February 2007
By Steve Werblow
Assessing an animal feeding operation’s manure storage and handling systems, and being sure to prevent discharges into waters of the state or U.S., can keep a producer from having to apply for an NPDES permit.
The livestock industry’s intense interest in upcoming revisions to the U.S. Environmental Protection Agency (US EPA) livestock water quality rule has renewed talk about the need for large Confined Animal Feeding Operations (CAFOs) to apply for National Pollutant Discharge Elimination System (NPDES) permits. Set to limit the discharges of pathogens, ammonia and other water quality parameters like biological oxygen demand, NPDES permits put the livestock operations, at some levels, in the same category as industrial facilities like wastewater treatment plants or paper mills.
The NPDES program covers approximately 15,500 CAFOs, which account for 60 percent of the manure generated by operations that confine animals for 45 days or longer over a 12-month period. But the good news for more than 34,000 producers is that the federal government is providing a golden opportunity for medium-sized outfits to avoid the permit requirement by simply preventing the discharge of manure to surface waters.
“Producers in the medium-sized category have the opportunity to do the right thing and by doing so can save themselves from having to get an NPDES permit,” says Steve Jann, deputy chief, NPDES Programs for US EPA Region 5 in Chicago, Ill. “By virtue of the way ‘medium-sized’ is defined, medium-sized producers have an opportunity to assess their production area and determine whether there are discharges. By assessing their operation and taking steps to stop discharges, they can avoid an NPDES permit.”
The trigger that trips the NPDES requirement for many medium-sized producers is the presence of a discharge from a production area through a ditch, flushing system or other similar man-made device to a water of the state, or if a water of the United States passes through the production area.
Not surprisingly, definitions are important.
For instance, “waters of the United States” can include streams, creeks, wetlands—even intermittent streams or dry creek beds. If they begin outside the production area and pass over, across or through it, the operation could meet US EPA’s discharge criteria.
The definition of “manure” is similarly broad—the CAFO rule actually applies to manure, litter and process wastewater, which includes flushing and washing water; water that is used for washing, swimming or spray cooling of the animals; and spillage or overflow from animal or poultry watering systems. Any water that comes into contact with any raw materials— or products and byproducts such as manure, feed, litter, bedding, milk or eggs—is also considered process water.
Another key term is “production area,” which for medium-sized Animal Feeding Operations (AFOs) does not include cropland, notes Jann. Instead, the production area includes the animal confinement area – open or housed lots, feedlots, stall or freestall barns, barnyards and other areas in which animals are maintained and vegetation is not maintained—and the manure storage area, which includes lagoons, ponds, pits, storage sheds and other places where manure, litter or the process water that contacts those materials is collected. Settling basins also fall into the same rule (compost piles count, too). Raw materials storage areas—whether in silos, bunkers or piles of bedding materials – are also considered part of the production area.
Despite the number of definitions in the regulations, there’s quite a bit of nuance in the rule as it stands, notes Rick Wilson of the Ohio Environmental Protection Agency, co-chair of the Animal Agriculture Committee for the Association of State and Interstate Water Protection Control Administrations. Key questions include:
1) What is considered a manmade conveyance?
2) What is the connection between the AFO and the receiving water? (For large CAFOs, discharges from either production areas or land application areas require permits. For medium-sized AFOs, the land is considered to be separate from the production portion of the operation, so field drainage doesn’t trigger a requirement for an NPDES permit.)
3) What are waters of the state (or the United States)?
Some operations raise clear red flags, Wilson notes. For instance, dairies need to be considered closely “because they have so many places where manure is stored and tracked,” he says. But the nuances come into play as soon as the manure starts to move.
“Once it runs off a feedlot pad into a small rivulet, is that a discharge?” he asks. Is the graded pad a conveyance, or does the rule apply only to drainage ditches or pipes? Is the rivulet that connects to a stream enough to qualify as a connection to waters of the state (or of the U.S.)? Is that a conveyance that should result in a point source regulation, or a nonpoint source?
US EPA’s Producer’s Compliance Guide to CAFOs (http://cfpub.epa.gov/npdes/afo/info.cfm#guidedocs) features several examples to help illustrate the definitions of AFO and CAFO.
For instance, a 600-cow dairy with year-round confinement and a tile outlet that carries parlor wash water to a nearby stream is easily identified as a CAFO. An 850-head beef confinement operation that conveys feedlot runoff through a settling basin, then via pipe and channel to a field in which the water leaches into the soil, doesn’t meet discharge criteria because the manure does not reach a water of the U.S. More subtle, a 400-head beef AFO that transports runoff from the feedlot pad via a properly constructed grass waterway to a field with no surface water also doesn’t meet discharge criteria. The waterway is indeed manmade, but the runoff doesn’t reach a water of the U.S. However, if a seasonal creek ran across the field where the runoff was directed, the operation could be categorized as a Medium CAFO and required to seek an NPDES permit.
Clearly, the bottom line is that anyone helping livestock producers navigate the regulatory straits will need to keep a close eye on the words used in the regulation, as well as EPA guidance on manmade devices “similar to” ditches.
The stakes, and the potential benefits, are high for both the medium-sized producer and the rest of the stakeholders in their watershed. Applying for an NPDES permit can be expensive and time-consuming—a particular challenge for relatively modest-sized farms—and compliance can require expensive modifications to a farm operation. Clear-eyed assessment and a clear sense of water quality regulations can help medium AFO operators protect water quality while reducing their regulatory burden.
At their most basic, CAFOs are animal feeding operations of roughly 1,000 animal units or more in which animals are confined or fed for 45 days or more in a 12-month period in an area where crops or vegetation is not maintained. Many CAFOs must file for NPDES permits as dictated in their required comprehensive nutrient management plans.
AFOs tend to be smaller operations with similar feeding or maintenance practices; however, if an AFO can or does discharge manure into a water of the state or a water of the U.S., it can be upgraded to a CAFO.
US EPA page on NPDES permits and CAFOs
US EPA’s Producer’s Compliance Guide for CAFOs
Link to CAFO Self-Assessment
Steve Jann’s summary of US EPA’s CAFO water quality rules presented at the Minnesota Pork Conference
A key distinction in US EPA permit requirements for livestock facilities is the size of the operation. Here’s how the agency defines “medium”:
| Animal Type | Range |
| Mature dairy cows | 200 – 699 |
| Veal calves | 300 – 999 |
| Heifers or beef cattle | 300 – 999 3,000 – 9,999 (under 55 lbs) |
| Swine | 2,500 (55 lbs or more) 10,000 (under 55 lbs) |
| Horses | 150 – 499 |
| Sheep or lambs | 3,000 – 9,999 |
| Turkeys | 16,500 – 54,999 |
| Chickens, liquid manure | 9,000 – 29,999 |
| Chickens, other than liquid manure | 37,500 – 124,999 (not laying hens) 25,000 – 81,999 (laying hens) |
| Ducks | 1,500 – 4,999 (liquid manure) 10,000 – 29,999 (other than liquid manure) |
It is important to note that the numbers of different animal types are not added together. A livestock operation is categorized as Medium or Large if a single type of animal meets the appropriate threshold. For a Medium AFO to be considered a Medium CAFO, it must also meet one of US EPA’s discharge criteria. Only then must the operation apply for an NPDES permit.

Manure systems that prevent discharges via manmade conveyance into a water of the state can keep medium-sized animal feeding operations from being classed as CAFOs. In turn, that keeps them from having to apply for NPDES permits.
Photo courtesy of USDA NRCS
One of the key drivers of EPA’s revisions to the water quality regulation governing CAFOs and AFOs is the 2005 decision in Waterkeeper Alliance v. EPA, which included several key determinations:
1) Only animal feeding operations (AFOs) that discharge or intend to discharge as a point source to waters of the U.S. need to apply for an NPDES permit;
2) AFOs that do not discharge do not have a duty to apply for an NPDES permit;
3) Ag stormwater discharges remain exempt;
4) Nutrient management plans must be developed as part of the NPDES permit process, and those plans are subject to public review.
State regulators can choose to adopt more stringent guidelines than the US EPA rules, but experts caution that the Waterkeeper decision could apply to state rules as well.
EPA’s summary of the Waterkeeper decision is available online.

Medium-sized AFOs do not have to apply for NPDES permits as long as they don’t allow discharge of manure or process water through manmade conveyances to creeks, streams, lakes or other waters of the state or U.S.
Photo courtesy of USDA NRCS: