R Essential Fish Habitat: Past and Present

ivers, estuaries, and the open ocean provide important habitat for fish, allowing them to feed, grow, and reproduce. 

Congress recognized the importance of habitat to fish in 1996, making significant revisions to the Magnuson-Stevens Fishery 

Conservation and Management Act (MSA). These revisions emphasized the need to protect fish habitat from the growing 

threats of human activity. Specifically, the MSA required that fishery management councils (Councils) identify as essential fish 

habitat (EFH) those areas necessary for fish to perform their basic life functions. By 1998, the Councils had identified EFH for

each federally managed fish species during each of their life stages. 

The MSA states that Councils must minimize to the extent practicable 

adverse effects to EFH caused by fishing activities. The National Marine 

Fisheries Service (NMFS) and the Councils are responsible for ensuring 

that impacts from fishing do not reduce the ability of habitat to support 

healthy fisheries. The MSA also requires federal agencies to consult with 

NMFS when their actions may adversely impact EFH. Together, these 

requirements form the foundation of fish habitat conservation under the 

EFH program, which seeks to ensure habitat protection for nearly 1,000 

managed fish species while providing efficient, flexible, and transparent 

review procedures.

EFH is defined as “...those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity.” 

“Waters” include aquatic areas and their associated physical, chemical, and biological properties that are used by fish. “Substrate” 

includes sediment, hard bottom, structures underlying the waters, and associated biological communities. “Necessary” means 

the habitat required to support a sustainable fishery and the managed species’ contribution to a healthy ecosystem; and 

“Spawning, breeding, feeding, or growth to maturity” covers a species’ full life cycle.

“. . . THOSE WATERS AND SUBSTRATE NECESSARY TO FISH FOR

SPAWNING, BREEDING, FEEDING, OR GROWTH TO MATURITY.”

Essential Fish Habitat
The eight regional fishery management councils and the 

NMFS Highly Migratory Species Division are responsible 

for drafting fishery management plans and describing and 

identifying EFH for each life stage of each managed species. 

EFH descriptions are based on the best available science, 

are developed through a public process, and are available 

on the EFH website (see footer).

Activities within EFH Designations

Identifying an area as EFH does not make it a marine 

protected area or indicate what kind of activities will be 

allowed or excluded from that area. The intent of the 

EFH provisions is to highlight the importance of habitat 

for fisheries. EFH management measures are handled 

separately from the process of describing and identifying 

EFH.

Essential Fish Habitat in State Waters

EFH occurs in state waters because certain life stages of 

many federally managed species use these waters. The 

requirement for the Councils and NMFS to minimize adverse 

impacts from fishing applies only to fishing activities 

occurring in federal waters that are regulated under a 

federal fishery management plan. However, NMFS and the 

Councils may provide states with recommendations for 

minimizing adverse impacts to EFH from fishing that takes 

place in state waters. Also, NMFS must provide conservation 

recommendations for non-fishing activities of other federal 

agencies in state waters that would adversely affect EFH.

Habitat Areas of Particular 

Concern

HAPCs are a subset of EFH that deserve special attention 

because they provide extremely important ecological 

functions and/or are especially vulnerable to degradation. 

For instance, HAPC designation may be warranted for areas 

that play a vital role in the reproductive cycle of a managed 

species (e.g., grouper spawning sites) or areas that contain 

a rare habitat type (e.g., corals) that may be sensitive to 

disturbance from fishing or other human activities. Councils 

may designate an area as a HAPC for one or more of the 

following reasons:

The habitat provides important ecological 

functions

The habitat is sensitive to human-induced 

environmental degradation

Development activities are, or will be, stressing 

the habitat

The habitat type is rare.

The Purpose of HAPCs

The purpose of HAPCs is to focus conservation, management, 

and research efforts on subsets of EFH that are vulnerable to 

degradation or are especially important ecologically for federally 

managed fish. The HAPC designation alone does not confer 

additional protection or restrictions to an area, but helps to focus 

EFH conservation, management, and research priorities. HAPC 

designation is a valuable way to acknowledge areas where we 

have detailed information on ecological function and habitat 

vulnerability, indicating a greater need for conservation and 

management. In some instances the Councils and NMFS may 

develop fishery management measures to conserve the habitat 

within the HAPC.

Designating HAPCs

The NMFS Highly Migratory Species Division and each Council have 

designated HAPCs for some of their managed species. Councils 

have designated HAPCs as discrete geographic areas or as all areas 

of a specific habitat type (e.g., seagrass). Aided by the research 

of NMFS and others, the Councils are continually improving their 

understanding of the life histories of fish species and their specific 

habitat requirements. As this understanding develops further, the 

Councils and NMFS may designate additional HAPCs or refine the 

existing designations.

HAPCs vs. EFH

HAPCs comprise only a small fraction of the areas identified 

as EFH. Healthy populations of fish require the total area 

described and identified as EFH. HAPCs identify specific 

areas for resource managers and users that may warrant 

more targeted protection measures. As NMFS strives 

to promote healthy and productive coastal and marine 

ecosystems, the conservation of both relatively small and 

larger habitat areas will be necessary.

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DESCRIBING & IDENTIFYING

Essential Fish Habitat

http://www.nmfs.noaa.gov/habitat/habitatprotection/efh/index.htm

Photo credit: Thomas Dunklin
Fishing Impacts on Essential 

Fish Habitat

NMFS’ concern for impacts to EFH includes non-fishing 

activities as well as the fishing activities it regulates. 

Examples of adverse effects from fishing practices can 

include altered physical terrain from bottom-tending gear, 

chemical modifications to the sediment and overlying water 

column, and biological changes to the benthic community 

by the removal of prey species.

Managing Fishing Impacts

The MSA requires that all fishery management plans 

minimize to the extent practicable adverse effects of fishing 

on EFH. All fishery management plans have measures in 

place, such as area closures, gear restrictions, and harvest 

limits that control fishing activities and provide benefits 

to EFH. 

For example, in Alaska, NMFS and the North Pacific Fishery 

Management Council approved several management 

measures in 2006 to conserve fish habitat, including the 

designation of the Aleutian Islands Habitat Conservation 

Area. The decision provides unprecedented conservation 

of fish habitat, such as sensitive deep water corals, by 

prohibiting bottom trawling in an area larger than the states 

of Texas and Colorado combined. The measures were 

developed with extensive input from the fishing industry 

and environmental groups and have been praised by all 

sides as a reasonable compromise.

Also, on the West Coast in 2006, NMFS and the Pacific 

Fishery Management Council approved a plan to establish 

and conserve as EFH more than 130,000 square miles of 

marine waters. This precautionary measure prohibits fishing 

methods, such as bottom trawling, that can cause longterm damage to the ocean floor. The plan, developed with 

support and advice from both environmental and fishing 

industry groups, conserves habitat in areas essential to the 

health of commercial and recreational fisheries. 

Some examples of other measures include:

Limiting access of bottom trawling to certain 

areas important to cod and scallops in New 

England

Restricting gear use in an area called Oculina 

Bank in the South Atlantic to protect sensitive 

coral habitats

Restricting the use of certain bottom gears in 

the Gulf of Mexico and the Caribbean to protect 

coral habitats.

NMFS continues to work with the Councils to develop 

additional measures to conserve EFH as data from ongoing 

research on fishing gear impacts and habitats become 

available. NMFS’ dedication to continually improving habitat 

protection and conservation is one part of an ongoing 

effort to move towards ecosystem-based approaches to 

sustainable fisheries management.

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http://www.nmfs.noaa.gov/habitat/habitatprotection/efh/index.htm

Photo credit: John Naughton
Once EFH has been described and identified, Congress 

mandated in the MSA that federal agencies consult with 

NMFS on activities that may adversely affect fish habitat. 

Through the EFH consultation process, NMFS provides 

recommendations to federal agencies to avoid, minimize, 

mitigate, or otherwise offset the effects of their actions on 

EFH. The consultation process requires that: (1) federal 

agencies provide NMFS with a description of impacts of an 

action through an EFH Assessment if they determine their 

actions may adversely affect EFH; (2) NMFS provides EFH 

conservation recommendations for any federal action that 

would adversely affect EFH; and (3) federal action agencies 

respond to NMFS’ recommendations in writing. If the action 

agency disagrees with NMFS’ advice, it must explain why. 

The procedures for EFH consultations are outlined in the 

EFH Consultation Guidance located on the EFH website and 

in the EFH regulations.

What Are Adverse Effects?

An adverse effect is any impact that reduces the quality 

and/or quantity of EFH. Adverse effects may include direct 

or indirect physical, chemical, or biological alterations of 

the waters or substrate and loss of, or injury to, benthic 

organisms, prey species and their habitat, and other 

ecosystem components. Adverse effects to EFH may result 

from actions occurring within or outside of EFH and may 

include site-specific or habitat-wide impacts.

Federal Actions and 

Essential Fish Habitat

http://www.nmfs.noaa.gov/habitat/habitatprotection/efh/index.htm

Consultation Approaches

NMFS offers five different approaches to complete EFH 

consultations. Each approach varies according to the type 

of action, its effect on EFH, and the level of information 

required from the action agency. NMFS also encourages 

federal agencies to work closely with NMFS early, before 

formally initiating an EFH consultation. Often, early 

coordination can streamline the EFH consultation process 

and lead to mutually beneficial outcomes for both EFH and 

the federal action agency (see box opposite page).

• Use of Existing Procedures

EFH consultations are often combined with existing 

environmental review procedures, such as those used under 

the National Environmental Policy Act and the Endangered 

Species Act, to streamline EFH consultation requirements 

and avoid duplication with other environmental reviews.

• Programmatic Consultations

Federal agencies and NMFS may consult on a group of 

similar actions that fall within a program--programmatic 

consultations. In many cases, when the federal action agency 

accepts programmatic EFH conservation recommendations, 

no further consultation is required.

• General Concurrences

A general concurrence identifies specific types of federal 

actions that may adversely affect EFH, but for which 

no further consultation will be required because NMFS 

determines that the actions do not cause greater-thanminimal adverse effects on EFH, either individually or 

cumulatively.
The consultation options listed above 

accommodate a variety of situations and 

minimize duplication, resulting in an effective, 

streamlined process. Close cooperation 

between NMFS and federal action agencies 

will provide a regulatory environment in 

which agencies can carry out activities while 

simultaneously considering the health of fish 

habitat.

Non-Federal Actions

• State Agencies: NMFS is required 

by the MSA to issue EFH conservation 

recommendations to state agencies if their 

actions would adversely affect EFH. However, 

state agencies are not required to consult with 

NMFS or respond to any EFH conservation 

recommendations NMFS may provide. 

• Private Landowners: Private landowners 

have NO responsibilities to consult with NMFS 

directly. Consultation is required ONLY if the 

project is funded, permitted, or authorized by a federal 

agency and the project may adversely affect EFH. In that 

case, the appropriate federal action agency undertakes the 

consultation with NMFS on behalf of the landowner.

http://www.nmfs.noaa.gov/habitat/habitatprotection/efh/index.htm

• Abbreviated Consultations

An abbreviated consultation is performed for those projects 

that may have an adverse effect on EFH, but for which the 

effects will not be substantial. An abbreviated consultation 

is only completed if no general concurrence, programmatic 

consultation, or existing environmental review process is 

available or appropriate for the federal action.

•Expanded Consultations

An expanded consultation is completed when no general 

concurrence, programmatic consultation, or existing 

environmental review process is available or appropriate 

for the federal action, and the action may result in 

substantial adverse effects on EFH. Procedures for expanded 

consultations allow for detailed analysis of effects by 

providing NMFS more time to coordinate with the action 

agency and develop EFH conservation recommendations.

Interagency Cooperation Leads to Habitat Protection in Puerto Rico

In 2001, the U.S. Environmental Protection Agency (EPA) and NMFS worked together to effectively protect hundreds of acres of submerged 

hard bottom, sand, and algal plain habitats in Puerto Rico from adverse effects of operating five wastewater treatment facilities. By 

initiating coordination early with NMFS, the EPA facilitated a smooth and successful implementation of their EFH consultation requirements. 

The effective and early coordination eventually led to agreement on all EFH conservation recommendations offered by NMFS and timely 

project completion. 

After receiving a permit proposal for five wastewater treatment facilities requesting exemption from required secondary treatment of 

wastewater under Section 301(h) of the Clean Water Act, the EPA contacted NMFS. The EPA opted to seek guidance from and work with 

NMFS before preparing an EFH Assessment on the project, identifying key fish habitat issues, potential impacts of the proposed permits, 

and mitigation strategies to avoid, minimize, or mitigate these impacts. As a result, the EPA’s EFH Assessment completely addressed the 

major issues and ensured the efficient approval of the proposed permits. Species with essential fish habitat in the project area included 

queen triggerfish, yellowtail snapper, banded butterflyfish, queen conch, and corals. 

The initial discussions ensured there were no surprises on either side of the EFH process. In its response to the EPA’s assessment, NMFS 

accepted the Clean Water Act waivers and agreed with the EPA that all wastewater treatment facilities follow strict monitoring requirements, 

effluent limitations, and other special conditions. EPA, in turn, accepted all of NMFS’ additional recommendations for the permit. 

The use of interagency coordination, especially early in planning stages, is a valuable asset to the EFH process. Cooperative efforts of EPA 

and NMFS led to agreement from all parties in this situation, both protecting fragile marine resources and fulfilling the permit applicant’s 

requests.

Photo Credit: Paige Gill
For more information on the Essential Fish Habitat Program and Regional contacts, 

please contact the Office of Habitat Conservation at 301-713-4300 or 

visit the Essential Fish Habitat homepage at:

http://www.nmfs.noaa.gov/habitat/habitatprotection/efh/index.htm

Photo credit: Chris Pickerell

June 2007