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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February 1: Is California Still Heading for a Multi-Year Drought?

by Jay Lund, Peter Moyle, and Andrew Rypel

This updates a post from December on the likelihood of California entering a second dry year. Normally, a second dry year brings drought operations for California’s overall water system operations.

Today, it is even likelier that California is entering a multi-year drought.

Precipitation conditions have improved somewhat with a nice atmospheric river this last week, but remain 51% of average for this time of year for the Sacramento Valley. (San Joaquin and Tulare basins are 61% and 47% of historical seasonal average precipitation so far.) Snowpack has improved somewhat with very recent storms, but is about as scarce as the precipitation.

The Sacramento Valley precipitation index today is about 14 inches below average. This translates statistically to about 16 inches of likely precipitation deficit this year (on average). From historical statistics, this averages 7.4 maf or 41% below average Sacramento Valley runoff this water year (on average), solely due to reduced precipitation. The scatter in the plot below gives little hope for a wet year.

The warmer temperatures of recent years, and this year, increase evapotranspiration which returns more precipitation to the atmosphere, leaving less for runoff and aquifer recharge than would have occurred historically. This increases the effective precipitation deficit. Estimates of this effect are substantial, but can vary considerably. So although reduced precipitation might reduce this year’s annual runoff by about 7 maf from average, runoff might be still lower because of depressed groundwater levels from last year’s runoff and more evapotranspiration from higher temperatures.

Reservoir storage conditions have mostly worsened, not refilling as much as usual from last year (which was dry) and the last dry season. Most large surface reservoirs are 50 – 75% of their long-term averages for this time of year. (This is good news for flood management this year, however.)

Groundwater in the Sacramento Valley is in good shape, and much of southern California’s groundwater storage also has refilled. Southern Central Valley groundwater has not recovered entirely from the 2012-2016 drought.

Although there is still some chance that this year could become average, wetter, or even have a major flood, it less likely.

Preparing for an impending drought?

“Plans are nothing, but planning is everything.” – Dwight Eisenhower

Californians should always be prepared for droughts (and floods, and apparently now wildfires). But this year, it looks wise to make more urgent preparations. Many actions below are probably happening, but others might be wishful thinking.

  • Farmers and irrigation districts with trees and vines will be making back-up water source arrangements, and consider how much groundwater to use – especially in areas with critical overdraft. Dry years now will increase difficulties of achieving SGMA groundwater objectives.
  • Cities will check their stocks, drought conservation and contingency plans, and drought finances (on top of COVID financial impacts on utilities and impoverished customers).
  • Wildlife refuges should plan to reduce water needs and arrange for back-up water sources for declining species such as riparian brush rabbits and tricolored blackbirds, resident waterfowl, and other birds. Similarly, managers should be identifying drought water sources for wetlands state-wide.
  • Fish managers should be preparing/improving refuges for declining and endangered fishes, such as Suisun Marsh, including implementing the Delta Smelt Resiliency Plan. This includes improving/expanding captive breeding programs.
  • Fisheries and water agencies, along with water regulators, should work together in advance to modify flow and habitat operations in California rivers to support struggling fish, especially salmon and steelhead, through even less favorable times. For the Sacramento Valley, implement the Sacramento Valley Salmon Resiliency Strategy and use it as model for drought-oriented strategies in other river systems.  
  • Salmon and steelhead hatcheries should prepare for reducing production in response to reduced cold water availability for hatcheries and downstream.
  • Delta managers, water project managers, and regulators should be planning now (ideally together) for low inflows and changed water operations in the coming year, including planning and permitting for salinity barriers in the coming years.
  • Fish agencies should monitor populations of all 62 California Fish Species of Special Concern and be prepare additional actions to protect populations threatened by drought. We assume such protection already exists for species formally listed as Threatened or Endangered (and we don’t need to lengthen this list).
  • Surprises are scenarios we did not expect. We seem to be in an age of surprises, especially the last 12 months. Organizations prepare for surprises by organizing adaptable plans and resources, collecting data, and developing rapid analytical capabilities, training to make flexible and fast decision (with inter-agency communications and exercises), and preparing to dedicate substantial resources rapidly. Surprises are the pop quizzes (or pop final exams) of organizational competence.

Will 2021 being dry make 2022 drier?

The same logic on a dry 2020 making a dry 2021 more likely applies now to prospects for 2022. Precipitation in northern California is poorly correlated across years, historically, as shown by the plot below.  The trend is essentially flat for precipitation.

However, a drier year in runoff tends to reduce the next year’s runoff a bit, as shown in the plot below for runoff.  So next year is likely to have a little less runoff even if we get average precipitation this year. 

Runoff is slightly correlated over time because precipitation accumulating in groundwater is likely to increase flow into streams in the next year, and lack of precipitation accumulating in groundwater tends to reduce streamflows in the next year.

Longer droughts have progressively larger economic, social, and environmental impacts.

We should prepare.

Jay Lund is a professor of civil and environmental engineering and Co-Director of the University of California – Davis Center for Watershed Sciences. Peter Moyle is an Emeritus Distinguished Professor of Wildlife, Fish, and Conservation Biology and an Associate Director of the Center for Watershed Sciences at UC Davis. Andrew Rypel is a professor of Wildlife, Fish, and Conservation Biology and Co-Director of the Center for Watershed Sciences at UC Davis.

Further reading

You can play with these data yourself, cheerfully supplied from DWR’s CDEC:

California Department of Fish & Wildlife. 2015.  Fish Species of Special Concern in California.  3rd edition.  Sacramento: California Department of Fish and Wildlife.

Durand, J., F. Bombardelli, W. Fleenor, Y. Henneberry, J. Herman, C. Jeffres, M. Leinfelder-Miles, J. Lund, R. Lusardi, B. Milligan, A. Manfree, J. Medellín-Azuara, and P. Moyle, “Drought and the Sacramento-San Joaquin Delta, 2012-2016: Environmental Review and Lessons,” San Francisco Estuary and Watershed Science, Vol. 18, Iss. 2, June 2020.

Escriva-Bou, A., J. Lund, J. Medellin-Azuara, and T. Harter “How reliable are Groundwater Sustainability Plans?,”, Posted May 10, 2020

Gailey, R., J. Lund, and J. Medellin-Azura, “Domestic well supply reliability during drought: stress testing for groundwater overdraft and estimating economic costs”, Hydrogeology Journal, Vol. 27, No. 4, pp 1159–1182, June 2019.

Klemes, V., 2000: Drought prediction: A hydrological perspective. Common Sense and Other Heresies: Selected Papers on Hydrology and Water Resources Engineering, Canadian Water Resources Association, 163–176

Lennox R.J., D.A. Crook, P. B.  Moyle, D. P. Struthers, and S. J. Cooke 2019. Toward a better understanding of freshwater fish responses to an increasingly drought-stricken world. Reviews in Fish Biology and Fisheries 29:71-92  Open Access.

Lord, B., B. Magnuson-Skeels, A. Tweet, C. Whittington, L. Adams, R. Thayer, and J. Lund, “Drought Water Right Curtailment Analysis for California’s Eel River,” Journal of Water Resources Planning and Management, ASCE, Vol. 144, No. 2: 04017082, February, 2018.

Lund, J. (2020), “Is California Heading for a Multi-Year Drought?,”, December 6

Lund, J.R., J. Medellin-Azuara, J. Durand, and K. Stone, “Lessons from California’s 2012-2016 Drought,” J. of Water Resources Planning and Management, Vol 144, No. 10, October 2018.


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A Swiss Cheese Model for Fish Conservation in California

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

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

The Swiss cheese respiratory pandemic defense model, as it appeared in the NY Times. Source:

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

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

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

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

Why is this relevant to water?

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Final Thoughts

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

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

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

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

Further Reading

Peer-reviewed papers

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

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

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

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

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

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

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

Kiernan, J.D., P.B. Moyle, and P.K. Crain. 2012. Restoring native fish assemblages to a regulated California stream using the natural flow regime concept. Ecological Applications 22: 1472-1482.

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

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

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

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

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

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

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

Web articles and germane reports:

NY Times Swiss cheese respiratory pandemic defense model.

Good biosecurity is multi-layered risk reduction.

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

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

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

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

Cited California WaterBlog

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Managing Groundwater Overdraft – Combining Crop and Water Decisions (without salinity)

by Yiqing “Gracie” Yao and Jay Lund

California’s Central Valley produces much of the nation’s food, including about 40% of the country’s fruits and nuts and has the nation’s second most pumped aquifer system. Its drier southern portion, the San Joaquin Valley, has decreasing surface water supply reliability due to frequent and prolonged droughts, stricter environmental regulations, and growing competition among water users. Many farmers pump groundwater to provide their unsupplied water demand. The resulting groundwater overdraft has numerous impacts on the Valley’s agriculture and residents. The 2014 Sustainable Groundwater Management Act (SGMA) requires local water agencies to end a decades-long overdraft (averaging about 2 maf/year) and bring groundwater basins into sustainable use by about 2040, a major challenge for San Joaquin Valley agriculture (Escriva-Bou et al. 2020).

Managing surface water and groundwater together, rather than separately, helps both supplies maximize overall regional benefits. This is referred as conjunctive water use, and is often a cost-effective way to help end overdraft (Harou and Lund 2008). Implementing SGMA has increased interest in expanding recharge programs, and also shows the need to reduce and modify agricultural groundwater use and production. The dry 2020 and so far dry 2021 underscore the importance of conjunctive water management for surface water, groundwater, and agriculture.

This post summarizes some recent research examining conjunctive water management for agriculture integrating hydro-economic optimization models on two timescales, neglecting for now salinity effects on crop yield: an intermediate term 10-year stochastic model of water and crop management spanning dry and wet years, and a far horizon (100 years of 10-year stages) management model which embeds intermediate-term model to represent longer-term aquifer targets (Yao 2020). The modeling was applied for conditions similar to California’s San Joaquin Valley.

Integrated economically-driven optimization of permanent and annual crop acreages and water management for these two timescales identifies some economically-promising strategies considering both crop decisions and water management to mitigate groundwater overdraft.  Some results of this investigation are:

  • Conjunctive use of surface water and groundwater can greatly smooth variability in water availability to support crop decisions, production, and agricultural profitability across different water years. More groundwater is pumped in drier years to support more profitable (often permanent) crops. More surface water is recharged in wetter years, often reducing wetter-year annual crop acreages to bank some water needed for artificial groundwater recharge.
  • Surface water is usually more valuable than groundwater, because of its lower operating cost, and because groundwater is ultimately recharged by often scarcer surface water. Table 1 shows how the economic value of surface water and groundwater vary with groundwater recovery targets and across dry to wet years. The high groundwater storage capacity means groundwater economic values are constant across hydrologic events.
Table 1. Summary of economic values of water ($/AF) in different water year types for different groundwater recovery goals (negative ∆GW draws down the aquifer). Orange shaded (drier) events have groundwater pumping. Blue shaded (wetter) events have artificial recharge. Bold italic events have annual crops planted. (Yao 2020)

  • Optimized intermediate-term and long-term decisions with overdraft limits differ in some ways. Intermediate-term optimal decisions propose more aggressive pumping to maximize profit (though pumping without limitation does not necessarily yield the highest profit when additional pumping cost exceeds the additional crop profit). Optimal shorter-term decisions often change when the longer-term context changes.
  • Long-term optimal solutions balance groundwater pumping across decades. Where sustainability goals are longer-term, these results adjust shorter-term crop and water decisions over time to achieve target groundwater levels (usually to end or recover groundwater overdraft), and are affected by financial interest (discount) rates. This finding is broadly consistent with past research on resource economics stating optimal depletion rates are close to the discount rate.  
  • For conditions similar to the San Joaquin Valley, salinity accumulation aside, drawdown initially increases with groundwater recovery delayed until the final stages before the sustainability target must be met (Figure 1).  The depth of drawdown and the delay in groundwater recovery both increase with higher discount rates due to the higher weight on near term benefits compared to more distant costs.

Figure 1. Higher interest rates further delay groundwater storage replenishment until the final time periods (here initial groundwater storage is 12 MAF with a 10 MAF target)
  • Higher discount or interest rates reduce planting of perennial crops, because these more profitable crops have higher initial costs and delayed initial benefits. Higher rates also reduce groundwater pumping in drier years needed to support these permanent crops.
  • The economic value of surface water is affected by climate and initial groundwater availability. A much drier climate can increase the economic value of remaining surface water for agriculture by several hundred dollars per acre-foot in a long-term timescale. Lower groundwater availability increases the economic value of surface water. A drier climate also increases the value of groundwater, without salinity, but less than its effect on surface water value.
  • Perennial crops, with high economic value, but high initial planting cost and inability to fallow in dry times, largely drive water and crop management in the model results. In shorter-term optimal decisions, permanent crop acreages are often limited by water availability in drier years, which also reduces annual crop acreage in drier years. However, in longer-term optimal decisions, perennial crop acreages are maintained as high as possible to reduce planting costs in later decades.

Overall, the modeling results agree with farming observations and economic theory. There is a transition from growing annual crops to increasing the planting of higher-value perennial crops to maximize the profit under water-scarce conditions. The results also suggest that aquifer recovery and ending overdraft will require substantial reductions in pumping and total net water use, with perennial crops being less affected, especially when aquifers are not degraded by salinity.

Further Reading

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.

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

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.

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.

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.

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

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2021: Is this the year that wild delta smelt become extinct?

by Peter Moyle, Karrigan Börk, John Durand, T-C Hung, and Andrew L. Rypel

Misty sunrise over former delta smelt habitat, Cache Slough, December, 2014.  Peter Moyle

2020 was a bad year for delta smelt. No smelt were found in the standard fish sampling programs (fall midwater trawl, summer townet survey). Surveys designed specifically to catch smelt (Spring Kodiak Trawl, Enhanced Delta Smelt Monitoring Program) caught just two of them despite many long hours of sampling. The program to net adult delta smelt for captive brood stock caught just one smelt in over 151 tries. All signs point to the Delta smelt as disappearing from the wild this year, or, perhaps, 2022. In case you had forgotten, the Delta smelt is an attractive, translucent little fish that eats plankton, has a one-year life cycle, and smells like cucumbers. It was listed as a threatened species in 1993 and has continued to decline since then. Former President Trump made it notorious when he called it a “certain little tiny fish” that was costing farmers millions of gallons of water (not true, of course).

Delta smelt, photo by Matt Young.

As part of the permitting process for Delta water infrastructure, the USFWS issued a Biological Opinion (BO), written by biologists, that found that increased export of water from the big pumps of the State Water Project and the Central Valley Project would further endanger the smelt. The BO was then revised by non-biologists to conclude that increased pumping would not hurt the smelt. The reason given was that large-scale habitat improvement efforts, plus the development of a facility for spawning and rearing of domesticated smelt, would save the species. We have written a short, fairly readable, article for a law journal that describes why the revised BO will not save the smelt. We will not write further about the paper in this blog but encourage readers to give the full article a read (it is a free download).

So, is this the year the smelt becomes extinct in the wild? Frankly, we are impressed by its resilience (see previous California WaterBlogs on smelt status) but small populations of endangered pelagic fish in large habitats tend to disappear, no matter what we do, partly the result of random events.

Looking for delta smelt

We trawl clear Delta water

And find emptiness.

Further Reading

Baumsteiger, J. and P.B. Moyle 2017. Assessing extinction.  Bioscience 67: 357-366. doi:10.1093/biosci/bix001

Baumsteiger, J, and P. Moyle 2017. Facing Extinction II: Making hard decisions. UCD Center for Watershed Sciences California WaterBlog   May 7, 2017

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

Bork, K. A. Rypel, and P.B. Moyle. 2020. New science or just spin: science charade in the Delta.  California WaterBlog.

Hobbs, J. and P. Moyle. 2018. Will delta smelt have a happy new year?  California WaterBlog  January 14, 2018.

Hobbs, J.A, P.B. Moyle, N. Fangue and R. E. Connon. 2017. Is extinction inevitable for Delta Smelt and Longfin Smelt? An opinion and recommendations for recovery.  San Francisco Estuary and Watershed Science 15 (2):  San Francisco Estuary and Watershed Science 15(2). jmie_sfews_35759. Retrieved from:

Moyle, P. 2015. Prepare for extinction of delta smelt.  California WaterBlog, March 18, 2015.

Moyle, P., K. Bork, J. Durand, T-C Hung, and A. Rypel. 2019. Futures for Delta smelt. December 15. California WaterBlog. Moyle, P.B., J. A. Hobbs, and J. R. Durand. 2018.  Delta smelt and the politics of water in California.  Fisheries 43:42-51.

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California’s Sacramento-San Joaquin Delta – a short history of big changes

Land subsidence in California’s Sacramento-San Joaquin Delta

by Jay Lund

Deltas globally adjust with changes and fluctuations in external conditions, internal dynamics, and human management.  This is a short history of big changes to California’s Sacramento-San Joaquin Delta (Delta) in the past and present, and its anticipated future.  This history is important for understanding how many of the Delta’s problems have developed, changed, and continue to change.

Sea level rise. California’s Delta is a product of sea level rise.  At the end of the last Ice Age, about 11,000 years ago, the sea was about 300 feet below today’s levels and the delta from the Sacramento and San Joaquin rivers formed in the Pacific Ocean, outside the Golden Gate.  As sea level rose, San Francisco Bay flooded, and about 6000 years ago, the rising sea level began to drown the confluence of the Sacramento and San Joaquin rivers, forming an inland delta at the Delta’s present location.  Sea level rise during this latter period was slow enough that the resulting immense tidal freshwater marsh arose with the sea level, forming the Delta’s deep peat soils of partially decomposed marsh plants.  These peat soils typically are deepest in areas longest affected by sea level rise.  Before 6000 years ago, today’s Delta was not a delta at all, but a river corridor subject to probably extensive seasonal flooding. (Atwater and Belknap 1980)

Poldering.  From the 1850s until the 1930s, most of the Delta’s 750,000 acres of wetlands were diked and drained to produce today’s agricultural Delta islands and tracts, which are predominantly agricultural with a few towns.  The Delta was California’s first large irrigated area, with year-round access to fresh water, near sea-level elevations that supported both field flooding and drainage with the tides, and location on steamship routes to markets.  However, the drainage of peat soils quickly accelerated their chemical decomposition, lowering the elevation of many island interiors by up to several inches per year.  After several decades, lowering lowland elevations required pumping for drainage and increasing costs for maintaining Delta dikes.  This dominant agricultural land use and increasing drainage and flood risk costs from land subsidence continues today, with occasional abandonment of islands to become flooded tracts (such as Big Break, Franks Tract, Mildred Island, and Liberty Island).  (Thompson 1957; Weir 1950)

Upstream diversions.  In the late 1800s, irrigation expanded using water upstream of the Delta, diverting from the Sacramento and San Joaquin rivers, and their tributaries.  Without major reservoirs, these upstream diversions occurred predominantly in the summer, and largely depleted summer inflows to the Delta in dry years during the early 1900s.  In the 1924 drought, the Carquinez Strait sugar plant was sending barges west to Marin, instead if east to the Delta, for freshwater.  By the 1930s drought, summer seawater intrusion extended inland to near Stockton.   Even today, most water taken from the Delta is diverted upstream. (Jackson and Paterson 1977)

In-Delta diversions.  By the 1930s, plans were being made to build reservoirs above the Central Valley to store water from winter for summer water supply and build pumps and canals from the Delta to thirst parts of the Bay Area, San Joaquin Valley, and southern California.  Preventing seawater intrusion by building a dam west of the Delta was considered, but rejected due to its high costs compared to the water cost of a “hydraulic barrier” of required Delta outflows.  Major in-Delta diversions began in 1949 by the USBR Central Valley project, growing faster with the State Water Project, to the present time.  These major in-Delta diversions, especially those from the southern Delta, caused major changes in the flow directions and magnitudes in Delta channels, and tied the Delta even more to the state’s economy as a whole. (DWR 1931)

Invasive species.  From the time of the Gold Rush, non-native species have been introduced to the Delta by ships hulls and ballast water, fishermen, fish agencies, and household aquarium owners.  Today’s Delta ecosystem is dominated by non-native species.  The Delta seems destined to be dominated by non-native species in highly altered habitat. However, efforts can be made to manipulate conditions to be more conducive for native species overall, recognizing that most non-natives will be impossible to eradicate. (Moyle et al. 2012)

Climate change.  Climate change will continue to shape the Delta, likely more rapidly than in the past century, especially from more rapid sea level rise and higher temperatures.  The maintenance of some subsided Delta islands will become less sustainable, with higher sea levels, continued land subsidence, less summer and more winter inflows (due to loss of snowpack), and more frequent flood flows and high water.  Temperature increases and more frequent droughts seem likely to further squeeze some native species and facilitate expansions of non-native species.  (Brown et al. 2013; DISB 2020)

Other human-induced changes.  Additional human-caused changes in the Delta should be expected from increased economic demands for Delta water exports from ending groundwater overdraft and more valuable agriculture, changes in conveyance and storage infrastructure, increased management for native species, and changes in environmental regulations and regulatory approaches (such as voluntary agreements).

What this means for Delta science and management.  Changes build upon changes.  Many old changes will continue, like sea level which has always defined the Delta, and there are more, mostly faster, and different changes to come.  The Delta’s ecosystems, water supplies, and communities will be challenged by these changes.  Managers, policymakers, and Delta communities will have to deal with all of these changes altogether – not one by one.  To be prepared, our scientific efforts must face these challenges in advance.

Historically, managing the Delta was about making planned changes, building and operating levees, pumps, canals, and land uses to provide services.  The future will include making planned changes, but management will increasingly be responding to changes driven from outside the Delta and the internal dynamics of Delta landscapes and ecosystems. 

Delta smelt - Wikipedia
Delta smelt

Further readings

Atwater, Brian F. (1982), Geologic maps of the Sacramento-San Joaquin Delta, California, Miscellaneous Field Studies Map 1401, USGS,

Atwater, B. F. and Belknap, D. F., 1980, “Tidal-wetland deposits of the Sacramento – San Joaquin Delta, California,” in Field, M. E., Bouma, A. H., Colburn, I.P.-;-Douglas, R. G., and Ingle, J. C., eds., Quaternary Depositional Environments of the Pacific Coast: Society of Economic Paleontologists and Mineralogists, Pacific Coast Paleogeography Symposium 4, p. 89-103.

Brown, Larry R., et al. “Implications for Future Survival of Delta Smelt from Four Climate Change Scenarios for the Sacramento–San Joaquin Delta, California.” Estuaries and Coasts, vol. 36, no. 4, 2013, pp. 754–774., doi:10.1007/s12237-013-9585-4.

Delta Independent Science Board, “Preparing for a Fast-forward Future in the Sacramento-San Joaquin Delta,” August 10, 2020 (Draft paper)

Division of Water Resources (1931), Report to the Legislature on State Water Plan 1930, Bulletin 25, State of California Department of Public Works, Sacramento, CA.

Jackson, W. T., and A. M. Paterson, The Sacramento–San Joaquin Delta and the Evolution and Implementation of Water Policy:  An Historical Perspective, California Water Resources Center, Contribution No. 163, University of California, Davis, June, 1977.

Lund, J., E. Hanak, W. Fleenor, R. Howitt, J. Mount, and P. Moyle, Envisioning Futures for the Sacramento-San Joaquin Delta, Public Policy Institute of California, San Francisco, CA, 300 pp., February 2007.

Lund, J., E. Hanak, W. Fleenor, W. Bennett, R. Howitt, J. Mount, and P. Moyle, Comparing Futures for the Sacramento-San Joaquin Delta, University of California Press, Berkeley, CA, February 2010.

Malamud-Roam, Frances, Michael Dettinger, B. Lynn Ingram, Malcolm K. Hughes, and Joan L. Florsheim. (2007), “Holocene Climates and Connections between the San Francisco Bay Estuary and its Watershed,” San Francisco Estuary and Watershed Science. Vol. 5, Issue 1 (February). Article 3. 3

Moyle, P., W. Bennett, J. Durand, W. Fleenor, B. Gray, E. Hanak, J. Lund, and J. Mount (2012), Where the Wild Things Aren’t: Making the Delta a Better Place for Native Species, Public Policy Institute of California, San Francisco, CA, 55 pp., June.

Moyle, Peter B., et al. (2013) “Climate Change Vulnerability of Native and Alien Freshwater Fishes of California: A Systematic Assessment Approach.” PLoS ONE, vol. 8, no. 5, 2013, doi:10.1371/journal.pone.0063883.

National Research Council. A Review of the Use of Science and Adaptive Management in California’s Draft Bay Delta Conservation Plan. National Academies Press, 2011.

Thompson, John, 1957, Settlement geography of the Sacramento San Joaquin Delta: Stanford University, Ph.D. thesis, Stanford, California, 551 p.

Weir, W., 1950, “Subsidence of peat lands of the Sacramento – San Joaquin Delta, California,” Hilgardia, v. 20, p. 37-56.

Whipple, A.; Grossinger, R. M.; Rankin, D.; Stanford, B.; Askevold, R. A. 2012. Sacramento-San Joaquin Delta Historical Ecology Investigation: Exploring Pattern and Process. SFEI Contribution No. 672. SFEI: Richmond.

Jay Lund is a Professor of Civil and Environmental Engineering and Co-Director of the Center for Watershed Sciences at the University of California – Davis

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We Wish You A Silly Fishmas

by Kim Luke

Night Before Fishmas

“Twas the night before Fishmas, when all through the space
Not a creature was stirring, not even a Dace;
The fyke nets were hung by the boat dock with care,
In hopes that St. Fish-olas soon would be there;

The salmon eggs were nestled all snug in their redds;
While visions of zooplankton danced in their heads;
Andd mamma in her life vest, and I in my cap,
Had just docked our boathouse for a long winter’s nap,

When out of the water there arose a fish ladder,
I sprang from my seat to see what was the matter.
Away to the port side I ran like a flash,
Tore up the shutters and threw up a sash.

The moon on the breast of the new-fallen snow;
Gave a lustre of midday to objects below,
When what to my wondering eyes did glimpse,
But a miniature boat and eight tiny rein-fish,

With a little old driver so lively and quick,
I knew in a moment he must be St. Fish.
More rapid than sailfish his coursers they came,
And he whistled, and shouted, and called them by name:

“Now, Bluegill! now, Largemouth! now, Sturgeon and Splitie!
On, Striped Bass! on, Sucker! on, Tule! and Crappie!
To the top of the dam! to the top of the trawl!
Now swim away! swim away! swim away all!”

As leaves that before the wild hurricane fly,
When they meet with an obstacle, swim to the sky;
So up to the boathouse the fishes they flew
With the boat full of toys, and St. Fish-olas too—

And then, in a twinkling, I heard with a swish
The flipping and flopping of each little fish.
As I drew in my head, and was turning around,
Into the cabin St. Fisholas came with a bound.

He was all dressed in fur, from his head to his fins,
And his clothes were tarnished with ag run-off—what a sin!;
A bundle of toys he had flung on his back;
And he looked like a peddler just opening his pack.

His eyes—how they twinkled! His lateral line, how merry!
His operculum like roses, his adipose fin like a cherry!
His droll little maxilla was drawn up like a bow,
And the beard on his chin was as white as the snow;

The stump of a pipe he held tight in his pharyngeal teeth,
And the smoke, it encircled his head like a wreath;
He had broad fins and a little round belly
That shook when he laughed, like a bowl full of jelly-(fishes).

He was chubby and plump, a right jolly old trout,
And I laughed when I saw him, T’was St. Fish, no doubt;
A wink of his eye and a twist of his head
Soon gave me to know I had nothing to dread;

He spoke not a word, but went straight to his work,
And filled all the tackleboxes; then turned with a jerk,
And laying his fin aside of his nose,
And giving a nod, up the cabin he rose; He sprang to his boat, to his team gave a whistle,
And away they flew like the down of a thistle.
But I heard his exclaim, ere he swam out of sight—
Happy Fishmas to all, and to all a good night!

Rudolph the Redear Sunfish

You know Bluegill and Crappie and Greenie and Largemouth
Smallmouth and Longear and Warmouth and Rock Bass
But do you recall
The most famous sunfish of all?

Rudolph the Redear Sunfish
Had a shiny opercle flap
And if you ever saw it
You would say “What’s up with that?”

All of the other sunfish
Used to laugh and call him names
They never let poor Rudolph
Join in any sunfish games

Then one foggy Christmas Eve
Santa came to say
“Rudolph, with your spot so bright
Won’t you guide my boat tonight?”

Then how the sunfish loved him
As they shouted out with glee
“Rudolph the Redear Sunfish
You’ll go down in history”

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Picture this research – a photo blog from the Center for Watershed Sciences

by Scientists at CWS

Holidays are a natural time of introspection on who we are, what we do, and why. Towards a bit of our own self-reflection, some researchers from UC Davis’ Center for Watershed Sciences (CWS) have each contributed a photo and short description of their work. We hope you enjoy reading about us and learning even more about us. It is hopefully a soft bookend to a wild 2020!

Sarah Yarnell

This is one of my favorite pictures because it captures the integrative and applied research and teaching we do at CWS. These students are part of the Ecogeomorphology field class, which brings together students from a range of science backgrounds to study and address conservation and management issues in watersheds in California and the Western US. From the foreground to the background, students are surveying channel topography, macroinvertebrate diversity, fish presence, and sediment texture on the Yampa River, a free-flowing unregulated river. When compared to survey data collected on the Green River, a river regulated by dams, students see the impacts of streamflow regulation on riverine ecosystems and discuss how conservation management practices balance ecological and human resource needs. My research seeks to similarly integrate biological and physical processes to better understand and inform stream restoration practices and environmental flow management in regulated rivers.

Jay Lund

The prosperity of civilizations in Mediterranean climates relies on water management, which involves eternally managing water disputes. The water court in Valencia, Spain has met weekly since medieval times in front of the city’s cathedral, and perhaps from Roman times in the same square. Unlike most water hearings in California, this one is a popular tourist attraction and the meeting ends after about 10 minutes. (a slightly pre-COVIN picture from February 2020).

John Durand

This photo captures the moment water is returning to a restored wetlands landscape. About a mile away, giant cranes crack open an levee, allowing water to flow up through meandering channels. Here a student researcher focuses quietly on recording water quality, but around her is all movement: the water rolling into the new channel, the crackling of dried vegetation being inundated, insects blowing up in clouds above the water followed by birds of all sorts swooping in to feed. The effect is dizzying and thrilling, to watch and hear the ancient ritual of water meeting land played out again for the first time in a century.

Ann Willis

These before-after photos capture the power of a living stream as it shifts and reshapes itself (and takes away my stilling well). This stream flows through an active cattle ranch, where the landowners recognize that stewardship includes both land and streamscapes. My research helps people like these ranchers preserve their heritage and livelihoods by guiding decisions about when and where to prioritize conservation. When science is combined with a coalition of the willing, we can have healthy rivers and rangeland.

Carson Jeffres

Here a Chinook Salmon is preparing to spawn in the Shasta River below Mt. Shasta. This is a reminder of how physical processes allow for ecological function. The snow that falls on Mt. Shasta percolates into the ground and emerges as nutrient rich springs. These nutrient rich springs provide a productive food web that allows the Chinook Salmon and other fishes to complete their life histories. It always amazes me that the snow you see in the background of this picture will come out of the ground 20-40 years after the photo was taken to benefit future generations of fish and other fauna.

Rusty Holleman

A drifter measuring position and shear in river currents floats down the San Joaquin River on approach to the Head of Old River. Data from drifter tracks helps keep our numerical models honest and provides a point of reference when studying how juvenile Chinook salmon navigate this junction on their way to the ocean. Hidden beneath the turbid waters is a network of hydrophones, recording the path of salmon smolts as they enter the Delta. By comparing data on the movements of water and fish, we learn about the swimming habits of the smolts, and how environmental cues can shape the path that they take through the Delta. Studies such as this one pave the way for effective stewardship of fisheries utilizing the Delta.

Ryan Peek

Rivers connect and carve the landscapes we live in and use. These systems are complex interconnected webs of life which we rely on and are part of, yet for every link that breaks, the systems become less diverse, and a little less stable or reliable. My research uses genetic and ecosystem data to help understand the connections between river organisms and changing environments, so we can prioritize and apply more effective conservation management.

Cathryn Lawrence

As the Watershed Center Assistant Director I keep the wheels on the Center and help move it forward. A picture of my normal work would be a picture of a computer screen with 50 windows open. On field trips, I’m the one who likes to point out and identify birds, even though I’m a limnologist and oceanographer by training. There are many more birds and bird species around us than people generally see without a bird-brain like me to enthusiastically point out even the little brown birds that do not tend to be crowd pleasers. Verdin picture is from the Grand Canyon field trip in 2014—cryptic in the tree until it popped out in the open. Long-earred Owl in Davis (December 2020)—a rarity here and very cryptic in the tree. It is left up to the ecologists to identify the location where I am “properly dressed” for birding including photography.

Rob Lusardi

The importance of salmon to ecosystem processes and food webs is well documented.  We were still surprised to witness this bobcat feasting on a fall-run Chinook salmon carcass on the upper Sacramento River immediately below Keswick dam. As an aquatic ecologist, I usually have my head in the water too often and need to remind myself that cross-ecosystem subsidies occur all the time and are critical to broader ecological function across the landscape.    

Andrew Rypel

I spent years researching lake ecosystems in Northern Wisconsin. The emergent aquatic plants in the foreground of this photo is naturally-occurring wild rice. Now I work on rice and agricultural floodplains in California. Juvenile Chinook salmon and many other native fishes once roamed vast floodplain habitats in the Central Valley. These natural wetland habitats are largely gone now (reduced by 95%); however we are examining whether agricultural floodplains including rice fields can be used in creative ways to facilitate the life-cycle of native CA fishes. Incidentally, the remote lake in the picture is one of only a handful of lakes I could ever find with truly “unfished” bluegill populations (note the lack of homes, docks and boat landings).

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