5 Well Disinfection Techniques, from a Water Doctor

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Need to disinfect your well after a natural disaster? Or just want to protect your family from potential microorganisms in your well supply?

Here, we’ve listed the 5 well disinfection techniques to use, depending on your circumstances.

📌 Key Takeaways:

  • Short-term emergency response well disinfection techniques are shock chlorination and boiling.
  • Long-term well disinfection techniques are UV water purification, chlorine injection, and water distillation.
  • When choosing a disinfection procedure for your well water system, consider your budget, whether you need an emergency or long-term solution, your preferences on chemical use, pre-treatment, and your other well contaminants.

🚨 2 Emergency Response Well Disinfection Techniques

Here are the two well disinfection techniques that we recommend in response to an emergency, such as contamination form a septic system, flooding, or a natural disaster.

Shock Chlorination

Shock chlorinating your well is the best way to kill coliform bacteria, viruses, and other microorganisms in well water.

You can use liquid household bleach (unscented bleach, not scented) for shock chlorination.

Here’s an overview of the process:

  1. Remove the well cap and pour the bleach inside.
  2. Wash down the inside of your well with a garden hose.
  3. Let the bleach solution sit for 6-12 hours (ideally overnight).
  4. Turn on all your faucets and fixtures to send the chlorinated water through your plumbing system. Flush your pipes until the chlorine odor is no longer present.
  5. Use chlorine test strips to check that the bleach solution has been flushed out of your well.
  6. After two weeks, do a coliform bacteria test again to check that your water is now pathogen-free.

Make sure to wear rubber gloves when handling the bleach solution. You can also wear protective goggles for extra safety.

👨‍🔧 We’ve shared a more more detailed guide to shock chlorinating a well water system in our well water shock chlorination article.

Contact a well contractor if you’re unable to effectively shock chlorinate your well. Your well construction may be damaged or degraded, and you might need to repair or even replace a section of your well.

Shock Chlorination
Source: uga.edu


  • Highly effective in disinfecting your entire well water system and plumbing
  • Rapid results – disinfects water within hours
  • More affordable than long-term disinfection methods
  • Simple process that can be carried out by the homeowner


  • May leave a residual taste and odor of chlorine
  • Handling chlorine solutions can be dangerous
  • You may miscalculate the amount of bleach that you need


Boiling water is another short-term emergency procedure for disinfecting well water.

Fill a pot under your water faucet, then bring the water to a rolling boil for 1 minute. The heat will kill bacteria, viruses, and other potential contaminants by damaging their structural components.

We recommend boiling your water as a short-term solution if you think your well has been contaminated with microorganisms, before you shock-chlorinate your well or look into a long-term disinfection solution.

Keep in mind that you can only boil water after it has left your faucet, so this solution won’t protect your home’s appliances or fixtures from pathogens.

Boiling water


  • Quick and easy
  • Affordable – you just need water from your faucet, a pot, and a stove
  • Effectively inactiates viruses, protozoa, bacteria, and other pathogens
  • Can store batches of boiled water for later drinking


  • Requires gas or electrical power (for your stove), which you may not have access to in an emergency situation
  • Point of use treatment – won’t protect your entire water supply
  • Won’t remove other potentially harmful impurities in contaminated water

🚰 3 Long-Term Well Disinfection Techniques

Looking for a long-term solution to disinfect water?

Treatment systems exist for this purpose. Here are the best long-term well water disinfection techniques:

UV Water Purification

UV water purification uses ultraviolet light to kill bacteria and other microorganisms.

UV water treatment devices are point of entry units, meaning that they treat your well water as soon as it enters your water supply, upstream of the water heater.

The UV disinfection process works by sending water through a UV chamber, where it’s treated with ultraviolet light. The UV rays damage the DNA of microorganisms, killing them and effectively disinfecting water.

UV disinfection is an effective way to kill all viruses, bacteria, and protozoa. However, some types of giardia and cryptosporidium have thick cell walls that protect them from penetration from UV light.

Increasing the UV power increases the system’s ability to penetrate and kill cryptosporidium and giardia.

Uv water purification system installed in basement


  • Natural, chemical-free process
  • More affordable upfront than chemical injection
  • Quick, effective process
  • Low-maintenance (UV lamp needs replacing about once a year)


  • Won’t work on turbid water
  • May not kill all microorganisms
  • Doesn’t leave a residual disinfectant in water

👨‍🔧 Check out the Expert Recommended UV Water Purifier Systems of September 2023

Chemical Injection

Chemical injection systems inject water with hydrogen peroxide or chlorine solutions, which kill microorganisms by breaking the chemical bonds in their molecules.

These systems consist of an injector pump and a tank for storing the water while it’s treated. Some systems also use a filtration media, like activated carbon, to remove the disinfection chemical before water is delivered to your home.

Other chemical injection systems are designed to oxidize and remove iron, manganese, and sulfur, and are often combined with birm or manganese greensand media to achieve this. They can also kill microorganisms as an added benefit.

An important part of any chemical injection system is the water retention tank. Water is held for up to 20 minutes to allow the chlorine to take effect. Without holding the chlorinated water before use, it may not have time to be properly disinfected.

Chlorine injection systems last up to 10 years, sometimes even longer, with proper maintenance.

Maintenance involves checking and refilling the hydrogen peroxide/chlorine solution (usually every 2-4 months), cleaning or replacing the injector pump tube, and replacing the filter media every few years.

These systems can effectively kill bacteria, iron bacteria, viruses, and other microorganisms in water. They may also treat hydrogen sulfide, manganese, and iron.

Pouring chlorine into chemical injection system


  • Long-lasting solution that requires easy maintenance
  • One of the only effective solutions for treating iron bacteria
  • Can be used with turbid water
  • May also target iron, sulfur, and manganese (depending on system design)


  • Doesn’t provide immediate disinfection
  • Chlorinated water has a poor taste & odor
  • Risk of exceeding the safe chlorine concentration in water

👨‍🔧 Looking for great deals? Here are the September 2023‘s Must-Have Chemical Injection Systems for Well Water Treatment

Water Distiller

A water distiller is a point of use system that can be used to purify and disinfect well water.

Water distillers have a high disinfection effectiveness because of their thorough purification process. These systems boil water, which kills microorganisms. The vaporized water travels out of the boiling chamber and condenses into a separate container, leaving the dissolved impurities behind.

You can use a water distiller to disinfect batches of drinking water. Distillation is a slow process, and whole-home water distillers don’t exist – so you can’t distill water that’s used throughout your home’s plumbing system.

Distillation can kill microorganisms including bacteria, viruses, protozoan cysts, and more.

Water distillers don’t contain filter media and they don’t use chemicals, so they’re a low-maintenance disinfection solution.

Water distiller on countertop


  • More affordable than point of entry disinfection systems
  • Kills microorganisms and removes virtually all other drinking water impurities
  • Virtually maintenance-free
  • Chemical-free water treatment


  • Can’t be used to disinfect a whole home water supply (drinking water only)
  • Lengthy process – takes around 5 hours to distill a 1-gallon batch of water
  • Distilled water has a “flat” taste

👨‍🔧 Read more: Exploring the 6 Best Water Distillers (Water Purification Made Easy)

🔎 Factors To Consider When Choosing Between Well Disinfection Techniques

When deciding on a well disinfection process for your situation, consider the following factors:

Your Budget

First, your budget will determine the disinfection water treatment systems you can afford.

If you just need to respond to a natural disaster or another source of contamination, shock chlorination is a low-cost solution. The price of household bleach is very low, and you can disinfect your well with less than $20 of product.

A long-term water treatment solution is costlier. The upfront cost of a point of entry system, such as a chlorine injection system or a UV purifier, is $1,000-$3,500 – possibly even higher if you need a particularly large or complex system.

Your safety is an important investment, but some of the more expensive water treatment systems, like chemical injection systems, might be too expensive for you to consider.

System TypeUpfront CostInstallation CostConsumables LifespanAnnual Costs
Chemical Injection$2,600-$3,400$150-$2,000+6-12 yrs$150-$250
UV Purifier$600-$1,300 $150-$5001 yr$100-$300
Water Distiiler$150-$400-6-12 mos$40-$100

Emergency Vs Long-Term

Also consider whether you need emergency one-off water disinfection or whether you want to disinfect all the water in your well supply in the long term.

Emergency disinfection is important if your well has been contaminated due to a natural disaster or another source (such as a leaking septic system) and you need to kill the microorganisms that have compromised your water safety.

You’ll also need to resolve the cause of the contamination to prevent re-contamination of the well.

Alternatively, you might prefer to disinfect your well water on a just-in-case basis, so you know for certain that your water is potable and safe to drink. Even if your well becomes contaminated with microorganisms, a water disinfection system will kill harmful pathogens, so you won’t get sick.

Chemical Vs Chemical-Free

If you’re looking at long-term disinfection for your well, you can choose between a chemical disinfection procedure and a chemical-free process.

We recommend UV systems because they offer the best chemical-free disinfection process, effectively killing microorganisms with ultraviolet light, which is safe, doesn’t compromise water quality, and doesn’t leave a chlorine odor. They’re also more affordable than chemical systems because of their simplistic design, costing around $1,000-$1,600.

However, UV purification has its setbacks. It can’t effectively treat turbid water, and it doesn’t prevent water from recontamination as it travels through your plumbing system.

If you prefer a chemical-based treatment that mimics the chlorination of municipal water, opt for a chemical injection system. This system treats water with a measured amount of chlorine, storing the water in a tank before delivering it to your home.

Due to the complexity of a chemical injection system, it has a higher upfront cost – usually $2,500-$3,800.

UV versus chemical injection for well water disinfection


Again, for long-term well disinfection, you might need a pre-treatment system, depending on your water quality.

UV purifiers can only effectively purify clear, non-turbid water supplies because suspended particulates in water may block the UV light from penetrating some pathogens in the water.

If your well contains tannins, sediment, rust, or other particles, you’ll need to install an appropriate pre-filter, like a sediment filter or a tannins filter.

Chemical injection systems usually only work with water that has a pH of 6-9. If your well supply has a low pH, you may need to install a calcite filter to raise the water’s pH to neutral.

Other Well Water Contaminants

Aside from microorganisms, there are other potential contaminants that may be present in your well water system.

These include:

  • Pesticides and herbicides
  • Hardness minerals
  • Fluoride
  • Arsenic, iron, manganese, and other heavy metals
  • Hydrogen sulfide
  • Nitrate and nitrite
  • VOCs
  • Radiological contaminants

The types of contaminants in your well water depend on where your well is located. Some contaminants are dangerous in large amounts, and some may cause aesthetic damage to your plumbing system and appliances. Some may give your water a poor taste or odor.

You’ll need to test your water for common well contaminants and look into installing additional water treatment systems if necessary. Contact your local authority if you don’t know which contaminants are common in your local groundwater.

Iron bacteria in water well

🔚 Final Word

Hopefully, you now know how to disinfect a well in response to an emergency (such as a natural disaster), and which methods of disinfection are best for long-term protection against bacterial contamination.

If you have any reason to believe that your well water has become contaminated with microorganisms, stop drinking your water and switch to bottled water or boil your water.

In the meantime, test your water for microbiological contamination. If pathogens are detected, shock disinfect your well with chlorine bleach, then consider installing a water treatment system to protect you from microorganisms in the long run.

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