Well depths and types (C) Carson Dunlop AssociatesFlooded or Bad Well Disinfection Procedure

  • WELL DISINFECTION PROCEDURE, POST FLOODING - CONTENTS: How to restore potability to a water well that has been flooded or resists usual well shocking steps, how to more effectively shock or sanitize a water well that is difficult dut to area flooding, casing contaminants or persistent aquifer contamination.
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Well disinfection, shocking, & restoration procedures to provide potable,sanitary water for difficult cases:

This article describes procedures recommended by the BC Canada Ministry of Heatlh & other expert sources to improve the chances of a successful well disinfection following area flooding or when the well casing has been contaminated with a biofilm or mineral deposits. We include the original experts' advice and add field experience comments as well as links to additional help with finding the well depth, finding well contaminant sources, and fixing other water well problems.

We include important well disinfection notes about adjusting the pH of well water & the pH of well disinfectant solution to assure adequate disinfection, & we repeat important safety warnings about handling chlorine or adding chlorine to water containing hydrogen sulfide H2S.

Page top sketch illustrating both deep and shallow water well construction and depths is provided courtesy of Carson Dunlop Associates.

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Special Well Cleaning & Well Disinfection Procedures after Area Flooding

Example of well casing deposits, BC Canada Ministry of Environment The following is adapated & expanded with additional references & details from the excellent Canadian documente cited just below. We cross-reference to other expert advice such as from the US EPA, health departments, university sources, & well drilling & service companies. CONTACT us to suggest changes, additions, or further research.

The illustration at left, from the BC ME cited below, provides an example of thick well casing deposits that can interfere with the success of usual well shocking procedures.

[Click to enlarge any image]

Physical cleaning of the casing may be required to cure a persistent bacterial contamination in a well that looks like this one.

The Canadian BC Ministry of Environment recommends eleven steps for successful post-flood water well disinfection

For a detailed procedure for disinfecting a well after area flooding see this helpful document cited both in our references and again just below:

When Standard Water Well Chlorination Procedures are Ineffective: fact Sheet developed for Well Drillers, Health Authority Staff and others involved in well recovery efforts after a flood [PDF linked to return to this article series] - British Columbia Ministry of Environment, retrieved 1/31/2014, original source: plan_protect_sustain/groundwater/ wells/factsheets/PFRA_well_recovery.pdf

The following information is adapted from & comments on the advice given in that document.

These suggestions will probably require the services of a well service company who have experience in well cleaning and restoration. They may be well beyond the scope of a homeowner. But following extensive area flooding it seems unlikely that the few experienced well service companies will be able to quickly address all of the contaminated water wells in an area.

A Twelve-Step Program for Disinfection of Problematic Contaminated Wells

The Eleven Steps detailed in the document cited above are, if we include a step of making necessary preparations, actually 12-steps. See the PDF Post Flood Well Disinfection for complete details.

  1. Prepare for well cleaning & disinfection by waiting for flood waters to subside, remove nearby contaminants, fix any broken wells seals, casings, pitless adapters, check and fix pump, wiring, controls, piping that are damaged or leaky

    Watch out: store a backup water supply sufficient for at least 24 hours, take any charcoal filters out of the disinfection loop, read safety procedures for handling chlorine, don't enter chlorine-vapor filled areas. Mechanical cleaning of the casing and pumpout of dirty cleaning debris may be needed before proceeding.

  2. Check & adjust the pH of the water in the mixing tank to 4.5 before adding the disinfectant. (Vinegar, 5% acetic acid, at 20L of 5% acetic acid per 1000L of water
  3. Find well depth & static head - needed to determine the disinfectant solution quantity. See STATIC HEAD and DEPTH of a WELL, HOW TO MEASURE
  4. Prepare the disinfectant solution - Start with clean potable water of sufficient quantity; check and adjust the water pH before adding the chlorine (bleach).

    To determine the amount of clean water needed to make the disinfectant solution see WELL DISINFECTANT TABLE, POST FLOODING given below

    The target water pH before adding bleach is 4.

    To determine the amount of bleach needed see WELL DISINFECTANT TABLE, POST FLOODING

    Watch out: for inadequate well disinfection: use enough bleach to reach the necessary concentration in the well and let the disinfectant remain in the well long enough (8-24 hours) - otherwise you may fail to adequately disinfect the well.

    Watch out: for excessive well disinfection: don't significantly "overdose" the well with bleach or chlorine or you may find that you have to waste a lot of water and time flushing out the chlorine bleach at the end of the disinfection period.

    Watch out for hydrogen sulfide (rotten egg or sulphur smell) in the water - see CHLORINE SAFETY WARNINGS

  5. Check the disinfectant solution pH and adjust it to between 6 and 7 if it is not in that range. See DISINFECTANT pH ADJUSTMENT
  6. Place disinfectant solution in the well, including washing down casing sides. A tremie line (pipe or rigid tubing that can be inserted below the water surface) is used to assure solution is placed throughout the static water in the well. Be sure well pumping equipment is turned off for this initial disinfectant insertion step.
  7. Circulate the disinfectant solution in the well, piping, and back to well top, washing down well casing (we see experts using a simple garden hose connected to an outside hose bibb - Ed.]
  8. Disinfect building piping by running the disinfectant through building fixtures as we describe at our standard PROCEDURE & QUANTITY of BLEACH NEEDED to SHOCK A WELL.
  9. Wait: to give adequate contact time. 6 hours minimum; 12-24 hours preferred.
  10. Flush disinfectant from the system. Flush for at least 60 minutes past the time you last detect chlorine smell; we like using chlorine test strips at this point. Don't flush disinfectant into the septic system or it may be damaged.

    Watch out: If significant debris, silt, sand or turbidity are observed in the well flushing water you may need to temporarily remove and then install new water filters if such are used on your system

    Watch out: if the well has a poor flow rate or poor yield you risk damaging the pump if the system does not include low-water protection equipment. For a low yield well you may need to flush the system more slowly and over longer or separated intervals.
  11. Restore the pump, well, and any water treatment equipment to normal use.
  12. Re-Test the drinking water after 2-3 days. Testing too soon risks giving false-negative results, indicating no problem when in fact a persistent contaminant source remains. See BACTERIA LEVEL INTERPRETATION and CHLORINE SOURCES in WATER.

    If the well water remains contaminated also see WELL WATER CONTAMINATION: CAUSES, CURES

The BC Ministry Post Flood Well Disinfection document includes 11 detailed steps recommended for well disinfection after a building flood, including the following Chlorine Quantity disinfection table

Post Area Flood Well Disinfection Table

Amount of Chlorine Required to Obtain a Chlorine Disinfectant Concentration of 200 PPM 1

Well Casing
Required Water Volume 
Required Amount
of Domestic
Chlorine Bleach
5.2% Strength
Required Amount of Industrial Sodium Hypochlorite 
More Information
Water needed per foot of water inside the well casing2 
Liters per Foot of Water3 
Liters per Foot of Water3 





1. Adapted from the BC Health Ministry publication cited, this table has been modified from the Canada-Alberta Water Wells that Last for Generations publication [5]

2. Water needed refers to clean (sanitary) water required to mix with disinfectant in a mixing tank to prepare the solution to be inserted into the well. The table is based on the concept that the volume of disinfection solution needed is two times the volume of water in the well.

Watch out: The BC document refers to "well casing" volumes but this is incorrect. The total volumes that should be considered need to address the total quantity of water in the well. Since in most locations a drilled water well extends for some distance into bedrock beneath the end of the well casing itself, the total well depth is what must be considered, not the "casing depth" (which would be a smaller quantity). - Ed.

3. Per Foot of Water refers to the total static head of water in the well when the well is at rest. If the well has been in use you should give time water to flow back into the well to bring the top of the water column to its normal (or seasonally-normal) resting height.

4. Watch out: this is milliliters, not liters of disinfectant. E.g. 19ml = 0.019 L of liquid. When you have multiplied these numbers by the number of feet of water in the static head in the well you may find it convenient to convert back to liters or fractions of liters for the actual measurement of disinfectant to be used.

Watch out: I'd add a caution that in addition to the problem that a too-strong bleach solution may actually shift the disinfection solution pH to make it ineffective, we have recurrent complaints from people who have had difficulty flushing out bleach after apparent overdosing.

The rate at which you can expect to flush disinfectant out of a treated well depends on both the pumping rate and the WELL YIELD DEFINITION - the rate at which water flows into the well from the aquifer.

Watch out: I'd also add that re-testing well-water for potability should be repeated even after an apparent well-disinfection, since as the Ministry pointed out, contaminants may have extended beyond the well casing to the aquifer itself. See BACTERIA LEVEL INTERPRETATION

Hopefully even if aquifer disinfection appears futile, a deeper aquifer that feeds a water well through rock fissures, and that was contaminated by flood waters entering the aquifer through the well casing itself, may be contaminated only locally close to the well (as it is difficult to force floodwaters far into rock fissures without high pressures).

This makes us optimistic that given sufficient time past the receding of the flood itself, a combination of disinfection and then well water flushing out may successfully remove contaminants brought by the flood itself.

Importance of adjusting the pH of Well Water & Well disinfectant Solution

Mark posted as a comments on 3/22/2013 & 1/31/2014


Bacteria can hide behind surface rust/debris on well casings. Taking two different samples, one from the casing and one from the aquifer should identify this situation: google this procedure; basically for casing samples you figure how much time it takes to pump the water in your discharge pipe out and add a minute to it, pump and take sample; for the aquifer sample you have to do the same basic procedure, but with figuring the amount of water in the well casing (no problem running well beyond such time, assuming that you're not risking running dry).

I've got a 35' well (been out of use for a good ten years, no real history, was left open) that I'll be rehabbing shortly. One of the things that I'll be doing is running a casing brush (WireHog) to clean the casing. I'll also be blowing out the well casing to make sure that there's not a bunch of crud in there.

Upon completion of this cleaning I will shock by back-flushing about 500 gallons of "treatment" (sodium hypochlorite and water) based on the optimal mixture ratio.

Watch out: if you use too strong a disinfectant solution you may not kill the bacteria: you end up increasing the pH level and defeating the biocidal capacity of the sodium hypochlorite, not to mention potential damage from increased pH levels on the casing, pumps and screens: test the pH and adjust with vinegar

Explanation of pH levels: adding vinegar is only a correct measure if the pH is too high - that is it is not sufficiently acidic. Solutions with a pH over 7 are considered basic or alkaline while solutions with a pH under 7 are considered acidic. A solution with a pH close to 7 is essentially neutral. - Ed.

I was ignorant of all of this and just dumped a gallon of bleach down the well. Clearly this didn't rectify my problem (and I now know why this might be so). The Alberta Agriculture and Rural Development has an excellent online page on Shock Chlorination [citation given in this article - Ed.].


Actually, one of the best places for bacteria to live is in the static to draw-down area.

I should have also stated that slime-forming bacteria can hide the real nasty stuff (coliform and e-coli). And the slime can inhabit all down the casing, the screens and out in to the aquifer. According to Well folks it can be necessary to brush out a well in order to achieve a good kill on the bacteria.

Again, pH IS EXTREMELY IMPORTANT! [The writer's reference citation from the Canadian BC Ministry of Environments given at the end of this section]

In general, they adjust water in a tank to a pH of 4.5 and THEN add chlorine. I wasn't aware of this procedure until after I mixed up my solution. Now that I have an actual personal experience in this I think that I can comment on it... I mixed up a 200ppm sodium hypochlorite solution (8.25% Clorox) in 275 gallons of pH neutral water (my spring water is nearly dead-on, 6.8 - 7.0 pH). I had ASSUMED, based on all the casual experts comments (in addition to information from various water publications [people that actually should be responsible]), that I shouldn't be too far off pH-wise- WRONG! I'm over 8.4 pH!

If you read the [BC health ministry document cited & linked below] you'll find that having a pH value that is much beyond neutral won't be effective as a biocidal. All of this should tell folks why they have difficulties really getting the job done and then have to end up shelling out a lot of money to pay a professional.

I am now trying to adjust the pH down... (don't have a lot of time before I lose the chlorine efficacy). Yes, there is a reason why the good professional well folks should earn what they do.


Re: Mark's 2013 comment

Excellent points Mark - which explains why it can be difficult to sanitize a well, but ONLY if there is actual exfoliating rust inside the well casing - which is not usually the case. Normal surface rust is not a substantive block to disinfectants used in a well. But a thick mineral deposit that may build up in some wells (in the area of the casing or well borehole that is normally water-filled) can make disinfection more difficult in those wells unless disinfection is accompanied by mechanical cleaning.

We agree that what is important is using a proper strength of disinfectant, for an adequate time, followed by through flushing of the well and after a suitable wait time, a follow-up test.

The well sanitizing procedures we document at InspectApedia cite U.S. & Canadian federal and state expert sources & health departments - those are the most expert people we can find.

Mark's 2014 comment was in regards to mine:

"it can be difficult to sanitize a well, but ONLY if there is actual exfoliating rust inside the well casing - which is not usually the case. Normal surface rust is not a substantive block to disinfectants used in a well."

We agree completely.Just below for reader convenience and also at References [5] we have cited and link to a PDF file copy of the helpful BC ministry document to which Mark refers. My original comment was directed at typical residential well disinfection and the PROCEDURE & QUANTITY of BLEACH NEEDED to SHOCK A WELL - and did not adequately focus on on pH adjustment and on disinfecting a well contaminated by area flooding - a more extreme situation that may have forced floodwaters into the aquifer itself.

For a detailed procedure for disinfecting a well after area flooding see this helpful document cited both in our references and again just below:

"When Standard Water Well Chlorination Procedures are Ineffective: fact Sheet developed for Well Drillers, Health Authority Staff and others involved in well recovery efforts after a flood " - British Columbia Ministry of Environment, retrieved 1/31/2014, original source: plan_protect_sustain/groundwater/ wells/factsheets/PFRA_well_recovery.pdf

In addition to the pH problem in disinfecting flooded wells, I add Manci's caution about giardia:

Chlorine kills bacteria, including disease-causing organisms and the nuisance organism, iron bacteria. However, low levels of chlorine, normally used to disinfect water, are not an effective treatment for giardia cysts. A chlorine level of over 10 mg/1 must be maintained for at least 30 minutes to kill giardia cysts. -- References [3]

The document from the BC ministry makes a sound point that it can be difficult to disinfect a water well following a flood, giving two reasons why well disinfection may be unsuccessful.

  1. The groundwater may still be contaminated with flood water or there may be a source of continuing contamination.
  2. The well was infrequently (or never) cleaned prior to the flood, and over time large quantities of mineral scale and biofilm have accumulated in the well. This material can greatly impair attempts to disinfect a well.


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