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The National Pollutant Discharge Elimination System (NPDES) is part of the US Clean Water Act.

Table of Contents

What is the NPDES?

What kinds of permits are included in NPDES?

Are there exemptions or exclusions?

What about nonpoint source pollution?

Are there opportunities for community advocacy?

Where can I find more information?

What is the NPDES?

The Clean Water Act ( was written to protect surface waters in the United States with a goal of restoring and maintaining their natural chemical, physical, and biological dynamics. Through the Clean Water Act, Congress authorized the declaration and enforcement of water quality standards and regulation of pollution discharge into surface waters. The National Pollutant Discharge Elimination System (NPDES) ( was established for this regulatory purpose, to ensure direct discharges to surface water bodies meet certain criteria.

Point sources only

The NPDES only applies to “point sources” of water pollution, specifically a “discernable, confined, discrete conveyance” into waters of the United States (CWA section 502(14)). Point sources include direct effluent pipes and conduits, ditches, tunnels, and more. #Stormwater is included as a point source of pollution, due to stormwater drain discharges, culverts, and other infrastructure that channel stormwater to a receiving surface water. Industrial sources and stormwater sources are regulated differently due to the reasonable control over pollutant input (e.g. direct effluent from a facility versus urban runoff), where stormwater permits are based more on “best management practices” rather than numeric water quality limits. There are also specific exemptions of industrial and stormwater point source pollution, and non-point sources of pollution like agricultural operations are not subject to NDPES permits.

It is worth noting that the definition of “water of the United States,” which are the receiving waters of NPDES-regulated sources, is currently a matter of contention. You can read the final 2015 definition here: The significant change to the former definition of “water of the United States” is that adjacent waters that have “a significant nexus” with navigable waters, interstate waters, and territorial seas are also considered as waters of the United States now. This expansion of the definition, which now includes some wetlands, is opposed by many in the agricultural industry (read more: and may be targeted for repeal under the current Administration (e.g.

What kinds of permits and limits are included in NPDES?

There are two kinds of permits issued under NPDES: individual and general. Individual permits are issued for major point sources, such as a city’s wastewater treatment plant or a large industrial facility. General permits are issued for smaller, more common sources, such as city stormwater or industrial sources that are expected to discharge sufficiently low amounts so as not to disrupt a water body’s physical, chemical, or biological state.

Individual permits

Individual permits are often written with both technology-based effluent limitations (TBELs) and water-quality-based effluent limitations (WQBELs). According to the Clean Water Act (section 301(b)(2), TBELs are limits based on the best available prescribed technologies and pollution control practices that are the “economically achievable” (read more her: TBELs are the default limits for NPDES permits, but if the TBELs are not sufficient to attain or maintain water quality standards in a given water body, then the NPDES permit will include WQBELs for those pollutants of concern. WQBELs include site-specific analysis of the receiving waters and the impacts of the permitted discharge on those water bodies (read more here: The specific pollutants that are regulated and monitored in an individual permit are based on analyses of the kinds of pollutants discharged from the industry category. Most individual permits include numeric limits on the “conventional pollutants” biochemical oxygen demand (BOD-5), total suspended solids (TSS), pH, fecal coliform, and “oil and grease.” Individual permits may include limits on additional “toxic pollutants” (such as heavy metals or organic contaminants), or “nonconventional pollutants” including ammonia, phosphorus, and other common pollutants. The full list of toxic and nonconventional pollutants are linked from this page:

General permits

General permits usually include “narrative limits” of best management practices that should be implemented to the “extent practicable,” such as public education for municipal stormwater permits, fences to routine leak checks for a facility, or fences to keep cattle out of streams on Concentrated Animal Feeding Operations (t is worth noting that most agricultural operations are not subject to NPDES permits; only CAFOs are technically considered point sources). Most NPDES general permits also include numeric limits for the conventional pollutants and a select few other pollutants based on the category of industry. For example, industrial cooling water discharges may be subject to temperature, residual chlorine, and flow limits. An example CAFO general NPDES permit can be found here:

Stormwater permits

Stormwater NPDES permits are required for Municipal Separate Storm Sewer Systems (MS4s), with different permit requirements based on the population size served. Most stormwater permits focus on the best management practices to the extent that they are practicable, including hosting educational programs about issues such as leaf litter and oil and grease disposal, implementing an infrastructure maintenance plan, and maintaining public access to water quality information. Large stormwater systems are also often subject to numeric water quality limits for conventional pollutants.

If a stormwater system or industrial effluent discharges into an impaired water body, they are subject to more stringent discharge limits. An impaired water body is one that a state has identified that does not meet the water quality standards established by the state, and for which normal TBELs are not sufficient to improve the receiving waters’ quality. Once a water body has been identified as such, it is included on the “Section 303(d) list,” referring to Section 303(d) of the Clean Water Act, which requires identification and improvement plans for such water bodies. The state water protection agency must develop a total maximum daily load (TMDL) for each impaired water body, detailing the daily pollutant load limit that each water body can accommodate while making progress toward better water quality. From the TMDL, each pollution point source contributing to that water body will receive a Waste Load Allocation (WLA) dictating the pollutant limit from each specific source. These WLAs will be included in permits for facilities and stormwater systems discharging into impaired waters. However, TMDLs and WLAs are aspirational, rather than strictly enforceable.

Are there exemptions or exclusions?

There are highly consequential exemptions listed in Section 402(l) of the Clean Water Act for point source pollution that is not subject to regulation. These include agricultural “return flows” and stormwater runoff from oil, gas, and mining operations.

Agricultural return flows are essentially runoff from irrigation, and could reasonably considered point source pollution, but they explicitly are not. Agricultural runoff is often a primary contributor of excess nitrogen and phosphorus, also called “nutrient pollution,” which can be devastating for ecosystems. Nutrient pollution stimulates algal blooms, which can rapidly decrease dissolved oxygen in the water as oxygen is consumed by decaying algae, resulting in oxygen-starved eutrophic waters that cannot support a lot of aquatic life. Fish kills are generally the result of nutrient pollution.

Stormwater runoff from oil, gas, and mining operations is poignantly exempted from NPDES regulation as well. These sites can contribute significant amounts of colloidal and suspended solids (TSS), and also can be a source of oil, heavy metals, sulfates, and synthetic pollutants used in operation.

What about nonpoint source pollution?

The absence of nonpoint source pollution from regulation through NPDES substantially limits state and federal agencies’ ability to limit pollution emanating from those sources. Nonpoint sources may be subject to waste load allocations if they discharge to severely impaired waters, but environmental agencies to not have authority to enforce those WLAs for nonpoint sources. Thus, agricultural operations, which are the largest contributors of excess nutrient pollution, are not regulated for such.

One approach to reduce pollution runoff from agricultural sources locally is through Water Quality Trading. This is an economic incentivisation, receiving credits for reducing effluent pollution in specific units or implementing best practices. Watershed alliances with agency, industry, and environmental groups can develop and implement productive water quality trading systems, a good example of which is the Upper Neuse River Basin Association, These programs are voluntary and rest upon good neighbor relationships as much as any scientific evidence. Some resources for promoting nonpoint source pollution mitigation are available on the EPA website,

Are there opportunities for community advocacy?

Community advocacy is important in the NPDES permitting system. The River Network, a nonprofit organization dedicated to protecting and restoring rivers, says: “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” (

For communities to be vigilant, seeking out information about existing NPDES permits, applications for permits, and permit renewal schedules. Finding existing NPDES permits can be challenging, depending on the state environmental agency. Even if permits are not readily accessible on state agency websites or on the facility’s website, there will be a contact person listed who can help residents who are interested in finding existing permits. For any new individual permits, the permitting authority will have to provide notice in a local newspaper, usually in the legal or classified section, and there is usually a short period for public comment, often 30 days. If you have any concerns about the permit, you have to raise them during that initial public comment period, as there will not be a later chance to express concerns that were not raised in the initial public comment period. For general permits, the public comment period is before the permit is fully developed, based on hypothetical situations. It is important to think about if the permit is appropriate for the worst case scenario of a facility that would be covered under the general permit. If the general permit is likely to be insufficient to protect the receiving waters, citizens can petition that a facility must seek an individual permit rather than being granted under a general permit.

Expired permits

Most NPDES permits are valid for five years. However, it is not uncommon for facilities to operate under expired permits for extended periods of time before receiving permit renewals. This is often due to lack of funding and personnel to review and approve of permits, and sometimes due to lengthy petition processes. Permit renewal periods are important opportunities for communities to petition for stricter limits.

Keeping abreast of water quality status of receiving waters, and whether or not those waters become or remain impaired, is important for communities. If a receiving waterbody is officially listed as impaired, waste load allocations will modify the NPDES permits.

For more community advocacy steps, please see The River Network’s Clean Water Act online course, steps 4-7:

Where can I find more information?

A thorough, plain-language resource from The River Network:

A useful summary from the EPA:


We're collecting and working our way through a range of questions about NPDES -- if you can contribute your own questions, or answer others', please do!

Ask a question about NPDES

Title Author Updated Likes
Are there any exemptions under the NPDES? @stevie 11 days ago
What types of NPDES permits are there? @stevie 11 days ago
How is stormwater regulated? @stevie 11 days ago

water-quality regulations stormwater wastewater npdes