Animal Waste and Water Quality: EPA’s
Response to the Waterkeeper Alliance Court
Decision on Regulation of CAFOs
Claudia Copeland
Specialist in Resources and Environmental Policy
November 8, 2011
Congressional Research Service
7-5700
www.crs.gov
RL33656
CRS Report for Congress
Pr
epared for Members and Committees of Congress
Animal Waste and Water Quality
Summary
In October 2008, the Environmental Protection Agency (EPA) issued a regulation to revise a 2003
Clean Water Act rule governing waste discharges from large confined animal feeding operations
(CAFOs). This action was necessitated by a 2005 federal court decision (Waterkeeper Alliance et
al. v. EPA, 399 F.3d 486 (2nd Cir. 2005)), resulting from challenges brought by agriculture
industry groups and environmental advocacy groups, that vacated parts of the 2003 rule and
remanded other parts to EPA for clarification.
The Clean Water Act prohibits the discharge of pollutants from any “point source” to waters of
the United States unless authorized under a permit that is issued by EPA or a qualified state, and
the act expressly defines CAFOs as point sources. Permits limiting the type and quantity of
pollutants that can be discharged are derived from effluent limitation guidelines promulgated by
EPA. The 2003 rule, updating rules that had been in place since the 1970s, revised the way in
which discharges of manure, wastewater, and other process wastes from CAFOs are regulated,
and it modified both the permitting requirements and applicable effluent limitation guidelines. It
contained important first-time requirements: all CAFOs must apply for a discharge permit, and all
CAFOs that apply such waste on land must develop and implement a nutrient management plan.
EPA’s 2008 revised regulation addressed those parts of the 2003 rule that were affected by the
federal court’s ruling: (1) it eliminated the “duty to apply” requirement that all CAFOs must
either apply for discharge permits or demonstrate that they have no potential to discharge, which
was challenged by industry plaintiffs; (2) it added procedures regarding review of and public
access to nutrient management plans, challenged by environmental groups; and (3) it modified
aspects of the effluent limitation guidelines, also challenged by environmental groups. The final
rule also modified a provision of the 2003 rule that the court upheld, clarifying the treatment of a
regulatory exemption for agricultural stormwater discharges. CAFOs were to apply for permits
and develop nutrient management plans by February 27, 2009. After that date, sources will have
three years to actually get permit coverage.
EPA’s efforts to revise the 2003 rule were controversial, particularly regarding the “duty to apply”
for a permit and agricultural stormwater exemption provisions. Environmental groups strongly
criticized EPA’s actions, arguing that the Waterkeeper Alliance court had left in place several
means for the agency to accomplish much of its original permitting approach, but instead EPA
chose not to do so. State permitting authorities also had a number of criticisms, focusing on key
parts that they argued would greatly increase the administrative and resource burden on state
regulators. Farm industry groups were generally supportive of the 2008 rule. Nevertheless, some
of them brought a legal challenge. In March 2011, a federal court agreed with the industry
petitioners and vacated a portion of the 2008 rule concerning the “duty to apply” requirement.
Congress has shown some interest in CAFO issues in the past, primarily through oversight
hearings in 1999 and 2001, before issuance of either the 2003 or 2008 rules.
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Animal Waste and Water Quality
Contents
Introduction...................................................................................................................................... 1
The 2003 Rule.................................................................................................................................. 2
The Waterkeeper Alliance Decision and EPA’s 2008 Revised Rule ................................................ 3
Duty to Apply for a Permit ........................................................................................................ 5
2008 Revised Regulation .................................................................................................... 7
Nutrient Management Plans ...................................................................................................... 7
2008 Revised Regulation .................................................................................................... 9
Aspects of the Effluent Limitation Guidelines for CAFOs ....................................................... 9
New Source Standards for Swine, Poultry, and Veal Operations ...................................... 10
Technology for Pathogen Control ..................................................................................... 10
Water Quality-Based Effluent Limitations........................................................................ 11
Agricultural Stormwater Discharges ....................................................................................... 12
2008 Revised Regulation .................................................................................................. 13
Responses to the 2008 Rule..................................................................................................... 14
Legal Challenge to the 2008 Revised Rule ....................................................................... 15
EPA’s Proposed Information Collection Rule ................................................................... 16
Congressional Interest ............................................................................................................. 17
Contacts
Author Contact Information........................................................................................................... 17
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Animal Waste and Water Quality
Introduction
According to the Environmental Protection Agency (EPA), the release of waste from animal
feedlots—the portion of the livestock industry that involves large, intensive animal raising and
feeding operations—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, which have occurred in a
number of locations in the United States. A variety of pollutants in animal waste can affect human
health in several ways, such as causing infections to the skin, eye, ear, nose, and throat.
Contaminants from manure can also pollute drinking water sources. Data collected for the EPA’s
2000 National Water Quality Inventory report identified agriculture as the leading known
contributor to water quality impairments in rivers and lakes. Animal feeding operations are only a
subset of the agriculture sector, but 29 states specifically identified animal feeding operations as
contributing to water quality impairment.1 Federal efforts to control these sources of water
pollution have accelerated in recent years, but they have been highly controversial.
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.
Although agricultural activities are generally not subject to requirements of environmental law,
discharges of waste from large feedlots, called concentrated animal feeding operations (CAFOs),
into the nation’s waters are regulated under the Clean Water Act (CWA). In the late 1990s, EPA
initiated a review of the CWA rules that govern these discharges. The rules had not been revised
since the 1970s, despite subsequent structural and technological changes in some components of
the animal agriculture industry. A proposal to revise the 1970s rules was released by the Clinton
Administration in December 2000 and was very controversial. Agriculture industry groups
opposed permitting requirements that they consider burdensome and costly, while others, such as
environmental groups, favored more stringent national standards that would require improved
control technology. During this period, Congress showed some interest in CAFO issues, through
oversight hearings held by House subcommittees in October 1999 and May 2001.
In December 2002, the Bush Administration issued a regulation revising the 1970s rules. The
revisions were published in the Federal Register in February 2003 and became effective April 14,
2003.2 The 2003 rule was challenged by multiple parties—environmental groups and agriculture
1 U.S. Environmental Protection Agency, “National Water Quality Inventory, 2000 Report,” August 2002, EPA-841-R-
02-001, 1 vol.
2 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. For additional information on the 2003 rule, see CRS Report
RL31851, Animal Waste and Water Quality: EPA Regulation of Concentrated Animal Feeding Operations (CAFOs),
by Claudia Copeland.
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industry groups—and in February 2005, a federal court issued a ruling that upheld major parts of
the rule, vacated other parts, and remanded still other parts to EPA for clarification, leaving all
parties unsatisfied to at least some extent. In response, EPA proposed revisions to the 2003 CAFO
rule which were finalized October 31, 2008. It took effect December 22, 2008, and required
CAFOs to apply for permits by February 27, 2009. Industry groups then challenged the 2008
revised rule, and in March 2011, a federal court vacated a portion of that regulation.
This report describes major features of the 2003 CAFO rule. It discusses the parts of the 2003 rule
that were addressed in the federal court’s 2005 decision and EPA’s response, as reflected in the
2008 revised regulation. It then describes legal challenges to the 2008 rule, and the federal court’s
March 2011 ruling. The report also provides an overview of perspectives of key interest groups—
the livestock and poultry industry, states, and environmentalists—on these issues.
The 2003 Rule
The CWA prohibits the discharge of pollutants from any “point source”3 to waters of the United
States unless authorized under a national pollutant discharge elimination system (NPDES) permit
that is issued by EPA or a qualified state. Any discharge from a point source, even one that is
unplanned or accidental, is illegal unless it is authorized by the terms of a permit. NPDES permits
limit the type and quantity of pollutants that can be discharged from a facility and specify other
requirements, such as monitoring and reporting. The specific discharge limitations in the permit
are derived from effluent limitation guidelines and standards (ELGs) that are separately
promulgated by EPA for specific categories of industrial sources. ELGs are technology-based
restrictions on water pollution, because they are established in accordance with technological
standards specified in the act. They vary depending upon the type of pollutant and discharge
involved, and whether the point source is new or already existing.
The act expressly defines CAFOs as point sources. EPA issued NPDES permitting rules for
CAFOs in 1974 (defining which animal feeding operations are subject to regulation4) and effluent
limitation guidelines in 1976. The 2003 rule did not redefine what is a CAFO, but it revised the
way in which discharges of manure, wastewater, and other process wastes from CAFOs are
regulated, and it modified both the NPDES permitting requirements and applicable ELGs. The
2003 rule required all CAFOs to apply for an NPDES permit. EPA estimated that this requirement
expanded the number of covered operations from about 12,800 under the pre-2003 rules to
15,500—primarily the largest CAFOs, in terms of numbers of animals raised or housed on-site—
or about 19% of all animal feeding operations of all size in the United States at that time. EPA
acknowledged that prior to the 2003 revisions, permitting and enforcement had been inadequate
and that only 4,000 CAFOs actually had permits.
3 Under the act, point sources are defined as any discernible, confined, and discrete conveyance, such as any pipe,
ditch, channel, or conduit from which pollutants are or may be discharged. In contrast, nonpoint source pollution,
which is not regulated by NPDES permits, is any source of water pollution that is not associated with a discrete
conveyance, including precipitation runoff from fields, forest lands, or mining and construction activities.
4 According to EPA rules, an animal feeding operation (AFO) is a facility in which livestock or poultry are raised or
housed in confinement for a total of 45 days or more in any 12-month period and animals are not maintained in a
pasture or on rangeland (40 CFR 122.23(b)(1)). CAFOs are a subset of AFOs. In addition to meeting the confinement
criteria, an AFO is a CAFO if it meets minimum size thresholds (those with more than specified numbers of animals
are CAFOs; those with fewer animals may be defined as CAFOs in some cases; 40 CFR 122.23(c)).
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The 2003 rule established ELGs that apply to the production areas of regulated CAFOs (including
the animal confinement area, manure storage area, raw material storage area, and waste
containment area) and, for the first time, to the land application area (referring to land to which
manure, litter, or process wastewater is or may be applied). These ELGs are non-numerical best
management practices. Discharges from a production area are subject to a performance standard
requiring facilities to maintain waste containment structures that generally prohibit discharges
except in the event of overflows or runoff resulting from a 25-year, 24-hour rainfall event.5
Similarly, discharges of pollutants from land application areas must comply with ELG best
management practices, such as the adoption of setback limits from surface waters or vegetative
buffer strips. In addition, the 2003 rule established a mandatory duty that a permitted CAFO must
develop and follow a plan, known as a comprehensive nutrient management plan (NMP), for
handling manure and wastewater and also must submit an annual performance report to EPA and.
The Waterkeeper Alliance Decision and EPA’s 2008
Revised Rule
The 2003 rule was challenged in court by a number of groups. The cases, brought by
environmental petitioners and by farm industry petitioners, were consolidated by the Second
Circuit Court of Appeals, which issued a decision in February 2005.6 The ruling reflected partial
victory for all of the parties, because the court upheld or did not address significant parts of the
regulation (such as the definition of what is a CAFO, for regulatory purposes). It upheld EPA’s
authority to regulate through permits the discharge of manure, litter, or process wastewater that a
CAFO applies to a land application area. It also upheld EPA’s interpretation that precipitation-
related discharges of manure, litter, or process wastewater from land application areas that are
applied in accordance with a nutrient management plan qualify as “agricultural stormwater” and
thus do not require permits.
The court agreed with some of the claims raised by both sets of petitioners: it vacated parts of the
regulation and remanded other parts to EPA for clarification. In response to the ruling, EPA
proposed revisions to the 2003 rule in June 2006. The parts of the rule affected by the court’s
ruling and EPA’s response are described in the next portion of this report.
During the time needed to develop a revised rule, EPA extended compliance dates in the 2003
rule for facilities that were affected by the Waterkeeper Alliance decision; ultimately, EPA
extended compliance until February 27, 2009—giving livestock operators another 19 months to
apply for discharge permits and to develop and implement manure management plans.7 This
extension affected the date for newly defined CAFOs (facilities not defined as CAFOs as of April
14, 2003—the effective date of the 2003 rule) to seek NPDES permit coverage and the date by
which all CAFOs must develop and implement NMPs. The compliance deadline extension did
5 This is a rainfall event with the probability of recurrence once in 25 years (or a 4% chance of being exceeded in a 24-
hour period in any single year). The amount of precipitation that constitutes a 25-year, 24-hour rainfall event varies by
location.
6 Waterkeeper Alliance et al. v. EPA, 399 F.3d 486 (2nd Cir. 2005).
7 U.S. Environmental Protection Agency, “Revised Compliance Dates Under the National Pollutant Discharge
Elimination System Permit Regulations and Effluent Limitations Guidelines and Standards for Concentrated Animal
Feeding Operations,” 72 Federal Register 40245-40250, July 24, 2007.
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not apply to new livestock operations (which were required by the 2003 rule to comply with those
rules when they begin operations) or to existing CAFOs that were covered by permits prior to
2003 (which also were required to comply when the 2003 rule became effective).
In March 2008, EPA released a supplement to the 2006 proposal, modifying it in two respects by
proposing additional options to respond to the Waterkeeper Alliance ruling, but not reopening the
entire 2006 proposal for additional public comment.
Several hundred public comments on EPA’s regulatory proposal were submitted by individual
citizens, environmental advocacy groups, state agencies (environmental, public health, and
agricultural departments), individual livestock and poultry producers, and groups that represent
livestock and poultry producers. Public comments addressed a number of general and specific
technical points, with particular focus on the “duty to apply” and agricultural stormwater
exemption provisions of the proposal (discussed below). Industry’s comments were generally
supportive of the proposal, approving deletion of the previous “duty to apply” provision and also
of EPA’s efforts to provide flexibility regarding nutrient management plan modifications—
especially to limit review and public participation requirements to only those changes that are
substantial. Environmental groups, on the other hand, strongly criticized the proposal, arguing
that the Waterkeeper Alliance court left in place several means for the agency to accomplish much
of its original permitting approach, but instead EPA chose not to do so. State environmental and
resource agencies, the primary implementers of CWA permitting, also had a number of criticisms.
They focused on key parts that they argued would greatly increase the administrative and
resource burden on states.
A final revised regulation was issued by EPA on October 31, 2008.8 The final rule substantially
adopted the 2006 proposal and the 2008 supplementary proposal, with some mainly editorial
modifications. In sum, the 2008 rule clarified the “duty to apply” provision to require that all
CAFOs apply for NPDES permits if they discharge or propose to discharge. It reiterated that a
CAFO could voluntarily self-certify compliance with the rule, but if a CAFO does not certify, in
an enforcement proceeding for failing to apply for a permit, the CAFO would have the burden of
proving that it did not propose to discharge. With regard to NMPs, the 2008 rule restated that
NMPs are an enforceable part of an NPDES permit and clarified that the terms of NMPs would
remain the same as specified in the 2003 rule. According to EPA, the revised rule applied to about
15,300 CAFOs that would need permit coverage (74% of the 20,700 CAFOs operating in 2008).9
The agency estimated that 9,000 CAFOs were covered by existing permits as of 2008, when the
revised rule was promulgated.
The next portion of this report discusses key portions of the 2003 regulation that were affected by
the Second Circuit’s ruling, beginning with discussion of issues that EPA addressed as a result of
the litigation. The issues are (1) the “duty to apply” requirement, which was challenged by
8 U.S. Environmental Protection Agency, “Revised National Pollutant Discharge Elimination System Permit
Regulation and Effluent Limitations Guidelines for Concentrated Animal Feeding Operations in Response to the
Waterkeeper Decision, Final Rule,” 73 Federal Register 225, November 20, 2008, pp. 70417-70486. See
http://www.epa.gov/npdes/regulations/cafo_final_rule_preamble2008.pdf.
9 EPA estimated that the CAFO industry had grown by about 22% between 2002 and 2008, due to industry expansion
and the trend toward larger, more concentrated facilities, but that changes in the 2008 rule, discussed below, reduced
the number of operations expected to seek permit coverage from 15,500 under the 2003 rule to 15,300 under the
revised rule.
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industry plaintiffs;10 (2) procedures regarding review of and public access to nutrient management
plans, challenged by environmental groups; and (3) aspects of the effluent limitation guidelines,
also challenged by environmental groups. It then discusses the agricultural stormwater issue
which the court did not reject or remand, but which EPA partially revised in the 2008 rule.
Duty to Apply for a Permit
The “duty to apply” provisions of the 2003 rule were among the most controversial, and they
remained so, even as revised in 2008—farm industry groups’ challenge to the 2003 rule focused
on this requirement and, as discussed below, so did these groups’ subsequent challenge to the
2008 revised rule.
The 2003 rule explicitly required all CAFOs to apply for an NPDES permit, or to demonstrate to
the permitting authority that they have no potential to discharge. EPA’s policy rationale for this
“duty to apply” provision was based on its “presumption that most CAFOs have a potential to
discharge pollutants into waters of the United States.”11 However, farm industry plaintiffs argued
that, unless there is a discharge of a pollutant, CAFOs and other point sources are neither
statutorily obligated to comply with EPA regulations, nor are they obligated to seek or obtain an
NPDES permit. The Waterkeeper Alliance court ruled in support of these plaintiffs and held that
EPA exceeded its authority under the CWA in ordering all CAFOs to apply for a permit, finding
that the law requires permits only where there is an actual discharge, not just a potential to
discharge.
In 2006, EPA proposed to replace the broad “duty to apply” requirement of the 2003 rule with a
requirement that all CAFOs that “discharge or propose to discharge propose to discharge” must
seek coverage under an NPDES permit. A similar requirement for all point sources already exists
under other parts of EPA regulations that were not affected by the Waterkeeper Alliance decision
(40 C.F.R. §122.21(a)(1)). The proposal deleted the 2003 rule’s provision allowing CAFOs to
demonstrate that they have no potential to discharge, saying that such a designation would be
irrelevant because the proposal would require only those CAFOs that discharge or propose to
discharge to seek coverage under a permit. EPA estimated that the change in the “duty to apply”
provision—that is, eliminating the permit requirement for CAFOs that have the potential to
discharge, as opposed to those that actually discharge or propose to discharge—meant that 25%
fewer CAFOs would ultimately seek permits and that CAFO operators would experience a $15.5
million per year reduction (or 26%) in administrative burden, compared with the 2003 rule.
EPA’s March 2008 supplementary proposal included a provision that would allow CAFOs to
voluntarily certify that the facility does not discharge or propose to discharge. This provision
would allow a CAFO to certify to the permitting authority, through an objective assessment, that
the operation does not discharge or propose to discharge and therefore does not need to obtain an
NPDES permit. To be eligible for this certification, the facility would be required to evaluate that
its production area will not discharge and to develop and implement an NMP similar to that for
permitted facilities. The certification process would be voluntary, but it would offer protection to
a farmer because in the event that a discharge from a certified CAFO occurs, the farmer would be
10 EPA’s resolution of the “duty to apply” issue in the 2008 revised rule was subsequently challenged by farm industry
groups, as discussed later in this report.
11 71 Federal Register at 37748.
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not liable for having failed to apply for a permit. The operator would still be subject to liability
for the discharge itself, however, and the certification would cease to be valid.
Public Comments
Both state permitting authorities and environmental groups opposed deletion of the requirement
in the 2003 rule that all CAFOs must apply for an NPDES permit. They said that in doing so, EPA
would change the entire permitting program from one that is pro-active to one that is reactive,
because it “would allow CAFO operators to decide whether their situation poses enough risk of
getting caught having a discharge to warrant the investment of time and resources in obtaining a
permit.”12 Although EPA estimated that 25% fewer CAFOs would seek permit coverage, states
argued that this overestimated the number that would voluntarily get permits, because under
EPA’s proposed revisions, there would be virtually no incentive to seek a permit. Further, states
contended that any cost savings experienced by CAFOs would be shifted to permitting authorities
which would be placed in a more adversarial position of first proving that a facility has a
discharge and then taking an enforcement action. As one state observed, the number of CAFOs,
permitted or not is the same, and EPA was thus expecting states to inspect those that don’t apply
for permit coverage, as well as process permits for those that do.13 Overall, states argued that the
administrative burden on states of EPA’s proposal to delete the “duty to apply” requirement would
be greater than under the 2003 rule, not less.
States and environmental groups also objected to allowing industry to voluntarily self-certify
compliance, saying that it would undermine the environmental protection provisions of the rule.
Industry groups also were critical, saying that requiring most feedlots to seek permits or face
retroactive penalties if an unpermitted discharge occurs would amount to a form of the “duty to
apply” concept that was rejected by the Waterkeeper court.
Agriculture industry commenters had other concerns about this aspect of EPA’s proposed
revisions. They had challenged the “duty to apply” provision of the 2003 rule, and the court had
upheld their argument that the CWA only requires facilities that actually discharge to seek permit
coverage. Industry groups fundamentally continue to disagree with any presumption that CAFOs
do discharge pollutants, contrary to EPA’s position in support of the 2003 rule or
environmentalists’ contentions.14 Thus, they objected to EPA’s proposal that CAFOs should
voluntarily seek permits and the specific addition of a permit requirement for those that “propose
to discharge.” According to this view, EPA may not lawfully establish permitting requirements
based on speculation as to possible future CAFO discharges. Any “duty to apply” triggered by
accidental discharges could arise (if at all) only after an actual discharge has occurred and should
be limited to facilities that accidentally discharge and fail after a reasonable time to identify the
cause and take appropriate corrective measures.15 One of EPA’s rationales for promulgating the
2003 rule was recognition that large numbers of unpermitted CAFOs were discharging wastes
12 Natural Resources Defense Council, Sierra Club, Waterkeeper Alliance, Comments on the revised CAFO regulation,
August 29, 2006, p. 9.
13 Ohio Department of Agriculture, Ohio Environmental Protection Agency, Ohio Department of Natural Resources,
Comments on the revised CAFO regulation, undated, p. 6.
14 National Pork Producers Council, United Egg Producers, American Farm Bureau Federation, National Council of
Farmer Cooperatives, National Corn Growers Association, “Comments on Proposed Post-Waterkeeper CAFO NPDES
Regulations,” August 29, 2006, p. 38.
15 Id., p. 14.
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that contribute to water quality impairments.16 Critics of industry’s position on this issue
contended that allowing CAFOs to self-regulate, self-report accidental releases, and then possibly
seek permit coverage would likely perpetuate those same conditions.
2008 Revised Regulation
The 2008 rule adopted the approach proposed in 2006, replacing the “duty to apply” requirement
in the 2003 rule with a requirement that a CAFO must seek permit coverage when it actually
discharges or proposes to discharge (i.e., based on an objective assessment that it is designed,
constructed, operated, or maintained such that a discharge will occur, not simply that it might
occur).
EPA recognized that some CAFOs that do not discharge or propose to discharge will not seek
permit coverage. But, in the event of a discharge from an unpermitted CAFO, the operator would
be in violation of the CWA, because any discharge from a CAFO, even one that is unplanned or
accidental, is illegal unless it is authorized by the terms of a permit or is agricultural stormwater.
Some CAFO operators were concerned that an accidental discharge from an unpermitted facility
would subject the CAFO to liability for the discharge and for failure to apply for a permit. Thus,
the revised rule included the option proposed in 2008 to allow a CAFO to certify to the permitting
authority that it is designed, constructed, operated, and maintained not to discharge. A certifying
CAFO is required to implement a nutrient management plan that, at a minimum, meets the NMP
requirements applicable to permitted CAFOs. A CAFO’s “no discharge” certification is not
subject to review by the permitting authority in order for it to become effective, and the
permitting authority is not required to make the certification available to the public for comment,
because the certification is not a permit application for which review is required. In the event of a
discharge from a certifying CAFO (other than agricultural stormwater), the facility would be
liable for any unpermitted discharge, but not for failure to apply for a permit.
Nutrient Management Plans
The 2003 rule mandated that NPDES permits for all CAFOs that land apply animal waste include
a new requirement that the permittee develop and implement a nutrient management plan that
includes minimum elements specified in the rule, such as ensuring adequate storage of manure,
litter, and process wastewater, and preventing direct contact of confined animals with waters of
the United States. CAFOs were to develop and implement an NMP by the same date that the rule
required them to comply with the rule’s land application provisions. The 2003 rule provided that
NMPs would be retained on-site at the CAFO. It must be available to EPA or the permitting
authority, but it is not considered part of the facility’s permit.
The environmental plaintiffs argued to the federal court that the NMP part of the 2003 rule was
unlawful under the Clean Water Act and the Administrative Procedure Act17 because it failed to
require that the terms of the NMP must be reviewed and be included in the NPDES permit
(inclusion in the permit would make the NMP enforceable by the government and private
citizens) and because it allowed permitting authorities to issue permits in the absence of any
16 See 68 Federal Register 7179-7181,
17 The Administrative Procedure Act, 5 U.S.C. §§ 551-559, contains provisions that govern federal agency rulemaking
proceedings.
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meaningful government or public review of this aspect of the permit. They also argued that the
permitting aspects of the rule violate the Clean Water Act’s public participation requirements by
effectively shielding the plans from public scrutiny and comment. The court agreed with the
environmental plaintiffs on these points and vacated these portions of the rule.
In response, EPA proposed in 2006 to require that CAFOs seeking permit coverage submit an
NMP as part of the permit application and that the permitting authority make the plan available
for review prior to developing the facility’s permit. The permitting authority would be responsible
for reviewing the NMP for completeness and sufficiency. The terms of the NMP (such as the
minimum elements described above) would become terms and conditions of the permit, as
required by the court. In its proposal, EPA distinguished between NMP terms, which must be
incorporated as enforceable conditions of the permit following the public review process, and the
plan as a whole, which must be submitted to the permitting authority for review. The NMP as a
whole, EPA said, will include underlying data, calculations, and other information such as
technical standards that provide a basis for the facility-specific requirements.
EPA rules generally allow permitting authorities to issue two types of permits: either individual
facility-specific permits, or general permits to cover multiple facilities without the need to receive
individual permit applications from facilities in advance of developing the permit. In the 2003
rule, EPA indicated that it expected that most permitting authorities would utilize general permits,
as a way of minimizing regulatory burden. The Waterkeeper Alliance ruling required EPA to
expressly address public participation in review of NMPs, since they must be included in a
permit. In the case of individual permits, existing NPDES rules already establish procedures for
public participation. Thus, because the NMP would be part of the individual permit application, it
would be subject to existing rules requiring public participation, and no rule changes were
needed.
EPA’s 2006 proposed response to the ruling contained new provisions for public participation in
review of NMPs for those facilities intending to be covered by a general permit, because there is
no provision in existing rules that explicitly addresses incorporation of site-specific NMP
requirements into a general permit. The proposal included mechanisms so that general permits for
CAFOs can be modified, once issued, to include the terms of an NMP applicable to a specific
CAFO and to provide an opportunity for public review of a CAFO’s Notice of Intent (including
the entire NMP) to be covered by a general permit, before the CAFO actually receives coverage
under the general permit. Under the proposal, the permitting authority (state or EPA) would have
discretion as to how best to provide public notification and comment in the context of general
permits.
In the March 2008 supplementary proposal, EPA presented alternatives to enable permitted
CAFOs some flexibility in developing their NMPs, with respect to specifying the rates of
application of nutrients in manure, litter, or process wastewater to land. Circumstances at a farm
change during the period of a permit (ordinarily five years), and agricultural operations often
modify their nutrient management and farming practices during the normal course of their
operations—for example, planting different crops that have different needs for nitrogen and
phosphorus. The alternatives were intended to allow CAFOs to make crop rotation and similar
changes without requiring formal modification of their NMPs. Such flexibility would reduce the
burden on permitting authorities and CAFO operators by decreasing the number of significant
changes to permits, which require public notice and comment. The alternatives would allow
CAFO operators to make routine changes at a facility that affect the rate of nutrient application to
land without changing the NMP itself. EPA proposed three alternatives, with increasing amounts
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of flexibility for the CAFO operator; each approach would require annual reporting requirements
to provide actual data that would be publicly available concerning compliance with permit
requirements during the previous year.
Public Comments
Many comments on the 2006 proposal focused on the complexity of nutrient management
planning and the administrative and resource burdens that NMPs would put on CAFO operators
and state permitting agencies. Recognizing the problem of burdens imposed on permitting
authorities, EPA’s proposal incorporated flexibility in various ways, such as allowing states the
discretion to decide how to provide for public notice. Other comments were critical that EPA was
proposing too much flexibility and discretion for permitting authorities and would not ensure
adequate public participation and review.
Industry commenters sought clarification of criteria that constitute the terms of the NMP (since
NMP terms become enforceable conditions of the permit), which EPA addressed in the 2008
supplementary proposal. However, other commenters asserted that the entire NMP should be
included in or expressly referenced by the permit, so as to ensure that the permit requires the
CAFO to comply with every discharge reduction or prevention measure in its NMP.
2008 Revised Regulation
The final rule adopted the approach that EPA proposed in 2006. The revisions did not change the
required contents of the NMP, but they added a requirement for CAFOs to submit the NMP as
part of their permit application or notice of intent to be covered by a general permit and added
public participation requirements to ensure opportunity for public review. The rule established
new procedures for permitting authority and public review of NMPs for CAFO general permits.
To respond to the Waterkeeper decision, the final rule specified minimum terms of the NMP that
must be enforceable requirements of a CAFO’s permit, but EPA did not agree with those
commenters who argued that all of the information in the NMP constitutes enforceable terms.
The court focused on rates of applications as perhaps the most important term of the NMP, and it
was an issue of concern to many commenters. Thus, the 2006 and especially the 2008
supplementary proposal addressed this issue in detail. The final rule modified the 2008
supplementary proposal to include two options for identifying the terms of the NMP with respect
to rates of application of nutrients. Each approach would provide a means for a CAFO to
articulate in its NMP annual maximum rates of application of animal waste by field and crop and
identify the minimum required terms of the NMP specific to that approach. One approach would
be suitable for operations with predictable crops and land application, EPA said, while the other
likely would benefit CAFOs that may need to adjust their rates of application because of changes
in soil levels of nitrogen and phosphorus, due, for example, to changes in crop rotations.
Aspects of the Effluent Limitation Guidelines for CAFOs
Specific effluent limitations contained in individual NPDES permits are dictated by the terms of
more general effluent limitations guidelines promulgated by EPA that typically specify the
maximum allowable levels of pollutants that may be discharged by facilities within an industrial
category or subcategory using specific technologies. While the limits are based on the
performance of specific technologies, they do not generally require the industry to use these
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technologies, but rather allow the industry to use any effective alternatives to meet the pollutant
limits. As noted above, in the 2003 rule, EPA established non-numerical effluent limitation
guidelines for the production areas of CAFOs, and did so for four subcategories of the CAFO
industry. The environmental petitioners challenged several aspects of the ELGs, and the
Waterkeeper Alliance court upheld parts of their claims. In this portion of the decision, the court
remanded the rule to EPA with instruction to present additional analysis and justification, so as to
clarify its decisionmaking rationale.
New Source Standards for Swine, Poultry, and Veal Operations
The CWA requires EPA to promulgate New Source Performance Standards (NSPS) for new, as
opposed to already existing, sources of pollution, based on what is determined to be the best
available demonstrated control technology. The 2003 rule dictated that new sources in this
subcategory meet a waste management standard of no discharge, except in the event of manure
runoff and precipitation from a 100-year, 24-hour rainfall event.18 The rule also allowed a less
restrictive alternative performance standard (a 25-year, 24-hour storm standard) for those
facilities that would voluntarily use new technologies and management practices that perform as
well as or better than the baseline ELGs at reducing pollutant discharges to surface waters from
the production area. The court held that EPA had not provided adequate statutory and evidentiary
basis for these portions of the rule and had not justified its decision to allow compliance through
an alternative standard. In its 2006 proposal to revise the rule, EPA deleted the provision allowing
CAFOs to meet the no discharge standard through the use of a 100-year, 24-hour rain event
containment structure, thus effectively prohibiting all discharge of manure, litter, and process
wastewater from the production area for new sources in this subcategory. EPA also proposed to
delete the voluntary superior performance standards provision, since the baseline for all new
facilities in this subcategory will now be no discharge.
In the 2008 final rule, EPA adopted the revisions proposed in 2006—deleting the use of a 100-
year, 24-hour rain event containment structure and deleting the voluntary superior performance
standards provision in the 2003 rule. The agency also promulgated a new provision that would
allow a CAFO using an open surface manure storage structure to request the permitting authority
to establish site-specific ELGs that incorporate the NSPS no discharge requirement. The new
provision was intended to create an incentive for the use of innovative technologies to meet the
no discharge requirement by providing an up-front determination that the CAFO will meet the
requirement prior to potentially expensive construction.
Technology for Pathogen Control
An effluent limitation guideline establishes the degree of pollutant reduction that is attainable by
industrial sources through the application of various levels of technology. The CWA requires that
ELGs be based on standards that are progressively more stringent: (1) best practicable control
technology currently available (BPT), the minimum technological requirement; (2) best control
technology for conventional pollutants (BCT); and (3) best available technology economically
achievable (BAT), representing the best control measures that have been developed or are capable
of being developed within the industrial category. The act required existing sources to meet BPT
18 This is a statistical event defined as the amount of rainfall that has a 1% chance of being exceeded in a 24-hour
period in any given year (or, once in 100 years).
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by July 1, 1977, and BAT by July 1, 1983. BCT is not an additional limitation, but it replaces
BAT for control of a group of pollutants that are naturally occurring in the aquatic environment,
are biodegradable, and are the traditional and primary focus of wastewater control. Five
pollutants are presently considered conventional pollutants; one of these, the pathogen fecal
coliform, is associated with manure discharges from CAFOs. Point sources that discharge
conventional pollutants are required to meet the BCT standard, but the act requires that, in
establishing BCT, EPA must conduct a “cost reasonableness” test of attaining more stringent
pollutant control than BPT.
In the 2003 rule, EPA said that the ELG requirements of the rule were not specifically designed to
reduce pathogens in animal waste but may, in EPA’s view, achieve some incidental reductions of
pathogens. The environmental plaintiffs argued that EPA had not presented adequate evidence to
justify establishing a BCT standard for pathogens that is no more stringent than the rule’s BPT
standard. The court upheld this complaint and ruled that EPA must make an affirmative finding
that the BCT-based ELGs adopted in the rule do in fact represent the best control technology for
reducing pathogens. In its 2006 proposal to revise the 2003 rule, EPA retained the BCT standard
promulgated previously and provided a lengthy narrative discussion and cost analysis justifying
its original rationale.
In the 2008 final rule, EPA presented what it termed an affirmative finding that the BCT
limitations adopted in the 2003 rule do, in fact, represent the best conventional control technology
limitations for fecal coliform. Thus, it retained the BCT standard in the 2003 rule with a more
complete explanation of how it made that determination.
Water Quality-Based Effluent Limitations
While technology-based NPDES permits derived from EPA’s ELGs may result in meeting state
water quality standards for individual waterbodies, the effluent guidelines program is not
specifically designed to ensure that the discharge from each facility meets the water quality
standards for that particular waterbody. For this reason, the CWA requires permitting authorities
to establish water quality-based effluent permit limitations (WQBELs), where necessary to attain
and maintain water quality standards, specifying discharge limitations that are more stringent than
the national ELGs. Where WQBELs are necessary, they are established without consideration of
treatment technologies or cost. In the 2003 rule, EPA included no requirements concerning
WQBELs. At the time, EPA said that it did not expect that WQBELs will be established for
CAFO discharges from land application areas since, as described above, any precipitation-related
discharges from those areas will be considered agricultural stormwater, which is exempt from
NPDES permitting.
The environmental plaintiffs challenged EPA’s failure to justify the lack of WQBELs for
discharges other than agricultural stormwater. They also charged that the 2003 rule would bar
states from promulgating WQBELs. The Waterkeeper Alliance court partly upheld these
complaints and directed EPA on remand to explain whether or not, and why, WQBELs are needed
to assure that CAFO discharges will not interfere with the attainment and maintenance of water
quality standards. The court also found that the Preamble to the 2003 rule was ambiguous about
whether states may promulgate WQBELs for discharges other than agricultural stormwater, and it
ordered EPA to clarify this issue.
In the 2006 proposal, EPA restated its view that precipitation-related discharges from land
application areas are statutorily exempt from any effluent limitations, including WQBELs,
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because they are agricultural stormwater, but it clarified that WQBELs can be applied in
appropriate cases to further limit discharges from CAFO production areas and with respect to
non-precipitation-related land application discharges. This reasoning would apply to state-issued
as well as EPA-issued permits. Further, EPA said that it is possible that a state, acting under its
own regulatory authorities, could impose additional requirements that are broader than the federal
NPDES program, if they so choose. Whether states will do so, however, is unclear.
In the 2008 final rule, EPA reiterated its view that nothing in the rule limits a state permitting
authority from including more stringent limitations on agricultural stormwater discharges under
its own state regulations. Thus, the agency said that a state could require WQBELs for new
sources that are subject to the rule’s no discharge standard (discussed above). But EPA also
reiterated its view that, as a practical matter, it is difficult to imagine circumstances in which
additional limitations would be necessary for CAFOs that already must comply with a stringent
no discharge requirement.
Agricultural Stormwater Discharges
One issue that the federal court upheld in 2005 concerns the rule’s treatment of a regulatory
exemption for agricultural stormwater discharges. This issue, which had been controversial
during development of the 2003 rule, arose in the context of the regulatory framework concerning
the land application of manure, litter, and process wastewater. As noted above, the CWA
expressly defines the term “point source” to include concentrated animal feeding operations. The
same provision of the act, Section 502(14), also expressly defines “point source” to exclude
“agricultural stormwater.” The court characterized this provision as “self-evidently ambiguous”
and observed, “the Act makes absolutely no attempt to reconcile the two.”19 When manure and
other waste are applied to land, precipitation-related runoff can transport nutrients, pathogens,
and other pollutants in the waste to nearby receiving waters.
To develop the 2003 rule, EPA had to interpret the statutory inclusion of CAFOs as point sources
and the agricultural stormwater exclusion consistently and to identify the conditions under which
discharges from the land application area of a CAFO are point source discharges that are subject
to NPDES permitting requirements, and those which are agricultural stormwater discharges and
thus are not point source discharges.20 The land application portion of the 2003 rule detailed
requirements to ensure that animal waste is applied to land in accordance with nutrient
management practices that ensure appropriate agricultural use of the nutrients in the waste. Under
the rule as promulgated, EPA determined that when manure or process wastewater is applied in
accordance with those practices, at appropriate agronomic rates, it is a beneficial agricultural
production input. Where such practices have been used, any remaining precipitation-related
discharge is agricultural stormwater which is exempt from permitting. In contrast, where
appropriate manure management practices have not been used, EPA argued that it is reasonable to
conclude that discharges of manure from a land application area have not been applied at
agronomic rates, are not agricultural stormwater, and thus are subject to NPDES permitting.
Under the 2003 rule, adherence to appropriate nutrient management practices eliminates any need
19 Waterkeeper Alliance et al. v. EPA, 399 F.3d at 507.
20 Production areas such as feedlots and lagoons are not eligible for the agricultural stormwater exemption, because
they involve the type of industrial activity that originally led Congress to single out CAFOs as point sources. See 68
Federal Register 7198.
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to seek permit coverage for land application discharges or submit a land application NMP to the
permitting authority.
Both groups of petitioners challenged this portion of the rule. Livestock and poultry industry
plaintiffs argued that land application runoff should be considered a point source discharge
subject to permitting only if it is collected or channelized prior to discharge. In contrast, the
environmental petitioners argued that the act’s definition of “point source” requires regulation of
all CAFO discharges, notwithstanding the statutory exemption for agricultural stormwater
discharges. The court found that EPA’s interpretation of the act in this regard was reasonable. The
court interpreted the rule as seeking to remove liability for agriculture-related discharges
primarily caused by nature, while maintaining liability for other discharges. “[W]here a CAFO
has taken steps to ensure appropriate agricultural utilization of the nutrients in manure, litter, and
process wastewater, it should not be held accountable for any discharge that is primarily the result
of ‘precipitation.’”21 It rejected the challenges by the parties, and it upheld this portion of the rule.
Although the court did not direct EPA to revise this provision, the agency stated in the Preamble
to the 2006 proposed revisions that it was considering adding a provision that would apply to
runoff from CAFO fields that are otherwise unpermitted because they do not discharge or propose
to discharge (and thus are considered to be agricultural stormwater). Under this addition, in order
to qualify as agricultural stormwater discharges and thus receive a permit exemption, unpermitted
large CAFOs would still be required to comply with nutrient management technical standards for
land application (field-specific standards, for example) that have been established by the
permitting authority (the state or EPA), in addition to the practices specified in the EPA rule.
Public Comments
Industry groups endorsed EPA’s proposal regarding agricultural stormwater, which assumed that
where land application is conducted in accordance with the rule’s nutrient management standards,
stormwater runoff is exempt from NPDES permitting. However, these groups strongly objected to
EPA’s suggestion in the Preamble to the 2006 proposal that it was also considering requiring
CAFOs to comply with additional technical standards established by a permitting authority,
because they maintained that such a change would unlawfully narrow the exemption.
Environmentalists, on the other hand, argued that this portion of the 2006 proposal would
unlawfully allow CAFOs to self-regulate, as it fails to require them to get permits in order to
claim the exemption. States expressed a similar view, contending that neither a state nor EPA can
take enforcement action against an unpermitted CAFO to comply with technical or other
standards. One state observed that EPA’s proposal represents “a circular arrangement that would
be quite difficult to enforce and administer,” and that courts would be skeptical of enforcement
cases against facilities that are exempt from regulation.22
2008 Revised Regulation
The revised rule included a provision described in the Preamble to the 2006 proposal. It stated
that in order for unpermitted large CAFOs to have their precipitation-related discharges qualify as
21 Waterkeeper Alliance et al. v. EPA, 399 F.3d at 509.
22 Illinois Environmental Protection Agency, Comments on the revised CAFO regulation, August 29, 2006, p. 4.
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agricultural stormwater discharges, they must apply manure, litter, or process wastewater to land
according to site-specific nutrient management practices that ensure appropriate agricultural use
of the nutrients in the waste. A full NMP is not required. While this was a new provision in the
rule, EPA stated that it was not a new requirement; rather, it clarified EPA’s existing interpretation
of the agricultural stormwater exemption in CWA Section 502(14).
Responses to the 2008 Rule
While there was no overall agreement among interest groups on the initial 2006 and 2008
supplementary proposals, they did concur on at least one point: EPA should provide much more
clarity and guidance on such key concepts as criteria or circumstances defining the need for a
CAFO to seek permit coverage and what terms in a nutrient management plan should be included
in a permit. EPA offered some examples on these points, but the public comments reflected
considerable uncertainty about issues that are fundamental to implementation of the rule.
EPA estimated that economic impacts of the final rule on CAFO operators would be nearly the
same as costs of the 2003 rule—$54 million annually. While approximately 25% of CAFO
operators subject to the 2003 rule would not need permit coverage under the 2008 revisions
(largely due to eliminating the universal “duty to apply” requirement), thus saving CAFOs
approximately $14 million in reduced permitting costs, other CAFOs face increases in annual
administrative burden due to the new NMP requirements and costs to qualify for the agricultural
stormwater exemption.
State permitting authorities were projected to incur administrative costs of about $17 million
annually—slightly higher than estimated in the 2003 rule. The smaller number of permitted
facilities was expected to reduce costs, while implementing the new NMP requirements was
expected to increase the administrative burden on states.
Industry groups were generally pleased that there was little change in the final rule from EPA’s
proposals, with the exception of the “duty to apply” provision, as discussed below. Questions
about implementation of the agricultural stormwater exemption persist, both with states and
environmental advocates, and many states continue to believe that EPA underestimated the
impacts of the rule on permitting authorities. A number of states and farm industry groups argued
that, even with EPA’s extension of compliance to February 27, 2009, that date was unattainable.
In the revised rule, EPA declined to modify that date, based on its view that CAFOs already had
the information that they would need to develop NMPs and would not need to wait for further
EPA action before doing so. Finally, environmental groups remained concerned about allowing
CAFOs to self-certify that they do not discharge, as well as about EPA’s failure to require
stringent technology for pathogen control.
While the CAFO regulations discussed in this report apply nationwide, EPA also is considering
regulatory changes that could affect CAFO operations located in the Chesapeake Bay watershed.
In May 2009, President Obama issued an Executive Order that declared the Bay a “national
treasure” and charged the federal government with assuming a strong leadership role in restoring
the Bay. One year later, EPA and other federal agencies issued a multi-agency strategy for
protecting and restoring the Chesapeake region consisting of specific environmental initiatives to
establish new clean water regulations on stormwater discharges and pollution discharges from
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animal feedlots in the Bay watershed, put new agricultural conservation practices on farms in the
region, and restore land and water habitat.23 Agricultural discharges of nutrients are believed to be
responsible for more than 50% of water quality impairment of the Bay.
As part of the federal strategy for Chesapeake Bay, EPA is initiating a rulemaking that will
consider more stringent CAFO permit standards to control nutrient discharges to the Bay. The
Bay-specific rules may consider expanding the universe of CAFOs by means which might
include (but are not limited to) making it easier to designate an AFO as a CAFO or increasing the
number of animal operations that would qualify as CAFOs. EPA will propose more stringent
permitting requirements for land application of manure, litter and process wastewater, such as
requiring next-generation nutrient management plans and off-site manure management. EPA
plans to propose the CAFO rule by June 30, 2012, and to take final action on the proposal by June
30, 2014. EPA is reviewing each Bay state’s CAFO program and is working with the states to
ensure that they meet the programmatic requirements of the 2008 CAFO rule. EPA will conduct a
review of each of the Chesapeake Bay states’ technical standards for nutrient management by
December 15, 2012, to ensure that they meet the requirements of the national CAFO regulations.
Some industry sources are concerned that the Chesapeake Bay-specific rules will also have
implications for EPA’s national CAFO regulations.
Legal Challenge to the 2008 Revised Rule
Not surprisingly, because of the differing perspectives on EPA’s action, further legal challenges
followed promulgation of the revised rule. Agriculture industry groups (although generally
satisfied with the rule) filed lawsuits in several federal appellate circuits, and environmental
groups also challenged portions of the rule. The various petitions were consolidated in the U.S.
Court of Appeals for the 5th Circuit.
EPA and the environmental petitioners began settlement negotiations in June 2009, and in May
2010, these parties signed a settlement agreement24 in which EPA agreed to develop a guidance
document that helps CAFOs determine if they have a discharge and thus should apply for a
permit. The agency issued the guidance document on May 28, 2010, as required by the
settlement.25 EPA also agreed to propose a rule in order to collect certain information from CAFO
owners or operators, such as number and types of animals, type and capacity of manure storage or
treatment process, and quantity of manure generated annually by the CAFO. This portion of the
settlement responds to concerns that EPA lacks adequate basic information about CAFOs, their
locations, size, characteristics, etc., to properly regulate them.26
Farm industry petitioners were not parties to that settlement, and their legal challenge to the 2008
revised rule continued. In the earlier litigation on the 2003 rule, the agriculture industry had
23 For information, see http://executiveorder.chesapeakebay.net/post/New-Federal-Strategy-for-Chesapeake-Launches-
Major-Initiatives-and-Holds-Government-Accountable-for-Progress.aspx.
24 National Pork Producers Council v. EPA, 5th Cir., No. 08-61093, May 25, 2010.
25 U.S. Environmental Protection Agency, Office of Water, “Implementation Guidance on CAFO Regulations –
CAFOs That Discharge or Are Proposing to Discharge,” May 28, 2010, EPA-833-R-10-006.
26 In September 2008, the Government Accountability Office issued a report that questioned EPA’s ability to
effectively regulate CAFOs, because the agency lacks comprehensive, accurate information needed to do so. See U.S.
Government Accountability Office, Concentrated Animal Feeding Operations—EPA Needs More Information and a
Clearly Defined Strategy to Protect Air and Water Quality from Pollutants of Concern, GAO-08-944, 80 p.
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challenged a provision of that rule that explicitly required all CAFOs to apply for an NPDES
permit, or to demonstrate that they have no potential to discharge. The Waterkeeper Alliance court
upheld their argument that the CWA only requires facilities that actually discharge to seek permit
coverage. Industry groups continued to disagree with any presumption that CAFOs do discharge,
thus they challenged EPA’s attempt in the 2008 revised rule to encourage CAFOs to voluntarily
seek permits and the specific addition of a permit requirement for those that “propose to
discharge.” According to this view, EPA may not lawfully establish permitting requirements based
on speculation as to possible future CAFO discharges.
The federal court issued its ruling in the case in March 2011.27 The court upheld the portion of the
rule requiring a CAFO to apply for a permit if the facility has an actual discharge. However, the
court vacated the part of the 2008 rule that created liability for failing to apply for a permit if the
CAFO only proposes to discharge, but does not actually do so, thus rejecting what the court
characterized as the “attempt by EPA to create from whole cloth a new liability provision.”28
The federal government did not seek a rehearing on the Fifth Circuit’s ruling, nor did it petition
the Supreme Court for a review. At least for now, EPA has no plans to revise the 2008 rule, having
concluded that the court’s ruling effectively simplifies permitting by removing uncertainty about
the “duty to apply” for a permit and thus is largely self-implementing. The agency has conducted
outreach to states on the effect of the ruling and expects at some point to post a disclaimer to the
guidance that it issued in May 2010 concerning CAFOs that discharge or propose to discharge.29
Section 510 of the Clean Water Act allows states to adopt or enforce water pollution standards or
discharge limitations that differ from but are no less stringent than federal requirements.
Consequently, although many states prohibit adoption of standards that are more stringent than
what is required by federal rules, CAFO operators in some locations may be subject to
requirements beyond those in EPA’s CAFO regulations. For example, state regulators in Michigan
require CAFOs to obtain water pollution discharge permits or prove they do not need them,
irrespective of whether they actually discharge—essentially the same provision in the 2003 EPA
rule that was invalidated in the Waterkeeper Alliance decision. In March 2011, the Michigan
Court of Appeals upheld the authority of state regulators to implement the requirement, pursuant
to state law, stating that the Waterkeeper decision was not relevant to the challenge to Michigan
law that had been brought by farm groups in the state.30
EPA’s Proposed Information Collection Rule
In October 2011, EPA proposed a rule that would require CAFOs to submit a specific set of basic
operational information to EPA, pursuant to the agency’s May 2010 settlement agreement with
environmental plaintiffs, described above. The proposal would require CAFOs to provide the
27 National Pork Producers Council v. U.S. EPA, 635 F.3d 738 (5th Cir. 2011).
28 Farm industry petitioners had also challenged a portion of the rule concerning inclusion of best management
practices in an NMP. The court disallowed this challenge, saying that it really was a challenge to part of the 2003 rule
and thus was time barred. The court also rejected a challenge by poultry industry petitions to certain EPA guidance
letters issued after promulgation of the 2008 rule, on the basis that the letters did not reject a final agency decision and
thus the court lacked jurisdiction to review them.
29 See infra footnote 25.
30 Michigan Farm Bureau v. Department of Environmental Quality, Mich. Ct. App., No. 209323, March 29, 2011,
http://coa.courts.mi.gov/documents/opinions/final/coa/20110329_c290323_30_290323.opn.pdf.
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following information: facility contact information; production area location; whether the CAFO
has a CWA permit; the number and type of animals at the CAFO; and the number of acres
available for land application of manure, litter, and process wastewater.31 EPA proposed two
reporting options. One option would require every CAFO to report the information to EPA, unless
states with authorized CWA programs choose to provide the information on behalf of CAFOs in
their state. The second option would require CAFOs in focus watersheds that have water quality
concerns associated with CAFOs to report information to EPA.32
EPA is accepting public comment on the two alternatives until December 20, 2011. Under the
court-approved agreement with environmental plaintiffs, EPA expects to take final action on a
rule by July 2012.
Both agriculture groups and environmental advocates criticized EPA’s proposal. Livestock groups
are not convinced that the rule is required in the first place and are concerned that supplying the
requested information would be a costly burden to farmers. EPA officials believe that burden
would be minimized by the limited data that the agency proposes to collect and also if states
voluntarily provide the information to EPA (under the first proposed option). Environmental
advocates, on the other hand, contend that the narrow scope of the proposed rule does not meet
the terms of the 2010 settlement agreement and falls short of the kind of information needed to
regulate CAFOs adequately. Environmental groups are skeptical of EPA’s assertion that the
agency can obtain site-specific answers to other questions—such as the quantity of manure
generated annually by the CAFO and quantities of manure transferred off-site—directly from
states, other federal agencies, specific CAFOs, or other sources.
Congressional Interest
Congress has shown some interest in CAFO issues in the past, primarily through oversight
hearings in 1999 and 2001, before issuance of either the 2003 or the 2008 CWA rules. The 112th
Congress has shown increased interest generally in the impact of EPA rules and requirements on
the agriculture sector.33 Whether these issues will receive more congressional attention in the
future, and what form it might take, are unknown for now.
Author Contact Information
Claudia Copeland
Specialist in Resources and Environmental Policy
ccopeland@crs.loc.gov, 7-7227
31 EPA’s authority to collect information is found in CWA Section 308(a)(3)(A), under which EPA may require owners
or operators of point sources to maintain records, make reports, and provide such other information as EPA may
reasonably require to carry out the objectives of the act.
32 U.S. Environmental Protection Agency, “National Pollutant Discharge Elimination System (NPDES) Concentrated
Animal Feeding Operation (CAFO) Reporting Rule; Proposed rule,” 76 Federal Register 65431-65458, October 21,
2011.
33 For information, see CRS Report R41622, Environmental Regulation and Agriculture, coordinated by Megan Stubbs.
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