An Introduction to the Clean Water Act

By: Ashley Dawn Anderson
March 14, 2025
Published as part of The Headwaters Report

The Clean Water Act (“CWA” or “Act”) is the primary federal law governing water pollution and surface water quality in the United States.  Congress passed the Act in 1972 in response to growing public concern and awareness of degraded water quality in the 1960s, including high bacteria levels in the Hudson River and the Cuyahoga River catching fire – for the third time.[i]  The Act aims to improve water quality through regulatory programs that Tribal Nations can implement over their reservation waters.  Tribes have used the CWA to protect water quality for ceremonies, fisheries, and other Tribal uses as an act of Tribal governance and sovereignty.  This overview describes the Act, its programs, how Tribal Nations obtain delegated authority for the implementation of such programs, and how Tribal Nations can use the CWA to protect water quality of their reservation waters. 

The Clean Water Act – Background

The CWA regulates water quality standards for surface water by controlling pollution of “waters of the United States.”[ii]  Congress enacted the CWA to “restore and maintain the chemical, physical, and biological integrity of the Nation’s waters.”[iii]  To accomplish this purpose, the CWA establishes multiple pollution control programs that are administered by the Environmental Protection Agency (“EPA”).  The central CWA program is the Water Quality Management program, and the water quality standards (“WQS”) promulgated under this program serve as a threshold for the Act’s other regulatory programs.  The Act allows states and authorized Tribes to set WQS that must meet the requirements of the Act.  States and authorized Tribes may set more stringent WQS if they choose.  If the state or Tribe does not submit WQS or submit WQS that fail to meet the requirements of the Act, the EPA may promulgate federal water quality standards until the state or Tribe submits adequate WQS.  Under the EPA’s supervision, states and Tribes that have received Treatment in a Similar Manner as a State (“TAS”) status can implement CWA programs, including:

  • Water Quality Management, CWA § 303
  • Nonpoint Source Management Program, CWA § 319
  • Water Quality Certifications, CWA § 401
  • National Pollutant Discharge Elimination System Program (NPDES), CWA § 402
  • Dredge or Fill Permit Program, CWA § 404   

Many CWA programs only apply to “navigable waters,” defined as “waters of the United States.”  As defined in federal regulation, “waters of the United States” are interstate waters, territorial seas, waters used in interstate or foreign commerce, and the tributaries and adjacent wetlands of these waters.  The scope of “waters of the United States” has inspired extensive litigation, primarily over the reach of the Act to wetlands and perennial water bodies that may be adversely affected by development.

In Sackett v. Environmental Protection Agency, the U.S. Supreme Court issued its most recent ruling interpreting the “waters of the United States,” narrowing the scope of the waters covered by the CWA.[iv]  According to the Court, the CWA only encompasses waters that are “relatively permanent, standing or continuously flowing bodies of water forming geographical features that are described in ordinary parlance as streams, oceans, rivers, and lakes.”[v]  Thus, “waters of the United States” now only include wetlands that have “continuous surface connection” to and are practically “indistinguishable” from traditionally navigable waters (e.g., oceans, rivers, lakes).[vi]  As a result of Sackett, the CWA does not extend to isolated wetlands or wetlands only connected to traditional navigable waters by streams that dry up and are, thus, not “continuous.”

The CWA regulates the discharge of pollutants – defined broadly to include any industrial, municipal, and agricultural waste – into the waters of the United States.[vii]  Specific examples of pollutants include chemical waste, radioactive materials, dredged soil, solid waste, sewage, garbage, heat, rock, and sand.  The EPA also maintains lists of toxic pollutants and priority toxic pollutants, which identify the pollutants most affecting waters of the United States.

CWA programs distinguish between water pollution caused by point sources and nonpoint sources.  A point source is a discrete conveyance, such as a drainage pipe or man-made ditch.  A nonpoint source is a conveyance of pollutants from natural runoff caused by rainfall or snowmelt, such as water flowing off a parking lot or agricultural field. 

Why Tribal Nations Should Care About the Clean Water Act

Tribal Nations are important to CWA implementation.  The Act represents collaborative federalism, which is a balance of state, Tribal, and federal powers to promote the protection of the waters within the United States.  Tribal Nations that want to obtain TAS status to manage CWA programs can effectuate standards that reflect Tribal needs and values that are otherwise not accommodated in state or federal standards.

TAS is a vehicle for Tribal regulatory authority over water quality both on and off the reservation.  If the EPA approves a Tribe’s TAS status for a CWA program, then the Tribe would assume the same responsibilities and funding as a state administering the same program.  Further, TAS is required for Tribes to access CWA grant programs that are not related to regulatory programs, such as technical assistance under Section 104, water pollution prevention under Section 106, and nonpoint source pollution under Section 319.

Tribes that attain TAS can establish WQS for all waters within the exterior boundaries of the reservation.  Thus, TAS helps alleviate regulatory hurdles created by checkerboard jurisdiction.  A TAS Tribe can also establish WQS more stringent than the adjacent state’s WQS, which the state must not violate.  Tribal WQS may not be less stringent than the minimum federal WQS.  

A Tribe’s WQS are enforced through CWA permit programs, such as NPDES permits (Section 402) and dredge or fill permits (Section 404).  A Tribe must separately obtain TAS for these permit programs to enforce compliance with their WQS.  Without TAS, the EPA enforces a Tribe’s WQS through these permit programs by requiring permit holders to comply with Tribal WQS.  The EPA or authorized Tribe may use fines or criminal prosecution to penalize parties who pollute reservation waters without the proper permit or violate a permit’s terms.  For example, in City of Albuquerque v. Browner, the court upheld the EPA’s decision requiring Albuquerque’s NPDES permit to comply with Tribal WQS, which were more stringent than the state’s WQS.[viii]  If the EPA improperly issues a permit or fails to prosecute a party that violate the permit, a Tribe can sue the EPA under the Administrative Procedure Act for failing to comply with the CWA.

A Tribe can use TAS status to establish WQS that protect values important to the Tribe.  For instance, Tribal WQS can account for preservation of cultural resources.[ix]  For example, the Isleta Pueblo’s WQS include a “ceremonial use standard,” which the EPA approved and the court upheld in City of Albuquerque v. Browner.[x]  In another example, the Hoopa Valley Tribe’s WQS account for “ceremonial and cultural water use, fish spawning, and water contact recreation.”  In creating Tribal WQS, Tribal Nations can assert water quality needs as enforceable standards that protect Tribal practices.

Applying for TAS

The CWA authorizes the EPA Administrator to treat a federally recognized Tribe as a state for CWA Sections 104, 106, 303, 305, 308, 309, 314, 319, 401, 402, 404, and 406.[xi]  A Tribe can obtain TAS for one or more of these programs by applying to the EPA.  A Tribe must separately apply and be approved for each CWA program the Tribe wishes to implement.

To qualify for TAS, a Tribe must demonstrate that it: (1) is federally recognized, (2) has a governing body that carries out substantial governmental duties and powers, (3) has authority over the water resources, and (4) has capacity to carry out the functions of the CWA program.  Essentially, the EPA requires the Tribe to prove it can implement the CWA program.  To apply for TAS for a particular program, Tribal leadership must submit a letter to the EPA Regional Administrator for the Tribe’s region describing how the Tribe meets these criteria.

Under the EPA’s 2016 rule, “Revised Interpretation of Clean Water Act Tribal Provision,” the EPA has interpreted the CWA as an express delegation of authority to Tribes to implement CWA programs for the waters within its reservation boundaries.  Thus, a Tribe can demonstrate the third application element – authority over its water resources – by submitting a map or legal description of its reservation boundaries.  The EPA’s 2016 rule reduces some burdens of applying for TAS because previously this element required the Tribe to prove it had “inherent authority” over its waters using the “Montana test.”[xii]  See EPA Fact Sheet on this rule for more information.

The EPA has streamlined the TAS application process for the WQS and Water Quality Certifications programs, so a Tribe need only use one application to become authorized for both programs.  Additionally, the EPA has created a TAS application template for Water Quality Standards and Water Certifications and Impaired Water Listing and TMDLs.  The templates for these programs are almost identical, and Tribes may apply for TAS for both programs at the same time.

TAS authorization for one program does not automatically qualify the Tribe for TAS authorization for another program.  However, a Tribe does not need to re-submit identical information for subsequent TAS applications after it has been approved for one TAS program.  For example, a TAS-authorized Tribe does not need to resubmit evidence that it is federally recognized or has a governmental body.  A Tribe will need to submit information on its capacity to carry out the function of the CWA program for each application.  For example, a Tribe with WQS (Section 303) authorization applying for NPDES permitting (Section 402) authorization would need to describe how the Tribal government would administer and implement the NPDES permitting program, which requires different functions from the Tribal government than WQS planning. 

TAS-Eligible CWA Programs

As noted above, the CWA authorizes Tribes to acquire TAS status to implement programs under CWA Sections 104, 106, 303, 305, 308, 309, 314, 319, 401, 402, 404, and 406.[xiii]  This section describes the major TAS-eligible regulatory programs.

Water Quality Standards and Implementation Plans – Section 303

CWA Section 303(c), the WQS program, is one of the most-implemented CWA programs by Tribal Nations.  Section 303(c) requires a state or authorized Tribe to describe the desired condition of the water bodies within its jurisdiction and develop WQS for each water body in order to protect or achieve that desired condition.  For Section 303(c), WQS are composed of three elements: (1) designated uses of the water body, (2) WQS criteria, and (3) antidegradation requirements.  The EPA must approve these three components of a state or Tribe’s proposed WQS if they meet CWA requirements.  To date, 84 Tribes are authorized to administer the WQS program, and the EPA has approved WQS for 52 Tribes.

  • Designated uses include protection of wildlife, cultural or traditional uses, public water supply, recreation, and agriculture.
  • WQS criteria are the numeric or narrative descriptions designed to protect the designated uses of a water body.  To illustrate the distinction, a numeric description includes the maximum pollutant concentration permitted in a water body, and a narrative description could be a statement about the desire for the water body to be free of pollutants that impair cultural activities.
  • Antidegradation requirements maintain and protect the existing water quality so that water quality does not fall below the standard that has already been achieved.  Antidegradation requirements must protect three tiers of water quality:
    • Existing uses, which have the minimum level of protection for all waters,
    • High-quality waters, which exceed the level necessary to support propagation of wildlife, and

CWA Section 303(d) requires states and TAS Tribes to identify and list impaired and threatened waters to the EPA every two years.  Using all existing and readily available information, the state or Tribe identifies the impaired water bodies, the pollutant(s) causing the impairment, the severity of the pollution, the sensitivity of use (for example, public water supply), among other factors.[xiv]  The state or Tribe uses this information to prioritize restoration efforts for the impaired water bodies.  Restoration involves the development of Total Maximum Daily Loads (“TMDLs”).  TMDLs are plans that identify how much pollution from various sources must be reduced for the water body to meet the WQS.  Implementation of the TMDLs typically involves pollution control permits for point sources, Best Management Practices (“BMP”) for nonpoint sources, and consistent monitoring.  A water body will remain on the impaired and threatened waters list until it meets the WQS.

The Water Quality Certification Program – Section 401

            Compliance with WQS is enforced through permit programs, and before a CWA permit – or any other federal license or permit – may be issued, a project proponent must obtain a water quality certification from the EPA or authorized Tribe or state.  TAS for Section 401 allows Tribes to grant or deny certifications to projects that may result in a discharge into waters of the United States and authorizes Tribes to participate in state water quality certification decisions as neighboring jurisdictions.  Currently, 84 Tribes have TAS for Section 401.

CWA Section 401 prohibits federal agencies from issuing any permit or license for a project that may result in any discharge into the waters of the United States – including mining operations, dams, and construction of highways – unless the EPA, authorized state, or TAS Tribe issues a Section 401 water quality certification or waives certification.  If applicable, Section 401 certification is a prerequisite for any federal permit or license, including any CWA permits (see Sections 402 and 404 below), hydropower licenses, and Rivers and Harbors Act Sections 9 and 10 permits.

In addition to certifying authority over federal permits and licenses, Section 401 TAS allows Tribes to participate in the neighboring jurisdiction process.  Under the neighboring jurisdiction process, the EPA notifies the TAS Tribe of proposed federal licenses or permits for projects originating in another jurisdiction if the proposed project “may affect” the Tribe’s water quality.  Then, the Tribe has 60 days to determine whether the project will violate any of its water quality requirements, including WQS or “any other water quality-related requirement” under Tribal law.  If the project violates any Tribal water quality requirement, the Tribe may object to the issuance of a federal permit or license and request a public hearing with the federal agency, certifying authority, project proponent, and EPA.  After the hearing, the federal agency must place conditions on the license or permit that will ensure the project complies with the Tribe’s water quality requirements.  If the project cannot meet the Tribe’s water quality requirements even with the conditions, then the federal agency is prohibited from issuing the license or permit.

For example, the Fond du Lac Band of Lake Superior Chippewa (“the Band”), a Section 401 TAS Tribe, successfully enforced the neighboring jurisdiction process to challenge the U.S. Army Corps of Engineers’ (“Corps”) issuance of a wetland dredge or fill permit (CWA Section 404) to PolyMet Corporation (now NewRange Copper Nickel, LLC).  Because the Band had obtained TAS for Section 401, the EPA was required to make a “may affect” determination and notify the Band of PolyMet’s Section 404 permit application for its proposed sulfide mine upstream of the reservation.  After notification, the Band determined the project would affect its reservation waters in violation of the Band’s water quality requirements and objected to the issuance of the Corp’s Section 404 permit.  After the Corps held the requisite hearing, the EPA confirmed the Corps could not add sufficient conditions on the permit to ensure PolyMet’s discharges complied with the Band’s water quality requirements.  Thus, the Corps was required to revoke PolyMet’s Section 404 permit, originally issued without appropriate EPA notification.  The Corps revoked the permit on June 3, 2023.

EPA’s Water Quality Certification Improvement Rule

Section 401 TASSection 401(a)(2) TAS
• Water Quality Certification Program
• Neighboring Jurisdiction Program		Neighboring Jurisdiction Program only

Tribal Nations also have the option to obtain TAS for the sole purpose of participating as a neighboring jurisdiction under CWA Section 401(a)(2).  As a result of the EPA’s 2023 Section 401 Water Quality Certification Improvement Rule, the EPA bifurcated TAS for Section 401 into two separate applications: (1) TAS for Section 401 in its entirety (both water quality certification and the neighboring jurisdiction program); and (2) TAS for Section 401(a)(2) which only authorizes the neighboring jurisdiction program.  With Section 401(a)(2) TAS authorization, a Tribe may only object to the issuance of a federal license or permit that may adversely affect the Tribe’s water quality through the neighboring jurisdiction process.  Section 401(a)(2) TAS does not authorize a Tribe to exercise Section 401 certifying authority over projects that require federal permits or licenses.  Section 401(a)(2) TAS allows Tribal Nations the flexibility to participate in the neighboring jurisdiction program and provide input on projects that may adversely affect the Tribe’s water quality without taking on the responsibility of the Water Quality Certification Program.

National Pollutant Discharge Elimination System – Section 402

The CWA prohibits the discharge of any pollutant from a point source into navigable waters unless the potential polluter first obtains a permit under CWA Section 402 issued by the EPA or an authorized state or Tribe.  The National Pollutant Discharge Elimination System (“NPDES”) permit program regulates the discharge of pollutants from discrete conveyances (i.e. point sources) into the waters of the United States.  The NPDES program controls water pollution by issuing permits that limit the amount of a pollutant a party may discharge into the regulated water body and by tracking and monitoring the permit holder.  A party discharging a pollutant without a NPDES permit or in violation of the permit’s terms will be subject to penalties (including fines or criminal prosecution), which are enforced by the EPA or authorized state or Tribe.

If the Tribe obtains NPDES TAS authorization, the Tribe can issue NPDES permits to itself or any party discharging pollutants into water within reservation boundaries.  Without TAS authorization for this program, the EPA issues NPDES permits within reservation boundaries, unless the EPA approved the state’s authority over reservations.  Currently, no Tribe has obtained TAS for the NPDES permit program.  (See “Considerations for Obtaining TAS” below.)

Dredged or Fill Material Permit Program – Section 404

The CWA prohibits the discharge of dredged or fill material from a point source into waters of the United States unless the potential polluter obtains a dredge or fill permit under CWA Section 404 from the Corps, authorized state, or TAS Tribe.  In the absence of state or Tribal authorization, the Corps issues Section 404 permits, and the EPA manages the program and reviews TAS applications (also called program “assumption”).  Currently, no Tribe has obtained TAS for the Section 404 permit program.  (See “Considerations for Obtaining TAS” below.)

The Section 404 permit program prohibits the discharge of dredged or fill material if (1) a practicable alternative exists that is less damaging to the aquatic environment or (2) the waters of the United States would be significantly degraded.  Dredged material is defined as material that is excavated or dredged from waters of the United States.  Fill material is defined as material placed in waters of the United States that either replaces any portion of a water with dry land or changes the bottom elevation of any portion of a water body.  A party discharging dredged or fill material without a permit, or in violation of the permit’s terms, will be subject to penalties (including fines or criminal prosecution), which are enforced by the EPA and Corps or by the authorized state or Tribe.

Conclusion

The CWA can be an effective vehicle for Tribes to assert regulatory authority over their reservation waters.  For example, Section 303 TAS allows Tribes to create WQS that protect water quality for important Tribal uses, including ceremonies and fisheries.  Additionally, Section 401 TAS authorizes Tribes to issue water quality certificates for federal permitting and licensing, giving Tribes the discretion to prevent projects that would adversely affect reservation waters, such as mining operations, infrastructure development, or hydroelectric dams.  Although no Tribes have obtained TAS for the NPDES and Dredge or Fill permit programs, these programs offer Tribes the opportunity (and responsibility) to enforce compliance with Tribal WQS and prosecute permit violations.  Tribes should carefully weigh the costs and benefits of TAS status before beginning the application process for any CWA program.  

Opportunities in Obtaining TAS

With TAS under the CWA, Tribes can:

  • Govern and mange reservation resources as an exercise of Tribal sovereignty,
  • Implement more environmentally protective programs than the EPA or a neighboring state,
  • Access CWA grants (including Section 104, Section 106, and Section 319),
  • Use cultural and traditional values to establish WQS,
  • Require upstream water users to follow downstream Tribal WQS,
  • Promulgate uniform water quality standards over the entire reservation,
  • Enforce NPDES and Dredged and Fill permits.

Considerations for Obtaining TAS

Even though TAS provides significant opportunities, Tribes should also consider that TAS can involve:

  • Lengthy, costly, and complex application processes,
  • Increased institutional capacity to administer CWA programs,
  • Significant costs to implement CWA programs, which may not be fully covered by CWA grants,
  • Uncertainty of the future of CWA programs and grant appropriations, given attacks on the CWA,
  • Hostility from neighboring states and businesses,
  • Vulnerability to litigation.

ADDITIONAL RESOURCES

Clean Water Act statute.

Clean Water Act regulations.

EPA, Case Studies, Video, and Publications on Tribal Water Quality Standards.

EPA, Fact Sheet on Revised Interpretation of Clean Water Act Tribal Provision.

EPA, Fact Sheet on Clean Water Act Section 404(g) Tribal and State Assumption Program Final Rule.

National Association of Wetlands Managers, FAQs: Treatment in a Similar Manner as a State (TAS) for Clean Water Act Programs (Nov. 2023) https://www.nawm.org/pdf_lib/tribal_wp/faqs_on_treatment_in_a_similar_manner_as_a_state.pdf.

TAS Application Templates

[i] 33 U.S.C. § 1251(a).

[ii] The CWA is codified at 33 U.S.C. §§ 1251-1387 and the relevant federal regulations implementing the statute can be found at 40 CFR Parts 104 – 140 (see Additional Resources).

[iii] 33 U.S.C. § 1251(a).

[iv] 598 U.S. 651 (2023).

[v] 598 U.S. 651, 671 (2023) (internal quotations removed); see also Rapanos v. United States, 547 U.S. 715, 739 (2006).

[vi] 598 U.S. at 678-79; see also Rapanos, 547 U.S. at 742, 755.

[vii] 33 U.S.C. § 1362(6).

[viii] 97 F.3d 415, 427 (10th Cir. 1996).

[ix] 33 U.S.C. § 1377.

[x] 97 F.3d at 429.

[xi] See CWA § 518(e).

[xii] The Montana test comes from Montana v. United States, 450 U.S. 544 (1981), and this case’s progeny. 

[xiii] See CWA § 518(e).

[xiv] See 40 C.F.R. §130.7(b)(4).

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