How to disinfect your well

If you’ve reached this page, you probably have a bacteriological sample that came back positive. This indicates that coliform (or e. coli) bacteria are in your water.

Coliform bacteria indicate that something is getting into your water lines. That may be from the well, or from the pipelines. It could even be from stagnant water (if the water hasn’t been used in a while). This generally indicates that there may be stuff in your water that you can get sick from.

E. Coli, sometimes known as fecal coliform, is the presence of harmful bacteria in your water. This bacteria can make you very ill.

Regardless of what kind of positive sample you have, you’ll want to treat your water. You can use this procedure for a one-time “shock chlorination” to disinfect the system. This often resolves the problem.

Before you begin

If your house has been empty for a while, the water may be stagnant. There may be bacteria inside the plumbing. You should flush the lines really well (for several hours) before taking a sample.

You may have a leak in a pipeline. If nothing else works, you might check for wet spots in your yard that can indicate a leak. Leaks can suck dirt into the pipelines – this can cause bacteria to show up in water tests.

Cut the power to the well pump. Right next to the pump controls – which are usually near the big blue (or brown) pressure tank – you should see a gray box with a lever. This is a main power disconnect switch for your well pump. Switch the lever to the OFF position (usually down). If you’re using a smart pump (or variable-frequency drive), turn the drive off and disconnect power.

Take care when the well is open. Be careful not to drop anything down the well, such as bolts or wrenches.* If you’re curious, you can shine a flashlight down the well. You’ll see the outer wall, which is usually steel casing. In the middle, you’ll see drop pipe that carries the water from your pump to your house. You’ll also see the submersible wire – this is watertight electrical wire that connects power to your pump.

Step 1: Gather your materials

You will need:

  • 2 adjustable wrenches
  • Disinfectant (2 gallons of bleach, or alternative)
  • 2 gallons of water
  • 8 hours for the disinfectant to work (or overnight)
  • 48 hours before collecting a second sample

For your disinfectant, you have a couple of options.

Option 1: Household bleach – Restaurants use diluted bleach water to clean and disinfect tables. Many public water systems use highly concentrated bleach as a disinfectant. You can use two gallons of regular household bleach, just like you find at the grocery store.

Option 2: A well disinfection kit – We sell these in the office (please call for availability). It’s a small box that contains disinfection tablets and instructions.

Step 2: Remove your well cap

You’ll need to take the cap off your well in order to add the disinfectant.

Your well is a piece of steel pipe sticking up out of the ground. It usually has a green, red, or metal cap on top, held in place by several bolts.

Start by using the two wrenches to remove the bolts. Use one wrench to hold the top of the bolt, and the second wrench to unscrew the nut underneath.

Tip: Once the bolt is out, reattach the nut so it doesn’t get lost.

Once the bolts are out, lift the well cap up. It should lift easily. There is a thin gasket that helps create a seal – don’t lose it. Set the well cap to the side.

You should see a bunch of electrical wires going down the well. That’s how your pump gets electricity to run. You may need to push those wires to the side so you don’t pour bleach on them.

Note: The wire down the well is designed to be waterproof. However, the connection to the wires that lead to your house may not be fully watertight. Avoid pouring liquids on the wires.

Step 3: Add your disinfectant

Pour both gallons of bleach down the well. Avoid pouring it on the electrical wires.

Next, pour both gallons of water down the well. This helps wash the bleach off the sides of the well and the drop pipe.

If you’re using tablets, just drop them down the well. They will dissolve in the water.

Step 4: Put the well cap back on

Align the gasket with the top of the well. Set the well cap back on the seal, and make sure the bolt-holes line up.

Reattach and tighten the bolts with your wrenches.

Step 5: Pump disinfectant throughout the house

Turn on each faucet in the house, and let the water run just long enough to smell chlorine.

Shut the water off, and let it set for 8 hours (or overnight).

Step 6: Flush the lines

After the disinfectant has done its work, you’ll need to flush all the disinfectant out of the lines. Turn on all the faucets in the house, and let the water run until you can’t smell chlorine anymore.

This can take anywhere from a few minutes to several hours.

Step 7: Resample

Idaho regulations say that you have to wait at least 48 hours after you disinfect the system before you can collect another sample.

Once you’ve waited 48 hours, you can call us to come collect a repeat sample. Or, if you’re familiar with water testing, you can collect your own sample for testing.


Congratulations! You’ve just disinfected and flushed your well. If you have any questions, you are welcome to send us an email, or give us a call.

*If you drop something down the well, you’ll never get it back. Most of the time, it won’t hurt anything lying at the bottom of the well. The pump isn’t usually powerful enough to lift metal objects. However, if you ever need to drill your well deeper, any metal objects in the well can severely damage a drill bit.