A Swiss Cheese Model for Fish Conservation in California

by Andrew L. Rypel, Peter B. Moyle, and Jay Lund

We read with great interest Nicholas Chistakis’s piece outlining a “Swiss Cheese Model For Combating Covid-19” in the Wall Street Journal. Christakis presents a model for considering the individual steps needed to achieve a larger goal, and how each step should fit into a larger strategy. He points out that each action used to limit the spread of Covid (handwashing, mask wearing, social distancing) creates a layer of imperfect defense akin to a slice of Swiss cheese. No action alone is 100% effective – there are holes. Yet in combination, multiple layers of the Swiss cheese become increasingly effective in limiting virus spread. This powerful analogy might be applied to other problems, from drinking water quality to fish conservation.

The Swiss cheese respiratory pandemic defense model, as it appeared in the NY Times. Source: https://www.nytimes.com/2020/12/05/health/coronavirus-swiss-cheese-infection-mackay.html

Indeed in water engineering, the “multiple barriers approach” is already a common strategy, e.g., for removing chemicals during the reuse of water (Marron et al. 2019). The Canadian government adopts a multiple barriers approach to water quality, stating:

“the multi-barrier approach takes all of these threats into account and makes sure there are “barriers” in place to either eliminate them or minimize their impact. It includes selecting the best available source (e.g., lake, river, aquifer) and protecting it from contamination, using effective water treatment, and preventing water quality deterioration in the distribution system. The approach recognizes that while each individual barrier may be not be able to completely remove or prevent contamination, and therefore protect public health, together the barriers work to provide greater assurance that the water will be safe to drink over the long term.”

In other fields, the Swiss cheese concept is described as “multi-layered risk management” (Felthman-King and McLeod 2020). Here, parallel concepts are applied to reduce safety risks and other threats. For example, a multi-layered approach is typical in financial institutions to mitigate fraud risk. In other cases, multi-layered risk management is applied in strategic planning to optimize asset allocation and prevent unfavorable outcomes. The video below describes a six-layered approach to physically securing Google’s data center (similar videos are available on multi-layered approaches to digital security):

Multi-layered approaches are attractive to diverse fields and applications, whenever individual solutions are imperfect, but consequences of failure are dire. Perhaps most importantly, a Swiss cheese or multiple barriers approach recognizes that many problems lack “silver bullet” solutions. Rather they require strategic, coordinated and sustained effort. Focusing on only one layer improves the function of that one layer, but reduces investment in other protective actions, and so can increase overall risk of failure. The additive benefit of multiple layers of activity is key.

Why is this relevant to water?

California water issues are notoriously complicated by a massive diversity of users, ecosystems, applications and futures. Indeed, water in the Delta has been described as a “wicked problem” indicating that these problems cannot be ignored and defy straightforward characterization and solutions. Below we highlight how a Swiss cheese model might be applied to vexing long-term declines in native fish populations in California. Our blog this week follows a recent update on the status of Delta Smelt – the iconic fish careening towards extinction in the wild. And while the analogy to the classic Swiss cheese model as applied to Covid isn’t perfectly aligned (e.g., we’re not trying to limit the spread of just one thing), the general idea is important – multiple actions taken together matter. Further, although this blog focuses on fish conservation as a proof-of-concept, the Swiss cheese/multiple barrier management approach is applicable to many environmental problems.

A Swiss cheese model for conservation of California’s native fishes

California has a highly endemic fish fauna under high major risk of extinction in the next 50 years. 83% of native species are declining, and 5% of species (e.g., Bull Trout, Clear Lake Splittail, Thicktail Chub) are already extinct (Moyle et al. 2011). Yet while these trends have persisted for decades, there remains a lack of consensus statewide strategy for recovering the fauna.

Declining native fishes fundamentally threaten water reliability, particularly agricultural and urban water diversions. For example, the inability of existing regulations, habitat, and environmental flows to protect native fishes is leading the State Water Board to only further increase environmental flow requirements. Climate change is raising water supply uncertainty further in an already variable climate by increasing the frequency and duration of droughts. These realities point towards a future where fish populations and ecological function need to substantially recover in order to better support agriculture, cities, and diverse communities.

Here we propose some conceptual scaffolding for a statewide approach to conserve and recover fish populations. It is a six point plan that, in combination, should improve conditions for fishes in powerful ways.

Watershed conservation framework for natural lake fisheries in MN, from Jacobson et al. (2016).

Layer 1: Protect the best remaining habitats; restore others. California is fortunate to have some exemplary fish populations and habitats remaining. In some cases, fishes have very limited distributions (e.g., Eagle Lake Rainbow Trout or Clear Lake Hitch); so protecting the watersheds for these sensitive species is essential. In other cases, watersheds should be preserved for their unique productive capacity. The McCloud River was once one of the most productive trout and salmon fisheries in North America, with all four runs of Chinook salmon, in addition to anadromous steelhead and other native salmonids like McCloud Redband Trout. Watersheds like the McCloud should be preserved to the fullest extent possible to retain this outstanding productive capacity.

Decisions over “what to protect” might benefit from a decision support tool. Above is a useful tool developed by Jacobson et al. (2016) to support integrated lake watershed and fish management in Minnesota. In the model, lakes are classified into one of four categories: vigilance, protection, full restoration, and partial restoration. Classifying California watersheds into similar categories might improve decision making. Dam removals are essential tools for restorative actions. Beaver rehabilitations are also key.

Layer 2: Deploy some protection for every native species. Securing a safe place for every native species in California helps reduce further population collapses from climate change and other anthropogenic effects. California is in a position to consider protecting every native species because total fish species richness is comparatively low given the state’s large size. Nonetheless, to protect this broad range of habitats, much more habitat work is needed. This is especially true for recently described or previously ignored species (e.g., the California roaches). The emerging concept of “freshwater protected areas” draws from conservation successes with marine protected areas. An important recent study found that small, community-based freshwater reserves were effective for sustaining freshwater fish diversity and fisheries in Thailand (Koning et al. 2020); parallel approaches could help protect fishes and freshwater diversity in California.

Example set of fishes (the California Roach complex – left) in need of additional protection. The Red Hills Roach (right) has very specific habitat requirements, and was only recently described. Map and photos from Peter Moyle.

Layer 3: Implement and expand environmental flows below dams. Even though some dams have outlived their functionality and are being removed, many large and still functional dams remain. Re-operating this infrastructure to be more wildlife-friendly will be essential to conserving and restoring diversity and ecological function, particularly in the Central Valley (Börk and Rypel 2020). Coldwater releases from Shasta Dam are essential to preserving winter-run Chinook salmon in the Sacramento River. In many cases, providing flows for fish is the central consideration of restoration efforts. Putah Creek is a different type of example we highlight often on the California WaterBlog. In the 20 years following reoperation of Monticello Dam to prevent the creek from drying up, the fish community shifted from one dominated by nonnatives to one dominated by natives, including fall-run Chinook salmon (Keirnan et al. 2012; Jacinto 2020).

View below Shasta Dam on the Sacramento River, CA. Water from the dam is released through five 15-foot penstocks leading to the five main generating units. Coldwater releases from Shasta Reservoir into the river help to support juvenile winter-run Chinook salmon, an endangered ESU that oversummers in the system and requires cold waters to survive. Photo source: Wikicommons.org

The California Environmental Flows Framework is a holistic, science-based process to support resource managers, water agencies, and NGOs working to restore the health of California’s rivers. The approach is largely compatible with 2018 Water Board policy, especially if implemented in a flexible way that incorporates water budgets. We encourage additional work on how the Framework can be used in environmental programs across diverse settings. A important ingredient will be delivering flows to improve ecosystem functions, such as fish production. By developing understanding of links between environmental flows and production of native fish species and assemblages, scientists will be able to recommend flow regimes that broadly benefit fisheries.

Layer 4: Develop a water right for aquatic animals, including fishes. According to the State Water Resources Control Board a water right is:

“A legal entitlement authorizing water to be diverted from a specified source and put to beneficial, nonwasteful use. Water rights are property rights, but their holders do not own the water itself. They possess the right to use it. The exercise of some water rights requires a permit or license from the State Water Resources Control Board (State Water Board), whose objective is to ensure that the State’s waters are put to the best possible use, and that the public interest is served.”

California provides legal protections for fishes, notably through California Fish and Game Code Section 5937 (water for fish) which states that dam owners are responsible to at all times release the water necessary to provide and keep in “good condition” the downstream ecosystem, its fish and other aquatic life. The code was successfully applied through lawsuits that sought to return flows for fish to Putah Creek and the San Joaquin River. The response of the Putah Creek ecosystem to delivery of water for fish has been an overwhelming ecological success (Jacinto 2020). Putah Creek is now a model of the impact and power of environmental flows when applied to declining native California fishes.

Yet, does California Fish and Game Code Section 5937 go far enough in protecting native California fishes and aquatic ecosystems? For example, how are streams kept in “good condition” for fishes when dams and dam owners are not in play? A water right for aquatic animals would solve this large and important loophole. For example, minimum flows could be established based on best available science that clearly outlines thresholds of water needed to sustain species of interest. These thresholds are particularly important to monitor in times of water scarcity (droughts). 

Putah Creek as it flows out Monticello Dam and Berryessa Reservoir. Photo source: Wikicommons.org

Layer 5: Identify, manage, & rehabilitate floodplain ecosystems. Floodplains are essential to riverine ecosystems, particularly in California’s Central Valley. Historical accounts show the valley’s floor was once a sprawling seasonal wetland teeming with fish and wildlife. Most native fishes in the Sacramento-San Joaquin basins are adapted to use floodplains. Fortunately, some water control structures for the Sacramento Valley allow some floodplain processes to remain in the Yolo and Sutter Bypasses. Despite this, ~95% of the original Sacramento Valley floodplain has been lost.

Flooded Yolo Bypass outside of Sacramento during winter 2017. Photo source: USFWS/Steve Martarano. Downloaded from Wikicommons.org

The presence of bypasses in the Sacramento Valley has likely saved many native fishes. This includes some iconic species that you might not immediately consider floodplain specialists, such as juvenile Chinook salmon (Katz et al. 2017). Yet the importance of floodplain management for juvenile salmon in our rivers is clear (Sommer et al. 2001, Holmes et al. 2020, Jeffres et al. 2020, Sommer et al. 2020). We must learn to better leverage the remaining floodplain ecosystems. However, managing floodplains requires working with non-traditional conservation partners (e.g., rice farmers and local water managers) to maximize the conservation value of these lands for fishes. Developing conservation programs that incentivize growers to participate in fish conservation will be important. Complementary programs that promote flood extension (more water and for longer periods) will be critical. Finally, stringent protections for existing floodplains (e.g., in the Cosumnes River) and efforts to manage for fishes in these habitats also are needed. We note that this work must also include protection and restoration of tidal marshes and managed wetlands in the delta that may serve related functions (Aha et al. 2021).

Layer 6: Cultivate hatcheries and reservoirs as emergency refugia for native fishes. Because many California reservoirs have expansive coldwater habitats, we have previously suggested that reservoirs could serve as emergency refuges for declining native fishes. Some California reservoirs have developed self-sustaining populations of Chinook salmon (Perales et al. 2015). Such populations may be needed as a backup plan if a disease or other disturbance threatens principal salmon runs. Reservoirs that support declining native fishes could be prioritized for infrastructure repair processes and as a conservation rubric in re-licensing processes.

Final Thoughts

There is no unified plan with broad buy-in to guide fish conservation decisions in California, despite various efforts to do so. The State of the Salmonids II report highlights risks facing trout and salmon in the California (Moyle et al. 2017). The Delta Science Council regularly creates a Science Action Agenda to guide support for delta conservation management projects; however it is mostly limited in scope to the Delta. The recently released water resilience portfolio details many excellent aspects of water management that could help fish, but doesn’t deal with fish conservation explicitly. CDFW has various species and statewide management plans, but they often are not utilized by other agencies and conservation partners. An actual statewide strategy with broad consensus buy-in is missing. What we present in this blog isn’t a plan per se either; however perhaps some ideas presented here could be helpful in such an endeavor.

Successful organizations spend substantial time developing, refining, and gaining feedback on strategic plans to help guide their organizations. In the early 2000s, Apple developed a strategic plan for developing hardware to facilitate portable music for the consumer (i.e., the iPod). Similar visioning and strategic planning is needed for fish conservation in California. Such a plan requires broad buy-in from the various stakeholders, agencies, and NGOs in the environmental and water sectors. Anything developed by fiat will be doomed. Without a widely-supported statewide plan, agencies will continue to struggle to prioritize and identify the best work. In the meantime, fish and water reliability will continue to decline.

In summary, the future of fish conservation in California needs a multi-layered approach. We end by noting that, while we clearly favor many of the above suggestions, a plan that incorporates just some of these layers can make all actions more effective. The key is to develop and codify a plan, such that critical decisions can be made to allocate resources towards a successful direction. Without a plan – we remain adrift and without control over obtaining the outcomes we collectively seek.

The noble face of a native Sacramento Pikeminnow from Putah Creek near Davis, CA. Photo source: Andrew Rypel

Further Reading

Peer-reviewed papers

Aha, N.M., P.B. Moyle, N.A. Fangue, A.L. Rypel, and J.R. Durand. 2021. Managed wetlands can benefit juvenile Chinook salmon in a tidal marsh. Estuaries and Coasts, Published Online.

Börk, K., and A.L. Rypel. 2020. Improving infrastructure for wildlife. Natural Resources & Environment.

Felthman-King, T., and C. Macleod. 2020. Multi-layered risk management in under-resourced antenatal clinics: a scientific-bureaucratic approach versus street-level bureaucracy. 22: 31-52. 

Holmes, E.J., P. Saffarinia, A.L. Rypel, M.N. Bell-Tilcock, J.V. Katz, and C.A. Jeffres. 2020. Reconciling fish and farms: Methods for managing California rice fields as salmon habitat. BioRxiv Preprint available https://doi.org/10.1101/2020.08.03.234062.

Jacinto, E.E. 2020. Long-term rehabilitation of a native freshwater fish assemblage in California. MS Thesis, University of California, Davis.

Jeffres, C.A., E.J. Holmes, T.R. Sommer, and J.V.E. Katz. 2020. Detrital food web contributes to aquatic ecosystem productivity and rapid salmon growth in a managed floodplain. PLoS One 1: e0216019.

Katz, J.V.E., C. Jeffres, J.L. Conrad, T.R. Sommer, J. Martinez, S. Brumbaugh, N. Corline, and P.B. Moyle. 2017. Floodplain farm fields provide novel rearing habitat for Chinook salmon. PloS one 12(6): e0177409.

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.

Koning, A.A., K.M. Perales, E. Flute-Chouinard, and P.B. McIntyre. 2020. A network of grassroots reserves protects tropical river fish diversity. Nature 588: 631-635.

Marron, E.L., W.A. Mitch, U. von Gunton, and D.L. Sedlak. 2019. A tale of two treatments: the multiple barrier approach to removing chemical contaminants during potable water reuse. Accounts of Chemical Research 52: 615-622.

Moyle, P.B., J.V.E. Katz, and R.M. Quiñones. 2011. Rapid decline of California’s native inland fishes: a status assessment. Biological Conservation 144: 2414-2423. 

Moyle, P.B., R. Lusardi, and P. Samuel. 2017. SOS II: Fish in hot water. Status, threats and solutions for California salmon, steelhead and trout. 

Perales, K.M., J. Rowan, and P.B. Moyle. 2015. Evidence of landlocked Chinook salmon populations in California. North American Journal of Fisheries Management 35: 1101-1105.

Sommer, T., B. Harrell, M. Nobriga, R. Brown, P. Moyle, W. Kimmerer, and L. Schemel. 2001. California’s Yolo Bypass: Evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture. Fisheries 26: 6-16.

Sommer, T., B. Schreier, J.L. Conrad, L. Takata, B. Serup, R. Titus, C. Jeffres, E. Holmes, J. Katz. 2020. Farm to fish: lessons from a multi-year study on agricultural floodplain habitat. San Francisco Estuary and Watershed Science 18(3).

Web articles and germane reports:


NY Times Swiss cheese respiratory pandemic defense model.



Good biosecurity is multi-layered risk reduction.




A path forward for California’s freshwater ecosystems – PPIC Report

Making the most of water for the environment: a functional flows approach for California’s rivers – PPIC Report

Managing California’s water: from conflict to reconciliation – PPIC Report

Managing California’s freshwater ecosystems: lessons from the 2012-16 drought – PPIC Report

Cited California WaterBlog

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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