How to Read and Manage NPDES Permits

Mismanaged or misinterpreted NPDES permits are a significant driver of non-compliance in wastewater. Here's how to manage and get clear on your obligations.


Key takeaways:

  1. NPDES permits are long, complex and at times difficult to interpret for non-experts, and responsibility for them is often shared across teams that have an incomplete understanding of their contents.
  2. Reading your NPDES permit properly and making sure you’re reading the right version can help avoid confusion and mistakes when planning monitoring and compliance.
  3. Good recordkeeping and data management systems that centralize all permit-related reporting and correspondence can help everyone at your organization make sure they’re on the same page when it comes to your NPDES permit.

Few permits are as central to wastewater as National Pollutant Discharge Elimination System (NPDES) permits. But they’re also long, complicated and can be difficult to parse, which can lead to challenges around compliance.Large utilities might have several people responsible for different parts of an NPDES permit, which means information can sometimes get mistranslated or lost in the shuffle.Worse, since permits must be re-issued every few years, facilities sometimes run the risk of employees reading from an old version with outdated information.In this article, we’ll translate your NPDES permit into plain language. We’ll also go over some common mistakes people make when reading them, and discuss how good record keeping can help everyone at your organization make sure they're on the same page when it comes to your NPDES permit.

What is an NPDES Permit?

Anyone who discharges pollutants from a point source into a water of the United States requires a National Pollutant Discharge Elimination System (NPDES) permit from their state or EPA Region.Each of these terms is defined very broadly by the Clean Water Act, as decades of litigation have resulted in a cautious approach.If you’re not sure whether something qualifies as a pollutant, point source, or water of the United States, assume it does until you can confirm it.


A pollutant is “any type of industrial, municipal, and agricultural waste discharged into water,” according to the EPA. Nearly anything you can think of can count as a pollutant — including some that aren’t obvious, such as soil, heat, and sand.

Point source

A point source is “any discernible, confined and discrete conveyance,” per the EPA, which is a fancy way of saying “the part where the waste comes out.” Pipes, ditches, channels, conduits, etc. count as point sources.

Water of the United States

A water of the United States, according to the EPA, is any “navigable waters, tributaries to navigable waters, interstate waters, the oceans out to 200 miles, and intrastate waters which are used: 

  • by interstate travelers for recreation or other purposes, as a source of fish or shellfish sold in interstate commerce
  • or for industrial purposes by industries engaged in interstate commerce.”

How Are Permits Issued?

Organizations apply for a permit through their state’s environmental regulatory agency or their regional EPA contact using the forms on the EPA’s NPDES portal.Who to apply to depends on the status of NPDES programs in your state or territory. If your state is partially authorized or unauthorized according to the map below, ask your regional EPA contact for guidance.

NPDES Program Authorizations as of July 2019

Permits are valid for five years. But that doesn’t mean you should file them away and forget about them. NPDES permits require regular upkeep to stay inside the bounds of the EPA’s guidelines.If your facility’s effluent output changes, for instance, you’ll need to update your permit.

What Does a Typical NPDES Permit Look Like?

NPDES permits can vary in appearance. State-issued permits might contain the logos of that state agency, for example. They might also use different terminology—for example, New York has its own version of NPDES called the State Pollutant Discharge Elimination System (SPDES). But each of these permits follow the same outline and use similar language.You can find digital copies of every federally-issued NPDES permit on the EPA website, and most state-issued permits are accessible through each state agency’s website. (California’s ​​State Water Resources Control Board makes all their permits available here, for example.)

The Main Parts of an NPDES Permit

All NPDES permits contain at least five sections:

  1. A Cover Page including the name of the discharger, the permit number and the exact location of the discharge(s) and outfalls covered by the permit.
  2. Effluent Limitations laying out what pollutants the permit holder can discharge, how much and how often.
  3. Monitoring and Reporting Requirements that outline what the permit holder will do to stay compliant.
  4. Standard or General Conditions that apply to all NPDES permits and delineate the legal, administrative, and procedural requirements of the permit. 
  5. Special Conditions that might include additional monitoring activities, special studies, best management practices (BMPs), and compliance schedules.  

Here’s what you can expect to find in each one:

1. Cover Page

The permit cover page is a snapshot pf the most basic information about your NPDES permit, including:

  • the name of the discharger
  • the discharger's address
  • a nine character NPDES permit number
  • the receiving waters
  • the exact location and coordinates of the discharge(s) and outfalls
  • when the permit comes into effect and expires

If you’re unsure whether the permit you’re looking at is up to date, the cover page should also have an Effective Date and an Expiration Date you can reference.The cover page is usually followed by a schedule or list of submittals, which summarizes which reports you’ll have to submit to stay compliant, including Discharge Monitoring Reports (DMRs); applications for permit renewal; and noncompliance reports.

2. Effluent Limitations

Effluent refers to the pollutants that remain in wastewater after it’s discharged to surface waters. This is the most important part of your permit—it’s the reason it exists.There are two categories of limits to know about:

  • Technology-based effluent limits are minimum standards that broad categories of facilities must meet.
  • Water quality-based effluent limits (WQBELs) are in place to deal with pollutant concerns in a specific body of water due to the specific pollutant being discharged.

WQBELs are usually in place in small streams with little flow, waters that are very close to violating water quality standards, or waters with very few pollutants that regulators feel should be protected.Effluent limits themselves are defined using the following terms:

  • Load limits refer to the total amount of pollutant allowed per day, usually in lbs.
  • Concentration limits refer to the amount of a particular pollutant that is allowed in a volume of water discharged, usually in milligrams per liter (mg/l) or parts per million (ppm).
  • Monthly or 30-day average refers to the amount of pollutant you can release per day, over a monthly period.
  • Weekly average means the same thing — but weekly.
  • Daily maximum is the highest total amount of a pollutant you can release per day.

Allowable wastewater flowThe average (design average flow) and maximum (design maximum flow) number of millions of gallons per day (MGD) of wastewater that your facility can discharge may be listed on your permit in this section.Effluent limits are usually recorded in table form, with effluents in the leftmost column and limits on the right.The Effluent Limit table on Page 5 of the NPDES permit for the Brightwater Wastewater Treatment Plant in King County, Washington, for example, lists five parameters: Biochemical Oxygen Demand (BOD), Total Suspended Solids (TSS), Total Residual Chlorine, pH and Fecal Coliform Bacteria.

Effluent Limits in an NPDES permit for the Brightwater Treatment Plant in King County, Washington State

3. Monitoring and Reporting Requirements

This section lays out what kinds of samples must be taken and how often they must be reported. Some key terms to look out for here include:Sample frequencyYour permit will let you know whether you must obtain samples daily, weekly, or monthly.Sample type

  • Continuous samples are taken constantly.
  • Grab samples are taken at a specific time not exceeding 15 minutes.
  • Composite samples are collected over time by continuous sampling or by mixing grab samples.

Whole Effluent Toxicity (WET) testingSome permits will require WET testing, which measures the chronic and acute toxicity of the effluent as a whole—instead of just the concentration of each pollutant.Instream monitoringSome permits will require you to monitor not just the output of your effluent, but its impacts. This could include surveying sea life for health, sampling upstream and downstream, and more.Stormwater contamination controlMunicipal operators are often required to plan for stormwater runoff — including how effluent will change, where the stormwater will go, and a detailed sitemap.Municipal pretreatmentMunicipal sewage plants will often have to spell out their pretreatment program. If your facility discharges more than 5 million gallons per day, you probably have one such program.

4. General Conditions

This is an all-inclusive housekeeping-type section that includes when the permit holder must reapply for a new NPDES permit, when the facility can be inspected, and how to comply with state-specific laws.It also deals with how the permit holder can navigate noncompliance, including their responsibilities and penalties for breaking rules. And it also lays out when, where, and how the permit holder must send notice to the authority for changes to their facility.

5. Special Conditions

This section outlines everything the permit holder needs to do to remain compliant outside of sticking to the effluent limitations outlined in the previous section. This might include:Additional monitoring and special studiesThis includes any sampling or testing that supplements or goes beyond regular monitoring. Treatability studies, toxicity identification evaluations, mixing or mixing zone studies, sediment monitoring, and bioaccumulation studies will all be referenced here.Best management practices (BMPs)These are any specific activities or prohibited practices your facility must adhere to, maintenance procedures it will have to follow, treatment requirements, and operating procedures to control things like spillage or leaks.Compliance schedulesSome permits may include a schedule that provides the permit holder with more time to fix issues identified with their facility in the past. Examples include construction and inspection dates, pretreatment program development, and sludge disposal program implementation.

Common Mistakes People Make When Reading an NPDES Permit

These permits are often dozens of pages long and contain a lot of confusing jargon. There are any number of mistakes one can make while reading through it. But the most common ones tend to fall under the following categories:

1. Ignoring State-Specific Rules

Make sure you’re interpreting your permit based on the rules in your state, since they vary. These are usually outlined in the “General Conditions” section.

For instance, some states list a design maximum and design average flow of wastewater in MGD — though many don’t. Some states define the weekly average as going through Sunday to Saturday, while others define it as Monday through Sunday.

If you’re ever unsure about a part of your NPDES permit, seek out your state's specific NPDES guidance documents or call your local authority for clarity.

2. Reading the Wrong Permit

Make sure you’re reading the most up-to-date permit available by checking the cover page for the Effective and Expiration dates of the permit.

Your organization may have altered its NPDES permit recently and it can do so at any time. 

Permits can be changed or updated when a wastewater treatment facility expands, changes ownership, updates its pollution control technology, or for many other reasons.

Permits will also be re-issued after they expire. But new permits are not always the same as the expired ones. 

You should receive a fact sheet along with your NPDES permit. That sheet should outline the changes. But don’t count on it — call your authority and ask to make sure.

3. Misinterpreting Sampling Requirements

The type and method of sampling will vary greatly from permit to permit. 

Know the difference between continuous, grab, and composite samples. Know what you’re sampling for. And know whether you’ll have to do WET testing, instream monitoring, or any of the other requirements listed above.

Remember, your permit will tell you whether you have to monitor your pollution output based on daily, weekly, or monthly averages.

4. Ignoring Additional Reporting Requirements

Every NPDES permit is different, and every wastewater facility is also different. Even if you’ve worked with other NPDES permits in the past, it pays to make sure you’re aware of all the rules and requirements that might be specific to your facility or organization.

How a Good Permit Management System Can Help

If navigating an NPDES permit itself wasn’t difficult enough, keeping track of all the additional paperwork involved in NPDES compliance—including Notices of Intent (NOIs), Municipal Separate Storm Sewer System (MS4) Program Reports, annual reports, and so on—can be downright frustrating.And it only gets worse when multiple staff members at your organization need access to that information.With all of that paperwork swirling around, the risk of making compliance decisions based on outdated permit information skyrockets.That’s why in addition to making sure staff are able to read and understand them, it’s crucial that organizations store all of their permit documentation and related correspondence in a single, centralized permit management system that allows team members to:

  • Keep track of and set alerts for important permit-related deadlines
  • Generate permit reports automatically
  • Break down silos and make reliable permit information available across departments
  • Prevent lost, duplicate or outdated documentation

Eliminate Permit Confusion With Klir

Klir is a single, unified operating system for water, pulling every aspect of wastewater management—including compliance, sampling, reporting and more—into an easy to use dashboard.Learn more about how Klir can help your organization manage permits, cut down on administration and record-keeping work, and provide a level of organization-wide visibility unmatched by other systems.

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