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Regulatory and Permitting Information Desktop Toolkit

Federal Clean Water Act Section 404 Permit Application Process (14-FD-a)

The Clean Water Act (CWA) (33 U.S.C. 1251 et seq.) is the primary federal law for regulating the discharge of pollutants into waters of the U.S. Under Section 404 of the Clean Water Act, Department of Army authorization from the United States Army Corps of Engineers (USACE) is required for the discharge of dredge or fill material into waters of the U.S., including wetlands (Michigan and New Jersey have assumed responsibility for the Section 404 Program for projects within their jurisdiction, so contact the appropriate State agency regarding Section 404 compliance). See 33 CFR 328 for the definition of waters of the U.S.

Regulations governing the Regulatory Program can be found at 33 CFR 320-332. Regulations specifically related to permits for the discharge of dredged or fill material into waters of the United States can be found at 33 CFR 323. Although Section 10 of the Rivers and Harbors Act of 1899 and Section 404 requirements differ in some ways, the application review process is generally the same except for projects that require an alternatives analysis under the Section 404(b)(1) Guidelines which is discussed in greater detail later.

In addition to the normal application review process, USACE has developed multiple general permits to authorize common activities that are minimally impacting both individually and cumulatively. These general permits are an expeditious way to receive authorization for a project that has been designed to meet the terms and conditions of the general permit.

USACE uses three types of general permits: Nationwide Permits, Regional General Permits, and Programmatic General Permits. The USACE Regulatory program is implemented by 38 district offices and not all districts use all types of general permits. In addition, many districts have regional conditions on Nationwide Permits so when determining if the project meets the terms and conditions of a Nationwide Permit, first verify which district the project is in and then visit the district website for the regional conditions. District offices can also answer any questions regarding the terms and conditions and/or applicability of a certain general permit to a proposed activity. Some general permits do not require any notification to USACE to use them while others may require notice to and verification from USACE prior to use.

In those cases where the activity cannot be designed to meet the terms and conditions of a general permit, an individual permit is required. The Individual Permit can be a Letter of Permission which is also an abbreviated process that is primarily used for Section 10 only activities that have minor impacts and no appreciable opposition. The other type of individual permit is a Standard Individual Permit and is most often just called an “Individual Permit.” This process is more detailed and is the primary focus of the remainder of this section and the associated flow chart.

Note that regardless of the type of permit, USACE must also comply with Section 7 of the Endangered Species Act, Section 106 of the National Historic Preservation Act, and its Tribal Trust Responsibilities. Additional information may be required from the developer for USACE to comply with these laws but such processes are not discussed in detail in this section since they are applicable to any federal action associated with the proposed activity. See On-Site Evaluation Process: 10

USACE may require compensatory mitigation for impacts to aquatic resources regardless of permit type. See 33 CFR 332 for more information.

The discussion below and flowchart assume that the developer already knows a permit is required. In cases where the developer is unsure if an aquatic feature, such as a wetland, at the potential project site is jurisdictional and subject to Section 404 permit requirements, he or she should contact the USACE district early in the process, prior to the project design stage if possible, to discuss any information that may be needed by USACE to make a jurisdictional determination, such as a wetland delineation report. To avoid delays during the application review process, such information should be provided to USACE as early as practicable.

Clean Water Act Section 404 Permit Application Process Process

14-FD-a.1 – Conduct Pre-Application Consultation for Major Applications

USACE will hold a pre-application consultation upon request by developers and in accordance with local procedures. See 33 CFR 325.1(b). The developer will be required to submit sufficient information to USACE to facilitate the pre-application meeting. Contact the appropriate district for the type of information needed. At the meeting, USACE project manager will provide the developer with information related to the application, including criteria used to assess the project. This process should be brief but thorough enough to allow the potential applicant to begin addressing the viability of some more obvious potential alternatives in the application. More informal pre-application meetings can be held for minor project proposals.

14-FD-a.2 to 14-FD-a.3 – Does the Proposed Activity Qualify for a General Permit?

The developer should first determine if the proposed activity qualifies for a general permit or contact the appropriate district if unsure. If there are no applicable general permits to fit the category of activity contemplated, the developer should contact the appropriate USACE district to determine whether an individual permit is necessary and if so, whether it is a Letter of Permission or a Standard Individual Permit.


There is a nationwide permit for "discharges of dredged or fill material associated with hydropower projects having: (a) Less than 5000 kW (5 MW) of total generating capacity at existing reservoirs, where the project, including the fill, is licensed by the Federal Energy Regulatory Commission (FERC) under the Federal Power Act of 1920, as amended; or (b) a licensing exemption granted by the FERC pursuant to Section 408 of the Energy Security Act of 1980 (16 U.S.C. 2705 and 2708) and Section 30 of the Federal Power Act, as amended." If the project falls within the nationwide permit, the developer need not complete this Clean Water Act Section 404 Permit Application Process but must submit a pre-construction notification to the district engineer prior to commencing activity.

(See USACE 2012 Nationwide Permits at 10).

14-FD-a.4 – Application for Department of the Army Individual Permit (ENG Form 4345)

When an individual permit is required, the developer should submit a complete application to the appropriate USACE district office. The application can be found at Engineering Form 4345. Note some districts may have joint permit applications with local or state agencies so please review the appropriate district website for application materials.

According the 33 CFR 325.1(d)(1), the application must include:

  • A complete description of the proposed activity including necessary drawings, sketches, or plans sufficient for public notice (detailed engineering plans and specifications are not required);
  • The location, purpose and need for the proposed activity;
  • Scheduling of the activity;
  • The names and addresses of adjoining property owners;
  • The location and dimensions of adjacent structures; and
  • A list of authorizations required by other federal, interstate, state, or local agencies for the work, including all approvals received or denials already made.

Further requirements for specific activities are listed in 33 CFR 325.1(d)(3)-(7) and (9). The application is deemed complete when it contains sufficient information to issue a public notice, as defined by 33 CFR 325.3(a). See 33 CFR 325.1(d)(10).

14-FD-a.5 to 14-FD-a.6 – Review Application Materials for Completeness

According to 33 CFR 325.2(a)(2), the district engineer must review the application for completeness and either issue public notice if complete or notify the applicant if incomplete. The application completeness review and notification must be done within 15 days of receipt of the application.

14-FD-a.7 to 14-FD-a.8 – Prepare and Publish Public Notice of Application; Comment on the Application

Within 15 days or receipt of a complete application, the USACE district office will issue a public notice of the submitted application. See 33 CFR 325.2(a)(2). The Public notice will be issued in accordance with the standard procedures specified in 33 CFR 325.3. The notice should include the items listed in 33 CFR 325.3(a) and a description of factors used to evaluate the application. Any comments received will be sent to the applicant for a response. USACE must address all comments in its Administrative record.

Once the public notice is issued, the district engineer may require the developer to submit additional information that is essential for the USACE to complete its NEPA documentation, public interest review, and, if applicable, an alternatives analysis under Section 404(b)(1) Guidelines and/or to and comply with other laws such as Section 7 of the Endangered Species Act and Section 106 of the National Historic Preservation Act.

14-FD-a.9 – Hold Public Hearing (Optional)

Whenever a public hearing is needed for USACE to make a permit decision or upon request by any person, in writing, during the comment period, a public hearing will be held on the proposed permit decision. See 33 CFR 327.4. When a public hearing is requested, USACE will only hold one if it determines such a hearing is necessary to make an informed decision.

14-FD-a.10 to 14-FD-a.11 – Has the Proposed Project Received State 401 Certification?

Under section 401 of the Clean Water Act (CWA), a federal agency may not issue a license authorizing the construction or operation of a project unless the appropriate state agency first issues a water quality certification for the project or waives certification by failing or refusing to act on a request for certification within a reasonable period of time. 33 USC 1341(a)(1). In order to allow the state agency sufficient time to analyze the impacts of the project on water quality and to meet the deadline for demonstrating compliance with section 401 of the CWA, the developer should request water quality certification from the appropriate state authority early on in the FERC licensing process.

USACE permit cannot be granted until the WQC is obtained or waived. See 33 CFR 325.2(b)(ii). Generally, a developer will apply to USACE and the WQC agency at the same time so the reviews can occur concurrently. Some USACE districts and WQC agencies use joint applications and issue joint public notices. Note it is the developer’s responsibility to notify each agency of changes required by another agency that could affect the application.


In Alaska, the Alaska Department of Environmental Conservation (ADEC) reviews and issues 401 Water Quality Certifications. ADEC reviews hydropower projects filed with the Federal Energy Regulatory Commission (FERC) in accordance with 18 AAC 15.180 and may issue a 401 WQC or waiver. For more information, see: 401 Water Quality Certification:


In California, the California State Water Resources Control Board and the regional water quality control boards implement Section 401 of the Clean Water Act. For more information, see:

401 Water Quality Certification:


In Colorado, the Colorado Department of Public Health and Environment Water Quality Control Division regulates water quality and wetlands through the State’s 401 Water Quality Certification Program. For more information, see:

401 Water Quality Certification:

New York

In New York, the New York State Department of Environmental Conservation (DEC) Division of Water Resources reviews and issues 401 Water Quality Certifications (WQC).

401 Water Quality Certification:


In Vermont, the Vermont Department of Environmental Conservation regulates water quality and issues 401 Water Quality Certifications pursuant to the Clean Water Act. For more information, see:

401 Water Quality Certification:


In Washington, the Washington State Department of Ecology (WSDE) reviews and issues 401 Water Quality Certifications (WQC). The developer must submit a 401 WQC application for any hydropower project requiring a FERC license, license amendment, or re-licensing. Washington currently does not require a 401 WQC for FERC exempted projects. For more information, see:

401 Water Quality Certification:

14-FD-a.12 to 14-FD-a.13 – Has the Proposed Project Received a CZMA Consistency Determination?

The developer must also apply for and receive Coastal Zone Management Act consistency determinations from the State, if applicable, prior to USACE rendering a permit decision. It is the responsibility of the developer to apply for and receive such approvals. Again, this can be applied for concurrently with USACE permit application.

For more information regarding CZMA determinations, see:

Coastal Zone Federal Consistency Determination:

Coastal Zone Federal Consistency Determination:

14-FD-a.14 to 14-FD-a.15 – Has Environmental Review Been Conducted?

The National Environmental Policy Act (NEPA) requires federal agencies to consider the potential environmental consequences of their proposed actions and any reasonable alternatives before undertaking a major federal action. The issuance of a permit by a federal agency is considered a major federal action. Consequently, a NEPA analysis must be performed before USACE can render a permit decision.

Depending on the category of activity involved, USACE must complete an Environmental Assessment (EA) and Finding of No Significance (FONSI), an Environmental Impact Statement (EIS), or a Categorical Exclusion (CatEX). See 33 CFR 325.2(a)(4). Information may be required from the developer for USACE to complete its review.

U.S. Army Corps of Engineers - NEPA Process:

For more information regarding NEPA implementation procedures for the USACE’s regulatory program, see 33 CFR 325, appendix B.

Similar to, and often combined with its NEPA analysis, is the USACE Public Interest Review. USACE must evaluate the proposed project impacts to determine whether or not the proposal is contrary to the public interest. See 33 CFR 320.4(a). The decision whether to issue a permit will be based on an evaluation of the probable impacts, including cumulative impacts, of the proposed activity and its intended use on the public interest. The benefits which reasonably may be expected to accrue from the proposal must be balanced against its reasonably foreseeable detriments. All factors which may be relevant to the proposal must be considered including the cumulative effects thereof: among those are conservation, economics, aesthetics, general environmental concerns, wetlands, historic properties, fish and wildlife values, flood hazards, floodplain values, land use, navigation, shore erosion and accretion, recreation, water supply and conservation, water quality, energy needs, safety, food and fiber production, mineral needs, considerations of property ownership and, in general, the needs and welfare of the people.

In cases where there is a discharge of dredged or fill material into waters of the U.S., as regulated under Section 404 of the Clean Water Act, USACE must also conduct an alternatives analysis in accordance with the Section 404(b)(1) Guidelines. This is a much more stringent requirement than NEPA since under the Guidelines, no discharge shall be permitted if there is a practicable alternative that would have a less adverse impact on the aquatic ecosystem, so long as the alternative does not have other significant adverse environmental consequences. See 40 CFR 230.10. This is often called the “LEDPA” which is the Least Environmentally Damaging Practicable Alternative. The alternative must be practicable in terms of cost, logistics and existing technology. USACE will review the proposed project and ensure impacts to aquatic resources are avoided, then minimized, and then appropriately compensated for, in that order. A developer cannot skip a step in the sequence and cannot “buy down” impacts with additional compensatory mitigation. Projects should be designed to avoid aquatic resource impacts to the extent practicable.

For unavoidable impacts to aquatic resources proposed under Section 404, regardless of whether or not the project qualifies for a general or individual permit, USACE may require compensatory mitigation. See 33 CFR 332.

14-FD-a.16 to 14-FD-a.19 – Prepare Administrative Record; Record of Decision (ROD) or Statement of Findings (SOF)

Once all public hearings and comment periods have concluded, and USACE has completed the analyses outlined above, USACE will prepare the Administrative Record. Before issuing the final permit decision, USACE develops a Record of Decision (ROD) or a Statement of Finding (SOF) depending on whether the environmental process required an EIS or EA. See 33 CFR 325.2(a)(6).

14-FD-a.20 to 14-FD-a.22 – Is the Permit Approved?; Section 404 Permit

Once the SOF or ROD is complete, the district engineer must either take action on the permit or forward the report, application, administrative record, and recommendation to the authorized officer, in accordance with 33 CFR 325.8. See 33 CFR 325.2(a)(6).

If the final decision is to deny the permit, USACE will advise the applicant in writing of the reasons for denial. See 33 CFR 325.2(a)(7). If the permit has been denied with prejudice, the developer may then appeal the decision in accordance with the procedures found in 33 CFR 331 et seq.

Note that the EPA has veto authority in accordance with Section 404(c) of the Clean Water Act for any Section 404 permits USACE issues. See 40 CFR 231. This occurs very rarely (approximately 14 times since 1972).

If the final decision is to issue the permit, USACE will forward the permit to the applicant for signature accepting the general and special conditions of the permit. The permit is not valid until signed by the permittee and countersigned by the District Engineer, or designated official. See 33 CFR 325.2(a)(7). The developer can also appeal the permit if he or she disagrees with any of the terms and conditions.

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