Biofilm and Effective Chemical Treatment for Disinfection in Wells

A degree in microbiology isn’t necessary to become better equipped to battle biofilm issues.

By Eric Duderstadt

Chlorine, the most widely used product for well disinfection, is part of a large family of oxidative chemicals which includes a number of household products. Photo courtesy Eric Duderstadt of Water Systems Engineering Inc.

The presence of biofilms within groundwater wells can be extremely problematic, influencing both production and water quality.

Despite being one of the most common fouling mechanisms within the well environment, the science behind biofilm formation and the role it plays in wells with regards to fouling, including its relation to coliform bacteria, is still not widely understood within our industry.

In a similar light, well disinfection is one of the most common forms of well maintenance. It has gone on relatively unchanged for more than 100 years, relying almost exclusively on the same product—chlorine. It is often mandated as part of new well construction, instituted within routine maintenance, used as a reactionary measure in accordance to regulated guidelines, and is the primary initial response to declining performance.

Yet common misconceptions surrounding the general process, improper use or application of the products being used, and often the urge to get the well back on-line as soon as possible often culminate in less than desirable results.

The good news is we don’t all have to have a degree in microbiology to become better equipped to battle biofilm issues or memorize the periodic table to make more informed decisions about the proper chemical application in order to improve the health of our wells. So, let’s take a moment to better understand biofilm presence within the well environment and how to form effective chemical treatment strategies for removal.

Biofilm Basics

First, let’s lay some groundwork about bacteria. In water, bacteria are either free swimming (planktonic) or they are attached to a surface (sessile). With regards to biofilms, we’re primarily interested in the latter, as it is through the extrusion of a slimy polysaccharide exopolymer bacteria produce when attaching themselves to surfaces that the building blocks of biofilm are formed.

Dense biofilm accumulation with protozoans, a type of biofilmconsuming microbe.

As bacteria exude this slime, a suburban community is formed where bacteria can propagate, capture needed nutrients, and gain protection by creating a barrier between themselves and external influences, such as disinfection efforts.

While this lifestyle may be enjoyed by the bacteria, it can become extremely problematic for well owners. As the growth of biofilm progresses and more bacteria join the party, the mass of the film expands and can become quite detrimental to water flow in a well as pathways become more and more restricted. Also, the same sticky characteristics of the slime that aids in surface attachment and nutrient capture is also an excellent source for the development of mineral scale within a well system.

Biofilms promote scale buildup by providing an excellent surface for adhesion of mineral-forming ions, further complicating well operation. Similarly, fine-grained sediments and debris, mobilized toward a well during operation, often become entrapped in biofilm, increasing the fouling potential. These surfaces can be screen or casing, pump components, gravel pack material, or the surfaces of the minerals which make up the aquifer formation.

Biofilm formation heavily entrained with iron oxides. The entrainment of naturally occurring minerals and other inorganic debris within
biofilm can enhance the overall degree of fouling within a well. Photos courtesy Eric Duderstadt of Water Systems Engineering.

Just like the individuals within our own towns and cities, we must also keep in mind that biofilms are not exclusively one type of bacteria. Rather they are a mixture of aerobic (oxygen present) and anaerobic (oxygen absent) bacteria. As biofilms mature and grow, they can develop a stratification in which the upper layers, where oxygen is still readily available, contain aerobic bacteria and overlay a lower anaerobic stratum where flow and oxygen content is restricted.

In addition to increasing the relative density and fouling potential of the biofilm, this stratification often results in the harboring of coliform bacteria, a commonly anaerobic or facultative anaerobic group of bacteria which have become the industry standard for determining drinking water’s sanitary quality due to regulatory actions put in place by the U.S. Environmental Protection Agency.

A group of closely related bacteria, coliforms have earned the role of “indicator” organisms due to their similarities to a variety of bacteria, parasites, and viruses known to be harmful if consumed in drinking water. In addition to providing nutrients for the proliferation of the coliform bacteria, the development of more mature biofilms within the well often acts as a shield, protecting coliforms from disinfection efforts. Thus, the greater the biofilm, the greater the potential is for coliform presence in a well.

Since the onset of the Total Coliform Rule in 1990, all public water systems are required to monitor for the presence of total coliforms in their water system and direct responses accordingly. When the rule was reauthorized in 2016, public water supplies were required to have a response plan in place should indicator organisms be identified.

The Chemistry Behind Disinfection

With a greater understanding of biofilm and how it relates to coliform presence, let’s now turn to the chemical side of disinfection. As mentioned earlier, although other products are now available for disinfection (bromine, hydrogen peroxide, chlorine dioxide, etc.), chlorine remains the most commonly used chemical today for the reduction or treatment of biological-related fouling issues within wells.

Chlorine is available in gas, liquid, and solid forms. In the liquid form, commonly as sodium hypochlorite, chlorine is available in a variety of strengths. From a chemical supplier, it is readily available in stronger solutions ranging from 10% to 15% strength as compared to 3% to 6% found in store-bought solutions.

When sodium hypochlorite is mixed together with water, both hypochlorous and hypochlorite ions are formed. The hypochlorous ion is considered to be several hundred times more biocidal than the hypochlorite ion, making it the preferred means of disinfection during treatment.

It is important to note that the distribution of hypochlorous and hypochlorite ions within the reaction is extremely pH dependent. The hypochlorous ion is present in greater concentration at lower pH values. While this seems a minor point, we must also remember that most commercial forms of chlorine are buffered to a higher, more alkaline, pH for safety.

This is done to limit the potential for chlorine gas to form, which is dangerous, as well as to reduce the potential for corrosion or damage from the oxidizing effects of chlorine. Thus, the result is a reduced concentration of hypochlorous ions and more limited biocidal effectiveness.

For example, at a pH of 6.5, the hypochlorous ion content is near 95% strength. At a pH of 7.5, the hypochlorous and hypochlorite ions will be present in near-equal concentrations with only minimal biocidal effectiveness. As the pH passes 8.0, the hypochlorous ion content falls to less than 4%, hindering biocidal activity significantly. This simple, but widely forgotten, phenomenon is why many disinfection efforts fail.

To improve the effectiveness of the chlorine chemistry, several additional enhancement chemistries are available to aid the process. Acids—including mineral and organic acids—are commonly employed in well cleaning. Buffered acids can serve to maintain the desired pH in the treatment solution to increase the hypochlorous acid production required during the process.

Additionally, the solubility of both minerals and organics is substantially increased using dispersants which act to prevent the reprecipitation and agglomeration of particles and ions which could interfere during the cleaning process.

And finally, surfactants are products that are designed to modify the surface tension of liquids against solids and help facilitate further penetration of the cleaning solution throughout the targeted area. NSF-certified products that use a combination of these supplemental chemistries are available to the market.

Customize Your Own Disinfection

Several treatment strategies, methods, and tools are used for disinfecting wells. Armed with a knowledge of biofilm and the chemistry being used, it’s time to take the next step to help improve the effectiveness of the disinfection process and custom design the procedure that fits your well.

A condition assessment can begin by first pumping the well to evaluate the need for additional cleaning efforts prior to disinfection. The removal of other fouling mechanisms complimentary to biological growth, such as mineral-based deposits, increase the likelihood of effective disinfection. Further, addressing potential sources of contamination—such as faulty well seals or breached casings—prior to disinfection also limit the potential for bacterial fouling to return or at least slow the process for future regrowth. This initial step can be particularly useful if the well has not been serviced or cleaned for an extended period of time.

After a bacteriological problem is recognized in a well, the offending party should be located, identified, and quantified using the laboratory or investigative tools necessary. Given the hazards, costs, and potential impacts of chlorination, the procedure should be part of a scientific-based process. With that knowledge in hand, a treatment can begin to be designed.

Calculating the correct dosage rates of chlorine solutions, as important as it may seem, is often done inaccurately or fails to take into account the well design. We recommend targeting a treatment volume equal to three to four times the standing well volume. A larger volume such as this is advantageous as it works to flood the entire well and extend the treatment solution beyond the confinement of the well interior into other hard to reach areas where bacterial growth may also reside.

An even worse error is to take the age-old approach of “more is better.” Research has shown concentrations of chlorine above 500 ppm generally fail to remove the targeted organisms (coliforms). These “super-chlorinated” solutions effectively work to burn or shrink the surface of a biofilm it contacts, creating a more dense and stubborn material to remove. The hardened biofilm also becomes less penetrable and is even more protective of the bacteria living within.

As a point of reference, most new wells, with lower degrees of fouling present, typically respond to chlorine concentrations of 50 to 150 ppm while older wells that exhibit more advanced fouling generally require concentrations of 200 to 400 ppm.

A proper disinfection treatment should also be based around the source water chemistry present. By confirming the pH and alkalinity of the water used to mix the chlorine with, you can identify the need for use of a chlorine enhancer and the neutralizing potential of the water prior to chlorine addition.

Adjusting the pH of the treatment solution to a range of 6.5 to 7.0 will maximize the production of hypochlorous acid and improve the biocidal efforts during treatment. However, be cautious not to lower the pH too drastically as at a pH level of 5.0 or lower, chlorine gas can be released.

Once the treatment solution is formulated, it becomes important to properly prepare the well and correctly apply the solution to ensure the previous efforts are not wasted.

First, for both new and old wells, it is advised to actively flush the well prior to treatment. For older wells, performing pretreatment cleaning or evacuation of the well prior to chlorination reduces the amount of biomass and debris that can readily degrade chlorine.

Second, dumping the prepared treatment solution from the top often fails to reach the target area. While it is true chlorine has a higher specific gravity than water, it is generally not sufficient to overcome the volumetric difference within the well column or remain effective as it dilutes in the well. An effective way to overcome this is to use a tremie pipe or similar means of application to spot the treatment solution evenly throughout the well, beginning at the bottom and working upwards. Once the solution is in place, applying agitation will help disperse the solution throughout the targeted treatment area and continually bring new chemical in contact with the bacteria which are the target of disinfection.

Finally, allow for sufficient contact time so the chlorine can go to work. As a rule of thumb, a minimum of 1000 “contact units” is recommended which is defined as the sum of the chlorine concentration multiplied by the contact time, in hours. For example, if you are using a solution of 250 ppm, you’ll need a minimum of four hours contact time.

When possible, allow the solution to stand overnight, downhole with periodic agitation. Regular monitoring of the downhole solution to ensure the chlorine solution remains viable is also good practice if possible. There are several commercially available test strips that allow you to monitor the chlorine residual. Maintain a minimum active concentration of 50 ppm downhole during treatment is suggested.

Cleaning Up

When the chlorination process is complete, the well should be thoroughly pumped, starting at the bottom and working up to assure effective removal of the chlorine solution and associated debris. Measuring conductivity, chlorine residuals, and turbidity can be helpful as well to determine when evacuation of the solution is complete. Proper disposal of chlorine solutions is an important final step and knowledge of your state’s requirements will guide the need to treat disinfection fluid discharges. When required, there are a variety of chlorine-neutralizing products on the market including NW-500, sodium bisulfite, sodium thiosulfate, and ascorbic acid. Generally, once sufficiently dechlorinated, the solution can be safely discharged.

Once disinfection efforts are completed, the well should be returned to an active operating schedule as soon as possible.


The development and presence of biofilms is a natural occurrence in well systems. If left unchecked or unmonitored, it is an effective fouling mechanism within the well, potentially impacting production as well as produced water quality.

Chlorine is a common chemical within the industry for treatment of biological fouling in wells. And well disinfection is a common practice within the scope of well maintenance. Yet the commonality shared by each of these entities does not entail simplicity.

Rather, effective removal of biofilms through a disinfection process requires one to comprehend the distinguishing features of groundwater bacteria, the chemistry that makes chlorine an effective biocide, and the techniques and practices that make disinfection an effective remedy for microbial growth within wells.

Taking the time to understand the biology present, the disinfection chemicals being used, and the proper application procedures will produce more effective maintenance efforts and improve well health.

Eric Duderstadt is an environmental biologist with Water Systems Engineering Inc. of Ottawa, Kansas, where he works as a consultant. He earned his bachelor’s degree in biology at Ottawa University in 2007 and has since become certified as a corrosion technician within the National Association of Corrosion Engineers. He also works within the firm’s research department and investigative laboratory centering on microbiology and chemistry. Duderstadt can be reached at eduderstadt