How to Clean Well Water

By: Jake Gallagher | August 23, 2023

I really can’t stress enough the importance of cleaning well water. Your well can quickly become a nest for dozens of contaminants if not treated regularly. 

If you own a private well, you are entirely responsible for its maintenance and treatment. After all, your whole family is dependent on this water supply, and you can’t put anyone at risk of ingesting fatal contaminants.

But how do you clean it? In this article, you’ll find the most common methods to help you keep your well water 100% safe.

Testing Well Water Quality 

Well water quality varies by region. Some groundwater has high levels of nitrates and nitrites, while arsenic is a chief concern in other areas. In most cases, you can’t see, smell, or taste the contaminants in well water, so it’s imperative you test it regularly. Without testing your water, you won’t know what treatment method to use because different cleaning processes apply to different contaminant types. 

According to the Environmental Protection Agency (EPA), you should test your water for coliform bacteria, nitrate, and nitrites yearly. You should also test for arsenic, manganese, lead, and radon once every three to five years. 

So, let’s discuss what methods you can use to test your wells.

Take a sample to your nearest laboratory

Contaminants like nitrites, arsenic, manganese, and lead can only be detected in a laboratory. You can get started by contacting your local health department and asking them if they have water testing programs or if they could recommend a laboratory certified to test private well water. 

Contact your laboratory and learn about their testing protocols. Read their instructions on taking a sample and follow the process carefully for accurate results.

You can also jump to the EPA’s database and find a certified laboratory near you. Or you could simply search Google to find a laboratory in your region. 

Testing at home

You can also test your well water at home using water testing kits. Testing at home increases the risk of human error and inaccurate results. In addition, there are no methods to test arsenic at home accurately. So it’s always better to leave it to the professionals in the laboratory. 

Nevertheless, keep an eye out for the following key water quality indicators. 


If your tap water starts smelling like a rotten egg, it is probably due to hydrogen sulfide gas or sulfur bacteria in your well. If it emits a sewage-like unpleasant odor, bacteria have most likely attacked your well water. In any case, finding the source of the smell is the first step. Sometimes, it’s just the inner lining of the faucet, plumbing system, or water heater causing the smell. 


Well water turning yellow is typically an indication of rusting iron pipes. Copper corrosion in the plumbing system can give a bluish green tint. In addition, if there’s a high magnesium concentration, well water turns black. 


If your water tastes funny, immediately stop drinking it and switch to another water source, such as bottled water. Water that tastes musty and earthy usually contains algae and bacteria. Water with high chlorine content will taste like bleach. Copper in water can cause it to have a bitter and medicinal taste. 


You can determine the pH of your drinking water by using a simple litmus paper test. This test will not indicate what contaminants are in your water, but it can show you how alkaline or acidic your water is.

According to the EPA, the ideal pH of well water is 6.5–8.5. If the pH is too high or too low, it can disrupt the plumbing system and cause the leaching of harmful metal ions into the water. 

Before Starting the Cleaning Process

Once you get your well water testing results, it’s time to find the source of the contamination and rectify it before you start the cleaning process. Here are some of the leading causes of contamination:

  • Seepage of surface water runoff due to a loose lid, cracked walls, or well casing not elevated above the surface level
  • Old well structure and rusty plumbing system
  • Malfunctioning water heaters, water softeners, or pressure tank
  • Leakage from your septic system
  • The presence of potential contamination sources, such as oil tanks or pesticide-laden farms, near your well

Point of entry vs. point of use

Before establishing a method for cleaning your contaminated well water, you need to figure out if you need a point-of-use (POU) or point-of-entry (POE) cleaning system. 

POE systems are installed at the location where well water enters the home. They deal with massive water flow and are responsible for filtering the entire water supply. POU systems, on the other hand, are placed right at your taps and faucets. 

Whether your system needs POU or POE purification systems depends on your budget and water quality.

POE filtration systems are cost effective, durable, and great for cleaning out smelly organic compounds and metals in your well water. 

However, if you want to further enhance the purity and taste of water coming from specific taps, such as kitchen faucets, you need POU advanced filtration systems. POU devices can treat contaminants coming from pipes and fixtures that a POE system will fail to address. 

You may need to install a combination of both types of water treatment systems for the best results. Discussing your needs with a local well contractor is the best way to go about this.

Water Treatment Methods

Unless you know enough to determine which treatment method will work best, you should contact a well water professional for advice. 

In general, though, cases of microbial contamination in well water can be remediated with shock chlorination, ozone, and ultraviolet light.

Shock chlorination

Many well owners perform shock chlorination themselves, as it’s a fairly easy process and doesn’t require professional skills. I’ve laid down the steps involved in this process:

Step 1

Measure the volume of water your tank can hold and buy an adequate amount of chlorine bleach to disinfect the well thoroughly. You can make your work easy if you find your well contractor’s report containing all the necessary information about your well, such as the well’s height, diameter, and static water level. 

Use unscented chlorine bleach to avoid adding any new contaminants to your well. Bleach is available in different concentrations, so buy according to the requirements of your well water. 

The National Ground Water Association (NGWA) doesn’t recommend using liquid household bleach for disinfection. Make sure to get chlorine bleach certified for disinfecting drinking water.

You can use this calculator by Public Health Ontario to calculate the amount of chlorine bleach you require for your well.

  • Before starting the disinfection process, collect enough water for 24 hours for personal use, such as flushing toilets and cleaning. Or arrange a different water source for drinking and cooking purposes.
  • Don’t forget to get yourself a pair of rubber gloves, safety glasses, mask, pliers, and a garden hose. 
  • Make sure you don’t have any activated carbon filters fitted in your water system. Carbon can filter out chlorine and hinder the disinfection process in the pipes beyond the filters. Also be sure to shut off your water heater. 

Step 2 

Now, wearing your protective equipment, open the wellhead and pour half of the chlorine bleach inside the well. Connect a hose to your water system, direct it into the well, and turn it on, so that bleach water starts circulating. Add the remaining bleach into your well.

In order for the chlorine to reach all the pipes and indoor faucets, turn on all the water taps in your home, hot and cold, and let the water run for a few minutes until you can smell the chlorine bleach odor.

Once the bleach mixture flushes all the pipes and plumbing system, turn off the faucets and let the treatment sit for 12–24 hours.

Step 3

After 12–24 hours, turn on the water hose connected to any tap outside and let the chlorinated water run until the smell diminishes and disappears. Make sure you drain the water in an area away from septic systems and vegetation. 

Water testing will not yield accurate results unless all the bleach has exited your water system. 

Retest the water after seven days of disinfection. Until then, use an alternate source or boil this water to use it for drinking and cooking. If the test is clear, your well water is safe to drink. It’s advisable to test your water again after three to four weeks and one to two months. 

NOTE: In case your well is again infected with coliform bacteria, the problem lies in groundwater, and you will need to go for other permanent water treatment systems.

Hydrogen peroxide disinfection 

Hydrogen peroxide is effective at removing iron bacteria in well water pipes and fixtures. It works by oxidizing iron into ferric iron (also called rust), which is then easily filtered out. Compared to chlorine bleach, hydrogen peroxide improves the taste of drinking water, leaving no by-products or strong bleachy smell in fixtures. 

But, according to the EPA, this method is not suitable for removing microbial contamination because hydrogen peroxide is a weak disinfectant. You will need to combine this process with ozone or UV filters to remove bacteria and viruses. 

Ultraviolet (UV) light unit

UV disinfection systems are effective against bacteria, viruses, and other microbes. This method can only kill harmful microorganisms in your system and not remove any other pollutants. 

Before installing a UV light unit, make sure you have a pre-filtration system to clean out heavy metals, organic matter, and salts, as these particles can disperse the UV rays and reduce their efficiency. The UV system becomes a powerful purification system when combined with other filtration devices. 

Ozone water disinfection system

Ozone water treatment removes bacteria, viruses, parasites, hydrogen sulfide, and metals, such as iron, copper, and manganese, from well water. 

Ozone oxidizes the organic matter in the cells of microorganisms and ruptures them. In addition, ozone oxidizes iron, copper, or manganese and turns them into solid, removable particles that can be filtered out using any mechanical filtration method.

During this disinfection process, you will not have to deal with chlorine bleach odor as you do with shock chlorination. It’s three times faster and more efficient than chlorination and doesn’t leave any by-products in the water. What’s more, it significantly improves the taste of your water.

The downside is that an ozone treatment system is quite expensive to install and can cost a few thousand dollars. 

Keeping Your Well Water Clean

After you’ve treated your contaminated water, you’ll want to keep it clean moving forward. There are several methods available for preventing contamination of private wells.

Water filtration

Water filtration is one of the most common ways for preventing contaminants in private wells. With several types of filters to choose from, it shouldn’t be too hard to find one that works for you. 

Carbon filters

Activated carbon filters can remove free chlorine, volatile organic compounds, dirt, smoke, and particles greater than 0.3 microns. It’s good for eliminating odor and improving water color. However, if your water test results indicate the presence of fluorides, nitrites, sodium, or microbes, carbon filters cannot remove them. Only some advanced carbon filters are used to filter out lead. 

Since carbon filters can miss out on other contaminants, you should use them in tandem with other purifying systems. 

Ion exchange filters

Ion exchange filters are great for removing calcium and magnesium in water, which is the cause of water hardness. Ion exchange filters are also used for deionization, or removing dangerous ions from water, such as lead, mercury, and arsenic. 

The system works by replacing unwanted ions with sodium ions. The ion exchange method is widely used for removing nitrates and nitrites from well water, as well as other contaminants.

Reverse osmosis (RO) filters

Reverse osmosis filters use pressure to filter contaminants through a semipermeable membrane and can remove arsenic, fluorides, volatile organic compounds (VOCs), nitrates, nitrites, herbicides, and pesticides from a contaminated well water system. Reverse osmosis also uses carbon filters to remove chlorine and odors from drinking water. Advanced RO filters offer a pore size of 0.1 nanometer that can effectively remove bacteria, viruses, and other microbes that range between 0.02-0.4 micron. 

RO filters are easy to install under the kitchen sink and don’t require much maintenance. 

Distillation systems 

Distillation is an old method for purifying water, but it is still used in some households. It effectively removes bacteria, VOCs, and heavy metals, such as lead, arsenic, and mercury. 

Distillation works on the principle of boiling water, turning it into vapors, and leaving behind the harmful compounds with a higher boiling point than water. The vaporized water is then condensed back to purified water in a separate container. 

The distillation method uses a lot of energy. Because this can be costly, it is only a suitable option for small quantities of water. 

Water softeners

If you live in a region where water hardness is a big issue, then a water softener is your best friend. It is a popular method for removing calcium and magnesium ions from water that cause hardness. For microbial and chemical contamination, however, you will need an additional treatment source. Read my article on the topic for more information about how a water softener works.

Final Thoughts

Your well water quality is highly dependent on where you live. Some regions have high levels of nitrates and nitrites in the groundwater, while other sites are rich in arsenic deposits. You can only identify them after regularly testing your well water in an accredited laboratory. 

In order to steer clear of toxic chemicals, you need to invest in a purification system or combination of filters as soon as you install a well or move to a new place with well water. Now that you know how to clean well water, you’re better prepared to take the next step to ensuring your drinking water is always safe and clean.