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Animal Waste NPDES Permits


Manure and wastewater from Animal Feeding Operations (AFOs) can contribute pollutants like nitrogen and phosphorus, organic matter, sediments, pathogens, hormones, and antibiotics to the environment. Large farms can produce more waste than some U.S. cities. In fact, a feeding operation with 800,000 pigs could produce over 1.6 million tons of waste a year. In high quantities, it can be a huge issue. Diseases can spread from farms and human health can suffer due to contaminated air and water quality. Because of all this, federal regulations and permits are in place. If you produce meat, milk, eggs, breeding stock, or stable horses, it is important to know if National Pollutant Discharge Elimination System (NPDES) permits for animal waste apply to you. This Fact File explains NPDES permits related to animal waste and defines who it applies to.


AFOs were first identified as potential pollutants in the 1972 Clean Water Act. They are agricultural operations where animals are kept and raised in confined situations. Specifically, an AFO is a lot or facility where the following conditions are met:

  • Animals have been, are, or will be stabled or confined and fed or kept for 45 days or more in any 12-month period, and
  • Crops, vegetation, forage growth, or post-harvest residues are not sustained in the normal growing season over any part of the lot or facility.

AFOs that meet the regulatory definition of a concentrated animal feeding operation (CAFO) are regulated under the NPDES permitting program. The 2008 final CAFO rule requires that only CAFOs which discharge or plan to discharge waste apply for permits. The NPDES program regulates the discharge of pollutants from point sources to waters of the United States.

CAFOs and AFOs

Since a CAFO is included in the requirement to apply for a permit under NPDES regulations, it is important to define a CAFO vs an AFO. A CAFO is an AFO where over 1,000 “animal units” are confined at the facility; or more than 300 animal units are confined at the facility and:

  • Pollutants are discharged into navigable waters through an artificial ditch, flushing system, or other similar device; or
  • Pollutants are discharged directly into waters that originate outside of and pass over, across, or through the facility or come into direct contact with the confined animals.

For a large CAFO, an animal unit is defined as an animal equivalent of 1,000 pounds live weight and equates to:

  • 1,000 head of beef cattle or veal calves,
  • 700 dairy cows,
  • 2,500 swine weighing more than 55 lbs.,
  • 10,000 swine weighing less than 55 lbs.,
  • 500 horses,
  • 10,000 sheep or lambs,
  • 55,000 turkeys,
  • 125,000 broiler chickens if using other than a liquid-manure handling system,
  • 82,000 laying hens or pullets if using other than a liquid-manure,
  • 30,000 ducks if using other than a liquid-manure handling system, or
  • 5,000 ducks if using a liquid-manure handling system

An AFO that meets the small or medium size thresholds can be designated as a CAFO by the permitting authority if certain criteria are met. This can include that the AFO is determined to be “a significant contributor of pollutants to waters of the United States.” An operation confining any animal type such as geese, emus, ostriches, bison, mink, or alligators which are not explicitly mentioned in the NPDES regulations and for which there are no Effluent Limitation Guidelines (ELGs) is subject to NPDES permitting requirements for CAFOs if:

  1. It meets the definition of an AFO, and
  2. If the permitting authority designates it as a CAFO.

Permit requirements and details

In general, CAFO permits will include limits for process wastewater discharges from the CAFO’s production area and land application area. Existing and new large CAFOs that confine horses and sheep may not discharge manure or process wastewater pollutants to waters of the U.S. from the CAFO. The only exception to the no-discharge standard is an overflow that occurs because of a rainfall event from a facility that is designed, constructed, operated, and maintained to contain all process wastewater plus the runoff from a 25-year, 24-hour rainfall event for the location of the CAFO. All duck CAFOs constructed after 1974 are new sources subject to a no-discharge standard that is identical to the standard for horses and sheep. CAFO existing and new sources for dairy cows, cattle, veal calves, swine, and poultry are also subject to a no-discharge requirement.


There are monitoring, record-keeping, and reporting requirements of NPDES permits for CAFOs. Monitoring requirements based off ELG includes daily and weekly visual inspections of specific aspects of the production area and land application monitoring requirements, including manure and soil analysis and land application equipment inspection.


CAFO operators should maintain in their records a copy of the current NPDES permit and any supplemental documents identified by the permitting authority. Records include but are not limited to: proof of adequate storage capacity, proof of mortality management, proof of diverting clean water, identification of what U.S. waters if any exist within the animal confinement areas and what is implemented to prevent animals from contacting waters, how chemicals are used, stored, or disposed, conservation practices to control runoff to U.S. waters, manure and soil testing, protocols for land application, records of the production area, records of inspections, weekly records of wastewater levels, and corrective actions. Records must be maintained for five years.


All NPDES permits for CAFOs include a requirement that the permittee submit an annual report with specific information defined in the regulation.

Applicable laws & regulations

40 CFR 122 – EPA Administered Permit Programs: The National Pollutant Discharge Elimination System

40 Part 412 – Concentrated Animal Feeding Operations (CAFO) Point Source Category

Related definitions

“Effluent Guidelines” mean national wastewater discharge standards that are developed by the Environmental Protection Agency (EPA) on an industry-by-industry basis.

“Liquid-manure handling system” means the facility uses pits, lagoons, flush systems (usually combined with lagoons), or holding ponds, or has systems such as continuous overflow watering, where the water meets manure and litter. In addition, operations that stack or pile manure in areas exposed to precipitation are considered to have liquid-manure handling systems.

“Point source” means any discernible, confined, and discrete conveyance, including to any pipe, ditch, channel, tunnel, conduit, well, discrete fissure, container, rolling stock, concentrated animal feeding operation, or vessel or other floating craft, from which pollutants are or may be discharged.

Key to remember

Under the CAFO regulations, multiple types of animals are not counted together to determine the type and size of a CAFO. But, once an operation is defined as a CAFO based on one animal type, all the manure generated by all animals confined at the operation are subject to NPDES requirements. If waste streams from multiple livestock species subject to different regulatory requirements are mixed at a CAFO, any facility NPDES permit must include the more stringent ELG requirements. In cases where immature animals (heifers and swine weighing less than 55 lbs.) are confined along with mature animals, the determination of whether the operation is defined as a CAFO depends on whether the mature or immature animals separately meet the applicable threshold. Operations that specialize in raising only immature animals have certain thresholds under the regulations.

Real world example

Feedlot penalties and citations can arise for various reasons. A sheep feedlot in Colorado, agreed to pay $16,000 for Clean Water Act violations. The feedlot discharged waste without a permit and had insufficient waste containment. Their facility can house up to 150,000 sheep and is on a portion of the Big Windsor Reservoir. The feedlot was discharging process wastewater to a roadside ditch which connects to a canal. The reservoir receives canal irrigation water and is used for fishing, swimming, boating, and camping. This facility directly put others at risk. People who were just trying to enjoy leisure activities were unknowingly in and on contaminated water. Think about others affected like this situation, before it is too late, and improperly managed animal waste negatively impacts people far and wide.