Lesson 2a: Pollution Discharge Permits

National Pollutant Discharge Elimination System

Under the Clean Water Act, all point source discharges of pollution require a permit. This basic principle is the foundation of water pollution prevention and control in the United States. Generally, anyone who discharges pollutants from a point source without a Clean Water Act permit is breaking the law. There is, of course, a corollary: it is perfectly legal to discharge pollutants if you have a valid permit and comply with its terms. Understanding how the permitting system works is critical for anyone wanting to use the Clean Water Act to protect a river.


Under the Clean Water Act, all point source discharges of pollution require a permit. This basic principle is the foundation of water pollution prevention and control in the United States. Generally, anyone who discharges pollutants from a point source without a Clean Water Act permit is breaking the law (40CFR122.1(b)(1)). There is, of course, a corollary: it is perfectly legal to discharge pollutants if you have a valid permit and comply with its terms. Understanding how the permitting system works is critical for anyone wanting to use the Clean Water Act.

Citizen involvement is important in all phases of the permit process. You don’t have to be a lawyer to make a difference, but you do need to understand the system’s basics. By developing a solid grasp of the following terms and concepts, you will be much better able to help prevent and control water pollution in your watershed.

Controlling point source pollution

The Clean Water Act’s primary point source control program is the National Pollutant Discharge Elimination System (NPDES). This system rests on the definition of point source: “any discernible, confined, and discrete conveyance” of pollutants to a water body. The definition of discrete conveyance includes, but is not limited to, “any pipe, ditch, channel, tunnel, conduit, well, discrete fissure, container, rolling stock, concentrated animal feeding operation, landfill leachate collection system, vessel or other floating craft from which pollutants are or may be discharged” (40CFR122.2).

As we will see, the definition of “point source” covers a wide and expanding variety of activities, beginning with direct discharges from factories and sewage treatment plants, and extending to a multitude of other sources. The Act provides one major exception to the point source definition: it specifically excludes “return flows from irrigated agriculture or agricultural storm water runoff”(40CFR122.3). This exempts many but by no means all, agricultural activities from the NPDES program.

Over the years, the EPA has regulated more sources of point source pollution. For example, in the early years of the Act, municipal stormwater pollution, or “urban runoff,” was considered an unregulated, nonpoint source. Much of it is collected in and discharged through stormwater pipes — clearly, in Clean Water Act parlance, “discrete conveyances.” The recognition of this fact (thanks to citizen suits in the 1980s) has led to the development of regulations and programs to control many forms of stormwater runoff under NPDES permits (see Lesson 2b: Stormwater Pollution Control Permits – available soon).

“Nonpoint source pollution”

The term “nonpoint source pollution” has been used in many different ways and in many different contexts over the past twenty-five years. Some define it as “polluted runoff from rain or snow,” others as pollution from “diffuse sources,” and still others, colorfully, as “poison runoff.” The most accurate, complete and enduring definition of the term is the very simplest. A “nonpoint source” is exactly what the words say: any source of pollution that is not a point source. (See Lesson 7: Nonpoint Source Pollution Control – available soon)

The Goal: Eliminate Discharge of Pollutants

In order to achieve the ultimate goal of the Clean Water Act, “to restore and maintain the chemical, physical and biological integrity of the Nation’s waters,” several other goals and policies, including the following, were established: “it is the national goal that the discharge of pollutants into the navigable waters be eliminated by 1985” (CWA101(a)(1)).

The NPDES has greatly reduced the impact of many existing discharges, but it certainly has not eliminated point source water pollution in the United States. In fact, while most pollution discharges have come under greater control since the Act was passed (with a few approaching “zero impact” ) very few have actually been phased out. Moreover, thousands upon thousands of new discharges — including many with significant impacts — have been permitted.

The NPDES performs admirably in those places where a well-informed public (a) keeps an eye on Clean Water Act goals, (b) monitors watershed activities, (c) understands how the NPDES and other CWA tools are supposed to work together, and (d) plays an active role in their ongoing implementation. In the absence of an ever-vigilant public, however, the NPDES can produce results that are quite the opposite of those intended.

The Clean Water Act calls for permits to be reviewed, adjusted as necessary, and renewed at least every five years. Far too often, however, the permit cycle is much longer than this. Delays in reviewing, adjusting and renewing permits are usually attributed to limited agency funding and staff.

EPA Runs Some NPDES Programs

The EPA has delegated primary NPDES program responsibility in most states to a state pollution
control agency. There are a few exceptions where the EPA retains lead responsibility for developing and/or enforcing NPDES permits. These are Idaho, Massachusetts, New Hampshire, New Mexico, the District of Columbia, Puerto Rico, the Pacific Territories and all tribal lands. The Virgin Islands are partially authorized.


There are two types of permits: individual and general permits. Each type has different requirements and different public review opportunities.

Individual permits

When a facility has its own specific permit, it is called an “individual permit.” These permits are site specific and usually much more detailed than general permits. The pollutant limits may be based on the category of discharge or they may be based on the water quality of the receiving water body. All municipal sewage treatment plants and “major industrial dischargers” must apply for individual permits. States may differ in how they define major industrial dischargers, but their definitions must be acceptable to the EPA.

Individual NPDES permits have many components. Some of the basic elements of a typical permit include:

  • Cover sheet: This will usually give the best snapshot of the permit. It lists the discharger’s name and address, description and location of discharge(s), condition of receiving water body, designated uses, effective date of the permit and its expiration date.
  • Pollutant limits: These are the “meat and potatoes” of the permit. All pollutants that are controlled or monitored from this discharge must be listed with the associated limits, such as dissolved oxygen >= 5mg/L.
  • Monitoring requirements: The pollutant limits page will also list the type and frequency of monitoring required for each pollutant or parameter (such as flow). For example, pH monitoring may only be required monthly, whereas, temperature monitoring may be required daily. Occasionally, the pollutant limits page will read only “monitor and report.” This may occur when there is uncertainty of the amount discharged and some screening is needed.
  • Fact sheet or rationale sheet: This section is often a separate attachment with useful detail about the permitted activity. It may include more information about the wastewater treatment process or more about the receiving water body. If the permitting agency properly implements the antidegradation policy, documentation of antidegradation analysis ought to be found in the fact sheet.
  • Other important information: The permit may also include a) additional annual or semi-annual pollutant screening to identify when new pollutant limits are needed, b) compliance schedules, c) details of the municipal wastewater “pretreatment program,” d) instream monitoring, or e) language that prohibits the discharge from contributing to violations of water quality standards.

The permit will usually also have several pages of “boilerplate” language at the end of the permit. In some states this has included requirements for identification tags on every pipe discharging into waters of the state. When reviewing permits, don’t skip this language. This section of the permit will often include crucial requirements.

Most importantly, public notice of every draft individual permit must be distributed to the interested and affected public. This is your opportunity to review and comment on permits. Get on the mailing list for permits in your watershed. Across the country, several state permitting agencies provide notice of permit applications long before the permit is drafted. Once you have developed relationships with agency staff you may get information on permits sooner.

General permits

Most citizens believe that every proposed discharger or regulated activity is specifically examined and that permit requirements are developed with that particular activity and location in mind. In reality, most of the activities permitted under NPDES are covered by general permits.

“General permits” are developed for numerous categories of activity within a political or geographic boundary that share similar operations and discharges, require similar limits or operating conditions, and require similar monitoring requirements (40CFR122.28). General permits are commonly used for stormwater pollution, concentrated animal feeding operations, many types of mining and often for categories of industrial discharge. If the owners of a business believe their enterprise qualifies under an existing general permit category, they can apply to be covered by that permit. They generally do so through an application called a “Notice of Intent” for coverage under the permit. The permitting agency has the authority to decline the application and to require an application for an individual permit.

The general permit is developed and renewed every five years and can vary considerably depending on what activity is being permitted to discharge. It will have a description of the activities for which the permit applies. It should discuss the potential impacts of these activities and specify when an activity does not qualify for the general permit. For example, if the activity is likely to affect fish when they are migrating or spawning, the permit could limit the timing and duration of the activity. The permit will also have a description of the information needed from every applicant and the compliance requirements.

Every applicant wanting to be covered by that permit must submit a “Notice of Intent” (NOI) form. The amount of information required by the NOI is variable, but very few are longer than two pages and little detail about the activity is required.

The general permits usually require less frequent monitoring and reporting than individual permits and sometimes none at all. Many general permit requirements are wrapped up in the development and implementation of management plans that are supposed to address likely pollution discharge and impacts to designated and existing uses through best management practices. However, these management plans, whether for stormwater or mining or feedlots, are seldom required to be submitted to the permitting agency.

General permits are subject to public notice and review only during the initial development of the permit and at the time of each five-year review of the permit. There is limited public and interagency review of each application for coverage under the general permit (notices of intent) throughout the five year period.

Bringing up specific concerns during the public review every five years is very important given that an unlimited number of permittees can be included under each general permit. Information on the permittees covered by each general permit is public and should be available from your permitting agency. If not, consider submitting a “Freedom of Information Act” (FOIA) request to obtain it.

If the general permit is not likely to protect the receiving water body, citizens can petition for requirement of an individual permit. An individual permit can be required by the permitting agency when: the discharger is out of compliance, better technology is available, circumstances in the receiving water body have changed so the general permit is no longer protective, or the discharger is a significant contributor of pollutants(40CFR122.28(b)(3)).


The level of treatment required of each discharger is determined by the category of discharge and the condition of the receiving water body. Minimum limits established for a category of discharges regardless of their location are called “technology-based.” Limits driven by the water quality standards and current conditions of the receiving waterbody are said to be “water quality-based.” In the Clean Water Act’s two-part system, each permit must contain limits for each pollutant based on the more stringent of the two types of controls in that particular situation. It is not unusual for a single permit to contain some limits of each type.

“Technology-based” permit limits

Clean Water Act regulations establish minimum pollutant control limits for numerous categories of industrial discharges, for sewage discharges and for a growing number of other types of discharges. Regardless of any site-specific considerations, all dischargers must meet at least the minimum limits that apply to all others in the same category. These limits are said to be “technology-based.” In each category, they represent levels of technology and pollution control performance that the EPA expects all dischargers in that category to achieve.

A “technology-based effluent limit” (TBEL) is simply a minimum level of performance that the EPA or a state permitting agency has decided must be achieved by dischargers in a given category, regardless of the nature or size of the “receiving water.” Decisions about how to best achieve that level of performance are typically left to permitees. Permits may prescribe specific point source control practices or technologies, or best management practices for non point sources, but they seldom do.

Many people understandably (but incorrectly) assume that technology-based limits represent the current state-of-the-art in pollution control technology. The Clean Water Act called for the technology-based limits to be based on the performance of the “best available technology economically achievable” (CWA, Section 301(b)(2)). This has been described as representing the average performance of the best performers. However, over thirty years after the passage of the Act, individual dischargers often are able to achieve a higher level of performance than what is specified by national technology-based limits. While EPA is continuing to develop technology-based limits for the categories of discharges that don’t yet have them, the agency has generally not been updating technology-based limits as technology advances.

Water quality-based permit limits

In many cases, technology-based limits are not enough to protect a receiving water body. If the discharge is large or highly concentrated, or if the receiving water is small or ecologically sensitive, the discharge can easily overwhelm the water body unless the discharger does more than simply meet the minimum technology-based limits.

The authors of the Clean Water Act understood that technology-based limits often would not be enough. Rather than discard the pre-1972 “receiving water quality-based” approach, they improved it by requiring that it be used as a backstop to the technology-based approach. This crucial backstop system requires each discharger to use as much additional treatment as necessary to meet water quality standards for the receiving water itself.

Water quality-based effluent limits (WQBELs) are often required when an applicant requests a permit for a relatively large-volume discharge to a relatively small stream. They may be necessary when the receiving water is naturally limited in its capacity to absorb pollution, or when a water body already carrying a heavy pollution burden cannot absorb any more without violating water quality standards. As pollution pressures in a watershed increase, permit limits are more frequently driven by water quality standards. Unlike the minimum technology-based effluent limits that have an economic feasibility component, water quality-based limits are set to assure that water quality standards (uses, criteria and antidegradation) are not violated, regardless of the economic consequences.

Monitoring compliance with these limits

Most of the monitoring of permitted discharges is done by permittees themselves. State and federal officials make spot checks (often in response to public concerns or questions), but the vast majority of the information about discharges and permit compliance is compiled and submitted by permittees.

Individual permittees submit monitoring reports to the permitting agency. The Discharge Monitoring Reports (DMRs) are typically due monthly. A failure to report properly and on time is a permit violation. The permitting agency compiles DMR information and must make it available to EPA and the public. When violations are evident, enforcement actions are in order. General permits usually do not have similar monthly reporting requirements, but they may have other requirements such as annual reporting.


The Clean Water Act provides for public comment and involvement in the NPDES permitting process. You will find several different formal opportunities for input, as well as a number of more informal opportunities.

Individual permits

It is essential to comment on NPDES permits in detail during the narrow (usually 30-day) public review period. If you decide to appeal (or otherwise contest) a permit decision to the agency or before a judge, you can usually raise only those issues that you raised during the initial public comment period. Therefore, if you do not have time to elaborate on an issue or concern during the public review period, it is important to at least raise it at that time. If you do go to court later, you may have to show that you have “exhausted all administrative remedies” for addressing your concerns.

General permits

The only times you can comment on general permits is when they are first developed (before any actual dischargers are applying for coverage) and every time they are up for renewal (which should be every five years). Even though general permits address the majority of activities covered under NPDES, once a general permit is finalized, the public is usually not given any notice or opportunity to comment on each particular activity or discharge submitted for “coverage” under that permit. Therefore, public comments on general permits may have to be based on hypothetical scenarios. Imagine the worst-case scenario when commenting on a general permit. How might an activity allowed under this general permit violate water quality standards? You can and should document the adverse impacts of general permitted activities. Such documentation can be used to improve the general permit or require individual permits in certain cases.

Preparing for NPDES permit review

1) Learn which permits have already been issued, or are proposed, for your area of interest — a stretch of your river, your whole watershed or your entire state. Your state agency and regional EPA (when the program is not “delegated” to the state) can provide this information. State and EPA websites will provide valuable information about discharge permits in your state. EPA maintains a Permit Compliance System online database that is worth examination.

2) Get on the mailing lists for public information. There should be a public notice that announces the public comment period when any new or renewing permit is drafted. Many states now post public notices on their websites. You may be able to request notification when permits in your watershed are under consideration. However, few states are able to notify by watershed.

3) Find out ahead of time when permits are due for renewal (theoretically every five years), or when new ones are open for public comment. Public comment periods are usually only 30 days, but you may be able to request an extension from the agency. Give it a try! Every day counts when you are trying to address a technical or legal question and build public awareness and support for your position.

4) Collect current state standards and data such as state water quality standards, the water quality inventory for your state (305(b)), the threatened and impaired waters list (303(d)), and any relevant Total Maximum Daily Load plans (see Lesson 4: Restoring Impaired Waters with TMDLs).

5) Set up a monitoring program. Design a monitoring program that fits your resources and answers your questions. If your questions include whether a facility is in compliance with its permit or whether a discharge is harming a water body (even if it is in compliance), you can monitor upstream and downstream of the discharge as well as in any defined mixing zone at the point of discharge. You don’t necessarily have to collect detailed scientific data. Watershed residents can provide valuable information about water quality problems to a state water quality agency and a permittee by paying attention to, documenting and reporting visual changes in the receiving water body. For example when is the water muddy? What species of fish and wildlife are present? What is noticeable downstream of each point source? If you can follow your state’s monitoring requirements, any data you collect will be more credible in the eyes of the water quality agency.


Regardless of whether a permit is new, modified or simply being reissued without any modifications, you will need most of the same information. More and more permits are available online, but the whole permit file is unlikely to be on the web.

Information to gather

  • Draft permit and old permit (if applicable)
    It is most important to find out what is changing in the new permit. Be sure to ask for the permit application and the fact sheet (sometimes called the rationale sheet).
  • Discharge monitoring reports (DMRs) – monitoring by permittee submitted monthly to agency
    You should review as many of these reports as you can get your hands on. Compare the reported levels of the pollutant with the limit in the permit. There is a column in DMRs to report exceedances of the limit, but sometimes reports with violations will be submitted and the agency will not notice them.
  • Summary of information on receiving waters
    To understand the quality of the receiving waters, you should review anything that is in the permit file on the receiving waters that may have been used to develop the permit limits. If there is nothing apparent, ask the agency what they used to assess the quality of the receiving water. On your own, you can track down and review the state’s water quality standards, the biennial water quality report to Congress (305(b) report – which must include the impaired waters list (303(d) list)), the list of restoration plans (Total Maximum Daily Loads, TMDLs), any fishing or recreation guides that may be published, drinking water protection plans, wild and scenic designations, etc.
  • Antidegradation analysis
    Does the draft permit propose a discharge increase in any way? That would be at least the case for all new permits and any renewing permits for which a) the volume is proposed to increase, b) the limits are weaker, c) the timing of the discharge is longer, d) there is an additional outfall, e) the mixing zone is larger, or f) fewer management practices are required. Request the antidegradation findings (which may be summarized in the permit) and the documentation of the analysis. The status and adequacy of antidegradation policies and implementation procedures vary considerably across the country (see Antidegradation section of Lesson 1).
  • Discharger’s past performance
    Look for “notices of noncompliance” or “notices of violation” in the permit file. If the permit is new, ask the agency about other permits held by the same entity.
  • Potential for water quality violation
    Look for a required analysis of the likelihood that the discharge will contribute to a violation of water quality standards (“reasonable potential analysis” (40CFR122.44(d)(1)(i))). A summary of the findings may be in the permit fact sheet.
  • Correspondence file
    Correspondence between the agency and the discharger and even among agency staff can be very enlightening and helpful in your review.
  • Response to comments from last permit renewal (if applicable)
    Concerns will often be raised during the comment period but not addressed during the finalization of the permit. By reading the comments and responses, you can find out additional information about problems caused by the discharger and ways that the agency proposed to address those problems. Assess whether the steps described in previous responses to comments have been taken.

Obtaining the necessary documents

Once you find out about an application for a permit or a draft permit that you want to review, you will need to request information from the permitting authority. In most states, it is the state water quality agency. Where EPA issues permits (New Hampshire, Massachusetts, Idaho, New Mexico, U.S. territories and tribal lands), you would contact your regional EPA office.

You may be able to request the information over the phone. Some states will actually send you copies of the documents! But in many cases, you will need to make an appointment to go in to the appropriate agency office and review the permit file. Most states have established a process for requesting public information. In any case, you may also use the federal “Freedom of Information Act” to obtain important documents. Be sure to ask how much copies will cost and, if you are a nonprofit organization, mention it. Citizens in Tennessee were subject to charges of 50 cents per page until they forced a change. Costs per page are now at a more common 10 cents per page.


Even after you’ve submitted your comments, your opportunities for public participation are far from over.

Time to ask for a public hearing

The Clean Water Act guarantees you the right to a public hearing before a NPDES permit is issued (CWA, section 402(a)(1)). It is not likely that agencies will hold a public hearing on a permit unless people request one, however. Some states require a certain number of requests before they will grant a hearing. The frequency of permit pubic hearings varies from state to state.

Detailed information on the permit may be provided at a public hearing, and sometimes questions will be answered. It can also be a valuable forum for making your concerns known to people other than your state agency, such as other interested citizens, decision-makers and members of the press. Many states hold hearings during the comment period. If any issues arise at the hearing, the comment period should allow sufficient time for the public to respond.

Appealing a permit

The steps to appeal an issued permit vary from state to state. There may be a limited time window for your appeal so be sure to ask the agency what the process is right away. If it appears likely that the permit is going to be issued, it wouldn’t hurt to ask about the appeal process even before it happens. That way, you have time to prepare whatever documentation and support (technical or legal) that you might need for the process.

In many states, the appeal first goes through an administrative process, such as a hearing before an administrative law judge or the board that oversees the agency. If that process is unsuccessful, state court (or federal court when EPA issues the permit) is usually the next step in the process. Some states require the appeal to be taken directly to court. It is important to determine whether the permit is valid or suspended while the appeal is on-going to avoid the construction of facilities or temporary discharge of pollutants that may ultimately be disallowed.

Modifying permits

Once a permit is granted, it is tough to change it. However, permits can be reopened if facilities or regulations change or if new information on the adverse effects of a permitted discharge becomes available((40CFR122.62(a))). If it is not possible to reopen the permit mid-cycle, continue to build your case for when the permit comes up for renewal.

Problems in the receiving stream should be documented and reported to the agency. If the water body is placed on the impaired waters list, and an existing discharge is contributing to the problems, the restoration plan (TMDL) for those problems must require changes to the permit. Listing of a receiving water body as threatened or impaired or completion of a TMDL should result in early revisions to the permit as well.

Stopping violations of a permit

Violations of NPDES permits can be enforced in three different ways: through 1) an agency’s civil enforcement actions (including administrative penalties), 2) criminal prosecution and 3) citizen suits. Permit enforcement actions can be triggered in a wide variety of circumstances. Some result from inspections, others from a review of the discharge monitoring reports submitted by a NPDES permittee and still others from complaints filed by citizens or current or former employees.

Civil Enforcement

Where the EPA delegates the NPDES permitting program to a state environmental agency, it also delegates primary civil enforcement responsibilities. When permits are violated, agencies base decisions on whether and how to pursue enforcement action on at least three factors: the violator’s culpability or mental state, the extent of environmental harm caused by the violation, and the economic benefit the violator gained through its failure to comply with the law. When a state agency documents a violation, it is supposed to issue a notice of noncompliance (NON) or notice of violation (NOV) to the violator. The most common civil enforcement action is the issuance of a civil penalty. The Clean Water Act provides for penalties of up to $32,500 per violation per day. In addition to imposing penalties, an enforcement authority may also:

  • require immediate actions to correct the violation;
  • require documentation of future compliance;
  • order facility operators to cease operations until problems are fully addressed;
  • revoke the discharger’s permit; or
  • refuse to renew a permit.

Criminal Prosecution

The Clean Water Act and state water quality statutes also contain criminal penalties for certain violations. Criminal prosecution is reserved for severe violations, but it is being used increasingly throughout the country. Criminal violations are prosecuted by United States Attorneys, State Attorneys General or local District Attorneys in the county in which the violation occurred.

In determining whether to prosecute criminally, most investigators and prosecutors look to whether the violation was committed intentionally (a “knowing” violation) or negligently, and whether the violation resulted in damage to the environment.

However, a violation need not be intentional to be subject to criminal prosecution. Nor must the extent of environmental damage necessarily be proven.

The most common criminal cases involve discharging without permits, bypassing pollution control equipment or falsifying discharge monitoring reports submitted to the states or the EPA.
Corporations as well as individuals may be criminally prosecuted. Criminal penalties may include substantial monetary fines as well as significant terms of imprisonment for individuals found guilty.

Citizen Suits

The Clean Water Act also grants private citizens the right to take independent enforcement actions for permit violations. Any person or entity that is or may be adversely affected by a permit violation may bring suit against the entity causing it (see Lesson 9: Enforcing the Act for more on citizen suits).

  1. Request a list of all permits (individual and general) in your area of interest.
  2. Choose the permits you wish to evaluate and ask for the permit, fact sheets, antidegradation analysis (if it isn’t in the fact sheet), discharge monitoring reports (for individual permits) and any notes from the file.
  3. Gather information on water quality standards (uses and criteria), current conditions in your watershed (i.e., is it listed as threatened or impaired?), and antidegradation policy and procedures for your state.
  4. Get on the mailing list for public notices and hearings associated with new and renewing permits. Limit these announcements to your watershed if possible. Ask when each permit in your basin is due for renewal.
  5. Find out how frequently your water quality agency verifies Discharge Monitoring Reports.
  6. Find out how your agency monitors and enforces required management practices, especially for stormwater permits.
  7. Investigate pollution prevention alternatives that should be considered when permits are due for renewal.
  8. Find out what types of general permits have been developed by your state agency and how many of each type have been issued in your watershed. Get a list. Ask how these general permits are issued, monitored and enforced.
  9. Find out whether and what enforcement actions have been taken against permit violators in your basin.
  10. Determine how to challenge a permit after it is issued. Is it an administrative appeal to the state agency or is it a court challenge?


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