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Essential Fish Habitat Consultations in the Pacific Islands

Through a essential fish habitat consultation process, NOAA Fisheries provides recommendations to federal agencies to avoid, minimize, mitigate, or otherwise offset the effects of their actions on essential fish habitat.

Corals thrive and support a wide diversity of reef fish in the sunny, shallow water at Baker reef. Corals thrive and support a wide diversity of reef fish in the sunny, shallow water at Baker reef.


The 1996 amendment to the Magnuson-Stevens Fishery Conservation and Management Act (MSA) created essential fish habitat (EFH) provisions that required the identification  and protection of important habitats for federally managed fisheries. EFH is described as, "Those waters and substrates necessary to fish for spawning breeding, feeding, or growth to maturity."

Federal agencies which fund, permit, or undertake activities that may adversely affect EFH are required to consult with NOAA Fisheries regarding the potential effects of their actions on EFH, and respond to the agency’s recommendations. The Pacific Islands Regional Office (PIRO) coordinates primarily with federal agencies to conserve EFH (although coordination with state and territorial governments is also possible). 

The MSA established the “council process,” through which federal commercial fisheries are managed and EFH is defined. PIRO works cooperatively with the Western Pacific Regional Fisheries Management Council and the NOAA Pacific Islands Fishery Science Center to cooperatively manage fishery species grouped into “management unit species” (MUS). MUS in the Pacific Islands are officially and fully described in the council’s Fishery Ecosystem Plans (FEPs), and include: bottom fish, crustaceans, coral reef ecosystem, precious coral, and pelagic fish species caught in quantities sufficient to warrant management or specific monitoring by NOAA Fisheries and the council. 

To assist in consulting with agencies, PIRO provides informal regional guidance specific to MUS and EFH in the Pacific Islands. To prepare their EFH assessment, federal agencies need to know if the proposed activity is within or adjacent to EFH for the MUS in the Pacific Islands region. The EFH Habitat Mapper and the Data Portal are  useful tools for this purpose, but official definitions are provided in the council’s FEPs. Once the federal action agency determines which EFH species and habitats are at risk from the proposed project activities, it can conduct the required adverse effects analysis of the effects of the proposed action on EFH. EFH adverse effects analyses are based on the specific MUS and life stages that may be adversely affected by the action. Therefore, the project description must be accurate enough to determine which stressors are likely to occur. Federal agency adverse effect determinations are derived from analyzing the anticipated adverse effects from expected stressors.  

Consulting federal agencies may utilize an existing interagency coordination processes, such as those pertaining to the National Environmental Protection Act, the Endangered Species Act, or the Fish and Wildlife Coordination Act. However, most commonly, an independent EFH Assessment is prepared and submitted to NOAA Fisheries when the federal agency initiates the consultation. 
Learn more about consultations for essential fish habitat

Preparing the EFH Assessment

There are two types of consultations, abbreviated and expanded. The type of consultation used depends on the magnitude of the adverse effect on EFH — substantial (expanded consultation) or less than substantial (abbreviated consultation).

Although the federal action agency is ultimately responsible for complying with the EFH consultation requirements of the MSA, the agency may designate a non-federal representative to conduct an abbreviated consultation or prepare an assessment on the agency’s behalf. Generally, this means that a permit applicant or consultant prepares the required EFH assessment. Applicants and consultants should only begin preparation of an assessment after receiving guidance from the federal action agency regarding the scope and level of effort appropriate for the assessment. This will ensure that the assessments submitted to NOAA Fisheries are adequate and complete.

Early Coordination

NOAA Fisheries recommends engaging with the agency on projects as early as possible. Through early coordination, NOAA Fisheries can provide technical assistance in a pre‐consultation setting (timing is subject to capacity and staff workload). Early coordination will reduce uncertainty and ensure maximum flexibility. NOAA Fisheries can provide this coordination throughout the federal agency’s planning process, typically leading to the identification of the types of information needed and the appropriate confidence level (i.e., resolution) of the appropriate supporting data (the standard of evidence) needed to move expeditiously through consultation. 

Consultation Initiation


The federal agency must notify NOAA Fisheries regarding a proposed action that may adversely affect EFH. It should describe the proposed activities to the fullest extent possible in both time and space, delineating methodologies and equipment types that would be used. Notification can take the form of a Public Notice (PN), Draft Environmental Assessment (EA), or Draft Environmental Impact Statement (EIS), or via direct correspondence (email or letter).


This is a written assessment of the effects of the action on EFH using the best scientifically available information. The level of detail contained within the EFH assessment should be commensurate with the degree of adverse effect to EFH. An EFH assessment must contain the following sections: 

  1. A description of the proposed action 
  2. Analysis of the potential adverse effect of the action on EFH
  3. The federal agency's conclusions regarding the effects of the action on EFH and the managed species
  4. Proposed mitigation measures taken to avoid and minimize adverse effects, and offset for adverse effects where appropriate

It may be helpful to include additional information to reduce uncertainty regarding the extent of adverse effects (especially for large-scale and complex proposals), such as but not limited to:

  • The results of an on-site inspection to evaluate habitat and site specific effects of the project
  • The views of recognized experts on the habitat or species that may be affected
  • A review of pertinent literature and relevant information
  • An analysis of alternatives to the proposed action including those alternatives that avoid or minimize the adverse effects on EFH
  • In cases where there are data gaps in the best available scientific information, obtaining novel information and including that in an EFH assessment will also reduce uncertainty and lead to more precise recommendations, without the need to make assumptions that benefit the resource (the precautionary principle).  

Agency Determinations

NOAA Fisheries will logically derive its determinations from the analysis in the EFH assessment, and any assumptions (if needed) will be based on the precautionary principle. A consultation is appropriate in cases where federal activities occur in the same location (such as in the water column or sea floor).

A useful “litmus test” is if best management practices (BMPs) are proposed, adverse effects to EFH may occur. For activities that would only generate temporary adverse effects to EFH (e.g., shading), an EFH consultation would be appropriate. 

PIRO categorizes adverse effect types in four categories: temporary, short‐term, long‐term, and permanent. The severity of the adverse effect depends on intensity and spatial extent of the stressor, while the adverse effect type is based on the recovery rate from the impact and the pervasiveness of the impact at the ecological scale. The PIRO standard EFH effects analysis normally will use the most sensitive and hard‐to‐replace EFH resources based on the recovery time back to the baseline or the highest following stable state likely. Considering recruitment and growth rates of impacted fauna, oceanographic and geomorphologic features, and anticipated future conditions, living EFH resources that are altered or lost can be quantified as a debt. Non‐living resources can also be adversely affected and lost, such as the removal or impairment of features that serve as shelter. These types of effects tend to be permanent.

Conservation Recommendations

After receiving the completed EFH assessment, PIRO will provide EFH conservation recommendations to the federal agency detailing additional measures that the agency can take to conserve EFH.

Agency Response

Within 30 days of receiving NOAA Fisheries recommendations, the federal agency must provide a detailed written response to NOAA Fisheries. In the case where a response is inconsistent with NOAA Fisheries’ recommendations, the federal agency must respond 10 days prior to taking action, and explain its reasons for not following the recommendations; including the scientific justification for any disagreements with NOAA Fisheries over the anticipated effects of the proposed action and the measures needed to minimize, mitigate, or offset such effects.

Understanding Essential Fish Habitat

Essential fish habitat includes coral reefs, kelp forests, bays, wetlands, rivers, and even areas of the deep ocean that are necessary for fish reproduction, growth, feeding, and shelter.

Mutton Snapper in Seagrass Photo Credit, Kurtis Gregg, NOAA.jpg