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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Making “productive” assessments of California’s ecosystems

by Andrew L. Rypel

Conservation science and restoration ecology are challenging and interdisciplinary fields. Managing for ecological function necessitates focus on multiple scales of ecological organization while simultaneously integrating feedback loops with critical environmental drivers like temperature, flow and habitat change. This means scientists working on these issues can emerge from diverse areas of inquiry including ecology, engineering, hydrological sciences, fisheries, geology, geography, and law. UC Davis’ Center for Watershed Sciences embraces this broad approach to water issues in California, but there are common challenges among fields. One particularly tricky proposition is the selection of appropriate “response metrics” when discussing restoration activities. 

A heuristic experience with Baldcypress trees

Fig. 1. Adult baldcypress trees in Lakeland, FL. Photo by Malcolm Manners and downloaded from

When I worked in rivers and reservoirs in the southeastern USA, I was always intrigued by the large Baldcypress trees (Taxodium distichum, a close relative to our California redwoods) growing in the middle of huge reservoirs. There were always only large trees – never any juveniles. It turns out these trees (which are long-lived, like redwoods) date back to the original floodplain, before the damming of rivers. Baldcypress are evolutionarily adapted to variable hydrological systems (Rypel et al. 2009). Thus while trees can persist as adults in reservoirs (flooded rivers), the seeds must fall into dry soil to germinate. In others words, reservoir cypress stands were now ecological sinks rather than sources – a form of extinction debt yet to be paid from dam construction. Yet a community ecologist might go out to reservoirs and, based on presence data, conclude that reservoirs are perfectly optimal habitats for Baldcypress trees. However these habitats clearly are not suitable to complete their life-cycle and these stands are in the process of decline because of hydrological impacts from dams – the decline is just very slow.

This example, while admittedly simple, offers a cautionary tale for how we can trick ourselves into focusing on pet ecological aspects and processes while ignoring critical ones. Holistic approaches are needed to isolate governing ecological dynamics and help guide management. In this blog, I’d like to briefly highlight one integrative metric I’ve gravitated to over time. The goal is not to convince that we should all measure or study secondary production. Rather, it is to illustrate the types of dynamics and thinking we might consider for evaluating effects of the vast water projects in California. While I focus on production, many other metrics could be equally relevant (e.g., nutrient cycling, decomposition, primary production, water circulation patterns, resilience) – essentially metrics classified as “ecosystem functions”.

What is “secondary production”?

Secondary production is the formation of biomass that crosses ecological trophic levels through time. It directly parallels the concept of primary production, but is intended for heterotrophic animals rather than plants. Both primary and secondary production are expressed in the exact same units (e.g., g m-2 y-1), meaning rates are comparable within or across food webs (Fig. 2, 3). It is also directly analogous to metrics of economic production such as GDP, only in this case, carbon is the currency of import. Although biomass is a representative static measure at a point in time, production is dynamic, and appropriately defined as a “flux”. And while correlated with biomass, production integrates a wider array of critical rate functions for animals including growth, reproduction, mortality, development time and lifespan. There is also the production-to-biomass ratio or “P/B”. P/B ratios provide an estimate of biomass turnover time and is a representative measure of productive capacity, expressed in units of inverse time (i.e., y-1). For these reasons, secondary production captures underlying dynamics related to energy availability, trophic relationships and turnover. Interestingly, it also can be quantified at any level of organization – from an individual (essentially growth), to a population (probably the most common approach), to a community or assembly of species (much rarer but still done), or even whole ecosystems (quite rare).

Fig. 2. Lindeman (1942) classically described the food web and trophic ecology of a small Minnesota lake (Cedar Bog Lake). The mathematical relationships Lindeman developed for describing energy fluxes (noted as Lambda values) quantify transfer of primary and secondary production units.

In a recent paper, we suggest secondary production is an underutilized metric for tracking efficacy of restoration initiatives. Dating back to Lindeman (1942) and before, ecologists have been interested in understanding the dynamics of energy transfer in food webs (Fig. 2). Yet most of the literature over the last 30 years has focused on benthic macroinvertebrate communities. The relative paucity of studies for other taxa may have something to do with a perception among other ecologists that these approaches require extensive data that are too costly or laborious to obtain. For example, if one were “starting from scratch” with study design, it can be difficult and costly to obtain all the data necessary to estimate secondary production rates. However, often we are not starting from scratch. For high profile fisheries and ecosystems, all the data needed to estimate secondary production are usually already available (Rypel et al. 2018). Furthermore, when data are not available, simple shortcuts can still provide useful paths (Rypel and David 2017). And usually these analyses yield important insights and patterns. Jeffres et al. (2020) highlight how detrital food webs facilitate the dramatically higher rates of salmon productivity observed on floodplains in the Central Valley. A recent analysis found that valuable fish populations were experiencing hidden overfishing only visible after patterns in fish production were calculated and examined relative to harvest rates (Embke et al. 2019). Another study of California oil platforms found these to apparently be some of the more productive marine habitats known (Claisse et al. 2014). 

Scope for secondary production in California and the Delta

Fig. 3. Results from a meta-analysis of 16 freshwater fish species highlighting the relationship between trophic position and fish production. Most productivity arises at the base of food webs.

As we consistently discuss in this blog, California’s natural aquatic resources face unprecedented threats, most of which stem from the sizable existence of human populations. Given the challenges of designing and implementing complex restoration studies in this context, it is unsurprising that many do not initially focus on production as a tool. For example, regulatory mechanisms consistently guide us towards species-based management even though many increasingly recognize these approaches as ineffective and in need of a total re-rewrite (Fogerty 2014; Sass et al. 2017). Holistic, ecosystem-based approaches offer potential for broad understanding of conditions that can support many species (even non-fishes!). Furthermore, focusing on ecological aspects that support general functionality is a more promising and realistic path to improved management. Attempting complete recovery of Delta Smelt is likely impossible at this point. Understanding the conditions that once promoted smelt production, but now support production of natives and similar non-natives (e.g., striped bass) is a worthwhile approach. This context can generate ideas on what actions are needed to boost the type of ecosystem productivity we desire and value.

Several larger points come to mind when considering how a production approach could be useful in California:

Synthesis now! In some cases, we already have enough data for production-based approaches and vital rate analyses that leverage oodles of previously collected data. We simply lack synthesis capacity to fund ecologists to do the work. Transparent and open databases are needed to encourage capacity for diverse scientists to innovate new approaches. Training students and researchers in synthesis, data science, and ecosystem ecology will be key.

Fig. 4. A simplified conceptual schematic on how flows, combined with other ecological drivers affect fish production (Lund et al. 2015).

Design monitoring programs wisely. Careful choice of focal taxa is needed. It is noble to want to protect and study all species, but this isn’t practical. Ideal monitoring programs would include multiple species, but these might not always be the species at most risk of going away. They should however be representative of the functionality that is valued. Then for each focal species, data on vital rates would be needed so production or key elements of production can be studied over time. Analyses of relationships between production and environmental variables (e.g., flow) would be the next logical step. Indeed frameworks incorporating this type of thinking have emerged before (Fig. 4).

Inventory existing monitoring programs. How satisfied are we with data currently collected as part of our monitoring programs? Are these data yielding a critical depth of understanding to manage ecosystems? Without giving up on core datasets, can we make small tweaks to incorporate critical elements to help scale to the ecosystem level? Existing review efforts by the Delta Independent Science Board and Delta Science Program may be useful in revealing some of these gaps (Brandt and Canuel 2019). 

Water is central to ecological production, but ecological efficiency is key too. Because secondary production is expressed per-unit-area, it is a mathematical certitude that more habitat (water) yields more production. We don’t need additional studies to show this basic relationship. However, understanding how to increase production per unit area is less well-understood. This is similar to agriculture – we know more crops can be grown by having a larger acreage in rotation. The more important challenge is how we grow more crops on the same amount of land? How can we get the most bang per habitat buck in the Delta? This central question can be understood and answered firmly with an ecosystem- or production-based approach.

Water reliability likely won’t increase without improved ecosystem function. Increasing costs and decreased exports combine with uncertain climate change impacts to create water reliability issues for contractors. Given current constraints, reliability simply won’t increase without increased ecological function. How do we get that? A good start might be to focus on defining the ecological functionality that we value or are required to ensure – fish and other ecological production is likely high on this list. We are ultimately in this together and should focus on metrics that lead to the goal.

Study ecology – and management. As shown by the Lindeman 1942 example, these are ancient and fundamental quests in ecology. Data collected in California in conjunction with management-relevant research can contribute to advancing basic ecological understanding. Reciprocally, ecology can help advance management by providing clues about how human actions affect ecosystem functionality. A new focus on vital rate functions would provide a rare bridge between basic and applied sciences that few explore. Doing so will invite more talent into California water and provide greater insights and comparability for needed ecosystem management alternatives. We can’t get lost in our silos – there is too much work to be done.

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

Further Reading

Managing ecosystem restoration: what does success look like?

Are numbers of species a true measure of ecosystem health:

Futures for delta smelt.

Functional flows can improve environmental water management in California.

Ten realities for managing the Delta.

Knowing the Delta’s past offers new ideas forward.

Striped bass control: cure worse than the disease? ps://

Benke, A. C. 2010. Secondary production. Nature Education Knowledge 3(10):23

Benke, A. C., and J. B. Wallace. 1997. Trophic basis of production among riverine caddisflies: implications for food web analysis. Ecology 78(4):1132-1145.

Brandt, S., and E. Canuel. 2019. Delta Independent Science Board: recent accomplishments and current activities. Delta ISB Update 8/22/2019.

Claisse, J. T., D. J. Pondella, M. Love, L. A. Zahn, C. M. Williams, J. P. Williams, and A. S. Bull. 2014. Oil platforms off California are among the most productive marine fish habitats globally. Proceedings of the National Academy of Sciences 111(43):15462-15467.

Embke, H. S., A. L. Rypel, S. R. Carpenter, G. G. Sass, D. Ogle, T. Cichosz, J. Hennessy, T. E. Essington, and M. J. Vander Zanden. 2019. Production dynamics reveal hidden overharvest of inland recreational fisheries. Proceedings of the National Academy of Sciences 116(49):24676-24681.

Fogarty, M. J. 2014. The art of ecosystem-based fishery management. Canadian Journal of Fisheries and Aquatic Sciences 71(3):479-490.

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 15(9): e0216019.

Kwak, T. J., and T. F. Waters. 1997. Trout production dynamics and water quality in Minnesota streams. Transactions of the American Fisheries Society 126(1):35-48.

Layman, C. A., and A. L. Rypel. 2020. Secondary production is an underutilized metric to assess restoration initiatives. Food Webs 25:e00174.

Lindeman, R. L. 1942. The trophic-dynamic aspect of ecology. Ecology 23(4):399-417.

Lund, J., S. Brandt, T. Collier, B. Atwater, E. Canuel, H. J. Shemal Fernando, J. Meyer, R. Norgaard, V. Resh, J. Wiens, J. Zedler. 2015. Flows and fishes in the Sacramento-San Joaquin Delta: research needs in support of adaptive management. A Review by the Delta Independent Science Board.

Parks, T. P., and A. L. Rypel. 2018. Predator–prey dynamics mediate long-term production trends of cisco (Coregonus artedi) in a northern Wisconsin lake. Canadian Journal of Fisheries and Aquatic Sciences 75(11):1969-1976.

Rypel, A. L., W. R. Haag. and R. H. Findlay. 2009. Pervasive hydrologic effects on freshwater mussels and riparian trees in southeastern floodplain ecosystems. Wetlands 29: 497–504. 

Rypel, A. L., and S. R. David. 2017. Pattern and scale in latitude–production relationships for freshwater fishes. Ecosphere 8(1):e01660.

Rypel, A. L., D. Goto, G. G. Sass, and M. J. Vander Zanden. 2018. Eroding productivity of walleye populations in northern Wisconsin lakes. Canadian Journal of Fisheries and Aquatic Sciences 75(12):2291-2301.

Sass, G. G., A. L. Rypel, and J. D. Stafford. 2017. Inland fisheries habitat management: lessons learned from wildlife ecology and a proposal for change. Fisheries 42(4):197-209.

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Is California Heading for a Multi-Year Drought?

by Jay Lund

Yes, California will have another multi-year drought.  California has immense hydrologic variability, with more droughts and floods per average year than any other part of the country.  California’s water users, managers, and regulators should always be prepared for droughts (and floods).  Eventually, California will have a multi-year drought worse than any we have ever seen.

More immediately, since the 2020 water year was dry in northern California, will this current 2021 Water Year be dry enough to put us into year two of a multi-year drought? (California’s water infrastructure and management system almost eliminates one-year drought effects for most uses in most years. This contrasts with the Eastern US, where rainfed corn or soybeans can die from a few weeks of drought.)

So far, we are early in the 2021 Water Year (October 2020 – September 2021) with essentially no October precipitation and almost none in November.  Although early in the wet season, this water year’s Sacramento, San Joaquin, and Tulare precipitation, so far, are the lowest, or among the lowest of record.  And the 2-week forecast shows no substantial precipitation.  Last year was definitely dry for northern California, so most of California’s reservoirs are drawn down a bit.  People also keep talking about El Nino.  Let’s look at some historical statistics on how these factors affect the likelihood that we are entering a multi-year drought, and what we should do about it.

Does a dry October and November mean 2021 will be another dry year?

Mostly no, at least not by itself.  The figure below plots annual northern California precipitation against October + November precipitation for each year since 1921.  There is only a little correlation.  The Sacramento Valley precipitation index today is about 6 inches below average.  Statistically, on average, we would expect this year’s total precipitation to be about 7.7 inches below average (statistically translating into about 3.5 maf or 20%, below average annual runoff).  We have a dry start to the 2021 water year, but the year can still become wet.  Given the lackluster forecasts, adding a dry December would make a dry year more likely, but still not guaranteed.

Will 2020 being dry make 2021 drier?

Precipitation in northern California does not seem correlated across years, at least not historically, as shown by the plot below.  The trend line is essentially flat for precipitation.

However, a drier year in terms of runoff tends to make the next year a little drier in runoff, as shown for a similar plot below for runoff instead of precipitation. 

So this year is likely to have a little less runoff because last year was dry, even if we get average precipitation this year.  (But precipitation this year seems unlikely to be affected by last year’s precipitation.)

Why is there a between-year correlation difference between precipitation and runoff?  Runoff is slightly correlated over time because precipitation accumulating in groundwater is likely to increase flow into streams in the next year.

What about El Niño/La Niña?

Below is a plot of the historical El Nino index against northern California annual streamflow.  The conclusion is pretty clear – La Niña/El Nino has little to do with annual runoff from northern California.  (The ENSO index plotted here is average of December-April for each water year.)

Although ENSO may signal significant weather changes elsewhere in the world, it seems to have little predictive capacity in Northern California where most of the state’s precipitation occurs. ENSO has better predictive value for Southern California (Schonher and Nicholson 1989).

So what should we do?

There is a significant probability that this year will be the second year of a multi-year drought, since last year was dry, and this year seems likely to be dry.  At this early time in the water year, the chances seem roughly even, but remain quite substantial.

Given such odds, it makes sense to prepare for another dry year, and perhaps several additional dry years.  Reservoir water levels are already below average from last year being dry, and groundwater will be a little lower as well.  So we have less water in reserve than last year at this time.

What to do? 

If your agency or interest has a drought plan, you are likely to be looking it over and updating it.

If your agency or interest does not have a drought plan, what state do you think you live in?  This is a good opportunity to develop a drought plan before you are desperate.  This applies especially for the Delta and many critical environmental and regulatory interests.

But this year could be wet or contain floods as well.  So, as usual for this time of year, Californians should be prepared for both floods and drought.

Finally, most technical people know Murphy’s Law, that “Anything that can go wrong, will go wrong (and at the worst possible moment).”  The inverse of this pragmatic “law” would hold that those who just made or updated a good drought plan should be less likely to see a drought.  (So update your flood plans as well!)  It is always good to be prepared.

Jay Lund is a professor of civil and environmental engineering 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:

Capitol Public Radio recently had a great story by the same title:

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

Schonher, T. and S. E. Nicholson (1989), “The Relationship between California Rainfall and ENSO Events,” Journal of Climate, Vol. 2, Nov. pp. 1258-1269.

El Niño/La Niña Resource Page, Golden Gate Weather Services, 2020ña-update

Impacts of El Niño and benefits of El Niño Prediction, National Oceanic and Atmospheric Administration 

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Functional Flows Can Improve Environmental Water Management in California

By Ted Grantham, Jeanette Howard, Belize Lane, Rob Lusardi, Sam Sandoval-Solis, Eric Stein, Sarah Yarnell and Julie Zimmerman

Over the past three years, a team of scientists from universities, NGOs, and state agencies across California have been working to provide guidance on how to better manage river flows for freshwater ecosystems throughout the state. A key product of this effort is the California Environmental Flows Framework (Framework), a guidance document and set of tools to help managers and stakeholders develop environmental flow recommendations for California’s rivers. The technical approach of the Framework relies on the concept of functional flows, defined as aspects of a river’s flow that sustain the biological, chemical, and physical processes upon which native freshwater species depend. Under the functional flows approach, environmental flows would be maintained at levels that preserve key ecosystem functions—such as sediment movement, floodplain inundation, and environmental cues for species migration and reproduction—to satisfy native freshwater species needs. Flow recommendations developed through the Framework would address ecosystem water needs throughout the year and preserve the many benefits to people from healthy rivers and streams.

The Framework is a departure from previous environmental flow approaches in California. Here, we describe key attributes of the Framework’s functional flows approach and highlight how it relates to past approaches and those recently adopted by the State Water Resources Control Board (Water Board). As described in the Framework Guidance document, previous publications (Yarnell et al. 2015; Yarnell et al. 2020), and recent policy reports (Grantham et al. 2020), a functional flows approach would involve:

  • Managing for ecosystem functions: Environmental flow management in California has traditionally focused on habitat needs for individual fish species, such as threatened salmon populations listed under the federal Endangered Species Act. A functional flows approach would shift the focus from single species needs to ecosystem needs. By protecting the underlying functions that sustain river ecosystems, this approach is likely to deliver broad benefits for freshwater biota, including listed fish species, as well as support valued ecosystem services, such as clean water, fisheries, and recreation.
  • Mimicking natural flow variation: The traditional focus on single species (or even single life history stages of individual species) has also tended to favor static environmental flow requirements that vary little within seasons and across years. However, California’s native freshwater biota are adapted to the high natural variability in river flows. A functional flows approach preserves elements of natural flow variation upon which native species depend.
  • Coupling flows with physical habitat and water quality improvements: Environmental flow protections have traditionally focused on water quantity, but have often overlooked water quality (temperature, salinity, contaminant loads, and other parameters) and physical habitat (the form and composition of the river channel, banks, and floodplains) in supporting ecosystem health. A functional flows approach recognizes that ecosystem benefits of environmental water are realized only when flows are coupled with suitable water quality and suitable physical habitat.

The total quantity of water required to implement a functional flows approach in any given watershed can be expected to vary depending on its hydrologic setting and water year. However, it is likely that additional environmental water, beyond the volumes currently protected as minimum instream flows, will be needed in rivers subject to high human water demands, such as in the Sacramento-San Joaquin River Basin. This raises the question: how does the functional flows approach compare with recent environmental flow regulations adopted by the Water Board for this region?

In 2018, the State Water Resources Control Board adopted new flow objectives as part of the Bay Delta Water Control Plan for the San Joaquin Rivers and its major tributaries: the Tuolumne, Merced, and Stanislaus Rivers. Under the Plan, environmental flows for these rivers are expressed as a percent of unimpaired flows – a fixed proportion of expected natural flows unaltered by upstream diversions, storage, or imported water. For the months of February to June, the default flow objectives are 40% of unimpaired daily flow, based on a minimum 7-day running average, from each of the Stanislaus, Tuolumne, and Merced Rivers. The policy also sets minimum flow requirements for the San Joaquin River.

The Water Board policy has some similarities and differences with the functional flows approach described above. Like the functional flows approach, a percent-of-unimpaired flows approach is designed to preserve natural patterns of flow variation that support ecosystem health. Establishing flow recommendations as a fixed proportion of unimpaired flows ensures that seasonal, sub-seasonal, and interannual variation in flow are preserved. However, there is a risk that flows implemented as a percent-of-unimpaired flow may be insufficient to support some ecosystem functions targeted by the functional flows approach. This is because many stream functions have a threshold response and reducing flows by a fixed percentage cannot support all functions similarly. As stated by Poff et al. (1997), “clearly, half of the peak discharge will not move half of the sediment, half of a migration motivational flow will not motivate half of the fish, and half of an overbank flow will not inundate half of the floodplain.” To maintain ecosystem functions, it is likely more than 40% of unimpaired flow will be required at particular times of year, and for other times, potentially less.

Environmental water allocated as functional flows (red line) preserves aspects of natural flow variation needed to support ecosystem functions, but differs from the full natural flow regime (yellow) and fixed percent-of-unimpaired flow regime (blue). Modified from Grantham et al. 2020.

Despite this apparent limitation in the percent-of-unimpaired flows approach, provisions in the new policy would allow environmental flow recommendations to more closely follow a functional flows approach (Mount et al. 2020). Specifically, the policy allows for negotiated agreements in which unimpaired flows can vary over a larger range (30-50%) and potentially allows for even further deviation from these levels by treating environmental flows as a block of water. Conceptually, this block of water could be managed as functional flows by allocating it to meet functional flow targets at specific times of year (Grantham et al. 2020).

A budgeted water approach could also bring needed flexibility to the way environmental flows are managed in California (Mount et al. 2019). Environmental flows in California have historically been established through a variety of regulatory and legal processes, but tend to be prescriptive, requiring flows to be maintained at or above specific thresholds following a set flow schedule. This approach offers certainty to environmental interests and water users, but a fixed flow schedule makes it difficult to adapt to changing ecosystem conditions or take advantage of unique opportunities to enhance ecosystem benefits (Horne et al. 2018). For this reason, implementation of functional flows as an ecosystem water budget—a fixed volume of water for each year that can be flexibly managed to maximize ecosystem benefits and that could also be stored, traded, or leased—is a promising approach for improving the effectiveness of environmental flows in achieving ecosystem management objectives (Grantham et al. 2020).

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 Framework has been acknowledged by the Governor’s Office as a key element in building the resilience of California’s water system (State of California 2020). Environmental organizations and water user communities have both recognized the potential value of the functional flows approach advanced by the Framework (Grantham et al. 2020). The functional flows approach is also largely compatible with the 2018 Water Board policy, especially if implemented as water budgets supported by adaptable, robust governance. Additional work is needed to understand how the Framework will be used to inform the development of environmental flow programs and guide their successful implementation in diverse settings. Even so, the strong technical foundation, broad support, and new regulatory directives suggest the Framework’s functional flows approach has significant potential to improve the scale and effectiveness of environmental water management in the state.

Ted Grantham is a cooperative extension specialist at UC Berkeley, Jeanette Howard is the director of science for The Nature Conservancy’s water program, Belize Lane is an assistant professor at Utah State University, Rob Lusardi is a senior researcher at the UC Davis Center for Watershed Sciences, Sam Sandoval-Solis is an associate professor and cooperative extension specialist at UC Davis, Eric Stein is a principal scientist with the Southern California Coastal Water Research Project, Sarah Yarnell is a senior researcher at the UC Davis Center for Watershed Sciences, and Julie Zimmerman is the lead scientist for freshwater at the The Nature Conservancy. These individuals have been working with government agency staff to develop the California Environmental Flows Framework.

Further Reading

Grantham, T.E., Mount, J., Stein, E.D., and Yarnell, S.M. 2020. Making the Most of Water for the Environment: A Functional Flows Approach for California’s Rivers. Public Policy Institute of California Water Policy Center Report.

Mount, J., Grantham, T., Gray, B., and Hanak, E. 2020. Setting aside environmental water for the San Joaquin River. PPIC Water Policy Center Blog, 26 October 26 2020,

Horne, A.C., Kaur, S., Szemis, J.M., Costa, A.M., Nathan, R., Angus Webb, J., Stewardson, M.J. and Boland, N., 2018. Active management of environmental water to improve ecological outcomes. Journal of Water Resources Planning and Management 144: 04018079.

Obester, A., Yarnell, S., Grantham, T. 2020. Environmental flows in California,

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

State of California. 2020. Water Resilience Portfolio: In Response to the Executive Order N-10-19,

Yarnell, S., Obester, A., Grantham, T., Stein, E., Lane, B., Lusardi, R., Zimmerman, J., Howard, J., Sandoval-Solis, S., Henery, R., and Bray, E. 2018. Functional flows for developing ecological flow recommendations,

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

Yarnell, S.M., Stein, E.D., Webb, J.A., Grantham, T.E., Lusardi, R.A., Zimmerman, J., Peek, R.A., Lane, B.A., Howard, J. and Sandoval‐Solis, S. 2020. A functional flows approach to selecting ecologically relevant flow metrics for environmental flow applications. River Research and Applications 36: 318-324

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Getting to the Bottom of What Fuels Algal Blooms in Clear Lake

By: Nick Framsted

Clear Lake is one of California’s oldest and most unique natural features. Nestled in Northern California’s coastal mountains, Clear Lake is the largest lake completely within California and is the oldest lake in North America with sediments dating back 480,000 years (Sims et al. 1988). Rich mineral deposits around the lake were historically mined for borax, sulphur, and mercury. Thus, Clear Lake continues to be polluted by mercury and methylmercury which bioaccumulates in the food chain (Suchanek et al. 2008). In spite of pollution, the lake boasts an impressive diversity of biological life. It is designated as an Important Bird Area by the Audubon Society, and has endemic species such as the Clear Lake hitch (Lavinia exilicauda chi, a planktivorous fish), the Clear Lake splittail (Pogonichthys ciscoides, now extinct), and Clear Lake gnat (Chaoborus astictopus)—the latter of which was targeted by heavy application of of the pesticide DDD to control large swarms (Lindquist et al. 1951). These pesticide applications earned Clear Lake a feature in Rachel Carson’s seminal novel Silent Spring for its negative impacts on Western Grebe populations.

Water Quality Issues in Clear Lake

Fig. 1. Operating a steam shovel to mine mercury, or quicksilver as it was called at the time, from a sulphur bank near Clear Lake. Photo from Anderson 1936.

Clear Lake continues to struggle with long-lasting impacts of nutrient pollution. High concentrations of nutrients such as nitrogen and phosphorus fuel large algal blooms and contribute to poor water quality in the lake. Phosphorus is particularly abundant in Clear Lake and its associated watershed. As a result, harmful phytoplankton known as cyanobacteria thrive here, some of which can produce toxins harmful to humans. Commonly known as blue-green algae, cyanobacteria are an ancient group of organisms that are actually unrelated to algae since they are considered bacteria and not plants. Perhaps the most important difference between cyanobacteria and algae is that some species of cyanobacteria have specialized cells called heterocysts that capture nitrogen gas from the atmosphere and transform it into usable forms through a process called nitrogen fixation–something that plants are not capable of. In fact, legumes like soybeans and clover actually have symbiotic relationships with other nitrogen-fixing bacteria in order to glean nitrogen for their own use. 

Fig. 2. Cyanobacterial bloom in the Oaks Arm of Clear Lake, CA in 2016. Photo courtesy of Holly Harris.

Nitrogen fixation gives cyanobacteria a competitive advantage in waters rich in phosphorus and relatively deficient in nitrogen–the exact conditions present in Clear Lake. Cyanobacteria thrive in Clear Lake and often form harmful algal blooms, or HABs, which are both ecologically damaging and dangerous to human health. In an effort to promote public safety, the Big Valley Band of Pomo Indians and the Elem Indian Colony collaboratively established an extensive cyanobacterial monitoring program to inform the public about current cyanotoxin levels around the lake. Annually, Clear Lake suffers major economic losses stemming from HABs, and a 1994 study estimated Lake County loses $7-10 million in tourist revenue annually due to HABs (Goldstein & Tolsdorf 1994). This value likely underestimates current tourism losses over 20 years later, and maintaining the economic viability of Clear Lake is paramount since it is located in the poorest county in the state. 

Restoring a Naturally Eutrophic Lake

Even before human settlement, Clear Lake was historically a productive lake due to phosphorus-rich rocks and sediments in the area (Bradbury 1988; Richerson et al. 2008). Eutrophic, or nutrient-rich lakes, do not inherently have poor water quality, despite their negative connotations. Clear Lake existed as a healthy, productive ecosystem for many thousands of years before European colonization. Algae forms the base of lake foodwebs, and algal abundances in Clear Lake create conditions that support trophy largemouth bass populations at higher densities than most other lakes.

Despite some ecological benefits of algae, there comes a point where too much becomes harmful. At high enough levels, massive algal blooms ultimately die and biodegrade. This dynamic ultimately depletes dissolved oxygen and robs waterbodies of vast swaths of habitat for fish and aquatic life. Such conditions contribute to fish kills, especially during increasingly prolonged bouts of hot temperatures (Till et al. 2019). In order to maintain suitable dissolved oxygen levels, nutrient levels must be managed to prevent large algal blooms. Therefore, efforts to restore Clear Lake have focused on identifying and managing phosphorus sources to curb their harmful effects. 

Phosphorus from the Deep: Internal Loading

Clear Lake has two main phosphorus sources: the surrounding watershed, and lake sediments, or muck, at the bottom of the lake. This muck consists of terrestrial particles that get washed into the lake and dead organisms that sink down and accumulate over time—just like dust settling on an old shelf. The resulting layer of sediment is densely packed with phosphorus and prone to releasing it to the lake during periods of low dissolved oxygen, or hypoxia, near the lake-bottom. When this occurs, lake sediments fertilize the lake and cause harmful algae blooms. This process is called internal loading, and it has been one of the main focuses of the UC Davis Tahoe Environmental Research Center’s (TERC) research in Clear Lake. With the help of the Lake County Water Resources Department and their long-term dataset on sediment-associated phosphorus, our team has been working to track how sediment phosphorus levels have changed over time.

Predicting Hypoxia and Internal Loading in Clear Lake

Fig. 3. Collecting intact sediment cores from the bottom of Clear Lake (left image) to investigate rates of phosphorus flux from sediments using incubations (middle and right images). Photos: Micah Swann.

We have taken a multi-pronged approach to estimating impacts of internal loading to Clear Lake. Since phosphorus only mobilizes from sediments during hypoxic conditions, TERC scientist Alicia Cortes has been leading an effort to develop a hydrodynamic model to predict hypoxia throughout the lake using simple meteorological data, temperature sensors, and dissolved oxygen sensors at sites across the lake (Cortes et al. in prep). Using phosphorus flux rates measured from incubations of intact sediment cores, this model will help estimate annual internal loads of phosphorus to the lake. Preliminary research indicates that internal loading accounts for nearly half of phosphorus inputs to the lake annually.

Fig. 4. Soluble reactive phosphorus (phosphate) flux in anoxic sediment cores sampled from 6 sites across Clear Lake, CA. Sites show significant spatial variability in phosphorus flux indicating “hot spots” of internal loading exist across the lake.

The UC Davis team is working with outside organizations to identify and test management solutions to control internal phosphorus loading that are both economical and environmentally responsible. Our goal is to inform the Blue Ribbon Committee – a committee of local stakeholders in Lake County, on adjusting existing total maximum daily limits on phosphorus loads entering the lake and recommend strategies for managing internal phosphorus loads.

Questions? Feel free to visit our website

Nick Framsted is a masters student in the Department of Environmental Science and Policy at the University of California, Davis and the UC Davis Tahoe Environmental Research Center.

Further Reading

Anderson, C. A. (1936). Volcanic history of the Clear Lake area, California. Bulletin of the Geological Society of America, 47(5), 629-664.

Bradbury, J. P. (1988). Diatom biostratigraphy and the paleolimnology of Clear Lake, Lake County, California. Late Quaternary Climate, Tectonism, Sedimentation in Clear Lake, Northern California Coasts. Geological Society of America, Boulder CO. 1988. p 97-129.

Goldstein, J. J., & Tolsdorf, T. N. (1994). An Economic Analysis of Potential Water Quality Improvement in Clear Lake: Benefits and Costs of Sediment Control, Including a Geological Assessment of Potential Sediment Control Levels: Clear Lake Basin, Lake County, California. US Department of Agriculture, Soil Conservation Service, Davis and Lakeport Offices.

Lindquist, A. W., Roth, A. R., & Walker, J. R. (1951). Control of the Clear Lake Gnat in California. Journal of Economic Entomology, 44(4).

Richerson, P. J., Suchanek, T. H., Zierenberg, R. A., Osleger, D. A., Heyvaert, A. C., Slotton, D. G., … & Vaughn, C. E. (2008). Anthropogenic stressors and changes in the Clear Lake ecosystem as recorded in sediment cores. Ecological Applications, 18(sp8), A257-A283.

Sims, J. D. (Ed.). (1988). Late Quaternary Climate, Tectonism, and  Sedimentation in Clear Lake, Northern California Coast Ranges (Vol. 214). Geological Society of America.

Suchanek, T. H., Eagles-Smith, C. A., Slotton, D. G., Harner, E. J., & Adam, D. P. (2008). Mercury in abiotic matrices of Clear Lake, California: human health and ecotoxicological implications. Ecological Applications, 18(sp8), A128-A157.

Till, A., Rypel, A. L., Bray, A., & Fey, S. B. (2019). Fish die-offs are concurrent with thermal extremes in north temperate lakes. Nature Climate Change, 9(8), 637-641.

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Planning for a shorter rainy season and more frequent extreme storms in California

By Claire Kouba and J. Pablo Ortiz Partida

California’s hydrologic future is muddled by a fundamental uncertainty: will the state get wetter or drier? Climate models disagree on this question, but provide insights on other important water management questions.

The wetter or drier question has been studied often in government reports (DWR CCTAG, 2015; U.S. Bureau of Reclamation, 2016) and a variety of academic studies (Connell-Buck et al., 2011; Dogan et al., 2019; Medellín-Azuara et al., 2008). Forecasts for California mean annual precipitation commonly range from at least 20% wetter to 20% drier on average.

This focus on the uncertainty of future mean annual precipitation has unnecessarily deterred investment in adaptive management of water resources (Persad et al., 2020). While there is little model agreement on change in mean annual precipitation, there is much more model agreement on other hydroclimate metrics relevant to water resources management, including:  

  • snowpack declines
  • increased fraction of precipitation on extreme rainfall days
  • a shorter, sharper rainy season
  • increased ET
  • higher frequency of extremely wet and extremely dry years, and
  • higher incidence of “whiplash” years where an extreme dry year follows an extreme wet year or vice versa.

Future shifts in these metrics were estimated in a recent study (Persad et al., 2020) using 10 statistically downscaled global climate models and two common emissions scenarios. These predicted shifts were used to alter the climate inputs to a regional hydrologic model for the Scott Valley in the Klamath Basin (Case Study 1), and to assess changes in Oroville reservoir storage based on outputs by Knowles et al.(Knowles et al., 2018)(Case Study 2).

Case Study 1 – Greater extremes threaten regional groundwater sustainability

In the first case, a more extreme rainfall regime was simulated in Scott Valley with primarily agricultural land cover using the Scott Valley Integrated Hydrologic Model (Foglia et al., 2018; Tolley et al., 2019). The objective was to estimate effects of increased average storm intensity on sustainable groundwater management.

To simulate the upper range of scenarios in this region with RCP 8.5 emissions, the historical rainfall record was altered so daily precipitation was redistributed within each water year such that the 5% of highest-rainfall days received 7% more water, and the remaining days with rain were proportionally reduced to keep total annual precipitation at its historical value for each water year. All other model inputs (reference ET, stream inflows, etc.) remained the same as estimated historical values.

The results suggest that a temporal concentration of rainfall increases both recharge through soils to the aquifer and crop irrigation demand (Figure 1). This is because there are fewer days when rainfall is sufficient for crop water needs (increasing the number of days when irrigation is needed), while the number of days when rainfall exceeds soil field capacity increases (increasing total volume of infiltration that becomes groundwater recharge rather crop transpiration). Also, because this case does not incorporate effects of other predicted phenomena, such as increased average ET, this is a conservative prediction of increased irrigation demand.

Notably, though the increases in recharge and irrigation demand are small (2% or less) over the whole model period, it can more substantially impact water use behavior and the sustainability of groundwater budgets in some years, such as 2010.

Figure 1. Changes in groundwater budget terms from more extreme precipitation. Water use in Scott Valley, California has higher sensitivity to redistribution of annual precipitation toward extreme days in water years with evenly spread precipitation (2010, yellow) than years with concentrated winter precipitation (2015, dark brown). These two water years had near average total annual precipitation for the 1991–2018 period (blue), showing the varying impacts of climate shifts across individual water years. Column values show the absolute change between the historical simulation and the altered precipitation simulation. Numbers above columns indicate percent change from the historical simulation.

Case Study 2 – Shifting inflows reduce reservoir storage

Continuing the current rates of heat-trapping gas emissions would likely further concentrate reservoir inflows into already wet winter months (November-March), as shown in many climate change studies for California since the late 1980’s (Cayan et al., 2008; Gleick, 1989; Hayhoe et al., 2004). The second case study assessed how changing seasonality of inflows from predicted shifts in timing and type of winter precipitation would affect Lake Oroville, California’s second largest reservoir.

Ironically, even though average reservoir inflows may be greater with severe climate change, the timing shift means the extra water would come when current operation rules require releasing excess water to protect against floods (Knowles et al., 2018). Because the extra outflows would occur in the wet winter months, when downstream agricultural water users don’t need it, such releases reduce average water storage in the reservoir and ultimately reduce water availability for the dry season. The data show that stored water declines by roughly 17 percent annually and by more than 35 percent during September and October, when reservoir storage is already at its lowest (Figure 2).

Figure 2. Changes in Oroville storage and outflows from climate change. Lake Oroville shows substantial changes in monthly mean seasonal storage (red curve) and outflows (blue curve) from historical (1980–2009) to RCP 8.5 end-of-century (2070–2099) climate change conditions.

Moving forward

To capture the variability of potential future climate, operational models driven by daily or subdaily inputs are needed (e.g., Willis et al., 2011) . Most current regional water system models use monthly inputs, making it more difficult to evaluate changes that might result from a higher frequency of extreme storms.  

Overall, with uncertainty in future mean annual precipitation, we need not rely on assumptions of stationarity in hydroclimate forecasts. These findings suggest that researchers and agencies can begin incorporating some less-discussed hydroclimate shifts into water planning efforts.


Cayan, D. R., Maurer, E. P., Dettinger, M. D., Tyree, M., & Hayhoe, K. (2008). Climate change scenarios for the California region. Climatic Change, 87(1), 21–42.

Connell-Buck, C. R., Medellín-Azuara, J., Lund, J. R., & Madani, K. (2011). Adapting California’s water system to warm vs. Dry climates. Climatic Change, 109(SUPPL. 1), 133–149.

Dogan, M. S., Buck, I., Medellin-Azuara, J., & Lund, J. R. (2019). Statewide Effects of Ending Long-Term Groundwater Overdraft in California. Journal of Water Resources Planning and Management, 145(9), 04019035.

DWR CCTAG. (2015). California DWR Climate Change Technical Advisory Group: Perspectives and guidance for climate change analysis. (Issue August).

Foglia, L., Neumann, J., Tolley, D. G., Orloff, S. B., Snyder, R. L., & Harter, T. (2018). Modeling guides groundwater management in a basin with river–aquifer interactions. California Agriculture, 72(1), 84–95.

Gleick, P. H. (1989). Climate change, hydrology, and water resources. Reviews of Geophysics, 27(3), 329–344.

Hayhoe, K., Cayan, D., Field, C. B., Frumhoff, P. C., Maurer, E. P., Miller, N. L., Moser, S. C., Schneider, S. H., Cahill, K. N., Cleland, E. E., Dale, L., Drapek, R., Hanemann, R. M., Kalkstein, L. S., Lenihan, J., Lunch, C. K., Neilson, R. P., Sheridan, S. C., & Verville, J. H. (2004). Emissions pathways, climate change, and impacts on California. Proceedings of the National Academy of Sciences of the United States of America, 101(34), 12422.

Knowles, N., Cronkite-Ratcliff, C., Pierce, D. W., & Cayan, D. R. (2018). Responses of Unimpaired Flows, Storage, and Managed Flows to Scenarios of Climate Change in the San Francisco Bay-Delta Watershed. Water Resources Research, 54(10), 7631–7650.

Medellín-Azuara, J., Harou, J. J., Olivares, M. A., Madani, K., Lund, J. R., Howitt, R. E., Tanaka, S. K., Jenkins, M. W., & Zhu, T. (2008). Adaptability and adaptations of California’s water supply system to dry climate warming. Climatic Change, 87(1 SUPPL).

Persad, G. G., Swain, D. L., Kouba, C., & Ortiz-Partida, J. P. (2020). Inter-model agreement on projected shifts in California hydroclimate characteristics critical to water management. Climatic Change, 21.

Tolley, D. G., Foglia, L., & Harter, T. (2019). Sensitivity Analysis and Calibration of an Integrated Hydrologic Model in an Irrigated Agricultural Basin with a Groundwater-Dependent Ecosystem. Water Resources Research, 55(8).

U.S. Bureau of Reclamation. (2016). Los Angeles Basin Study: Summary Report.

Willis, A. D., Lund, J. R., Townsley, E. S., & Faber, B. A. (2011). Climate Change and Flood Operations in the Sacramento Basin, California. San Francisco Estuary and Watershed Science, 9(2).

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