DNA Unveils New Freshwater Fish Species in California

By Peter B. Moyle & Matthew A. Campbell

No doubt you have watched a crime show where DNA analysis reveals the identity of a victim or criminal. Or, you have read accounts of how Neanderthal genes are part of our DNA. It is still astonishing to think that such uses of DNA did not exist until the Human Genome Project, finished about 20 years ago at the cost of millions of dollars. Even more astonishing is that low-cost methods of examining the genome of any animal or plant are now available. Specifically, the genomes of fishes can be examined to determine evolutionary relationships among species and to identify new ‘cryptic’ species of fishes that otherwise are harda to identify. This means that ancient fish biologists (like Moyle) can team up with geneticists steeped in new methodologies (like Campbell) to explore fish genomes. We can identify ‘new’ (to us) species and confirm (or deny) species identified by standard methods, such as counting scales and fin rays.

Moyle’s first venture into the genomic world, with postdoc Jason Baumsteiger as his guide, was to explore the genome of California roach (Hesperoleucus symmetricus), a small fish endemic to much of central and coastal California. They found that the single species recognized when they started was actually five species (Baumsteiger et al. 2019). In this blog, we summarize our findings that the Riffle Sculpin (Cottus gulosus) is also multiple species based on analysis of the genome (genomics) but supported by other genetic, distributional, and meristic studies (Moyle and Campbell 2022).

Freshwater sculpins as a family (Cottidae, 42+ recognized species) are good subjects for genomic analysis because the species are naturally hard to tell apart, being small (usually less than 80 mm in length), with no scales, and with habits and color patterns that keep them camouflaged. Most species are indicators of high water quality, inhabiting cool, clear streams and lakes throughout the northern hemisphere. Their frequent preference for permanent headwaters leads to isolation and formation of new species, some with ironically hilarious scientific names such as Cottus perplexus and C. confusus. They are typically abundant and important parts of the ecosystems they inhabit, coexisting with diverse trout and salmon species, as well as other endemic fishes.

The Riffle Sculpin species “complex” we discuss here consists of the following three species and four subspecies:

Cottus pitensis, Pit Sculpin Bailey and Bond 1963

Cottus gulosus, Inland Riffle Sculpin (Girard 1854)

            C. g. gulosus: San Joaquin Riffle Sculpin (Girard 1854), nominate subspecies

            C. g. wintu: Sacramento Riffle Sculpin, Moyle and Campbell 2022, new subspecies

Cottus ohlone, Coastal Riffle Sculpin Moyle and Campbell 2022, new species

            C. o. ohlone, Ohlone Riffle Sculpin Moyle and Campbell 2022, new subspecies

            C. o. pomo, Pomo Riffle Sculpin Moyle and Campbell 2022, new subspecies.

Left: Four species/subspecies of riffle sculpin endemic to California. A. San Joaquin Riffle Sculpin, B. Sacramento Riffle Sculpin, C. Ohlone Riffle Sculpin, D. Pomo Riffle Sculpin. Right: Map of current distribution of Riffle Sculpin species/subspecies. Note the fragmentation of distributions, which is the result of habitat alteration by people. From Moyle and Campbell 2021. Photos by Irene Englis. Map by Amber Manfree.
Pit Sculpin, from Bailey and Bond (1963).

The Pit Sculpin was described as a distinct species in 1963, using conventional taxonomic techniques, but its distinguishing features were minor, indicating its close relationship to the Inland Riffle Sculpin. Our genomic study showed that it did indeed merit continued recognition as a separate species. This is the only sculpin species in the Pit River watershed of northeastern California and the tributaries to Goose Lake in Oregon.

The Inland Riffle Sculpin was described in 1854 by pioneering ichthyologist Charles Girard. His description was brief and confusing and was applied to all Riffle Sculpins in California (including the Pit Sculpin). Our genomic study showed that Girard’s sculpins in the Pit, Sacramento, and San Joaquin rivers and their tributaries, as well as in San Francisco Bay tributaries and the Russian River, were distinct from each other. Girard’s description seems to have been mainly based on fish from the San Joaquin River, so C. gulosus was retained as the scientific name of the Inland Riffle Sculpin.

Our genomic analysis indicated that the Inland Riffle Sculpin contained two distinct evolutionary lineages that we designated as subspecies because the genetic differences were less than we found between species-level lineages in our data set. Yet the differences are substantial and correspond to the major river basins, so we recognized the San Joaquin Riffle Sculpin (C. g. gulosus) and the Sacramento Riffle Sculpin (C. g. wintu). One outcome of our genomics study was finding that the Sacramento Riffle Sculpin is a hybrid lineage of ancient origin, with a nuclear genome largely of the Inland Riffle Sculpin lineage but with maternally-inherited mitochondrial DNA of the Pit Sculpin type. Surveying only mitochondrial DNA with barcoding approaches would be misleading in this case and is an argument to apply genomic approaches when possible.

Baumsteiger et al. (2012, 2014), in part by using mitochondrial DNA, found that the sculpins in San Francisco Bay drainages were quite different genetically from the inland sculpin populations. This finding is what prompted our study using the more complete genetic picture provided by genomics, which examines the entire genome. Our study led to the designation of coastal and SF Bay populations as a new species Coastal Riffle Sculpin (C. ohlone),with two subspecies, Ohlone Riffle Sculpin (C. ohlone ohlone) and Pomo Riffle Sculpin (C. o. pomo).The two subspecies were named to honor the native peoples that lived in the watersheds they occupied, coexisting with the fishes for thousands of years.

Today, the Ohlone Riffle Sculpin lives mostly in the headwater streams of the Guadalupe River which drains the Santa Clara Valley. These streams flow through and are highly altered by urban areas of San Jose. They also are found in a few small streams that flow directly into the Bay (e.g., Coyote Creek). The Pomo Riffle Sculpin is present in the upper Russian River watershed, above the mouth of Mark West Creek. Their range includes the East Fork Russian River, as well as tributaries to northern San Francisco Bay: Napa River, Petaluma River, Sonoma Creek, and smaller tributaries. These SF Bay streams had connections in the past to the Russian River, via the shifting headwaters of Sonoma Creek. For both subspecies the exact distribution needs to be clarified, as does the status of each isolated population.

Our finding of ‘new’ species and subspecies of sculpin is an example how genomics can be used to identify cryptic species in the California fish fauna. The five sculpin lineages we have identified cannot, for the most part, be told apart using non-genetic techniques. Furthermore, the use of mitochondrial barcoding techniques would also not have captured the entire picture of sculpin diversity in California. These discoveries increase our appreciation of the uniqueness of California fish fauna, where over 80% of the species are endemic to the state or shared with parts of watersheds in Oregon or Nevada (Moyle 2002, Leidy and Moyle 2022). If these special species are going to be around for future generations to admire, including the species and subspecies of Riffle Sculpin, a way must be found to systematically protect aquatic habitats statewide while surveying for cryptic diversity. There are other cryptic species waiting to be discovered!

Peter Moyle is an Emeritus Professor and Associate Director of the Center for Watershed Sciences, UC Davis; Matthew Campbell is a Research Scientist in the Genomic Variation Laboratory, UC Davis.

Further Reading

Bailey, R.M. & Bond, C.E. (1963). Four new species of freshwater sculpins, genus Cottus, from western North America. Occasional Papers of the Museum of Zoology, University of Michigan 634: 1-27. https://deepblue.lib.umich.edu/handle/2027.42/57070

Baumsteiger, J., Kinziger, A.P. & Aguilar, A. (2012). Life history and biogeographic diversification of an endemic western North American freshwater fish clade using a comparative species tree approach. Molecular Phylogenetics and Evolution, 65: 940–52. https://doi.org/10.1016/j.ympev.2012.08.015

Baumsteiger, J., Kinziger, A.P., Reid., S.B. & Aguilar, A. (2014). Complex phylogeography and historical hybridization between sister taxa of freshwater sculpin (Cottus). Molecular Ecology 23: 2602–2618. https://doi.org/10.1111/mec.12758

Baumsteiger, J. & Moyle, P.B. (2019). A reappraisal of the California Roach/Hitch (Cypriniformes, Cyprinidae, Hesperoleucus/Lavinia) species complex. Zootaxa 4543 (2): 2221–240.

Leidy, R.A. & Moyle, P.B. (2021). Keeping up with the status of freshwater fishes: a California (USA) perspective. Conservation Science and Practice 3(8): e474. https://doi.org/10.1111/csp2.474.

Moyle, P.B. (2002). Inland Fishes of California. Revised and Expanded. University of California Press, Berkeley, 517 pp.

Moyle, P. B. and M.A. Campbell. (2022). Cryptic species of freshwater sculpin (Cottidae, Cottus) in California, USA. Zootaxa 5154 (5): 501-507.

Moyle, P.B., Katz J.V.E. & Quiñones, R.M. (2011). Rapid decline of California’s native inland fishes: a status assessment. Biological Conservation 144: 2414–2423. https://doi.org/10.1016/j.biocon.2011.06.002

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Is the Drought Over? Reflections on California’s Recent Flood-Drought Combo

By Andrew L. Rypel, Jay Lund, and Carson Jeffres

Early January was an unusually wild ride of atmospheric rivers. Nine sizable systems produced a train of storms beginning about New Years and lasting for several weeks across almost all of California. After three years of drought, the storms reminded us that California has flood problems similar in magnitude to its drought problems, and that floods and droughts can occur in synchrony. As the dust begins to settle, let’s look at the impacts of these early January floods and examine if the recent three-year drought and its longer-term drought impacts might be ending.

Accumulated precipitation for northern California as of publication of this blog. Graph from the Department of Water Resources, California Data Exchange Center https://cdec.water.ca.gov/cgi-progs/products/PLOT_ESI.pdf

Impact of the Floods

Recent storms have been the proximate cause of about a billion dollars of damage to public infrastructure, private homes and businesses, not all from floods, but also from high winds and landslides. Homes and cars were smashed by downed trees, and roads eroded or washed away by streams and coastal waves. Some piers and harbors were damaged or closed. 

More surprising was the number of deaths. Around 20 deaths have been attributed to the storms, about 6 of which were flood-related drownings. Of the thousands of miles of flood levees in California, only two areas seem to have suffered levee failures – a Merced suburb (from a levee failure on Bear Creek) and Wilton (Sacramento County) on the Consumnes River, which had several levee failures. Flooding on major rivers was limited by low storage in most reservoirs, which let them capture large amounts of water rather than discharging it.

For a local reclamation district perspective on the Cosumnes River flooding, see the video below:


Modern flood forecast, warning, and evacuation systems have greatly reduced flooding deaths in the US since the early 1900s. These integrated national, state, and local alert systems appear to have functioned well, although some weaknesses will be evident. A major cause of flood-related drownings nationally is people driving into rising or moving water, erroneously thinking a car can pass safely. Most recent drownings were people in cars. In flood-prone areas, warnings and signage need to improve concerning driving through floodwaters. After more than a decade of levee improvements, no levees failed in protecting major cities. But failures did occur on smaller streams and tributaries. Overall, most of California’s massive network of levees passed the test, but weaknesses should be systematically identified and addressed before the memory of flooding recedes.

Slusser Road in Windsor California, January 14, 2023. Photo credit: Sarah Stierch. Downloaded from commons.wikimedia.org

Although the increasingly older dam and reservoir spillway infrastructure in California (Rypel et al. 2020) did not fail, it was not thoroughly tested due to most large reservoirs being relatively empty at the start of the year and in the process of filling. In some reservoirs, normal flood reservoir releases were required (as with Folsom), resulting in the usual complaints of ‘water being wasted to the sea’ (Cloern et al. 2017). Yet such episodic high flows are important to ecosystems of California, and its unique biodiversity.

As featured in last week’s blog (Mount et al. 2023), our early January storms might be described as ‘nature’s gift to nature’. Ecologically, these storms have been a bonanza for species and ecosystems that rely on floodplain and wetland habitats. In general, habitat science and management in aquatic ecosystems greatly lags that for terrestrial environments (Sass et al. 2017). In California, access to floodplain habitat for freshwater species is of the highest importance (Opperman et al. 2017). Both the Freemont (Yolo Bypass) and Tisdale Weirs overtopped during recent storms, allowing massive habitat use by our Sacramento River natives. Salmon of several run types were captured in recent surveys of flooded fields along with many native and non-native species. Unfortunately, flooding arrived after some fairly low annual returns of salmon, especially winter-run Chinook salmon. Nonetheless, for the progeny of successful salmon spawners this year, conditions have been optimal so far. And because outmigration survival increases with river flows (Michel et al. 2021), these floods will help buoy Central Valley salmon stocks to some extent following several punishing drought years. There are some active scientific research projects in the floodplains this year that will be informative for learning more about how to manage floods and winter flows for California’s biodiversity. The floods are extremely beneficial for these efforts.

Is the drought over?

There are many ways a drought can be indexed and measured, summarized conceptually in Table 1. 

Storms so far this year have done well at replenishing soil moisture, which is good for annual pastures, dryland crops, forests, and shortening the wildfire season, so far. Ample soil moisture also means future storms will produce more runoff to streams, reservoirs, and aquifers. But two and a half months remain in the wet season, and the 2-week forecast is mostly dry.

Reservoir levels as of 1/20/2023. Graph from the Department of Water Resources, California Data Exchange Center https://cdec.water.ca.gov/cgi-progs/products/rescond.pdf

Water levels in California reservoirs are much improved across the board. Smaller reservoirs have filled and started discharging to make room for managing potential floods. Large reservoirs are refilling now to undo the cumulative impacts of a multiyear drought. This is partly because atmospheric rivers often soak a relatively narrow region with high precipitation, and until recently, most of the fire hose was pointed at the Central Sierra Nevada. With the recent storms, reservoirs are accumulating water. Shasta Lake is filling well at 86% of average for this time of year. Lake Oroville is at 108% of average for this date, having essentially recovered from the drought. However, Trinity Lake is only at 49% of its average for this date. Even major reservoirs can fill fairly quickly from major storms, but it can still be months if storms are smaller. Snow conditions are excellent. Statewide snowpack is currently 141% of the January average and 160% and 119% for the Sacramento and San Joaquin rivers, respectively. More reservoir filling will occur as the accumulated snow melts during spring and early summer. Alternatively, snowpack could grow more with more storms, and in some places, we could have snowmelt floods if the spring is warm. 

But many aspects of long and deep droughts end slowly, sometimes over years, and often only after several wet periods. Despite the welcome precipitation, the drought is over only in some facets, but not others. With more storms, many drought impacts will be reduced further.

Table 1. Is the drought over? Which drought?

Drought typeEffectsCurrent status
Soil moisture storageForests, Unirrigated crops and pasture, reduced runoff for human and ecosystem uses, longer wildfire seasonsDrought over.
Reservoir storageLess water supply for irrigated crops, recreation, cities, hydropower, and cold water for salmon. Empty storage reduces flood risksMuch better, but still a ways to go. Many reservoirs might fill this year.
Groundwater storageIrrigated crops, well-dependent households, towns, cities, spring and groundwater-dependent wetlands and ecosystems A bit better, but perhaps years to go.
EcosystemsReduced survival rates of salmon, increased abundance of non-native species, harmful algal blooms, species at risk of extinctionQuite bad. CA freshwater ecosystems are functionally exposed to chronic, long-term drought every year. Actual droughts impose an additional step in the declining direction.
Lingering impacts· Dead forest trees prolong fire risks for years
· Drawn-down aquifers increase pumping costs and new well costs
· Need to replace drought pumping from aquifers can fallow lands in later wet years
· Depleted fish and bird populations can take years to recover
Too late, we’ll have these for years to come.

The chronic drought for ecosystems

Ecosystem impacts of droughts have been some of the most stubborn for managers and regulators. California’s aquatic ecosystems have been systematically exposed to long-term chronic drought because of dam building and massive water storage, diversions, and extractions. These are good things for humans, but the debt is real for ecosystems. For some species like the Delta smelt, the end game is now as managers race to release hatchery fish into a fundamentally changed, and apparently hostile, Delta ecosystem. Longfin smelt are tracking closely behind. For other species, like Chinook salmon, the trend is not good. Last ditch actions like two-way trap-and-haul above Shasta are being tried to correct decades of decline. Although there is a tendency to divert as much water as regulations allow during high flows, it is important to recognize that periodic major storms and flooding help support the ecology and geomorphology of our remnant ecosystems, and make them more durable. Flooded bypasses provide a glimpse into a future of green infrastructure that might extend the duration and spatial footprint of flooding. Our flood protection system was designed without ecosystem priorities and with a different understanding of ecological benefits of seasonal flooding. Managed floodplains are a needed feature of our water management system, with many benefits (Torres et al. 2022).

Groundwater recharge is another nature-based solution linked to the multi-decadal drought experienced by ecosystems. California has modest systematic groundwater monitoring, so changes in groundwater stores are difficult to track. In general however, Sacramento basin groundwater has a history of refilling aquifers better and more efficiently than the drier and more overdrafted San Joaquin and Tulare basins. Depleted groundwater in overdrafted basins is likely to extend the drought in these areas and accelerate State Groundwater Management Act (SGMA) actions to reduce pumping. Under SGMA, additional pumping during the drought has increased the overdraft debt that must be repaid by 2040. One potential lesson from this round of storms is the need for faster permitting or pre-event permitting to allow flooding of lands for groundwater recharge. And because increased groundwater recharge ultimately benefits people and ecosystems (especially local streams), this green infrastructure solution could be implemented more nimbly in the future.


The drought is not over, yet. Furthermore, many legacies from the current drought will endure for years. Impacts from recent flooding were intense and expensive, but the state fared mostly okay during the deluge. As usual, native biodiversity continues its stair step pattern of decline from droughts. For groundwater, pumping will need to be further reduced during wet years, just to restore aquifers to 2015 levels needed to comply with SGMA. Nonetheless, at halftime for this wet season, the recent storms have provided hope that the current drought may be ending from multiple perspectives. Another dry year remains plausible, but looks much less likely than it did a month ago. And major floods are now a bit more likely this year.

But as always for California, both floods and droughts are inevitable in the future, and we should prepare.

Yolo Bypass at the intersection with US Interstate 80

Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences. Jay Lund is a Professor of Civil and Environmental Engineering at University of California, Davis, and Vice Director at its Center for Watershed Sciences. Carson Jeffres is Field and Lab Director and a Senior Researcher at the Center for Watershed Sciences.

Further reading

Cloern, J.E., J. Kay, W. Kimmerer, J. Mount, P.B. Moyle, and A. Mueller-Solger. 2017. Water wasted to the sea? San Francisco Estuary and Watershed Science 15(2).

Lund, J., Rypel, A.L., and J. Medellin-Azuara. 2021. California’s New Drought. https://californiawaterblog.com/2021/03/14/californias-new-drought/

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

Mount, J., P.B. Moyle, A.L. Rypel, and C. Jeffres. 2023. Nature’s gift to nature in early winter storms. https://californiawaterblog.com/2023/01/15/natures-gift-to-nature-in-early-winter-storms/

Opperman, J.J., P.B. Moyle, E.W. Larsen, J.L. Florsheim, and A.D. Manfree. 2017. Floodplains Processes and Management for Ecosystem Services. University of California Press. 

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 42:197-209.

Rypel, A.L., C.A. Parisek, J. Lund, A. Willis, P.B. Moyle, Yarnell, S., and K. Börk. 2020. What’s the dam problem with deadbeat dams? https://californiawaterblog.com/2020/06/14/whats-the-dam-problem-with-deadbeat-dams/

Rypel, A.L. 2022. Nature has solutions…What are they? And why do they matter? https://californiawaterblog.com/2022/03/

Torres, F., M. Tilcock, A. Chu, and S. Yarnell. 2022. Five “F”unctions of the Central Valley floodplain. https://californiawaterblog.com/2022/05/08/five-functions-of-the-central-valley-floodplain/

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Nature’s gift to nature in early winter storms

By Jeffrey Mount, Peter B. Moyle, Andrew L. Rypel, and Carson Jeffres

The current wet spell, made up of a parade of atmospheric rivers, is a welcome change from the last three years of record dry and warm conditions. For very good reasons, the focus during these big, early winter storms is first and foremost on flood management and public safety. There is of course also great interest in the potential of these storms to relieve water shortages for communities and farms. What is not always appreciated is the role of these early winter storms  in supporting the health of freshwater ecosystems.

For millennia, California’s biodiversity evolved strategies to take advantage of these infrequent, but critical high flow events. Benefits from recent storms are now being realized throughout the state, from temperate rainforests of the North Coast to semi-arid and arid rivers in the south. 

As an example, here is a sample of some of the vital ecological processes that take place during winter wet periods in the Central Valley and San Francisco Estuary:

A juvenile Chinook salmon captured on the Sutter Bypass with its lunch packed on the way to the Pacific Ocean (photo curtesy of Eric Holmes).
  • Shaping of rivers and their habitat. Floods are when the work of a river gets done.  Important geomorphic thresholds are crossed during these high flows, leading to erosion, transport and deposition of sediment, and channel migration and formation. This is essential to creating habitat heterogeneity, abundance, and quality. A healthy river is one that does not hold still, but is constantly adjusting its channel and floodplain.
  • Dispersal of plants and animals. Large flow events are vital to moving everything, from fish to trees. For some fishes, such as endangered winter- and spring-run Chinook salmon, high flow events give an essential lift to juveniles, transporting them downstream, and enhancing outmigration survival rates to the Pacific Ocean. For riparian trees like willows and cottonwoods, these events send pieces of vegetation downstream, depositing them on newly-formed sandbars where they sprout in the spring.
  • Increased spawning success of native fishes. Native fishes including Chinook salmon, white sturgeon, Sacramento splittail, Sacramento sucker, hitch, and other species generally show an increase in populations following wet years, in part from the increase in floodplain spawning and rearing habitat. Indeed, a high fraction of native fishes in the Central Valley evolved to take advantage of floodplain habitats when available, either for rearing or spawning. Splittail, for example, only spawn on floodplains.
  • Access to more river margin habitat. During the summer and fall, low flows on rivers reduce the amount of available habitat. High flows open access to channel margin habitat, which are good places for fishes and other aquatic organisms to hold, feed, and escape predators. Increased flooding and access to river margin habitat, in turn, also generates a positive feedback cycle whereby these habitats become more likely to support riparian vegetation. And increased vegetation is of exceptional value to migratory songbirds, beaver, and other wildlife. Good things lead to more good things.
  • Wetting of seasonal wetlands. Large storms play an essential role in delivering water to seasonal wetlands, whether through direct rainfall, overflow from rivers and streams, or irrigation canals. This helps spread out migratory waterbirds, increasing available habitat and food resources, and reducing disease transmission. Increasing the amount and duration of flooding in the Central Valley has long been a solid conservation goal for diverse practitioners. All this rain provides these restorative benefits for free.
  • Priming the floodplain. Floodplains of the Central Valley are an essential part of river ecological productivity. As days grow longer and air temperatures increase, the water pushed onto floodplains in winter warms, slowly turns into a rich soup of aquatic insects. Numerous fishes—most notably juvenile Chinook salmon—make use of floodplains as a place to fatten up. Like packing a lunch for a long trip, salmon subsequently use these resources during their journey to the ocean and once they get there if resources are not plentiful.
  • Groundwater recharge. Winter floods play a large role in maintaining shallow groundwater levels throughout the Central Valley. Perennial wetlands, floodplain lakes, and streams and rivers are fed by shallow groundwater, particularly over the dry season, making ideal, productive habitat for an array of plants and animals. Today, with many basins facing overpumping and groundwater level declines, there’s renewed interest in using floodwaters for recharge—a boon for water supplies and for nature.
  • Estuarine rejuvenation. Life in the San Francisco Estuary—not the largest on the west coast, but a very important one—is adapted to and dependent upon pulses of fresh water, nutrients, and sediment that come from the watershed during winter floods. These pulses are especially important to building and maintaining tidal marsh habitat, which is the signature habitat of the Sacramento-San Joaquin Delta and much of the rest of the estuary. The biodiversity of this estuary is closely linked to these flood pulses.

These are just a few items from the long list of ecological benefits associated with large winter floods. The history of water and land management in California has muted these important processes. Reservoirs store floods and trap sediment. Thousands of miles of levees built to reclaim land for cities and farms have reduced or eliminated the historic connections that sustained wetlands, primed the productivity of the floodplain, and recharged groundwater. River channels have been straightened and simplified to speed water off the land for flood control. Overpumping of groundwater has disconnected many groundwater dependent wetlands. And all these changes have resulted in greatly diminished estuaries—most notably the San Francisco Estuary—that are no longer productive and have become home to numerous non-native species. This moment is also a reminder that the many efforts underway in California to improve freshwater ecosystems need to consider the potential value of winter flood pulses, and crafting strategies to restore these essential functions, such as including timing of flow releases and reconnecting water to land.

Still, even in our highly changed landscapes, high flow events like those unfolding this month (roughly once a decade on average, with the last big early winter flows in 2017) are very helpful in managing river and estuarine ecosystems. So while the news is rightfully focused on water supply and flood damages, it is worth keeping in mind that there are other important, often unseen benefits for our natural environment.

Jeffrey Mount is a senior fellow at the Water Policy Center, Public Policy Institute of California and founding director at the UC Davis Center for Watershed Sciences. Peter B. Moyle is a Distinguished Professor Emeritus at the University of California, Davis and is Associate Director of the Center for Watershed Sciences. Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences. Carson Jeffres is Field and Lab Director and Senior Researcher at the Center for Watershed Sciences.

Further Reading:

Cloern, J. E., J. Kay, W. Kimmerer, J. Mount, P. B. Moyle, and A. Mueller-Solger. 2017. Water wasted to the sea? San Francisco Estuary and Watershed Science 15(2).

Moyle, P., J. Opperman, A. Manfree, E. Larson, and J. Florsheim. 2017. Floodplains in California’s future. https://californiawaterblog.com/2017/09/10/floodplains-in-californias-future/

Rypel, A.L., P.B. Moyle, and J. Lund. 2021. A swiss cheese model for fish conservation in California. https://californiawaterblog.com/2021/01/24/a-swiss-cheese-model-for-fish-conservation-in-california/

Sturrock, A.M., Ogaz, M., Neal, K., Corline, N.J., Peek, R., Myers, D., Schluep, S., Levinson, M., Johnson, R.C. and Jeffres, C.A., 2022. Floodplain trophic subsidies in a modified river network: managed foodscapes of the future? Landscape Ecology 37(12): 2991-3009.

Torres, F., M. Tilcock, A. Chu, and S. Yarnell. Five “F”unctions of the Central Valley floodplain. https://californiawaterblog.com/2022/05/08/five-functions-of-the-central-valley-floodplain/

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

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Drought and the Colorado River: Localizing Water in Los Angeles

By Erik Porse and Stephanie Pincetl

Parker Dam and Lake Havasu, 2009 (Photo Credit: Alan Stark, Flickr)

In October 2022, water agencies in Southern California with Colorado River water rights announced plans to reduce water diversions. The agencies offered voluntary conservation of 400,000 acre-feet per year through 2026. This annual total is nearly 10% of the state’s total annual usage rights for the Colorado River. The cutbacks help prepare for long-term implications of climate change for the river’s management, which are starting to be acknowledged. In urban Southern California, an important aspect of this need is reducing imported water reliance through investments in local water resources.

Diversion rights along the Colorado River are over a century old. In 1922, states signed an agreement to allocate the river’s resources. Native Americans were excluded, but some of the sovereign nations have subsequently gained water rights through legal decisions and agreements. Arizona did not ratify the compact until 1944. Within the 1922 agreement, the river’s originally estimated 16.5 million acre-feet of annual yield was divided, with 7.5 million acre-feet allocated to states in both the upper and lower basins. A paltry 1.5 million acre-feet was allocated to Mexico in the 1944 Treaty with Mexico. Subsequent research estimated the historic volume of available water on the Colorado closer to 14 million acre-feet, and from 2000-2020, average inflow volumes were 12.5 million acre-feet. These numbers leave the river dry at its ultimate destination, the Colorado River Delta in Mexico. In recent decades, no flows reached the Gulf of California until 2014, when agencies negotiated a timed release of flows from Lake Mead that wetted the Delta for a few days as part of an international agreement between the U.S. and Mexico (Minutes 319 & 323).

In 2022, the river’s available water was projected to be just 8.4 million acre-feet of inflows into Lake Powell, another year well below historical averages. Huge reservoirs along the river, namely Lake Mead and Lake Powell with over 50 million acre-feet of storage, buffer against dry periods. But today the reservoirs are nearly drained after decades of severe dryness. Existing agreements developed over 15 years outline how states in the Upper and Lower Basins must adaptively reduce demand during drought based on reservoir storage levels. Given the stark forecasts through 2024, in June 2022 the U.S. Bureau of Reclamation (USBR) issued an ultimatum to parties along the river: develop plans to reduce draws by 2 to 4 million acre-feet that address chronic overuse and align with agreed conservation plans, or be subject to federal determinations. Among the Lower Basin states, California was not required to reduce draws until Lake Mead reached 1,045 feet in elevation. As of November 30, 2022, its elevation was 1,043 feet. Recovering the basin’s reservoir levels will require continued conservation along with multiple wet years.

What would happen if Southern California lost access to Colorado River water for an extended period? Almost a decade ago, we looked at this question for urban areas in Los Angeles (L.A.) County. Cities use less than 30% of California’s 4.4 million acre-feet of Colorado River water allocations. This is mostly for the Metropolitan Water District of Southern California (MWD) and San Diego County Water Authority.  The remaining California water use from the Colorado River is for agricultural districts and Native American sovereign nations. The percentages can vary between years based on decades of complex water sharing and storage agreements. End-of-year projections for 2022 forecasted that MWD would receive 25% of California’s total Colorado River diversions. Within areas of Los Angeles, Orange, Riverside, San Bernadino, and San Diego Counties served by MWD, Colorado River water supplies are critical. MWD balances imported water supplies from the Colorado River and Northern California to maintain sufficient storage in its reservoirs, helping augment local groundwater, stormwater capture, and recycled water.

To investigate the impacts of reduced imported water supply in Los Angeles, we modeled scenarios of full (100%) to no (0%) imported water availability for L.A. County water agencies that supply 10 million people. We examined impacts on urban water operations, trees, and landscapes, along with opportunities to update existing groundwater rights allocations. At the time, we didn’t anticipate that as soon as 2022, L.A. County agencies could face little to no available new water allocations from both the State Water Project and Colorado Rivers.

Results present a window into water management futures in Los Angeles. Overall, L.A. County water agencies could likely reduce long-term water reliance on imported supplies, especially the Colorado River, to 30% of total demand. Agencies would need to boost stormwater capture and recycled water production, while also investing in many more climate-appropriate landscapes. In recent years, agencies have increased investments in these strategies. Continued conservation is also key. The modeled scenarios included water allocations for health and safety, as well as estimated irrigation requirements for the urban tree canopy (if irrigated appropriately). Total per capita use was 80-100 gallons per capita per day (gpcd) in scenarios with reduced imported water availability.

The analysis captured many current trends. For instance, water use in L.A. County has continued to decline, most recently facilitated by severe drought since 2020. Recent total urban per capita use was approximately 100 gpcd across Southern California agencies in 2019-2020. In modeled scenarios, landscape transformation was a key contributor to long-term conservation. In addition, agencies have continued to invest in stormwater capture and groundwater recharge projects, especially through the county-wide Safe Clean Water Program approved in 2018. Modeled scenarios also showed the importance of water storage, not only in MWD’s reservoirs, but also in groundwater basins. Groundwater continues to be an important source that has historically averaged 35% of supply in both L.A. County and urban Southern California more broadly. We didn’t model any new ocean desalination projects in L.A. County because no such plans were underway.

We also missed some key developments. The modeled scenarios included existing and planned recycled water projects at the time, but did not account for large scale water reuse projects by the Los Angeles Department of Water and Power (LADWP), MWD, and L.A. County Sanitation. Additionally, we modeled household water needs for health and safety as 50-55 gpcd, which was the legislative standard at the time. The current indoor standard is slated to drop to 42 gpcd through 2030. Last, we didn’t explicitly include significant policy and behavioral changes that have emerged. For instance, research supported by MWD estimated that a rebate-funded turf replacement project yields an additional two turf replacement projects not funded through incentives. So-called “non-functional” turf on commercial, industrial, and institutional properties will likely become much less common in Southern California.

Achieving equitable local water reliance will require key policy changes. Many of L.A. County’s groundwater basins were adjudicated years ago and the remaining ones have been brought under regulations through the Sustainable Groundwater Management Act or “SGMA”. In adjudicated basins, existing water rights for pumping will need to offer broader access to agencies that may be unable to fund new projects. This would further incentivize stormwater capture and would spur agencies to address current adjudications, including possible municipalization of pumping rights. New water financing strategies are also needed to pay for large water projects such as countywide water recycling. Agencies will need to increase retail rates to subsidize affordable water for low-income households (within Proposition 218 restrictions). Tradeoffs in water availability for recycled water and environmental instream flows will need to be resolved, likely through guidelines for seasonal releases.  Finally, increased and sustained funding streams for landscape transformation will be needed, supported by cooperation between water agencies and the landscaping and nursery industries. Nascent programs are already taking root.

Much work remains to adapt Southern California’s water use habits to future climate conditions. The Colorado River will remain an important source of supply for coming years, but expectations of availability will change. Southern California’s cities have significant fiscal resources and planning capacity to adapt. The hardest hit areas will likely be rural and agricultural communities in California that rely on Colorado River water. Yet, cities use food grown by farms and, over decades, water management practices between urban and rural agencies in the region have become entwined. The result is a system where everyone is affected. As we face more dry years in California and the Pacific Southwest, empathy for the livelihoods of fellow Californians is perhaps our most potent resource for climate adaptation.

Erik Porse is a Research Engineer at the Office of Water Programs at Sacramento State and an Assistant Adjunct Professor at UCLA’s Institute of the Environment and Sustainability.

Stephanie Pincetl is a Professor at UCLA’s Institute of the Environment and Sustainability and Founding Director of the California Center for Sustainable Communities at UCLA.

The results were part of projects from a multi-university team that also included Mark Gold, Diane Pataki, Terri Hogue, Katie Mika, Kim Manago, Elizaveta Litvak, Madelyn Glickfeld, and Felicia Federico.

Further Reading:

Davis, Margaret Leslie. 1993. Rivers in the desert: William Mulholland and the inventing of Los Angeles, 1st ed. HarperCollins Publishers, New York, NY.

Erie, Steven, HD Brackman. 2006. Beyond Chinatown: the Metropolitan Water District, growth, and the environment in southern California. Stanford University Press, Stanford, CA.

Felicia Federico, A. Youngdahl, S. Subramanian, C. Rauser, M. Gold. 2019 Sustainable LA Grand Challenge Environmental Report Card for Los Angeles County Water. UCLA

Galt, Joe. Sharing Colorado River Water: History, Public Policy and the Colorado River Compact. University of Arizona Water Resources Research Center. August 1997.

MWD. Integrated Water Resources Plan: 2020 Update. Technical Appendices. Los Angeles, CA.

MWD. 2020 Urban Water Management Plan. Los Angeles, CA. June 2021.

Mika, Kathryn B., E. Gallo, E. Porse, T. Hogue, S. Pincetl, and M. Gold. 2017. LA Sustainable Water Project: Los Angeles City-Wide Overview. UCLA, Los Angeles, CA

Ostrom, Elinor. 1965. Public Entrepreneurship: A Case Study in Ground Water Basin Management. Ph.D. Dissertation, University of California, Los Angeles

Ostrom, Vincent. 1962. “The political economy of water development.” The American Economic Review 52.2: 450-458.

Porse, Erik, KB Mika, E Litvak, KF Manago, K Naik, M Glickfeld, TS Hogue, M Gold, DE Pataki, and S Pincetl. 2017. “Systems Analysis and Optimization of Local Water Supplies in Los Angeles.” Journal of Water Resources Planning and Management. 143, no. 9 (2017): 04017049.

U.S. Bureau of Reclamation. Annual Operating Plan for Colorado River Reservoirs 2022. December 8, 2021.

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California WaterBlog: 2022 In Review

By Christine Parisek

The California WaterBlog is completing its 11th year. As we enter 2023, we take a moment to to thank our many readers, partners, authors, and friends. The California WaterBlog’s central mission is to provide stimulating ideas and commentary on critical challenges of water issues, resource management, and ecosystem restoration, in a digestible form. 

Figure 1. Word Cloud displaying frequent
      themes in 2022 WaterBlog titles.

In 2022, California WaterBlog published 49 blogs. This year, 64 unique authors contributed to California WaterBlog (an increase from last year), and on July 10th we surpassed our 500th blog post! The blog currently reaches readers in 74 countries worldwide with almost 14,000 subscribers and over 103,000 visitors this year. As usual, blog posts covered a breadth of themes, including Watershed outreach, the recent mass local die-off of white sturgeon, effect of drought on California’s intermittent streams, thiamine deficiency in salmon, native fishes and reservoirs, and being patient and persistent with nature.

Especially popular topics included California’s drought status and drinking water systems, environmental water rights, what to do when shift happens, a conservation bill you’ve never heard of [that] may be the most important in a generation (the Recovering America’s Wildlife Act), an exposé on the silent extinction of freshwater mussels, and farmer-researcher team science initiatives. We hope you continue enjoying CaliforniaWaterBlog and that the list below helps if you missed any blogposts.

Christine Parisek is a PhD candidate in the Graduate Group in Ecology at UC Davis and a science communications fellow at the Center for Watershed Sciences.

Table 1 (Further Reading). Top 17 blog posts in 2022, as ranked by “View” statistics.

6,128California’s 2022 Water Year – Both Wet and DryJay Lund
5,674Saving Clear Lake’s Endangered ChiPeter Moyle and Thomas Taylor
2,879Considerations for Developing An Environmental Water Right in CaliforniaKarrigan Börk, Andrew Rypel, Sarah Yarnell, Ann Willis, Peter Moyle, Josué Medellín-Azuara, Jay Lund, and Robert Lusardi
2,820Drought Year Three in California, 2022Jay Lund
2,746Who governs California’s drinking water systems?Kristin Dobbin and Amanda Fencl
2,580Continued drought early in a possibly wet yearJay Lund
2,283The Failed Recovery Plan for the Delta and Delta SmeltPeter Moyle
2,232Shift happensMiranda Bell-Tilcock, Rachel Alsheikh, and Malte Willmes
2,147A conservation bill you’ve never heard of may be the most important in a generationAndrew Rypel
1,957Follow the Water!Jay Lund
1,936Nature has solutions…What are they? And why do they matter?Andrew Rypel
1,758The Putah Creek Fish Kill: Learning from a Local DisasterAlex Rabidoux, Max Stevenson, Peter Moyle, Mackenzie Miner, Lauren Hitt, Dennis Cocherell, Nann Fangue, and Andrew Rypel
1,697Approaches to Water PlanningJay Lund
1,589Losing mussel mass – the silent extinction of freshwater musselsAndrew Rypel
1,483Five “F”unctions of the Central Valley FloodplainFrancheska Torres, Miranda Tilcock, Alexandra Chu, and Sarah Yarnell
1,434Unlocking how juvenile Chinook salmon swim in California riversRusty Holleman, Nann Fangue, Edward Gross, Michael Thomas, and Andrew Rypel
1,434Rice & salmon, what a match!Andrew Rypel, Derrick Alcott, Paul Buttner, Alex Wampler, Jordan Colby, Parsa Saffarinia, Nann Fangue, and Carson Jeffres
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The Collapse of Water Exports – Los Angeles, 1914

This is a re-post from 2019 with updated links for pictures and further readings.

by Jay Lund

Collapse of Los Angeles aqueduct pipeline through Antelope Valley from a major flood in February, 1914 (3-months after the aqueduct’s official opening)

“In February, 1914, the rainfall in the Mojave Desert region exceeded by nearly fifty per cent in three days the average annual precipitation.

Where the steel siphon crosses Antelope valley at the point of greatest depression, an arroyo or run-off wash indicated that fifteen feet was the extreme width of the flood stream, and the pipe was carried over the wash on concrete piers set just outside the high water lines. The February rain, however, was of the sort known as a cloud-burst, and the flood widened the wash to fifty feet, carried away the concrete piers, and the pipe sagged and broke at a circular seam. The water in the pipe escaped rapidly through the break under a head of 200 feet, and the steel pipe collapsed like an emptied fire hose for nearly two miles of its length. In some places the top of the pipe was forced in by atmospheric pressure to within a few inches of the bottom. The pipe is ten feet in diameter, and the plates are 1/4 and 5/16 of an inch thick. Many engineers pronounced the collapsed pipe a total loss, and advised that it be taken apart, the plates re-rolled and the siphon rebuilt.

The damage was repaired, however, by the simple expedient of turning the water on after the break was mended, relying on the pressure to restore the pipe to circular form. The hydraulic pressure, under gradually increasing head, restored the pipe to its original shape without breaking any of the joints or shearing the rivets, and a month after the collapse the siphon was as good as new. The total cost of repairing the siphon was only $3,000. It would have cost about $250,000 to take it apart and rebuild it.” [1]

Water management and policy has always faced challenges, even unexpected ones following great technical triumphs.  But sometimes challenges require only some simple creativity based on fundamental insights and a willingness to venture forth and adapt.  Sometimes.

Further reading

[1] Complete report on construction of the Los Angeles aqueduct, Los Angeles Board of Public Service Commissioners, Los Angeles, CA 1916. (pp. 20-21) https://openlibrary.org/works/OL13802476W/Complete_report_on_construction_of_the_Los_Angeles_aqueduct

[2] http://waterandpower.org/museum/Construction_of_the_LA_Aqueduct.html

[3] LADWP historic photo archives – https://tessa2.lapl.org/digital/collection/dwp/search

[4] YouTube – Construction of the Owens Valley Project

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The Largest Estuary on the West Coast of North America

By Jeffrey Mount and Wim Kimmerer

For decades the San Francisco Estuary, which includes San Francisco Bay and the Sacramento-San Joaquin Delta, has been routinely described as “the largest estuary on the west coast of North America.” This appeared in publications of all types, presumably to emphasize the importance and unique nature of the estuary. But this claim is wrong. While the San Francisco Estuary is quite large, with many unique features, the Salish Sea Estuary is the largest by far.

Estuaries were defined six decades ago as semi-enclosed bodies of water where rivers mix with ocean water. This definition reflected the scope of estuarine studies of that era, which were conducted mainly in large river mouths in Europe and eastern North America. This traditional view of estuaries may have influenced current thinking that the San Francisco Estuary is the largest. But, the definition of what constitutes an estuary has since been broadened to include all coastal enclosed water bodies, including those without substantial freshwater input (for example, Tomales Bay).

The San Francisco Estuary, including its historic wetlands, covers an area greater than 1,900 square miles (Figure). The Salish Sea Estuary—made up of Puget Sound, Strait of Juan de Fuca, Georgia Strait, and Desolation Sound—covers 7,200 square miles, almost four times larger. It is the biggest on the west coast and is even larger than the Chesapeake Bay Estuary.

Sources: Salish Sea Atlas (Flower 2021), Adapting to Rising Tides East Contra Costa Shoreline Flood Explorer. Prepared by Gokce Sencan, PPIC.

Notes: For the San Francisco Estuary, boundaries of a 100-year storm event were used as rough boundaries of the estuary. For the Salish Sea Estuary, the topographic map was adjusted to include elevations up to 2 meters (approximately 6 feet). Actual areas of estuaries might be smaller due to factors like historical modifications and rounding in calculations.

This contrast in size stems from the geologic processes that originally formed the two estuaries.

Most large estuaries are formed by sea level rise. From around 19,000 years to 5,000 years ago, melting of continental glaciers induced a rapid rise in sea level that inundated valleys and canyons formerly occupied by rivers and streams around the globe.

Before the late Pleistocene/Holocene rise in sea level, the ancestral Sacramento River emerged from the Central Valley through the Carquinez Strait and spread out into an alluvial plain in what is now San Pablo and San Francisco Bay. The river then flowed through a narrow canyon at the Golden Gate and formed a large delta adjacent to the Farallon Islands, more than 300’ below present sea level.

By the time early Native Americans arrived, perhaps more than 10,000 years ago, there were vast floodplains, marshes, riparian forests and massive dune fields in what is San Francisco Bay. As sea level rose, brackish and freshwater tidal marsh formed along shorelines throughout the area. About 5,000 years ago, sea level rise pushed into the area near the confluence of the Sacramento and San Joaquin rivers. Here, accumulation of organic material and river sediment kept up with sea level rise—which slowed considerably—forming the Sacramento-San Joaquin Delta.

Until they were subsequently drained or filled, the marshes formed by sea level rise throughout the estuary were the unique characteristic of the relatively shallow San Francisco Estuary. They fueled what must have been one of the most productive estuarine ecosystems in North America, teeming with abundant fish and wildlife (today it has become rather unproductive owing to changes in hydrology, loss of wetlands, and the introduction of countless species from around the world).

The origins of the Salish Sea are quite different, but it is, by modern definitions, an estuary. The glaciers that covered much of the North American continent 25,000 years ago spilled over into the Salish Sea region, carving steep-walled, deep canyons. The ice in some regions was nearly a mile thick, with its base grinding out canyons well below sea level. Around 16,000 years ago these glaciers retreated rapidly, completely disappearing as the oceans began to rise and flood glacial outwash sediments in Juan de Fuca Strait, Puget Sound, and Georgia Strait. Depths in the Salish Sea today reach more than 2,000 feet in some areas. It is one of the deepest estuaries in North America: even deeper than the St. Lawrence Estuary, which is by far the largest. And unlike the San Francisco Estuary, which has one large watershed at its head, many rivers discharge into the former glacial canyons.

The San Francisco and Salish Sea Estuaries are the West Coast’s largest. Their differences in origin shape their hydrodynamics, salinities, and ecology, along with their human uses. But the differences in origins also led to big differences in size. As important as the San Francisco Estuary is to the region’s history, economy, culture, and biodiversity, it is not the biggest. That crown goes to the Salish Sea Estuary.

Jeffrey Mount is a senior fellow at the Water Policy Center, Public Policy Institute of California and founding director at the UC Davis Center for Watershed Sciences. Wim Kimmerer is Estuary and Ocean Science Center Research Professor, San Francisco State University, Romberg Tiburon Campus.

Further reading

Johnson, K. A. and G. W. Bartow, eds. 2018. Geology of San Francisco, California, United States of America. Association Engineering Geologists, Geology of Cities of the World Series.

Lasmanis, R. and E. S. Cheney, eds. 1994. Regional Geology of Washington State. Washington Division of Geology and Earth Resources, Bulletin 80.

Malamud-Roam, F., M. Dettinger, L. B. Ingram, et al. 2007. Holocene Climates and Connections between the San Francisco Bay Estuary and its Watershed: A Review. San Francisco Estuary and Watershed Science, 5 (1).

McLusky, D. S. and M. Elliott, M. 2004. The Estuarine Ecosystem: Ecology, Threats and Management. New York: Oxford University Press.

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The 2020-2023 drought continues for a fourth year?

by Jay Lund

After three years of drought and two dry months, plus two wet weeks, into California’s “wet” season for 2023, California has become unsettlingly settled into this long drought.  Most cities have decreased their water use, some more than others.  Agricultural fallowing has been modest statewide, but large in the Sacramento Valley, with major economic effects in areas depending on rice-growing.  Impacts to native fish and forests have been accumulating, and are dire in some cases.

What is California’s water situation in early December 2022?

What are some drought lessons so far?

What are prospects and preparations for additional dry years?

Storage in Major Surface Reservoirs

Reservoir levels remain low, but within California they are slightly improved from last year at this time.  Nevertheless, there is little surface water reserve to be drawn down if this winter remains dry, and much of that would be needed for Delta outflows to keep the Delta freshish this coming summer.

The ongoing depletion of lower Colorado River water storage means that overall storage available to California is diminished (perhaps including any remaining California water “banked” in the Colorado River basin), and embroils California with increasingly dire Colorado River issues, especially for the Salton Sea.

The immense Colorado River reservoirs have been draining rapidly, about 3 million acre-ft in the last year, to supply about a third of water use in the lower basin and Mexico (about 9 maf). Continued drawdown in these reservoirs could jeopardize the ability to use some dam outlet structures this coming summer.

The good news is these low reservoir levels make flooding less likely this water year, so far at least.

Surface Storage as of October 31, 2022 (water year 2023):

Precipitation so far

It remains too soon to say much about precipitation for the 2023 water year.  After the first 2 months, precipitation is currently 85% of average for northern California.  So far, it has not been wet, but there is time for this to change, with the wettest months of the water year still ahead. The last week has put some water in this wet season, but the water year is still young.

Snowpack so far – Very early, but with the last week or so of storms, California is at 150% of average for this time of year.  An unusual time recently where snow is above average and total precipitation is a bit below average.

Drought damages so far

Just before Thanksgiving, a group led from UC Merced produced an insightful report on the impacts of this drought on agricultural water use, production, and economic performance (Medellin-Azuara et al. 2022).  The table below summarizes from this report, and adds results from the worst two years of the previous drought (from Howitt et al. 2014, 2015).

Condensed Summary of Recent Drought Impacts to Agriculture:

Note: *2014 and 2015 estimates were done using somewhat different methods and baselines, and not corrected for inflation, and so are only roughly comparable.

Some pretty interesting preliminary results stand out (highlighted in the table), which are discussed more in the original reports:

  1. All four drought years were similarly dry overall, but 2015 was the worst.
  2. There was a big and unusual shift of surface water supply reductions in 2022 to the Sacramento Valley from the Tulare basin, helping explain the large fallowing of rice lands in the Sacramento Valley in 2022.
  3. Additional groundwater pumping due to drought seems to have diminished in the post-SGMA drought years, unless this difference stems from differences in estimation methods. (I’ll be hopeful for now.)
  4. Net water shortages were more balanced across river basins in the 2021-22 drought years, shifting fallowing more to the Sacramento Valley from the Tulare basin.
  5. Economic losses in terms of value added from crop and livestock production seem pretty similar across droughts, but job losses were a little larger recently.
  6. These newer agricultural drought impact studies are more complete.

Some of these differences might be due to differences in methods and baselines, especially between the two droughts.  We’ll have to see how more detailed post-drought analyses come out.  It would be nice to see such regular assessments on ecological and rural community drought impacts.

The quantities of water shortages and land fallowing during these drought years is roughly what we should expect to see permanently with the implementation of SGMA. 

Prospects for another dry year

The likelihood of additional dry years is high enough to prepare for more drought.  Low reservoirs and declining groundwater make such preparations even more prudent.  DWR’s minimal initial State Water Project water allocations for the coming year are along this line.

DWR recently released an interesting survey of urban water shortage likelihoods for next year.  There was widespread expectation of an additional dry year, with quite a few agencies expecting cuts in their regular water sources.  However, of hundreds of sizable urban water suppliers, very few expected great difficulty in accommodating these water source reductions, having made preparations for alternative sources (from groundwater, purchases from farmers, additional water conservation, etc.).  Urban areas appear to be mostly well prepared, as they should be.  Urban water use supports over 90% of California’s economy and population, while using about 10% of its water.

Groundwater levels are declining.  DWR’s new SGMA website shows local and regional trends in groundwater levels (and is a great advance in groundwater data communication).  For the Central Valley, there continues to be sizable declines in groundwater levels in many areas, particularly the San Joaquin Valley and now in parts of the Sacramento Valley.  The need to replenish the additional pumping of this drought, as well as accumulating overdraft since 2014, during the hopefully coming wet years will extend the agricultural impacts of this drought for many years to come, especially if 2040 sustainability targets are to be met.

Rural communities often struggle in drought and from accumulating groundwater contamination.  State aid seems more available and organized than in previous droughts.  But we still have a long way to go on these problems.

Ecosystems impacts of drought remain California’s sector with the least drought management success.  For waterbirds, we seem relatively well organized and mostly successful.  But not for most fish and forests, with post-drought impacts extending for many years from wildfires and more species becoming more endangered.

What to do?

The previous drought highlighted the need to manage groundwater and resulted in California’s Sustainable Groundwater Management Act.  This drought confirms the need to move solidly and deliberately to implement this law at the aquifer level, which will reduce irrigated acreage by 500,000 – 1,000,000 acres permanently.  This will be painful, but necessary for long-term rural health, prosperity, and ecosystems across drought and wetter years.  State and county education and development programs can help ease and accelerate this unavoidable transition.

This drought highlights the growing urgency and unavoidability of reducing agricultural and urban water uses, and the needs to rationalize environmental water management and rural water supplies. 

In the meantime, stay calm and hopeful, but prepare for both floods and drought, as usual.

Further reading

Precipitation data: https://cdec.water.ca.gov/precipapp/get8SIPrecipIndex.action

Reservoir data: https://cdec.water.ca.gov/reservoir.html

Groundwater data: https://sgma.water.ca.gov/CalGWLive/#groundwater

Here is a data garden to play in:  http://cdec.water.ca.gov/reportapp/javareports?name=8STATIONHIST

Medellín-Azuara, J., et al. (2022). Economic Impacts of the 2020-2022 Drought on California Agriculture (2022). A report for the California Department of Food and Agriculture. Water Systems Management Lab. University of California, Merced 35p. Available at http://drought.ucmerced.edu

Howitt, R.E., D. MacEwan, J. Medellín-Azuara, J.. Lund, D.A. Sumner (2015). “Economic Analysis of the 2015 Drought for California Agriculture”. Center for Watershed Sciences, University of California – Davis, Davis, CA, 16 pp.

Howitt, R.E., Medellin-Azuara, J., MacEwan, D., Lund, J.R. and Sumner, D.A. (2014). Economic Analysis of the 2014 Drought for California Agriculture. Center for Watershed Sciences, University of California, Davis, California. 20p.

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

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Managing source water for maximum benefit in a challenging climate

By Amber Lukk and Ann Willis

Figure 1. A site in the study reach of the Little Shasta River during summer baseflows. (Image credit: Amber Lukk).

In drought-prone northern California, limited water resources, private water rights allocations, and inefficient transport and use of water resources causes tension between freshwater conservation and private landownership (Garibaldi et al. 2020, Vissers 2017). In the face of a changing climate, drought curtailments will likely become more frequent, ratchetting stress on all water users (Vissers 2017). From an engineering perspective, efficiently managing water rights as arid landscapes become drier and less predictable will be essential to preservation of working landscapes and the environment.

Water purchases and leases are a common tool for securing water rights for environmental purposes. California recently considered a budget proposal to allocate $1.5 billion to buy-back private agricultural water rights to mitigate drought and support ecological uses (Bork et al. 2022). However, water right purchases can be incredibly expensive, and understanding which water rights are most likely to achieve maximal environmental benefit is vital for optimized management. Especially in coldwater habitats, the quality of water sources included in buy-backs will determine success of such efforts.

In our recent study (Lukk et al. In Press), we explore these concepts using a case study of a stream where water rights affect both spring-fed and surface water sources. The study focused on restoration of a portion of the Little Shasta River (Siskiyou County, Northern California) through reconnection of Evans Spring. This natural coldwater spring was historically a tributary to the Little Shasta, but is currently diverted for agricultural use. In the study, we explore effects of increasing stream flow using alternative water sources (e.g., in-stream runoff versus off-channel springs) to enhance coldwater habitat along a working cattle ranch.

Of the simulated scenarios, piping water directly from Evans Spring to the Little Shasta showed the greatest thermal benefits, with a maximum temperature reduction of 2.7°C. This scenario (Piping Scenario B) would provide substantive ecological benefits, especially for salmonids of conservation concern. The addition of surface water runoff, however, did not provide thermal benefits to the Little Shasta River. But while piping spring water provided the largest temperature benefit, this same strategy sacrifices potential benefits of off-channel habitat and restoration of the historical spring-fed channel. The trade-offs associated with piping versus historical channel restoration are important, as one option provides immediate benefit to existing habitat during current conditions when extreme low flows and warmer stream temperatures occur during the summer; the other reflects a more long-term conservation strategy.

No matter which option is pursued, the implications of these findings are that the source of water transfers is vital to success of an environmental water dedication. Water management practices aimed at increasing quantity of water dedications often overlook water quality in favor of an emphasis on quantity alone. When planning water inputs to a coldwater ecosystem, especially for the purposes of conservation, the water quality of the source water should be taken into consideration. Natural coldwater sources have considerable value for California’s native ecosystems, whereas their thermal quality is of little value for agricultural uses (Garbach et al. 2014). In contrast, other dedications may increase the amount of water available to streams, but result in little benefit because they have marginal ecological quality.

Figure 2. Results from the temperature model showing the differences in water temperature between the baseline measurement and the projected values from each alternative management scenario.

With the challenging unpredictability of freshwater resources, understanding the best possible uses for high-quality coldwater sources may provide the greatest benefits to the environment as well as adjacent working landscapes. For coldwater ecosystems, preservation of natural thermal regimes will be key to conservation efforts in the face of a changing climate (Willis et al. 2021). Prioritizing different water sources and when to use them may provide considerable benefits for the future of water resource and stream management in California.

Amber Lukk is an Assistant Specialist at the Center for Watershed Sciences. Dr. Ann Willis was a Senior Research Engineer at the Center for Watershed Sciences and is currently the California Regional Director at American Rivers; her research focuses on water management for stream conservation in working landscapes.

Further Reading:

Börk, K., A.L. Rypel, S. Yarnell, A. Willis, P. Moyle, J. Medellin-Azuara, J. Lund, and R. Lusardi. 2022. Considerations for developing an environmental water right in California. https://californiawaterblog.com/2022/06/12/considerations-for-developing-an-environmental-water-right-in-california/rBlog

Garbach, K., Milder, J.C., Montenegro, M., Karp, D.S., and DeClerck, F.A.J. 2014. Biodiversity and ecosystem services in agroecosystems. Encyclopedia of Agriculture and Food Systems 2: 21-40. https://doi.org/10.1016/B978-0-444-52512-3.00013-9

Garibaldi, L.A., F.J. Oddi, F.E. Miguez, I. Bartomeus, M.C. Orr, E.G. Jobbagy, C. Kremen, L.A. Schulte, A.C. Hughes, A.C., C. Bagnato, G. Abramson, P. Bridgewater, D.G. Carella, S. Diaz, L.V. Dicks, E.C. Ellis, M. Goldenburg, C.A. Huaylla, M. Kuperman, H. Locke, Z. Mehrabi, F. Santibanez, and C.D. Zhu. 2020. Working landscapes need at least 20% native habitat. Conservation Letters 14: e12773. https://doi.org/10.1111/conl.12773

Lukk, A.K., R.A. Lusardi, and A.D. Willis. In Press. Water management for conservation and ecosystem function: modelling the prioritization of source water in a working landscape. Journal of Water Resources Planning and Management.

Vissers, E. 2017. Low Flows, High Stakes: Lessons from Fisheries Management on Mill, Deer, and Antelope Creeks During California’s Historic Drought. Hastings Environmental Law Journal 23:169. https://repository.uchastings.edu/cgi/viewcontent.cgi?article=1026&context=hastings_environmental_law_journal

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

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The Flow of California Water Policy – A Chart

by Jay Lund

California water policy is often discussed and depicted as being impossibly complex.  In its essentials, it can be seen much more simply, as in the flow chart below.  Without extreme events (such as floods and droughts), the policy process would be simpler, but ironically less effective, and less well funded.

California’s remarkable water history shows that frequent extreme events have activated enough innovation and preparations over 170 years such that floods, droughts, and earthquakes are now much less threatening to California’s population and economy.  However, frequent failures have not yet motivated adequate preparation and management for ecosystems and rural water supplies.

Given predictions of climate and ecological disasters, the future looks simultaneously bright, terrible, and worse for those not prepared.

Further reading

Pinter, N., J. Lund, and P. Moyle. “The California Water Model: Resilience through Failure,” Hydrological Processes, Vol. 22, Iss. 12, pp. 1775-1779, 2019.

Dynamic inaction – https://www.thedailybeast.com/when-in-doubt-mumbledynamic-inaction-may-be-our-best-hope; https://www.youtube.com/watch?v=EcDvJTazDd0

Yes Minister – https://en.wikipedia.org/wiki/Yes_Minister

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