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Water: Wetlands

Memorandum for the Field

Subject: Special Emphasis Given to Coral Reef Protection under the Clean Water Act, Marine Protection, Research, and Sanctuaries Act, Rivers and Harbors Act, and Federal Project Authorities


Executive Order 13089 (E.O. 13089) on Coral Reef Protection, signed by the President on June 11, 1998, recognizes the significant ecological, social, and economic values provided by the Nation's coral reefs and the critical need to ensure that Federal agencies are implementing their authorities to protect these valuable ecosystems. E.O. 13089 directs Federal agencies, including the Environmental Protection Agency (EPA) and the Army Corps of Engineers (Corps), whose actions may affect U.S. coral reef ecosystems, to take the following steps:

  1. Identify their actions that may affect U.S. coral reef ecosystems;
  2. Utilize their programs and authorities to protect and enhance the conditions of such ecosystems; and
  3. To the extent permitted by law, ensure that any actions they authorize, fund, or carry out will not degrade the conditions of such ecosystems.

This guidance is intended to clarify and reemphasize the protection afforded the Nation's valuable coral reef ecosystems under the Clean Water Act (CWA) Section 404 regulatory program, the Marine Protection, Research, and Sanctuaries Act (MPRSA) Sections 102 and 103 provisions, Rivers and Harbors Act (RHA) Section 10 requirements, and Federal Projects conducted by the Corps.

Protection for Coral Reefs under CWA Section 404

Section 404 of the CWA provides for a permit program to regulate the discharge of dredged or fill material into waters of the United States. The CWA Section 404(b)(1) Guidelines (Guidelines) establish the environmental standards to be used by EPA and the Corps in the review of permit applications, and as part of the evaluation of Corps feasibility studies, to discharge dredged or fill material in the Nation's waters, including marine waters that are home to coral reefs. Fundamental to the Guidelines is the alternatives analysis, the focus of which is to ensure avoidance of potential adverse environmental impacts associated with activities requiring a Section 404 permit or the application of the Guidelines to Corps feasibility studies. The Guidelines provide (Section 230.10(a)) that no discharge shall be permitted if there is a practicable alternative available that would have less adverse environmental impact. Moreover, the Guidelines impose an explicit, but rebuttable, presumption that alternatives to discharges in special aquatic sites are less damaging to the aquatic ecosystem and are environmentally preferable. Consistent with the general burden of proof under the Guidelines, it is the permit applicant's responsibility to demonstrate that each of these presumptions is rebutted before a permit may be issued. Likewise the Corps must also demonstrate the rebuttal of this presumption in its feasibility reports where there is anticipated to be a discharge of dredged or fill materials into the Nation's waters.

Thus, the Guidelines establish a higher level of review for activities affecting special aquatic sites. The Guidelines specifically recognize coral reefs as one of only five examples of special aquatic sites deserving this higher level of protection. (Subpart E, Section 230.44) Special Aquatic Sites are generally characterized as "geographic areas, large or small, possessing special ecological characteristics of productivity, habitat, wildlife protection, or other important and easily disrupted ecological values. These areas are generally recognized as significantly influencing or positively contributing to the general overall environmental health or vitality of the entire ecosystem of a Region." (Section 230.3(q-1))

The agencies should be particularly careful to consider potential direct, indirect, and cumulative impacts to coral reefs because of their important ecological values, their greater susceptibility to even small environmental changes, and the difficulties associated with effective coral reef replacement/mitigation. In particular, coral reefs are very sensitive to even small increases in turbidity and nutrient loading. Impacts to be considered should include those resulting from sediments from dredging or dredged material disposal, discharges of particulates or nutrients close to the coral reefs, and degradation or destruction of ecosystems that protect and are integral to the coral reef system, in addition to direct damage to the corals. It is important to recognize that there are circumstances where the impacts of the proposed activity are so significant that even if alternatives are determined not to be available, the permit should be denied regardless of compensatory mitigation that is proposed.

Protection for Coral Reefs under MPRSA Sections 102 and 103

Unless authorized by a permit issued under the Act, the MPRSA generally prohibits the transportation of material from the U.S., and from locations outside the U.S. by U.S. vessels, for the purpose of ocean dumping (MPRSA Section 101(a)). Ocean waters subject to the MPRSA include the territorial sea and ocean waters lying seaward of the territorial sea 1 (MPRSA Section 3(b)). It is the policy of EPA and the Corps to apply their authorities under the MPRSA to avoid adverse impacts on coral reefs.

The MPRSA Sections 102 and 103 describe the criteria to be applied to the selection of proposed sites for the discharges of dredged material by EPA and the Corps, respectively. Section 102 of the MPRSA requires EPA, in consultation with the Corps, to develop environmental criteria which must be met before any proposed ocean disposal activity is allowed to proceed. Section 102 also gives EPA authority to designate ocean disposal sites within and beyond the territorial sea, and directs the Corps to use such EPA-designated sites to the maximum extent feasible (MPRSA Section 102 (c) and Section 103(b)). Section 103 authorizes the Corps to select ocean disposal sites for project-specific use if one is needed by the Corps to carry out its dredging responsibilities and if the use of a site designated by EPA is not feasible. Site selection is subject to compliance with EPA's site designation criteria and subject to EPA concurrence (MPRSA Section 103(b)).

Protection of coral reefs should be carefully addressed during site designation by EPA under Section 102(c) or selection of an alternative site by the Corps under Section 103(b). In particular, the applicable site designation criteria require consideration of the potential site's location in relation to breeding, spawning, nursery, feeding, and passage areas of living marine resources and amenity areas (40 C.F.R. 228.6(a)(2) and (3)), interference with recreation and areas of special scientific importance (40 C.F. R. 228.6(a)(8)), and existence of any significant natural or cultural features at or in close proximity to the site (40 C.F.R. 228.6(a)(11)). These criteria should be applied by EPA and the Corps during the site selection process so as to identify and avoid any candidate disposal sites which might result in adverse effects on coral reefs, including consideration of potential transport of the material from the site by currents or storm events.

In addition, under Section 102(c)(3) of the MPRSA, site management plans are required for designated dredged material disposal sites. In cases where there is any potential for coral reef impacts, the required plans should be carefully developed to provide for early detection of any such impacts. The special conditions required for inclusion in site management plans by MPRSA Section 102(c)(3)(C) should clearly specify any conditions necessary to protect coral reefs from the effects of dumping.

Impacts to coral reefs should be avoided during the site selection process by selecting sites that avoid areas with reefs or areas where reefs may be affected by subsequent disposal. However, avoidance of impacts to coral reefs also may need to be considered during the permitting process. Under 40 C.F.R. 227.18 and 227.21, impacts on esthetic, recreational, and economic values and other existing and potential uses of the ocean are to be considered in the permitting process, and as necessary permit conditions should be required to ensure protection of coral reefs from dumping impacts. In addition, pursuant to MPRSA Section 104(a)(4) and (5), permits or authorizations for site use should include as part of their terms and conditions any requirements deemed necessary to ensure protection of coral reefs. As under Section 404 of the CWA, there are circumstances where the impacts of the proposed activity are so significant that no conditions can ensure compliance with the ocean dumping criteria, and the permit should be denied.

Protection for Coral Reefs under RHA Section 10

Section 10 of the River and Harbors Act applies to waters subject to the ebb and flow of the tide and to waters lying inward of the territorial sea. The RHA requires a permit for any work or structure, including fill material discharges, in or affecting the course, condition, location, or capacity of navigable waters of the U.S. and artificial islands, installations, or other devices on the Outer Continental Shelf. The permit process involves consideration of public interest by balancing potential project benefits against potential adverse impacts. It is during the public interest review process that concerns surrounding any potential impacts to corals and coral reef systems would be considered. As a general matter, adverse impacts to coral reefs and coral reef systems are detrimental to the public interest. Corps findings for Section 10 permits should document how these impacts have been avoided.

Protection for Coral Reefs under the Coastal Zone Management Act

Section 307(c)(1) of the Coastal Zone Management Act (CZMA) requires that activities a Federal agency conducts or supports that affect the coastal zone be consistent with the enforceable policies of the Federally-approved State coastal management plan to the maximum extent practicable. As a general matter, State coastal management plans for areas that include coral reefs, include specific provisions to ensure that these valuable ecosystems are not harmed. Consistent with the provisions of Section 307(c)(3) of the CZMA, the Corps will not issue any permits or authorizations under CWA Section 404, MPRSA Section 103, or RHA Section 10 that do not have a State CZMA consistency determination. Similarly, EPA will not designate an ocean dumping site under MPRSA Section 102 without meeting the requirements of the CZMA.

Protection for Coral Reefs under Corps Federal Projects

Although the Corps does not process and issue itself permits for the activities it conducts pursuant to Congressionally authorized projects (e.g., projects authorized under the Water Resources Development Act), the Corps must make findings that demonstrate compliance with the substantive requirements of relevant law. Among these laws are CWA Section 404, MPRSA Sections 102 and 103, RHA Section 10, and the Federally-approved State management plan under the Coastal Zone Management Act (CZMA), as appropriate. Therefore the Corps will implement the specific protections provided for coral reefs under the above statutes when undertaking Federal projects.

Corps regulations provide that the preferred alternative must be the least costly plan that meets the environmental standards established by the Section 404(b)(1) evaluation process or the ocean dumping criteria, as set forth in the National Economic Development Plan for new works projects (ER 1105-2-100) or as the Federal Standard for required maintenance dredging of existing projects. During the Corps' project planning process, a national economic development objective is designed to maximize a project's benefits while also remaining consistent with protecting the Nation's environment. The Corps must consider all practicable and reasonable alternatives for proposed discharges of dredged or fill material into waters of the U.S. or ocean waters, in identifying the least costly alternative consistent with engineering and environmental requirements. Specifically, the Corps is responsible under the National Environmental Policy Act for evaluating alternatives for the discharge of dredged material, including cost, technical feasibility, and potential environmental impact. Any potential impacts to coral reefs, and how these impacts can be avoided, should be documented in the Corps' findings, consistent with the relevant environmental requirements.


Coral reefs are widely recognized as highly productive, ecologically valuable, and economically important ecosystems that, because of their particular sensitivity to environmental changes, are experiencing a world-wide decline. The CWA, MPRSA, RHA, and Federal Projects conducted by the U.S. Army Corps of Engineers, by statute and implementing regulations, give particular attention to protecting coral reefs as special aquatic sites from adverse chemical, biological, and physical impacts associated with discharges into the Nation's waters, including marine waters. Projects that may directly or indirectly adversely affect coral reefs will be given the highest level of protection. This guidance reemphasizes the protections intended for coral reefs under the laws our agencies implement and should ensure that agency field staff are applying these regulations to ensure effective protection for these critical marine ecosystems.


J. Charles Fox
Assistant Administrator
U.S. Environmental Protection Agency
Joseph W. Westphal
Assistant Secretary (Civil Works)
Department of the Army


1. Section 404 of the CWA also applies to the territorial sea. However, under the CWA Section 404(b) (1) guidelines, ocean dumping of dredged material in the territorial sea is primarily to be regulated under the MPRSA, with placement of fill material in the territorial sea (e.g., beach nourishment, artificial reefs) to be addressed by CWA Section 404 (40 C.F.R. 230.2(b).

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