Common NPDES Permit Problems (and How We Fix Them!)

Solving the 8 BIGGEST NPDES Permit Problems

We’ll be straight with you: NPDES (National Pollutant Discharge Elimination System) permits are complicated. Even the most organized companies struggle with applications, sampling, reporting, and permit conditions. And the truth is, most facilities have at least one gap in their compliance program.

And that gap might not feel urgent in the moment… until it leads to a failed inspection, a fine, or worse, a lawsuit. We’ve seen it happen. Again and again (and again).

At RMA, we help companies across the U.S. identify and fix their NPDES problems before they become bigger (and more expensive) headaches. Here are the most common issues we see in the field - and how we step in to fix them.

And if you’re experiencing any of these problems and want a hand getting back on track, reach out to us here. Okay, let’s jump in.

Table of Contents

• NPDES Application and Renewal Problems
• Monitoring and Sampling Problems
• Reporting and Documentation Problems
• Permit Condition Problems
• People and Organizational Problems
• Inspection and Enforcement Problems
• Legal and Liability Problems
• Treating NPDES Like a Once-a-Year Task
• How to Get NPDES Help!
• Additional NPDES Permitting Information

1. NPDES Application and Renewal Problems

Getting a permit isn’t always straightforward (in fact, it’s usually not). NPDES regulations are highly dependent on your location, the regulatory body that oversees them, and your industry – meaning it's hard to get the right information without spending hours on Google. Things can get especially confusing when you have multiple locations across state lines.

Companies often don’t even know what type of permit they even need, which is the very first step in the process. A general permit? An individual permit? Is a non-exposure certification enough? What goes into an application? When do we pay our renewal fees? Is our SWPPP the same as our permit? (Hint: it’s not!)

Missed discharge points, incomplete or flat-out incorrect applications, and blown renewal deadlines are common and costly. And that’s assuming you’re not in the group of folks who don’t even realize they need a permit in the first place!

How we fix it: We start by confirming what permit you really need. From there, we handle applications, renewals, modifications, and supporting documents. Most importantly, we make sure your permit requirements, SWPPP, and site conditions all align - so nothing slips through the cracks. Check out the cost below!

2. Monitoring and Sampling Problems

You’d think collecting stormwater samples would be simple. But we constantly see teams sampling from the wrong location, using the wrong containers, or missing qualified sampling events altogether (that's right, not every rainstorm is fair game). Heck, even the technique you use can throw your samples way out of whack - don’t scoop too deep or you’ll collect sediment!

What’s worse is that staff turnover makes it even harder. You finally have a guy (or gal!) who knows the protocol, when to sample, how to sample, the whole enchilada. And then suddenly, they leave for another position, or get promoted, or are out on a month-long vacation, and… you’re back to square one and have no idea what to do.

How we fix it: We don’t write your sampling plan (that’s built into your permit), but we do train your staff on exactly where, when, and how to collect samples properly. We also walk you through lab reports so you actually know what your results mean and how to avoid compliance mistakes.

3. Reporting and Documentation Problems

Discharge Monitoring Reports (DMRs) are commonly required as part of NPDES permits. The government has issued you a permit that says “you need to stay within these limits” and requires you to test your discharges to make sure you are. It’s only natural that they would want to see the numbers themselves to confirm… and potentially punish you if not.

And these reports are… to put it bluntly… a minefield of problems for lots of facilities. The most common issues we see include late submissions, unit errors, decimal mistakes, or even lost lab reports. Regulators don’t care if it was a simple typo - the record is what counts.

But DMRs are just the beginning - your SWPPP and other required documentation are just as important! Do you have a system for organizing all this stuff, or is it all strewn about an office in various drawers and messy binders? Could you produce documented proof that you’re in compliance on the spot? If not, you’re asking for a violation the second an inspector walks through the door.

How we fix it: We can file DMRs on your behalf, or we can coach your team to keep them accurate and on time. And if we’re not handling them ourselves, we’ll send you friendly reminders so your due dates don’t get missed. We also review supporting documents to make sure your SWPPP, inspection logs, and reports are all consistent and audit-ready. If they’re a mess? We’ll clean them up and hand over a neat, organized portfolio of your NPDES documents (and help you keep them that way).

4. Permit Condition Problems

Sometimes the problem isn’t necessarily that you aren’t cut out for keeping up with your permit, it’s that the permit itself is totally broken. Individual permits in particular can contain vague, confusing, or even unrealistic requirements. We’ve seen pollutant limits set at numbers LOWER than they’re already naturally occurring in the river down the road – good luck staying under those!

How does this happen? Too often, permits are written by someone in a government office who’s never actually set foot at your facility. They might even be fresh out of college and have never done one of these before. And if you don’t know what you’re looking at when you get the draft approval, you might accept permit terms that you could have (and should have) disputed.

How we fix it: If you’re starting from scratch and still need to get a permit, you’re in good hands. We’ll make sure it’s realistic and actually aligns with your site and reflects what you can (and can’t) do. We’ll talk to the agencies on your behalf, review drafts, and push back if it’s warranted. If you’ve already got a permit, we’ll help you understand what’s in it - and when it might make sense to raise a flag or seek a modification. Our job is to translate the legal jargon into plain English, highlight what’s realistic, and help you work with regulators to resolve what isn’t.

5. People and Organizational Problems

Sometimes the problem isn’t the permitting process or the requirements - it’s the people – your people. Look, we’re not here to point fingers. Environmental compliance is tough, especially if you’re managing multiple regulations (and especially especially if you’re already wearing another day-to-day hat). This stuff is confusing, it’s complicated, it’s time-consuming… and that’s why it’s one of the first things to get pushed to the back-burner when your plate is already full.

We’ve seen five different departments all assume someone else is handling NPDES, which means no one actually is. Can you honestly say that you have a dedicated, qualified person or team handling your NPDES requirements that’s got it totally under control? If the answer is yes – give them a raise! But since you’re here… we’ll assume the answer is “not really” or “kind of” at best. Now add in turnover and lack of training, and compliance can completely fall apart.

How we fix it: We build accountability into your program. That means training your staff, assigning clear roles, and in some cases, stepping in as your outsourced environmental department to take the reins. We’ll completely run your NPDES program for you, or we’ll just provide the backup you need to keep things running smoothly. Either way, you’ll have a clear picture of exactly who is doing exactly what.

6. Inspection and Enforcement Problems

Oh boy, this is the one that most people are terrified of. A government inspector shows up with a clipboard and a bad attitude and starts poking around your site, scribbling notes and taking pictures. Will this end in a violation? A fine? Can they shut us down on the spot? It happens all the time (and if it hasn’t happened to you yet – don’t consider yourself too lucky, you might be due next!).

Most inspection problems don’t come from lack of caring. They come from being unprepared. Disorganized records, undocumented corrective actions, or messy sites can all draw unwanted attention from regulators. The result? You’re constantly stressed and on your toes waiting for the day you “might get caught”. That’s not a fun way to operate.

How we fix it: We prepare you for inspections before they happen. That means organizing files, running mock audits, and building systems that make compliance easy to demonstrate. When inspectors show up, you’ll be ready… and maybe even a little excited to show off that you’ve got your program running like a well-oiled machine.

7. Legal and Liability Problems

And here’s what’s probably fueling the fear of the last one. Lawsuits. Court dates. Shut-down orders. Bad press. Yikes! Here’s the thing, though – most companies are only concerned about half of the risk here – legal problems stemming from getting in trouble with regulators. And yes, that’s a very real and very serious possibility. But it’s not the full story.

The truth is, your NPDES record isn’t private. It’s the 21^st century, and everything is online for all to see. People kayak past your site with HD smartphone cameras in their pockets. Amateur drone enthusiasts fly a little too close for comfort. And yes, environmental groups can (and do) review compliance histories online. Nothing whips people into a frenzy faster these days than a “big corporate polluter”. That means sloppy reports, repeat violations, missing records, and bad site conditions can leave you open to citizen lawsuits and bad press.

How we fix it: We make sure your compliance story is accurate, defensible, and complete. That way, you avoid unnecessary legal exposure, and keep your reputation intact. We’ll keep you out of the press (and the courtroom) by making sure you’re doing things the right way… before anyone has a chance to turn it into a media circus, public outrage, or class-action suit.

8. Treating NPDES Like a Once-a-Year Task

Too many companies treat NPDES like a box to check once a year. The renewal rolls around, someone dusts off the binder, fills out a form, and then it goes right back on the shelf until next year. Sound familiar? The problem is, compliance doesn’t work that way.

Your permit isn’t static. It requires ongoing monitoring, inspections, reporting, and recordkeeping throughout the year. Ignore it for months at a time and you’re almost guaranteed to miss something - whether it’s a sample that didn’t get collected, a DMR that wasn’t filed, or site conditions that have changed and no longer match your SWPPP. By the time you circle back to it, you’re not just catching up… you’re scrambling to patch a dozen holes, often with regulators breathing down your neck.

This once-a-year mindset also leads to a dangerous false sense of security. You might think, “We didn’t hear anything last year, so we must be fine.” But in reality, problems could have been piling up all along. And when they come to light, the penalties, violations, and reputation damage hit all at once… and hard.

How we fix it: We help you move from reactive to proactive. Instead of panicking once a year, we build systems that make compliance an ongoing, manageable program. That means consistent tracking, organized documentation, and regular check-ins so you’re never left guessing. When renewal time comes, it won’t feel like a fire drill, it’ll feel like just another step in a process you’ve already got under control.

Getting the Help You Deserve: Let’s Fix Your NPDES Problems Before They Become Bigger Ones

NPDES compliance isn’t something you can afford to “hope for the best” on. A missed renewal, a late DMR, or a sloppy sampling record might feel small in the moment, but regulators (and even the public) won’t see it that way. Fines, violations, lawsuits, and reputational damage often come from problems that started as minor oversights.

The good news? None of this is new to us. We’ve been helping companies of all sizes manage NPDES compliance since 1992. We’ve seen every type of problem - permits written with impossible conditions, sites that missed years of sampling data, teams scrambling after a surprise inspection - and we’ve fixed them. Sometimes that means walking a client through a single permit renewal. Other times it means stepping in as a fully outsourced environmental department. Whatever the need, we know how to steady the ship and keep it that way.

If you’re even a little worried about your NPDES program, that’s your sign to act. Don’t wait for the letter in the mail, the inspector at your gate, or the news story you never wanted to see. Call us before those things happen. We’ll make sure your permits, plans, and programs are clear, defensible, and set up to protect your business, not jeopardize it.

Contact us today, and let’s get your NPDES compliance where it needs to be: organized, proactive, and built to last.