How to Clean Well Water (2024)

Reviewed by: James Layton
Updated on:
March 5, 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 and treating 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 Solution: 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 microbes. Many well owners perform shock chlorination themselves because it’s a fairly easy process and it’s super cheap.

This treatment will only kill microbes; it is not a solution to any other common well water issues. If your problem isn’t microbes and you need a more permanent solution to a wide range of well water issues, jump to our recommendations for well water treatment systems.

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 consistently contaminated with microbes. If your well water tests positive for microbes, such as coliform bacteria, you really should nail down how it became infected.

The main sources of microbes in private wells are malfunctioning septic systems and sewer lines. To prevent this kind of contamination, it’s important to have your well far enough away from your septic tank. The minimum is 50 feet.

If the problem is to do with your septic tank or the structural integrity of your well, shock chlorination will not solve your problem unless you also fix what’s broken.

However, acute microbial contamination can result from recent flooding, especially for shallow wells or wells with the well cap set too low to the ground. In such a case, shock chlorination is appropriate. It’s also suitable for new wells, wells that have sat unused, or wells that have recently been serviced.

Follow these steps to shock chlorinate your well with a liquid solution.

Step 1: Preparation

  • Working with bleach comes with hazards, so make sure you take the following precautions.
  • Collect enough water for 24 hours or arrange a different water source for cleaning, flushing toilets, bathing, drinking, and cooking.
  • Remember to disconnect any filters fitted to your water system to avoid damaging the filter media.
  • Collect the necessary supplies: rubber gloves, safety glasses, a mask, a funnel, and a garden hose. 
  • Use only unscented chlorine bleach containing 5%–6% sodium hypochlorite.

Step 2: Adding the chlorine bleach 

Remove the well cap.

For a 100-foot well six inches in diameter, mix 1.5 quarts of bleach with 6–10 gallons of water (you’ll need multiple buckets). For measurements specific to your well, you can use this calculator from Public Health Ontario.

Drop one end of the garden hose into your well as far as it can go. Using your funnel, begin adding bleach to the well. As you do, raise and lower the garden hose repeatedly to ensure the bleach reaches as much of the well as possible.

When all of your bleach solution has been added to the well, remove the hose and replace the well cap.

Next, run all your taps until you can smell chlorine. This should ensure the bleach mixture reaches your entire water system.

Let the treatment sit for 4–12 hours, or overnight. Do not use or drink the water during this period.

Step 3: Flushing the system

After enough time has passed, run all of your fixtures and faucets until you no longer smell chlorine. Make sure you never drain the water near aquatic ecosystems or storm drains. 

Step 4: Retesting

Retest the water two to five days after 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: If your well is still infected, 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.

Long-Term Water Treatment

While shock chlorination is a good solution for treating one-time microbial infection of your well, it is not a long-term solution to improving the overall quality of your well water. If you have ongoing contamination from common well water impurities, you’ll want to install a permanent filtration system.

All the following treatment systems are effective against specific contaminants, but none is a one-size-fits-all solution. You’ll need a different filter for microbes than you will for sediment, and the same goes for lead, iron, chemicals, and myriad other contaminants.

Your water test will help you decide which filter or combination of filters you need.

Ultraviolet (UV) light purification

Starting with UV because we’ve covered the one-time microbial contamination solution, UV is an ongoing solution to microbes, perhaps from groundwater contaminated by nearby livestock. (However, it still can’t take the place of repairing a damaged septic tank or well casing.)

UV disinfection systems are effective against bacteria, viruses, and parasites. This method can only kill harmful microbes in your system. It is not effective against anything else. 

Before installing a UV light unit, make sure you install a sediment filter or activated carbon filter, if necessary, to prevent solid particles from reducing the efficacy of the ultraviolet rays.

We’ve reviewed the best UV purifiers to help you get started.

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, 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 fluoride, 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.

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.

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 a highly exact method for purifying water. 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 everything. 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.

Leading Causes of Well Water Issues

Some sources of well water contamination can be solved, such as a malfunctioning septic tank. Some, however, are just the way it is due to the location of your home relative to industry or agriculture, or simply the geology of your region.

Here are some of the leading causes of well water contamination:

  • Surface water runoff
  • Old well structure or plumbing system
  • Malfunctioning water heaters
  • Leakage from your septic system
  • Mining, industrial or manufacturing plants, and farms
  • Rock and other natural earth formations

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

DIY tests increase 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.

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 water that’s been subjected to bacteria or other pathogens through repair, recent flooding, or other acute causes, you can shock chlorinate your well. It’s easy and cheap.

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

For everything you need 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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