 pounds per salmon, would have equated to about 310,000 to 625,000 salmon. Current valley-wide numbers oscillate between only a few thousand to upwards of 25,000 adults (Fig. 2).

Surprise 2 – While it is hard to imagine now, the San Joaquin River at one time contained the most abundant population of spring-run Chinook salmon in the Central Valley, perhaps due to the extirpation of all the other great spring-run populations originally found throughout the Valley (Yoshiyama et al 1998). Most of these fish spawned in the upper reaches of the watershed in the Sierra Nevada where strong coldwater habitats allowed fish to over-summer as described above. Following the completion of Friant Dam, spring-run Chinook salmon in the San Joaquin River were predictably extirpated in rapid succession. Identical stories of dams built without fish passage and subsequent salmon declines exist for every major river draining into the Central Valley. Yet in addition to blocking access to coldwater habitat in the Sierra Nevada, completion of Friant Dam and a chain of dams upstream (e.g., Kerckhoff Dam/Millerton Reservoir) also facilitated diversion of high proportions of water from the San Joaquin River such that ~ 60 miles were left completely dry when the project was completed (Matthews 2007). 

Fig. 3. Aerial photo revealing the landscape of the San Joaquin River, CA. Photo by Ken Lund, downloaded from, 4/14/20

Surprise 3 – Despite continued degradation of the river (Fig. 3), and its status as perennial contender for “America’s most endangered river”, spring-run Chinook salmon have been on the comeback trail for the last five years. Much of this success is largely due to a massive habitat restoration and reintroduction effort, spear-headed by the San Joaquin River Restoration Program (SJRRP). The SJRRP has developed a comprehensive reintroduction strategy for spring-run Chinook salmon intended to overcome the various obstacles that impede reestablishment of a viable spring-run Chinook salmon population. Habitat projects include restoring connectivity in the river, increasing flows to provide suitable habitat to complete all phases of the life cycle, and removal and reconfiguration of structures that obstruct movement of salmon. The phased goals of the program include reintroduction of spring-run Chinook salmon (supported by a conservation hatchery operated by CDFW), establishment of self-sustaining local populations under contemporary river conditions, and finally long-term maintenance of a population of 30,000 spawning adults with negligible hatchery influence.

It is of note that spring-run fish from the Feather River Hatchery were used to initially jumpstart the conservation hatchery broodstock for the San Joaquin River. Thus, we can never truly “bring back” the original upper San Joaquin spring-run – a notable consequence of extinction overall.  However, a recently published genomic study on Central Valley Chinook salmon (Meek et al. 2020) revealed that Feather River Hatchery spring-run have distinctive genetic elements that set it apart from the two other Central Valley spring-runs (i.e., Mill/Deer Creek, and Butte Creek) as well as from the Feather River Hatchery fall-run. This finding in turn suggests the Feather River Hatchery spring-run likely retains ancestral genetic elements from the original Feather River spring-run varieties. Hence, the new reintroduced San Joaquin spring-run population is aiding in preservation of Feather River spring-run ancestry, but also, overall genetic diversity of Central Valley Chinook populations – this is a good thing.

Science to inform adaptive management of spring-run Chinook salmon

Over the last 4 years, our team has been developing science that can be used to facilitate adaptive management of reintroduced spring-run Chinook salmon in the San Joaquin River. The centerpiece to this work has been a set of focused acoustic telemetry studies on juvenile salmon released each spring. Beginning each year in early March, our team usually tags 750 juvenile spring-run Chinook salmon produced at the Salmon Conservation and Research Facility (SCARF; Friant, CA) with miniature Juvenile Salmon Acoustic Telemetry System (JSATS) transmitters. Similar to a recent blog, these transmitters produce sounds that are then “heard” by receivers maintained by our team throughout the river (Fig. 4). Fish with uniquely coded transmitters swim past receivers and data are registered allowing us to study survival rates, routing and other fish behaviors of interest. The JSATS transmitters are the smallest available on the commercial market, allowing us to track fish as small as ~72mm in length, although we prefer to tag larger smolts.

Fig. 4. (Top) Taggable-size spring-run Chinook salmon from the SCARF hatchery. Resting on top of the fish is a miniature acoustic transmitter ready to implant in the fish. (Bottom) Finishing JSAT implantation surgery on a juvenile spring-run Chinook salmon. Photos by Gabriel Singer.

Currently, spring-run Chinook salmon are confined to only the lower San Joaquin River (below Friant Dam). Therefore, we track fish through this area which includes the lower region of the Restoration Area, but also continues through the Sacramento-San Joaquin Delta, San Francisco Estuary, and entrance to the Pacific Ocean. We also maintain (fancier and more expensive) real-time receivers at the federal and state pumping facilities which provide a rapid window into how many juvenile fish are being entrained and salvaged at the water pumping facilities. These receivers transmit data in real time via cell phone towers. See example of real-time telemetry data from this year’s spring-run tagging.

With three years of data now in the bag, some patterns are notably clear. First, as is typical with juvenile salmon in the Central Valley – water matters! Years during which there was increased precipitation and high flows, survivorship to the ocean was higher. In 2017 (a wet year – remember Oroville Dam!), we estimated out-migration survival to the Golden gate at 2-5%, but in 2018 (a drier year) survivorship plunged to only 0.5%. In a wetter year, 2019 survivorship increased again to 5%. In 2020, real time receivers at Benicia Bridge estimate that so far only 0.5% of our fish have successfully out-migrated to the ocean – ouch again! As a comparison, telemetry studies for other runs of Chinook salmon in the Sacramento during 2019 suggested outmigration survival rates upwards of 15-20%. Our data therefore indicate survivorship is uniformly low for salmon in the San Joaquin River overall, and that flows here probably really matter for the fish. Most of the tagged fish that enter the interior Delta simply don’t make it out. 

Finally, we have found that many of our tagged fish are plucked out of the river at the fish salvage facilities located at the Central Valley Project and State Water Project (pumping facilities). Interestingly, these fish often have higher survivorship to the ocean versus fish remaining in the mainstem San Joaquin River or freely swimming through the interior Delta. This pattern is likely not because being salvaged is “good for fish” but rather, because upon salvage, fish are physically trucked around the interior Delta to the San Francisco Bay. Previous studies on fall-run salmon smolts in the system found highly similar patterns (Buchanan et al. 2018). Furthermore, a temporary fish barrier is often installed by the Department of Water Resources (DWR) at the head of Old River to prevent fish from being drawn towards the pumping facilities (DWR 1992). Yet it now seems possible that this barrier, originally installed to prevent fish from accessing an assumed low survival route in low discharge years, may sometimes actually block access to the highest survival out-migration pathway (salvage). It is notably sad and ironic perhaps, that the quality of habitat in the lower river is so poor that the best migration path for salmon appears to be as a salvaged fish, trucked around the Delta by DWR or BOR staff.


While the data we have paint a grim ecological picture for spring-run Chinook salmon in the San Joaquin River, the situation is beginning to trend positive. At the end of May 2019, at least 23 adult spring-run salmon returned to the river, capping at least a 370 mile round trip journey to the ocean and back again. It also marked the first time in 65 years that adult spring-run Chinook salmon returned volitionally to the San Joaquin River to spawn. In fall of 2019, more than 200 redds were counted, a 4-fold increase from the previous year. Wild smolts have been increasingly captured in screw traps, indicating successful reproduction is occurring in the wild independent of hatchery efforts. 

As we continue to gain data on the biology of reintroduced salmon in the San Joaquin River, we will be able to provide increased information valuable for conservation. For example, we are conducting focused experiments on specific areas of the interior delta that we think may be especially problematic for salmon smolts (e.g., Frank’s Tract). We are also conducting innovative studies on the physiology of salmon smolts experimentally exposed to different parts of the river. Finally, we are conducting in-depth habitat assessments to further inform why there are major “hotspots of death” for salmon in the lower portions of the ecosystem. In the future, adding more upriver habitat to the current migration corridor for spring-run may be worth consideration. For example, historically, the very best spring-run Chinook habitat was in the areas below and between where Friant and Kerckhoff Dams now stand. While these areas are now mostly flooded, remnants of deep pool habitat do exist below Kerckhoff Dam, making restoration a possibility in these areas. Unfortunately, there is not a ton of spawning habitat to go with the deep pool habitat in these areas as the canyon below Kerckoff is fairly narrow except where it expands at Temperance Flat. This is also an area where another dam has been proposed. Nonetheless, if these pools could be managed for coldwater through summer months, small runs of spring-run Chinook salmon above Friant may also be possible.

Finally, what we have encountered all along the way has been a constant dedication to the fish and ecosystem from biologists of all stripes at agencies, universities, fishing groups and others. We work hand-in-hand with a number of agencies conducting concurrent telemetry studies in the Sacramento River and Delta, and are constantly impressed by the professionalism and dedication needed to help recover our fish populations. It is heartening that against all odds, spring-run Chinook salmon are staging a comeback (albeit small currently) in one of the most endangered rivers in the USA. We are proud to be part of these interdisciplinary studies that provide, not only information needed immediately for conservation, but also as a training ground for the future of fisheries biology. There are so many to praise for these advances.

Fig. 5. View from the top of Friant Dam pointing downriver. The raging whitewater on the left is the Friant-Kern Canal which pulls ~75% of its water from Friant. The more docile waterbody to the right is the San Joaquin River. Photo by Gabriel Singer.

Andrew Rypel is an Associate Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and an Associate Director of the Center for Watershed Sciences. Gabriel Singer is a postdoctoral research associate in the Rypel Lab at University of California, Davis. Nann Fangue is a professor and Chair of the Department of Wildlife, Fish & Conservation Biology at University of California, Davis.

Further reading:

2019 Spring-Run Redds Set Record!

Azat, J. 2019. GrandTab 2019.05.07 California Central Valley Chinook Population Database Report. California Department of Fish and Wildlife, Sacramento, CA USA. 

Buchanan, R.A., Brandes, P.L., Skalski, J.R., 2018. Survival of Juvenile Fall-Run Chinook Salmon through the San Joaquin River Delta, California, 2010–2015. North American Journal of Fisheries Management 38: 663–679.

California Department of Water Resources. 1992. South Delta Temporary Barriers Project: monitoring, evaluation, and management program. California Department of Water Resources, Sacramento, CA USA.

Matthews, N. 2007. Rewatering the San Joaquin River: A Summary of the Friant Dam Litigation. Ecology Law Quarterly 34(3): 1109–1135.

Meek, M.H., M.R. Stephens, A. Goodbla, M. May, and M.R. Baerwald. 2020. Identifying hidden biocomplexity and genomic diversity in Chinook salmon, an imperiled species with a history of anthropogenic influence. Canadian Journal of Fisheries and Aquatic Sciences 77: 534-547.

Moyle, P. B., R. Lusardi, and P. Samuel. 2017. State of the Salmonids II: Fish in hot water. Status, threats and solutions for California salmon, steelhead and trout. University of California-Davis, CA USA.Yoshiyama, R. M., F. W. Fisher, and P. B. Moyle. 1998. Historical abundance and decline of chinook salmon in the Central Valley region of California. North American Journal of Fisheries Management 18: 487-521.

Yoshiyama, R. M., F. W. Fisher, and P. B. Moyle. 1998. Historical abundance and decline of chinook salmon in the Central Valley region of California. North American Journal of Fisheries Management 18: 487-521.


This research is being funded by the Delta Science Council, with additional support from the California Department of Fish and Wildlife (CDFW) and the US Fish and Wildlife Service (USFWS). Our larger team of scientists at UC Davis working on this project includes Dennis Cocherell, Colby Hause, Leah Mellinger, Sarah Baird, Michael Thomas, Amanda Agosta, Heather Bell, Matthew Pagel, Emily Jacinto, Mackenzie Miner, Wilson Xiong. We also thank past scientists at UC Davis including A. Peter Klimley and Eric Chapman for their important contributions in the early years of this work. Lori Smith and Pat Brandes (USFWS), Don Portz (SJRRP), Towns Burgess (SJRRP), John Kelly (CDFW), Matt Bigelow (CDFW), and Josh Isreal (USBOR) have all been critical to supporting and continuing this work. We thank Peter Moyle, Ronald Yoshiyama and Towns Burgess for reviewing earlier versions of this blog.

About Andrew Rypel

Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences.
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