Current Progressive Dairy digital edition

0307 PD: Manure storage and treatment systems

John W. Worley Published on 06 March 2007

Animal waste storage and treatment systems have historically been selected and designed to efficiently use valuable fertilizer nutrients for crop production while protecting soil, air and water quality. The primary reason to store manure is to allow the producer to land-apply the manure at a time compatible with the climatic and cropping characteristics of the land receiving the manure.

Manure nutrients can be best utilized when spread near or during the growing season of the crop. Therefore, the type of crop and method of manure application are important considerations in planning manure storage and treatment facilities.



Alternative storage and treatment systems

Many dairy operations use liquid or slurry manure storage and handling systems. The discussion here will focus on liquid systems. However, slurry systems will also be discussed in order to enhance understanding of the difference between the goals and management strategies of the two systems.

Dry systems (systems where manure is handled as a solid) will also be discussed. Some systems use solids separation devices to remove some of the solids from the liquid stream. These systems are really a combination of liquid and dry systems and must be handled as such.

Liquid storage systems (lagoons)

Lagoons are probably the most common form of liquid manure handling system. A lagoon is a waste treatment system as well as a storage facility for manure, and it represents the most economical means currently available for reducing the waste stream in liquid systems.


A properly operating lagoon will reduce odors and convert much of the organic matter into gases which are given off to the air. Odor reduction comes as a result of purple sulfur bacteria which grow near the surface of the lagoon and convert odorous compounds (primarily hydrogen sulfide) into less offensive gases.

Lagoons reduce the amount of manure solids and nitrogen by converting organic nitrogen into nitrogen gas and ammonia. Phosphorus and potassium remain in the lagoon but tend to settle to the bottom and are stored in the sludge. If properly designed, constructed and managed, a lagoon will minimize seepage of nutrients into the ground below and will present little risk of overflow into surface waters.

Advantages of lagoon storage of manure may include treatment of manure to reduce odors and potential to handle manure with conventional pumping and irrigating equipment.

Disadvantages of lagoons include the need for a large earthen structure requiring more area than simple storage and the need for solids separation or sludge removal equipment if bedding or other non-biodegradable materials are present. In addition, the effluent from a lagoon is less well balanced with crop needs, since nitrogen is released, and phosphorus and potassium remain in the lagoon.

Manure slurry storage systems

Manure slurry storage systems tend to be used when the need for nutrients for crop growth in the area is high since these systems tend to maintain higher levels of nutrients (particularly nitrogen) than do lagoons. Manure storage facilities include fabricated (concrete or steel) or earthen structures. Fabricated structures may be above ground, or partially or fully below ground.


Manure is usually scraped or flushed from the production buildings and may flow into these tanks by gravity or be pumped into the tank from a collection sump or reception pit. Adequate agitation is necessary to suspend solids and facilitate complete removal of the contents of these manure tanks. Fabricated tanks are usually the least costly to cover, which is sometimes desirable for odor control.

Slurry manure may also be stored in earthen structures or basins. Because storage volume can usually be obtained at less cost in an earthen basin than in a fabricated facility, these facilities are often used when manure and wastewater volumes are relatively large due to washwater use or lot runoff. Earthen structures require a relatively high degree of planning and preliminary investigation to ensure proper soil materials are available to create a seal and that the seal is constructed properly.

These facilities are basically similar to lagoons, but much smaller since less water is added to the manure. Maintenance requirements may be greater with earthen structures because of the need for maintaining and mowing a vegetative cover on the berm area and keeping it free of weeds, trees and shrubs.

Agitation is equally important in earthen structures, and access points for agitation and pumping should be part of the design plan. Some earthen storage units are partially or completely lined with concrete and built with an access ramp so that loading and hauling equipment can enter the basin. Earthen storage structures are more difficult to cover than tanks if odor control is needed.

Odor is generally a greater problem in slurry storage structures than in a properly operating lagoon, but if coverage is necessary, it is less costly in a slurry storage facility because of the smaller size.

Advantages of storing manure in the slurry form may include less volume, adaptability to tank storage, possibility of covering the manure storage facility to reduce odors, higher nutrient retention and the potential to collect and transport hydraulically.

Disadvantages may include higher odor potential (unless storage unit is covered) and odor and runoff potential, if the slurry is spread without injection or incorporation.

Dry systems and solids separators

Dry manure storage can be as simple as using the confinement building itself as storage. In cases where crop needs do not coincide with the need to clean out a dairy lot, manure is often stacked either in a building or outside until it can be utilized by a crop. These stacks should always be covered to protect them against runoff in case of rain, or the runoff should be contained and treated as a liquid waste.

Another type of “dry” storage is a settling basin used to separate solids from a liquid stream. Typically, these basins are designed to store three to four weeks of manure, with two or more basins being utilized in order to allow one basin to drain while the other one is being filled. This design allows more flexibility in timing the application of solids onto crops and pastures. These basins are lined with concrete and the runoff from them flows into a lagoon to prevent contamination of surface waters.

Mechanical solid separators are also used. These devices usually produce a dryer product than a settling basin which is better for composting or hauling to remote sites or off the farm. Their main disadvantage is that, being mechanical systems, they do break down and require periodic maintenance. They also have a cost of operation involved since they require energy to operate. The solids from these systems are typically stored on a covered concrete pad or protected to ensure that runoff goes into a lagoon or storage structure.

Basic design principles


A lagoon must be sized to provide adequate storage for manure, dilution water (ensuring proper microbial digestion will occur), storage of sludge (indigestible materials that settle to the bottom), storage of rainwater and washwater and a safety margin in case of severe storms. Adequate sizing of a lagoon depends upon location, the number and size of animals using the lagoon, whether or not solids separation will be used and how long sludge will be allowed to build up before being removed. In addition, good management practices such as loading the lagoon on a uniform basis, maintaining proper vegetation on berms, regular inspections and maintaining safe levels in the lagoon, are necessary to provide safe, efficient operation.

Lagoons must be designed by a properly trained engineer (NRCS or consulting engineer). The berms (walls) must be designed to be stable under load, and the lagoon must be properly lined with either a compacted clay or synthetic liner to prevent leakage into groundwater. The owner or operator should understand the limitations of the system and how the expansion of animal numbers may prevent the lagoon from operating properly. He or she should know the capacity of the lagoon, how many animals it is supposed to handle, how often it should be pumped down and to what level it should be pumped down. Any major expansion or change in the operation of a facility would require a reassessment by the design engineer.

Manure slurry storage

The actual size of a manure slurry storage structure needed depends upon the same factors used in sizing a lagoon with the notable exception that no treatment volume of water must be added since microbial breakdown of manure is not desired. Manure is left in a more solid state, which hinders bacterial growth. Also, sludge accumulation is not accounted for since this facility should be completely emptied one or more times per year.

The design storage period plays a significant role in sizing these structures. Storage period needed depends primarily upon cropping system, climatic conditions and labor or equipment availability. Most operations utilizing a single, full-season annual row crop or small grain crop will need at least six months of manure storage to schedule land spreading around cropping operations. Experience has shown that even a full year’s storage is beneficial when wet conditions may make fall application difficult and manure needs to be stored until spring.

A manure storage facility for a given number of animals is much smaller than a lagoon for the same farm, since no storage space is needed for dilution water. However, adequate size must still be supplied for manure storage, rainwater and a safety factor for severe storms.

As in the case of lagoons, a manure slurry storage system should be designed by an NRCS or properly trained consulting engineer, whether it is an earthen basin or a concrete or steel structure. The engineer should also be consulted before any expansion or major change in the operation takes place.

Dry systems and solid separators

If manure is to be stored in a building, the building should be designed to safely handle the loads it will experience, and it should be designed to withstand the corrosive atmosphere in which it will exist while manure is stored in it. Assistance on building design is available from the NRCS or the Cooperative Extension Service. Concrete floors are recommended, but clay floors are acceptable if mortality composting is not to be done in the facility.

Storage of manure in stacks outside a building should be avoided when possible. Stacks can be covered with plastic which will protect them from leaching while in place, but when the stack is removed and spread on a field, it is almost impossible to remove all of the manure, and the remaining manure can leach into the soil.

Settling basins for separating solids should be designed to be structurally sound and to be large enough to provide flexibility in the timing of manure application from the basin. Again, assistance can be obtained from the NRCS or Cooperative Extension Service.

Effects on nutrient management

The amount of nutrients available for use on crops is affected by the method used to store manure, as well as the application method. In estimating the total amount of nutrients available for use annually, the total nutrients excreted must be adjusted for storage and application losses. When applying material from an aerobic lagoon for instance, up to 90 percent of the excreted nitrogen can be lost during the anaerobic treatment of the waste. This nitrogen is lost to the atmosphere primarily in the forms of nitrogen gas and ammonia.

There are also losses of phosphorus and potassium, but unlike nitrogen, these nutrients accumulate in the sludge layer of the lagoon, which must eventually be removed and applied to the land unless some arrangements can be made to remove the sludge from the farm. For this reason, 90 to 95 percent of excreted phosphorus and potassium should be accounted for in the overall farm nutrient management plan.

Operation and monitoring of lagoons and slurry storages

Lagoons combine storage and treatment functions and thus are more sensitive to management inputs than are solid or slurry facilities. The establishment and maintenance of desirable microbiological populations in lagoons requires more specific procedures in the way lagoons are loaded and monitored.

Start-up and loading procedures

Lagoon start-up is an important factor in developing a mature lagoon that has an acceptable odor level and will perform in the expected manner over the long term. Lagoons are designed with a treatment volume that provides an environment for development and maintenance of a bacterial population that degrades and stabilizes manure.

The size of the treatment volume is based on a volatile solids (VS) loading rate, which depends primarily upon temperature. (Volatile solids are those that can be converted to gases by bacteria.) The proper VS loading rate is achieved only if the lagoon contains a volume of water equal to the treatment volume at start-up.

It is very important to have sufficient water in a lagoon at start-up. The treatment volume should be used as a target. Achieving this goal may require identifying a water source (pond, lake) and implementing the needed pumping procedures to transfer the desired volume of water to the lagoon.

Since bacteria are more active at warmer temperatures, consideration should be given to starting a lagoon in the spring or early summer. In this way, bacteria will have a warm season to establish themselves before activity slows during the winter. Spring start-up of lagoons often requires special planning of construction schedules and animal procurement.

In addition to start-up, long-term loading procedures are critical to lagoon performance. A somewhat common and unfortunate practice in the livestock industry is to expand animal numbers without expanding lagoon size. This results in a proportionate increase in VS loading, and associated problems can be expected to develop. Volatile solids loading should not be increased beyond the facility’s design. Alternatives to reduce VS loading (or expand animal numbers) include solids separation, construction of additional lagoon volume or pretreatment of manure.

Lagoons should also receive manure in a consistent manner (no “slug” loading). This is usually accomplished in modern production systems utilizing hydraulic transport of the manure to the lagoon. Sludge must be periodically removed from the lagoon, as a buildup of sludge also reduces treatment volume, reducing the effectiveness of bacterial treatment. Sludge should be maintained at or below the design level.

Overall monitoring activities

Certain activities are advisable and necessary in maintaining a manure storage structure and ensuring it is performing as expected. Some of these activities may be required by regulation, but all are evidence of good management and stewardship regardless of regulatory requirements.

Monitoring during pumping activities

Experience has shown unplanned discharges and spills most often occur with pumping activities. Sources of such unplanned discharges include burst or ruptured piping, leaking joints, operation of loading pumps past the full point of hauling equipment and other factors. Hence, pumping activities should be closely monitored, especially in the start-up phase, to ensure no spills or discharges occur. Continuous pumping systems such as drag-hose or irrigation systems can be equipped with automatic shut-off devices (which usually sense pressure) to minimize risk of discharge in the event of pipe failure.


Liners in earthen manure storage impoundments are designed and constructed to provide an adequate barrier between the potential contaminants in the impoundment and groundwater. Hence, liner integrity is extremely important in maintaining an environmentally sound manure storage facility. To the extent possible, liners should be regularly inspected for signs of damage, erosion or other compromising factors.

Wave action can cause liner erosion at the level of the liquid in the impoundment. If this condition is severe, consideration might be given to the use of riprap or similar mitigation methods to preserve liner integrity.

The area around the pipes that discharge into the impoundment is also subject to erosion, especially if the pipes discharge directly onto the liner surface. A better configuration is to install inlet pipes such that they discharge into at least 4 feet of liquid, which may require a supporting structure for the end of the pipe. Concrete or rock chutes should be used with inlet pipes that discharge onto the liner surface.

Agitation is also an activity that can damage liners. Care should be taken to operate agitators a sufficient distance above the liner so liquid velocities are reduced enough to ensure erosion does not occur. Heavy or unusual rainfall events can also erode liners, and special attention should be given to liner inspection after such storm events.

Logbooks and record keeping

Certain data and record keeping involving manure storage structures can aid in overall maintenance and management, and it is also evidence of responsible operation and good record keeping. In addition to periodic inspections, manure levels in a storage structure should be monitored and recorded. This data can illustrate the effects of excessive rainfall and lot runoff and help in planning pump-down or other land application activities.

Manure levels should be observed and recorded frequently enough to provide a feel for the rate of accumulation, and pumping activities should be scheduled accordingly. When a lagoon is pumped or other manure storage structure is emptied, the date of the activity should be recorded along with the volume or amount of manure removed, locations where the manure is spread and the nutrient content (from a lab analysis) of the manure.

Calibration of pumping equipment is necessary to accurately estimate amounts pumped. This information may be required by the regulatory agency for interim or year-end reports or may be useful in the event of litigation.

Pump-down or manure-level markers

Pump-down or manure-level markers, or indicators, are a simple but important component of a manure storage facility. Such a marker enables the operator to ascertain quickly and easily the degree of fill of the manure storage facility, the point at which pumping or emptying should begin and the point at which it should end. The presence of a durable, easily read marker gives inspection or regulatory personnel confidence a manure storage facility is being managed properly.

Experience has shown that pump-down markers must be made of durable materials and properly installed to afford the long life needed. The operator or inspector should be able to ascertain the following information when observing a pump-down marker:

•the level at which pumping operations should begin and end

•the level at which overflow will occur

•the fraction of total storage currently filled

A common practice is to install steel fenceposts at the upper and lower pump-down levels for earthen impoundments. While this approach provides basic information on beginning and ending pump-down, experience has shown that more knowledge is needed.

Also, fenceposts installed in this manner are subject to damage and displacement. A good pump-down marker will indicate the level, or elevation, of manure throughout the possible range (from lower pump-down level to overflow, or spillway) in the storage facility. A pump-down marker can be made from PVC pipe with all ends left open to allow water to flow into the pipe.

Weather stations

A simple weather station that indicates or records rainfall can be a useful tool in maintaining and managing a manure storage structure. Rainfall has a significant impact on open storage structures and structures serving open lots, so knowledge of rainfall amounts can be very useful. Some permits are written that provide for a legal discharge under certain climatic events. A weather station can aid in the documentation of such events without resorting to off-site data from stations that may not be descriptive of conditions at the storage facility. Recorded rainfall data is also evidence of good stewardship.

Aesthetics and appearance

Aesthetics and appearance may not be critical factors in protecting the environment or complying with environmental regulations; however, these characteristics are major factors in the perceptions formed by the general public, who may not be intimately associated or familiar with the livestock industry. Therefore, aesthetics and appearance should be given major priority for the overall benefit and viability of animal agriculture.

The general cleanliness and sanitation characteristics of a livestock enterprise are often perceived as a measure of the concern for environmental stewardship. A clean, well-landscaped production area will project a positive image for the operation. Typical items of concern for livestock production enterprises include leftover construction debris or refuse; old, unused vehicles; worn-out equipment; rusted equipment from the buildings (farrowing crates, pen dividers, feeders); torn and worn-out ventilation curtains; and loose roofing panels, etc.

All livestock production operations experience animal death loss. A specific plan for managing animal mortalities should be developed and implemented. The perceptions generated by the presence of dead animals in or around the production facility are highly offensive. Additionally, poorly managed mortalities represent a very real health and disease risk to the enterprise.

Few activities undertaken by the producer are as effective as frequent mowing in conveying a positive image of livestock production. Producers who maintain “front yard quality” around the production and manure storage facilities provide a powerful first impression of pride and responsibility. Also, routine inspections for seepage, rodent burrowing, erosion or other damage are much more effective if the areas have been mowed at regular intervals.

Control of surface water

As confined production units become larger, control of surface water in the production area is a primary concern. Wider, longer buildings, placed relatively close together, create high rates of discharge from roof and paved areas. Special considerations and landscaping are needed to manage this water in a manner that does not create erosion, unwanted ditches and washed-out culverts or waterways. A surface water management plan should be developed based on a design storm event, expected runoff rates, soil types and erosive velocities and properly designed and vegetated channels for carrying surface water away from the production area. Some states may require surface water from production areas be contained and checked for contaminant levels before discharge to a watercourse.

Closure of waste impoundments

If a lagoon or waste storage facility ceases to be used, it will need to be cleaned out at some point so it no longer represents an environmental threat. The Natural Resources Conservation Service (NRCS) has written a conservation practice standard that covers this subject. It is Code 360, Closure of Waste Impoundments. A summary of the document follows.

There are three options for managing the earthen impoundment after closure:

•complete closure and fill

•breaching the lagoon berm

•conversion to a farm pond or irrigation storage structure

In any case, the first steps are the same:

1. Remove all pipes or other structures that convey waste into the structure. Pipes should be dug up and ditches refilled.

2. Remove as much of the stored waste and sludge as practical. This can be done by agitating the lagoon and pumping as much material out as possible, refilling with water and repeating until most material has been removed. Alternatively, the effluent (relatively dilute liquid on top) can be pumped out, and the sludge can be removed using a slurry pump or excavation equipment.

3. All material must be land-applied at agronomic rates (such that crops can utilize the nutrients).

If the lagoon is to be completely closed, it should then be filled in and the land returned to its approximate original contours. Soil should be mounded slightly in the lagoon area (5 percent slope) in order to allow for settling and to encourage surface water to run away from the site. Vegetation should be established on the site to prevent erosion. If the lagoon berm is to be breached, all surface water runoff should first be diverted away from the lagoon. The breach should have sufficient side slope to prevent erosion (maximum 3-to-1 slope). The NRCS can help with this design. It should be low enough to allow all water to flow from the structure and prevent ponding. Vegetation should be established on the entire site, including the sides of the breach to prevent erosion.

If the lagoon is to be used as a farm pond, a watering source for livestock or an irrigation storage pond, the structure should meet the requirements for these types of structures. A properly designed lagoon will probably meet those requirements without major alterations, but the NRCS should be able to provide technical assistance to assure this requirement is met.

Water quality samples should be taken and submitted to assure safety before allowing livestock to drink from a converted lagoon. Dissolved oxygen (DO) levels should be higher than 3 milligrams per liter and nitrate nitrogen should be below 30 milligrams per liter.


Lagoons, manure slurry storage structures and dry systems each have advantages and disadvantages. Lagoons reduce the nitrogen and organic matter in the waste stream by volatilizing them (converting them to gases and moving them into the air.) They also reduce the odor released compared to a slurry storage, but they are more expensive because of their larger size and must be carefully managed to maintain a healthy bacterial population.

Slurry storage structures are smaller (do not include treatment volume or sludge storage), conserve more nutrients in the waste and are easier to cover, but they tend to produce more odor if not covered.

Dry systems keep manure in a concentrated form making it more transportable and less likely to flow into surface waters, but it must be handled as a solid which usually requires more labor than liquid systems which can use automated pumps. Solids separation devices remove much of the solids going into a liquid system and thus reduce the required volume for treating the waste, but they do require a financial investment and require two types of manure handling equipment (liquid and dry).

Whichever type of system is used, it is important to understand that it cannot perform as designed unless it is managed properly. For a lagoon, that includes starting it about one-third full of water before waste is added (preferably in the spring), loading it evenly and maintaining the level between the minimum and maximum levels. For a slurry storage, it includes cleaning it out on a regular schedule, according to crop needs, and minimizing the amount of water entering the storage. Solids separating systems must have the solid fraction removed regularly (within the flexibility provided in the design) in order to keep them operating properly, and mechanical systems must be regularly maintained to avoid breakdowns. PD

References omitted but are available upon request by e-mailing .

—Excerpt from “Small Farm Nutrient Management Primer”