Protecting California’s Aquatic Biodiversity in a Time of Crisis

by Peter Moyle, Jeanette Howard, Ted Grantham

Fig. 1. Walking in the Putah Creek Riparian Reserve on the UC Davis campus, where wide trails permit social spacing of hikers. The flow of the creek is regulated to favor native fish and wildlife.

“Nowhere is the biodiversity crisis more acute than in freshwater ecosystems” (Tickner et al. 2020)

Weeks of being confined indoors under shelter-in-place orders increases our appreciation of the natural world. Walking and exercising outdoors, especially along a local stream like Putah Creek, is one of the best ways to escape the news cycle and to restore a sense of well-being.  Quiet streets and pathways have invited a growing chorus of bird song and can even inspire  interest in watching hatches of mayflies rising off gurgling stream waters. Online livestreaming of  wildlife cameras has surged. These experiences remind us how California’s natural environments and rich biological diversity improve the quality of our lives.  They also remind us that this natural heritage is threatened. California harbors more unique plants and animals than other state in the U.S but an estimated 30 percent of our native species are now threatened with extinction (Mooney and Zavaleta 2016).

Sustaining the amazing diversity of life on this planet and in California in particular is a major challenge of this frenetic era. The importance of this protection is reflected in the growing realization that maintaining the diversity of native species living in healthy ecosystems also results in an environment that is good for people. However, the demand of California’s ever-increasing citizenry for intensive use of our land and water makes this challenge extremely hard to meet. Meeting the challenge has just been made even more urgent by the new finding that since 2000 California and the western USA has been experiencing a megadrought, in part because of the aggravations of climate change. This era is being pegged as the driest period in over 500 years and there is no reason to think it is not going to continue, despite occasional wet years.

A major response to the state’s biodiversity challenge by the state has been the California Biodiversity Initiative of 2018, which was supported by Governor Brown and continues to be supported by Governor Newsome. The initiative proposes statewide measures to halt the decline of native species and ecosystems, under the leadership of the Department of Fish and Wildlife and the Department of Food and Agriculture.

We applaud this initiative as a good beginning, even if stalled by the effects of the present pandemic. However, it also has a major flaw: it is so focused on terrestrial ecosystems and native plants that it overlooks the needs of native aquatic (freshwater) species, habitats, and ecosystems. California’s aquatic biodiversity is particularly imperiled, as it is worldwide (Tickner et al. 2020). This problem is most clearly reflected in status of our native fishes. Of our 125+ native fishes, seven species are already extinct and 100 species are in decline and may be ultimately threatened with extinction. These include 31 species already listed as Threatened or Endangered under the state and federal Endangered Species Acts and 62 species listed as Species of Special Concern by CDFW (Moyle et al. 2011, 2015). These species include salmon and steelhead that are both iconic and support valuable fisheries.

Native fish declines are mirrored by other freshwater taxa. Howard et al. (2015) conducted the first statewide status assessment of California’s freshwater taxa. They found that of about 2,000 freshwater vascular plants, macroinvertebrates, and vertebrates for which adequate information was available, half were ranked as vulnerable (data were lacking for the other ~2,000 freshwater taxa in the state). California’s vulnerable aquatic organisms were mostly endemic species, found nowhere else in the world. But among the vulnerable taxa, only 113 (6%) were listed as endangered or threatened under the federal or state ESAs indicating a general neglect of non-charismatic species.

California has taken notable steps to protect its biodiversity, primarily through the establishment of protected lands under various programs. Unfortunately, efforts to protect terrestrial habitats and ecosystems rarely do an adequate job of protecting aquatic biodiversity; most of the key rivers that support threatened fishes, for example, flow outside of protected areas (Grantham et al. 2016). Of course, because terrestrial ecosystems drain into or encompass freshwater systems, management of terrestrial habitats is important for conserving aquatic habitats. However, most protected areas in the state are not explicitly managed to maintain freshwater ecosystems and their biota.

If native freshwater biodiversity is to be conserved, a systematic, statewide approach is required. Building on previous work by Howard et al. (2018), Grantham et al. (2016), Moyle (2002) and Moyle and Yoshiyama (1996), we argue that such an approach should be centered on the designation of priority watersheds and/or habitats for freshwater species management. Moyle (2002) identified a network of streams, lakes, spring systems, wetlands, and watersheds throughout the state that could potentially support all of the state’s native freshwater fishes and include representative examples of all of California’s aquatic habitats (as described by Moyle and Ellison 1991). Grantham et al. (2016) and Howard et al. (2018) extended this approach by using systematic conservation planning methods (Linke et al. 2011) to identify a network of watersheds in California that most efficiently encompass the distribution of all native freshwater taxa. Collectively, these studies provide an ecosystem-based blueprint for pursuing a systematic, statewide approach to freshwater biodiversity conservation, through Freshwater Protected Areas (FPAs), inspired by California’s system of Marine Protected Areas (MPAs).

In addition to the designation of FPAs, water supplies must also be secured for aquatic biodiversity protection. All aquatic species depend upon a sufficient quantity and quality of water throughout the year, no matter what type of habitat they live in. This is particularly true of riverine species that have adapted to the natural variation in seasonal flows – including winter high flows and summer low flows – that characterize the state’s rivers and streams. Yet most of California’s flowing waters have been dammed, diverted, and otherwise modified (Grantham et al. 2014), activities which have altered natural flow patterns and impaired aquatic habitats (Zimmerman et al. 2018). Only a small proportion of the state’s rivers and streams have environmental flow protections and many of these are managed mainly for single species, such as ESA-listed salmon and steelhead. Recently, a working group of researchers and agency staff has been developing a California Environmental Flows Framework (Obester et al. 2020; The Framework includes technical tools and guidance for developing environmental flow standards in streams throughout the state, focusing on specific functional elements of the flow regime linked to ecosystem health (i.e., functional flows). The overall goal of the Framework is to support a more consistent, and comprehensive approach to managing water for the environment in California.

The protection of California’s aquatic biodiversity, incorporating the above approaches, will require a large-scale effort. This effort should start now and accelerate when people and conservation agencies are less distracted by the effects of the COVID-19 epidemic, including a distressed economy. We can envision actions to protect aquatic biodiversity as being part of the economic recovery efforts for California.

Priority actions include:

1. Update and invest in mapping and assessment of freshwater taxa and habitats.

One reason that the state has been unable to implement a systematic strategy for managing native freshwater biodiversity is the limited collection, poor organization, and inaccessibility of data. Several recent efforts, including the PISCES database for tracking of the distribution of native fishes (Santos et al. 2013) and the California Freshwater Species Database for tracking additional freshwater species (TNC 2015), have been difficult to update and sustain because of lack of funds and personnel. Other data sources are either inaccessible to the public (e.g, California Natural Diversity Data Base) or are poorly organized (e.g., Biogeographic information and Observation System [BIOS]). These should be vetted, reorganized, and published, following modern data management and open source principles. TNC’s California State of Salmon website attempts to provide accessible data for all watersheds with salmon and steelhead monitoring ( However, monitoring programs are inadequate for accurately tracking the status of even these iconic species. Most other species are either monitored opportunistically or not at all. Successful management of the state’s freshwater biota and ecosystems cannot be achieved without a robust, comprehensive monitoring program.

2.  Designate and manage Freshwater Protected Areas (FPAs).

We already have a good idea where many of the most important areas for freshwater species conservation are located. However, there has been no formal designation or concentrated effort to identify and prioritize such areas for conservation and management actions. The 2018 Biodiversity Initiative aims to protect 20 percent of each major ecosystem type in the state, including freshwater ecosystems and to restore 15 percent of each ecosystem type from its degraded status. While this sounds good, the numbers are arbitrary and reflect terrestrial thinking. For rivers, for example, how do you protect an ”ecosystem type” that has not been clearly defined and changes as it flows downstream? Does it mean establishment of a statewide network of watersheds focused on their restoration and protection? If that is the case, how big (hydrologic unit) should each watershed in the system be? Whatever the units, FPAs should provide habitat for as much of the native aquatic biota as possible, throughout the state. Previous work by Moyle (2002), Grantham et al. (2016), and Howard et al. (2018) establish a blueprint for delineating FPAs that could efficiently protect native freshwater biodiversity and habitats.  With this information, a team of scientists, such that assembled for the California Biodiversity Initiative, should be able to come up with a site-specific plan to implement an FPA strategy, if California is willing to support it. The plan would, based on both expert opinion and computer algorithms, could provide preliminary designations of potential FPAs, much as Moyle and Randall (1998) did for Sierra Nevada watersheds. These could then be investigated more closely and appropriate action taken to protect the most imperiled FPAs.

3. Accelerate implementation of environmental flows.

California Environmental Flows Framework provides guidance for developing flow recommendations to maintain healthy freshwater ecosystems. The Framework provides a set of flow criteria (based on predictions of functional flows informed by reference stream hydrology) that can be used to immediately establish environmental flow standards in rivers where they do not exist. In rivers and streams with existing flow protections, the Framework can be applied to refine standards so that they are more effective in supporting ecosystem health. On-the-ground pilot projects are needed to implement the Framework across the diversity of California’s rivers and management contexts. As the foundation of the Framework, the functional flows approach also recognizes that environmental flow protections be coupled with strategic investments in physical habitat improvements, such as levee setbacks and barrier removals. For large rivers, it is particularly important to restore their connectivity to their floodplains to support the biological and physical functions that sustain salmon and other native species.

In short, California does a poor job of protecting aquatic biodiversity. A bold and imaginative, systematic effort is needed to protect and manage aquatic biodiversity. This will take leadership, money, and dedication to getting the job done by federal, state, and local agencies. As a biodiversity hotspot with an economy bigger than most nations, California should be leading the country and the world in protecting its aquatic systems. We have the tools at hand, but have been unable to muster the will to do the hard work. But as we reflect upon the natural world during the current public health crisis, it just may be that our growing appreciation of California’s biological richness is what is needed to inspire meaningful action.

Peter Moyle is an emeritus professor at the Center for Watershed Sciences, UC Davis. Jeanette Howard leads The Nature Conservancy’s freshwater science team for California; Ted Grantham is a Co-operative Extension Specialist in the Department of Science, Policy, and Management, UC Berkeley.

Fig. 2. The Long Valley speckled dace is an undescribed fish species that is now found in only one small stream and wetland in the wild, the Owens Valley region. The headwaters of the stream is hot springs that are now a public swimming pool. Its habitat needs protection if the fish is to survive. This is an example of an aquatic system that could be declared an FPA and managed appropriately.

Further Reading

Grantham, T.E., J. H. Viers, and P.B. Moyle. 2014 Systematic screening of dams for environmental flow assessment and implementation. Bioscience 64: 1006-1018.

Grantham, T. E., K.A. Fesenmyer, R. Peek, E. Holmes, R. M. Quiñones, A. Bell, N. Santos, J.K. Howard, J.H. Viers, and P.B. Moyle. 2016. Missing the boat on freshwater fish conservation in California. Conservation Letters. DOI: 10.1111/conl.12249.

Howard J.K. and 20 others. 2015. Patterns of freshwater species richness, endemism, and vulnerability in California. PLoS ONE 10(7): e0130710. doi:10.1371/journal.pone.0130710.

Howard, J.K. and 10 others. 2018.   A freshwater conservation blueprint for California: prioritizing watersheds for freshwater biodiversity. Freshwater Science 37(2): 417-431.

Linke, S., E. Turak, and J. Nel.  2011. Freshwater conservation planning: the case for systematic approaches. Freshwater Biology 56(1): 6-20.

Mooney, H. and E. Zavaleta. Ecosystems of California. Berkeley: University of California Press, 2016.

Mount, J., B. Gray, K. Bork, J. E. Cloern, F. W. Davis, T. Grantham, L. Grenier, J. Harder, Y. Kuwayama, P. Moyle, M. W. Schwartz, A.Whipple, and S.Yarnell. 2019.  A Path Forward for California’s Freshwater Ecosystems.  San Francisco: Public Policy Institute of California. 32 pp.

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

Moyle, P. B., and J. Ellison.  1991.  A conservation-oriented classification system for California’s inland waters.  California Fish and Game 77:161-180.

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

Moyle, P.B., R. 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.

Moyle, P. B., and P. J. Randall.  1998.  Evaluating the biotic integrity of watersheds in the Sierra Nevada, California. Conservation Biology 12:1318-1326.

Moyle, P. B., and R. M. Yoshiyama.  1994.  Protection of aquatic biodiversity in California: A five-tiered approach.  Fisheries 19:6-18.

Obester, A., S. Yarnell, and T. Grantham.  2020. Environmental flows in California.  California WaterBlog, March 18, 2020.

Santos, N.R., J.V.E. Katz, P.B. Moyle, and J. H. Viers. 2013.  A programmable information system for management and analysis of aquatic species range data in California. Environmental Modeling & Software 53:13-26.

Zimmerman, J.K., Carlisle, D.M., May, J.T., Klausmeyer, K.R., Grantham, T.E., Brown, L.R. and Howard, J.K., 2018. Patterns and magnitude of flow alteration in California, USA. Freshwater Biology, 63(8):859-873.

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About Andrew Rypel

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.
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