You are here

Water Resources (including Wetlands, Stormwater Management, Floodplains)

NEPA requires analysis and consideration of the effects of a proposed project on water resources, including coastal zones, floodplains, navigable waterways, water quality and stormwater, wetlands and other Waters of the U.S., as appropriate (e.g., a landlocked state does not need to consider coastal zones). Each of these topics is discussed in further detail below.

Coastal Zone Management

What is the Coastal Zone Management compliance process?

If a transit project will directly affect the coastal zone of any state with an approved  Coastal Zone Management (CZM) Program, the environmental document must show whether the project will be consistent with the CZM Plan. The Coastal Zone Management Act of 1972 (16 USC § 1451 et seq.), as amended, established a voluntary federal-state partnership to protect, restore, and responsibly develop our nation’s coastal communities and resources. Thirty-three of eligible , territories, and commonwealths (collectively referred to as coastal states) currently participate in the Coastal Zone Management Program.

The state agency managing the program, called the principal 306 agency, is usually the state Department of Natural Resources, Department of Ecology, or equivalent agency. Its procedures are used for determining consistency with the state’s federally approved CZM Plan, and FTA must obtain its opinion on whether the proposed project is consistent with the state's program. The environmental document should document that the project is (or is not) consistent with the CZM program and the consultation with the state agency.

The Coastal Barrier Resources Act (16 USC § 3501 et seq.) (CBRA) designates a protected network of undeveloped coastal barriers located on the Atlantic and Gulf Coasts called the Coastal Barrier Resources System. (Congress later passed the Great Lakes Coastal Barrier Act (Public Law 100-707), pursuant to which the Dept. of Interior identified additional System units along the .)  Section 5 of this Act prohibits federal expenditures for construction of any facilities, structures, roads, bridges, airports, etc., within the System. Exceptions can be made for some activities such as the maintenance of existing channel improvements and related structures, and the maintenance, replacement, reconstruction, or repair (not expansion) of publicly-operated roads or facilities which are essential links in a larger network or system. Consultation with the U.S. Department of the Interior is required. When a proposed project impacts a coastal barrier unit, the environmental document should:

  • Include a map showing the relationship of each alternative to the coastal barrier unit(s)
  • Identify direct and indirect impacts to the coastal barrier unit(s), qualifying and describing the impacts as appropriate
  • Discuss the results of early coordination with the U.S. Fish and Wildlife Service, identifying any issues raised and how they were addressed
  • Identify any alternative which (if selected) would require an exception under the Act

Any issues identified or exceptions required for the preferred alternative should be resolved prior to its selection. This resolution should be documented in the environmental document.

Additional Resources:
Coastal Zone Management Act of 1972 (16 USC § 1451 et seq.)
Established a voluntary program in which 28 states are currently participating

Coastal Barrier Resources Act (16 USC § 3501 et seq.)
Designates a protected network of undeveloped coastal barriers located on the Atlantic and Gulf Coasts

National Oceanic Atmospheric Administration, Office of Ocean and Coastal Resource Management (OCRM) 
Administers and coordinates a range of federal-state programs and gives technical and financial help, and training, to states working to manage coastal areas.

Fish and Wildlife Service Division of Habitat Conservation 


What is a floodplain? 

A floodplain is the lowland adjacent to a river, lake, or ocean. Most known floodplains in the U.S. have been mapped by the Federal Emergency Management Agency’s (FEMA) Flood Insurance Administration (FIA), which designates them by the rarity of the flood that is large enough to inundate them. For example, a 10-year floodplain would be inundated by a flood that is likely to occur only once every 10years, and a 100-year floodplain by a flood that is likely to occur only once every 100 years. Flood frequencies, such as the "100-year flood," are determined by plotting a graph of the size of all known floods for an area and determining how often floods of a particular size occur. This practice has unavoidable shortcomings: it is based on past flooding (when built environments may have been much different) and it relies on probabilities. Thus, a “10-year-flood” may occur more often than every ten years. Changing climate conditions have added to the difficulty of making accurate predictions. In support of the National Flood Insurance Program, Federal Emergency Management Agency’s (FEMA) identifies flood hazard areas throughout the United States and its territories. Most areas of flood hazard are commonly identified on Flood Insurance Rate Maps (FIRMs).

What is the floodplains compliance process?

Executive Order 11988Floodplain Management, recognizes the importance on floodplains and directs federal agencies to avoid conducting, allowing or supporting actions on a floodplain. FIA will show FIRMs if a proposed public transportation project site lies within the 100-year floodplain.  If any part of the proposed project is located within a floodplain, the environmental document should include a detailed floodplain analysis as specified in U.S. Department of Transportation Order 5650.2Floodplain Management and Protection(April 23, 1979). Since building in a floodplain can worsen flood impacts, the analysis should discuss any risk to, or resulting from, the action, the impacts on natural and beneficial floodplain values, the degree to which the action provides direct or indirect support for development in the floodplain and measures to minimize harm or to restore or preserve the natural and beneficial floodplain values affected by the project.

If the preferred alternative involves significant encroachment of the floodplain the final environmental document must include:

  • FTA's finding that the proposed action is the only practicable alternative and
  • Supporting documentation reflecting consideration of alternatives to avoid or reduce adverse impacts on the floodplain.

Significant encroachment involves one or more of the following impacts:

  • A considerable probability of loss of human life.
  • Likely future damage associated with the encroachment that could be substantial in cost or extent, including interruption of service on or loss of a vital transportation facility A notable adverse impact on natural and beneficial floodplain values (as defined in the Order), although it may nevertheless require mitigation of adverse impacts to the floodplain.

Additional Resources:
Executive Order 11988, Floodplain Management 
Directs federal agencies to avoid to the extent possible adverse impacts associated with floodplains and to avoid direct or indirect support of floodplain development.

USDOT Order 5650.2, Floodplain Management and Protection (April 23, 1979) 

Prescribes policies and procedures for ensuring that proper consideration is given to the avoidance and mitigation adverse floodplain impacts in agency actions, planning programs, and budget requests.

FEMA National Flood Insurance Program 

Navigable Waterways

What are navigable waterways?

Navigable waterways are those “Waters of the United States” that are subject to the ebb and flow of the tide shoreward to the mean high water mark, and that are presently used, have been used in the past, or may be susceptible to use for transport of interstate or foreign commerce. Public transportation projects that affect navigable waterways are subject to permitting and review.

What is the navigable waterways compliance process?

River and Harbor Act of 1899 The Rivers and Harbors Act of 1899 requires that the Secretary of the Army issue permits for:

Section 9 of the Act requires authorization from the U.S. Army Corps of Engineers (USACE)  applies to any dredging or disposal of dredged materials, excavation, filling, rechannelization, or any other modification of a navigable water of the U.S It applies to all structures, from the smallest floating dock to the largest commercial undertaking. It further includes, without limitation, any wharf, dolphin, weir, boom breakwater, jetty, groin, bank protection (for example, riprap, revetment, bulkhead), mooring structures such as pilings, aerial or subaqueous power transmission lines, intake or outfall pipes, permanently moored floating vessel, tunnel, artificial canal, boat ramp, aids to navigation, and any other permanent or semi-permanent obstacle or obstruction.

  • Section 9 and Section 10 Permits:Certain work performed, or structures constructed, in navigable waters could require permits pursuant to both Sections 9 and 10 of the Rivers and Harbors Act. A project involving dredging in navigable waters would require both a Section 10 and a Section 404 permit because  pertains to "Waters of the United States" which includes more than navigable waters. The  (33 USC § 401 et seq.) of construction of a dam or dike across a navigable water of the U.S.
  • Section 10 of the Act requires USACE authorization before construction of any structure over, excavation from, or disposal of materials into navigable waters. Even structures or work outside the limits defined for navigable waters of the U.S. require a Section 10 permit if the structure or work affects the course, location, or condition of the water body.

The USACE commonly adopts the DOT environmental document to support its permitting decision. Therefore, FTA should coordinate closely to make sure that the FEIS or EA includes all the environmental analysis that the Corps will need to evaluate the Section 9 or Section 10 permit.

Coordination with U.S. Fish and Wildlife Service: The Fish and Wildlife Coordination Act (16 USC § 661 et seq.) requires consultation with the U.S. Fish and Wildlife Service (FWS) and the appropriate state wildlife agency when a project will impound, divert, channelize, or otherwise control or modify the waters of any stream or other body of water. Generally, if a permit is required under Sections 9 or 10 of the Rivers and Harbors Act of 1899, or Section 402 or Section 404 of the Clean Water Act, the consultation requirement will apply. Permit applications will be forwarded to the FWS, which will review them according to their Guidelines for the Review of Fish and Wildlife Aspects of Proposals in or Affecting Navigable Waterways (published in the Federal Register on December 1, 1975).

The environmental document must evaluate how the federal project may affect fish and wildlife resources and include measures to minimize harm, such as features to reduce turbidity during construction, stabilizing the shoreline with planting suitable for use by wildlife, or compensation for habitat that may be lost. FWS’s mitigation policy can be consulted when planning mitigation measures. The final environmental document should include The results of the consultation.

Additional Resources:
River and Harbor Act of 1899 (33 USC § 401 et seq.)
Requires the Secretary of the Army to issue permits for projects that affect navigable waterways (for example, bridges, dams, or other structures).

Fish and Wildlife Coordination Act (16 USC § 661 et seq.)
Requires consultation with the U.S. Fish and Wildlife Service and the appropriate state wildlife agency when a project will impound, divert, channelize, or otherwise control or modify the waters of any stream or other body of water.

Guidelines for the Review of Fish and Wildlife Aspects of Proposals in or Affecting Navigable Waterways 
U.S. Fish and Wildlife Service guidance for interpretation of 16 USC § 661.

Water Quality and Stormwater Management

Public transportation projects can impact water quality by depositing contaminants, increasing runoff or altering surface or subsurface drainage patterns. If a project results in discharge of wastewater into the stormwater system, a permit may be required under the National Pollutant Discharge Elimination System (NPDES).

What is the process for protecting water quality? 

Transit projects can affect water quality in various ways. Wastewater generated by  maintenance and storage facilities can contain a number of pollutants that, through improper handling or treatment, can be released into stormwater systems. Typical bus garage effluent contains concentrations of oil and grease, detergents, chemicals and metals, and solid materials that pass into the sewer system. Environmental documents for a proposed project should discuss any activities that could generate wastewater (for example, steam cleaning, vehicle washing, and floor wash-downs) and the provisions for containing possible pollutants.

stormwater runoff from transit parking areas may contain harmful pollutants such as lead, zinc, and cadmium. The environmental document should describe The project's potential for increasing runoff, and measures that will be used to reduce runoff or prevent pollutants from entering stormwater systems (e.g., of bus or rail parking or maintenance facilities).

In addition, if a transit project changes the existing runoff pattern it could contribute to local flooding. Examples include paving of an area where previously a permeable surface existed, modifying a drainage system, or channeling existing runoff.In such cases, the EIS or EA should evaluate the magnitude of the impact and identify measures that will be used to reduce the potential for flooding. The analysis also should include the findings of the appropriate local or state agencies (for example, public works agencies or flood control districts).

A National Pollutant Discharge Elimination System (NPDES) permit issued under Section 402 of the Clean Water Act(33 USC § 1342) may be required if wastewater is discharged into the stormwater system. The U.S. Environmental Protection Agency (EPA) sets pretreatment effluent limits for NPDES permits and issues the permits (or a state may issue them under delegated authority). The environmental document should state whether an NPDES permit is required and whether there are local or state pretreatment requirements. Depending on specifics, the project may also require an NPDES to cover potential discharges from construction activities. 

Mitigation measures should be used to control chemical and detergent use and to remove oil, grease, and solid materials at the source. As a mitigation measure, dry detention facilities may be preferable to wet detention ponds because the transformation of particulate metals (from diesel exhaust emissions) to soluble forms that are susceptible to washout can be minimized. The soluble form is much more toxic to aquatic organisms than the particulate form. Periodically, pipes should be flushed, exterior pavement washed, and sediments removed from detention ponds in dry weather.

Additional Resources:
Section 402 of the Clean Water Act (33 USC § 1342)
National Pollution Discharge Elimination System (NPDES)

U.S. Environmental Protection Agency Office of Water

Wetlands and Other Waters of the U.S.

Wetlands provide a number of ecosystem benefits, including flood control, water quality filtration, and habitat, among others. Responding to decades of steady wetlands loss, President Carter’s 1977 Executive Order 11990, Protection of Wetlands directs agencies first and foremost “to avoid to the extent possible the long- and short-term 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.” Executive Order 11990 cites NEPA as one of its primary authorities and therefore applies to all wetlands, not just those under the jurisdiction of the U.S. Army Corps of Engineers (USACE).

U.S. Department of Transportation (USDOT) Order,  Preservation of the Nation's Wetlands, DOT Order 5660.1A, implements Executive Order 11990. It requires USDOT agencies to avoid undertaking or providing assistance for new construction located in wetlands unless the agency finds:

  • That there is no practicable alternative to such construction; and
  • That the proposed action includes all practicable measures to minimize harm to wetlands that may result.

Complying with Section 404 (see below) commonly assures satisfaction of these requirements.

What are wetlands? 

Wetlands are lowland areas that are inundated or saturated by surface or ground water at a frequency that, under normal circumstances, supports a prevalence of vegetation typically adapted for life in saturated soil conditions. Wetlands generally include swamps, marshes, bogs, and similar areas. Where a federally assisted transportation project affects a wetland, the environmental document must analyze potential wetland impacts.

What are “other “Waters of the U.S.”?.”? 

The Clean Water Act, which regulates wetlands, applies to “waters of the United States.” These are:

  • All waters which are currently used, or were used in the past, or may be susceptible to use in interstate or foreign commerce, including all waters which are subject to the ebb and flow of the tide
  • All interstate waters including interstate wetlands
  • All other waters such as intrastate lakes, rivers, streams (including intermittent streams), mudflats, sandflats, wetlands, sloughs, prairie potholes, wet meadows, playa lakes, or natural ponds, the use, degradation or destruction of which would affect interstate waters or interstate commerce waters

Determining whether an area is a “jurisdictional wetland”(a wetland over which the federal government has jurisdiction under the Clean Water Act) requires technical expertise and can require interagency coordination to resolve.

How are wetlands considered during the environmental review process? 

As noted above, USDOT Order 5660.1A requires that an analysis of project impacts to wetlands. The analysis should assess the impacts on wetlands and associated wildlife resulting from both construction and operation of the project. It should also include measures to minimize adverse impacts and avoid, to the fullest extent possible, drainage, filling or otherwise disturbing wetlands. Alternatives that would avoid new construction in wetlands must be studied. If the preferred alternative requires new construction in wetlands the analysis must demonstrate that there are no practicable alternatives to the use of the wetlands, and all practicable measures to minimize harm have been included. A significant impact on wetlands will usually trigger an Environmental Impact Statement.

What is the wetlands permitting program?

The Section 404 permitting process applies to projects that may discharge dredged or fill material to waters of the US, including wetlands. The process is established under the  Clean Water Act, Section 404 (33 USC § 1344) and jointly run by the U.S. Army Corps of Engineers (USACE) and the U.S. Environmental Protection Agency (EPA). It is administered and enforced by the USACE as described in Section 404 Permitting Program (33 CFR Part 320 et seq.). In general, the permitting program operates according to the principle of "no net loss of wetlands”; requiring a sequence of "avoid, minimize, enhance and compensate." Guidance on the contents of the permit application and the evaluation criteria are described in the EPA's Section 404(b)(1) Guidelines (40 CFR Part 230).

The USACE can issue either of two types of permits: individual permits that require case-by-case evaluations of specific projects; and general permits that are issued on a nationwide or regional basis for groups of activities that are substantially similar in nature and cause, and have only minimal environmental impacts. For actions covered by a general permit, no further reporting or written communication is required at the time the individual activity is initiated.

The information that is needed for compliance with Section 404 of the Clean Water Act can be integrated into the National Environmental Policy Act (NEPA) compliance process.  Normally this information includes a formal jurisdictional delineation of wetlands, a functional assessment of those wetlands, and proposed mitigation measures. The permit itself does not have to be obtained (and usually is not obtained) before FTA makes its environmental determination. The grant applicant submits a permit application to the USACE, which initiates a public comment period, and notifies the EPA of the application. The EPA reviews the application and has the authority to deny a permit.

A permit application for an activity that involves the discharge of dredged or fill material must include the purpose of the discharge; a description of the type, composition, and quantity of the material; the method of transportation and disposal of the material; and the location of the disposal site. If the project involves construction of a filled area, piles, or platforms, the description should include the use of and specific structuresto be erected on the fill or platform. Section 230.10 of the EPA's guidelines explain in detail what information should be included in the permit application. FTA’s environmental document should discuss this information, but typically not in the same level of detail as required by the permit application. 

Additional Resources:
Clean Water Act, Section 404 (33 USC § 1344)
Gives authority to the U.S. Army Corps of Engineers to regulate discharges of dredged or fill material into waters of the United States, including wetland areas. This includes fill that occurs as a result of infrastructure development, such as a light rail line or a bus terminal. Permit applicants must demonstrate that they have attempted to avoid wetland impacts where practicable. Where impacts do occur they must be compensated by restoration or creation of wetlands.

Section 404 Permitting Program (33 CFR Part 320 et seq.)
Federal regulations for the U.S. Army Corps of Engineers (USACE) permitting program describing USACE's authority to operate the program, and general policies for implementing the program.

Section 404(b)(1) Guidelines (40 CFR Part 230)
Guidance regarding the substantive criteria to be used in evaluating permit applications.

Protection of Wetlands, Executive Order 11990 
Requires federal agencies to avoid direct or indirect support of new construction in wetlands wherever there is a practicable alternative.

Preservation of the Nation's Wetlands, USDOT Order 5660.1A 
Sets forth the US Department of Transportation (DOT) policy for interpreting Executive Order 11990. Requires that transportation facilities and projects should be planned, constructed, and operated to assure the protection, preservation, and enhancement of the nation's wetlands to the fullest extent practicable, and establishes procedures for implementation of the policy.

U.S. Army Corps of Engineers Wetlands Delineation Manual 
Field manual used by the agencies to identify and delineate wetlands for purposes of Section 404 of the Clean Water Act.

Applying the Section 404 Permit Process to Federal-Aid Highway Projects (September 1988) 
Discusses ways to improve interagency coordination on federal-aid highway projects, and ways to integrate the National Environmental Policy Act and Section 404 requirements.

U.S. Army Corps of Engineers 

U.S. Environmental Protection Agency, Office of Water

Federal Highway Administration, Wetlands Information 

2007 Nationwide Permits, Conditions, Further Information, and Definitions (with corrections)

Assessing wetland functions:

U.S. Environmental Protection Agency’s Wetlands compensatory mitigation:

U.S. Army Corps of Engineers, Wetlands Delineation Manual, Part III: Characteristics and Indicators of Hydrophytic Vegetation, Hydric Soils, and Wetland Hydrology (1987) 
Jurisdictional delineation manual considers (1) Wetland hydrology, (2) Hydric soils, and (3) Hydrophytic vegetation 

40 CFR Part 230: Section 404(b)(1) Guidelines for Specification of Disposal Sites for Dredged or Fill Material 

U.S. Army Corps of Engineers Regulatory Guidance Letter: Jurisdictional Determinations (June 26, 2008)
To help implement Section 404 of the Clean Water Act and Sections 9 and 10 of the Rivers and Harbors Act of 1899, explains the differences between jurisdictional determinations (JDs) and preliminary JDs, and provides guidance on when an approved JD is required.

U.S. Army Corps of Engineers Regulatory Guidance Letters 
A list of documents that provide guidance on regulations regarding waterbodies.

Updated: Wednesday, March 16, 2016
Submit Feedback >