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

by Eric Chapman, Emily Jacinto, and Peter Moyle

2017 was another good year for Chinook salmon in Putah Creek.

Putah Creek is just a small stream flowing through Yolo and Solano counties, fed by releases of water from Lake Berryessa. For decades, Chinook salmon were rare in the creek.

Yet, now, with salmon populations struggling throughout the Central Valley, Putah Creek numbers are on the rise. Over the past five years the estimated number of adult spawners has increased from eight in 2013 to over 500 in each of the past three years (200-500 in 2014, 500-700 in 2015, 1500-1700 in 2016, and 700 in 2017).

When much of California was in the historic drought of 2012-2016, hatcheries resorted to trucking juvenile Chinook salmon far downstream to the Delta. The intent was to increase the number of juveniles reaching the ocean because survival is poor in the rivers during low water years (Michel et al. 2013, Michel et al. 2015). While trucking can sustain adult populations, it increases the rate of adult straying into other watersheds upon return from the ocean, rather than homing to their natal watershed (Johnson 1990, Lasko 2012).

However, ongoing restoration and management efforts in Putah Creek have made conditions favorable for attracting salmon. Flashboards blocking access to the creek at the Los Rios Check Dam in the Yolo Bypass are removed every year in November and salmon attraction flows are released for five consecutive days from the Putah Diversion Dam in Winters, CA.

Map of Putah Creek from the Putah Diversion Dam (PDD) to the Toe Drain (yellow star). Salmon migrate through the yellow area to and from the spawning grounds in red. Number of adult carcasses sampled (blue circles and numbers) in different sections (black circles) of the spawning grounds. The location of the rotary screw trap is above Winters, CA (yellow star).

Minimum flows were established to enhance rearing habitat for juvenile salmon and to facilitate outmigration (Kiernan et al. 2012). During summer and fall, the Solano County Water Agency has also been using heavy equipment to scarify (turn over) the bottom of selected reaches of the creek; this process exposes spawning gravel that has been buried by years of siltation and compaction.

Over the past two years, salmon spawning has been observed on nearly every patch of gravel from the Putah Diversion Dam to Davis, a distance of ~25 kilometers. Fish were observed spawning on the newly exposed areas and on sites from previous scarification efforts. Use by salmon seems to keep the sites from becoming cemented in again.

In Winters, people watched salmon spawning below the pedestrian bridge. This reach was site of a major restoration project that removed a concrete dam and recreated a meandering stream, greatly improving salmon habitat.

Where did these fish come from and are they spawning successfully? Are juveniles making it out of Putah Creek to the ocean and are any of them returning as adults to spawn? UC Davis and the Solano County Water Agency set out to answer these questions by sampling both adult and juvenile life stages.

Adult Sampling

In 2016, researchers from the UC Davis Department of Wildlife Fish and Conservation Biology began conducting carcass surveys throughout the creek. Surveys did not begin until December in 2016, but in 2017 they coincided with the arrival of adults in the creek. The researchers poled canoes from the Putah Diversion Dam to Davis at least once during every week of the run. This allowed them to estimate the number of fish throughout the creek from week to week.

Colby Hause, a researcher at UC Davis, poles a canoe during carcass surveys. (photo: Eric Chapman)

The 2017 estimate of 700 fish is likely within ± 20%.  In the future, we hope to employ other methods as well to estimate abundance, such as use of special cameras to record passing fish.

During the two years of carcass surveys, otoliths (ear bones) were collected in order to determine the origin and age of salmon spawning in Putah Creek. Genetic samples were also collected, and tiny, coded wire tags (CWTs) were extracted from fish missing their adipose fin. The missing fin indicates they were of hatchery origin.

Results from 23 CWT fish from 2016 found that 20 were from the Mokelumne River Hatchery, two were from the Nimbus Hatchery on the American River, and one from the Feather River Hatchery. All of the tagged fish were fall-run Chinook salmon that had been trucked downstream to be released closer to the ocean during the drought.

Two otoliths collected from a carcass and location of coded wire tags (CWT). Note that the head of this fish is pointing upwards (photo: Eric Chapman)

These 23 fish were a subsample of the 126 carcasses recovered on the creek. Otolith microchemistry from the 91 fish with an intact adipose fin was determined at the University of California Davis Interdisciplinary Center for Plasma Mass Spectrometry, focusing on Strontium (Sr) isotope ratios (87Sr/86Sr). These isotope ratios vary among rivers in the Central Valley of California. The strontium isotopes are incorporated into each otolith on a daily basis, allowing for assignment of natal origin of individual fish by measuring the isotope ratios at the core of the otolith.

The microchemistry of the otolith center reflects where the fish was hatched and reared. Unfortunately, considerable overlap exists among the strontium signatures of possible natal sources, including between rivers and hatcheries, making some results difficult to interpret. For example, the strontium signature of Chinook salmon from Putah Creek overlaps with that of the wild Feather River fish but not with those in fish produced in the Feather River Hatchery.

Gabriel Singer with a large male sampled during carcass surveys. (photo: Eric Chapman)

The otolith microchemistry showed that there were at least five stocks of fish in Putah Creek in 2016. One fish was sampled that could have been of Putah Creek origin but it could have also been a naturally produced Feather River fish. To determine the difference between Putah Creek and the Feather River, it will be necessary to incorporate other trace elements or isotope systems in the future.

Juvenile Sampling

In the spring of 2017, a rotary screw trap (RST) was deployed to determine spawning success and to describe emigration timing of the juveniles. This was an extremely high water year, with Lake Berryessa overflowing during much of late winter. Because of the hazards of running a trap at high flows, the trap wasn’t operated until May 1st when the water subsided. On May 2nd there were nine juvenile fall run Chinook salmon in the trap; juveniles were captured daily until May 20th,with a peak of over 30 fish on May 10th.

The screw trap used to sample juvenile Chinook in Putah Creek. Photo credit: Ken Davis

The 215 juvenile salmon sampled into June 2017 were large, averaging 97 millimeters in length and 11.4 grams in weight. This indicates that high flows did not push them out of Putah Creek, rather it provided rearing conditions that enabled them to thrive prior to migration. These conditions were likely found on the edges of the creek and outside of the banks where floodplain conditions exist.

Daily catch summary of juveniles sampled in Putah Creek during 2017.

The jury is still out on successful spawning and rearing in 2018. The RST has been deployed again in 2018, and hundreds of small outmigrating  juveniles were captured as of January-March.  One hundred of the largest fish will receive an acoustic transmitter that will be surgically implanted to track their survival and migratory behavior. Receivers that detect the transmitters will be situated at the base of the creek, enabling the researchers to determine emigration survival from Putah Creek. An array of receivers collaboratively deployed by UCD and fisheries agencies outside the creek will enable modelling of survival through the Delta and San Francisco Estuary all the way to the Golden Gate, which has the last line of receivers prior to the Pacific Ocean.

Typical juvenile salmon caught in the RST during 2017 spring sampling (photo: Eric Chapman)

Putah Creek is a success story for salmon because water releases from a dam and habitat restoration projects have worked together to attract salmon and to allow them to spawn and rear successfully. It is likely that at least some adult salmon that returned to spawn were themselves spawned in Putah Creek. It seems possible that in the future a run could develop that is not dependent on hatchery strays, but is made up of natal fish from the creek.

Otoliths and genetics help us understand what happens when a creek is reborn and made available to fish. Spawner surveys and juveniles caught in the rotary screw trap confirm that restoration actions are working and that Putah Creek offers habitat that is suitable for producing fall-run Chinook salmon on an annual basis. Putah Creek is already regarded as model for restoration of habitat for native fishes and other plants and animals. To add wild salmon to this trajectory of success requires continued management of the creek to benefit salmon, including expansion of habitat restoration projects.


We thank the Solano County Water Agency for funding this project and for all of their help throughout the project. We would also thank Malte Willmes and James Hobbs for processing the otoliths in the mass spectrometer. Finally we thank all of the members of the UCD Biotelemetry Laboratory (Gabriel Singer, Colby Hause, Tommy Agosta, Christopher Bolte, and Patrick Doughty), volunteers, and students for their help during field work.

Eric Chapman, the lead researcher, works in Peter Moyle’s fisheries laboratory in the Center for Watershed Sciences. Emily Jacinto is a lab assistant at UC Davis. Peter Moyle is professor emeritus at the University of California, Davis, and Associate Director of the Center for Watershed Sciences. 

Further reading

Johnson, S.L., Solazzi, M.F. and Nickelson, T.E., 1990. Effects on survival and homing of trucking hatchery yearling coho salmon to release sitesNorth American Journal of Fisheries Management10(4), pp.427-433.

Kiernan, J.D., P. B. Moyle, and P. K. Crain. 2012. Restoring native fish assemblages to a regulated California stream using the natural flow regime concept.  Ecological Applications  22:1472-1482.

Lasko, G.R. 2012. Straying of late-Fall-run Chinook salmon from the Coleman National Fish Hatchery into the lower American River, California. Masters thesis, California State University, Sacramento.

Michel, C.J., Ammann, A.J., Chapman, E.D., Sandstrom, P.T., Fish, H.E., Thomas, M.J., Singer, G.P., Lindley, S.T., Klimley, A.P. and MacFarlane, R.B., 2013. The effects of environmental factors on the migratory movement patterns of Sacramento River yearling late-fall run Chinook salmon (Oncorhynchus tshawytscha). Environmental biology of fishes96(2-3), pp.257-271.

Michel, C.J., Ammann, A.J., Lindley, S.T., Sandstrom, P.T., Chapman, E.D., Thomas, M.J., Singer, G.P., Klimley, A.P. and MacFarlane, R.B., 2015. Chinook salmon outmigration survival in wet and dry years in California’s Sacramento River. Canadian Journal of Fisheries and Aquatic Sciences72(11), pp.1749-1759.

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