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Water Quality/Wetlands


This section provides brief summaries of federal water quality and wetlands requirements applicable to the transportation community. Topics include the following:

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.

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Water Quality Basics

Water quality management requirements for transportation agencies are related to implementation of the NPDES program along with the water quality certification program under the CWA.

Currently there are three areas related to water quality that are having a significant impact on transportation practice nationwide:

  1. NPDES requirements for obtaining permits for operation and maintenance of Municipal Separate Storm Sewer Systems (MS4s).
  2. NPDES requirements for permitting Stormwater Discharges Associated with Construction Activities.
  3. NPDES requirements for compliance with effluent standards related to established Total Maximum Daily Loads or other effluent discharge standards that may be required by the state regulatory agency.

[Note: Water quality issues span a broad range of concerns that overlap into many areas of science and numerous environmental issues and concerns. This section deals only with the primary issues of stormwater quality and that impact the detailed design and construction of transportation facilities. Other water related issues, such as ground water, water supply, water and stormwater quantity, aquatic habitat, etc., are not addressed here.]

National Pollutant Discharge Elimination System (NPDES) Municipal Separate Storm Sewer Systems (MS4) Permitting Requirements under CWA Section 402

To achieve its objectives, CWA Section 402 considers all point source discharges into the nation’s waters unlawful, unless authorized by a permit. Thus industrial and municipal entities that discharge any type of water such as waste water or stormwater, must obtain permits from EPA or a designated state program, under the NPDES.

Stormwater runoff from transportation facilities and construction projects is considered by broad definition under the CWA to be a point source discharge and has been identified as a major source of pollutants discharged into the nation’s waters.

Therefore, as part of the implementation of the NPDES, permits are required for operation of MS4s. Under the initial implementation of the MS4 Phase I program (1990) stormwater discharge permits were required for urbanized areas with populations greater than 100,000. These are called “large and medium MS4s.” Most state transportation agencies had facilities in one or more of the regulated MS4s and were required to obtain individual permit coverage or joint coverage with the municipal jurisdiction. These permits must be renewed on a 5-year cycle. A detailed summary of the Phase I Program is available in EPA's Overview of the Stormwater Program.

Phase II permits required stormwater quality monitoring programs for wet weather and dry weather discharges, and the development of detailed stormwater management programs (SWMPs). Stormwater management programs also were required to implement public education and outreach on stormwater impacts, public involvement/participation, illicit discharge detection and elimination, construction site stormwater runoff control, post-construction stormwater management in new development and redevelopment, pollution prevention/good housekeeping for municipal operations.

The Phase II rules include many of the State transportation agencies that were not included in the Phase I permits. Phase II includes urbanized areas with over 50,000 in population with storm sewer systems that discharge into waters of the U.S. not covered by Phase I. These are referred to as “small MS4s.” State transportation agencies will work with municipalities in small urbanized areas to obtain their permits and contribute to the development and implementation of a Stormwater Management Program (SWMP).

A SWMP must include measurable goals for each of the “minimum control measures.”

  • Public Participation/Involvement
  • Public Education and Outreach
  • Illicit Discharge Detection and Elimination
  • Construction Site Runoff Control
  • Post-Construction Runoff Control
  • Pollution Prevention/Good Housekeeping

While the SWMP must address all six of these minimum measures, two of these – post-construction runoff control and pollution prevention/good housekeeping – are having a significant impact on current and future development of highway and other transportation systems. The requirement for post-construction runoff control requires that new and redevelopment projects address stormwater runoff with permanent best management practices (BMPs) of some type. For rural corridors the vegetated roadside is generally sufficient to handle normal stormwater discharges. However, in urban areas where space is limited more reliance must be placed on active treatment systems. This is probably the next area of focus, particularly for those transportation agencies in large metropolitan areas.

The Phase II requirement for good housekeeping is also an area of impact that has been given less attention but has been a significant challenge to many transportation agencies. The areas of greatest impact are departmental equipment maintenance yards, bulk storage areas for deicing materials and aggregates, rest areas and roadside parks, and other permanent facilities operated by the transportation agency. Many of these facilities require the implementation of special controls and management measures to control stormwater runoff.

At this time all state departments of transportation are working on implementing their SWMPs to address the six minimum measures. Because there is such variety in the implementation strategy the individual states should be contacted for specific program information.

NPDES Stormwater Management for Construction Sites

The rules implementing the NPDES required that eleven categories of industrial activity obtain permits to discharge stormwater. Because stormwater discharges from construction sites are significantly different than other types of industrial stormwater, EPA opted to permit construction activities separately from other industrial activities. The rules require stormwater discharge permits for sites of one acre or greater. Some states classify sites of one to five acres as “small sites.” Sites of five acres or more are classified “large sites,” and they have different permitting requirements from state to state.

The permitting requirements for construction projects should not be confused with other management requirements of the MS4 permits. Although construction is a temporary activity, the loss of surface cover exposes the soil and will result in accelerated erosion if not properly managed. By volume, soil particles are the number one pollutant in the nation’s waters. Sediment-bearing runoff from construction sites has been identified as a source of pollutants that can result in significant damage to water quality. As runoff moves over a construction site, it mobilizes all available pollutants, which may include: soil particles which may bond with other chemicals, surface debris, soluble chemicals, pathogens, grease and oil, etc. If this runoff is allowed to reach a water body or a conveyance that is connected to a water resource it can result in significant adverse impacts.

The NPDES stormwater program recognizes that construction site runoff represents a pollution risk that is significantly different from other industrial stormwater discharges. Therefore the NPDES requires operators of constructions sites of one acre or larger (including smaller sites that are part of a larger common plan of development) to obtain authorization to discharge stormwater under a state or federal NPDES construction stormwater permit. The Construction General Permits (CGPs) issued by states and EPA require the filing of a Notice of Intent, the development of a Storm Water Pollution Prevention Plan (SWPPP) and filing a Notice of Termination once the construction site has been restabilized. The key document is the SWPPP which details how the site will be managed to prevent the pollution of adjacent waters.

EPA has delegated the construction permitting authority to most of the state resource agencies; however, EPA remains the permitting authority in a few states, territories, and on most federal and Indian lands. For construction on EPA regulated lands, construction projects must seek coverage under the EPA Construction General Permit (CGP). State construction general permits have a similar structure to EPA’s CGP, but individual states may have additional requirements that are tailored to protect the unique characteristics of their water resources.

Coverage of NPDES general permits for construction stormwater discharges is limited to five years.

Total Maximum Daily Loads (TMDLs): Establishment of State-based Water Quality Standards under Clean Water Act Section 303

Under section 303(d) of the Clean Water Act, all states must develop a list of impaired water bodies. This list is generally referred to in regulatory documents as the “303(d) list.” For all of the water bodies on the 303(d) list the rule requires that total maximum daily loads (TMDLs) be established in order to return impaired water bodies to fishable and/or swimmable condition. The TMDL places an upper limit on the amount of a particular pollutant, such as nutrients, sediments, pathogens, or other chemical pollutants, that can be discharged into a specific water body. These loads are then distributed across all permittees that discharge into that water body.

In addition to the effluent standards required by an established TMDL, many states are adding effluent standards to their general permits for stormwater discharges for construction activities. Many standards being developed are focused on protecting high quality waters and to ensure that the combined BMPs used for stormwater control on construction sites are protecting adjacent waters and determining the actual effectiveness of stormwater BMPs.

Under Section 303(d), states, territories, and authorized tribes are required to develop lists of impaired waters. These impaired waters do not meet water quality standards that states, territories, and authorized tribes have set for them, even after point sources of pollution have installed the minimum required levels of pollution control technology. The law requires that these jurisdictions establish priority rankings for waters on the lists and develop TMDLs for these waters.

A TMDL specifies the maximum amount of a pollutant that a waterbody can receive while still meeting water quality standards, and it allocates pollutant loadings among point and non-point pollutant sources. As TMDLs and WLAs are developed for the impaired waters, dischargers, including highway agencies, must implement Best Management Practices (BMPs) to reduce contributions from transportation-related land uses.

By law, EPA must approve or disapprove lists and TMDLs established by states, territories, and authorized tribes. If a state, territory, or authorized tribe submission is inadequate, EPA must establish the list or the TMDL. EPA issued regulations in 1985 and 1992 that implement CWA section 303(d). Once a TMDL is developed for a surface water body, a waste load allocation (WLA) must be developed specifying how much of a given constituent can be contributed to a particular water body by each discharge and discharger.

While TMDLs have been required by the Clean Water Act since 1972, until recently states, territories, authorized tribes, and EPA have not developed many. Several years ago citizen organizations began bringing legal actions against EPA seeking the listing of waters and development of TMDLs. According to EPA, there have been about 40 legal actions in 38 states to date. EPA is under court order or consent decrees in many states to ensure that TMDLs are established, either by the state or by EPA.

On July 21, 2003, EPA issued Guidance for 2004 Assessment, Listing and Reporting Requirements Pursuant to Sections 303(d) and 305(b) of the Clean Water Act. The guidance is intended to be used by states in developing their integrated lists of impaired waters under Section 303(d) of the act and their reports describing the quality of their waters under Section 305(b). Additional information is available on the EPA TMDL website, including the policy memo “Establishing Total Maximum Daily Load (TMDL) Waste-Load Allocations (WLAs) for Stormwater Sources and NPDES Permit Requirements Based on Those WLAs.” This memo clarifies EPA's policy on waste-load allocations (WLAs), specifically that NPDES-regulated stormwater must be included in the WLA component of the TMDL and affirms EPA's view that an iterative, adaptive management BMP approach is appropriate.

Stormwater Provision in SAFETEA-LU

The Safe, Accountable, Flexible, Efficient Transportation Equity Act: A Legacy for Users (SAFETEA-LU) modified the eligibility of Federal-aid funds to participate in environmental restoration and pollution abatement (stormwater runoff) activities to minimize or mitigate the impacts of transportation projects. According to FHWA guidance, this section primarily deals with the impacts of transportation facilities that were built prior to the current, more stringent requirements for abatement of stormwater runoff. These transportation facilities may have been constructed with limited or no stormwater treatment controls.

The guidance specifies that SAFETEA-LU provides the means to fund retrofits and the construction of stormwater treatment systems to address water pollution and environmental degradation that is caused in whole or in part by a transportation facility. These measures may be implemented under two basic scenarios:

  • a stand-alone project, one that is developed solely to address stormwater concerns and is not associated with a transportation project that is being developed or is under construction; or
  • in conjunction with a project that is currently being developed for the reconstruction, rehabilitation, resurfacing, or restoration of a transportation facility. In this case, the costs for environmental restoration and pollution abatement may not exceed 20 percent of the total cost of the project.

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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, Sixth Circuit Court of Appeals issued an order in October 2015 staying the new Clean Water Rule nationwide, pending a determination by the court on jurisdiction to review the rule. Thus, the Clean Water Rule is stayed, and the prior 1986 regulations are in effect nationwide. The two agencies are evaluating the order and its implications for the litigation that is currently pending in district courts. In the meantime, the Corps is not implementing the Clean Water Rule, and is using the 1986 regulations and applicable guidance (those in effect prior to August 28, 2015) in making jurisdictional determinations or taking other actions based on the definition of "waters of the United States." For more information, link to the U.S. Army Corps' Jurisdictional Information web page.

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.

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