Increasing groundwater salinity changes water and crop management over long timescales

by Yiqing “Gracie” Yao and Jay Lund

Salinity has often become a major limit for irrigated agriculture in semi-arid regions, from ancient Mesopotamia to parts of California today. A previous blog post showed that conjunctive use with more saline groundwater can differ fundamentally from freshwater aquifers. Higher salinity limits groundwater use for irrigation during dry years, when less surface water is available to dilute groundwater salinity, and increases aquifer pumping in wetter years to avoid water-logging. Brackish groundwater can no longer serves as drought storage, but becomes a supplemental water supply in all years, limited by availability of fresh surface water for diluting salts. This greatly reduces groundwater’s ability to support permanent crops and increases variability in annual crop acreage across different water years, thus reducing profit.

This post extends the analysis timescale of groundwater management with salinity to a century, examining groundwater storage management and cropping patterns as salts accumulate in an undrained aquifer. This discussion is based on results from a recent hydro-economic optimization model (Yao 2020), which conjunctively manages surface water and groundwater for irrigating a mix of annual and permanent crops over a range of dry to wet years to maximize agricultural profits. The modeling examined conditions similar to California’s western San Joaquin Valley.

The biggest change in long-term groundwater management with salinity is that more net recharge of groundwater storage and less overall pumping occurs in early decades to slow the rise in groundwater salinity. This prolongs the use of groundwater to supply some irrigation water (when diluted with available surface water), particularly for more profitable perennial crops.

With low initial groundwater salinity, greater early pumping lowers groundwater storage to a minimum allowable level, raising early profits, and groundwater recharge occurs in the last decades to recover aquifer levels (when recharge cost is most discounted). With modest groundwater salinity, costly artificial recharge occurs in early decades (Figure 1.a) when initial groundwater storage is low, to achieve the final storage target and slow accumulation of salinity to prolong the viability of more profitable perennial crops. With higher initial groundwater storage, aquifer levels are only lowered to the storage target towards the end (Figure 1.b) for the same reason.

Figure 1. Groundwater management strategy changes greatly with modest salinity (  = 500 mg/L) with a discount rate of 3.5% and final storage target of 10 MAF.

When initial groundwater salinity is high enough to reduce perennial crop yields, groundwater recharge is increased and occurs earlier to slow groundwater salination (Figure 1.a). Net extraction moves to the last decades if initial groundwater storage is high (Figure 1.b), which means profit from pumping in the first decades cannot offset losses in later decades from groundwater salinity accumulating from early pumping.

From an earlier blog post on conjunctive use without groundwater salinity, high initial planting costs and profits for perennial crops lead to maintaining perennial crop acreages as high as possible to reduce planting costs in later decades. However, in an undrained basin, as groundwater salinity grows, perennial crop acreage must shrink, driven by low fresh surface water availability in dry years to dilute more saline groundwater. However, the high value of salt-sensitive perennial crops drives the model to suppress growth in groundwater salinity in early stages to prolong crop yields.

The cost of groundwater salinity becomes huge. When groundwater salinity becomes high enough, it is no longer suitable for irrigation and must be disposed of to avoid water-logging. In our modeling, restoring the aquifer with fresher surface water never makes more profit than managing the salinated aquifer at a near-constant level and pumping away excess drainage. However, slowing the increase in groundwater salinity occurs in early decades when benefits of larger early less-impaired perennial crop acreages are less discounted. 

It is almost impossible to lower groundwater salinity without extensive artificial recharge or expensive desalination. So, over time groundwater salinity gradually increases and perennial crop acreage decreases. The loss in total profit over 10 decades from initial groundwater salinity of 500 mg/L to 1,500 mg/L can be several hundreds of million dollars. Salination diminishes groundwater’s ability to serve as a drought reservoir for drier years and eventually makes groundwater unfavorable for agricultural water supply by reducing crop yields.

Interest rates are important (Figure 2). Lower discount rates further increase the value of controlling groundwater salinity by early aquifer recovery, deferring net extraction to the last decades when the initial groundwater salinity is still low (Figure 2.a). When initial groundwater salinity is higher, more water than required is recharged to the aquifer in early decades to slow salination and prolong production, despite some recharged water being wasted to meet the final storage goal (Figure 2.b).

Figure 2. Lower discount rates cause more aggressive groundwater recharge in early decades and shift pumping to the last decades.

A drier climate worsens conditions for irrigated agriculture with groundwater salination. It is the battle between recharging the aquifer to have lower groundwater salinity for middle decades and pumping to irrigate more perennial crops to make more profit in early decades. However, a drier climate dramatically increases the cost of recharging (especially in the first decades) because less available surface water can dilute less groundwater, meaning fewer less-impaired perennial crops can be supported, while less deep percolation from crops requires more artificial recharge in wetter years for aquifer recovery, reducing annual crops. A drier climate further increases the loss from groundwater salinity, by 200 M$ in this example.

Overall, groundwater salinity changes conjunctive water management for decadal timescales, shifting pumping from drier years to wetter years, when more surface water can dilute more saline groundwater for irrigation. Groundwater salinity also changes groundwater management at longer timescales, moving artificial recharge to earlier decades and shifting pumping to later decades (only to avoid water-logging). Even with these changes, agricultural production suffers greatly from groundwater salinity, which reduces crop yields and diminishes groundwater ability to serve as a drought backup.

In undrained parts of California and the world, irrigated agriculture faces problems of excess salinity, even if groundwater overdraft ends.

Dr. Gracie Yao recently completed her PhD in Civil and Environmental Engineering at the University of California – Davis.  Jay Lund is a Professor of Civil and Environmental Engineering at the University of California – Davis

Further reading

Yao, Y. and J. Lund (2021), Managing Groundwater Overdraft – Combining Crop and Water Decisions (without salinity),, January 17, 2021

Yao, Y. and J. Lund (2021), Managing Water and Crops with Groundwater Salinity – A growing menace,, March, 2021

Yao, “Gracie” Yiqing (2020), Managing Groundwater for Agriculture, with Hydrologic Uncertainty and Salinity, PhD dissertation, Department of Civil and Environmental Engineering, University of California – Davis.

Dogan, M., I. Buck, J. Medellín-Azuara, J. Lund (2019). Statewide Effects of Ending Long-Term Groundwater Overdraft in California, Journal of Water Resources Planning and Management, Vol 149, No. 9, September.

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, Vol. 265, 110426, June 2020.

Faunt, C., ed. (2009). Groundwater Availability of the Central Valley Aquifer, California: U.S. Geological Survey Professional Paper 1766, 225p. USGS Professional Paper 1766: Groundwater Availability of the Central Valley Aquifer, California.

Hansen, J. A., Jurgens, B. C., & Fram, M. S. (2018). Quantifying anthropogenic contributions to century-scale groundwater salinity changes, San Joaquin Valley, California, USA. Science of the Total Environment, 642, 125-136.

Harou, J. and J. Lund (2008). Ending groundwater overdraft in hydrologic-economic systems, Hydrogeology Journal, Volume 16, Number 6, September, pp. 1039-1055.

Howitt, R., Kaplan, J., Larson, D., MacEwan, D., Medellín-Azuara, J., Horner, G., Lee, N. The Economic Impacts of Central Valley Salinity. Final Report to the State Water Resources Control Board Contract. March 2009.

Pauloo, R.A., Fogg, G.E., Guo, Z., Harter, T. (2021), Anthropogenic Basin Closure and Groundwater Salinization (ABCSAL), Journal of Hydrology, Vol. 593, 125787, February 2021.

Pauloo, R.A., Fogg, G.E. (2021), “Groundwater Salinization in California’s Tulare Lake Basin, the ABCSAL model,”, Posted on February 21, 2021    

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Looking for a new challenge? – Retrain as a Delta Smelt

Cool smeltHelp restore one of California’s most endangered species while supporting California’s water supplies in a time of drought.

The Federal government is beginning a program for the unemployed to retrain as much-needed Delta Smelt.  Following a two-day course, candidates will learn to:

  • Seek out turbid waters
  • Spawn in sand at secret locations
  • Surf the tides
  • Make themselves present for counting in mid-water trawls

Major California water projects and water users are preparing to hire successful graduates for 1-2 year non-renewable contracts.  Minimum qualifications:Smelt 2

  • Must be shorter than three inches
  • Swim poorly
  • Smell slightly of cucumber
  • Be translucent

Occupational risks include:

  • Consumption by bass
  • Entrainment by pumps
  • Getting lost in Delta channels
  • Relocation to Southern California

As an endangered species, actual employment conditions will likely comply with State social distancing requirements.

For information, please contact:

Smelt touch

Looking for a new career?

What do you want to do ?

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Field courses help young people see the real world

by Andrew L. Rypel

It was perhaps unsurprising I wound up a field ecologist. Raised in Wisconsin, I spent almost all my childhood free time roaming largely unchaperoned in nature, pre-internet. It was there that I developed a deep love for nature, water and fish that would stay with me my whole life. It was a privileged upbringing. And yet somehow it was years later, when I was 22 and taking a university field course, that I finally figured out I wanted to pursue a career in fish and ecology. It’s unclear how many biologists trace their paths back to experiences like these, but I suspect there are many. Field courses are so impactful, and we need them now, more than ever before. 

As a young college student, I struggled at my mid-sized liberal arts college to find a curricula that connected my outdoors interests (nature, fishing, camping, hiking) together. Years later, I recognized that field broadly as ecology, but at the time, I didn’t know that’s what I was searching for. Most of the science courses and majors at my institution were annoyingly pre-health. I briefly toyed with the idea of a double major in English and a natural science field. Eventually I declared the best major I could find – environmental science (awarded through the geology department) with biology as a minor. At that time, environmental programs were somewhat rare at many US institutions, so I was happy enough I had majored in something vaguely reflecting my values.

Group photo from 2002 “Biology of the Southern Appalachians”. Yours truly looking dour and scraggly in the back row. Photo from Meredith Latimer.

I finally took my first real field course during my Master’s program in fisheries several years later at Auburn University (War Eagle!). The course was Biology of the Southern Appalachians, taught by Professor George Folkerts. It hadn’t been offered in years, and I had privately heard it was something special. Now, I could write an entire series of blogs on George, but most people who know Auburn, or natural history of the southeastern USA, or Tuesday trivia night in Auburn – all knew George. He was gentle, patient, brilliant, and a walking encyclopedia of biodiversity and ecology, especially rare and declining organisms like bog plants, salamanders, turtles, beetles, arthropods of longleaf forests – basically everything. I consider him one of my “academic parents”, and he was later a close friend.

George took about 15 students including myself (~50/50 undergrad/grad) in vans for the better part of two months collecting plants and animals from Auburn, AL northeast to parts of Maryland. It was one of the best periods in my life. To help write this blog, I resurrected my old field notebook from the course to recall some of what we collected. For example, I see that we collected a black racer snake, hiked through a stand of smoke trees, observed cave bats, snorkled for freshwater mussels, observed rare bog turtles, collected aquatic insects, seined for fishes, captured a jumping mouse with our bare hands, used live traps for small mammals, sampled terrestrial snails, collected at least five species of cockroach (!), identified millipedes, collected a baker’s dozen species of salamanders, hiked to the top of Clingman’s Dome to see the completeness of the damage done to forests by acid rain and the balsam woolly adelgid, visited a cataract bog with stands of live mountain sweet pitcher plants (I described them as uniformly tall, beautiful, and with insects trapped in the pitchers). And this list was just for the first half of our trip!

From the dusty bottom of moving boxes – my field notebook from 2002. 

One afternoon, early in the trip, we were hiking through Joyce Kilmer National Forest in NC – famous for its old growth tulip trees. We’d been hiking for an hour or so when George stopped at the base of a large tulip tree. He sat down, pensively, and swigged some water out of his canteen. He then said something I’ve never forgot

“Don’t let anyone tell you to get into the real world. Science and academics is the search for knowledge. And it’s more real than anything you’ll ever find in the “real world”.”

I’d never considered science as a career before then. Was I good at that? I had always figured I would get a fisheries degree, find a great job at a state or federal agency, and move back near home. Over time, I came to learn that I was good at science, and it became a passion. I wanted to understand how things worked – and I wanted to use that information to improve conservation, especially for my beloved fishes.

Over the years, I’ve come to realize my experience wasn’t unique. Many students pursue environmental and science-based careers after taking field courses. We observe this frequently at the Center for Watershed Sciences at UC Davis. Many of our students, alumni, and staff began their journeys after taking Ecogeomorphology (EcoGeo for short). The brain child of Jeff Mount and Peter Moyle, EcoGeo is an interdisciplinary idea, where upper level undergraduate students study watershed issues in multidisciplinary teams. The course culminates with an extended summer field trip to the watershed where field research is conducted. UC Davis teams have traveled to places like the Kobuc River (AK), Santa Cruz Island (CA), Grande Ronde (OR/WA), Skeena River (BC), Copper River (AK), and the Grand Canyon (several times). So many UC Davis students have started careers with these courses; it is one of the great and enduring legacies of the Center, and one that I would like to see multiplied in coming years.

UC Davis EcoGeo students and instructors are gathered in the Grand Canyon in the nightly Circle of Science, where each night a student makes a presentation on some issue relevant to river management. Then everyone discusses how the topic relates to different disciplines. Photo credit: Joe Proudman

We know these courses are effective at generating extraordinary learning outcomes. Elkins and Elkins (2007) demonstrated that for introductory geology information, there was significantly higher improvements in basic geoscience understanding for field course students compared to 29 other introductory geoscience courses from across the United States. Durrant (2015) showed that aside from basic intellectual gains, students of field courses themselves realized integrative learning gains had taken place while attending a field course. These results suggest field courses also work on sharpening metacognition or ‘thinking about how you think’ – considered one of the higher forms of human thought. 

Finally, field courses can reset our values framework. For many young people, especially those without privilege, nature has never been fully experienced. Our society, especially in California, is increasingly urban, populated, and disconnected from nature and wilderness. We work and manage within reconciled contexts – urban parks, working landscapes, backyard ecology. These frameworks are necessary to realistically preserve and manage the ecological function we have left. Yet there is also a need to visit, study and protect the best – wild places – where the true real word is right in front of you. It is important for humans to experience these environments. 

In an alarming study by Soga and Gaston (2016), we see that children especially are having decreased basic contact with nature. For example, the percentage of children who had never fished increased from ~20% in 1998 to ~50% in 2009. The percentage of children who had never climbed a mountain increased from ~50% in 1998 to ~70% in 2009. Other simple indicators of participation (climbing trees, catching bugs, birdwatching) have all declined in young people over time. This is scary – and may do us in faster than many other existential threats that we worry about! 

It is rightful to ask, “How will our society be capable of protecting nature if many have never fully experienced it?” Field courses don’t solve this problem alone, but they do address the root of the problem for those who take them. Field courses also represent an opportunity to aid in diversifying the fields of natural resource management and conservation, which are notably lacking in recruitment and retention of women and people of color. For our part, we will journey on. Maybe you’ll see some of our graduates out on the river, or fighting for science-based decision-making in a meeting or public forum near you.

Further reading

UC Davis Center for Watershed Sciences education webpage,

Durant, K.L. 2015. The Integrative Learning Value of Field Courses. Journal of Biological Education 49: 385-400.

Elkins, J.T., and N.M.L. Elkins. 2007. Teaching Geology in the Field: Significant Geoscience Concept Gains in Entirely Field-based Introductory Geology Courses. Journal of Geoscience Education 55: 126-132.

Soga, M., and K.J. Gaston. 2016. Extinction of experience: the loss of human-nature interactions. Frontiers in Ecology and the Environment 14: 94-101.

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That Time Warren Buffett Got Involved in California Water

by Andrew L. Rypel

Famous quote by Warren Buffett

As if 2020, wasn’t completely strange enough, it wound up also being a time when Warren Buffett was plunged headlong into California water. Buffett of course is an American business tycoon – primarily an investor, and currently the 4th richest person on the planet. Although 90 years old, Buffett continues as chairman and CEO of Berkshire Hathaway – a multinational holding company headquartered in Omaha, Nebraska – Buffett’s hometown. Buffett is also a mega-philanthropist that has pledged to give away 90% of his wealth, mostly through the Bill & Melinda Gates Foundation. Thus it was with some surprise that last year Warren Buffett found himself recently embroiled in a hugely important California water issue – removal of the Klamath River dams.

The socioecological effects of dams on the Klamath River have been massive, almost uniformly negative, and ongoing. The Klamath watershed has been estimated as the third-most productive drainage on the West Coast for salmon and steelhead. Yet salmon runs declined substantially over the last century in part because dams fragment and isolate salmon from their historical upland spawning habitats (Brown et al. 1994, Hamilton et al. 2016). Other complicated ecological problems that harm salmonids persist in the basin and can vary by taxa and watershed position (Quiñones et al. 2014). Finally, climate change and certain aspects of current dam operations increase vulnerability of salmon to disease, notably C. shasta (Som et al. 2019, Lehman et al. 2020). 

Klamath River before and after installation of Iron Gate Dam. Photo source:

Indigenous peoples have disproportionately dealt with the brunt of ecological impacts from dams on the Klamath River (Most 2007, Norgaard and Reed 2010, Hormel and Nogaard 2009). Fish kills and declining salmon populations have left indigenous nations and fishers scrambling to adapt, and developing legal strategies for defending their ancestral heritage and sacred natural resources. And as if fighting legal battles for the river and salmon weren’t enough, examples abound of tribal members being harassed for hunting and fishing using traditional methods. Technicalities and cover-ups were used to arrest and harass indigenous peoples and negate fishing rights. The landmark Boldt Decision of 1974 re-affirmed the rights of indigenous people to hunt and fish using ancestral methods, and to also co-manage their fisheries with the US and its state governments. Nonetheless, various other methods and campaigns were created after the Boldt Decision to functionally invalidate tribal fishing rights. These battles mirror unsavory behavior in other inland fisheries following the Boldt Decision, such as with the walleye fishery in the Ceded Territory of Wisconsin (Nesper 2002).

Plans to remove four large hydroelectric dams along the Klamath River have been developing for some time. The genesis of the Klamath Dam removals is multi-faceted. Part of it comes from endangered species like salmon and the native Klamath River suckers having gained protective ascendancy under the law. In addition, tribes have been exercising their senior water rights, which can date back to original treaties – making tribal nation owners some of the oldest water right holders on the river. However, there is also an important business case for removing the dams. Like all dams, these four (Iron Gate, John C. Boyle and Copco Dams 1 & 2) have been ageing. And unlike fine cheeses and wines, dams tend to get worse with age – not better. For example, there are concerns about structural stability and costs to rehabilitate or retrofit them for functionality and safety in the coming century. Ultimately, to renew the operating license for the dams, PacifiCorp would have had to shell out $400M for upgrades to ensure compliance. Part of this compliance would have included installation costs for fish ladders at each of three dams for fish migration. Removing the dams would likely cost less, but the theme is the same – PacifiCorp is the major entity on the hook.

Photo of salmon carcasses taken 9/28/02 along the banks of the Klamath River. Photo source: Ron Winn/The Herald And News via AP

Berkshire Hathaway, under Buffett’s leadership, acquired Pacificorp in 2006 for $9.4B from Scottish Power – a UK company. And while Buffett made his name on a reputation for acquiring good companies and letting them run more or less autonomously, that is not how the Pacificorp acquisition unfolded. Rather, the day of the merger with MidAmerican (Birkshire’s energy holdings subsidiary), Pacificorp was reorganized into three separate units and an East and West Division. Almost all top managers were replaced and a top-down chain-of-command structure established to run the company in the Birkshire way. That is – using financial discipline, respecting the chain-of-command, and focusing on the bottom line. Thus, the history of Birkshire’s involvement in the Pacificorp yielded a window into how the company might approach the Klamath dams quagmire.

A 2016 accord provided hope that the removals would indeed occur. Under this agreement, Pacificorp would transfer its federal hydroelectric licenses for the dams to the Klamath River Renewal Corporation – a nonprofit coalition of stakeholders deeply invested in the project. The removal cost is estimated at $450M, so the cost is more than the $400M it would take for PacifiCorp to upgrade the infrastructure – but not much more. Under the 2016 agreement, Pacificorp customers would contribute $200M for the project while the utility would avoid additional liability costs. The additional $250M would come from a 2014 water bond approved in California.

Artistic rendering of the Klamath River at Copco Lake before versus after dam removal.

But things got spicy again in summer of 2020. The Federal Energy Regulatory Commission (FERC) decided to approve the transfer of the FERC license from PacifiCorp to the Klamath River Renewal Corporation, but on the stipulation that PacifiCorp remain as co-licensee. FERC expressed concerns that while the new nonprofit could likely carry out the work, they would undoubtedly be faced with issues they may not be equipped to deal with. This was a game changer because it meant PacifiCorp and its rate payers, and by proxy, Berkshire, would be on the hook for liabilities from any fish kills, lawsuits, blue green algae blooms, and other issues. 

Copco Dam on the Klamath River, one of the four large dams slated to be removed. Photo source:

Fortunately, an accord was again struck in fall of 2020 with Buffett and Berkshire. Governors Gavin Newsom (CA) and Kate Brown (OR), together with partner tribes and NGOs, pushed Berkshire and Buffett hard towards a new solution. In the new agreement, California and Oregon will sign on as co-licensees of the dams alongside the Klamath River Renewal Corporation. The stipulation is that the two states and PacifiCorp will split costs equally should the project overrun funds set aside for the project. However, the deal still requires approval of the FERC board that rejected the previous proposal, so nothing is final yet. At a press conference announcing the deal, the Chairman of the Yurok tribe, Joseph James articulated the following (watch also in video below): 

“To me this is who we are. We have a free-flowing river, just as those who have come before us, and here now for those generations to come. This is a place in time for our prayers, our songs, our dances, our ceremonies which will continue with more water and more fish. Our ecosystem will continue to heal and provide substance to all of us. We are connected with our heart and our prayers to these creeks, lands, animals, and our way of life will thrive with these dams being out. We’ll be able to have salmon and our traditional food once again because there is no other place than our villages and sense of place than along the Klamath River. I’d also like to highlight and discuss who we are. We’re a prayer people. We’re traditional people. We’re a natural resource tribe. It is our duty and our oath to bring balance to the river. In this effort, it is fulfilling that duty.”

The Berkshire Energy Chair Greg Abel later commented that “It was an honor to be there for the important milestone, which underscored his company’s commitment to “economic, social and racial justice.

As is often the case, the road to water policy change in California has been long and winding. Some have pointed out that the deal isn’t perfect, claiming that the new deal struck is a bad one for California and Oregon taxpayers that are now on the hook for costs and liability. The dam removals also cut into the capacity to have a more reliable source of energy available for an ailing electric power grid. However, the Klamath dams are an example of what it takes to build real solutions for complex water problems. Critical decisions that were difficult to predict threw wrenches into already complicated processes. There will be more detours and problems in the coming years. Stakes are high. Patience is essential. Compromises were made. Yet culture, economics, politics, and ecology collide to pave and sometimes divert the road towards something quite special in California – this should be celebrated. The solution struck seems reasonable and ensures the Klamath River will finally have a chance to recover. We hope to provide more blogs on the Klamath dam removals and related Klamath basin topics in the coming years.

Klamath River. Photo source:

Further Reading

Brown, L. R., P. B. Moyle, and R. M. Yoshiyama. 1994. Historical decline and current status of coho salmon in California. North American Journal of Fisheries Management 14(2):237-261.

Hamilton, J. B., D. W. Rondorf, W. R. Tinniswood, R. J. Leary, T. Mayer, C. Gavette, and L. A. Casal. 2016. The persistence and characteristics of Chinook salmon migrations to the upper Klamath river prior to exclusion by dams. Oregon Historical Quarterly 117(3):326-377.

Hormel, L. M., and K. M. Norgaard. 2009. Bring the salmon home! Karuk challenges to capitalist incorporation. Critical Sociology 35(3):343-366.

Lehman, B., R. C. Johnson, M. Adkison, O. T. Burgess, R. E. Connon, N. A. Fangue, J. S. Foott, S. L. Hallett, B. Martinez–López, and K. M. Miller. 2020. Disease in Central Valley Salmon: Status and Lessons from Other Systems. San Francisco Estuary and Watershed Science 18(3).

Most, S. 2007. Salmon people: crisis and continuity at the mouth of the Klamath. California History 84(3):5-22.

Nesper, L. 2002. The Walleye War: The Struggle for Ojibwe Spearfishing and Treaty Rights. University of Nebraska Press, Lincoln, Nebraska USA.

Norgaard, K. M., and R. Reed. 2010. Salmon Feeds Our People: Challenging Dams on the Klamath River. Conservation International.

Quiñones, R. M., M. Holyoak, M. L. Johnson, and P. B. Moyle. 2014. Potential factors affecting survival differ by run-timing and location: linear mixed-effects models of pacific salmonids (Oncorhynchus spp.) in the Klamath River, California. PloS One 9(5):e98392.

Som, N. A., N. J. Hetrick, R. Perry, and J. D. Alexander. 2019. Estimating annual Ceratonova shasta mortality rates in juvenile Scott and Shasta River coho salmon that enter the Klamath River mainstem. U.S. Fish and Wildlife Service, Technical Report.

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California’s New Drought

By Jay Lund, Andrew L. Rypel, and Josue Medellin-Azuara

As March begins to drag on with little precipitation in the forecast and few weeks left in California’s traditional wet season, we are in another dry year. This is California’s second dry year in a row since the 2012-2016 drought.  Statistically, California has the most drought and flood years per average year than anywhere in the US.  This statistical fact seems to becoming increasingly extreme, as predicted by many climate change models.

Figure 1. Some major current reservoir levels today and over the last few years, including the 2012-2016 drought (US Army Corps of Engineers)

As Californians have adapted to drought over the last 150 years, drought damages and losses have changed.  Traditional drought water supply losses to cities and agriculture have fallen tremendously, as a percent of urban and agricultural economies.  The 2012-2016 five-year drought had total direct damages of about $10 billion statewide, without direct loss of life (Lund et al 2018).  For a state economy exceeding $2 trillion/year, drought impacts were often large locally, but statewide water shortage impacts were less than 0.09% of the state’s economy.  Traditional drought impacts are important, but are manageable if managed well (we sometimes have trouble with this).

Yet, wildfires in the four following years worsened considerably from the drought-related deaths of over a hundred million forest trees and other factors.  These wildfires caused a record of over $55 billion in direct property losses and 175 direct deaths, with many weeks of widespread air pollution with still larger and more widespread economic and health impacts, including estimates of more than 1,000 additional deaths.  Additional health impacts from these events are likely chronic and poorly understood (such as increased risk of cancer and lung damage from particulate inhalation). The drought was not responsible for all these wildfire impacts, but probably some substantial share of them.

Arguably, the 2012-2016 drought’s impacts occurred mostly after the drought ended.  And most economic and health drought impacts were to people who suffered no water shortages.

California’s new drought, with higher temperatures and greater resulting wildfire and air pollution impacts, and perhaps other untold ecological and human health impacts, is a new aspect and era for drought in California.  Wildfire-related air pollution affects almost everyone in California, even the majority who don’t see traditional water shortages – but do see often-delayed drought-related shortages of safe air to breathe.

State of this drought today. Today, northern California has about 52% of average precipitation for this time of year.  Snowpack levels are at 62% of average, but this is less important because California’s reservoirs are only 57% of long term average total storage.

Some of California’s major reservoirs are as low in this second year of drought as they were in the third and fourth years of the 2012-2016 drought.  Today, storage in Shasta reservoir is 2.28 million acre feet. Since 2012, only 2014 had a lower storage at this time of the year (at 1.94 million acre feet). These conditions pose major challenges for endangered fishes like winter-run Chinook salmon that have extended freshwater rearing periods during the summer. If temperatures are as warm as the last drought, we might see problems supplying cold water for young winter-run salmon below Shasta dam, a problem which killed more than 90% of this salmon run in 2014 and 2015.

High drought temperatures seem likely again, as temperatures have been high for recent years, including the previous drought.  In the last drought, higher temperatures were responsible for about 25-30% of the drought’s total moisture deficit, which increased tree mortality in forests.  Higher temperatures also make it harder to maintain cold water for salmon and other species.  Less cold water is available, and it warms faster as it travels downstream.  Increasing temperatures have been noted as a major challenge for the embattled delta smelt, which is near extinction.  Its close threatened relative, longfin smelt, also is sensitive to temperature (Yanagitsuru et al. 2021). We have barely begun to understand, detail, or try to manage the more complex effects of warm droughts, especially for ecosystems.

Groundwater Redux and Future

The biggest traditional drought impacts are likely to occur from increased agricultural groundwater pumping to partially compensate for reduced surface water supplies: 

  • Many rural community and household wells will be left dry or become contaminated as deeper wells pull nitrate contamination deeper (Stone and Gailey 2019). 
  • Some environmental surface flows will be drawn underground by lower aquifer levels.
  • Additional land subsidence will reduce capacities for surface canals and floodways.
  • Accumulated overdraft from additional drought years and the years elapsing during this drought will make achieving SGMA groundwater sustainability objectives harder without additional reductions in agricultural acreages in deeply overdrafted basins.  (The magical magnitudes of water espoused from Flood-MAR will become still less plausible, even though plausible amounts remain useful.  Droughts often test our assumptions.)

The Delta

The Delta is always a pivotal weak point in California’s water system.  Managers are always very attentive to Delta management and its drought challenges.  Much will depend on details we don’t know yet about this drought.  A few things to watch:

  • Reduced water supplies from the Delta are certain in the drought, but the exact amount of reductions won’t become clear for some time.
  • Warmer temperatures and lower Delta channel flows seem to have accelerated the spread of invasive aquatic plants during the last drought.  This might well happen again.  These same conditions also could increase harmful algal blooms, with both water quality and potential public health impacts, and are being studied by a variety of agency and independent scientists.
  • Delta salinity barriers are likely under continued severe conditions. 
  • Struggles for native Delta fishes remains a perennial issue which peaks in times of drought.  Will this be the true end of Delta Smelt?

Other usual, but still important, impacts

  • California’s hydropower generation, usually about 15% of state electricity production, will fall.
  • Continued shifts in forest and rangeland ecosystems can be expected.
  • Agricultural water shortages, and resulting unemployment and financial stress to irrigation districts.
  • Local urban water shortages, and financial stress to water utilities from reduced water sales and perhaps to poorer water customers
  • Water markets – prices up
  • Water right curtailments – seem likely, with details becoming clearer in the months ahead.

Drought in California is always an old story and a new one.  Alas, we probably will need the N-95 masks episodically after the pandemic to combat drought impacts in the coming years.

Some data sources

Here are some data-rich sites useful for folks who want to follow the drought.  The main overall go-to data site is DWR’s excellent CDEC, – Bon apetit!



Reservoir levels:

A nice table of major reservoir storages throughout California, produced at the end of each month.

A nice table comparing major reservoir levels for this time over the last few years, including the previous drought.

Jay Lund and Andrew Rypel are professors and Co-Directors of the Center for Watershed Sciences at the University of California – Davis.  Josue Medellin-Azuara is a professor at the University of California – Merced.

Happy Pi Day! (3/14)

Further reading

Durand JR, Bombardelli F, Fleenor WE, Henneberry Y, Herman J, Jeffres C, Leinfelder–Miles M, Lund JR, Lusardi R, Manfree AD, et al. 2020. Drought and the Sacramento-San Joaquin Delta, 2012–2016: Environmental Review and Lessons. San Franc Estuary Watershed Sci. 18(2). doi:10.15447/sfews.2020v18iss2art2.

Lund J, Medellin-Azuara J, Durand J, Stone K. 2018. Lessons from California’s 2012–2016 Drought. J Water Resour Plan Manag. 144(10):04018067. doi:10.1061/(ASCE)WR.1943-5452.0000984.

Stone, K. and R. Gailey (2020),Economic Tradeoffs in Groundwater Management During Drought,”, June 10, 1919.

Ullrich, P.A., et al. (2018), “California’s Drought of the Future: A Midcentury Recreation of the Exceptional Conditions of 2012–2017”, Earths Future. 2018 Nov; 6(11): 1568–1587.

Woodhouse, C. A., Pederson, G. T., Morino, K., McAfee, S. A., and McCabe, G. J. (2016), Increasing influence of air temperature on upper Colorado River streamflow, Geophys. Res. Lett., 43, 2174– 2181, doi:10.1002/2015GL067613.

Yanagitsuru, Y., et al. (2021), “Effects of temperature on hatching and growth performance of embryos and yolk-sac larvae of a threatened estuarine fish: Longfin smelt (Spirinchus thaleichthys),” Aquaculture, Vol. 537.

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Managing Water and Crops with Groundwater Salinity – A growing menace

by Yiqing “Gracie” Yao and Jay Lund

Salinity is an eventual threat to agriculture and groundwater sustainability in parts of California, and other irrigated parts of the world. Irrigation, lower groundwater levels, and natural conditions have dramatically increased groundwater salinity in parts of California over the last 150 years (Hansen et al. 2018). Nearly two million tons of salt accumulates per year in the San Joaquin Valley (CV-SALTS), where 250,000 acres of irrigated land have been fallowed, 1.5 million acres are potentially salt-impaired (Great Valley Center 2005), with $1.2 – $2.2 billion/year losses by 2030 (Howitt et al. 2009) without management. Managing groundwater with salinity can differ fundamentally from conjunctive water management without salinity, which was summarized in a previous blog post.

Salts accumulate in soils and shallow groundwater in arid and semi-arid areas because higher evapotranspiration rates and lower precipitation leave salt in the soil, requiring more irrigation water (also containing salts) to leach soil salinity to groundwater or drainage systems. However, without drainage from a basin, as occurs when low groundwater tables prevent salt drainage to rivers, soil salinity collects in underlying aquifers and groundwater salinity can only increase with time (Pauloo and Fogg 2021). 

With every pumping-and-recharge cycle, the groundwater becomes saltier. This is common in western parts of California’s San Joaquin Valley (Hansen et al 2018). Salts in soil and irrigation water reduce crop yield and quality, with foreseeable salinization and agricultural losses for the San Joaquin Valley.

Groundwater salinity and conjunctive use of surface water and groundwater

A recently-completed hydro-economic optimization model examines conjunctive water use and cropping patterns for extensive irrigated agriculture with increasingly saline groundwater (Yao 2020). It models crop planting and water management to maximize profits over a 10-year period with surface water availability varying from dry to wet years (event 1 = driest to event 5 = wettest), considering salinity’s harm to crop yields. The modeling was applied for conditions similar to the western San Joaquin Valley. For simplification, the model assumes blended irrigation water to reduce salinity effects on crop yields. 

Model results show that conjunctive use with more saline groundwater differs fundamentally from conjunctive use without salinity (Figure 1). With little groundwater salinity, semi-arid agricultural regions tend to pump more groundwater in drier years to supplement scarcer surface water. As groundwater become saline enough to reduce crop yields, economically optimal conjunctive use shifts to pumping less in drier years and pumping more in wetter years (Figure 1), when surface water can dilute more saline groundwater.

Figure 1. More saline groundwater fundamentally shifts groundwater operations from pumping more in dry years to pumping more in wetter years, when more saline groundwater can be diluted with fresher surface water (Yao 2020), while maintaining groundwater storage.

Cropping patterns and crop water use with groundwater salinity

Figure 2 shows water use for perennial and annual crops over the range of dry to wet years for different groundwater salinities.

At low groundwater salinities, more perennial crop acres are grown. As groundwater salinity rises to the salt tolerance of the perennial crop, groundwater’s ability to furnish useable water for dry years to grow perennial crops diminishes rapidly, because driest years have the least surface water to blend with more saline groundwater. Otherwise, perennial crop yields decrease uneconomically. Reduced pumping in drier years substantially reduces a region’s ability to support perennial crops and can eliminate annual crops with lower value in dry years.

To maintain groundwater levels, groundwater pumping increases in wetter years when more surface water is available to dilute more saline groundwater, but the additional pumping is used to grow lower-value annual crops. With higher groundwater salinities, annual crop acreage in wetter years is limited by irrigation water salinity. If all available water (surface water plus groundwater) is used to grow crops in the wettest years, the additional deep percolation forces more groundwater pumping to avoid waterlogging. More pumping increases salinity in irrigation water as the amount of surface water is fixed for each water year type, while more saline irrigation water reduces crop yields. Therefore, fewer annual crops are planted, and excess water must be disposed from the basin (brown arrows in Figure 2). 

Figure 2. Relationship between crop water requirement and irrigation with no overdraft. Brown arrows in the wettest year for high salinity cases are unused water externally drained.

Economic value of water with groundwater salinity

Table 1 summarizes how groundwater salinity affects the economic value of surface water and groundwater. When groundwater salinity is low, groundwater has greater value, as it can help support more perennial crops in dry years (when surface water is unavailable). With higher groundwater salinity, this drought buffering is unavailable and becomes a cost to agriculture, as pumping makes irrigation water too salty for perennial crops, reducing both crop yield and profit. At the two highest groundwater salinities, groundwater is so undesirable (in this model) that saline groundwater is pumped only for discharge outside the basin to avoid waterlogging (imposing pumping and disposal costs without profit).

Table 1. Summary of economic values of water ($/AF) in different hydrologic events with different groundwater salinities for a no-overdraft goal.

Salination of groundwater makes surface water more economically valuable, as it makes useable water scarcer overall. Surface water availability in the driest years limits the extent of profitable perennial crops, making farmers willing to pay more for this water (roughly the cost of desalted water in this case). The range of economic values for surface water widens across years as groundwater becomes more saline. For low salinities, the availability of fresh groundwater dampens water price variation across years. But with more saline groundwater, the variability in surface water’s economic value expands, rising for dry years and declining, eventually to zero, for wetter years. 

A drier climate further increases the value of surface water in the driest year and reduces agricultural profit. When groundwater salinity is low, overall usable dry-year water scarcity is less, and we value groundwater more. However, if groundwater salinity is too high, groundwater reduces agricultural profitability for drier climates.

Artificial recharge in the context of groundwater salinity

From Figure 2, high groundwater salinity leads to externally discharging water in the wettest years to physically remove both salt and excess recharge (deep percolation) from the basin. In such cases, raising water tables can be more profitable (if waterlogging is not an issue), by reducing need to pump (and waste) saline groundwater, having the same acreages of perennial crops with more lower-value annual crops in wettest years (Figure 3) as no pumping occurs in these years and irrigation water salinity is not a concern anymore. Artificial recharge of fresh surface water also can reduce groundwater salinity, at least locally, to make more groundwater fresher for dry year use in the future. Starting artificial recharge with fresh surface water early can slow groundwater salination and reduce its effects on water and crop management.

Figure 3. With high groundwater salinity (Cgw = 6,000 mg/L), mild aquifer recovery can be more profitable. Also, artificial recharge somewhat dampens the difference in surface water variability in wetter years.

Unlike pumping decisions, which are limited by irrigation water salinity, artificial recharge occurs in wetter years when perennial crops are irrigated only by fresh surface water. Therefore, artificial recharge still serves the original function of conjunctive use to dampen surface water variability. Annual crop acreage in years without artificial recharge should never exceed annual crop acreage in years with artificial recharge, and annual crop acreage is the same across years with artificial recharge (Figure 3).


For parts of California where salts accumulate in groundwater without drainage from the basin (mostly western San Joaquin Valley), growing groundwater salinity seems destined to bring a somber future for agriculture. Here eventually, salinizing groundwater will have diminishing ability to serve as a drought reservoir for drier years, and perennial crop acreage will become limited by surface water available in drier years, with greater annual crop acreage fluctuations. Profitable agriculture will still exist, but will be smaller, less profitable, and more variable across wetter and drier years. Though costly, earlier restoration of the aquifer levels, with reduced pumping and increases surface water recharge, can slow salination of groundwater and prolong the value of the aquifer for agriculture.

Many variants of this problem and solutions can be explored; some will be helpful.  Desalting of groundwater for irrigation will continue to be intensely explored and advocated, but will always remain expensive and unsuitable for lower-valued crops.  There is no cheap and permanent escape from the Valley’s water and salt balance problems.

Salinity accumulation is an ancient menace for irrigated agriculture, from ancient Mesopotamia to the present day. After groundwater overdraft is tamed, groundwater salinity will drive changes in groundwater management and overlying agriculture. 

Dr. Gracie Yao recently completed her PhD in Civil and Environmental Engineering at the University of California – Davis.  Jay Lund is a Professor of Civil and Environmental Engineering at the University of California – Davis

Further Reading

Yao, Y. and J. Lund (2021), Managing Groundwater Overdraft – Combining Crop and Water Decisions (without salinity),, January 17, 2021

Yao, “Gracie” Yiqing (2020), Managing Groundwater for Agriculture, with Hydrologic Uncertainty and Salinity, PhD dissertation, Department of Civil and Environmental Engineering, University of California – Davis.

Dogan, M., I. Buck, J. Medellín-Azuara, J. Lund (2019). Statewide Effects of Ending Long-Term Groundwater Overdraft in California, Journal of Water Resources Planning and Management, Vol 149, No. 9, September.

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, Vol. 265, 110426, June 2020.

Faunt, C., ed. (2009). Groundwater Availability of the Central Valley Aquifer, California: U.S. Geological Survey Professional Paper 1766, 225p. USGS Professional Paper 1766: Groundwater Availability of the Central Valley Aquifer, California.

Hansen, J. A., Jurgens, B. C., & Fram, M. S. (2018). Quantifying anthropogenic contributions to century-scale groundwater salinity changes, San Joaquin Valley, California, USA. Science of the total environment, 642, 125-136.

Harou, J. and J. Lund (2008). Ending groundwater overdraft in hydrologic-economic systems, Hydrogeology Journal, Volume 16, Number 6, September, pp. 1039-1055.

Howitt, R., Kaplan, J., Larson, D., MacEwan, D., Medellín-Azuara, J., Horner, G., Lee, N. The Economic Impacts of Central Valley Salinity. Final Report to the State Water Resources Control Board Contract. March 2009.

Marques, G., J. Lund, and R. Howitt (2010). Modeling Conjunctive Use Operations and Farm Decisions with Two-Stage Stochastic Quadratic Programming, Journal of Water Resources Planning and Management, Vol 136, Issue 3, pp. 386-394.

Pauloo, R.A., Fogg, G.E., Guo, Z., Harter, T. (2021), Anthropogenic Basin Closure and Groundwater Salinization (ABCSAL), Journal of Hydrology, Vol. 593, 125787, February 2021.

Pauloo, R.A., Fogg, G.E. (2021), “Groundwater Salinization in California’s Tulare Lake Basin, the ABCSAL model,”, Posted on February 21, 2021

Reilly, T., K. Dennehy, W. Alley, and W. Cunningham (2008). Groundwater Availability in the United States: U.S. Geological Survey Circular 1323, 70p. USGS Circular 1323.

Singh, A (2014). Conjunctive use of water resources for sustainable irrigated agriculture, Journal of Hydrology, Volume 519, Part B, pp. 1688-1697, November 2014.

Zhu, T., G. Marques, and J. Lund (2015). Hydroeconomic Optimization of Integrated Water Management and Transfers under Stochastic Surface Water Supply, Water Resources Research, Vol 51, Issue 5, pp. 3568-3587.

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Celebrating Black Scientists in Fisheries & Biology

By Kim Luke, Christine Parisek, Rachelle Tallman, Marissa Levinson, Sarah Yarnell, Miranda Bell Tilcock, Andrew Rypel, and Jay Lund

In honor of Black History Month, the Center for Watershed Sciences would like to highlight the contributions of Black scientists in our field. These prominent researchers have not only pushed the social and scientific boundaries of fisheries biology, but have also acted as dedicated mentors. We recognize that scientists of color, and women, experience discrimination and have had more strenuous journeys to succeed in their fields. Out of respect for their lived experiences, the focus of this article is to share their important work, not speak on behalf of their experiences as scientists of color.  

First in her Field

Dr. Roger Arliner Young was a marine biologist, and the first Black woman to receive a PhD in zoology in 1940 from the University of Chicago. Dr. Young was also the first Black woman in her field to have her research paper “On the Excretory Apparatus of Paramecium” published in the journal Science in 1926. She was the student of another prominent Black marine biologist, Dr. Ernest Everett Just, who recruited Young during her undergraduate studies at Howard University. Dr. Young assisted Dr. Just with his pioneering experiments on marine organism fertilization at the Marine Biological Laboratory at Woods Hole. She went on to teach at several universities and head the Department of Zoology for Dr. Just while he was overseas. 

Fisheries & Anthropogenic Issues

Dr. Daniel Pauly is a fisheries biologist and professor at the University of British Columbia. He has worked all over the world, focusing his research on overfishing and global fish trends, particularly in developing parts of the world. Some of Dr. Pauly’s notable contributions include the fish encyclopedia FishBase, the modeling program Ecopath, and the research initiative for fisheries data, Sea Around Us. One of his papers, “Fishing down marine foodwebs” is widely considered to be one of the preeminent classics, and required reading for many fisheries courses. This paper was also included in the book “Foundations of Fisheries Science” that features reprints of critical fisheries work. Dr. Pauly has also written many books on fisheries and marine ecosystems, and has been given seven honorary doctorates from universities in Europe and Canada.

Working in the Public Sector

Dr. Mamie Parker is a fish and wildlife biologist, and was the first African American Fish and Wildlife Service Regional Director. She also served as FWS Chief of Staff, and Assistant Director of Habitat Conservation/ Head of Fisheries. One of the many highlights of Mamie’s work with fish habitat management, was her role in negotiating with General Electric to clean up the Hudson River. Dr. Parker now works as a principal consultant, success coach, and public speaker.

Population Genetics in Fisheries

Dr. Sheila Stiles has been a research geneticist at the Northeast Fisheries Science Center for more than 50 years. Dr. Stiles received a B.S. in Biology from Xavier University (Louisiana, USA), an M.S. from University of Connecticut (Storrs, USA), and finally, Ph.D. from the University of Massachusetts (Amherst, USA) in fisheries and genetics. Dr. Stiles was the first African American woman hired at the Milford Laboratory which later became part of the Northeast Fisheries Science Center when NOAA was created in 1970. Dr. Stiles is the project leader of a collaborative research program with a tiered focus on mussel breeding, molecular genetics, and field work in order to provide various economic and conservation applications. Dr. Stiles is also strongly involved in recruitment, retention, and mentoring activities of young scientists from elementary to college level.

Science meets Management

Dr. Cecil Jennings is Unit Leader at the USGS Georgia Cooperative Fish and Wildlife Unit in the Warnell School of Forestry & Natural Resources at the University of Georgia. He holds a bachelor’s degree in biology, natural science, and conservation from Carthage College, a master’s degree in wildlife and fisheries ecology from Mississippi State University, and a Ph.D. in fisheries science from the University of Florida. He has studied fisheries for over >32 years.

Dr. Jennings is widely known for developing science for improving conservation management of freshwater fishes throughout North America. He has worked extensively with rare and diverse fish species in the southeastern USA, but also fisheries with intense connections to people and communities. He has highly cited papers detailing aspects of the biology and management of sturgeons, suckers and paddlefish. Over his career, Dr. Jennings has mentored a small army of graduate students, post-doctoral research associates, and technical staff who continue to protect and manage fisheries for future generations. In 2020, Dr. Jennings was selected as the 2nd Vice President of the American Fisheries Society.

Founder of “Minorities in Aquaculture”

Imani Black founded Minorities in Aquaculture. Imani is currently a faculty research assistant working at the Horn Point Laboratory in University of Maryland’s Center of Environmental Sciences (UMCES), and soon-to-be graduate student at UMCES in 2021. Imani entered the aquaculture field through internships and trainings at the Oyster Restoration Team at Chesapeake Bay Foundation (Virginia) and Virginia Institute of Marine Science’s Oyster Aquaculture Training Program (OAT), and through work as an assistant hatchery manager at Hooper Island Oyster Company (Cambridge, MD). Imani was bothered that little to no people of color held management or leadership roles in aquaculture around her. With a desire to improve recruitment and retention of women and diversity in the marine sciences, Imani became founder and president of a new non-profit organization “Minorities in Aquaculture”.

Diversity, equity, and inclusivity in the ecology and fisheries workforce promotes a rich variety of perspectives, worldviews, creativity, innovation, skills, and experiences required to tackle the  complex socio-ecological issues we face. We must create individual and systemic changes to foster a scientific community to reflect this. We acknowledge that we selected just a few trailblazers, but we encourage readers to continue honoring Black History Month year round by researching other Black scientists and activists. 

“In fisheries science, we often celebrate the biodiversity of species. That celebration, however, exists in tension with the low diversity of gender and race or ethnicity in our workforce.”

Arismendi and Penaluna 2016 

To learn more about the featured scientists experiences, research, and accomplishments visit the following sites:

Dr. Roger Arliner Young:

Dr. Daniel Pauly:

Dr. Mamie Parker:

Dr. Sheila Styles :

Dr. Cecil Jennings:

Imani Black:

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Groundwater Salinization in California’s Tulare Lake Basin, the ABCSAL model

By Rich Pauloo and Graham Fogg

Lower groundwater levels can prevent drainage of water and salts from a basin and increase aquifer salinity that eventually renders the groundwater unsuitable for use as drinking water or irrigation without expensive desalination. Pauloo et al. (2021)  demonstrate this process for the Tulare Lake Basin (TLB) of California’s Central Valley. Even if groundwater pumping does not cause overdraft, it can cause hydrologic basin closure leading to progressive salinization that will not cease until the basin is opened by allowing natural or engineered exits for groundwater and dissolved salt. The process, “Anthropogenic Basin Closure and Groundwater Salinization (ABCSAL)”, is driven by human water management. 

Salts do not accumulate in aquifers when outlets exist to discharge groundwater and its salt load from the basin (Figure 1A). Salt load (TDS) is inherent to groundwater due to natural, ubiquitous subsurface rock-water weathering reactions. Many closed basins without salt drainage exist globally, including Death Valley, Salar de Uyuni (Bolivia), and saline lakes like the Great Salt Lake (USA) and the Dead Sea (Middle east). In all of these basins, the dominant exit for water, including groundwater, is evaporation that leaves salts behind. Changes in groundwater management, such as more pumping, recharge, or evapotranspiration can change the groundwater quality sustainability by merely closing the basin. This study investigated the time scales and ultimate magnitudes for groundwater basin salinization that can be expected in the TLB as it has shifted to a closed basin due to pumping and irrigation. 

Figure 1: Conceptual model of ABCSAL. (A) Open “drained” basin, pre-groundwater development: surface and groundwater systems connect. Groundwater discharges salts to surface water which exits the basin. Groundwater here is predominantly fresh (less than 1,000 mg/L). (B) Closed “undrained” basin: groundwater pumping eliminates baseflow to streams. Lower groundwater levels cause subsurface inflow to drain from adjacent basins. Pumped groundwater is concentrated by evapotranspiration (ET) in irrigation. Salts migrate into the production zone of the aquifer by vertical hydraulic gradients from recharge and pumping. 

Prior to groundwater use for irrigation in California, the TLB was drained by baseflow to surface water, lateral subsurface flow, and episodic spill from Tulare Lake into the San Joaquin Valley to the north (Figure 1B). A basin can transition from open or “drained”, to closed or “undrained”, when groundwater pumping lowers groundwater levels so saturated groundwater becomes disconnected from streams, and the direction of lateral groundwater flow reverses, causing the basin to drain adjacent areas (Figure 1B). Thus, the basin is “closed” in the sense that groundwater can no longer drain salts out of the basin. Closed basins naturally salinate over time.

Figure 2: Water budgets for the TLB in California’s southern Central Valley shows substantial change from(A) early-groundwater-development to(B) post-groundwater-development (C2VSim). Gaining streams become losing streams, with increased pumping, evapotranspiration, and recharge (from diversions and natural sources, like streams, lakes, and watersheds). 

The model results for the TLB show that salinization proceeds from the top of the aquifer down, as recharge water drives evapoconcentrated water at the land surface into shallow and then deeper aquifers over decadal to century long timescales (Figure 3). Impacts occur in shallow aquifers (around 100 feet deep) within decades, and in deep aquifers (greater than 500 feet) within two to three centuries. Results agree with measured TDS changes (Hanson et al., 2018; Pauloo et al., 2021) in shallow aquifers from historic to modern times in the TLB. The causes of basin closure are groundwater pumping and evapotranspiration (ET) from irrigated crops. Over the last century in the TLB, exits for groundwater have shifted from baseflow and lateral subsurface flow to ET, which now accounts for nearly all groundwater discharge and accommodates no salt discharge (Figure 2). 

Figure 3: Progression of groundwater salinization ensemble results for scenarios with and without rock-water interactions. The blue and purple lines show the ensemble median concentration for the two scenarios. The interquartile range of the ensemble simulations is shown in grey shading. The black dashed line is the freshwater TDS maximum contaminant level (MCL).

Groundwater basins can become closed or “undrained” due to moderate amounts of pumping, even without chronic declines in groundwater storage or overdraft. If the dominant land use in these basins is irrigation, then salinization from ABCSAL is likely already underway and if unchecked, the groundwater will eventually become unusable without expensive desalination. Pauloo et al. (2021) show the timescale of this process in the TLB is similar to groundwater basin exhaustion from overdraft. This raises the interesting question: “How could ABCSAL be avoided?” The answer is simple — the hydrologic basin would have to be opened (become “drained”) by managing it in a way that allows exits for groundwater and its entrained salts by baseflow to streams and wetlands, lateral flow to adjacent basins, or regional agricultural drains. This would require careful groundwater monitoring and management that maintains water table elevations such that the basin is sufficiently “full” to drain groundwater and salt to the surface and eventually to destinations beyond the basin. 

In groundwater basins undergoing salinization and significant overdraft, like the Tulare Lake Basin, it may seem far-fetched to suggest the hydrologic balance of these systems can ever be reversed sufficiently to open them. In basins not yet in advanced stages of overdraft and ABCSAL, however, it would be prudent to develop groundwater management that moderates pumping while maximizing recharge to maintain hydrologically open, “drained” conditions. A necessary ingredient in this water management would likely emphasize subsurface storage of water much more than in the past, possibly prioritizing subsurface water storage over the more common and familiar surface storage. 

The Central Valley has at least three times the subsurface water storage “space” than California’s entire surface reservoir storage capacity, highlighting opportunities to better use subsurface storage. Basin salinization challenges long term groundwater quality sustainability under the Sustainable Groundwater Management Act (SGMA). Solutions to slow or reverse salinization should emphasize managed aquifer recharge to increase groundwater storage, improve water quality, reduce pumping costs, and secure clean irrigation and drinking water. 

Figure 4: Animated progression of groundwater salinization for the scenario without rock-water interactions (blue line in Figure 3 above). Shallow aquifers are impacted within decades and deep aquifers, within centuries.

Dr. Rich Pauloo ( is a scientist at Larry Walker Associates and a co-founder of the Water Data Lab (  Dr. Graham Fogg is a Professor Emeritus of Hydrogeology and Hydrogeologist in the Agricultural Experiment Station at the University of California Davis.

Further reading

Hansen, J. A., Jurgens, B. C., & Fram, M. S. (2018). Quantifying anthropogenic contributions to century-scale groundwater salinity changes, San Joaquin Valley, California, USA. Science of the total environment, 642, 125-136.

Pauloo, R. A., Fogg, G. E., Guo, Z., & Harter, T. (2021). Anthropogenic basin closure and groundwater salinization (ABCSAL). Journal of Hydrology, 593, 125787.

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Eat Prey Loon: lessons from juvenile loons in Wisconsin

by Brian A. Hoover, Andrew L. Rypel and Walter H. Piper

Do you remember when you first moved from home, and were completely on your own in new surroundings? How did you decide where to live, or which restaurants to try for the first time? Did you try places randomly, or did you seek familiar food chains and businesses where you knew what to expect? 

Familiarity comes from experience, and familiarity can be important when an animal finds itself in a new habitat. Familiarity means you have previous experience with a specific situation, and so have a good idea of what to do (and what not to do!) if you find yourself in similar conditions again. For example, a young animal that learns how to find food and avoid predators in one habitat can apply those same lessons in a new similar habitat. But what if this same individual visits new habitat, which offers a different type of food that needs collecting in a different way? Learning new skills requires practice, and practice takes time. For young animals just starting out on their own, there might not be much time, or margin for error.

Identifying familiar habitats can be beneficial, but which habitat traits actually matter? A new study ( examines this question for juvenile common loons (Gavia immer) in lakes in northern Wisconsin. In central California we generally see loons in the winter, mostly in coastal ocean waters and also at some large reservoirs in Solano and Yolo County. But in summer, these large birds are icons of northern Minnesota, Wisconsin, New England, and Canada (e.g., the Canadian one-dollar coin is engraved with a loon and affectionately known as the “loonie”). There, loons thrive within landscapes carved by glaciers and dotted with natural lakes. Loons are highly territorial, with a single pair often defending an entire small to medium-sized lake. This territoriality leads to the loons’  famous vocal wails and yodels, which carry across the lakes and warn of dangers or intruders. Below is a short clip of one of the study bird adults wailing on Silverbass Lake in northern Wisconsin in 2020.

Loons raise 1-3 chicks in the summer, feeding them a variety of small fish, crayfish, leeches, snails, and other small food items. In the fall, chicks increasingly forage by themselves, and by the time they fledge, are on their own. After fledging, juvenile loons start visiting nearby lakes. Working with loons, the difficult part is identifying which birds are which and where they go! Fortunately, the Loon Project, started by Dr. Piper in 1993, has been banding adult and juvenile loons in Oneida and Vilas County in Wisconsin for 28 years, and the unique color band IDs given to each loon enable observers to quickly ID birds from shore or canoes. Consequently, observers can quickly track which juvenile loons are present when they start to visit different lakes in the study area.

Juvenile loons showing color bands on Muskellunge Lake. Photo credit: Linda Grenzer

This banding system allows us to understand where these juveniles are going, and what kinds of lakes are they visiting. And how the lakes of north Wisconsin differ from each other, in terms of their habitats.  One of the authors, Andrew Rypel, has been examining this last question in terms of fish communities and physical lake features (Rypel et al. 2019), and identified “classes” of lakes, based on distinct fisheries and their relationship to lake size and trophic complexity (complex – simple), temperature (warm – cold) and water clarity (dark – clear). Using these lake classes and physical lake variables, the study found that juvenile loons in the region follow a specific pattern:

1) Regardless of the lake that  juveniles grow up on, ALL juveniles prefer visiting large and complex lakes.

2) Juveniles prefer visiting lakes with pH similar to their home lake.

Randomization test showing the average pH difference (red vertical line) between the origin lake of juvenile loons and the destination lakes they visited. The histogram simulates what the pH differences should look like randomly if you calculate the pH difference between loon lakes and all other lakes in the study area (not just destination lakes)…. and then repeat this 10,000 times! The red line shows that juvenile loons are choosing to visit lakes much closer in pH to their home lake than would be randomly expected.

Point 1 makes sense – loons are large birds (large males can weigh up to 11 lbs) that require ample food supplies. Large complex lakes are likely to still have abundant fishes to feed on in late fall, especially energy-rich pelagic fishes, like Cisco (Coregonus artedi). In contrast, smaller lakes may be depleted by fall and generally lack larger, calorie-rich fish that would be especially attractive to a young bird trying to add mass for its first migration south.

Point 2 is just…interesting! Why would a juvenile prefer a lake with a pH similar to where it was raised? Interestingly, adults show a very similar behavior, as they prefer to breed on lakes that are similar in both size and pH to the lakes on which they were born (Piper et al. 2013). This behavior is believed to provide strong advantages to individuals that practice it. The idea is that if a young animal survives, the environment it grew up in likely indicates a reasonably high quality habitat. Thus, seeking out similar environments as an older individual could help improve survival and fitness. For example, loons might not really care about pH in particular, but pH may indicate or reflect something that loons DO care about, such as the smell of a particular habitat type where they know how to find and catch fishes. Perhaps a wandering juvenile loon looking for the right lake to visit is just like a human faced with an unfamiliar new menu, searching for a familiar and trusted childhood food? These patterns raise another question: if loons prefer habitats similar to home, what do other birds do? These types of questions might be especially relevant to the ecology of birds in California. For example, are some reservoirs/lakes in California more heavily used by migratory water birds than others? Do similar “rules” apply here? And ultimately, the behavior is intriguing, but the mechanisms and reasons for this behavior still need to be disentangled. Coupling loon movements with critical limnological dynamics promise more insights to come.

A parent looks on as a juvenile loon eats a bluegill (Lepomis macrochirus). Photo credit: Linda Grenzer

Brian Hoover is a GCI Postdoctorate Fellow in the Schmid College of Science and Technology at Chapman University in Orange CA. 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 Co-Director of the Center for Watershed Sciences. Walter Piper is a Professor of Biology in the Schmid College of Science and Technology at Chapman University in Orange CA. 

Further Reading

North Woods loons adopt duckling. 

BA Hoover, KM Brunk, G Jukkala, N Banfield, AL Rypel, WH Piper. (2021). Early evidence of natal‐habitat preference: Juvenile loons feed on natal‐like lakes after fledging. Ecology and Evolution Published Online

WH Piper, MW Palmer, N Banfield, MW Meyer. (2013). Can settlement in natal-like habitat explain maladaptive habitat selection? Proceedings of the Royal Society B: Biological Sciences 280 (1765), 20130979

AL Rypel, TD Simonson, DL Oele, JDT Griffin, TP Parks, D Seibel, CM Robers, S Toshner, LS Tate, J Lyons. (2019). Flexible classification of Wisconsin lakes for improved fisheries conservation and management. Fisheries 44 (5), 225-238

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Can Japanese Smelt Replace Delta Smelt?

by Peter Moyle

Wakasagi. Photo by Rene Reyes, USBR

A question I get asked on occasion is: Why all this fuss about endangered delta smelt when there is another smelt that looks just the same that can takes its place? The smelt being referenced is the wakasagi (Hypomesus nipponensis), which is indeed similar to the delta smelt (Hypomesus transpacificus). In fact, both species were once thought to be a single species (H. olidus), the pond smelt, with populations scattered along the Pacific Rim, from California to Japan. In 1963, Don McAllister, a Canadian ichthyologist and smelt expert, examined all populations and concluded that the populations in Japan and California were different from the intervening populations. But he also concluded that the two comprised just one species, with the scientific name noting their trans-Pacific distribution. Because having one freshwater species in two locations separated by thousands of miles made no sense from an evolutionary perspective, the species was later split into two species. This left the delta smelt stranded with the transpacificus epithet, following standard rules of zoological nomenclature.

The natural separation of the two species was broken by biologists from the California Department of Fish and Game (CDFG) in 1959. CDFG thought the pond smelt, then recognized as just one widespread species, would be the perfect forage fish for trout and salmon if planted in cold-water reservoirs. Because of the difficulty of collecting smelt in California, CDFG imported 3.6 million smelt eggs from Japan, where the smelt was cultured as a valuable food fish. The transplant was very successful and populations of wakasagi were soon widely established in reservoirs. The reservoirs included Folsom and Oroville reservoirs, whose water flows into the Sacramento River and Delta, via the American and Feather rivers, respectively. When the reservoirs spilled, smelt were spilled as well. Wakasagi probably reached the Delta by the 1970s but they went largely undetected until the early 1990s, presumably because of their similarity to the abundant delta smelt (Stanley et al, 1995, Trenham et al. 1998).

Once the presence of wakasagi in the Delta was realized, records of capture in sampling programs improved. Biologists trained in fish identification found they can identify wakasagi by sight, using the ‘gestalt’ of slightly narrower body, somewhat larger eye, and somewhat larger mouth; wakasagi also grow to larger sizes than delta smelt so any fish >90 mm is likely a wakasagi. Identifications can be supported by counting dark chromatophores on the ‘chin’ (isthmus; delta smelt has 0 or 1), although a few wakasagi (<5%) also have low numbers of chin chromatophores (Jenkins et al. 2020). Jenkins et al (2020) recommend that field identifications of wakasagi be confirmed with photographs and/or genetic tests to reduce uncertainty.

Wakasagi (top), delta smelt (middle), and wakasagi x delta smelt hybrid (bottom). From Jenkins et al.(2020)

But despite recognition, the wakasagi has remained scarce in the Delta and in rivers below the lowermost dams. In 149,455 trawl or seine pulls made during 1980-2017 in eight long-term surveys, only 364 contained wakasagi. Most of the catch was by the United States Fish and Wildlife Service Beach Seine Survey in the lower Sacramento River, below the mouth of the American River. There was a relatively high catch in 2011, a wet year, presumably of fish being blown out of the reservoirs (D. Stompe, UCD, unpublished analysis). This analysis indicates that most wakasagi in the Delta came from reservoirs.

Around 1997, a bogus scientific paper became widely circulated that claimed that the delta smelt, like the wakasagi, was a Japanese import. This false report gained some credence among water agencies, so Dr. Randy Brown of the Department of Water Resources asked if I would do genetic studies to determine if the claim was false. Not being a geneticist, I arranged with Dr. Bradley Shaffer, UCD herpetologist, to have his graduate students do the study (Stanley et al. 1995, Trenham et al. 1998). The results were clear. The delta smelt was indeed a distinct California species, whose closest relative was the surf smelt (Hypomesus pretiosus), a marine fish common along the California coast. The studies also showed that the closest relative of the wakasagi was also a marine smelt, found along the Japanese coast. The delta smelt and wakasagi were also shown hybridize (see above photo). Hybrid fish are rare and only maternal backcrosses are known, a genetic dead-end, so the rarity of both smelts combined with their distant genetic relationship has maintained the genetic integrity of wild delta smelt (Benjamin et al. 2018).

So, there is no question that the wakasagi is a species of smelt quite distinct from delta smelt, even if they look alike. But can the wakasagi substitute for delta smelt in the San Francisco Estuary? The answer is definitely ‘no’. They likely persist in the Delta mainly through continuous re-introductions from reservoirs. Presumably, the same poor environmental conditions that suppress delta smelt also suppress wakasagi. The failure of this Japanese smelt may also throw light on the potential for delta smelt to become re-established through repeated introduction of captive-bred fish. In contrast, the success of wakasagi in reservoirs suggests promise may also exist in some reservoirs for supporting delta smelt.

Further Reading

Benjamin, A., Sağlam, İ.K., Mahardja, B. et al. 2018. Use of single nucleotide polymorphisms identifies backcrossing and species misidentifications among three San Francisco estuary osmerids. Conservation Genetetics 19: 701–712.

Jenkins, J., N. Ikemiyagi, B. Schreier, B.E. Davis. 2020.  Exploring secondary field identification of delta smelt and wakasagi using image software. IEP Newsletter, October 2020.

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

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

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

Stanley, S. E., P. B. Moyle, and H. B. Shaffer.  1995.  Allozyme analysis of delta smelt, Hypomesus transpacificus and longfin smelt, Spirinchus thalichthys, in the Sacramento-San Joaquin estuary, California. Copeia 1995: 390-39

Trenham, P. C., H. B. Shaffer, and P. B. Moyle.  1998.  Biochemical Identification and assessment of population subdivision in morphologically similar native and invading smelt species (Hypomesus) in the Sacramento-San Joaquin Estuary, California. Transactions, American Fisheries Society 127: 417-424.

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