Animal Waste and Water Quality: EPA Regulation of Concentrated Animal Feeding Operations (CAFOs)

Animal Waste and Water Quality:
EPA Regulation of Concentrated
Animal Feeding Operations (CAFOs)
Updated November 17, 2008
Claudia Copeland
Specialist in Resources and Environmental Policy
Resources, Science, and Industry Division

Animal Waste and Water Quality: EPA Regulation of
Concentrated Animal Feeding Operations (CAFOs)
According to the Environmental Protection Agency, the release of waste from
animal feedlots to surface water, groundwater, soil, and air is associated with a range
of human health and ecological impacts and contributes to degradation of the nation’s
surface waters. The most dramatic ecological impacts are massive fish kills. A
variety of pollutants in animal waste can affect human health, including causing
infections of the skin, eye, ear, nose, and throat. Contaminants from manure can also
affect human health by polluting drinking water sources.
Although agricultural activities are generally not subject to requirements of
environmental law, discharges of waste from large concentrated animal feeding
operations (CAFOs) into the nation’s waters are regulated under the Clean Water
Act. In the late 1990s, the Environmental Protection Agency (EPA) initiated a
review of the Clean Water Act rules that govern these discharges, which had not been
revised since the 1970s, despite structural and technological changes in some
components of the animal agriculture industry that have occurred during the last two
decades. A proposal to revise the existing rules was released by the Clinton
Administration in December 2000. The Bush Administration promulgated final
revised regulations in December 2002; the rules took effect in February 2003.
The final rules were generally viewed as less stringent than the proposal, a fact
that strongly influenced how interest groups have responded to them. Agriculture
groups said that the final rules were workable, and they were pleased that some of the
proposed requirements were scaled back, such as changes that would have made
thousands more CAFOs subject to regulation. However, some continue to question
EPA’s authority to issue portions of the rules. Many states had been seeking more
flexible approaches than EPA had proposed and welcomed the fact that the final rules
retain the status quo to a large extent. Environmentalists contended that the rules
relied too heavily on voluntary measures and fail to require improved technology.
This report provides background on the 2003 environmental rules, the previous
Clean Water Act rules and the Clinton Administration proposal, and perspectives of
key interest groups on the proposal and final regulations. It also identifies several
issues that could be of congressional interest as implementation of the revised rules
proceeds. Issues include adequacy of funding for implementing the rules, research
needs, oversight of implementation of the rules, and possible need for legislation.
The revised CAFO rules were challenged by multiple parties, and in February
2005, a federal court issued a ruling that upheld major parts of the rules, vacated
other parts, and remanded still other parts to EPA for clarification. In October 2008,
EPA issued revisions to the rules in response to the 2005 court decision; for
information, see CRS Report RL33656, Animal Waste and Water Quality: EPA’s
Response to the “Waterkeeper Alliance” Court Decision on Regulation of CAFOs.

In troduction ......................................................1
Livestock Production and Animal Waste................................2
Animal Waste and the Environment...................................4
Previous Clean Water Act Regulations.................................6
Problems with CAFO Regulation.................................7
How States Regulate AFOs and CAFOs............................8
Revising the CAFO Regulations......................................9
Additional Data Considered.....................................10
Public Response..............................................11
The Final Revised CAFO Rules.....................................11
Environmental and Economic Benefits of the Rules..................14
Economic Costs of the Rules....................................15
Comparing the Proposed and Final Rules..........................16
Reactions to the Final Rules........................................17
Technology Requirements......................................18
Air Emissions................................................19
Resources Needed to Implement the Rules.........................20
Other Industry Views..........................................21
Other Views of Environmental Groups............................22
Issues for Congress...............................................23

Animal Waste and Water Quality:
EPA Regulation of Concentrated
Animal Feeding Operations (CAFOs)
Agricultural operations often have been treated differently than other types of
businesses under numerous federal and state laws. In the area of environmental
policy, agriculture is “virtually unregulated by the expansive body of environmental
law that has developed in the United States in the past 30 years.”1 Some laws
specifically exempt agriculture from regulatory provisions, and some are structured
in such a way that farms escape most, if not all, of the regulatory impact. The Clean
Water Act (CWA), for example, expressly exempts most agricultural operations from
the law’s requirements, while under the Clean Air Act (CAA), most agricultural
sources are not subject to that law’s regulatory programs because most of those
sources do not meet the CAA’s minimum emission quantity thresholds.
One exception to this general policy of exemption from environmental rules is
the portion of the livestock industry that involves large, intensive animal raising and
feeding operations. These facilities, which include concentrated feeding operations
and feedlots, are a specialized and significant part of the livestock production
process, largely separate from cropland agriculture. Certain large animal feeding
operations are subject to explicit regulations under the Clean Water Act (33 U.S.C.
1251 et seq.) that are intended to restrict discharges of animal wastes which could
degrade the quality of the nation’s rivers, streams, lakes, and coastal waters.
However, existing regulations, promulgated in the 1970s, have not been amended to
reflect significant structural and technological changes in some components of the
animal agriculture industry that have occurred, particularly during the last two
decades. In addition, manure and waste-handling and disposal problems from
intensive animal production have begun to receive attention as these facilities
increase in size and the effects of these problems reach beyond the industry to affect
others in nearby communities.
In the late 1990s, the Environmental Protection Agency (EPA), the federal
agency responsible for implementing the CWA, initiated a review of the existing
CWA rules that govern waste discharges from large animal feeding operations. The
review was part of overall Administration efforts to address problems of animal
waste affecting the environment, including EPA’s response to a court-ordered
schedule to revise several CWA rules. A proposal to revise the existing rules for

1 J.B. Ruhl, “Farms, Their Environmental Harms, and Environmental Law,” Ecology Law
Quarterly, vol. 27, no. 2 (2000), pp. 263-349, 265.

animal feeding operations was released by the Clinton Administration in December
2000. After two years of reviewing the proposal, the Bush Administration issued
final revised regulations in December 2002.
The proposed rules were controversial for a variety of reasons. Livestock and
poultry groups, as well as general agriculture advocacy groups, opposed the rules,
arguing that they would be too costly. Environmental groups generally supported the
rules. States were divided: some favored a strengthened national approach to
regulating animal waste, while many favored greater flexibility. The final revised
rules adopt some elements of the proposal, modify other parts, and largely retain the
structure of the previous rules. The final rules are generally viewed as less stringent
than the proposal, a fact that strongly influences how interest groups have responded
to them.
This report describes the 2003 environmental rules, the background of previous
rules, the Clinton Administration proposal, and perspectives of key interest groups.
It also identifies several issues that could be of congressional interest as
implementation of the revised rules proceeds.
The revised CAFO rules discussed in this report were challenged by multiple
parties — environmental groups and agriculture industry groups — and in
February 2005, a federal court issued a ruling that upheld major parts of the rules,
vacated other parts, and remanded still other parts to EPA for clarification
(Waterkeeper Alliance et al. v. EPA, 399 F.3d 486 (2nd Cir. 2005)), leaving all
parties unsatisfied to at least some extent. In October 2008, EPA announced
revisions to the CAFO rules in response to the court’s decision. The revised rules
require compliance by February 2009. EPA’s revised regulations are not
discussed here, but are discussed in CRS Report RL33656, Animal Waste and
Water Quality: EPA’s Response to the “Waterkeeper Alliance” Court Decision
on Regulation of CAFOs.
Livestock Production and Animal Waste
There are an estimated 1.2 million farms with livestock and poultry in the
United States, according to the U.S. Department of Agriculture’s (USDA) 1997
Census of Agriculture. This number includes all operations that raise beef or dairy
cattle, hogs, and poultry and includes both confinement and non-confinement (i.e.,
grazing and rangefed) production. Of these, about 238,000 are defined as animal
feeding operations (AFOs, or feedlots; see box on “EPA Definitions of AFOs and
CAFOs,” p. 3), where livestock and poultry are confined, reared, and fed. An
estimated 95% of these are small businesses: most AFOs raise small numbers of
animals (i.e., fewer than 300). Concentrated animal feeding operations (CAFOs),
which confine large numbers of animals and meet certain pollutant discharge criteria
(see box, p. 3), are a small fraction of all AFOs (less than 5%), but these largest
operations raise more than 40% of U.S. livestock that are reared in confined facilities.
In recent years, livestock raising has become more concentrated in fewer but larger
operations. From 1982 to 1997, the total number of livestock operations decreased

by 24%, and total operations with confined livestock similarly fell by 27%. At the
same time, the number of animals raised at large feedlots increased by 88%, and the
number of large feedlots/CAFOs increased by more than 50%.2
EPA Definitions of AFOs and CAFOs3
An Animal Feeding Operation (AFO) is a facility in which livestock or
poultry are raised or housed in confinement, and where the following conditions
are met: (1) animals are confined or maintained for a total of 45 days or more in
any 12-month period, and (2) crops are not sustained in the normal growing
season over any portion of the lot or facility (i.e., animals are not maintained in
a pasture or on rangeland).
Concentrated Animal Feeding Operations (CAFOs) are a subset of AFOs.
In addition to meeting the above conditions, an AFO is a defined as a CAFO if it
meets minimum size thresholds (AFOs with more than 1,000 animals are CAFOs;
those with 300-999 animals may be CAFOs, depending on discharge
characteristics; and those with fewer than 300 may be CAFOs in some cases) and
either one of these conditions: (1) pollutants are discharged into navigable waters
through a manmade ditch or similar manmade device, or (2) pollutants are
discharged directly into waters of the United States that originate outside of and
pass over, across, or through the facility, or otherwise come into direct contact
with the confined animals. (40 C.F.R. Part 122, App. B)
By animal type, swine and poultry operations have seen the most dramatic
change in the manner of production, in terms of animals being raised in confinement
at very large animal feeding operations. From 1982 to 1997, there was a 12-fold
increase in numbers of swine raised at large AFOs, with the greatest geographic
concentration now in Oklahoma, Arkansas, North Carolina, northern Iowa, and
southern Minnesota. During the same time period, poultry production at the largest
operations increased 218%, with geographic concentration today in southeastern
states, coastal states of Florida, Georgia, North Carolina, South Carolina; Minnesota
and the surrounding areas; and western coastal states.4
Animal manure can be and frequently is used beneficially on farms to fertilize
crops and add/restore nutrients to soil. However, the changes in animal agriculture,
especially the increasing trend toward raising livestock on large feedlots, have
resulted in more extensive problems associated with using and disposing of animal

2 U.S. Department of Agriculture, Natural Resources Conservation Service, “Manure
Nutrients Relative to the Capacity of Cropland and Pastureland to Assimilate Nutrients:
Spatial and Temporal Trends for the United States,” Publication no. nps00-579, December

2000, p. 18. Hereafter cited as USDA, “Manure Nutrients.”

3 These definitions were adopted in regulations promulgated in 1974. As discussed later in
this report, in 2003 EPA revised these regulations but retained the definitions of AFOs and
CAFOs in the 1974 rule.
4 Ibid., pp. 44, 46.

waste. As livestock production has become denser and more spatially concentrated,
the amount of manure nutrients relative to the assimilative capacity of land available
on farms for application has grown, especially in high production areas including the
central northern states from New York to Nebraska, West Coast states and Arizona,
and scattered areas through the Southeast.
According to USDA, in 1997, 66,000 operations had farm-level excess nitrogen
(an imbalance between the quantity of manure nutrients produced on the farm and
assimilative capacity of the soil on that farm) and 89,000 had farm-level excess
phosphorus.5 USDA believes that where manure nutrients exceed the assimilative
capacity of a region, the potential is high for runoff and leaching of nutrients and
subsequent water quality problems. Geographically, areas with excess farm-level
nutrients correspond to areas with increasing numbers of confined animals, and farms
with poultry accounted for about two-thirds of the farm-level excess nitrogen and
over one-half of the farm-level excess phosphorus. Some of these operations can
export manure to surrounding properties. Even accounting for off-site transfers,
USDA believes that the number of counties with excess manure nutrients has
increased by approximately 60% since 1982 and that in 1997, 165 counties had
county-level excess manure nitrogen, and 374 counties had potential excess manure
phosphorus. Counties with potential animal waste problems tend to be grouped
together. Nearly all of the counties with excess nitrogen were in the Southeast in a
region extending from Arkansas and Louisiana to Virginia. Counties with excess
phosphorus were also numerous throughout the Southeast, as well as in the Northeast
(including the Delmarva Peninsula), extreme Northwest, California, and the Great
Plains.6 Poultry operations comprised 82% of the operations with farm-level excess
nitrogen in those counties, and poultry, dairy, and swine operations comprised nearly

90% of those with farm-level excess manure phosphorus.7

Animal Waste and the Environment
Animal waste, if not properly managed, can be transported over the surface of
agricultural land to nearby lakes and streams. Leaching from manure storage lagoons
and percolation through the soil of fields, where animal waste is applied can
contaminate groundwater resources. According to EPA, the release of waste from
animal feedlots to surface water, groundwater, soil, and air is associated with a wide
range of human health and ecological impacts and contributes to the degradation of8
the nation’s surface waters. Data collected for the EPA’s 2000 National Water

5 In the agriculture context, assimilative capacity is the amount of nutrients taken up and
removed at harvest for cropland and the amount that could generally be applied to
pastureland without accumulating nutrients in the soil.
6 USDA, “Manure Nutrients,” op. cit., p. 85.
7 Ibid., pp. 75-81.
8 U.S. Environmental Protection Agency, “Environmental and Economic Benefit Analysis
of Final Revisions to the National Pollutant Discharge Elimination System Regulation and
the Effluent Guidelines for Concentrated Animal Feeding Operations,” December 2002, p.

Quality Inventory identify agriculture as the leading contributor to water quality
impairments in rivers and lakes and the fifth leading contributor to impairments in
the nation’s estuaries. Animal feeding operations are only a subset of the agriculture
category, but 29 states specifically identified animal feeding operations as
contributing to water quality impairment. 9
The primary pollutants associated with animal wastes are nutrients (particularly
nitrogen and phosphorus), organic matter, solids, pathogens, and odorous/volatile
compounds. Animal waste also contains salts and trace elements, and to a lesser
extent, antibiotics, pesticides, and hormones. Pollutants in animal waste can impact
waters through several possible pathways, including surface runoff and erosion,
direct discharges to surface waters, spills and other dry-weather discharges, leaching
into soil and groundwater, and releases to air (including subsequent deposition back
to land and surface waters). Pollutants associated with animal waste can also
originate from a variety of other sources, such as cropland, municipal and industrial
discharges, and urban runoff.
The most dramatic ecological impacts associated with manure pollutants in
surface waters are massive fish kills. Highly publicized incidents have occurred in
nearly every state — from California to Maryland. In addition, manure pollutants can
seriously disrupt aquatic systems by over-enriching water (in the case of nutrients)
or by increasing turbidity (in the case of solids), processes that can disrupt aquatic
ecosystems. Excess nutrients cause fast-growing algae blooms that reduce the
penetration of sunlight in the water column and reduce the mount of available oxygen
in the water, thus reducing fish and shellfish habitat and affecting fish and
invertebrates. EPA’s 2000 Water Quality Inventory report indicates that excess algal
growth alone is among the leading causes of impairment in lakes, ponds, and
A variety of pollutants in animal waste can also affect human health. Over 150
pathogens in livestock manure are associated with risks to humans; these include the
bacteria E. coli and Salmonella species and the protozoa Giardia species. Contact
with pathogens contained in manure during swimming or boating can result in
infections of the skin, eye, ear, nose, and throat. Shellfish such as oysters, clams, and
mussels can carry toxins produced by some types of algae that are associated with
excess nutrients. These can affect people who eat contaminated shellfish. Further,
contaminants from manure can also affect human health through drinking water
sources and can result in increased drinking water treatment costs. For example,
nitrogen in manure and liquid waste can be transported to drinking water as nitrates,
which are associated with human health risks and which EPA has identified as the
most widespread agricultural contaminant in drinking water wells. Elevated nitrate
levels can cause nitrate poisoning, particularly in infants (this is known as
methemoglobinemia, or “blue baby syndrome”). Nitrate contamination of private

8 (...continued)
9 U.S. Environmental Protection Agency, “National Water Quality Inventory, 2000 Report,”
August 2002, EPA-841-R-02-001, 1 vol.

wells that has been linked to nearby livestock and poultry operations has occurred in
several areas, including Delaware, the Maryland Eastern Shore, and North Carolina.
Previous Clean Water Act Regulations
Since it was enacted in 1972, the Clean Water Act’s predominant focus has been
the control of wastewater from manufacturing and other industrial facilities and
municipal sewage treatment plants, termed “point sources,” which are regulated by
discharge permits. As point source pollution has been brought under regulation,
uncontrolled discharges in the form of runoff from “nonpoint sources” have become
not only greater in absolute terms, but also proportionally a larger share of remaining
water pollution problems. Nonpoint pollution occurs in conjunction with surface
erosion of soil by water and surface runoff of rainfall or snowmelt from diffuse areas
such as farm and ranch land, construction sites, mining and timber operations, and
residential streets and yards. Most agricultural activities are considered to be
nonpoint sources, since they do not discharge wastes from clearly identifiable pipes,
outfalls, or similar “point” conveyances. Nonpoint sources are not subject to the
permit, compliance, and enforcement regime that applies to point sources.
Under the CWA, most AFOs are considered to be nonpoint sources. However,
CAFOs (large AFOs) are specifically defined in the law as point sources and are
treated in a manner similar to other industrial sources of pollution, such as factories.
They are subject to the act’s prohibition against discharging pollutants into waters of
the United States without a permit. In 1974 and 1976, EPA issued regulations
defining the term CAFO for purposes of permit requirements (40 C.F.R. §122.23)
and effluent limitation guidelines, specifying limits on pollutant discharges from
regulated feedlots (40 C.F.R. Part 412). These regulations cover CAFOs that confine
beef and dairy cattle, swine, poultry (chickens and turkeys), ducks, sheep, or horses.
Discharge permits issued pursuant to the Part 122 rules, under the act’s National
Pollutant Discharge Elimination System (NPDES) permit program, establish limits
on the amounts and types of pollutants that can be released into waterways. Permits
are issued for a fixed term, not to exceed five years, and must be renewed thereafter.
NPDES permits may be issued by EPA or a state authorized by EPA to implement
the NPDES program. Currently, 45 states have been authorized by EPA to
administer this permit program, in lieu of EPA (Oklahoma has been authorized to
issue permits for most sources but not for CAFOs). The CWA allows states to
impose additional requirements on permittees and to regulate more conduct and more
types of operations than those governed by the federal NPDES rules. The two basic
types of NPDES permits are individual permits, which are tailored for a specific
facility, and general permits, issued by a permitting authority to cover multiple
facilities with similar characteristics. Because of the large number of CAFOs, EPA
and states increasingly are using general permits to regulate these facilities.
EPA’s regulations define a CAFO based on the length of time animals are
confined, the number of animals confined, and whether or not the facility directly
discharges pollutants into waters of the Untied States. In addition to criteria that
define an animal feeding operation (see box on “EPA Definitions of AFOs and

CAFOs,” p. 3), the rules for defining a CAFO contain a three-tier structure based on
the number of animal units10 at the facility.
!The facility is a CAFO if it holds more than 1,000 animal units.
!If the facility holds from 300 to 999 animal units, the facility is a
CAFO if pollutants are discharged from a manmade conveyance or
are discharged directly into waters passing over, across, or through
the site.
!Animal feeding operations that include fewer than 300 animal units
may be designated as CAFOs if EPA or the permitting authority
determines that the facility contributes significantly to water
The regulations nominally impose a zero discharge limitation on regulated
operations, because they prohibit discharge of pollutants into waters of the United
States, except in the event of discharges that might occur during the worst 24-hour
storm in a 25-year period (termed the 25-year, 24-hour storm exception). These
regulations do not specifically address discharges to surface water or leaching to
groundwater that may occur from animal waste or manure which are applied to land.
Nor do they address odor problems from animal agriculture operations. These topics,
if regulated at all, have been subject to varied state and local authority, not federal
law or regulation.
Problems with CAFO Regulation
A number of problems with the CAFO regulatory system that had existed since
the 1970s were widely recognized. These problems limited its effectiveness in
preventing environmental problems from livestock production.
!Less than 30% of CAFOs have CWA permits — about 4,100 out of
the approximately 12,700 that meet the EPA regulatory definitions
described above. One explanation is the historic emphasis by federal
and state permitting authorities on regulating other large industrial
and municipal dischargers rather than agricultural sources, since
most of agriculture is not subject to the act. Another factor is that
the 25-year, 24-hour storm exemption has allowed a large number
of operations to avoid obtaining discharge permits if they discharge
waste only during such a storm event.
!Some sources went unregulated because the EPA rules did not
reflect changes in animal waste management technology. In

10 As defined by USDA, an animal unit is 1,000 pounds of live weight of any given livestock
species or combination. The term varies according to animal type; one animal is not always
equal to one animal unit. An EPA animal unit is equal to 1.0 beef cattle, 0.7 mature dairy
cow, 2.5 pigs weighing more than 55 pounds each, 100 chickens (broilers or layers), 10
sheep or lambs, or 0.5 horses.

particular, the 1970’s rules only applied to poultry operations that
have a continuous overflow watering or liquid manure handling
system (i.e., “wet” systems) and thus excluded poultry CAFOs with
dry manure handling systems, which predominate in this sector
today. This exemption allowed more than 2,000 confined poultry
operations to avoid obtaining permits.
!The federal regulations contained no requirement for plans to
establish manure application rates for fields based on technical
standards for nutrient management.
!CAFO inspections by federal and state regulators and compliance
enforcement activities have been limited, often occurring only after
citizen complaints or accidental releases following large rainfall
events or equipment failures. In addition, according to the General
Accounting Office (GAO), EPA’s limited oversight of the states has
contributed to inconsistent and inadequate implementation by states,
which are the authorized permitting entities for the large majority of
facilities, CAFO and other.11
How States Regulate AFOs and CAFOs
Since NPDES permits are the CWA vehicle for implementing the CAFO rules,
and states carry out most NPDES permit activities, the nature and scope of state
programs for regulating feedlots is an important consideration in evaluating overall
effectiveness of current efforts. An EPA compendium of state programs for
managing animal feedlots illustrates the variations and complexity of state
activities.12 According to EPA, state regulation of AFOs and CAFOs often involves
both federal and state laws and regulations and several different state-level agencies,
with numerous variations in approaches, requirements, and jurisdiction. Forty-five
states are authorized by EPA to implement the base NPDES program to regulate
CAFOs. Seven states regulate CAFOs exclusively under this authority, while 32
states administer a state NPDES CAFO program in combination with some other
state permit, license, or authorization, such as a construction or operating permit. Six
states, while generally authorized to implement the NPDES program, have chosen
to regulate CAFOs under separate state non-NPDES programs. Further, five states
are not authorized to administer the NPDES program, and EPA retains responsibility
to issue CAFO permits. In three of these states, EPA permits are the sole CAFO
regulation, and the other two impose some form of non-NPDES program
requirement, in addition to the federally-issued permit. Substantively, state programs

11 U.S. General Accounting Office, “Livestock Agriculture: Increased EPA Oversight Will
Improve Environmental Program for Concentrated Animal Feeding Operations,” January

2003, GAO-03-285, p. 7.

12 U.S. Environmental Protection Agency, Office of Wastewater Management, State
Compendium, Programs and Regulatory Activities Related to Animal Feeding Operations.
May 2002. Another report presents a detailed comparison of features and requirements of
programs in seven states. See, Environmental Law Institute, State Regulation of Animal
Feeding Operations, January 2003, 80 p.

vary widely in defining what is a CAFO (hence, the scope of the regulatory program),
permit conditions and siting requirements, details for waste management plans (if
required), and enforcement procedures.
Because of the wide variability, it is difficult to say whether the glass is “half-
full” or “half-empty” with regard to the adequacy of state regulatory activities. EPA
concludes that state non-NPDES AFO programs are often more stringent than
NPDES programs and often extend coverage to smaller classes of facilities. Further,
according to EPA, the implementation of state non-NPDES programs often receives
more state agency attention than implementation of NPDES programs, with several
states actively choosing not to use NPDES permits. However, the GAO recently
found inconsistent and inadequate implementation of CWA requirements by states
that have been authorized to administer CAFO permitting. Permits do not meet all
EPA requirements, and several states evaluated by GAO do not issue any type of
permit to CAFOs, thereby leaving facilities and their wastes essentially unregulated.13
In revised CAFO rules proposed in December 2000 (discussed below), EPA said that
the number of non-NPDES permits issued to AFOs greatly exceeds the number of
NPDES permits issued — there are nearly 20 times more non-NPDES permits.
Many would not meet the standards for approval as NPDES permits, EPA said, and
because they are not NPDES permits, none meets the requirement for federal
Revising the CAFO Regulations
In the early 1990s, environmental groups sued EPA for failure to revise existing
Clean Water Act permit regulations for a number of industry categories and failure15
to adopt new rules for unregulated industries. Settlement of that lawsuit put EPA
under a court-ordered schedule to issue revised or new Clean Water Act rules for
CAFOs and more than a dozen other industries. Under the consent decree, which has
been modified several times, revised CAFO rules were to be proposed by December

2000 and finalized by December 15, 2002.

In response to this deadline and as part of broader efforts by EPA and the U.S.
Department of Agriculture to address water quality problems associated with animal
feeding operations, the Clinton Administration proposed rules to modify the existing
CAFO regulations in December 2000.16 To address shortcomings in the existing
regulations, the rules proposed to clarify the conditions under which an AFO is a
CAFO and is, therefore, subject to permit requirements. It proposed to increase the
number of facilities required to obtain Clean Water Act permits and to restrict land
application of wastes.

13 GAO, op cit., pp. 7-11.
14 66 Federal Register 2969, January 12, 2001.
15 Natural Resources Defense Council v. Reilly, U.S. District Court, D.C., Civ. Action No.

89-2980, April 23, 1991.

16 66 Federal Register 2959, January 12, 2001.

EPA co-proposed and asked for public comment on two alternative approaches
for defining CAFOs. The first would retain the existing three-tier structure (see page
7), but with modifications and clearer criteria regarding the middle tier (1,000
Animal Units or more would be CAFOs, operations with 300 to 999 Animal Units
would be CAFOs but could be exempt from permits by demonstrating no potential
to discharge wastes, and fewer than 300 Animal Units would be CAFOs only if
designated by the permit writer). The second option proposed a two-tier structure
(500 Animal Units or more would be defined as CAFOs, fewer than 500 Animal
Units would be CAFOs only if designated by the permit writer). EPA estimated that
under the proposed two-tier structure, 25,590 operations would need a permit,
compared with 12,700 under existing regulations. Under a revised three-tier
structure, 31,930 operations would need a permit, while an additional 7,400 in the
middle tier were potentially affected, but these operations were expected to be able
to avoid permitting by certifying that they are not CAFOs.
In addition, permitting requirements would be extended to some livestock
categories not previously regulated (i.e., dry-manure poultry operations and stand-
alone immature swine and heifer operations). EPA also proposed to require that
permitted facilities develop and implement site-specific plans which identify the
amount of nutrients generated at the facility and determine rates for the application
of the waste to agricultural land. Finally, it proposed a co-permitting system, in
which permits would cover not just the grower or farmer, but also corporate owners
(integrators) who contract out to farmers to raise the animals or poultry and exercise
substantial operational control over the facility.
There was a 120-day public comment period following publication of the
proposal in the Federal Register in January 2001, and on March 26, 2001, the EPA
Administrator authorized an additional 75-day public comment period, through July
30. EPA held nine public hearings to review the proposal in the spring and early
summer of 2001. Because of the change in Administrations immediately following
release of the proposal, new appointees at EPA undertook a detailed and thorough
review of the proposal and public comments on it before releasing final rules in
December 2002.
Additional Data Considered
In November 2001, EPA published a Federal Register Notice of Data
Availability (NODA) in which the Agency described information, data, and material
received during the public comment period and subsequently concerning rule-related
issues such as cost and economic impact and technology options for managing
animal waste.17 EPA said it was considering changes to certain aspects of the
proposed CAFO rules. The Agency did not formally re-propose the rules, but it
outlined the types of changes being considered and sought additional public comment
on the specific data and issues identified in the Notice. For example, EPA said it was
considering alternative definitions of what type of feedlot is a “concentrated” feedlot
for certain types of livestock operations (which could result in fewer numbers of
facilities being subject to regulation than under the Clinton proposal) and also was

17 66 Federal Register 58556, November 21, 2001.

considering some alternatives that would give states the flexibility to “opt -out” of
the federal regulatory program.
In July 2002, EPA published a second Notice of Data Availability that discussed
three additional issues for which the Agency was considering changes to the
proposal.18 The issues were: (1) potential new regulatory thresholds for chicken
operations with dry litter management practices that would lower the number of
facilities defined as CAFOs; (2) potential alternative performance standards to
encourage CAFOs to voluntarily install new wastewater treatment technologies
and/or management practices; and (3) discussion of new financial data that EPA was
considering to evaluate the economic effects of regulatory options.
Public Response
The Clinton Administration-proposed rules were highly controversial for many
reasons. Livestock and poultry groups, as well as general agriculture advocacy
groups, opposed the rules, arguing that they would impose excessive economic
burden on farmers and ranchers. They also criticized the proposal for taking a
uniform national approach to problems that they asserted were better suited to
management by state and local agencies. Environmental groups generally supported
the rules (while arguing that parts should be strengthened), based on their concern
that excessive nutrients and other contaminants in animal waste are polluting
waterways and groundwater. Although lengthy agency review of public comments
on a regulatory proposal is not unusual, many in these groups feared that EPA was
planning to weaken the Clinton proposal, based on discussion in the first and second
NODAs. States were divided on the rules: some favored a uniform national approach
to regulating animal waste pollution from the livestock industry based on
strengthened EPA rules, while many favored greater state flexibility. States were
concerned about diverting resources to CAFO permitting and thus undermining other
water quality programs. Congress expressed some interest in the revised rules: in
May 2001, a House Transportation and Infrastructure subcommittee held an oversight
hearing on the proposal. The hearing focused on impacts and costs on animal
agriculture producers, especially small producers.
The Final Revised CAFO Rules
After nearly two years’ review of the Clinton Administration proposal, EPA
issued final revised CAFO regulations on December 11, 2002. The new rules were
published in the Federal Register on February 12, 2003, with an effective date of
April 14, 2003.19 The regulations include a number of elements of the proposal and

18 67 Federal Register 48099, July 23, 2002.
19 U.S. Environmental Protection Agency, “National Pollutant Discharge Elimination
System Permit Regulation and Effluent Limitation Guidelines and Standards for
Concentrated Animal Feeding Operations (CAFOs); Final Rule,” 68 Federal Register 7175-

7274, February 12, 2003.

a number of modifications, with retention of much of the regulatory structure in the
existing rules. Highlights include the following:
!Definition of a CAFO. The definition of what is a CAFO remains
the same, unchanged from the prior rule (see box on “EPA
Definitions of AFOs and CAFOs,” p. 3). Also, the revised rules
retain the previous three-tier structure for defining a CAFO, based
on the number of animals housed at the facility. The rules retain the20
size thresholds for most of the regulated categories. As was
proposed, the final rules eliminate use of the term “animal unit”
equivalents for each animal sector and replace it with the less
confusing concept of numbers of animals in each sector.
!Duty to apply. The revised rules adopt an explicit duty for all
CAFOs to apply for an NPDES permit, as EPA had proposed. Thus,
the rules remove a permitting exemption in the previous rules that
had allowed facilities which meet the definition of a CAFO, but
claim to only discharge in the event of a large storm, to avoid
applying for permits. However, a permit exemption can be claimed
by a facility that can certify that it has no potential to discharge
waste into waters of the United States.
!Poultry. As noted above, the previous rules only applied to poultry
operations that have a continuous overflow watering or liquid
manure handling system. The final rules include revisions, as
proposed, to clarify applicability of the regulations to all types of
poultry operations, regardless of the type of manure handling system.
The inclusion of all poultry operations, regardless of manure
handling system, brings in all large broiler and dry layer feeding
operations and adds an estimated 2,198 operations to the number of
regulated facilities.
!Immature animals. The final rules also regulate facilities that
confine stand-alone immature animals (swine and heifers), which
previously were not covered separately. As a result, 488 of these
operations are now subject to regulation.
!Operations required to apply for a permit. EPA estimated that
under the previous rules, 12,813 animal feeding operations were
subject to regulation and should have had NPDES permits. The total
includes 8,438 large facilities (more than 1,000 animals) and 4,375
medium facilities (300 to 999 facilities) which either are defined as
CAFOs by size or discharge characteristics, or have been designated
as CAFOs by permitting authorities. By adding all poultry
operations and stand-alone, immature animal operations, the final

20 The threshold for duck operations with dry manure-handling systems was changed from
5,000 to 30,000 animals for large operations, thus reducing the number of regulated
operations from 157 under the previous rules to 25 under the final rules.

rules are estimated to cover an additional 2,554 operations (15,437
facilities in total, consisting of 10,754 large and 4,613 medium
operations).21 The total is 34% of all large and medium animal
feeding operations and about 19% of operations of all size in the
United States, based on USDA’s 1997 Census of Agriculture.
!Required performance standard. Also as described above, the
previous rules prohibited discharges from a CAFO except in the
event of wastewater or manure overflows or runoff from a 25-year,
24-hour rainfall event. The proposed and final rules retain this
design criterion without change. However, under the final rules,
new sources in the swine, poultry, and veal categories must meet a
more stringent design standard: storage structures must be designed
and maintained to contain the runoff from a 100-year, 24-hour storm
event. The final rules include a provision that was not in the
proposal allowing existing CAFOs to request permit limits based on
site-specific alternative technologies established by the permitting
authority, to encourage innovative technologies, according to EPA.
Under the new rules, alternative technology limits are required to
provide pollutant control equal to or better than under the baseline
!Best Management Practices. The revised rules include Best
Management Practices (BMPs) for land application and animal
production areas. BMPs are measures or methods that have been
determined to be the most effective, practical means of preventing
or reducing pollution from nonpoint sources. The requirements for
land application areas are to ensure the proper application of manure,
litter, and other process wastes to land that the CAFO controls.
They include measures such as specified setbacks from streams,
vegetated buffers, and determination of application rates, to
minimize the transport of phosphorus and nitrogen from the field to
surface waters, in accordance with technical standards of the
permitting authority. BMPs for animal production areas also are
specified, including daily and weekly inspections, maintenance of
depth markers in lagoons and other impoundments to determine the
design capacity, and on-site recordkeeping.
!Nutrient management plans. As part of the land application
requirements, the final rules require a CAFO operator to develop a
plan for managing the nutrient content of animal manure and process
wastewater. The previous rules had no such requirement. The plan
must be maintained on-site and available on request to EPA or the
state, but it is not considered part of the facility’s permit. Under this
plan, manure is to be analyzed annually for nitrogen and phosphorus

21 U.S. Environmental Protection Agency, “Development Document for the Final Revisions
to the National Pollutant Discharge Elimination System Regulation and the Effluent
Guidelines for Concentrated Animal Feeding Operations,” December 2002, pp. 9-3 to 9-15.

content, and land application areas are to be analyzed every five
years for phosphorus content, to evaluate nutrient build-up in excess
of amounts that crops can utilize.
!Compliance schedule. The final rules establish time frames for
compliance. Operations defined as CAFOs under the previous rules
are expected to already have applied for permits and, presumably,
are in violation of the rules if they have not done so. Operations
newly defined as CAFOs under the revised rules, such as dry litter
poultry operations, must apply for permits by April 13, 2006. 22 A
new source must seek permit coverage 180 days prior to the date it
commences operation. CAFOs that are existing sources are required
to develop and implement nutrient management plans and other land
application requirements by December 31, 2006. That date is based
on EPA’s belief that, by then, there will be sufficient technical
experts available to develop and implement nutrient management23
plans. The land application and nutrient management plan
requirements apply immediately to new sources. States with
existing NPDES permitting programs must adopt state rule revisions
to reflect the federal rules within one year. States which must amend
or enact a statute to conform with the rules were required to make
needed rule changes within two years (by April 13, 2005).
!Proposed provisions not in the final rules. Finally, the final rules
omit several provisions of the proposal. In addition to not adopting
reduced thresholds for defining a CAFO, EPA decided not to include
requirements for co-permitting of entities that exercise “substantial
operational control” over the CAFO, require zero discharge to
groundwater beneath the CAFO production area where there is a
direct hydrologic connection to surface water, or require that permit
nutrient plans be developed by a certified expert and be re-certified
every five years.
Environmental and Economic Benefits of the Rules
A number of environmental and human health benefits were expected to result
from requirements of the final rules, according to EPA. These include recreational
and non-use benefits from improved water quality in freshwater rivers, streams, and
lakes; reduced fish kills; reduced nitrate and pathogen contamination of sources of
drinking water; reduced public water treatment costs; and reduced livestock mortality
from contamination of livestock drinking water.

22 EPA subsequently extended this date to February 27, 2009. See 72 Federal Register

40245, July 24, 2007.

23 EPA also extended the deadline by which permitted CAFOs are required to develop and
implement nutrient management plans to February 27, 2009. 42 Federal Register 40245.

EPA quantified the pollutant reductions associated with the final rules. It
estimated that nutrient loadings (nitrogen and phosphorus) will be reduced by 23%
(166 million pounds per year), sediment loadings by 6% (2.2 billion pounds), and
metals discharges by 5% (one million pounds), compared with pre-regulation
baseline pollutant loadings.24 In contrast, the proposed rules estimated pollutant
reductions of 179 to 187 million pounds of nutrients, 75 to 77 billion pounds of
sediment, and 42 to 44 million pounds of metals (depending on which regulatory
option was finalized).25
EPA also estimated that the environmental benefits of the final rules, such as
improved surface water quality and reduced water treatment costs, will result in
annual estimated economic benefits ranging from $204 to $355 million (2001
dollars).26 Annual benefits of the proposed rules were estimated to be $146 to $163
million (1999 dollars).
Economic Costs of the Rules
The proposed and final rules also presented EPA’s estimates of the costs of
revised regulation. EPA estimated that the total incremental compliance costs for
CAFOs is $326 million annually (pre-tax, 2001 dollars), consisting of $283 million
for large CAFOs, $39 million for medium CAFOs, and $4 million for facilities that
are designated as CAFOs. Federal and state permitting authorities were projected to
incur $9 million per year in costs to implement the rules. Estimated annual
incremental costs of the proposed rules were $831-$930 million for CAFO operators,
plus $6-8 million for permitting authorities (1999 dollars).
EPA also evaluated financial effects in terms of the number of operations that
will experience affordable, moderate, or stress impact because of the rules. Overall,
EPA concluded that the rules are economically achievable. For the veal, dairy,
turkey, and egg laying sectors, no facility closures are projected. In the beef cattle,
heifer, hog, and broiler sectors, EPA’s analysis showed that some existing facilities
will experience financial stress. An estimated 285 facilities, or 3% of all large
CAFOs, might be vulnerable to closure, according to EPA (3% of affected beef
CAFOs, 9% of heifer operations, 5% of hog operations, and 1% of broiler
operations). 27
EPA estimated that about 6,200 facilities affected by the rules are small
businesses, which the Small Business Administration defines in terms of average
annual receipts (or gross revenue), accounting for 40% of all affected facilities.
Among large CAFOs, about 2,330 operations are small businesses; most are in the

24 68 Federal Register 7239, Table 7.2, February 12, 2003.
25 66 Federal Register 3116, January 12, 2001.
26 U.S. Environmental Protection Agency, “Environmental and Economic Benefit Analysis
of Final Revisions to the National Pollutant Discharge Elimination System Regulation and
the Effluent Guidelines for Concentrated Animal Feeding Operations,” December 2002, pp.

11-3 - 11-4.

27 68 Federal Register 7245-46, February 12, 2003.

broiler sector. Among medium CAFOs, about 3,870 operations are small businesses
(accounting for the majority of operations in this size category), and most are in the
hog, dairy, and broiler sectors. EPA’s analysis further estimated that about 262 of
these operations (4% of all affected small business CAFOs) are vulnerable to closure
as a result of the new requirements. They are predominantly beef cattle operations.28
Comparing the Proposed and Final Rules
One obvious difference between the proposed and final rules was retention of
the previous definition and numerical categorization of regulated facilities.
Commenting on the proposal’s options for either a two-tier structure or a modified
three-tier structure, EPA said that it agreed with commenters, including many states,
that changing to a two-tier structure would be very disruptive to ongoing programs.
EPA also said that it did not adopt the proposed new set of conditions for
determining when a facility in the middle of the three-tier structure (300 to 999
animals) is a CAFO because doing so would not necessarily have improved the
clarity or effectiveness of the rules, as intended, but would have caused substantial
permitting burdens and imposed costs on essentially all operations above 300
The previous discussion concerning costs and benefits of the revised rules
partially illustrates difficulties in comparing impacts of the proposed and final rules.
Some differences in EPA’s discussions of the two are notable, but they do not
necessarily affect outcomes. For example, the 2000 proposed rules stated that of the
12,700 medium and large CAFOs that should have been subject to permits under the
previous rules, but that permits had been issued for approximately 2,270 facilities.
In the final rules, while continuing to acknowledge that few operations have permits,
EPA stated that the number of permitted facilities is 4,100.30
The Notice accompanying the final rules stated, “As a result of today’s action,
EPA is regulating close to 60 percent of all manure generated by operations that
confine animals.”31 However, the proposed rules stated that an estimated 49% of
total manure would be controlled by retaining a CAFO definition threshold of 1,000
animals (as adopted in the final rules) and would increase to 64% to 72% under the
regulatory options that EPA co-proposed in December 2000 which would have
adopted a definition with a lower threshold.32 The differences in estimated pollutant
reductions and amounts of manure controlled under the proposed and final rules were
not fully explained. Concerning amounts of manure controlled, part of the difference
between the two could be explained by the final rules’ inclusion of more poultry

28 68 Federal Register 7246-47, February 12, 2003.
29 Ibid., 7189-7190.
30 Compare 66 Federal Register 2969, January 12, 2001, with U.S. Environmental
Protection Agency, “Development Document for the Final Revisions to the National
Pollutant Discharge Elimination System Regulation and the Effluent Guidelines for
Concentrated Animal Feeding Operations,” December 2002, at p. 9-12.
31 68 Federal Register 7180, February 12, 2003.
32 66 Federal Register 2986, January 12, 2001.

operations and stand-alone, immature animal operations than under the previous rules
— except for the fact that the proposed rules also included these additional
In comparing impacts of the revised requirements to a baseline, neither the
proposed nor the final rules were precisely clear about what baseline was utilized.
Consequently, evaluating impacts of changes is difficult. The baseline could be
assuming full compliance and control of pollutant runoff from feedlots by the 12,700
operations covered by the previous rules. Alternatively, the baseline could be the
partial compliance, and corresponding current water discharges, resulting from that
fact that 30% or less of covered facilities are actually operating under NPDES
permits. If the baseline assumed complete current compliance (which is not
occurring, in fact), then the incremental pollutant reduction improvements of the
revised regulatory requirements would be less than if the baseline assumed partial
compliance by currently regulated facilities. There is some indication that, for
estimating environmental improvements, the baseline of the proposed rules was
current partial compliance with previous rules,33 while in the final rules, the baseline
was assumed to be complete compliance with the existing rules. That might explain
the large estimated differences in pollutant reduction between the two; see, for
example, the above discussion about estimates of reduced sediment loadings and
metals discharges.34
These differences are not satisfactorily explained or addressed in the final rules,
but they are significant for evaluating the regulation. In response to inquiries about
these issues, an EPA official indicated that, during review of the rules, the Agency
completed more extensive modeling of previously available data to assess impacts,
including disaggregation for better geographic treatment to address differences in
climate, soil type, and conservation practices, and that the improved analysis
contributed to the apparent differences between the proposal and final rules.35
Reactions to the Final Rules
The final rules were generally viewed as less stringent than the December 2000
proposal, a fact that strongly influenced how interest groups have responded to them.

33 However, in the proposed rules, EPA stated that, for purposes of estimating compliance
costs, it assumed that all CAFOs subject to revised regulations are currently in compliance
with the existing regulatory program, even though it recognized, as a practical matter, that
this is not true. EPA did not estimate the additional costs of complying with existing
requirements, because it did not consider those costs part of the incremental costs of revised
rules. 66 Federal Register 3080, January 12, 2001.
34 US. Environmental Protection Agency, “Environmental and Economic Analysis of
Proposed Revisions to the NPDES Regulation and the Effluent Guidelines for Concentrated
Animal Feeding Operations,” January 2001, p. 4-18.
35 Telephone conversation, Paul Shriner, U.S. EPA, Office of Water, Office of Science and
Technology, March 3, 2003.

Agriculture industry groups36 indicated that they believed the final rules were
workable, and they were generally pleased that some of the proposed requirements
were scaled back, including reduced definition thresholds and co-permitting of
corporate owners of livestock as well as of farmers who actually raise the animals.
However, some continue to question EPA’s authority to issue portions of the rules.
Many states, too, had been seeking more flexible approaches than EPA originally
proposed, and thus welcomed the fact that the final rules retain the status quo to a
large extent. Impacts on states will vary, depending on the changes in existing state
programs needed to comply with the new requirements, however. Both industry and
states were greatly concerned about adequacy of resources to implement the
requirements. Environmentalists contended that the rules relied too heavily on
voluntary measures to control runoff, instead of mandating strict compliance with
national standards, and fail to require improved technology. In the weeks
immediately after publication of the rules, environmental groups and several
agriculture industry groups filed lawsuits challenging the rules in a number of
different federal courts.
Technology Requirements
Environmental groups criticized EPA for omitting a provision in the proposal
that would have required zero discharge from the CAFO’s production area to ground
water that has a direct hydrologic connection to surface water. A hydrologic
connection refers to the interflow and exchange between surface impoundments such
as lagoons and surface water through an underground corridor or ground water. The
proposal would have required CAFOs to determine whether such a direct hydrologic
connection exists and, if so, to monitor ground water up gradient and down gradient
to ensure that zero discharge to ground water is achieved. The proposal also would
have adopted a stringent zero discharge standard for regulated swine, veal, and
poultry CAFOs, with no exception for chronic storm overflows. This issue was a key
concern to environmentalists who point out that rural areas, where most CAFOs are
located, often rely on ground water for drinking water supplies. In addition, they
criticized the final rules for omitting proposed special requirements that would have
restricted land application of wastes to frozen, snow-covered, or saturated soil. In the
final rules, EPA explained that the proposals were rejected because pollutant
discharges to surface water via ground water or as a result of application to frozen or
saturated soil are highly dependent on site-specific variables, such as climate,
distance to surface water, etc. Thus, a national technology-based standard is
inappropriate, according to EPA.

36 On most issues affecting agriculture, there often is a subset of interests most affected and
likely to express views on legislation, regulations, etc. Their views may differ or coalesce
on a given issue. The CAFO rules discussed here were of considerable interest to groups
representing livestock and poultry producers, such as the National Chicken Council, Port
Producers Council, and National Cattlemen’s Beef Association, as well as groups that
represent agriculture as a whole, such as the Farm Bureau. In EPA’s discussion of the rules
(e.g., the Federal Register Notice accompanying the final rules), when referring to
“industry,” it did not distinguish among these groups, nor does this CRS report. It appears
that, at least in EPA’s judgment, these groups generally reflected similar interests and
concerns on the CAFO rule issues. Other agriculture industry groups, representing interests
of cropland producers, for example, had limited involvement in these rules.

Further, environmentalists asserted that the final rules fail to require
performance standards consistent with the best available technology. The rules
perpetuate that status quo, they said, because they do not require phaseout of the use
of lagoons. Many environmental advocates believe that lagoons are outmoded
technology that can pollute both surface and ground water as a result of weather
events, human error, and system failures and, thus, are an unacceptable risk to public
health and the environment. Likewise, advocates believe that sprayfields, where
waste is sprayed onto crops or pastureland, pose significant risks, and many support
the position that manure waste that is land applied should be injected or incorporated
into the soil.
Industry groups, on the other hand, disputed environmentalists’ belief that
stringent national standards requiring zero discharge would encourage development
of new technologies. In industry’s view, the previous rules’ zero discharge standard
(even with the allowance for chronic storm event discharges) had virtually ensured
the use of lagoons and holding ponds to store CAFO wastewater on site. Industry
urged EPA to adopt final rules that would encourage alternative technologies. They
argued that CAFOs — like other point sources regulated under the Clean Water Act
— should be allowed to treat wastes to an established level of quality that does not
impair lakes or streams and to release treated wastes to the environment. The final
rules appeared to respond to industry’s concern in this area: while retaining the
previous rules’ nominal zero discharge standard, they also allow a CAFO to request
a permit based on site-specific alternative technologies established by the permitting
authority that are equivalent to the baseline standard or better. EPA believed that this
flexibility would encourage innovative technologies, but environmentalists believed
that allowing CAFOs to “treat and release” animal waste is weaker than the previous
rules and effectively allows alternative technologies to have a discharge that may
harm the environment.
Air Emissions
Environmentalists also were disappointed that the final rules did not address or
restrict emissions of air pollutants. AFOs can emit various pollutants, including
ammonia, hydrogen sulfide, methane, volatile organic compounds, and particulate
matter. Environmental impacts can vary, depending on the design and operation of
the facility. Scientists generally believe that emissions present a number of issues of
environmental concern but not a large public health problem, although more research
on public health impacts is required. Some air emissions are important on a local
scale (hydrogen sulfide, odor), and others are significant nationally or globally
(ammonia, which can be redeposited to earth and contribute to water quality
degradation, and the greenhouse gas methane). Industry groups pointed out that
water pollution control technologies, which were the subject of the CAFO rules, do
not address air emissions and that proven air abatement technologies are needed
before adopting regulations.
A 2002 National Research Council report recommended developing improved
approaches to estimating and measuring emissions of key air pollutants from AFOs
and initiating long-term coordinated research by EPA and USDA with the goal of
eliminating release of undesirable air emissions. Nitrogen emissions from production
areas are substantial, the report found, and control strategies aimed at decreasing

emissions should be designed and implemented now. For example, implementation
of feasible management practices, such as incorporating manure into soil, that are
designed to decrease emissions should not be delayed while research on mitigation
technologies proceeds.37 In the Notice accompanying the final rules, EPA estimated
that the rules would not significantly alter ammonia emissions from CAFOs but will
reduce hydrogen sulfide emissions and methane emissions by 12% and 11%,
respect i v el y. 38
Resources Needed to Implement the Rules
Adequacy of resources to implement the revised regulations is an important
issue for the animal agriculture industry and states, and these groups focus on the
need for federal support to meet the new federal requirements. Livestock operators
face costs for manure handling requirements, developing and implementing nutrient
management plans, and record-keeping. A key federal financial assistance program
for producers is the Environmental Quality Incentives Program (EQIP), administered
by the Natural Resources Conservation Service of USDA. EQIP provides technical
assistance, cost sharing, and incentive payments to assist livestock and crop
producers with conservation and environmental improvements using land
management and structural practices, such as site-specific nutrient management or
animal waste management facilities. In the 2002 farm bill (P.L. 107-171), Congress
increased funding for EQIP from $200 million to $1.3 billion per year by FY2007.
Spending for this program is mandatory. Sixty percent of the available funding is to
be targeted at practices relating to livestock production. EQIP funds can be used to
cover 75% of the cost of measures to control manure runoff, and, under the 2002
farm bill amendments, livestock operators of all sizes including large CAFOs are
eligible to receive funding. The amendments limit total payments to $450,000 per
participating producer (changed from $50,000 per contract) through FY2007.
The 2008 farm bill (P.L. 110-246) reauthorized EQIP at levels increasing
annually up to $1.75 billion in FY2012. However, it lowered the EQIP payment limit
to $300,000 in any six-year period per entity, except in cases of special
environmental significance including projects involving methane digesters, as
determined by USDA. The enacted bill retained the requirement that 60% of funds
be made available for cost-sharing to livestock producers, including an incentive
payments for producers who develop a comprehensive nutrient management plan.
USDA, EPA, and federal agencies such as the Small Business Administration
(SBA) administer a number of other assistance programs, which EPA summarized
in a 2002 report.39 The SBA, for example, administers a pollution control loan

37 National Research Council, Board on Agriculture and Natural Resources, Board on
Environmental Studies and Toxicology, “Air Emissions from Animal Feeding Operations:
Current Knowledge, Future Needs, Final Report,” December 2002, 241 p.
38 68 Federal Register 7242, February 12, 2003. The time period for achieving these
anticipated reductions is not specified.
39 U.S. Environmental Protection Agency, “Financial Assistance Summaries for AFOs,”

program that can be used by small and large animal feeding operations that are small
businesses. Several of the EPA Clean Water Act programs described in the report,
such as nonpoint source pollution management grants, can be used by AFOs, but
generally not by CAFOs which are regulated as point sources under that act.
A 2003 GAO report found that neither states nor EPA are equipped to
implement the program, having not made provisions for additional staffing to process
permits, conduct required inspections, and take enforcement actions.40 GAO reported
that the changes will create resource and administrative challenges for states, and
meeting these new demands will require additional personnel. However, most of the
states reviewed by GAO cannot hire additional staff and would have to reassign
personnel from other programs. EPA, too, will have to redeploy staff resources.
GAO commented in the report on EPA’s limited past oversight of state CAFO
programs and concluded that the Agency will need to increase its oversight of state
regulatory programs to ensure that the new requirements are properly adopted and
carried out by states.
For state agencies that implement the NPDES permit program, the principal
existing source of financial assistance is grants under Section 106 of the Clean Water
Act, which states already use for various activities to develop and carry out water
pollution control programs. States currently use Section 106 grants, supplemented
by state resources, for standard setting, permitting, planning, enforcement, and
related activities. In light of budgetary problems confronting many states, it is
unclear how state agencies will find the resources needed to carry out their
responsibilities under the revised rules without reducing resources for other important
Other Industry Views
Fundamentally, agricultural interests emphasize that most farmers are diligent
stewards of the environment, since they depend on natural resources of the land,
water, and air for their livelihoods and they, too, directly experience adverse impacts
on water and air quality, when they do occur. Many believe that environmental
problems caused by some individual farmers do not require national solutions or
standards, and most are very concerned that regulatory requirements will adversely
affect the economic viability of the industry, especially compared with international
While agriculture industry groups reportedly considered the final rules workable
(especially with increased resources provided by the 2002 farm bill), it was also clear
that many objected to some basic elements of the regulations that were not eliminated
or were changed little from the December 2000 proposal. These concerns were
reflected in comments on the proposed rules. For example, livestock and general

39 (...continued)

2002. Available at [].

40 U.S. General Accounting Office, “Livestock Agriculture, Increased EPA Oversight Will
Improve Environmental Program for Concentrated Animal Feeding Operations,” January

2003, GAO-03-285.

agriculture groups questioned EPA’s basic authority to impose a number of the rules’
requirements. These groups generally opposed eliminating the previous permitting
exemption for facilities that discharge only in a large storm event, saying that such
operations should not be covered by permits.
Industry also opposed imposing on CAFOs a duty to apply for permits and
questioned EPA’s legal authority for requiring permits from CAFOs that claim not
to discharge pollutants, since in their view the Clean Water Act only requires permits
for actual discharges. Some questioned EPA’s finding that many CAFOs are
discharging without a permit (which EPA had cited as a key reason for revising the
regulations) and said that voluntary programs are working adequately to address the
excess manure issue. Some objected to putting the burden on the CAFO to show that
it does not discharge into waterways and argued that the CAFO should not be
required to apply for a permit in the absence of evidence of an actual discharge.
Some industry commenters also argued that EPA lacks authority to include
permit requirements governing land application of manure and process wastewater,
because in their view runoff from land application areas is a nonpoint source
discharge that is not subject to Clean Water Act permitting. EPA’s view is that land
application areas are integral to CAFO operations, and, because there have been
significant discharges from them, non-regulatory controls alone are insufficient.
Other Views of Environmental Groups41
Environmental groups were critical of several other provisions in the proposal
that were omitted from the final rules. Chief among these was EPA’s decision not
to require co-permitting of both the farmer who raises the livestock and the large
companies that actually own the animals and contract with farmers. This was one of
the most controversial parts of the proposed rules. Environmental advocates believe
that co-permitting makes large corporations responsible for wastes produced on the
farms with which they contract, while the agriculture industry said it would make
corporations liable for waste management decisions over which they have no
practical control.
Environmental groups also had strongly favored lowering the threshold for
defining when an AFO is a CAFO, which would ensure that more operations are
subject to uniform controls and enforcement.
These groups criticized changes in the final rules that they believed will limit
public involvement and oversight. In particular, they said that, by not requiring that

41 Within agriculture, there are some groups that reflect many interests similar to those of
environmental groups, such as the Sustainable Agriculture Coalition, which promotes
policies based on economically profitable, environmentally sound, family-farm based
systems of agriculture and livestock production methods at small and mid-size operations
that do not use animal confinement. Concerning CAFO issues, sustainable agriculture
groups favored strategies based on nationally uniform standards, alternatives to large CAFO
production, public accountability in issuance of CAFO permits, and legal liability for
corporate owners of confined animals.

nutrient management plans be publicly developed and available, the public will not
have adequate access to the plans. Many environmental advocates favored including
nutrient management plans in a CAFO permit, which would make the plans an
enforceable element of the permit. Agriculture industry groups argued that the plan
would contain proprietary information and that making it publicly available would
both discourage innovation in developing waste management technologies and could
make CAFOs vulnerable to lawsuits. EPA pointed out that the final rules require
CAFOs to submit annual nutrient management reports that will be public and will
provide information on numbers of animals, amounts of manure generated, and how
the manure is being handled. Advocates also said that, by not requiring that nutrient
management plans be developed by a certified expert or be approved by the
permitting authority, as had been proposed, the revised rules essentially allow
farmers to write their own requirements without technical or permitting authority
Issues for Congress
Implementation of the revised CAFO rules will present large challenges for
those who are directly affected by the regulations — the animal agriculture industry,
states, and EPA — as well as interested members of the public. Likewise, several
issues of congressional interest are apparent.
!Adequacy of funding. Requests for funding assistance to help
affected groups comply with the rules are expected to increase —
especially by feedlot operators seeking EQIP funds. However, even
at the higher EQIP contract limit provided by the 2002 farm bill
($450,000 per farmer), there was concern that the ceiling would
effectively diminish some farmers’ interest in the program. The
more recent 2008 farm bill (P.L. 110-246) lowers the EQIP payment
limit to $300,000 per entity. In addition, both states and EPA are
likely to face difficulties in meeting new program and permitting
responsibilities within current budgetary constraints. At issue is
whether adequate resources will be provided and funding priority
given as needed.
!Research needs. A large number of treatment technologies and best
management practices exist for pollution prevention at animal
feeding operations, as well as for handling, storage, treatment, and
land application of wastes.42 EPA believes, however, that storage
lagoons and sprayfields have been and remain the most widely used
technologies. Research to encourage new technologies and
demonstration of technologies and practices that may pose less
environmental risk could be environmentally and economically

42 Technologies are discussed extensively in: U.S. Environmental Protection Agency,
“Development Document for the Final Revisions to the National Pollutant Discharge
Elimination System Regulation and the Effluent Guidelines for Concentrated Animal
Feeding Operations,” December 2002, Chapter 8.

beneficial. In this regard, researchers may be interested in a program
established by the 2002 farm bill that authorizes USDA to provide
innovation grants to leverage federal investment in environmental
protection through the use of EQIP, including demonstrating
innovative nutrient management technology systems for AFOs. In
addition, the National Research Council’s recent report on air
emissions from AFOs recommends that EPA and USDA
aggressively pursue research in that area and identifies priorities for
short- and long-term research programs.
!Oversight of implementation. As noted previously, GAO has been
critical of EPA’s past oversight of state CAFO permitting activities,
and EPA has acknowledged that neither federal nor state agencies
have previously given much priority to regulating feedlot wastes. At
issue now will be how EPA and states demonstrate through planning
and actions their commitment to implement the new requirements.
USDA’s commitment to supporting farmers’ implementation of the
rules also will be of interest.
!Is federal legislation needed? There also is the issue of whether
the revised regulatory program reflects Congress’ intent and
expectations concerning management of animal waste and its
environmental impacts. Some questions of congressional intent
were raised in legal challenges brought by agriculture industry and
environmental groups to the rules, such as, did Congress intend to
authorize EPA to regulate land application of wastes? At the same
time, some may conclude that legislation amending the Clean Water
Act is needed to guide EPA, states, and industry by clarifying
Congress’ current view of key issues, compared with that act’s
enactment in 1972 — considering, for example, whether the scope
of requirements should be narrowed. Alternatively, some who see
gaps in parts of the final rules may favor legislation to broaden
requirements — for example, concerning co-permitting or
technology standards. Finally, some may believe that another
legislative vehicle entirely — such as the farm bill administered by
USDA — is a more appropriate tool for addressing animal waste
management issues.