Section 401 of the Clean Water Act (33 U.S.C. 1341) requires any applicant for a federal license or permit to conduct any activity that may result in a discharge of a pollutant into waters of the United States to obtain a certification from the State in which the discharge originates or would originate, or, if appropriate, from the interstate water pollution control agency having jurisdiction over the affected waters at the point where the discharge originates or would originate, that the discharge will comply with the applicable effluent limitations and water quality standards. A certification obtained for the construction of any facility must also pertain to the subsequent operation of the facility.

Section 307(c) of the Coastal Zone Management Act of 1972, as amended (16 U.S.C. 1456(c)), requires federal agencies conducting activities, including development projects, directly affecting a state's coastal zone, to comply to the maximum extent practicable with an approved state coastal zone management program. Indian tribes doing work on federal lands will be treated as a federal agency for the purpose of the Coastal Zone Management Act. The Act also requires any non-federal applicant for a federal license or permit to conduct an activity affecting land or water uses in the state's coastal zone to furnish a certification that the proposed activity will comply with the state's coastal zone management program. Generally, no permit will be issued until the state has concurred with the non-federal applicant's certification. This provision becomes effective upon approval by the Secretary of Commerce of the state's coastal zone management program. (See 15 CFR part 930).

The Fish and Wildlife Act of 1956 (16 U.S.C. 742a, et seq. ), the Migratory Marine Game-Fish Act (16 U.S.C. 760c–760g), the Fish and Wildlife Coordination Act (16 U.S.C. 661–666c) and other acts express the will of Congress to protect the quality of the aquatic environment as it affects the conservation, improvement and enjoyment of fish and wildlife resources. Reorganization Plan No. 4 of 1970 transferred certain functions, including certain fish and wildlife-water resources coordination responsibilities, from the Secretary of the Interior to the Secretary of Commerce. Under the Fish and Wildlife Coordination Act and Reorganization Plan No. 4, any federal agency that proposes to control or modify any body of water must first consult with the United States Fish and Wildlife Service or the National Marine Fisheries Service, as appropriate, and with the head of the appropriate state agency exercising administration over the wildlife resources of the affected state.

The Endangered Species Act (16 U.S.C. 1531 et seq. ) declares the intention of the Congress to conserve threatened and endangered species and the ecosystems on which those species depend. The Act requires that federal agencies, in consultation with the U.S. Fish and Wildlife Service and the National Marine Fisheries Service, use their authorities in furtherance of its purposes by carrying out programs for the conservation of endangered or threatened species, and by taking such action necessary to insure that any action authorized, funded, or carried out by the Agency is not likely to jeopardize the continued existence of such endangered or threatened species or result in the destruction or adverse modification of habitat of such species which is determined by the Secretary of the Interior or Commerce, as appropriate, to be critical. (See 50 CFR part 17 and 50 CFR part 402.)

The Marine Mammal Protection Act of 1972 (16 U.S.C. 1361 et seq. ) expresses the intent of Congress that marine mammals be protected and encouraged to develop in order to maintain the health and stability of the marine ecosystem. The Act imposes a perpetual moratorium on the harassment, hunting, capturing, or killing of marine mammals and on the importation of marine mammals and marine mammal products without a permit from either the Secretary of the Interior or the Secretary of Commerce, depending upon the species of marine mammal involved. Such permits may be issued only for purposes of scientific research and for public display if the purpose is consistent with the policies of the Act. The appropriate Secretary is also empowered in certain restricted circumstances to waive the requirements of the Act.

The primary intent of Section 106 of the National Historic Preservation Act of 1966 (NHPA; 16 U.S.C. 470) in relation to Section 10 and 404 permitting is to help the USACE make informed decisions on the treatment of historic properties, and to avoid, minimize, or mitigate adverse effects to historic properties whenever possible. NHPA provides public comment that is taken into account decisions affecting historic properties, but does not mandate any given outcome. Federal agencies with Section 106 issues are obligated to seek the opinions of the State Historic Preservation Officers of the state in which there are affected historic properties, and, if an undertaking affects sites of cultural or religious significance to any federally recognized American Indian tribe or tribes, or on tribal lands, the opinions of the respective tribe's Tribal Historic Preservation Officer or designated historic preservation representative. Ultimate decisions regarding historic properties and an undertaking’s effects to them remain the responsibility of the responsible Federal Agency official having jurisdiction, namely the head of that governmental unit (e.g., the District Engineer).

The USACE is required under the regulations governing its Regulatory authorities, to consider effects to historic properties, often referred to as cultural resources, in its permitting decisions. In addition, under Section 106 of the NHPA, Federal agencies that have direct or indirect jurisdiction over a Federal, or federally assisted undertaking having authority to license, permit, or fund any undertaking, are required to do two things prior to funding or issuing such permits or licenses: 1) take into account the effects of its actions on historic properties (cultural resources); and 2) allow the Advisory Council on Historic Preservation a reasonable opportunity to comment on such actions. Historic properties are defined for the purposes of Section 106 as those districts, sites, structures or objects listed on, or eligible for listing in, the National Register of Historic Places (NRHP). Under the USACE regulations governing its permitting authority (33 Code of Federal Regulations 320-332), the USACE may consider effects to other historic properties as well.

The Advisory Council on Historic Preservation (ACHP) is a small, independent Federal agency created by the National Historic Preservation Act to advise the President and Congress and Federal agencies on matters involving historic properties, or sites, and historic preservation. It was created as an independent agency to act as a neutral advisor. The Advisory Council's authority is restricted, advisory only, and not prescriptive; ultimate decisions involving historic properties affected by Federal actions remain the responsibility of the head of the Federal agency having jurisdiction over an undertaking. While the Advisory Council is supposed to provide an independent and balanced viewpoint, the NHPA, and the intent of Congress is not. Section 2 of the NHPA (16 U.S.C. 470-1) reads, in part: "It shall be the policy of the Federal Government, in cooperation with other nations and in partnership with the states, local governments, Indian tribes, and private organizations and individuals to: 1) Use measures including financial and technical assistance, to foster conditions under which our modern society and our prehistoric and historic resources can exist in productive harmony and fulfill the social, economic, and other requirements of present and future generations; and 2) encourage the public and private preservation and utilization of all usable elements of the Nation’s historic built environment."

The concern of Congress for the preservation of significant historical site, and particularly those of an archaeological nature, is also expressed in the Preservation of Historical and Archeological Data Act of 1974 (16 U.S.C. 469 et seq.), which amends the Archaeological Recovery Act of 1960, itself an outgrowth of the Historic Sites, Buildings and Antiquities Act of 1935. The 1935 Act was the first federal legislation in this country to declare a national policy on historic preservation. Under the 1974 Act, whenever a federal construction project or federally licensed project, activity, or program alters any terrain such that significant historical or archeological data is threatened, the Secretary of the Interior may take action necessary to recover and preserve the data prior to the commencement of the project.

Other important legislation and Executive Orders concerning historic properties which the USACE may sometimes need to consider in its permitting decisions are the Archaeological Resources Protection Act of 1979, the Abandoned Shipwreck Act of 1987, the Native American Graves Protection and Repatriation Act of 1990, the American Indian Religious Freedom Act of 1978, and Executive Order 11593, the latter codified as Section 110 of the NHPA (16 U.S.C. 470h-2).

The National Environmental Policy Act of 1969 (42 U.S.C. 4321–4347) declares the national policy to encourage a productive and enjoyable harmony between man and his environment. Section 102 of that Act directs that "to the fullest extent possible: (1) The policies, regulations, and public laws of the United States shall be interpreted and administered in accordance with the policies set forth in this Act, and (2) All agencies of the Federal Government shall "* * * insure that presently unquantified environmental amenities and values may be given appropriate consideration in decision-making along with economic and technical considerations * * *". (See Appendix B of 33 CFR part 325.)

Section 302 of the Marine Protection, Research and Sanctuaries Act of 1972, as amended (16 U.S.C. 1432), authorizes the Secretary of Commerce, after consultation with other interested federal agencies and with the approval of the President, to designate as marine sanctuaries those areas of the ocean waters, of the Great Lakes and their connecting waters, or of other coastal waters which he determines necessary for the purpose of preserving or restoring such areas for their conservation, recreational, ecological, or aesthetic values. After designating such an area, the Secretary of Commerce shall issue regulations to control any activities within the area. Activities in the sanctuary authorized under other authorities are valid only if the Secretary of Commerce certifies that the activities are consistent with the purposes of Title III of the Act and can be carried out within the regulations for the sanctuary.

The Federal Power Act of 1920 (16 U.S.C. 791a et seq. ), as amended, authorizes the Federal Energy Regulatory Agency (FERC) to issue licenses for the construction and the operation and maintenance of dams, water conduits, reservoirs, power houses, transmission lines, and other physical structures of a hydro-power project. However, where such structures will affect the navigable capacity of any navigable water of the United States (as defined in 16 U.S.C. 796), the plans for the dam or other physical structures affecting navigation must be approved by the Chief of Engineers and the Secretary of the Army. In such cases, the interests of navigation should normally be protected by a DA recommendation to FERC for the inclusion of appropriate provisions in the FERC license rather than the issuance of a separate DA permit under 33 U.S.C. 401 et seq. As to any other activities in navigable waters not constituting construction and the operation and maintenance of physical structures licensed by FERC under the Federal Power Act of 1920, as amended, the provisions of 33 U.S.C. 401 et seq. remain fully applicable. In all cases involving the discharge of dredged or fill material into waters of the United States or the transportation of dredged material for the purpose of disposal in ocean waters, section 404 or section 103 will be applicable.

The Interstate Land Sales Full Disclosure Act (15 U.S.C. 1701 et seq. ) prohibits any developer or agent from selling or leasing any lot in a subdivision (as defined in 15 U.S.C. 1701(3)) unless the purchaser is furnished in advance a printed property report containing information which the Secretary of Housing and Urban Development may, by rules or regulations, require for the protection of purchasers. In the event the lot in question is part of a project that requires DA authorization, the property report is required by Housing and Urban Development regulation to state whether or not a permit for the development has been applied for, issued, or denied by the Corps of Engineers under section 10 or section 404. The property report is also required to state whether or not any enforcement action has been taken as a consequence of non-application for or denial of such permit.

The Deepwater Port Act of 1974 (33 U.S.C. 1501 et seq. ) prohibits the ownership, construction, or operation of a deepwater port beyond the territorial seas without a license issued by the Secretary of Transportation. The Secretary of Transportation may issue such a license to an applicant if he determines, among other things, that the construction and operation of the deepwater port is in the national interest and consistent with national security and other national policy goals and objectives. An application for a deepwater port license constitutes an application for all federal authorizations required for the ownership, construction, and operation of a deepwater port, including applications for section 10, section 404 and section 103 permits which may also be required pursuant to the authorities listed in §320.2 and the policies specified in §320.4 of this part.

Section 7(a) of the Wild and Scenic Rivers Act (16 U.S.C. 1278 et seq. ) provides that no department or agency of the United States shall assist by loan, grant, license, or otherwise in the construction of any water resources project that would have a direct and adverse effect on the values for which such river was established, as determined by the Secretary charged with its administration.

The Ocean Thermal Energy Conversion Act of 1980, (42 U.S.C. section 9101 et seq. ) establishes a licensing regime administered by the Administrator of NOAA for the ownership, construction, location, and operation of ocean thermal energy conversion (OTEC) facilities and plantships. An application for an OTEC license filed with the Administrator constitutes an application for all federal authorizations required for ownership, construction, location, and operation of an OTEC facility or plantship, except for certain activities within the jurisdiction of the Coast Guard. This includes applications for section 10, section 404, section 103 and other DA authorizations which may be required.

Section 402 of the Clean Water Act authorizes EPA to issue permits under procedures established to implement the National Pollutant Discharge Elimination System (NPDES) program. The administration of this program can be, and in most cases has been, delegated to individual states. Section 402(b)(6) states that no NPDES permit will be issued if the Chief of Engineers, acting for the Secretary of the Army and after consulting with the U.S. Coast Guard, determines that navigation and anchorage in any navigable water will be substantially impaired as a result of a proposed activity.

The National Fishing Enhancement Act of 1984 (Pub. L. 98–623) provides for the development of a National Artificial Reef Plan to promote and facilitate responsible and effective efforts to establish artificial reefs. The Act establishes procedures to be followed by the Corps of Engineers in issuing DA permits for artificial reefs. The Act also establishes the liability of the permittee and the United States. The Act further creates a civil penalty for violation of any provision of a permit issued for an artificial reef.