Monday, June 17, 2013

What to Do About Discolored Well Water After Heavy Rain

 In Virginia where I volunteer with VAMWON as part of the rural household water quality program run by Virginia Tech, it is estimated that 34% of the population obtains their drinking water from private groundwater wells, more than twice the national average. The most frequent call I get is for well water that turns suddenly brownish or discolored after a heavy rain. If you own a well, then the responsibility for ensuring that your family and friends are drinking safe water rests with you. While you cannot taste bacterial contamination from human and animal waste, nor nitrate/ nitrite contamination, brownish water after a heavy rain storm is an indication that you likely have one of two contamination problems with your well. Brownish or “dirty” water always associated with rain, is likely the fast infiltration of rainwater from the surface, but could also be caused by a nearby failing septic system that is overwhelmed by the rain.

After rust in the household fixtures there are five causes for well water to be discolored or brownish: surface infiltration, well collapsing or water level dropping, iron – iron bacteria and/or manganese in the water, pump system or well casing rusting and worst of all contamination from a nearby septic system. The likely causes of dirty looking water after heavy rains is surface infiltration, but contamination from a failing septic system is also possible and should be investigated. A bacterial test will confirm what your problem is. I would recommend taking a water sample to a local certified laboratory, and have the water tested for coliform bacteria and if positive e-coli and fecal coliform bacteria. However, there might not be a laboratory near your home in which case you could consider a home test. If your water is discolored after a heavy rains, take your sample while the water is discolored. If this is a local infiltration problem, the water will clear after several hours and could be bacteria free (but the bacteria could have infected the plumbing system and if you have it the water treatment system in the house. Event caused coliform bacteria do not always show up in every sample. They can be sporadic and sometimes seasonal when they occur in a water supply. Be concerned but do not panic if coliform bacteria are detected.

Coliform bacteria are commonly found in soil, on vegetation, and in surface water. Coliform bacteria also live in the intestines of warm-blooded animals and humans. Some coliform bacteria strains can survive in soil and water for long periods of time. Most coliform bacteria will not cause illness. However, because coliform bacteria are associated with sewage or surface waters, the presence of coliform bacteria in drinking water may indicate that other disease-causing organisms (pathogens) may be present in the water and the water supply is not sanitary. There are three different groups of coliform bacteria; total coliform, fecal coliform and Escherichia coli (E. coli) each has a different level of risk. Coliform bacteria do not occur naturally in most aquifers, but are mostly harmless. Fractured or creviced bedrock aquifers in Karst terrain that are close to the surface are the possible exception. Testing for e. coli and fecal coliform and nitrogen will differentiate the harmless coliform from contamination that is from surface infiltration of water from bacteria contamination that might impact your health and is from sewage or animal feces.

If your well tests positive for coliform bacteria and negative for fecal coliform and E. coli bacteria, you have an infiltration problem that may be persistent, but can be addressed and dealt with by the suggestions below. If your well tests positive for fecal coliform or E. coli your water is not safe to drink. Boiling the water will concentrate nitrogen that is commonly present with fecal contamination and can be lethal to infants. Call the Health Department. You are drinking water impacted from a septic system and the water is unsafe especially for children and the elderly. To make this drinking water safe the septic system must be repaired and/or a new well drilled. Public water systems routinely recycle water, but they have entire water treatment plants and constant water testing to address the problem.
From Penn State Cooperative Extension

Occasional impact from surface infiltration is a much more pedestrian problem. Bacteria washed into the ground by rainfall or snowmelt are usually filtered out as water seeps through the soil, so properly constructed water wells do not typically harbor Coliform bacteria. Surface infiltration of water is due to impaired pump, casing or well seal system. Often what fails in the typical 6 inch diameter pipe well with immersion pump is the grouting. Look at your well. A properly build and functioning well should not be impacted by rain, but wells get old and systems deteriorate. Items to look for and fix are:

  • A missing or damaged well cap would allow rain to enter the well. Make sure to check seals around wires, pipes, and where the cap meets the casing may be cracked, letting in contaminants. A new sanitary sealing well cap can be purchased on-line or from a well driller. 
  • Contaminant may be seeping through the well casing. Cracks or holes in the well casing allow water that has not been filtered through the soil to enter the well. This seepage is common in the wells made of concrete, clay tile, or brick. This can also happen to a steel pipe well that was hit by a piece of equipment such as a car, snow blower, lawn tractor or mower or that has rusted. A well driller can often install a sleeve to line the well casing. Wells installed in Virginia after 1992 (or in Prince William County since 1980) should have at least 40 feet of steel casing to protect the well from collapse and infiltration of shallow groundwater(less than 20-40 feet deep that may contain coliform bacteria. 
  • Contaminants can enter the well by seeping along the outside of the well casing. Many older wells were not sealed with grout when they were constructed or the grouting has failed. Check the grouting carefully especially if water seems different after severe rains. Also, make sure that rainfall does not puddle against the well, but drains away. Repacking the soil might help.
  • Well flooding is a common problem for wellheads located below the ground in frost pits that frequently flood during wet weather. Wells that are located in pits are commonly impacted by rain water pooling in the pit and entering the well. This can be corrected by having a well driller install an extension on the well pipe to raise the top, or create a drain for the pit. 

Hopefully, one of the simple items above will turn out to be your problem and can be quickly and easily resolved without need to drill a new well or install disinfection equipment. To use your well that has been impacted by coliform bacteria from storm related infiltration you need to chlorine shock your well after each rainfall until the problem is solved by one of the above suggestions, or you drill a new well. Yeah, I know what that costs, so temporary fixes are often necessary. Look, this is not the best idea, but it will disinfect your well each time it is impacted by surface infiltration. Water that looks dirty after a storm is a gross infiltration problem- there is a big leak somewhere, not the invisible coliform problem that is more easily addressed by an in-house disinfection system using either UV light or chlorine. Coliform bacteria are associated with warm-blooded animals, so they are normally found in surface water and in shallow groundwater (less than 20-40 feet deep). Most bacteria (with the exception of fecal and e-coli) are not harmful to humans, but are used as indicators of the safety (sanitary condition of the water.

The instructions below are standard procedure from various state department of health and the US EPA:

Run your hoses (away from your septic system and down slope from your well) to clear the well. Run it for an hour or three and see if it runs clear. If not let it rest for 6-12 hours and run the hoses again. Several cycles should clear the well. What we are doing is pumping out any infiltration within the well area and letting the groundwater carry any contamination away from your well. In all likelihood the well will clear of obvious discoloration. Then disinfect your well. This is an emergency procedure that will kill any bacteria for 7 to 10 days. After 7 to 10 days you need to test your well for bacteria to make sure that it is safe.

Determine what type of well you have and how to pour the bleach into the well. Some wells have a sanitary seal which must be unbolted. Some well caps have an air vent or a plug that can be removed. On bored or dug well, the entire cover can simply be lifted off to provide a space for pouring the bleach into the well.

Take one gallon of bleach of non-scented household liquid bleach and carefully pour the bleach down into the well casing using a funnel if necessary. Wear rubber gloves, old clothes and protective glasses to protect you from the inevitable splashes. After the bleach has been added, run water from an outside hose into the well casing until you smell chlorine coming from the hose. You can also use chlorine test strips for swimming pools to test for chlorine, but usually, the smell method works. Then turn off the outside hose. Now go into the house and one bathroom and sink at a time, turn on all cold water faucets, until the chlorine odor is detected in each faucet, then shut it off and move on to the next sink, or bathroom (if you have an automatic ice maker and water in your refrigerator dump the ice and run the water on the refrigerator also. If you have a water treatment system, switch it to bypass before turning on the indoor faucets. Once the inside system has been done, go back to the outside spigots and run the hoses until you smell chlorine coming out.

Wait 8 to 24 hours before turning the faucets back on. It is important not to drink, cook, bathe or wash with this water during the time period it contains high amounts of chlorine whose by products are a carcinogen. After at least 8 hours, run the water into a safe area where it will not kill your lawn, your trees or plants pollute lakes, streams or septic tanks. Run the water until there is no longer a chlorine odor. Turn the water off. The system should now be disinfected, and you can now use the water for 7 to 10 days when the effects of the disinfections wear off at that time test your well to make sure it is still safe to use. It is important not to run all the treated water into your septic system because the chlorine will kill all the bacteria in the septic system and the system will not function. This is the one time I might recommend adding bacteria to the septic system to account for any kill off that might occur from the minor amounts of chlorine treated water that was run through the plumbing system.

Final note. In the March 2012 Good Housekeeping magazine they evaluated home water testing kits. To test the home contaminant-detection kits, the Good Housekeeping Research Institute worked with the Water Sciences Laboratory at the University of Nebraska at Lincoln. Lab researchers spiked water samples with measured concentrations of contaminants the kits claimed to be able to detect, including two herbicides, nitrate, copper, lead, and bacteria. Then after following the kit's instructions, evaluated its performance at detecting the known contaminants. They found the PurTest kit to be the most accurate and easiest to use, but the second ranked First Alert test kit and the was also good and significantly cheaper. Make sure you test for both coliform bacteria and fecal coliform bacteria.


  1. could it be something other than the well

  2. Yes.Check out another post

  3. I’m so thankful to have found your blog posts!! I just wish it was sooner. We have had problems on and off for years with our laundry getting discolored with possible tiny rust spots and lately after days of rain the whites come out dingy.

    We have tried so many things: new water heater, new washer, and replaced the two huge tanks to our water care filtration system which I think is basically for the water softener. And after last night I can add ER visit including a EKG to the list of water related expenses­čśť because I accidentally got quite a bit of rust remover on my fingers that had hydrofluoric acid in it. Most people would probably be fine with the lower concentration level but my fingers really started to react possibly from my autoimmune diseases that already cause issues to my finger tips. I was hoping to determine with the rust remover which type of stains might be rust, or bacteria or something else but all of them got better or immediately disappeared probably because of the hydrofluoric acid. So my hypothesis is that hydrofluoric acid also removes other causes of stains other than rust. I had a few different all over dingy color catchers that I washed in my new washing machine. Some by themselves, done with and without detergent and some with white shirts. Then I had a color catcher that sat in a bowl of cold water and after a while developed 3 different spots that become yellow. I tried the bowl of cold water test because it is not only my washing machine causing problems. I have soaked a dirty item of clothing overnight before and it sometimes pops up with tiny looking rust spots. The rust remover immediately took out the 3 yellow spots but that color catcher was still wet. The dingy color catcher was completely dry but it looked significantly whiter where I put the Rust Remover The rust remover even helped remove some pink bacteria in my shower.

    My husband has ordered an RO filter that he is going to put in our laundry room and probably our kitchen sink. He is really hoping (for me at least) that this will prevent any more laundry issues that have caused so much stress.

    But since the all over dingyness started after lots of rain I really would like to get our water tested after reading your information!!! It could be our septic but we also have had some quite a bit of sand in one of our small filters by our water softener over an unknown amount of time (it is possible that the water system maintainence guy didn’t replace the filter for a long time) and our toilet bowls have some sand too so we could have a well problem. My husbands view is to put the money into the RO filter instead of water testing but now I really think we need to investigate the cause first.

    Our water care company even came out to retest our water right after the rain and dingyness started and they said it was fine. Just a little high PH from all the new water softener stuff. I do need to ask them what else they tested for and for them to help me understand how they are filtering out the iron/manganese to determine if they are doing it the best way. I would really like to send in my water in for evaluation but I haven’t found a kit that includes all the bacteria you mentioned and the dissolved solids. Do you have one specifically you recommend? When I looked for the PurTest ones you mentioned all I can find is the super cheap ones on Amazon that maybe test for 10 things.

    Thanks so much for all your help!



    1. Try National Testing Laboratory.

  4. I know this article is older but some advice and wisdom stand the test of time. Relative newbies to living with a well - been a year and half now - we've never had any issues but after EXTREME rain (several inches in one day) we find ourselves with yellow-tinged water. It has to be rain related because it was fine until a day after the deluge. I'm headin out to get a bacteria test kit at the hardware store and if it comes back positive, we'll flush the well as you recommend, hopefully till it's clear again. I plan to retest and if still positive I'll follow your steps to chlorinate. I am guessing that doing this ourselves can save us alot of money and I appreciate that. Our well cap is probably not high enough but there was no standing water around the top of the well so it must be infiltration. Our well sits about 50 ft across from and about 60-80 feet above a creek that is normally pretty calm but with the storms its a brown muddy river. Am thinking that has probably infiltrated the aquifer. Anyway, sorry to ramble, but I wanted to thank you for such an easy to understand article that offer good country advice. And yes, if it continues we'll have the water lab tested and then contact the well guy. Fingers crossed it corrects as quickly as it came! Thanks again. Elizabeth (western Oregon, Lane County)

    1. Elizabeth, I just experienced a shocking brown water well tonight 1/12/20. I am sure hoping it is just infiltration as spoken about, I have never had an issue with this well in the 15 yrs we;ve lived here. It has rained HEAVY the last 24-18 hrs though. Hoping this is an easy to solve issue.

    2. My well is giving me brown like red water. I never experienced this before and it happened just after heavy rain that took about 2 weeks.

      Could that be the reason of heavy rain?

      Please help.

      South Africa

  5. Our well water is green..Help! What do we do???

    1. This comment has been removed by the author.

    2. The water flowing out of the tap is green colored? Wow. Is it Toxic Avenger green, St. Patty's day beer green, or some other type green? The first thing you do is get a comprehensive analysis. Go to
      buy the standard package and follow instructions. Sample ahead of any treatment equipment you may have and send your test results to Let's see what you have. In the meantime, don't drink it.

  6. I have a question- after all this rain this weekend oit water turned yellow the day after. It fits your description. Do we have to add bleach to our well if it clears up on its own? Also, do we use bleach or chorine? I'm kind of confused on that. Thanks in advance!

  7. After rust in the household fixtures there are five causes for well water to be discolored or brownish: surface infiltration, well collapsing or water level dropping, iron – iron bacteria and/or manganese in the water, pump system or well casing rusting and worst of all contamination from a nearby septic system. The likely causes of dirty looking water after heavy rains is surface infiltration, but contamination from a failing septic system is also possible and should be investigated. A bacterial test will confirm what your problem is. I would recommend taking a water sample to a local certified laboratory, and have the water tested for coliform bacteria and if positive e-coli and fecal coliform bacteria.
    Most likely it will clear up on its own. However, the advise to chlorinate the well is not to change the color of the water, but to sanitize the well. The yellow water after a rain is an indication that water from the surface is getting into the well.

  8. After a snow melt my well water is cloudy. No color change. What could be wrong