[Federal Register: November 20, 2008 (Volume 73, Number 225)]
[Rules and Regulations]
[Page 70417-70486]
[DOCID:fr20no08-24]

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Part II

Environmental Protection Agency

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40 CFR Parts 9, 122, and 412

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

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ENVIRONMENTAL PROTECTION AGENCY

40 CFR Parts 9, 122, and 412

[EPA-HQ-OW-2005-0037; FRL-8738-9]
RIN 2040-AE80

Revised National Pollutant Discharge Elimination System Permit
Regulation and Effluent Limitations Guidelines for Concentrated Animal
Feeding Operations in Response to the Waterkeeper Decision

AGENCY: Environmental Protection Agency (EPA).

ACTION: Final rule.

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SUMMARY: Under the Federal Water Pollution Control Act (Clean Water Act
or CWA), EPA is revising the National Pollutant Discharge Elimination
System (NPDES) permitting requirements and Effluent Limitations
Guidelines and Standards (ELGs) for concentrated animal feeding
operations (CAFOs) in response to the order issued by the U.S. Court of
Appeals for the Second Circuit in Waterkeeper Alliance et al. v. EPA,
399 F.3d 486 (2d Cir. 2005). This final rule responds to the court
order while furthering the statutory goal of restoring and maintaining
the nation's water quality by ensuring that CAFOs properly manage
manure generated by their operations.
    This final rule revises several aspects of EPA's current
regulations governing discharges from CAFOs. EPA is modifying the
requirement to apply for a permit by specifying that an owner or
operator of a CAFO that discharges or proposes to discharge must apply
for an NPDES permit. The final rule also includes an option for an
unpermitted CAFO to certify to the permitting authority that the CAFO
does not discharge or propose to discharge. In addition, EPA is
clarifying how the agricultural stormwater discharge exemption criteria
are interpreted for unpermitted Large CAFOs. EPA is also requiring
CAFOs seeking permit coverage to submit their nutrient management plans
(NMPs) with their applications for individual permits or notices of
intent to be authorized under general permits. Permitting authorities
are required to review the NMPs and provide the public with an
opportunity for meaningful public review and comment. Permitting
authorities are also required to incorporate terms of NMPs as NPDES
permit conditions. Additionally, this action removes the provision that
allowed CAFOs to use a 100-year, 24-hour containment structure to
fulfill the no discharge requirement for new source swine, poultry, and
veal calf operations. Instead, this action authorizes permit writers,
upon request by swine, poultry, and veal calf CAFOs that are new
sources, to establish best management practice no discharge effluent
limitations when the facility demonstrates that it has designed an open
containment system that will comply with the no discharge requirements.
    This final rule also responds to the court's remand orders
regarding water quality-based effluent limitations (WQBELs) and
pathogens. EPA is clarifying that WQBELs may be required in permits
with respect to production area discharges and discharges from land
application areas that are not exempt as agricultural stormwater.
Finally, EPA is making the finding that the best conventional
technology (BCT) limitations established in 2003 also apply to fecal
coliform.

DATES: These final regulations are effective December 22, 2008. For
judicial review purposes, this final rule is promulgated as of 1 p.m.
Eastern Daylight Time, on December 4, 2008, as provided in 40 CFR 23.2.

ADDRESSES: The record for this rulemaking is available for inspection
and copying at the Water Docket, located at the EPA Docket Center (EPA/
DC), EPA West 1301 Constitution Ave., NW., Washington, DC 20004. The
record is also available via EPA Dockets at http://www.regulations.gov
under docket number OW-2005-0037. The rule and key supporting documents
are also available electronically on the Internet at http://
www.epa.gov/npdes/caforule.

FOR FURTHER INFORMATION CONTACT: For additional information contact
Rebecca Roose, Water Permits Division, Office of Wastewater Management
(4203M), Environmental Protection Agency, 1200 Pennsylvania Ave., NW.,
Washington, DC 20460, telephone number:<PHONE_NUMBER>, e-mail address:
<EMAIL_ADDRESS>For additional information specific to New
Source Performance Standards and BCT Limitations contact Paul Shriner,
Engineering and Analysis Division, Office of Science and Technology
(4303T), Environmental Protection Agency, 1200 Pennsylvania Ave., NW.,
Washington, DC 20460, telephone number:<PHONE_NUMBER>, e-mail address:
<EMAIL_ADDRESS>
SUPPLEMENTARY INFORMATION:

I. General Information
    A. Does This Action Apply to Me?
    B. How Can I Get Copies of This Document and Other Related
Information?
    C. Under What Legal Authority Is this Final Rule Issued?
    D. What Is the Comment Response Document?
II. Background
    A. The Clean Water Act
    B. History of Actions To Address CAFOs Under the NPDES
Permitting Program
    C. Ruling by the U.S. Court of Appeals for the Second Circuit
    D. What Requirements Still Apply to CAFOs?
    E. EPA's Response to the Waterkeeper Decision
III. The Final Rule: Revisions to the 2003 CAFO Rule in Response to
Waterkeeper
    A. Duty to Apply for a Permit
    B. Agricultural Stormwater Exemption
    C. Nutrient Management Plans
    D. Compliance Dates
    E. Water Quality-Based Effluent Limitations
    F. New Source Performance Standards for Subpart D Facilities
    G. BCT Limitations for Fecal Coliform
IV. Impact Analysis
    A. Environmental Impacts
    B. Administrative Burden Impacts
    C. Response to Public Comment on the Proposal
V. Cross-Media Considerations and Pathogens
    A. Cross-Media Approaches
    B. Pathogens and Animal Feeding Operations
VI. Statutory and Executive Order Reviews
    A. Executive Order 12866: Regulatory Planning and Review
    B. Paperwork Reduction Act
    C. Regulatory Flexibility Act
    D. Unfunded Mandates Reform Act
    E. Executive Order 13132: Federalism
    F. Executive Order 13175: Consultation and Coordination With
Indian Tribal Governments
    G. Executive Order 13045: Protection of Children From
Environmental Health and Safety Risks
    H. Executive Order 13211: Actions Concerning Regulations That
Significantly Affect Energy Supply, Distribution, or Use
    I. National Technology Transfer and Advancement Act
    J. Congressional Review Act

I. General Information

A. Does This Action Apply to Me?

    This action applies to concentrated animal feeding operations
(CAFOs) as specified in section 502(14) of the Clean Water Act (CWA),
33 U.S.C. 1362(14) and defined in the NPDES regulations at 40 CFR
122.23. Table 1.1 provides a list of standard industrial codes for
operations potentially regulated under this revised rule. The rule also
applies to States and Tribes with authorized NPDES Programs.

                            Table 1.1--Operations Potentially Regulated by this Rule
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                                                                               North American       Standard
                                                                                Industry         Industrial
                Category                    Examples of regulated entities     Classification    Classification
                                                                               System (NAICS)         (SIC)
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Industry...............................  Operators of animal production
                                          operations that meet the
                                          definition of a CAFO:
                                            Beef cattle feedlots (including             112112              0211
                                             veal calves).
                                            Beef cattle ranching and farming            112111              0212
                                            Hogs............................             11221              0213
                                            Sheep and Goats.................      11241, 11242              0214
                                            General livestock except dairy               11299              0219
                                             and poultry.
                                            Dairy farms.....................             11212              0241
                                            Broilers, fryers, and roaster                11232              0251
                                             chickens.
                                            Chicken eggs....................             11231              0252
                                            Turkey and turkey eggs..........             11233              0253
                                            Poultry hatcheries..............             11234              0254
                                            Poultry and eggs................             11239              0259
                                            Ducks...........................             11239              0259
                                            Horses and other equines........             11292              0272
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    This table is not intended to be exhaustive, but rather provides a
guide for readers regarding entities likely to be regulated by this
action. This table lists the types of entities that EPA is now aware
could potentially be regulated by this action. Other types of entities
not listed in the table could also be regulated. To determine whether
your facility is regulated under this rulemaking, you should carefully
examine the applicability criteria in Sec.  122.23. If you have
questions regarding the applicability of this action to a particular
entity, consult the person listed in the preceding FOR FURTHER
INFORMATION CONTACT section.

B. How Can I Get Copies of This Document and Other Related Information?

    1. Docket. EPA has established an official public docket for this
action under Docket ID No. EPA-HQ-OW-2005-0037. The official public
docket consists of the documents specifically referenced in this
action, any public comments received, and other information related to
this action. Although listed in the index, some information is not
publicly available, e.g., Confidential Business Information (CBI) or
other information whose disclosure is restricted by statute. Certain
other material, such as copyrighted material, will be publicly
available only in hard copy. Publicly available docket materials are
available either electronically in www.regulations.gov or in hard copy
at the Water Docket in the EPA Docket Center, EPA West, 1301
Constitution Ave., NW., Washington, DC. The Public Reading Room is open
from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal
holidays. The telephone number for the Public Reading Room is (202)
566-1744, and the telephone number for the Water Docket is (202) 566-
2426.
    2. Electronic Access. This Federal Register document and key
supporting documents are also electronically available on the Internet
at http://www.epa.gov/npdes/agriculture.

C. Under What Legal Authority Is This Final Rule Issued?

    This final rule is issued under the authority of sections 101, 301,
304, 306, 308, 402, and 501 of the CWA. 33 U.S.C. 1251, 1311, 1314,
1316, 1317, 1318, 1342, and 1361.

D. What Is the Comment Response Document?

    EPA received a large number of comments on the 2006 proposed rule
(71 FR 37,744-87; June 20, 2006) and the 2008 supplemental proposal (73
FR 12,321-40; March 7, 2008). EPA evaluated all of the comments
submitted and prepared a Comment Response Document containing both the
comments received and the Agency's responses to those comments. The
Comment Response Document complements and supplements this preamble by
providing more detailed explanations of EPA's final action. The Comment
Response Document is available in the Docket.

II. Background

A. The Clean Water Act

    Congress enacted the Federal Water Pollution Control Act (1972),
also known as the Clean Water Act (CWA), to ``restore and maintain the
chemical, physical, and biological integrity of the nation's waters''
(CWA section 101(a)). Among the core provisions, the CWA establishes
the NPDES permit program to authorize and regulate the discharge of
pollutants from point sources to waters of the U.S. (CWA section 402).
Section 502(14) of the CWA specifically includes CAFOs in the
definition of the term ``point source.'' Section 502(12) defines the
term ``discharge of a pollutant'' to mean ``any addition of any
pollutant to navigable waters from any point source'' (emphasis added).
EPA has issued comprehensive regulations that implement the NPDES
program at 40 CFR part 122. The Act also provides for the development
of technology-based and water quality-based effluent limitations that
are imposed through NPDES permits to control the discharge of
pollutants from point sources. CWA sections 301(a) and (b).

B. History of Actions To Address CAFOs Under the NPDES Permitting
Program

    EPA began regulating discharges of wastewater and manure from CAFOs
in the 1970s. EPA initially issued national effluent limitations
guidelines and standards for feedlots on February 14, 1974 (39 FR
5704), and NPDES CAFO regulations on March 18, 1976 (41 FR 11,458).
    In February 2003, EPA issued revisions to these regulations that
focused on the 5% of the nation's animal feeding operations (AFOs) that
presented the highest risk of impairing water quality and public health
(68 FR 7176-7274; February 12, 2003) (``the 2003 CAFO rule''). The 2003
CAFO rule required the owners or operators of all CAFOs\1\ to seek
coverage under an NPDES permit, unless they demonstrated no potential
to discharge.

A number of CAFO industry organizations (American Farm Bureau
Federation, National Pork Producers Council, National Chicken Council,
and National Turkey Federation (NTF), although NTF later withdrew its
petition) and several environmental groups (Waterkeeper Alliance,
Natural Resources Defense Council, Sierra Club, and American Littoral
Society) filed petitions for judicial review of certain aspects of the
2003 CAFO rule. This case was brought before the U.S. Court of Appeals
for the Second Circuit. On February 28, 2005, the court ruled on these
petitions and upheld most provisions of the 2003 rule but vacated and
remanded others. Waterkeeper Alliance, et al. v. EPA, 399 F.3d 486 (2d
Cir. 2005). The court's decision is described in detail below.
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    \1\ The Clean Water Act regulates the conduct of persons, which
includes the owners and operators of CAFOs, rather than the
facilities or their discharges. To improve readability in this
preamble, reference is made to ``CAFOs'' as well as ``owners'' and
``operators'' of CAFOs. No change in meaning is intended.
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    The revisions to the 2003 CAFO rule being published today relate
directly to the changes required by the court's decision and continue
to maintain the focus on regulating discharges from the universe of
high-risk AFOs.

C. Ruling by the U.S. Court of Appeals for the Second Circuit

    The Second Circuit's decision in Waterkeeper upheld certain
challenged provisions of the 2003 rule and vacated or remanded others,
as follows.
1. Issues Upheld by the Court
    This section discusses provisions of the 2003 CAFO rule that were
challenged by either industry or environmental petitioners, but were
upheld by the Waterkeeper Court and therefore remain unchanged. EPA is
not revising any of these provisions and did not solicit comment on
them.
(a) Land Application Regulatory Framework and Interpretation of
``Agricultural Stormwater''
    The Waterkeeper Court upheld EPA's authority to regulate, through
NPDES permits, the discharge of manure, litter, or process wastewater
that a CAFO applies to its land application area. The court rejected
the industry petitioners' claim that land application runoff must be
channelized before it can be considered to be a point source discharge
subject to permitting. The court noted that the CWA expressly defines
the term ``point source'' to include ``any * * * concentrated animal
feeding operation * * * from which pollutants are or may be
discharged,'' and found that the Act ``not only permits, but demands''
that land application discharges be construed as discharges ``from'' a
CAFO. 399 F.3d at 510.
    The Waterkeeper Court also upheld EPA's determination in the 2003
CAFO rule that precipitation-related discharges of manure, litter, or
process wastewater from land application areas under the control of a
CAFO qualify as ``agricultural stormwater'' only where the CAFO has
applied the manure in accordance with nutrient management practices
that ensure ``appropriate agricultural utilization'' of the manure,
litter, or process wastewater nutrients. EPA's interpretation of the
Act in this regard was reasonable, the court found, in light of
Congressional intent in excluding agricultural stormwater from the
meaning of the term ``point source'' and given the precedent set in an
earlier Second Circuit case, Concerned Area Residents for the
Environment v. Southview Farm, 34 F.3d 114 (2d Cir. 1994). 399 F.3d at
508-09.
(b) Effluent Guidelines
    The court rejected the environmental organizations' claim that EPA,
in developing best available technology effluent limitations
guidelines, had failed to consider the single best performing CAFO and
adopt limitations that reflected its performance. The court found that
EPA had collected extensive data on the waste management systems at
CAFOs and had considered approximately 11,000 public comments on the
proposed CAFO rule. The court determined that EPA had either adopted as
the basis for its limitations the best performing technology or
declined to do so for permissible reasons. 399 F.3d at 513.
    The court upheld EPA's decision in the 2003 rule relating to
groundwater controls. In the 2003 rule, EPA stated that the Agency
believed that requirements limiting the discharge of pollutants to
surface water via groundwater that has a direct hydrologic connection
to surface water should be addressed on a site-specific basis. The
Agency also stated that nothing in the 2003 rule was to be construed to
expand, diminish, or otherwise affect the jurisdiction of the CWA over
discharges to surface water via groundwater that has a direct
hydrologic connection to surface water. 399 F.3d at 514-15.
    The court upheld the analytic methodologies that EPA used for
determining whether the technology-based permit requirements for CAFOs
set in the 2003 rule would be economically achievable by the industry
as a whole. 399 F.3d at 515-18.
2. Issues Vacated by the Court
    The following are the elements of the 2003 rule that the
Waterkeeper Court found to be unlawful and therefore vacated.
(a) Duty To Apply
    The CAFO industry organizations argued that EPA exceeded its
statutory authority by requiring all CAFOs to either apply for NPDES
permits or demonstrate that they have no potential to discharge. The
court agreed with the CAFO industry petitioners on this issue and
therefore vacated the ``duty to apply'' provision of the 2003 CAFO
rule.
    The court found that the duty to apply, based on the potential to
discharge, was invalid because the CWA subjects only actual discharges
to permitting requirements rather than potential discharges. The court
acknowledged EPA's policy considerations for seeking to impose a duty
to apply based on the potential to discharge but found that the Agency
lacked statutory authority to do so. 399 F.3d at 505.
(b) Nutrient Management Plans (NMPs)
    The court concluded that the 2003 CAFO rule impermissibly: (1)
Empowered permitting authorities to issue permits without any
meaningful review of a CAFO's NMP, (2) failed to require that the terms
of the nutrient management plan be included as effluent limitations in
the NPDES permit, and (3) violated the CWA's public participation
requirements. The court agreed with the environmental petitioners on
these three issues.
    The court relied on provisions of the Act that authorize point
source discharges only where NPDES permits ``ensure that every
discharge of pollutants will comply with all applicable effluent
limitations and standards,'' citing CWA sections 402(a)(1), (a)(2), and
(b). Because the 2003 CAFO rule did not provide for permitting
authority review of a CAFO's nutrient management plan before the permit
was issued, the court found that the rule did not ensure that each
CAFO's discharges comply with these CWA provisions. The court also
found that the terms of the NMP themselves are ``effluent limitations''
as that term is defined in the Act and therefore must be made part of
the permit and be enforceable as required under CWA sections 301 and
402. The court also held that as effluent limitations, those terms must
be made available for public review. 399 F.3d at 499-502.
3. Issues Remanded by the Court
    The Waterkeeper Court also remanded other aspects of the CAFO rule
to EPA ``for further clarification and analysis.''

(a) Water Quality-Based Effluent Limits
    The court agreed with EPA that agricultural stormwater is excluded
from the meaning of the term ``point source'' and therefore is not
subject to water quality-based effluent limitations in permits.
However, the court directed EPA to ``clarify the statutory and
evidentiary basis for failing to promulgate water quality-based
effluent limitations for discharges other than agricultural stormwater
discharges as that term is defined in 40 CFR 122.23(e),'' and to
``clarify whether States may develop water quality-based effluent
limitations on their own.'' 399 F.3d at 524.
(b) New Source Performance Standards--100-Year Storm Standard
    The 2003 CAFO rule set new source performance standards (NSPS) for
swine, poultry, and veal calf CAFOs at no discharge. A CAFO in these
categories could fulfill this requirement by showing that either (1)
its production area was designed to contain all manure, litter, or
process wastewater, and precipitation from a 100-year, 24-hour storm,
or (2) it would comply with ``voluntary superior environmental
performance standards'' based on innovative technologies, under which a
discharge from the production area would be allowed if it was
accompanied by an equivalent or greater reduction in the quantity of
pollutants released to other media (e.g., air emissions). The court
found that EPA had neither justified in the record nor provided an
adequate opportunity for public comment for either of these provisions.
As a result, the court remanded these provisions to EPA to clarify, via
a process that adequately involves the public, the statutory and
evidentiary basis for them. 399 F.3d at 520-21.
(c) BCT Effluent Guidelines for Pathogens
    The court held that the 2003 CAFO rule violated the CWA because EPA
had not made an affirmative finding that the BCT-based Effluent
Limitations Guidelines (ELGs), i.e., the ``best conventional
technology'' guidelines for conventional pollutants such as fecal
coliform, do in fact represent BCT for pathogens. The court remanded
this issue to EPA for such a finding. 399 F.3d at 519.

D. What Requirements Still Apply to CAFOs?

    The Waterkeeper decision either upheld or did not address most
provisions of the 2003 CAFO rule. This section describes certain key
portions of the rule that were not challenged in Waterkeeper. These
unchallenged provisions are addressed in this final rule only to
provide background information and are not in any way reopened or
affected by this rulemaking.
    The definitions provided in 40 CFR 122.23(b) of the 2003 CAFO rule
remain in effect and are unchanged. First, an operation must be defined
as an animal feeding operation (AFO) before it can be defined as a
concentrated animal feeding operation (CAFO). 40 CFR 122.23. The term
``animal feeding operation'' is defined by EPA regulation as a ``lot or
facility'' where animals ``have been, are or will be stabled or
confined and fed or maintained for a total of 45 days or more in any 12
month period and crops, vegetation, forage growth, or post harvest
residues are not sustained in the normal growing season over any
portion of the lot or facility.''
    Whether an AFO is a CAFO depends primarily on the number of animals
confined, which is also unchanged. Large CAFOs are AFOs that confine
more than the threshold number of animals detailed in 40 CFR
122.23(b)(4). Medium CAFOs confine fewer animals than Large CAFOs and
also: (1) Discharge pollutants into waters of the U.S. through a man-
made ditch, flushing system, or other similar man-made device; or (2)
discharge pollutants into waters of the U.S. which originate outside of
and pass over, across, or through the facility or otherwise come into
direct contact with the confined animals. 40 CFR 122.23(b)(6)(ii). The
NPDES permitting authority also may, on a case-by-case basis, designate
any medium or small AFO, as a CAFO after conducting an on-site
inspection and finding that the facility ``is a significant contributor
of pollutants to waters of the United States.'' 40 CFR 122.23(c). The
permitting authority may not exercise its authority to designate a
small AFO as a CAFO unless pollutants are discharged into waters of the
U.S. through a man-made ditch, flushing system, or other similar man-
made device, or are discharged into waters of the U.S. which originate
outside of the facility and pass over, across, or through the facility
or otherwise come into direct contact with the animals confined in the
operation. 40 CFR 122.23(c)(3).
    As previously described, the court upheld EPA's definition of
``agricultural stormwater discharge'' in relation to discharges from
land application areas under the control of a CAFO in 40 CFR 122.23(e).
Discharges of manure, litter, or process wastewater from land
application areas under the control of a CAFO are discharges from the
CAFO (i.e., point source discharges) unless they are agricultural
stormwater discharges, which are exempt from permit requirements.
Section 122.23(e) provides that precipitation-related discharges of
manure, litter, or process wastewater from a CAFO's land application
areas are agricultural stormwater discharges, provided that ``the
manure, litter, or process wastewater has been applied in accordance
with site-specific nutrient management practices that ensure
appropriate agricultural utilization of the nutrients in the manure,
litter, or process wastewater, as specified in Sec.  122.42(e)(1)(vi)-
(ix).''
    The court ruling also did not affect the nutrient management
planning requirements for permitted CAFOs established in the 2003 CAFO
rule. All CAFOs that apply for permits must develop and implement an
NMP that meets the requirements of 40 CFR 122.42(e) and, for Large
CAFOs subject to 40 CFR part 412, subpart C or D, 40 CFR 412.4. The NMP
identifies the necessary actions to ensure that runoff is eliminated or
minimized through proper and effective manure, litter, or process
wastewater management, including compliance with the ELGs as
applicable. Permitted CAFOs must comply with all applicable
recordkeeping and reporting requirements, including those specified in
Sec.  122.42(e).
    The court ruling also did not affect the ELG requirements for Large
CAFOs, with the exception of new source performance standards (NSPS)
for swine, poultry, and veal calf operations. ELG requirements ensure
the appropriate storage of manure, litter, and process wastewater and
proper land application practices. They vary depending upon the type of
animals confined: Subpart A for horses and sheep; subpart B for ducks;
subpart C for dairy cattle, heifers, steers, and bulls; and subpart D
for swine, poultry, and veal calves. 40 CFR part 412. Additionally,
NSPS for beef and dairy operations were not affected by the decision
and remain unchanged (40 CFR 412.35).
    Permitted small and medium CAFOs are not subject to the ELGs
specified in part 412. Rather, they must comply with technology-based
requirements developed by the permitting authority on a case-by-case
basis (i.e., best professional judgment (BPJ)), pursuant to CWA section
402(a)(1)(B) and as defined in 40 CFR 125.3(c)(2) and (d).

E. EPA's Response to the Waterkeeper Decision

    On June 30, 2006, EPA published a proposed rule to revise the
Agency's regulations governing discharges from

CAFO's in response to the Waterkeeper decision. 71 FR 37,744. In
summary, EPA proposed to require only owners or operators of those
CAFOs that discharge or propose to discharge to seek authorization to
discharge under a permit. Second, EPA proposed to require CAFOs seeking
authorization to discharge under individual permits to submit their
NMPs with their permit applications or, under general permits, with
their notices of intent. Permitting authorities would be required to
review the NMP and provide the public with an opportunity for
meaningful public review and comment. Permitting authorities would also
be required to incorporate terms of the NMP as NPDES permit
requirements. Additionally, EPA proposed a process for modifying a
CAFO's NPDES permit to incorporate changes to the NMP during the permit
term by designating permit modifications in accordance with that
process to be ``minor modifications of permits'' under 40 CFR 122.63.
The 2006 proposed rule also addressed the remand of issues for further
clarification and analysis. These issues concerned clarifications
regarding the applicability of water quality-based effluent limitations
(WQBELs) to CAFO discharges; NSPS for swine, poultry, and veal CAFOs;
and BCT effluent limitations guidelines for fecal coliform.
    A March 7, 2008, Federal Register notice supplemented the 2006
proposed rule by proposing additional options considered by EPA for
inclusion in this final rule in response to the Second Circuit's
decision in the Waterkeeper decision. In that notice, EPA proposed a
voluntary option for a CAFO to certify that the CAFO does not discharge
or propose to discharge based on an objective assessment of the CAFO's
design, construction, operation, and maintenance. EPA also proposed a
framework for identifying the terms of the NMP and three alternative
approaches for addressing rates of application of manure, litter, and
process wastewater when identifying terms of the NMP to be included in
the permit. In the 2008 supplemental proposal, EPA sought comment only
on the issues presented in the 2008 supplemental proposal.
    In addition to the changes made through this rulemaking, EPA
extended certain deadlines in the NPDES permitting requirements and
ELGs in two separate rulemakings in order to allow the Agency adequate
time to complete this rulemaking in response to the Waterkeeper
decision, in advance of those deadlines. The principal purpose of these
rulemakings was to provide additional time for the Agency to complete
this final rule. Neither of these date extension rules addressed any of
the substantive issues addressed in this final rule or promulgated any
provisions in response to the Waterkeeper decision. The first rule
revised dates established in the 2003 CAFO rule by which facilities
newly defined as CAFOs were required to seek permit coverage and by
which all CAFOs were required to develop and implement nutrient
management plans. 71 FR 6978-84 (February 10, 2006). EPA extended the
date by which operations defined as CAFOs as of April 14, 2003, that
were not defined as CAFOs prior to that date, were required to seek
NPDES permit coverage, from February 13, 2006, to July 31, 2007. EPA
also amended the date by which operations that become defined as CAFOs
after April 14, 2003, due to operational changes that would not have
made them a CAFO prior to April 14, 2003, and that are not new sources,
were required to seek NPDES permit coverage, from April 13, 2006, to
July 31, 2007. Finally, EPA extended the deadline by which CAFOs were
required to develop and implement nutrient management plans, from
December 31, 2006, to July 31, 2007. That rulemaking revised all
references to the date by which CAFOs must develop and implement NMPs
as specified in the 2003 CAFO rule.
    As a result of the extensive array of public comments on the issues
raised by the Waterkeeper decision, EPA was unable to complete this
final rule prior to July 31, 2007. Thus, EPA published a second
revision of the compliance dates on July 24, 2007, extending the dates
from July 31, 2007, to February 27, 2009. The preamble to the second
date change rule explained EPA's belief that the February 27, 2009,
deadlines were appropriate because they would provide additional time
for States, the regulated community, and other stakeholders to adjust
to the new regulatory requirements. See 72 FR 40,245-50. In the 2008
supplemental rule, EPA requested comment on further extending the
compliance deadline. For additional discussion of compliance dates, see
section III.D of this preamble.

III. The Final Rule: Revisions to the 2003 CAFO Rule in Response to
Waterkeeper

    This final rule responds to the Second Circuit Court's vacature and
remand orders.

A. Duty To Apply for a Permit

1. Provisions in the 2003 CAFO Rule
(a) Duty To Apply
    The 2003 CAFO rule required all CAFOs to seek authorization to
discharge under an NPDES permit unless the Director, i.e., the
permitting authority, determined that the CAFO had no potential to
discharge.
(b) ``No Potential To Discharge'' Determination
    The 2003 CAFO rule included a process for CAFOs to seek a ``no
potential to discharge'' determination by the Director. Where the
Director determined, based on information supplied by the CAFO
operator, that a CAFO had no potential to discharge manure, litter, or
process wastewater to waters of the U.S., the CAFO operator had no duty
to apply for a permit, unless circumstances at the facility changed
such that the facility would have the potential to discharge. Examples
of facilities that possibly would have qualified for this exemption
included facilities in very arid areas, facilities that are down slope
from waters of the U.S., and facilities with completely enclosed
operations.
2. Summary of the Second Circuit Court Decision
    The Second Circuit Court of Appeals vacated the provision that
required all CAFO owners or operators with a potential to discharge to
apply for an NPDES permit. The court held that the Clean Water Act
(CWA) authorizes EPA to require permits for the actual discharge of
pollutants, but not for mere potential discharges. Because the 2003
CAFO rule imposed an obligation on all CAFOs to either apply for an
NPDES permit or affirmatively demonstrate that they have no potential
to discharge, the court ruled that it exceeded EPA's authority under
the CWA. Waterkeeper Alliance et al. v. EPA, 399 F.3d 486, 506 (2d Cir.
2005).
3. This Final Rule
    To address the court's decision on the duty to apply, EPA is
revising the 2003 CAFO rule in three ways:
     Deleting the requirement that all CAFOs apply for an NPDES
permit to provide instead that all CAFOs that ``discharge or propose to
discharge'' have a duty to apply when they propose to discharge;
     Eliminating the procedures for a no potential to discharge
determination; and
     Establishing a voluntary option for unpermitted CAFOs to
certify that they

do not discharge or propose to discharge.
(a) Duty To Seek Permit Coverage
    EPA proposed to replace the ``duty to apply'' requirement adopted
in the 2003 rule, which states that all CAFO owners or operators must
seek coverage under an NPDES permit unless they demonstrate ``no
potential to discharge'' (40 CFR 122.21(a)(1) and 40 CFR 122.23(a) and
40 CFR 122.23(d)(1)) with a modified ``duty to apply'' provision. The
2006 proposed rule would have required that all CAFOs that ``discharge
or propose to discharge'' seek coverage under an NPDES permit, which is
the same language that applies generally to point sources under
longstanding NPDES regulations at Sec.  122.21(a)(1).
    This rule adopts the approach in the 2006 proposed rule by
replacing the ``duty to apply'' requirement of the 2003 rule with a
requirement that a CAFO that ``discharges or proposes to discharge''
must seek authorization to discharge under an NPDES permit. Because a
number of commenters misunderstood, or were confused by, the term
``propose to discharge,'' EPA is providing additional clarification in
this rule and preamble on how operators should evaluate whether they
discharge or propose to discharge. While commenters generally agreed
that the changes proposed by EPA were consistent with the Second
Circuit decision, some commenters thought that ``propose to discharge''
and ``potential to discharge'' were not sufficiently distinguishable,
and that ``proposed'' discharges could be understood as contrary to the
Waterkeeper court's holding that only ``actual'' discharges are subject
to CWA requirements.
    EPA disagrees with these commenters. Including a duty to apply for
CAFOs that ``propose to discharge'' is not the same as requiring a
permit for CAFOs with only a ``potential to discharge.'' Unlike the
2003 rule, which categorically required a permit for any CAFO with a
``potential to discharge,'' this final rule calls for a case-by-case
evaluation by the CAFO owner or operator as to whether the CAFO
discharges or proposes to discharge from its production area or land
application area based on actual design, construction, operation, and
maintenance. ``Potential'' connotes the possibility that there might--
as opposed to will--be a discharge, which, as the Waterkeeper court
held, is not sufficient under the CWA to trigger NPDES permitting
requirements. In contrast to the 2003 rule, this rule requires a case-
by-case assessment by each CAFO to determine whether the CAFO in
question, due to its individual attributes, discharges or proposes to
discharge. Therefore, revised Sec.  122.23(d)(1) requires only CAFOs
that actually discharge to seek permit coverage and clarifies that a
CAFO proposes to discharge if based on an objective assessment it is
designed, constructed, operated, or maintained such that a discharge
will occur, not simply such that it might occur. Consistent with the
Waterkeeper decision, CAFOs that are required to seek permit coverage
must do so when they propose to discharge. (See below for discussion of
the provision relating to when a CAFO must seek permit coverage, 40 CFR
122.23(f).) Thus, it is the responsibility of the CAFO owner or
operator to seek authorization to discharge at the time they propose to
discharge. A CAFO that discharges without a permit is in violation of
the CWA section 301(a) prohibition on such discharges and additionally
has the burden of establishing that it did not propose to discharge
prior to the discharge (unless the permitting authority has a current,
complete certification from that CAFO as provided by 40 CFR
122.23(j)(2), discussed below). If it is determined that it did, in
fact, propose to discharge prior to the discharge (that is, it was
designed, constructed, operated, or maintained such that a discharge
would occur), it is also in violation of the Sec.  122.23(d)(1) duty to
apply. Section 122.23(j)(2) also clarifies how a CAFO may satisfy the
burden of establishing that it did not propose to discharge.
    Under section 301(a) of the CWA, only those CAFO discharges
authorized by an NPDES permit (or otherwise authorized by the statute),
regardless of the volume or duration of the discharge, are allowed. 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. While EPA recognizes that not every discharge
indicates that the CAFO will discharge in the future, an operator
should certainly consider any unplanned or accidental discharge that
may have occurred in the past in deciding whether to seek permit
coverage. CAFO operators must objectively assess whether a discharge
from the CAFO, including from the production area or land application
areas under the control of the CAFO, is occurring or will occur for
purposes of determining whether to obtain permit coverage.
    It is well established that ``discharge'' is not limited to
continuous discharges of pollutants from a point source to waters of
the U.S., but also includes intermittent and sporadic discharges.
``Intermittent or sporadic violations do not cease to be ongoing until
the date when there is no real likelihood of repetition.'' Chesapeake
Bay Foundation v. Gwaltney of Smithfield, 890 F.2d 690, 693 (4th Cir.
1989). Such intermittent, sporadic, even occasional, discharges may in
fact be the norm for many CAFOs, but they are nonetheless
``discharges'' under the CWA and are prohibited unless authorized under
the terms of an NPDES permit. CAFOs that have had such intermittent or
sporadic discharges in the past would generally be expected to have
such discharges in the future, and therefore be expected to obtain a
permit, unless they have modified their design, construction,
operation, or maintenance in such a way as to prevent all discharges
from occurring.
    EPA received a number of comments concerning past discharges. Some
commenters asserted that a prior discharge is not, by itself, a
sufficient basis for requiring a permit and observed that it is quite
possible that a CAFO may have eliminated the cause of the discharge.
EPA agrees that not every past discharge from a CAFO necessarily
triggers a duty to apply for a permit; however, a past discharge may
indicate that the CAFO discharges or proposes to discharge if the
conditions that gave rise to the discharge have not changed or been
corrected. See, e.g., Gwaltney of Smithfield. Ltd. v. Chesapeake Bay
Foundation, 484 U.S. 49, 57 (1987) (``a reasonable likelihood that a
past polluter will continue to pollute in the future'' is a continuous
or intermittent violation); American Canoe Ass'n v. Murphy Farms, Inc.,
412 F.3d. 536 (4th Cir. 2005) (CWA violation continues where corrective
measures are insufficient to eliminate real likelihood of repeated
discharges). The same rationale that led the courts in these cases to
conclude that the point sources in question were discharging in
violation of the CWA underlies the final rule's requirement that CAFOs
must seek permit coverage when they discharge or propose to discharge
(i.e., are designed, constructed, operated, or maintained such that a
discharge will occur). Sections 122.23(d)(1) and (f).
    An uncorrected past discharge is not the only indicator that
operators should consider in assessing whether the CAFO discharges or
proposes to discharge. Other key factors the operator should consider
include the proximity of the production area to waters of the U.S.,
whether the CAFO is upslope from waters of the U.S., and climatic
conditions. Similarly, the type of waste storage system, storage
capacity, quality

of construction, and presence and extent of built-in safeguards are
important factors. Standard operating procedures and level of
maintenance are also critical factors for the operator to consider when
assessing whether a CAFO discharges or proposes to discharge. Such
considerations contributed to EPA's decision to include in this final
rule an option for unpermitted CAFOs to certify that they do not
discharge or propose to discharge by meeting the criteria in 40 CFR
122.23(i)(2), discussed in detail below. EPA encourages unpermitted
CAFOs that choose not to certify to consider the set of criteria for
certification eligibility when deciding whether to seek permit
coverage, and this final rule provides in Sec.  122.23(j)(2) that these
same criteria may be used to establish that a CAFO did not propose to
discharge prior to a discharge occurring.
    As a result of the revisions to 40 CFR 122.23(d) and (f), only
CAFOs that discharge or propose to discharge are required to seek
permit coverage, and a CAFO that proposes to discharge must seek
coverage as soon as it proposes to discharge in order to avoid having
unpermitted discharges. In the event of a discharge from an unpermitted
CAFO, the CAFO operator would be in violation of the CWA prohibition
against discharging without a permit. Under this final rule, if the
CAFO proposed to discharge prior to the discharge, the CAFO would also
be in violation of the requirement in Sec.  122.23(d)(1) and (f),
implementing sections 308 and 402 of the CWA, that CAFOs seek permit
coverage when they propose to discharge.
    In revised Sec.  122.23(d)(1), EPA is clarifying that ``a CAFO
proposes to discharge if it is designed, constructed, operated, or
maintained such that a discharge will occur.'' EPA intends that the
CAFO operator should make an objective assessment of the operation to
determine whether the CAFO will discharge. Such an objective assessment
would take into account not only the characteristics of the manmade
aspects of the CAFO itself, but climatic, hydrological, topographical,
and other characteristics beyond the operator's control that impact
whether the CAFO will discharge, given the design, construction,
operation and maintenance of the CAFO.
    To assist CAFO operators in making this objective assessment and to
provide assurance for CAFOs deciding not to seek permit coverage that
they are not required to obtain permit coverage, EPA is finalizing a
voluntary certification option, proposed in the 2008 supplemental
proposal. This option provides a means for a CAFO to certify that it
does not discharge or propose to discharge. The voluntary certification
provisions are discussed below in section III.A.3(c) of this preamble.
    This rule is consistent with the Waterkeeper decision because the
duty to apply for a permit only arises when a CAFO discharges or
proposes to discharge, that is, when it discharges or is designed,
constructed, operated, or maintained such that a discharge will occur.
It is also consistent with Chesapeake Bay Foundation v. Gwaltney of
Smithfield, discussed above, which found a violation under the CWA
where it is reasonably likely that a discharge will occur due to
existing circumstances. This rule derives from sections 402(a)(3) and
308 of the CWA, 33 U.S.C. 1342(a)(3), 1318. Under section 402(a)(3),
EPA is required to establish a permit program that, among other things,
ensures compliance with all applicable requirements of sections 301
(requirements for establishing technology-based and water quality-based
effluent limitations), 306 (requirements for establishing new source
performance standards), 308 (requirements relating to inspections,
monitoring and entry, including requests for information to determine
compliance status or support development of effluent limitations) and
402 (NPDES permits).
    Section 301(a) prohibits the discharge of pollutants, except in
compliance with specific provisions in the CWA. Particularly relevant
to CAFOs, section 301(b) provides that ``there shall be achieved''
effluent limitations controlling pollutants discharged from point
sources. Section 308(a) provides EPA broad authority to require the
owner or operator of any point source (including CAFOs) to provide
information necessary to develop effluent limitations, to ``carry out''
section 402, and to ``carry out'' the objectives of the Act, which are
set forth in CWA section 101(a). Under section 501(a) EPA is authorized
to prescribe ``such regulations as are necessary to carry out'' its
functions under the CWA. Any permit program established to carry out
section 402 must, of necessity, require point sources that discharge or
propose to discharge to submit information to allow the permitting
authority to determine prior to issuance of a permit what effluent
limitations should apply to a discharger and be included in its permit
(including providing the public and any other affected State notice and
opportunity for public comment, as required by section 402(b)(3)). It
is therefore reasonable for EPA to require those CAFOs that discharge
or propose to discharge to apply for NPDES permit coverage.
    Some commenters on the 2006 proposed rule opposed regulating
entities that ``propose'' to discharge, or alternatively, suggested
that EPA should clarify that ``propose'' means ``intend'' or ``plan.''
While EPA acknowledges that ``propose'' to discharge could be
understood to mean ``intend'' or ``plan'' to discharge, under this
final rule ``propose to discharge'' means that the CAFO is designed,
constructed, operated, or maintained such that it will discharge. This
is consistent with the Waterkeeper decision because a mere
``potential'' to discharge is not sufficient to trigger the revised
duty to apply. Accordingly, as previously discussed, revised Sec.
122.23(d)(1) clarifies that ``a CAFO proposes to discharge if it is
designed, constructed, operated, or maintained such that a discharge
will occur.'' The CAFO's decision as to whether to apply for a permit
should be based on an objective assessment of conditions at that
operation. As discussed below, under this final rule, a CAFO that is
not designed, constructed, operated, or maintained in a manner such
that the CAFO does or will discharge is not required to seek permit
coverage under Sec.  122.23(d)(1) and may choose to take advantage of
the voluntary no discharge certification.
    Some commenters on the 2006 proposed rule requested that EPA
specifically state in the regulation that facilities designed to the
25-year, 24-hour design standard have not ``proposed'' to discharge.
One commenter questioned whether existing operations should be required
to obtain permit coverage if they have installed structures and
production area BMPs using Natural Resources Conservation Service
(NRCS) standards and if they have been operating without discharging.
The commenter indicated that ``since EPA is requiring that a zero
discharge standard be met only for certain new CAFOs and not existing
CAFOs, it is unreasonable to expect all existing animal operations that
do not otherwise come under a permit to meet a zero discharge
standard.''
    EPA disagrees that CAFOs designed for the 25-year, 24-hour storm
should be categorically excluded from the requirement to apply for a
permit simply based on their design standard. EPA also believes that it
is reasonable to expect unpermitted CAFOs to meet a zero discharge
standard. The CWA is very clear that point source discharges from CAFOs
are illegal unless the operator has applied for and obtained an NPDES
permit. Thus, ``zero discharge'' is the only standard to which EPA can

hold unpermitted CAFOs under the CWA. Large storms and chronic rainfall
events do occur and production areas built to the 25-year, 24-hour
storm design standard can and do discharge during precipitation events.
Under the CWA, as previously discussed, a violation of the prohibition
against discharging without a permit occurs even if the discharge was
not planned or intended. Conversely, in the event of a discharge from a
permitted CAFO, the discharge will not violate the CWA if the CAFO is
in compliance with its permit.
    EPA notes that design is only one aspect for a CAFO to consider
when assessing whether or not to apply for a permit. Construction,
operation, and maintenance are equally important components of a CAFO's
operation and can make the difference between a CAFO that discharges
and one that does not. With regard to the commenter's question about
the applicability of NRCS standards, a CAFO's decision as to whether to
seek permit coverage should be based on an objective assessment of
conditions at the operation, including, but not limited to, the manure
storage design standard. EPA notes that whether or not a CAFO is
designed according to NRCS standards may be an important component of
the objective evaluation it undertakes to assess whether it is
designed, constructed, operated, or maintained such that a discharge
will occur. A CAFO that does not discharge or propose to discharge is
not required to seek permit coverage under Sec.  122.23(d)(1) and may
be eligible for no discharge certification under 40 CFR 122.23(i).
    CAFO NPDES permit requirements include, but are not limited to,
best management practices (BMPs) to eliminate discharges from the
production area under most circumstances and to ensure appropriate
agricultural utilization of nutrients in manure, litter, and process
wastewater that is applied to land under the CAFO's control. EPA
expects that an unpermitted CAFO would also need to implement BMPs in
order to ensure that it does not discharge or propose to discharge.
However, in many, if not most, cases the BMPs called for will be more
rigorous than those required for permitted CAFOs, because the operator
of an unpermitted CAFO is never authorized to discharge under CWA
section 301(a). Permitted CAFOs have greater flexibility because, in
addition to being authorized to discharge under the circumstances
prescribed by the permit, other discharges can be excused when the
conditions contained in EPA's upset and/or bypass regulations are met.
See 40 CFR 122.41(m) and (n).
    In contrast to commenters who believe that some non-discharging
CAFOs will needlessly go through the permitting process, other
commenters expressed concern that some CAFOs that should have permits
will not seek needed permit coverage. They contended that many CAFOs
are currently discharging without a permit and objected to having CAFOs
make the determination themselves as to whether or not they discharge
or propose to discharge, as such an approach would, in their view,
establish a self-permitting scheme. These commenters further contended
that the administrative record from the 2003 rule supports the
presumption that all Large CAFOs actually discharge and, therefore,
such CAFOs should be required to obtain a permit.
    EPA does not agree that the rule establishes a self-permitting
scheme. As is the case with all point sources, it is up to the operator
to determine whether or not to apply for a permit in the first
instance, by assessing whether the point source (CAFO) discharges or
proposes to discharge. Point sources that do not discharge or propose
to discharge are not subject to CWA permitting requirements. See Sec.
122.21(a)(1). Regarding the administrative record for the 2003 rule,
that rule established a duty to apply for all CAFOs unless the CAFO
could demonstrate to the satisfaction of the permitting authority that
it had no ``potential to discharge.'' That provision was vacated by the
Second Circuit, which noted that EPA did not argue that the
administrative record supported a regulatory presumption that all Large
CAFOs actually discharge. 399 F.3d at 506, n.22. Thus, consistent with
the Waterkeeper decision, EPA is promulgating a rule which requires
those CAFOs that discharge or propose to discharge, but not CAFOs with
a mere ``potential'' to discharge, to seek permit coverage on a case-
by-case basis. With regard to the comments that EPA should establish a
categorical presumption that all Large CAFOs discharge, the Agency is
evaluating various options for exploring the nature of discharges from
Large CAFOs.
    Finally, this rule revises the regulatory provisions for when a
CAFO must seek permit coverage and the duty to maintain permit coverage
for CAFOs. The final rule clarifies that those CAFOs that are required
under Sec.  122.23(d)(1) to seek permit coverage must do so ``when the
CAFO proposes to discharge,'' unless a later deadline, such as February
27, 2009, is specified for the specific category of operation. EPA is
recodifying 40 CFR 122.23(g) as Sec.  122.23(f) because the paragraph
codified as Sec.  122.23(f) in the 2003 rule is being removed. See
section III.A.3(b) of this preamble. Revised Sec.  122.23(f) is
consistent with the revised duty to apply requirement in Sec.
122.23(d)(1) and EPA's authority under sections 301, 308 and 402 of the
CWA to require CAFOs that actually discharge to seek permit coverage.
None of the specific timeframes for the various categories of CAFOs in
paragraphs (1)-(5) of Sec.  122.23(f), as amended by the 2007 date
change rule (72 FR 40,245), is affected by this rule. The revised
language in the introductory paragraph of Sec.  122.23(f) simply
conforms to the requirements of Sec.  122.23(d)(1).
    EPA is making corresponding revisions to the regulatory text
requiring CAFOs to maintain permit coverage. Due to the fact that Sec.
122.23(f) as codified in 2003 is being removed, EPA is recodifying 40
CFR 122.23(h), ``Duty to Maintain Permit Coverage,'' as Sec.
122.23(g). See section III.A.3(b) of this preamble. Also, in the 2006
proposed rule, EPA proposed to revise this provision to address the
Waterkeeper court's decision vacating the requirement for all CAFOs to
seek permit coverage unless they obtained a no potential to discharge
determination. See 71 FR 37,785. In this final rule (as in the proposed
rule), a CAFO would not need to reapply based solely on the fact of
having had a permit, if the permit had been terminated in accordance
with the NPDES provisions at 40 CFR 122.64(b). Since a CAFO that
terminated permit coverage is no longer a permitted CAFO, it is not
subject to the duty to maintain permit coverage provision. Consistent
with the requirement that only CAFOs that discharge or propose to
discharge seek NPDES permit coverage, new Sec.  122.23(g) excludes
CAFOs that will not discharge or propose to discharge upon expiration
of the permit from the requirement to reapply 180 days in advance of
permit expiration.
(b) ``No Potential To Discharge'' Determination
    In this final rule, EPA is deleting the regulatory provisions
adopted in the 2003 CAFO rule allowing CAFOs to demonstrate that they
have no potential to discharge and authorizing the Director to make
such a determination. 40 CFR 122.23(d)(2) and 122.23(f). Because EPA is
not requiring CAFOs to seek permit coverage based merely on potential
to discharge, this provision is no longer relevant to determining
whether or not a facility needs to seek permit coverage. This final
rule is

unchanged from the 2006 proposed rule in this respect.
    Overall, most commenters supported eliminating the ``no potential
to discharge'' provisions in the CAFO regulations, noting that it is no
longer necessary because only CAFOs that discharge or propose to
discharge must apply for permits. One State observed that the ``no
potential to discharge'' criteria could still be useful to CAFOs in
determining whether they need to apply for a permit. While these
criteria may continue to be useful to CAFO owners and operators for
that purpose, EPA is eliminating these provisions from 40 CFR 122.23 of
the regulations.
(c) Voluntary No Discharge Certification
    In this final rule, the Agency is adopting a new provision that
allows CAFOs to voluntarily certify that the CAFO does not discharge or
propose to discharge. As discussed above, EPA received several hundred
comments on the 2006 proposed rule related to how a CAFO operator would
decide whether to seek permit coverage under a revised rule that
requires CAFOs that discharge or propose to discharge to apply for a
permit or submit a Notice of Intent for coverage under a general
permit. Several commenters were particularly concerned with the
consequences for an unpermitted CAFO that has an ``accidental
discharge'' because they understood EPA's proposal to mean that a CAFO
that does not apply for a permit and subsequently has a discharge of
pollutants to waters of the U.S. would be liable for two violations,
one associated with the discharge itself and another violation for
failing to apply for a permit for authority to discharge. In response
to these comments, in the 2008 supplemental proposal, EPA requested
public comment on an option that would allow a CAFO that determines,
based on an objective assessment, that it does not discharge or propose
to discharge to certify to the permitting authority that it is
designed, constructed, operated, and maintained not to discharge. In
the unlikely event that a properly certified CAFO discharges (which
would constitute a violation of section 301(a) of the CWA), the CAFO
would not be liable for failing to apply for a permit prior to the
discharge in accordance with the permit application requirements of 40
CFR 122.23(d)(1) and (f).
    EPA received many comments on the proposed voluntary certification
option. Commenters were divided, with some generally supportive and
others generally opposed to the concept of a voluntary certification
option for unpermitted CAFOs. Those in favor stated that certification
would assist CAFOs that do not discharge or propose to discharge by
providing a structured process for CAFOs to notify the permitting
authority that they are not required to seek permit coverage. Some
commenters opposed to certification believe the Agency's record
supports a regulatory presumption that all CAFOs discharge, and,
therefore, the no discharge certification process is a further
departure from the decision of the Waterkeeper court. The majority of
State permitting authorities commenting on the 2008 supplemental
proposal were opposed to the certification option, as proposed.
    In this final rule, EPA has addressed both the decision from the
Waterkeeper court that CAFOs with only a potential to discharge are not
subject to NPDES permitting requirements and the concerns expressed by
commenters that some CAFOs may be uncertain as to whether they
discharge or propose to discharge. In the NPDES program, the first step
is for a point source to decide whether it needs to seek permit
coverage. Generally, the question of whether a point source needs
permit coverage is easily answered; indeed other point sources are
typically designed to discharge to waters of the U.S. After careful
consideration of the comments and in light of the unique
characteristics of CAFOs among point sources, EPA has concluded that
providing a voluntary option for unpermitted CAFOs to certify to the
Director that the CAFO does not discharge or propose to discharge based
on an objective assessment of the CAFO's design, construction,
operation, and maintenance is reasonable and appropriate for CAFOs.
However, in response to comments received on the proposed certification
option, EPA is clarifying several aspects of the process, eligibility
requirements, and effect of certification as discussed below. The
Agency is also making several changes to the proposed option to ensure
that certification will be properly implemented.
    Under this final rule, and as proposed in the 2008 supplemental
proposal, a CAFO operator may certify that the CAFO does not discharge
or propose to discharge by signing and submitting a certification
statement to the Director. The objective assessment necessary for the
CAFO to qualify for certification takes into account the CAFO's
production area design and construction and its operating and
maintenance procedures and practices as described in its nutrient
management plan (NMP) in accordance with the eligibility criteria,
described in detail below. The certification option established by this
rule does not change the requirement that CAFOs that propose to
discharge must seek permit coverage when they propose to discharge
pursuant to Sec.  122.23(f). It does, however, provide a structured
process for CAFOs that wish to certify to establish by objective means
that they do not discharge or propose to discharge. EPA believes that
such a structured process is helpful to CAFOs as they decide whether to
seek permit coverage. 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
under section 402 of the CWA. EPA wishes to emphasize that submission
of a no discharge certification is voluntary and the process for
obtaining a certification has been developed with that underlying
principle in mind.
    As explained in detail above, under Sec.  122.23(d)(1) a CAFO that
does not discharge or propose to discharge is not required to apply for
an NPDES permit. A certification in accordance with this final rule
documents the CAFO operator's basis for making an informed decision not
to seek permit coverage because the CAFO does not discharge or propose
to discharge. A CAFO that certifies in accordance with the requirements
of this final rule, discussed in detail below, is properly certified so
long as the CAFO maintains its eligibility. EPA believes that providing
a properly certified CAFO assurance that it is not required by Sec.
122.23(d)(1) to seek permit coverage is reasonable and justified. The
threshold question regarding which CAFOs are required to seek permit
coverage--whether the CAFO discharges or proposes to discharge--is the
same for all CAFOs. A CAFO that does not discharge or propose to
discharge can choose to certify or not. Certification in accordance
with the requirements of 40 CFR 122.23(i) requires a CAFO owner or
operator to undertake and document a rigorous analysis of the
operation's structure and design, and to be committed to operation and
maintenance protocols designed to ensure no discharge, discussed in
detail below.
    EPA is adding subsection (j) 40 CFR 122.23 to clarify the effect of
certification. As provided in new paragraph (j)(1), a CAFO certified in
accordance with Sec.  122.23(i) is presumed not to propose to
discharge. A CAFO that is ``certified in accordance with

Sec.  122.23(i)'' has submitted a complete certification that is in
effect pursuant to 40 CFR 122.23(i)(4). In the unlikely event that such
a CAFO does discharge, it will not be in violation of the requirement
that CAFOs that propose to discharge seek permit coverage pursuant to
Sec.  122.23(d)(1) and (f), with respect to that discharge, provided
the CAFO maintained its certification by continuing to be designed,
constructed, operated, and maintained in accordance with the
eligibility criteria in 40 CFR 122.23(i)(2). This is because meeting
the eligibility criteria at the time of the discharge establishes that
the CAFO did not propose to discharge. If a certified CAFO does
discharge, and the Director believes that the CAFO's certification was
invalid at the time of the discharge (i.e., not in accordance with the
eligibility criteria in Sec.  122.23(i)(2)), the presumption means
that, in any enforcement action alleging failure to seek permit
coverage prior to the discharge, the burden is on the Director to
establish that the CAFO ``proposed to discharge'' prior to the
discharge. EPA notes that any unpermitted discharge from a properly
certified CAFO is still a violation of CWA section 301(a) and
terminates the certification pursuant to Sec.  122.23(i)(4). Moreover,
if subsequent to the discharge event the CAFO is designed, constructed,
operated, or maintained such that a discharge will occur, it must seek
permit coverage under Sec.  122.23(d)(1) and (f). For additional
discussion of past discharges from unpermitted CAFOs see section
III.C.3(a) of this preamble.
    To further clarify the effect of voluntary certification, EPA is
also including in the final rule a provision specifically related to
uncertified CAFOs. As provided in 40 CFR 122.23(j)(2) of this final
rule, in any enforcement proceeding for failure to seek permit coverage
under Sec.  122.23(d)(1) or (f) that is associated with a discharge
from an unpermitted CAFO that has not submitted certification
documentation as provided in 40 CFR 122.23(i)(3) or 40 CFR
122.23(i)(6)(iv), the CAFO would have the burden to establish that it
did not propose to discharge prior to the discharge. Also, a CAFO that
had submitted a certification more than five years prior to the
discharge (and not recertified within the past five years) or that had
withdrawn its certification pursuant to 40 CFR 122.23(i)(5) prior to
the discharge would also have the burden to establish that it did not
propose to discharge. EPA's intent is to clarify that when an
unpermitted CAFO discharges and the permitting authority does not have
a current, signed certification from that CAFO, it is the CAFO's
responsibility to show that it was not required to have applied for
permit coverage (i.e., did not propose to discharge) prior to the
discharge. Section 122.23(j)(2) provides that the CAFO can satisfy this
burden by establishing that at the time of the discharge the CAFO's
design, construction, operation, and maintenance were all in accordance
with the certification eligibility criteria of Sec.  122.23(i)(2).
    Unlike the 2003 rule that required all CAFOs to seek permit
coverage in order to operate unless they obtained a determination of
``no potential to discharge,'' the certification provision is entirely
voluntary. The requirement for a CAFO to apply for a permit is
triggered if a CAFO discharges or proposes to discharge, regardless of
whether it has certified or not. Any CAFO operator's decision as to
whether to seek permit coverage should be made based on an objective
assessment of the CAFO's design, construction, operation, and
maintenance, in contrast to the 2003 rule, which required the operator
either to seek permit coverage or prove to the satisfaction of the
Director that the CAFO had no potential to discharge. Therefore, under
Sec.  122.23(d)(1) and (i), the operator must evaluate based on such an
objective assessment whether it discharges or proposes to discharge. If
it does it must seek and obtain permit coverage; if it does not it may
operate without a permit and decide either (1) to certify under the
provisions at Sec.  122.23(i); or (2) to operate without a permit and
without certifying. The purpose of certification is to provide a
voluntary mechanism for the CAFO to establish in advance that it does
not discharge or propose to discharge. As previously discussed, a CAFO
that operates without a permit must be designed, constructed, operated,
and maintained such that no discharge will occur, because any discharge
(other than agricultural stormwater) is prohibited from unpermitted
CAFOs pursuant to CWA section 301(a), while permitted CAFOs are allowed
to discharge under specified conditions and may also have defenses for
upset and bypass. NPDES permit coverage reduces CAFO operator risk and
provides certainty to CAFO operators regarding activities and actions
that are necessary to comply with the CWA. In contrast, certified CAFOs
are not allowed to discharge under any conditions (other than
discharges of agricultural stormwater), and are liable for any
unpermitted discharge pursuant to CWA 301(a), but they will not
additionally be held liable for a violation of the duty to apply,
provided their certification is valid and still in effect at the time
of discharge. EPA strongly recommends that all CAFOs that have any
doubt about their ability to operate under all circumstances without
discharging seek to obtain NPDES permit coverage, and believes it is in
their interest to do so. However, in accordance with the Waterkeeper
decision, EPA is requiring CAFOs to seek permit coverage only if they
discharge or propose to discharge.
    The final rule provisions for certification eligibility and
submission, and conditions for a valid certification are discussed in
detail below.
(i) Certification Eligibility Criteria
    EPA is establishing specific eligibility criteria for CAFO
certification at 40 CFR 122.23(i)(2). Meeting these criteria
establishes that the CAFO does not ``discharge or propose to
discharge'' for purposes of 40 CFR 122.23(d)(1), for as long as the
certification is valid. Eligibility for certification means meeting the
criteria described below at the time certification is established and
continuing to meet the eligibility criteria throughout the period of
certification as new information or situations arise. The three
criteria are as follows: (1) An objective evaluation which shows that
the CAFO's production area is designed, constructed, operated, and
maintained so as not to discharge, (2) development and implementation
of an NMP to ensure no discharge (other than agricultural stormwater
discharges) that, at a minimum, addresses the elements set forth in 40
CFR 122.42(e)(1) and 40 CFR 412.37(c), including operation and
maintenance practices for the production area and land application
areas under the control of the CAFO, and (3) maintenance of the
documentation required for certification either on site, at a nearby
office, or where it can be made readily available to the permitting
authority upon request. A statement that describes the basis for the
CAFO's certification that it satisfies these eligibility criteria must
be submitted to the Director, but there is no requirement for
permitting authority review in order for the certification to be valid.
    The first two criteria concern the existing physical and
operational conditions at the CAFO. In addition, meeting these criteria
includes making proper accommodations during the certification period
to address changes to the operation. For example, if an increase in
animals will cause the CAFO to exceed the existing storage capacity for
precipitation, manure and process

wastewater required for no discharge, in order to remain certified, the
CAFO must remedy the storage capacity problem prior to bringing the
additional animals to the operation. Operation and maintenance
practices may need to be modified to accommodate changes to the CAFO.
For example, a reduction in fields available for land application would
trigger the need to reevaluate the adequacy of manure storage and
handling protocols. The third eligibility criterion requires a
certified CAFO to maintain records needed to support the basis for the
certification throughout the duration of the certification, such as
monitoring and inspection records, records of maintenance and repairs,
and land application records, including updated documentation to match
current conditions and circumstances at the CAFO. Certified CAFOs, like
any other permitted or unpermitted CAFO, may be asked to send
information to the permitting authority that is relevant to
implementation of the CWA, or inspected by EPA or authorized State
inspectors. During an inspection the certified CAFO could be required
to produce the documentation showing that it meets the eligibility
criteria, including that the CAFO has been and is being operated and
maintained in accordance with an NMP that has been updated as
necessary.
    Commenters offered numerous perspectives on the proposed
eligibility criteria. Some commenters asserted that the proposed
criteria were too extensive, stringent, and complex, and therefore
would make it unlikely that self-certifying CAFOs could accurately
demonstrate their eligibility. These commenters indicated that, as
proposed, the eligibility criteria would be expensive to implement and,
thus, would serve as a disincentive for a CAFO to choose to certify. In
response to these comments, EPA emphasizes that certification is
voluntary, and CAFOs may choose not to certify. As noted above, EPA
believes that it is generally in an operator's best interest to obtain
permit coverage. However, EPA has provided the certification option for
CAFOs that choose not to seek permit coverage but would like to
establish up front that they do not discharge or propose to discharge.
The final rule contains stringent eligibility criteria because in light
of the CWA prohibition against unpermitted discharges, the eligibility
criteria for certification must establish that the CAFO does not
discharge or propose to discharge. Only CAFOs that establish
eligibility and meet all of the certification provisions in 40 CFR
122.23(i)(2)-(3) will receive the benefit of certification, which is
that a validly certified CAFO that discharges will not be in violation
of the requirement to apply for a permit pursuant to Sec.  122.23(d)(1)
and 40 CFR 122.23(f). As EPA is clarifying in 40 CFR 122.23(j), without
a certification, an unpermitted CAFO that discharges has the burden of
establishing that it did not propose to discharge in an enforcement
action arising from a discharge from the CAFO.
    In contrast, other commenters indicated that the proposed criteria
do not ensure that a certified CAFO will not discharge and, therefore,
additional requirements and procedures should be imposed for
certification eligibility. In response to these comments, the
certification eligibility criteria in this final rule have been
modified from the 2008 supplemental proposal in order to clarify what
EPA expects of a certified CAFO. The final rule clarifies that the
CAFO's NMP must include any operation and maintenance practices that
are established by the technical evaluation of production area open
storage structures as necessary to ensure no discharge. Also, EPA
reminds unpermitted CAFOs considering certification that many site-
specific factors, such as location and the facility's discharge
history, must be taken into account when demonstrating certification
eligibility in accordance with this final rule. A CAFO in close
proximity to waters of the U.S. or a conduit to waters of the U.S. may
need to take additional protective measures for design, construction,
operation and maintenance in order to be able to demonstrate that it
will not discharge. A CAFO operator who intends to establish
eligibility for certification should be mindful that, as stated above
in the discussion of revised Sec.  122.23(d)(1), a CAFO that has
discharged in the past would generally be expected to discharge in the
future, and therefore be expected to obtain a permit, unless it has
modified the design, construction, operation or maintenance in such a
way as to prevent any discharges from occurring.
    The first eligibility criterion for valid certification covers the
design, construction, operation, and maintenance of the CAFO's
production area. As proposed, 40 CFR 122.23(i)(2)(i) of this final rule
requires the CAFO to demonstrate that the CAFO's production area is
designed, constructed, operated, and maintained so as not to discharge.
Due to the variations in production area design based on the type of
containment system used at the operation, EPA proposed and is
finalizing today a rule with two parts for the first eligibility
criterion: the first for open manure storage structures and the second
for any part of the production area not considered to be open
containment.
    Consistent with the 2008 supplemental proposal, under the final
rule, any CAFO with an open manure storage structure seeking to certify
that it does not discharge or propose to discharge is required to
perform a technical evaluation under 40 CFR 122.23(i)(2)(i)(A). To
demonstrate that the CAFO meets the production area requirement for
certification, this evaluation must be conducted in accordance with the
elements of the technical evaluation required for open storage new
source swine, poultry and veal calf operations seeking to demonstrate
no discharge under 40 CFR 412.46(a)(1)(i)-(viii), as revised by this
action. EPA clarifies that, although this provision references the new
source performance standard (NSPS) for swine, poultry and veal calf
operations, this eligibility criterion applies to any unpermitted CAFO
with open manure storage seeking to certify that it does not discharge
or propose to discharge, not just new sources in the swine, poultry and
veal calf sectors with open storage.
    Elsewhere in this final rule, EPA is revising the provisions at 40
CFR 412.46(a)(1) to allow such new sources with open containment to
meet the no discharge requirement for their NPDES permit using best
management practices based in part on a rigorous site-specific
technical evaluation that includes use of the most recent versions of
the Animal Waste Management (AWM) software, or equivalent software, and
the Soil Plant Air Water (SPAW) Hydrology Tool, or an equivalent model.
For a discussion of the technical evaluation and the AWM and SPAW
modeling tools, see section III.F of this preamble.
    Several commenters expressed the need for evaluation criteria
specific to beef cattle feedlots, based on their belief that reliance
on swine, poultry, and veal calf new source provisions is inappropriate
for all animal sectors. As described in more detail in Section III.F of
this preamble, AWM software is a planning and design tool for animal
feeding operations that can be used to estimate the production of
manure, bedding, and process water and determine the size of storage
facilities necessary to meet no discharge. AWM (CCE version 2.3.0)
currently provides manure characteristics for eight animal types with
the ability to modify these characteristics and add animal types as
necessary. The field and pond hydrologic analyses conducted with the
SPAW model are not specific to any animal species. Therefore beef and
dairy

operators can use the AWM and SPAW tools to establish the appropriate
design, construction, operation and maintenance of their facility to
meet the no discharge requirement of certification.
    EPA also received comments seeking clarification regarding how the
technical evaluation for new source swine, poultry and veal calf
operations can apply to existing facilities given that EPA stated in
the preamble to the 2003 CAFO rule that the no discharge performance
standard was not economically achievable for existing facilities. While
EPA has determined that the no discharge performance standard was not
appropriate to require for existing facilities on a national basis (see
68 FR 7218), EPA acknowledges that there are existing CAFOs that could
meet the standard. Existing CAFOs that feel it is not economically
achievable to meet a no-discharge standard always have the option of
applying for a permit.
    In order to meet the second part of the first eligibility
criterion, the final rule requires, in 40 CFR 122.23(i)(2)(i)(B), that
any certifying CAFO must demonstrate that all of its production area,
as defined at 40 CFR 122.23(b)(8), not just open containment
structures, is designed, constructed, operated, and maintained such
that there will be no discharge of manure, litter, process wastewater,
or raw materials, such as feed, to surface waters. For a CAFO without
open containment, this provision requires a demonstration of no
discharge from the entire production area. For a CAFO that has an open
containment structure, this provision requires a demonstration that the
remainder of the production area (other than the open containment
structure subject to the demonstration in Sec.  122.23(i)(2)(i)(A)),
also will not discharge. Because of the special risk of discharge from
open manure storage structures, greater specificity is provided
regarding the elements of the demonstration in Sec.
122.23(i)(2)(i)(A); however, the demonstration in Sec.
122.23(i)(2)(i)(B) must be technically sound and must be adequate to
demonstrate that the production area is designed, constructed,
operated, and maintained for no discharge. This demonstration must be
based on an evaluation of site-specific characteristics, including,
among others, the amount of manure generated during the storage period,
the size of the storage structure, control measures to ensure diversion
of clean water, and seasonal restrictions on land application. The
preamble to the 2003 rule provides additional information regarding
production area design for total containment and closed manure storage
systems, such as lagoon covers, underhouse pit storage systems, and
stockpile storage sheds. See 68 FR 7176, 7219-20. Some CAFOs may have a
combination of open manure storage structures and covered structures,
while others will house all animals and store all manure, feed and by-
products under cover. In either case, all parts of the production area
must be included in the demonstrations required under Sec.
122.23(i)(2)(i)(A) and (B).
    In addition, as proposed under 40 CFR 122.23(i)(2)(i)(C), this
final rule requires any certified unpermitted CAFO to implement the
measures set forth in 40 CFR 412.37(a) and (b) for the production area.
These additional measures pertain to operation and maintenance and
include provisions for visual inspections, depth markers for all open
surface liquid impoundments, corrective action, mortality handling and
recordkeeping. This final rule also requires these measures for
permitted new swine, poultry and veal calf operations to meet a no
discharge standard. Since both these permitted new source operations
and unpermitted certified CAFOs need to ensure no discharge from the
production area under the permit and certification requirements,
respectively, it is appropriate to rely, in part, on those provisions
to establish eligibility criteria for no discharge certification. The
documents that are necessary to satisfy the first eligibility
criterion, which addresses the CAFO's design, construction, operation,
and maintenance of the entire production area, include design
documentation and all recordkeeping and operation and maintenance
planning necessary to address the elements of Sec.  122.23(i)(2)(i),
which includes the measures set forth in Sec.  412.37(a) and (b).
    In the preamble to the 2008 supplemental proposal, EPA requested
comment on whether a recordkeeping checklist for use by certified CAFOs
would be a useful tool. EPA suggested the possibility of making such a
checklist available to all CAFO operators. Commenters generally
supported the concept of a recordkeeping checklist that could be used
by certified CAFOs, since the checklist could be used to document
``expectations for risk management.'' Commenters added that the
checklist should be developed in concert with the States. EPA plans to
work with States to develop a checklist and consider whether State-
specific checklists would also be appropriate.
    The second eligibility criterion requires the CAFO to have
developed and be implementing an NMP that addresses, at a minimum, the
elements set forth in Sec.  122.42(e)(1) and 40 CFR 412.37(c), and all
site-specific operation and maintenance practices necessary to ensure
that the CAFO will not discharge. The NMP must include provisions
regarding nutrient management in the production area as well as in all
land application areas under the control of the CAFO where the CAFO
will land-apply manure. Because operation and maintenance practices and
procedures are critical to discharge prevention, implementation of an
NMP is an essential component of any CAFO's efforts to ensure that it
will not discharge from its production or land application areas.
Furthermore, in order for any certified CAFO that land applies to
ensure that the only discharges from the land application areas are
non-point source agricultural stormwater discharges, the CAFO would, at
a minimum, need to land apply in accordance with practices that ensure
appropriate agricultural utilization of nutrients, including
conservation practices and agronomic rates of application. For detailed
discussion of unpermitted CAFOs and the agricultural stormwater
exemption, see section III.B of this preamble.
    EPA received comments indicating that the final rule should
establish a link between a facility's open storage structure design and
the land application practices outlined in a CAFO's NMP. In the 2008
supplemental proposal, EPA intended that the CAFO's NMP would reflect
any operation and maintenance practices related to and assumed in the
technical evaluation performed for open containment structures. To
clarify this intent, 40 CFR 122.23(i)(2)(ii)(B) of this final rule
states that the operation and maintenance practices required to be part
of the NMP must include ``any practices or conditions established by a
technical evaluation pursuant to paragraph (i)(2)(i)(A),'' the
provision applicable to CAFOs with open containment. For example, an
existing facility may develop an NMP and then use AWM and the SPAW
model to evaluate the adequacy of the designed storage facility and
overall water budgets for the operation, respectively, which will rely
upon inputs from the CAFO's NMP such as the number and type of animals,
soil profiles and planned crop rotations. In such a scenario, the CAFO
may learn from the technical evaluation that more frequent lagoon
drawdowns are necessary in order to achieve no discharge. To be
eligible for certification under the final rule, the CAFO's NMP

would then need to be revised to include the adjusted operation and
maintenance practices resulting from the technical evaluation. It is
these changed operation and maintenance practices that EPA is referring
to in the Sec.  122.23(i)(2)(ii)(B) requirement for the NMP to address
``any practices or conditions established by'' the technical evaluation
required for CAFOs with open containment structures under the first
eligibility criteria.
    Commenters requested that EPA define what criteria can be used to
meet the NMP eligibility requirement (e.g., whether a comprehensive
nutrient management plan (CNMP) would suffice). As EPA stated in the
2008 supplemental proposal, a CAFO may rely upon a CNMP \2\ for
purposes of certification eligibility, so long as the minimum NMP
requirements of Sec.  122.42(e)(1) and Sec.  412.37(c) are met by the
CAFO's plan, including all necessary operation and maintenance
protocols.\3\
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    \2\ Technical Guidance for Developing Comprehensive Nutrient
Management Plans, USDA Natural Resources Conservation Service
(2003), available at http://policy.nrcs.usda.gov/
viewerFS.aspx?id=3073.
    \3\ It is common for an operation to have one or more operation
and maintenance plans in order to properly implement a number of
NRCS conservation practice standards simultaneously. Also, to the
extent that the necessary operation and maintenance requirements to
implement any provision of the NMP are not included in the NMP
itself, those requirements need to be implemented and included in an
operation and maintenance plan to be maintained on site or at a
nearby location.
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    As discussed below, 40 CFR 122.23(i)(4) requires the certified CAFO
to at all times be designed, constructed, operated, and maintained such
that it meets the eligibility criteria to establish that the operation
does not discharge or propose to discharge. Thus, to maintain a valid
certification, a certified CAFO must update its NMP if any of the
design specifications, practices, or other NMP provisions change over
time. For example, if a certified CAFO operator decides to land-apply
manure on a field that is not included in the NMP, the CAFO will need
to calculate rates of application in accordance with the protocols for
land application consistent with 40 CFR 122.42(e)(1)(viii) and revise
the NMP to include the new field and the corresponding application
rates and any other land application practices for the field in
accordance with the protocols. Furthermore, since the eligibility
criteria require the certified CAFO to implement the ``up-to-date''
NMP, the CAFO would then need to land apply in accordance with the
application rates and other practices incorporated into the NMP for
that field.
    In the 2008 supplemental proposal, EPA stated that it would
encourage CAFOs seeking certification to consult with qualified third-
party professionals, but did not propose to require such consultation.
Some commenters supported EPA's position, while others believe that a
third-party validation of the certification by an NRCS-certified
technical service provider and professional engineer should be a
required element of the eligibility criteria. Commenters expressed
concerns that many CAFOs do not have the requisite knowledge to make
technically sound determinations regarding how to meet the eligibility
criteria for certification. EPA continues to believe that it is
appropriate that the third-party consultation be recommended but not
required because certification is voluntary and it is the CAFO owner or
operator who must certify to the operation's eligibility. Because a
CAFO's certification will not be approved by the permitting authority,
it is up to the CAFO operator to be certain that the certification is
valid in order to benefit from the presumption that it does not propose
to discharge. Therefore, EPA recommends consultation with a qualified
third-party. As stated in the preamble to the 2008 supplemental
proposal, any professional consulted by the CAFO should have the
requisite training, experience and expertise to conduct and/or
substantively review the required analyses, and to advise the owner or
operator as to whether the CAFO is, in fact, designed, constructed,
operated, and maintained such that it will not discharge.
    The third eligibility criterion for certification established by
this final rule, 40 CFR 122.23(i)(2)(iii), requires that the CAFO
maintain the documentation required by the first two criteria ``either
on site or at a nearby office, or otherwise make such documentation
readily available to the Director or Regional Administrator upon
request.'' The 2008 supplemental proposal included a regulatory
requirement that the NMP and other documentation of eligibility be
maintained by the CAFO ``on site.'' Many commenters expressed the need
for the final rule to include regulatory language allowing all
documentation of the certification eligibility criteria to be held on-
site or made readily available upon request. These commenters were
primarily concerned that a requirement to maintain the documentation on
site would be unreasonably burdensome on facilities that have multiple
production sites with one central office. EPA agrees that the
documentation necessary to demonstrate certification eligibility,
including the CAFO's site-specific NMP, should be maintained either on
site or at a nearby office, or otherwise made readily available to the
permitting authority upon request. The final rule established today
includes this revision to the proposed language, which is also
consistent with the provision established today applicable to the
agricultural stormwater discharge exemption for unpermitted CAFOs,
discussed in section III.B of this preamble. EPA recommends that
operators maintain the necessary documentation on-site to ensure proper
implementation of all operation and maintenance procedures.
(ii) Submitting the Certification
    Under the certification option promulgated by this action, a CAFO
seeking to certify that it does not discharge or propose to discharge
is required to submit the certification to the permitting authority.
Under 40 CFR 122.23(i)(3), the submission to the Director must include:
(1) The CAFO owner or operator's name, address and phone number; (2)
information regarding the CAFO's location, including latitude and
longitude; (3) a description of the basis for the CAFO's certification
that it satisfies the eligibility requirements of 40 CFR 122.23(i)(2);
(4) the certification statement set forth in 40 CFR 122.23(i)(3)(iv);
and (5) an official signature that meets the signatory requirements of
40 CFR 122.22.
    The signed certification makes the CAFO legally responsible for its
representations to the Director regarding the design, construction,
operation, and maintenance of the CAFO. As EPA noted in the preamble to
the 2008 supplemental proposal, the language regarding legal liability
for making a false statement under the certification option is
consistent with language in 40 CFR 122.26(g) which applies to
facilities seeking to obtain a ``no exposure'' exclusion from the
requirement for an industrial stormwater discharge permit. EPA
clarifies that under the applicable signatory requirements in Sec.
122.22, signing the certification signifies that the signer is
certifying that the certification was prepared under his/her direction
or supervision in accordance with a system designed to assure that
qualified personnel properly gathered and evaluated the information
submitted and that based on the responsible official's inquiry of the
person or persons who manage the system, or those persons directly
responsible for gathering the

information, the information submitted is, to the best of their
knowledge and belief, true, accurate and complete.
    This final rule makes no changes to the existing regulations
concerning how CAFOs may make Confidential Business Information (CBI)
claims with respect to information they must submit to the permitting
authority and how those claims will be evaluated. A facility may make a
claim of confidentiality under the existing regulations at 40 CFR part
2, subpart B.
    The third item the Agency is requiring for submission to the
Director, as listed above, is a statement describing the basis for the
CAFO's certification that it is designed, constructed, operated, and
maintained in accordance with the certification eligibility criteria.
EPA's expectation for what this description should include is unchanged
from the 2008 supplemental proposal. In the preamble to the 2008
supplemental proposal, EPA requested public comment on whether the
scope and type of information included in the description of
eligibility submitted to the Director should include: (1) The type and
number of animals; (2) the type and capacity of manure and wastewater
storage and/or containment; (3) storm size used as the basis for
containment design; (4) whether the CAFO consulted with a professional
engineer or technical service provider (TSP); (5) identification of the
documents maintained on site in accordance with the eligibility
criteria; and (6) any technical standards, tools (e.g. , RUSLE and
Phosphorus Index) and formulas used to calculate application rates of
manure, litter, and process wastewater.
    Commenters expressed differing viewpoints as to what documentation
must be provided to the Director for the no discharge certification.
Some commenters felt that the 2008 supplemental proposal would have
required the submission of too much information, and that CAFOs should
only be required to submit a list of the documents created to establish
a facility's eligibility. Some of these stated that submission of any
facility design or operation specifics is superfluous given that there
is no review by the permitting authority. In contrast, other commenters
believed that the extent of documentation to be submitted to the
Director was insufficient to establish that a facility is designed,
operated, and maintained in a way to ensure that it is not discharging.
Specifically, these commenters desired that submissions include all
documents associated with meeting the eligibility criteria for
certification.
    After consideration of these comments, EPA believes that the list
of information presented in the preamble to the supplemental proposal
balances the need of the Director to be informed of critical aspects of
the certified CAFO's operation with the fact that the certification is
not subject to review by the Director in order to become effective. It
is reasonable that the description of the CAFO's basis for
certification be submitted as part of the certification, including the
type of information listed above, as proposed in the supplemental
proposal. EPA also recognizes that depending on site-specific
conditions at a particular facility, certain information may not be
necessary (e.g. , an operation with no land application areas would not
need to provide information about application rates of manure, litter,
and process wastewater). Furthermore, if the Director is concerned that
a CAFO that discharges or proposes to discharge has submitted a
certification, the Director has the authority to request additional
information from the CAFO, as discussed below.
    The authority given to the permitting authority under section 308
of the CWA to conduct inspections at operations is not affected by this
rule. Section 308 authorizes, among other things, EPA to require owners
or operators of point sources to establish records, conduct monitoring
activities and inspections, and make reports, to enable the permitting
authority to determine whether there is any violation of any
prohibition, or any requirement established under section 308, 402, or
504 of the CWA. Therefore, any CAFO, whether it is certified,
permitted, or neither, may be subject to an information gathering
request or inspection, at the Director's discretion and for any of the
reasons provided by section 308 of the CWA. 33 U.S.C. 1318.
    Under this final rule, 40 CFR 122.23(i)(4), a ``certification that
meets the requirements of paragraphs (i)(2) and (i)(3) * * * shall
become effective on the date it is submitted, unless the Director
establishes an effective date of up to 30 days after the date of
submission.'' A certification is effective if the CAFO meets the
eligibility criteria in Sec.  122.23(i)(2) and submits the signed
certification statement and other required information in accordance
with Sec.  122.23(i)(3). This rule also requires the use of certified
mail or an equivalent method of documentation for identifying the date
of submission, consistent with the supplemental proposal, in order to
notify the Director that the CAFO has chosen to self-certify.
    EPA notes that under the final provision, the Director may, but is
not required to, establish that certifications will become effective
after a specified number of days, not to exceed 30 days, following
submission of the certification if the Director deems such action
appropriate, as discussed below. Regardless of whether the permitting
authority chooses to establish an effective date in accordance with
Sec.  122.23(i)(4), a certification becomes effective (either on the
date it is submitted or on the date established by the Director)
without acceptance or approval by the permitting authority. A decision
by the permitting authority to delay the effective date would allow the
permitting authority to become aware of the CAFO's certification prior
to it going into effect. A delayed effective date of up to 30 days
could provide the opportunity for the permitting authority and the CAFO
to have a focused exchange of information before the certification
becomes effective. For example, as a result of such an exchange the
CAFO may choose to consider making revisions to its certification to be
assured it has submitted a certification that meets all the
requirements of Sec.  122.23(i)(2) and (3). Also, such an exchange
could provide an opportunity for the CAFO to obtain additional
information about maintaining a valid certification after it goes into
effect. The permitting authority can also request information from an
unpermitted CAFO, as provided in section 308 of the CWA, and provide
feedback to the CAFO operator if the Director believes that the CAFO
has not met the certification requirements.
    EPA emphasizes that the final rule does not require Director review
of the certification. Therefore, if, for example, the permitting
authority establishes that certifications in that State will become
effective 30 days after submission, a certification from a CAFO that
has met the eligibility and submission requirements in Sec.
122.23(i)(2)-(3) will go into effect on day 30 regardless of any
activities that take place during the 30-day period, so long as the
CAFO maintains eligibility throughout that period. Similarly, because
the certification is not subject to permitting authority review and
approval, inaction on the part of the permitting authority at any time
during or after the 30 days does not indicate that the CAFO either has
or has not met the eligibility and submission requirements. An
effective date that is no more than 30 days after submission provides
sufficient time for the permitting authority to receive the
certification and have an exchange with

the CAFO, but it does not constitute an unreasonable delay for the CAFO
to obtain a valid certification. Given these underlying principles, EPA
has determined that it is appropriate to allow the Director discretion
to establish an effective date that is up to, but not more than, 30
days after submission.
    EPA received comments concerning the submission process for no
discharge certifications. Numerous commenters expressed concerns with
the lack of any explicit requirement for Director review and approval
of certifications. Some commenters asserted that the lack of review and
public participation under the 2008 supplemental proposal violates the
CWA and the Waterkeeper decision, and that without such review,
certification provides no assurance of ``no discharge'' and creates an
impermissible permitting structure based on self-regulation. Other
commenters indicated that Director review of key documentation is
necessary to ensure that a facility's certification meets applicable
criteria. Some commenters requested that the documents necessary to
meet the eligibility criteria also be subject to review by the Director
and that approval of the no discharge certification be made contingent
on such review.
    EPA does not agree that the lack of a requirement for Director
review is contrary to the CWA or the Waterkeeper decision. The
voluntary certification option is available only to CAFOs that do not
discharge or propose to discharge and, therefore, are not required to
seek NPDES permit coverage. Neither the CWA nor the Waterkeeper
decision requires a permitting authority to review no discharge
certifications or to subject such information to public participation.
Under the CWA, such requirements apply only to the permitting process.
In addition, EPA emphasizes that certification is not a substitute for
a permit. Rather, a valid certification simply allows an unpermitted
CAFO that is designed, constructed, operated, and maintained not to
discharge to establish and document that it does not discharge or
propose to discharge, in exchange for the assurance provided by a no
discharge certification that it is not subject to the regulatory
requirement to seek permit coverage in 40 CFR 122.23(d)(1) and (f). It
is the CAFO's choice and responsibility to establish and maintain a
valid certification or lose the benefits afforded by the certification.
Furthermore, as mentioned above, the final rule allows the permitting
authority to establish an effective date for certification of up to 30
days after the date of submission by the CAFO. Allowing States the
discretion to delay the effective date of certification addresses some
comments from States expressing uncertainty about the role of the
permitting authority in the certification process.
(iii) Limitations on Certification
    This rule includes several limitations on certification related to
the term of a certification, withdrawal of certification, and
recertification after a certification becomes invalid.
    Consistent with the 2008 supplemental proposal, under this final
rule, a no discharge certification will expire five years after the
effective date, unless the CAFO voluntarily withdraws the certification
or the certification becomes invalid (i.e., the CAFO has either
discharged or ceases to be designed, constructed, operated, and
maintained in accordance with certification eligibility criteria)
during the five-year term. See 40 CFR 122.23(i)(4). Some commenters
agreed with the proposed five-year term of certification, because the
limited term of certification would ensure that the CAFO reevaluates
eligibility. Other commenters contended that facilities should
recertify on a more frequent basis, either annually or triennially, to
ensure more frequent reevaluation of their certification. A number of
commenters did not believe that a term of certification should be
prescribed; several of these commenters maintained that if a facility
remains in compliance with the certification criteria and does not make
any significant changes in operation, the certification should remain
valid indefinitely.
    After considering the comments regarding the appropriate term for
certification, EPA has concluded that the proposed five-year term is
appropriate. At the end of this term the certification can be renewed,
if desired by the CAFO. Since CAFOs commonly alter their operations
over time, it is reasonable for the CAFO to periodically reevaluate and
update its certification submission. In addition, renewal every five
years does not create an undue burden on the CAFO or the permitting
authority because CAFOs that have not had major changes in operations
may be able to use much of the same documentation as prepared
previously, and permitting authorities are not required to review and
approve the certification. A shorter term for certification, such as
one or three years, is not necessary because a properly certified CAFO
needs to evaluate the facility at regular intervals as part of the
inspection and recordkeeping requirements. Thus, a five-year term is
reasonable.
    Under 40 CFR 122.23(i)(5) a CAFO may withdraw its certification at
any time by notifying the Director, by certified mail or equivalent
method of documentation, that it is withdrawing its certification. The
certification is effectively withdrawn on the date the notification is
submitted to the Director. If a CAFO's certification becomes invalid as
provided in Sec.  122.23(i)(4), discussed below, Sec.  122.23(i)(5)
requires the CAFO operator to withdraw its certification within three
days of the date on which the CAFO becomes aware that the no discharge
certification is invalid. As proposed, this final rule does not require
the CAFO operator to notify the Director of the reason for withdrawing
the certification because certification is voluntary.
    EPA received a number of comments concerning the withdrawal of
certification. These comments generally focused on the need for a
certified CAFO to provide more information regarding its actions
leading to the withdrawal. Some commenters observed that in order to
withdraw certification, CAFOs should have to submit the reasons for
such withdrawal to the Director. EPA believes it is reasonable for a
CAFO to be able to withdrawal its voluntary certification at any time
without additional explanation. The decision to certify is voluntary,
and thus, it is appropriate to allow a CAFO to decide to withdraw its
certification for any reason with no further explanation. However,
certain situations require the CAFO to withdraw its certification. This
final rule requires that a CAFO withdraw its certification by notifying
the Director in the event that the certification is no longer valid,
either because of a discharge or because the CAFO ceases to meet the
eligibility criteria. See Sec.  122.23(i)(4) and (5). Notifying the
Director that a CAFO is withdrawing its certification provides the
information necessary for the Director to maintain an up-to-date record
of certified CAFOs. A CAFO that fails to withdraw its certification
within three days of becoming aware that the certification is invalid
would be in violation of this regulatory requirement. EPA believes
these provisions appropriately balance the voluntary nature of
certification with the value to the Director of maintaining accurate
records of the universe of certified CAFOs.
    This final rule describes in Sec.  122.23(i)(4) the situations that
cause a certification to become invalid. First, in the unlikely event
of a discharge from a properly certified CAFO, the

certification would cease to be valid and would no longer be in effect.
Second, should a CAFO fail to continue to meet any of the eligibility
criteria, the CAFO's certification would no longer be valid.
Circumstances that could result in the certification becoming invalid
include, for example, an increase in animals that exceeds the capacity
of the production area for manure storage and handling or a loss of
land application areas such that the assumptions in the NMP concerning
land application would no longer be appropriate, if the CAFO's
operations, NMP and certification documentation were not revised to
address these changed circumstances. EPA emphasizes that failure by a
certified CAFO to continue to meet the eligibility requirements in 40
CFR 122.23(i)(2) is not, in and of itself, a violation of any
regulatory requirement because certification is strictly voluntary. For
example, failure to implement the measures set forth in 40 CFR
412.37(a)-(b), which are required for no discharge certification
eligibility under 40 CFR 122.23(i)(2)(i), is not a violation of Sec.
412.37(a)-(b) but renders the certification invalid. However, failure
to withdraw a certification that has become invalid is a violation of
the requirement to do so.
    As explained in the 2008 supplemental proposal, once a
certification ceases to be valid, the operator cannot rely on it if a
subsequent enforcement action is brought for a violation of the duty to
apply for a permit that is triggered after the certification becomes
invalid. In other words, once a CAFO's certification becomes invalid,
the CAFO is in the same position as any other unpermitted and
uncertified CAFO. After withdrawing the invalid certification, the
operator may be interested in seeking to recertify that the CAFO does
not discharge or propose to discharge or, if the CAFO does discharge or
propose to discharge, the CAFO is required to seek permit coverage, as
stated in 40 CFR 122.23(i)(5)(ii).
    In the 2008 supplemental proposal, EPA proposed to allow a
previously certified CAFO to recertify by revising its operations to
address the deficiency that led to the invalid certification and
submitting a new certification statement. Under the proposal, if the
certification was rendered invalid by a discharge, in order to
recertify a CAFO would have to submit to the Director the information
required under 40 CFR 122.23(i)(3) and additional information
describing the discharge and the steps taken by the CAFO to permanently
address the cause of the discharge. As proposed, such a recertification
submission, like the initial submission, would not be subject to
review.
    Under this final rule, if a CAFO's certification becomes invalid
due to a failure to meet the eligibility criteria, as opposed to
because of a discharge, and the CAFO wishes to recertify, the owner or
operator would need to make the changes necessary to establish
eligibility under Sec.  122.23(i)(2). The provisions applicable to the
recertification submission and effective date would be the same as for
any certification. See Sec.  122.23(i)(3) and (4). If the CAFO wishes
to recertify after a discharge has occurred, the CAFO would need to
meet the additional requirements of 40 CFR 122.23(i)(6), discussed in
detail below.
    Commenters expressed several viewpoints with regard to the proposed
provisions for recertification after a discharge. Some commenters
supported the recertification process as proposed. These commenters
generally recognized that CAFOs may encounter unusual circumstances
that result in a discharge and that it is appropriate to allow for
recertification once the conditions that resulted in the discharge are
addressed. Certain other commenters argued that subsequent to a
discharge any recertification should be reviewed by the permitting
authority and open to public comment to ensure a rigorous assessment of
whether recertification is appropriate. Some commenters asserted that
recertification after a discharge should not be allowed at all under
the CAFO regulations. Furthermore, some commenters believe it would be
inequitable for unpermitted CAFOs to discharge and recertify if other
discharging operators are required to seek permit coverage. Several of
these commenters asserted that any CAFO that discharges should be
required to obtain an NPDES permit.
    EPA emphasizes that it will be highly unlikely for a CAFO that is
designed, constructed, operated, and maintained in accordance with the
eligibility criteria in Sec.  122.23(i)(2) to discharge. Furthermore,
EPA maintains its position, stated in the preamble to the 2008
supplemental proposal, that the Agency generally considers a recurring
discharge as evidence that a CAFO is not eligible for certification or
recertification and needs to seek permit coverage. However, given the
possibility of a discharge from a properly certified CAFO, albeit
remote, EPA believes it is necessary for the final rule to include
provisions specifically for a CAFO seeking to recertify after a
discharge.
    In response to comments, EPA has established specific criteria in
this final rule that limit a CAFO's ability to recertify after a
discharge to those situations where (1) the certification was valid at
the time of the discharge, meaning the CAFO continued to be designed,
constructed, operated, and maintained for no discharge in accordance
with all provisions of the NMP and any operation and maintenance plans
included in the certification; (2) the operator has made any necessary
changes to the CAFO's design, construction, operation and maintenance
to permanently address the cause of the discharge and ensure that no
discharge from this cause occurs in the future; and (3) the CAFO has
not previously recertified after a discharge from the same cause. The
first criterion limits the availability of recertification after a
discharge by excluding CAFOs that discharge after allowing the
certification to lapse. EPA believes that a CAFO that certifies under
penalty of law that it is and will continue to be designed,
constructed, operated, and maintained so as not to discharge, that then
fails to satisfy this criterion and subsequently discharges, should not
be given the opportunity to once again obtain the benefits of a no
discharge certification. The second criterion ensures that a CAFO will
only recertify after it has carefully evaluated the cause of the
discharge and taken whatever action is necessary to ensure that a
discharge from the same cause will not occur again. Finally, the third
criterion constrains a CAFO from engaging in a cycle of recertifying
after multiple discharges from the same cause. The voluntary
certification option established in this rule is not intended to be a
mechanism for discharging CAFOs to avoid obtaining permit coverage, a
concern cited by several commenters who opposed the certification
option. On the contrary, EPA is providing the certification option to
allow CAFOs that meet the eligibility criteria to establish up front
that they do not discharge or propose to discharge.
    The final rule provides that the CAFO's recertification will not
become effective until 30 days from the date of submission. The
operator is also required to submit the following information for
review by the Director: A description of the discharge, including the
date, time, cause, duration and approximate volume of the discharge,
and a detailed explanation of the steps taken by the CAFO to
permanently address the cause of the discharge. This 30-day review
period provides an opportunity for the Director to consider the
circumstances leading to the discharge, any actions taken by the CAFO
to permanently address the cause of the discharge, and any other
relevant

compliance information regarding the facility. EPA encourages State
permitting authorities to take advantage of this opportunity to
consider such information. As is true for the general certification
process described above, when a CAFO seeks to recertify after a
discharge, the Director has the authority to collect additional
information from the CAFO, assess whether the criteria in this rule are
satisfied, and provide feedback to the CAFO if he/she believes that the
CAFO has not met the recertification criteria. For example, the 30-day
review period will allow the Director to assess whether or not the CAFO
has previously recertified after a discharge from the same cause.
However, as with the initial certification, the Director is not
required to take any action for a certification to become effective at
the end of the 30-day review period and inaction does not indicate that
the CAFO has met the recertification criteria. After considering public
comments on the 2008 supplemental proposal regarding recertification
after a discharge, EPA has determined that this 30-day review period is
reasonable and prudent to allow the Director to review situations where
a previously certified CAFO has had an actual discharge.
    Overall, the limited conditions under which a CAFO can recertify
following a discharge, the description of the discharge submitted to
the permitting authority, and the required 30-day review period prior
to the recertification becoming effective, provide an opportunity for
the Director to determine whether the CAFO discharges or proposes to
discharge and must seek coverage under an NPDES permit. For example, as
provided in 40 CFR 122.28(b)(2)(vi), the Director has the authority to
direct that the CAFO be covered under a general permit if one is
available.
    EPA believes the final rule provisions covering recertification
after a discharge provide an appropriate balance of the flexibility
offered by voluntary certification and the need for scrutiny of
previously certified CAFOs that have discharged. Additionally, under
the final rule, any previously certified CAFO that discharges or
proposes to discharge is subject to the permit application requirements
of 40 CFR 122.23(d)(1) and (f), and therefore must apply when the CAFO
proposes to discharge. A CAFO that has permanently addressed the cause
of the discharge such that the CAFO does not ``discharge or propose to
discharge'' is not required to seek permit coverage regardless of
whether it recertifies. For further discussion of the effects of a past
discharge on a CAFO's permit application requirements, see the duty to
apply discussion at section III.A.3(a) of this preamble.

B. Agricultural Stormwater Exemption

1. Provisions in the 2003 CAFO Rule
    The discharge of manure, litter, or process wastewater from a land
application area under the control of a CAFO is a discharge subject to
NPDES permitting requirements, unless the discharge is an
``agricultural stormwater discharge,'' which is excluded from the
meaning of the term ``point source'' under 33 U.S.C. 1362(14). In the
2003 CAFO rule, EPA differentiated between discharges from land
application areas under the control of the CAFO that are point source
discharges and those that are ``agricultural stormwater discharges''
exempt from NPDES permit requirements.
    In the 2003 rule, EPA promulgated a definition of agricultural
stormwater for CAFO land application areas that referenced 40 CFR
122.42(e)(1)(vi)-(ix). The referenced regulatory text includes
requirements for edge-of-field buffers or equivalent measures, testing
of manure and soil, land application at site-specific agronomic rates,
and recordkeeping. While not explicitly included in the definition of
agricultural stormwater, technical standards established by the
Director, in accordance with effluent limitations guidelines (ELGs) in
40 CFR 412.4(c) applied to Large CAFOs' nutrient management plans for
land application. These more specific limitations implemented the
general requirements at Sec.  122.42(e)(1)(vi)-(ix), and because the
2003 rule required all CAFOs with a potential to discharge to obtain
permits, virtually all Large CAFOs were required to comply with them.
2. Summary of the Second Circuit Court Decision
    The Second Circuit upheld EPA's definition of agricultural
stormwater established by the 2003 rule. In addition, ELG requirements
of 40 CFR 412.4(c) concerning land application for Large CAFOs were not
challenged. The court did not, however, specifically address the
applicability of these requirements to unpermitted Large CAFOs seeking
to claim the agricultural stormwater exemption for land application
discharges, in light of its vacature of the duty to apply for all Large
CAFOs. Waterkeeper Alliance et al. v. EPA, 399 F.3d 486 (2d Cir. 2005).
3. This Final Rule
    As a result of the regulatory revisions being made by this action
in response to the Waterkeeper decision, which held that EPA does not
have authority to require facilities with solely a potential to
discharge to obtain permits, Large CAFOs are not required to seek NPDES
permit coverage unless they discharge or propose to discharge. For
those Large CAFOs that obtain NPDES permit coverage, provisions for
determining whether precipitation-related discharges from their land
application areas qualify for the agricultural stormwater exemption
were promulgated in the 2003 rule and codified at 40 CFR 122.23(e). As
explained above, under the 2003 rule, Large CAFO NPDES permits must
require the development and implementation of nutrient management plans