Water System Permitting and Compliance 101

Key takeaways:

  1. While managing the mountain of permitting and other compliance-related responsibilities involved in running a utility can feel daunting, surveying the compliance landscape and developing familiarity with major EPA programs is a great starting point.
  2. Becoming acquainted with the EPA’s new eReporting requirements and preparing for them is a great way to cut down on administrative work and signal that your utility is serious about streamlining reporting processes.
  3. Staying ahead of new regulations related to PFAS and Lead and Copper will be key to staying on top of compliance challenges and building robust permitting management programs.

Managing the storm of permits, rules and other regulations involved in running a water system can be a time-intensive, daunting, and even exasperating task. It isn’t unusual for larger utilities in the U.S. to juggle hundreds or even thousands of permits and regulatory responsibilities at any particular moment. 

The rules in these programs can change often, and the knowledge required to stay on top of them often lives inside the heads of a handful of veteran employees. If you’re just starting out, wrapping your head around everything you need to do to stay compliant can feel impossible.

One of the most effective ways to reduce the time you spend tracking and organizing mandated testing for these permits is to adopt an effective permit management system like Klir.

But it also helps to take a step back and to acquaint yourself with federal and state organizations that issue permits, reporting requirements, and recent changes.

To bring you up to speed, this guide reviews three important topics in water permitting:

  1. First, we’ll introduce some of the most important permit-issuing authorities in the United States at the federal and state level.
  2. Second, we’ll take a look at the reporting requirements for those programs, including important changes to those requirements, like the EPA’s eReporting initiatives.
  3. Finally, we’ll review some of the newest regulations in water and what you can do to prepare for them today.

EPA-Related Permits and Regulations

As a federal agency, the Environmental Protection Agency (EPA) is necessarily responsible for key permits relevant to water systems.

EPA permitting covers the mandates of the Safe Water Drinking Act (SWDA), hazardous waste permitting regulations, and the National Pollutant Discharge Elimination System (NPDES). It also covers the Clean Air Act (CAA), which is relevant to water facilities producing certain minimum amounts of air pollution.

SDWA Drinking Water Standards

Through the Public Water System Supervision (SWSS) program, the EPA protects 90 percent of the USA’s drinking water. In partnership with individual states, the EPA monitors the analytic testing results of samples taken by water systems, ensuring they stay within threshold amounts of chemical and microbial contaminants.

Consumer Confidence Reports (CCR)

The EPA also partners with states to make sure that local water systems follow the Consumer Confidence Report (CCR) rule.

This rule requires local water systems to prepare and distribute a brief annual report summarizing information about water sources, compliance, detected contaminants, and educational programs. 

The aim is to increase consumer awareness about how their water systems run, provide information on safe water use, and increase dialogue between consumers and their water utilities.

The water system must deliver a copy of this report to state authorities. Additionally, if it serves over 100,000 customers, it must post the report online using EPA’s CCR iWriter tool.

Hazardous Waste Permitting Regulations

The EPA also partners with states to administer hazardous waste permitting regulations. These regulations are intended as a “cradle to the grave” management system for hazardous wastes, controlling how they’re produced, transported, stored, and eventually disposed of.

That being said, hazardous waste permits aren’t only relevant to facilities that manage and dispose of waste. Gasoline, diesel, and batteries all qualify as hazardous wastes. And facilities running industrial boilers, furnaces, or generators may also need permits to operate.

Clean Air Act (CAA) Permits

When a water system produces enough air pollutants, it’s required to obtain a Clean Air Act (CAA) permit—typically, a Title V Permit. In some cases, this is provided by an EPA Regional Office. But typically CAA permits are handled by state, local, and tribal authorities.

Title V permits

Broadly, any source that has the potential to emit (PTE) 100 tons per year of air pollutants is classified under the CAA as a “major source,” and needs a Title V permit to operate. Pollutants fall into six categories:

    • Particulate matter
    • Carbon monoxide
    • Ozone
    • Lead
    • Sulfur dioxide
    • Nitrogen dioxide

A source also qualifies if it emits more than 100,000 carbon dioxide equivalent tons per year, uses a solid waste incinerator, or meets a few other specific thresholds. You can learn more about qualifying for a Title V permit here.

Title V permits last for five years after they’re issued. In order to keep their permit, a major source must monitor, record, and report their pollutant output. The specific methods for measuring and reporting vary according to each type of pollutant.

Other Permits at the Federal Level

Outside those permits directly administered by EPA, there are a number of federal-level permits that water systems may need to obtain.

Section 401 Water Quality Certifications

Under Section 401 of the Clean Water Act (CWA), before any federal agency issues a permit allowing discharge into US waters, the state or tribe responsible for the area where the discharge originates must issue a Section 401 permit

They can also waive certification—either expressly, or by failing to issue a 401 within a reasonable amount of time.

Even though they’re administered at the state and tribal level, 401s are federally mandated; there’s nowhere in the USA that a water system can get a federal permit to discharge into US waters without applying for a 401.

US Army Corps of Engineers Permits

In order for a water system to perform any construction or dredging in the USA’s navigable waters, it must apply for a permit from the US Army Corps of Engineers.

There are two types of permits:

  1. Individual or standard permits, issued when projects have “more than individual or cumulative impacts,” and must be evaluated based on environmental criteria, requiring a public interest review.
  2. General permits, issued for projects that will have minimal impact. They’re issued on the individual, nationwide, or category-specific level. 

Federal Energy Regulatory Commission (FERC) Preliminary Permits and Licenses

Any water utility involved in the construction of a hydroelectric project must be licensed by FERC. The licensing process typically begins with application for a preliminary permit, good for four years, that reserves the organization a spot in FERC’s queue of license applicants while the organization explores the potential location and other considerations prior to beginning construction. In order to start construction, the organization must obtain a hydropower license from FERC.

State and Local Level Permits

The permits covered above are all administered at the federal level, often in partnership with states and tribes. But, in order for any given water utility to carry out day-to-day activities, they must apply for and manage a swath of permits at the state and municipal level. 

While these permits are absolutely necessary and may in fact comprise the better part of a water system’s compliance and reporting tasks, they’re so specific to each particular utility and locale that it’s impossible to cover them in detail here.

If you’re unsure about permit requirements at the local level for water systems, get in touch with your municipal and state authorities.

Know You’re Compliant With Klir

Tracking permits is a massive task. Klir gives you an all-in-one solution that guarantees nothing slips through the cracks. Learn more about Klir’s powerful permit management solution and book a demo today.

What Is Electronic Reporting, and What Does It Mean for Utilities?

Rather than requiring you to stay compliant by submitting reports via physical mail or e-mail, the EPA is increasingly requiring utilities to do their reporting through online portals like NetDMR and the Central Data Exchange (CDX).

In most states the only report you’re currently required to e-report is the Discharge Monitoring Report (DMR), the form wastewater utilities use to self-report compliance with environmental law in the United States on a weekly or monthly basis.

But according to the EPA’s eReporting rule, utilities across the country will soon have to start using these portals to submit other reports like:

These reports are longer than DMRs and require a lot more manual work, which will make moving important reporting data out of paper and spreadsheets and into platforms like Klir all the more important.

An exhaustive list of all the reports that utilities will have to start reporting under the eReporting rule is available under the “Phase 2” heading of the EPA’s eReporting website.

CROMERR and What It Means for Electronic Reporting

The Cross-Media Electronic Reporting Regulation (CROMERR) establishes standards for the systems that receive reports and other documents that utilities submit to satisfy many of the programs mentioned above.

CROMERR-compliant systems ensure the integrity of electronic documents, that a Copy of Record is created, and that documents are signed with a proper Electronic Signature.

Why eReporting Is Important

Because many of the EPA’s eReporting requirements aren’t due to kick in for another few years, you might wonder whether preparing for it now is worth the time and money.

It absolutely is. Eliminating paper documents and manual data entry from your workflows can save you hours a week in administration work and free up your staff for more important tasks. 

Electronic reporting also cuts down on the risks of error, makes it easier to follow reporting requirements, and shows regulators that you’re serious about streamlining your reporting processes.

New Compliance Challenges and What They Mean for Utilities

In addition to changes around electronic reporting methods, regulators are also constantly changing and refining the contents of regulatory programs themselves.

Staying compliant means anticipating and preparing for new regulations, like the ones around effluents on the EPA’s UCMR lists. Here’s a brief rundown of the most important changes in the pipeline and what you can do now to prepare.


Per- and Polyfluoroalkyl Substances (PFAS — pronounced “PEE-Fass”) are a class of synthetic “forever chemicals” that have been linked to everything from cancer to high cholesterol.

We’re currently in the eye of storm when it comes new PFAS-related regulations. Maine has already banned the chemicals, 29 states have introduced numerical PFAS limits for water, and the White House is publicly detailing its anti-PFAS plan. Recently the EPA announced that 29 of the next 30 pollutants it would look at under its Unregulated Contaminant Monitoring Rule (UCMR) would be PFAS. Most experts agree that it’s only a matter of time before utilities will have to start sampling discharges and biosolids for many of the chemicals on this list.

The EPA has awarded millions in grants for PFAS research and mitigation. The agency said data gathered from the latest Unregulated Contaminant Monitoring Rule “will also serve as a potential source of information for systems with infrastructure funding needs for emerging contaminant remediation,” which makes compliance with UCMR 5 crucial.

Lead and Copper

Last year the EPA released the biggest overhaul to its Lead and Copper rule since 1991, and in November Congress included $15 billion for lead pipe replacement in its infrastructure plan, signaling that U.S. regulators were finally getting serious about lead in drinking water.

One of the biggest changes to the EPA’s Lead and Copper rule so far has to do with sampling—specifically the new rule that requires a fifth-liter (L5) sample at homes with lead service lines (LSLs) rather than the original first-liter (L1) sample to demonstrate compliance with water lead level (WLL) limits.

In preparation for the effort to replace all lead service lines with copper ones, utilities must also start building out lead service line inventories, which collect as much information as possible about which service lines in a distribution system are made of lead.

In most cases the EPA has delegated responsibility for inventory requirements to states, which means rules around how exhaustive these inventories must be will vary. Municipalities without access to complete historical records for lead line installations, for example, might be able to apply probabilistic approaches to determining how much lead is in their system.

How Klir Can Help

Klir is a single, unified operating system for water, pulling 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.

Wastewater-Based Epidemiology Is Already Here. How Should Utilities Prepare?

Wastewater-based epidemiology is a scientific field that’s surged in popularity during the COVID-19 pandemic. 

Researchers have used wastewater to predict surges before they happen — a breakthrough that’s helped governments focus on preparation instead of reaction. 

And it isn’t limited to COVID. Once the pandemic becomes endemic, researchers will still be on the hunt for pathogens that can cause issues for public health. In the best-case scenario, scientists could catch the next pandemic before it happens.

But the strategy requires gathering and sorting through huge amounts of data. That presents privacy and data management issues for utilities to overcome. We spoke with two experts about the possibilities of wastewater-based epidemiology, and what utilities should be doing now to prepare.

What Is Wastewater Epidemiology?

Think of wastewater-based epidemiology as reading tea leaves, but grosser. 

Scientists take samples of human waste and analyze them for pathogens, like the virus that causes COVID-19. Researchers can then use the data to predict surges based on trends in where the pathogen is found and how much of it is there.

That allows local governments to ramp up public health measures like expanding health-care facilities and instituting mandates like masking or lockdowns.

The International Effort to Track COVID Using Wastewater

Most people have learned about wastewater epidemiology through the pandemic. Researchers’ ability to predict COVID trends has led to the field’s expansion

Some public health officers have found it’s less helpful in their municipalities, though they’re sometimes not sure why. In a sign of the field’s still-emerging status, experts have debated just how much wastewater sampling can tell us about COVID.

In the United States and Canada, and many other jurisdictions, wastewater sampling decisions lie with local governments, limiting the data’s scope. But projects like COVIDPoops19 show the method’s worldwide spread and a glimpse of what it could become.

Its creator, University of California Merced professor Colleen Naughton, said she hopes every city in the world will eventually have its own wastewater epidemiology outpost — though she noted it’ll take a while to get there. Even though it’s cheaper than individual testing, “it still requires resources and … utility-level sampling, and then courier services, and then labs to analyze it,” she said.

What Could Wastewater Epidemiology Be Used for in the Future?

Some experts believe COVID tracking is just the beginning. 

Naughton noted that the method was used to track polio outbreaks in the past. The U.S. Centers for Disease Control and Prevention (CDC) now hopes to catch influenza, norovirus, fungal infections, hepatitis A and B, and antimicrobial-resistant (AMR) pathogens — bugs that have evolved to be resistant to antimicrobial drugs. 

“We’ve had large hepatitis A outbreaks in California and Michigan, so it would have been nice to have more of a warning system about that,” she said.

Experts have long warned of AMR “superbugs” that could ravage the world in a similar — or worse — way to COVID-19. Wastewater epidemiology could potentially identify them before they spiral out of hand. 

Wastewater testing could also be tested for opioids and other illicit drugs to combat the overdose epidemic, Naughton said.

Future-Proof Your Sampling Operation With Klir

Interested in learning how better data management can help you run more effective sampling programs? Book a demo of the Klir sampling module today.

What Challenges Will Wastewater-Based Epidemiology Create for Drinking and Wastewater Utilities?

Naughton and epidemiologist David Larsen raved, unprompted, about partnering and working with wastewater treatment plants. 

“They don’t get a lot of recognition for their important role,” Naughton said. “We go to the treatment plants and they’re always running around, you know, the phone’s ringing off the hook, and they’re like, ‘Yeah, sure, we’ll take an extra sample for you.’ It’s just been amazing what they’ve done to help. So we really appreciate it.”

Plant operators are “really excellent people,” Larsen said. “They’re a huge contributor to this public health initiative. And so I’m just really glad to be working with them and they’ve been great so far.”

Clearly, utilities are doing something right. But for those that want to get ahead of the game as wastewater testing expands in the coming years, the professors had some tips:

Equipment and Staffing

Some water utilities have absorbed extra epidemiological sampling requirements with ease. But others — especially rural and smaller plants — don’t have the equipment, time, or staff to spare, Naughton said.

Some that can only do a grab sample once per day have tried to time it with the morning flush to get the most data, Naughton said. But the “gold standard” of 24-hour composite sampling yields more complete data, Larsen said. 

Naughton recommended small utilities keep an eye out for programs like the one from the CDC and Water Environment Federation (WEF) where they could apply for free autosamplers. 

Smaller plants will also have more difficulty hiring enough people to carry out the sampling, then shipping it off, Larsen said. 

Lots of government grants are going to labs for analysis — but more cash should be flowing to utilities to hire more staff to carry out the increased sampling load, Naughton said. Public health is “chronically underfunded,” Larsen said, adding that any increased burden shouldn’t come out of utilities’ budgets.

Coordination With Researchers

Scientists analyzing wastewater samples rely on utilities’ knowledge of their systems, the experts said. Things like the amount of industrial waste the facility processes, or how much salt is used on the roads in winter can make a big difference to sampling, Naughton said. 

“So when we see things that are weird with the data, they can be like, ‘Oh, that clarifier went offline then, or we had this industrial flow,’” she said. 

Developing those relationships is critical to a smooth working partnership, Larsen said. 

“Know who the epidemiologists are and know who the environmental epidemiologists are,” he said.

Naughton added that she invites utilities she works with to meetings so they can ask questions and engage with public health departments. 

Data Privacy

Health data is a sensitive topic, and utilities need to make sure security is top-of-mind.

As the population sample decreases, the privacy risk increases, Larsen said. Sampling for COVID-19 and other illnesses at a city level can’t put any individuals’ or groups’ data at risk. But what data is made public from sampling at smaller levels must be considered thoughtfully, the experts said. Generally, sampling becomes a data privacy risk at under 3,000 people, Naughton said.

“It’s public information that public money is going towards… so you should see that data. But we do need to be sensitive to how that data is shared and what it’s used for, and if it’s targeting communities more than helping communities,” she said.

Larsen recommended reading the World Health Organization’s guidelines on public health surveillance. Arizona State University has also studied the field’s privacy implications.

And if local public health units opt to sample for drugs, Naughton said it should be to find out which neighbourhoods need more support — not to increase incarceration or otherwise punish communities.


Fortunately, there’s lots of reading on wastewater-based epidemiology for utilities to do — potentially an “overwhelming” amount, Naughton said. 

She pointed to resources from the Canadian Water Network as a great starting point. Videos like the WEF’s that show what happens to samples can be helpful for utilities as well, she said. 

“Our plants love seeing the data, and getting it back, and (knowing) that it’s being used for something,” she said.

Better data management can help utilities better prepare for wastewater epidemiology

Wastewater epidemiology requires sampling large amounts of data. Klir’s sampling module allows you to stay on top of it all, so you can be ready when researchers come knocking.

Book a demo today to find out how Klir can help you streamline data throughout your organization. Learn more and book a demo today.

Striving for a ‘One Utility, One Platform’ Approach at Halifax Water

“One of the difficulties with diving into the digital world is that you end up having an app for this, and then an app for that. The fact that Klir had so many different modules that can talk and communicate with each other was really appealing to us. Users don’t have to learn eight different applications: ideally they’re only going to know the SCADA system and Klir.”

As Data Analyst for the Halifax Regional Water Commission’s Water Quality Programs, Adam McKnight has a privileged vantage point over Nova Scotia’s largest water system.

Serving a population of more than 350,000 in the Halifax Regional Municipality, the utility manages 8 water supply plants, 14 wastewater treatment facilities and more than 1,500 kilometers of water mains in Canada’s second-fastest growing municipality, all of which must be constantly monitored for compliance through a rigorous sampling program.

“A lot of the time, compliance data drives our operational decision making. If we’re reporting a number to a regulator, we need to make sure that we’re doing what we need to do operationally to meet those targets,” points out McKnight.

But getting those thousands of data points in front of the right people can be a challenge, especially when you consider the patchwork of offline and online systems that water workers like McKnight have to navigate.

That’s why Halifax Water set out to transform the way it manages its water data, merging multiple data sources and processes into a single collaborative platform and paving the way for a more proactive, collaborative and resilient water data management program.

More Data, More Challenges

When Halifax Water first considered implementing Klir to manage its compliance data in 2020, it had already spent decades using software tools to transition away from paper and binder-based recordkeeping and do more with their existing data.

But while compliance-specific web tools had helped Halifax Water take one step into a digital future, as the utility grew and the number of different people and departments using those tools increased, the utility’s data management system became increasingly strained. 

“We focused on getting drinking water data into the digital realm, then we expanded on that and incorporated wastewater compliance and sampling, then we added more research-based groups.”

The result was a work process that, from a data and reporting perspective, was unsustainable in a few ways:

  • Sampling data remained difficult to access, living “either in physical log sheets at the treatment facilities, digital spreadsheets, or in the time series data management system that stores our SCADA data. Having data in so many locations and formats makes it really difficult to pull the data together for comparison and analysis, especially when it is needed quickly.”
  • Spreadsheets were being used as databases, creating data opacity and discouraging proactive data management.
  • Even when users could get data in and out of the system, it wasn’t built for collaboration and often became disorganized with too many hands in the pot.

“We didn’t really have a solid water quality data governance or structure. It was kind of a free for all, which led to a lot of challenges,” says McKnight.

Implementing a New Approach to Water Data Management

It became clear that Halifax Water would need to adopt a new approach to water quality data management—one that took the patchwork of tools it had depended on in the past and turned it into one truly integrated system. 

To do that, the utility turned to Klir, an operating system (OS) for water management that integrates compliance, sampling and all other aspects of water and wastewater data management into one integrated, centralized and easy to use system.

Presented with the opportunity to switch to Klir, McKnight says it didn’t make sense not to make the jump.

“We have all of this operational data, we have all of this compliance data—it didn’t make sense not to have that data be brought together.”

With the help of Klir and a renewed commitment to the One Utility, One Platform approach, Halifax Water aims to:

1. Maintain High Quality Drinking Water

Klir dovetailed with a longstanding desire at Halifax Water to do more with data and move from reactive problem solving to an approach whereby compliance personnel, operators and engineers worked proactively to mitigate drinking water and wastewater issues.

“Over the last three years we’ve been trying to look at our compliance data as early as possible, especially when data is beginning to trend differently. We began by getting our compliance inspectors to send us emails when they’re noticing things in the distribution systems or at treatment facilities when data is outside normal thresholds.”

Klir presented McKnight’s department with the opportunity to see the bigger compliance picture, notice trends before they become problems, and make sure the right people have access to the right data at the right time.

“That way, we’re able to get ahead of things and maintain high quality drinking water.”

2. Decrease Dependence on Individuals

The complicated routines of a water sampling program as large as Halifax Water’s will often live, to some extent, inside the desk drawer or head of a single employee. That can create problems if that information—or person—ever goes missing.

“That’s a lot to put on one person,” points out McKnight. “And if that one person leaves, you’re stuck.”

Klir gave Halifax the ability to offload that information into a universally-accessible system, decreasing dependence on individuals and building a system that was more resilient, more secure and less prone to information loss.

3. Centralize Compliance Data and Cut Down on Data Chasing

Larger utilities like Halifax Water often struggle to maintain a single set of compliance data, which can sometimes lead to confusion or even overlapping, contradictory information about water and wastewater quality.

“Sometimes data used in reporting is calculated from a combination of compliance and operational sampling program data. However, confusion can result when datasets unintentionally referenced are not the authoritative source of the information and have become outdated. We need one single source of truth, where people know they can go to reference authoritative data at any time.”

Linking and centralizing compliance, monitoring, research, operational and other data together to create a single source of truth provides Halifax Water’s users with a new level of decision-making confidence, allowing operators and staff preparing reports to have a full and clear picture of what is actually going on in the utility.

4. Use Fewer Apps to Build a More Efficient, Secure System

It’s not uncommon today for operators, engineers and compliance professionals at large utilities to use separate tools for compliance reporting, sampling, pretreatment and FOG, backflow prevention & cross-connection control. 

McKnight says that can become a frustrating challenge for a utility trying to build a system that works, and is also precisely why Halifax Water chose Klir.

“The fact that Klir had so many different modules that can talk and communicate with each other was really appealing to us. Users don’t have to learn eight different applications: ideally they’re only going to know the SCADA system and Klir.”

McKnight says that in addition to reducing the time Halifax Water spends training new users, it also allows the utility to avoid situations where someone leaves the company and takes access to and familiarity with an app with them.

“From an auditing perspective that can be a huge red flag. If you’re only using a handful of applications, that’s a lot easier from a security perspective.”

5. Break Down Departmental Silos and Promote Collaboration

Halifax Water made a multi-year commitment to become a “One Water” operation, integrating stormwater, wastewater and drinking water into one seamless system. 

“Our big objective is to break down silos and have more communication between the different business units, departments and divisions. Alongside that, internally we’ve also [adopted] the slogan of ‘one water, one data.’ Those two goals really go hand in hand.”

Klir has helped accelerate that transformation within Halifax Water, helping form bridges between different groups within the utility, giving all user groups easy access to water quality data, and helping decision makers at the utility get on the same page when it comes time to problem-solve.

“It only helps make us stronger, because we’re going to be working together and everyone has a common goal rather than feeling like there’s different groups that are working against each other.”

One Water, One Data

With Klir, Halifax Water foresees making serious progress on its goals to encourage interdepartmental collaboration as a One Water utility, set the stage for further data integration in the near future, as well as:

  • Adopting a proactive approach to problem solving, helping it maintain water of high quality for its customers and the environment.
  • Decrease dependence on individuals, reducing the risk of information loss.
  • Create a single source of truth, avoiding overlapping or contradictory reporting and streamlining the compliance process as a whole. 
  • Use fewer apps to build a system that is easier to use, takes less training time to master, and is better prepared from an audit and security perspective.
  • Break down departmental silos and promote collaboration, allowing the utility to deliver on its One Water, One Data vision.

Bring a ‘One Water’ Approach to Your Utility

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

Request a Demo

Book a demo with our team and receive the latest industry insights and exclusive offers.

Building the Utility of the Future

Receive our free comprehensive report on how to bring your utility into the 21st century and tackle the compliance data challenge.

Request a Demo

Book a demo with our team and receive the latest industry insights and exclusive offers.