The Chemistry and Biology of Well Development

Published On: February 19, 2024By Categories: Art of Wells Columns, Drilling

Chemical and biological conditions can significantly impact the ability to develop a well.

By Marvin F. Glotfelty, RG

My last column in the November 2023 issue of Water Well Journal was titled “The Physics of Well Development,” and this column expands on that discussion.

Figure 1. Examples of calcite (CaCO3) mineral scale. The top sample is a large calcite buildup that formed in a vertical turbine pump. The samples on the right and bottom (insert) are calcite scale deposits that formed on pump column pipes.

It does so by incorporating considerations of the chemical reactions and biological processes that are closely related to the physical forces in water wells, which significantly impact our ability to effectively develop or redevelop a well.

My previous column about well development physics described how the velocity of water during well development (e.g. from jetting, swabbing, etc.) relates to the amount of kinetic energy that is created, and how that energy achieves the development of the well.

While physical attributes of well development are critical to the well development process, those physical attributes do not stand alone as important variables to be considered. The physical conditions that are involved with well development are inexorably related to the chemical and biological conditions in and around the well.

Detrimental impacts may result from chemical interactions between the groundwater chemistry, the geochemistry of the formation that was penetrated by the well, and the chemistry of the well’s construction materials (as well as the drilling fluid chemistry during drilling). The comingling of these chemistries may increase the solubility (dissolution) of solids and mobilize them, or the combined chemistries may decrease the solubility (precipitation) of constituents and cause clogging of pore spaces with mineral deposits.

There can also be a detrimental impact on the performance of a well from the accumulation of metabolic byproducts (scale or biofilm) that are deposited by microbial organisms (naturally occurring bacteria) in the subsurface. Biochemical scale or biofilm deposits can clog pore spaces and impede the flow of groundwater to and from the well.

The importance of these chemical and biological impacts to well performance are what prompted me to provide the cautionary closing statement in my previous column: “Be mindful of the chemical and biological aspects that impact the water well environment, and how those aspects interact with one another to influence the well’s performance throughout its operational life.”

An effective approach to well development (for a new well) or redevelopment (for an existing well) necessitates understanding the nature of the chemical and biological processes that are causing the problem.

Thus, let’s consider the fundamental attributes of how the chemical and biological conditions of a well may present these challenges to us. The particulars of chemical and biological clogging of wells span a broad range from place to place and from well to well, but we can review a few common conditions and generalized principles that will enable us to better address the development and redevelopment of water wells in
a pragmatic and effective manner.

Chemical Clogging

Figure 2. Conceptual oxygen corrosion cell. Scale deposits from iron-related bacteria (orange-brown colored) and sulfate-reducing bacteria (black colored) can result in corrosion/deposition from the flow of electrons (yellow arrows) when an oxygen corrosion cell is established.

The stratification and geologic complexity of an aquifer can isolate different bodies of groundwater into separate aquifers, and those aquifers often have different water chemistry. In addition, the different geologic strata will have unique geochemical profiles that reflect the mineral content of the formation, and each of those unique geochemical formations may impact the groundwater flowing through it.

Due to these conditions, groundwater can become enriched or even supersaturated with salts or other soluble elements and compounds such as sodium (Na), calcium (Ca), iron (Fe), magnesium (Mg), chloride (Cl), sulfate (SO4), carbonate (CO3), oxygen (O2), etc.

Any combination of these constituents can be precipitated as mineral deposits on the casing or screen surfaces, or within the pore spaces of the filter pack media. Mineral deposits can be hard and difficult to remove, and in some cases, the mineral deposits can accumulate to form thick scale deposits.

Examples of calcite (CaCO3) deposits that have accumulated on pump equipment are shown in Figure 1. Although calcite is probably the most common mineral scale, the potential also exists for numerous other mineral scales to be deposited in water wells as long as the components of the mineral are at or near the saturation level. Other common mineral scales include gypsum (CaSO4·2H2O), barite (BaSO4), and manganite (MnO OH).

Biochemical Clogging

Mineral scale deposits are a common problem in water wells, but in my experience, the accumulation of biologically derived scale or biofilm is an even more prevalent problem in water wells.

Figure 3. Scale deposits from iron-related bacteria that have grown into elongate, stalactite-shaped tubercles.

Naturally occurring bacteria exist in the subsurface of the earth, and from a practical standpoint, we cannot avoid biochemical clogging of water well screens by siting our wells away from locations where the bacteria occur.

Colonies of bacteria are essentially ubiquitous and have been documented at depths of more than a mile deep within the earth and have been identified on every continent on the earth. Therefore, biochemical clogging is a potential problem in every water well (although its severity varies from place to place).

When a water well is being pumped, it draws groundwater from a broad radius and that groundwater delivers nutrients to the bacteria that live on the surface of the well screen and casing. Thus, the bacteria may survive in other portions of the aquifer environment, but they thrive in the water well environment.

One of the most common types of bacteria in wells is iron-related bacteria. This type of bacteria generally prefers an oxygen-rich (aerobic) environment, and they get their energy from dissolved iron in the aquifer, as well as iron from the well casing and screen.

Iron-related bacteria oxidizes the casing and screen material to form deposits of iron oxide or iron hydroxide, which form tubercles (lumps of scale deposit which serve as a home for the bacteria) as shown in the top photograph in Figure 2. In some cases, iron-related scale can grow in elongate columns that resemble a stalactite from a cave formation that is composed of iron oxide (Figure 3).

Figure 4. Two perspectives of slime-forming biofilm accumulation on a louvered well screen. Images are screen captures from the side-view lens of a well video.

Another type of biochemical scale results from sulfate-reducing bacteria, which generally prefer oxygen-deficient (anaerobic) environments. These bacteria often reside in portions of the well with stagnate water where the lack of circulation causes the anaerobic conditions, although they may also occur in aquifers composed of carbonate rocks or shale, especially if the formations contain hydrocarbons (written communication, Stuart Smith, 2024).

Sulfate-reducing bacteria obtain their energy by reducing sulfate (SO4) to hydrogen sulfide (H2S), which creates a corrosive environment and can result in holes in the steel surface. Scale from this type of bacteria is often dark or black in color, as shown in the bottom photograph in Figure 2. Scale from sulfate-reducing bacteria may have a sulfur smell due to the emission of H2S.

Sulfate-reducing bacteria can also form a symbiotic relationship with iron-related bacteria, when the outer metabolic layer on a tubercle formed by iron bacteria prevents oxygen from penetrating the tubercle. This sets the stage for sulfate-reducing bacteria to grow beneath the tubercle in the anaerobic environment that is formed in the oxygen-deficient area beneath the tubercle.

The relationship of side-by-side aerobic and anaerobic environments on the outside and underside of the tubercle sets the stage for an oxygen corrosion cell (Figure 2). Like corrosion or deposition on the poles of an automobile battery, the flow of electrons is initiated between the anode and cathode portions of the oxygen corrosion cell, which exacerbates the corrosion of the steel surface beneath the tubercle and the
deposition of corrosion byproducts in the area surrounding the tubercle (which causes clogging).

Some types of bacteria produce a layer of bonded sugar molecules (referred to as a polysaccharide layer) that provides a protective slime coating around the bacteria colony (Figure 4). Bacteria that form polysaccharide layers can exist in both aerobic and anaerobic environments, and an increase in the flow of groundwater and associated nutrients or oxygen can cause the slime to grow rapidly (Chemical Cleaning, Disinfection & Decontamination of Water Wells, Schnieders, J.H., 2003).

For example, the louvered screen shown in Figure 4 had been cleaned only 60 days prior to the date of the screen capture images from a well video. The changed conditions from cleaning the well two months earlier (to address different types of iron and manganese scale) resulted in rapid and extensive development of slime-forming biofilm.

Lessons Learned from Experience

Some lessons are provided to us by the experience of our past evaluations of well conditions. Based on many wells at various locations, we know that biochemical scale does not grow equally on all steel types. Due to the higher iron content of low-carbon steel, a much greater amount of biochemical scale will be expected to develop on casing and screen composed of that material, as opposed to stainless steel or other steel alloys.

Figure 5. Variable scale growth on different steel types. Screen capture images from a video of a well in El Paso, Texas, with alternating stainless steel screen and low-carbon steel blank casing.

It is difficult to draw a valid comparison of water wells made of different steel types since such wells are generally installed at different locations, by different drillers, at different points in time.

However, screen capture images from a video survey of a well in El Paso, Texas, provide us with a good comparison of scale accumulation on these different steel surfaces. The unusual attribute of the El Paso well is that it has alternating stainless steel screen sections (top photograph in Figure 5) and low-carbon steel blank casing sections (middle and bottom photographs in Figure 5). As can be seen in the figure, the stainless steel portions of the well have minimal scale accumulation, while the low-carbon steel portions of the well have significant biochemical scale buildup.

Another less obvious lesson that has been provided by past experience comes from occasions when a well was decommissioned or modified, such that the filter pack material was removed and could be inspected.

We tend to interpret how much well development (or more commonly, redevelopment) is needed for a particular well on the basis of what we observe in downhole videos of the well. It is important for us to recognize that the biological and chemical clogging doesn’t occur only on the inside of the well screen. A significant amount of clogging can also be located outside the screen within the filter pack envelope and sometimes even in the adjacent formation.

Figure 6 shows examples of filter pack sand that was removed from a well that had been completely clogged with scale to become a solid conglomerate of scale-cemented filter pack sand.

Recommendations and Referrals

Figure 6. Examples of filter pack sand that was removed from wells which had become entirely clogged with scale deposits. Dime is used for scale.

An overview of the chemical and biological clogging elements to be addressed during chemical and biological well development/redevelopment were provided in previous paragraphs, but I’ve made no mention of the methods, materials, or other considerations that will be needed to achieve effective well development/redevelopment.

That’s because the topic exceeds the limits of this column, both in terms of the allotted text area and my limited expertise on the topic of chemical and biological well development. For that reason, my best advice is to seek bona fide expertise on the topic.

The generalized considerations I’ve outlined are inadequate to cover the numerous conditions that are routinely encountered at various well sites, and the few bits of experience I’ve provided may not be applicable to specific challenges in upcoming projects.

That’s why my recommendation is to contact one of the individuals who are listed at the right. I’ve worked with and professionally interacted with each of these guys, and while they are not the only qualified experts in the field of chemical and biological well development/redevelopment, they are definitely some of the most capable and experienced individuals in the groundwater industry. I recommend all of them (listed in alphabetical order):

Each of these individuals have an exemplary track record for success and they all adhere to sound scientific principles. So, I recommend contacting these individuals for project-specific advice on the chemical/biological aspects of well development.

Learn The Art of Water Wells
Get The Art of Water Wells by Marvin F. Glotfelty, RG, a 2019 book from NGWA Press that is a comprehensive overview of well systems and delivers practical information applicable to real-world situations. The book is ideal for everyone working in the groundwater field. It provides practical information of water wells—covering everything from site selection to design, drilling methods, economics, and more. Click here to order it, call (800) 551-7379, fax (614) 898-7786, or email
Have a Drilling Question for Glotfelty?
Is there a drilling issue that you have wondered about for a long time? A question you have wanted a second opinion on for a while? Send them to The Art of Water Wells column author Marvin F. Glotfelty, RG, and he will utilize his more than 35 years of experience to tackle the question for you. Email Glotfelty at, and the answer will appear in an upcoming WWJ video.

Marvin F. Glotfelty, RG, is the principal hydrogeologist for Clear Creek Associates, a Geo-Logic Associates Co. He is a licensed well driller and registered professional geologist in Arizona, where he has practiced water resources consulting for more than 35 years. He is author of The Art of Water Wells (NGWA Press, 2019) and was The Groundwater Foundation’s 2012 McEllhiney Lecturer. Glotfelty can be reached at

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