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Our precious marine habitats


Commercially valuable fish stocks have been declining for years. Although overfishing has historically been blamed for this decline, coastal habitat loss may also be an important factor. Population expansion, and its associated development, are major causes of coastal habitat loss and degradation.

The National Marine Fisheries Service (NMFS), part of the United States Department of Commerce's National Oceanic and Atmospheric Administration, is charged with the protection, management, and enhancement of the nation's marine fishery resources. The Essential Fish Habitat (EFH) provisions of the Magnuson-Stevens Fishery Conservation and Management Act, as well as the Fish and Wildlife Coordination Act, authorizes the NMFS to evaluate development projects proposed or licensed by federal agencies, including the U.S. Army Corps of Engineers and the Federal Energy Regulatory Commission. If coastal development projects have the potential to adversely affect marine, estuarine, or anadromous species or their habitat, the NMFS makes recommendations on how to avoid, minimize, or compensate these impacts.

Each year the NMFS Northeast Regional Office reviews almost two thousand requests for federal permits to dredge wetlands and waterways, deposit dredged material in nearshore waters, build coastal structures, fill waterways or wetlands, build dams, and perform other in-water work. The NMFS's technical reviews are supported by the agency's research on the biological effects of human activities, the value of coastal habitats, and methods of reducing habitat loss and degradation.

Activities Affecting Coastal Habitat

The NMFS Northeast Region, extending from Maine through Virginia, is the most populated and visited areas in the United States. Since colonization by European settlers, humans have greatly modified the natural coastal geography in this region by dredging, filling, and other construction activities. As a direct consequence of these activities, only a small portion of the formerly expansive coastal marshes remain. Similar patterns of loss have occurred in other coastal habitats, notably aquatic vegetation beds and intertidal flats. As part of its mandated responsibilities, NMFS works closely with the U.S. Fish and Wildlife Service, the U.S. Environmental Protection Agency, the U.S. Army Corps of Engineers, and other federal and state agencies to ensure that future development projects have minimal impact on aquatic habitats and species.

When performed in or near the coastal zone, most construction activities have the potential to harm aquatic species. For example, dredging can damage seagrasses or other aquatic bed communities by changing water depths, causing sedimentation or erosion in surrounding areas, or creating sediment plumes which decrease light penetration through the water column. Reducing the spatial extent of these communities affects many other species by eliminating an important source of food and shelter. In addition, dredging can resuspend pollutants, nutrients, or sediments in the water column, potentially making them available for uptake in living organisms. These particular impacts have been shown to cause decreased reproductive success and mortality among many shellfish and finfish species. Similarly, damming rivers for water storage or hydropower may restrict migration access by anadromous species and block vernal floodwaters and their associated nutrients from reaching estuarine systems downstream. Accompanying changes in salinity and nutrient regimes may degrade habitat quality in these estuarine nurseries.

Perhaps the greatest risk associated with coastal and watershed development projects is that the magnitude and scope of their environmental effects are not easily identified. For example, we are only beginning to realize the importance of managing non-point source impacts from motor oil, sewage, industrial wastes, pesticides, and fertilizers. These non-point source pollutants are often associated with drainage from urban centers, residential areas, and agricultural lands. It is important to consider the potential impacts of non-point source pollutants as projects are designed, evaluated, and authorized. Responsible management of these and other coastal activities is necessary to ensure that suitable habitat remains available for aquatic species.

Habitat Conservation

NMFS's Habitat Conservation program was established to assess the effects of infrastructure, commercial, and residential development on the nation's stocks of fish and shellfish, and to make appropriate recommendations to federal regulatory agencies to protect the stocks and the habitats needed for their survival. The Habitat Program conducts environmental assessments of coastal and open water ecosystems. These environments are linked by the water cycle and the species that depend on them for spawning grounds, nurseries, feeding areas, or a mixture of these biological requirements.

The predominant habitat types of the Northeast Region include the rocky shores of New England, the sandy beaches of the Mid-Atlantic, and the extensive salt marsh system that runs along the back bays and river basins form Maine to Chesapeake Bay. The nation's living marine resources depend on the rivers, estuaries, marshes, tidal flats, and shallow waters of these areas. It is the interconnection of these habitats that make them so biologically productive.


Rivers provide spawning, nursery, and other important habitat functions for anadromous species (those that swim up rivers from the sea to spawn, e.g. salmon), catadromous species (those that swim down rivers to the sea to spawn, e.g. eels), and resident species (those that live in the area year round, e.g. perch). Atlantic salmon, American shad, and striped bass are among the most sought after anadromous species which are dependent on riverine habitat for early lifestage survival. American eels, our only catadromous species, grow in river systems after hatching in the Sargasso Sea.

Rivers support and transport the first levels of the aquatic food chain; receiving nitrogen and phosphorus (from decaying organic matter and fertilizers) and moving these nutrients and primary producers (phytoplankton) downriver to coastal waters. Phytoplankton are the single celled plants upon which primary consumers such as small fish feed. The primary consumers are, in turn, preyed upon by carnivorous species, including many commercially-important fish and shellfish.


Estuaries are formed where rivers meet the ocean and salt water is diluted by fresh. The input of nutrients, fresh water, and abundant food combine to provide unique, shallow habitats. Estuaries provide sanctuary from the harsh action of ocean currents and waves. These systems are often fringed by salt marshes and tidal flats and may contain valuable beds of subaquatic vegetation such as eelgrass and widgeongrass. As many as forty percent of commercially and recreationally important species of the Northeast depend on estuaries for some part of their life cycle.

Salt Marshes:

Salt marshes fringe portions of the protected coastline of the Northeast Region. Salt marshes filter pollutants from streams and rivers protecting fragile estuarine nurseries, and they buffer shorefront property from wave and water damage during storms and floods. Striped bass and bluefish depend on these areas for food, while the prey species, such as killifish and silversides, use the channels and marsh interiors as habitat throughout their lives.

Nontidal Wetlands:

As one moves farther south in the Northeast Region, nontidal wetlands become increasingly important both in terms of acreage and their association with coastal plain rivers and estuaries. Nontidal wetlands provide numerous indirect values to anadromous and estuarine fish resources. For example, nontidal wetlands lying adjacent to rivers and streams enhance or maintain the quality of anadromous fish instream spawning and nursery habitat.

Tidal Flats:

Tidal flats typically exist between mean sea level and the low tide line. Often composed of fine sediments, they characteristically extend offshore from the waterward edge of a salt marsh. Nutrients and particulate biological matter washing from the adjacent marshes make tidal flats prime habitat for primary producers, grazers, and scavengers. As the tide rises, an abundance of resident bivalves, worms, and crustaceans attract more mobile predators to the area, which are, in turn, consumed by a variety of commercially and recreationally important species.


Submerged shallows and offshore banks, such as Stellwagen and Georges, are unique areas where nutrients from the land and ocean mix over preferred substrates. These components combine to create unique and highly productive habitats for commercially valuable stocks such as cod and flounder.


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Last Updated: May 31, 2014
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