Diagnosing Problems

Are you having problems with your well? Here are a few of the more common problems. Click on the problem and you will see the possible solution. If your problem is not on this list, please contact us, we can help.

Iron bacteria/slime bacteria in wells and piping systems

Odors in wells or systems

Corrosion in wells and piping systems

Discoloration of water from wells

Coliform bacteria, Ecoli, or fecal coliform bacteria

Calculate pumping costs


Before ImageIron bacteria/slime bacteria in wells and piping systems

Iron bacteria is a name of a specific group of bacteria that really produce stalk like tubes
rather than slime. The industry has always referred to slime problems in wells as iron bacteria, but the terminology is not correct.

Over the past 10 years, our tests indicate iron bacteria is actually only found in approximately 8-10% of all slime types of problems. Pay attention to any changes that appear in a well, whether it be reduced yields, odors, corrosion, etc. You can physically check your pipelines or fittings near the well for evidence of bacterial growths. Be aware, you can find plugging in a piping system and may not always be present in a well. The further from the well any sampling is done, the chances are reduced that the problem starts from the well. Specific laboratory tests can be done at the well head and at various areas within a pipeline or large system to determine the location of growths. See "Lab Services".

After ImageRecords that include monitoring Specific Capacity of wells can actually determine if any plugging is present. (See, "Cleaning Wells and Pipelines" for instructions on monitoring your well performance.) Unfortunately, if you are already having problems, it is not the time to start monitoring well performance. You should establish a baseline when the well is new or when no problems exist. Contrary to traditional thinking, iron bacteria or slime bacteria can NOT be killed or removed by chlorine. Chlorine, even in large volumes, only oxidizes the outer surface and can make it more difficult to treat later. The problem will always return with shorter treatment frequencies. Iron bacteria/slime bacteria can be removed in wells and systems for long periods of time (years) if the well is properly treated, developed, and the chemistry is monitored to determine when the well is clean. See, "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services", e-mail or call us for technical recommendations.

>> Back to Top


Odors in wells or systems

“Rotten egg” odors or Hydrogen Sulfide Gas (H2S)

In groundwater, a rotten egg odor is created by a bacteria called Sulfate Reducing bacteria (SRB). These are anaerobic in nature, meaning they survive in an environment where oxygen is not present. In wells, these areas could include a sump below the screen or non producing areas of a screen or formation. These are also found in wells that are not pumped frequently as the oxygen dissipates when wells sit and these bacteria can thrive. These are naturally occurring, soil bacteria and can be found in formations like silty sands, clay or shale lenses that have low flow conditions. These areas must provide the low oxygen environment and the sulfate levels or gypsum to survive.

SRBs reduce sulfates in the water, but sulfate levels above 50 ppm provide the opportunity for massive growth. They can survive with only trace amounts of sulfate, however, with limited nutrient would not provide significant growth. As they process sulfates, these bacteria release an organic acid which is very corrosive. The natural pH of water can even be effected if the growth is severe. A hydrogen sulfide gas is released during this process. H2S (hydrogen sulfide gas) can also be processed;


Chemically by acids often associated with sites around oil drilling/oil production areas or solution mining applications. It is thought this chemical process releases gas from sulfur and lowers natural pH of the groundwater. This enhances sulfur in the environment and sulfur oxidizing bacteria growths can increase substantially. SRBs then have an environment to thrive as well. The bacteria are often well into the formation and the gas can be carried with water flow toward the well.


Biologically through the SRBs. In groundwater applications, we would expect as much as 95% of H2S gas is a result of SRBs.

H2S gas can cause a milky appearance in water when reaching atmospheric pressure from a pump. As H2S dissolves in water, it increases the S ion which can force sulfate formation. This happens when calcium sulfate or in rare cases, magnesium sulfate comes out of solution. H2S can result in a decline in the natural pH of water which can actually force dissolved minerals out of solution, creating a discoloration in water.

>> Back to Top


Rotten Egg Odors in New Wells:

These bacteria are naturally occurring soil organisms and can be present in the aquifer before it is drilled. Drilling contractors should be aware these bacteria can be present in silty sands, clay lenses, and shale lenses (low Permeability) but not often found in clean sands, sandstone lenses, or areas of high flow rates (high Permeability). Low Permeability areas act as a sponge by holding large amounts of water, but not allowing the water to move easily, allowing the oxygen to dissipate.

One field study was done in an area know for this H2S odor. The drillers log included 20-30’ of shale lenses in the upper portion of the aquifer in-between clean sandstone and the bottom 50-60’ was clean sandstone. A test hole was drilled to determine the location of the shale lenses. This test hole was reamed to 5’ below the deepest shale lens. Casing was installed and grouted. The remainder of the formation was drilled to the completed depth in just the clean formation. No odors. 8 more wells were drilled in this same area with no odors in 7 of the 8 wells.

Solution: Chemical treatment, chlorination, or shock chlorination will do nothing to retard or eliminate this odor other than a temporary 1 week fix. Check into aeration or water treatment alternatives. Be aware that simple aeration will cause minerals in solution to oxidize as solids. This could plug pipes and any water treatment media. Aeration with an iron removal media bed can work quite effectively.

>> Back to Top


Odors in Older Wells (greater than 3 months to several years):

If this odor was never present in your well and suddenly appears or gets noticeably stronger, we suggest the following:


Did you recently replace an old metal (generally galvanized) pressure tank with the newer style bladder tank?

If so, the old metal tanks allowed a water to air contact inside the tank allowing the gas produced by these bacteria to dissipate. The new bladder tanks force water into a rubber bladder and the air inside the tank provides pressure. The water never has a direct contact with air until it comes out of the faucet. Hence, the odor is now present and you think you have a new problem when you may not. Simply go to an aeration prior to filling the tank.


If nothing has changed in the pressure tank, the problem may be in the well or a piping system.

The presence of these bacteria may also indicate massive slime growths and/or mineral scale deposits. Remember these bacteria are anaerobic only, and are generally found under these growths and scale where there is little oxygen available. Any biological mass would include layers of aerobic slime formers on the surface and anaerobic bacteria at the base.

Sometimes when a pump is pulled, the pump scrapes the sidewall of the casing and exposes the anaerobic bacteria and hence, an odor suddenly appears.

Treatment for rotten egg odors in older wells Chlorination or shock chlorination of a new well or an older well will not eliminate this odor but may contain it for a few weeks.

Sometimes this odor may not be present until a well is treated with acids and the outside protective shell (scale or slime) is removed by acids. If the well is only treated with acids, the odor often remains long after the treatment, as these bacteria have now been exposed.

We highly recommend to wire brush the entire casing and screen to physically remove the debris on the inside of the well. Be very careful, as the human body can only withstand a certain level of H2S gas. See the “Slime Bacteria” section of "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services" for treatment guidelines.

>> Back to Top


Oily, musty, or swampy odors

We often see well owners testing for toxic organic compounds when an oily odor exists. There are several bacteria capable of producing an oily, musty, or swampy odors. Often, these are associated with any number of iron bacteria families. These bacteria will secrete a corrosive enzyme to consume a nutrient. The byproduct is sometimes a gas associated with any of these odors. Generally this happens in wells which are greater than a month old. A well can be in operation for several years before odors become obvious. If there is any change in a well, it may be due to an increase in bacterial activity. Chlorination will not be successful at removing these odors for more than a couple of weeks. See the “Slime Bacteria” section of our brochure "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services", for treatment guidelines.

>> Back to Top


Corrosion in wells and piping systems

Corrosion in groundwater is more likely due to high total dissolved solids (TDS), stray ground currents (DC), or bacterial activity, rather than corrosive water. You can review the water chemistry for a determination if the water is actually corrosive.

Water Chemistry-Corrosive Tendencies
Follow these guidelines to understand if your water chemistry is corrosive.
- pH lower than 7.0 (pH is logarithmic so declines 10 fold for every point)
- dissolved oxygen exceeds 2 ppm
- carbon dioxide exceeds 50 ppm (H2S) greater than 1 ppm
- chlorides (salt) greater than 500 ppm
- Ryznar Stability Index (calculated) at greater than 7 (logarithmic)

If you don’t have any water chemistry information, we would suggest an accredited laboratory run
some initial water quality tests for corrosion. If no laboratory is available, we can do these tests for you.
See "Lab Services."

If the water chemistry does not indicate corrosive tendencies, check the following items for other potential causes.

>> Back to Top


Total Dissolved Solids (TDS)

There are several TDS meters on the market or have any local laboratory check for total dissolved solids (TDS). If greater than 600 ppm, there is a chance corrosion is the result of bimetallic corrosion, sometimes called “Electrolysis” or “Galvanic” corrosion. The greater the TDS, the greater the corrosion potential. High TDS water is very conductive to electrical currants. If dissimilar metals are immersed in high TDS water, corrosion will occur on the lower or less noble of the metals (say aluminum or mild steel) and deposit will occur on the more noble of metals (say stainless steel). You can check the Galvanic Series for metals in most metallurgical books or e-mail/call us. If TDS is lower than 400-500 ppm, corrosion is likely to be caused by something else.

>> Back to Top


Stray AC or DC currents

Contact your local electrical power company and ask them to check for stray AC and DC currants around the well or in the electrical wiring. They should be able to determine if stray currant exists and to what degree of severity any currants may be causing corrosion. If stray AC currants are present, the source should be found to eliminate the problem. DC stray currants can be caused by local cathodic protection of water or oil pipelines, phone lines, electric fences, etc. DC currents can cause severe damage in low amounts. 1 AMP of DC voltage can corrode 20 pounds of steel in a year.

In some cases, a sacrificial anode can be buried with a connection to the steel well casing. This creates corrosion to the sacrificial anode and not the well casing. This will last for several years. Your local electric company, a corrosion control company, or a pipeline company can provide you with sacrificial anodes.

If electrolysis is creating problems with the pump or column pipe to the pump, a thick aluminum cable can be banded to the pump and column pipe to act as a sacrificial anode. This should be periodically checked to determine the life expectancy of the anode. Contact a reputable pump contractor for services.

>> Back to Top


Bacteria can cause corrosion

If no stray currants are present, the problem may be bacterial in nature. There are many types of bacteria which produce corrosive enzymes that can dissolve metals. Sometimes corrosion is related to odors released by these same bacteria. Iron bacteria and Sulfate Reducing Bacteria are two of the most commonly found bacteria that can cause this problem. Note any changes in the water quality like a lowering of pH, or any odors that suddenly appear. Any or all may indicate bacterial activity. You should then contact us for a bacterial study to determine the severity of any bacterial activity. See “Lab Services” for more information.

>> Back to Top


Discoloration of water from wells

Discoloration in a potable water application can be caused by high minerals in solution, corrosion, or bacterial growths.

High minerals: The color will depend upon the mineral in solution.
Red or yellow coloration will generally mean high iron. Look for iron greater than 3-4 ppm.
Black or gray will indicate manganese. Look for manganese greater than 0.1 ppm.
Green or blue may also mean corrosion of copper pipes as well. A simple water test can indicate the potential.
White or milky color may indicate Sulfate Reducing bacteria. See “Odors”.

A simple water quality test will determine the problem and generally water treatment is a simple solution.

Corrosion: See “Corrosion.” Chemical additives can be added to control corrosion. See a water treatment specialist for recommendations.

Bacterial: Bacteria will process a variety of minerals in water and the color of slime may indicate what nutrient has been processed. Often, the discoloration is intermittent as bacteria sloughs off because of water velocity. You can have bacterial growths in a pipeline and not necessarily find a problem in a well. See “Iron Bacteria & Slime Bacteria” for more information.

>> Back to Top


Coliform bacteria, Ecoli, or fecal coliform bacteria

Positive coliform bacteria in new wells
Positive counts of coliform in a new well is often related to pH of the natural water, placement of chlorine, or debris in a well hiding coliform from chlorine such as:


bentonite used by the direct drilling method


debris smeared by cable tool rigs


air pockets lodged into the formation by air drilling methods.

First check the natural pH of your water. If it’s over 7.0, refer to our brochure, "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services" The placement of chlorine can also be an issue and is covered in the same brochure.

New wells are often drilled using the present (old) buried pipeline to transmit water. This pipeline can contain mineral scale or slime bacteria deposits which can hide coliform. If a positive count occurs in this situation, lift the pump and test the well only. If negative, the pipeline must be cleaned prior to testing in the building. See the “Cleaning Buried Pipeline” section of our brochure, "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services"

If a new well was drilled with a direct rotary drilling method using bentonite as a drilling fluid, the well may not be fully developed and bacteria may be hiding behind bentonite still left in the well. Bentonite has a very strong polyaccrilimide polymer chain which constitutes around. 2% and is almost impossible to breakdown.

If chlorination efforts are failing, remaining bentonite in the borehole may have to be removed before a negative count is obtained. Breaking this polymer chain in bentonite requires a 1500 PPM solution of sodium hypochlorite (liquid chlorine). We generally recommend the 12-15% industrial concentration on larger wells but a 5% unscented household bleach can be used as well.

Recommended procedure:


Calculate the volume of water in the screen or open borehole in gallons.


Multiply this volume times 2 or 3 to double or triple the volume of the screen/open borehole.


Have a tank at the surface large enough to hold the gallons in step 2.


Fill the tank with the required gallons of water.


Mix a 1500 ppm chlorine solution into the water in the tank and circulate to mix. For 12-15% industrial
strength, use .012 gal of sodium hypochlorite per gallon in the tank. For 5% household bleach, use .03 gal of bleach per gallon in the tank.


Install a pipeline called a tremie pipe near the top of the screen or borehole. If either is less than 50’ thick. If greater than 50’, we recommend to install in equal increments throughout the screen or borehole in 50’ sections.


Surge the well with a surge block to agitate this solution. (See “Development” section in our brochure,“Cleaning Wells and Pipelines”


Let set overnight.


In the morning, surge the well with a surge block and over pump the well with an airline (airlift development) or a pump.

The oxidation process of the 1500 ppm sodium hypochlorite solution will break this polymer chain of bentonite. Expect a malty appearance of the solution being pumped from the well.

>> Back to Top


Positive coliform in old wells

Often coliform bacteria will grow undetected under mineral scale or microscopic slime bacteria growths in wells. When a pump is pulled, this debris on the casing can be scratched, exposing coliform bacteria, and a positive count occurs. If slime is forming on the well casing due to bacterial growths, it can slough or breakaway from the casing due to water flow, exposing coliform. In either condition, chlorine will most always be ineffective in removing coliform. See our brochure, "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services"under “Slime bacteria” for recommendations for cleaning.

>> Back to Top


Continuing or multiple positive coliform samples

If you continue to have positive counts in water tests, ask your local laboratory to do the following tests:



Actual identification of coliform on a nutrient plate. There are some naturally occurring soil organisms that will show false positives on the 24 hour, positive/negative test kits. A positive is possible due to bacteria that may not be a health issue, but could be related to surface contamination. A physical problem in the well may be the real problem.


MPN (Most Probable Number) of the actual coliform. This will help determine the severity of the problem. If the MPN is 2 coliform, we may recommend you pump the well for a week and simply retest. If the MPN number is greater than 20, other steps would be required. Refer to the “Slime bacteria” section of our brochure, "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services"for cleaning directions.


Heterotrophic bacteria counts. Some labs refer to these as “background” bacteria or “congruent” bacteria. If the number is greater than 250-300, there may be premature slime formation that chlorine is not able to penetrate and any chlorination may fail. Refer to the “Slime bacteria” section of our brochure, "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services"for cleaning directions.

Allow the well to sit overnight. Turn the pump on and take the sample 3-5 minutes on domestic wells. A second test can be taken at 60 minutes of continued pumping and used as a comparison to the first test. This will give you an idea of normal aquifer numbers to see where the problem exists. If the numbers decline, the problem may be near the well. If the numbers go up in the aquifer sample, it may be a contaminent issue. We often use our Design Water Technology Anaerobic and Aerobic bacterial tests to do the same thing. For municipal or industrial wells, refer to "Lab Services."

If local labs can not do these tests, refer to our "Lab Services." If you have any questions, please call out toll free line or e-mail for further recommendations.

>> Back to Top


E coli, or fecal coliform bacteria

These are pathogens and will present health problems. Do not drink the water. These bacteria require a warm bodied source or a fecal contaminant for existence. If you have a positive count, suspect something in the well is causing the problem or a contaminant source near the well, i.e., sewer system, a swamp, surface water, etc. The well must be airlift pumped to maximize the velocity at the bottom of the well to remove any contaminant from the well. If nothing is found during the airlifting (development) of the well and the problem continues, suspect a contaminant source near the well or faulty grout of the well casing area. A simple colored dye test may prove if the grout around the casing is suspect. Refer to "Understanding Well Problems" for further explanations and recommendations for treatment. If you have questions on how to determine your well problems, you can go to "Lab Services".

Chlorination is NOT THE ANSWER! Chlorination will not eliminate the source and will only be a temporary solution, at best. Unless you find the source, you will continue to have problems.

>> Back to Top