Schooling Fish: Behind the Scenes of Putah Creek Fish Sampling

By Christine A. Parisek, Peter B. Moyle, Joshua Porter, and Andrew L. Rypel

It’s a curious thing, teaching a classroom of future fish conservationists about revitalizing degraded ecosystems. Putah Creek was an unconventional place to teach ecology. After the creek turned bad, it stayed that way for decades – deteriorated habitat, nonexistent flow, garbage, rusted cars, even gravel mining. And while conditions have improved, many students, and even some scientists, still remain skeptical that this ecosystem could ever be anything but a spoilt ecosystem. Is it really possible to genuinely rehabilitate an ecosystem like that through improved management and community building? Those lessons work in other cases, for other ecosystems, but surely not this one. 

This blog explores the outcome of environmental stewardship over time, of patience and persistence that pays off, and of some extremely cool fishes you wouldn’t guess live in our local creek today. It’s a story that catches students, and even many members of the community, off guard. Those who have ties to the area, whether in growing up here or as UC Davis alumni, may vividly remember a time when the creek was a very different place.

Putah Creek Fish Sampling 

Professors Peter Moyle and Andrew Rypel introduce the Biology & Conservation of Fishes class to the start of a Putah Creek field trip. Photo by Christine Parisek.

On the crisp morning of November 4th, the UC Davis fish class (WFC 120) ventured on their annual field trip to Putah Creek, located just on the outskirts of campus. The most recent field trip expands a long-term student-generated dataset on Putah Creek spanning nearly 50 years. Students have spent most of this academic quarter learning about native and introduced fish species in California. A major goal of the course is cultivating an appreciation for the status of our fishes, and what we can do to protect them from extinction. Prior to this class, many of these students had never touched a fish before. The field trip is an opportunity to see local fish diversity up close, learn about our local watershed, and try a hand at different sampling methods. It is also a chance to tell the story of Putah Creek – a positive narrative about collaboration, team science, and diverse people uniting to successfully realize a shared vision.

Prickly sculpin (Cottus asper; Native). Left: Lateral view. Right: Dorsal view. Photo by Christine Parisek.
Sacramento sucker (Catostomus occidentalis; Native). Left: Ventral view showing the Sacramento sucker’s fleshy papillose suction-like lips. Right: Several Sacramento sucker in a well-aerated aquarium for the afternoon’s field trip demonstrations. Photo by Christine Parisek.

Class leaders and representatives from the East Bay Park District demonstrate a variety of active (shoreline seining, boat electrofishing, backpack electrofishing) and passive (gill nets, minnow traps, clover traps) sampling techniques for the students (under an approved Scientific Collection Permit and IACUC protocol). These data also support a reliable inventory of the fishes in the creek (e.g., Table 1). Some fishes are more or less likely to be captured via a particular method; thus we use a suite of tools for more robust data collection. Fishes caught during the trip are identified, counted, measured, and returned to the creek. A subset of unique fishes are kept in accessible well-aerated aquaria for students to observe up close during the day, and to use for practicing common measurements on fishes. In addition to the students, we often also get to chat with folks from the community passing by on their weekend jaunts. Another significant aspect of our collaboration with the East Bay Park District (EBPD) was that several of these collected fish, including many native fishes, went on to be incorporated into the EBPD Mobile Fish Exhibit and various visitor center aquariums in the East Bay; this has allowed EBPD to expand outreach and educate thousands of children (and adults) in the Bay area on the importance of native fish in California. We are especially grateful for the supportive and dedicated graduate students, research personnel, and East Bay Parks District representatives who help put on an experiential learning opportunity like this for the students every time – it truly takes a village!

Fish sampling in action during the Putah Creek field trip. Top left: Largemouth bass (Micropterus salmoides; Introduced). Top middle: Black crappie (Pomoxis nigromaculatus; Introduced). Top right: Sacramento sucker (Catostomus occidentalis; Native). Bottom left: Sacramento sucker (Catostomus occidentalis; Native). Bottom middle: Fall-run Chinook salmon  (Oncorhynchus tshawytscha; Native). Bottom right middle and bottom right: Class and community members gather to hold and learn about fish. Photos by Christine Parisek (top left, top middle, bottom right), Dave Ayers (bottom left, bottom middle, bottom right middle), John Durand (top right).
Passive and active fish sampling techniques in action. Top left: Seining. Bottom left: A group is boat electrofishing. Top right: Demonstrating a Sacramento sucker’s fleshy papillose lips. Middle right: A group gets ready to backpack electrofish. Bottom right: A group gathers around fish aquaria. Photos by Dave Ayers (top left), Christine Parisek (top and bottom right), and John Durand (bottom left, middle right).
Top left: Juvenile Sacramento pikeminnow (Ptychocheilus grandis; Native). Bottom left: Sacramento tule perch (Hysterocarpus traskii traskii; Native). Middle: Largemouth bass (Micropterus salmoides; Introduced). Top right: Black crappie (Pomoxis nigromaculatus; Introduced). Bottom right: Redear Sunfish (Lepomis microlophus; Introduced). Photos by Dave Ayers (bottom left) and Christine Parisek (others).

By now you may be thinking – Wait a minute, all these fishes can live Putah Creek? Salmon, too??!! I thought that place was a hole…

Ripple effects of reconciling ecosystems  

People are frequently shocked by the diversity of fishes in Putah Creek today. Yet in a landscape as heavily modified as California’s Central Valley, we often take for granted our ability to, with patience and persistence, improve the vibrancy of nature’s ecosystems. As the Tanzanian Proverb goes: “Little by little, a little becomes a lot.” 

For those that don’t know it – the Sacramento region historically had prolific salmon runs (Brown et al. 1994; Yoshiyama et al. 1998; Yoshiyama 1999). That is until dams, water diversions, and pollution significantly reduced habitat quality. In Putah Creek, humans ultimately desiccated the creek bed and, coupled with the construction of dams, quickly extirpated the anadromous fishes. Afterwards, the fish assemblage shifted to one dominated by invasive species. We often joke that even the cars couldn’t survive in the creek anymore (see below figure). Motivated by enforcement of California Fish and Game Code 5937, an Accord in 2000 prompted the creek be kept in better condition for fishes (see: Marchetti & Moyle 1995; Moyle et al. 1998). The Accord developed standards for minimum base flows, seasonal pulse flows, and a robust monitoring program in Putah Creek. With just 5% of flows returned to the creek, patience and persistence with nature, and stakeholder and community collaboration and commitment – rehabilitating the creek ecosystem transitioned from aspiration to reality. 

Putah Creek at 2 locations before and after the Accord. Photographs <2018 by Peter Moyle and ≥2018 by Emily Jacinto. Figure adapted from Jacinto et al. 2023.

Reconciled ecosystems like Putah Creek gain the ecological benefits from restoration interventions but also continue to support human needs (e.g., recreation, agriculture, cities). And there is no going back in time for Putah Creek. The creek is so deeply incised from years of poor land management that very little of the historical riparian ecosystem remains. It bears little resemblance to what it once did historically and it would be functionally impossible to engineer it back to that state. Yet through science-based management, we can approximate conditions that on the whole are good for native species. Managing in this general direction improves the ecosystem slowly, and over time, ecological processes begin to heal. The creek now has a regularly returning salmon run whose numbers appear to be growing, and improvements to the bird community are apparent too (See: Dybala et al 2018; Chapman et al. 2018; Rypel 2022; Jacinto et al. 2023b). 

Dr. Andrew Rypel holds an adult Chinook salmon (Oncorhynchus tshawytscha) that was making its way up Putah Creek during the 2023 fall field trip. Photo by Dave Ayers.

And this year marked the first time ever that an adult Chinook salmon Oncorhynchus tshawytscha was caught on the annual class field trip. The return of salmon to Putah Creek means a lot to the community, to cultural values, and to ecosystem services. The creek also means a lot to the UC Davis community. It is amazing that the university now has a run of Chinook salmon in its own backyard. Past decades of students from WFC 120 are noticing the change too, and it is heartening that we are all able to witness tangible evidence of the benefits of proactively managing this reconciled creek patiently and persistently. This is a tribute to a long list of concerned citizens, scientists, and managers who worked tirelessly for the creek over the years. 

Just imagine if there were more reconciled ecosystems managed and acting as natural labs like Putah Creek, scattered all over the state, each one once again serving its ecosystem function and in doing so reminding us all of the invaluable lesson that little by little, a little becomes a lot. Small changes that we have control over can make a big impact, and we shouldn’t take that for granted. Students from the class have gone off to become leaders in the California water and environmental communities. Others have become professors and scholars in other parts of the world. It is an important example for all of us to see in how to translate science into practice.

Christine A. Parisek is a Ph.D. candidate in the Graduate Group in Ecology at UC Davis and a science communications fellow at the Center for Watershed Sciences. Peter B. Moyle is an emeritus professor in the Center for Watershed Sciences, University of California, Davis. Joshua Porter is currently a Fisheries Biologist, focusing on angler education, with the Louisiana Department of Wildlife & Fisheries and was previously an Aquatic Exhibits & Fisheries Resource Analyst with the East Bay Parks District in California. Andrew L. Rypel is a professor of Wildlife, Fish, & Conservation Biology and Director of the Center for Watershed Sciences at the University of California, Davis.

Students from the 2023 fish class holding various fish during the field trip. Photo by Dave Ayers.
Class photo from the 2023 field trip to Putah Creek, California. Photo by Dave Ayers.
Left: Green sunfish (Lepomis cyanellus; Introduced.). Right: Bluegill sunfish (Lepomis macrochirus; Introduced).

Table 1. Fish species typically observed or collected during the Putah Creek class field trip. Take a look at their profiles on the UC-ANR California Fish website!

Native Fishes
Fall-run Central Valley Chinook Salmon (Oncorhynchus tshawytscha)
Central Valley Steelhead (Oncorhynchus mykiss); present in the system but not during the Fall field trip. 
Sacramento Tule Perch (Hysterocarpus traskii traskii)
Sacramento Sucker (Catostomus occidentalis occidentalis)
Sacramento Speckled Dace (Rhinichthys osculus subspecies)
Sacramento Pikeminnow (Ptychocheilus grandis)
Sacramento Perch (Archoplites interruptus)
Prickly Sculpin (Cottus asper subspecies)
Pacific Lamprey (Entosphenus tridentata)
Introduced Fishes
Spotted Bass (Micropterus punctulatus)
Largemouth Bass (Micropterus salmoides)
Smallmouth Bass (Micropterus dolomieu)
Mississippi Silverside (Menidia beryllina subspecies)
Mosquitofish (Gambusia affinis)
Goldfish (Carassius auratus)
Common Carp (Cyprinus carpio)
Green Sunfish (Lepomis cyanellus)
Bluegill Sunfish (Lepomis macrochirus)
Redear Sunfish (Lepomis microlophus)
Brown Bullhead Catfish (Ameiurus nebulosus)
Black Bullhead Catfish (Ameiurus melas)
Channel Catfish (Ictalurus punctatus)
White Crappie (Pomoxis annularis)
Black Crappie (Pomoxis nigromaculatus)
Bigscale Logperch (Percina macrolepida)
* The sampling methods described in this blog are under an approved Scientific Collection Permit and IACUC protocol. Fishes are identified, counted, measured, handled with love, and returned to the creek. Before you fish, it is always a good idea to check your local fishing regulations.

Further Reading – Understanding Putah Creek (Reverse Chronological Order)

Jacinto, E., Fangue, N.A., Cocherell, D.E., Kiernan, J.D., Moyle, P.B. and Rypel, A.L., 2023a. Increasing stability of a native freshwater fish assemblage following flow rehabilitation. Ecological Applications, p.e2868.

Jacinto, E., N.A. Fangue, D.E. Cocherall, J.D. Kiernan, P.B. Moyle, and A.L. Rypel. 2023b. Putah Creek’s rebirth: a model for reconciling other degraded streams? California WaterBlog. 

Rypel, A.L. 2023. Facing the Dragon: California’s Nasty Ecological Debts. California WaterBlog. 

Rabidoux, A., M. Stevenson, P.B. Moyle, M.C. 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. California WaterBlog. 

Rypel, A.L. 2022. Being patient and persistent with nature. California WaterBlog. 

Rypel A.L., P.B. Moyle, and J. Lund. 2021. A Swiss Cheese Model for Fish Conservation in California. California WaterBlog.

Willmes, M., Jacinto, E.E., Lewis, L.S., Fichman, R.A., Bess, Z., Singer, G., Steel, A., Moyle, P., Rypel, A.L., Fangue, N., Glessner, J.J., Hobbs, J.A. and Chapman, E.D. 2021. Geochemical tools identify the origins of Chinook Salmon returning to a restored creek. Fisheries 46:22-32. 

Willmes M., A. Steel, L. Lewis, P.B. Moyle, and A.L. Rypel. 2020. New insights into Putah Creek salmon. California WaterBlog. 

Moyle, P.B. 2020. Crawdads: Naturalized Californians. California WaterBlog. 

Chapman, E., E. Jacinto, and P.B. Moyle. 2018. Habitat Restoration for Chinook Salmon in Putah Creek: A Success Story. California WaterBlog. 

Dybala, K.E., Engilis, A., Trochet, J.A., Engilis, I.E. and Truan, M.L., 2018. Evaluating riparian restoration success: long-term responses of the breeding bird community in California’s lower Putah Creek watershed. Ecological Restoration, 36(1), pp.76-85.

Moyle, P.B. 2017. What do stream fish do during flood flows? California WaterBlog. 

Tilcock, M. 2016. The Horror of a Salmon’s Wheel of Misfortune. California WaterBlog. 

Moyle, P.B. 2015. Salmon finding a home in my backyard – Could it be? California WaterBlog. 

Austin, C. 2014. Reconciling ecosystem and economy. California WaterBlog. 

Grantham, T., and P.B. Moyle. 2014. Flagging problem dams for fish survival. California WaterBlog. 

Börk, K.S.  J. F. Krovoza, J. V. Katz, and P. B. Moyle. 2012. The rebirth of California Fish & Game Code 5937: water for fish. University of California Davis Law Review 45: 809-913. 

Kiernan, J.D., Moyle, P.B. and Crain, P.K., 2012. Restoring native fish assemblages to a regulated California stream using the natural flow regime concept. Ecological Applications, 22(5), pp.1472-1482.

Marchetti, M. P., and P. B. Moyle.  2001Effects of flow regime on fish assemblages in a regulated California stream. Ecological Applications 11:530-539. 

Marchetti, M. P., and P. B. Moyle. 2000Spatial and temporal ecology of native and introduced fish larvae in lower Putah Creek, California. Environmental Biology of Fishes 58:75-87.

Yoshiyama, R.M., 1999. A history of salmon and people in the Central Valley region of California. Reviews in Fisheries Science, 7(3-4), pp.197-239.

Yoshiyama, R.M., Fisher, F.W. and Moyle, P.B., 1998. Historical abundance and decline of chinook salmon in the Central Valley region of California. North American Journal of Fisheries Management, 18(3), pp.487-521.

Moyle, P.B., Marchetti, M.P., Baldrige, J. and Taylor, T.L., 1998. Fish health and diversity: justifying flows for a California stream. Fisheries, 23(7), pp.6-15.

Marchetti, M. and Moyle, P., 1995. The case of Putah Creek: Conflicting values complicate stream protection. California Agriculture, 49(6), pp.73-78.

About Christine Parisek

Christine A. Parisek is a Ph.D. candidate in the Graduate Group in Ecology at UC Davis and a science communications fellow at the Center for Watershed Sciences. Website:
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3 Responses to Schooling Fish: Behind the Scenes of Putah Creek Fish Sampling

  1. Joseph Buckley says:

    This is such great work. There are many streams around California that could benefit from having similar programs. Some even in the other college towns. The long-term collections in Putah Creek dating back to early Moyle days truly is special. So glad to see it has continued strong.

  2. Jeffery Williams says:

    Where can we view the longitudinal data for the species abundance and size?

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