Water Quality and Wetlands Background

The Federal Water Pollution Control Act (1972), referred to as the Clean Water Act (CWA) when amended in 1977, is the principal federal law protecting surface waters in the United States. The CWA establishes the regulatory authority which is administered by the Environmental Protection Agency (EPA) and/or U. S. Army Corps of Engineers (Army Corps), directly or in concert with the states and tribes, to manage and control the discharge of pollutants into U.S. surface waters. The principal enforcement mechanisms of the law are pollutant discharge limits and permitting programs. Toward that end, the legislation authorizes EPA to establish and enforce pollution control performance standards; assist states and tribes with establishing and enforcing water quality criteria and pollution control programs; provide financial and technical assistance to states and municipalities for constructing waste water treatment facilities; and oversee other federal agencies implementing various sections of the Act or conducting activities controlled under the Act. In 1972 the CWA Section 404 established control of discharges into U.S. waters associated with dredging and filling activities. This provision has since been used to control and mitigate the loss of wetlands. The regulatory program developed to implement Section 404 of the CWA is administered by the Army Corps with oversight by EPA.

Beginning in 1987, Congress amended the Clean Water Act to broaden the definition of point sources to include stormwater discharges from industrial activities. The first phase of the program (Phase I) required certain industrial dischargers, medium and large municipal separate storm sewer systems (MS4s), and operators of construction sites greater than five acres to obtain National Pollutant Discharge Elimination System (NPDES) permits. The second phase of the program (Phase II) directed EPA to designate certain categories of dischargers for regulation under the NPDES program. Phase II requirements address urbanized areas usually with a population over 50,000 and construction projects of one acre or more. The program is designated to the States in 45 cases, usually in their State water quality agencies.

Implementation of the wetlands regulations (Section 404) and the NDPES (Section 402), along with Water Quality Certification (Section 401) programs have had the greatest impact on the transportation industry, and they will continue to have significant impacts in the future as the programs mature.

Emphasis of CWA programs over the last two decades also is shifting from a program-by-program, source-by-source, pollutant-by-pollutant, approach to more regional or watershed-based strategies. Transportation agencies increasingly are adopting watershed approaches to prevent and mitigate impacts to wetlands and other aquatic resources.

Under the watershed approach equal emphasis is placed on protecting healthy waters and restoring impaired ones. A full array of issues are addressed, not just those subject to CWA regulatory authority. The identification and adoption of watershed-based pollutant loading objectives and limits called Total Maximum Daily Loads (TMDLs) are the central elements of this approach. (More information about TMDLs is provided below.) Involvement of stakeholder groups in the development and implementation of watershed-based strategies for achieving and maintaining state water quality and other environmental goals is essential.

Wetlands Basics

Wetlands and similar surface waters are typically important and valuable transition areas between uplands and deep water habitats. Their recognized ecological values have led to a variety of governmental protection measures, most notably the policies and regulatory programs operating under the CWA. Federal authorities beyond the CWA include Executive Order 11990, Protection of Wetlands. This Executive Order directs federal agencies and their partners receiving federal assistance to avoid to the extent possible adverse impacts associated with the destruction or modification of wetlands and to avoid direct or indirect support of new construction in wetlands wherever there is a practicable alternative. It also directs that impact mitigation be implemented when avoidance is not practicable. The Order covers all wetlands, not just those falling under jurisdiction of CWA regulatory programs. Other Federal programs designed to conserve and protect wetlands include the Emergency Wetlands Protection Resources Act of 1986 (16 U.S.C. 3921-3931), the North American Waterfowl Management Plan (16 U.S.C. 4401(a)(12)), and the Wetlands Reserve Program (16 U.S.C. 3837).

In addition, there can be state and local wetland protection programs and regulations that must be met when planning and building transportation projects in certain locations. This website will not attempt to list those requirements as there are too many to cover and they may apply only in limited situations. Nevertheless they can be important considerations during the development of transportation improvements and need to be followed according to state and local procedures.

Regulation And Permitting Requirements on the Discharge of Dredged and Fill Material under Clean Water Act Section 404

Section 404 of the CWA prohibits discharges of dredged and fill material into wetlands and other “waters of the United States,” except as authorized by a permit issued under this section. The responsibility for implementing the Section 404 program is divided among several agencies. At the federal level, the Corps is responsible for issuing Section 404 permits, while EPA is responsible for establishing the guidelines that the Corps must follow when making permitting decisions. In addition, EPA has authority under some circumstances to veto permits issued by the Corps. State governments also play an important role. Before the Corps can issue a permit, the project applicant must obtain certification under CWA Section 401 from the state water quality agency that the proposed activity meets state water quality standards.

In addition, the CWA allows the Corps to delegate its Section 404 permitting authority to a state agency having an approved assumption program. The Clean Water Act provides that the states may assume administration of Section 404 in certain waters within the state. A.

Section 404(b)(1) Guidelines

Under Section 404, the EPA issued regulations to guide the Corps permitting decisions. These regulations are commonly known as the “Section 404(b)(1) Guidelines.” They are codified at 40 CFR Part 230. The Guidelines establish criteria that must be met before a Section 404 permit can be issued. These criteria preclude issuance of a Section 404 permit if there is a practicable alternative that causes less harm to the aquatic ecosystem, unless that less-damaging alternative has “other significant adverse environmental consequences.” This requirement is commonly referred to as the “Least Environmentally Damaging Practicable Alternative” (LEDPA) requirement.

Individual and General Permit Programs and Letters of Permission

The Corps regulations implementing the Section 404 permitting program establish the process for filing permit applications and describe the information that needs to be included in those applications. The regulations allow for both individual permits and general permits. General permits are issued for categories of projects that have similar, and most often, minor impacts. General permits include both regional programmatic permits and nationwide permits. The Corps Divisions issue regional permits. They only apply in the geographic area covered by the Division for activities involving specific types and amounts of fill or dredged material. Nationwide permits are issued at the national level and can be used in all areas of the country subject to individual state approval and other specific restrictions and requirements. Nationwide permits generally are effective for five years, after which the Corps will reissue the general authorizations for another five years with or without revision. Revisions to the program may include new permits, direct changes to existing permits, new and adjusted conditions that permit users must observe, or revoked permits.

Corps Districts can also authorize work under Section 404 with letters of permission. Letters of permission can be issued in situations where the USACE District Engineer determines the proposed work would be minor, would not have significant individual or cumulative impact on environmental values, and would not encounter significant opposition. Section 404 letters of permission can be issued only in cases where the District Engineer has previously approved similar activities under the letter of permission procedures (see 33 CFR 325.2, subsection (e)(1). Requesting a letter of permission may be an appropriate and expedient way to comply with Section 404 for many localized and non-controversial actions.

Wetlands Jurisdiction

The CWA defines “waters of the United States” as “navigable waters.” When the Corps first issued regulations to implement the Section 404 program, they limited the program’s jurisdiction to traditionally navigable waters, including adjacent wetlands, excluding many small waterways and most wetlands. Due to several subsequent court decisions and other policy shifts, the Corps eventually included waters not immediately adjacent to those that are traditionally navigable. These areas became the so-called “isolated waters” and were afforded jurisdictional protection under the CWA 404 permit program.

The Supreme Court ruling in Solid Waste Agency of Northern Cook County v. Corps of Engineers, 531 U.S. 159 (2001) (SWANCC) raised new questions regarding the jurisdictional reach of federal wetlands regulations. The ruling invalidated the so-called Migratory Bird Rule as a way to establish federal jurisdiction over certain isolated U.S. waters. The ruling stated that the Corps cannot legally assert jurisdiction over intrastate, non-navigable isolated waters when the only tie to interstate commerce is the use of the waters by migratory birds. Essentially, this decision removed intrastate, non-navigable isolated waters from Section 404 coverage unless there is some other reason that demonstrates use of such waters for traditionally navigable or interstate commerce purposes. The EPA and the Corps issued a joint policy memorandum which formally instructs their field offices not to assert jurisdiction over intrastate, non-navigable isolated waters when the only reason they have for asserting jurisdiction is the Migratory Bird Rule. If those offices intend to assert jurisdiction on other factors, such as interstate commerce on such waters, they must first seek the approval of their headquarters unit. [For further information, see FHWA Information and Guidance on Jurisdictional Coverage of Isolated, Non-Navigable Intrastate Waters, January 2003.]

In a subsequent decision, the Supreme Court ruled further on the jurisdictional reach of the Section 404 permit program by remanding two recent cases back to a lower court for adjudication. These cases, Rapanos, et al v. U.S. and Carabell, June, et al. v. Corps of Engineers challenged the jurisdictional reach of federal wetlands regulations, specifically the government’s interpretation of “adjacent to navigable waters” and “connected to the tributary system of navigable waters.” While court did not specifically invalidate the previous determinations of jurisdiction, the majority opinion raised major concerns about the reasoning used in the lower court decision. The Court concluded that in both cases the lower court opinions had misjudged the factors necessary to determine whether the lands in question had, or did not have, the required nexus to navigable waters and remanded the case for further review to determine if, in fact, there is sufficient connection to justify the government’s claim of jurisdiction. For further information, see the Rapanos opinion.

On June 5, 2007, EPA and the Corps issued guidance on jurisdiction based on the two Supreme Court decisions. Based on public comments received on the guidance, the agencies issued a revised version on Dec. 2, 2008.

The 2008 revised guidance, Clean Water Act Jurisdiction Following the U.S. Supreme Court’s Decision in Rapanos v. United States & Carabell v. United States, The 2008 guidance includes a summary regarding how the two agencies will determine jurisdiction.

Waters of the U.S. Rule and Litigation

In May 2015, The U.S. Army Corps of Engineers and EPA published a joint final rule for the definition of Waters of the U.S. under the Clean Water Act. Following several legal challenges, EPA and the Corps published a joint final rule redefining the scope of federal jurisdiction over rivers and wetlands. The final rule, called the “Navigable Waters Protection Rule,” amends the definitions of what are considered and what are not considered waters under federal jurisdiction, for the purposes of discharge and wetlands permitting. The final rule includes, among other things, the new concept of a “typical year” to be used when determining whether a stream is intermittent and protected, or ephemeral and unprotected. The water levels of an aquatic body during a “typical year” are based on a rolling 30-year average of precipitation. The rule took effect in June 2020. For more information, see the EPA Navigable Waters Protection Rule website.

Wetlands Mitigation

Avoidance, minimization, and compensation of impacts are the key elements of the basic federal authorities protecting wetland resources. As mentioned above, Executive Order 11990, the Section 404(b)(1) Guidelines, and the Section 404 permitting regulations are the primary directives setting these measures of wetland mitigation. But there are also various other supporting policies and rules which transportation agencies should also recognize and implement.

The FHWA implements the regulatory and national policy requirements stated above. The Intermodal Surface Transportation Efficiency Act (ISTEA), the Transportation Equity Act for the 21st Century (TEA-21), and the Safe, Accountable, Flexible, Efficient Transportation Equity Act: A Legacy for Users (SAFETEA-LU) all recognized wetlands management regulations, procedures and processes, and included important new authorities for participation in costs of wetlands mitigation with Federal transportation funds. Discussion of this participation is found in the FHWA regulation concerning mitigation of wetlands [See Mitigation of Impacts to Wetlands and Natural Habitat – Final Rule, 65 FR 82913; 12/29/00)].

TEA-21 and SAFETEA-LU specify a preference for mitigation banking to compensate for unavoidable losses to wetlands or other natural habitat caused by transportation projects receiving Federal assistance under Title 23 of the US Code. [See Federal-aid Eligibility of Wetland and Natural Habitat Mitigation, Federal Guidance on the Use of the TEA-21 Preference for Mitigation Banking to fulfill Mitigation Requirements under Section 404 of the Clean Water Act and Federal Guidance for the Establishment, Use and Operation of Mitigation Banks.]

In 2008, EPA and the U.S. Army Corps of Engineers jointly promulgated regulations revising and clarifying requirements regarding compensatory mitigation. According to the regulations, compensatory mitigation means the restoration (re-establishment or rehabilitation), establishment (creation), enhancement, and/or in certain circumstances preservation of wetlands, streams and other aquatic resources for the purposes of offsetting unavoidable adverse impacts which remain after all appropriate and practicable avoidance and minimization has been achieved.

Under the regulations, there are three mechanisms for providing compensatory mitigation (listed in order of preference as established by the regulations): mitigation banks, in-lieu fee programs, and permittee-responsible mitigation. For more information and link to the regulations, see EPA’s Compensatory Mitigation page.