How to Disinfect your Well

If you recently had a positive/present result on a coliform test, this page has Do-It-Yourself instructions for shock-disinfecting your well.

First of all, don’t panic! Coliform bacteria are an indicator that something is getting into the water. That might be a surge in water in the springtime (especially if you’re near a canal or river), or stagnant water if the house has been setting empty for a while.

If you have a positive result on the E. Coli test, you should boil your water before you drink it. E. Coli can make you sick. It’s an indicator that human or animal waste is getting into your water.

With that said, if you’re selling your house, the lender will probably require the coliform test to come back clean.

Step 1: Gather your tools

You will need:

  • 2 adjustable wrenches
  • 1 gallon of household bleach (Sodium Hypochlorite)
  • 1 gallon of water
  • A funnel (optional)
  • Plastic storage container (optional)
  • WD-40 or penetrating oil (optional)
  • Safety gear – coveralls and eye goggles
  • Bottled water for drinking

Step 2: Plan your work

You’ll want to let the chlorine set in the plumbing for at least 8 hours. You can disinfect in the morning and let it set all day while everyone is at work/school. Or you can do the disinfection in the evening and let it set overnight.

While the system is disinfecting, it’s OK to use some water from the faucet, but avoid heavy use like showers or irrigation. The water should be OK to drink, but I would keep bottled water on hand for drinking.

You’ll be working with bleach, which can damage your clothes. I suggest wearing old clothes, like the kind you’d wear for painting. If you have coveralls, those are a great option.

Please wear eye protection, in case there’s a splash. You don’t want to get bleach in your eyes. (If you do get bleach in your eyes, flush your eyes out with water for several minutes and seek medical attention.)

Step 3: Open your well

Your well is usually a piece of steel pipe sticking up out of the ground. Some wells may be in old cisterns or well pits underground.

Opening a well cap

In most cases, your well is sealed with a well cap, which is secured by several bolts. Use your adjustable wrenches to remove the bolts, then lift the cap off. A plastic storage container is a good place to put the bolts.

Note: If the bolts are stuck or rusty, you can spray them with a little penetrating oil or WD-40. Wait a few moments, then try again.

Opening a well seal

If you have an older well, especially in a well pit, your well may be secured by a well seal. These usually look like a flat piece of metal on top of the well, with a pipe sticking out of the top. You won’t be able to get the seal out, because the weight of the pump is hanging on that piece of pipe.

Fortunately, most well seals have a little plug that you can take out. It might be red plastic, or it might be a metal plug with a square top. Use your adjustable wrench to turn the plug counter-clockwise until it comes out.

Put a funnel into the opening where the plug was.

Note: Be careful with the open well. If you drop a bolt or a tool down the well, it’s gone for good. If you’re curious, you can shine a light down the well to see what’s down there. A hand-mirror to reflect sunlight works better than a flashlight!

Step 4: Add the disinfectant

Carefully pour 1 gallon of household bleach down the well. If your well uses a well seal, use a funnel to pour the chlorine through the port without spilling.

After you’ve poured the bleach down the well, follow up by pouring 1 gallon of water down. This will rinse the bleach off of any equipment that’s above water, to help prevent corrosion.

Household bleach is the same chemical that many public water systems use to keep their water safe to drink. Public water systems use a higher concentration that’s not available in stores. Although it’s not a perfect solution, bleach is a much safer solution than bacteria in the water.

Note: Some people like to use 2 gallons of bleach. For most situations it isn’t necessary, but it won’t hurt. Some practical reasons might be for a repeat disinfection, a poorly-sealed well, or a well with a larger diameter (10″ or greater).

Step 5: Seal the well back up

Collect all the bolts and have them ready. Put the well cap back on, and make sure the gasket is in place. Replace the bolts and tighten them with your wrenches. After the bolts are secure, go back around to each one and make sure they’re snug.

If you have a well seal, just replace the plug and screw it back in clockwise with the wrench.

Note: You don’t need to worry too much about surface contaminants getting into your well water during this process. Obviously, don’t dump a bunch of chemicals or objects down the well. If a little dirt gets into the well, it will get flushed out later in the process.

Step 6: Pump the chlorine into the household plumbing

Turn each faucet on cold for a few moments, just until you smell the chlorine. Then turn off the water and let it set for at least 8 hours.

Flushing toilets or light cleaning is fine. It should be OK to drink the water, even with the chlorine, but I would have some bottled water on hand for drinking.

Note: You’ll probably be very aware of how much you depend on water when you can’t use it!

Step 7: Flush the chlorine out

After the bleach has done its work for 8 hours, you’ll need to flush it out of the plumbing.

Just turn all the faucets full-blast on cold, and let them run until you can’t smell the chlorine anymore. This can take anywhere from 10 minutes to a couple hours, depending on your plumbing and the size of your pump.

Step 8: Wait 48 hours

We have to wait 48 hours after disinfection before we can come back and take a second coliform test.

Most of the time, this kind of shock-chlorination of a well will knock out any bacteria that might be in the well and plumbing, and you’ll be back to normal.

Step 9: Collect a repeat sample

The whole point of this process is to disinfect your well, and then prove that the water is potable (POTE-uh-bull) – meaning safe to drink.

I can help you get your repeat sample, or you can do it yourself. This is usually up to the lender – most lenders want a disinterested third party doing the sampling. I don’t have any stake in the sale, so I have no reason to influence the results one way or the other.

Optionally, you can work with the lab to take a test sample before an official one, just to be sure the disinfection worked. That might be more cost-effective than paying for drive time, especially if you end up having to chlorinate a second time. I can always come out and take an official sample once you know the disinfection worked.

Step 10: The results

Most of the time, a single disinfection is enough to clear up the bacteria in a well and get a clean result.

Occasionally, though, it doesn’t. If some kind of material is getting into your well, like surface water or soil, it can cause the repeat sample to come back positive.

If your second coliform sample comes back positive, you can try disinfecting/flushing/resampling again. If a third coliform test comes back positive, then you’ll probably need a permanent treatment system for your water.

One way to treat your water is using an Ultraviolet (UV) Disinfection system. Basically, it runs the water past ultraviolet light, which deactivates the bacteria. Another solution is a Reverse Osmosis (RO) system, which is a fancy kind of filter.

I don’t install or replace equipment, but I can offer recommendations.

What happened? Why did I have bacteria in my well water?

As mentioned above, the usual causes are either the house sat empty for too long without running the water, or there’s a change in the flow of groundwater that’s affecting your well.

One example might be if you live near a canal. The canal system distributes irrigation water through a series of ditches and canals throughout the area. These canals aren’t lined or sealed, they’re just open to the dirt – which means that some of the water soaks down into the ground. That canal water can work its way into your well, and trickle down into the well water.

If you have an older well, it may be that the surface seal isn’t secure. Wells should have a surface seal to prevent rainwater from running down into your well. (Rainwater picks up all kinds of gunk on the surface, from pesticides to petrochemicals to fertilizers.) Most modern wells have a surface seal to prevent this kind of contamination. A surface seal should be 38′ deep, and it uses a special kind of clay called bentonite that swells up when it gets wet. Older wells might not have been required to meet those standards, but were grandfathered in.

Another possibility could be the location of a septic tank or drainfield. Idaho has requirements for the distance between a septic system and the water source of 100 feet. But not all properties were constructed with these standards in mind.

There may be a few other sources of bacteria in your water, but the vast majority of the time it’ll be one of these.

I hope you found this information helpful! If you have any questions or concerns, please get in touch!