By Lauren G. Hitt, Malte Willmes, Mackenzie C. Miner, Max Stevenson, Carson A. Jeffres, Robert A. Lusardi, Nann A. Fangue, and Andrew L. Rypel

For the third year in a row, regulators have canceled California’s commercial Chinook salmon fishing season.Poor spawning salmon returns in 2024 and low predicted numbers of salmon in the ocean during 2025 prompted the decision. These issues, in a nutshell, are symptoms of the persistent pressures that California salmon populations face. In particular, Chinook salmon in the Central Valley face chronic habitat loss due to dams and wetland conversion (Yoshiyama et al. 2001), warming water temperatures (Williams et al. 2016), poor migration survival rates (Michel et al. 2015), impacts from hatchery management (Williamson and May 2005), changing diets in the ocean (Mantua et al. 2021), and drought-related and worsening climate effects (Herbold et al. 2023), among other concerns.  

Despite these threats, we uncovered cause for hope right next to the UC Davis campus in Putah Creek, a waterway beloved by the communities of Davis and Winters. Prior work on the creek has examined the resurgence of native fishes, the first cohorts of salmon in the creek, and the results of a recent severe weather event. Our newest research, published in March in the journal Ecosphere, provided evidence for the first time that Chinook salmon can complete their full life cycle using Putah Creek. Although the vast majority of salmon spawning in Putah Creek are hatchery-origin fish that strayed into the creek via the Yolo Bypass, researchers have suspected there might be a few salmon among the hatchery fish that were born in Putah Creek, and detecting those fish of Putah Creek origin has been a goal of Solano County Water Agency (SCWA) and UC Davis. Our new study documented that, indeed, juvenile salmon hatched in Putah Creek returned from the ocean 2-4 years later to spawn as adults. This remarkable finding signals the first step in what could become a new population of Chinook salmon in California. Our findings also highlight how restoration and reimagined flow management can help us leverage even highly modified waterways into viable salmon habitat at a time when bolstering California’s salmon populations is of dire importance.

For the first time, Putah Creek-origin Chinook salmon

In our new paper, we studied the annual adult Chinook salmon migration to Putah Creek, where the fish spawn and ultimately die (Figure 1). Over a period of five years, we collected otoliths (‘ear-stones’) from salmon carcasses and applied two geochemistry methods to match the otolith chemical signatures to water chemical signatures from different Central Valley rivers and fish hatcheries (Barnett-Johnson et al. 2008). In other words, we used the natural chemicals in fish ear bones to find out where individual fish lived over the course of their lives. Using these techniques, we determined whether each salmon that we sampled in Putah Creek was a hatchery-origin stray, a stray from another wild population, or one of the lucky few Putah Creek-origin salmon that successfully navigated from Putah Creek to the Pacific Ocean and back during their life cycle. For three of the five years we studied, we observed at least one salmon of Putah Creek origin. In the most recent year of our study (2021), we identified the highest number of Putah Creek salmon yet: nine fish, or 12% of that year’s sample(Figure 2). 

It takes a team: The roles of community engagement, collaboration, and restoration

The presence of Chinook salmon of any origin in Putah Creek would not have been possible without substantial investment in the creek and in long-term science conducted by local communities. Beginning in the 1990s, organizing and community-led lawsuits culminated in the Putah Creek Accord (2000), which marked a turning point in both the management of the creek and collaborative efforts to restore the ecosystem. There are many agencies and organizations helping to promote Putah Creek’s restoration, including partners like SCWA, Lower Putah Creek Coordinating Committee, California Department of Fish & Wildlife, city governments of Davis and Winters; non-profits including Putah Creek Council and Yolo Basin Foundation; researchers from UC Davis in addition to private consultants and contractors; farmers and landowners bordering the creek; undergraduate students studying the creek in their courses and volunteer work; and engaged community members who recreate in and around the creek. Together, these partners completed many substantial restoration goals for Putah Creek. Some of these (many!) goals include structuring an environmental flow regime via dam releases to better support native fish, gravel scarification to break up armored river sediment to encourage fish spawning, gravel augmentation to replace gravel mined for construction operations, re-grading channelized segments from steep banks to flatter floodplains, improved fish passage, community clean-up days, removal of introduced plants like Himalayan blackberry brambles, and growing and planting native species. Many of these projects are ongoing, and new plans for a restored wetlands park along Putah Creek outside Davis are in motion. Also noteworthy is the annual Winters Salmon Festival, which celebrates the return of salmon to the Putah Creek waterway every year and highlights the strong ties between communities and the creek’s fish.

Not yet a fairytale ending: Ongoing issues in Putah Creek

It’s easy to look at the positive development of the salmon population and other native fishes (e.g., Jacinto et al. 2023) at Putah Creek and call it ‘case closed.’ However, many obstacles still affect salmon using the creek. The most concerning of these obstacles was revealed by a 2021 atmospheric river event that had the unlucky timing to coincide with the arrival of migrating adult salmon to Putah Creek. This atmospheric river created a ‘perfect storm’ of problems, including debris and ammonia-saturated waters washing into the creek, that resulted in low oxygen levels in Putah Creek for months and ultimately, killed nearly all adult salmon that returned to Putah Creek to spawn in 2021, which was the final year of our otolith study. This suggests that of the nine Putah Creek-origin salmon we detected, the largest cohort of natal fish in our study, none were able to spawn and contribute a next generation of Putah Creek salmon, certainly a setback in the development of a ‘Putah Creek run’ of salmon. However, management changes in the years following the 2021 fish kill, regarding the timing of migration cues for salmon and the seasonal removal of barriers to the creek, will ideally prevent future, similar setbacks.

Another ongoing obstacle to the development of a Putah Creek salmon population is, paradoxically, the same phenomenon that led to the rapid establishment of salmon in the creek in the first place: the high number of hatchery-origin salmon straying into the creek each year. Hatcheries often truck juvenile salmon directly to the sea instead of releasing them into rivers to undertake their migrations, and though this practice may improve juvenile salmon survival, it results in returning adult salmon that get lost and stray into adjacent watersheds in unnaturally high numbers (Sturrock et al. 2019). As long as hatcheries continue trucking juveniles, the development of a fully self-sustaining Putah Creek salmon population is unlikely. Looking into the future, the potential impacts of climate change on Putah Creek salmon will also be important to consider, as warming temperatures, worsening droughts, and more frequent extreme events may impact Putah Creek’s ability to support salmon on the Central Valley floor.

There is still much to celebrate about Putah Creek. Returns of adult salmon to Putah Creek (Figure 3) in recent years are reaching record highs, and ongoing restoration and community engagement on the creek continue to promote quality habitat that supports Chinook salmon and other native species. This is not the last you’ll be hearing about research on Putah Creek, as studies on salmon genetics, juvenile outmigration success, and ecosystem effects of salmon carcass fertilization are currently in the works. Most importantly, the story of Putah Creek provides a blueprint that can be replicated in other highly modified rivers throughout California and the larger Pacific coast. This project should also provide perspective for the time restoration takes to recover salmon in California – it has taken years of flow management and restoration in Putah Creek for significant numbers of Putah Creek salmon to be detected. In times of crisis with fishery closures, drought, and climate change, Putah Creek has shown that playing the long-game of landscape-level change can pay dividends. This work not only supports the survival of Chinook salmon in California but also strengthens the connections between communities and the waterways that support them. We can’t wait to see which restored California stream will be next to support salmon.

About the Authors

Lauren G. Hitt completed her Master’s degree in Ecology at UC Davis in 2023 studying the Putah Creek salmon population. She is currently a PhD candidate at the University of Canterbury in Christchurch, New Zealand, where her dissertation work focuses on lake ecosystems and populations of threatened galaxiid fishes. 

Malte Willmes is a researcher at the Norwegian Institute for Nature Research (NINA) and an affiliate at UC Santa Cruz.

Mackenzie C. Miner was a project lead and graduate student researcher at UC Davis, where she focused on the lifecycle monitoring of Chinook salmon in Putah Creek and completed her Master’s degree in Animal Biology in 2022. She now leads a regional monitoring program, the Yolo Bypass Fish Monitoring Program, supporting science-based fisheries management. 

Max Stevenson is Streamkeeper with Lower Putah Creek Coordinating Committee and Solano County Water Agency.

Carson A. Jeffres is a Senior Researcher, as well as Field and Lab Director, of the UC Davis Center for Watershed Sciences

Robert A. Lusardi is an Assistant Professor in the Department of Wildlife, Fish, & Conservation Biology and Associated Director of the Center for Watershed Sciences. 

Nann A. Fangue is a UC Davis Professor and Chair of the Wildlife, Fish, & Conservation Biology Department. Nann studies California native fish physiology and conservation.  With her team of students and staff, their work focuses on understanding how changes in the environment influence fish responses and how we can use our understanding of these responses to find creative solutions to tough environmental problems.  Prof. Fangue received her PhD from the University of British Columbia in 2007, joined the UC Davis faculty in 2009, and is a UC Davis Chancellor’s Fellow.  

Andrew L. Rypel is an Adjunct Professor in the Department of Wildlife, Fish, & Conservation Biology at UC Davis and past Director of the Center for Watershed Sciences. He is currently Director of the School of Fisheries, Aquaculture, and Aquatic Sciences at Auburn University.

Further reading

Hitt, L.G., M. Willmes, G. Whitman, M.C. Miner, C.A. Jeffres, R.C. Johnson, D.E. Cocherell, N.A. Fangue, and A.L. Rypel. 2025. Early evidence for establishment of a Chinook salmon population in a restored watershed. Ecosphere16(3): e70207. https://doi.org/10.1002/ecs2.70207

https://www.ucdavis.edu/climate/news/restored-stream-supports-new-wild-salmon-run

https://www.cbsnews.com/sanfrancisco/video/uc-davis-researchers-look-into-resurgence-of-wildlife-at-restored-creek/#x

https://www.sfgate.com/local/article/chinook-salmon-study-northern-california-creek-20236728.php

Putah Creek’s rebirth: a model for reconciling other degraded streams?

The Putah Creek Fish Kill: Learning from a Local Disaster

New insights into Putah Creek salmon

Habitat Restoration for Chinook Salmon in Putah Creek: A Success Story

Works Cited

Barnett-Johnson, R., T. E. Pearson, F. C. Ramos, C. B. Grimes, and R. Bruce MacFarlane. 2008. Tracking Natal Origins of Salmon Using Isotopes, Otoliths, and Landscape Geology. Limnology and Oceanography 53: 1633–1642. https://doi.org/10.4319/lo.2008.53.4.1633.

Herbold, B., S. M. Carlson, and R. Henery. 2018. Managing for Salmon Resilience in California’s Variable and Changing Climate. San Francisco Estuary and Watershed Science 16(2): 1–23. https://doi.org/10.15447/sfews.2018v16iss2art3

Jacinto, E., N.A. Fangue, D.E. Cocherell, J.D. Kiernan, P.B. Moyle, and A.L. Rypel. 2023. Increasing stability of a native freshwater fish assemblage following flow rehabilitation. Ecological Applications 33(5): e2868. https://doi.org/10.1002/eap.2868

Mantua, N., R. Johnson, J. Field, S. Lindley, T. Williams, A. Todgham, N. Fangue, C. Jeffres, H. Bell, D. Cocherell, J. Rinchard, D. Tillittt, B. Finney, D. Honeyfield, T. Lipscomb, S. Foott, K. Kwak, M. Adkison, B. Kormos, S. Litvin, and I. Ruiz-Cooley. 2021. Mechanisms, impacts, and mitigation for thiamine deficiency and early life stage mortality in California’s Central Valley Chinook salmon. North Pacific Anadromous Fish Commission Technical Report 17: 92-93. https://doi.org/10.23849/npafctr17/92.93

Michel, C.J., A.J. Ammann, S.T. Lindley, P.T. Sandstrom, E.D. Chapman, M.J. Thomas, G.P. Singer, A.P. Klimley, and R.B. MacFarlane. 2015. Chinook salmon outmigration survival in wet and dry years in California’s Sacramento River. Canadian Journal of Fisheries and Aquatic Sciences 72(11). https://doi.org/10.1139/cjfas-2014-0528

Rabidoux, A., M. Stevenson, P. B. Moyle, M. Miner, L. G. Hitt, D. E. Cocherell, N. A. Fangue, and A. L. Rypel. 2022. The Putah Creek fish kill: Learning from a local disaster. Calif. WaterBlog. https://californiawaterblog.com/2022/04/24/the-putah-creek-fish-kill-learning-from-a-local-disaster/.

Sturrock, A. M., W. H. Satterthwaite, K. M. Cervantes-Yoshida, E. R. Huber, H. J. W. Sturrock, S. Nusslé, and S. M. Carlson. 2019. Eight Decades of Hatchery Salmon Releases in the California Central Valley: Factors Influencing Straying and Resilience. Fisheries 44: 433–444. https://doi.org/10.1002/fsh.10267.

Willmes, M., E.E. Jacinto, L.S. Lewis, R.A. Fichman, Z. Bess, G. Singer, A. Steel, P.B. Moyle, A.L. Rypel, N. Fangue, J.J.G. Glessner, J.A. Hobbs, and E.D. Chapman. 2021. Geochemical tools identify the origins of Chinook salmon returning to a restored creek. Fisheries 46(1): 22-32. https://doi.org/10.1002/fsh.10516

Williams TH, Spence BC, Boughton DA, Johnson RC, Crozier LG, Mantua NJ, O’Farrell MR, Lindley ST. 2016. Viability assessment for Pacific Salmon and Steelhead listed under the Endangered Species Act: Southwest. U.S. Department of Commerce, NOAA Technical Memorandum NMFS-SWFSC-564. https://repository.library.noaa.gov/view/noaa/12013

Williamson, K. S., and B. May. 2005. Homogenization of Fall-Run Chinook Salmon Gene Pools in the Central Valley of California, USA. North American Journal of Fisheries Management 25: 993–1009. https://doi.org/10.1577/M04-136.1.

Yoshiyama, R. M., E. R. Gerstung, F. W. Fisher, and P. B. Moyle. 2001. Historical and Present Distribution of Chinook Salmon in the Central Valley Drainage of California. California Department of Fish and Game Fish Bulletin 179(1): 71-176. https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=3563