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« Atlantic Salmon Ecosystems Research Team

Critical Habitat

Picture of freshwater habitat
Picture of freshwater habitat Two examples of freshwater habitat available in Maine for Atlantic salmon. On the top, diverse substrate provides instream structure; well rooted banks prevent erosion and minimize sedimentation and turbidity; significant canopy cover provides shade and buffers against high water temperatures; runs, riffles and pools provide a diversity of habitat for several Atlantic salmon life stages. On the bottom, the homogenous substrate provides little habitat diversity or instream cover; there is no refuge during times of drought, and a shade-providing overstory canopy is lacking.
Picure of critical habitat Here are some of the conditions a returning adult may encounter. Navigating high velocity stretches of river (above) requires an extreme energy expenditure, necessitating holding areas where adults can recuperate. If drought conditions occur (below), adults must find refuge in deep pools. Picture of river during drought Picture of Veazie Dam
Prime spawning habitat Prime spawning habitat
Arial shot of two trawlers Above, two trawlers work together to pair tow a net in Penobscot Bay. The postsmolt trawl is conducted during the smolt emigration period (late spring/early summer). The net is towed at the survace and guides postsmosts and other species occupying the same space safely into an "aquarium" at its codend. Biological information is then obtained from these captured postsmolts and other on-target species.
Map of Atlantic salmon migration Once Atlantic salmon smolts leave their natal river, they undertake a migration that takes them far from shore into the North Atlantic Ocean and as far as Western Greenland.
Picture of Greenland

Western Greenland, where Atlantic salmon over-winter and feed after emigrating from US and Canadian rivers.

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Every single species on Earth needs a specific set of environmental conditions to live and thrive.  As the ecological footprint of humans grows, however, the habitat required by a variety of species (including Atlantic salmon) is becoming increasingly unavailable.  Subsequently, a number of populations have become unstable to the point where extinction is a real possibility.

Under the Endangered Species Act (ESA), a species' critical habitat (CH) refers to the physical, chemical and biological features, or primary constituent elements (PCEs), that are essential for its survival and reproduction.  Thus, the rationale for designating CH is that particular habitats, when lost, are disproportionately limiting to populations and therefore must be prioritized for protection. 

AN ACT to provide for the conservation of endangered or threatened species of fish, wildlife, and plants, and for other purposes.
Be it enacted by the Senate and House of Representatives of the United States of America in Congress assembled, That this Act may be cited as the "Endangered Species Act of 1973."
(5)(A) The term "critical habitat" for a threatened or endangered species means --
(i) the specific areas within the geographical area occupied by the species, at the time it is listed in accordance with the provisions of section 4 of this Act, on which are found those physical or biological features (I) essential to the conservation of the species and (II) which may require special management considerations or protection; and
(ii) specific areas outside the geographical area occupied by the species at the time it is listed in accordance with the provisions of section 4 of this Act, upon a determination by the Secretary that such areas are essential for the conservation of the species...

Excerpt from the Endangered Species Act of 1973

The ESA requires that a species' CH be designated by either the U.S. Fish and Wildlife Service or NOAA-Fisheries at the time of its listing.  In reality, the process is inherently time consuming and costly, and designation usually occurs after the listing and sometimes not at all.  Reasons for this are:

  • Operational definitions, approaches, and information for identifying CH remain poorly defined.
  • Defining CH involves multiple aspects of population biology—ranging from local habitat effects on individual growth and survival to large-scale population and landscape issues.
  • While there is an overabundance of information about threats facing imperiled species, optimal habitat requirements are frequently unknown.
  • Public comment a complete economic analyses of the impacts of CH designation must occur before the designation's finalization.

As a species cannot exist in the absence of habitat, CH designations are sometimes perceived as duplicating protections already afforded under the ESA through listing.  However, designating CH affords species additional and very important protections under the ESA that listing alone does not. 

For instance, when designating CH, a determination must be made regarding whether a species’ current range is adequate or if additional habitat within the species’ historic range is required to ensure the its continued existence into the foreseeable future (100 years).  Designating unoccupied habitat that is essential for a species’ recovery is the only mechanism under the ESA that can ensure its protection and availability to the species. 

Another benefit of designating CH is that federal agencies are forced to clearly identify PCEs—what they are and what geographical area they’re associated with.  By fully understanding what habitat features are essential, the agencies are in a better position to identify what is needed to preserve, protect or enhance those features required for the species’ survival, reproduction and recovery.  NEST is currently identifying the PCEs for Atlantic salmon—this is especially challenging since Atlantic salmon have several distinct life history phases that are identified by specific changes in their behavior, physiology, and habitat requirements. 

Atlantic salmon have a complex life history strategy that includes freshwater and marine residencies and extensive migrations over an extremely large range.  Because each life stage has very distinct and different habitat requirements, NEST must identify PCEs and designate CH for each.


Map depicting the scale at which critical habitat is designated
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Map depicting the scale at which critical habitat is designated for Atlantic salmon in freshwater. As an example, the basin draining the Downeast region of Maine has a HUC of 6. The next smallest level is the sub-basin (HUC 8), which can be broken down even further into a watershed (HUC 10). This map shows the Narraguagus watershed as it falls within the sub-basin that drains the coastal Downeast rivers and basin that drains the downeast region of Maine.

The scale at which CH is being designated for the freshwater life stages of Atlantic salmon is at the watershed scale.  Specifically, the U.S. Geological Survey’s hydrologic unit code (HUC) of 10 (~60-390 square miles) is being used.

Although watersheds with naturally reproducing populations of Atlantic salmon vary widely in physical characteristics, habitat must exist within a watershed for spawning, feeding, sheltering and overwintering.  Atlantic salmon habitat is often identified by life stage specific such as depth, water velocity, substrate, and cover.  Some additional PCEs of freshwater habitat include:

  • Water quality
  • Instream structure
  • Species composition
  • Water chemistry
  • Space
  • Riparian canopy cover

It is necessary to look at habitat from the vantagepoint of a watershed because what happens on the land within a basin affects its water resources.  For instance, removing riparian vegetation (that which borders a waterbody) eliminates an important source of nutrients and instream structure (e.g. woody debris), and can result in increased water temperature and sediment loads.  Furthermore, groundwater extractions can increase surface water temperatures and affect dissolved oxygen concentration.  And landuse activities occurring within the drainage basin can alter water chemistry (e.g. pH).  All of these activities, and many more, can result in changes in the aquatic biota, as aquatic plants and animals that are better adapted to the altered environment thrive while those that are not decline.

As an example of the complexity of freshwater habitat required by Atlantic salmon, take the returning adult life stage.  Adults return from sea to their natal river in early spring where they can spend nearly five months in a freshwater environment before spawning.  They may encounter conditions along the way (such as high water temperatures, extremely high/low flows, predators and obstructions, like the dam pictured below) that tax their limited energy reserves and test their ability to reach their spawning grounds at the exact time when conditions allow for maximum spawning success. 

For an adult to successfully migrate to suitable spawning grounds, holding areas must be available en route.  These allow for resting and provide refuge in the event that adverse conditions occur.  Holding areas can include deep pools or deadwaters, lakes and ponds, and even the estuary.  On occasion, an adult will reach the spawning ground weeks or even months in advance of spawning.  These early arrivers require holding areas in proximity to spawning areas that provide shade, cover from predators, and protection from environmental variables such as high flows, high temperatures and sedimentation.

Optimal spawning habitat is gravel substrate with adequate water circulation to keep buried eggs well oxygenated.  As such, spawning sites (redds) are typically positioned within flowing water to allow for percolation of water through the gravel or where upwellings of groundwater occur.

A redd that is constructed in waters that are too shallow are at risk of desiccation or freezing, while  one that is too deep may not have enough flow for adequate permeation of oxygenated water through the substrate to the eggs.  Additionally, water velocities that are too low can result in accumulation of fine sediments in the redd and prevent the proper cleaning of eggs—flows that are too high can result in excessive scouring and cause redd excavation.  

Finally, spawning adults require adequate space.  A typical redd encompasses slightly more then 40 square feet of spawning habitat.  If sufficient space is not available, or access to spawning areas are impeded, there is an increased risk that redds will become superimposed by other females seeking to spawn (superimposition occurs when a female digs a redd on top of an already existing redd).  The result is near complete reproductive failure of the earlier spawner and thus decreased overall spawning success for the population.


During the smolt life history stage, juvenile Atlantic salmon undergo a physiological transformation that prepares them for life at sea.  Migrating from Maine’s rivers, smolts transition into estuarine and nearshore marine environments.  As postsmolts, they leave the Gulf of Maine and make their way to into feeding grounds in the North Atlantic Ocean where they spend one winter before becoming adults. 

The scale at which critical habitat is designated for marine life stages of Atlantic salmon falls within 300 miles of the U.S. coast.  Currently, the habitat requirements of Atlantic salmon in offshore marine environments are largely unknown due to the difficulties associated with collecting data at sea.  However, NESTs nearshore postsmolt trawl survey provides information related to postsmolt feeding and movement. 

Identification of the habitat features essential for Atlantic salmon survival and reproduction is a crucial component of the recovery process.  Designating CH not only improves manager’s abilities to make informed decisions but also maximize protection of essential habitat features under the ESA.

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