Two-way thinking in natural resource management

By Andrew L. Rypel

“I have more confidence in the ability of institutions to improve their thinking than in the ability of individuals to improve their thinking” ~Daniel Kahneman

It is long recognized that there are two dominant modes of thinking (Glatzeder 2011). New research and empirical data support the elemental interplay between these modes in our behavior, summarized in the book Thinking, Fast and Slow by Nobel Prize winning economist Daniel Kahneman. These two modes or systems of thinking are dynamic and influence our behavior in a vast variety of subtle and less so ways. System 1 is ‘fast’ and intuitive, operating almost unconsciously, and relies on learned associations. It is tempting to rely on this mode for decisions that must be made quickly. The problem is that this mode is often wrong. System 2 by contrast uses reason, and the slow process of reasoning. Immanuel Kant wrote“All our knowledge begins with the senses, proceeds then to the understanding, and ends with reason. There is nothing higher than reason.” Yet reason and System 2 require deliberate focused effort, and training to get better at. It is ‘slow’. The enlightenment was fueled largely by a growing appreciation for System 2. System 2 thinking is also endemic to science and the scientific method which developed as a way of using reason and rational thought. This is the system used to conduct what is now colloquially and increasingly referred to as ‘deep work’. Sadly many of us, while claiming to rely extensively on System 2, in fact spend most of our time in System 1. A prime example is our politics. How often are any of us swayed by excellent arguments from the other side, even following a rational debate?

The question for this blog is: Can Kahneman’s ideas be applied to group decisions, and thus to natural resource management? It’s a bit murky, but there are clues, and I have some thoughts. In Thinking, Fast and Slow  Kahneman was clearly writing about the combination of the two systems in each person – not groups of people. Yet it seems plausible that a well-managed team of people could avoid the excesses and extract the best elements of thinking from each system. But, different teams of people invariably have different mixes of System 1- or 2-leaning thought. Further, the appropriate mix of thinking needed for each environmental problem may differ, and change over time. 

Reflecting on the usefulness and practicality of both systems of thinking is probably universally helpful. This exercise is an example of ‘metacognition’, which can be defined generally as: thinking about how you think. Metacognition is a high order abstraction that might help us personally, but also collectively as team members or leaders in organizations. System 1 is needed to make timely decisions and prevent gridlock and lack of progress. It is the system in which we spend most of our time, and there is a reactive ease to its use. But this system has inherent flaws and is vulnerable to poor judgment. Humans generally avoid decisions perceived as risky because of loss aversion, which has evolutionary foundations. Thus, we often default towards safe and familiar decisions, even when a riskier choice might be better. System 2 can help reduce loss aversion (by better thinking through the pros and cons of a decision), provided there is enough time, and often the best available science. It is increasingly clear that Kahneman himself believes group decisions can be improved, primarily through slower processes and better decision making structures (see above opening quote to this blog found in this recent piece).

Fig. 1. Idealized natural resource management system adapted from Nielson 1999

Potential applications to natural resource management

Natural resource management, including water management, balances the needs of organisms, ecosystems and people (Fig. 1). Effective management occurs at the nexus of all three areas. Yet because many resource agencies are political, there are discrete time pressures on decisions. This could be because elected and appointed leaders hold power for only short periods, laws and regulations change alongside attitudes, political circumstances favor or preclude decision-making, or because an ecosystem or resource is collapsing in front of us. The time-sensitive nature of these decisions makes resource management agencies vulnerable to biases and issues associated with both thinking systems. Quality resource management might therefore hinge on a general ability to balance Systems 1 and 2 thinking.

It remains unclear how most extant water or conservation organizations lean disproportionately towards System 1 or 2 thinking. One might argue that, given their famously grinding speed, government organizations rely overly on System 2, perhaps to prepare for politically-opportune times or to avoid the controversy of actually making decisions. However, there are also abundant examples of government decisions being made rashly and without the time needed to fully appreciate key dynamics. The private sector ostensibly seems to favor System 1 for its faster decision-making and links to constantly changing financial markets. Yet it is also clear that most folks staking large sums of private capital on a venture extensively reason the issue from multiple angles before a risky decision. 

The value of two-way thinking

There is usefulness to both systems. Do we appreciate the value of both systems and find ways to organize and challenge ourselves and our organizations for the missing piece? For example, we need to organize our science and policy-makers to spend time on problems and solutions well in advance of short political windows of decision-making opportunity. This implies a need for greater organization of science syntheses to continually prepare policymakers for the types of decisions they will need to make over their tenure. Scheffer et al. 2013 articulates another undervalued benefit, specifically to slow decision making. That is, that many breakthroughs come outside the confines of the traditional workplace. By supplying enough time, stronger decisions might emerge through simple activities like dog walks, bowling adventures, or picnics where novel thoughts and conversations might take place. Can organizations and leaders deliberately generate the space for unstructured conversations and serendipity? Can this lead towards new compromises? New conservation and business successes? A recent survey of CEOs found that dealing with complexity was often identified as the greatest institutional challenge (Kleiman 2011). The CEOs then identified several directions for overcoming rising complexity; this included increasing creativity, increasing dexterity, and improving customer relationships. Yet budgeting time for developing these skills or encouraging person-to-person interactions are rarely prioritized in strategic plans or time planning exercises.

In many natural resource organizations, it probably helps to have people highly skilled in System 2 thinking. There are good reasons for System 1 thinking, but too often, it is simply wrong, and bad decisions can be avoided with a slower process. Perhaps there is not enough time to develop full blown science studies on a topic. Nonetheless, can we quickly summarize and synthesize previous scientific information from similar enough work to infuse elements of System 2 thinking into fast decision making? This is an advantage to having in-house science bureaus or R&D arms in organizations. And also a sad aspect to their (often hyperpolitical) demise. It is a challenge to have System 2 ecosystem management in a System 1 political world. 

Conversely, are there examples where we ‘research topics to death’? Clearly, the answer is yes. Perhaps what we really want is the ability to make decisions with System 2 thoroughness but with closer to System 1 speed. In California, we know the Sacramento-San Joaquin Delta is in a prolonged state of decline and the status quo is not working – at best. Time is increasingly limited before more species go extinct. More research along the lines of the last 40 years is unlikely to yield novel breakthrough information and abate the trajectory. More research is always needed, but more decisions are also needed – if they are the right decisions. However, it is challenging, especially given the ever-changing mix of system thinking needed for each problem and through time. This disorientation contributes to our bad intuition about probability, poor perception of time, and faulty decisions overall (Nowotny 2016). 

What can we do about all this?  Well, the adaptive cycle of natural resource management might be inevitable. We will need to experiment – a lot – and build on things that seem to work. Lund (2022) provides an overview for ‘rational water planning’, which is simply an in-depth look at one kind of System 2 approach. We can learn from prior experiments, even if they produced negative or null results. Large experiments, likely perceived to be ‘risky’, probably have a better chance at saving our California biodiversity, and to some extent us. To accomplish this, we will need well-trained scientists and managers skilled in System 2 to help design and monitor the great experiments of the future. We also need leaders unafraid and supported enough to pull the trigger on changing the status quo in a timely manner (i.e., those with an appreciation for the need to exercise System 1). Finally, we should expect the unexpected – and be prepared to try new experiments when the last great thing fails. 

Bog wetlands in the fall. Photo by 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 Co-Director of the Center for Watershed Sciences.

Acknowledgements: I thank Jay Lund and Steve Carpenter who provided thoughts and comments on earlier versions of this essay.

Further Reading:

Glatzeder, B. 2011. Two modes of thinking: evidence from cross-cultural psychology. pp 233-247 in S. Han and E. Poppel, eds Cultural and neural frames of cognition and communication: on thinking. Springer, Berlin, Germany.

Kahneman, D. 2013. Thinking Fast and Slow. Farrar, Straus and Giroux, New York, NY USA.

Kleiman, P. 2011. Learning at the edge of chaos. SISHE-J: The All Ireland Journal of TEaching and Learning in Higher Education 3: 62.1-62.11.

Lund, J. 2022. Approaches to water planning.

Newport, C. 2016. Deep Work: Rules for Focused Success in a Distracted World. Grand Central Publishing, New York, NY USA.

Nielson, L. A. 1999. History of inland fisheries management in North America. Pages 3-30 in C. C. Kohler, and W. A. Hubert, editors. Inland Fisheries Management in North America. American Fisheries Society, Bethesda, MD USA.

Nowotny, H. 2016. The Cunning of Uncertainty. Wiley, Hoboken, NJ USA.

Rypel, A.L., P.B. Moyle, and J. Lund. 2021. A swiss cheese model for fish conservation in California.

Scheffer, M., J. Bascompte, T.K. Bjordam, S.R. Carpenter, L.B. Clarke, C. Folke, P. Marquet, N. Mazzeo, M. Meerhoff, O. Sala, and F.R. Westley. 2013. Dual thinking for scientists. Ecology and Society 20: 3.

Understanding noise in human judgements

Posted in Uncategorized | 2 Comments

The Great Lakes and Invasive Species

This week’s CaliforniaWaterBlog post is an excerpt (Box 1) from a recent Delta Independent Science Board report on non-native species and the California Delta.  This excerpt summarizes the experience of the Great Lakes, and how its physical and ecological management has led to waves of profoundly disruptive species invasions, resulting in a sequence of “novel” ecosystems.  This sequence of invasions seems likely to continue to shape the Great Lakes.  This history is a wake-up and warning for policymakers and those working on California’s Delta.  Dan Eagan’s 2018 book is an excellent and readable history of these cyclic invasions and attempts to manage and cultivate them.

The Great Lakes are one of the most well-studied and invaded ecosystems in the world. Nearly every aspect of management is impacted by invaders (Egan 2018). The Great Lakes’ aquatic ecosystem developed following the last Ice Age by the recession of continental glaciers. Native species evolved from remnant populations in local and regional streams and a few that swam upstream. The Great Lakes’ topography, particularly Niagara Falls, limited species introductions to the upper Great Lakes until commercial navigation expanded in the early 1800s with the construction of New York’s Erie Canal and the Welland Canal that linked the lower Great Lakes to the upper Great Lakes.

Among these invasive species was the sea lamprey (Petromyzon marinus), which spread through the Great Lakes over several decades and depleted native predators particularly the lake trout (Salvelinus namaycush), which lacked any defenses. After years of scientific study, it was found that sea lamprey could be suppressed (but not eliminated) by treating specific stream reaches with a species-specific poison at specific times of the year when they were most vulnerable. Sea lamprey populations were reduced by about 90%, but control efforts continue, costing more than $20 million annually (Kinnunen 2018).

The herring-like alewife (Alosa pseudoharengus) also entered the Great Lakes, replacing intermediate species in the food web. With sea lamprey suppressing native predators, alewife boomed so high, they experienced massive annual die-offs that had to be removed from Chicago beaches by bulldozers. Commercial fishing began on alewife. To further help control the alewife population, several species of Pacific salmon (Oncorhynchus spp.) were introduced (Parsons 1973). Salmon survived well in the Great Lakes and triggered a massive sports fishery that bought billions of dollars annually to the Great Lakes. Annual stocking of (non-native) salmon raised in hatcheries became a major fisheries management priority and now stocking rates are tied to the production of its main prey, the non-native alewife.

The opening of the Saint Lawrence Seaway eventually brought larger, faster commercial ships and their ballast water to the Great Lakes, resulting in the new introduction of a wide range of species. Most notably, the introduction of zebra mussels (Dreissena polymorpha) to the Great Lakes in the late 1980s is considered the poster child of a successful invader. It has had profound impacts on the ecology and economy of the Great Lakes that range from clogging of water intakes for drinking and water-power operations (estimated costs into the billions) to loss of native clams to the decimation of primary production and disrupted food webs including the salmon recreational fishery. Interestingly, the invasion of the Great Lakes by zebra mussels was predicted more than a century before, based on shipping connections between the Great Lakes and areas where the mussel was well established (Carlton 1991). Quagga mussels (Dreissena rostriformis bugensis) invaded a few years later and have largely out-competed zebra mussels throughout the deeper portions of the Great Lakes. Both mussels have since spread throughout much of the Midwest and well into the west including California, Nevada, and Texas.

There is now concern about further invasions, including the movement of several Asian carp species (Cyprinus spp.) up the Mississippi River to the Great Lakes through the Chicago Sanitary and Ship Canal.

At each stage in this continuing history, local and regional interests and different state, provincial, national governments, and international bodies have acted, often out of necessity to manage these ecosystems or control major pathways such as ship ballast water. Management efforts to control invaders once established have been very limited. The entire Great Lakes ecosystem has been transformed by invasive species.


Carlton, J. (1991). Predictions of the arrival of the zebra mussel in North America. Dreissena Polymorpha Information Review, 2:1.

Delta Independent Science Board (2021), The Science of Non-native Species in a Dynamic Delta, Delta Independent Science Board, Sacramento, CA.

Egan, Dan (2018), The Death and Life of the Great Lakes, W. W. Norton & Company, 384 pp.

Kinnunen, R. (2018). Great Lakes sea lamprey control is critical. Michigan State University Extension, Michigan State Sea Grant.

Parsons, J.W. (1973). History of Salmon in the Great Lakes, 1850 – 1970. Technical Paper 68. U.S. Bureau of Sport Fisheries and Wildlife, Great Lakes Science Center.

Posted in Uncategorized | 1 Comment

Follow the Water!

by Jay Lund

People often have strange ideas about how water works.  Even simple water systems can be confusing.  When water systems become large complex socio-physical-ecological systems serving many users and uses, opportunities for confusion become extreme, surpassing comprehension by our ancient Homo sapien brains.

When confused by conflicting rhetoric, using numbers to “follow the water” can be helpful.  The California Water Plan has developed some such numbers.  This essay presents their net water use numbers for 2018, by California’s agricultural, urban, and environmental uses by hydrologic region. 

Net water use is the amount by which a water use deprives water from other uses.  This differs from gross water use (a.k.a. applied water use) which includes both the net use plus any water returned after use which is available downstream for other uses.  The biggest net water uses, which deplete the most available water, are evapotranspiration from crops, urban landscapes, and wetlands, as well as required flows to the ocean.  Even large instream environmental or hydropower flows high in a watershed can have little net water use if reused downstream. 

The water accounting for agricultural and urban net water use is fairly strong here, but accounting for environmental flows remains primitive, and should probably be a lower bound.  Much past accounting conveniently (and sloppily) quantified “environmental water use” as all water not consumed by agriculture and cities, which inflated environmental water use.  The environmental water accounting here includes only evapotranspiration from interior environmental purposes (mostly wetlands) and outflows to the ocean required by law and regulation.

Here are the raw regional net water use numbers for 2018 by hydrologic region (arranged mostly north to south) by major purpose.  Details and data are available at

Table 1. Net water uses in 2018 by hydrologic region and use category

If the average water availability in California is about 75 million acre-ft per year, clearly there will be more “surplus” ocean outflows and some greater water use in wetter years, and less “surplus” outflow and water use in drought years.  In this large, diverse, and complex water system, it is hard to catch every drop before it reaches the ocean.  Even in very dry years, some water escapes the clutches of water managers and users.

Table 2. Percent of net water use in each hydrologic region by major water use

Table 2. Percent of net water use in each hydrologic region by major water use

California’s tremendous hydrologic and water use diversity jumps out from Table 2.  In the North Coast, net water use is 94% environmental (mostly outflow from wild and scenic rivers), with very little other uses (agricultural use here might be a bit more from illegal agriculture).  Most of California’s hydrologic regions have less than 10% of their water use being environmental, including the major urban regions and three of the largest the agricultural use regions.  All regions could be called unbalanced, individually, in different ways, which makes the state on average seem more balanced than it really is. 

When presented as percent of net water use, agriculture is the largest overall water use in California, and urban use is a distant third, as least in 2018.  Urban water conservation is good and merits some attention, but we clearly obsess with it disproportionately from a statewide perspective.  Agriculture is the big water use, and it is important how this use is managed (and largely reduced) for the future and for droughts.  Slash and burn approaches to water conservation hurt people and often ecosystems.

Other DWR data would show that total environmental use varies wildly from dry to wet years because much of it is for wild and scenic river flows. 

Table 3. Percent of net water use for each major use, by hydrologic region

96% of net environmental water use is in just two northern regions. Most regions in California have less than 1% of total state net water use for environment.  89% of agricultural water use is concentrated in just four regions.  73% of urban water use occurs in just two regions.  We often talk about how important or unimportant water uses are for California overall, while neglecting how even small uses statewide can dominate in some regions, and how some uses of large statewide concern are almost absent from many regions.

We should make more use of numbers in water policy. For example, Greg Gartrell et al. (2017 and 2022) have done insightful analyses of Delta inflows and outflows, which dispel several myths and put Delta water balance in perspective.  Grafton et al. (2018) show how water conservation based on gross water use is often ineffective and misleading for saving water.  A recent Delta Independent Science Board (2022) report reviews how we might make better water numbers and put them to better use for current and future challenges.  Implementing the Sustainable Groundwater Management Act will require far better and more available numbers for groundwater, surface water, and water demands than we have ever had.

We need insightful numbers to challenge and improve our current conceptions and prepare a more common basis for the difficult water discussions needed for a better future.  

Jay Lund is a Professor of Civil and Environmental Engineering and Co-Director of the Center for Watershed Sciences at the University of California – Davis. He is easily confused, so numbers help him think things through.

Further reading

Delta Independent Science Board. 2022. Review of Water Supply Reliability Estimation Related to the Sacramento-San Joaquin Delta. Report to the Delta Stewardship Council. Sacramento, California.

DWR, California Water Plan water use data

Gartrell, G., J. Mount, and E. Hanak (2022), “Tracking Where Water Goes in a Changing Sacramento–San Joaquin Delta, Technical Appendix: Methods and Detailed Results for 1980–2021,” PPIC, San Francisco, CA.

Grafton et al. (2018), “The Paradox of Irrigation Efficiency”, Science,

Posted in Uncategorized | 8 Comments

Saving Clear Lake’s Endangered Chi

By Peter B. Moyle and Thomas L. Taylor

‘Tens of thousands of these fish once ascended streams in Spring. They are of major cultural importance to the Pomo people who harvested them as a valued food source.’ When you read statements like this, most likely it is salmon that come to mind. Yet this statement characterizes the Clear Lake Hitch or Chi, a non-salmonid fish, that ascends the tributaries to Clear Lake (Lake County) to spawn each spring (Thompson et al. 2013, Pfieffer 2022). Spawners are typically 10-14 inches long. They once moved up the streams in large numbers as soon as spring rains created sufficient stream flows to attract the fish (Moyle 2002, Moyle et al. 2015, Feyrer 2019).

We had the good fortune to be able to observe runs in the 1970s when we were studying Clear Lake’s unique fish fauna, following in the bootsteps of John Hopkirk. Hopkirk (1973) described the Clear Lake hitch and other Clear Lake fishes as unique forms adapted for life in this ancient (2.5 million years!) lake. Moyle was studying the lake’s fishes, while Taylor was documenting the distribution and ecology of the stream fishes (Taylor et al 1982.). Taylor also was (and still is) fascinated with photographing native fishes. The abundant hitch made good subjects. The photographs here show hitch spawning in streams in the 1970s and in 1990, when they were considerably more abundant than they are today, a reminder of what we are now missing.

Lure imitating a juvenile Clear Lake hitch. Lucky Craft Pointer 100-089.

In the same period, graduate student Eugene Geary conducted a life history study of hitch because of their abundance and predictability, perfect for a M.S. thesis study (Geary and Moyle 1980). We were concerned about their long-term persistence in the lake because they were thought of as ‘rough fish’(Rypel 2021) and knew that another stream spawner, the Clear Lake splittail, had already been extirpated (Moyle 2002, Moyle et al. 2015). When exploring the spawning streams, at times we would see dozens of fish that were dead for no apparent reason. We were told that local kids had a tradition of ‘hitching’, killing fish for the fun of it. There was also a commercial fishery in Clear Lake that, while focused on Sacramento blackfish, harvested hitch every year as well. Non-native predators also took their toll. Local largemouth bass anglers still use a lure made to look like a juvenile hitch (see photo above). Yet, in the 1970s, hitch were abundant enough so that they were labeled as a “persistent” native fish in the paper on their life history (Geary and Moyle 1980).

This optimistic view of their persistence was overshadowed by the fate of splittail and thicktail chub which had been extirpated from Clear Lake, and by Sacramento perch, which were rare (and are now extirpated from the lake). In 1989, the California Department of Fish and Wildlife listed Clear Lake hitch as a Fish Species of Special Concern. In 2014, the California Fish and Game Commission listed it as Threatened. This year, the USFWS has agreed to consider listing it as Threatened (see Taxonomic issues that might have prevented listing have now been resolved (Baumsteiger and Moyle 2019).

The causes of its rapid decline toward extinction are multiple and are tied to large-scale changes to Clear Lake and its watershed (Thompson et al. 2013, Moyle et al. 2015). However, the single biggest cause of the recent decline seems to be stream habitat degradation, including barriers, gravel mining, and loss of crucial spring flows for spawning and early development, as well as for transport of the larval fish back to Clear Lake. These problems are exacerbated by the current severe drought (e.g., Larson 2022). This spring, spawning hitch were found in only two tributaries (Kelsey, Adobe creeks) and many of those fish had to be rescued and returned to the lake, when streams stopped flowing (Pfeiffer 2022). Any eggs and larvae produced by these fish were stranded in the drying streams.

The fate of Clear Lake hitch is tied to restoring spring flows to spawning streams, along with barrier removal and other habitat restoration actions. Such restoration will take continued leadership by the Pomo people in the watershed, cooperation among the numerous agencies with authority in the region, citizen volunteer efforts (such as stream surveys), and lots of funding from state and federal sources.

Ideally, the actions to protect Clear Lake hitch would also stimulate interest in other remaining endemic lake-dwelling species such as Clear Lake tule perch, Clear Lake sculpin, and Sacramento blackfish. Saving the Clear Lake hitch could open a whole new chapter for fish conservation in Clear Lake and its tributary streams.

Peter B. Moyle is a Distinguished Professor Emeritus at the University of California, Davis and is Associate Director of the Center for Watershed Sciences.Thomas L. Taylor is a retired fish biologist with a long history of working on California fishes. He is a native fish enthusiast and has spent thousands of hours in streams photographing fish.

Further reading

Baumsteiger, J., M. Young, and P. B. Moyle. 2018. Using the Distinct Population Segment (DPS) concept to protect fishes with low levels of genomic differentiation: conservation of an endemic minnow (Hitch). Transactions of American Fisheries Society 148:406-416. 10.1002/tafs.10144.

Feyrer, F. 2019. Observations of the spawning ecology of the imperiled Clear Lake Hitch. California Fish and Game 105:225-23

Geary, R. E., and P. B. Moyle. 1980. Aspects of the ecology of the Hitch, Lavinia exilicauda (Cyprinidae), a persistent native cyprinid in Clear Lake, California. The Southwestern Naturalist 25: 385-390.

Hopkirk, J.D. 1973. Endemism in Fishes of the Clear Lake region in Central California. University of California Publications in Zoology 96.

Larson, E. 2022. State, local, and tribal officials partner to rescue stranded Clear Lake Hitch. Lake County News, April 30, 2022.,threatened.

Moyle, P.B. 2002. Inland Fishes of California, Revised and Expanded. Berkeley: University of California Press.

Moyle, P. B., R. M. Quiñones, J. V. E. Katz, and J. Weaver. 2015. Fish Species of Special Concern in California. 3rd edition. Sacramento: California Department of Fish and Wildlife.

Pfeiffer, J. 2022. Why I am fighting for a fish I have never seen. High Country News. May 25, 2022.

Rypel, A.L., P. Saffarinia, C.C. Vaughn, L. Nesper, K. O’Reilly, C.A. Parisek, M.L. Miller, P.B. Moyle, N.A. Fangue, M. Bell-Tilcock, D. Ayers, and S.R. David. 2021. Goodbye to “rough fish”: paradigm shift in the conservation of native fishes. Fisheries 46: 605-616 .

Rypel, A.L. 2021. Defending ‘Rough Fish.’ California Water Blog. University of California, Davis, Center for Watershed Sciences. December 19, 2021.

Taylor, T. L., P. B. Moyle, and D. G. Price. 1982. Fishes of the Clear Lake Basin. Pages 171-223 in P. B. Moyle, ed., Distribution and Ecology of Stream Fishes of the Sacramento-San Joaquin Drainage System, California. Publications in Zoology 115, University of California Press, Berkeley, California.

Thompson, L.C., G.A. Giusti, L.Weber, and R. F. Keiffer. 2013. The native and introduced fishes of Clear Lake: a review of the past to assist with decisions of the future. California Fish and Game 99(1):7-41.

Posted in Uncategorized | 5 Comments

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:

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,

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

Posted in Uncategorized | Leave a comment

Uncertainty in modeling, an Art Gallery

Water resource planners regularly rely on computer models to illuminate relationships between human- and natural-systems. Anyone who has tinkered with one of California water supply models knows this is a deeply left-brained exercise. During Winter 2021, as part of Jay Lund’s Art and Water class, water resource engineering students took a break from creating and analyzing mathematical models to exercise the right side of their brains and enjoy some art. Please enjoy this collection of art pieces curated by a group of graduate students who can’t quite figure out how to unplug…

“War (The First Discord)” (19th c.) – DeScott Evans

This piece illustrates the struggle and discord that can occur in hydrologic modeling practice. As these cherubs fight over the apple shown in the bottom left, we can imagine two experts fighting to model nuanced environmental processes to create a “more perfect” model. In the heat of battle, they fail to consider how the model informs effective policy and meaningful change. Is creating the most accurate model always worth the toil, resources, and effort? Instead, the cherubs could collaborate to share the apple and create a model that worked well enough to inform policy and promote meaningful change. – Abbey Hill

Composition II in Red Blue and Yellow” (1930) –  Piet Mondrian 

Uncertainty in modeling is inescapable. Instead of making the solution very complicated, why not make things easier? This painting by Mondrian consists only of straight lines and blocks of colors. We can’t predict the variability of precipitation and other key variables in the future, but simplified (Mondrian-esque) models can still be useful and inform water-saving policies. –  Zhendan Cao

Tree Cathedral (Cattedrale Vegetale) – Giuliano Mauri (2010)

This work of Earth art represents both the carefully planned infrastructure and unavoidable uncertainty inherent to modeling. Just as models build on known and existing systems, this work originates with the architectural history of Gothic cathedrals. However, models must also allow space for flexibility, which Wilby and Dessai (2010) describe as a “framework for robust adaptation.” The Tree Cathedral is built with rigid support structures to manipulate the tree growth pattern, but as time passes, the support cages rot and fall away, allowing the trees to stand on their own. The adaptable and flexible nature of the Tree Cathedral becomes apparent over the years as it continues to grow. Will the tree canopies form the roof of the Cathedral as planned? Will the trees continue to grow as intended? Uncertainty is central to the beauty of the Tree Cathedral and to the functioning of models. There is no way to control or plan for every possible eventuality. Will the Tree Cathedral stay standing, or will exposure to the elements cause it to fall? How will future climate outcomes compare to model predictions of increased drought or storms?  – Eleanor Fadely

“Bad Lemon (Creep)” (2019) Kathleen Ryan

Emerging artist Kathleen Ryan creates intricate mosaics of precious gemstones to create larger-than-life monuments to spoiled fruit. The artist’s process resembles that of a water resource planning model-builder. The modeler finds beauty when complex mathematical feedbacks and uncertainties nest neatly together and produce reasonable results. Stepping back and applying modeling to real-life scenarios (such as climate change and drought) reveals rotten dilemmas for water resource managers.  – Lindsay Murdoch

Dove (1949), The Flying Dove with a Raibow I and II (1952) and The Dove of Peace (1949) by Pablo Picaso; and The Birds by Georges Braque (1960)

This collection of Dove sketches by Pablo Picasso presents a parallelism between different models used in water planning, design and operation. If a real dove represents the watershed to water managers, the first painting illustrates the utopic model that perfectly simulates/forecasts existing hydrology, incorporating all heterogeneity and complexity. The second sketch would be physically-based, spatially distributed hydrologic models to predict hydrologic processes, accurate depiction of the dove, with some spatial heterogeneity at fine spatial resolutions, represented by the feather details. The next simple dove sketch would illustrate simpler physically based models with a few hydrologic processes, clearly depicting a dove but with less detail. The second to last sketch nicely relates to conceptual models in which each block represents a separate hydrologic process, for instance Tank Model (Sugawara 1972) for subsurface runoff and baseflow, that individually do not provide useful information, but when arranged meaningfully, can produce realistic watershed outputs (Klemes 1982). Thus, generating the dove shape. Finally, George Braque’s painting illustrates an empirical model in which the resemblance to a dove is exclusively due to its construction using watershed data. As such, if provided to other water managers, they might recognize them as a different bird or even E letters with humps, showing that empirical models are useful for the specific watershed they are developed for. – Francisco Bellido

Autumn Rhythm by Jackson Pollock (1950)

Despite the shocking global trend of rising temperature, its local implications can be obscure. As some pointed out, “There is a low level of agreement amongst climate models even about the sign of the seasonal rainfall” over large areas. Future climate projections do share some similarities with Jackson Pollock’s paintings. In this notable piece called “Autumn Rhythm”, the artist used a variety of dripping and pouring methods to create disordered lines and patches. This certainly reminds us about the numerous uncertainties embedded into climate predictions. Viewers often appreciate this painting for its randomness, abstractness, and the delivery of vitality and flow. As engineers, we also hope to uncover trends and beauty in the turmoil of the future.

Bridge Over a Pond of Water Lilies – Claude Monet (1993)

A low level of agreement amongst climate models on projected changes in key variables such as the magnitude of warming or the magnitude and sign of seasonal precipitation has led many to recommend dynamic adaptive management as an alternative to taking big actions now. There is undeniably some common sense to this “wait and see” approach. However, adaptive management merely supplants uncertainties in projecting climate with a myriad of other uncertainties such as the social, economic, and political environments around decisions planned to be made in the future, environments which may in fact be more conducive to decisions made today. Imagine Claude Monet’s universally admired painting, “Bridge Over a Pond of Water Lilies”, without the bridge – does the scene appear more untamed and wild? The notion of adaptive management is like the bridge: its elegant structure transforms the landscape into an orderly, calm and serene atmosphere. But it only appears that way. In reality, the chaotic unpredictability of the environment is more likely to undermine our adaptive plans, plans which are assuredly more embellished and highly dimensioned than Monet’s bridge. In sum, we cannot simply create a bridge over uncertainty, no matter how alluring it may be. – Wyatt Arnold

Further Reading

Klemes, V (1982), “Empirical and Causal Models in Hydrology,” Scientific basis of water resource management, National Academy Press, Washington, DC.

Wilby, R.L.  and S. Dessai (2010) “Robust adaptation to climate change,” Weather, Vol. 65, No. 7, July.

Posted in Uncategorized | Leave a comment

California’s continued drought

By Andrew L. Rypel

As California’s drought deepens, it is worth checking in on the status of water supplies and what might be in store for the rest of the summer, and beyond.

What started with the promise of a wet water year, ended up dry, again. In January, the 8-Station Index showed precipitation totals keeping pace with the wettest year on record. Then it got dry and accumulated totals flat-lined. The final result is a below average water year, although not one of the driest years on record. To be precise, we are 13.3 cumulative inches below the long-term average for the northern Sierras.

Fig. 1. Accumulated precipitation for northern California during the current water year. Graph from the California Department of Water Resources, California Data Exchange Center

Current conditions in reservoirs are a mixed bag. Shasta Reservoir remains low at only 40% of capacity, and 49% of the historical average. On this same date in 2021, Shasta was 41% of capacity and 51% of long-term average. Thus conditions in Shasta are very similar to those observed last year. So holding coldwater to support eggs and juvenile winter-run Chinook salmon in the Sacramento River will again be a major challenge this summer. On the heels of a mostly failed year class of winter-run Chinook salmon in 2021, the run is now at perilous risk of extinction. After all, these salmon operate on just a three year life-cycle. Perhaps because of this, efforts have accelerated to move adult winter-run Chinook salmon into coldwater habitats above Shasta Reservoir and into upper Battle Creek. Juvenile outmigrants would have to be trapped and moved around structures on their way out (‘two-way trap and haul’), or fishways re-operated for the specific benefit of salmon (‘one-way trap and haul’). Neither management approaches have been attempted at scale before in these systems. Two-way trap and haul is notoriously expensive and managers have reluctantly avoided it in the past (Lusardi and Moyle 2017).

Comparison of California reservoir levels in 2021 (left) to the same date in 2022 (right). Figures and data from the California Department of Water Resources, California Data Exchange Center

Other reservoirs are faring better than one might expect. Oroville is at 53% of capacity and 67% of the historical average. For comparison, at this same point in 2021, Oroville was at 36% capacity and 46% of the historical average. Folsom Reservoir stands at a whopping 88% capacity and 111% of the long-term average – quite good for this point in the drought. This also compares favorably to only 34% of capacity and 43% of the long-term average for Folsom at the same date in 2021.

One potentially interesting observation is that many locally-operated reservoirs appear to be doing particularly well. New Bullard’s Bar and Don Pedro sport 102% and 82% of long-term average, respectively. These reservoirs were also decently full during 2021. Yet, the architecture of these reservoirs may partially explain this dynamic. For example, New Bullard’s Bar is a large capacity reservoir (969,600 acre-foot) but drains a watershed that is comparatively small; the entire Yuba River watershed is 857,600 acres. Similarly, Don Pedro has a capacity of 2,030,000 acre-foot and the entire Tuolumne River drains a watershed of 1,253,120 acres. In this sense, reservoirs with a high capacity:watershed ratio reservoirs may be more slowly impacted, and thus more durable over longer drought. Grantham et al. 2014 ranked all major dams in California based on their degree of regulation (DOR). Both of these reservoirs had DOR values well >1, which was a threshold identified in the study for strong hydrologic regulation. 

It is likely that high air and water temperatures will occur again this summer, as temperatures have been high for recent years. This will have specific and diffuse socioecological impacts. During the last drought, increased temperatures led to parched soils and stressed trees, and ultimately major forest mortality events (Keen et al. 2022). Obviously, drought also increases frequency and severity of wildfires. The top seven largest wildfires in California history all occurred within the last 4 years. Last summer, the Dixie Fire was the largest of the 2021 wildfires, burning close to 1M acres in Butte, Plumas, Shasta, Tehama, and Lassen Counties. As of writing, there are already seven active wildfires burning. How many major wildfires will accumulate during 2022?

Groundwater is taking a major hit. Water right curtailment orders will occur again this growing season. Growers that have planted annual crops will likely rely on groundwater in an attempt to finish. Tree growers with young crops may be forced to use groundwater or purchase water at high prices to try to keep trees alive. California produces ~80% of the world’s almonds and acreage planted has been growing, despite drought risk. Declining groundwater stores will stress rural wells that will run dry or become contaminated by nitrates. Land subsidence from reduced groundwater will impact the capacity for canals to operate properly. Finally, overdraft of groundwater supplies from this year (and previous years, such as 2021) will make SGMA objectives even more difficult to obtain, and require repayment of aquifers for additional drought pumping in future years for many basins.

The Delta ecosystem continues its sad decline. The delta smelt is virtually extinct from the wild, and although releases of hatchery smelt have been initiated, the habitat issues that historically plagued smelt remain unaddressed. To a large extent they have gotten worse. Water temperatures continue to increase, and increased temperatures are a major factor in recruitment failures of smelt (Komorosky et al. 2015). Longfin smelt are declining behind delta smelt (Eakin 2021). Warmer temperatures and clearer waters (due to effects of non-native clams) have intensified the rate of spread of invasive aquatic plants. The switch of fish habitats from cold turbid waters to warm, clear and plant filled habitats has shifted the ecological regime in the Delta to favor non-native fishes such as black basses. These species in turn, compete and predate on native fishes, which cause further declines in Sacramento Valley and Delta endemics.

Castaic Reservoir as seen at 46% capacity during the 2014 drought. Photo from Planet Labs Inc, and downloaded from

Other drought-related impacts are emergent. Water prices are increasing across the board. San Diego County Water Authority will be charging close to $2,000 per acre foot for untreated water in 2023. Many growers that have elected to sell water rather than grow have received record sale prices. These effects are being further compounded by macroeconomic inflation. Urban water restrictions have already been put in place in much of the state. The economic fallout of agricultural water shortages will result in rising unemployment and financial stress to agricultural communities and various irrigation districts. Amidst drought conditions, an interesting plan emerged earlier this month that involved the state potentially purchasing senior water rights. The details and fate of this plan remain murky. As water becomes more expensive and scarce, there may be less interest and prioritization of environmental programs, even though drought is the time when these programs might be most needed by wildlife.

Andrew L. Rypel is a professor of Wildlife, Fish & Conservation Biology and Co-Director of the Center for Watershed Sciences at the University of California, Davis.

Further reading

Börk, K., A.L. Rypel, S. Yarnell, A. Willis, P.B Moyle, J. Medellin-Azuara, J. Lund, and R. Lusardi. 2022. Considerations for developing an environmental water right in California,

Börk, K., A.L. Rypel, and P. Moyle. 2020. New science or just spin: science charade in the Delta,

Eakin, M. 2021. Assessing the distribution and abundance of larval longfin smelt: what can a larval monitoring program tell us about the distribution of a rare species? California Fish and Wildlife Special CESA Issue: 189-202.

Grantham, T.E., J.H. Viers, and P.B. Moyle. 2014. Systematic screening of dams for environmental flow assessment and implementation. Bioscience 64: 1006-1018.

Keen, R.M., S.L. Voelker, S.Y.S. Wang, B.J. Bentz, M.L. Gouldon, C.R. Dangerfield, C.C. Reed, S.M. Hood, A.Z. Csank, T.E. Dawson, A.G. Merschel, and C.J. Still. 2022. Changes in tree drought sensitivity provided early warning signals to the California drought and forest mortality event. Global Change Biology 28: 1119-1132. 

Jessoe, K., J. Medellin-Azuara, P. Moyle, J. Durand, and A. Willis. 2021. A few lessons for California’s new drought. California Waterblog

Komoroske, L.M., R.E. Connon, K.M. Jeffries, and N.A. Fangue. 2015. Linking transcriptional responses to organismal tolerance reveals mechanisms of thermal sensitivity in a mesothermal endangered fish. Molecular Ecology 24: 4960-4981.

Lund, J., T. Harter, R. Gailey, R. Frank, G. Fogg. 2015. The Earth is falling! – land subsidence and water management in California. California Waterblog

Lusardi, R.A., and P.B. Moyle. 2017. Two-way trap and haul as a conservation strategy for anadromous Salmonids. Fisheries 42: 478-487.

Moyle, P., K. Börk, J. Durand, T.C. Hung, and A.L. Rypel. 2021. 2021: Is this the year that wild delta smelt become extinct?

Rypel, A.L. 2021. Do largemouth bass like droughts?

Posted in Uncategorized | 2 Comments

Considerations for Developing An Environmental Water Right in California

By Karrigan Börk, Andrew L. Rypel, Sarah Yarnell, Ann Willis, Peter B. Moyle, Josué Medellín-Azuara, Jay Lund, and Robert Lusardi

Tuolumne River Northwest of Tuolumne Meadows, Yosemite National Park. Photo by Dick Witt, downloaded from

This week, news emerged of a State Senate plan that would spend upwards of $1.5B to purchase senior water rights from California growers. Under California’s first-in-time, first-in-right water allocation system, senior water rights are filled first, before more junior right holders get their water. The proposal is ostensibly promising. Because of widespread diversions, the aquatic biodiversity of California has been effectively exposed to chronic drought every year, and additional flows may help native species. If purchases can quickly add additional water to rivers in the right places and at the right times, they could benefit ecosystems and endangered species, like Chinook salmon and delta smelt (Moyle et al. 2019, Obester et al. 2020). But it could also easily become a payoff for wealthy water holders with marginal benefit for ecosystems, species, and people. The potential for abuse is particularly troubling when the State is using public funds to buy water, which technically belongs to the people of the state and which the State can already regulate to achieve the same aims. As the old saying goes, the devil is in the details. 

This blog highlights some important considerations for decision makers on making effective environmental water right purchases. Below are several questions and themes for a successful water purchasing program.

Does purchasing water rights actually result in more water for ecosystems?

Water rights in California are complicated, and there are many ways a water right purchase could not add appreciable water for ecosystems. 

First, many water rights exist only on paper. Some right holders only use a portion of their water right in most years and can only use the full right occasionally, e.g., in very wet years. The state of the data and reporting system in California, especially for senior water rights, makes it challenging to know how much water senior right holders are entitled to and how much water they actually use. And we’re most interested in their consumptive use – the share of water use that becomes available and legal to sell under California law – a quantity that’s even harder to pin down. Established legal and regulatory process exist to dedicate real water rights to the environment. California Water Code Section 1707 provides a mechanism to transfer water rights to instream use, and it, combined with other water code sections on water transfers, does a fair job of making sure that what’s being transferred is real water that will actually increase flows and be protected from other users. Practitioners have already developed practical guidelines for successfully completing the 1707 process. The State must take care to purchase real wet water rights that will result in enforceable instream flows. 

Second, water transferred to instream use needs to stay instream. On many rivers, the full flow of the river is already spoken for through existing rights, often many times over; California has allocated up to 1000% of natural surface water flow, with most of these water rights issued in the Sacramento and San Joaquin rivers. If purchased rights are simply retired or not otherwise protected for ecosystem purposes, then holders of other existing water rights can (and often will) simply take the water. 

Third, even with an effective mechanism for selecting real water rights and protecting them instream, improvements to monitoring and enforcement are essential to ensure true increases in instream flows. Many diversions are only roughly monitored, such that neither the water user nor the State knows exactly how much water is being used. Many river stretches lack flow gages, so it is difficult to quantify how much water remains instream (though SB 19 is attempting to address the limited network of stream gages in California). And the Water Board lacks adequate resources to enforce existing limits on water rights. The State needs open and reproducible data on diversions and flows, along with a meaningful enforcement threat to ensure any water set aside for environmental benefit remains in the ecosystem.

Finally, these water rights should be “new” water. The Water Board, through its Bay Delta Water Quality Control Plan, is already reducing water rights to protect public trust uses and water quality in the Bay Delta watershed. Water users are negotiating over Voluntary Agreements that could be a part of that Plan. In addition, many growers will need to fallow some fields to meet the mandates of SGMA. Many state and federal laws already circumscribe many water rights to protect instream water uses. Purchases with public funds should be focused on water rights that right holders would otherwise use, so the funds don’t go to pay for water that would have remained instream anyway.

What price should California pay?

The Water Board already has the power to reduce water rights to protect the public trust or to ensure water is used reasonably so as not to destroy public resources, and it has previously exercised that power. They consistently win the resulting lawsuits. California could legally and constitutionally acquire much of this water through other mechanisms, without paying for it. So what exactly is the State paying for here? 

In a nutshell, the state would pay for acquiring water quickly, with less political resistance and bureaucratic wrangling, and with less political ill-will and fewer messy and protracted lawsuits. That might make sense; we’re in a climate crisis, and salmon and many of California’s imperiled species don’t have time to waste. But it also means the State should not be paying full price. Water use reductions to support instream flows could occur through other government actions, without a State buyback. A water right that is sometimes curtailed by the state during drought due to endangered species or public trust concerns simply isn’t worth as much as a water right that doesn’t face such regulation. The question is whether water right holders get paid something now for their right or lose some of this water right with no payment after a protracted and expensive fight into a rapidly changing future. Prolonged litigation isn’t as advantageous to current water rights holders as they might seem. Longer and deeper curtailments are possible given the trajectory of California’s climate, meaning the right could become worth even less in the future.

The best approach to pricing might be something like the reverse auctions that The Nature Conservancy is already using to generate migratory bird habitat. Under this approach, water right holders bid to sell their water to the state, and the lowest bids would be more favored, provided that they are real wet rights, as discussed above. This should be coupled with continued pressure from the Water Board to exercise their existing powers to reduce water available to right holders, as they did in the last drought, to generate conditions that would encourage water right holders to sell. And, as we’ll discuss in further detail, another complexity is that it’s not just the cheapest water the state should buy, but the cheapest real water in the right place at the right time for the ecosystem (see point 3 below). Paying full price for water rights could amount to a giveaway to wealthy water right holders, but the reverse auction model can avoid this pitfall.

Paying public money for a publicly-owned and regulated resource will strike some advocates as morally wrong. They might argue it sets a dangerous precedent of buying out those who oppose regulation or treating water rights as a more concrete form of property than they actually are. Legislators should be aware of this philosophical opposition and must carefully craft the purchase program to ensure it provides enough water and ecological benefits to merit the actual and political costs. Because California water already belongs to all Californians, and water rights are subject to continuing State supervision, the State should make sure the funds they dedicate go as far as possible.

What water, when, and where?

What are the precise goals of these purchases? The plan may become the beginnings of an ‘environmental water right’. This would be a positive step. 83% of California’s endemic fish species are declining (Moyle et al. 2011). Furthermore, outmigration survival of juvenile Chinook salmon is strongly linked in a threshold manner to river flows (Michel et al. 2021). Thus additional flows could benefit endangered species, especially if deployed strategically. However, if additional flows are simply gobbled up by other water users downriver or deployed in the wrong places and times, the environmental benefit to people and ecosystems could be nil. Water budget and accounting mechanisms are needed to ensure water is getting where and when it is most needed.

“When” matters.

The ecological value of water changes over time; both between seasons and across years. For example, additional flows during drought may yield more ecological return on investment than increased flows in wet years. As one heuristic, average annual runoff in California is 71M acre-feet. Thus a total of 200,000 acre-feet of additional water (the figure provided in the linked article above) is only 0.3% of the average water budget. However, runoff in drought years is much lower. Runoff during the 1977 drought year was only 15M acre-feet; so 200,000 acre-feet is 1.3% of the water budget in such dry years. An accounting or water budget that details when additional flows would be available is needed to accurately track the availability of surplus water.

The value of water for economic uses also changes over time. Opportunity costs of water in the irrigation season of dry years are particularly high. Thus creating a buffer in wet years might be more cost effective than buying out agricultural water use during dry years. A buyback program that considers a baseline amount plus dry-year option may reduce uncertainties for both farming and ecosystem needs.

Monticello Dam provides flows tailored to help native fishes in lower Putah Creek, photo from Bureau of Reclamation

“Where” matters.

There are better and worse places for additional water. Adding high quality water is valuable, so water rights in spring-fed streams and groundwater-dominated rivers have high potential for adding higher value than simply additional flow volume due to their unique water quality. Spring-fed and groundwater-dominated streams are more resilient to climate change than strictly surface runoff-dominated streams, and, as a result, they support robust ecosystems

Adding significant amounts of water to tributaries can make a significant difference, in part because less water is needed to enhance these habitats. Similarly, adding water to coastal rivers, which may be less complicated and easier to monitor, could result in significant gains.

On maintem rivers, giving juvenile salmon and other native fishes better access to productive riparian and floodplain areas could support aquatic biota. Data from a host of studies demonstrate that salmon grow better when exposed to floodplain habitats (e.g., Katz et al. 2017, Holmes et al. 2021), and new studies are testing potential survival benefits for floodplain-reared salmon. But this may not require purchases of water rights; permanent easement arrangements, long-term conservation easements and/or NRCS programs could provide similar benefits at less cost and with more impact than just adding water to maintem rivers. Strategic tributary investments are likely to often provide greater and more sustainable ecosystem value compared to large mainstem purchases, where many other users, especially in the Central Valley, bid up water prices and the marginal proportions of flow improvements are smaller.

Equity and Social Justice.

In 2021, the California Water Board released Resolution No. 2021-0050, titled “Condemning Racism, Xenophobia, Bigotry, and Racial Injustice and Strengthening Commitement to Racial Equity, Diversity, Inclusion, Access, and Anti-racism.” This remarkable document acknowledged that the “Water Boards’ programs were established over a structural framework that perpetuated inequities based on race,” and it provides extensive background on the systematic exclusion of many groups from the water right acquisition process. The most senior water rights in California, those targeted by this purchase program, were acquired during a period when racism was the norm, when women often lacked independent legal identity, and when Asian people were unable to become citizens, even though citizenship was open to most other races. Indigenous peoples were still subject to state-sponsored genocide and systematically disenfranchised of their land and water rights. As a result, most minorities and many women were excluded from acquiring water rights or land with appurtenant water rights. Most senior water rights were originally claimed by white men, and that disparity has continued. Buying out water rights now, as opposed to rationally regulating them, risks perpetuating that tradition. Because of the State’s continuing ownership and regulatory interest in water rights, the State still has opportunity to redress past injustices, as the Water Board resolution acknowledges. Early drafts of the legislation for the purchase program appear to recognize this history and attempt to mitigate some of the lasting harm through funding for increased access to drinking water for disadvantaged communities. Without intentional engagement to address these past injustices, the broader purchase program might result in better public control of water, but at the cost of extending inequities. 


The State Senate proposal offers the promise of real change in California water. It might help to move past a decades-long stalemate, protect important tributary and coastal rivers, and ensure the survival of imperiled species. It offers quick action that could create long-sought environmental water rights. But the details matter. This proposal could just as easily result in a very minor increase in mainstem flows that does little to benefit ecosystems, or even pay for water rights that aren’t worth the paper they’re written on. A decade from now, this might be seen as a turning point or just another expensive water scheme. 

At some point, transdisciplinary water and ecosystem experts need to be brought into the room. Scientists can assist policy makers to identify the locations, times, and dynamics of flows that can have the most environmental benefit (e.g., California Environmental Flow Framework). Further, transparent cost benefit analysis, water balance modeling, or ecological optimization provide important insight on when and how (e.g., functional flows) to best use additional water for the environment.

Although engaging with experts can be challenging and can occasionally stymie progress, scientists also deliver data-driven frameworks for optimizing investments and learning the most from an experiment. This knowledge works to ensure that decisions are ultimately based on sound science while also looking at economic and distributional effects in water reallocations. Management plans/processes that are transparent, reproducible and science-based often help. Indeed, some states have adopted democratic boards with a science-based mission to oversee management of natural resources within the context of the public trust. A similar model may be useful here.

Strong legal and scientific oversight will be essential to maximize the ecological benefits of purchases. We hope these suggestions provide encouragement and guidance for decision makers as they further consider water right purchases for the environment.

Yuba River near Bridgeport, California. Photo by Michael Nevins, United States Army Corps of Engineers, downloaded from

Karrigan Börk is an Acting Professor of Law at the UC Davis School of Law and an Associate Director at the Center for Watershed Sciences. Andrew L. Rypel is a professor of Wildlife, Fish & Conservation Biology and Co-Director of the Center for Watershed Sciences at the University of California, Davis. Sarah Yarnell is a Research Hydrologist at the Center for Watershed Sciences. Ann Willis is a Research Engineer at the Center for Watershed Sciences. Peter B. Moyle is a Distinguished Professor Emeritus at the University of California, Davis and is Associate Director of the Center for Watershed Sciences. Josué Medellín-Azuara is an Associate Professor at the University of California, Merced. Robert Lusardi is an Assistant Adjunct Professor and Research Ecologist in the Department of Wildlife, Fish & Conservation Biology and the Center for Watershed Sciences at UC Davis. 

Further Reading

Bellido-Leiva, F.J., Lusardi, R.A. and Lund, J.R., 2021. Modeling the effect of habitat availability and quality on endangered winter-run Chinook salmon (Oncorhynchus tshawytscha) production in the Sacramento Valley. Ecological Modelling, 447, p.109511.

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

Börk, K., A.L. Rypel, and P. Moyle. 2020. New science or just spin: science charade in the Delta,

Grantham, T.E., and Viers, J.H. (2014). 100 years of California’s water rights system: patterns, trends and uncertainty. Environmental Research Letters 9(8), 084012.

Grantham, T.E. and Viers, J.H. (2014). California water rights: You can’t manage what you don’t measure. California Waterblog.

Holmes, E.J., P. Saffarinia, A.L. Rypel, M.N. Bell-Tilcock, J.V. Katz, and C.A. Jeffres. 2021. Reconciling fish and farms: Methods for managing California rice fields as salmon habitat. PLoS ONE 16(2): e0237686.

Hollinshead, S.P. and J.R. Lund, “Optimization of Environmental Water Account Purchases with Uncertainty,” Water Resources Research, Vol. 42, No. 8, W08403, August, 2006.

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.

Lusardi, R.A., Nichols, A.L., Willis, A.D., Jeffres, C.A., Kiers, A.H., Van Nieuwenhuyse, E.E., et al. (2021). Not All Rivers Are Created Equal: The Importance of Spring-Fed Rivers under a Changing Climate. Water 13(12), 1652.

Medellín-Azuara, J., Paw U, K.T., Jin, Y. Jankowski, J., Bell, A.M., Kent, E., Clay, J., Wong, A., Alexander, N., Santos, N., Badillo, J., Hart, Q., Leinfelder-Miles, M., Merz, J., Lund, J.R., Anderson, A., Anderson, M., Chen, Y., Edgar, D., Eching, S., Freiberg, S., Gong, R., Guzmán, A., Howes, D., Johnson, L., Kadir, T., Lambert, J.J., Liang, L., Little, C., Melton, F., Metz, M., Morandé, J.A., Orang, M., Pyles, R.D., Post, K., Rosevelt, C., Sarreshteh, S., Snyder, R.L., Trezza, R., Temegsen, B., Viers, J.H. (2018). A Comparative Study for Estimating Crop Evapotranspiration in the Sacramento-San Joaquin Delta. Center for Watershed Sciences, University of California Davis.

Michel, C.J., J.J. Notch, F. Cordoleani, A.J. Ammann, and E.M. Danner. 2021. Nonlinear survival of imperiled fish informs managed flows in a highly modified river. Ecosphere 12: e03498.

Middleton Manning, BR. 2018. Upstream: Trust Lands and Power on the Feather River. Tucson: University of Arizona Press. 256 pp.

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., K. Börk, J. Durand, T. Hung, A.L. Rypel. 2019. Futures for Delta Smelt,

Moyle, P.B. 2021. Drought makes conditions worse for California’s declining native fishes.

Rypel, A.L. 2022. Nature has solutions…What are they? And why do they matter?

Rypel, A.L., D.J. Alcott, P. Buttner, A. Wampler, J. Colby, P. Saffarinia. N. Fangue, and C.A. Jeffres. 2022. Rice and salmon, what a match!

Rypel, A.L., P.B. Moyle, and J. Lund. 2021. A swiss cheese model for fish conservation in California.

Willis, A.D., Peek, R.A., and Rypel, A.L. (2021). Classifying California’s stream thermal regimes for cold-water conservation. PLOS ONE 16(8), e0256286. doi: 10.1371/journal.pone.0256286.

Yarnell, S.M., Petts, G.E., Schmidt, J.C., Whipple, A.A., Beller, E.E., Dahm, C.N., Goodwin, P. and Viers, J.H., 2015. Functional flows in modified riverscapes: hydrographs, habitats and opportunities. BioScience, 65(10), pp.963-972.


Posted in Uncategorized | 7 Comments

Demystifying mist as a source of water supply

Source: Wikicommons
Fog envelopes the Golden Gate Bridge. Source: Wikimedia Commons

By Jay Lund

(originally posted in 2015)

In some of the world’s driest places, atmospheric moisture is a major source of water for native ecosystems. Some algae, plants and insects in the Israeli and Namibian deserts get much of their water from fog, dew and humidity. The spines of some cacti species have evolved to collect fog droplets. California’s redwood forests derive a significant amount of their moisture from fog.

Some drought-minded California residents along the coast, perhaps yearning for a clear ocean view, have suggested harvesting fog as a water supply.

Globally, few places get drinking water from coastal fog. They are mostly rural areas with abundant fog but little other available water. Communities along the parched northern coast of Chile have captured fog for some of its water supply by erecting large fences of synthetic fiber cross-wise to the coastal wind. The condensate on the netting is channelled for collection and use.

A fog fence or catcher supplies water to poor residents of Lima, Peru. Source: Wikimedia Commons

Fog harvesting yields from 1 quart to 3 gallons of water daily per square yard of fog mesh [1].

What would this mean for a typical coastal household?

A household of three that uses 300 gallons a day would need 1,030 to 12,300 square feet of fog mesh [2]. To fit on a typical single-family lot,  the length of the fog fence would be limited to about 50 feet. That means the fence would need to stand 21 to 250 feet tall, about the height of the State Capitol dome.

To fit on a typical single-family lot, the length of the fog fence would be limited to about 50 feet. That means the fence would need to stand 21 to 250 feet tall, about the height of the State Capitol dome. Illustration by Stephanie Pi, UC Davis.
To fit on a typical single-family lot, the length of the fog fence would be limited to about 50 feet. That means the fence would need to stand 21 to 250 feet tall, about the height of the State Capitol dome. Illustration by Stephanie Pi, UC Davis.

Building such a fence would cost a household thousands of dollars and require cleaning (algae tends to grow on the mesh) and repair (the mesh becomes a big sail in a storm). Homeowners probably also would want a sizable water tank to fill for periods of clear weather.

For virtually all homeowners, a fog water supply would almost always be costly and inconvenient. Some households might use fog as a supplemental supply, but it usually will be at a steep additional cost.

If these numbers were scaled up for San Francisco, population 800,000, the fog fence would need to cover 10 to 120 square miles, or 20 percent to 2.5 times the area of the city (47 square miles). Fog will unlikely be a major water supply for California.

But this is only for atmospheric fog. More petty forms of fog frequently blur discussions of water in California. If we could demistify some of this haze, we might condense our discussions and diminish our droughts.

Jay Lund is a professor of civil and environmental engineering and director of the Center for Watershed Sciences at UC Davis.

May 2016 update:

Oddly enough, apparently a SF Bay Area vodka maker is experimenting using fog-collected water in its distilling: $125 per bottle.  At that price, I expect it is economical.

[1] The density of liquid water is 1,000 kg per cubic meter. The density of water in fog might range from 0.05 to 0.5 grams per cubic meter. If the fog mesh can wring 10 to 50 percent of the water from a coastal breeze blowing 2 miles per hour for half the day, then 1 cubic meter of fog mesh would produce roughly 1 cup to 2.5 gallons of water a day. Not a bad agreement between theory and practice.

[2] To meet a daily water demand of 300 gallons, the coastal household would need a giant square fog mesh of 32 to 111 feet on each side for a total area of 1,030 to 12,300 square feet, which is larger than most California houses.

Further reading

Dawson, T. E. (1998), “Fog in the California redwood forest: ecosystem inputs and use by plants,” Oecologia, Volume 117, Issue 4, December, pp 476-485

Estrela, M.J., J.A. Valiente, D. Corell, M.M. Millán. 2008. “Fog collection in the western Mediterranean basin (Valencia region, Spain)”. Atmospheric Research, Volume 87, pp. 324–337

Friedmann, I., Y. Lipkin, and R. Ocampo-Paus. 1967. “Desert Algae of the Negev (Israel)”. Phycologia, 6:4, 185-200

Goodman, J. 1985. “The collection of fog drip”. Water Resources Research, Vol. 21, No. 3, pp. 392-394. A very small field experiment on coastal Montara Mountain south of San Francisco, Calif.

Henschel, J.R. and M.K. Seely. 2008. “Ecophysiology of atmospheric moisture in the Namib Desert”. Atmospheric Research, Volume 87, Issues 3–4, March 2008, Pages 362–368

Ju, J., H. Bai, Y. Zheng, T. Zhao, R. Fang, and L. Jiang. 2012. “A multi-structural and multi-functional integrated fog collection system in cactus”. Nature Communications, 4 Dec. 2012

Klemm, O. et al. 2012. “Fog as a Fresh-Water Resource: Overview and Perspectives”. Ambio. Mar 2012; 41(3): 221–234

Snyder, R.L. 1992. “Fog contribution to crop water use”. Drought tips, No. 92-40, UC Davis

Victoria, M. and M. Jaen. 2002. “Fog water collection in a rural park in the Canary Islands (Spain)”. Atmospheric Research, Volume 64, pp. 239–250


Posted in Uncategorized | Tagged , , , | 19 Comments

The Failed Recovery Plan for the Delta and Delta Smelt

By Peter Moyle

Few native species are as controversial as Delta Smelt. It is a 3-4 inch translucent fish that lives only in the California Delta, where the Sacramento and San Joaquin rivers meet. This place also happens to be the heart of California’s complex water supply system which provides fresh drinking water to 35-million Californian’s and supports a multi-billion dollar agricultural industry. As water demand increased over the years, the smelt declined, approaching extinction. This blog probes into lessons we can learn from the failure of efforts to protect the smelt, laid out in the 1990s.

Delta Smelt

In 1993, the Delta Smelt was listed as a threatened species, under the Federal Endangered Species Act of 1973 (ESA). Once listed, actions were initiated to “recover” the species under the powerful, no-nonsense provisions of the ESA. On December 19, 1994, critical habitat for the smelt was defined as essentially the entire Delta, plus the dynamic extent of the low salinity zone (technically, the location of the 2 ppt isohaline or X2), to make sure responses of different life history stages to variability in freshwater outflow were included. On November 11, 1996, the US Fish and Wildlife Service adopted the recovery plan (the Plan) discussed here. The ultimate goal of this Plan was to improve habitat conditions for Delta Smelt so it could be removed from the ESA list once it was no longer threatened with extinction. Twenty-five smelt generations later, this goal has not been achieved, and Delta Smelt populations have declined further.

Today Delta Smelt exist mainly as hatchery fish that are raised, from egg to adult, at two locations. This year, over 55 thousand hatchery Delta Smelt were released into their historical habitat areas and there is now some early evidence of their survival and spawning. But the question remains: can we really expect a self-sustaining population of smelt to re-develop in habitat which has failed to support them in the past?

Recovery Plan

Delta Smelt. Photo credit: Renee Reyes. USBR.

In this blog, I focus on the recovery plan to obtain insight into why recovery efforts have failed, despite a large body of research findings on what smelt populations need for survival. I have a personal interest in the recovery plan because in 1995 I was appointed Team Leader to prepare (officially, to assist), for the USFWS, The Recovery Plan for the Sacramento/San Joaquin Delta Native Fishes (the Plan). The Team consisted of 10 scientists with knowledge of the Delta and its fishes, representing academia, state and federal agencies, and water agencies[1]. Given the perceived urgency of our task we met frequently with a high level of participation from all members, finishing the Plan in about a year.

Early in process, the Team proposed broadening our efforts to include other native fishes that were in decline from poor habitat conditions in the Delta. Our argument was basically that recovering multiple species together fit well under Section 2 of the ESA which says that a primary purpose of the ESA is to provide a means for the conservation of ecosystems on which endangered and threatened species depend. To my surprise, the proposal was accepted by USFWS. “Accordingly, the purpose and scope of this recovery plan is to outline a strategy for the conservation and restoration of the Sacramento-San Joaquin Delta that currently supports or has the potential to support Delta native fishes (USFWS 1996, p.1)”

To create a multi-species plan, we established five criteria for adding additional species to the Plan and chose seven species: Delta Smelt, Longfin Smelt, Sacramento Splittail, Green Sturgeon, Sacramento Late Fall-run Chinook Salmon, Spring-run Chinook Salmon, and San Joaquin Fall-run Chinook Salmon. We did not include Sacramento Winter-run Chinook salmon because it had been listed previously and had its own recovery plan. Sacramento Perch were added by the USFWS after the initial draft of the Plan was completed, even though it was extirpated from the Delta.

A Naïve Approach

In retrospect, this idealistic approach was naïve. Only the Delta Smelt had legal clout, so other species could be largely ignored by managers, at least until Longfin Smelt, Spring-run Chinook, and Green Sturgeon also became listed under the ESA. Sacramento Splittail were listed for a short period but became delisted as more and better information on their biology developed (Moyle et al. 2004). An ecosystem-based approach to management of the Delta also emerged from the signing of the Bay-Delta Accord on December 15, 1994, which was supposed to restrict exports and set salinity standards that restricted outflow, to an extent. Yet the Accord (as CALFED Bay-Delta program) failed in its mission, at least as far as native fishes are concerned, despite the development of the Strategic Plan for the Ecosystem Restoration Program (ERP, issued in 1998). For Delta Smelt and other listed fishes, the goals of the recovery Plan were incorporated the ERP. The expectations were that other native fishes would have increasing or stable populations in 25 years (i.e. by 2023). The evidence is clear that this has not happened [2]. So, the rest of this blog focuses in on why the Plan also failed to recover the Delta Smelt and Delta fish habitats.

I reread the Plan after a long absence and the first thing that struck me was how little we knew about Delta Smelt at the time. We relied heavily on a few older published studies, agency reports where smelt were incidental catches, anecdotal and unpublished reports, and the life history study by Moyle et al. (1992). For quantitative assessment of distribution and abundance, such as it was, the Team relied on data from the Fall Midwater Trawl Survey of CDFW, which we thought had the best representation of both adult smelt numbers and distribution. This sampling program was established to monitor the abundance of Striped Bass, not smelt, but was regarded as generally useful for monitoring all pelagic fishes in the upper estuary and Delta.

Causes of Smelt Decline

The Team generally agreed Delta Smelt had declined to a small fraction of their historical population size, which was assumed to be represented by base-lined data from 1967-1981. The reduced populations in 1982-1992 were used for comparison, although 1987-92 were drought years. After the initial decline, most smelt seemed to be confined to the Sacramento River channel between Collinsville and Rio Vista. The Team outlined several plausible explanations for the decline. In the Plan, the causes of decline were stated to be “multiple and synergistic but seemed to be in the following order of importance (p. 19):”

1. Reduction in outflow

2. Entrainment losses to water diversions

3. High outflows

4. Changes in food

5. Toxic substances

6. Disease, competition, and predation.

Reduction in inflow to the Delta, the result of decades of dam construction and diversions, was considered to be a logical cause, because subsequent outflow from the Delta was seemingly insufficient to carry juvenile smelt to their most productive rearing area, Suisun Bay, as outflow. However, Delta Smelt numbers showed a positive relationship with outflow (X2) before 1981-82 and negative relationship after that (Kimmerer 2002). In contrast, other pelagic fishes such as Striped Bass, Longfin Smelt and American Shad showed a fairly strong positive relationship between numbers and outflow in all years.

Estimates of fish entrainment in water diversions, especially in the big state and federal pumping plants in the south Delta, were largely based on analyses of CDFG (now CDFW) that entrainment of juvenile Striped Bass was a major cause of bass decline. This justified a hatchery program for rearing Striped Bass and a program for taking young-of-year bass from the salvage operations and rearing them in cages, to increase survivorship. For Delta Smelt, Kimmerer (2008) was the first to demonstrate potential large effects of the pumping plants on their survival.

High outflows were included as a possible cause of decline because the period of decline included both years with low outflow (1987-91) and years with exceptionally high outflows (1982, 1986). It was speculated that high outflow years could “flush” Delta Smelt, and their planktonic food supply, to unfavorable habitats downstream. The Team speculated that the combination of both exceptionally high and low outflows during the evaluation period created unfavorable conditions for smelt.

Changes in food reflected a general recognition that zooplankton seemed less abundant in Delta Smelt rearing habitat than they once were. Three lines of evidence were presented: the shift in copepod species from native to non-native species, blooms of the diatom Melosira, which was regarded as low quality food for zooplankton, and the invasion of the overbite clam, Corbula amurensis, which by 1986-87, was demonstrably depleting zooplankton populations in Suisun Bay. The first two causes of change were largely dismissed, but it was quickly accepted that the overbite clam invasion was likely depleting plankton populations (Kimmerer et al. 1994). The problem from a Delta Smelt perspective is that the invasion occurred after the major smelt decline had taken place. So, the clam might be preventing recovery but was regarded as an unlikely cause for the initial decline.

Toxic substances (contaminants), especially agricultural pesticides, were listed as a potential threat but unstudied. Subsequent laboratory studies indicated contaminants of various sorts were potentially a problem, but impacts of individual toxins were hard to pin down. Delta waters at times seemed a soup of contaminants, unhealthy for fish.

The Plan found “no evidence that disease, competition, or predation has caused Delta Smelt populations to decline, despite the abundance of introduced species in the estuary (p.22-23).” It was implied, however, that further study might show that species such as Striped Bass and Mississippi Silversides were having a negative impact. It was noted that CDFW stopped planting Striped Bass in the estuary in 1992 because of potential predation on endangered species.

The loss of genetic integrity due to hybridization of Delta Smelt with non-native Wakasagi had no published support. Later studies indicated this was not a problem.


The Plan and scientific thinking in the 1980s and 90s revealed no ‘smoking gun’ causes of decline of Delta Smelt. But the Team agreed the key to recovery of smelt was habitat restoration for each major life stage: spawning, larval and juvenile transport, rearing, and adult migration. This meant having adequate outflows for each life stage, each living in a food-rich environment that was relatively free of toxins and had low entrainment in diversions. The Plan indicated the smelt population would be considered restored “when its population dynamics and distribution pattern within the estuary are similar to those that existed in the 1967-1981 period.” The distribution requirement was particularly important because recovery of endangered fish species is usually focused on population size, not distribution. The Team developed very specific criteria for distribution, because before the decline Delta Smelt were widely distributed in the Delta, including the south and central Delta. The temporary resurgence of a smelt population in the 1990s almost met the abundance and distributional requirements for delisting. Rapid changes after that made recovery no longer possible.

Figuring out how to make recovery possible required a major research program, which was quickly instituted. Generous funding for research was important for producing the insights into smelt biology that were gained. Meanwhile, the decline continued, to the point that the natural population has largely disappeared, and hatchery smelt have been planted in ‘vacant’ Delta habitat. But the total amount of suitable habitat for Delta Smelt has further diminished by invasions of aquatic plants, especially Egeria densa. These plants now line Delta channels, slowing outflow and tidal flows, filtering out sediment and organic matter and making the water clearer and warmer. Habitat in the south and central Delta is now largely free of Delta Smelt and most other open-water fishes. Instead, it is lake-like habitat that supports common non-native species such as Largemouth Bass, Bluegill, and Black Bullhead. Elsewhere, Asian and overbite clams suppress zooplankton populations while fishes such as Mississippi Silverside prey on larval smelt and other fishes. Clearly, habitat for Delta Smelt has not recovered, nor has it for other species in the Delta Native Fishes Recovery Plan, with the possible exception of Sacramento Splittail (but see )

Failure of the Plan

The causes of decline and suppression of Delta Smelt and other native fishes continue to be multiple and are covered elsewhere (e.g., Moyle et al. 2018. Hobbs et al. 2017) so are beyond the scope of this blog. But it is clear that habitat for native fishes has worsened dramatically since the 1996 Plan was adopted. This trend continues with sea level rise, climate change, new invaders, and other factors. The questions then become: “How much habitat remains available for native fishes? Is it possible to create sufficient habitat through restoration?” Can we work with rapid environmental change in ways that favor native fishes or do we just ‘roll with the punches’? The discussion of alternative responses to climate-related changes in Suisun Marsh (Moyle et al. 2014) provides some ideas of how to respond.

In short, developing the Recovery Plan for the Sacramento/San Joaquin Delta Native Fishes was basically a good idea because it amounted to a Delta native fish habitat recovery plan. It failed in part because it was never instituted on a large enough scale under a coherent plan of shared governance among state and federal agencies. Providing water to agriculture has almost always trumped providing significant water for the Delta ecosystem and its fishes. This inequity is increasingly being recognized as a violation of the Public Trust, which has a particularly long history in relation to sharing water and has been undergoing a revival in recent years in California litigation. (e.g., D. Des Jardins. 2022,

But the Plan also failed because the governance structure for Delta water and fishes has not been prepared for unanticipated changes to Delta habitats, especially those related to climate change and invasive species. Even the scientific community has been surprised by the rate of change, if not the trajectory. A grand experiment is underway to see if current Delta habitat can support a re-established, self-sustaining population of Delta Smelt. Regardless, the severe decline of Delta Smelt is a major indicator of the Plan’s failure and of the failure of more recent management efforts (Börk et al. 2020). Unless large-scale action is taken to make Delta habitats more favorable to native freshwater fishes, the other native fishes in the Plan (and outside the Plan) will likely follow the trajectory of Delta Smelt, if on longer time scales.


An ecosystem-based approach is needed to allow native aquatic species and their ecosystems to persist (Mount et al. 2019). As the recovery Plan and the CalFed strategic plan show, using this approach has attractive features, but so far the approach has failed to protect native fishes. One option is to develop biological goals for the Delta and then use multiple linked species models to define habitat conditions needed to reach those goals (Dahm et al. 2019). Then, all it takes is strong cooperative leadership, especially from state and federal fish and water agencies, to develop and use an ecosystem-based approach and to acquire the resources to implement it. Can these agencies actually work together, along with NGOs and diverse groups with interests in the Delta, to create conditions favorable for recovery of desirable species? In particular, can sufficient water be provided for the environment under the Public Trust or other laws? Or is it too late to ‘restore’ appropriate habitats? If the latter is the case, we need to decide what the Delta ecosystem of the future should look like and what species we want living there. Otherwise, nature will decide for us.

Peter B. Moyle is a Distinguished Professor Emeritus at the University of California, Davis and is Associate Director of the Center for Watershed Sciences. This blog is originally posting on Dr. Moyle’s birthday. Happy birthday Dr. Moyle!!! 🙂

Further Reading

Börk, K.S., P. Moyle, J. Durand, T. Hung, and A. L. Rypel. 2020. Small populations in jeopardy: a Delta Smelt case study. Environmental Law Reporter 50 ELR 10714 -10722 92020.

Dahm, C., W. Kimmerer, J. Korman, P. B. Moyle, G. T. Ruggerone, and C.A. Simenstad. 2019. Developing Biological Goals for the Bay-Delta Plan: Concepts and Ideas from an Independent Scientific Advisory Panel. A final report to the Delta Science Program. Sacramento: Delta Stewardship Council.

Hobbs, J.A, P.B. Moyle, N. Fangue and R. E. Connon. 2017. Is extinction inevitable for Delta Smelt and Longfin Smelt? An opinion and recommendations for recovery. San Francisco Estuary and Watershed Science 15 (2): San Francisco Estuary and Watershed Science 15(2).

Kimmerer, W.J. 2002. Effects of freshwater flow on abundance of estuarine organisms: physical effects or trophic linkages? Marine Ecology Progress Series 243:39-55.

Kimmerer WJ. 2008. Losses of Sacramento River Chinook salmon and Delta smelt to entrainment in water diversions in the Sacramento-San Joaquin Delta. San Francisco Estuary Watershed Science 6(2).

Mount, J., B. Gray, K. Bork, J. E. Cloern, F. W. Davis, T. Grantham, L. Grenier, J. Harder, Y. Kuwayama, P. Moyle, M. W. Schwartz, A. Whipple, and S. Yarnell. 2019. A Path Forward for California’s Freshwater Ecosystems. San Francisco: Public Policy Institute of California. 32 pp.

Moyle, P.B., R. D. Baxter, T. Sommer, T. C. Foin, and S. A. Matern. 2004. Biology and population dynamics of Sacramento splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: a review. San Francisco Estuary and Watershed Science [online serial] 2(2):1-47.

Moyle, P.B., J. Durand, and C. Jeffres. 2018. Making the Delta a Better Place for Native Fishes. White Paper, Orange County Coastkeeper and Center for Watershed Sciences, University of California. 63 pp.[available from author]

Moyle, P.B., J. A. Hobbs, and J. R. Durand. 2018. Delta smelt and the politics of water in California. Fisheries 43:42-51.

Moyle, P.B., A. D. Manfree, and P. L. Fiedler. 2014. Suisun Marsh: Ecological History and Possible Futures. Berkeley: University of California Press.

Moyle, P.B., R. M. Quiñones, J.V.E. Katz, and J. Weaver. 2015. Fish Species of Special Concern in California. 3rd edition. 842 pp. Sacramento: California Department of Fish and Wildlife.

[1] I apologize for giving the ERP Strategic Plan such short shrift. It has many good features including taking an adaptive management approach and basing management recommendations on conceptual models (full disclosure: I was a member of the Core Team that produced the document).

[2] Team members were Peter Moyle, Robert Pine (Executive Secretary, USFWS), Larry R. Brown (USGS), C.H. Hanson (Hanson Environmental), Bruce Herbold (USEPA), Kenneth M. Lenz (USBR), Lesa Meng (USFWS), Jerry J. Smith (San Jose State University), Dale Sweetnam (CDFG), and Leo Winternitz (CDWR).

Posted in Uncategorized | 4 Comments