Raton Basin
Common Problems/Solutions

Common Well Water Quality Problems: Causes and Management

There are many issues that can affect the quality of water from a private water well. Periodic testing of your well and its water chemistry can help monitor for existing or developing problems. Testing for a comprehensive suite of analytes from an environmental or agricultural laboratory can tell you about the quality of water from your well, and may even tell you about the condition of the well itself.

For well water quality problems common to Colorado visit Environmental Protection Agency’s (EPA’s) private water well information document: 



Private Water Well Common Problems

Effervescent Water

Cause:  Off-gassing of methane or other dissolved gases in your well water. The source of dissolved methane gas in the well water could be from coal seams native to the area, deep subsurface microbial gas (from CO­2 reduction), or near surface microbial gas from the decaying of organic matter.

Management:  A build-up of flammable gases is a serious issue that needs to be managed right away. Not all gases are flammable, but it is highly recommended to properly vent your well bore, well house, and or add a vented outdoor cistern to decrease a possible explosion hazard from contained flammable gases. Visit the following websites for more information on management of flammable and other gases in water wells: 


Rust Colored Water, Black Suspended Particles, and or “Rotten Eggs” Smell 

Cause:   Infestation of Iron Related Bacteria (IRB) and Sulfate Reducing Bacteria (SRB) in combination with Slime Forming Bacteria (SLYM) can cause an abundance of dissolved iron or hydrogen sulfide gas in your well system. These are common nuisance soil bacteria that can contaminate the well environment. If left untreated, the bacteria can cause plugging and/or corrosion of well pipes in addition to poor water potability. Visit the following website for more information on how to test for these bacteria in your water well: 


Management:  Visit the following websites for more information on how to disinfect your water well to manage the bacteria (will not correct chemical contamination):

Decreased Yielding Performance or Cloudy/Turbid Water

Cause:  Possible cause is plugging of the well screen and pipes by biomass infestation.

Management:  Please see the cause and management above to rust colored water and the following link:


Cause:  Other possible causes are damage to the well itself, such as casing failure, pump wear, or a declining water level in the aquifer from over-pumping.

Management:  For private well design, maintenance and other general information on water wells visit the following websites:

Scaly Residue or Scum Build-up on Fixtures, Sinks, Showers, and Bathtubs

Cause:  Hard water caused by calcium and magnesium salts natural to water in the area.

Management:  A hard water softener that will replace the calcium and magnesium salts with sodium salts is needed. Calcium and magnesium salts dissolved in the water are more likely to fall out of solution as conditions change from the aquifer environment to your well and home. By nature sodium salts are more likely to stay dissolved in the water instead of precipitating.  Please see the following links on the pros and cons of using hard water:

 Detergent Odor or Foaming Water

Cause:  Overflow or seepage of nearby septic tanks.

Management:  Inspect the nearby septic tank for cracks, breaks or over-filling. Test your well water for possible contamination of pathogenic or opportunistic bacteria common to septic tank environments. Total and fecal coliform tests can give you an overall indication of such contamination. For more information on well testing and a homeowner’s guide to septic tanks:


Household Members or Guests Suffer Gastrointestinal Illness after Consumption

Cause:  After ruling out other causes of gastrointestinal illnesses, a possible cause could be contamination by bacteria, or elevated nitrate and sulfate in your water.

Management: Test your well water for total coliform bacteria, nitrate and sulfate. For more information on well testing visit the following website:

Drinking Water Quality Common Problems

Water is often described as the universal solvent because it dissolves many natural substances in the environment or helps to transport them. It is the “stuff” in the water that is responsible for the quality of the drinking water. Although some stuff is acceptable, water with too much dissolved or suspended solids can cause foul tasting or smelling water, and/or can be a health concern. The following links are items commonly found in water wells in drinking water and what to test for (please see above link from the CDPHE on laboratory testing): 

Heavy Metals or pH imbalance

Cause:  Elevated heavy metal concentrations in well water could be from natural subsurface filtration and interaction with rock and soil environments, or elevated concentrations could be from man-made sources, such as lead and copper pipes, or leakage of a nearby landfill.

The toxicity of the metal can depend on the pH of the water, and is different per metal per pH.  pH is a measure of the acidity or basicity of the water, with 7.00 as neutral pH.  Anything below 6.50 can be too acidic and anything above 8.50 can be too basic for aesthetic drinking water quality.

For water wells within the Raton Basin, iron and manganese are two metals that are occasionally measured above their respective secondary standards, 0.3 milligrams per liter (mg/L) and 0.05 mg/L, referenced in document 5 CCR 1002-41 of the Water Quality Control Commission (WQCC) Colorado Department of Public Health and the Environment (CDPHE).

Management:  Ask the lab to test for drinking water metals and physical parameters such as pH, EC, and total dissolved solids (TDS). For further information on heavy metal and chemical concentrations, visit:

For further information on water pH imbalance, visit the following website:

Inorganic Material and TDS

Cause:  Elevated inorganics, such as nitrate, nitrite, fluoride, and sulfate, can be caused by natural subsurface filtration and interaction with rock and soil environments, or they can be attributed to man-made contamination sources, such as agricultural and residential run-off.

These major inorganics usually compose the majority of the solids measured in the water.  Total dissolved solids (TDS) analyte is largely a measure of the inorganic salts or ions dissolved in the water, and it is related to the electrical conductance of the water.  TDS analyte provides an overall water quality assessment of the water.  Total suspended solids (TSS) analyte is a measure of the suspended particles in the water.  These are the particles that can be separated from the water by a filter, and are thus usually larger than the dissolved solids.

For water wells within the Raton Basin fluoride is an organic ion that is occasionally measured above its CDPHE primary, human health standard of 4.0 mg/L.  TDS is also occasionally measured at an elevated concentration compared to it CDPHE secondary standard of 500 mg/L for aesthetic conditions.

Management:  Ask the lab to test for major cations and anions and physical parameters such as pH, EC, TDS, and TSS. For further information on inorganic concentration, visit:


Organic Material

Cause:  Possible sources of organic polutants include improper waste disposal of household products, such as paints, cleaning products, pesticide and fertilizer storage, leakage from nearby landfills, or gasoline/hydrocarbon spills.  Spills onto the soil can leach into groundwater and affect the well water for household use.

Management:  If a spill from a household organic product is suspected, please inform the lab of the type of product.  They may be able to assist you with the list or organics to analyze.  Possible organic analytes include BTEX, TPH-GRO, TPH-DRO, volatile organic compounds (VOCs), semi-volatiles, or polyaromatic hydrocarbons (PAHs).


Microorganisms Contaminants

Cause:  Microorganism contamination can occur from the select breeding and overpopulation of native soil bacteria due to the introduction of a non-native component to the soil environment, such as a water well, or by the infestation of coliform type bacteria or parasites due to a nearby septic tank leach field, surface water runoff from pastures or feedlots, etc.

Management:  Ask the lab to test for Total coliform and Biological Activity Reaction Tests (BART) for water well samples.  The BART sample analyses can also be conducted on your own by following directions found at the following site from the manufacturer of these fields test.

Common test kits for water wells contain the Iron Related Bacteria (IRB), Sulfate Reducing Bacteria (SRB), and Slime Forming Bacteria (SLYN).  Follow-up samples may be required for both BART tests and coliform testing following a disinfection plan for positive results.

For further information on microorganisms in water wells and disinfection of well water, visit:

For further information on BART tests and native soil bacteria specifically, visit:

For further information on coliform testing specifically, visit:

Livestock and Irrigation Use Water Quality Common Problems

The quality of well water required for irrigation and livestock use varies from human drinking water quality. For instance, irrigation water with elevated sodium concentrations can interact with the soil particles to leave behind large amounts of sodium, often called sodic soils. Waters with elevated TDS can leave behind saline soils. Both of these soil conditions can be detrimental to crops. There are also some potentially toxic substances in drinking water for livestock, including high salinity. 


Drinking Water Contamination for Livestock Use

Cause: The causes of pollutants in livestock drinking water from well water are the same as natural and man-made sources of human drinking water contamination (see above). If using surface water sources, heavy growth of algae can also threaten the quality of water for livestock use.

Management: For further information on the most common water quality problems of livestock, visit:


Water Contamination for Irrigation Use

Cause: The causes of pollutants in irrigation use from well water are the same natural and man-made sources of human drinking water contamination (see above). When using irrigation ditches or channels, run-off is one possible source of additional pollutants to the water.

Management: Further information on testing soils and water for irrigation use, please visit the Colorado United States Department of Agriculture (USDA) Natural Resources Conservation Service (NRCS) website:

For management and further information of irrigation water quality: