Initial Sampling of the Carp-DEUM Project

By Kim Luke, John Durand, Rachel McConnell, Aaron Sturtevant, Nina Suzuki, Andrew L. Rypel

This spring, the Carp-Dependent Urgent Management (Carp-DEUM) Project began its first round of sampling in the UC Davis Arboretum before the Covid-19 lockdown. The project has two planned phases; a population estimate of common carp (and other arboretum fishes) in the Arboretum and a subsequent carp exclosure experiment. We want to know if removing carp can improve water quality and reduce harmful algal blooms, HABs. Carp are widely known to bioturbate sediments where previously deposited nutrients like phosphorus are bound (see YouTube video below). Re-suspension of phosphorus by carp leads to HABs, creating an interesting link between fish and human health. At the same time, this exercise also provides an opportunity to evaluate the unique fish community and limnological conditions within the Arboretum. 

Challenges in the Arboretum 

The Arboretum is the former pathway of Putah Creek, before the creek was diverted to the south of town in 1871 as part of bringing the railroad through. The channel has been heavily re-shaped by humans, making it a challenging place to sample. Natural banks have been replaced by concrete banks with steep, landscaped sides. However, a series of weirs on the eastern end of the Arboretum allow for periodic draining of parts of the Arboretum, which in turn present opportunities for studying fish. During spring this year, when the weirs were open, we prevented fish from escaping sampling sections with a block net, drained the water to a wade-able height and used a beach seine to sample every possible fish in the three middle sections (Figures 1 and 2). Of the five available sections, the three middle were chosen for initial sampling due to their relatively straight and narrow form.

Fig. 1. Undergrads Aaron and Kim setting up the block net. Photo: Nina Suzuki

Seining Methods

Once the sections were drained and the water level lowered, we began seining. A beach seine is a long net pulled manually by two poles (or brailers) on each end. The top of the net has a line of floats and the bottom a line of weights. We pulled the net along the channel from the lower weir to the upper weir, and rolled the seine up until it was flush against the concrete bank (because there is no beach to land it on). We then lifted the net from the water, and transferred the live fish into a large aerated container of water. We seined the lowest section just once because of the quantity of detritus and other debris on the bottom. The middle section was seined four times and the upper section five times in an effort to catch most of the fish present.

Fig 2. Undergrads Aaron and Kim seining for fishes. Photo: Gregory Urquiaga

What We Found

We found an abundance and diversity of fish in these sections, as well as turtles, crawfish–and even a cash register! The predominant fish species found in these sites were 1058 Fathead Minnow (Pimephales promelas), and 743 Black Bullhead (Ameiurus melas). We also seined 358 Mosquitofish (Gambusia affinis), 149 Green Sunfish (Lepomis cyanellus), and 263 native Sacramento Blackfish (Orthodon microlepidotus) (Figures 4). A few carp were found in two of the three sections, and a goldfish was found as well. We found fewer carp than anticipated, though we still suspect they are an abundant fish, as they are easily spotted in many other reaches of the Arboretum. The weir sections might make it difficult for carp to pass upstream, limiting the accessibility of carp to these sections compared to lower parts of the Arboretum where more carp are typically seen.

Fig. 3. Undergrad Rachel with a Carp. Photo: Gregory Urquiaga

One particularly interesting species found in abundance was the Sacramento Blackfish. Like Common Carp, this species also belongs to the cyprinid family, but unlike carp, they’re native to the Sacramento and San Joaquin watersheds. Sacramento Blackfish prefer the warm, turbid water of off-channel floodplain habitats that once dominated the Sacramento Valley in spring and summer. As adults, they eat algae and organic matter floating in the water–widely available in the Arboretum in summer. Given its murky waters full of algae, the Arboretum is an ideal habitat for Sacramento Blackfish. While preventing HAB’s and improving water quality is our goal, we will need to consider how removal of carp could affect the habitat of a native fish with a declining population.

Fig. 4. Species abundance data from initial fish sampling in the Arboretum waterway. Fish graphics from;;;;;

What’s Next?

Based upon our preliminary work, we intend to sample other sections of the Arboretum, potentially with different methods. The larger, more open areas in the lower west end of the Arboretum appear to host many more carp, which can often be seen by people above water cruising, rooting and feeding. Because it may be even more difficult to sample these sections with a seine, we will use fyke nets, which are a kind of modified fish trap made from netting to conduct mark-and-recapture experiments. Once we have a better estimate on the total carp population and biomass, we will move on to the second part of the project, installing exclosures, removing carp from exclosures, and monitoring the change in vegetation and water quality in the exclosures and control plots. Given the shutdown in response to the Covid-19 pandemic, further sampling is postponed for now. We will resume once we can do so safely. In the meantime, the western end of the Arboretum can be a safe place for exercise, fresh air and carp-viewing during this time. If you visit the Arboretum, be sure to wear a face mask, and maintain a safe social distance from other human visitors of at least 6 feet.

Kim Luke is a junior specialist at the Center for Watershed Sciences at the University of California, Davis. John Durand is a Research Scientist at the Center for Watershed Sciences. Rachel McConnell and Aaron Sturtevant are graduating from UC Davis and are researchers at the Center for Watershed Sciences community. Nina Suzuki is the Waterway Steward at the UC Davis Arboretum and Public Garden. Andrew Rypel is an associate professor of fish ecology and the Peter Moyle & California Trout Chair at UC Davis and an associate director at the Center for Watershed Sciences.

Further Reading

Lake Wingra carp removal –

Lake Kegonsa carp removal –

The “Carp Cannon” –

Carp Removal Studies

Lathrop, R. C., D. S. Liebl, and K. Welke. 2013. Carp removal to increase water clarity in shallow eutrophic Lake Wingra. Lakeline 33:23-30.

Carp and Macrophytes

Miller, S., and T. Crowl. 2006. Effects of common carp (Cyprinus carpio) on macrophytes and invertebrate communities in a shallow lake. Freshwater Biology 51:85-94.

Carp Effects on Water Quality

Bajer, P. G., and P. W. Sorensen. 2015. Effects of common carp on phosphorus concentrations, water clarity, and vegetation density: a whole system experiment in a thermally stratified lake. Hydrobiologia 746:303-311. 

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People, Agriculture, and Water in California

by Jay Lund


Farmworker housing in Corcoran, CA, 1940

Agriculture is California’s predominant use of managed water.  Agriculture and water together are a foundation for California’s rural economy.  Although most agriculture is economically-motivated and commercially-organized, the sociology and anthropology of agriculture and agricultural labor are basic for the well-being of millions of people, and the success and failure of rural, agricultural, and water and environmental policies.

The economic, ethnic, and class disparities and opportunity inequalities in urban life are urgent problems today.  Similar problems continue to exist in the structure of rural communities.  These rural problems often are more dire and difficult because the lower densities of rural settlement make these problems harder to observe, bring greater difficulties for organization, information, and logistics, and increase per-capita expenses for actions that provide services (water, education, transportation, housing, and all manner of human services).  The anthropologist Walter Goldschmidt observed these difficulties in California’s San Joaquin Valley in the 1940s (as John Steinbeck did in the 1930s).

Most serious social scientists and policy wonks of California agriculture (and agriculture in general) have read Walter Goldschmidt’s As You Sow (1947).  Those who haven’t should.

Despite decades of subsequent research, much of this work could be written and read insightfully today, and it retains much influence, as seen in Mark Arax’s recent history of California’s water development (2019).

Some, of many, points made in Goldschmidt’s book include:

  • History, expectations, and economic structure have implications for local social structure and the experience and opportunities of people individually and as social groups. The San Joaquin Valley’s social structures arose and arise from a history of demographic, economic, and social transitions built around migrations, farming, and perceived economic opportunities.  Goldschmidt discusses how these transitions often involved efforts to limit opportunities for some groups, particularly individuals and groups providing farm labor.
  • The book is a nice example of a fairly classical anthropological/ethnographic approach to studying social structure and public policy issues, showing how social scientists have long produced insightful results for policy problems, in this case on social, economic, and policy implications of modernization in agriculture and the urbanization of agriculture and rural life. (Feel free to comment on this post with citations and links to additional great examples – a few appear under further reading.)
  • The original presentation of what became the “Goldschmidt hypothesis,” that areas dominated by family farms tend to have more desirable socioeconomic conditions than industrial farming areas. This idea has been both supported and not supported by many more recent studies (cited under further readings), and might be less relevant today as remaining commercial family farms have grown in industrial scale since the 1940s.
  • The importance of effective local social and governmental organization and expectations for providing good schools, social services (human services, police, etc.) and infrastructure services (water, sewer, transportation, housing, energy, and solid waste). This applies for everyone, everywhere and at all times, I think.
  • Fundamental objectives of policy – these seem eternal and relate to more than just rural and agricultural policy (p. 254): “Three fundamental principles must underlie any constructive farm policy consistent with American democratic tradition:
    • The full utilization of American productive capacity to insure the welfare of all the people and the strength of our nation;
    • The preservation of our national resources to insure that maximum production can continue without loss from earlier exploitation of the land;
    • The promotion of equity and opportunity for those whose life work is devoted to the production of agricultural commodities.”
  • One footnote I enjoyed were references to the scholarly work of Clark Kerr on farm labor and policy in the 1930s. Clark Kerr went on to oversee the progressive transformation of the University of California in the 1960s as UC President.

This is another great book on California, agriculture, and water (one of many).  It nicely focuses on people, and some of the most economically and socially underprivileged people in California, then and now.  These places, and their like, still exist with social and economic structures that affect human health, well-being, and water management (Ramsey 2020).  Struggles to better achieve the universal political and economic objectives summarized by Goldschmidt in 1947 continue.

Considering people in agriculture is among the hardest and most central issues as California works to adapt agriculture to reduce groundwater overdraft and contamination, manage the Delta more sustainably, improve rural water services, protect ecosystem health, and improve rural life and opportunities.

As I read recently, “Read old to stay sharp.”  And then read some more.

Jay Lund is a Professor of Civil and Environmental Engineering at the University of California – Davis.  His now-ancient MA thesis at the University of Washington, Seattle, was an ethnographic study of urban liveaboards.

Further Reading

Arax, M. The Dreamt Land: Chasing Water and Dust Across California, Penguin Random House Books, 2019.

Goldschmidt, Walter R. (1947). As You Sow: Three Studies in the Social Consequences of Agribusiness. Montclair, N.J: Allanheld, Osmun and Co. Publishers, Inc.

Hoggart, K. (1987) Income Distributions, Labour Market Sectors and the Goldschmidt Hypothesis: the Nonmetropolitan United States in 1970 and 1980,” Journal of Rural Studies. Vol. 3. So. 3. pp. 31-245.

Peters, D. 2002. Revisiting the Goldschmidt Hypothesis: The Effect of Economic Structure on Socioeconomic Conditions in the Rural Midwest. P-0702-1. MERIC, Missouri Department of Economic Development.

Works by Michael Eissinger:–papers.html

Ramsey, A.R. (2020), “The Great Divide: California communities battle for rights to water,” Fresno Bee, 5 June,


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What’s the dam problem with deadbeat dams?

by Andrew L. Rypel, Christine A. Parisek, Jay Lund, Ann Willis, Peter B. Moyle, Sarah Yarnell, Karrigan Börk

Damming rivers was once a staple of public works and a signal of technological and scientific progress. Even today, dams underpin much of California’s public safety and economy, while having greatly disrupted native ecosystems (Quiñones et al. 2015, Moyle et al. 2017), displaced native peoples (Garrett 2010), and deprived residents of water access when streamflow is transported across basins. California’s dams are aging and many will require expensive reconstruction or rehabilitation. Many dams were built for landscapes, climates and economic purposes that no longer exist. California’s current dams reflect an accumulation of decisions over the past 170 years based on environmental, political, and socio-economic dynamics that have changed, sometimes radically. Former Secretary of the Interior Bruce Babbitt remarked, “Dams are not America’s answer to the pyramids of Egypt… Dams do, in fact, outlive their function. When they do, some should go.

Is California prepared for updating or removing this infrastructure, and what would be the consequences of inaction?

Fig. 1. Transformation of the West through government funded irrigation. From: Donald J. Pisani, To Reclaim a Divided West: Water, Law, and Public Policy, 1848-1902 125 (University of New Mexico Press, 1992)

We examined the National Inventory of Dams (NID) to assess the state of California’s dams. This database is a large data product curated by the US Army Corps of Engineers and contains information on most large dams in the USA (Fig. 2, 3, Table 1). Across the nation there are 91,468 NID dams, with 1,580 in California. Because there are multiple dams on some reservoirs, we estimate a total of 80,101 and 1,444 NID reservoirs in the USA and California, respectively.

Mean age of USA dams is 59 years old; but mean age of California dams is 72 years (Fig. 3). The 25% oldest CA dams are 93 years or older. California’s total reservoir storage capacity behind NID dams is 45 million acre-feet with a total reservoir surface area of 713,146 acres. For comparison, the total surface area of all managed natural lakes in Wisconsin is 943,130 acres, supporting a massive tourism industry (Rypel et al. 2019). Unfortunately, 1,097 (69%) of California NID dams are listed as high or significant hazards to human communities if they fail (Fig. 2, Table 2). These counts greatly underestimate problematic dams. In the USA, there are hundreds of thousands of smaller (often old) dams that fall outside of state and federal lists, and so are not included in the NID. This issue is broader than just dams too – infrastructure of all varieties is aging, representing a growing problem for humans and wildlife (Börk and Rypel 2020).

Fig. 2A. Map of all California dams in the NID.
Fig. 2B. Map of all NID dams in the contiguous USA. In both maps red circles represent dams classified in the NID as “high hazard” (i.e.,the potential for dam failure or facilities mis-operation to result in loss of human life, in addition to lower risk characteristics such as potential for economic and environmental losses). Gray circles represent all other dams.

Fig. 3. Histograms describing characteristics of dams and reservoirs in the USA and California. All data are from the National Inventory of Dams database. All log transformed data are (Log+1) transformations, however mean values in text boxes are non log-transformed values. Year Dam Completed was cropped at >1750 for ease of viewing.

We have already witnessed examples of the high cost of inaction. Recently in Michigan, two dams (Edenville and Sanford) failed and forced the evacuation of 10,000 residents in the midst of the COVID-19 pandemic – essentially a worst case scenario. Extreme rain in the midwest led to historic flooding in the Tittabawasse and Tobacco Rivers. Federal regulators had worried about failures at the Edenville Dam for 30 years due to an undersized spillway (see related news stories 1, 2, 3, 4).

Table 1. Summary statistics on age and storage capacity of dams and reservoirs in the USA and California.

Fig. 4. Oroville’s failing primary spillway during spring 2017. Photo source:

In California, we recall a near miss when the Oroville Dam spillway failed in early spring 2017. Floods damaged the primary spillway such that the California Department of Water Resources stopped flow over the spillway to better assess damage. Lake levels continued to fill and ultimately overtopped the emergency spillway, triggering unexpected erosion around the emergency spillway and the evacuation of 188,000 residents downstream. An independent forensic report of the Oroville incident highlights several lessons, including the need for periodic review of dam design and performance. Dams in California have failed before and a list of major events can be found here and here. Recent evaluations have indicated that conditions of California dams are below average, with one reporting a statewide grade of “C-” (Moser and Hart 2018;

Table 2. Summary of hazard classifications for USA and California dams based on the NID. The NID defines hazard potentials as: “High” –  dam failure is likely to result in loss of human life. “Significant” – likely no risk to human life, but a likelihood to cause economic and/or environmental losses. “Low” – likely no risk to human life and low anticipated economic and/or environmental losses. “Undetermined” – hazard designation not assigned; here, dams classified as “undetermined” were grouped with dams that had an N/A hazard potential.

Dams also can have catastrophic effects on natural ecosystems, especially in productive and species-rich large rivers (Poff et al. 1997). Dams fragment the hydrologic connectivity of ecosystems, and create massive physical barriers for migratory species, including salmon. American rivers are so extensively fragmented by dams, that Benke (1990) estimated only 42 high quality free-flowing rivers remain in the USA – zero in California. In the Sacramento Valley, abundant spring-run Chinook salmon would once migrate long distances and over-summer high in cold mountain streams. Now, spring-run Chinook salmon are listed under the US Endangered Species Act, largely because of disruptions from dams. In the San Joaquin River, construction of Friant Dam preceded a rapid eradication of spring-run Chinook from this ecosystem. Expensive efforts to reintroduce spring-run Chinook salmon hold promise; but fish are still fundamentally blocked from naturally cold habitats by rim dams. The McCloud River once had all four runs of Chinook salmon, plus steelhead and bull trout. None of these species occur in the McCloud River anymore, and bull trout have gone extinct in California. Helfman (2007) suggested that ~70% of global freshwater fish extinctions can be attributed to “habitat change,” including effects of dams.

Fig. 5. Migratory salmon are strongly and negatively affected by dams. This photo shows the types of habitats that salmon often cannot ascend to in California any longer. “Salmon on spawning beds” by John Cobb 1917 in Pacific Salmon Fisheries. Annual Report to the Secretary of Commerce, 1915-1916, Washington DC. Downloaded from Wikicommons and the Freshwater and Marine Image Bank.

Beyond the catastrophic failures and ecological impacts of individual dams, California’s dams create disastrous outcomes for disadvantaged communities, including Native American Tribes. Tribes along the Klamath have spent years struggling to preserve the river and its sensitive salmon populations. Removing deadbeat dams like the four major dams on the Klamath River along the CA-OR border exemplify the types of projects where removal makes economic sense to dam owners and begins to address damage to indigenous communities of color and aquatic ecosystems. NGOs have long been interested in dam removals like this. However, the slow speed of these removals highlights the complicated details involved in removal. Such experiences suggest efforts addressing aging dams must start early.

The California Division of Safety of Dams (DSOS) has existing responsibilities that include: 1) Performing independent analyses to understand dam and appurtenant structures performance; 2) Overseeing construction to ensure work is being done in accordance with approved plans and specifications; and 3) Inspecting dams on an annual basis to ensure it is safe, performing as intended, and is not developing issues. Roughly 1/3 of these inspections include in-depth instrumentation reviews of the dam surveillance network data. Every state (except GA) has a dam safety program, and the CA program is the largest in the USA. Therefore, the DSOD plays a major role in working with dam owners to identify deficiencies in California. The size of the DSOS program suggests this resource could be leveraged in CA to take a leading role in dam safety. Response to aging dams has been mostly reactive. Studies of dam behavior during earthquakes has been a long focus of research, and such questions are obviously important in California. In a 1977 USGS analysis of dam structural behavior during Earthquakes, half the study systems were in California. Many of the major dam failures in California were triggered by earthquakes.

California is well-positioned to lead in proactively addressing aging dams; however, the window for leadership is likely closing. The challenge will be in developing balanced approaches that prioritize the dams, rivers and people in most need of help (Null et al. 2014). To advance policy on dealing with obsolete dams, we suggest California should:

(1) Form a “California Dams Blue Ribbon Panel”. Given recent experiences in California and nationally, it seems timely for the State of California to take stock and assess the long-term performance of its dam regulation capabilities. Efforts are needed to assist the public, local governments, and dam owners in identifying at-risk dams in need of action. A California dams blue ribbon panel would help develop a framework for decision making that could be applied to dams across the state. The panel’s charge would be to: i) evaluate the state’s existing regulatory framework for evaluating public safety and environmental performance of dams; ii) estimate overall magnitude of current and future dam safety and environmental problems (especially with climate change); iii) recommend improvements to state regulatory capacities and support for owners in terms of dam safety and environmental performance. Panel findings might be published as a white paper for others to use and reference. The panel should have broad representation from multiple stakeholder groups including roles for Native American tribes and other disadvantaged and at-risk communities. Ultimately, a blue ribbon panel and white paper format would produce faster results than a larger task-force style effort, but could lead to a larger effort if necessary.

(2) Develop a structured assessment tool. An objective science-based prioritization framework would be useful. Structured assessments are a class of tools that can more transparently and objectively analyze natural resource management decisions in a careful and organized way (Gregory et al. 2011). Such models are popular in some federal agencies and have already aided decision-making in other areas of CA state government, such as welfare services. A directed action to build such a tool could rapidly aid agencies charged with managing aging dams and scoring restoration projects. Once the tool is available, proposed on-the-ground restoration projects could be scored more transparently. Projects that propose work on high priority dam sites might then be prioritized for funding. Thus restoration projects funded through state bond propositions (e.g., Prop 1 and Prop 68) net the state and its investors the most “bang for their buck”, while simultaneously leveraging science and enhancing transparency and accountability. Improvements to the assessment method could form a way of incorporating new scientific findings or ways of thinking over time.

(3) Revisit existing legal frameworks. Dams sit at the crossroads of state and federal law and so face a complex mess of state and federal laws and regulation. Prominent legal issues will include liability for flooding and for environmental damages associated with dam removal (which will differ between privately and publicly owned dams), environmental reviews mandated under state and federal endangered species and environmental impact laws, and the myriad dam-specific laws. This is an area of active research in environmental law (see here recents legal debates on issues facing dams in the Western USA). Some examples of laws that have legal relevance to the operation and use of dams include the California Fish and & Game Code 5937 – “Water for Fish” (Börk et al. 2012). Additionally, under the authority of the Federal Power Act, the Federal Energy Regulatory Commission (FERC) retains exclusive authority to license non-federal hydropower projects on navigable waterways, federal lands, or areas connected to the interstate electric grid. Opportunities for dealing with deadbeat dams also present themselves during the FERC relicensing process. Indeed this was a critical piece to the removal of the Klamath Dams. Most dams currently face little regulation and receive little attention from policy makers.

(4) Explore reservoirs as novel habitats for declining fishes. Because many California reservoirs contain expansive coldwater habitats, scientists have occasionally suggested reservoirs could be capable of serving as emergency rooms for declining native fishes. Some California reservoirs have developed self-sustaining populations of Chinook salmon (Perales et al. 2015). These populations may be needed as a backup plan in the event a disease or other disturbance afflicts the primary Sacramento River salmon runs. We support this concept and note that some reservoirs and dams may hold hidden value in this regard. Reservoirs successfully managed as novel habitat for native fishes might ultimately be scored higher for dam renovation or repurposing funds.

Every dam is unique and there will be no one-size-fits-all approach. Ultimately dams are owned by entities ranging from the state of California, water agencies and districts, counties, cities, homeowner’s associations, private companies, or private citizens. Hansen et al. 2020 identified that in general dams can be mitigated, renovated, repurposed, or eliminated. In California, dams have been important in controlling water availability, both reducing the frequency of catastrophic floods and making water available for cities and irrigated agriculture in our highly variable Medeterranean climate. They will remain vital in the future, perhaps even more so with anticipated changes in climate. Ultimately, some dams will be fine, some will need to be removed, and some modified. At this point however, an overarching strategy is needed to guide efforts to identify which dams are suited to our uncertain future and which are more risky than worthwhile, then rank them with the best rubric we can devise (e.g..Quiñones et al. 2015). Planning for aging dams is not unlike planning for a pandemic. It seems as though you don’t need it…until you do.

Fig. 6. The upper Klamath River in Oregon was once accessible to salmon migrating from the Pacific Ocean through California. The Klamath dam removals promise to reconnect some of these habitats. Photo by Bob Wick, source

Further Reading

ASCE Committee on America’s Infrastructure. 2017. Infrastructure in California. ASCE: Reston, Virginia. https://

Benke, A.C. 1990. A perspective on North America’s vanishing streams. Journal of the North American Benthological Society 9: 77-88.

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

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

France, J.W., I.A. Alvi, P.A. Dickson, H.T. Falvey, S.J. Rigbey, and J. Trojanowski. 2018. Independent forensic team report Oroville Dam spillway incident. Technical Report.

Garrett, B.L. 2010. Drowned memories: the submerged places of the Winnemem Wintu. Archaeologies 6: 346–371.

Gregory, R., L. Failing, G. Long. T. McDaniels, and D. Ohlson. 2011. Structured Decision Making: A Practical Guide to Environmental Management. Wiley-Blackwell, West Sussex, UK

Grabowski, Z.J., H. Chang, and E.F. Granek. 2018. Fracturing dams, fractured data: Empirical trends and characteristics of existing and removed dams in the United States. River Research and Applications 34: 526-537. 

Grantham, T., and P. Moyle. Flagging problem dams for fish survival. California WaterBlog, October 24, 2014.

Hansen, H.H., E. Forzono, A. Grams, L. Ohlman, C. Ruskamp, M.A. Pegg, and K.L. Pope. 2020. Exit here: strategies for dealing with aging dams and reservoirs. Aquatic Sciences 82.

Helfman, G.S. 2007. Fish conservation: a guide to understanding and restoring global aquatic biodiversity and fishery resources. Island Press, Washington D.C. USA.

Moser, S.C., and J.F. Hart. 2018. Paying it forward: the path toward climate-safe infrastructure in California. A report of the climate-safe infrastructure working group to the California State Legislature. Technical Report.

Null, S.E., J. Medellin-Azuara, A. Escriva, M. Lent, and J. Lund. 2014. Optimizing the  195–215Dammed: Water Supply Losses and Fish Habitat Gains from Dam Removal in California. Journal of Environmental Management 136: 121-131.

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

Poff, N.L., J.D. Allan, M.B. Bain, J.R. Karr, K.L. Prestegaard, B.D. Richter, R.E. Sparks, and J.C. Stromberg. 1997. The natural flow regime. BioScience 47: 769-784.

Quiñones, R.M, T. Grantham, B. N. Harvey, J. D. Kiernan, M. Klasson, A. P. Wintzer and P.B. Moyle. 2015. Dam removal and anadromous salmonid (Oncorhynchus spp.) conservation in California. Reviews in Fish Biology and Fisheries 25: 195–215. 

Rypel, A.L., T.D. Simonson, D.L. Oele, J.D.T Griffin, T.P. Parks, D. Seibel, C.M. Roberts, S. Toshner, L.S. Tate, and J. Lyons. 2019. Flexible classification of Wisconsin lakes for improved fisheries conservation and management. Fisheries 44: 225-238.

US Army Corps of Engineers: Federal Emergency Management Agency. National Inventory of Dams. 2018. Washington, DC USA


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Black Lives Matter

We have elected to suspend our regular posts for this week. 

Institutional racism is urgent and real, and should divert us from topics of California water at this time. The deaths of George Floyd, Breonna Taylor, Ahmaud Arbery, and countless others are horrific, and the effects of a pandemic are disproportionately affecting communities of color. At the Center for Watershed Sciences, we acknowledge that while we strive for equity and inclusion in our science in line with our Principles of Community, we have a long way to go to address racism and unconscious bias. 

We admire all who have flooded our social media and news this week with demonstrations of the great power of diversity in our nation and our scientific fields. We support and encourage everyone to have the hard conversations and do the hard work to learn more about how to better support all people in our communities. It is moments like this that remind us that bearing witness to racism and injustice is critical and must be a core part of our mission.

These are difficult and challenging times, where current thinking and actions have been inadequate. We have provided a list of resources courtesy of the Graduate Group in Ecology’s Diversity Committee to advance our work of creating a community that is safe, welcoming, and inclusive. We ask you to join us in advocating for and creating safe and equitable environments for living, working, and practicing science.


Executive Committee, Center for Watershed Sciences: Andrew L. Rypel, Jay Lund, Sarah Yarnell, Ryan Peek, Cathryn Lawrence, Thomas Harter

Principal Investigators, Students, Postdocs, and Researchers, Center for Watershed Sciences: Ann Willis, Carson Jeffres, John Durand, Anna Sturrock, Robert Lusardi, Rusty Holleman, Peter Moyle, Josue Medellin-Azuara, Katrina Jessoe, Caroline Newell, Amber Lukk, Scout Carlson, Ryan Hitchings, Francine DeCastro, Kimberly Luke, Elsie Platzer, Dylan Stompe, Brian Williamson, Aaron Sturtevant, Malte Willmes, Avery Kruger, Meghan Holst, Mollie Ogaz, Kelly Neal, Nick Corline, Priscilla Vasquez-Housley, Adriana Alarcon, Eric Holmes, Madeline Frey, Sage Lee, Miranda Tilcock, Marisa Levinson, Alexandra Chu, Christine Parisek, Rachelle Tallman, Gabriel Singer, Colby Hause, Emily Jacinto, David Ayers, Chris Jasper, Mattea Berglund, Parsa Saffarinia

Further Reading

Teaching and higher education:

Haynes, C., & Bazner, K. J. (2019). A message for faculty from the present-day movement for black lives. International Journal of Qualitative Studies in Education, 32(9), 1146-1161.

Aggie Brickyard Spring: Vol VIII 2019 ‘What’s On Your Mind?’: Everyday Actions to Up Your Inclusivity Game, by the GGE Diversity Committee:

Teaching in times of crisis:

Ways white people can take action for racial justice:

5 ways white people can take action in response to white and state-sanctioned violence:

75 things white people can do for racial justice:

Guide to allyship:

Anti-racism resources for white people:

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An Introduction to State Water Project Deliveries

By Nicole Osorio

Most people in California receive some of their drinking water supply from the State Water Project (SWP). The SWP also supplies water to over 10% of California’s irrigated agriculture.  The SWP and its service area span much of California, delivering water to 29 wholesale contractors shown in Figure 1.

Each year, the Department of Water Resources announces SWP Table A allocations which inform water contractors’ SWP deliveries: “Table A”, “Carryover”, and “Article 21.”  What are these different SWP delivery categories and how do they work?

Fig 1

Figure 1: State Water Contractors (SWC) of California by Region (“Update on Delta Conveyance” 2019)

Table A, Carryover, and Article 21 are three types of SWP deliveries described in this post. Some additional, more minor, deliveries are made as: transfer and exchange Table A, and Pool Water deliveries.

The 2020 water year is dry, but the recent May storms led to the increased 2020 SWP Allocation from  15% to 20% of SWP contractors requested “Table A” delivery amounts. Figure 2 compares the initial and final SWP allocations from 1996-2020. Some lessons from this graph include:

  • 2006 was the last 100% allocation year, 14 years ago.
  • Final allocations usually increase significantly from the initial allocation estimate sent to SWP contractors (usually in October). However, final allocations (usually in May) could be less than initial allocation estimates in extreme dry years.
  • Drought years tend to have little or no increases from initial to final SWP allocations (such as 2007-2009 and 2012-2015).
  • It is likely that 2020’s final allocation will be 20%. The last 20% final allocation year was in 2015, one of the driest years on record.


Figure 2: Historical SWP Initial and Final Allocations (1996-2020) (CA DWR 2020b). May 2020 allocation seems likely to become the 2020 final.

Figure 3 shows Table A, Carryover, and Article 21 deliveries from 2000-2017. Minimum, average, and Maximum Table A and carryover statistics were combined because both are categorized under Table A water while Article 21 deliveries are made above the approved Table A amounts. 2014 had the least Table A and carryover deliveries at 475 TAF while 2003 contained the most at 3202 TAF.

fig 3

Figure 3: Historical SWP Deliveries (TAF) by category from 2000-2017 (Data from CA DWR 2009, 2012, and 2018).

What is Table A?

Table A allocations represent “a portion or all of the annual Table A amount requested by SWP water contractors and approved for delivery by DWR (CA DWR 2019).” DWR and the public water agencies and local water districts developed the SWP’s long-term water supply contracts in the 1960s. Table A contract amounts originated from these long-term contracts and have been amended. The 1994 Monterey Agreements significantly revised the long-term water supply contracts. Table 1 presents each contractor’s maximum Table A contract delivery amount, adding up to 4.17 million AF, anticipated to be the SWP’s ultimate delivery capability in the 1960s (an amount rarely actually available). As a wet year example, the last column indicates how much each water contractor utilized their Max Table A amount in 2006, a 100% allocation year. San Joaquin contractors were more likely to take their full Table A and supplement water supplies with Article 21 water, described later.


Table 1: Share of total Maximum Table A amount (4.17 MAF) between all 29 SWP Contractors at Calendar Year 2020 (CA DWR 2019) and % Utilization of Table A deliveries at 100% Allocation year in 2006 (CA DWR 2015). Largest Table A contract holders and highest 100%  allocation utilizers highlighted. 2006 total deliveries also include turnback pool water.

What is Carryover water?

Carryover water is a portion of Table A water that contractors may save for next year’s delivery. Carryover requests allow SWP contractors to store some of their annual allocation for the next year, and not lose undelivered allocation at the end of the SWP contract year, December 31. When contractors request carryover for next year’s delivery, that water is stored in the SWP’s share of San Luis reservoir in Merced County.

However, storing carryover water in San Luis reservoir has a low operating priority and so brings a risk. SWP contractors can lose this stored carryover water when San Luis Reservoir fills. In the 2017 wet year, some contractors (Santa Barbara County , Crestline Lake Arrowhead Water Agency and San Gorgonio Pass Water Agency) needed to transfer their carryover water from San Luis to another non-SWP facility to prevent losing their carryover storage. Figure 4 shows how San Luis filled in 2017 for the first time since 2011, following the 2012-2016 drought.


Figure 4: San Luis reservoir levels (TAF) from January 2000 to April 2020 with wettest and driest water year designations using the Sacramento Valley Index (CA DWR 2020a; c).

Overall, San Luis carryover water provides water contractors with a safety net in dry years, like 2020. During the 2012-2016 drought, contractors almost exclusively relied on only Table A and carryover. 2014 was the only year when carryover deliveries (383 TAF) exceeded those of Table A (92 TAF) (Figure 3). Carryover storage acts as a “savings bank account” which water agencies can draw on in dry conditions, but at some risk in very wet years.

What is Article 21 water?

Article 21 (described in water contracts) allows water contractors to take deliveries above approved and scheduled Table A amounts (CA DWR 2019). Article 21 is sometimes called interruptible, unscheduled, or surplus water.  It is offered predominantly in wet years (2005, 2006, 2011, and 2017) (Figure 5).


Figure 5: Historical Article 21 deliveries from 2000-2017 (Maven’s Notebook, 2018)

As an ephemeral surplus supply, contractors cannot “request” and schedule Article 21 deliveries in advance. DWR can only offer Article 21 deliveries when (CA DWR 2018, 2019; CA WATER COMMISSION: Article 21 water, explained):

  1. Article 21 deliveries do not interfere with SWP allocations.
  2. Excess water is available in the Delta.
  3. Conveyance is not being used for SWP purposes or scheduled SWP deliveries.
  4. Article 21 water may not become Carryover water, stored in SWP facilities.

The different types of SWP deliveries are akin to managing household finances. Table A deliveries are like a monthly paycheck for fixed recurring expenses. Carryover requests let you save part of your “Table A paycheck” for the future. Lastly, Article 21 deliveries are like an unusual annual bonus. You could splurge your “Article 21 water” bonus for direct retail delivery, or save it in an aquifer or reservoir outside the SWP.

In California’s highly variable climate, each water contractor must match these SWP water supplies, other local and regional water resources, and water demands for this year’s water use and in preparing for future droughts. In this dry 2020 year, SWP contractors are likely aware that the next drought could be just around the corner.

Nicole Osorio is a first year Master’s student of Water Resources Civil Engineering at the University of California, Davis.

Further Readings

CA DWR and State Water Contractors. (1994). The Monterey Agreement – Statement of Principles by the State Water Contractors and the State of California, Department of Water Resources for Potential Amendments to the State Water Supply Contracts. < > (May 04, 2020)

CA DWR. (1996). Bulletin 132-95: Management of the California State Water Project. Sacramento, CA. <; (May 04, 2020)

CA DWR. (2009). DRAFT: The State Water Project Delivery Reliability Report 2009. Sacramento, CA.

CA DWR. (2015). The State Water Project Final Delivery Capability Report 2015. Sacramento, CA.

CA DWR. (2018). The Final State Water Project Delivery Capability Report 2017. Sacramento, CA.

CA DWR. (2019). Bulletin 132-17: Management of the California State Water Project. Sacramento, CA, 547.

CA DWR. (2020a). “California Data Exchange Center.” California Data Exchange Center, <; (Apr. 27, 2020).

CA DWR. (2020b). “State Water Project Historical Table A Allocations: Years 1996-2020.” <; (Apr. 25, 2020).

CA DWR. (2020c). “Water Year Hydrologic Classification Indices.” Department of Water Resources California Data Exchange Center, <; (May 23, 2020).

Maven’s Notebook. (2018). “CA Water Commission: Article 21 water, explained.” MAVEN’S NOTEBOOK | Water news, <; (Apr. 25, 2020).

Update on Delta Conveyance.” (2019). <; (Nov. 14, 2019).

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Drawing boundaries with DNA to improve conservation

by Ryan Peek

Foothill Yellow-legged Frogs have begun to spawn, laying small snow-globe sized egg masses in streams and rivers. They are one of the few stream-breeding frogs endemic to California and Oregon. This species is a good indicator of stream health because they link aquatic and terrestrial ecosystems and are strongly tied to natural seasonal cues associated with local hydrology. Historically, they occurred in streams and rivers throughout California and Oregon, but, as with many amphibians, they have precipitously declined in many parts of their range due to river regulation, habitat loss, and disease.

First petitioned for listing under the California Endangered Species Act (CESA) in 2016 by the Center for Biological Diversity, the California Fish and Game Commission recently listed Foothill Yellow-legged Frogs (Rana boylii) in February 2020. But unlike other species listed under CESA, Foothill Yellow-legged Frogs are one of the first species where genetic data were used to introduce more nuance into the regulatory process. Only a few other species have used a genetic basis to identify groups for listing under the CESA. For example, Coho Salmon Oncorhynchus kisutch (listed in 1995) used a single status listing for the species based on existing genetic data. Similarly, the Fisher (Pekania pennanti) was also listed/not listed using evolutionarily significant units (ESUs), but the species is extremely geographically separated, unlike the historically wide-ranging Foothill Yellow-legged Frog. For Foothill Yellow-legged Frogs, different genetically distinct groups were given different listing status (Threatened, Endangered, or listing not warranted at this time). This listing is not an endpoint, it reflects successful collaboration between researchers and regulators to provide a pathway to better prioritize long-term management and conservation of one of California’s iconic species.

Fig. 1. A Foothill Yellow-legged Frog (Rana boylii).

While protecting and conserving one of our few native frog species is important, using the same uniform listing and management strategy for every frog population in California may not be practical. The Foothill Yellow-legged Frog has a large range that historically encompassed most of California, thus a blanket approach to listing and conservation management across the state may not be very effective. Different regions of the state have different impacts on the species; therefore it makes sense and is likely more effective and cost-efficient to manage conservation at a regional scale. A more nuanced approach also avoids placing a regulatory burden on entities in areas where the species appears to be doing well. Finding options to build more flexibility into the system we use to manage and conserve our natural resources is important for long-term success. The crux of this success is best illustrated by a deceptively straightforward map (Figure 2). Despite its simplicity, this map is a result of several years of genetic research and collaboration between multiple agencies and universities. Its use in the state listing process is a relatively novel application of conservation genetics.

Ultimately the boundaries on this map provide a flexible but robust way to prioritize each clade or genetic group  independently. Because each group is genetically distinct, the map allows us to describe each group using metrics that include genetic diversity as well as landscape change and flow alteration. Measuring genetic diversity within and among each of these groups is important because genetic diversity provides a species with the ability to adapt to changing conditions (i.e., evolve). A loss of diversity often signals extreme population and range reductions, and is associated with a loss of fitness (reproductive success and survival). Genetic data enables us to quantify which groups had more or less genetic diversity, and this was combined with regional information about the impacts of flow regulation, habitat alteration, and disease, to identify which groups may be most at risk of extinction. This allowed the CDFW to identify, prioritize, and list each clade separately, and make clade-specific listing recommendations, which provided a much more practical way to evaluate and apply CESA in a historically wide-ranging species (CDFW 2020).

And importantly, there was consensus in these findings; a separate independent study conducted at UCLA found a strikingly similar pattern, lending additional support to these genetic boundaries (McCartney-Melstad et al. 2018). The boundaries on this map can be updated, and these data provide additional benchmarks that give us insight into the status and health of different populations which can be compared across time and location. Translating the information that DNA provides us provides a powerful tool to help bridge the need for “the best available science” in conservation, but ultimately the most effective tools rely on our ability to collaborate and communicate across boundaries.

The map shows the genetic boundaries for distinct interbreeding populations, called clades, for the Foothill Yellow-legged Frog. This map helped define how and where the Foothill Yellow-legged Frog would be listed under CESA, and it provides a unique and powerful way to use DNA as a way to inform conservation.

Fig. 2. Foothill Yellow-legged Frog (Rana boylii) genetic groups or “clades.” (Peek 2018).

Drawing boundaries with DNA is not new. Delineating geographic ranges for organisms based on their underlying genetic code has been one of the foundational components of population genetics, but integrating this information into legal conservation frameworks like the state and federal Endangered Species Acts has been a slow process. The Endangered Species Act requires decisions be based on the “best available science.” While this sounds like a decision that would be heavily based on quantifiable data, it requires judgement and interpretation to incorporate the full spectrum of biological data when classifying a species as Endangered, Threatened, or listing not warranted. With the advent of modern genetics, the types of data that can be used can be powerful and informative, but also complicated and very dense. So how do we use genetic tools and translate this information into defensible policy and legal conclusions?

In an era where we can generate more data than ever before, where specializations abound, and the competition to maintain funding to conduct research has greatly emphasized novelty, the ability to translate across disciplines and find ways to effectively apply science may seem rare. Ultimately, there is a continuum between research and management, and from a management perspective, the best information is actionable, discrete, and can be integrated into existing policy frameworks. For scientists interested in applied research, this means understanding the context where the research may be used, identifying what gaps exist within a given framework, and actually talking with the folks who will use the science.

When I started my dissertation, I tried to think critically about what would be useful for management. I spent time talking to resource managers at state and federal agencies, and I tried to maintain communication and collaborations throughout the process. In particular, I tried to ask what pieces of information or research would be critical for helping inform conservation of the species. Maps are crucial for identifying, prioritizing, and planning, so identifying and refining boundaries for conservation units (distinct populations, or clades) was an important component in the listing process. In the end, some key pieces of my dissertation were used in the Status Review used for the California Department of Fish & Wildlife (CDFW) listing recommendations for the Foothill Yellow-legged Frog (CDFW 2019). While it is bittersweet to work with a species that is at risk of extinction, it is encouraging to participate and contribute in a meaningful way to a conservation process as a scientist.

Ryan Peek is a post-doctoral researcher at the Center for Watershed Sciences, UC Davis.

Further Reading:

California Department of Fish and Wildlife (CDFW). (2019). A Status Review Of The Foothill Yellow-legged Frog (Rana boylii) In California.

CDFW. (2020). Notice of Findings for Foothill Yellow-legged Frog (Listing Decision).

McCartney-Melstad, E., Gidiş, M., & Shaffer, H. B. (2018). Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining Foothill Yellow-legged Frog. Heredity121(2), 112–125.

Peek, R.A. (2018). Population Genetics of a Sentinel Stream-breeding Frog (Rana boylii) [Ecology]. PhD Dissertation. University of California, Davis.

Peek, R. (2020). Rana boylii Population Genetics website.


Laura Patterson has been instrumental as an contributor and collaborator; she coordinated and prepared the status review report for CDFW. In addition, Brad Shaffer, Sarah Kupferberg, Amy Lind, Sarah Yarnell, and Jennifer Dever have all provided data and critical research towards conservation of this species.

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How reliable are Groundwater Sustainability Plans?

by Alvar Escriva-Bou, Jay Lund, Josue Medellin-Azuara, and Thomas Harter

Earlier this year, the first local Groundwater Sustainability Plans (GSPs) were submitted to California’s Department of Water Resources for basins with the most severe groundwater overdraft.  To comply with the Sustainable Groundwater Management Act, these plans must address any “significant and unreasonable” impacts of groundwater overdraft that occurred after January 1, 2015, including lowering groundwater levels and other “undesirable results.” The math for ending overdraft is simple: groundwater basins must balance their budgets, by increasing groundwater recharge and reducing pumping.

In principle, evaluating the adequacy of these plans to achieve sustainability should also be simple: Does the anticipated reduction in pumping plus increase in recharge equal or exceed the basin’s long-term rate of overdraft?

In practice, however, it’s not so simple. Water supply in California is dynamic and variable, and groundwater overdraft can vary widely from year to year. In dry years more groundwater is pumped to replace reductions in surface water deliveries, while in wet years more water is recharged. Cropping patterns also vary annually with market conditions, agronomic conditions (fallowing, salinity, etc.), and labor availability, all of which can affect regional water use. Even estimates of long-term average overdraft have considerable uncertainty, due to California’s hydrologic variability and uncertainties in data and models used to estimate water balances. For instance, model estimates of average statewide groundwater overdraft for different periods range from 1.4 to 9.1 million acre-feet (maf) per year (Brush et al., 2013; Escriva-Bou, 2019; Famiglietti et al., 2011; Faunt et al., 2009; Xiao et al., 2017). Considering all these uncertainties, plans based on rigid and static assumptions are bound to miss their targets.

So how do we know if a proposed Groundwater Sustainability Plan will succeed? Or, put another way, how can we plan for sustainability given all these uncertainties?

Although we can’t ever be sure, we can make reasonable estimates that account for the range of uncertainties. In a recent paper, we outline a method for estimating the likelihood of achieving groundwater sustainability. This method highlights the relationship between restrictions on groundwater pumping and the likelihood of maintaining groundwater levels, trade-offs between pumping restrictions and agricultural revenue losses, and implications of defining thresholds—such as minimum groundwater levels—as part of sustainability plan rules.

Our analysis highlights the dynamic character of hydrology and water use in California’s Central Valley. Although we illustrate the method using regional modeling estimates of overdraft and hydrology that were available prior to the release of the new GSPs, the analysis is relevant for groundwater sustainability agencies as they implement and refine their plans going forward. The method can be applied to help estimate uncertainties in these plans, reduce these uncertainties over time, and plan adaptively for sustainability, considering the economic consequences of varying pumping restrictions and thresholds.

Here we highlight some of the paper’s main lessons.

Greater pumping restrictions increase the likelihood of ending overdraft

Uncertainty in overdraft arises from the state’s highly variable climate, uncertainties in future water use decisions, and imperfections in models and data representing water balances.

We estimated uncertainty in annual overdraft for 21 Central Valley sub-regions using the results of recent hydrologic history (1975-2003) of two Central Valley groundwater models (USGS’ CVHM and DWR’s C2VSIM).  Each model’s results show variability in annual water balances and overdraft. The differences between these models’ results can represent the uncertainty of data and models.

Our analysis directly combines both sources of uncertainty. A simple approach is to estimate average annual overdraft as the average of model results, and estimate the variability of annual overdraft from the standard deviation of these results.  A simple statistical equation can be used to estimate the probability of accumulated future overdraft for a given net reduction in pumping over a specified number of years. By defining sustainability as the inter-annual fluctuation of the groundwater table that does not exceed a minimum threshold (Figure 1), it is possible to estimate the probability of achieving sustainability as a function of the net reduction in groundwater use.

Figure 1 blog

Figure 1: Hypothetical representation of changes of groundwater storage over time and definition of minimum thresholds to define sustainability


Figure 2 shows results for all 21 Central Valley sub-regions. A net reduction in water use equaling the average level of overdraft has a 50% chance of achieving sustainability in any time period. Greater reductions in net water use increase the probability of ending overdraft, although the rates (the slope of the curves) vary across sub-regions depending on local conditions. For example:

  • Sub-regions that are sustainable (but that could become unsustainable with unfavorable conditions). Sub-regions 9 (Delta) and 12 (Turlock Basin) are sustainable on average, with positive average annual change in groundwater storage. Without net water use reductions their chances of balancing groundwater levels in 20 years exceed 70%, but with unfavorable hydrologic conditions they would have to reduce net water use to ensure sustainability.
  • Sub-regions with low levels of unsustainable pumping. Sub-regions 10 (Delta-Mendota Basin) and 11 (Modesto and southeast San Joaquin Basin) have some average annual overdraft (< 10 taf/year). Without net water use reduction, they would have almost a 50% chance achieving sustainability over next 20 years. To ensure sustainability for any future hydro-climatic conditions, they would have to reduce water use by much more (~ 80 taf/year).
  • Sub-regions with large values of unsustainable pumping. Sub-regions 8 (the valley floor east of the Delta) and 13 (Merced, Chowchilla, and Madera Basins) have larger average annual overdraft (55 and 116 taf/year respectively). Their larger variances also make the curves flatter. These sub-regions still have a 20% chance of becoming sustainable without reducing water use. Net use reductions at least three times the current level of overdraft are needed to reliably achieve sustainability.

For longer regulatory horizons, the range of pumping reductions for different probabilities narrows around the estimated average annual overdraft because the statistical average becomes more likely to dominate over rare favorable or unfavorable hydrology over longer periods.

Two caveats are worth mentioning. First, this analysis assumes all overdraft is addressed by net reductions in groundwater use. Smaller reductions will be needed if groundwater recharge can be increased in wet seasons and years. Some estimates find that 15-30% of long-term overdraft in the Central Valley could be supplied by additional groundwater replenishment (DWR 2018; Kocis and Dahlke 2017, Escriva-Bou and Hanak 2018). This could significantly reduce the economic impact of pumping restrictions. Second, our results are based on DWR’s C2VSim and USGS’s CVHM models, developed for the Central Valley. These models may have some difficulties representing local groundwater basins—the relevant geographic focus for GSPs. Even if GSPs are able to incorporate more accurate local estimates of overdraft and historic hydrology, it will still be important for these plans to estimate the uncertainties of these and other parameters in evaluating the likelihood of attaining groundwater sustainability.

Figure 2 blog

Figure 2. Probability of ending groundwater overdraft in year 2040 for a range of net groundwater pumping reductions for all Central Valley sub-regions

Increasing the likelihood of achieving sustainability rapidly raises agricultural economic losses

We also estimated economic costs and probabilities of achieving sustainability over different periods. Here, we assumed the sub-regions achieve sustainability only by reducing agricultural water use, with internal water markets within each sub-region.

Trade-off curves of the reliability of achieving sustainability versus economic costs of reducing farm water use follow an S curve (Figure 3). Small water use reductions have low likelihood of achieving sustainability, and lower economic costs for agriculture. Achieving sustainable groundwater levels with higher reliability requires more pumping reductions and much higher economic costs, because this requires curtailing water for more valuable crops. For example, the average cost to achieve a 50% chance of groundwater sustainability in sub-region 15 over 20 years is $10 million/year. However, to achieve nearly 100% reliability of sustainability would cost roughly six times more in lost crop revenues. Much longer compliance horizons lessen the tradeoff between farm sector costs and reliability of attaining sustainability.

Figure 3 blog

Figure 3: Higher likelihood of achieving groundwater sustainability reduces farm revenues (example for sub-region 15)

An important caveat is that we only account for agricultural revenue losses from reducing overdraft in this study. Plans would also need to consider costs of not reducing overdraft, including infrastructure damage related to land subsidence, capital costs of stranded wells, higher pumping costs, dry drinking water wells, and harm to groundwater-dependent ecosystems.

Some lessons

  1. Initial overdraft estimates will almost certainly be wrong. Uncertainties in data and models should be considered when developing overdraft estimates for Groundwater Sustainability Plans, and the plans should provide ranges of estimates. For instance, overdraft estimates for different historical periods could show the potential range of hydrologic variability, and the implications of this variability for attaining sustainability.
  2. Groundwater pumping restrictions will need to vary across years. To accommodate future droughts within the compliance horizon for attaining sustainability, required reductions in water use will need to vary across years.  Groundwater demand is generally higher during droughts, when less surface water is available. As droughts progress and groundwater is drawn down, pumping shares should be adjusted to avoid reaching the minimum threshold for groundwater levels too early, potentially causing significant investment losses in perennial crops.
  3. Long-term pumping and recharge efforts will likely need to adjust over time. Anticipating and building such adjustments into local groundwater plans should make it easier to implement plans and to anticipate changes in groundwater availability, as well as make it easier for state agencies to evaluate plans.
  4. Successful groundwater sustainability plans and institutions will analyze uncertainty to prepare to adapt to variable hydrology and new estimates of overdraft. Adaptive methods to account for California’s hydrologic variability and the inherent uncertainties are essential for a dynamic response to changing conditions. SGMA’s requirement that GSPs update their plans at least every five years provides an important opportunity to incorporate new information and lessons, and adapt to changing conditions.
  5. State regulators can help by providing common regional templates, data, and models for analysis and institutional response. To facilitate the transition to stronger sustainability accounting—incorporating uncertainties—state technical assistance should focus on standardizing and improving the quality of the data, documentation, modeling, and other key tools for GSP planning and implementation. DWR’s Draft Handbook for Water Budget Development (2020) may be a step in this direction.

Data availability and replicability

The data and code to replicate all the analyses included in this paper are available at

Further reading

Escriva-Bou, A., R. Hui, S. Maples, J. Medellín-Azuara, T. Harter, and J. Lund (2020) “Planning for Groundwater Sustainability Accounting for Uncertainty and Costs: an Application to California’s Central Valley,” Journal of Environmental Management, Volume 264, 110426,

Brush, C.F., Dogrul, E.C., Kadir, T.N., 2013. Development and Calibration of the California Central Valley Groundwater-Surface Water Simulation Model (C2VSim), Version 3.02-CG. California Department of Water Resources, Bay-Delta Office.

DWR (California Department of Water Resources) 2018 Water Available for Replenishment Report (Sacramento CA: California Department of Water Resources) (Now seemingly unavailable from the DWR website)

DWR (California Department of Water Resources), 2020. Draft Handbook for Water Budget Development. With or Without Models.

Escriva-Bou, A., and Hanak, E. (2018), Appendix A: Update of the San Joaquin Valley’s Water Balance and Estimate of Water Available for Recharge in 2017. In Hanak et al (2018) Replenishing Groundwater in the San Joaquin Valley. PPIC.

Escriva-Bou, A. (2019), Appendix A: Update Assessment of the San Joaquin Valley’s Water Balance. In Hanak et al (2019) Water and the Future of the San Joaquin Valley, PPIC

Famiglietti J S, Lo M, Ho S L, Bethune J, Anderson K J, Syed T H, Swenson S C, de Linage C R and Rodell M 2011, “Satellites measure recent rates of groundwater depletion in California’s Central Valley,” Geophy. Res. Lett. 38

Faunt C C 2009 Groundwater availability of the central valley aquifer, California, USGS Professional paper No. 1766.

Kocis, T.N. and H.E. Dahlke, 2017. Availability of high-magnitude streamflow for groundwater banking in the Central Valley, California. Environmental Research Letters.

Orth, D. “SGMA IMPLEMENTATION: David Orth gives his observations on how sustainable groundwater management is playing out in the San Joaquin Valley,” summarized by Maven March 19, 2020

Scanlon B R, Faunt C C, Longuevergne L, Reedy R C, Alley W M, McGuire V L and McMahon P B 2012 Groundwater depletion and sustainability of irrigation in the US high plains and central valley Proc. Natl Acad. Sci. 109 9320–25

Xiao M, Koppa A, Mekonnen Z, Pagán B R, Zhan S, Cao Q, Aierken A, Lee H and Lettenmaier D P 2017 How much groundwater did California’s Central Valley lose during the 2012–2016 drought? Geophy. Res. Lett. 44 1–8

Alvar Escriva-Bou is a Research Fellow with the Public Policy Institute of California. Jay Lund is the Director of the Center for Watershed Sciences and a Professor of Civil and Environmental Engineering at the University of California, Davis. Josue Medellin-Azuara is an Associate Professor of Environmental Engineering at the University of California, Merced. Thomas Harter is a Professor of Hydrology and Cooperative Extension Specialist at the University of California, Davis.


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Protecting California’s Aquatic Biodiversity in a Time of Crisis

by Peter Moyle, Jeanette Howard, Ted Grantham

Fig. 1. Walking in the Putah Creek Riparian Reserve on the UC Davis campus, where wide trails permit social spacing of hikers. The flow of the creek is regulated to favor native fish and wildlife.

“Nowhere is the biodiversity crisis more acute than in freshwater ecosystems” (Tickner et al. 2020)

Weeks of being confined indoors under shelter-in-place orders increases our appreciation of the natural world. Walking and exercising outdoors, especially along a local stream like Putah Creek, is one of the best ways to escape the news cycle and to restore a sense of well-being.  Quiet streets and pathways have invited a growing chorus of bird song and can even inspire  interest in watching hatches of mayflies rising off gurgling stream waters. Online livestreaming of  wildlife cameras has surged. These experiences remind us how California’s natural environments and rich biological diversity improve the quality of our lives.  They also remind us that this natural heritage is threatened. California harbors more unique plants and animals than other state in the U.S but an estimated 30 percent of our native species are now threatened with extinction (Mooney and Zavaleta 2016).

Sustaining the amazing diversity of life on this planet and in California in particular is a major challenge of this frenetic era. The importance of this protection is reflected in the growing realization that maintaining the diversity of native species living in healthy ecosystems also results in an environment that is good for people. However, the demand of California’s ever-increasing citizenry for intensive use of our land and water makes this challenge extremely hard to meet. Meeting the challenge has just been made even more urgent by the new finding that since 2000 California and the western USA has been experiencing a megadrought, in part because of the aggravations of climate change. This era is being pegged as the driest period in over 500 years and there is no reason to think it is not going to continue, despite occasional wet years.

A major response to the state’s biodiversity challenge by the state has been the California Biodiversity Initiative of 2018, which was supported by Governor Brown and continues to be supported by Governor Newsome. The initiative proposes statewide measures to halt the decline of native species and ecosystems, under the leadership of the Department of Fish and Wildlife and the Department of Food and Agriculture.

We applaud this initiative as a good beginning, even if stalled by the effects of the present pandemic. However, it also has a major flaw: it is so focused on terrestrial ecosystems and native plants that it overlooks the needs of native aquatic (freshwater) species, habitats, and ecosystems. California’s aquatic biodiversity is particularly imperiled, as it is worldwide (Tickner et al. 2020). This problem is most clearly reflected in status of our native fishes. Of our 125+ native fishes, seven species are already extinct and 100 species are in decline and may be ultimately threatened with extinction. These include 31 species already listed as Threatened or Endangered under the state and federal Endangered Species Acts and 62 species listed as Species of Special Concern by CDFW (Moyle et al. 2011, 2015). These species include salmon and steelhead that are both iconic and support valuable fisheries.

Native fish declines are mirrored by other freshwater taxa. Howard et al. (2015) conducted the first statewide status assessment of California’s freshwater taxa. They found that of about 2,000 freshwater vascular plants, macroinvertebrates, and vertebrates for which adequate information was available, half were ranked as vulnerable (data were lacking for the other ~2,000 freshwater taxa in the state). California’s vulnerable aquatic organisms were mostly endemic species, found nowhere else in the world. But among the vulnerable taxa, only 113 (6%) were listed as endangered or threatened under the federal or state ESAs indicating a general neglect of non-charismatic species.

California has taken notable steps to protect its biodiversity, primarily through the establishment of protected lands under various programs. Unfortunately, efforts to protect terrestrial habitats and ecosystems rarely do an adequate job of protecting aquatic biodiversity; most of the key rivers that support threatened fishes, for example, flow outside of protected areas (Grantham et al. 2016). Of course, because terrestrial ecosystems drain into or encompass freshwater systems, management of terrestrial habitats is important for conserving aquatic habitats. However, most protected areas in the state are not explicitly managed to maintain freshwater ecosystems and their biota.

If native freshwater biodiversity is to be conserved, a systematic, statewide approach is required. Building on previous work by Howard et al. (2018), Grantham et al. (2016), Moyle (2002) and Moyle and Yoshiyama (1996), we argue that such an approach should be centered on the designation of priority watersheds and/or habitats for freshwater species management. Moyle (2002) identified a network of streams, lakes, spring systems, wetlands, and watersheds throughout the state that could potentially support all of the state’s native freshwater fishes and include representative examples of all of California’s aquatic habitats (as described by Moyle and Ellison 1991). Grantham et al. (2016) and Howard et al. (2018) extended this approach by using systematic conservation planning methods (Linke et al. 2011) to identify a network of watersheds in California that most efficiently encompass the distribution of all native freshwater taxa. Collectively, these studies provide an ecosystem-based blueprint for pursuing a systematic, statewide approach to freshwater biodiversity conservation, through Freshwater Protected Areas (FPAs), inspired by California’s system of Marine Protected Areas (MPAs).

In addition to the designation of FPAs, water supplies must also be secured for aquatic biodiversity protection. All aquatic species depend upon a sufficient quantity and quality of water throughout the year, no matter what type of habitat they live in. This is particularly true of riverine species that have adapted to the natural variation in seasonal flows – including winter high flows and summer low flows – that characterize the state’s rivers and streams. Yet most of California’s flowing waters have been dammed, diverted, and otherwise modified (Grantham et al. 2014), activities which have altered natural flow patterns and impaired aquatic habitats (Zimmerman et al. 2018). Only a small proportion of the state’s rivers and streams have environmental flow protections and many of these are managed mainly for single species, such as ESA-listed salmon and steelhead. Recently, a working group of researchers and agency staff has been developing a California Environmental Flows Framework (Obester et al. 2020; The Framework includes technical tools and guidance for developing environmental flow standards in streams throughout the state, focusing on specific functional elements of the flow regime linked to ecosystem health (i.e., functional flows). The overall goal of the Framework is to support a more consistent, and comprehensive approach to managing water for the environment in California.

The protection of California’s aquatic biodiversity, incorporating the above approaches, will require a large-scale effort. This effort should start now and accelerate when people and conservation agencies are less distracted by the effects of the COVID-19 epidemic, including a distressed economy. We can envision actions to protect aquatic biodiversity as being part of the economic recovery efforts for California.

Priority actions include:

1. Update and invest in mapping and assessment of freshwater taxa and habitats.

One reason that the state has been unable to implement a systematic strategy for managing native freshwater biodiversity is the limited collection, poor organization, and inaccessibility of data. Several recent efforts, including the PISCES database for tracking of the distribution of native fishes (Santos et al. 2013) and the California Freshwater Species Database for tracking additional freshwater species (TNC 2015), have been difficult to update and sustain because of lack of funds and personnel. Other data sources are either inaccessible to the public (e.g, California Natural Diversity Data Base) or are poorly organized (e.g., Biogeographic information and Observation System [BIOS]). These should be vetted, reorganized, and published, following modern data management and open source principles. TNC’s California State of Salmon website attempts to provide accessible data for all watersheds with salmon and steelhead monitoring ( However, monitoring programs are inadequate for accurately tracking the status of even these iconic species. Most other species are either monitored opportunistically or not at all. Successful management of the state’s freshwater biota and ecosystems cannot be achieved without a robust, comprehensive monitoring program.

2.  Designate and manage Freshwater Protected Areas (FPAs).

We already have a good idea where many of the most important areas for freshwater species conservation are located. However, there has been no formal designation or concentrated effort to identify and prioritize such areas for conservation and management actions. The 2018 Biodiversity Initiative aims to protect 20 percent of each major ecosystem type in the state, including freshwater ecosystems and to restore 15 percent of each ecosystem type from its degraded status. While this sounds good, the numbers are arbitrary and reflect terrestrial thinking. For rivers, for example, how do you protect an ”ecosystem type” that has not been clearly defined and changes as it flows downstream? Does it mean establishment of a statewide network of watersheds focused on their restoration and protection? If that is the case, how big (hydrologic unit) should each watershed in the system be? Whatever the units, FPAs should provide habitat for as much of the native aquatic biota as possible, throughout the state. Previous work by Moyle (2002), Grantham et al. (2016), and Howard et al. (2018) establish a blueprint for delineating FPAs that could efficiently protect native freshwater biodiversity and habitats.  With this information, a team of scientists, such that assembled for the California Biodiversity Initiative, should be able to come up with a site-specific plan to implement an FPA strategy, if California is willing to support it. The plan would, based on both expert opinion and computer algorithms, could provide preliminary designations of potential FPAs, much as Moyle and Randall (1998) did for Sierra Nevada watersheds. These could then be investigated more closely and appropriate action taken to protect the most imperiled FPAs.

3. Accelerate implementation of environmental flows.

California Environmental Flows Framework provides guidance for developing flow recommendations to maintain healthy freshwater ecosystems. The Framework provides a set of flow criteria (based on predictions of functional flows informed by reference stream hydrology) that can be used to immediately establish environmental flow standards in rivers where they do not exist. In rivers and streams with existing flow protections, the Framework can be applied to refine standards so that they are more effective in supporting ecosystem health. On-the-ground pilot projects are needed to implement the Framework across the diversity of California’s rivers and management contexts. As the foundation of the Framework, the functional flows approach also recognizes that environmental flow protections be coupled with strategic investments in physical habitat improvements, such as levee setbacks and barrier removals. For large rivers, it is particularly important to restore their connectivity to their floodplains to support the biological and physical functions that sustain salmon and other native species.

In short, California does a poor job of protecting aquatic biodiversity. A bold and imaginative, systematic effort is needed to protect and manage aquatic biodiversity. This will take leadership, money, and dedication to getting the job done by federal, state, and local agencies. As a biodiversity hotspot with an economy bigger than most nations, California should be leading the country and the world in protecting its aquatic systems. We have the tools at hand, but have been unable to muster the will to do the hard work. But as we reflect upon the natural world during the current public health crisis, it just may be that our growing appreciation of California’s biological richness is what is needed to inspire meaningful action.

Peter Moyle is an emeritus professor at the Center for Watershed Sciences, UC Davis. Jeanette Howard leads The Nature Conservancy’s freshwater science team for California; Ted Grantham is a Co-operative Extension Specialist in the Department of Science, Policy, and Management, UC Berkeley.

Fig. 2. The Long Valley speckled dace is an undescribed fish species that is now found in only one small stream and wetland in the wild, the Owens Valley region. The headwaters of the stream is hot springs that are now a public swimming pool. Its habitat needs protection if the fish is to survive. This is an example of an aquatic system that could be declared an FPA and managed appropriately.

Further Reading

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.

Grantham, T. E., K.A. Fesenmyer, R. Peek, E. Holmes, R. M. Quiñones, A. Bell, N. Santos, J.K. Howard, J.H. Viers, and P.B. Moyle. 2016. Missing the boat on freshwater fish conservation in California. Conservation Letters. DOI: 10.1111/conl.12249.

Howard J.K. and 20 others. 2015. Patterns of freshwater species richness, endemism, and vulnerability in California. PLoS ONE 10(7): e0130710. doi:10.1371/journal.pone.0130710.

Howard, J.K. and 10 others.   A freshwater conservation blueprint for California: prioritizing watersheds for freshwater biodiversity. Freshwater Science 37(2): 417-431.

Linke, S., E. Turak, and J. Nel.  2011. Freshwater conservation planning: the case for systematic approaches. Freshwater Biology 56(1): 6-20.

Mooney, H. and E. Zavaleta. Ecosystems of California. Berkeley: University of California Press, 2016.

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. 2002. Inland Fishes of California: Revised and Expanded. Berkeley: University of California Press.

Moyle, P. B., and J. Ellison.  1991.  A conservation-oriented classification system for California’s inland waters.  California Fish and Game 77:161-180.

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

Moyle, P.B., R. 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.

Moyle, P. B., and P. J. Randall.  1998.  Evaluating the biotic integrity of watersheds in the Sierra Nevada, California. Conservation Biology 12:1318-1326.

Moyle, P. B., and R. M. Yoshiyama.  1994.  Protection of aquatic biodiversity in California: A five-tiered approach.  Fisheries 19:6-18.

Obester, A., S. Yarnell, and T. Grantham.  2020. Environmental flows in California.  California WaterBlog, March 18, 2020.

Santos, N.R., J.V.E. Katz, P.B. Moyle, and J. H. Viers. 2013.  A programmable information system for management and analysis of aquatic species range data in California. Environmental Modeling & Software 53:13-26.

Zimmerman, J.K., Carlisle, D.M., May, J.T., Klausmeyer, K.R., Grantham, T.E., Brown, L.R. and Howard, J.K., 2018. Patterns and magnitude of flow alteration in California, USA. Freshwater Biology, 63(8):859-873.

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Supreme Court Ruling Finds Old, New Middle Ground on Clean Water Act’s Application to Groundwater


Groundwater Replenishment Facility in Coachella, Calif. Photo: Kelly M. Grow/ California Department of Water Resources

By Thomas Harter, Steph Tai, and Karrigan Bork

In 1972, the U.S. Clean Water Act (CWA) created a permit system for point source discharges to navigable waters of the United States – rivers, lakes, and coastal waters – with the goal of restoring and protecting their water quality. Typically, these permits are issued by the U.S. EPA or through state agencies to dischargers of wastewater, e.g., from urban and industrial wastewater treatment plants and to other dischargers of potentially contaminated water that reach streams by a pipe or similar conveyance. The goal was to provide some degree of regulatory oversight over such discharges.  In California, the State Water Resources Control Board implements the federal Clean Water Act using its authority under the Porter-Cologne Water Quality Control Act (Water Code, §13000 et seq.). Under the CWA, neither EPA nor the states are required to issue permits for pollutant discharges into groundwater or to nonpoint source dischargers.

This week, the Supreme Court decided on a case involving discharge from a wastewater reclamation facility owned and operated by the County of Maui.  In this case, the facility discharged 3 to 5 million gallons of treated wastewater per day into four injection wells about half a mile from the ocean.  Recent research showed that much of the injected waste eventually discharges to the ocean. Environmental groups sued the county for not obtaining a CWA permit, arguing that point source discharge of pollutants that eventually reach surface water is governed under CWA. All sides agreed that the case at hand involved a point source of pollutant discharge and that the pollution eventually reached the ocean. The disagreement was whether the CWA requires the permit only if the pollutant discharge is directly into surface water, as argued by the defendants (a “bright-line test”). Environmental groups argued that even if the pollutant discharge is via groundwater to surface water, the CWA permit must be obtained. The district court and the Ninth Circuit court ruled in favor of the plaintiffs. The Ninth Circuit court held that permits are required when “pollutants are fairly traceable” from the point source to surface water.

In its final 6-3 decision, the Supreme Court majority now rejects both sides’ arguments as too extreme and returned the case to the lower courts with further guidance.  On the “bright-line test”, Justice Breyer, writing for the majority, wrote “we do not see how Congress could have intended to create such a large and obvious loop hole in one of the key regulatory innovations of the Clean Water Act.”  On the “fairly traceable” approach, the opinion stated that such interpretation “would require a permit in surprising, even bizarre circumstances”.


Groundwater discharge to a nearby agricultural canal in Yolo County. Photo: 2013 by John Chacon / California DWR

Instead, the Court decision introduces the concept of a “functional equivalent of a direct discharge” as a guideline for when a point source discharge must obtain a permit. It cites the case of an injection well receiving pollutant discharge that then travels a few feet through groundwater into navigable waters as a clear case of “functional equivalent” to direct discharge. But it rejects the notion that such a “functional equivalent” exists in a case with “100 year migration of pollutants through 250 miles of groundwater to a river” and “likely does not apply” if “the pipe ends 50 miles from navigable waters”. The Court acknowledges that the concept of “functional equivalence” as the Court’s guideline leaves many point source discharges to groundwater somewhere between these extreme cases.  It relegates consideration of those cases back to regulators and lower courts, suggesting they consider the various groundwater flow and transport factors underlying individual cases – travel time and distance in particular, but also soils and geology, geochemical reactions, the locations where pollutants subsequently enter navigable waters, and “the degree to which the pollution (at that point) has maintained its specific identity.”

Importantly, the majority opinion does not expect a “vastly” expanded scope of the CWA, such that permits would be required, e.g., for the country’s 20 million septic systems. It does so in two ways: by emphasizing (and affirming) the long history of CWA implementation, which has, at times, required permits even if pollutant discharge was via groundwater into surface waters, but not under other circumstances. And, secondly, both the majority and dissenting opinions repeatedly underscore the important role and sovereignty of states in regulating discharges to groundwater and nonpoint source pollution (groundwater pollutant discharge to surface water is sometimes considered nonpoint source pollution of surface water).

The decision will not make it easier than in the past for either regulators or lower courts to make their determinations as to whether a point source pollutant discharge to groundwater that eventually affects surface water is subject to a CWA permit. But the decision sides squarely with the use of science. And it shows a remarkable acknowledgement of hydrologic sciences and the interconnectedness of surface water and groundwater: “Virtually all water, polluted or not, eventually make its way to navigable water. This is as true for groundwater.” Perhaps this statement missed the nuance that some groundwater, particularly in the western U.S., will instead be pumped by wells onto crops or pulled by plant roots from the water table to be evapotranspired into the atmosphere. But it underscores that the court made its decision knowing and applying hydrologic science. “Given the power of modern science, The Ninth Circuit’s limitation, ‘fairly traceable’, may well allow EPA to assert permitting authority over the release of pollutants that reach navigable waters many years after their release […] and in highly diluted forms.”, an application that the justices find inconsistent with the CWA.

The dissenting opinion of Justice Alito rejects the introduction of the “functional equivalence” concept as too vague and inconsistent with the language of CWA.  Given the authorities of states on matters of groundwater and nonpoint source pollution, he supports the “bright-line test”.  But importantly, Justice Alito instead refers to the definition of “point source” as a means to avoid the loopholes cited in the majority opinion as reason to reject the “bright-line test”:  He points out that, according to CWA, “point source[s] include [….] ‘any discernible, confined and discrete conveyance… from which pollutants … may be discharged.’ §1362(14).” The opinion continues to describe how the pathway created by pollutant discharge from a pipe onto a beach and ending in the ocean” or many of the cases that trouble the Court” would easily be covered by applying common definitions of “conveyance”, “discernable”, and “confined”.  Groundwater hydrologists may further point out something not mentioned and perhaps not considered by Justice Alito: that we do have scientific tools (as referred to by the majority opinion) to similarly describe some groundwater pathways as a conveyance that is indeed discernable and confined, “i.e., held within bounds”.  So perhaps Justice Alito’s argument, from a scientific perspective, would in practice not be substantively different from the scientific criteria that the majority opinion associated with defining “functional equivalent” point source discharge. Such an interpretation would add further support and a consistent angle to the overall spirit of the Court’s decision.

The Maui decision is already having a ripple effect in other areas of environmental


Submarine Groundwater Discharge, USGS

concern.  Environmentalists have long been advocating against the use of coal ash impoundments—open pits for disposal of toxic byproducts left over from burning coal.  Many of these byproducts have allegedly moved from these impoundments through groundwater into streams and rivers.  Prior to the decision in Maui, power companies argued the CWA permitting program was inapplicable to impoundments.  But the Maui decision will likely lend weight to these challenges.

The Maui decision also will likely impact litigation over the federal administration’s repeal of the Water of the United States rule, a regulation under the Obama administration which clarified the views of the Environmental Protection Agency and the U.S. Army Corps of Engineers about the reach of the Clean Water Act.  In this repeal, this administration specifically stated, in response to commenters, that “A groundwater or subsurface connection could also be confusing and difficult to implement, including in the determination of whether a subsurface connection exists and to what extent.” U.S. Army Corps of Engineers and Environmental Protection Agency, The Navigable Waters Protection Rule: Definition of ‘‘Waters of the United States,” 85 Fed. Reg. 22,250, 22,313 (Apr. 21, 2020).  Promulgated by the agencies before the Maui decision came out, the agencies will likely have to wrestle with the Maui decision in subsequent challenges.

While the decision leaves some previous uncertainty over the interpretation of the CWA, and perhaps adds some, California dischargers are unlikely to face additional regulation under this decision. Under the Porter-Cologne Water Quality Control Act, California already requires permits for discharges to groundwater, even if they don’t meet the “functional equivalent” test outlined by Justice Breyer’s majority opinion. California regulators may need to adjust their approach to reflect that some of these permits will also serve as CWA permits under the state’s authority, but this should not impose significant new burdens on regulated entities. California’s robust implementation of a strong groundwater quality regulatory program, implementing state laws (including the Sustainable Groundwater Management Act, SGMA) and other federal laws governing discharge of pollutants to groundwater (Safe Drinking Water Act, Toxic Substances Control Act, Resources Conservation and Recovery Act, state and federal Superfund programs) puts it in an excellent position to have little to worry about a new layer of bureaucracy and restrictions.

The decision’s reliance on strong groundwater science marks another significant step in the emerging integration of groundwater and surface water. The California courts and legislature have long regarded surface water and groundwater as legally distinct, but over the last decade that legal fiction has begun to break down. In 2014, SGMA explicitly recognized the relationship between groundwater and surface water, requiring groundwater managers to avoid significant and unreasonable adverse impacts on beneficial uses of surface water. In 2018, a California appellate court ruled that the public doctrine applies to groundwater extraction if it adversely impacts a navigable waterway. This decision validates the hard work of water scientists working to protect critical freshwater systems in the context of integrated watershed and water resources management, including efforts to protect many of these freshwater resources that depend on high quality groundwater discharge. And it reminds us to keep hard at working to achieve the larger vision of the Clean Water Act.

Professors Harter and Tai were both authors of an amicus brief in this Supreme Court case.

Thomas Harter is a Professor of Hydrologic Sciences and a Cooperative Extension Groundwater Specialist at the University of California, Davis.  He is currently Acting Director of the UC Davis Center for Watershed Sciences and Chair of the Hydrologic Sciences Graduate Group.

Steph Tai is a Professor of Law at the University of Wisconsin Law School.  Their research focuses on areas of science, risk, and environmental and food regulation.

Karrigan Bork is an Acting Professor of Law and an Associate Director of the Center for Watershed Sciences at the University of California, Davis. His research focuses on water law, environmental law, and natural resource conservation.

Further readings

Supreme Court opinion, County of Maui v. Hawaii Wildlife Fund, 2020:

Supreme Court Docket, No. 18-260 (County of Maui v. Hawaii Wildlife Fund, 2020):

Brief amici curiae of Aquatic Scientists and Scientific Societies, filed July 19, 2019:

Karrigan Bork, 2019:  What water is covered by the Clean Water Act? California Water Blog



Science Magazine:

Brownstein Hyatt Farber and Schreck:

Frank, R. (2020), Here Today, Gone to Maui – U.S. Supreme Court Issues Environment-Friendly Ruling in Major Clean Water Act Case


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Science of an underdog: the improbable comeback of spring-run Chinook salmon in the San Joaquin River

By Andrew L. Rypel, Gabriel Singer, and Nann A. Fangue

Fig. 1. (Left) U.S. Fish and Wildlife Service biologists and partners prepare to release ~90,000 spring-run Chinook salmon into the San Joaquin River, 3/6/17. USFWS Photo/Steve Martarano, downloaded from (Right) Transferring juvenile spring-run Chinook salmon prior to release. Photo by Gabriel Singer.

“You can’t design a worse evolutionary strategy for the Anthropocene”

There are many variants on this quote, and we’ve heard them often in reference to the status of native fishes in California and other freshwater organisms worldwide. Indeed, the statement rings true for Pacific salmon, but especially spring-run Chinook salmon (Oncorhynchus tshawytscha) in California. And although the current situation certainly looks bleak overall for endangered salmon (Moyle et al. 2017), there are signs in a few corners that the arrow may finally be pointing up. For the last four years, our team at UC Davis has been conducting scientific studies on reintroduced spring-run Chinook salmon in the San Joaquin River and we wanted to take a minute to share some of what we’ve learned. Plus, everyone loves a good comeback story right?

Primer on the life-history of spring-run Chinook salmon

The complicated life-histories of Chinook salmon in the Pacific are well-known. Indeed they are a frequent topic of blog posts here! (examples, 1, 2, 3). Living as adults in the Pacific Ocean and migrating into freshwater tributaries, adults spawn and subsequently die leaving their carcasses to fertilize freshwater ecosystems with marine-derived nutrients. Young salmon must outmigrate from freshwater habitats to the ocean (and survive!) where they feed and live as adults. In California, we think of late summer and into fall, and maybe even into winter as prime time adult Chinook salmon migration time. But, spring-run Chinook salmon are different. These fish enter freshwater in spring months as sexually immature adults, and historically migrated long distances upriver to coldwater refuges in the mountains. Here, they “oversummer”, often congregating in deep coldwater plunge pools high in the landscape where they survived on their fat reserves, which dwindled as they continued to mature. When rains and flows increase in the late fall, barriers to movement suddenly become passable and fish would migrate further into the high California landscape to spawn in the fall. When you consider this life-history, and the current human-dominated landscape of California (think dams built without fish passage, climate change, landscape alterations), it is little wonder that this species (technically an “ESU, Ecologically Significant Unit”) has declined to where it is listed under the CA and US Endangered Species Act. Yet, spring-run Chinook salmon are full of surprises. Here’s some of them: 

Fig. 2. Long-term trends in adult abundances of spring-run Chinook salmon in the Sacramento Valley. Data are from CDFW Status Report (1998), and Grandtab (Azat 2019). Historical (pre-1900) abundance estimates are based on extrapolations from cannery records.

Surprise 1 – Spring-run Chinook salmon historically were co-dominant with the fall-run in the Central Valley and in some years may even have exceeded the fall-run in overall abundance. Today, we tend to consider fall-run Chinook salmon as the main run of salmon in California, but alas, it was the spring-run that originally predominated in the early commercial salmon fishery due to its great abundance, wide distribution and higher food quality. In one year alone (1883), at least 567,000 spring-run salmon were reported caught in the commercial fishery, not to mention all the fish that escaped the fishery and spawned in their home streams. Through the 1880s, total commercial harvests (composed primarily of spring-run fish) generally hovered around 5 million to 10 million pounds — which, at an average weight of 16 pounds per salmon, would have equated to about 310,000 to 625,000 salmon. Current valley-wide numbers oscillate between only a few thousand to upwards of 25,000 adults (Fig. 2).

Surprise 2 – While it is hard to imagine now, the San Joaquin River at one time contained the most abundant population of spring-run Chinook salmon in the Central Valley, perhaps due to the extirpation of all the other great spring-run populations originally found throughout the Valley (Yoshiyama et al 1998). Most of these fish spawned in the upper reaches of the watershed in the Sierra Nevada where strong coldwater habitats allowed fish to over-summer as described above. Following the completion of Friant Dam, spring-run Chinook salmon in the San Joaquin River were predictably extirpated in rapid succession. Identical stories of dams built without fish passage and subsequent salmon declines exist for every major river draining into the Central Valley. Yet in addition to blocking access to coldwater habitat in the Sierra Nevada, completion of Friant Dam and a chain of dams upstream (e.g., Kerckhoff Dam/Millerton Reservoir) also facilitated diversion of high proportions of water from the San Joaquin River such that ~ 60 miles were left completely dry when the project was completed (Matthews 2007). 

Fig. 3. Aerial photo revealing the landscape of the San Joaquin River, CA. Photo by Ken Lund, downloaded from, 4/14/20

Surprise 3 – Despite continued degradation of the river (Fig. 3), and its status as perennial contender for “America’s most endangered river”, spring-run Chinook salmon have been on the comeback trail for the last five years. Much of this success is largely due to a massive habitat restoration and reintroduction effort, spear-headed by the San Joaquin River Restoration Program (SJRRP). The SJRRP has developed a comprehensive reintroduction strategy for spring-run Chinook salmon intended to overcome the various obstacles that impede reestablishment of a viable spring-run Chinook salmon population. Habitat projects include restoring connectivity in the river, increasing flows to provide suitable habitat to complete all phases of the life cycle, and removal and reconfiguration of structures that obstruct movement of salmon. The phased goals of the program include reintroduction of spring-run Chinook salmon (supported by a conservation hatchery operated by CDFW), establishment of self-sustaining local populations under contemporary river conditions, and finally long-term maintenance of a population of 30,000 spawning adults with negligible hatchery influence.

It is of note that spring-run fish from the Feather River Hatchery were used to initially jumpstart the conservation hatchery broodstock for the San Joaquin River. Thus, we can never truly “bring back” the original upper San Joaquin spring-run – a notable consequence of extinction overall.  However, a recently published genomic study on Central Valley Chinook salmon (Meek et al. 2020) revealed that Feather River Hatchery spring-run have distinctive genetic elements that set it apart from the two other Central Valley spring-runs (i.e., Mill/Deer Creek, and Butte Creek) as well as from the Feather River Hatchery fall-run. This finding in turn suggests the Feather River Hatchery spring-run likely retains ancestral genetic elements from the original Feather River spring-run varieties. Hence, the new reintroduced San Joaquin spring-run population is aiding in preservation of Feather River spring-run ancestry, but also, overall genetic diversity of Central Valley Chinook populations – this is a good thing.

Science to inform adaptive management of spring-run Chinook salmon

Over the last 4 years, our team has been developing science that can be used to facilitate adaptive management of reintroduced spring-run Chinook salmon in the San Joaquin River. The centerpiece to this work has been a set of focused acoustic telemetry studies on juvenile salmon released each spring. Beginning each year in early March, our team usually tags 750 juvenile spring-run Chinook salmon produced at the Salmon Conservation and Research Facility (SCARF; Friant, CA) with miniature Juvenile Salmon Acoustic Telemetry System (JSATS) transmitters. Similar to a recent blog, these transmitters produce sounds that are then “heard” by receivers maintained by our team throughout the river (Fig. 4). Fish with uniquely coded transmitters swim past receivers and data are registered allowing us to study survival rates, routing and other fish behaviors of interest. The JSATS transmitters are the smallest available on the commercial market, allowing us to track fish as small as ~72mm in length, although we prefer to tag larger smolts.

Fig. 4. (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.

Currently, spring-run Chinook salmon are confined to only the lower San Joaquin River (below Friant Dam). Therefore, we track fish through this area which includes the lower region of the Restoration Area, but also continues through the Sacramento-San Joaquin Delta, San Francisco Estuary, and entrance to the Pacific Ocean. We also maintain (fancier and more expensive) real-time receivers at the federal and state pumping facilities which provide a rapid window into how many juvenile fish are being entrained and salvaged at the water pumping facilities. These receivers transmit data in real time via cell phone towers. See example of real-time telemetry data from this year’s spring-run tagging.

With three years of data now in the bag, some patterns are notably clear. First, as is typical with juvenile salmon in the Central Valley – water matters! Years during which there was increased precipitation and high flows, survivorship to the ocean was higher. In 2017 (a wet year – remember Oroville Dam!), we estimated out-migration survival to the Golden gate at 2-5%, but in 2018 (a drier year) survivorship plunged to only 0.5%. In a wetter year, 2019 survivorship increased again to 5%. In 2020, real time receivers at Benicia Bridge estimate that so far only 0.5% of our fish have successfully out-migrated to the ocean – ouch again! As a comparison, telemetry studies for other runs of Chinook salmon in the Sacramento during 2019 suggested outmigration survival rates upwards of 15-20%. Our data therefore indicate survivorship is uniformly low for salmon in the San Joaquin River overall, and that flows here probably really matter for the fish. Most of the tagged fish that enter the interior Delta simply don’t make it out. 

Finally, we have found that many of our tagged fish are plucked out of the river at the fish salvage facilities located at the Central Valley Project and State Water Project (pumping facilities). Interestingly, these fish often have higher survivorship to the ocean versus fish remaining in the mainstem San Joaquin River or freely swimming through the interior Delta. This pattern is likely not because being salvaged is “good for fish” but rather, because upon salvage, fish are physically trucked around the interior Delta to the San Francisco Bay. Previous studies on fall-run salmon smolts in the system found highly similar patterns (Buchanan et al. 2018). Furthermore, a temporary fish barrier is often installed by the Department of Water Resources (DWR) at the head of Old River to prevent fish from being drawn towards the pumping facilities (DWR 1992). Yet it now seems possible that this barrier, originally installed to prevent fish from accessing an assumed low survival route in low discharge years, may sometimes actually block access to the highest survival out-migration pathway (salvage). It is notably sad and ironic perhaps, that the quality of habitat in the lower river is so poor that the best migration path for salmon appears to be as a salvaged fish, trucked around the Delta by DWR or BOR staff.


While the data we have paint a grim ecological picture for spring-run Chinook salmon in the San Joaquin River, the situation is beginning to trend positive. At the end of May 2019, at least 23 adult spring-run salmon returned to the river, capping at least a 370 mile round trip journey to the ocean and back again. It also marked the first time in 65 years that adult spring-run Chinook salmon returned volitionally to the San Joaquin River to spawn. In fall of 2019, more than 200 redds were counted, a 4-fold increase from the previous year. Wild smolts have been increasingly captured in screw traps, indicating successful reproduction is occurring in the wild independent of hatchery efforts. 

As we continue to gain data on the biology of reintroduced salmon in the San Joaquin River, we will be able to provide increased information valuable for conservation. For example, we are conducting focused experiments on specific areas of the interior delta that we think may be especially problematic for salmon smolts (e.g., Frank’s Tract). We are also conducting innovative studies on the physiology of salmon smolts experimentally exposed to different parts of the river. Finally, we are conducting in-depth habitat assessments to further inform why there are major “hotspots of death” for salmon in the lower portions of the ecosystem. In the future, adding more upriver habitat to the current migration corridor for spring-run may be worth consideration. For example, historically, the very best spring-run Chinook habitat was in the area where Kerckhoff Dam (Millerton Reservoir) now stands, upriver from Friant. While these areas are now mostly flooded, remnants of deep pool habitat do exist below Kerckhoff Dam, making restoration a possibility in these areas. If these pools can be managed for coldwater through summer months, small runs of spring-run Chinook salmon above Friant may also be possible.

Finally, what we have encountered all along the way has been a constant dedication to the fish and ecosystem from biologists of all stripes at agencies, universities, fishing groups and others. We work hand-in-hand with a number of agencies conducting concurrent telemetry studies in the Sacramento River and Delta, and are constantly impressed by the professionalism and dedication needed to help recover our fish populations. It is heartening that against all odds, spring-run Chinook salmon are staging a comeback (albeit small currently) in one of the most endangered rivers in the USA. We are proud to be part of these interdisciplinary studies that provide, not only information needed immediately for conservation, but also as a training ground for the future of fisheries biology. There are so many to praise for these advances.

Fig. 5. View from the top of Friant Dam pointing downriver. The raging whitewater on the left is the Friant-Kern Canal which pulls ~75% of its water from Friant. The more docile waterbody to the right is the San Joaquin River. Photo by Gabriel Singer.

Andrew Rypel is an Associate 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 an Associate Director of the Center for Watershed Sciences. Gabriel Singer is a postdoctoral research associate in the Rypel Lab 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.

Further reading:

2019 Spring-Run Redds Set Record!

Azat, J. 2019. GrandTab 2019.05.07 California Central Valley Chinook Population Database Report. California Department of Fish and Wildlife, Sacramento, CA USA. 

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.

California Department of Water Resources. 1992. South Delta Temporary Barriers Project: monitoring, evaluation, and management program. California Department of Water Resources, Sacramento, CA USA.

Matthews, N. 2007. Rewatering the San Joaquin River: A Summary of the Friant Dam Litigation. Ecology Law Quarterly 34(3): 1109–1135.

Meek, M.H., M.R. Stephens, A. Goodbla, M. May, and M.R. Baerwald. 2020. Identifying hidden biocomplexity and genomic diversity in Chinook salmon, an imperiled species with a history of anthropogenic influence. Canadian Journal of Fisheries and Aquatic Sciences 77: 534-547.

Moyle, P. B., R. Lusardi, and P. Samuel. 2017. State of the Salmonids II: Fish in hot water. Status, threats and solutions for California salmon, steelhead and trout. University of California-Davis, CA USA.Yoshiyama, R. M., F. W. Fisher, and P. B. Moyle. 1998. Historical abundance and decline of chinook salmon in the Central Valley region of California. North American Journal of Fisheries Management 18: 487-521.

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


This research is being funded by the Delta Science Council, with additional support from the California Department of Fish and Wildlife (CDFW) and the US Fish and Wildlife Service (USFWS). Our larger team of scientists at UC Davis working on this project includes Dennis Cocherell, Colby Hause, Leah Mellinger, Sarah Baird, Michael Thomas, Amanda Agosta, Heather Bell, Matthew Pagel, Emily Jacinto, Mackenzie Miner, Wilson Xiong. We also thank past scientists at UC Davis including A. Peter Klimley and Eric Chapman for their important contributions in the early years of this work. Lori Smith and Pat Brandes (USFWS), Don Portz (SJRRP), Towns Burgess (SJRRP), John Kelly (CDFW), Matt Bigelow (CDFW), and Josh Isreal (USBOR) have all been critical to supporting and continuing this work. We thank Peter Moyle, Ronald Yoshiyama and Towns Burgess for reviewing earlier versions of this blog.

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