How to Remove Bacteria from Water

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Whatever the cause, bacteria in your drinking water is never a good sign. While some bacteria are harmless, others can make you sick – and it’s not worth the risk of drinking water containing bacteria and hoping you’ll get away with it.

In this guide, I’ll be looking at the ways that bacteria can get into drinking water, and, most importantly, how to remove bacteria from water using UV disinfection, chemical disinfection, distillation, or sub-micron filtration.

🦠 What Bacteria Are Commonly Found in Water?


Cryptosporidium can contaminate both well and city water, and can spread quickly in a water source. When consumed, it can cause severe stomach cramps and diarrhea in a disease known as cryptosporidiosis. It’s essential that water is properly treated to kill this parasite.

E. coli

Escherichia Coli, or E, Coli for short, is one of the most common types of bacteria found in water. When consumed, this bacteria can cause vomiting, nausea, diarrhea and abdominal pain. You will usually experience symptoms between one and eight days after drinking contaminated water.


Coliform is most commonly found in well water. While most coliform is not harmful, someone that has been exposed may experience vomiting, fever, diarrhea or upset stomach and elderly or children are more at risk.


Giardia Lamblia, otherwise referred to as giardia, causes a type of infection known as giardiasis. You may experience nausea, diarrhea, stomach cramps, and gas with this infection, which can last for up to two weeks.


Legionella is another bacteria that can be found naturally in the environment. You’re especially likely to find legionella in warm waters, and it poses a particularly high health risk when inhaled (such as while showering or through an air conditioning unit), causing a lung condition called Legionnaires disease.


Shigella causes shigellosis, one of the most contagious bacterial diseases. This bacteria can get into water in numerous ways, including in polluted stormwater runoff and sewage overflows, and after flooding. Shallow wells are especially at risk of shigella contamination.

🤔 When Would Drinking Water Be Contaminated With Bacteria?

Bacteria may be present in all water sources, which is why it’s so important to only drink treated water, to stay on the safe side. Even if you get your water from a public city system, there’s still a risk of bacterial contamination.

You can find some of the most common occurrences that can result in bacterial contamination below.

After a Natural Disaster

Natural disasters, such as earthquakes, storms or major flooding events, can contaminate both well water and public drinking water supplies.

An earthquake could damage a water supply line, allowing bacteria to enter. Storms or flooding could cause untreated floodwater to flood wells and municipal water reservoirs, contaminating clean water systems with dirty, potentially bacteria-laden water.

From a Contaminated Well

If you’re a private well owner, it’s your responsibility to test your well for potential contaminants and implement treatment methods when necessary.

Wells can become contaminated with bacteria in many ways, and older well systems are more susceptible to bacterial contamination as they’re less study in structure and more likely to experience leaks and breakages.

From Untreated Surface Water

As I mentioned earlier, bacteria has the potential to linger in any untreated surface water source. That crystal-clear lake or shimmering waterfall might look clean to you, but it could still be teeming with bacteria.

Think twice before drinking untreated surface water from lakes, rivers or streams while you’re hiking or camping. If you do choose to use this water, make sure to boil it or run it through a portable water filter before drinking, which will kill or remove any potential bacteria.

🩺 Health Risks of Drinking Water Contaminated With Bacteria

The exact health risks of drinking water contaminated with bacteria depend on which bacteria are present. Some of the health effects of bacteria are as follows:

Nausea, Vomiting and Stomach Cramps

The most common side-effects of drinking water containing bacteria are vomiting, nausea, and stomach cramps. E. Coli for instance, produces a toxin called shiga, which damages the lining of the small intestine, resulting in abdominal pain and diarrhea. These symptoms can range from mild to severe, depending on the type of bacteria you’ve consumed. cryptosporidiosis is a particularly severe diarrheal disease caused by bacterial contamination.


Bacterial pneumonia is caused by inhaling bacteria in water, such as during showering. Legionnaires disease is a particularly common type of pneumonia caused by bacteria in drinking water. This disease causes cough, fever, shortness of breath, headaches, and muscle aches, and can be fatal.

There’s also a less serious infection caused by legionella, known as pontiac fever. This causes muscle aches and fever, but doesn’t result in pneumonia.

Fever, Headaches and Fatigue

Alongside symptoms of nausea, vomiting and stomach cramps, you may also experience headaches, fever and fatigue after consuming water that contains bacteria. Shigella can cause fever and headaches as well as diarrhea and vomiting. E. Coli and legionella can also cause these symptoms.

✅ How to Remove Bacteria from Water

You should now have a better idea of how bacteria get into water, and which types of bacteria are more common. Let’s look at how to remove bacteria from water, both at home or while you’re on the go.

UV Disinfection

UV disinfection is one of the most effective point-of-entry bacteria removal methods. You can use a UV purifier system to remove bacteria from drinking water in your home or RV, or even while you’re out and about, in a UV purifier bottle.

A UV disinfection system uses a UV lamp that sits inside a chamber. When water flows through the chamber, the ultraviolet rays alter the DNA of waterborne pathogens, killing them and preventing them from reproducing.

When you drink water that has been disinfected with UV treatment, it will still technically contain bacteria, but this bacteria will no longer be able to make you sick.

UV disinfection doesn’t only kill bacteria in drinking water. It is also effective against all protozoa and viruses. 

A UV filter can usually last for about 1 year before the lamp needs to be replaced. This makes UV disinfection a low-maintenance option that’s worth considering if you don’t want the hassle of filter changes or chemical top-ups.

UV filter bottles can cost between $50 and $100, while complete UV disinfection systems are priced at around $400-$600, depending on the model.

uv purification system
UV purification system

Chemical Disinfection

Chemical disinfection is an affordable means of killing bacteria, viruses and protozoa in water.

This form of water treatment is widely used by municipal water suppliers to affordably treat large batches of potentially contaminated water before it is sent to our homes.

Chlorine is the most commonly used chemical for disinfection. Chloramine, a chlorine byproduct, is also used in some states.

Chlorinated water is almost guaranteed to be free from pathogenic bacteria, viruses and protozoa. This is because chlorine breaks the chemical bonds that bind these molecules together, killing them and stopping them from being able to multiply.

You can use a whole home chlorine injection system to remove bacteria from well water by injecting a measured amount of chlorine into the water. This system features a tank that water will sit in for several minutes, allowing it enough contact time with chlorine for disinfection to take place.

Because chlorine injection systems are whole home filters, you can benefit from bacteria-free water throughout your home, including in your showers, appliances, drinking water, and plumbing.

The biggest setback of a chlorine injection system is that it affects water quality by introducing chlorine, which can give water an unpleasant taste. You may want to use a water filter system to remove this chlorine after using it to disinfect your water, which will cost more money. You will also need to pay for chlorine top-ups when required.

chlorine injection system
Chemical injection system


Distillation can be used to purify drinking water at home. A countertop unit known as a water distiller is used to boil water until it evaporates into a gas, before cooling and condensing into liquid form in a separate container.

The distillation process is one of the most thorough water treatment techniques available today. It doesn’t just remove bacteria from water – it also removes iron, manganese, fluoride, chlorine (in chlorinated water), other disease-causing pathogens like viruses, chemicals like pesticides and herbicides, and much more.

You can buy a water distiller system for around $100-$300, depending on its features.

Distiller systems are portable, and are easy to take with you to work or on a road trip. However, they do need to be plugged into a power source to boil the water, so you can’t use them while camping or in an emergency situation.

While distillation is highly effective, and can remove bacteria and a whole host of other impurities from drinking water, it isn’t a fast purification process. It can take between 3 and 5 hours for a distiller to produce a single batch of distilled water.

The advantage of distiller systems, however, is that they’re virtually maintenance-free and cost very little to operate. Some distillers come with a small carbon filter, which will need to be replaced occasionally, at a low yearly cost. Other than that, you’ll just need to clean out the boiling chamber between uses.

countertop water distiller
Countertop distiler

Sub-Micron Filters

A sub-micron filter uses a microporous screen that is small enough to trap bacteria, viruses (some but not all), and other pathogens in drinking water.

You can find sub-micron filters in some at-home water filter systems, as well as portable water filters designed for filtering natural surface water sources, like straw filters and hanging gravity filters.

These filters are also known as microfilters. As well as bacteria and some viruses, a sub-micron filter can usually remove microplastics, chemical matter, silt, and cloudiness.

The majority of sub-micron filter systems need to be periodically flushed or backwashed, which involves sending water backward through the filter and removing any large contaminants that are blocking the filter’s pores.

This process is essential to prevent the filter from becoming completely blocked with contaminants, which is likely, because of the tiny size of its pores.

The benefit of sub-micron filters is that many of them have long lifespans of several years, as long as they’re properly maintained. This makes sub-micron filters especially ideal for storing away for emergency use.

sawyer mini portable hiking water filter
Sawyer Mini sub-micron filter

❔ Frequently Asked Questions

Do Water Filters Remove Bacteria?

Most water filters are incapable of removing bacteria from drinking water, because their micron rating is too high.

A filter’s micron rating refers to its pore size. The lower the micron rating, the smaller the filter’s pores. Most water filters have a micron rating of between 1 and 10. Bacteria can be as small as 0.3 microns, and can slip through the pores of these filters.

You might be wondering – why don’t all filters just have smaller pore sizes to remove bacteria? The answer is that the smaller the pores, the greater the contaminant removal, and the faster the filter becomes clogged. If your typical carbon filter had tiny pores that could trap bacteria, it would probably last a couple of weeks at most before it would need replacing. 

Which Bacteria Filter is Best for Emergency Use?

If you’re looking to buy a water treatment system that can remove bacteria from water in an emergency situation, I would recommend using an emergency preparedness portable water filter.

Straw water filters, bottle filters and gravity-fed water filters are all good options for emergency preparedness, as they don’t need water pressure or electricity to operate.

Make sure that the filter you choose can remove bacteria, as not all filters can (see above). You can read my full guide on emergency preparedness water filters if you’re interested in learning more.

Can Reverse Osmosis Water Filters Remove Bacteria?

Most reverse osmosis water filters can usually reduce and possibly remove bacteria, and you can certainly consider these systems as an option for bacterial removal. Always check the manufacturer’s data to determine if their system is designed for the contaminants you are looking to reduce/remove. However, I wouldn’t recommend this type of water treatment if you’re purely looking to get rid of bacteria in water. Here’s why.

Reverse osmosis water filters are another highly effective water treatment solution, using a membrane to remove almost every existing drinking water contaminant, including bacteria and some viruses.

However, reverse osmosis systems provide a very expensive purification process, costing around $500-$1000 or even more, depending on the system you buy. You’ll also need to pay to replace the membrane and filters periodically. This is a big investment if all you need to remove from your water is bacteria.

With that said, if you are looking to fully purify your water as well as removing bacteria, reverse osmosis water filters are worth considering. Just keep in mind that the majority of reverse osmosis water treatment units are designed for under-sink or countertop installation, so they won’t protect you from inhaling legionella.

Will I Know If My Water Contains Bacteria?

Based on sight or taste alone, no. You will only know your water contains bacteria when it’s too late – unless you test for it in advance.

Bacteria in water supplied to the public is uncommon, as water is treated to kill or remove this contaminant before it is delivered to our homes. Public water providers are required by the Environmental Protection Agency to test their water quality and disinfect water with chlorine or chloramine to ensure it is safe for drinking.

If public testing finds disease-causing bacteria, your local authority should inform you of the detection and issue a boil water advisory or notice.

For well water supplies, the owner of the well is responsible for testing for bacteria in water. The CDC recommends testing for total coliforms and fecal coliforms, including E. Coli. If you carry out regular bacterial testing, you should be able to resolve a contamination issue before it makes you sick.

Is Chlorine A Safe Means Of Removing Bacteria?

Yes. Chlorine is widely used for public water disinfection, and in small amounts, can make your water safe to drink without posing an additional health risk. However, chlorine will affect your water quality, and some people would rather use water filters to remove bacteria and viruses because they don’t give water an unpleasant taste. Additionally, with the use of chlorine, there’s always the risk that you might add too much chlorine to your water during treatment, which could be dangerous.

Which Bacteria Water Filters Are Best For Hiking and Camping?

Any bacteria water filters that are small and portable are suitable for hiking and camping trips. Straw filters, water bottle filters and hanging gravity filters are all good choices. Using a portable bacteria filter means that you won’t have to worry about boiling water before drinking, or bringing enough bottled water to see you through. Some of these can also remove viruses – it depends on the pore size.

  • Jennifer Byrd
    Water Treatment Specialist

    For 20+ years, Jennifer has championed clean water. From navigating operations to leading sales, she's tackled diverse industry challenges. Now, at Redbird Water, she crafts personalized solutions for homes, businesses, and factories. A past Chamber President and industry advocate, Jennifer leverages her expertise in cutting-edge filtration and custom design to transform water concerns into crystal-clear solutions.

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