Your Well Tested Positive for Coliform. Now What?

By Trent, owner of Palouse Water Pros · Moscow, Idaho · September 2026

A lab report that says "total coliform: present" is something plenty of well owners around Moscow, Troy, Deary, Genesee, and the rest of Latah County run into. It often lands during a home sale or after a wet spring. Here's what the result means, what to do today, how to find where bacteria are getting in, why shock chlorination often doesn't hold, and when a well needs continuous disinfection.

Total coliform vs. E. coli: two very different results

• Total coliform is a broad group of bacteria found in soil, surface water, plants, and animal guts. Most don't make people sick on their own. They are an indicator: something is letting surface water or soil into a supply that should be sealed off. The EPA's health goal for total coliform in drinking water is zero, because a path that lets in harmless bacteria can let in harmful ones too.
• E. coli (or "fecal coliform" on some reports) is a subset that lives in human and animal intestines. The CDC says a positive E. coli result likely means feces — and the germs that come with it — have gotten into the well. This is the result that needs you to change what you drink today.

What to do right now

1. Don't panic — read the report. Total coliform without E. coli is a warning light, not an emergency.
2. If E. coli is present, stop drinking the water untreated. Use bottled water, or boil it. CDC guidance is a rolling boil for one minute (three minutes above 6,500 feet), and the treated water should be used for drinking, baby formula, brushing teeth, washing produce, and ice.
3. Know when boiling is the wrong answer. Boiling kills germs but concentrates nitrate. If your well is close to a septic system or livestock, have nitrate tested too — Idaho Health and Welfare recommends private wells be tested for bacteria and nitrate at least once a year — and use bottled water until you know.
4. Confirm the result. A dirty faucet or sloppy sample can cause a positive. A second, properly collected sample (see below) tells you which you have.
5. Call your local health district if E. coli shows up. Latah County is served by Public Health – Idaho North Central District, which publishes well disinfection instructions for private wells.

Where the bacteria are getting in

A well that is properly sealed from the surface normally tests free of coliform. When it shows up, extension and health department guidance points to the same short list:

• A missing, loose, or damaged well cap that lets in insects, small animals, or runoff.
• Cracks or holes in the upper casing, or a failed grout seal that lets surface water run down the outside of the casing.
• Grading that drains toward the wellhead, so rain and snowmelt pond around the casing.
• Septic systems or animal waste too close to the well, or a failing drainfield.
• Flooding and heavy rain — sometimes a one-time event.
• Recent work on the system — a pump, pressure tank, or plumbing repair that wasn't disinfected afterward.

On the Palouse, what I typically find is older wells with shallow casings and caps that have been bumped, buried, or patched over the years — and positives that show up after wet springs, when the ground is saturated and surface water has more ways in.

Inspecting the wellhead

Before anyone pours bleach down the well, go look at it. The casing should stick up above grade, not sit in a pit or a flower bed. The cap should be tight and sealed, with no gaps where the wiring enters. The ground should slope away. Look for cracks, rust-through, or a gap between casing and soil, and note what's nearby — septic tank, drainfield, animal pens, low spots that hold water. Casing or grout seal repairs are a job for a licensed well driller; a new cap or regrading is usually simpler.

Shock chlorination: what it is and why it often doesn't hold

Shock chlorination means putting a high dose of chlorine into the well and the plumbing, letting it sit long enough to kill bacteria in the well and water system, then flushing it out. Follow a published procedure rather than improvising — good ones come from Oregon State University's Well Water Program, Penn State Extension, and the local health district.

The general outline looks like this:

1. Fix the wellhead problem first, if you found one. Shocking a well with an open cap just resets the clock.
2. Bypass treatment equipment. I put softeners, carbon filters, and reverse osmosis units on bypass before a shock — strong chlorine is hard on resin, loads up carbon, and damages RO membranes.
3. Add plain, unscented household bleach in the amount the instructions call for based on the water in your well. Extension guidance generally targets roughly 50 to 200 parts per million of chlorine.
4. Circulate chlorinated water back into the well, then run each faucet until you smell chlorine.
5. Let it sit. Published instructions range from several hours to overnight or longer.
6. Flush it out somewhere other than the septic system — the chlorine will kill the bacteria the septic system depends on — and away from gardens, lawns, and streams.

Here's the part that isn't always explained: shock chlorination is a one-time kill with no protection left once the chlorine is gone. If the path is still open, bacteria come back. Penn State Extension found that only about 15 percent of wells with coliform were cured by shock chlorination plus a sanitary well cap — mostly wells with low bacteria counts to begin with. For the rest, the fix is either a well repair or continuous disinfection.

When to retest

Don't sample while there's still chlorine in the water — it will give you a false negative. Once the chlorine smell is gone, retest. Penn State suggests roughly 10 to 14 days after the shock, and if that comes back clean, another test two to three months later. Two clean results suggest a one-time event; a positive on either means the source is still there. After that, test yearly and after any flood, well work, or change in taste or clarity.

When continuous disinfection makes sense

If coliform keeps coming back after the wellhead is fixed and the well is shocked, continuous disinfection is the next step. Both common approaches have to be designed around the rest of your water — especially on Palouse wells with iron, manganese, and hardness.

Chlorination with contact time

A small feed pump adds chlorine continuously, and the water needs time in contact with it — a general rule is about 30 minutes — which usually means a retention tank. Chlorine also oxidizes dissolved iron and manganese into particles, which changes the whole treatment train: those particles have to be filtered out, and any leftover chlorine has to be removed with carbon before it reaches a softener or RO membrane, because chlorine breaks down softener resin over time. Done in the wrong order, it fouls everything downstream. See iron and manganese removal for how that side of it works.

Ultraviolet (UV)

UV adds nothing to the water, which is why people like it. But it only works on water the light can pass through. Iron, manganese, and hardness coat the lamp's quartz sleeve, and cloudy water shields bacteria from the light. Penn State Extension also advises against UV where total coliform counts exceed about 1,000 per 100 mL or fecal coliform exceeds about 100. On a typical Palouse well, that means UV goes last, after iron and manganese removal and a softener — and it only protects water at the moment it passes through, with no residual in the pipes.

This is why any positive coliform history changes the treatment design. A UV unit bolted onto hard, iron-heavy water, or a softener fed chlorinated water, will fail. Disinfection, iron and manganese removal, and softening have to be planned together, in the right order.

Quick decision table

Buying a home where the seller "shocked it and it came back clean"? Ask whether the cause was found and whether there's a history of positives — more in buying a home with a well in Latah County. How to read a well water test covers the rest of the report, and the Palouse well water guide explains how iron, manganese, and hardness fit together. Not sure where to start? Take the 2-minute water quiz, see water testing, check the FAQ, or get in touch.