Animal Agriculture’s Effect on Water Quality: Waste Storage

Purdue Extension publication WQ-8-W


Alan L. Sutton, Department of Animal Sciences


Indiana’s large and varied livestock industry makes up almost half of the state’s agricultural commodity sales. Due to economics, labor efficiencies, equipment and other factors, confinement systems of livestock production are prevalent. Confinement systems require the difficult task of col- lection and disposal of large volumes of manure in a relatively small area. Proper management of animal waste protects the quality of Indiana’s water supplies.

Waste by-products from livestock production that must be stored and utilized, include: animal excrement (manure and urine), waste water, spilled feed and sometimes bedding. The specific components in animal waste which can cause contamination are: nitrogen, phosphorus, inorganic salts, carbon compounds and microorganisms.

To protect Indiana’s waterways from pollution by livestock feedlot operations, the state legislature in 1971, enacted the Indiana Confined Feeding Control Law, requiring operations above certain sizes or those identified as polluters to obtain approval for their manure management systems. Approval is the responsibility of the Indiana Department of Environmental Management (IDEM). The law requires that livestock operations subject to the law provide: (1) adequate storage capacity for feedlot runoff and manure to permit timely disposal on the land; and (2) adequate equipment and land for waste disposal.

Figure 1. Open feedlot showing settling basin used with a holding pond and grassed infiltration area. Runoff from shelter roofs is directed to grass channels around the building.

Figure 1. Open feedlot showing settling basin used with a holding pond and grassed infiltration area. Runoff from shelter roofs is directed to grass channels around the building.

Storage facilities for animal waste allow producers to apply manure when conditions for contamination are reduced and nutrients can best be utilized. Management practices to prevent or reduce the risk of contamination from liquid or solid waste storage facilities are discussed in this bulletin.

Lagoons and Earthen Pits

Common methods for collecting and storing liquid waste are earthen lagoons, holding ponds and pits. Other methods used for waste storage include above or below ground tanks of concrete or steel. Generally these types of storage pits have little opportunity to affect water quality.

Lagoons hold diluted waste for 6 to 24 months. They are designed to allow waste to partially decompose before field application. Smaller than lagoons, earthen pits store liquid manure from one to six months. Little decomposition occurs because of the short holding time and little dilution. Consequently, nutrient levels are higher in earthen pits than lagoons.

Animal manure “seals” the bottom of earthen basins, such as lagoons and pits, constructed in heavy-textured, clayey soils. The bottom seal minimizes most downward nutrient leaching. Earthen basins — constructed in sandy, well-drained soils, in high water table areas or where bedrock containing useable ground water is within 30 feet of the surface — require additional precautions to prevent leaching of nutrients into ground water supplies.

The bottom of earthen basins should be lined with compacted bentonite clay or synthetic lagoon lining materials to control leaching. Earthen basins should also be lined on the inside walls to prevent leaching through the wall when the liquid level changes. Otherwise, the soil on the walls can dry and crack as the level drops. Leaching then occurs through the walls as the level rises. Old tile lines must be completely sealed at the location of the earthen basin to avoid drainage to waterways.

Holding Ponds

Figure 2. Levels of an earthen basin waste storage facility.

Figure 2. Levels of an earthen basin waste storage facility.

Used for short-term storage of feedlot runoff, holding ponds are smaller than lagoons. Little decomposition occurs in holding ponds. The runoff is held in the pond until application to crop land through irrigation systems.

The same considerations of sealing lagoons against leaching also apply to holding ponds. Uncontaminated runoff from shelter roofs should be kept out of the waste facilities and diverted to a separate drainage system.

A settling basin located between the feedlot and holding pond collects between 60-75 percent of the solid waste (Figure 1). With a settling basin, the holding pond can be a smaller size and will produce fewer odors. The life of the holding pond will also be extended. With less solid matter, the runoff can be applied by smaller irrigation systems.

The grass banks of lagoons and ponds must be maintained to reduce erosion. Prevent groundhogs or muskrats from digging burrows into the banks. During a heavy rainstorm these weakened areas can break down.

Lagoon and pond volumes should allow for a large and sudden amount of rain. A recommended 12-inch grass spillway will absorb any overflow and reduce erosion (Figure 2).

Solid Waste Storage

Figure 3. Solid waste storage on a concrete pad.

Figure 3. Solid waste storage on a concrete pad.

Solid manure storage is used when manure sufficiently dries or where enough bedding is added to form a stackable solid. The manure is usually piled on a concrete pad to prevent leaching to ground water and to facilitate loading (Figure 3).

It is a violation of Indiana law to allow livestock waste and lot runoff to reach any drainage area or waterway. Runoff control measures also must be provided for solid manure storage.

Covering the storage area with a roof will prevent rain and snow from causing runoff, and maintain the nutrient value of the manure. Collect run- off from the solid storage and dispose of on growing crops to prevent ground water contamination. A filtering channel of grass around the storage area will also help absorb runoff and utilize nutrients.


Composting is an aerobic microbial treatment of solid manure. Com- posting reduces manure volume and transforms the manure into a more stable nutrient form. The stable nutrients (mostly in organic form) are less likely to leach or be transported with runoff water.

Horse and poultry wastes are most often used in composting. Commercial sale of compost can provide a second enterprise for large livestock operations. Currently composting is not a common practice in Indiana. Very few markets have been developed in the state.


In addition to minimizing nutrient leaching from feedlots, barnyards and manure lagoons, the location of these facilities with respect to water supply wells is also important. Water supply wells can become contaminated with bacteria and nitrate associated with animal manures.

Maintaining a distance of at least 100 feet between animal quarters or manure holding areas and properly constructing water wells decreases the risk of contamination and its potential health effects. In addition, replacing shallow wells with deeper wells, properly encased at upper levels, often eliminates problems from nitrate and bacteria contamination.

For Further Information:

For further information on livestock production and water quality contact your county Cooperative Extension Office. The following bulletins in the WQ series may be helpful:

WQ-1-W Water Testing Laboratories
WQ-7-W Animal Agriculture’s Effect on Water Quality Pastures and Feedlots

Other sources:

ID-101-W Utilization of Animal Manure as Fertilizer
ID-114-W Runoff Control Systems for Open Livestock Feedlots
PIH-153 Pork Industry Handbook
MWPS-18-1 Manure Management Systems Series: Manure Characteristics

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Published: July 1990

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