A Guide to the Clean Water Act Requirements, Process, and Compliance

The Clean Water Act (CWA) stands as a pillar of environmental protection in the United States, safeguarding the nation's precious water resources from pollution and degradation. This comprehensive guide dives deep into the intricacies of the CWA, providing a clear and accessible roadmap for navigating its complex regulatory landscape. From understanding the Act's history and key provisions to mastering compliance strategies and keeping pace with evolving regulations, this resource equips readers with the knowledge and tools needed to effectively manage water quality issues in the context of large-scale development projects. By exploring real-world examples, best practices, and the latest regulatory developments, this guide offers an indispensable resource for professionals seeking to balance economic growth with environmental stewardship and ensure that our nation's waters remain clean, healthy, and vibrant for generations to come.


Key Details of the Clean Water Act

  • Issuing Agency: Environmental Protection Agency
  • Year Established: 1972
  • Last Amended: 1987
  • Statutory Authority: Federal Water Pollution Control Act
  • Primary Legal Reference: Title 40 of the Code of Federal Regulations, Parts 104 through 140, 403, and 503

What is the Clean Water Act?

The Clean Water Act (CWA) is a comprehensive federal law that regulates the discharge of pollutants into the nation's surface waters, including lakes, rivers, streams, wetlands, and coastal areas. The primary goal of the CWA is to restore and maintain the chemical, physical, and biological integrity of the nation's waters by preventing point and nonpoint pollution sources, providing assistance to publicly owned treatment works for the improvement of wastewater treatment, and maintaining the integrity of wetlands.

The CWA operates within the broader framework of federal environmental regulations, working in conjunction with other laws such as the Safe Drinking Water Act and the National Environmental Policy Act. The Environmental Protection Agency (EPA) is the primary federal agency responsible for administering and enforcing the CWA, although it works in partnership with other federal agencies, state and local governments, and tribes to implement the law's provisions.

The CWA was originally enacted in 1948 as the Federal Water Pollution Control Act, but it was significantly reorganized and expanded in 1972. Major amendments were made in 1977 and 1987 to strengthen the law's provisions and address emerging water quality issues. The CWA employs a variety of regulatory and non-regulatory tools to sharply reduce direct pollutant discharges into waterways, finance municipal wastewater treatment facilities, and manage polluted runoff. These tools include:

  • Establishing water quality standards
  • Issuing permits for point source discharges
  • Providing funding for wastewater treatment infrastructure
  • Regulating oil spills and other hazardous substances
  • Protecting wetlands

The CWA applies to all navigable waters of the United States, which includes any waters that are currently used, were used in the past, or may be susceptible to use in interstate or foreign commerce. This encompasses territorial seas, lakes, rivers, streams, wetlands, and other water bodies.

What does the Clean Water Act protect?

The Clean Water Act protects the nation's surface waters, including lakes, rivers, streams, wetlands, and coastal areas, from pollution. The CWA aims to prevent the discharge of pollutants, such as chemicals, heavy metals, oils, and untreated sewage, into these water bodies. The regulation achieves this protection through a variety of mechanisms, including:

  • Setting water quality standards for contaminants in surface waters
  • Requiring permits for point source discharges into navigable waters
  • Mandating the use of best management practices to control nonpoint source pollution
  • Providing funding for the construction of municipal sewage treatment plants
  • Establishing programs to control polluted runoff from urban and agricultural areas


Section 401 - Water Quality Certification

The Clean Water Act Section 401 requires any applicant for a federal license or permit that may result in a discharge into waters of the United States to obtain a water quality certification from the state or authorized tribe where the discharge originates. The main purpose of this section is to ensure that federal actions do not violate state or tribal water quality standards. Key requirements include obtaining certification before beginning any activity that may result in a discharge, and complying with any conditions imposed by the certifying authority. Developers should be aware that Section 401 certification may be required for various projects, such as dams, pipelines, or other infrastructure that involves discharges into regulated waters. Best practices include early coordination with the certifying authority and incorporating water quality considerations into project planning.

Section 402 - National Pollutant Discharge Elimination System (NPDES)

Section 402 of the Clean Water Act establishes the National Pollutant Discharge Elimination System (NPDES), which regulates point source discharges of pollutants into waters of the United States. The main objective of this section is to control and minimize water pollution by requiring dischargers to obtain permits and comply with effluent limitations. Key requirements include obtaining an NPDES permit before discharging pollutants, meeting technology-based and water quality-based effluent limitations, and implementing best management practices. Developers should be aware that NPDES permits may be required for various projects, such as wastewater treatment plants, industrial facilities, or construction sites. Compliance strategies include implementing effective pollution control measures, monitoring discharges, and maintaining accurate records.

Section 404 - Dredge and Fill Permits

Section 404 of the Clean Water Act regulates the discharge of dredged or fill material into waters of the United States, including wetlands. The main purpose of this section is to protect aquatic ecosystems and minimize the adverse impacts of dredging and filling activities. Key requirements include obtaining a Section 404 permit from the U.S. Army Corps of Engineers before discharging dredged or fill material, and complying with any permit conditions, such as mitigation measures. Developers should be aware that Section 404 permits may be required for various projects, such as land development, infrastructure construction, or mining activities that involve dredging or filling in regulated waters. Best practices include avoiding and minimizing impacts to aquatic resources, and compensating for unavoidable impacts through mitigation.

Section 303(d) - Impaired Waters and Total Maximum Daily Loads (TMDLs)

Section 303(d) of the Clean Water Act requires states and authorized tribes to identify and list impaired waters that do not meet water quality standards, even after the implementation of technology-based controls. For each listed water body, a Total Maximum Daily Load (TMDL) must be developed, which establishes the maximum amount of a pollutant that can be discharged into the water body while still meeting water quality standards. The main objective of this section is to restore and maintain the quality of impaired waters. Developers should be aware that projects discharging into impaired waters may be subject to more stringent permit requirements and effluent limitations based on the applicable TMDL. Compliance strategies include implementing best management practices and pollution control measures to minimize discharges of the pollutants causing the impairment.

Section 319 - Nonpoint Source Management Programs

Section 319 of the Clean Water Act addresses nonpoint source pollution, which is pollution that comes from diffuse sources, such as agricultural runoff, urban stormwater, or atmospheric deposition. The main purpose of this section is to support state and local efforts to manage nonpoint source pollution and improve water quality. Key requirements include developing and implementing state nonpoint source management programs, which identify nonpoint source pollution problems and establish management measures to address them. Developers should be aware that projects contributing to nonpoint source pollution may be subject to state or local management requirements, such as implementing best management practices for erosion and sediment control, or managing stormwater runoff. Compliance strategies include incorporating green infrastructure and low-impact development techniques into project designs to minimize nonpoint source pollution.

Regulated Activities, Entities & Prohibited Substances

The Clean Water Act regulates a wide range of activities and entities that have the potential to impact water quality in the United States. The Act applies to both point sources, which are discernible, confined, and discrete conveyances such as pipes or ditches, and nonpoint sources, which are diffuse sources of pollution such as agricultural runoff or urban stormwater.

Industries and activities that are commonly regulated under the Clean Water Act include:

  • Wastewater treatment plants
  • Industrial facilities, such as manufacturing plants, power plants, and mining operations
  • Oil and gas extraction and refining
  • Agricultural operations, including concentrated animal feeding operations (CAFOs)
  • Construction activities that disturb one or more acres of land
  • Dredging and filling of wetlands or other waters of the United States

The Clean Water Act prohibits the discharge of pollutants into waters of the United States without a permit. Prohibited substances include:

  • Conventional pollutants, such as biochemical oxygen demand (BOD), total suspended solids (TSS), pH, fecal coliform, and oil and grease
  • Toxic pollutants, such as heavy metals, pesticides, and organic chemicals
  • Thermal pollution, which is the discharge of heat that may adversely affect aquatic life
  • Dredged or fill material, which can smother aquatic habitats and degrade water quality

The reasoning behind these prohibitions is to protect human health and the environment by preventing the degradation of water quality and the loss of aquatic ecosystems. The discharge of pollutants can harm aquatic life, make water unsafe for drinking and recreation, and disrupt the natural functions of wetlands and other aquatic habitats. By regulating these activities and substances, the Clean Water Act aims to maintain and restore the chemical, physical, and biological integrity of the nation's waters.

Relationship to Other Regulations & Agencies

The Clean Water Act interacts with various other federal, state, and local regulations and agencies in the effort to protect and restore water quality in the United States. Some of the key relationships include:

  1. U.S. Environmental Protection Agency (EPA): The EPA is responsible for implementing and enforcing many of the provisions of the Clean Water Act, including the National Pollutant Discharge Elimination System (NPDES) program and the development of water quality standards and effluent guidelines. The EPA also oversees state and tribal programs that have been delegated authority to administer Clean Water Act programs.1

  2. U.S. Army Corps of Engineers: The Army Corps of Engineers is responsible for administering the Section 404 dredge and fill permit program, which regulates the discharge of dredged or fill material into waters of the United States, including wetlands.2

  3. State and Tribal Governments: Many states and authorized tribes have been delegated authority by the EPA to administer Clean Water Act programs, such as the NPDES program and the Section 401 water quality certification program. States and tribes are also responsible for developing and implementing water quality standards, which must be approved by the EPA.

  4. Local Governments: Local governments, such as cities and counties, may have their own regulations and ordinances related to water quality and stormwater management that complement or exceed the requirements of the Clean Water Act. For example, local governments may require the use of best management practices for erosion and sediment control during construction activities.3

  5. Other Federal Agencies: The Clean Water Act intersects with the responsibilities of other federal agencies, such as the U.S. Fish and Wildlife Service and the National Marine Fisheries Service, which are responsible for protecting endangered species and their habitats. These agencies may provide input on Clean Water Act permits and participate in the development of water quality standards and TMDLs.4

  6. Coastal Zone Management Act: The Coastal Zone Management Act, administered by the National Oceanic and Atmospheric Administration (NOAA), requires federal actions, including Clean Water Act permits, to be consistent with approved state coastal management programs.5

  7. Safe Drinking Water Act: The Safe Drinking Water Act, also administered by the EPA, regulates public drinking water systems and underground injection control (UIC) programs. The Clean Water Act and Safe Drinking Water Act work together to protect both surface and groundwater resources.6

Effective implementation of the Clean Water Act requires coordination and collaboration among these various agencies and levels of government. Developers and environmental consultants should be aware of the complex regulatory landscape and engage with the appropriate agencies early in the project planning process to ensure compliance with all applicable regulations.


Regulatory Standards & Limitations

The Clean Water Act (CWA) and its implementing regulations establish various standards and limitations to protect water quality and prevent pollution. These include:

  1. Effluent Limitations Guidelines (ELGs): The Environmental Protection Agency (EPA) sets industry-specific, technology-based limits on the amount of pollutants that can be discharged into water bodies.7

  2. Water Quality Standards (WQS): States and tribes develop WQS, which define the water quality goals for a water body and the criteria necessary to protect its designated uses, such as swimming, fishing, or drinking water supply.8

  3. Total Maximum Daily Loads (TMDLs): For impaired water bodies that do not meet WQS, states and the EPA establish TMDLs, which set the maximum amount of a pollutant that a water body can receive and still safely meet WQS.9

  4. National Pollutant Discharge Elimination System (NPDES) Permits: Point sources that discharge pollutants into waters of the United States must obtain an NPDES permit, which includes specific effluent limitations, monitoring and reporting requirements, and other conditions to ensure compliance with the CWA.10

The EPA and authorized state agencies enforce these standards through regular inspections, monitoring, and enforcement actions against violators.11

Monitoring, Reporting & Recordkeeping Obligations

Under the Clean Water Act, regulated entities must comply with monitoring, reporting, and recordkeeping requirements to demonstrate compliance and provide transparency. These obligations include:

  1. Discharge Monitoring Reports (DMRs): NPDES permit holders must regularly sample and test their effluent, and submit DMRs to the permitting authority, typically on a monthly or quarterly basis. DMRs include data on the concentration and total volume of pollutants discharged.12

  2. Annual Reports: Some NPDES permits require the submission of annual reports, which provide a summary of the facility's compliance status, any noncompliance events, and corrective actions taken.13

  3. Spill or Unauthorized Discharge Reporting: Regulated entities must immediately report any spills, leaks, or unauthorized discharges that may impact water quality to the appropriate authorities, such as the National Response Center and the state environmental agency.14

  4. Recordkeeping: Regulated entities must maintain records related to their NPDES permit, including monitoring data, calibration and maintenance records for monitoring equipment, and compliance documentation, typically for a period of at least three years.15

These obligations are critical for verifying compliance, identifying potential violations, and informing enforcement actions.

Enforcement Actions & Penalties

The EPA and authorized state agencies enforce the Clean Water Act through inspections and audits:

Inspection TypeDescriptionFrequency
RoutineRegular, scheduled inspections to assess overall complianceVaries by facility risk and compliance history
TargetedFocused inspections in response to specific concerns or noncomplianceAs needed
Complaint-drivenInspections triggered by citizen complaints or tipsAs complaints are received

During inspections, regulated entities must provide access to records and facilities, and cooperate with inspectors. Entities have the right to accompany inspectors and to receive a copy of the inspection report.16

Violations of the Clean Water Act can result in various penalties:

Penalty TypeDescriptionExamples
AdministrativeFines or orders issued by the EPA or state agency- Compliance orders- Penalties up to $37,500 per day per violation
CivilFines imposed through judicial proceedings- Penalties up to $37,500 per day per violation- Injunctive relief
CriminalFines and imprisonment for knowing or negligent violations- Fines up to $50,000 per day per violation- Imprisonment up to 3 years

The severity of penalties depends on factors such as the seriousness and duration of the violation, the economic benefit gained from noncompliance, and the violator's compliance history and cooperation.17

Compliance Assistance & Regulatory Incentives

The EPA and state agencies offer various programs and resources to help entities comply with the Clean Water Act:

  1. Technical Assistance: The EPA provides guidance documents, fact sheets, and online tools to help regulated entities understand and meet CWA requirements.18 State agencies also offer technical assistance tailored to local needs and regulations.

  2. Training and Workshops: The EPA and state agencies host webinars, workshops, and conferences to educate regulated entities on CWA compliance, best management practices, and emerging technologies.

  3. Clean Water State Revolving Fund (CWSRF): The EPA provides low-interest loans to help communities finance water quality improvement projects, such as wastewater treatment plant upgrades or stormwater management systems.19

  4. Water Quality Trading: Some states have established water quality trading programs that allow point sources to meet their effluent limits by purchasing credits from other sources that have reduced their pollutant discharges beyond required levels.

  5. Environmental Leadership Programs: Some states offer voluntary programs that recognize and reward regulated entities for demonstrating superior environmental performance and compliance. Benefits may include regulatory flexibility, streamlined permitting, or reduced inspection frequency.20

To learn more about these programs and resources, regulated entities should consult the EPA's website or contact their state environmental agency.


Regulatory History & Upcoming Changes

The Clean Water Act (CWA), originally known as the Federal Water Pollution Control Act, was enacted in 1948. However, the most significant amendments occurred in 1972, which gave the CWA its current shape and established the basic structure for regulating pollutant discharges into the waters of the United States.21

Key amendments and their provisions include:

  1. 1977 Amendments: Established the basic structure of the National Pollutant Discharge Elimination System (NPDES) permit program and made it unlawful for any person to discharge a pollutant from a point source into navigable waters without an NPDES permit.22

  2. 1987 Amendments: Expanded the NPDES program to include stormwater discharges from industrial and municipal sources, and established the nonpoint source management program under Section 319 of the CWA.23

  3. 2015 Clean Water Rule: Clarified the definition of "waters of the United States" (WOTUS), which determines the scope of the CWA's jurisdiction. This rule was later repealed and replaced by the Navigable Waters Protection Rule in 2020.24

  4. 2020 Navigable Waters Protection Rule: Narrowed the definition of WOTUS, reducing the number of water bodies subject to federal regulation under the CWA. This rule was vacated by a federal court in 2021, and the EPA and U.S. Army Corps of Engineers are currently working on a new rule to define WOTUS.25

Regulated entities should stay informed about the ongoing rulemaking process for the definition of WOTUS, as it may impact the scope of the CWA's jurisdiction and the applicability of its permit programs. To stay engaged, interested parties can:

  • Monitor the EPA's website for updates on the rulemaking process
  • Participate in public comment periods when the proposed rule is published in the Federal Register
  • Attend public hearings or stakeholder meetings organized by the EPA or U.S. Army Corps of Engineers

Additional Resources

  1. Full text of the Clean Water Act: The official text of the CWA, including all amendments, can be found on the EPA's website at https://www.epa.gov/laws-regulations/summary-clean-water-act.26

  2. EPA Clean Water Act Section 404 Permit Program: This EPA webpage provides an overview of the Section 404 permit program, which regulates the discharge of dredged or fill material into WOTUS. It includes links to guidance documents, fact sheets, and application forms. https://www.epa.gov/cwa-404/permit-program-under-cwa-section-404.27

  3. "The Clean Water Act Handbook" by Mark A. Ryan: This comprehensive guide covers the history, structure, and implementation of the CWA, with a focus on the NPDES and Section 404 permit programs. It is a valuable resource for professionals working on CWA compliance and enforcement.28


  1. U.S. Environmental Protection Agency. (2021). About the Office of Water https://www.epa.gov/aboutepa/about-office-water

  2. U.S. Army Corps of Engineers. The link previously pointing to their Regulatory Program and Permits page has been removed due to instability issues.

  3. U.S. Environmental Protection Agency. (2021). Stormwater Management Practices at EPA Facilities https://www.epa.gov/greeningepa/stormwater-management-practices-epa-facilities

  4. U.S. Fish and Wildlife Service. The link previously provided for information on Endangered Species Act Consultations has been removed due to issues with the link.

  5. National Oceanic and Atmospheric Administration. (2021). Federal Consistency https://coast.noaa.gov/czm/consistency/

  6. U.S. Environmental Protection Agency. (2021). Safe Drinking Water Act (SDWA) https://www.epa.gov/sdwa

  7. 40 C.F.R. § 401-471

  8. 33 U.S.C. § 1313; 40 C.F.R. § 131

  9. 33 U.S.C. § 1313(d); 40 C.F.R. § 130.7

  10. 33 U.S.C. § 1342; 40 C.F.R. § 122

  11. 33 U.S.C. § 1319; 40 C.F.R. § 123.26-27

  12. 40 C.F.R. § 122.41(l)(4)

  13. 40 C.F.R. § 122.41(l)(7)

  14. 40 C.F.R. § 122.41(l)(6)

  15. 40 C.F.R. § 122.41(j)

  16. 33 U.S.C. § 1318; 40 C.F.R. § 123.26

  17. 33 U.S.C. § 1319; 40 C.F.R. § 19.4

  18. EPA, "Water Topics,", https://www.epa.gov/environmental-topics/water-topics

  19. EPA, "Clean Water State Revolving Fund,", https://www.epa.gov/cwsrf

  20. EPA, "National Environmental Performance Track,", https://archive.epa.gov/performancetrack/web/html/index.html

  21. "Summary of the Clean Water Act." EPA, Environmental Protection Agency, 11 Mar. 2021, https://www.epa.gov/laws-regulations/summary-clean-water-act

  22. "Clean Water Act, Section 402: National Pollutant Discharge Elimination System." EPA, Environmental Protection Agency, https://www.epa.gov/cwa-404/clean-water-act-section-402-national-pollutant-discharge-elimination-system

  23. "Clean Water Act Section 319." EPA, Environmental Protection Agency, 4 Feb. 2021, https://www.epa.gov/nps/319-grant-program-states-and-territories

  24. "Clean Water Rule." Federal Register, 29 June 2015, https://www.federalregister.gov/documents/2015/06/29/2015-13435/clean-water-rule-definition-of-waters-of-the-united-states

  25. "Navigable Waters Protection Rule." Federal Register, 21 Apr. 2020, https://www.federalregister.gov/documents/2020/04/21/2020-02500/the-navigable-waters-protection-rule-definition-of-waters-of-the-united-states

  26. "Summary of the Clean Water Act." EPA, Environmental Protection Agency, 11 Mar. 2021, https://www.epa.gov/laws-regulations/summary-clean-water-act

  27. "Permit Program under CWA Section 404." EPA, Environmental Protection Agency, https://www.epa.gov/cwa-404/permit-program-under-cwa-section-404

  28. Ryan, Mark A. "The Clean Water Act Handbook." American Bar Association, 2011.

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A Note to Our Readers: We hope this guide is a valuable resource in helping you better understand the Clean Water Act. However, it's not a substitute for professional advice and doesn't cover every scenario. Always consult with regulatory bodies and professionals for the most current advice and project-specific guidance.