Drought Makes Conditions Worse for California’s Declining Native Fishes

Long Valley speckled dace and Whitmore Marsh, its last natural native habitat in the Owens Valley. Other habitats have been heavily modified by poor landuse and mostly dried up.  Photos by J. Katz and P. Moyle.

by Peter Moyle and Andrew Rypel

California is home to 131 kinds of native fishes that require freshwater for some or all of their life-cycle. Most of these fishes are found only in California and most (81%) are in decline (Moyle et al. 2015, 2020). Thirty-two (24%) are already listed as threatened or endangered by state and/or federal governments. Declines are usually the result of fishes losing the competition with humans for California’s water and habitat (Leidy and Moyle 2021). This competition is heightened by the ongoing severe drought.  Thus, there is a petition circulating to declare the delta smelt extinct to make supposedly large amounts of water available to farmers, even though the smelt is not extinct and the amount of water devoted to delta smelt is small (Börk et al. 2020). Winter-run Chinook are being vilified because they require cold-water releases from Shasta Reservoir even though the lack of cold water mostly results from poor management of the reservoir’s pool of water. In the Klamath River Basin, farmers are angry because they are not being provided with water from Upper Klamath Lake, blaming the demands of endangered suckers and salmon, even though juvenile salmon in the river are already dying in this extraordinary drought.

One response to these ongoing problems is federal and state financial relief for farmers.  For example, California politicians have proposed state and federal funding to improve canals that deliver water to farmers in the San Joaquin Valley. Yet deterioration of the canals was created by over-drafting ground water, causing land and canals to subside. Some $800 million in government funds is proposed to subsidize this infrastructure repair, that will mostly go to improving the ability of farmers to take water away from fish. An equivalent bill to improve access of native fishes to water or improve their habitats does not seem to be in the works.

              If native fishes are going to persist through this extended drought (there is no end in sight), a statewide program of monitoring, emergency, and preparatory actions is needed. This program needs to check on the condition of all native fishes annually, with the capacity to take action if key habitats are drying up or are otherwise becoming unsuitable.  Here are some examples that reflect the diversity of actions that are ongoing or needed to keep California’s native fishes viable despite the combined immediate threats of competition for water with people and loss of habitat by drought. In general, species listed under the federal Endangered Species Act (ESA) are more likely to have resources devoted to their recovery than are species that are not listed. More complete information on these example species can be found in Moyle et al. 2015, 2017.

              The central coast Coho salmon is listed as endangered under federal and state ESAs  because of loss of habitat combined with reductions in stream flows, often drought related. This fish has been brought back from the brink of extinction by a combination of intensive management of Lagunitas Creek (Marin County) and an innovative captive breeding program at the Dry Creek Hatchery. Coho have the advantage of being charismatic, as sleek sea-run fish that are highly visible when they spawn, reminding people that California coho once supported extensive sport and commercial fisheries.

              The Sacramento splittail once lived throughout the Central Valley and upper San Francisco Estuary.  The only population remaining today spawns on flooded vegetation especially in the Yolo Bypass. After spawning the fish return to their main rearing area, Suisun Marsh, followed by the juveniles a few months later.  They were listed as a federally threatened species for a short time but the designation was rescinded when studies revealed their remarkable resilience, even during short droughts. But their total distribution is increasingly restricted and persistence through long droughts will be increasingly difficult, without help, such as providing more reliable floodplain habitat for spawning.

              The northern California roach is a small minnow largely confined to springs and isolated small streams in the upper Pit River watershed in California and Oregon. Its original description as a distinct species in 1908 was largely ignored by subsequent workers. Baumsteiger and Moyle (2017), however, using genomic techniques, validated the species distinctiveness. Its current status, especially in California, is poorly known but most of its known habitats are degraded by poor land management (e.g., livestock grazing) and other factors, exacerbated by drought. This species may easily disappear unnoticed from California if steps not taken to protect it and its habitats.

              The Long Valley speckled dace is another small minnow headed for extinction because it had not been seen as unique. An unpublished genomics study reveals that it is quite different from other dace and has been isolated for thousands of years in the streams and marshes of the Owens Valley region. These habitats are disappearing as the water disappears.  Its last natural refuge is Whitmore Marsh, which is watered by a hot spring, now converted to a swimming pool.  The only other population is in a small pond monitored by CDFW at the White Mountain Research Station. Neither population can be regarded as secure.

              Green sturgeon are ancient survivors, reaching 2-3 m in length and living 50-75 years or more. Like salmon, they are anadromous, spending most of their time in the ocean.  Unlike salmon however, they spawn many times throughout their long lives. There are two distinct populations recognized, the southern green sturgeon and the northern green sturgeon. The former consists of small population that spawns in the Sacramento River, while the latter spawns in north coast streams, principally the Klamath River and the Rogue River (Oregon). The southern population is listed as a threatened species and is likely further threatened by drought-reduced flows in the Sacramento River. Thanks to its being ESA-listed, however, considerable resources have been devoted to it, so managers can take advantage of new knowledge of its life history requirements. The northern population in the Klamath River supports a small tribal fishery which is threatened by reduced flows and temperatures. The 2002 fish kill in the lower Klamath, caused by low flows in combination with disease, is famous for killing thousands of adult salmon and also killed a few green sturgeon.

              Clear Lake Hitch is a native fish that is found exclusively in Clear Lake, Lake County, where it was once an abundant food for the indigenous Pomo people.  Formerly, it ascended tributary streams by the thousands to spawn in the spring. Hitch numbers are greatly reduced due to alteration and diversion of its spawning streams and to predation by non-native fishes in the lake. Reductions in flows are particularly a problem in drought years. Furthermore, Clear Lake struggles with blue-green algae blooms, especially during hot summers, which functionally limits the oxythermal habitat of fishes like the Clear Lake hitch, and can also can fish kills (Till et al. 2019). Importantly, Clear Lake also has a history of native fish extinctions; the Clear Lake Spilttail (another species only found in Clear Lake) has not been captured since 1970 and is presumed extinct. Local people monitor the hitch populations but funding for habitat restoration and other actions is limited, so the future of these fish is far from secure, despite being listed as Threatened under the state ESA and despite its importance to Pomo culture.

Each of California’s native fishes have a similar story, even species not threatened with extinction. But the most threatened species need special attention. The more obscure species need be protected by champions who watch out for their welfare, such as the CDFW biologist who checks up on Red Hills roach in their tiny streams, ready to mount a rescue operation if needed. Ultimately, each species needs protection in their special habitats, preferably as a statewide system of managed watersheds that protect more than just threatened fish (Howard et al 2018). We discussed many of these issues at length in a recent blog post.

Winter-run Chinook salmon and Delta smelt are examples of species that have been saved from extinction so far by extraordinary measures, as prescribed under the state and federal ESAs. These acts have managed to prevent extinction of most listed California fishes so far, but drought, combined with threats from activities by people, is pushing ESA protections to the breaking point.

Further reading

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

Baumsteiger, J. and P. B. Moyle. 2019.A reappraisal of the California Roach/Hitch (Cypriniformes, Cyprinidae, Hesperoleucus/Lavinia) species complex. Zootaxa 4543 (2): 2221-240. https://www.mapress.com/j/zt/article/view/zootaxa.4543.2.3  (available as open-access download)

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

Howard, J.K, K. A. Fesenmyer, T. E. Grantham, J. H. Viers, P. R. Ode, P. B. Moyle, S. J. Kupferburg, J. L. Furnish, A. Rehn, J. Slusark, R. D. Mazor, N. R. Santos, R. A. Peek, and A. N. Wright. 2018. A freshwater conservation blueprint for California: prioritizing watersheds for freshwater biodiversity.  Freshwater Science 37(2):417-431. https://doi.org/10.1086/697996

Leidy, R. A. and P. B. Moyle. 2021. Keeping up with the status of freshwater fishes: a California (USA) perspective.  Conservation Science and Practice. 2021;e474. https// doi.org/ 10.1111/csp2.474. 10 pages. Open Access.

Lennox R.J., D.A. Crook, P. B.  Moyle, D. P. Struthers, and S. J. Cooke 2019. Toward a better understanding of freshwater fish responses to an increasingly drought-stricken world. Reviews in Fish Biology and Fisheries 29:71-92  https://doi.org/10.1007/s11160-018-09545-9.  Open Access.

Moyle, P., J. Howard, and T. Grantham, 2020. Protecting California’s Aquatic Biodiversity in a Time of Crisis. California Water Blog. https://californiawaterblog.com/2020/05/03/protecting-aquatic-biodiversity-in-california/

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

Moyle, P., R. Lusardi, P. Samuel, and J. Katz. 2017. State of the Salmonids: Status of California’s Emblematic Fishes 2017.  Center for Watershed Sciences, University of California, Davis and California Trout, San Francisco, CA. 579 pp. https://watershed.ucdavis.edu/files/content/news/SOS%20II_Final.pdf

Moyle, P.B., R. M. Quiñones, J.V.E. Katz, and J. Weaver. 2015.  Fish Species of Special Concern in California.  3rd edition.  Sacramento: California Department of Fish and Wildlife. https://www.wildlife.ca.gov/Conservation/Fishes/Special-Concern

Moyle, P.B., D. Stompe, and J. Durand. 2020. Is the Sacramento splittail an endangered species?  https://californiawaterblog.com/2020/03/03/is-the-sacramento-splittail-an-endangered-species/

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

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

Peter Moyle is Distinguished Professor Emeritus at the University of California, Davis and is Associate Director of the Center for Watershed Sciences. Andrew Rypel is a professor of Wildlife, Fish, and Conservation Biology and Co-Director of the Center for Watershed Sciences at the University of California, Davis.

About jaylund

Professor of Civil and Environmental Engineering Director, Center for Watershed Sciences University of California - Davis
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24 Responses to Drought Makes Conditions Worse for California’s Declining Native Fishes

  1. Joseph Rizzi says:

    Cold Fish – 1 mile apart fishing holes dug or dredged to about 50 to 60 feet deep to create nice fishing holes where the fish can rest and the hole area stays cold. Added benefit is holes add more water into water table due to added area exposed to water and water depth adds pressure.

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