Order Code RL33656
Animal Waste and Water Quality:
EPA’s Response to the Waterkeeper Alliance
Court Decision on Regulation of CAFOs
April 11, 2007
Specialist in Resources and Environmental Policy
Resources, Science, and Industry Division
Animal Waste and Water Quality:
EPA’s Response to the Waterkeeper Alliance
Court Decision on Regulation of CAFOs
On June 30, 2006, the Environmental Protection Agency (EPA) proposed
regulations that would revise a 2003 Clean Water Act rule governing waste
discharges from large confined animal feeding operations (CAFOs). This proposal
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 for analysis and 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 a facility can discharge are
derived from effluent limitation guidelines promulgated by EPA for categories of
point sources. 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 proposal for revisions addresses those parts of the 2003 rule that were
affected by the federal court’s ruling: (1) it would eliminate the “duty to apply”
requirement that all CAFOs either apply for discharge permits or demonstrate that
they have no potential to discharge, which was challenged by industry plaintiffs, (2)
it would add procedures regarding review of and public access to nutrient
management plans, challenged by environmental groups, and (3) it would modify
aspects of the effluent limitation guidelines, also challenged by environmental
groups. EPA’s proposal also considers modifying a provision of the rule that the
court upheld, concerning the treatment of a regulatory exemption for agricultural
Public comments addressed a number of general and specific technical points,
with particular focus on the “duty to apply” for a permit and agricultural stormwater
exemption provisions of the proposal. Industry’s comments were generally
supportive of the proposal, approving deletion of the previous “duty to apply”
provision and also EPA’s efforts to provide flexibility regarding nutrient
management plan modifications. Environmental groups 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 permitting authorities also have a number of criticisms,
focusing on key parts that they argue will greatly increase the administrative and
resource burden on states. EPA officials have indicated that they intend to
promulgate revised regulations by June 2007. Congress has shown some interest in
CAFO issues, primarily through oversight hearings in 1999 and 2001.
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
The 2003 Rule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
The Waterkeeper Alliance Decision and EPA’s Response . . . . . . . . . . . . . . . . . . 3
Agricultural Stormwater Discharges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Duty to Apply for a Permit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Nutrient Management Plans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Aspects of the Effluent Limitation Guidelines for CAFOs . . . . . . . . . . . . . . 7
Standards for New Sources of Swine, Poultry, and Veal Operations . . 8
Technology for Pathogen Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Water Quality-Based Effluent Limitations . . . . . . . . . . . . . . . . . . . . . . 9
Public Response to EPA’s Proposal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Duty to Apply . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Agricultural Stormwater Exemption . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Animal Waste and Water Quality: EPA’s
Response to the Waterkeeper Alliance
Court Decision on Regulation of CAFOs
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 identify
agriculture as the leading 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 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
U.S. Environmental Protection Agency, “National Water Quality Inventory, 2000 Report,”
August 2002, EPA-841-R-02-001, 1 vol.
industry. A proposal to revise the existing rules was released by the Clinton
Administration in December 2000. These regulatory activities and proposals have
been very controversial. Agriculture industry groups have opposed permitting
requirements that they consider burdensome and costly, while others, such as
environmental groups, have favored more stringent national standards that 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.
The Bush Administration issued final revised regulations in December 2002,
which 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 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 June 2006, EPA issued proposed revisions to the CAFO rule in response
to the court’s decision which have been criticized by a number of stakeholder groups.
This report describes major features of the 2003 CAFO rule. It discusses the
parts of the rule that were addressed in the federal court’s decision and EPA’s
response to the court, as presented in proposed regulatory revisions. Finally, the
report provides an overview of comments on the June proposal that were submitted
by several varied interest groups: the livestock and poultry industry, states, and
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
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, Feb. 12,
2003. For additional information on the rule, see CRS Report RL31851, “Animal Waste and
Water Quality: EPA Regulation of Concentrated Animal Feeding Operations (CAFOs),” by
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.
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. Under the 2003 rule,
all CAFOs are required to apply for an NPDES permit. EPA estimated that this
requirement expanded the number of covered operations from about 12,800 to 15,500
— primarily the largest CAFOs, in terms of numbers of animals raised or housed onsite — or about 19% of all animal feeding operations of all size in the United States.
EPA acknowledged that prior to the revisions, permitting and enforcement had been
inadequate and that only 4,000 CAFOs actually had permits.
The 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, a permitted facility is required
to submit an annual performance report to EPA and to develop and follow a plan,
known as a comprehensive nutrient management plan (NMP), for handling manure
The Waterkeeper Alliance Decision
and EPA’s Response
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 on
February 28, 2005 (Waterkeeper Alliance et al. v. EPA, 399 F.3d 486 (2nd Cir. 2005)).
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. 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 1,000 animals are CAFOs; those with fewer animals may be defined
as CAFOs in some cases).
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.
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), but it 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 court’s ruling, EPA has proposed
revisions to the 2003 rule.6 The public comment period on this proposal concluded
on August 29. EPA officials have indicated that they expect to promulgate revised
regulations by June 2007.
The remainder of this report discusses key portions of the regulation that were
affected by the court’s ruling, beginning with one key issue which the court did not
reject or remand. Following that is discussion of issues that EPA addressed in its
proposal as a result of the litigation: (1) the “duty to apply” requirement that all
CAFOs either apply for NPDES permits or demonstrate that they have no potential
to discharge, which was challenged by industry plaintiffs, (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.
Agricultural Stormwater Discharges
One issue that the court upheld concerns the rule’s treatment of a regulatory
exemption for agricultural stormwater discharges. This issue, which was one of the
most 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.” 7 When
manure and other waste is applied to land, precipitation-related runoff can transport
nutrients, pathogens, and other pollutants in the waste to nearby receiving waters.
To develop the 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. 8 The land application portion of the rule details requirements to ensure
that animal waste is applied to land in accordance with nutrient management
U.S. Environmental Protection Agency, “Revised National Pollutant Discharge Elimination
System Permit Regulation and Effluent Limitation Guidelines for Concentrated Animal
Feeding Operations in Response to Waterkeeper Decision; Proposed Rule,” 71 Federal
Register 37744-37787, June 30, 2006.
Waterkeeper Alliance et al. v. EPA, 399 F.3d at 507.
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.
practices that ensure appropriate agricultural utilization 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 discharge is agricultural stormwater which is exempt from
permitting. In contrast, where such 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 rule, adherence to appropriate nutrient
management practices eliminates any need 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 had 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.’” 9 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 June proposal that it is considering adding a requirement 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, such CAFOs that do not have permits would still
be required comply with any more prescriptive 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.
Duty to Apply for a Permit
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.” 10 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
Waterkeeper, p. 509.
71 Federal Register at 37748.
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 its proposal to revise the regulation, EPA would replace the “duty to apply”
requirement of the 2003 rule with a requirement that all CAFOs that “discharge or
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 CFR §122.21(a)(1)).
The proposal deletes 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 requires 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 means that 25% fewer CAFOs would ultimately receive
permits and that CAFO operators will experience a $15.5 million per year reduction
(or 26%) in administrative burden, compared with the 2003 rule.
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 (generally
December 31, 2006, under the original rule; after the Waterkeeper Alliance decision,
EPA extended the deadline to July 31, 2007). The 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 that the NMP part of the rule was unlawful
under the Clean Water Act and the Administrative Procedure Act11 because it failed
to require that the terms of the NMP 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
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 proposes to require that CAFOs seeking permit coverage
submit an NMP as part of its permit application and that the permitting authority
make the plan available for review prior to developing the facility’s permit. The
The Administrative Procedure Act, 5 U.S.C. §§701-706, contains provisions that govern
federal agency rulemaking proceedings.
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 distinguishes 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 says, will include underlying data, calculations, and other
information such as technical standards that provide a basis for the facility-specific
EPA allows 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 response to the Waterkeeper Alliance ruling does contain 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 includes 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. The proposal gives the
permitting authority (state or EPA) discretion as to how best to provide public
notification and comment in the context of general permits.
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 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.
Standards for New Sources of 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. 12 The rule also allowed a less restrictive alternative
performance standard (a 25-year, 24-hour storm standard) for those facilities that will
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 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 proposes to delete
the voluntary superior performance standards provision, since the baseline for all new
facilities in this subcategory will now be no discharge.
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 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 June proposal to revise the 2003 rule, EPA retains the
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).
BCT standard promulgated previously and provides a lengthy narrative discussion
and cost analysis justifying its rationale.
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, that
specify 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, saying that it did not expect that WQBELs will be established for CAFO
discharges from land application areas since, as described above, any precipitationrelated 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 other than agricultural stormwater discharges. They also charged that
the 2003 rule bars 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 is ambiguous about whether states may
promulgate WQBELs for discharges other than agricultural stormwater, and it
ordered EPA to clarify this issue. In the June proposal, EPA restated its view that
precipitation-related discharges from land application areas are statutorily exempt
from any effluent limitations, including WQBELs, 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 nonprecipitation-related land application discharges. This reasoning applies to stateissued 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 many states will do so, however, is unclear.
Public Response to EPA’s Proposal
Several hundred public comments on EPA’s June 2006 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. 13
Materials in the EPA docket for this rulemaking, No. EPA-HQ-OW-2005-0037, including
EPA documents and public comments on the proposal, can be found at [http://www.
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. Industry’s comments were generally supportive of the
proposal, approving deletion of the previous “duty to apply” provision and also
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 have a number of
criticisms. They focus on key parts that they argue will greatly increase the
administrative and resource burden on states.
Duty to Apply. Both state permitting authorities and environmental groups
are unhappy with EPA’s deletion of the requirement that all CAFOs must apply for
an NPDES permit. They concur 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.”14 Although EPA estimates that 25% fewer CAFOs will seek
permit coverage, states argue that this overestimates the number that will voluntarily
get permits, because under EPA’s proposed revisions, there is virtually no incentive
to seek a permit. Further, states contend that any cost savings that CAFOs will
experience will be shifted to permitting authorities which will 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 expects states to inspect those that don’t apply for permit
coverage, as well as process permits for those that do. 15 Overall, states believe that
the administrative burden on states of EPA’s proposal to delete the “duty to apply”
requirement will be greater than under the 2003 rule, not less, as EPA concluded.
Agriculture industry commenters have very different concerns about this aspect
of EPA’s proposal. They challenged the “duty to apply” provision of the 2003 rule,
and the court upheld their argument that the CWA only requires facilities that
actually discharge to seek permit coverage. Industry groups fundamentally disagree
with any presumption that CAFOs do discharge pollutants, contrary to EPA’s
position in support of the 2003 rule or environmentalists’ contentions. 16 Thus, they
object to EPA’s attempts to get CAFOs to voluntarily seek permits and the specific
Natural Resources Defense Council, Sierra Club, Waterkeeper Alliance, Comments on the
revised CAFO regulation, Aug. 29, 2006, p. 9.
Ohio Department of Agriculture, Ohio Environmental Protection Agency, Ohio
Department of Natural Resources, Comments on the revised CAFO regulation, undated, p.
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,
addition of a permit requirement for those that “propose to discharge” (see page 6).
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. 17 One of EPA’s rationales for promulgating the 2003 rule was recognition
that large numbers of unpermitted CAFOs were discharging wastes that contribute
to water quality impairments. 18 Critics of industry’s position on this issue contend
that allowing CAFOs to self-regulate, self-report accidental releases, and then
possibly seek permit coverage will likely perpetuate those same conditions.
Agricultural Stormwater Exemption. Industry groups endorse EPA’s
proposal regarding agricultural stormwater, which assumes 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 object to EPA’s suggestion in the Preamble to the rule that it is also
considering requiring CAFOs to comply with additional technical standards
established by a permitting authority (see page 5), because they maintain that such
a change would unlawfully narrow the exemption.
Environmentalists, on the other hand, argue that this portion of the proposal
would unlawfully allow CAFOs to self-regulate, as it fails to require them to get
permits in order to claim the exemption. States express 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 will be skeptical of enforcement cases against
facilities that are exempt from regulation. 19
While there is no overall agreement in the views of these varied interest groups,
they do 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, what terms in a nutrient management plan should be
included in a permit, and what constitutes a substantial change to a NMP (since nonsubstantial changes could be incorporated in a permit without time-consuming
review). The Preamble to the proposal offers some examples on these points, but the
public comments indicated that considerable uncertainty still exists about issues that
are fundamental to implementation of the rule.
Id., p. 14.
See 68 Federal Register 7179-7181,
Illinois Environmental Protection Agency, Comments on the revised CAFO regulation,
August 29, 2006, p. 4.
Further, agriculture industry groups and states generally agreed on one other
issue. As previously noted, EPA expects to promulgate a final revised rule by June
2007. The proposal did not include an extension of the existing July 31, 2007,
deadline for compliance with the rule, apparently assuming that states have already
adopted provisions of the 2003 rule and would simply need to rescind provisions of
the vacated rule and replace them with language of a revised rule. States consider
that date “unrealistic and unattainable,” because most states likely stopped their
rulemaking adoption of the 2003 rule during the Waterkeeper Alliance challenge. 20
Industry groups argued that one month is not enough time for CAFOs to decide
whether to apply for a permit, prepare the permit application, and prepare or update
their NMPs to meet the new regulatory requirements. Thus, many of their comments
urged EPA to extend the compliance deadline.
Finally, because of the differing perspectives on EPA’s proposal, one can
anticipate that whatever revised regulation emerges from the current process will be
challenged. Some of the discussions in the public comments echoed criticisms that
were made of the 2003 rule and seem to preview legal critiques that are likely to be
raised in future challenges. Thus, it is nearly as difficult to estimate when the issues
discussed here will ultimately be resolved, as it is to estimate how they will be
Association of State and Interstate Water Pollution Control Administrators, Comments
on revised CAFO regulation, August 29, 2006, p. 4.