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EPA’s NCI: Reducing Significant Non-Compliance with National Pollutant Discharge Elimination System (NPDES) Permits strives to improve surface water quality and reduce potential impacts on drinking water by assuring that all Clean Water Act National Pollutant Discharge Elimination System (NPDES) permittees are complying with their permits.

Over 29 percent of the approximately 46,000 major and minor NPDES-permitted facilities were in significant noncompliance (SNC) with their permits in FY 2018! EPA’s NCI aims to reduce this number by half by the end of FY 2022.

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Issue SummaryWastewater

Local governments are responsible for designing, planning, constructing, financing, operating and maintaining wastewater treatment facilities, and their conveyance systems, known as publicly owned treatment works (POTWs), in compliance with Clean Water Act (CWA) regulations. POTWs collect wastewater from homes, commercial buildings and industrial facilities and transport it via a series of pipes, known as a collection system, to the treatment plant. Here, the POTW removes harmful organisms and other contaminants from the sewage, so it can be discharged safely into the receiving waters.

Generally, POTWs are designed to treat domestic sewage only, but they also receive wastewater from industrial users. EPA’s General Pretreatment Regulations establish responsibilities of federal, state and local government, industry and the public to implement Pretreatment Standards. The Standards aim to control pollutants originating with industrial users which may pass through or interfere with POTW treatment processes or which may contaminate sewage sludge.

Collection systems that were designed to carry stormwater as well as sewage (combined systems) can also raise compliance issues when, during and after wet weather events, they exceed the conveyance and treatment capacity of the POTW and result in untreated discharges (combined sewer overflows, or ’CSOs’).

Other wastewater collection and treatment activities that have compliance obligations include laboratory operations, biosolids management and disposal, chemical storage/hazardous materials management and vehicle/equipment management.


EPA administers the CWA programs with which local government must comply. Under the CWA, a permit is needed to discharge a pollutant from a point source, such as a POTW, into the waters of the United States. CWA implementation is primarily carried out by states and several tribes under delegated authority. EPA retains direct regulatory authority in a few states, all U.S. territories, and much of Indian Country. Implementation includes issuing NPDES permits to owners/operators of POTWs.

Permittees must comply with their designated discharge limitations and submit ’discharge monitoring reports’ (DMRs) showing their compliance with permit conditions. EPA establishes primary and secondary treatment standards, which are minimum, technology-based requirements for municipal wastewater treatment plants.

Permittees must also prevent unauthorized discharges, such as sanitary sewer overflows (SSOs) and CSOs. This includes implementation of control strategies and, in the case of CSOs, long-term control plans.

Sanitary Sewer Overflows and Prevention

Most collection systems constructed since the 1950s use dedicated sanitary sewers. However, these sometimes suffer from infiltration and inflow (I/I) of stormwater or groundwater, often during wet weather events. Large volumes of I/I can cause sanitary sewer overflows and operational problems at the wastewater treatment facility serving the collection system. Sewage overflows can be caused by other problems such as blockages, equipment failures, broken pipes or vandalism.

SSOs that reach waters of the U.S. are considered point source discharges. This means SSOs are prohibited unless authorized by a NPDES permit. Under the Supreme Court’s recent decision in County of Maui v. Hawaii Wildlife Fund (’Maui decision’), SSOs that are discharged to groundwater and conveyed to waters of the U.S. may also constitute violations. Moreover, SSOs, including those that do not reach waters of the U.S., may indicate that sewer systems are being improperly operated or maintained and may violate NPDES permit conditions.

SSOs can be prevented or controlled by following facility and operational best practices, including:

  • Sewer system cleaning and maintenance
  • Reducing infiltration and inflow through system rehabilitation and repairing broken or leaking service lines
  • Enlarging or upgrading sewer, pump station or sewage treatment plant capacity and/or reliability
  • Limiting fats, oils and grease (FOG) into the sewer systems
  • Construction of wet weather storage facilities
  • Expanding the capacity of the treatment works
  • Public education

Combined Sewer Overflows

CSOs convey untreated or partially treated human and industrial waste, toxic materials and stormwater. EPA has prescribed nine minimum controls for operators of CSSs to implement. Permittees must prepare and implement a long-term control plan to eliminate the CSO and meet water quality standards. The nine minimum controls are:

  1. Proper operation and regular maintenance programs for the sewer system and CSO outfalls
  2. Maximum use of the collection system for storage
  3. Review and modification of pretreatment requirements to ensure that CSO impacts are minimized
  4. Maximization of flow to the POTW for treatment
  5. Elimination of CSOs during dry weather
  6. Control of solid and floatable materials in CSOs
  7. Pollution prevention programs to reduce contaminants in CSOs
  8. Public notification to ensure that the public receives adequate notification of CSO occurrences and CSO impacts
  9. Monitoring to effectively characterize CSO impacts and the efficacy of CSO controls.

Biosolids Program

CWA regulations apply to management of biosolids, a byproduct of wastewater treatment. Section 405(d) of the CWA requires EPA to establish numeric limits and management practices that protect public health and the environment from the reasonably anticipated adverse effects of chemical and microbial pollutants during the use or disposal of sewage sludge. EPA also reviews biosolids regulations every two years to identify any additional pollutants that may occur and establishes regulations for those pollutants that prove harmful to human health or the environment.


EPA oversees implementation of these programs and may take direct enforcement action even in states and tribes that have received approval to operate these permit programs. EPA and the U.S. Department of Justice have brought enforcement actions against cities and municipal POTWs, entering into consent decrees (agreements filed with federal courts) with the municipalities to ensure correction of violations and investment of funds.

EPA’s Office of Wastewater Management (OWM) oversees programs protecting the nation's waters and watersheds. Its mission focuses on control of water and wastewater that is collected in discrete conveyances (also called point sources), including pipes, ditches and sanitary or storm sewers. OWM is home to the Clean Water State Revolving Fund, focused on providing low-cost financing for local wastewater treatment systems, nonpoint source projects and estuary protection through support of state revolving funds. OWM also administers the Water Infrastructure Finance and Innovation Act (WIFIA) program established in 2014, a federal loan program for water and wastewater infrastructure projects.

OWM’s website offers a substantial set of resources, rulemakings and guidance documents helpful for local governments. ’

NPDES Municipal Wastewater Portal. Information on municipal wastewater management and treatment, permitting, financing, reporting and technologies.

EPA Water Enforcement Policy, Guidance and Publications. Comprehensive collection of EPA guidance documents on enforcement of the CWA and Safe Drinking Water Act.

CWA Analytical Methods Update Rule. Identifies methods used by municipalities and industries and their laboratories to analyze the chemical, physical and biological components of wastewater, identify pollutants, satisfy reporting requirements and document compliance with applicable requirements.

Memorandum on Interim Strategy for Per- and Polyfluoroalkyl Substances (PFAS) in Federally Issued NPDES Permits. Recommended actions for implementing EPA's interim PFAS strategy. Listed actions focus on adapting NPDES permitting practices to increase monitoring for PFAS in NPDES permitted facilities. Also details EPA's future plans to promulgate information-sharing on PFAS monitoring between facilities.

CWA Analytical Methods for PFAS. Information on EPA's development of analytical methods to test for PFAS in wastewater, groundwater and surface water.

Pretreatment Standards & Limits. Program requirements for pretreatment of industrial wastes and related requirements.

Maui Guidance Memorandum. Guidance to the regulated community and permitting authorities on the impact of the Supreme Court's Maui decision on the CWA Section 402 NPDES permit program. Outlines seven non-exclusive factors to evaluate whether a point source pollutant discharge that travels through groundwater can be treated as the equivalent of a direct discharge to Waters of the United States.



State Regulations Resource Locator. Find environmental regulations, link to state agencies, retrieve agency news and download sector-specific resources.

Organizations/Non-Government Programs


The Water Environment Federation (WEF). International not-for-profit educational and technical organization of over 40,000 water experts. Provides webinars, technical assistance trainings and guidance documents on wastewater system management.

Association of Clean Water Administrators (ACWA). National association of the state, interstate and territorial regulators administering water pollution control and clean water programs.

National Association of Clean Water Agencies (NACWA). National association of public wastewater and stormwater agencies and utility districts.



Making Water a Career of Choice: Water Workforce Case Studies. Nine case studies of communities in the U.S. and their unique initiatives to improve recruitment and retention of water and wastewater professionals. Strategies include increased outreach to youths and minority communities and development of leadership training programs.

Pipeline to a Sustainable Workforce: Decentralized/Onsite Wastewater Occupations. Report on occupational characteristics, growth projections and basic education and training requirements for professionals working in the decentralized wastewater sector.

It's Hot and Getting Hotter: A Report for Utilities on Heat Impacts. Projects heat impacts on utility personnel and assets through the year 2070 and provides adaptation procedures to reduce heat-related harm to outside utility workers and infrastructure including HVAC systems, water treatment plants, pumps and motors.

Rural and Small Systems Guidebook to Sustainable Water and Wastewater Utility Management. Walks small system operators through best practices in 10 key areas of sustainable system management (Product Quality, Customer Satisfaction, Employee & Leadership Development, Operational Optimization, Financial Viability, Infrastructure Stability, Operational Resiliency, Community Sustainability & Economic Development, Water Resource Adequacy, and Stakeholder Understanding & Support). Provides further guidance on conducting system assessments and identifying priority areas for improvement. Information on conducting workshops and trainings on this manual is available in EPA's companion publication, "Workshop in a Box: Sustainable Management of Rural and Small Water and Wastewater Systems Workshops."

Making the Right Choices for Your Utility: Using Sustainability Criteria for Water Infrastructure Decision Making. Provides water and wastewater utilities with a six-step process to compare and choose between competing infrastructure alternatives. The process highlights considerations, including the creation of sustainability and performance goals and the determination of common and relevant evaluation criteria, to ensure that a municipality's selected infrastructure will meet its regulatory requirements.

Camden County Municipal Utilities Authority: A Wet Weather Case Study of Incorporating Community Interests into Effective Infrastructure Decision-Making. Camden County, New Jersey case study on successful integration of community stakeholder involvement, long-term sustainability considerations and cost effectiveness into the preparation of a Long Term Control Plan to address CSO.

EPA Case Studies on Implementing Low-Cost Modifications to Improve Nutrient Reduction at Wastewater Treatment Plants. Empirical data and experiences of non-advanced wastewater treatment plants that have improved their nutrient reduction capabilities with low-cost techniques and no costly infrastructure upgrades.

Local Limits Development Guidance. Assistance for municipalities that own or operate publicly owned treatment works (POTWs) on developing and implementing local pretreatment programs.

Databases and Tools


Wastewater Technology Clearinghouse. Information-sharing platform focused on cost-effectiveness and performance, separated into databases on centralized and decentralized treatment systems. Provides reports, case studies and webinars.


For more information on available funding and financing strategies, please visit the "Wastewater and Stormwater" section of our Financing page.