Reasons for Chlorinating a Well

Spring is here and it is an odd number year, so, I will be planning on chlorinating my well if. Though normally thought of as a method to sanitize a well contaminated with coliform bacteria, there are so many benefits of chlorination that you might want to consider it a regular part of home maintenance. I do it to knock back the iron bacteria and keep my water tasting good.

Iron bacteria, while not a health hazard, are an incredibly common nuisance in water wells, and once you have it you will always have it. I have never come across a well that did not have it. Iron bacteria are a type of reducing bacteria that uses dissolved iron in the water as an energy source and leave slimy deposits of red iron hydrate as a by-product. Reducing bacteria can also thrive on sulfur and/or manganese. Elevated levels of iron, manganese and sulfate in groundwater are ideal for iron bacteria to grow. Iron bacteria are present in soil and surface water in this area of Virginia and in many other parts of the country and can be introduced into a well during drilling or repair. There are tests that can look for these micro-biologicals. After testing my well for reducing bacteria about 15 years ago, I just began regularly chlorinating the well to keep the bacteria in check.

I test my well water each year either during the annual water clinic the Prince William Extension Office hosts or every few years from a private company for all primary and secondary pollutants under the safe drinking water act. Iron bacteria is not part of those tests. The standard bacteria tests do not test for iron bacteria. I tested my well water for iron/reducing bacteria after noticing the typical symptoms (slime in the orange toilet tank and foam in my ATU tank). The test found a significant levels of reducing bacteria present. National Testing Laboratories sells mail in test for $85 including shipping if you want to test your well. That is what I used. The test cost $150 when I bought it back in the day.

Now, I just monitor the iron bacteria by checking my toilet tanks. The slime from iron bacteria builds up in toilet tanks and can be felt on the flapper. Also, the iron bacteria makes it look orange in the tank. I’ve noticed that the slime builds up at different rates in different bathrooms, I’ve not figured out why that is, maybe use. Anyone who has thoughts on the topic or a theory share it in the comments.

Iron bacteria once introduced into the well cannot be easily wiped out. Instead, it continues to get worse, ultimately binding up your pump and fouling the well. Iron bacteria can grow on pump intakes and screens openings, reducing the yield and efficiency of the well. In addition, the bacteria will make the water smell and taste vaguely unpleasant. Iron bacteria also cause foam to form in the ATU tank of some kinds of alternative septic systems. A much earlier symptom is the slime on the toilet tank flipper. 

It is common practice to regularly treat public supply wells to prevent biofilm buildup from reducing bacteria and mineral encrustation. Preventive maintenance is to chemically treat and flush the production well.  However, this has not been  practiced in private water wells in the past. Now, several state health departments and Canadian Provinces are recommending the regular chlorination of private wells to push back the iron bacteria.

From Penn State Extension: “As a water well ages, the rate at which water may be pumped tends to decrease.” Penn State attributes this decrease in performance of a well to incrustations and biofouling (with reducing bacteria) of well screens and rock fractures or borehole, saying: “In severe cases, the obstruction to flowing water can render the well useless. Major forms of incrustations can occur from build-up of calcium and magnesium salts, iron and manganese compounds, or plugging caused by slime producing iron bacteria or other similar organisms (biofouling).”

Private well owners typically try to treat the symptoms rather than the cause of the problem. Eliminating iron bacteria once a well is heavily infested can be difficult. However, treating the well is your best chance for a fix that will last a couple of years.  Iron bacteria cannot be eliminated by most common water filtration methods or water softeners. Iron bacteria will foul that equipment.  However, though it is difficult to eliminate, it is actually very easy to control – just oxidize the heck out of the well. This is accomplished by chlorine shocking of the well with adequate chlorine concentration and several hours of mixing accomplished by recirculation.  

Personally, I chlorinate my own well every few years or so to prevent the buildup of a biofilm in my well and plumbing system and maintain the aesthetic quality of my water. I drain and flush the hot water heater annually to protect it from biofilm and mineral buildup and keep the temperature above 145 degrees to prevent the growth of reducing bacteria.  If you have treatment equipment like a water softener, you might want to consider chlorinating your well annually and treating your media to prevent a bio mat from forming in the media tanks.

There are so many things that regular chlorination will solve or prevent that you might want to consider a regular part of home maintenance. The first couple of times I chlorinated my well, so much reddish-brown mucus like gunk came out that after recirculating the well for three hours I ran the water off for three hours. Then upped the chlorine concentration and recirculated it again before I pulled the water into the house and sealed the well. 

These days when I chlorinate, I tend to reddish brown tinged water after a few hours of recirculating the chlorine water mixture.  At that point, I seal up the well and don't use any water. Once the well has sat for 12-14 hours with the chlorine mixture, I run the hoses to a non-sensitive area for at least an additional 14 hours till it runs clear, and the chlorine level drops towards non-detect. Though it can take an additional week to clear a well of every trace of chlorine under normal use. 

When I replaced my pump and pressure tank in 2020, I used a heck of a lot of chlorine in the powder form (a couple of cups or more of high-test calcium hypochlorite) to sanitize the well. I probably should have replaced the black pipe which as you can see below was coated (likely inside and out) with iron bacteria slime. Unfortunately, I did not think of it in time.

Jason pulling the pump. Note the orange look of the black pipe

The entire pipe should be black as is the top section

When you replace the pump, you are to let it sit for 24 hours and I was not able to mix the chlorine adequately.  Mixing the chlorine is accomplished by recirculating the water for a couple of hours which uses the pump. The result was that after running the hoses for about 12 hours the water appeared near clear but still had a measurable but low level of chlorine. So, I need to keep diluting the chlorine solution by running the hoses to rid my well.

I ended up running the hoses for around days. During this time, I was able to use water in the house (just don’t do laundry or cook with it). Pockets of discolored water kept appearing for days. Though I cannot run my well dry-it recharges faster than I can pump, I only ran the hoses only about 6-12 hours a day whenever a pop of rust colored water reappeared.  It would still be almost 5 days before all traces of the chlorine and rust colored water was flushed from the system, and the water remained consistently clear, but we were good with filtered water for coffee until then.

During well chlorination, free chlorine is introduced into the well water; there is no one standard for how much chlorine and methods to accomplish this disinfection so your experience will vary from mine, but adequate amounts of chlorine will flush the mineral build up, iron in solution in the water and reducing bacteria out of the well.  The more iron you have, the more iron bacteria the higher concentration of chlorine you will need.  Based on a survey of emergency disinfection protocols performed by Dr. Kelsey J. Pieper et. al and published earlier this year “Improving state-level emergency well disinfection strategies in the United States”, the scientists found that there were many differences in the protocols for chlorine disinfection. 

Most of the protocols for chlorination recommend that high chlorine doses be introduced into the well, circulated throughout the system, and stagnated for several hours up to 24 hours. The scientists point out that it is important that residual chlorine be measured at the faucet before you stagnate the system. This is because if too much of the chlorine solution reacts with iron or organic substances present in the well the concentration of chlorine and thus its effectiveness is reduced. This is key because when iron or iron bacteria or other reducing bacteria react with chlorine (are oxidized) and are flushed out of the well into the water. If there is enough chlorine, the well will shed brown water and be disinfected. 

Five days was the longest it has ever taken to flush all the gunk out of the well which I attribute to not mixing the chlorine adequately and using a heck of a lot of chlorine. My husband was briefly worried that I had somehow ruined the well or water supply because it seemed to go on and on. No worries, by the next week the water was clear and tasty. It takes patience to clear a well. Your well will clear, also.  However, the next time I change my pump, I will also replace the pipe to remove that excess iron bacteria source.