Safeguarding Wells and Springs from Bacterial Contamination

Techniques on how to construct wells and springs to minimize the possibility of harmful microorganisms entering water supplies. Read about other measures that will help keep drinking water biologically safe.

Many Pennsylvanians rely on their own wells or springs for their water supplies, and the quality of their drinking water depends in large part on how effectively they manage their systems. As private operators, they must take steps to ensure that their water is safe to drink. It must be free of pathogenic bacteria, viruses, and harmful chemical impurities. It should also be clean, clear, and nonstaining, without offensive tastes or odors.

Bacterial contamination is one of the most common problems but also one of the simplest to prevent. It may result from poor location or construction of the water system.

Water supply management

Managing a water system to provide safe drinking water requires three steps:

  • Finding out what to do and how to do it. Reading this publication is a good start.
  • Taking action, such as having the water tested periodically or installing water treatment equipment.
  • Maintaining a complete file of water management records, including water test reports, treatment-equipment warranties, and owner's manuals, along with information about the well itself, such as depth and yield. Records are especially useful if water quality or quantity is problematic because they provide information that the owner or a professional can use to diagnose the problem and to find a solution.

Well location

Since a well's location determines the quality and quantity of the water obtained, one should plan carefully before choosing the site. In an area where unconsolidated materials like sands and gravels exist, a well can be located anywhere and the chances of obtaining adequate quantities of water will be good. In consolidated bedrock, however, the greatest amounts of water occur in fractures and weathered openings along fractures and bedding planes. This holds true even in porous rocks like sandstones. If a high-yielding well is desired and if space permits some flexibility in siting, it is best to locate the well on a zone of fracture, or even better, at the intersection of two such zones.

A technique has been developed to allow zones of fracture concentration to be mapped on aerial photographs. To determine the location of such zones, trained hydrogeologists study the alignment of surface sags and depressions, soil tonal differences, and vegetation patterns. These features can be identified on aerial photographs, and potential sources of pollution can be noted. Field observation and geologic maps are used to determine the type of rock at the drilling site. Also, historical data can help determine the quality and quantity of water obtained from different rocks. All of this information may then be used to locate the well.

Well location influences the quality and quantity of the water obtained. Groundwater that supplies wells is usually free of microorganisms because the overlying soil acts as a filter. But soils differ greatly in their filtering ability. Clays and fine sands are better filters than gravels, coarse sands, and porous subsoils. Usually, the further water travels through a good filtering bed, the safer it becomes.

It is difficult to specify at what distance from a septic tank or any other source of contamination a well should be located to yield safe water. However, there are general guidelines. Wells should be located upslope from contamination sources, although this alone will not guarantee water purity. The Pennsylvania Department of Environmental Protection (DEP) recommends that wells be built at the following minimum distances from various contamination sources:

  • Storm drains - 25 feet
  • Sewers and drains for domestic sewage or industrial wastes - 50 feet
  • Septic tanks - 50 feet
  • Privies - 50 feet
  • Sewage seepage pits and cesspools - 100 feet
  • Subsurface sewage disposal fields - 100 feet

In general, the further the well is from sources of contamination, the less likely it is that the water supply will become contaminated.

Selecting a well driller

The same care should be exercised in selecting a well driller as would be taken in contracting to build a house. The driller must be licensed by the Commonwealth of Pennsylvania, and certification by the National Water Well Association is desirable. The driller's past performance can be checked by contacting former clients. Finally, the driller should be insured, and a contract that specifies services and costs should be prepared.

Well construction

The quality of well water often is determined by the care taken in well construction. If surface water enters an improperly constructed well, groundwater may be contaminated. Any aquifer that is penetrated should be protected from such contamination, and an appropriate amount of casing should be installed with grouting along the casing's entire length (Figure 1).

Pitless Adapter

Figure 1. Pitless adapter with submersible pump installation for basement storage. (Source: Adapted from Manual of Individual Water Supply Systems, EPA-430/9-74-007, U.S. Environmental Protection Agency.)

Several basic steps are involved in making sure that a well is properly constructed. The borehole for bedrock wells must be straight to allow for proper casing placement and pump access. Well depth should rarely exceed 300 feet. Properly constructed wells usually yield sufficient water at depths of less than 200 feet. If sufficient water is not encountered before reaching a drilling depth of 300 feet, a new borehole should be started at a different location. Wells drilled deeper than 500 feet in Pennsylvania may yield extremely salty water that is unsuitable for most uses. The temptation to extend borehole depths to increase storage capacity should be resisted. At a drilling cost of $6 per foot, each gallon of storage space in a well having a 6-inch diameter costs $4. In addition, there is always a chance that poorer-quality water will be encountered at greater depths.

In Pennsylvania, most wells are drilled in bedrock, but there are areas in the glaciated northern regions of the state where sand and gravel aquifers may be found. In these areas, well drilling and construction methods may differ because wells may be jetted with water under pressure to scoop out a borehole. Casing must extend the entire length of the borehole to prevent cave-ins, and a well screen must be used to keep sand out of the borehole. A flowing mixture of cement or grout should be forced into the space between the well casing and the sides of the borehole. Grouting should be done above the water-bearing sand or gravel deposit.

The casing should be new and able to withstand strong pressures. The casing joints should be watertight. Steel and thermoplastic pipe may be used for casing materials. If plastic casing is used, it should conform to American Society for Testing Materials (ASTM) standard F-480-76 or National Sanitation Foundation (NSF) standards (NSF seal on pipe).

In consolidated rock, casing is lowered into the borehole to the top of the bedrock, and grout is pumped into the bottom of the casing and forced up along the outside of the casing until it flows onto the ground. An alternate grouting technique requires that the borehole be plugged at the bedrock contact, filled with grout, and the casing set in the borehole.

If loose sand or gravel is encountered during drilling, a well screen may be required. Well screens are not usually required when drilling in bedrock, but they may be necessary when drilling on zones of fracture. Screens are designed in a range of sizes to prevent sand and larger particles from entering the well.

Well development (removing fine cuttings or sands) is sometimes required to provide maximum yield and to prevent clogging where sand and mud are encountered during drilling. The most common method of development is called "surging," the rapid movement of a plunger up and down the well to dislodge small particles retarding groundwater flow to the well. Once the particles settle to the bottom, they may be removed by bailing.

All well casings should be extended at least 8 inches above ground or high enough so that flood waters can never enter the well via the top of the casing. Well pits or buried casings should never be installed. A pitless adapter, pitless unit, or above-ground discharge adapter should be used for water line access. The pitless adapter (Figure 2) is used most often, since it allows the water service line to the home to enter the well casing through a sanitary seal located below the frost line. This protects the well from both frost and contamination. A sanitary well seal should be provided for the top of the casing. If the seal has a compressible gasket, it also should have a screened vent.

Clamp-on Pitless Adapter

Figure 2. Clamp-on pitless adapter for submersible pump installation. (Source: Manual of Individual Water Supply Systems, EPA-430/9-74-007, U.S. Environmental Protection Agency.)

The yield of the well should be determined at the time of construction. The simplest method of conducting a pumping test is to have the well driller use a bailer to determine the average amount of water removed from the well during some elapsed time, usually expressed as gallons per minute (gpm). The change in water level from the beginning to the end of the test is also measured and recorded. Wells already in service should be pumped at full capacity for a predetermined period of time, and the change in water level, along with the pumping rate (gpm) and the elapsed time from the start of the test, should be measured and recorded. To obtain the most reliable information, pump tests should be done in dry and wet seasons of the year. This information will be useful in the event that diminished well yields are experienced in the future.

Measuring the water level in small-diameter wells that are in service is sometimes very difficult because it is impossible to drop a weighted string or tape down the well. In such cases, a solid copper or rigid plastic tube may be inserted down the well until the end is under water. The submerged end of the tube should be at least two feet above the pump to prevent incorrect readings. A pressure gage and a hand air pump are attached to the other end of the tube and air is introduced into the tube until the pressure gage reading remains constant. The pump is then started and run for a predetermined period of time. At the end of the measurement period, with the pump still running, the pressure gage reading is recorded. The second pressure gage reading is subtracted from the first and is multiplied by 2.3 feet to determine the change in water level.

Before well construction is completed, the well must be disinfected using the shock chlorination procedure described in Box 1. Care should be exercised to ensure that the entire system is disinfected. When construction is completed, a copy of the completion report (Box 2) should be obtained from the well driller and kept with other water supply records.


In rural areas springs often are used for water supplies. Springs occur where groundwater discharges to the land surface. Depending on the geology of an area, the discharge may bubble from a fairly distinct point, (e.g., from fractured bedrock) or may surface as seepage areas with no well-defined discharge po1nt, as when an impervious layer of soil channels groundwater to the surface.

Although springs can be a good source of water, they may not provide enough water throughout the year to be a reliable supply. Many springs are fed by water that is fairly close to the soil surface so that during periods of drought there may not be enough water in these areas to keep the spring flowing at a sufficient rate.

Another problem with springs fed by shallow groundwater is that they are contaminated easily by microorganisms and other pollutants from the land surface. For this reason it is important that no contamination sources be located upslope from the spring and that any surface runoff be diverted away from the spring development. Fenc1ng to keep livestock out of the catchment area is advisable. Because springs are so easily contaminated, installation of disinfection equipment usually is necessary.

Springs that become muddy shortly after a rain shower probably should not be developed as water supplies because surface water provides much of their flow. These springs are likely to be highly unreliable and may be contaminated.

Before proceeding with development, the total daily flow from the spring should be estimated to ensure that it at least equals the daily water need. (Provisions for peak water use can be met by using a storage tank.) To make a crude estimate of the spring's flow, the flow rate should be measured during the lowest flow period (usually in the late summer or fall) by constructing a temporary clay dam below the spring to channel the water. A pipe is placed through the dam and the time required to fill a container of known volume is recorded. Then the flow rate is calculated.

Figures 3 and 4 provide examples of spring development under various conditions. For maximum protection against contamination, a properly developed spring should have the following characteristics:

  • absence of contamination sources
  • a collection system to concentrate and channel the flow (e.g., a cutoff wall or a system of perforated pipe located where the water is at least 3 feet below the surface)
  • a reinforced-concrete spring box with a secure cover, an overflow pipe, and provisions for emptying, access, and cleanout (Figure 5)
  • additional storage capacity and disinfection equipment, if necessary

Spring development in creviced rock

Figure 3. Spring development in creviced rock. (Source: Adapted from Spring Development, Plan 800-166, Department of Agricultural Engineering, The Pennsylvania State University.)

As with wells, spring developments also should be disinfected after construction (Box 1). After disinfection, the water should be tested for bacteria.

Spring Development in a Seep

Figure 4. Spring development in seep area. (Source: Adapted from Spring Development, Plan 800-66, Department of Agricultural Engineering, The Pennsylvania State University.)

Testing water for bacteria

Pathogenic bacteria may be present in sewage and animal manures. Sometimes these microorganisms find their way into the groundwater that supplies wells or springs, infecting humans who drink the water. The most common illnesses associated with water-borne bacteria are gastrointestinal ailments such as diarrhea and stomach cramps. Diseases such as hepatitis (a virus) and giardiasis (caused by a protozoan) can also be transmitted by water.

Bacteria, viruses, and giardia cysts in the Intestines of sick people or animals are excreted with fecal waste. In rural areas most human waste is treated by a septic system that discharges effluent (still containing microorganisms) into the soil. Microorganisms in manure spread on cropland can also get into the soil. In both of these cases, harmful microorganisms will probably not contaminate groundwater because the microorganisms are filtered by the soil and die in this hostile environment. However, soil does not always remove harmful microorganisms. In saturated soils with large pore spaces, for example, water may move through the soil too quickly or not come into contact with enough soil particles for the water to be rid of these infectious agents.

To find out the quality of the water supply, a sample should be tested by a DEP-accredited laboratory. The labs test for the presence of total coliform bacteria which are found in the intestines of warm­ blooded animals and elsewhere. Testing for coliform is easier and less expensive than testing for individual, disease-causing microorganisms, so this group of bacteria is an indicator of contamination by sewage or animal waste. Most coliform bacteria do not cause illness, but if they are in the water, then pathogenic bacteria, viruses, or protozoans may also be there. Drinking water should contain no coliform bacteria.

Water should be tested for bacteria at least once a year, preferably every six months. To obtain the names of area water testing laboratories, check the telephone directory or call an Extension or DEP office. Ask the laboratory for instructions on how to collect and handle a water sample.

Sources of bacterial contamination

Bacteria and other microorganisms that contaminate a water supply may come from any number of sources, including the following:

Septic systems

Improper design, location, construction, or maintenance of septic systems can result in groundwater pollution. To lessen the load on the system, water conservation devices can be installed in the home. The tank should be pumped at recommended intervals. Septic tank "cleaners" should be avoided because they may damage the system or put chemicals into groundwater.

Silos and barnyards

If it finds a path to the groundwater supply, seepage from a silo or runoff water from a barnyard or manured field can also cause problems. Manure and silo liquids are highly contaminated with bacteria and cause water to turn dark and take on an objectionable odor.


These depressions or low spots in limestone areas provide a direct connection to the groundwater below. Contaminated water that flows into a sinkhole may reach groundwater without being filtered by soil. This water may flow through solution channels in the limestone, polluting wells and springs some distance away. Garbage, farm wastes, or dead animals should never be thrown into sinkholes or left where the drainage from them can infiltrate the groundwater supply.

Abandoned and active wells

Any well provides a conduit from the land surface directly to groundwater. Polluted surface water may enter the well and move rapidly to the underlying aquifer, contaminating groundwater. Because the well borehole may penetrate several aquifers, if a polluted aquifer lies above an unpolluted one, water from the polluted aquifer may drain through the well and contaminate the aquifer that lies below. Abandoned wells should be filled (with cement grout or clay) in such a way as to prevent water movement within the borehole and groundwater pollution. Active wells should be properly located and grouted. (See well construction section. Procedures vary with specific site conditions.)

Continuous disinfection of water supplies

If a water test indicates bacterial contamination, both the water supply location and the construction of the system should be checked for contamination pathways. Necessary improvements should be made and the system shock chlorinated. After two weeks, the water should be retested. If contamination is still present, the owner should find a new source of water or should continuously disinfect the present one.

Figure 5. Spring Box

Figure 5. Spring box. (Source: Adapted from Manual of Individual Water Supply Systems, EPA-430/9-74-007, U.S. Environmental Protection Agency.)

It may be cheaper to disinfect bacterially contaminated water than to risk the expense of developing another source that may also be unsafe. Sources of water that are otherwise clean, adequate, and protected from surface pollution can be made safe for domestic use by chlorination, iodination, or ultraviolet light. Sources that are high in suspended solids or that sometimes appear muddy or discolored should be filtered prior to disinfection because disinfection, by whatever method, is effective only in clear water.

Commercially available disinfection equipment will effectively treat bacterially contaminated water, but other pathogens, such as certain viruses and giardia cysts, may not be killed by this equipment. In cases where these pathogens are present, special disinfection procedures or additional water treatment such as filtration are usually required. If you have any questions about the effectiveness of disinfection equipment, consult your equipment dealer and a DEP or Extension representative.


A common method of disinfecting water is to inject a chlorine solution into the water by means of a chlorinator (there are several types). Chlorine compounds such as sodium hypochlorite or calcium hypochlorite are used to make the solution. Sodium hypochlorite solution is available as household laundry bleach (about 5 percent available chlorine) or as swimming pool disinfectant (about 15 percent available chlorine). Calcium hypochlorite (65 to 75 percent available chlorine) comes in a powdered or tablet form. Container labels indicate whether drinking water disinfection is an approved use of the product.

Normally, all of the water from a given source must be chlorinated, but the quantity of chlorine can be regulated for different conditions. Disinfection is not instantaneous. There must be a period of contact time, and pipe coil or a baffled tank can provide space for this to occur. In most cases, at least 0.4mg/L of free residual chlorine should be in contact with the water for not less than 30 minutes.


Iodine, a well-known germicidal agent for cuts, scratches, and skin abrasions, can be used to disinfect water. A small quantity of an iodine solution mixed with water kills most bacteria in about thirty minutes of contact time. Although iodine is a good disinfectant, because of possible effects on the thyroid gland, it is not recommended for continuous consumption. However, in situations where no one will be drinking the water over a long period of time-such as at a vacation home or hunting camp-iodination may be a good choice.

An iodinator regulates the amount of iodine solution going into the water. The iodinator has no moving parts and requires no electricity for operation. It can be used on a gravity water system provided there is sufficient pressure in the supply line. A small tank containing iodine crystals is connected to the water line, and some water is diverted from the line into the tank. The crystals are dissolved to form a saturated solution, which is fed into the supply line. It may be difficult to set the feed accurately to achieve disinfection while minimizing taste problems.

Ultraviolet Light

This method uses an ultraviolet light tube sealed in a quartz sleeve inside a stainless steel cylinder, which is connected to the water supply line. The untreated water from the source comes in at one end of the cylinder, passes around the ultraviolet tube, and exits through the opposite end into the safe water line. Ultraviolet light emanating from the tube kills the bacteria. Unlike chlorination, the ultraviolet light process does not leave a residual disinfectant in the water and the possibility exists for water to be recontaminated. For this reason the ultraviolet light unit should be installed at the end of all underground piping.

There is no simple test to determine whether the ultraviolet light is operating effectively. Ultraviolet rays must reach bacteria to kill them. To ensure proper operation, the ultraviolet light bulb should be replaced when it weakens. If the manufacturer does not supply an ultraviolet intensity indicator on the unit, the bulb should be replaced once a year. Some units are equipped with a photocell that indicates whether the light is on or off. This does not provide sufficient protection against light failure, because the light may be intense enough to indicate that it is operating, yet ultraviolet light output could be diminished to the point of ineffectiveness.

Other contaminants

Although bacterial contamination of private, individual water supplies is a very common problem, contamination by other substances, both natural and synthetic, may also occur. Before a new well or spring is put into service, the water should be tested for other possible contaminants. In addition to the test for bacteria, tests for pH, nitrate, total dissolved solids, and turbidity should be run. If the water's pH is less than 7.0 or if the water has more than 500 mg/L total dissolved solids, it may be corrosive to metallic plumbing. If the plumbing is copper and corrosion is suspected, tests for copper and lead should be made on a water sample that has stood in the pipes overnight. If the plumbing is galvanized iron, test for zinc and cadmium. In areas where particular contaminants are known (or suspected) to be present, additional testing for these contaminants should be done. The local Extension or DEP office can offer advice on testing procedures and can help interpret the results.

The water quality of existing wells and springs should be continuously monitored by periodic testing. In addition to testing for bacteria every six months, chemical tests should be performed at least every three years. Of course, if there is any change in the appearance, taste, or odor of the water, or if there is a change in land use in the area that may affect the water supply, the appropriate water tests should be conducted immediately.

Water-supply management steps

To ensure safe water supplies, water systems must be managed effectively:

  • Locate and construct wells and springs properly to protect them from contamination sources.
  • Test the water regularly.
  • Use treatment equipment, if necessary, and maintain the equipment according to the manufacturer's recommendations.
  • Keep records of all management actions.

Box 1. How to shock chlorinate wells and springs

If the water contains suspended particles, the well should be pumped until it clears. Mix household laundry bleach approved for water disinfection (see Table 1 to determine quantity) with 5 to 10 gallons of water in a non-metallic container. Pour this solution into the well. To mix the chlorine with the well water, run a hose from a faucet beyond the pressure tank and circulate the water back into the well, washing down the sides of the casing, for fifteen minutes. Close the faucet and reseal the well. Next, open a faucet at the far end of the system, let it run until you smell chlorine, then turn it off. Do this with all the other faucets to disperse chlorine throughout the system. The next morning pump the chlorinated water out of the well onto the ground away from any water bodies containing fish, then flush the pipes by letting the faucets run until the chlorine odor is gone.

Dug or bored wells should be disinfected in the same way as drilled ones. Lower the water level as much as possible; remove any sand, silt, and debris; and treat the water with a chlorine solution (Table 1). Do not try to disinfect an unprotected, unlined well because contaminated seepage or surface contamination may flow into the water as fast as you can disinfect it.

For springs, mix about ½ cup of household bleach with 5 gallons of water and use this solution to scrub the walls of the spring box. Make sure there is adequate ventilation. Shock chlorination for springs operates on the same principle as for wells. Make a disinfection solution by mixing 3 pints of household bleach with several gallons of water in a nonmetal container. This will be enough to disinfect about 100 gallons of water. (A spring box holds 7% gallons of water for each 1 cubic foot of storage space.) If the spring flow is low enough it may be possible to keep the disinfectant in the spring box for the required time. Otherwise you may have to add disinfectant continuously throughout the period.

In an emergency, small quantities of water should be boiled vigorously for 1 full minute, while larger quantities can be treated with chlorine bleach approved for this use. Follow the instructions on the container label or mix 2 drops of the bleach (about 5 percent available chlorine) thoroughly with each quart of clear water and let it stand for 30 minutes. This treatment should produce a mild odor of chlorine in the water. If it does not, repeat the dose and wait another 15 minutes.

Iodine may also be used. Add 5 to 10 drops of tincture of iodine for each quart of clear water to be disinfected and mix thoroughly. Wait 30 minutes before using it. Commercially prepared tablets containing iodine or chlorine can be purchased from drug and sporting-goods stores. Follow the label instructions for correct use.

  Well diameter, in.
6 8 10 24 32 36
10 1 c
1 c 2 c
3 qt
4 qt
6 qt
20 1 c 2 c
4 c
5 qt
8 qt
10 qt
30 2 c
4 c
3 pt
1 pt
2 pt
4 pt
60 2 pt
3 pt
6 pt
80 2 pt
4 pt
7 pt
100 3 pt
5 pt
4 qt
150 5 pt
4 qt
6 qt

Note: The table shows the quantity of household laundry bleach (5.25 percent chlorine, approved for water disinfection) required to develop a concentration of 100 ppm of chlorine in clear water standing in the well. If you can not determine the depth of the water in your well, use the following guidelines: For wells up to 8 inches in diameter holding less than 80 feet of water, mix a minimum of ½ gallon of chlorine bleach with about 10 gallons of water. For wells with more than 80 feet of water, use 1 gallon of bleach. In any case, it is better to use too much chlorine than too little.

Source: Adapted from How to Disinfect a Water System, Agricultural Engineering Fact Sheet SW4.

Well Completion Report

Box 2. Well Completion Report

Prepared by Joe Makuch, Department of Agricultural Engineering water quality specialist, Chesapeake Bay Project, and William E. Sharpe, associate professor of forest hydrology, School of Forest Resources and the Environmental Resources Research Institute. The Chesapeake Bay Program is a cooperative project between the Pennsylvania Department of Environmental Resources and related organizations, as well as county, state, and federal agencies. Development of this publication was supported in part by a grant from the Pennsylvania Department of Environmental Resources.

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Safeguarding Wells and Springs from Bacterial Contamination



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