In the past 20 years, there has been a dramatic change in animal agricultural production, or livestock farming, in the United States. The overall size of individual operation has increased from smaller, family-owned farms to larger farm operations raising more animals per operation. There has also been a shift toward raising poultry and certain livestock within production barns as a way to increase production efficiencies. 

In the past 20 years, there has been a dramatic change in animal agricultural production, or livestock farming, in the United States. The overall size of individual operation has increased from smaller, family-owned farms to larger farm operations raising more animals per operation. There has also been a shift toward raising poultry and certain livestock within production barns as a way to increase production efficiencies.

An animal feeding operation (AFO) is a facility where animals are confined or stabled and fed for 45 days or more in a 12-month period and crops, forage or other vegetative ground cover is not sustained over at least 50% of the confinement area. A concentrated animal feeding operation (CAFO) is an AFO that confines more than 1,000 animal units. Animal units are based on the weight of the animal.

1,000 animal unit equals:

  • 1,000 beef cows
  • 700 dairy cows
  • 2,500 swine (pigs)
  • 100,000 chicken boilers

Designing CAFOs requires careful planning and considerations, including how to handle the amount and concentration of animal waste produced by the CAFO, as well as the associated odors and noise. The federal Clean Water Act identifies CAFOs as possible point sources for water pollution. New technologies and modern waste-management systems help properly manage animal waste by providing a safe, reliable fertilizer source for farming operations. Proper waste management protects the environment and ultimately makes a farm more productive. Protecting the environment and the agricultural industry is a shared responsibility and doing so may have a positive impact on the environment, our food supply and local and state economies. Learn more about Missouri's CAFO laws and regulations below.

An operation is defined as an animal feeding operation (AFO) if the facility confines, stables or feeds animals for 45 days or more in a 12-month period and a ground cover of vegetation is not sustained over at least 50% of the confinement area. An operation is defined as a concentrated animal feeding operation (CAFO) if it meets the definition of an animal feeding operation and also confines more than 1,000 animal units (1,000 animal units is equal to 2,500 swine, 100,000 broilers, 700 dairy cows or 1,000 beef steers).

An operation's "class size" is a category that is based upon the total number of animal units confined at an operation. The Class 1C, 1B and 1A are categories that start at 1,000, 3,000 and 7,000 animal units respectively and are required by state regulation to obtain a permit.

Class II operations confine less than 1,000 animal units and by definition, are only an animal feeding operation. Class II operations are not required to have a permit, although many voluntarily obtain one anyway. The department can also require a Class II operation to obtain a permit when an unauthorized discharge has occurred or when a discharge results in a violation of water quality standards. The Class II operations that appear on maps include only those that are currently permitted and do not represent the total statewide count of all Class II operations in Missouri. The department does not track nor have records of non-permitted Class II Operations.

New technologies and modern waste-management systems help properly manage animal waste by providing a safe, reliable fertilizer source for farming operations. Proper waste management protects the environment and ultimately makes a farm more productive.
ease production efficiencies. 

Length of Permit

The department issues this general permit for a five year period. The effective date is March 1, 2023 and expires Feb. 29, 2028. If a facility applies for and receives this permit on June 1, 2026, their permit will expire Feb. 29, 2028. 

Laws, Rules and Regulations

Missouri's CAFO laws and regulations are designed to minimize risks and are important for the long-term protection of the environment. Laws and regulations are also important to preserve and maintain a strong and profitable agricultural industry for generations to come. State regulations are available at 10 CSR 20-6.300 and 8.300, while federal regulations are located in 40 CFR Parts 122 and 412. Protecting the environment and the agricultural industry is a shared responsibility and doing so may have a positive impact on the environment, our food supply and local and state economies

At the state level, water quality is protected through the department’s permit application and approval process. Water pollution construction and operating permits are a requirement for all sizes and types of CAFOs. These permits typically have a list of very specific and stringent requirements to follow and operations are expected to keep detailed records of farm-related activities and submit them to the state agency for review each year. In addition, the department has developed stringent state technical standards that CAFOs must follow and relate to the handling and land application of animal manure.

How to Apply

Applications

Fact Sheets

Fees

  • Applicants will pay the following fees to operate an animal feeding operation or concentrated animal feeding operation.
  • $5,000 per year for a national pollutant discharge elimination system permit or a Missouri state operating permit for a class IA concentrated animal feeding operation as defined by the commission
  • $450 per year for a national pollutant discharge elimination system permit for a class IB concentrated animal feeding operation as defined by the commission
  • $350 per year for a national pollutant discharge elimination system permit for a class IC or class II concentrated animal feeding operation as defined by the commission
  • $300 per year for a Missouri state operating permit for a class IB concentrated animal feeding operation as defined by the commission
  • $150 per year for a Missouri state operating permit for a class IC or class II concentrated animal feeding operation as defined by the commission

Timeline/ Process

The department must issue or deny a master general permit within 60 days of receiving the permit application. If a public notice is required as part of the process, the department will issue or deny the permit within 90 of receiving the permit application. The department will request additional information if the application is not complete, which will delay the review process.

Public Participation

Neighbor Notice

State regulations require Neighbor Notice letters to be sent prior to submitting an operating permit application. Letters are required to contain specific information about the operation and must be sent to all landowners within one and one half times the buffer distance (information included under the Requirements Tab), the county governing body and the department. The department is required to accept neighbor comments for a period of 30 days, which begins the date the application is received. The neighbor notice will expire if an operating permit application has not been received within 12 months of initiating the neighbor notice requirements.

General Public Notice

Public notification of the issuance of this general permit to an individual applicant is not required by state regulations. Public notices are issued on this master general permit every 5 years. The only exception to this rule, 10 CSR 20-6.020, is when a facility applies for the first time the following master general permits.

  • Airport
  • Chemical manufacturing
  • Fabricated structured metal
  • Foundries
  • Limestone and rock quarries
  • Lubricant manufacturing
  • Petroleum storage greater than 50,000 gallons
  • Wood treaters

However, the department does provide a 15-day public notice comment period on Concentrated Animal Feeding Operations.

Administrative Hearing Commission

Anyone who is adversely affected by the director's decision to issue, deny, suspend or revoke a permit must appeal within 30 days of the decision to the Administrative Hearing Commission as provided by 621.250.3 RSMo. All appeals must be filed by petition and send to:

Administrative Hearing Commission
PO Box 1557
Jefferson City, MO 65102
Phone: 573-751-2422
Fax: 573-751-5018
Website: Administrative Hearing Commission

Requirements

Buffer Distances

State regulations require Class I CAFOs to meet buffer distance requirements from the operation to an existing public building or occupied residence that is not owned by the CAFO. The buffer distance is measured in a radius around any lagoon and from each confinement building or area. Any public building or non-owned occupied residence within the buffer zone must sign a waiver to allow the construction or expansion of the operation. This waiver must be recorded with the County Recorder and filed with the chain of title for the property of which the landowner has agreed to the shorter buffer distance.

Wastewater Construction Permit

This master general permit does not cover construction activities that may be required as part of the project. If you plan to construct, install or modify any earthen basin, collection system or wastewater treatment facility, you may be required to obtain a Site-Specific Wastewater Construction Permit.

Major Water User

Any surface or groundwater user with a water source and the equipment necessary to withdraw or divert 100,000 gallons (or 70 gallons per minute) or more per day combined from all sources from any stream, river, lake, well, spring or other water source is considered a major water user in Missouri. All major water users are required by law to register water use annually.

Reporting

Permittees must submit the following reports to the department. Additional monitoring and reporting requirements are included with in the Concentrated Animal Feeding Operation CAFO MO G010000 general permit. 

  • Any spill, overflow or other discharge(s) not specifically authorized are unauthorized.
  • If an unauthorized discharge cause or permit any contaminants to discharge or enters waters of the state or crosses property boundaries, the discharge must be reported to the department’s regional office as soon as practicable but no more than 24 hours after the discovery of the discharge.
  • Spills or leaks that are contained on the property shall be reported to the department within 24 hours, if the spill or leak exceeds 1,000 gallons per day.
  • Register with the department’s Missouri Gateway for Environmental Management (MoGEM) system to submit the facility’s Electronic Discharge Monitoring Reports. All reports should be easily identifiable, such as “CAFOAnnualManureExportReport2023.”
  • Concentrated Animal Feeding Operation Annual Report Form MO 780-1953 – submit annual report by Feb. 15 for the previous calendar year. This report is required yearly.
  • Within seven days of the date that an earthen basin’s level comes within 4 inches of the upper operating level, the permittee shall notify the department with information that identifies the earthen basin, the level in inches below the emergency spillway and actions taken to reduce the levels.
  • Operational Monitoring Report – Lagoon Form MO 780-2801

Renewal

Unless terminated, the permittee shall submit the permit application listed above no later than 30 days prior to the permit’s expiration date for renewal. When a facility submits a timely and complete application and the department is unable through no fault of the permittee to issue a renewed permit prior to expiration of the previous permit. The terms and conditions of the expired permit are administratively continued and will remain fully effective and enforceable until such time when a permit action is taken. Failure to submit a renewal application is a violation of the Missouri Clean Water Law.

Resources

Construction of an earthen basin or holding structure requires a construction permit. CAFO waste and wastewater storage system modifications shall be designed and constructed in accordance with 10 CSR 20-8.300. Instructions on how to apply for and receive a construction permit are located on the department’s Wastewater Construction Permits and Engineering webpage. Construction may not begin on new or expanding CAFOs until an operating permit is issued. Questions regarding permit requirements may be directed to department’s Water Protection Program phone line at 573-751-1300 or toll free at 800-361-4827.

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