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The Decline of North American Freshwater Fishes

Stephen J. Walsh, Howard L. Jelks, and Noel M. Burkhead


The fishes of North America’s inland waters, the most diverse of any temperate region, currently face an unprecedented conservation crisis.

  • About 40% are imperiled or presumed extinct, and the portion of imperiled fishes is increasing.
  • Threats to this fauna include habitat destruction, introduced species, altered hydrology, pollution, disease, over-exploitation, and other factors.
  • Extinctions and imperilment of fishes occur among diverse taxonomic groups, across regions, and in a variety of habitats.

June 2009


Fly fisherman above Ojo Calenti Bend on the Firehole River, Wyoming, USA, October 2007. Photo: Mike Cline.

Freshwater fishes are in crisis.

North America has a broad array of freshwater ecosystems because of the continent’s complex geography and geological history. Within a multitude of habitats—that include streams, large rivers, natural lakes, springs, and wetlands—rich assemblages of fishes reside, representing diverse taxonomic groups with unique ecological requirements. They face an unprecedented conservation crisis.1 In the last few decades, the proportion of inland fishes of North America, which are considered imperiled or extinct, increased from 20 to 40%.2 Although extinctions have occurred, many species and populations are declining in range size and abundance. The fish biota of the continent as a whole remains diverse; however, we can take action to stem any further declines.

Fish biodiversity is prolific.

Globally, fishes outnumber all other vertebrates combined and have the highest rate of discovery of new species.3 Fishes exhibit a remarkable diversity of morphological attributes and biological adaptations and occur in most aquatic habitats on Earth. Even in North America, where scientific knowledge of the fauna is advanced, new species are described every year. These discoveries are the combination of applied technologies, such as gene sequencing, which increase recognition of biodiversity at all levels, and the documentation of new, morphologically distinct forms and populations. Biological taxonomy is the discipline of classifying and naming organisms using an internationally accepted system or code. Because of the dynamic nature of fish taxonomy, and the extent of unexplored areas of the planet with potentially many undescribed species, statements or conclusions about numbers and percentages of species occurring in particular habitats or geographical regions are but rough approximations. Published information reveals the following:

  • A conservative estimate is that as many as 32,500 extant (living) fish species may exist in the world.3 This number may eventually prove greater, however, with approximately 30,000 currently recognized as valid and over 300 new species described each year.4

  • Fresh water constitutes only about 1% of the Earth’s surface area and less than 0.01% of its water by volume.

Almost half of fishes are found in fresh waters.
  • About 12,000 species, or approximately 43% of all currently named fishes, occur exclusively in fresh waters. A small number are diadromous, regularly living part of their lives in rivers, streams, or lakes, and part in the oceans.

  • North America has the greatest taxonomic richness of freshwater fishes among temperate regions of the world,1 although it is greatly surpassed in number of species by less documented areas of the tropics—especially the biological hotspots of South America, Africa, and southeast Asia.5,6 Currently, there are approximately 1,200 recognized fish species that occur in inland waters of the continental United States, Canada, and Mexico.

  • Collectively, the fish fauna (ichthyofauna) of North America’s freshwater ecosystems has at least 435 imperiled species, another 72 species with distinct populations in trouble, and 36 species that are extinct from the wild.2

  • Worldwide, historical, and emerging trends in the conservation of fishes and fishery stocks portray continued or even accelerated population decreases; yet, there are reasons for optimism, as well as potential for recovery and protection of these declining resources given societal resolve.7

Threats to freshwater fishes and habitats

Threats to freshwater ecosystems are so widespread that many endemic species—those naturally restricted to a single drainage or ecoregion—are imperiled simply because restricted geographic distribution makes them more vulnerable to human modification of landscapes. The most important documented threats to fishes in freshwater habitats include:1,7,8,9

Habitat loss for fish is a major concern.
  • Destruction or modification of habitat resulting in reduced range size and/or loss of populations. Examples include dam construction, channelization, mining, clearing of natural forests for agriculture, urban development, and other intensive land-use practices.

  • Water depletion. Some desert fishes have become extinct because of human exploitation of limited groundwater resources.

  • Pollution from point and non-point source contaminants. Runoff from urban areas, and the compound effects of multiple pollutants, often reduces water quality to the point that only the most tolerant species remain in receiving water bodies.

  • Erosion and sedimentation. Fine sediments can smother bottom substrates, to the detriment of many bottom-dwelling (benthic) species, whose prey and reproductive success are dependent on clean substrates and good water quality.

Fishing has overexploited populations.
  • Overexploitation for commercial, recreational, scientific, or educational purposes. Examples of fishes that have been overharvested include salmons, whitefishes, trouts, striped bass, and sturgeons.

  • Disease or parasitism. For instance, whirling disease, a microscopic parasite introduced from Europe, has ravaged many wild and hatchery populations of trouts and salmons in the U.S. and Canada.

  • Other anthropogenic factors—including introduction of non-native species—which may result in hybridization, competition, and predation. Numerous introductions of fishes and other aquatic organisms, both from outside of North America and intracontinental transplants, have had severe negative impacts on native species,including some that have caused extinction.10

  • Climate change. Regional variation in rainfall patterns, storm events, and droughts can affect habitats and potentially have negative consequences for rare species.

Conservation status

Land animals make better news than aquatic animals.

Media coverage of conservation issues about the world’s animals is often greatest for species that are particularly endearing to humans, such as mammals and birds, whereas perils to aquatic faunas, including fishes, are often much less publicized. This disparity is due, in part, to taxonomic bias in research and funding in the field of conservation biology.11 Based on published scientific literature, fishes, amphibians, reptiles, and invertebrates are greatly underrepresented in conservation studies relative to the proportion of species of each group known worldwide,11 and organisms in the freshwater and marine realms receive much less coverage than those in terrestrial environments.12 Among invertebrates, however, it is notable that mollusks and crustaceans, of which many species are aquatic, are generally better studied than the vast diversity of arthropods—especially insects, with the exception of butterflies and moths. Even within freshwater fishes, game, and commercial species often receive greater attention than non-game species.

Fish funding and research is lacking.

Major deficits in funding for faunal surveys, monitoring, basic research, and the general lack of public awareness about the conservation status of fishes across taxonomic groups and ecosystems is a significant problem. Given the myriad of threats to aquatic habitats throughout the world; the degree to which degradation of these habitats is accelerating; and the overall proportion of biodiversity represented, exceptional natural resources are at risk of being severely diminished or lost. In particular, freshwater habitats are some of the most threatened in the world.8,9,13 Moreover, aquatic systems are inextricably linked to terrestrial habitats, and pollutants and sediments from perturbed landscapes flow into lakes, streams, and rivers.

New studies reveal fish are in peril.

The Endangered Species Committee of the American Fisheries Society (AFS-ESC) has tracked the plight of imperiled fishes in North America for over 30 years, with the explicit aim of providing objective and unbiased status assessments independent of the influence of policy or regulatory considerations. Recently, the AFS-ESC—represented by 16 scientists from the United States, Canada, and Mexico, with the assistance of numerous colleagues— evaluated the conservation status of the entire continental fish fauna.2 In the latest assessment, approximately 40% of described North American freshwater and diadromous fish species are documented as imperiled or extinct, representing a substantial increase over previous assessments. Past conservation assessments by the AFS were limited to determining the status of distinct species and subspecies. Undescribed forms, or those not named in the scientific literature using classic Linnaean binomial nomenclature, were included where sufficient data were available to document taxonomic distinctiveness, as evidenced by unique morphological, genetic, or other attributes.

In the most recent assessment, additional infraspecific taxa were included in the form of distinctive populations, or what are sometimes referred to in the scientific community as evolutionarily significant units (ESUs) or distinct population segments (DPSs, although this term has certain legal connotations under the Endangered Species Act within the U.S.).14 A taxon (taxa, plural) is a unit used in biological classification and is defined based on a natural relationship, formally recognized as one or more lineages (= clades) of descendants sharing a common ancestry.

700 freshwater fish taxa in N.A. are in peril.

Seven hundred fish taxa are considered imperiled in North America’s inland waters, currently, which represent 133 genera in 36 families (see Figure 1).2 The majority of taxa are named species (63%), followed by named subspecies (13%), populations (12%), undescribed species (7%), and undescribed subspecies (5%). Previous lists from 1979 and 1989 also had about 63% listed species and 37% infraspecific taxa. Of the total taxa currently listed,

  • 280 taxa are endangered (E), i.e., in imminent (fewer than 50 years) danger of extinction, or extirpation (loss of populations) throughout most portions of a taxon’s range.
  • 190 are threatened (T), or in imminent danger of becoming endangered.
  • 230 are vulnerable (V), that is, in imminent danger of becoming threatened, which is comparable to a designation of “Special Concern” by many agencies and conservation organizations.
  • 61 are presumed extinct (X), meaning a taxon that has not been observed for over 50 years. Two subcategories are included: Possibly Extinct (Xp), a taxon suspected to be extinct, as evidenced by more than 20 but less than 50 years since living representatives were observed, and Extirpated in Nature (Xn), where all populations in natural habitats are presumed eliminated but surviving individuals are maintained in captivity.

Figure 1

Chronological increase in the number of fish taxa imperiled in North American freshwater ecosystems, as assessed by the American Fisheries Society Endangered Species Committee.2 Assessments were conducted in 1979, 1989, and 2008. Delisted taxa are those that appeared on a previous list but were removed due to improved status, taxonomic invalidity, or extralimital distributions.

The number of imperiled fishes represents a 92% increase over a nearly 20-year period dating to 1989. The list of imperiled taxa encompasses fishes that span a remarkable diversity of lineages, morphologies, life histories, and habitats. A taxonomic breakdown of the list and comparison to known, described species reveals disparities by family.

  • Nearly one quarter of all imperiled taxa belong to the most species-rich family of North American freshwater fishes, the Cyprinidae, represented by the minnows and their allies.

The Candy Darter is a vulnerable species found in the New River system of Virginia and West Virginia. Darters are a colorful, species-rich group of small-bodied fishes limited in distribution to North America; their greatest diversity is in uplands of central and eastern U.S. Photograph by N.M. Burkhead.

  • Another 15% is represented by the second-most diverse family—the Percidae—that includes a large number of darters—small, colorful fishes that have their greatest diversity and abundance in clear-flowing streams of the central and eastern U.S.

  • The Salmonidae—trouts, salmons, ciscoes, and their allies—comprise nearly 12% of all imperiled taxa, but are disproportionally represented in comparison to other families by large numbers of infraspecific taxa.

Imperiled species include minnows and salmon.

There are distinct geographic trends evident for imperiled North American fishes based on distributions within natural hydrologic units or ecoregions (defined by a combination of physical drainage features and faunal similarity, see Figure 2).12 Concentrations of at-risk fishes occur in the southeastern U.S., the mid-Pacific coast, the lower Rio Grande, and coastal and south-central inland regions of Mexico.1 Of particular note is the distribution of imperiled fishes in North America within ecoregions; 80% of all taxa are confined (endemic) to a single ecoregion, and another 10% are limited to two ecoregions. Much of the imperilment of the inland continental fish fauna is attributed to a combination of limited range sizes of many species and broad-scale habitat degradation.


Figure 2

Numbers of imperiled freshwater and diadromous fishes by ecoregions, within North America, based on the most recent conservation assessment by the American Fisheries Society’s Endangered Species Committee.2

Why be concerned about the decline?

Fish declines affect humans and other species.

Loss of biodiversity on planet Earth is thought by some to be the greatest impending environmental crisis currently facing humanity.15 The decline of North American fish species and populations, as with elements of biodiversity throughout the world, directly or indirectly impacts other faunas, is detrimental to freshwater ecosystems in general, and affects humankind in a variety of ways. Freshwater fishes are important sentinels of environmental conditions and play a crucial role in the ecology and sustainability of natural ecosystems.

The natural balance of both aquatic and terrestrial communities, including birds, mammals, reptiles, and other fishes, is dependent on fish populations that provide critical functions, such as cycling nutrients and serving as prey to a large variety of carnivores. The larvae of native freshwater mussels, called glochidia, require fish hosts in order to complete their life cycles. Some migratory fishes—such as shads, smelts, chars, and salmons—serve as keystone species of entire ecosystems. For instance, a variety of predators and scavengers feed on adults of migrating and spawning salmon, their eggs, fry, and their decaying carcasses. The nutrients that are transferred from the sea and incorporated into the food chain contribute to the health of forests adjacent to streams in which salmon spawn, thereby illustrating the linkage between terrestrial and aquatic habitats.7,16,17

Herbivorous species provide important functions in terms of cropping algae and plants or disseminating seeds and fruits. Humans derive extensive recreational, commercial, and intangible benefits from fish and fishery resources; and our welfare is linked directly to their protection and sustainability. Conversely, degraded aquatic ecosystems—with simplified communities and altered food webs—can lead to an increase in vectors, such as mosquitoes and snails, water-related diseases like malaria, schistosomiasis, and cholera.18

Ecosystems suffer from fewer fish species.

These are but a few examples of the global importance of freshwater fishes, their habitats, and the need for the conservation of both. Overall, fish species, and communities in the inland streams, rivers, lakes, and wetlands of North America, provide countless ecosystem services. Beyond the economic value of fish, fisheries, and freshwater habitats, healthy natural aquatic ecosystems may have profound positive effects on the human spirit and well-being.

What can be done to ensure effective conservation?

Although the status and future prospects for many North American fishes may be discouraging, many actions can reverse declining trends, recover populations, and provide solutions. In a review of a number of studies, G.S. Helfman summarized the following solutions to environmental problems associated with the conservation of fishes and their habitats7:

Society can take action to reverse the trends.
  • Enforce existing laws that protect native assemblages and habitats.

  • Create reserves, protected land areas, and water bodies. Large reserves provide the greatest impact for protecting multiple species and communities.

  • Promote ecosystem-based management.

  • Be precautionary and proactive. Act despite uncertainty and without waiting for scientific consensus. Conservation crises may become irreversible, and management actions may be required before supporting scientific data are available.

  • Monitor results and manage adaptively. Make adjustments to improve conservation actions and implement successful ones for the long term.

Stephen J. Walsh, Ph.D., Howard L. Jelks, M.Sc., and Noel M. Burkhead, M.Sc. are research biologists with the U.S. Geological Survey in Gainesville, Florida, and they serve as co-chairs of the American Fisheries Society’s Endangered Species Committee. All three scientists have broad research interests in ichthyology and have conducted studies on freshwater fishes in the central and southern U.S. for over three decades. They have authored many journal articles, book chapters, and books on the biology, ecology, and conservation of fishes.

The Decline of North American Freshwater Fishes

BioScience Articles

  • » “Overfishing of Inland Waters.” Systematic overfishing of fresh waters is largely unrecognized because of weak reporting and because fishery declines take place within a complex of other pressures. Read why recognizing this is so important in the December 2005, BioScience article, “Overfishing of Inland Waters,” by Allan et al. Free to read.
  • » “Freshwater Ecoregions of the World: A New Map of Biogeographic Units for Freshwater Biodiversity Conservation.” In this May 2008, BioScience article, Abell et al. present a new map depicting the first global biogeographic regionalization of Earth’s freshwater systems. Read the abstract or log in to purchase the full article.

American Fisheries Society Endangered Species Committee

This website provides a link to the AFS report on imperiled North American freshwater and diadromous fishes, interactive maps, and the ability to generate lists of imperiled species and populations based on geographic distribution.

Convention on Biological Diversity

This website represents a global initiative to protect biodiversity through international agreement, as first signed in 1992 at the Earth Summit in Rio de Janeiro, Brazil. Canada and Mexico are parties to the convention, whereas the U.S. is not.

Millenium Ecosystem Assessment: Biodiversity

The Millenium Ecosystem Assessment examined the consequences of ecosystem change for the well-being of humanity. The biodiversity synthesis report is a primer for the role of biodiversity and why humans must protect it globally for long-term ecological, economic, and sociopolitical welfare.

NatureServe Explorer

A valuable source of information on rare and endangered species and threatened ecosystems, with a searchable encyclopedia of more than 70,000 plants and animals of the United States and Canada may be found here.


FishBase is an extensive database containing information on the distribution, biology, human use, and bibliography of fishes worldwide and provided in several languages.

USFWS Fisheries and Habitat Conservation

The USFWS Division of Fisheries and Habitat Conservation (FHC) includes multiple programs that are oriented toward the conservation and restoration of habitats and fish and wildlife resources. The National Fish Hatchery System includes technological centers that provide research support and propagation of rare species for reintroductions into native habitats.

Committee on the Status of Endangered Wildlife in Canada

COSEWIC is a committee of experts who assess and designate which species of wildlife in Canada are jeopardized or likely to be, in order to provide scientifically sound information that can be incorporated into conservation programs.

Mexican protected fishes

This lists imperiled fishes in Mexico that are officially recognized by the government as part of Norma Oficial Mexicana regulations.

Catalog of Fishes

A technical database oriented to the scientific researcher, this website contains information on names, taxonomy, and authority of all formally described fish species.

North American Native Fish Association

This is a nonprofit corporation dedicated to the appreciation, study, and conservation of native fishes. This website provides useful links, including to state and provincial government lists of protected fishes.

National Fish Habitat Action Plan

This is a cooperative nationwide program in the U.S. to engage all stakeholders in efforts to protect, restore, and enhance fish habitats. A series of Fish Habitat Partnerships serve to coordinate conservation activities.

National Fish and Wildlife Foundation (NFWF)

The NFWF is a nonprofit organization that supports grassroots conservation programs by combining federal and private funds within the U.S. The freshwater fish conservation initiative is designed to assist in implementing the National Fish Habitat Action Plan by providing funds and direction to recovery and protection efforts for fishes and aquatic habitats.

International Union for the Conservation of Nature (IUCN)

IUCN is the world’s oldest and largest professional global environmental network. The IUCN provides leadership throughout the world in conserving natural resources. The organization maintains its Red List as the world’s most comprehensive inventory of the global conservation of plants and animals, with the aim to convey the urgency and scale of conservation problems and to motivate the global community to strive to reduce species extinctions.

World Wildlife Fund (WWF)

The WWF is the largest multinational conservation organization in the world and for nearly half a century has been a leader in the stewardship of nature. The WWF works to preserve the diversity and abundance of life and healthy ecosystems by protecting natural areas and associated plants and animals, and by promoting sustainable approaches to the use of renewable resources and energy by minimizing negative ecological impacts.

American Rivers

Founded in 1973, American Rivers is a leading conservation organization with a mission to protect and promote rivers as valuable assets that are vital to human health, safety, and quality of life. Through a series of campaigns and working with a network of strategic partners, American Rivers strives to educate, improve water quality, promote water conservation, and restore degraded aquatic habitats. American Rivers releases an annual list of America’s most endangered rivers.

Conservation Fisheries

Conservation Fisheries is a nonprofit organization dedicated to the captive propagation, reintroduction, and monitoring of critically imperiled fishes of the southeastern U.S. With a small staff, this organization has played an important role in the recovery and protection of endangered species, such as the smoky madtom, a diminutive catfish once thought to be extinct.

  1. Page, L. M., and B. M. Burr. 1991. A field guide to freshwater fishes, North America north of Mexico. Boston, MA: Houghton Mifflin Company.
  2. Jelks, H. J., S. J. Walsh, N. M. Burkhead, S. Contreras-Balderas, E. Díaz-Pardo, D. A. Hendrickson, J. Lyons, N. E. Mandrak, F. McCormick, J. S. Nelson, S. P. Platania, B. A. Porter, C. B. Renaud, J. J. Schmitter-Soto, E. B. Taylor, and M. L. Warren, Jr. 2008. Conservation status of imperiled North American freshwater and diadromous fishes. Fisheries 33(8): 372–407.
  3. Nelson, J. S. 2006. Fishes of the world, 4th ed. Hoboken, NJ: John Wiley & Sons.
  4. Eschmeyer, W. N. 1998. Catalog of fishes. California Academy of Sciences. 3 vol., 2,905 pp. (see “Learnmore” links for updated, online version).
  5. Lundberg, J. G., M. Kottelat, G. R. Smith, M. L. J. Stiassny, and A. C. Gill. 2000. So many fishes, so little time: an overview of recent ichthyological discovery in continental waters. Annals of the Missouri Botanical Garden 87(1): 26–62.
  6. Abell, R., M. L. Thieme, C. Revenga, M. Bryer, M. Kottelat, N. Bogutskaya, B. Coad, N. Mandrak, S. Contreras Balderas, W. Bussing, M. L. J. Stiassny, P. Skelton, G. R. Allen, P. Unmack, A. Naseka, R. Ng, N. Sindorf, J. Robertson, E. Armijo, J. V. Higgins, T. J. Heibel, E. Wikramanayake, D. Olson, H. López, R. E. Reis, J. G. Lundberg, M. H. Sabaj Pérez, and P. Petry. 2008. Freshwater ecoregions of the world: a new map of biogeographic units for freshwater biodiversity conservation. BioScience 58(5): 403–414.
  7. Helfman, G. S. 2007. Fish conservation: a guide to understanding and restoring global aquatic biodiversity and fishery resources. Washington, D.C.: Island Press; 584 pp.
  8. Master, L. L., S. R. Flack, and B. A. Stein (eds). 1998. Rivers of life: critical watersheds for protecting freshwater biodiversity. The Nature Conservancy, 71 pp. (accessed February 10, 2009).
  9. Abell, R. A., D. M. Olson, E. Dinerstein, P. T. Hurley, J. T. Diggs, W. Eichbaum, S. Walters, W. Wettengel, T. Allnutt, C. J. Loucks, and P. Hedao. 2000. Freshwater ecoregions of North America: a conservation assessment. Washington, D.C.: Island Press; 319 pp. Clark, J. A., and R. M. May. 2002. Taxonomic bias in conservation research. Science 297: 191–192.
  10. Fuller, P. L., L. G. Nico, and J. D. Williams. 1999. Nonindigenous fishes introduced into inland waters of the United States. American Fisheries Society Special Publication 27.
  11. Clark, J. A., and R. M. May. 2002. Taxonomic bias in conservation research. Science 297: 191–192.
  12. Irish, K. E. and E. A. Norse. 1996. Scant emphasis on marine biodiversity. Conservation Biology 10(2): 680.
  13. Abell, R. A. and 26 co-authors. 2008. Freshwater ecoregions of the world: a new map of biogeographic units for freshwater biodiversity conservation. BioScience 43(1): 406–414.
  14. DPSs, although this term has certain legal connotations under the Endangered Species Act within the U.S.
  15. Eldredge, N. 1998. Life in the balance: humanity and the biodiversity crisis. Princeton, NJ: University Press.
  16. Helfield, J. M., and R. J. Naiman. 2001. Effects of salmon-derived nitrogen on riparian forest growth and implications for stream productivity. Ecology 82: 2403–2409.
  17. Willson, M. F., S. M. Gende, and B. H. Marston. 1998. Fishes and the forest. BioScience 48:455–462.
  18. Millenium Ecosystem Assessment. 2005. Ecosystems and human well-being: wetlands and water synthesis. Washington D.C.: World Resources Institute, (accessed February 10, 2009).
  19. U.S. Federal Register 66[195]: 51362-53166. Endangered and Threatened Wildlife and Plants: 12-month finding for a petition to list the Bonneville cutthroat trout as threatened throughout its range.


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