How to Clean Well Water (2024)

Updated on:
January 26, 2024

Key Takeaways

If you own a private well, you are entirely responsible for its maintenance and treatment. But that doesn’t need to be as scary as it sounds. Cleaning your well water is easy once you know how.

If you’d prefer to skip the how-tos and science lessons, check out our list of the best whole-house water filters for well water.

One-Time Solutions

If your well has been acutely contaminated by recent flooding or servicing of your well, which opens the well cap and risks pathogens entering, a one-time solution could be effective for killing the pathogens and giving your well a fresh start.

If you need to clean your well water with an ongoing solution, jump to our recommendations for well water treatment systems.

Shock Chlorination

Shock chlorination is the process of pouring liquid chlorine bleach into your well for the purpose of killing bacteria, viruses, and other harmful microorganisms.

Many well owners perform shock chlorination themselves because it’s a fairly easy process and it’s super cheap.

Before I tell you how to shock chlorinate your well, I first must warn you that this is not a long-term solution to well water contaminated with microbes.

If you’ve tested your water and found bacteria, you really should nail down why your well has bacteria. If your well casing or septic tank is damaged, you’ll need to have it repaired or replaced. Shock chlorination will not solve your problem. Nor will help if your groundwater is contaminated with bacteria, which can sometimes happen.

Now, if you do need to clean your well because it’s new, hasn’t been used in a long time, or has recently been repaired or flooded, keep reading to learn how to clean it with shock chlorination. 

Step 1

Step one of shock chlorination is preparation. Working with bleach comes with hazards, so make sure you take the following precautions:

  • First, 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 with different concentrations of chlorine, but the ideal concentration for shock chlorination is between 5% and 5.25%.

  • Determine the volume of water your tank can hold. For drilled wells, add 5 ounces of bleach for every 25 feet of water. For a 100-foot well, you’d add 20 ounces of bleach. For an 800-foot well, 160 ounces. You can also use this calculator from Public Health Ontario.

  • Before starting the disinfection process, collect enough water for 24 hours for personal use, or arrange a different water source for cleaning, flushing toilets, bathing, drinking, and cooking purposes.

  • Collect the necessary supplies: rubber gloves, safety glasses, a mask, pliers, and a garden hose. 

  • Disconnect 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.

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.

Do not use or drink the water during this period.

Step 3

After 12–24 hours, you can drain the chlorine out of your well system. Turn on the water hose connected to any tap outside and let the chlorinated water run until the smell diminishes and disappears. Water testing will not yield accurate results unless all the bleach has exited your water system. 

Make sure you drain the water in an area away from septic systems and vegetation. 

Step 4

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 to ensure the bacteria has not returned. 

NOTE: In case your well is again infected with coliform bacteria, the problem lies either in the groundwater, and you will need to go for a more permanent water treatment solution, or your well or septic tank is damaged, and you need to have them assessed.

Hydrogen peroxide disinfection 

Hydrogen peroxide is effective at removing iron, hydrogen sulfide, other odors, or tannins in well water pipes and fixtures. It works by oxidizing molecules into solid particles, which can then be 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 it’s slightly more expensive, and slightly less effective at killing microbes. 

According to the EPA, hydrogen peroxide is a weak disinfectant. You should combine this process with shock chlorination, ozone, or UV filters to remove bacteria and viruses. 

Hydrogen peroxide disinfection works just like chlorination, with a few differences.

To use hydrogen peroxide, you must first have your water tested so you know how many ppm of contaminants you have.

You’ll then inject 1 ppm of a 7% concentration of hydrogen peroxide for every ppm of iron or manganese, and 2 ppm of hydrogen peroxide for every 1 ppm of hydrogen sulfide gas.

Cycle your water just as you would with chlorine, but hydrogen doesn’t stay in the water as long as chlorine because it turns into oxygen.

Long-Term Water Treatment Methods

While shock chlorination or hydrogen peroxide injection is a good solution for treating one-time microbial infection of your well, it is not a long-term solution to improving the quality of your well water.

All of the following purification systems are effective at treating a wide range of contaminants, but none is a one-size-fits-all solution.

You need to have your water tested to narrow down a solution.

Ultraviolet (UV) light purification

UV disinfection systems are effective against bacteria, viruses, and other microbes. This method can only kill harmful microorganisms in your system. It will 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 because these particles can disperse the UV rays and reduce their efficiency.

We’ve reviewed the best UV purifiers on the market.

Sediment filtration

Impurities such as dirt, sand, silt, and clay can make their way into your well through groundwater. If you don’t want these substances building up in your water heater or clogging your water treatment system, let alone polluting your drinking water, a sediment filter is what you need.

Sediment filters come with various micron ratings based on the size of the sediment particles in your water. Large particles, high micron rating. Tiny particles, small micron rating.

Sediment filters are among the most affordable water filters, and they’re super easy to install and maintain.

Check out our list of the best sediment filters.

Activated carbon filtration

Activated carbon can remove free chlorine, volatile organic compounds, dirt, smoke, and particles greater than 0.3 microns. It’s also good for eliminating odors 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. 

Here’s a list of the best whole-house carbon filters.

Ion exchange (water softening)

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 that cause water hardness.

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.

For microbial and chemical contamination, however, you will need an additional treatment source.

Ion exchange filters might also remove other ions from water, such as nitrate, sulphate, and arsenic. However, you may not want to trust a water softener to remove these potentially dangerous contaminants.

See our list of the best water softeners.

Reverse osmosis (RO) filtration

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 come in several kinds, and we’ve reviewed every kind to help you choose the best one for your house.


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. 

Find the best water distiller for you by reading our review.

Ozone water disinfection system

Ozone water treatment removes bacteria, viruses, parasites, hydrogen sulfide, and metals, such as iron, copper, and manganese, from well water, but it is extremely complex and expensive, so I don’t really recommend it for household use. 

However, it’ll probably show up in your research as you go about choosing a water treatment system, so here’s how it works.

Ozone disinfection systems inject ozone into the water as it passes through the filter. There, it 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.

Testing Your Well Water

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, you should test your well water annually. Only through testing can you properly treat for coliform bacteria, nitrate, nitrites, arsenic, manganese, lead, radon, and other common well water contaminants. 

So, let’s discuss what methods you can use to test your well water quality.

Accredited laboratory testing

Sending a sample of your water to an accredited laboratory is the best and most accurate way to test your well water. In fact, contaminants like nitrites, arsenic, manganese, and lead can only be detected in a laboratory.

We’ve been in the water treatment game for a long time, and we’ve come to trust Tap Score with all our testing needs. Tap Score has a specific test for every type of water.

For accurate, fast, and trustworthy results, have your water tested by Tap Score.

Testing at home

Testing at home increases the risk of human error and inaccurate results. Furthermore, these tests can’t test for every contaminant, including the scariest ones. For example, there are no methods to test arsenic at home accurately.

So, it’s always better to leave it to the professionals in the laboratory. 

However, if you’re determined to DIY this essential step to achieving clean well water, see our list of the best DIY water testing kits for well water.

Other indicators of well water quality

If it’s not yet time to send your water off to a lab but you have misgivings about your water quality, 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. 

If it turns out you do have a sulfur problem in your well, one of these best sulfur filters for well water will sort you out.


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, it may be cause for concern, it may not. Consider switching to another drinking water source, such as bottled water, until you can narrow down the cause.

Water that tastes musty and earthy might contain tannins, 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. 

Only a proper water test can tell you exactly what you’re tasting.


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.

If you’re interested in customizing the pH of your water, here’s a list of the best water ionizers

Leading Causes of Well Contamination

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 well water 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

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. 

To clean well that’s been subjected to bacteria or other pathogens through repair, recent flooding, or other acute causes, you can shock chlorinate your well. Another one-time treatment includes hydrogen peroxide.

But if your well water needs cleaning on a more permanent basis, you’ll need to install a well water treatment system.

For everything you to know about well water, read our well water treatment guide.

We at Drinking Water are committed to helping you achieve the best water quality you can. To elevate your understanding of water treatment, check out the following articles and guides:

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