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

By Emily Jacinto, Nann A. Fangue, Dennis E. Cocherell, Joseph D. Kiernan, Peter B. Moyle, and Andrew L. Rypel

Putah Creek is an aquatic ecosystem embedded within a truly human-dominated landscape. Photo of Lower Putah Creek near Davis CA, January 2011 (photo credit: Peter Moyle).

It’s hard to look at native fishes in Putah Creek and not grin a little. Be it a Sacamento Pikeminnow (below), a Sacramento Sucker, a Tule Perch, or even a Chinook Salmon – Putah Creek has become a treasured resource in our local community. The stream and its riparian areas are a nature refuge for local residents, a field site for teaching students, and increasingly a science lab for studying restoration.

A native Sacramento Pikeminnow captured from Putah Creek. Photo credit: Andrew Rypel

As often discussed on this blog, California’s freshwater ecosystems face numerous challenges due to human activities (Moyle and Rypel 2023, Rypel and Moyle 2023, Rypel 2023). These are not just California problems, they are global problems, especially in regions that share our Mediterranean style climate. Putah Creek exemplifies the scope and challenges of human pressures on the environment. It is a reconciled stream tucked into a landscape fully dominated by humans (above picture). In this blog, we delve into results from our recent paper (Jacinto et al. 2023). The paper expands on those of Keirnan et al. 2012 and examines trends in the Putah Creek fish assemblage since the 1990s. It shows the multiple ways in which the assemblage has improved following implementation of the Putah Creek Accord, and suggests similar strategies could be used to recovering ecological capacity in other degraded streams.

Damming and Draining Putah Creek

In 1957, a large capacity dam (Monticello Dam, below left) was constructed on Putah Creek. The dam dramatically transformed the natural flow regime, channel structure, geomorphic processes, and overall ecological character of the stream. In addition, a diversion dam (Putah Creek Diversion Dam, below right) was constructed ~13km downstream from Monticello Dam that diverts flows into a canal for use in agriculture and urban areas. Over time, a reduction in downstream flows, particularly during summer months, resulted in an aquatic assemblage completely dominated by warm-water nonnative species. Meanwhile, native species struggled to survive and were relegated to subordinate roles. Anadromous fishes, such as Chinook salmon, which were once present, but in variable numbers (Shapovalov 1947), were extirpated. During the 1990s, the creek regularly dried for prolonged periods because of lack of flow releases and drought.

An Accord for Ecosystem Rehabilitation

Recognizing the massive ecological degradation caused by reduced flows below the dams, a court-mediated Accord was ratified in 2000. The Accord stemmed from a lawsuit (Putah Creek Council vs. Solano Irrigation District and Solano County Water Agency, Sacramento Superior Court Number 515766) that was filed to provide a more natural flow regime under Section 5937 of the California Fish and Game Code which requires that fish populations below dams be kept in “good condition” (Börk et 2012; Moyle et al. 1998). The Accord aimed to restore a more natural flow regime that specifically benefited native and anadromous fish species. At the time, legal issues focused on keeping the creek from drying, developing spring flows for native fish (which are needed for spawning and for dispersal and survival of juveniles), creating fall attraction flows for spawning Chinook salmon, and generating high flows to displace nonnative fish and to promote natural channel processes. Implementation of the Accord marked a significant turning point in the rehabilitation of the creek.

How has the Putah Creek Assemblage Changed Over Time?

Number of native and nonnative fish species have changed over time in Putah Creek. Upstream sites (A-D) have seen major declines in nonnative (gold) and no change or increases in native species (blue). Downstream sites (E-F) have largely remained unchanged. Initiation of the Accord is indicated by a vertical line.

Since the 1990s, researchers have collected standardized fish community data at a series of sites along the longitudinal profile of Putah Creek. To assess the long-term effects of the restoration, we analyzed the full comprehensive dataset spanning pre- and post-Accord years. In particular, we focused on the numbers of native and nonnative species and overall stability of the ecosystem.

Analyses revealed compelling results that generally highlight success and limitations of the approach. Richness of nonnative species consistently declined at every monitoring site following the implementation of the Accord. In contrast, native species richness either increased or remained stable over time. Notably, the most upstream sites demonstrated the strongest recovery of native species richness, with all upstream sites surpassing nonnative richness over time. Yet in more downstream reaches, the recovery rate of native species decreased.This finding suggests recovery of the native assemblage was more pronounced closer to flow releases and habitat rehabilitation activity.

Rank-abundance curves showed that species evenness (inequality) remained low throughout the study. Therefore, stream rehabilitation activities did not change the underlying assembly dynamics of the fish community. Rather, it reordered the species to be increasingly dominated by natives than nonnatives. And again, there was a notable shift in dominance from nonnative to native species in the upstream sites, coinciding with more intensified rehabilitation efforts.

Rank-abundance curves describe many key aspects of ecological community dynamics, including richness (number of species) and evenness (slope of the curve). In this figure, rank–abundance curves are shown for every site across time – each year is presented by a single curve. We show that proportional abundance changed for native (solid blue circles) versus nonnative (solid orange circles) species (Panels A-F, left). The center (b) and right (c) panels show the same curves, but highlight two native (Rainbow Trout = solid blue circles and Prickly Sculpin = solid green circles), and two nonnative (Largemouth Bass = solid orange circles and Common Carp = solid red circles) species. Initiation of restorative flows from the Accord is indicated by a gray vertical line.
Mean rank shifts, a measure of ecosystem stability, have declined over time. Thus, Putah Creek is becoming an increasingly stable fish assemblage.Again, initiation of the Accord is indicated by a vertical line.

Finally, we document another encouraging finding – increased stability (=less variability) in the assemblage over time. Mean rank shifts in abundance, which measures variability in species ranks, decreased over the years, indicating a more stable and balanced ecosystem with time. This shift towards greater stability is attributed to the increasing dominance of native species; however the exact mechanisms for the stability remain unclear and worth further study.

Putah Creek as a Model for Recovering Ecological Functions

Adult Chinook salmon ascending Putah Creek, late fall 2022. Photo: Anne Boyd.

The rebirth and recovery of Putah Creek stands as a compelling model for others seeking to enhance the functionality of degraded freshwater ecosystems. Perhaps of most public attention was the return of anadromous salmon to the system circa 2015 (Willmes et al. 2020, Willmes et al. 2021). Thus while salmon numbers decline and crash across the Pacific Rim, in Putah Creek, salmon numbers appear to be increasing. Combined with the fish assemblage story outlined here, these lines of evidence suggest something quite positive has indeed occurred.

By prioritizing native species and implementing measures to recover key aspects of natural flow regimes, rehabilitation efforts in Putah Creek have been successful. These changes functionally reversed a dominance by nonnative species and bolstered recovery of native fishes. Similarly degraded stream ecosystems abound in California. And some streams (e.g. the Kern River in Bakersfield) still run dry even though these streams are still below dams and subject to California Fish and Game Code 5937. What is perhaps most stunning is the extent of ecological changes that occurred with just a marginal improvement in flows. 95% of flows in Putah Creek are still diverted for human use. Thus, the change described here represents that which can be done with only 5% of flows. Just imagine how our ecosystems would respond with more! These findings suggest there is much that can be accomplished with an environmental flows approach (Yarnell et al. 2015), and perhaps the voluntary agreements, if executed thoughtfully.

Putah Creek between Davis and Winters CA. Photo: Andrew Rypel

Emily Jacinto was a graduate student at UC Davis and is now an Environmental Scientist with California Department of Fish and Wildlife. Nann Fangue is a Professor and Chair of the Department of Wildlife, Fish & Conservation Biology at University of California, Davis. Dennis E. Cocherell is a Lab Manager and Staff Research Associate in Wildlife, Fish, and Conservation Biology at the University of California, Davis. Joseph Kiernan is a Research Scientist at NOAA based at the Southwest Fisheries Science Center. Peter B. Moyle is a Distinguished Professor Emeritus at the University of California, Davis and is Associate Director of the Center for Watershed Sciences. Andrew L. Rypel is a Professor of Wildlife, Fish, and Conservation Biology and Director of the Center for Watershed Sciences at the University of California, Davis.

Further Reading:

Börk, K., J. Krovoza, J. Katz, and P. Moyle. 2012. The Rebirth of California Fish & Game Code Section 5937: Water for Fish. University of California Davis Law Review 45: 809–913.

Collins, S.L., M.L. Avolio, C. Gries, L.M. Hallett, S.E. Koerner, K.J. La Pierre, A.L. Rypel, E.R. Sokol, S.B. Fey, D.F.B. Flynn, S.K. Jones, L.M. Ladwig, J. Ripplinger, and M.B. Jones. 2018. Temporal heterogeneity increases with spatial heterogeneity in ecological communities. Ecology 99: 858-865.

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: e2868.

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:

Marchetti, M. P., and P. B. Moyle. 2001. Effects of flow regime on fish assemblages in a regulated California stream. Ecological Applications 11: 530–9.

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

Moyle, P.B., and A.L. Rypel. 2023. Monster fish: lessons for sturgeon management in California. https://californiawaterblog.com/2023/05/14/monster-fish-lessons-for-sturgeon-management-in-california/

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. https://californiawaterblog.com/2022/04/24/the-putah-creek-fish-kill-learning-from-a-local-disaster/

Rypel, A.L. 2023. Facing the dragon: California’s nasty ecological debts. https://californiawaterblog.com/2023/06/11/facing-the-dragon-californias-nasty-ecological-debts/

Rypel, A.L., and P.B. Moyle. 2023. Hatcheries alone cannot save species and fisheries. https://californiawaterblog.com/2023/04/30/hatcheries-alone-cannot-save-species-and-fisheries/

Shapovalov, L. 1947. Report on Fisheries Resources in Connection with the Proposed Development of the United States Bureau of Reclamation. California Fish and Game 33: 61–8.

Willmes, M.,  E.E. Jacinto, L.S. Lewis, R.A. Fichman, Z. Bess, G.P. Singer, A. Steel, P.B. Moyle, A.L. Rypel, N.A. 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: 22-32.

Willmes, M., A. Steel, L. Lewis, P.B. Moyle, and A.L. Rypel. 2020. New insights into Putah Creek salmon. https://californiawaterblog.com/2020/10/18/new-insights-into-putah-creek-salmon/

Yarnell, S. M., G. E. Petts, J. C. Schmidt, A. A. Whipple, E. E. Beller, C. N. Dahm, P. Goodwin, and J. H. Viers. 2015. Functional flows in modified riverscapes: hydrographs, habitats and opportunities. Bioscience 65: 963–72.

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

  1. Ricardo Amon says:

    thanks for the research effort to document the improvements made to Putah creek over the past decades. i would like to know more about the role that Putah Creek plays in recharging the west Davis aquifers, and how silt built up can limit recharge rates and if there are efforts to further remove silt from the creek beds? gracias, Ricardo Amon

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