Animal Feeding Operation Permits and Regulations in Missouri - PUB2351

Federal and state regulations, as well as permitting requirements for animal feeding operations (AFO), have undergone several changes in recent years. This guidance provides an overview of federal and state regulations relating to AFOs and Concentrated Animal Feeding Operations (CAFO) in Missouri. It also describes the different permits that can be required and outlines the permit application process. Not all regulatory and permit requirements are listed so producers are encouraged to contact the department early in the planning stages, particularly if questions or unusual circumstances arise. AFO owners and operators are also encouraged to become be familiar with all state and federal regulations. Operations should also check with local government as several counties and townships have health or planning and zoning ordinances relating to AFOs. These can be more stringent than state and federal regulations.

Most permits issued by the Missouri Department of Natural Resources are issued in accordance with National Pollutant Discharge Elimination System (NPDES) Electronic Reporting Rule as well as state and federal regulations. NPDES is a permitting program under Section 402 of the Clean Water Act, which is intended to reduce discharges of pollutants from point sources. Non-NPDES permits are issued in accordance with state regulations.

Permit Coverage Requirements

State regulations require all Class I CAFOs to obtain coverage under a NPDES or State No-discharge Operating Permit. Class II AFOs that are defined or designated as a CAFO due to discharging, must obtain a NPDES operating permit also. State regulations also require a construction permit for certain construction activities for new or expanding Class I CAFOs. To determine if either of these permits are required for a specific operation, the class size must be determined, and if the operation is an AFO or CAFO.

 Class Size Determination

 The class size category is based on the number of Animal Units (AU) in confinement at an operation. This does not include animals that are kept in pasture. The class size category can be determined in the following ways:

• AU can be calculated by dividing the number of animals by the conversion factor for that animal category from Table 1. (ex. 5000 swine over 55 pounds ÷ 2.5 = 2000 animal units).
• Class size category can also be determined by using Table 2, which lists the range animal numbers for each animal type by class size category. 

Table 1. Animal Unit Conversion Factors

1 Animal Unit =

1	Beef cow, feeder, veal calf, cow/calf pair and dairy heifer
0.5	Horses
0.7	Mature Dairy cows
2.5	Swine weighing over 55 pounds
10	Swine weighing under 55 pounds
10	Sheep, lambs, and meat and dairy goats
30	Chicken laying hens, pullets and broilers with a wet handling system
55	Turkeys in growout phase
82	Chicken laying hens without a wet handling system
125	Chicken broilers and pullets, and turkey poults in brood phase, all without a wet handling system
300	Ducks without a wet handling system
5	Ducks with a wet handling system

Table 2. Class Sizes and Animal Numbers

Animal Class Category	Class IA 7,000 AUs*	Class IB 3,000 to 6,999 AUs*	Class IC 1,000 to 2,999 AUs*	Class II 300 to 999 AUs*
Beef cows, feeder cattle, veal calves, cow/calf pairs and dairy heifers	7,000	3,000 to 6,999	1,000 to 2,999	300 to 999
Horses	3,500	1,500 to 3,499	500 to 1,499	150 to 499
Mature Dairy Cows	4,900	2,100 to 4,899	700 to 2,099	200 to 699
Swine weighing over 55 pounds	17,500	7,500 to 17,499	2,500 to 7,499	750 to 2,499
Swine weighing under 55 pounds	70,000	30,000 to 69,999	10,000 to 29,999	3,000 to 9,999
Sheep, lambs, meat and dairy goats	70,000	30,000 to 69,999	10,000 to 29,999	3,000 to 9,999
Chicken laying hens, pullets and broilers with a wet handling system	210,000	90,000 to 209,999	30,000 to 89,999	9,000 to 29,999
Turkeys in growout phase	385,000	165,000 to 384,999	55,000 to 164,999	16,500 to 54,999
Chicken laying hens without a wet handling system	574,000	246,000 to 573,999	82,000 to 245,999	24,500 to 81,999
Chicken broilers and pullets, and turkey poults in brood phase, all without a wet handling system	875,000	375,000 to 874,999	125,000 to 374,999	37,500 to 124,999
Ducks without a wet handling system	210,000	90,000 to 209,999	30,000 to 89999	10,000 to 29,999
Ducks with a wet handling system	35,000	15,000 to 34,999	5000 to 14,999	1,500 to 4999

*Animal Units

To be a Class I operation there must be 1000 AU or more of one animal category at one operating location. Once an operation becomes Class I, the animal units of all animal categories in confinement are added together to determine if it is Class IA, IB or IC. Operations with less than 300 AU are unclassified.

AFO or CAFO

An AFO is defined as a lot, building or complex at an operating location where animals are stabled or confined, and fed or maintained for a total of 45 days or more in any 12-month period, and crops, vegetation, forage growth or post-harvest residues cannot be sustained over at least 50% of the animal confinement area within the normal crop growing season.

A CAFO is an AFO that meets the criteria for the Class I size category, or a Class II operation where pollutants are discharged into waters of the state through a manmade ditch, flush system or other similar man-made device; or pollutants are discharged directly into waters of the state which originate outside of and pass over, across or through the production area or otherwise come into contact with the animals confined in the operation. The department can designate an AFO as a CAFO if it has determined it should be regulated as a CAFO after an on-site inspection has been conducted.

Permit Types

One or more of the following permits may be required for the construction and/or operation of a CAFO.

Construction Permit

This is a non-NPDES permit and is required for a new or expanding Class I CAFO for the construction or major modification of an earthen storage structure to hold, convey, contain, store or treat domestic, agricultural or industrial process wastewater.

As of Aug. 28, 2013, all other industrial construction activities are exempt from construction permitting requirements. All exempted construction activities designed to hold, convey, contain, store or treat domestic, agricultural or industrial process waste shall be designed by a professional engineer registered in Missouri in accordance with 10 CSR 20-8.300 and 6.300 and constructed according to the design plans.

CAFO Operating Permits

Operating permit coverage must be obtained prior to the operation of a waste management system at a CAFO and before any animals can be placed in confinement. There are two different general operating permits available.

• NPDES – This permit allows for a discharge from an uncovered liquid storage structure due to a catastrophic storm or chronic weather event. A discharge for any other reason is not allowed.
• State No-discharge – Discharges are not allowed for any reason.

Each type of general operating permit issued contains the same monitoring and reporting requirements. Some of the requirements may not be applicable to certain operations due to the type of waste management system used by the operation. Permits are effective for fixed five- year period. Both general permits can be viewed on the department’s Concentrated Animal Feeding Operation (CAFO) webpage.

Class IA CAFOs are excluded from obtaining general permit coverage and must obtain a site specific operating permit.  A site-specific permit NPDES operating permit is written with monitoring and reporting requirements that are specific to that operation.

Additional Permits

There are two other permits that may also be required for construction activities, even if construction or operating permits are not required. These permits authorize activities and discharges that are not covered in the construction or operating permits.

• A land disturbance permit is required if one acre or more of land is to be disturbed during the construction process. This permit must be obtained before any clearing, excavating or grading occurs.
• Section 404, Clean Water Act Permit – This permit is obtained from the U.S. Army Corps of Engineers and is required prior to disturbing, placing fill or discharging material into waters of the United States, which also includes wetlands. Activities include, but are not limited to, building dams or levees, road crossings and stream bank disturbances. If an operation is planning to conduct any construction activity in or along a drainage way, even if the channel is dry, they should contact the appropriate USACE office to determine if this permit is required.

Permit Applications and Fees

To apply for a permit, the appropriate application form and required additional documents, along with a permit fee must be submitted. If applying for more than one permit, or applying for permits at different operating locations, a separate application form and fee must be submitted for each permit. Contact the department’s Water Protection Program for appropriate form and current permit fees.

Regulatory Requirements

All CAFOs and AFOs, regardless of size, are subject to Missouri Revised Statute 644.051, which pertains to water contaminants that are likely to or have entered waters of the state and violated the general criteria for water quality standards in 10 CSR 20-7.031(3). In addition, all Class I CAFOs are required to comply with state regulations in 10 CSR 20-6.300 and 10 CSR 20-8.300, as well as federal regulations in 40 CFR 122 and 40 CFR 412, Subpart A through Subpart D.

No Discharge

All CAFOs in Missouri must be designed, constructed, operated and maintained as no-discharge. Uncovered liquid storage structures must be able to contain all manure, litter or process wastewater, plus the precipitation and runoff from chronic weather events and a catastrophic storm. CAFOs meet the no discharge requirement by having adequate storage volumes and land applying all manure, litter and process wastewater to agricultural fields.

Discharges of manure, litter or process wastewater from the production area and land application areas are prohibited by state regulations unless allowed for by an operating permit. CAFO operating permits allow for discharges under following conditions:

• When manure, litter or process wastewater has been land applied according to the operations Nutrient Management Plan (NMP) and the Missouri Concentrated Animal Feeding Operation Nutrient Management Technical Standard (NMTS), a precipitation-related discharge from land application areas under control of the CAFO, is considered to be an agricultural stormwater discharge.
• NPDES permits allow for discharges from uncovered liquid storage structures when it has been designed and maintained in accordance with regulations and permit requirements, and the criteria for a chronic weather event or a catastrophic storm has been exceeded.

Even though these discharges are allowed, they must not violate water quality standards in 10 CSR 20-7.031(3). Discharges for any other reason are not authorized and is a violation.

Nutrient Management Plans (NMP)

Prior to issuance of an operating permit an operation must develop a field specific NMP and implement the NMP upon issuance of the permit. The NMP must meet the requirements in 10 CSR 20-6.300(3)(G) 2., 10 CSR 20-6.300(5) and the NMTS. The NMP at a minimum must address the following areas:

• Ensure adequate storage of manure, litter and process wastewater and procedures for proper operation and maintenance of the storage facilities.
• Ensure proper mortality management.
• Ensure that clean water is diverted from the production area.
• Prevent direct contact of confined animals with waters of the state.
• Ensure that chemicals and other contaminants are disposed of properly.
• Identify site specific conservation practices to be implemented.
• Identify protocols for testing of manure, litter and process wastewater and soil.
• Establish protocols for land application of manure, litter, and process wastewater that ensure appropriate agricultural utilization of nutrients.
• Ensure appropriate recordkeeping.

All land application areas that are under operational control of the CAFO owner or operator whether they are owned, leased or rented must be included in the NMP before receiving any land application of manure, litter or process wastewater.

Buffer Distances and Neighbor Notice

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 (see Table 4). 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 land owner has agreed to the shorter buffer distance.

State regulations also 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, 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.

Table 3. Buffer and Neighbor Notice Distances

Class Size	Buffer Distance (ft.)	Neighbor Notice (ft.)
Class IA	3000	9,000
Class IB	2000	6,000
Class IC	1000	3,000
Class II and smaller	Not required	Not required

Odor Control Plans

Many factors affect the level of odors coming from a CAFO including number and type of animal, manure storage structure type, prevailing winds, topography as well as other operational and environmental factors. The buffer distance requirements are intended to address odor concerns by providing an area for odors to disperse. In addition to the buffer distance, Class IA CAFOs are required to prepare and implement an odor control plan as described by the Air Pollution Control Program under its odor emission regulations. The odor control plan requires a detailed analysis of a Class IA CAFOs odor sources and a corresponding plan to reduce odor emissions. All other sizes of CAFOs are exempt from these regulations.

Air Pollution Control Program odor emission regulations require facilities to restrict their odor emissions so they cannot be perceived above a defined level after it leaves the facilities' property. Failure to comply with the odor standard can result in a violation and penalty. The odor emission level for Missouri is defined as follows:

• No person may cause, permit or allow the emission of odorous matter in concentrations and frequencies or for durations that odor can be perceived when one volume of odorous air is diluted with seven volumes of odor-free air for two separate trials not less than 15 minutes apart within the period of one hour. This odor evaluation shall be taken at a site not at the installation.

Setbacks

There are required minimum setback distances for confinement buildings, open lots, manure storage structures and mortality composters in the production area from certain features. Additionally, there are setbacks for the land application of manure, litter and process wastewater at land application areas. These setbacks are meant to protect surface waters and wells.

Table 4. Production Area Setback Distances

Setback Feature	Setback distance (ft.)
Public water supply lines	10
Property lines	50
Public road	50
Wetland or impoundment for non-human water consumption	100
Lake or impoundment for human water consumption	300
Perennial or intermittent stream	100
Perennial or intermittent losing stream or sinkhole	300

Table 5. Land Application Setback Distances

Set back Feature	Application Conditions	Setback distance (ft.)
Public or private drinking water well or impoundment, or drinking water intake structure	All application methods	300
Classified waters of the state not used as a water supply	Permanently vegetated buffer	35
	No or insufficient vegetated buffer	100
Public or private impoundments not used as a water supply	Permanently vegetated buffer	35
	Up-gradient, or no or insufficient vegetated buffer	100
	Down-gradient, or no or insufficient vegetated buffer	35
Perennial or intermittent stream, wetland	Permanently vegetated buffer	35
	Up-gradient, or no or insufficient vegetated buffer	100
	Down-gradient, or no or insufficient vegetated buffer	35
Tile line inlet, (if left unplugged during application	Up-gradient, Permanently vegetated buffer	35
	Up-gradient, or no or insufficient vegetated buffer	100
	Down-gradient	0
Losing stream cave, spring, or sinkhole	All application methods	300
Perennial or intermittent losing stream or sinkhole	All application methods	300
Public use area, non-owned residence or business	Spray irrigation only	150
Public road or property boundary	All application methods	50

In addition to the setbacks in Table 5, other limitations for land application include:

• No land application on slopes greater than 20%.
• No surface application when soil is frozen, snow covered or saturated.
• No surface application if a precipitation event that is likely to create runoff is forecasted within 24 hours of the planned application.

Setback distances from wells apply to confinement areas, land application areas, waste storage structures, mortality composter or other potential water contamination sources also. Minimum setback distances are found in 10 CSR 23-3.010 and were established by the Missouri Clean Water Commission and the Well Installation Board.

There were no Missouri well installation rules before November 1987. The well construction setback distances rules adopted after that date are summarized in Table 7. Wells constructed prior to the Missouri Well Construction Rules, but after adoption of the Clean Water Commission rules for minimum separation distances, are reviewed and approved on a case-by-case basis and may involve water sample testing or dye tracing for indications of contamination.

Existing operations with wells installed after rules adoption that do not meet the minimum separation distance requirements will be resolved by either setting modification requirements or requiring a new well to be drilled. The new amendments to the Missouri Well Construction Rules became effective June 30, 1996.

Table 6. Well Construction Rules and Setback Distances

Setback from a water well to:	Setback distance (ft.) by regulation effective date
	June 30, 1996	Jan. 1, 1994	Nov. 1, 1987
Storage area for commercial fertilizer or chemicals	300	300	150
Cesspool	100	100	100
Below-grade manure storage area	300	100	100
Animal or poultry yard, building or privy	100	100	75
Other contaminants that may drain into the soil	100	100	75
Lagoon	300	300	Case-by-case
Earthen, concrete or other manure storage structure or lagoons	300	1/	1/
Land application areas for animal waste	300	300	2/
Uncovered animal composters	300	1/	1/
Enclosed composters with concrete floor and roof	100	1/	1/
Dry litter storage in poultry building during normal operations.	100	1/	1/
Single family lagoon	100	1/	1/

1/ Not covered by Missouri Well Construction Rules, but Clean Water Commission rules recommend 300 feet and require a minimum of 100 feet.

2/ Not covered by Missouri Well Construction Rules, but April 15, 1989, Clean Water Commission rules require a minimum of 300 feet.

Inspections, Recordkeeping and Reporting

Operating permits include requirements for inspections, recordkeeping and reporting. The operation is to perform regularly scheduled visual inspections of stormwater diversion devices, manure storage structures including liquid level, water and wastewater lines and land application equipment. These inspections are to protect surface water and wells and help to prevent unauthorized discharges. Any deficiencies discovered during a visual inspection should be corrected as soon as possible.

The operation must maintain records of permits, visual inspections, mortality management, discharges, land application and manure transfers. These records must be kept for five years and made available to the department upon request. Recordkeeping requirements are listed in the permits and in the NMTS. The department has developed a CAFO Record Keeping Form Checklist (form MO 780-2153) that has forms for all recordkeeping required by general operating permits.

An annual report is required by all operating permits. The type of information required in the report varies by permit and is listed in each operating permit. These reports may be submitted on the CAFO Annual Report (form MO 780-1953) that is provided by the department or on another form that includes the equivalent information.

CAFOs are also required to report any discharge to the department within 24 hours of the CAFO becoming aware of the discharge. The date, time, duration and approximate volume of the discharge is to be reported.

Permitting Process

During the planning and design stages all regulatory requirements and water quality issues at the site are to be considered. Other items to consider are manure storage capacities, mortality management, manure handling and adequate land application areas.

Permit Application Review

When applications and permit fees are received, they are processed and assigned to a permit writer. It can take 60 to 180 days or more from the date the application is received until the permit is issued depending on the type of permit applied for and if any required documents are missing or if more information is needed.

Upon receiving the application, the permit writer will conduct a completeness check to determine if the application includes all of the required documents. If the application is incomplete, or if more information is needed, the applicant or the engineer will be notified and provided an opportunity to provide the information. The 30-day neighbor comment period also begins on the day the application is received.

Once the application is complete, a technical review of the application begins. During this review, the department verifies compliance with applicable laws and regulations. If the department determines revisions are needed, all questions or comments on the application will be directed to the applicant or engineer for response. Once a satisfactory response is received, the department will proceed with issuing the permit.

After a permit is issued or denied by the department, the applicant or opponent has 30 days to appeal the decision. Appeals must be made to the Administrative Hearing Commission, which upon hearing the case will make a recommendation to the Missouri Clean Water Commission. The Clean Water Commission will either accept or reject the recommendation.

Construction Permit Applications

Construction permit application and permit fee should be submitted at least 180 days prior to the starting construction. Construction permitting requirements are listed in 10 CSR 20-8.300/6.010.  An application for an operating permit and permit fee shall be included with the construction permit application. Both permits will be issued concurrently after completion of the completeness check, technical review, neighbor comment period and public notice, if required.

General Operating Permit Applications

With the construction permit requirement exemption, much of the information and review that done with a construction permit application must now be done with the operating permit application. This includes buffer distances, neighbor notice and comment period, NMP, production area setbacks and manure storage.

The operating permit application should be submitted at least 90 days prior to the proposed starting date of operation. This will allow for time to correct any deficiencies in the application. While not required, the department recommends applications be submitted prior to the start of construction. The additional documents required to be submitted with the application include:

• Title page of engineering report or similar document including name and address of the operation, date the report was prepared, name and address of firm preparing the report, seal and signature of the engineer and a statement indicating the project was designed in accordance with 10 CSR 20-8.300 and 10 CSR 20-6.300.
• Narrative project summary. This shall include a summary of the existing and/or proposed modifications of operating conditions including the number of confinement buildings or areas, the total design capacity in animal units and actual animal numbers for each type of animal and an explanation of the existing and/or proposed modifications to the waste management system.
• Calculations showing the amount of manure generated annually, storage volume calculations and days of storage of all manure storage structures, including mortality composter.
• A recent aerial or topographic map showing the extent of the production area including;
  • All existing and proposed confinement buildings, open lots, manure storage structures.
  • Surface waters and areas subject to a 100-year flood event within or adjacent to the production area.
  • Production area setback distances to public water supply lines, property lines, public roads, impoundments, intermittent and perennial streams (gaining and losing), and wells in accordance with 10 CSR 20-8.300 (5)(B).
• Nutrient Management Plan
  • NPDES permit – applications for a new or modified permit shall include the operations nutrient management plan.
  • State no-discharge permit – applications for a new permit shall include the operations nutrient management plan.
  • For export only operations, completing parts 5-11 of Form W - Concentrated Animal Feeding Operation (CAFO) Operating Permit Application MO 780-2112 meets this requirement.
• Applications for Class I CAFOs shall also include:
  • An aerial or topographic map showing  the production area buffer and neighbor notice distances and all property lines and owners within the neighbor notice area in accordance with 10 CSR 20-6.300(3)(C)4;
  • Proof that neighbor notice was sent to property owners in neighbor notice area, county government and the department in accordance with 10 CSR 20-6.300(3)(C).

Permit Maintenance

While permits do allow for some flexibility for the day-to-day operation and management of CAFOs, it reflects circumstances and operating conditions of the operation on the date of issuance. Certain changes to the operation can require the permit to be modified, require a different permit or no longer be required to have a permit.

Permit Modification

Certain changes or additions to an operation require a modification of the permit. Changes include but are not limited to, adding a new confinement building or area, changing the footprint of an existing confinement building or area, adding or modifying a manure storage structure, change of ownership or revisions to the NMP that result in changes to the terms of the NMP in a NPDES permit. Some of these changes could affect the buffer zone requiring another neighbor notification, or change in animal units that could increase the class size.

Permit Renewal

All operating permits have an expiration date. The permittee is required to submit an application for renewal and appropriate fee. For general operating permits, the application and fee for renewal of a must be submitted at least 30 days prior to the expiration date. If an application for renewal is submitted within the appropriate time frame, permit coverage will continue under the current permit until the department issues the new permit; if not, the permit will expire and the operation will be considered operating without a permit, which is a violation.

Permit Termination

In the event a permitted operation closes, the operating permit can be terminated. Class I operations must submit a closure plan for all manure storage structures to the department for review and approval. Operating permit coverage must be maintained until all manure storage structures are properly closed. All manure, litter, process wastewater, sludge and compost must be removed from all manure storage structures and land applied at agronomic rates. Once the plan has been approved and all waste storage structures are properly closed, the permittee may submit a completed Request for Termination of Operating Permit MO 780-2814 to the department.

Class II and smaller operations can close manure storage structures in accordance with 10 CSR 20-6.300(6)(B) or maintain them so there is no discharge. Class II and smaller AFOs that have obtained voluntary permit coverage may terminate permit coverage at any time by submitting a request, since these operations are not required to be permitted.

Appeal Procedure

Any parties adversely affected or aggrieved by the Department’s decision to approve a permit request and issue a final NPDES permit may appeal to the Administrative Hearing Commission by filing a written petition within 30 days from issuance.