Bacteria in Your Well Water: What You Should Know and How to Keep Your Water Clean and Safe

If you get your drinking water from a private well, you already know how good it feels to have your own water source. But here’s the thing — your well water doesn’t get checked, treated, or maintained by anyone but you.

One of the biggest risks to your water is something you can’t even see: bacteria.

Let’s talk about the types of bacteria that can show up in well water (including some you might not expect), how they get into your well (sometimes thanks to bugs, mice, and even lawn mowers!), what tests you should run, and how to get rid of bacteria — including why a whole-house UV system might be worth it.

What Kind of Bacteria Are We Talking About?

Even if your water looks and tastes perfectly fine, bacteria might still be lurking. Here are some of the most common types that show up in wells:

Coliform bacteria — These are the standard “red flag” bacteria. They aren’t always harmful themselves, but they let you know something’s wrong — like contamination from surface water, sewage, rodent or insect infestation.
E. coli — A specific kind of coliform that can make you sick with stomach cramps, diarrhea, or worse.
Iron bacteria — Not dangerous to your health, but they leave rusty slime in your pipes and can clog things up.
Sulfur bacteria — These are the ones responsible for that “rotten egg” smell.
Pseudomonas — These bacteria thrive in moist environments and can cause infections, especially if your immune system is weakened. They also create slimy biofilms in plumbing.
Mycoplasma — Tiny bacteria that don’t have a cell wall. They’re more known for causing respiratory infections, but have been found in water systems on rare occasions.

How Do Bacteria Even Get Into a Well?

Good question — and the answer might surprise you. Your well is supposed to be sealed and protected, but even tiny gaps or damage to the well cap or casing can let bacteria, insects (and sometimes critters) sneak in. Earwig infestation in water wells has become a common problem across the US.

Here’s how:

A hole in the cap — Even a small hole in the top of your well cap can let in insects, spiders, earwigs, or dirt. Never hide your wellhead in a flower bed with bushes or mulch. It just invites insect infestation.

Missing or torn vent screen — Every well has a vent covered by a screen, so it can “breathe,” but with a rusted or torn vent screen, it’s basically an open door for bugs and even mice. This picture shows a well infested with earwigs. The earwig parts entered the household plumbing and plugged up the aerator on the faucet. I've seen this happen many times, and yes, it's gross. I had to shut the wells down, call a well company to repair them, sanitize them, and flush the wells. I sanitized the whole house and flushed the well for twenty-four hours. I then took a water sample to the lab for testing. To ensure the water was safe to drink again. We had to rebuild and sanitize all their water treatment equipment, as well. So this was not an inexpensive repair. Earwigs are known to carry coliform bacteria in their body.
Cracked well casing — The casing (the pipe that lines the well) can crack over time, letting surface water — and all the bacteria in it — seep down. Cracked well casings and well caps are frequently caused by lawn mowers bumping into the well and damaging it. Be extra careful when mowing around your well! The photo above shows earwigs in the kitchen aerator screen. I had a customer who hit his well while mowing the lawn, knocking a fist-sized hole in the side of the well casing and loosening the well cap (similar to the photo on the right here). When I took the well cap off, the well was filled solid with earwigs. That was the first time I found an infestation of earwigs in a well, and I found it first at the kitchen aerator screen. They complained about "Low water pressure."

Loose or damaged cap — If the well cap isn’t sealed properly, anything can get in — including leaves, rainwater, insects, and even mice.

Well Cap Inspection Video

That’s why it’s so important to check your wellhead regularly, keep the area around it clear, and make sure everything stays in good shape.

What Tests Should You Run?

If you haven’t tested your water in a while (or ever!), now’s the time. You can’t see bacteria, so testing is the only way to know what’s really in there.

When you call a lab or water professional, ask for:

✅ Total coliform test — This is the standard, and tells you if your water is at risk.
✅ E. coli test — Usually done at the same time as coliform, and is more specific.
✅ Heterotrophic plate count (HPC) — A general count of bacteria in your water.
✅ Specific tests — If you’re worried about something like Pseudomonas or Mycoplasma, ask the lab. These bacteria aren’t usually part of a standard test, but they can test for them if requested.

You should test your well water at least once a year, and after heavy rain, flooding, or if you’ve had work done on the well.

TapScore - Water Testing Lab

How Do You Get Rid of Bacteria?

So your water tested positive for bacteria — now what? Don’t panic! There are plenty of ways to fix it:

Shock chlorination — A one-time, high dose of chlorine to disinfect the well, followed by flushing the well for 24 hours. Perfect for emergencies, after well repairs, or a positive test for coliform bacteria. Shock Chlorination Quick Guide: Disinfecting Your Well Water

Continuous chlorination — A system that adds a low level of chlorine to your water all the time, keeping bacteria at bay, with a contact tank, followed by carbon filtration, water softening, and a reverse osmosis system for quality drinking water.

Ozone treatment — Another option that uses ozone gas instead of chlorine to kill bacteria.

Ozone Integration for Improved Water Filtration

UV disinfection — This one’s a favorite — it’s chemical-free, simple, and really effective.

Well Water Disinfection is Your Responsibility

Why UV Disinfection is a Game-Changer

A UV system uses ultraviolet light to kill bacteria, viruses, and even protozoa by messing up their DNA and neutralizing them. Here’s why so many well owners love it:

It treats all the water coming into your house if you install it at the point of entry (POE).
It doesn’t add anything to the water — no chemicals, no weird taste or smell.
It’s easy to maintain — just replace the UV bulb about once a year.

If you’re looking for a whole-house solution, a UV system at the point of entry (along with a pre-filter to keep the water clear) is an excellent way to keep your family — and your guests — safe from bacteria.

Viqua VH410-F20 UV Home Water Treatment System with Integrated Pre Filter System

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Keeping Your Well Water Clean and Safe

Here’s the bottom line: Your well water can be safe, clean, and delicious — but it’s up to you to keep it that way.

Here are a few easy steps to stay on top of things:

✅ Check your wellhead every few months — fix any holes, cracks, or missing screens.
✅ Be careful when mowing near your well to avoid damaging the cap or casing.
✅ Test your water at least once a year (more if anything changes).
✅ If bacteria show up, treat for it right away.
✅ Consider installing a whole-house UV disinfection system for peace of mind.

With regular care and the right treatment, you can enjoy worry-free water every day.

Your well is more than just a source of water — it’s a lifeline for you and your family. But because no one else is checking it for you, it’s your responsibility to keep it safe, clean, and reliable.

Bacteria can sneak in through the smallest cracks, holes, or missing screens, and you might not even know it’s there without testing. With regular maintenance, annual testing, and proven treatment methods like shock chlorination, chlorine injection, UV disinfection, or an ozone filtration system, you can keep your water healthy and safe.

Take the time to inspect your well twice a year, test your water, and consider investing in a whole-house treatment system. Your future self, family, and your guests will thank you every time they pour a fresh, clean glass of water.

Clean, safe water is possible — and it starts with you.

I wish you Good days and Good water!

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