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  2. Small and Rural Wastewater Systems
  3. About Small Systems

Lagoon Wastewater Treatment Systems

Many small, rural, and Tribal communities across the United States rely on lagoon systems to treat their municipal wastewater. As we learn how to keep the water clean and protect the environment, new regulatory requirements can require installing more complex and costly wastewater treatment technology to comply with permits. This can be particularly challenging for rural, small, and Tribal communities as they may need more financial and technical capacity to identify the best-fit, most effective technologies or process improvements for their lagoon system. They may also need more capacity to successfully seek funding for infrastructure investments to achieve associated water quality improvements; this can lead to human health, recreational, and aquatic life impacts in small communities.

  • Fact Sheet: Technical Assistance for Lagoon Wastewater Treatment Systems (pdf) (87.99 KB)

On this page:
  • Lagoon Wastewater Treatment Action Plan
  • Lagoon Inventory Dataset
  • Universe of Lagoons Report
  • Financial and Technical Assistance Tools

Lagoon Wastewater Treatment Action Plan 2022-2026

The Implementation of a Lagoon Action Plan between 2022 and 2026 supports small, rural, and Tribal communities, identify alternative and retrofit technologies, and provide other assistance to make progress toward the vision of creating workable programs that result in clean waterways that small, rural, and Tribal communities can sustain.

  • Lagoon Action Plan (pdf) (12.85 MB)

As part of this plan, EPA's Office of Water and Office of Compliance are focusing their efforts on the following areas of need:

  • Identifying the Universe (Inventory) of Lagoons Nationally
  • Developing Cost and Performance Data for Alternative or Retrofit Technologies
  • Developing Financial and Other Technical Assistance Tools
  • Developing Regulatory Support Tools, Including Tools to Streamline Economic Impact Evaluations
  • Developing plans for community engagement, communication, and partnerships to support the Lagoon Action Plan

Lagoon Inventory Dataset

The Lagoon Inventory Dataset contains information on  over 4,500 known discharging lagoon wastewater treatment systems with National Pollutant Discharge Elimination System (NPDES) permits that are publicly or semi-publicly owned, in which lagoons serve as the main form of secondary treatment (without more advanced treatment or add-on technologies). This list of lagoons was compiled from 18 datasets containing lagoon facilities from EPA, states, and the Rural Community Assistance Partnership (RCAP). The following data for facility locations are also included:

  • Compliance data (from EPA’s Enforcement and Compliance History Online (ECHO) database as of September 20, 2021)
  • Socioeconomic data (from U.S. Census American Community Survey using Census place-level geography five-year averages from 2015-2019)

This lagoon inventory dataset was updated in May 2022 to reflect the most up-to-date information from states, while The Universe of Lagoons Report (see below) was written based on a previous version of the dataset. In July 2022, EPA revised the dataset to incorporate updates provided by the state of New Hampshire and to clarify if each NPDES permit is state or EPA-issued.

  • Lagoon Inventory Dataset (xlsx) (2.58 MB)

Universe of Lagoons Report

The Universe of Lagoons Report describes the methodology used to aggregate state and Tribal lagoon wastewater treatment systems in the Lagoon Inventory Dataset. The report includes an analysis of lagoon wastewater treatment system data, including socioeconomic, and compliance data patterns in communities that use lagoons based on data gathered in 2020-2021.

  • Universe of Lagoons Report (pdf) (1.79 MB)

Financial and Technical Assistance Tools

The following tools support lagoon operators, technical assistance providers, and local leadership. The tools were developed under the Lagoon Action Plan.

Read EPA's News Release announcing the new tools.

First Stop Toolbox for Lagoon Systems

EPA has released a lagoon troubleshooting diagnostic tool called First Stop Toolbox, to aid in quickly diagnosing and determining workable paths forward to resolve brief or persistent system disruptions that lead to discharge non-compliance. 

The First Stop Toolbox guides users through questions to identify the best resources to use when addressing a lagoon’s challenges. It may be useful to operators, community decisionmakers, technical assistance providers and circuit riders, and others familiar with issues affecting a specific lagoon.

  • Access the First Stop Toolbox

View the webinar below for an overview of how to use the tool to address technical or compliance challenges facing a particular lagoon:

Ammonia Water Quality Standards (WQS) Variance Tools for Small Communities with Lagoon Wastewater Treatment Systems

EPA developed two regulatory support tools that states, authorized Tribes, and communities with lagoon wastewater treatment systems may use when conducting the economic impact analyses for ammonia-specific WQS variances:

  • Small Lagoon Community Economic Streamlining Tool, or “SLCES Tool”
  • Individual Lagoon Tool, or “ILT”

Both tools provide a user-friendly, streamlined way for a state, Tribe, or community to apply EPA’s economic guidance to evaluate whether a WQS variance may be appropriate for a small community experiencing lagoon system compliance challenges related to ammonia. The tools are accompanied by an implementation document that describes when each tool is most useful and how to use the tools’ results to construct a WQS variance consistent with EPA’s regulation.

  • Learn more about and access Ammonia WQS Variance Tools for Small Communities with Lagoon Wastewater Treatment Systems.

Troubleshooting Manual for Small Wastewater Lagoon Systems

This detailed manual assists operators of small wastewater lagoon systems diagnose and troubleshoot the causes of a system's noncompliance, optimize system performance, and attain compliance with their NPDES permit.

  • Troubleshooting Manual for Small, Facultative, Partial-Mix Aerated, and Complete-Mix Aerated Wastewater Lagoons (pdf) (1.57 MB)

Understanding Lagoon Requirements Under 40 C.F.R. Part 503: Best Management Practices for Use or Disposal of Sewage Sludge, Part 1 – Land Application of Sewage Sludge Removed from Lagoons

The Clean Water Act (CWA), Section 405 required EPA to develop a regulation to protect public health and the environment from any reasonably anticipated adverse effects of pollutants that might be present in sewage sludge. This regulation, 40 C.F.R. Part 503, Standards for the Use or Disposal of Sewage Sludge, was published on February 19, 1993 (58 FR 9248). 40 C.F.R. Part 503 (or “Part 503”) contains requirements for sewage sludge when it is applied to land, incinerated in a sewage sludge incinerator, or placed on a surface disposal site.

This document summarizes Part 503 requirements and best management practices for the land application of sewage sludge removed from a lagoon.

  • Understanding Lagoon Requirements Under 40 C.F.R. Part 503: Best Management Practices for Use or Disposal of Sewage Sludge: Part 1 – Land Application of Sewage Sludge Removed from Lagoons (pdf) (2.42 MB)

Small and Rural Wastewater Systems

  • About Small Systems
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    • Lagoon Systems
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Contact Us About Small and Rural Wastewater Systems
Contact Us About Small and Rural Wastewater Systems to ask a question, provide feedback, or report a problem.
Last updated on May 30, 2025
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