Man and boy fishing at pier

Habitat Conservation





Habitat science looks at the relationships between species and their environment. Habitat information is needed in almost every one of our programs, as it provides important scientific advice on both the current status and future trends of habitats. This information is used for habitat management and restoration, stock assessments, ecosystem-based management, and throughout other programs.

The Magnuson-Stevens Act requires the eight regional fishery management councils (link) to identify essential fish habitat—areas used by fish throughout their lives for spawning, feeding, nursery grounds, migration, and shelter—and for NOAA Fisheries to assist in conserving and enhancing them. Fish might change their habitat throughout life stages, for example, when Coho salmon migrate from a marine environment into freshwater streams and rivers to mate. This means it is important to conduct research to understand the different types of habitats and their different characteristics, like types of reefs or nutrient levels, to figure out how best to manage different marine species.

As the climate changes and oceans warm, fish populations are moving in search of cooler waters like in New England where fishermen have been catching black sea bass and longfin squid in the Gulf of Maine, far north of the animals’ usual range. Understanding and predicting the effects of climate change and other human-caused impacts on marine species will also require an increased focus on habitat science.

Understanding habitat can also improve stock assessments and integrate them into an ecosystem-based management system. Our habitat science activities include coordination with research and management activities and implementation of the Marine Fisheries Habitat Assessment Improvement Plan.

Habitat Science in the Regions



In the Alaska region, we are responsible for more than 70 percent of the nation’s continental shelf habitat and conduct research to support the management of 60 stocks of fish and shellfish. The sheer physical immensity and northern geography of Alaska can pose major challenges to conducting habitat research.

We have a long history of habitat research in the region and even pioneered the use of submersibles to conduct deep-water habitat assessments, but the habitat assessments conducted in Alaska are generally in small geographic areas of high interest. Recent interest in the conservation of deep-sea corals resulted in habitat assessments in areas of high coral and sponge fisheries bycatch. We also conduct research and assessments in nearshore habitats.

Our scientists are facing new challenges stemming from the effects of climate change on habitat in Alaska. These include the loss of sea ice, ocean acidification, and shifts in the distribution of species and the habitats they use, particularly in the northern seas. These changes are not unique to Alaska, but the changes expected to happen here may be extreme and help serve as a warning for the rest of the world.

Learn more about habitat science in Alaska


In the Northwest, we conduct habitat research in the California Current Large Marine Ecosystem in partnership with other federal and state agencies as well as academic institutions, covering almost 500,000 square miles. We conduct research on marine habitats of more than 100 species of fish stocks, like Pacific Coast Groundfish and Pacific Coast Salmon. Our scientists develop models for managing multi-species fisheries, define essential fish habitats for key groundfish species, and try to understand the complex relationships between commercially and recreationally important fisheries and their habitats in the Pacific Northwest.

Working with Oregon State University, we developed the Pacific Coast Ocean Observing System West Coast Habitat Data Portal to integrate geological, geophysical, biological, fisheries, and physical oceanographic data in one portal. Almost 50 full-time staff conduct habitat-related research or provide habitat-related data and information used to support fisheries research and management for Pacific Coast stocks.


Most, if not all, of California’s coastal ecosystem has been dramatically altered by intense, continuous recreational and commercial fishing, beginning at least as far back as the 1940s, and by population growth and coastal development. These human-induced changes partnered with natural, but unpredictable, environmental changes make it challenging to identify and understand changes in coastal habitats.

Our Southwest scientists conduct research in the freshwater and marine environments of California, as well as in parts of the Antarctic, Mexico, and open-ocean international waters. The Southwest region, like the Northwest, is part of the California Current Large Marine Ecosystem, and is made up of five general habitat categories: 1, 2, 3, 4, and 5.

Habitat restoration has been done in a piecemeal fashion that might actually have contributed to the major declines in 2008-09 salmon fisheries, and scientific advice on what would be the most effective habitat restoration activities is badly needed.

Challenges and concerns in the region include damage to seafloor habitats due to fishing, effects of climate change (including the consequences of northward shifts in fish distributions with increased ocean temperatures), effects of marine protected area management, and invasive species like the recent invasion of jumbo squid in the California Current Ecosystem. We have more than 30 full-time staff that conduct research on marine habitats of more than 110 stocks and species, and our habitat research is designed describe and protect essential fish habitat and to improve stock assessments, as well as to understand and predict the effects of climate and environmental change on fish populations and marine ecosystems.


There is an extensive amount of research on habitat use and its value in the Southeast Region, especially on estuarine habitats, the habitats that occur where rivers meet the sea. We provide science to help manage 77 stocks in a wide variety of habitats throughout three large marine ecosystems: the Southeast Shelf, the Gulf of Mexico, and the Caribbean Sea. Fisheries in the region are diverse, and range from artisanal traps for fish and crustaceans on coral reefs to open ocean longlines and trawls that sweep the muddy bottom of the Gulf of Mexico for shrimp. The large number of habitats in the oceanic and coastal regions, combined with the number of fishery species, makes habitat research in the Southeast a challenge.

Many fishery species in the region live in continental shelf waters as adults but spend the early part of their lives in estuarine nurseries like seagrass beds, coastal wetlands, oyster reefs, and tidal mudflats. This special connection means that their ecosystems and habitats are vulnerable to human development on the coast. Threats to healthy habitats in the region include damage and change from fishing, hurricanes and storms, climate change and rising sea levels, coral bleaching, disease, and uptake of toxins. Invasive species like lionfish, offshore aquaculture impacts, and the rise of harmful algal blooms and dead zones are some more recent habitat concerns.

We have emphasized research on the estuarine habitats where many species spend part of their lives in the last 30 years. Some of the earliest studies on the value of seagrass beds and estuarine shrimp habitats were started in our laboratories. Because many estuarine habitats are being lost to coastal development, we are exploring techniques to restore habitat and define the cost of restoring habitat while factoring in the benefit to fishery species we depend on every day.

As part of our habitat efforts, we have a regional Habitat Science ListServ for the Southeast to increase communication between scientists, habitat managers, and the NOAA Restoration Center. To join the Southeast habitat assessment ListServ, send an email to with "join" in the subject line.


In the Northeast, we are responsible for the Northeast Shelf large marine ecosystem, which ranges from Maine to Cape Hatteras, North Carolina. This ecosystem is heavily exploited and human activities include commercial and recreational fishing, whale watching, navigation, aquaculture, military operations, pipeline and cable construction, wind and wave energy production, offshore oil and gas development, and mining of sand and gravel.

Habitats range from fine clay to cold-water corals, and ocean conditions in the northeast are complex because of influxes from the warm Gulf Stream in the south as well as cold, often fresher waters from the Scotian Shelf in the north. The diversity of these habitats, the two fishery management councils (New England and Mid-Atlantic) we support, and the numerous state agencies we work with create a complicated challenge for our scientists that work to provide habitat data and advice for management decisions. We have a group of staff that works on habitat science and data, including: collecting habitat data, developing products like maps and tools, and doing habitat assessments.

Pacific Islands

The Pacific Islands area of responsibility includes a vast expanse (1.7 million square miles) of the western and Central Pacific Ocean that supports a wide range of habitats, including shallow reefs, islands, banks, deep slopes, seamounts, and the oceanic seascape. The region is responsible for management of 56 species, including bottomfish and groundfish, coral reefs, crustaceans, pelagic species (also known as highly migratory species), and precious corals. The islands, reefs, and banks that make up most of the habitat in the Pacific Islands are extremely vulnerable to human-caused effects.

The culturally diverse fishing communities in this region, ranging from commercial oceanic longline fishermen to individual fishers on remote islands who sell their reef catches at local markets, are a unique challenge to habitat-related data collection, research, and management. Most habitat related research has been conducted as a part of research commissioned to study pelagic fishes, sea turtle bycatch, coral reef conservation, and other protected species.