The rapid invasion of Mississippi silverside in California

by Peter B. Moyle

Mississippi silversides sampled from South San Francisco Bay.
    Photo by Jim Ervin.

The Mississippi silverside (Menidia audens[1]) is one of the most abundant fishes in the San Francisco Estuary and in the fresh waters of California in general. As the name indicates, it is not native to the state but was introduced into Clear Lake, Lake County, in 1967, from which it quickly spread widely, via the California aqueduct system and through angler introductions as a bait and forage fish (Moyle 2002). It is a small fish, 7-12 cm (3-4 inches) adult length but typically occurs in large schools. Its impact on native fishes is poorly understood but is most likely negative. This blog tells the story of how it came to be introduced, as a classic example of the Frankenstein Effect, where a well-intentioned, science-based introduction created an out-of-control monster. I then discuss the extent of its spread, including into marine environments, and attempt to explain why it has been so successful in California and why it is probably having negative impacts on native fishes.

The silverside was brought to California in 1967 from Lake Texoma, Oklahoma, as a joint project of the Lake County Mosquito Control Agency and the California Department of Fish and Game (as it was known then) (Cook and Moore 1970). The goal was permanent control of the Clear Lake gnat (Chaoborus astictopus). This non-biting gnat, once an important component of the food web of Clear Lake, was regarded as a nuisance species because in summer, adults emerged from the lake in enormous numbers at night and were attracted to electric lights. Gnat hatches restricted or interfered with barbeques and other important human outdoor activities.

As a result, starting in 1949, TDE (a relative of DDT) was applied to the entire 180 km2 (68 mi 2) lake. The application was deemed a success until 1957, when concern over the detrimental, cumulative effects of TDE on birds and people shut the program down. This problem was made famous by Rachel Carson (1957) in Silent Spring, who used Clear Lake as an example; she said: “Here the problem was resolved in favor of those annoyed by gnats, and at the expense of an unstated…risk to all who took food and water from the lake (p 59).” The response was, in 1962, to switch to lake-wide application of methyl-parathion (Prine et al. 1975). I watched the last application of this pesticide in 1973 and was awed by seeing large barges loaded with barrels of pesticide being towed back and forth across the lake, leaving a toxic wake. This event was the last application because parathion was not working well, apparently due to increased pesticide resistance on the part of the gnat. So, the gnat problem returned and the search was on for a ‘biological control’ which presumably would be less harmful than chemical control. The choice of an agent settled on the Mississippi silverside.

(Top) Mississippi silverside and (bottom) map showing rapid spread in California, 1967-84. It is no doubt present now in many other bodies of water. Drawings by Chris M. van Dyck, from Moyle (2002).

The silverside seems to have been chosen because it was a known planktivore/insectivore, had a one-year life cycle so could build up populations quickly, and could tolerate a wide range of temperatures and salinities. It was also readily available. It quickly became one of the most abundant fish species in the lake. This was demonstrated by our catches in the 30 foot long, quarter inch mesh, minnow seines that my colleague Hiram Li and I used, with students, to sample shallow water during a summer field course. In order to return captured fish to the water as quickly as possible, each student determined how many fish were in a handful and then reported counts in “standard handfuls,” which were converted to rough numbers. Hundreds of fish were captured in many of the hauls.

Unknown at the time of introduction was a feature that made silversides even more likely to be able to control the gnat population. While silversides were extremely abundant in shallow water during the day (littoral zone), at night they were scarce in our seine hauls. We found that silversides were moving off-shore at night, into the pelagic zone. This movement occurred at the same time as the nocturnal gnat larvae were emerging from the bottom of the lake to feed on zooplankton (Wurtsbaugh and Li 1985). As a result, gnats became scarce because of silverside predation. From a biological control perspective, the introduction thus was successful; the gnats at least have not been a problem since then. However, the effect that silversides have had on the Clear Lake ecosystem overall (Eagles-Smith et al. 2008) and to other systems they have subsequently invaded is not well understood but appears to be negative.

The rapidity with which silversides moved from Clear Lake and spread is impressive. I first collected them in lower Cache Creek, the outlet of Clear Lake, and Putah Creek in 1972. By 1975 they were well established in the SF Delta and by 1981 they were abundant in a number of coastal and southern California reservoirs (Moyle 2002). Subsequently, they have spread to most coastal streams in southern California, from the San Gabriel River on north. Swift et al. (2014) indicate that much of this recent dispersal has been through marine waters along the California coast, from the large populations now present in some estuaries. Their ability to survive in marine environments indicates that they should be expected in other estuaries and coastal environments, as well as in freshwater habitats. For example, UC Davis scientist Levi Lewis and his crew have found silversides to be one of the most abundant fishes in south San Francisco Bay, with occasional population increases (e.g., 2020) that have been characterized as fish “tsunamis” (L. Lewis, pers. comm. and

In the San Francisco Estuary, they occur in water ranging from fresh to near-marine. In the Delta they are most abundant in the warm (25-30 degrees C), turbid water that occurs in summer when inflows are low (Mahardja et al. 2016). In South Bay, they live under warm, near-marine conditions and coexist with brackish and marine species. If their behavior in the estuary is the same as that in Clear Lake, then they are interacting with other fishes in both the littoral (inshore) and pelagic (offshore, open water) zones. It may be significant that, in the Delta, silversides have increased, while abundance of other plankton feeding fishes have decreased (Mahardja et al. 2016). In particular, the decline of Delta smelt and longfin smelt may be related to silversides foraging in shallow water habitats where the smelt spawn. Their eggs and larvae would be easy prey. Moyle and Bennett (1996) note that under experimental conditions silversides can be effective predators on fish larvae of other species. Likewise, even when smelt are scarce, delta smelt DNA can be detected in guts of some silversides (Baerwald et al. 2012). Silversides themselves are frequent prey for non-native predators, such as largemouth bass, white and black crappie and other inshore fishes. It remains to be seen whether or not they have reciprocal interactions with these species, such as embryo and larval predation.

In short, Mississippi silversides are a hyper-invasive fish species. They can colonize new, diverse habitats rapidly and quickly become abundant. They have demonstrated extreme adaptability to highly altered habitats in California, including polluted or otherwise altered lakes, streams, and estuaries, under salinities ranging from fresh to salt. They co-occur with a diverse array of fishes including both potential predators and prey. It therefore is important to discover what regulates silverside populations and how to reduce negative effects where possible. Understanding their biology and interactions with other species (more than fishes!) is especially important for the San Francisco Estuary where millions of dollars are being spent for native fish conservation. Their story is also a good lesson in why bringing new species of any sort into California should be avoided if at all possible. It is predictable that new introductions will have unexpected consequences.

[1] The Mississippi silverside has been considered by many as part of the widespread Inland silverside (Menidia beryllina) complex (e.g., Moyle 2002), but recent studies indicate it is a distinct freshwater species. See discussion in Fluker et al. (2016).

Peter Moyle is an emeritus professor in the Center for Watershed Sciences and Department of Wildlife, Fish and Conservation Biology, University of California, Davis.

Further reading

Baerwald, M.R., Schreier, B.M., Schumer, G. and May, B., 2012. Detection of threatened Delta Smelt in the gut contents of the invasive Mississippi Silverside in the San Francisco Estuary using TaqMan assays. Transactions of the American Fisheries Society141(6): 1600-1607.

Cook Jr, S.F. and Moore, R.L., 1970. Mississippi silversides, Menidia audens (Atherinidae), established in California. Transactions of the American Fisheries Society 99(1):70-73.

Eagles-Smith, C.A., Suchanek, T.H., Colwell, A.E., Anderson, N.L. and Moyle, P.B., 2008. Changes in fish diets and food web mercury bioaccumulation induced by an invasive planktivorous fish. Ecological Applications 18(sp8): A213-A226.

Fluker, B.L., Pezold, F. and Minton, R.L., 2011. Molecular and morphological divergence in the inland silverside (Menidia beryllina) along a freshwater-estuarine interface. Environmental Biology of Fishes91(3): 311-325.

Mahardja, B., Conrad, J.L., Lusher, L. and Schreier, B., 2016. Abundance trends, distribution, and habitat associations of the invasive Mississippi Silverside (Menidia audens) in the Sacramento–San Joaquin Delta, California, USA. San Francisco Estuary and Watershed Science14(1).

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

Moyle, P.B., and Bennett W.A. 2008. The future of the Delta ecosystem and its fish. In: Lund J, Hanak E, Fleenor W, Bennett W, Howitt R, Mount J, Moyle P. 2008. Comparing futures for the Sacramento–San Joaquin Delta. San Francisco (CA): Public Policy Institute of California. Technical Appendix D. Available from: http:// pdf

Prine, J.E., G. G. Lawley, and P.B. Moyle (1975). A multidisciplinary approach to vector ecology at Clear Lake, California. Bulletin of the Society of Vector Ecologists 2: 21-31.

Swift, C.C. Howard, S., Mulder, J., Pondella, D.J., and T.P. Keegan. 2014. Expansion of the non-native Mississippi Silverside, Menidia audens (Pisces, Atherinopsidae), into fresh and marine waters of coastal Southern California. Bulletin of the Southern California Academy of Sciences 113(3):153-164,

Wurtsbaugh, W. and Li, H., 1985. Diel migrations of a zooplanktivorous fish (Menidia beryllina) in relation to the distribution of its prey in a large eutrophic lake 1. Limnology and Oceanography 30(3): 565-576.

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Explaining water units to real people (who like basketball)

by Jay Lund

It’s March madness once again as we try to explain water conditions in California to real people in the midst of additional basketball madness.

We all enjoy and suffer with basketball.  This commonality can make it a useful unit of volume among the many units of volume used for water.

A basketball has the volume of about 1/4 cubic feet (4 basketballs per cubic foot).  So a flow of 1,000 cubic feet per second (cfs) has a volume equivalent of having 4,000 basketballs coming at you every second. 

An acre-foot (af) is a volume one foot deep over an acre of area.  It has a volume of 43,560 cubic feet or 325,850 gallons, or 174,240 basketballs.

One cfs flowing for one day (24 hours) discharges almost 2 acre-feet (1.98) of volume (348,480 basketballs/day).

A million gallons per day (mgd) has the same volume as 1.87 million basketballs per day. (There are 7.48 gallons per cubic foot)

A cubic meter (m3) is about 35.3 cubic feet, which equals about 141 basketballs of volume.

Here is a California water units translator (rounded some, highlighting the most useful conversions):

For California’s water infrastructure, the Sacramento Valley flood bypass system has a conveyance capacity of almost 750,000 cubic feet per second (600,000 cfs in the lower Yolo Bypass and 130,000 cfs in the Sacramento River main stem).  This is equivalent to the volume of 3 million basketballs per second (260,000 mega-basketballs per day – mbd).

California’s largest reservoir has a storage capacity of 4.55 million acre-feet, or almost 800 billion basketballs.

In terms of water use, most of California’s roughly 8 million acres of irrigated agriculture uses 3-4 acre-ft per acre annually (520,000-700,000 basketballs per acre/year) each year totaling about 26 million acre-ft per year, or 4.5 trillion basketballs of water per year.

California’s urban water users, almost 40 million people, use roughly 140 gallons per capita per day (74 basketballs/person-day or 27,100 basketballs/person-year), totaling about 7 million acre-ft per year, or 1.2 trillion basketballs of water per year of urban water use.

Maybe this basketball lens for California water use is helpful for “#SciComm” junkies and others at pains to communicate scienterrific things to real people.  As a civil engineering undergraduate student, it seemed that a third of all my calculations were unit conversions. We might have learned more with a single standard international unit such as basketballs (since metric hasn’t caught on much here).  (Still, if I made a mistake in the table, let me know.)

Welcome to March Madness!

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Hiding in plain sight: newly described freshwater fishes from the Los Angeles area and elsewhere in California

By Peter B. Moyle, Nicholas Buckmaster, and Yingxin Su

Lahontan Speckled Dace (left) and Santa Ana Speckled Dace (right), showing typical body shape and coloration of dace of the genus Rhinichthys, among rocks in which they can hide to avoid predators. Photos by Thomas L. Taylor and Jennifer Pareti. The fish shown are about three inches long.

Lulu Miller in her wonderful 2020 book, Why Fish Don’t Exist, describes how fish exist to us humans only if they have been assigned proper names. The Santa Ana Speckled Dace is a local case in point. This small fish has been living in southern California streams for about a million years, yet has been largely ignored because it was assumed to be just another population of the Speckled Dace. This dace has been regarded as the most widely distributed ‘true’ freshwater fish species in western North America, found in streams and lakes from Canada to Mexico and California. Speckled Dace from throughout this vast range all look alike – blunted-snouted minnows with a tiny mouth and eyes, a nearly cylindrical body, wide caudal peduncle, and active behavior. They are often covered with speckles that coalesce into a dark band, either under or through the eyes. They typically locate under rocks during the day and emerge to forage on invertebrates at night, so are easy to overlook.

This blog is an announcement that the Santa Ana Speckled Dace exists, and now has an official name, which includes its new scientific name, Rhinichthys gabrielino (Moyle et al. 2023). Rhin-ichthys means “snout-fish” while gabielino honors the native peoples who lived comfortably with Santa Ana Speckled Dace for thousands of years. Today this fish is missing from about half its historic habitats in the Los Angeles, San Gabriel, and Santa Ana rivers [see map below]. Because it now has an official name, it is more likely to gain the attention of conservation agencies, much like the Santa Ana Sucker (Pantoseus santannae), which is listed as a Threatened species under state and federal Endangered Species Acts. A petition to similarly list the Santa Ana Speckled Dace has been filed by the Center for Biological Diversity. After thriving in the Los Angeles Region for a million years, disregard for its welfare by people may lead to its extinction in the next 50 years or less.

Moyle et al. (2023) used genomic (DNA) analyses as a major basis for providing, not only a name for Santa Ana Speckled Dace, but for all dace populations in California. There are now two other species of Speckled Dace in California, each with three subspecies (below). All are cryptic and similar, so hard to tell apart, unless you look at their DNA.

Santa Ana Speckled Dace, Rhinichthys gabrielino, new species

Desert Speckled Dace, Rhinichthys nevadensis, new common name

            Lahontan Speckled Dace, R. nevadensis robustus, new combination

            Amargosa Speckled Dace, R. nevadensis nevadensis, new combination

            Long Valley Speckled Dace, R. n. caldera, new subspecies

Western Speckled Dace, Rhinichthys klamathensis, resurrected species

            Klamath Speckled Dace, R. klamathensis klamathensis new combination

            Sacramento Speckled Dace, R. klamathensis achomawi new subspecies

            Warner Speckled Dace R. klamathensis goyatoka new subspecies

Top: Santa Ana Speckled Dace male in spawning colors, by Jennifer Pareti CDFW. Bottom: maps showing past and present distribution of Santa Ana Speckled Dace, in relation to the location of public lands. Map provided by Center for Biological Diversity.

What follows is an explanation of how we arrived at these names. First, I determined which populations of dace in California might merit species/subspecies status based on review of an abundance of previous studies. These studies used standard morphometrics and meristics, mitochondrial DNA and knowledge of the geology and zoogeography of the western USA to try to find names for the scattered Speckled Dace populations, mostly without success. The literature review showed that Speckled Dace in California were indeed cryptic species, with no obvious characters separating populations in regions long isolated from one another.

Second, Su et al. (2022) performed an analysis of dace genomics which required obtaining samples of Speckled Dace tissues from likely distinct populations in the state, plus some outside populations for comparison. The basic hypothesis tested was that Speckled Dace in California were divided up into three evolutionary lineages, each representing a separate colonization of California and long isolation from one another: Lahontan, Klamath-Sacramento, Southern California. The results of the genome analysis, using methods described in Su et al. (2022), largely validated these lineages and revealed likely species and subspecies. The determination of species and subspecies was based on phylogenetic trees generated by the analyses. Branches on each tree represent evolutionary lineages leading to isolated populations that we can recognize as species and subspecies.We therefore were able to label lineages with broad genomic separationfrom other lineages as species and geographically isolated lineages with less genomic differentiation as subspecies. See Su et al. (2022) and Moyle et al.(2023) for details on the methods. Once the genomics analysis was finished, Buckmaster reviewed the latest geologic information to see if the geologic history was reflected in the DNA-based branching; it was.

The species and subspecies that came out of this analysis are each distinctive in their own way. The Santa Ana Speckled Dace were the example that opened this blog, so here are some comments on the rest of the speckled dace taxa we described or unveiled. Distribution of each taxon is shown on map at end of text.

Type specimens of four new Speckled Dace species and subspecies, described in Moyle et al. (2023). A. Santa Ana Speckled Dace. B. Long Valley Speckled Dace. C. Warner Speckled Dace, D. Sacramento Speckled Dace. Each individual is about 79 mm (3 inches) total length. Photo and specimens from Museum of Wildlife, Fish, and Conservation Biology, UC Davis.

Desert Speckled Dace is a new common name for all the dace found in the Death Valley-Owens Valley region and over a vast area of the Great Basin, mostly in Nevada and California. The scientific name originally applied only to Speckled Dace in the Death Valley region which our genomics study showed were most closely related to Lahontan Speckled Dace. They tend to be found in any waterway with permanent water, despite the great distances of desert often separating populations. This broad distribution reflects that during the Pleistocene period the region was much wetter and now-dry basins and connecting streams were full of water. Genomics revealed three subspecies.

Lahontan Speckled Dace was originally described as a full species inhabiting much of the Great Basin; it was demoted to a subspecies by later workers, mainly because it could not be told apart using non-genetic techniques from Speckled Dace from other watersheds, such as the Sacramento. It inhabits a wide variety of habitats including Lake Tahoe. Today the Lahontan Speckled Dace is considered to be a subspecies of R. nevadensis, rather than R. osculus.

Amargosa Speckled Dace is the name for dace inhabiting springs, small streams, and ditches in Death and Owens valleys. The geologic history has the Owens and Death Valley regions once connected by the Amargosa River, now mostly dry. All these populations are threatened with extinction from various factors, but only the Death Valley populations are listed under the federal ESA. All should now be included in the listing.

Long Valley Speckled Dace is a new subspecies that is native to small streams and ditches of the Long Valley region. This region was shaped by a volcanic caldera – the result of an eruption that occurred about 750,000 years ago. The scientific name we gave to this fish is consequently R. nevadensis caldera. Today, despite having survived that massive eruption, the Long Valley Speckled Dace is likely the most endangered fish in California. It has just one small population remaining in its native range, in the marshy outflow of a public swimming pool, operated by the Town of Mammoth Lakes. The pool is fed by a hot spring, which formerly flowed directly onto the marsh. A second population lives in a small pond outside the native range, at the White Mountain Research Station, in which everything is artificial including the pumped water supply and the old tires which form the principal cover for the fish. Survival in both places depends on the continuous attention of those who control the water supply (Moyle et al. 2015).

Western Speckled Dace is the name used by Markle (2020) and others for the dace that live in the combined immense watersheds of the Klamath and Sacramento Rivers, plus the Warner Valley and some small coastal drainages in southern California, north of those occupied by the Santa Ana Speckled Dace. This dace was first described as just the Klamath Speckled Dace (hence R. klamathensis) but our genomics study showed that the dace that inhabited streams over a broader area were part of the same evolutionary lineage. See Moyle et al. (2023) for further explanation.

Klamath Speckled Dace are perhaps the most abundant and widespread ‘true’ freshwater fish in the Klamath River watershed in Oregon and California. It has also been introduced into the Eel River, a California watershed previously without Speckled Dace.

Sacramento Speckled Dace so baffled early ichthyologists in California by its similarity to Lahontan Speckled Dace (and others) that it was ignored, even by David Starr Jordan. Jordan was the best-known ichthyologist in the world during his day, who named hundreds of species (Miller 2020). Sacramento Speckled Dace lived in streams close to his doorstep at Stanford University but the best he could do was to say “These California and Nevada forms may be distinct species, but if so, we are unable to define them (Jordan and Evermann 1896:312)”. Sacramento Speckled Dace are abundant and widespread in the Sacramento watershed and managed to colonize rivers as far south as the Santa Maria River. They have disappeared from a number of streams in which they once lived, suggesting that many populations are not secure.

Warner Speckled Dace are known only from streams that flow into the arid Warner Valley, Oregon, including Twelve Mile Creek which has its headwaters in California. The watershed has been heavily invaded by non-native fishes, so the dace (and other endemic fishes) need protection.

Approximate distribution of Speckled Dace species and subspecies in California. Map by Amber Manfree.


Our findings demonstrate the need to conserve the diversity of forms and taxa in this fascinating group of small fishes; if action is not taken to protect them and their habitats, many will disappear. It is therefore important to assign names to the diverse lineages, as we have done for California populations (Moyle et. al. 2023). They all still exist today but only with our sufferance. We can only hope, given the rapid changes taking place on this planet today, that we humans will allow some humble Speckled Dace species and subspecies to survive into the next century and with them the diverse aquatic biota that share their habitats.

Peter Moyle is an emeritus professor in the Center for Watershed Sciences and Department of Wildlife, Fish and Conservation Biology, University of California, Davis. Yingxin Su is a graduate student in the Animal Biology Graduate Group, University of California, Davis. Nicholas Buckmaster is Fisheries Program Supervisor for the Inland Desert Region, California Department of Fish and Wildlife, Bishop, California.

Further reading

Baumsteiger, J., Moyle, P.B., Aguilar, A., O’Rourke, S.M. & Miller, M.R. (2017) Genomics clarifies taxonomic boundaries in a difficult species complex. PLoS ONe, 12 (12), e0189417.

Center for Biological Diversity (2020) Petition to List Three Populations of Speckled Dace (Rhinichthys osculus) in the Death Valley Region under the Endangered Species Act: Amargosa Canyon Speckled Dace, Long Valley Speckled Dace, Owens Speckled Dace. Submitted to US Fish and Wildlife Service, 8 June 2020, 1–48.

Jordan, D.S. & Evermann, B.W. (1896) The Fishes of North and Middle America. Bulletin, US National Museum, 47, Part 1, 1–1240.

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.

Markle, D.F. (2016) A Guide to the Freshwater Fishes of Oregon. Oregon State University Press, Corvallis, Oregon, 140 pp.

Miller, L. (2020) Why Fish Don’t Exist: a Story of Loss, Love, and the Hidden Order of Life. New York: Simon & Schuster, 225 pp.

Moyle, P.B. (2002) Inland Fishes of California, Revised and Expanded. University of California Press, Berkeley, California, 405 pp.

Moyle, P.B., Buckmaster, N. and Su, Y. 2023. Taxonomy of the Speckled Dace species complex (Cypriniformes: Leuciscidae, Rhinichthys) in California, USA. Zootaxa

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

Moyle, P.B., Quiñones, R.M., Katz, J.V.E, & Weaver, J. (2015) Fish Species of Special Concern in California. 3rd Edition. Sacramento, California Department of Fish and Wildlife. Available from: (accessed 8 February 2023)

Su, Y., Moyle, P.B., Campbell, M.A., Finger, A.J., O’Rourke, S., Baumsteiger, J. & Miller, M.R. (2022) Population genomic analysis of the Speckled Dace species complex identifies three distinct lineages in California. Transactions of American Fisheries Society, 151, 695–710.

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Will more wildfire and precipitation extremes mussel-out California’s freshwater streams?

By Andrew J. Lawrence and Andrew L. Rypel

Fig. 1. Graphical overview of the impacts of wildfire runoff on freshwater mussels and native fishes. Image credit: Vlastimil Novak, Lawrence Berkeley National Laboratory.

Apocalyptic scenes of wildfires and floods are now familiar to Californians. However, the ecological impacts from these events remain understudied in California and across the world. Gaps in awareness and understanding on the issue are especially intense for freshwater mussels, whose cryptic and sedentary life-histories belie their importance to freshwater ecosystems and biodiversity (see previous post on freshwater mussels). One difficulty in studying effects of wildfire on freshwater ecosystems is that there is often a “right time in the right place” factor to appropriately conduct the science. For example, researchers and biologists often need to be studying a population or ecosystem before a burn so effects afterwards can be quantified – ideally alongside nearby unaffected control sites. Yet such natural experiments are rare because we never know when and where major wildfires will strike.

The 2020 Dolan Fire in Monterey County became an opportunity to document effects of this ‘one-two punch’ on freshwater mussels and some native fishes, described in our recently published paper (Lawrence et al. 2022). Shortly before the fire began, populations of native freshwater mussels were documented in headwater streams of the Nacimiento and San Antonio rivers in Monterey County, California (Fig. 2A). Species encountered included California floaters (Anodonta californiensis/nuttalliana; Fig. 2D) and western ridged mussels (Gonidea angulata), the latter being a current candidate for listing under the Endangered Species Act. Unfortunately, the excitement that accompanies finding previously undiscovered populations of imperiled species was quickly dampened by the catastrophic wildfires engulfing the landscape. The Dolan Fire burned about 20,432 ha (50,488 acres) above our study site in the San Antonio River headwaters region beginning in August 2020 (Fig. 3) and left behind a severely charred and exposed landscape. The fire was followed by an exceptionally dry period that was finally interrupted by a major atmospheric river that produced 38–51 cm (15–20 in) of rain over three days in late January 2021, resulting in significant hydric erosion across the burned area. Large unseasonal atmospheric rivers on their own (without burns) are already known to harm native fish diversity, including the induction of large fish kills (Rabidoux et al. 2022).

Fig. 2. Photos of the San Antonio River in Monterey County, California, USA, before wildfire in July 2020 (A; photo credit Andrea Adams), (B) the study pool after wildfire and flood in February 2021, (C) sedimentation of entire study pool and growth of algae and new vegetation within the river in August 2021, and (D) a live California floater mussel (Anodonta californiensis/nuttalliana).

What happened to the mussels?

Following the major storm, sediment from wildfire ash and exposed soil nearly filled our entire study site pool, such that the pool’s thalweg (i.e., the deepest point) decreased from 1.77 m to just 0.2 m (Fig. 2B, 2C). While mussels can move throughout some substrates (Watters et al. 2001), the potential interactive effect of volatile compounds and substantial depth of new sediment seemed to exceed survival and movement capabilities. We found no live mussels during post-fire visual and tactile surveys and found no mussel eDNA at the study site (Fig. 3). Although California floaters inhabit diverse aquatic habitats (Jepsen et al. 2012), this population was apparently extirpated by wildfire runoff. The western ridged mussel was not identified at this particular site before the sedimentation; but limited access during the fire and short time until the post-fire survey does not eliminate the possibility that the mussel also occurred elsewhere in this system.

Fig. 3. Study site location (yellow triangle) in the San Antonio River, boundary of Fort Hunter Liggett (black line), and area burned by the Dolan Fire (orange) in Monterey County, California, USA, 2020. Green circles represent positive detection of California floaters (Anodonta californiensis/nuttalliana) from eDNA surveys, while red circles represent no detection.

What about native fishes?

Before the wildfire, we found mature and juvenile Monterey sucker, (Catostomus occidentalis mnioltiltus), Monterey roach (Lavinia symmetricus subditus), and Sacramento pikeminnow (Ptychocheilus grandis) at the site. Even during periods of severe drought, the large and deep pool held stable water levels and was likely a refuge for fishes and other aquatic organisms. During post-wildfire surveys, we saw several dead mature Monterey suckers, while smaller-bodied fishes (Monterey roach and speckled dace [Rhinichthys osculus]) persisted in the shallow waters of the significantly altered stream.

Are freshwater mussels in California doomed?

We don’t think so…yet. But, keeping them around will require our help. More work is needed to identify broader regions and finer-scale stream characteristics most at-risk to wildfire runoff. This need is incidentally also true for other aquatic organisms including fishes, waterfowl, other freshwater invertebrates, aquatic herpetofauna, plants, aquatic mammals, and other dimensions of freshwater biodiversity. For freshwater mussels and other freshwater taxa eking out a living in California’s harsh Mediterranean climate, individuals often need remnant pools as refugia during the dry season (Bogan et al. 2019). Yet as we have seen in the San Antonio River, these pools can be rapidly filled by heavy sedimentation events. In these cases, previously beneficial refugia can quickly become “ecological traps” (Battin 2004). Climate change effects are never simple or straightforward.

Had the rainfall been spread out over weeks or months, perhaps runoff and corresponding impacts on the ecosystem would have been less severe. Unfortunately, this will be a common pattern in the coming century. California’s Mediterranean climate is becoming a more extreme version of itself, with increases in the frequency and intensity of precipitation events, coupled with larger and hotter wildfires overall (Touma et al. 2022). Will the habitat conditions and aquatic organisms of impacted streams return to their previous state? They might get close, but fully recovering would likely take a long time, especially given the long turnover rates of most mussel populations (Haag and Rypel 2011). Knowing how much sediment is too much for mussels to survive will also require further work, as effects can vary among species (Imlay 1972, Brim Box and Mossa 1999). Ultimately, California’s native freshwater mussels need much more research and extensive conservation work. Ironically, the unlisted status of California’s native mussels under the ESA has likely limited opportunities for research and conservation. This may change given petitions to list some native mussel taxa, and their reliance on native fishes in California to reproduce – these host fishes are also declining at alarming rates.

Fig. 4. The San Antonio River study site in Monterey County, CA with receding floodwaters during January 2023. Exposed soils in severely burned areas still contribute sediment to the river. Photo credit: Andrew Lawrence.

Andrew Lawrence is an interdisciplinary ecologist with Colorado State University’s Center for Environmental Management of Military Lands (CEMML). 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.

Further Reading

Battin, J. 2004. When good animals love bad habitats: ecological traps and the conservation of animal populationsConservation Biology 18: 1482-1491.

Blevins, E., Jepsen, S., Box, J.B., Nez, D., Howard, J., Maine, A. and O’Brien, C. 2017. Extinction risk of western North American freshwater mussels: Anodonta nuttalliana, the Anodonta oregonensis/kennerlyi clade, Gonidea angulata, and Margaritifera falcata. Freshwater Mollusk Biology and Conservation 20: 71-88.

Bogan, M.T., Leidy, R.A., Neuhaus, L., Hernandez, C.J. and Carlson, S.M. 2019. Biodiversity value of remnant pools in an intermittent stream during the great California drought. Aquatic Conservation: Marine and Freshwater Ecosystems 29: 976-989.

Box, J.B. and Mossa, J. 1999. Sediment, land use, and freshwater mussels: prospects and problemsJournal of the North American Benthological Society 18: 99-117.

Haag, W.R. and Rypel, A.L. 2011. Growth and longevity in freshwater mussels: evolutionary and conservation implicationsBiological Reviews 86: 225-247.

Imlay, M. J. 1972. Greater adaptability of freshwater mussels to natural rather than to artificial displacement. Nautilus 86: 76-79.

Jepsen, S. C. LaBar, and J. Zamoch. 2012. Anodonta californiensis (Lea, 1852)/Anodonta nuttalliana (Lea, 1838) California Floater/Winged Floater Bivalvia: Unionidae. The Xerces Society for Invertebrate Conservation, Portland, Oregon.

Lawrence, A.J., Matuch, C., Hancock, J.J., Rypel, A.L. and Eliassen, L.A. 2022. Potential local extirpation of an imperiled freshwater mussel population from wildfire runoffWestern North American Naturalist 82: 695-703.

Rypel, A.L. 2022. Losing mussel mass – the silent extinction of freshwater mussels

Silva, V., Abrantes, N., Costa, R., Keizer, J.J., Goncalves, F. and Pereira, J.L. 2016. Effects of ash-loaded post-fire runoff on the freshwater clam Corbicula fluminea. Ecological Engineering 90:180-189.

Swain, D.L., Langenbrunner, B., Neelin, J.D. and Hall, A. 2018. Increasing precipitation volatility in twenty-first-century California. Nature Climate Change 8: 427-433.

The strange, savage life of a freshwater mussel

Touma, D., Stevenson, S., Swain, D.L., Singh, D., Kalashnikov, D.A. and Huang, X. 2022. Climate change increases risk of extreme rainfall following wildfire in the western United States. Science Advances 8: 1-11.

Watters, G.T., O’Dee, S.H. and Chordas III, S. 2001. Patterns of vertical migration in freshwater mussels (Bivalvia: Unionoida). Journal of Freshwater Ecology 16: 541-549.

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A Guide for New California Water Wonks

by Jay Lund

Water is a universal foundation for every problem and opportunity in California.  Most people use it every day, yet even experts with decades of experience don’t know it all.   (Alas, too many advocates and pundits almost don’t know it at all.)  Welcome!

Immense numbers of books and articles have been written on California water.  Here is a selection of some readings and websites useful for folks who want to become California water wonks as serious journalists, students, agency and NGO leaders or workers, consultants new to the area, professors and instructors, or just obsessed members of the public. 

Bon appétit!  

Some General Readings on California Water

The Dreamt Land (2019) by Mark Arax is probably the best single overall work on California water.  It is a wonderful well-written human history with a great deal of context and science woven in.  It was reviewed in CaliforniaWaterBlog.

A list of 14 good wonk-producing readings is at Some springtime reading on California water (2019).  The list is annotated to help you get started.

For folks who want go get deeper into some interesting historical documents, here is another list – Old Readings on California Water (2020).  Oldies but goodies. There are few truly new water ideas in California.

The best 4-pages on California water is probably Joan Didion’s (1977), “Holy Water,” in her book, The White Album (1979). 

Water in the News Websites and Listserves

To keep up-to-date and become regularly exposed to a wealth of details and ideas, there are some good websites and listserves:

Maven’s notebook (The Best single site for aggregation, dissemination, and interpretation!)

DWR’s Water News compilations

Brown & Caldwell WaterNews compilations

Water Education Foundation (tours, events, compilations, public information publications, etc.)

CaliforniaWaterBlog (weekly water essays and findings from UC Davis)

Data and Graphics Websites for California Water Wonks

Many websites present interesting and useful data on water in California, for those who like to follow our floods, droughts, and storms.  Here are a few on some common topics.  The time you take to explore these is worthwhile.  (True wonks will download some data for their own analyses.)

River and Flood Forecasts from California -Nevada River Forecasting Center (CNRFC)

Precipitation (California Department of Water Resources, CDEC)  

Lots of good charts and options here, for all except southern California:

Nice depictions of precipitation forecasts for all west coast –

Snowpack – How much snow is in the mountains for different parts of California relative to earlier years.

Reservoir levels – Take some time to explore this these.

A newer, pretty neat depiction:

US Army Corps of Engineers California flood operations See how some of the major reservoirs are being operated as storms come and go, and in preparation and operation for snowmelt.

Groundwater Live (California Department of Water Resources) – The best California groundwater site that I’m aware of.

California and the World needs more and better water wonks! Go play in the water.

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.  He likes to read and mess around with numbers.

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Green Sturgeon in California: Hidden Lives Revealed From Long-Term Tracking

By Scott F. Colborne, Lawrence W. Sheppard, Daniel R. O’Donnell, Daniel C. Reuman, Jonathan A. Walter, Gabriel P. Singer, John T. Kelly, Michael J. Thomas, and Andrew L. Rypel

Fig. 1. An adult Green Sturgeon Acipenser medirostris. CDFW photo, taken by Mike Healy.

You gotta respect fishes that have been around since the dinosaurs, such as the 27 described sturgeon species. Unfortunately, the majority of these fishes currently face a high risk of extinction. Extinctions happen to these gentle giants. The Chinese Paddlefish went extinct following a long-term decline – finished off by the Three Gorges Dam (Zhang et al. 2020). California has two sturgeon species: White Sturgeon and Green Sturgeon. Recently, Schreier et al. 2022 published a blog on the status of White Sturgeon in California focused on impacts from a mass die off during a red tide event in the summer of 2022. Here we focus on the southern distinct population segment (DPS) of Green Sturgeon (Fig. 1), a federally ‘threatened’ species under the US Endangered Species Act. Green Sturgeon are fully anadromous and live primarily in the ocean as adults, but spawn in freshwater rivers in the spring. High-quality habitat is essential for the life-history of native fishes, especially in California (Sass et al. 2017, Hause et al. 2022). Yet despite their large size and historical importance to many communities, there is still much we don’t know about Green Sturgeon biology in California.

Fig. 2. Acoustic receivers through San Fransisco Bay and the Sacramento-San Joaquin watershed 2006-2018.

Acoustic telemetry is a method for tracking animals using ultrasonic tags that transmit unique identification codes via sound waves in the water, combined with listening devices, called receivers, that decode these sounds and record when they are heard. Acoustic telemetry has become commonplace for studying aquatic animal movements because GPS tags are not well suited for animals that do not frequently surface, particularly because GPS signals do not transmit well through water. In California, acoustic telemetry has been used to study fish movements since at least 2001 with construction and maintenance of a large array of receivers throughout the Sacramento River and Sacramento-San Joaquin Delta (Fig. 2). In total, more than 450 km of the Sacramento River have been covered in acoustic receivers. This array was supported by several state and federal agencies in California that foresaw the great potential of telemetry approaches to advance understanding and management of our native fish populations. A team of researchers at UC Davis, led by A. Peter Klimley, originally developed and maintained this array for many years. 

We recently published a paper (Colborne et al. 2022) synthesizing 12 years of acoustic telemetry data for Green Sturgeon in the Sacramento River and Sacramento-San Joaquin Delta. It had been observed that enough telemetry data had accumulated that a synthesis science effort could contribute additional value beyond the original purposes of previous studies. Our team included academic researchers from across the US, international collaborators, and leaders from state and federal agencies in California. This research advances our understanding of the life-history and specifically migration timing of Green Sturgeon in several ways. First, we showed that during spring months (Fig. 3, left), there is a single pulse of upriver migrants towards spawning grounds in the upper Sacramento River, consistent with other observations (Steel et al. 2018). The upriver migration occurs during March and April, but fluctuates within that time range across years. Second, Green Sturgeon return to the ocean in two groups separated in time by several months (Fig. 3, right). Earlier returning sturgeon begin migrating downriver during mid-June; however, the second group over-summers in the river where they remain until mid-December. 

Fig. 3. Distributions of (left) swim-up and (right) swim-down dates for Green Sturgeon.
Fig. 4. A Green Sturgeon sampled during the fall in Suisun Bay. Photo by Davis Dominquez of USFWS.

It’s not yet known if these two migration groups reflect divergent life-history strategies, sexual differences in migration timing, or fish becoming increasingly trapped upriver by low summer flows. The timing of outmigration in both groups is significantly related to river flow conditions such that early migrants are cued by higher discharge values in the spring/early summer whereas late migrants begin outmigration when the hydrograph begins to rise in the fall. Interestingly, downriver migrants show some fidelity to the timing of downriver migrations, such that late migrants are statistically more likely to be late migrants during their second monitored spawning year. When migrants did change the timing of outmigration,they tended to migrate late when flow rates during the early period of the year were low compared to the years when they migrated early. Combined, our findings suggest water managers may have a capacity to help sturgeon migrate, potentially by strategically releasing pulse flows from dams. The idea of sturgeon pulse flows may ostensibly seem new, but we are already accustomed to managing flows for Pacific salmon, which also have distinct life-history variations based on run timing.

Our work exposes how synthesis science of telemetry data specifically has important utility in today’s matrix of California water science activities. Broad-scale collaborative efforts like these deliver actionable science to decision makers concerned with the decline of sturgeon and other native species. Few studies in California have leveraged prior large and long-term investments in the core array, tags, and various specific studies. Individual telemetry studies are exceedingly expensive, considering the costs of tags, personnel, receivers, transportation, etc. Oftentimes, there is “more juice in the orange,” and investments in synthesis and team science groups allows full value extraction from prior investments. Furthermore, the high expense of these studies may limit the intellectual capacity that can be applied to these problems by restricting access to data and hypothesis testing (Nguyen et al. 2017). Open science and team science help solve these problems. And we are not the only ones – there are synthesis science efforts popping up all around the California water world. This is a great thing. Hopefully, using all our efforts and ways of knowing, we can generate information to keep sturgeon and other native species alive and well in California for a long time to come.

Acknowledgements. This synthesis work was supported by a grant from the Delta Stewardship Council, Delta Science Program, and the US Bureau of Reclamation (award: 18204; Synchrony of native fish movements). We recognize A.P. Klimley for his leadership and efforts in organizing the initial “core 69 kHz array,” and CDFW for funding it. We also recognize the contributions of numerous people in the UC Davis Biotelemetry Laboratory over the years that made this extensive Green Sturgeon dataset a possibility. The number of people involved with these projects across multiple agencies and institutions is too numerous to list everyone here, but we express a deep gratitude to anyone that has collected data, turned on tags, tagged fish, maintained receivers, downloaded data, curated data etc.

Scott F. Colborne was a postdoctoral researcher at University of California Davis and is currently a Research Specialist at the Quantitative Fisheries Center at Michigan State University. Lawrence W. Sheppard is a Research Scientist at the Marine Biological Association in the UK, Daniel R. O’Donnell was a postdoctoral researcher at University of California Davis and is currently a Senior Scientist at CDFW. Daniel C. Reuman is a Professor in the Department of Ecology and Evolutionary Biology at the University of Kansas and a Senior Scientist at the Kansas Biological Survey. Jonathan A. Walter is a Senior Researcher at the Center for Watershed Sciences at University of California Davis, Gabriel P. Singer is a Senior Environmental Scientist at CDFW, John T. Kelly is a Senior Environmental Scientist and Statewide Sturgeon Coordinator at the CA Department of Fish and Wildlife, Fisheries Branch, Michael J. Thomas was a Staff Researcher at University of California Davis and is currently a Fish Biologist at U.S. Army Corps of Engineers. Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair in Coldwater Fish Ecology at University of California Davis, and the Director of the Center for Watershed Sciences.

Further Reading

Colborne, S.F., L.W. Sheppard, D.R. O’Donnell, D.C. Reuman, J.A. Walter, G.P. Singer, J.T. Kelly, M.J. Thomas, and A.L. Rypel. 2022. Intraspecific variation in migration timing of green sturgeon in the Sacramento River system. Ecosphere 13: e4139.

Hause, C.L., G.P. Singer, R.A. Buchanan, D.E. Cocherell, N.A. Fangue, and A.L. Rypel. 2022. Survival of a threatened salmon is linked to spatial variability in river conditions. Canadian Journal of Fisheries and Aquatic Sciences 79: 2056-2071.

Heublein, J.C., J.T. Kelly, C.E. Crocker, A.P. Klimley, and S.T. Lindley. 2009. Migration of green sturgeon, Acipenser medirostris, in the Sacramento River. 84: 245-258.

Kelly, J.T., A.P. Klimley, and C.E. Crocker. 2007. Movements of green sturgeon, Acipenser medirostris, in the San Francisco Bay estuary, California. Environmental Biology of Fishes 79: 281-295.

Miller, E.A., G.P. Singer, M.L. Peterson, E.D. Chapman, M. Johnston, M.J. Thomas, R.D. Battleson, M. Gingras, and A.P. Klimley. 2020. Spatio-temporal distribution of Green Sturgeon (Acipenser medirostris) and White Sturgeon (A. transmontanus) in the San Francisco Estuary and Sacramento River, California. Environmental Biology of Fishes 103: 577-603. 

Mora, E.A., R.D. Battleson, S.T. Lindley, M.J. Thomas, R. Bellmar, L.J. Zarri, and A.P. Klimley. 2018. Estimating the annual spawning run size and population size of the southern Distinct Population Segment of Green Sturgeon. Transactions of the American Fisheries Society 147: 195-203.

Moser, M.L.. J.A. Isreal, S.T. Lindley, D.L. Erickson, B.W. McCovey Jr., and A.P. Klimley. 2016. Biology and life history of Green Sturgeon (Acipenser medirostris Ayres, 1854): state of the science. Journal of Applied Ichthyology 32: 67-86.

Nguyen, V.M., J.L. Brooks, N. Young, R.J. Lennox, N. Haddaway, F.G. Whoriskey, R. Harcourt, and S.J. Cooke. 2017. To share or not to share in the emerging era of big data: perspectives from fish telemetry researchers on data sharing. Canadian Journal of Fisheries and Aquatic Sciences 74: 1260-1274.

Rypel, A.L., P.B. Moyle, and J. Lund. 2021. A swiss cheese model for fish conservation in California.

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.

Schreier, A., P.B. Moyle, N.J. Demetras, S. Baird, D. Cocherell, N.A. Fangue, K. Sellheim, J. Walter, M. Johnston, S. Colborne, L.S. Lewis, and A.L. Rypel. 2022. White sturgeon: is an ancient survivor facing extinction in California? 

Steel, A.E., M.J. Thomas, and A.P. Klimley. 2018. Reach specific use of spawning habitat by adult green sturgeon (Acipenser medirostris) under different operation schedules at Red Bluff Diversion Dam. Journal of Applied Ichthyology 35: 22-29.

Thomas, M.J., A.L. Rypel, G.P. Singer, A.P. Klimley, M.D. Pagel, E.D. Chapman, and N.A. Fangue. 2022. Movement patterns of juvenile green sturgeon (Acipenser medirostris) in the San Francisco Bay Estuary. Environmental Biology of Fishes 105: 1749–1763.

Zhang, H., I. Jaric, D.L. Roberts, Y. He, H. Du, J. Wu, C. Wang, and Q. Wei. 2020. Extinction of one of the world’s largest freshwater fishes: lessons learned for conserving the endangered Yangtze fauna. Science of the Total Environment 710: 136242.

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Resistance is Futile – Agriculture is Key to Fixing Lower Colorado River Water Shortages

by Jay Lund and Josué Medellin-Azuara

The lower Colorado River has been out of balance for about 40 years, using more water than has been available.  As their reservoirs empty, the three lower basin states, federal government, and water users are getting around to addressing this problem.  

The Colorado River reservoir system has immense storage capacity, about 4 times the river’s average annual historical inflow.  These Colorado River reservoirs (Lake Mead behind Hoover Dam and Lake Powell behind Glen Canyon Dam) have filled only once since their completion in 1963, in 1983.  Lower basin water demands have grown and a warming climate has reduced river flows and increased evaporation in the last century (Figures 1 and 2).  The reservoirs seem unlikely to refill anytime soon with this growing imbalance.  This long-term depletion of the basin’s surface reservoirs is paralleled by widespread overpumping of the region’s groundwater (Castle et al. 2014). 

Such immense reservoirs being full in 1983 might have prolonged inattention to fundamentals.  For managers, water users, and political leadership, starting with full reservoirs in 1983 has meant difficult policy choices could be postponed for almost two generations.

But with depletion of remaining reservoir storage progressing at a rate of about 3 million acre-ft per year, people are becoming concerned, and major decisions will need to be made within this or the next election cycle.  After 40 years, lower Colorado River basin reservoirs are falling to elevations where outlet structures can no longer release water or generate hydropower reliably.

Some imaginative and very expensive measures are being proposed (such as desalination, barring growth in Arizona, building new reservoirs, dragging icebergs upriver from Mexico, etc.).  However, the great majority of Colorado basin water use is for irrigated agriculture, mostly for animal feed, which seems far cheaper to fallow than the cost of most other proposed actions.

Figure 1. Lower Colorado River Reservoir Storage for 40 years (data from John Fleck)
Figure 2. Declining annual and 10-year average natural flow at Lees Ferry, Colorado River (maf/yr) (USBR data)
Figure 3: The Colorado River supplies seven states and Mexico

The Colorado River is a medium-sized river and the largest surface water supply for a region of more than 40 million people, 5.5 million acres of irrigated cropland, 22 federally-recognized tribes, and many national and state parks and wildlife refuges directly involving 7 western states and Mexico (Figure 3).

An agreement in 1922 and subsequent agreements and treaties allocate Colorado River water across 7 states and Mexico (Table 1) and set the basis for building the large lower basin reservoirs.  These initial allocations assumed unusually high average inflows from before 1922. At that time, the basin had more water than was being used by cities and agriculture, and seemed to allow for continued growth in water use.  The negotiations were eased somewhat by assuming a high average river flow and omitting tribal water rights and future reservoir evaporation.  Despite these flaws, this agreement helped hold the peace on the river for almost 100 years, aside from a few colorful episodes. 

A negotiated settlement for current shortages will be more difficult with today’s water scarce conditions, sizable water over-use in the lower basin, potential further water use growth in the northern basin, basin aridification from climate warming, and more pressing tribal water rights. 

Location1922 allocation (maf/yr)Recent actual use (maf/yr)
Average total water available16.412.5-14?
Upper basin7.54.8 (2018) **
   Colorado   3.86   2.4
   Utah   1.71   1.0
   Wyoming   1.04   0.4
   New Mexico   0.84   0.5
   Arizona   0.05   0.03
   Upper reservoir evap/losses   0.5
Lower basin states7.57.5 (2020)
   Nevada   0.3   0.3
   Arizona   2.8   2.8
   California   4.4   4.4
Reservoir evaporation1.5 (approximately)
Total Use~615.3
Annual Shortage-9 (surplus)3 (approximately)
Table 1: Colorado River water availability, allocations, and uses 1922 and recently * Under Minute 319 to the US-Mexico treaty, Mexico’s allocation can drop as much as 125 taf/yr in extreme droughts.
**USBR (2019) Provisional Upper Colorado River Basin 2016-2020.

Shortage is large

The Federal government has recently sought to reduce Colorado River water use by 2-4 maf/year.  A recent proposal from the states envisions a 2 maf/yr reduction to address depletion of water reserves.  The rough accounting in Table 1 indicates a sizable reduction of about 20%-30% of current water use is needed to balance supply and demand.

For the reservoirs to accumulate storage for future dry years, still greater cuts are needed.  The reservoirs are currently quite low, so it might be prudent to reduce water use by more so remaining supplies become more reliable.

Who’s most at risk?

The Colorado River supplies with water, energy, and recreation for tens of millions of people, trillions of dollars of economic activity, and some iconic landscapes and ecosystems.  So it is easy to panic about the Colorado River “running out of water.” 

Water use in the lower Colorado River basin is 70-80% for irrigated agriculture, with about four-fifths of this supporting feed crops for livestock.  Agricultural water use’s share of the economy is about 4%, and some fallowing historically has been a buffer for dry times. Urban water use is about 20-30% of Colorado River basin water use, but supports over 90% of the economy and people. Hydropower and recreation from the reservoirs mostly use water on its way downstream to consumptive agricultural and urban water users,

Few of these activities are at risk if the system is managed wisely, but hundreds of millions of dollars of losses are unavoidable, given the basin’s permanent water scarcity.  The costs of these shortages will be far greater ($ billions) and more widespread if the river’s available water is not managed and allocated well.

What to do?

Many options have been considered:

Clearly, expanding surface water storage capacity in the Colorado River basin will not improve its water supplies.  The lower basin lacks water to fill existing reservoir storage capacities even partially.  More storage capacity will not produce more water.

Desalinating seawater on the California or Mexican coasts has been proposed.  While technologically possible, coastal desalination’s roughly $2,000-$3,000/af cost greatly exceeds the economic value of most water uses.  The USBR’s less expensive brackish water desalination plant in Arizona has been mothballed for decades. 

Wastewater reuse already occurs throughout the basin, and almost no wastewater returns to the Sea of Cortez in Mexico.  So additional local wastewater reuse would merely take water from a current downstream user to expand a consumptive reuse of wastewater upstream.

Urban water conservation is important and will help some, but even draconian urban conservation cannot eliminate the need to permanently fallow irrigated croplands.  More importantly, urban conservation helps decouple water use from economic prosperity and population.   Southern California has imported about the same amount of water for decades, with a growing economy and population.  Conserve water in urban areas, but understand that this will not spare water-intensive agriculture from major reductions in water use. 

Nearly all the Colorado River Basin’s long-term water shortage will require permanent reductions in irrigated acreage.  Permanent reductions of 1-2 million acres of irrigated land will be needed in the lower basin states, about 20-30% of irrigated agriculture in the basin. 

An idea to facilitate permanent reductions in agricultural water use is a fee on all water use from the lower Colorado River to fund voluntary permanent buy-backs of agricultural water across the basin and some local costs of re-adjustment.  Well-established buyback schemes can help reduce cost of fixed reductions to all users.

California’s large agricultural water use has become a reserve water supply for southern California cities since the 1980s.  Since the 1980s, southern California cities have purchased water from more senior agricultural water-right holders, supplementing remaining agricultural profits with payments for fallowing and effective water conservation, often including some funds for local economic and social impacts.  The expansion of higher-valued crops in California and Arizona might increase costs of fallowing, but enough less profitable irrigated agriculture remains to achieve the needed water use reductions. 

Game theory

For most parties, the political game now is how to extract the most money from the Federal government and the most water from California so other lower-priority parties can reduce water use less.

Some interesting ideas for updating Colorado River allocations and their management include:

  • Firm up federal water rights for tribes outside of the 1922 agreement in a way that allows tribes to sell water anywhere so a) tribes win and their water claims are formally settled, b) a sizable water volume is shifted out of the 1922 agreement into a more flexible situation.  (This would disproportionately reduce California use and provide fungible long-term support for tribes.)
  • Do the same with evaporative losses from the reservoirs.  This was proposed recently by a group of six states (excluding California).
  • Human health and safety priority for some water, perhaps established at 55 gpcd (the current California drought standard) for residents depending on Colorado River water.  This would be a backstop for urban users, especially in Nevada and Arizona, supporting about 38% of current Phoenix and 50% of current Las Vegas water use.  The remainder of use could be from purchases of remaining allocations (perhaps across state lines) or other sources.
  • As a condition for Federal adjustment funds, states must allow their Colorado River water users to sell water to users in other states.  This allows the most important water uses in any state to be supplied reasonably, with compensation to users who give up more water than the law requires.

An important economic problem of how to minimize the economic and human impacts of unavoidable fallowing of irrigated lands.  Markets within states and perhaps across states can allocate remaining water to crops and people which provide greater economic benefits (and usually employ more and better paid workers). 

A subsequent environmental problem and opportunity for landowners, environmentalists, and local, state, and federal governments will be what to do with 1-2 million acres of permanently fallowed cropland. 

This need to reconfigure water management, agriculture, and land use in the lower Colorado River basin is not unique.  Many parts of the western US have overdeveloped water use and agriculture, worsened by climate change with deep environmental degradation.  Strikingly similar problems and solutions exist for addressing groundwater overdraft in California’s San Joaquin Valley, with very similar acreages of permanent fallowing needed.  Maintaining the Great Salt Lake in Utah, groundwater in Arizona, waterfowl and fish in the Klamath basin, and other terminal lake and playa and groundwater systems in the West (and globally, Lake Urmia in Iran and Aral Sea) all suffer from over-use of water mostly for irrigated agriculture. 

Human and ecological prosperity in the West with a changing climate and newer economic structures will require deep changes in water use and management similar to changes when these regions shifted from mining economies to agricultural economies.  Federal and state leadership, structure, and incentives can make these transitions occur more efficiently, quickly, and justly than will occur otherwise.

Jay Lund is a Professor of Civil and Environmental Engineering at the University of California – Davis.  Josué Medellin-Azuara is an Associate Professor of Civil and Environmental Engineering at the University of California – Merced. 

Further reading

USBR, Colorado River Basin Water Supply and Demand Study Executive Summary, US Bureau of Reclamation, December 2012

Castle, S., B. Thomas, J. Reager, M. Rodell, S. Swenson, and J. Famiglietti. “Groundwater Depletion during Drought Threatens Future Water Security of the Colorado River Basin.” Geophysical Research Letters 41, no. 16 (2014): 5904–11.

Bruce Babbitt (2022), “Department of Interior needs to review agricultural use of water amid negotiations for Colorado River cuts,” The Nevada Independent.

Porse, E. and S. Pincetl (2023), “Drought and the Colorado River: Localizing Water in Los Angeles,”, 8 January 2023.

Some other insightful media work:

Lower Colorado River Reservoir Evaporation the Focus of New Analysis.” 2022. KUNC. October 26, 2022.

Recent proposals from states:


Other states

John Fleck – Deadpool Diaries: The numbers in the states’ two proposals (1 February 2023)  

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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 CWS staff.
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.

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.

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.

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.

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.

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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

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

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

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.

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.

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?

Rypel, A.L. 2022. Nature has solutions…What are they? And why do they matter?

Torres, F., M. Tilcock, A. Chu, and S. Yarnell. 2022. Five “F”unctions 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.

Rypel, A.L., P.B. Moyle, and J. Lund. 2021. 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.

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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