Unlocking how juvenile Chinook salmon swim in California rivers

By Rusty C. Holleman, Nann A. Fangue, Edward S. Gross, Michael J. Thomas, and Andrew L. Rypel

Despite years of study and thousands of research projects, some aspects of the biology of Chinook salmon remain altogether mysterious. One enduring question is how outmigrating salmon smolts behave and swim through our waterways to somehow find their way into the ocean. For example, it has long been noted that salmon ‘shoulder’ (hold on the river’s edge) at certain times along their oceanward journey, and that they tend to school and travel in packs alongside one another. Are they actively swimming through these habitats? Or merely drifting with the currents, akin to riding an innertube down the river. A better understanding of Chinook salmon swimming behavior could be helpful for managers. If salmon actively navigate, could we provide flows or otherwise manage water to promote salmon survival?

Fig. 1. (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.

Improved acoustic tagging technologies (such as juvenile salmon acoustic tags, “JSAT”) now allows researchers to study the movements of juvenile salmon as small as 65–75mm long along their entire journey (Fig. 1). The tags produce high frequency sounds detectable with hydrophones (underwater microphones) placed throughout waterways. With enough hydrophones in a small area, it then even becomes possible to track behaviors of salmon, including second-by-second motions inside critical areas of interest. In the Delta, areas of particular interest include areas near water pumping facilities and channel junctions (forks in the river), where the fate of salmon can be quite different if fish go one direction versus another.

Fig. 2. Map of study site including (a) Sacramento-San Joaquin Delta, including San Joaquin River and fish release locations. (b) Head of Old River study site, with computational grid and bathymetry, and the layout of the hydrophone array. White arrows show the downstream flow direction (noting that tidal flow reversal is possible on the downstream section of the San Joaquin River). (c) Location of gages relative to study site.

We studied swimming behavior of juvenile spring-run Chinook salmon in the San Joaquin River (Holleman et al. 2022). Spring-run are being reintroduced into the San Joaquin River, and a team at UC Davis has studied this population for the last 5 years, primarily using acoustic telemetry. One aspect of this work was an array of hydrophones at the Head of Old River to track salmon behavior at this critical junction (Fig. 2). These results build from related model development and analytical work published by this same interdisciplinary group (Gross et al. 2022). During typical flow conditions, most salmon ‘hang a left’ at this junction, meaning fish will arrive at the state or federal water facilities. Any fish salvaged at these facilities receive a truck ride to Chipps Island at the western boundary of the Delta where they are released back into the Estuary. In contrast, salmon that ‘go right’ at the junction traverse the engineered channels and predation exposure in the South Delta, including the deepwater Port of Stockton, before exiting the Delta at Chipps Island. Research with spring-run (Singer 2019, Hause et al. 2022) and fall-run (Buchanan et al. 2018) show fish that follow this route have very poor survivorship — sadly, even worse than those salvaged at the pumping facilities. Nonetheless, because the fate of fish hinges on this left/right route selection, it is an intriguing location to examine salmon swimming behavior.

Fig. 3. Location of water velocity measurements and model–data comparisons. Velocity vectors in the horizontal for
each transect showing modeled (green) and observed (black) velocities averaged over the top 2 m of the water column.

To complement data on fish movement we also studied hydrodynamics of the river at this same location. Using a boat-mounted acoustic doppler current profiler (ADCP), we mapped water velocity of the river at nine transects — six above the junction, one at the junction, and one below the junction on each branch. These data supported a three-dimensional hydrodynamic model of the study area (Fig. 3), which in turn provided estimates of water velocity along each observed smolt’s path. By comparing the water velocity and smolt’s movement we calculated a swimming speed and direction for each tagged fish. Such swim velocity vectors can identify longitudinal (upstream or downstream) and lateral (river right or river left) swimming components for each fish.

A key difference between this study and many previous swim speed studies is the focus on swimming behavior (what a fish chooses) rather than swimming capacity (what a fish is capable of). Over the 147,991 detections from tagged salmon, most swimming speeds were 0.15–0.20 m s-1 (Fig. 4), or 2–3 body lengths per second (BL s-1). These speeds are similar to, but slower than, previously observed swim capacity speeds for juvenile Chinook Salmon, often ~4 BL s-1. The observed long tail of high velocities is comparable to the result of Lehman et al. 2017 who measured maximum sustained swim speeds of ~7 BL s-1. While the smolts are capable of much faster movement, these data paint a picture of emigrating smolts cruising along at a relatively “comfortable” speed.

Fig. 4. Distributions of swimming speeds for juvenile Chinook salmon in the study.

In the absence of swimming or vertical movement, smolts would be passively transported with the flow, matching the velocity of the river. Our data show that smolts were almost always moving downstream, but slower than water velocities. This indicates that salmon smolts are actively navigating the river and not displaying passive behavior dominated by water flow. Positive rheotaxis (turning to face the current, see YouTube video above for a visual) was broadly observed. Further, this kind of behavior increased with water velocity, and was consistent with smolts moving through the area more slowly than the mean flow velocity. It’s unclear whether fish face into the flow for feeding, to observe and respond to predators, or if they just like to feel the wind in their face. Diurnal variations in swimming also indicated greater positive rheotaxis or downward vertical migration during daylight hours, along with greater lateral swimming. Understanding these behaviors is a fundamental component of answering important questions of route selection and transit time of emigrating Chinook Salmon smolts.

Overall, we learned that Chinook salmon smolts are far from simple passengers riding the flow of the rivers and tides to the sea. This study showed that smolts actively swim along the way, often pointed into the current or traversing the river side-to-side, and generally at a pace less than half of their top speed. It also showed how novel technologies such as acoustic telemetry can be leveraged to study very old questions in fisheries, natural resource management, and even behavioral ecology. More studies that combine these technologies will give increasing comparative information on how salmon smolts behave in different rivers and junctions. These results will help managers understand how salmon will react to various proposed water infrastructure and operating decisions.

Rusty Holleman is a Senior Researcher in Civil and Environmental Engineering at the Center for Watershed Sciences at University of California, Davis. Ed Gross is a research Engineer in the Department of Civil and Environmental Engineering 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. Andrew Rypel is Co-Director of the Center for Watershed Sciences and a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis.

Further Reading

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.

Gross, E.S., R.C. Holleman, M.J. Thomas, N.A. Fangue, and A.L. Rypel. 2021. Development and evaluation of a Chinook salmon smolt swimming behavior model. Water 13(20) 2904.

Hause, C.L., G.P. Singer, R.A. Buchanan, D.E. Cocherell, N.A. Fangue, and A.L. Rypel. 2022. Survival of a threatened salmon is linked to spatial variability in river conditions. Canadian Journal of Fisheries and Aquatic Sciences In Press. bioRxiv preprint available: https://www.biorxiv.org/content/10.1101/2021.08.24.456882v1

Holleman, R. C., E.S. Gross, M.J. Thomas, A.L. Rypel, and N.A. Fangue. 2022. Swimming behavior of emigrating Chinook salmon smolts. PLoS ONE 17(3): e0263972. 

Lehman B, D.D. Huff, S.A. Hayes, S.T. Lindley. 2017. Relationships between Chinook Salmon Swimming Performance and Water Quality in the San Joaquin River, California. Transactions of the American Fisheries Society 146: 349–358.

Rypel, A.L., G. Singer, and N.A. Fangue. 2020. Science of an underdog: the improbable comeback of spring-run Chinook salmon in the San Joaquin River, https://californiawaterblog.com/2021/12/05/science-of-an-underdog-the-improbable-comeback-of-spring-run-chinook-salmon-in-the-san-joaquin-river/

Singer, G.P. 2019. Movement and survival of juvenile Chinook salmon in California’s Central Valley. Ph.D. Dissertation, University of California, Davis.

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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