Document ID: EPA-HQ-OW-2005-0037-0917
Agency: epa
Document Type: Rule
Title: Revised National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitations Guidelines for Concentrated Animal Feeding Operations in Response to the Waterkeeper Decision
Posted Date: 2008-11-20T05:00Z

[Federal Register: November 20, 2008 (Volume 73, Number 225)]
[Rules and Regulations]               
[Page 70417-70486]
From the Federal Register Online via GPO Access [wais.access.gpo.gov]
[DOCID:fr20no08-24]                         

[[Page 70417]]

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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

[[Page 70418]]

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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: (202) 564-0758, e-mail address: 
roose.rebecca@epa.gov. 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: (202) 566-1076, e-mail address: 
shriner.paul@epa.gov.

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.

[[Page 70419]]

                            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.

[[Page 70420]]

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.''

[[Page 70421]]

(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

[[Page 70422]]

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

[[Page 70423]]

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

[[Page 70424]]

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

[[Page 70425]]

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

[[Page 70426]]

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

[[Page 70427]]

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

[[Page 70428]]

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

[[Page 70429]]

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

[[Page 70430]]

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\
---------------------------------------------------------------------------

    \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.
---------------------------------------------------------------------------

    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

[[Page 70431]]

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

[[Page 70432]]

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

[[Page 70433]]

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

[[Page 70434]]

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 
for land application in accordance with the ELG in 40 CFR part 412. 
Nutrient management plans for land application in accordance with 40 
CFR 412.4(c) include application rates and other practices for manure, 
litter, and process wastewater developed in compliance with technical 
standards, as well as other requirements. These land application 
requirements are then incorporated into the permit pursuant to 40 CFR 
122.42(e)(1). Therefore, for permitted Large CAFOs that land apply 
manure, litter, or process wastewater, ``site-specific nutrient 
management practices * * * as specified in Sec.  122.42(e)(1)(iv)-
(ix)'' in Sec.  122.23(e) include land application rates and other 
practices determined in compliance with technical standards.
    The 2003 rule at Sec.  122.23(e) specifies how Large CAFOs that 
have NPDES permits qualify for the agricultural stormwater exemption. 
Specifically, under the existing regulation, the permit must set forth 
the site-specific nutrient management practices that ensure appropriate 
agricultural utilization of nutrients as specified in 40 CFR 
122.42(e)(1)(vi)-(ix) in order for precipitation-related discharges 
from such land application areas to be exempt agricultural stormwater 
discharges. EPA did not propose to amend the existing agricultural 
stormwater discharge exemption provision in Sec.  122.23(e), nor has 
EPA otherwise reopened the provision.
    In this rule, however, EPA is adopting a new regulatory provision 
clarifying what constitutes agricultural stormwater for unpermitted 
Large CAFOs. The Waterkeeper court held that Large CAFOs with a mere 
potential to discharge were not required to obtain permits. Because the 
existing regulations could be construed as

[[Page 70435]]

applying only to Large CAFOs with NPDES permits, EPA explained in the 
preamble to the 2006 proposed rule that a CAFO with no discharges other 
than precipitation-related discharges from its land application areas 
would not be considered to ``discharge'' if it applies manure, litter, 
or process wastewater to land under its control in accordance with 
nutrient management practices that ensure appropriate agricultural 
utilization of the nutrients in the manure, litter, or process 
wastewater as specified Sec.  122.42(e)(1)(vi)-(ix). The Agency also 
expressly stated in its 2006 proposal that, for unpermitted Large CAFOs 
to qualify for the statutory agricultural stormwater exemption, manure, 
litter, and process wastewater must be applied in compliance with 
technical standards, noting that technical standards are, in 
significant part, intended to ensure the appropriate agricultural 
utilization of the nutrients contained in the manure, litter, or 
process wastewater. 71 FR 37,750. EPA also requested comment on whether 
to codify language to require that unpermitted Large CAFOs that land 
apply manure, litter, or process wastewater must comply with the 
technical standards established by the Director in order to qualify for 
the agricultural stormwater discharge exemption for precipitation-
related discharges from land application areas under their control.
    In the preamble to the 2006 proposed rule, EPA also discussed the 
reference to the documentation requirement found in 40 CFR 
122.42(e)(1)(ix). EPA noted that documentation is a crucial element for 
determining whether a CAFO is land applying manure, litter, or process 
wastewater in a manner that ensures the appropriate agricultural 
utilization of nutrients such that any runoff from land application 
areas under a CAFO's control consists only of exempt agricultural 
stormwater discharges. 71 FR 37,750.
    The provision established in this rule at Sec.  122.23(e)(1) 
clarifies that in order for unpermitted Large CAFOs to have their 
precipitation-related discharges qualify as agricultural stormwater 
discharges, they must land apply manure, litter, or process wastewater 
``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).'' This interpretation of the statutory 
agricultural stormwater exemption was upheld by the Second Circuit in 
the Waterkeeper decision. In addition, the new provision established at 
40 CFR 122.23(e)(2) requires unpermitted Large CAFOs to have nutrient 
management planning documentation on site, at a nearby office, or 
otherwise make it readily available upon request to support assertions 
that the only discharges from their land application areas are 
precipitation-related discharges that qualify for the agricultural 
stormwater exemption. As noted above, EPA has not reopened any aspect 
of the 2003 CAFO rule applicable to permitted CAFOs. Rather, the new 
provisions clarify how the agricultural stormwater exemption applies to 
Large CAFOs that do not have an NPDES permit. This is not a new 
requirement for unpermitted CAFOs, but rather a clarification of EPA's 
existing interpretation of the agricultural stormwater exemption in CWA 
section 502(14).
    EPA is modifying the interpretation articulated by EPA in the 2006 
proposal of how technical standards apply to unpermitted CAFOs seeking 
to have their precipitation-related discharges from land application 
areas qualify for the agricultural stormwater exemption. Under this 
final rule, a precipitation-related discharge from land application 
areas under the control of an unpermitted Large CAFO constitutes an 
agricultural stormwater discharge where the CAFO has land applied 
manure, litter, or process wastewater 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). Nutrient 
management practices and rates of application satisfy the requirements 
of 40 CFR122.42(e)(1)(viii) when they are in accordance with technical 
standards established by the Director. The form, source, amount, 
timing, and method of application of nutrients are essential components 
of the protocols for land application of manure, litter, or process 
wastewater specified in Sec.  122.42(e)(1)(viii). As explained below, 
CAFOs that land apply using nutrient management practices based on 
standards other than the technical standards established by the 
Director would have to demonstrate that such practices ensure the 
appropriate agricultural utilization of the nutrients in the manure, 
litter, or process wastewater as specified in Sec.  122.42(e)(1)(viii).
    Technical standards established by the Director provide an 
objective basis for determining when precipitation-related discharges 
from land application areas are exempt from NPDES permit requirements. 
Such technical standards are reviewed and determined by the permitting 
authority to provide a technically sound framework for establishing 
rates of application that generally would satisfy the requirements of 
Sec.  122.42(e)(1)(viii). Such technical standards specify the method 
or methods for determining whether land application rates are to be 
based on nitrogen or phosphorus, or whether existing nutrient loads in 
the soil preclude land application, and also address the form, source, 
amount, timing, and method of application on each field to achieve 
realistic production goals while minimizing movement of nitrogen and 
phosphorus to surface waters. Thus, technical standards provide an 
objective and reliable framework for developing rates of application 
and other practices for each field, taking into account a range of 
critical factors. For purposes of Sec.  122.42(e)(1)(viii), rates of 
application developed using technical standards must encompass and 
include all of the factors discussed above.
    Because the technical standards established by the Director 
represent the permitting authority's judgment as to practices that 
ensure appropriate agricultural utilization of nutrients, as discussed 
above, they provide a sound basis for determining and documenting that 
a precipitation-related discharge from land application areas will meet 
the requirements of Sec.  122.42(e)(1)(viii). If a facility chooses to 
take a different approach and follow other standards, the facility 
would need to demonstrate not only that its practices accorded with 
such alternative standards, but also that the standards provided a 
reliable, technically valid basis for meeting the terms of Sec.  
122.42(e)(1)(viii). While technical standards established by the 
Director would have undergone careful review by the Director to 
determine their validity for purposes of applying the agricultural 
stormwater exemption, there may not have been a comparable review in 
place for alternative standards. Thus, the CAFO may have to demonstrate 
both the appropriateness of alternative standards and that its 
practices conformed to them in order for its discharges to qualify for 
the agricultural stormwater exemption.
    EPA recognizes that there may be other standards that are developed 
besides those established by the Director that may also provide 
guidance to producers regarding appropriate agronomic nutrient 
management practices and the development of rates of application. Under 
this rule, owners and operators of unpermitted CAFOs are not precluded 
from relying on such other standards. However, while other

[[Page 70436]]

standards may provide useful guidance, in the absence of being reviewed 
and established by the Director, it is the CAFO's responsibility to 
demonstrate that such alternative standards do, in fact, ``ensure 
appropriate agricultural utilization of the nutrients in the manure, 
litter, or process wastewater,'' as required by Sec.  
122.42(e)(1)(viii).
    In determining whether a CAFO's site-specific nutrient management 
practices do ``ensure appropriate utilization of the nutrients'' in the 
land applied manure, litter, or process wastewater, EPA will evaluate 
an unpermitted CAFO's nutrient management practices using the technical 
standards established by the Director as a baseline and expects the 
same of authorized States. As discussed, EPA considers the technical 
standards established by the Director to be a sound measure for 
determining whether the form, source, amount, timing, and method of 
application meet the requirements of Sec.  122.42(e)(1)(viii).
    As noted above, in order for an unpermitted Large CAFO without an 
NPDES permit to establish that the only precipitation-related 
discharges from its land application areas are agricultural stormwater 
discharges, it must have documentation showing that its nutrient 
management practices are in accordance with Sec.  122.23(e)(1). This is 
not a new concept, as one of the requirements specified in Sec.  
122.23(e) promulgated in the 2003 rule is to maintain documentation as 
required by 40 CFR 122.42(e)(1)(ix). Section 122.42(e)(1)(ix) requires 
specific records to be maintained to document the implementation of the 
elements of Sec.  122.42(e)(1)(vi)-(viii). As stated in the preamble to 
the 2006 proposed rule, the necessary documentation includes both the 
nutrient management planning documents and the additional recordkeeping 
that demonstrates the actual nutrient management practices that have 
been implemented. See 71 FR 37,750. Such documentation is essential for 
determining whether precipitation-related discharges from a land 
application area are agricultural stormwater discharges or point source 
discharges.
    It is reasonable and appropriate that unpermitted CAFOs be required 
to demonstrate that their nutrient management practices, including 
rates of application, meet the regulatory definition of agricultural 
stormwater promulgated in 2003, and to do so means maintaining 
documentation of their nutrient management practices. Without adequate 
documentation, it would be difficult, if not impossible, to know 
whether such precipitation-related discharges are unpermitted point 
source discharges or are exempt agricultural stormwater discharges.
    Because unpermitted CAFOs are not subject to the place and time 
recordkeeping requirements of Sec.  122.42(e)(2), EPA is in this rule 
requiring that unpermitted CAFOs that land apply manure, litter, or 
process wastewater maintain on site or at a nearby office, or otherwise 
make available upon request documentation showing that precipitation-
related discharges from their land application areas are agricultural 
stormwater discharges. The requirement for documentation is referenced 
in Sec.  122.42(e)(1)(ix), and is authorized by section 308(a) of the 
CWA. Section 308(a) gives EPA authority to require any point source to 
establish and maintain records for determining whether ``any person is 
in violation'' of a prohibition, including the section 301(a) 
prohibition against point source discharges unless authorized under an 
NPDES permit. Section 308(a)(4) authorizes EPA to require records, 
reports, and other information when required to carry out provisions of 
the CWA, including sections 301 and 402. The inclusion of this 
requirement for unpermitted CAFOs to keep the documentation on site or 
to make it readily available upon request is for the purpose of giving 
States and EPA a basis for determining whether the CAFO's land 
application discharges are within the statutory exemption for 
agricultural stormwater. EPA expects that, in general, CAFOs will 
maintain their nutrient management plans for land application on site 
because they set out the protocols that must be followed in practice. 
Documentation of the site-specific nutrient management practices that 
is not produceable to an inspector at the time of a permitting 
authority's inspection would not be considered to be made ``readily 
available'' and, further, would raise questions as to whether it is 
actually being properly used by the CAFO.
    EPA received comments in support of its position that a facility 
need not have an NPDES permit in order for precipitation-related 
discharges from land application areas to be deemed agricultural 
stormwater discharges. Other commenters disagreed for a variety of 
reasons. First, commenters asserted that the proposal was inconsistent 
with the approach EPA established in the 2003 rule. Second, some 
commenters argued that allowing the CAFO owner or operator to determine 
whether its nutrient management practices meet the requirements of the 
rule creates a similar ``impermissible self-regulatory permitting 
scheme'' as that struck down by the Second Circuit Court of Appeals in 
the Waterkeeper decision. They argued that these nutrient management 
practices must be subject to review and consideration by the permitting 
authority and the public.
    EPA does not agree that only CAFOs with NPDES permits should be 
allowed to claim that discharges from their land application areas are 
agricultural stormwater discharges. The question is whether a 
precipitation-related discharge from a CAFO's land application area is 
exempt from permitting requirements as an ``agricultural stormwater 
discharge'' or whether it is a point source discharge that requires a 
permit. As the Court of Appeals for the Second Circuit reiterated in 
the Waterkeeper decision, ``a discharge from an area under the control 
of a CAFO can be considered either a CAFO discharge that is subject to 
regulation or an agricultural stormwater discharge that is not subject 
to regulation.'' 399 F.3d 486 at 508 (citing Concerned Area Residents 
for the Environment v. Southview Farms, 34 F.3d 114 (2d Cir. 1994)). 
The assessment of whether a discharge is exempt as agricultural 
stormwater or a point source discharge subject to permitting 
requirements is not part of the permitting process, but rather precedes 
it.
    For the same reason, EPA does not agree that a self-regulatory 
regime is created by allowing unpermitted CAFOs to claim that 
precipitation-related discharges from their land application areas are 
exempt if they land apply manure, litter, or process wastewater in 
accordance with appropriate nutrient management practices as required 
by Sec.  122.23(e). In the context of the agricultural stormwater 
discharge exemption, nutrient management practices are not effluent 
limitations, which can only be established and enforced through NPDES 
permits. NPDES permits are authorized by section 402 of the CWA for the 
``discharge of any pollutant'' under the terms of that section, 
including compliance with effluent limitations. Section 502(12) defines 
``discharge of a pollutant'' and ``discharge of pollutants'' as ``the 
addition of any pollutant * * * from any point source.'' The definition 
of ``point source'' in section 502(14) expressly excludes 
``agricultural stormwater discharges and return flows from irrigated 
agriculture.'' Therefore, NPDES permits are necessary for point source 
discharges, but not for agricultural stormwater discharges. 
Consequently, the site-specific nutrient

[[Page 70437]]

management practices that a CAFO must implement in order for 
precipitation-related discharges from areas under the CAFO's control to 
be considered agricultural stormwater discharges are not effluent 
limitations. Rather, they are preconditions for determining whether the 
agricultural stormwater exemption applies for discharges from land 
application areas under the CAFO's control. Because the site-specific 
nutrient management practices are not effluent limitations, they are 
not subject to the requirements in section 402 for public review and 
comment. However, persons who believe that an unpermitted Large CAFO's 
nutrient management practices are not sufficient to qualify for the 
agricultural stormwater exemption are free to bring citizen suits under 
CWA section 505 alleging that the CAFO is discharging without a permit.
    The Waterkeeper court upheld EPA's construction of the definition 
of point source as articulated in Sec.  122.23(e) as reasonable. In 
this rule, EPA has not in any way reopened this provision of the 2003 
rule. Nor is EPA changing any aspect of Sec.  122.23(e) with respect to 
what is required in order for precipitation-related discharges from 
land under the control of a CAFO where manure, litter, or process 
wastewater is applied to qualify as ``agricultural stormwater 
discharges.'' The approach taken in this rule is simply to describe how 
a CAFO without an NPDES permit may come within the scope of the 
existing language in Sec.  122.23(e).

C. Nutrient Management Plans

1. Provisions in the 2003 CAFO Rule
    Under the 2003 CAFO rule, an NPDES permit issued to a CAFO must 
include a requirement for the permittee to develop and implement a 
nutrient management plan (NMP). At a minimum, the NMP is required to 
include best management practices (BMPs) and procedures necessary to 
achieve effluent limitations and standards, to the extent applicable, 
including the minimum requirements of 40 CFR 122.42(e)(1)(i)-(ix). 
Effluent limitations for Large CAFOs are set forth in the effluent 
limitations guidelines (ELG) in 40 CFR part 412, which contain specific 
NMP requirements applicable to both the production area and the land 
application areas under the control of Large CAFOs in the cattle, 
swine, poultry, and veal calf subcategories. For small and medium 
CAFOs, and other operations not subject to 40 CFR part 412 
requirements, effluent limitations, including those applicable to land 
application areas, are established on the basis of the best 
professional judgment (BPJ) of the permitting authority pursuant to CWA 
section 402(a)(1)(B) and defined in 40 CFR 125.3(c)(2).
2. Summary of the Second Circuit Court Decision
    The U.S. Court of Appeals for the Second Circuit found that the 
terms of an NMP are effluent limitations and vacated the 2003 CAFO rule 
insofar as the rule allowed permitting authorities to issue NPDES 
permits to CAFOs without (1) reviewing the terms of the NMPs; (2) 
providing for adequate public participation in the development, 
revision, and enforcement of the nutrient management plans; and (3) 
including the terms of the NMP in the permit. Waterkeeper Alliance et 
al. v. EPA, 399 F.3d 486, 498-504 (2d Cir. 2005). The decision did not 
affect the substantive requirements for NMPs established at 40 CFR 
122.42(e)(1) and 412.4(c) in the 2003 CAFO rule.
3. This Final Rule
    To address the court's decision, EPA is revising the 2003 CAFO rule 
and other provisions of the NPDES regulations to provide for:
     Receipt and review of the NMP by the permitting authority 
prior to issuing an individual permit or granting coverage under a 
general permit;
     Adequate public participation prior to issuing an 
individual permit or granting coverage under a general permit;
     Incorporation of the terms of the NMP into the NPDES 
permit; and
     The process to address changes to the NMP once permit 
coverage is granted, for both individual and general permits.
    The individual permitting process already allows for review of NMPs 
by the permitting authority and the public, and incorporation of the 
terms of the NMP into the individual permit consistent with the CWA. 
This is not the case, however, for general permits. Given that fact, in 
promulgating these revisions, EPA is devoting particular attention to 
the process for issuance of general permits. Furthermore, EPA expects 
most CAFOs to be covered by general permits.
    To effectuate these changes, EPA is revising 40 CFR 122.21, 122.23, 
122.28, 122.42, 122.62, and 122.63. As mentioned above, EPA extended 
the deadlines set in the 2003 CAFO rule for NMP development and 
implementation, as well as for newly defined CAFOs to seek permit 
coverage in separate rulemakings. 71 FR 6978 (February 10, 2006); 72 FR 
40,245 (July 24, 2007).
    The preamble discussion that follows is divided into eight sections 
to separately address each of the following issues:
     CAFO permit application or notice of intent requirements;
     Procedures for permitting authority review and public 
participation prior to permit coverage;
     Identification of terms of the NMP;
     Process for incorporating terms of the NMP into a general 
permit;
     Changes to a permitted CAFO's NMP;
     Process for review of changes to an NMP and for modifying 
terms of the NMP incorporated into the permit;
     Annual reporting requirements; and
     EPA nutrient management plan template.
(a) CAFO Permit Application or Notice of Intent Requirements for 
Nutrient Management Plans
    EPA is revising 40 CFR 122.21(i)(1)(x) to require the applicant to 
submit, as part of its permit application or notice of intent (NOI) to 
be covered by a general permit, an NMP developed in accordance with the 
provisions of 40 CFR 122.42(e) and, for Large CAFOs subject to subparts 
C or D of 40 CFR part 412, the requirements of 40 CFR 412.4(c), as 
applicable. Although this change is codified in the section of the 
regulations applicable to individual permit applications (40 CFR 
122.21(i)(1)), it also applies to NOIs, because the regulation 
governing NOIs (40 CFR 122.28(b)(2)(ii)) cross-references the 
requirements of Sec.  122.21(i)(1). EPA revised Application Form 2B to 
reflect these changes, and the revised form is provided as Appendix A 
of this notice.
    The final rule adopts the approach that EPA proposed. This approach 
is consistent with the Waterkeeper decision, which left undisturbed the 
substantive requirements for nutrient management plans in the 2003 CAFO 
rule but held that such plans must be submitted to the permitting 
authority for public review prior to permit coverage. These revisions 
do not change the required contents of the NMP, but add a requirement 
for CAFOs to submit their NMP as part of their application for an 
individual permit or NOI to be covered under a general permit. This 
differs from the requirements of the 2003 rule, which required that 
NMPs be submitted only at the request of the Director.
    In the 2006 proposed rule, EPA proposed requiring an applicant to 
submit, as part of its permit application or NOI, an NMP developed in 
accordance with the provisions of 40 CFR 122.42(e)(1) and if 
applicable, 40

[[Page 70438]]

CFR 412.4(c)(1). The permitting authority would then make the NMP 
available for review prior to issuing an individual permit or providing 
coverage under an NPDES general permit.
    Many commenters supported the proposed requirements to submit NMPs 
with the initial permit application or NOI. One State commented that a 
CAFO should be allowed to submit the NOI information in batches so that 
the permitting authority could begin processing the NOI before a 
facility has completed its NMP to prevent delays in the review and 
approval process. The commenter added that authorization to discharge 
under the permit could not be granted until the permitting authority 
had received, processed, and reviewed all required NOI and NMP 
information according to the regulations.
    Nothing in this rule prohibits permitting authorities from 
accepting permit application information in batches, provided that the 
application information and submission process satisfies all applicable 
requirements. For example, existing NPDES regulations address, in 
relevant part, the effective date of an application and the processing 
of a permit. See 40 CFR 124.3. EPA recognizes that early communication 
between the owner or operator of a CAFO and the permitting authority 
can help facilitate the permitting process, and EPA encourages CAFOs to 
work closely with their permitting authorities.
    EPA received some comments suggesting that the Director issue a 
general permit that defines the terms of the NMP and details BMP 
options for a range of possible conditions combined with a requirement 
for the CAFO to submit a summarized NMP. The summarized NMP would 
include site-specific facility information needed to apply the 
management approach prescribed by the general permit. One State 
recommended that, for general permits, CAFOs submit a ``universal NMP'' 
with their NOI that contains decision-making tools used by producers to 
determine application rates, dates, and methods rather than including 
site-specific information in the permit. This would allow for the 
public to comment on a generic ``universal NMP'' and would reduce the 
number of comments that the State regulatory agencies would need to 
review and consider if comments were provided for each individual NMP 
submitted for a general permit.
    EPA weighed these comments in deciding what information needed to 
be submitted to the Director for review to comport with the CWA 
requirements cited by the Waterkeeper Court. The final rule requires 
any CAFO seeking coverage under a general permit to submit with the NOI 
an NMP that meets the requirements of Sec.  122.42(e) and applicable 
effluent limitations and standards. EPA did not identify any other 
specific regulatory alternatives that substantially reduce burden while 
still providing for meaningful permitting authority and public review 
of site-specific NMPs prior to permit coverage. Thus, EPA is 
promulgating an approach that is consistent with the Waterkeeper 
decision and the NPDES CAFO permit program requirements, while 
continuing to allow for the use of general permits for CAFOs.
    EPA also received a comment that production and land application 
areas should have separate permitting requirements such that a facility 
that does not land apply would not need to submit an NMP that addresses 
its land application area. EPA is not revising the NMP requirements 
established in the 2003 CAFO rule that added land application 
requirements for permitted CAFOs. Under the NPDES regulations 
established in the 2003 rule, permits issued to CAFOs apply to the 
entire facility, including land application areas. Furthermore, the NMP 
provisions address discharges that can originate either from production 
areas or from land application areas. Thus, NMPs have been designed to 
be comprehensive documents required of all permitted CAFOs. The NMP 
provisions at Sec.  122.42(e)(1) must be included in a CAFO's NMP ``to 
the extent applicable.'' Thus, if a facility does not land apply 
manure, litter, or process wastewater, the land application provisions 
of the regulation would not be applicable. CAFOs should note, however, 
that even facilities that do not land apply manure, litter, or process 
wastewater, but transfer all manure, litter, or process wastewater to 
other persons, are required by 40 CFR 122.42(e)(3) to provide the 
``most current nutrient analysis'' to the recipient.
    Although EPA is not revising the substantive requirements of 
paragraph (e)(1) in this rule, EPA is modifying the introductory 
paragraph to conform to the procedural requirements promulgated in this 
rule. Because this rule requires an NMP to be submitted as part of the 
CAFO's permit application or NOI, EPA is removing, from paragraph 
(e)(1), the permit condition for development of an NMP once permit 
coverage is granted. EPA is thus revising Sec.  122.42(e)(1) simply to 
require that any individual or general NPDES permit issued to a CAFO 
require the implementation of an NMP that contains best management 
practices (BMPs) as specified in 40 CFR 122.42(e)(1)(i)-(ix) and the 
applicable effluent limitations and standards. Applicable effluent 
limitations include, for Large CAFOs, the requirements of 40 CFR part 
412, and for other CAFOs BAT requirements set on a best professional 
judgment (BPJ) basis.
    EPA notes that the definition of ``BMPs'' in the NPDES regulations 
(40 CFR 122.2) is very broad and includes both practices and procedures 
to be implemented by a permittee. For this reason, EPA is also changing 
the phrase in the introductory paragraph of Sec.  122.42(e)(1) 
concerning the contents of an NMP from ``best management practices and 
procedures'' to simply reference ``best management practices'' without 
intending any change in the actual scope of what must be included in an 
NMP.
(b) Procedures for Permitting Authority Review and Public Participation 
Prior to Permit Coverage
    This rule promulgates 40 CFR 122.23(h), which provides new general 
permit procedures for CAFO general permits. The provisions of Sec.  
122.23(h) supplement the general permitting requirements of 40 CFR 
122.28 with specific provisions for review and incorporation of CAFO 
NMPs into general permits for CAFOs. These provisions implement the 
decision of the Waterkeeper courts concerning public review of NMPs and 
incorporation of the terms of the NMP into CAFO permits, specifically 
for CAFOs seeking authorization under a general permit.
    After the permitting authority receives an application or an NOI 
from a CAFO, it is the permitting authority's responsibility to review 
the application or NOI to ensure that it meets the requirements of the 
regulations, and for general permits, the requirements of the general 
permit. This includes determining whether the nutrient management plan 
meets the requirements of 40 CFR 122.42(e)(1) and, for Large CAFOs 
subject to 40 CFR 412 subpart C or D, the applicable requirements of 40 
CFR 412.4(c). As part of that process, the Director must review the NMP 
for both completeness and sufficiency, as required by the Waterkeeper 
decision. Also, because the Waterkeeper decision requires terms of the 
NMP to be incorporated as permit terms, the Director must provide for 
adequate public participation in the process of establishing permit 
terms based on each CAFO's NMP.
    The general permit issuance process and the individual permitting 
process

[[Page 70439]]

differ in how a permit is developed and the means by which individual 
facilities obtain authorization to discharge. A general permit covers 
multiple facilities, and is made available to facilities seeking permit 
coverage after it is finalized. When the permitting authority develops 
a draft general permit, it must provide the public (including potential 
future permittees) an opportunity to review the permit, submit 
comments, and request a hearing. After considering comments submitted, 
the permitting authority then finalizes the general permit. Facilities 
may then submit an NOI seeking coverage under the final general permit. 
Typically, the permitting authority may then, without the need for 
further public notice and comment, either grant coverage under the 
general permit, require the facility to seek coverage under an 
individual permit, or deny permit coverage. Existing regulations 
establish a right for any interested person to petition the Director to 
require a facility authorized under a general permit to apply for an 
individual permit. See 40 CFR 122.28(b)(3).
    For individual permits, the NMP will be submitted and reviewed as 
part of the permit application. The decision-making procedures in 40 
CFR part 124 apply to the Director's review of the application, which 
includes the NMP. Part 124 requires review of the completeness and 
sufficiency of the permit application, includes an opportunity for the 
CAFO to modify the plan or provide additional information to the 
permitting authority, and requires a final decision by the Director 
after an opportunity for the public to comment and request a hearing.
    Although a review process for data submitted by applicants, 
including NMPs, is already provided for in existing NPDES regulations 
that address issuance of individual permits, such a process has not 
previously been expressly available in the regulations for CAFO general 
permits. Following the Waterkeeper decision, general permits for CAFOs 
must include the terms of an NMP applicable to each specific CAFO 
authorized under the permit. Moreover, Waterkeeper requires that the 
public have an opportunity to review each CAFO-specific NMP and comment 
on terms of the NMP to be incorporated into the permit. Thus, a second 
round of public notice and comment is necessary when providing coverage 
for CAFOs under a general permit. To fill these gaps and address the 
Waterkeeper decision, this rule creates new provisions at Sec.  
122.23(h) that establish a process for permitting authority and public 
review of NMPs for CAFO general permits.
(i) Permitting Authority Review of Nutrient Management Plans
    As discussed above, the Waterkeeper court held that NMPs must be 
reviewed by the permitting authority before permit coverage is issued 
to any CAFO. Waterkeeper, 399 F.3d at 498-502. The process for 
permitting authority review of NMPs for CAFOs seeking coverage under a 
general permit is established by this final rule at 40 CFR 
122.23(h)(1). Section 122.23(h) requires the Director to review the NOI 
submitted by a CAFO owner or operator to ensure that the NOI includes 
the information required by 40 CFR 122.21(i)(1), including an NMP that 
meets the requirements of 40 CFR 122.42(e) and applicable effluent 
limitations and standards, including those specified in 40 CFR part 
412. Section 122.23(h)(1) also provides that if, upon review, the 
permitting authority determines that additional information is 
necessary to complete the NOI or clarify, modify, or supplement 
previously submitted material, the Director will notify the CAFO owner 
or operator and request that the appropriate information be provided. 
When the NOI is complete, the Director must then proceed with the 
public notification process required by this rule and discussed below.
    In the 2006 proposed rule, EPA proposed a new regulatory provision 
to establish permitting authority review of NMPs for general permits. 
This provision would require the Director to review the NMP submitted 
with the NOI and to take appropriate steps to ensure that the NMP meets 
the applicable requirements of 40 CFR 122.42(e)(1) and, for Large 
CAFOs, 40 CFR 412.4(c). Upon review of the NMP, the permitting 
authority would request from the CAFO owner or operator any additional 
information needed to complete the NOI or clarify, modify, or 
supplement the submitted material. The permitting authority would then 
notify the public of its receipt of a complete NOI and of the terms of 
the NMP proposed to be incorporated into the general permit. After 
allowing time for public comment and a public hearing, if needed, the 
permitting authority would decide whether to authorize coverage under 
the general permit.
    Many commenters disagreed with the proposed modified general permit 
process that would add permitting authority review of the NMP. The 
primary concern was that the permitting authorities may have 
insufficient resources to review all NMPs, which could limit the 
usefulness of general permits. To address this concern, a number of 
commenters suggested variations on the proposed process. These 
suggestions are addressed in more detail below under the corresponding 
discussion for the respective stage of the general permitting process.
    The Waterkeeper decision held that permitting authorities must 
review the permit application and the NMP to ensure that all applicable 
requirements have been met. The court made no distinction between 
individual or general permits with regard to this requirement. Because 
existing regulations do not provide for a review process that addresses 
the submission and review of NMPs for inclusion in a general permit, 
and given that EPA expects many CAFOs to be permitted under general 
permits, EPA is adopting provisions at Sec.  122.23(h) that provide for 
permitting authority review of the CAFO NOI and NMP, as well as 
opportunity for the public to comment and request a hearing on the NOI, 
NMP, and the terms of the NMP to be incorporated into the permit.
    The procedure for review and notice of CAFO NOIs and NMPs will 
impose some increased burden on permitting authorities and will add 
steps to the process of administering a general permit. However, EPA 
has worked to adapt these new requirements to a two-stage review 
process that comports with the Waterkeeper decision and the CWA and 
adds some flexibility to the parallel NPDES permit procedure 
regulations of 40 CFR part 124.
    Commenters stated that EPA should establish a correlation between 
the timing of the application process and permit coverage. These 
commenters wanted the regulation to automatically authorize discharges 
within 60 days from the date of application/NOI submission unless the 
permitting authority denied permit coverage within that period, even if 
the public review process was incomplete. They took the view that CAFOs 
should not be penalized by a review process that could vary in length 
based on factors out of the control of the CAFO. Similarly, some 
commenters stated that EPA's final regulation should provide a clearly 
defined process with a limited length of time for permitting authority 
review. Suggestions for a time limit ranged from 30 to 60 days.
    To provide permitting authorities flexibility to review NMPs of 
varying complexity, this action does not require a specific timeframe 
for completion of the permitting authority review process. This 
approach is consistent with the existing NPDES regulations in part 124 
for other industries, which similarly do

[[Page 70440]]

not specify a timeframe for automatic authorization to discharge or for 
the completion of the permitting authority and public review processes.
    Commenters expressed concern over the additional workload that 
reviewing individual NMPs would create, and suggested alternatives to 
reduce permitting authority workload, including: Submission of a 
``universal NMP'' with permit applications for use in determining 
application rates, timing, and methods rather than including site-
specific information in the permit; and combining a detailed, clear 
general permit with the submission of a summarized NMP for review.
    In developing the 2006 proposed rule EPA evaluated alternative 
approaches for reducing operator and permitting authority workload. For 
example, EPA considered the use of an NMP template as a voluntary tool 
to facilitate completion and review of the NMP by CAFO applicants and 
permitting authorities, respectively. 71 FR 37,752. Such a template 
could serve as one of many tools available to support CAFO permitting 
and reduce permitting authority workloads. See preamble section 
III.C.3(h) for a discussion of the template. EPA also plans to develop 
additional tools and guidance to reduce the burden on both the CAFO 
operator and the permitting authority to meet the requirements of the 
NPDES regulations. For example, EPA is developing a training course 
that focuses on development and review of NMPs to comport with this 
final rule. EPA plans to first make the course available to State and 
federal permitting authorities in 2009.
    Another possible approach for minimizing permitting authority 
resource expenditures is utilizing a third-party for NMP review. A few 
commenters noted that having permitting authority staff review NMPs 
that have already been prepared by a State-certified planner is 
duplicative and unnecessary. Commenters believe that, due to their 
extensive training, certified planners are in the best position to 
review and certify NMPs coupled with appropriate public agency 
oversight. This is one State commenter's established NMP review 
process. Commenters noted that, in some States, another State agency 
(typically the State agricultural agency) reviews and approves NMPs. A 
State commenter asserted that the final rule would meet the intent of 
the Waterkeeper decision if it allowed NMP review by qualified 
professionals meeting educational and technical training requirements 
as set forth by the Director. Such professionals should be properly 
trained and subject to a quality assurance protocol. One commenter 
asserted that this flexibility is imperative for effective State 
programs.
    The permitting authority is responsible for reviewing NMPs and for 
ensuring that the terms of the NMP meet the applicable requirements of 
the NPDES process. There is no reason, however, why a State cannot 
obtain assistance and advice from technical experts, or tailor its 
review based on the development or certification of NMPs by State-
certified nutrient management planners. However, it is the permitting 
authorities' responsibility to ensure that comments are properly 
addressed and the final permit terms are incorporated.
    Regarding the increased workload permitting authorities may 
experience due to review of NMPs, EPA notes that 30 out of the 44 
States that regulate CAFOs currently require NMPs to be submitted with 
a CAFO's request for NPDES permit application coverage. Further, 28 of 
these States allow for public review of these NMPs. Thus, even though 
EPA did not specifically require this in the 2003 CAFO rule, such a 
review process already exists for many State regulatory authorities.
(ii) Public Review of Nutrient Management Plans
    In the Waterkeeper decision, the Second Circuit held that ``The 
CAFO rule deprives the public of the opportunity for the sort of 
participation that the Act guarantees because the Rule effectively 
shields the nutrient management plans [NMPs] from public scrutiny and 
comment.'' 399 F.3d at 503. This rule responds to the Waterkeeper 
decision by establishing public participation requirements that ensure 
adequate opportunity for public review of both a CAFO's NMP and the 
terms of the NMP to be incorporated into the permit prior to the CAFO 
obtaining authorization to discharge under the permit.
    As previously discussed, procedures for public participation in the 
issuance of individual permits are already established in the NPDES 
regulations. See 40 CFR part 124. Because this rule requires CAFOs to 
submit their NMP as part of their permit application (see discussion at 
section III.C.3(a) of this preamble; 40 CFR 122.21 and 122.23)), the 
public will have access to the NMP prior to permit issuance and will 
also have full opportunity to comment on the adequacy of the plan and 
on the nutrient management terms in the draft NPDES permit developed 
for the specific CAFO facility. This individual permit process 
addresses the court's decision in this respect.
    To preserve the option of general permits for CAFOs and to conform 
to the Waterkeeper decision which requires the terms of each CAFO's NMP 
to be incorporated into the CAFO's permit, this rule establishes new 
provisions, at 40 CFR 122.23(h), that require the permitting authority 
to allow public review of both the NMP and the terms of the NMP to be 
included in a general permit.
    In Sec.  122.23(h), the rule establishes new general permitting 
procedures for CAFOs that require permitting authorities to incorporate 
the terms of site-specific NMPs, which must be submitted with the NOI, 
into CAFO general permits when authorizing coverage under a general 
permit. These procedures require the Director to notify the public that 
the permitting authority is proposing to grant coverage for a facility 
under the general permit and make available for public review and 
comment the CAFO's NOI (including its NMP) and the draft terms of the 
NMP to be incorporated into the permit. The public will also have an 
opportunity to request a hearing on this information before the CAFO is 
authorized to discharge under the general permit.
    After making a preliminary determination that the NOI meets the 
requirements of 40 CFR 122.21(i)(1) and 122.42(e), the Director has 
discretion as to how best to provide the requisite public notification 
in the general permit context. For example, public notification may be 
provided on the permitting authority's Web page or through other 
electronic means. Another alternative is to use the notice or fact 
sheet for the general permit to establish a procedure allowing any 
person to request notice by mail or electronically of the receipt of an 
NOI, the permitting authority's proposed action, and the terms of the 
NMP proposed to be incorporated into the permit. These are appropriate 
ways to balance the competing concerns of providing adequate 
notification to the public, providing flexibility to the permitting 
authority, and ensuring the practicality of general permits.
    Under this rule, the Director also has discretion to establish an 
appropriate period of time for public review of the NOI and draft terms 
of the NMP proposed to be incorporated into the permit. Under 40 CFR 
122.23(h)(1), the Director may establish by regulation or in the 
general permit an appropriate period of time for the public to comment 
and request a hearing. This differs from the specifications in 40 CFR 
124.10, which sets a 30-day public notice period for proposed coverage 
under individual permits. Having the

[[Page 70441]]

Director set the time period for public review by regulation or in the 
general permit process will allow the public and other interested 
parties an opportunity to comment on the sufficiency of that time 
period. Factors the permitting authority might consider when 
establishing an appropriate time period include the number of NOIs 
being publicly noticed at any one time, the complexity of the material 
made available for public review, the expected level of public interest 
based on prior notices of CAFOs seeking coverage, the opportunity for 
the public to request an extension of the comment period for one or 
more facilities, and whether individuals can request and receive 
individual notification of CAFOs seeking authorization to discharge 
under the permit in a timely fashion.
    As mentioned above, the Director must also provide an opportunity 
for the public to request a hearing. The procedures for requesting and 
holding a hearing on the terms of the NMP to be incorporated into the 
general permit are the same as those for draft individual permits, 
which are provided in 40 CFR 124.11 through 40 CFR 124.13. When 
granting permit coverage, the Director must respond to all significant 
comments received during the comment period as provided in 40 CFR 
124.17, and if necessary, require the CAFO owner or operator to revise 
their NMP.
    Additionally, under the procedures promulgated in Sec.  
122.23(h)(1) of this rule, if after the public notice period and the 
conclusion of any hearings, the Director decides to authorize discharge 
under the permit, the permitting authority must notify the CAFO and 
inform the public. Such notification is necessary to ensure that the 
applicant and interested individuals are aware of the Director's final 
decision on granting authorization to discharge under the general 
permit and incorporating site-specific NMP terms into the general 
permit. Furthermore, the provision provides notification equivalent to 
that required when CAFOs are issued coverage under individual permits 
consistent with this rule revision.
    EPA is promulgating 40 CFR 122.23(h)(2), which establishes 
additional procedures for EPA-issued permits. Paragraph (h)(2) requires 
the EPA Regional Administrator to notify each person who has submitted 
written comments on the proposal to grant permit coverage and the draft 
terms of the NMP of the final permit decision. A person affected by the 
general permit can either challenge the general permit in court, or 
apply for an individual permit as authorized in 40 CFR 122.28.
    The public notice process described above also includes providing 
notice to other affected States, as required by the CWA. Section 
402(b)(3) of the CWA provides that the Administrator, in approving a 
State program, shall make sure the State has adequate authority to 
ensure notice to ``any other State the waters of which may be 
affected.'' Section 402(b)(5) provides that the Administrator must 
ensure that any State ``whose waters may be affected by the issuance of 
a permit may submit written recommendations to the permitting State,'' 
and that if those recommendations are rejected, the permitting State 
must notify the affected State in writing of the reasons for the 
rejection. The public notice provisions in this rule provide 
notification to affected States as well as to the public in general. 
Additionally, the permitting authority's response to all significant 
comments will include responses to comments from affected States.
    This rule balances several competing concerns regarding public 
participation procedures for general permitting of CAFOs. First, the 
final rule maintains the utility of a general permit program as a 
resource-efficient method by which to authorize multiple CAFOs under an 
NPDES permit while meeting the Second Circuit's directive to ``provide 
for adequate public participation'' in the development of site-specific 
effluent limitations. Waterkeeper, 399 F.3d at 524. Second, the final 
rule provides sufficient flexibility for State permitting authorities 
to adopt their own procedures while ensuring that they meet the public 
participation requirements of the CWA. Because of the large number of 
CAFOs that may seek permit coverage, the Agency considers it 
appropriate to have procedures that allow and encourage permitting 
authorities to continue the use of NPDES general permits as a means for 
applying CWA limitations and standards to CAFOs on a timely basis. Of 
course, existing regulations give the Director authority to require a 
facility to apply for an individual permit instead of allowing coverage 
under a general permit (even after coverage under a general permit has 
been granted). The Director may thus choose not to issue a general 
permit for CAFOs, but instead to require all CAFOs seeking permit 
coverage to obtain coverage under individual permits.
    The 2006 proposed rule included procedures for public review of 
NOIs and draft terms of the NMP substantially the same as the 
procedures promulgated today in Sec.  122.23(h). EPA solicited comment 
on the proposal to give the Director discretion regarding the means of 
public notification and the length of the public notice period, and 
also on the possibility of fixed minimum time frames for public review. 
The Agency also specifically sought comment on whether the proposed 
public participation process achieved an appropriate balance between 
the competing interests of maintaining the utility of general permits 
for CAFOs and providing adequate public review of permit terms.
    Several commenters expressed concern that public review of the NMP 
would eliminate the use of general permits, noting that States have 
limited resources for accommodating a public review process. Several 
commenters stated that the proposed process provided inadequate 
opportunity for public input. Some believed that the proposed public 
participation process is inconsistent with the general permitting 
approach and that only individual permits are appropriate for CAFOs 
since the terms of the NMP constitute site-specific effluent 
guidelines. Others felt that the public participation process needed to 
begin before the development of the NMP to provide an opportunity for 
comment on the specific best management practices (BMPs) to be included 
in the plan.
    The procedures for public participation in this final rule preserve 
the availability of general permits for CAFOs. As discussed above, the 
changes to the CAFO general permit process made in this rule are 
necessary to meet the requirements of the Waterkeeper decision. In 
addition, EPA has provided flexibility where it could with regard to 
how a permitting authority provides public notice and makes key 
information available. Further, the rule provides permitting 
authorities with flexibility to establish an appropriate time period 
for public review. Finally, the rule does not change any of the 
existing regulations that allow a permitting authority to require an 
individual permit when appropriate. Overall, the final rule maintains 
the utility of a CAFO general permit program as a resource-efficient 
method for authorizing multiple CAFOs under an NPDES permit while 
meeting the court's directive to ``provide for adequate public 
participation'' in the development of site-specific effluent 
limitations.
    One commenter stated that public access to the entire NMP will 
strongly compel operators to risk noncompliance by operating without 
authorization under a permit. Some commenters were concerned that 
sensitive information will be made available to the public.

[[Page 70442]]

    EPA understands the sensitivity of some information that may be 
contained in a CAFO's NMP. However, public availability and permitting 
authority review of a CAFO's NMP is not a new practice; rather, it is 
one that is currently employed in many State NPDES CAFO programs. As 
stated above, 30 of the 44 States that permit CAFOs request that NMPs 
be submitted as part of their permit application process. In most of 
those States the permitting authority conducts a comprehensive 
technical review of the NMPs prior to granting authorization to 
discharge under the permit. These NMPs have already been publicly 
available in these States for some time. Moreover, most of these States 
provide notice to the public of the availability of these plans and 
seek public review, with some conducting public meetings as well. Any 
information submitted to the permitting authority as part of a permit 
application or NOI must be made available for public review and 
comment, unless it is confidential business information (CBI). See 40 
CFR 122.7.
    EPA disagrees with commenters who believe that the permitting 
process provides inadequate opportunity for public input or that such 
opportunity should arise earlier in the process. The final rule 
provides ample opportunity for the public to comment on the terms and 
conditions of the general permit, including for each permitted CAFO, 
the opportunity to comment on permit coverage and the terms of the NMP. 
This rule requires that the public have access to the NOI and the NMP 
when reviewing and commenting on BMPs and other terms of the NMP to be 
incorporated as enforceable conditions of the permit.
    Several commenters supported permitting authority discretion on the 
method of providing public notice of the opportunity to comment on an 
NMP or request a hearing. One commenter stated that EPA should allow 
applications to be processed jointly so that the permitting authority 
could provide notice to the public of multiple NMPs at the same time. 
Another commenter supported web-based or other electronic notice. One 
commenter suggested that the general permit fact sheet be utilized to 
establish a procedure allowing any person to request notice by mail or 
electronically of the receipt of an NOI, the permitting authority's 
proposed action, and the terms of the NMP proposed to be incorporated 
into the permit. Such an approach would provide flexibility to the 
permitting authority and reduce the number of notices that must be 
published.
    As stated above, this rule allows the permitting authority 
discretion as to how best to provide such public notification in the 
general permit context. For example, public notification may be 
provided on the permitting authority's Web page or through other 
electronic means. The final rule does not restrict the ability of a 
permitting authority to provide notice of multiple NMPs at one time 
provided the all applicable procedural and substantive permitting 
requirements are satisfied. However, notice must be adequate, and the 
opportunity to comment must be meaningful.
    Some commenters expressed that EPA should require a minimum of 30 
days for public review and that the 2006 proposed rule provided 
permitting authorities too much discretion. Others stated that the 
public participation process should be limited, with many suggesting no 
more than 30 days for an initial submission. In addition, commenters 
requested that EPA limit the circumstances under which the comment 
period could be extended. EPA believes that the decision as to how much 
time should be allowed for public participation is best decided by the 
Director for reasons discussed above, including that the public will 
have an opportunity to comment on the length of the public notice 
period when reviewing either the draft regulations or draft general 
permit.
    EPA also received comments suggesting that EPA specify that each 
facility would be subject to only one public hearing on a draft permit; 
that the decision to hold a public hearing on a draft permit and NMP 
should be based on a finding of a significant degree of public interest 
and limited to issues germane to permitting; and that public review of 
a general permit be limited to the terms of the NMP that are 
incorporated into the permit. Several commenters were concerned that 
without some limitations, the public review process could be misused. 
This rule specifies that permitting authorities follow the procedures 
set forth in Sec.  124.11-124.13. These protocols are well established 
for NPDES permits and allow the Director to weigh the relevant 
circumstances in addressing each of the issues raised by commenters.
    State commenters were generally supportive of EPA's proposed 
approach and the flexibility it allows for permitting authorities in 
the general permit process. In particular, these commenters said that 
establishing timeframes for public review should be left to the 
permitting authority.
    One State suggested that the public participation aspects of the 
2006 proposed rule be limited to only new Large CAFOs and that NMP 
terms for previously authorized Large CAFOs be made available as part 
of a modified annual reporting requirement. The public participation 
requirements in this final rule are applicable to all CAFO NPDES 
permits. The Waterkeeper decision did not distinguish between new 
facilities seeking permit coverage for the first time and existing 
facilities seeking permit reissuance for purposes of public 
participation in reviewing CAFO NMPs. Such a distinction would not make 
sense given that the Second Circuit found that the terms of NMPs are 
effluent limits that must be included in the permit and presented for 
public review and comment. Providing the NMP terms to the public only 
in an annual report would not address the Waterkeeper requirement that 
the permitting authority must provide for public notice and the 
opportunity to comment on the NMP terms and that the NMP terms must be 
enforceable.
    EPA regulations applicable to State NPDES programs specify that 
where notice and opportunity for comment must be provided, a permitting 
authority must respond to significant public comments (Sec.  124.17). 
Several commenters said EPA should specifically narrow what constitutes 
a significant comment warranting a response by the permitting 
authority. Their general position was that comments must have a 
technical or scientific basis, or address errors, omissions, or 
misrepresentations in order to be considered significant. Some said 
that comments should be limited only to issues under the purview of the 
CWA, and generalized grievances about the operation or location should 
be identified as insignificant and not warrant any response by the 
permitting authority. Other commenters, namely State agencies, 
identified the need to provide the permitting authority with 
flexibility for determining which comments are significant and warrant 
a response. They also indicated that the permitting authority will have 
limited resources for responding to all comments on a draft permit and 
NMP.
    EPA intends that this final rule be consistent with existing 
regulatory provisions addressing public participation in the NPDES 
program and believes that it provides a reasonable amount of discretion 
and flexibility for permitting authorities to determine and respond to 
those comments deemed to be significant.

[[Page 70443]]

(c) Identification of Terms of the NMP
    In the Waterkeeper decision, the Second Circuit held that because 
the terms of the NMP constitute effluent limitations, the CAFO Rule, 
``by failing to require that the terms of the nutrient management plans 
be included in NPDES permits--violates the CWA and is otherwise 
arbitrary and capricious in violation of the Administrative Procedure 
Act.'' 399 F.3d at 502.
    To respond to the Waterkeeper decision, the Agency is promulgating 
40 CFR 122.42(e)(5) in order to specify the minimum terms of the 
nutrient management plan (NMP) that must be enforceable requirements of 
a CAFO's NPDES permit. As discussed in the preambles to both the 2006 
proposed rule and 2008 supplemental proposal, EPA is not revisiting the 
decisions the Agency made in 2003 with respect to the contents of the 
nutrient management plan because the Waterkeeper decision did not 
affect these requirements. This rule requires that, based on the 
provisions promulgated in 2003 that define nutrient management plans 
(40 CFR 122.42(e)(1) and 412.4(c)), the ``terms'' of the nutrient 
management plan become terms and conditions of the permit, as required 
by the Second Circuit decision.
    The Waterkeeper court clearly indicated that the terms of the NMP 
must be included in the permit and that the terms must include ``waste 
application rates'' developed by Large CAFOs pursuant to their NMPs. 
399 F.3d at 502. Paragraph (e)(5) includes two alternative approaches 
for specifying terms of the NMP with respect to rates of application, 
which are needed to satisfy the requirement that the NMP include 
``protocols to land apply manure, litter, or process wastewater * * * 
that ensure appropriate agricultural utilization of the nutrients.'' 40 
CFR 122.42(e)(1)(viii). For Large CAFOs, use of either of these 
alternative approaches also satisfies the requirements set forth in 40 
CFR 412.4
(i) Background
    In the 2006 proposed rule and 2008 supplemental proposal, EPA 
discussed how the ``terms'' of a CAFO's NMP could be identified so as 
to address the nine minimum required elements in 40 CFR 
122.42(e)(1)(i)-(ix)) and 412.4(c) (for Large CAFOs, as applicable).
    The 2006 proposed rule preamble identified a number of factors that 
are necessary to the development of an NMP and discussed the need to 
allow a CAFO some flexibility in managing its operation. 71 FR 37,753-
55. With respect to portions of the NMP that would be incorporated as 
permit terms, the Agency also proposed regulatory language for 
accommodating changes to the NMP that involve changes to the terms 
during the permit period. 71 FR 37,756.
    EPA received many comments on the NMP issues highlighted in the 
2006 proposed rule preamble concerning the complexity associated with 
nutrient management planning, particularly with respect to land 
application, and seeking clarification of what constitutes the terms of 
the NMP. In particular, commenters sought clarification for terms 
regarding rates of application, given the complexity of factors used to 
determine rates of application and the dynamics associated with such 
factors.
    In light of these concerns, EPA in March 2008, issued a 
supplemental proposal that proposed what elements of the NMP would be 
terms of the NMP that would be required to be included as enforceable 
terms of a CAFO's NPDES permit. EPA received many comments on the 
supplemental proposal that identified the need for some further 
revisions to EPA's proposed approach concerning the terms of the NMP.
(ii) Terms of the NMP To Be Included in the Permit
    In this final rule, EPA is promulgating 40 CFR 122.42(e)(5) to 
identify the minimum terms of an NMP to be included in a CAFO's NPDES 
permit as enforceable requirements of the permit. Paragraph (e)(5) 
establishes that any permit issued to a CAFO must require the CAFO to 
comply with the terms of the CAFO's site-specific nutrient management 
plan.
    Paragraph (e)(5) states that the terms of the NMP ``are the 
information, protocols, best management practices, and other 
conditions'' identified in a CAFO's nutrient management plan and 
determined by the permitting authority to be necessary to meet the 
requirements of 40 CFR 122.42(e)(1). For Large CAFOs subject to the 
land application requirements of the effluent limitations guideline, 
the terms would include the best management practices necessary to meet 
the requirements of 40 CFR 412.4(c) in addition to the requirements of 
40 CFR part 122. This requirement is thus broadly applicable to all of 
the measures required to be included in a CAFO's NMP. EPA believes that 
this clarification should address the concerns of some commenters that 
the proposed terms of the NMP were limited to land application 
requirements only.
    The ``information, protocols, best management practices, and other 
conditions'' that constitute the terms of a CAFO's NMP include what the 
CAFO operator would be required to do to properly implement its NMP and 
determinative conditions upon which such actions are based. For 
example, both the structural design capacity necessary to satisfy the 
storage requirement of 40 CFR 122.42(e)(1)(i) and the associated 
operational and maintenance conditions necessary to ensure adequate 
storage, would be considered terms of the NMP. Likewise, the terms of 
the NMP would need to ensure, for example, proper management of 
mortalities and diversion of clean water. However, the number of 
animals confined would not necessarily need to be a term of the NMP 
because a CAFO operator would be required to properly operate and 
maintain the CAFO's storage facilities regardless of the number of 
animals or the volume of manure, litter, or process wastewater 
generated.
    Some commenters asserted that the entire NMP should be included in 
or expressly referenced by the permit and that all the elements of a 
CAFO's NMP must be included in a CAFO's NPDES permit so as to ensure 
that the permit requires the CAFO to comply with every discharge 
reduction or prevention measure in its NMP. These commenters disagreed 
with EPA's interpretation of Waterkeeper and felt that the 2006 
proposed rule put forth a more narrow meaning of the word ``terms'' 
than intended by the court. They also felt that the proposed rule 
provided the permitting authority too much discretion for determining 
what constitutes the ``terms'' of the NMP.
    The Agency agrees that the enforceable terms of the NMP must be 
clear so as to provide notice, both to the operator and to the public, 
about what is enforceable and to ensure compliance with the discharge 
reduction and prevention measures in the NMP. However, EPA does not 
agree that the all of the information in the NMP constitutes 
enforceable terms. By establishing the information, protocols, best 
management practices, and other conditions or activities necessary to 
meet the requirements of 40 CFR part 122 and part 412, this rule 
ensures that effluent limitations in the permit will be fully 
implemented, consistent with the NPDES regulations, the effluent 
guidelines, and the Waterkeeper decision. In addition, this approach 
preserves NMPs as comprehensive management tools used to guide a wide 
range of practices regarding nutrient production, storage, and use. 
Regarding the degree of discretion afforded to the Director, the 
requirements of this final

[[Page 70444]]

rule concerning terms of the NMP and the opportunity for public review 
of the full NMP together with the draft terms of the NMP to be 
incorporated into the permit provides a check on the exercise of that 
discretion.
    Moreover, whether the NMP has been properly developed, whether the 
information in the NMP is accurate, and whether calculations are 
correct and consistent with applicable requirements are issues which 
are properly addressed when the NMP is reviewed by the Director and by 
the public. This is analogous to the types of calculations and data 
submitted in a permit application and found in the fact sheet that 
accompanies a draft NPDES permit for other types of permitted point 
sources.
    Other commenters observed that NMPs do not fit well in this 
regulatory context due to their design and the way in which they have 
been used by CAFO operators. Rather, they asserted that NMPs are 
developed to guide management decisions regarding nutrients and, by 
necessity, must remain flexible to address the many conditions that 
affect nutrient generation and management.
    The final rule allows for the incorporation of the key NMP terms in 
a regulatory context without overburdening the permitting process or 
completely recasting the NMP itself. As discussed above, the terms of 
the NMP include whatever is contained in the NMP that is necessary to 
ensure compliance with Sec.  122.42(e)(1) and, for Large CAFOs, 40 CFR 
412.4. Additional content of the NMP that is beyond the scope of 
compliance with those regulatory requirements would not be a term of 
the NMP.
    Some commenters on the 2006 proposed rule urged EPA to provide 
greater clarity, guidance, and certainty in the final rule on the 
meaning and significance of the distinction between the NMP and the 
``terms'' of the NMP. As proposed in the 2008 supplemental proposal, 
the final rule establishes more specific requirements for terms of the 
NMP applicable to CAFOs that land apply manure, litter, and process 
wastewater than were included in the proposed rule. For such CAFOs, 
paragraph (e)(5) includes as terms the fields available for land 
application, field-specific rates of application, and timing 
limitations for land application.
    As stated above, with respect to land application, the terms of 
every NMP must include the fields the CAFO plans to use for land 
application. The site-specific elements of the NMP can only be properly 
represented in the NMP by the inclusion of field-specific information 
that must be made available for review by the Director and for public 
review in determining, for example, the appropriate conservation 
practices and rates of application to be included in the plan and, 
ultimately, in the permit. Compliance with the permit during the period 
of coverage would require any new fields (i.e., fields not addressed 
specifically in the terms of the permit) to first be added to the NMP 
and the permit, in accordance with the requirements of 40 CFR 
122.42(e)(6), discussed below, before they could be used by the CAFO 
for land application. Similarly, as discussed in greater detail below, 
field-specific, crop-specific application rates would be terms of the 
NMP, as would certain factors needed to determine the rates. However, 
background information that is fixed and unchangeable, such as actual 
historic yields used in the development of an NMP, while important for 
determining rates of application, would not need to be terms of the 
NMP. Such information is also relevant and important for public review 
of the draft permit, in order to ascertain that the terms relating to 
rates of application are correct and enforceable. In other words, this 
is an example of information necessary for the development of the NMP, 
but is not relevant for compliance or enforcement purposes.
    Finally, the terms of the NMP must include any timing limitations 
in the NMP that would make fields unavailable for land application at 
certain times or under certain conditions.\4\ Insofar as the NMP 
includes such limitations, the resulting limitations are terms of the 
NMP and thus enforceable.
---------------------------------------------------------------------------

    \4\ There are two types of ``timing'' referred to in this rule 
regarding land application. One type relates specifically to rates 
of application, i.e., the availability of nutrients for crop uptake 
based on the timing (and method) of application. There are also 
timing limitations, such as restrictions on applying under certain 
conditions, such as on saturated or frozen fields, or at certain 
times of the year. The latter types of timing restrictions are the 
subject of this paragraph.
---------------------------------------------------------------------------

(iii) Rates of Application
    40 CFR 122.42(e)(1)(viii) requires the nutrient management plan to 
include ``protocols to land apply manure, litter, or process wastewater 
in accordance with site-specific nutrient management practices that 
ensure appropriate agricultural utilization of the nutrients in the 
manure, litter, or process wastewater.'' As EPA noted in the 2006 
proposed rule, the Waterkeeper court focused on rates of application as 
perhaps the most important term of the NMP, in particular the 
provisions of the effluent limitations guidelines in 40 CFR 412.4(c), 
and emphasized their site-specific nature. 71 FR 37,753. In the 2008 
supplemental notice, the Agency proposed regulatory requirements to 
ensure that legally-enforceable field- and crop-specific application 
rates are included in the permit as part of the protocols for land 
application required to be in the NMP under Sec.  122.42(e)(1)(viii).
    This rule promulgates two alternative approaches for expressing the 
terms of the nutrient management plan with respect to rates of 
application. 40 CFR 122.42(2)(5)(i)-(ii). Each approach provides a 
means by which a CAFO may articulate in its NMP annual maximum rates of 
application of manure, litter, and process wastewater by field and crop 
for each year of permit coverage and identify the minimum required 
terms of the NMP specific to that approach. One approach expresses 
field-specific maximum rates of application in terms of the amount of 
nitrogen and phosphorus from manure, litter, and process wastewater 
allowed to be applied. This is called the ``linear approach.'' The 
other approach expresses the field-specific rate of application as a 
narrative rate prescribing how to calculate the amount of manure, 
litter, and process wastewater allowed to be applied. This is called 
the ``narrative rate approach.''
    Each of the approaches requires the CAFO operator to develop an NMP 
that projects for each field and for each year of permit coverage the 
crops to be planted, crop rotation, crop nutrient needs, expected 
yield, amount of nitrogen and phosphorus to be land applied, and 
projected amounts of manure, litter, and process wastewater to be 
applied. However, each approach is different in identifying which of 
these projections would be required to be ``terms of the NMP.'' In 
neither approach is the projected amount of manure, litter, and process 
wastewater to be land applied a term of the permit because these 
projected amounts must be adjusted at least once a year.
    Several commenters suggested that the NMP and permitting authority 
review of the NMP should focus on how agronomic rates are developed in 
the NMP rather than the specific rate determined in the NMP, based on 
the difficulty of developing accurate application rates for a five-year 
term and because agency review of specific application rates for each 
field would be too burdensome. As discussed above and in the 2006 
proposed rule, the Waterkeeper court focused on rates of application as 
perhaps the most important term of the NMP and emphasized their site-
specific nature.

[[Page 70445]]

To comply with the decision of the Waterkeeper court with regard to the 
terms of the NMP and to allow flexibility both for CAFO operators to 
develop NMPs in a manner appropriate for a particular operation as well 
as for States to develop regionally-appropriate program requirements 
that meet the needs of a particular agency, EPA in this final rule is 
providing two alternatives for expressing rates and determining the 
associated terms of the NMP.
    Rates of application are field-specific and are designed to ensure 
that crops receive sufficient nutrients to meet yield goals, while 
minimizing the amounts of nutrients that could be transported from the 
field. The discussion that follows summarizes the basic process for 
establishing rates of application in an NMP, in light of the comments 
received in the 2008 supplemental proposal, as an introduction to the 
specific discussion of the two approaches promulgated in this final 
rule.
    To develop appropriate land application rates for each field where 
land application will occur, CAFOs must identify the crops to be 
planted and the planned crop rotations, or other uses, and the nitrogen 
and phosphorus needs of these crops or other uses. The NMP also must 
identify the realistic yield expected from the crop or crops planted in 
the field, in order to calculate the proper amount of nutrients to 
apply. A crop's nutrient needs are generally determined in accordance 
with the nutrient recommendations for a given crop (or other planting, 
such as forage or pasture) and the per acre realistic yield goal for 
that crop. The State land grant university typically provides these 
values or the formulas for calculating these values. The realistic 
yield goal can also be based on historic field-specific yield data.
    Because a CAFO operator could plant more than one crop on a field 
in a given year, the plant available amount of nitrogen and phosphorus 
needs to be calculated with reference to the nutrient needs of all the 
crops to be planted on such field in a given year in order to be 
accurate. This includes accounting for other field uses, such as 
pasture and cover crops.
    A properly developed NMP must also evaluate the condition of the 
fields to be used for land application. A field-specific assessment 
based on soil test nutrient levels and other factors required by the 
technical standards established by the Director provides information 
needed to determine whether land application of manure is appropriate 
for a site. The capacity of the field for manure, litter, or process 
wastewater application generally depends on the capacity of the soil to 
retain phosphorus. The phrase ``outcome of the field-specific 
assessment of the potential for nitrogen and phosphorus transport from 
each field,'' as used in this rule, reflects the terminology typically 
associated with the use of the phosphorus index, which is one of three 
field-specific risk assessment methods discussed in NRCS conservation 
practice standard 590. However, in this final rule, EPA is using this 
phrase to reflect the results of whichever method is required by the 
technical standards established by the Director, including the soil 
test phosphorus method and the phosphorus threshold method.
    One commenter suggested that, for some States, it may be 
appropriate to require that the field-specific assessment of the 
potential for nitrogen and phosphorus transport be conducted on an 
annual basis. EPA recognizes that some States require, for example, use 
of a phosphorus index that factors into the calculated risk rating the 
amount of manure applied to the field in the previous year. EPA agrees 
that, for these States, it would be appropriate to require 
recalculation of the phosphorus index on an annual basis and 
anticipates that such States would include the appropriate requirements 
in technical standards, permits, or other requirements applicable to 
CAFOs. Furthermore, EPA encourages CAFO operators to reevaluate field-
specific assessments of the potential for nitrogen and phosphorus 
transport as frequently as necessary to ensure minimization of nutrient 
transport from each field.
    Ultimately, the purpose of the field-specific assessment of the 
potential for nitrogen and phosphorus transport is to determine the 
appropriate limiting nutrient for developing land application rates, 
i.e., whether phosphorus or nitrogen limits the amount of manure, 
litter, or process wastewater that can be applied and the degree to 
which the limiting nutrient restricts land application, or whether land 
application is to be avoided altogether. State technical standards 
typically allow nitrogen-based application rates on fields with a low 
phosphorus risk rating. For fields that have a moderate to very high 
phosphorus risk rating, State technical standards generally limit the 
amount of phosphorus that may be added to a field.
    In determining rates of application where phosphorus is the 
limiting nutrient, the amount of phosphorus that may be land applied is 
based on the annual phosphorus removal rate for each crop or other 
field use. In deciding how much manure may be land applied, the amount 
of plant available phosphorus already in the field is not deducted 
because State technical standards identify the rate of application 
based on the crop removal rate. Because soil levels tend to change 
incrementally, depending on the buffering capacity of the soil, and 
because a phosphorus-based application rate doesn't reduce the amount 
of phosphorus already in soil, phosphorus-based rates of application 
may remain relatively constant for a period of several years or longer, 
so long as the outcome of the assessment of phosphorus transport does 
not change during that time. However, any multi-year phosphorus 
application must be done in accordance with State technical standards.
    In determining rates of application where nitrogen is the limiting 
nutrient, the NMP must consider the total amount of plant available 
nitrogen for each crop from residual nitrogen already in the field and 
the nitrogen added for a particular field. Residual nitrogen is the 
nitrogen that remains from prior applications of manure, litter, 
process wastewater, or chemical fertilizer, or from other sources such 
as crop residues and nitrogen fixing legumes. The addition of nitrogen 
to a field includes application of chemical fertilizer as well as 
application of manure, litter, or process wastewater and other 
materials such as biosolids.
    Crediting for all residual nitrogen in the field that will be plant 
available, as a result of prior additions (e.g., crop residue, legume 
credits, and previous manure applications), should be done in 
accordance with the directions provided in the technical standards 
established by the Director (required for all permitted Large CAFOs). 
Since organic forms of nitrogen typically become plant available when 
they are converted to inorganic forms, such as nitrate and ammonium, 
crediting generally identifies the amount of organic nitrogen likely to 
be converted to inorganic forms that will be plant available. Credits 
are calculated using soil test results included in the NMP and 
projected applications of nitrogen from manure, litter, and process 
wastewater during intervening years, as well as other additions, 
including from crops (e.g., where crops are plowed under or residues 
are left on the field or where nitrogen-fixing legumes are grown), and 
other sources of nitrogen remaining on the field that would be plant 
available during the next growing season.
    EPA expects a complete NMP also to account for any other additions 
of plant available nutrients during the crop year,

[[Page 70446]]

such as chemical fertilizer, irrigation water (groundwater may have 
measurable concentrations of nutrients), and biosolids, where applied.
    The forms of nitrogen and phosphorus to be factored into 
calculations for rates of application are generally identified in the 
technical standards established by the Director or in other 
documentation referenced in the State's technical standards. Typically, 
the amount of plant available phosphorus is determined based on the 
amount of various forms of phosphate added to or present in the soil 
and the amount of organic phosphorus that will mineralize during the 
growing season. The amount of plant available nitrogen is based on the 
amount of inorganic nitrogen (e.g., nitrate and ammonium-nitrogen) 
added to or present in the soil and the amount of organic nitrogen that 
will mineralize during the growing season. The amount of plant 
available nitrogen also depends on losses due to volatilization, which 
is calculated using the nitrogen volatilization rate associated with 
the source of nutrients and the timing and method of land application. 
As previously discussed, it is the forms of nitrogen and phosphorus 
that will be available to a given crop that are most relevant in 
determining rates of application. In this final rule, the appropriate 
forms of nitrogen and phosphorus to be factored into these calculations 
must be expressed in chemical forms determined to be acceptable by the 
Director, such as in the permit or in the technical standards 
established by the Director.
    As discussed above, the NMP must include calculations projecting 
for the length of the permit term the amount of manure, litter, or 
process wastewater, in tons or gallons, to be land applied in order to 
meet, but not exceed, crop nutrient needs (after considering residual 
nutrients and other additions of nutrients and results of the most 
recent manure test) based on the outcome of the field-specific 
assessment of the potential for nitrogen and phosphorus transport, 
i.e., whether application rates will be limited by nitrogen or 
phosphorus. These calculations must also take into account, with 
respect to each crop to be grown or other agricultural use, the source 
and form of nutrients to be land applied; the method of application of 
manure, litter, and process wastewater; and the timing of when 
application will occur. Although a properly developed NMP addresses all 
of these factors, some operators may have multiple sources of manure, 
litter, or process wastewater and may need to make the determination as 
to which source to draw from for land application to a particular field 
in a given year at some point in time after the NMP has been developed. 
The method of application depends on the source and form of manure, 
litter, or process wastewater; the location of a particular field and 
the equipment available for such field; the soil nutrient status; and 
the crop to be planted. For example, wastewater could be spray-
irrigated, otherwise surface applied, or injected, whereas poultry 
litter is most likely to be surface applied by a manure spreader.
    Whereas one CAFO operator may wish to follow the planned sequence 
of steps for planting crops and applying manure, litter, and process 
wastewater described in the NMP submitted to the Director, another 
operator may want or need to vary from that linear sequence of events, 
due to choices made in the course of normal operations, or in response 
to events or circumstances beyond the CAFO's control, such as weather, 
crop failure, or market conditions. EPA has addressed this concern in 
this final rule by including two alternative approaches for determining 
the terms of an NMP, as discussed below.
    As indicated above, EPA is promulgating two approaches for defining 
the terms of an NMP for rates of application, rather than the three 
approaches that were proposed in the 2008 supplemental notice. While a 
number of commenters encouraged EPA to include all three proposed 
approaches in the final rule to allow operators the greatest number of 
alternative options, many commenters were critical of the matrix 
approach. Some commenters suggested EPA should finalize only the 
narrative rate approach because they felt that the linear and matrix 
approaches were too inflexible to be useful. Others suggested that the 
inclusion of three approaches would create a program that is too 
complicated for permittees, permitting authorities, and the public. One 
commenter stated that the matrix approach fails to fully address the 
complexity of the decision-making process facing the CAFO operator. 
Several industry commenters found the matrix approach to be less 
flexible than necessary and overly burdensome. Environmental group 
commenters found the matrix approach to be too rigid to ensure 
protection of water quality and not inclusive of critical information. 
In reviewing the comments, EPA agrees that the matrix approach does not 
adequately address the complexity of the nutrient management decisions 
to be made by the CAFO operator and that it could result in over-
application of manure, litter, or process wastewater. In addition, EPA 
agrees that having three approaches to identifying terms of the NMP 
with respect to application rates is unduly complicated and would be 
unnecessarily burdensome. Moreover, EPA believes that the improvements 
and clarifications to the linear and narrative rate approaches 
promulgated in this final rule make inclusion of the matrix approach 
unnecessary. In considering comments that criticized the inability of 
the matrix approach, as proposed, to more directly address the complex 
dynamics relating application rates to crop needs, EPA would have 
needed to make adjustments that would have made the matrix approach 
either more like the linear approach or more like the narrative rate 
approach. As a result, and in consideration of comments stating that 
including three approaches is unnecessary and burdensome, EPA has 
decided to eliminate the matrix approach as an option for identifying 
the terms of the NMP for rates of application.
    Some industry commenters indicated that CAFOs should be allowed to 
choose from either approach as long as they maintain the same approach 
for the five-year permit term while another industry commenter stated 
that CAFOs should be allowed to switch approaches during the permit 
term. This final rule does not address the possibility of switching 
approaches during a permit term. It is up to the discretion of the 
Director whether such a change would be allowed. However, because each 
approach differs in what are the terms of the permit, switching 
approaches during the permit term would require a permit modification 
to include the terms of the NMP associated with the selected approach 
into the permit.
    Under both of the approaches, the terms of the NMP are required to 
include specific factors used for the development of rates of 
application. These include:
     The outcome of the field-specific assessment of the 
potential for nitrogen and phosphorus transport from each field;
     The crop or crops to be planted in each field or any other 
uses such as pasture or fallow fields;
     The realistic yield goal for each crop or use identified 
for each field; and
     The nitrogen and phosphorus recommendations from sources 
specified by the Director for each crop or use identified for each 
field.
    Both of the approaches account for other information necessary for 
determining the amount of manure, litter, and process wastewater to be 
land applied. This information relates to: (1)

[[Page 70447]]

Credits for residual nitrogen available in each successive year during 
the five year term of the permit; (2) consideration of any multi-year 
phosphorus application; (3) accounting for additions of commercial 
fertilizer and other additions of nitrogen and phosphorus during each 
successive year; (4) the form (liquid, solid) and source (e.g., lagoon, 
compost, process wastewater) of the material to be land applied; (5) 
nitrogen and phosphorus content of the manure, litter, or process 
wastewater; (6) timing of application; and (7) method of application 
(e.g., spreading, spray, injection). However, the two approaches differ 
in the way they incorporate this information in expressing the rates of 
application as terms of the NMP. The following sections of the preamble 
describe the two approaches and how each approach accounts for this 
information.
(A) Linear Approach--Rates Expressed in Pounds of Nitrogen and 
Phosphorus From Manure, Litter, and Process Wastewater
    The first approach (see 40 CFR 122.42(e)(5)(i)) allows the CAFO to 
express rates of application as pounds of nitrogen and phosphorus from 
manure or litter, and process wastewater. The terms of the NMP include 
maximum application rates for each year of permit coverage, for each 
crop identified in the NMP, in pounds per acre, per year, for each 
field to be used for land application. In addition, the terms of the 
NMP include the following factors:
     The outcome of the field-specific assessment of the 
potential for nitrogen and phosphorus transport from each field;
     The crop or crops to be planted in each field or any other 
uses such as pasture or fallow fields;
     The realistic yield goal for each crop or use identified 
for each field;
     The nitrogen and phosphorus recommendations from sources 
specified by the Director for each crop or use identified for each 
field;
     Credits for all nitrogen in the field that will be plant 
available;
     Consideration of multi-year phosphorus application;
     Accounting for all other additions of plant available 
nitrogen and phosphorus to the field;
     The form and source of manure, litter, and process 
wastewater to be land applied; and
     The timing and method of land application.
    The terms also include the methodology by which the NMP accounts 
for the amount of nitrogen and phosphorus in the manure, litter, and 
process wastewater to be applied.
    This approach is considered a ``linear'' approach because it is 
based on the use of only those crops included in the planned crop 
rotations in the NMP; the amounts of nitrogen and phosphorus from 
manure, litter, and process wastewater to be land applied according to 
the planned schedule for land application (including source and method 
and timing of application); and the projected values for plant 
available nitrogen and phosphorus from other sources. Under this 
approach, a single set of field-specific rates of application would be 
established, based on the predicted sequence of activities the CAFO 
plans to follow in implementing its NMP, and a CAFO would be required 
to follow the sequence identified in the NMP for each field-specific 
crop rotation and each planned step for land application of manure, 
litter, or process wastewater.
    Under this linear approach, a CAFO must land apply manure, litter, 
and process wastewater in amounts that will result in application of no 
more than the amounts of nitrogen and phosphorus from manure, litter, 
and process wastewater specified for each field in the NMP, following 
the schedule and the methods of application described in the NMP. When 
applying manure, litter, and process wastewater, CAFOs will need to 
take into account manure test results, including for Large CAFOs the 
annual manure test results required by the 2003 final rule, so as to 
not exceed the nutrient needs of the crops. Medium and small CAFOs must 
apply manure, litter, and process wastewater consistent with Best 
Professional Judgment (BPJ)-based requirements established in the 
permit for accounting for the nutrient content of the manure. Large 
CAFOs using the linear approach must calculate the maximum amount of 
manure, litter, and process wastewater to be land applied at least once 
each year using the results of the most recent representative manure, 
litter, and process wastewater tests for nitrogen and phosphorus taken 
within 12 months of the date of land application.
    The methodology used for translating the amounts of nutrients in 
pounds into the amount of manure, litter, and process wastewater to be 
land applied, in tons or gallons, is a term in the linear approach. 
This includes incorporation of manure test results in determining such 
rates.
    The final rule differs from the proposed linear approach with 
respect to the expression of the rates of application. EPA proposed 
that application rates in the linear approach be expressed in terms of 
tons or gallons of manure, litter, and process wastewater. Several 
commenters stated that the application rate under the linear approach 
should be expressed in terms of pounds of nitrogen and phosphorus 
rather than tons and gallons of manure and wastewater. The commenters 
felt that this approach would more accurately account for the actual 
nutrient content of the manure and wastewater being applied. EPA agrees 
with the commenters and has changed the linear approach accordingly to 
address this concern. The key advantage of this change is that it 
ensures that the results of manure testing, which for Large CAFOs is 
required to be done annually, are used in determining the actual amount 
of manure, litter, and process wastewater to be applied. EPA believes 
that expressing the rate in terms of pounds of nitrogen and phosphorus 
from manure, litter, and process wastewater provides greater 
environmental protection by requiring operators to adjust the actual 
amount of manure, litter, and process wastewater applied based on the 
most current manure nutrient test results.
    The utility of this approach, nevertheless, hinges on the CAFO 
making accurate predictions in the NMP that are not disrupted by 
changes to the CAFO's operation or by circumstances beyond the control 
of the CAFO operator. Any changes to the terms of the NMP would 
constitute a change to the terms of the permit, which would require a 
permit modification. See discussion in section III.C.3(e) of this 
preamble, ``Changes to a Permitted CAFO's Nutrient Management Plan.'' 
For example, any change to the planned crop sequence, such as the 
addition of a second crop to a field, requires a permit modification.
    On the other hand, the advantage of this approach is its relative 
simplicity for CAFOs with predictable crops and land application. The 
linear approach would be particularly suitable for operations that 
consistently plant one crop or two crops in rotation on the same 
fields, using the same source and form of manure, litter, or process 
wastewater, and that land apply on a regular annual schedule using the 
same application method(s).
    EPA notes that even under the linear approach, operators may 
provide themselves some flexibility by specifying more than one field-
specific crop rotation plan in the NMP, with application rates of 
nitrogen or phosphorus specified for each alternative plan for 
inclusion in the permit. This might be practical for operators who are 
reasonably confident

[[Page 70448]]

that they will follow one of two or three potential crop rotations. EPA 
is promulgating the other approach for operators seeking a greater 
degree of flexibility.
(B) Narrative Rate Approach--Rates Derived From Total Amounts of Plant 
Available Nitrogen and Phosphorus
    This final rule includes a second approach that would allow rates 
of application to be expressed as a narrative rate that includes the 
total amount of plant available nutrients from all sources combined 
with a specific, quantitative method for calculating the amount, in 
tons or gallons, of manure, litter, and process wastewater allowed to 
be land applied. (See 40 CFR 122.42(e)(5)(ii).) Unlike the linear 
approach, in this quantitative narrative rate approach, the terms of 
the NMP include the maximum amounts of nitrogen and phosphorus from all 
sources of nutrients for each crop or other field use identified in the 
NMP, in chemical forms determined to be acceptable to the Director, in 
pounds per acre, for each field.
    As required at 40 CFR 122.42(e)(5)(ii)(A), the narrative rate 
approach also includes as terms the following four factors:
     The outcome of the field-specific assessment of the 
potential for nitrogen and phosphorus transport from each field;
     The crop or crops to be planted in each field or any other 
uses such as pasture or fallow fields;
     The realistic yield goal for each crop or use identified 
for each field; and
     The nitrogen and phosphorus recommendations from sources 
specified by the Director for each crop or use identified for each 
field.
    In addition, this narrative rate approach includes as a term of the 
NMP the methodology by which the NMP accounts for certain factors when 
calculating the amounts of manure, litter, and process wastewater to be 
land applied. A CAFO using the narrative rate approach is required to 
apply in accordance with the resulting calculations. This final rule 
requires the methodology in NMPs developed using this approach to 
account for the following factors:
     Results of soil tests conducted in accordance with 
protocols identified in the nutrient management plan, as required by 40 
CFR 122.42 (e)(1)(vii);
     Credits for all nitrogen in the field that will be plant 
available;
     The amount of nitrogen and phosphorus in the manure, 
litter, and process wastewater to be applied;
     Consideration of multi-year phosphorus application;
     All other additions of plant available nitrogen and 
phosphorus to the field;
     The form and source of manure, litter, and process 
wastewater;
     The timing and method of land application; and
     Volatilization of nitrogen and mineralization of organic 
nitrogen.
    The factors listed above are not themselves required to be terms in 
the narrative rate approach, but the methodology used to account for 
them in the CAFO's permit is a term. Thus, the CAFO operator will be 
bound by the methodology and the way in which these factors must be 
accounted for in calculating the actual amount of manure, litter, or 
process wastewater allowed to be applied to the field. The terms of the 
NMP under this approach do not include the amount of nitrogen and 
phosphorus in the manure, litter, or process wastewater allowed to be 
land-applied as set forth in the NMP, but they do include the 
methodology prescribed in the NMP for calculating these amounts. And 
while the terms of the NMP do not include the predicted source, form, 
timing, and method of application of manure, litter, or process 
wastewater set forth in the NMP, they include the methodology that 
accounts for these factors in determining the amount of manure, litter, 
or process wastewater allowed to be applied. This allows the actual 
inputs and results for these factors to be something other than what 
was projected in the NMP during the period of permit coverage, using 
the methodology, while ensuring that the CAFO meets the requirements of 
40 CFR 122.42(e)(1) and, for Large CAFOs, 40 CFR 412.4, by applying in 
accordance with the methodology and other terms of the NMP.
    This approach requires that the CAFO apply manure, litter, or 
process wastewater according to the results of this calculated amount. 
For example, if the NMP projected an amount of manure to be applied 
based on incorporation of solid manure, the operator could apply 
process wastewater from the lagoon by spraying the field instead. In 
this example, the methodology must account for factors of form, source, 
and method of application such that these inputs and results can be 
other than what was projected in the NMP and the amount of manure 
allowed to be applied will be predictably and accurately calculated. In 
other words, the methodology and requirement that application be in 
accordance with the rate calculated using that methodology are 
enforceable term that must be complied with at the time of determining 
how much, from which source, in what form is allowed to be applied to 
the field using which method of application.
    40 CFR 122.42(e)(5)(ii)(C) clarifies that the amount of manure, 
litter, and process wastewater to be applied as projected in the NMP 
submitted with the permit application or NOI is not a term of the NMP 
under the narrative rate approach. As explained above, the amount of 
manure, litter, and process wastewater is to be calculated using the 
methodology included in the NMP and based on actual amounts of plant 
available nitrogen and phosphorus from all sources at the time of land 
application. Other projections that must be included in the NMP but are 
not terms are the CAFO's planned crop rotations for each field; credits 
for all nitrogen in the field that will be plant available; 
consideration of multi-year phosphorus application; accounting for all 
other additions of plant available nitrogen and phosphorus to the 
field; the predicted form, source, and method of application of manure, 
litter, and process wastewater for each crop; and the timing of 
application for each field, insofar as it concerns the calculation of 
rates of application (permitting authorities may establish in permits 
or technical standards for nutrient management land application timing 
restrictions, such as prohibitions on land application to frozen or 
saturated ground, that would be permit terms).\5\
---------------------------------------------------------------------------

    \5\ See footnote 4.
---------------------------------------------------------------------------

    As specified at 40 CFR 122.42(e)(5)(ii)(B), NMPs for which terms 
are identified using the narrative rate approach may also include 
alternative crops not included in the planned rotation in the NMP, so 
long as the NMP includes for each crop realistic yield goals, nitrogen 
and phosphorus recommendations from sources specified by the Director, 
and maximum amounts of nitrogen and phosphorus from all sources. The 
terms and factors associated with alternative crops would be the same 
as the terms and factors required for the crops included in the planned 
rotation in the NMP.
    EPA received several comments on the proposed terms and factors for 
the narrative rate approach. Commenters requested that EPA refer only 
to ``plant available'' nutrients in the narrative rate approach. Some 
confusion may have been caused by EPA's reference in the preamble to 
the 2008 supplemental proposal to the ``maximum amount of total 
nitrogen and phosphorus'' with regard to expression of the application 
rate under the narrative approach. This

[[Page 70449]]

language was intended to refer to the total amounts of nitrogen and 
phosphorus, rather than referring to a specific chemical form (``total 
nitrogen'' or ``total phosphorus''). This has been corrected in this 
final rule and preamble by removing the word ``total.'' The final rule 
refers to plant available forms of nutrients with regard to determining 
credits for nitrogen in the field and accounting for all other 
additions of plant available nitrogen and phosphorus to the field. 
Otherwise, the rule requires expression of application rates in 
chemical forms determined to be acceptable to the Director, such as 
indicated in the technical standards established by the Director, or in 
the permit.
    One commenter suggested that crop yields be included as a factor 
under the narrative rate approach and that yield goals should be 
adjusted for operations that consistently fail to meet them. This final 
rule includes realistic yield goals as a term under both approaches. 
Realistic yield goals will be included in the NMP and, therefore, will 
be subject to review by the permitting authority and the public. In 
addition, States may establish in their technical standards criteria 
for deriving realistic yield goals including criteria for adjusting 
yield goals based on actual crop yields. EPA believes that this is 
sufficient to ensure that the yield goals used to calculate application 
rates in NMPs are appropriate. Upon subsequent permit issuance, the 
public will have the opportunity to review yield goals in light of 
actual yields reported by the CAFO in its annual reports (see 40 CFR 
122.42(e)(4)(viii)).
    The narrative rate approach would eliminate certain issues 
associated with a five-year planning cycle previously discussed in 
connection with the linear approach presented above. A key difference 
of the narrative rate approach, is that it would require application 
rates for manure, litter, and process wastewater to be recalculated at 
least annually using the methodology specified in the NMP (40 CFR 
122.42(e)(5)(ii)(D)). Unlike the linear approach, the narrative rate 
approach allows CAFOs that may need to adjust their rates of 
application of manure, litter, and process wastewater due to changes in 
soil levels of nitrogen and phosphorus to do so without requiring the 
permit to be modified. Therefore, it is important to ensure that the 
actual changes in soil levels of plant available nitrogen and 
phosphorus are taken into account, rather than relying on five-year 
projections of fluctuations provided in the NMP.
    The narrative rate approach requires an annual determination of 
soil levels of nitrogen and phosphorus. For nitrogen, the annual 
determination must include a concurrent calculation of nitrogen that 
will be plant available consistent with the methodology specified in 
the NMP. As described above, this methodology must account for the 
factors that would affect soil nitrogen levels on an annual basis such 
as the form and timing of previous land application(s); the actual 
amount of nitrogen in the manure, litter, and process wastewater 
previously applied; and volatilization and mineralization rates for 
nitrogen. For phosphorus, the annual determination must include the 
results of the most recent soil test conducted in accordance with 
sampling requirements approved by the Director. As in the case of other 
technical determinations to be made by the Director as part of this 
final rule, the Director's determination concerning sampling 
requirements may be made in the technical standards established by the 
Director, in the permit, or by an equivalent determination made 
elsewhere. Many States require sampling to be done every two or three 
years, for most conditions. Some require more frequent sampling 
generally, and others require more frequent sampling at higher 
concentrations of soil test phosphorus. If sampling is conducted more 
frequently than required by the Director, then the determination must 
be based on the results of the most recent test.
    EPA proposed that CAFOs using the narrative rate approach would be 
required to test soils annually for nutrient content and that these 
data be used in recalculating the amount of manure, litter, and process 
wastewater to apply annually. Many commenters opposed annual soil 
testing for phosphorus. These commenters stated that annual testing is 
inconsistent with State land grant university guidance, is unnecessary 
because phosphorus levels in the soil do not change significantly from 
year to year and that such testing would be cost-prohibitive for many 
operations. A number of commenters suggested alternative testing 
frequencies ranging from three to five years. Several commenters 
suggested that annual phosphorus testing be required only where the 
soil phosphorus level is already high or previous applications have 
exceeded the crop phosphorus removal rate (such as where manure is 
applied at a nitrogen-based rate). A few commenters asked EPA to 
clarify that annual soil testing only applies to fields that will 
receive manure in the year the testing is performed. One commenter 
indicated that, under certain circumstances, manure nutrient testing 
should be required more frequently than annually. Although the 
supplemental proposal did not specifically propose to require annual 
soil nitrogen testing, several commenters indicated that such testing 
should not be required, citing limitations in accuracy and 
effectiveness of the testing methods currently available. EPA agrees 
with commenters that, in a number of States, annual soil testing for 
phosphorus has been determined to be unnecessary. EPA recognizes that 
soil test requirements vary from State to State, and may include 
testing for nitrogen as well as phosphorus. Based on these responses 
from a range of commenters and the various suggested alternatives, EPA 
has replaced the proposed annual soil testing requirement for the 
narrative rate approach with the requirement that an annual 
determination of soil nutrient levels be based on current data and 
calculations as described above to support ``real time'' calculation of 
appropriate application rates. This final rule does not specify a 
minimum frequency for soil phosphorus testing, but instead requires 
CAFOs to include the results of the most recent soil tests for 
phosphorus conducted in accordance with soil testing requirements 
approved by the Director.
    The annual recalculation of the amount of manure, litter, and 
process wastewater allowed to be applied must also rely on the results 
of the most recent representative manure, litter, and process 
wastewater tests taken within 12 months of the date of land 
application. These data along with the annual determination of soil 
levels of nitrogen and phosphorus must be used to calculate, in real 
time, the amount of manure, litter, and process wastewater to be 
applied to supply the remaining nitrogen and phosphorus needed for the 
actual crop being planted on the field. Commenters requested that the 
narrative rate approach express application rates in terms of pounds of 
nutrients rather than tons of manure to allow appropriate utilization 
of nutrients in manure whose nutrient content varies over time. In 
practice, the narrative rate approach requires that amounts of manure, 
litter, and process wastewater to be land applied be calculated first 
in pounds of nutrients and then translated into tons or gallons of 
manure, litter, and process wastewater using current manure nutrient 
analyses. The information presented to the public in the CAFO's NMP 
will include the projected amounts for the planned crop rotation, in 
tons or gallons of manure,

[[Page 70450]]

litter, or process wastewater, since this is the endpoint of the 
calculation of the amount to be applied. As discussed above, these 
projected amounts are not themselves terms, since they will need to be 
recalculated each year based on updated information.
    One commenter suggested that EPA specify that manure tests and 
plant tissue tests also be used in the annual rate recalculation. As 
described above, this final rule does require consideration of recent 
manure test results in annual application rate recalculations. Plant 
tissue testing may be an effective tool for determining nitrogen 
deficiencies (and the need for supplemental nitrogen application), as 
well as for determining excess nitrogen. However, plant tissue tests 
are typically taken after manure applications have been made on a field 
and thus are unavailable at the time the operator is determining rates 
of application. A CAFO's NMP may include plant tissue testing as part 
of the CAFO's methodology so long as it is done consistently with State 
technical standards.
    In addition to accounting for the crop and field information, the 
methodology for the annual recalculation of the amount of manure, 
litter, and process wastewater to apply must account for a number of 
other variables, including the form and source of the manure, litter, 
and process wastewater and the timing and method of application, as 
described above. The operator may not apply more than the maximum 
amount of nitrogen and phosphorus calculated using the methodology.
    Under this approach, the NMP will include planned crop rotations 
for each field and corresponding projected amounts, in tons or gallons, 
of manure, litter, and process wastewater to be applied, including all 
of the calculations for determining such projected amounts, for the 
period of permit coverage. This will give the permitting authority and 
the public an opportunity to review, prior to permit issuance, the 
adequacy of the CAFO's methodology and the way the CAFO uses the 
methodology to calculate the appropriate amount of manure, litter, and 
process wastewater to be applied, based on the operator's planned crop 
rotation at the time of permit issuance. Again, these planned crop 
rotations and projected amounts are not terms, as they will need to be 
recalculated each year based on updated information; however these 
projections will allow the public to see how the methodology (which is 
a term) is applied to a projected set of facts to calculate the amounts 
to be land applied.
    Several commenters expressed concerns about the enforceability of 
the narrative rate approach, citing the lack of an objective rate and 
public availability of supporting information used to calculate the 
rate. The narrative rate approach requires the CAFO to recalculate the 
amount projected in the NMP of manure, litter, and process wastewater 
to be land applied, using the methodology in the NMP, at least once a 
year, throughout the period of permit coverage. In recalculating these 
amounts, a CAFO will be required to use concurrent calculations of 
credits for all plant available nitrogen in the field and the results 
of the most recent soil tests for phosphorus in the field. The CAFO 
will then calculate the maximum amount of nitrogen and phosphorus from 
manure, litter, and process wastewater allowed to be applied, as a 
portion of the total amount of nitrogen and phosphorus from all 
sources, using the methodology in the NMP. Under the narrative rate 
approach, the CAFO must use the methodology specified in the NMP (which 
is a term) to account for the amount of nitrogen and phosphorus in the 
manure, litter, and process wastewater to be applied when calculating 
the maximum amount of manure, litter, and process wastewater allowed to 
be applied. To ensure that such recalculations are made available to 
the Director and the public, the recalculations and the new data from 
which they are derived are required to be reported in the CAFO's annual 
report for the previous twelve months. In other words, the rate of 
application would be an objective, enforceable rate, because the permit 
will specify the methodology required for calculating the amount of 
manure, litter, and process wastewater allowed to be applied, certain 
values or sources of information required to be used in the 
methodology, and will limit the total amount of nitrogen and phosphorus 
from all sources for each crop. Failure to comply with the rate 
established under the permit would be a violation of the permit, and 
the Director and the public will be able to determine whether the rate 
was complied with from the annual report.
    Most commenters who commented on the narrative rate approach were 
supportive of the approach in terms of its degree of flexibility. Some 
commenters suggested that it should be the only approach adopted in the 
final rule. EPA believes that the flexibility of the narrative rate 
approach will reduce the burden on permitting authorities and CAFO 
operators by decreasing the number of substantial changes to the permit 
which require public notice and comment, arising from changes to the 
CAFO's crop rotations, while ensuring that all effluent limitations 
applicable to a permitted CAFO are incorporated as terms of the permit, 
as required by the Waterkeeper decision.
    As many commenters on the 2006 proposed rule pointed out and EPA 
recognizes, there may be changes in field conditions or practices at a 
CAFO, including, for example, those that alter the projected levels of 
plant available nitrogen and phosphorus in the soil or in the manure 
over the period of permit coverage. Such changes introduce some 
uncertainty in setting application rates for five years as enforceable 
terms of the permit. The narrative rate approach is designed to 
accommodate these concerns by allowing a CAFO to compensate for changes 
in soil levels of plant available nutrients, in manure nutrient 
content, or in the timing and method of application, by adjusting the 
application rates accordingly without the need for a permit 
modification. However, the operator will be limited to the total crop-
specific amount of nitrogen and phosphorus from all sources and will 
have to adhere to a methodology that establishes the way in which such 
rates are to be calculated. Thus, in the second and later years of the 
permit term, this approach will provide an accurate and verifiable 
means of achieving realistic production goals while minimizing 
transport of phosphorus and nitrogen from the field. This will help 
CAFOs avoid the possibility of over-application of nitrogen or 
phosphorus because of increased levels of nutrients in the soil, 
compared to what was projected at the time of permit issuance, and, 
conversely, the possibility of failing to meet crop agronomic needs due 
to under-application of nitrogen or phosphorus.
(d) Process for Incorporating Terms of the Nutrient Management Plan 
Into a General Permit
    The Agency is also promulgating procedural requirements for 
incorporating the terms of the NMP into an NPDES general permit, in new 
paragraph 40 CFR 122.23(h)(1).
    Once the processes for publicly reviewing the NMP and the terms of 
the NMP have been completed, the Director must address all significant 
comments raised and make a final decision whether to grant coverage 
under a general permit. As necessary, the Director will require a CAFO 
owner or operator to revise their NMP to address issues raised during 
the review process. Once the Director determines that the

[[Page 70451]]

process for the development of a CAFO's NMP is complete, the Director 
must make the final decision whether to grant permit coverage to the 
CAFO under the general permit. If coverage is granted, the Director 
must incorporate the relevant terms of the NMP into the general permit 
(as described later) and inform the CAFO owner or operator and the 
public that coverage has been authorized and of the applicable terms 
and conditions of the permit. Once a CAFO obtains authorization to 
discharge under an NPDES permit, the CAFO must implement the terms and 
conditions of the nutrient management plan as incorporated into the 
permit, as of the date of permit coverage authorization.
    The preamble to the 2006 proposed rule discussed and requested 
comment on approaches for the Director to identify the terms of the NMP 
to be incorporated into the permit. These options ranged from attaching 
the entire NMP to the permit to identifying specific elements to be 
included in the permit as terms. Based on comments received on the 
proposed rule, EPA is specifying certain elements of NMPs with respect 
to land application as ``terms of the NMP'' that must be incorporated 
into the permit. EPA is not, however, requiring a single approach 
whereby the terms are made part of the permit, leaving to the Director 
the discretion to decide whether, for example, to attach the entire NMP 
to the permit and require compliance with the terms of the NMP or to 
specify the terms of the NMP and specifically identify each of them in 
the permit. Under this final rule, incorporation of the terms of a 
particular CAFO's NMP into a general permit is not a permit 
modification subject to 40 CFR 122.62. Rather, it is an extension of 
the CAFO general permitting process itself. As discussed above, EPA 
intends the process proposed in 40 CFR 122.23(h) to generally parallel 
the procedures in 40 CFR part 124.
    Commenters supported an approach allowing a permitting authority to 
incorporate the entire NMP as a condition of the permit without 
distinguishing between the NMP and the ``terms'' of the NMP. Some 
supported attaching an NMP to the permit or general permit and 
requiring that the CAFO implement that NMP as a permit condition. As 
discussed above, this rule requires that a permit include the terms of 
a site-specific NMP. However, EPA is not prescribing the manner in 
which this incorporation takes place. The permitting authority may 
satisfy this requirement by incorporating a CAFO's NMP by reference 
into the permit or as described in the preamble to the 2006 proposed 
rule, the permitting authority may extract the terms of the NMP and 
attach them to the permit. Either way, the terms of the NMP are 
enforceable terms of the NPDES permit.
    Other commenters sought greater State discretion in implementing 
NMP requirements as permit conditions. These commenters recognized the 
importance of implementing the NMP provisions but did not want this 
rule to interfere with effective existing State approaches. In 
addition, these commenters wanted to preserve the administrative 
advantages of using general permits.
    This rule provides some State discretion by allowing permitting 
authorities to determine which NMP provisions to include as terms of 
the permit. The rule specifies what must be included at a minimum in 
the permit as terms of the NMP. However, States have the authority to 
adopt additional or more stringent requirements, under CWA section 510.
(e) Changes to a Permitted CAFO's Nutrient Management Plan
    It is well understood that agricultural operations modify their 
nutrient management and farming practices during the normal course of 
their operations. Such alterations may require changes to a permitted 
CAFO's NMP during the period of permit coverage.
    As discussed in the preamble to the 2006 proposed rule, the permit 
does not need to be modified for all operating changes. Because of the 
way NMPs are developed and the flexibility provided by the two options 
for developing the terms of the nutrient management plan at 40 CFR 
122.42(e)(5), most routine changes at a facility should not require 
changes to the NMP itself. For example, a CAFO using the narrative rate 
approach would not ordinarily need to change its NMP when it makes 
changes to factors that are not themselves terms but are accounted for 
in the methodology. To minimize the need for revision, nutrient 
management plans should anticipate and accommodate routine variations 
inherent in agricultural operations such as anticipated changes in crop 
rotation, as well as changes in numbers of animals and volume of 
manure, litter, or process wastewater resulting from normal 
fluctuations or a facility's planned expansion. Typically, an NMP is 
developed to accommodate, for example, normal fluctuations in herd or 
flock size, capacity for manure, litter, and process wastewater 
storage, the fields available for land application and their capacity 
for nutrient applications. Moreover, as discussed in this preamble, EPA 
would encourage operators to develop an NMP that includes reasonably 
predictable alternatives that a CAFO may implement during the period of 
permit coverage. However, unanticipated changes to a nutrient 
management plan may nevertheless be necessary.
    The final rule includes 40 CFR 122.42(e)(6), which requires a CAFO 
to notify the Director of changes to the CAFO's NMP. Section 
122.42(e)(6) excludes the results of calculations made in accordance 
with 40 CFR 122.42(e)(5)(i)(B) and 122.42(e)(5)(ii)(D) from the 
requirements of paragraph (e)(6). The results of these calculations, 
which are required of Large CAFOs using the linear approach and all 
CAFOs using the narrative rate approach, must be reported in the CAFO's 
annual report. Thus, there is no need to provide this information 
pursuant to the requirements of paragraph (e)(6).
    In the 2006 proposed rule, EPA proposed a process that CAFOs and 
the permitting authority would need to follow when a CAFO makes changes 
to its NMP. The proposal also included criteria for determining when a 
change to a CAFO's NMP should be considered a substantial change. In 
the 2008 supplemental notice, the Agency solicited comment on several 
modifications to the 2006 proposal including a list of changes to the 
NMP that would constitute a substantial change.
    In this final rule, EPA is including a list of changes to the NMP 
that would constitute a substantial change to the terms of a facility's 
NMP, thus triggering public notice and permit modification. Substantial 
changes include: (1) Addition of new land application areas not 
previously included in the CAFO's NMP; (2) any changes to the maximum 
field-specific annual rates of application or to the maximum amounts of 
nitrogen and phosphorus derived from all sources for each crop, as 
expressed in accordance with, respectively, the linear approach or the 
narrative rate approach; (3) addition of any crop not included in the 
terms of the CAFO's NMP and corresponding field-specific rates of 
application; and (4) changes to field-specific components of the CAFO's 
NMP, where such changes are likely to increase the risk of nitrogen and 
phosphorus transport from the field to waters of the U.S.
    This final rule also makes one exception to the first type of 
substantial change (a land application area being

[[Page 70452]]

added to the nutrient management plan), where such additional land is 
already included in the terms of another existing NMP incorporated into 
an existing NPDES permit. If, under the revised NMP, the CAFO owner or 
operator applies manure, litter, or process wastewater on such land 
application area in accordance with the existing field-specific terms 
of the existing permit, such addition of new land would not be a 
substantial change to the terms of the CAFO owner or operator's NMP.
    EPA received a number of comments on the list of substantial 
changes in the 2006 proposed rule and 2008 supplemental proposal. One 
commenter encouraged EPA to state that substantial changes under the 
narrative rate approach only occur when the CAFO changes the system 
used to determine maximum allowable application rates. EPA agrees that 
changes in the methodology may be substantial changes to the terms of 
the NMP if they result in changes to the maximum rates of application 
or maximum amounts of nitrogen and phosphorus derived from all sources 
for each crop or if they result in changes likely to increase the risk 
of nutrient transport to waters of the U.S. However, EPA does not agree 
that there are no other changes that are substantial changes under the 
narrative rate approach. EPA believes that the four substantial changes 
identified in this final rule are appropriate for both of the 
approaches for determining rates of application. For example, proper 
implementation of the narrative rate approach depends on identification 
of the fields to be used for land application, so use of a new field 
for land application that had not been previously covered in the 
facility's (or another facility's) permit terms would constitute a 
substantial change. In addition, under the narrative rate approach a 
change to the field-specific maximum amounts of nitrogen and phosphorus 
derived from all sources is a substantial change to the NMP, because it 
defines the upper bounds on nutrient additions.
    Some commenters suggested that EPA expand the list of substantial 
changes to include changes such as the maximum number of animals 
allowed for the CAFO site; production area changes that alter the 
volume and composition of waste; using soil, manure, plant tissue test 
results to refine the NMP; and changes in the status of the receiving 
waterbodies. With regard to the number of animals confined and the 
volume of waste generated, EPA has stated that the number of animals 
confined at a CAFO would not necessarily be a term of the NMP because a 
CAFO operator is required to properly operate and maintain the CAFO's 
storage facilities regardless of the number of animals or the volume of 
manure, litter, or process wastewater generated. For the same reasons, 
EPA believes that changes to these factors will not necessarily trigger 
substantial change to a CAFO's permit, although accommodating an 
increase in the number of animals or volume of manure could lead to 
changes to the NMP that would constitute substantial changes to terms 
of the NMP (and the permit). With regard to the use of soil and manure 
tests, both approaches discussed above for expressing land application 
rates in NMPs and associated terms allow for consideration of manure 
testing on an annual basis; and the narrative rate approach also 
requires consideration of the most recent soil test results. Finally, 
NPDES permits for all types of dischargers, including CAFOs, typically 
include reopener provisions under which the Director may revise the 
permit during the permit term based on factors such as changes to the 
status of the receiving water body. EPA believes that such standard 
NPDES provisions are sufficient to allow permit revisions necessary to 
support the criteria and standards established for receiving waters.
    The Agency believes that the list of substantial changes included 
in this final rule address changes that most directly affect 
fundamental components of the NMP that relate to the land application 
of manure, litter, and process wastewater, which was a primary focus of 
the Waterkeeper decision. First, by identifying the addition of new 
land application areas not originally included in the terms of the NMP 
as a substantial change, the Agency makes clear that the fields to be 
used for land application must be permit terms, as all permitted CAFOs 
that land apply manure, litter, and process wastewater are required to 
do so at field-specific agronomic rates. The identification of land 
application areas in the NMP is essential for determining the effluent 
limitations applicable to a particular CAFO, which the Waterkeeper 
decision required be made available for public review and comment and 
incorporated into the permit. Thus, the public must have an opportunity 
to comment on the fields planned for land application during both the 
initial permit issuance phase and any subsequent permit modification 
phase. The exception for the addition of new fields already covered by 
an existing NPDES permit is consistent with the Waterkeeper decision 
because the rates of application for those land application areas will 
have already been publicly reviewed, approved, and incorporated into a 
permit as required by Waterkeeper.
    Some commenters supported the addition of new land application 
areas as a substantial change. They also commented that adding or 
reducing land application areas would require a recalculation of the 
application rate. Some commenters were concerned that the addition of 
new land application areas as a substantial change is 
counterproductive, severely limits flexibility for producers to plan, 
does not add water quality benefit, discourages producers from adding 
land to their NMP and will hinder a CAFO's ability to quickly add more 
fields to the NMP. These commenters suggested the addition of land 
application areas can be addressed by requiring producers to submit 
this information with their annual reports. Some commenters also 
suggested granting States the flexibility to define when and what types 
of land application area additions would be considered a substantial 
change. Some commenters suggested that only the loss of land 
application areas should be treated as a major modification which 
requires public participation. As discussed above, under Waterkeeper, 
the public must have opportunity to review the fields planned for land 
application during both the initial permit issuance phase and any 
subsequent permit modification phase in order to determine whether 
field-specific rates of application have been properly developed. For 
this reason, the addition of new land application areas not already 
addressed under an existing NMP and permit must be considered a 
substantial change and made available for public review.
    The second substantial change is any change to the field-specific 
maximum rates of application. The Waterkeeper decision makes clear the 
importance of these rates as terms of the NMP. Some commenters 
indicated this change should not apply to NMPs developed using the 
narrative approach, since the appropriate application rate should be 
calculated using the approved methodology. This final rule clarifies 
that, for the narrative rate approach, a substantial change is 
triggered by a change in the field-specific maximum amount of nitrogen 
and phosphorus derived from all sources.
    The third substantial change is the addition to the NMP of crops or 
other uses not previously included in the CAFO's NMP, together with the 
corresponding maximum field-specific

[[Page 70453]]

rates of application for those crops or other uses. Because rates of 
application are based on the yield goals for each specific crop, any 
crops or other uses newly added to the plan will require corresponding 
newly calculated rates of application. In addition, because the maximum 
rates of application must be made available to the public for review 
prior to incorporation as terms of the permit, consistent with 
Waterkeeper, the addition of new crops or other uses and their 
corresponding rates of application is considered a substantial change.
    Finally, any change to site-specific components of the CAFO's 
nutrient management plan that is likely to increase the risk of 
nitrogen and phosphorus transport to waters of the U.S. is a 
substantial change. The Agency recognizes a number of changes as 
potentially triggering this requirement, including the following 
examples: (1) Alternate timing of land application that would diminish 
the potential for plant nutrient uptake; (2) methods of land 
application not provided for in the NMP calculation of amount of 
manure, litter, and process wastewater to be applied; (3) changes to 
conservation practices; and (4) changes in the CAFO's procedures for 
handling, storage, or treatment of manure, litter, and process 
wastewater. The actual crop planted, timing and method of land 
application, crop uptake, and conservation practices utilized with 
respect to the land application areas are all key factors that affect 
nitrogen and phosphorus runoff from the land application area. Changes 
to any of the planning considerations listed above can directly (and 
measurably) alter the outcome of the decisions made in an NMP and the 
efficacy of that plan in ensuring appropriate agricultural utilization 
of those nutrients that are land applied.
    An advantage of the narrative rate approach is that it reduces the 
likelihood that changes to a CAFO's operation would result in a 
substantial change to the terms of the CAFO's NMP. For example, a 
change to the method or timing of application would be a substantial 
change to the terms of the NMP for CAFOs using the linear approach if 
the Director determines that it is likely to increase the risk of 
nutrient transport to surface waters. For a CAFO using the narrative 
rate approach, a change in the method or timing of application would 
not be a change to the terms of the NMP, and therefore not a 
substantial change, so long as the methodology in the NMP (itself a 
permit term) accounts for the change in method or timing.
    Because changes to the NMP could result in a change to a permit 
term, the 2006 proposed rule provided that whenever a CAFO makes any 
change to its NMP, the owner or operator would be required to provide 
the Director with the revised NMP and identify the changes from the 
previous version submitted. Of course, any change to the CAFO's 
implementation of its NMP that does not constitute a change to the NMP 
itself would not be submitted to the Director. For example, for CAFOs 
following the narrative rate approach, any change in crop rotation or 
substitution of crops in a given rotation with alternative crops 
identified in the NMP for a given field would not be a change and thus 
would not need to be submitted to the Director prior to implementation.
    Some commenters felt that substantial changes could be addressed by 
making those changes part of the annual report. For example, some 
commenters recommended that CAFOs using the narrative rate approach be 
required to include information associated with the addition of new 
crops in their annual reports. The annual report does not provide 
sufficient public notice for making changes to the terms of the NPDES 
permit. Those procedures are detailed below.
(f) Process for Review of Changes to an NMP and for Modifying Terms of 
the NMP Incorporated Into the Permit
    When a permitted CAFO operator revises its NMP, this rule requires 
the CAFO operator to submit the revised NMP to the permitting authority 
for review and for the permitting authority to incorporate any revised 
terms of the NMP into the permit. This rule includes provisions that 
enable the Director to determine whether revisions to the CAFO's NMP 
necessitate revisions to the terms of the NMP incorporated into the 
permit, and if so, whether such changes are substantial or non-
substantial. This rule identifies several specific types of changes 
that must be considered substantial changes to the NMP, and this 
preamble provides further guidance for distinguishing between 
substantial and non-substantial changes. This final rule also 
establishes a streamlined process for formal public notice and comment 
that the permitting authority must follow for permit modification when 
a CAFO is seeking to make substantial changes to the terms of its NMP. 
Non-substantial changes to the terms of the NMP are not subject to 
public notice and comment before the permit is revised. Finally, this 
rule establishes provisions for incorporating both substantial and non-
substantial revisions to terms of the NMP into the permit as a minor 
permit modification. These procedures apply to all permitted CAFOs, 
regardless of whether they are covered under an individual permit or 
under a general permit. These procedures are discussed in greater 
detail, below.
    As mentioned above, this final rule requires that whenever a CAFO 
makes any change to its NMP (see discussion in section III.C.3(e) of 
this preamble, ``Changes to a Permitted CAFO's Nutrient Management 
Plan''), the owner or operator must provide the Director with the 
revised NMP and identify the changes from the previous version 
submitted to the permitting authority. See 40 CFR 122.42(e)(6)(i). 40 
CFR 122.24(e)(6)(ii) requires the Director to then review the revised 
plan to ensure that it still meets the requirements of 40 CFR 122.42(e) 
and applicable effluent limitations and standards, including those 
specified in 40 CFR part 412. This rule also requires the Director to 
determine whether the changes necessitate revision to the terms of the 
NMP that were incorporated into the permit issued to the CAFO. If not, 
the Director must notify the CAFO that the permit does not need to be 
modified. Upon such notification the CAFO may implement the revised 
nutrient management plan.
    If, on the other hand, the Director determines that the changes to 
the NMP do require that the terms of the NMP that were incorporated 
into the permit be revised, the Director must next decide whether or 
not the change is substantial. The Director will evaluate the change 
based on the provisions in Sec.  122.42(e)(6)(iii) discussed above. 
Pursuant to 40 CFR 122.42(e)(6)(ii)(A), for non-substantial changes, 
the Director must make the revised nutrient management plan publicly 
available and include it in the permit record, revise the terms of the 
nutrient management plan incorporated into the permit, and notify the 
owner or operator and inform the public of any changes to the terms of 
the nutrient management plan that are incorporated into the permit. 
Upon such notification the CAFO may implement the revised nutrient 
management plan.
    If the changes to the terms of the NMP are substantial, the 
Director will also modify the permit as necessary by incorporating 
revised terms of the NMP, but only after the public has had the 
opportunity to review and comment on the NMP changes pursuant to the 
requirements of 40 CFR 122.24(e)(6)(ii)(B). The process for public 
comments, hearing requests, and the hearing process if a hearing is

[[Page 70454]]

granted must follow the procedures for draft permits set forth in 40 
CFR 124.11-13. The Director must respond to all significant comments 
received during the comment period as provided in 40 CFR 124.17, and 
require the CAFO owner or operator to further revise the nutrient 
management plan if necessary. Once the Director incorporates the 
revised terms of the nutrient management plan into the permit, the 
Director must notify the owner or operator and inform the public. A 
permit modification to revise the terms of the NMP incorporated into 
the permit may be appealed in the same manner as the initial final 
permit decision.
    The Director may establish by regulation, or in the general permit 
for CAFOs authorized under a general permit, an appropriate period of 
time for the public to comment and request a hearing on the proposed 
substantial changes to the terms of the nutrient management plan 
incorporated into the permit that differs from the time period 
specified in 40 CFR 124.10. EPA is providing this discretion to the 
Director to allow CAFOs to implement revised nutrient management 
practices in accordance with growing seasons and other time sensitive 
circumstances. As is stated above in section III.C.3(b) of this 
preamble regarding public review of NMPs during the general permit 
process, the public will have an opportunity to comment on the 
sufficiency of the time period when the Director proposes it, either in 
the regulations or general permit.
    Because the process in Sec.  122.42(e)(6)(ii) allows for public 
review of substantial changes to the terms of nutrient management plans 
and the underlying data and calculations, the incorporation of changes 
to the permit through this process will be treated as a minor permit 
modification, under 40 CFR 122.63(h), and not require additional 
review. EPA considered requiring that any change to the NMP be 
considered a permit modification subject to procedures under 40 CFR 
122.62, but rejected this interpretation as it would significantly 
limit permitting authorities and CAFO operators' ability to make 
necessary and timely minor changes to NMPs as discussed above.
    Commenters identified several issues associated with the proposed 
process for making substantial changes to NMPs. Several commenters 
indicated that the need for the permitting authority to review, provide 
public notice and comment, and approve substantial changes to NMPs will 
likely result in significant delays which will impact the operational 
ability of many CAFOs to make timely nutrient management decisions. 
Some commenters suggested that the process for making such changes be 
streamlined or time-limited. Other commenters requested that EPA 
provide flexibility to accommodate existing State criteria and 
procedures for determining and addressing substantial changes. Some 
State commenters indicated that they already have effective procedures 
in place. Some commenters simply asserted that the State Director 
should have discretion whether or not to require a permit modification.
    The NPDES regulations at Sec.  122.62 specifically require that any 
change to permit terms and conditions requires permit modification to 
be subject to public review and comment procedures, unless it falls 
under a minor modification listed at 40 CFR 122.63. In this rule, EPA 
has accounted for the frequent operational changes unique to CAFOs 
which are not typical for other NPDES-regulated industries. This 
tailoring is an effort to balance environmental protection with the 
burden to CAFOs and permitting authorities as well as the need to allow 
other operational changes that would not trigger the substantial 
modification requirements.
    The process in this rule for making changes to NMPs and 
incorporating such changes in permits is necessary as a result of the 
Waterkeeper decision, which held that terms of the NMP are effluent 
limitations and that the CWA requires that the terms of each NMP be 
incorporated into a corresponding permit and be subject to public 
notice and comment and permitting authority review. Within this 
context, EPA has worked to streamline the process to the extent 
possible. This includes promulgating a process for revising NMPs that 
delineates what are substantial changes to the terms of the NMP and 
allows non-substantial changes to proceed in an expedited manner. It 
also includes provisions that allow a CAFO to develop NMPs with 
operational contingencies to minimize the number of substantial changes 
that must be made. As explained herein, the process and criteria in 40 
CFR 122.42(e)(6) are reasonable and necessary to provide permitting 
authorities an effective mechanism to maintain linkage between the NMP 
and the permit in a manner consistent with the Waterkeeper decision.
    Commenters suggested changes to the process in the 2006 proposed 
rule. Several commenters requested that EPA approve certain substantial 
changes as long as the CAFO continues to comply with all applicable 
technical requirements. Such substantial changes could include adding a 
new and substantially different field or increasing the animal 
headcount so as to exceed the previously identified ``maximum'' amount 
of manure in the NMP. In addition, one commenter recommended that the 
permitting authority inspect the CAFO before allowing any substantial 
changes to the NMP.
    The final rule does not expressly provide that a permitting 
authority can pre-approve certain substantial changes, unless they are 
specified in an NMP that encompasses normal fluctuations or variations, 
because the Waterkeeper decision dictates that NMPs must be subject to 
permitting authority review and the terms of the NMP available for 
public comment. In addition, EPA does not believe an inspection is 
needed prior to allowing any substantial change to an NMP. Apart from 
the burden this would entail, EPA expects that self-reported 
information is credible and notes that there are significant penalties 
for submitting false or misleading information.
    Many commenters supported the proposal that non-substantial changes 
would require only that the CAFO submit a revised NMP and that the 
permitting authority would notify the public of the change without 
allowing for public comment. Commenters encouraged EPA to clarify that, 
upon submission, the CAFO may proceed to implement such changes if the 
CAFO believes they are non-substantial. Many commenters stated that 
there is a need to ensure that CAFOs can quickly make changes to NMPs. 
One commenter recommended that EPA allow CAFOs to accumulate minor 
changes and submit them as a group when renewing their permit. Another 
commenter suggested that any changes incurred during a given year be 
reported in an annual NMP update form. EPA decided that, because the 
terms of the NMP are enforceable terms and conditions of the permit, 
CAFOs must submit changes to the NMP to the permitting authority and 
receive approval before a change is made, not annually or at the 
beginning of each new permit cycle.
    Commenters were generally unsupportive of the proposed 180-day 
temporary approval period for implementation of certain substantial 
changes. Numerous commenters stated that this would not be helpful to 
CAFO owners because they would be hesitant to invest significant 
amounts of money to make substantial changes based only on a temporary 
approval, since final approval would remain subject to an uncertain 
regulatory status. Others

[[Page 70455]]

requested clarification regarding what happens if a change is 
implemented and then not approved. Some of these commenters suggested 
as an alternative that EPA require the permitting authority to process 
the applications in fewer than 45 days, and then allow seven days of 
public review.
    Another commenter stated that the temporary approval period is 
inadequate because 180 days is longer than the crop growing season. 
This commenter observed that the temporary approval would allow CAFOs 
to change their entire land application patterns for an entire crop 
season without having public comment and review by the permitting 
agency. This commenter suggested that CAFOs plan in advance for any 
substantial changes and that only if the substantial changes are the 
result of unforeseen circumstances outside the control of the CAFO, 
should it be allowed temporary approval.
    Based on comments, EPA reevaluated the usefulness of the 180-day 
temporary approval. In light of the comments, EPA recognizes that such 
an approach may be problematic for both industry and permitting 
authorities. Some industry commenters stated that the 180-day grace 
period would be meaningless because no operator would employ expensive 
changes without knowing if they would be approved. States commented 
that any permit modification must be approved before it is implemented. 
There is no requirement precluding operators from purchasing new land; 
rather, practices on the land cannot be employed until approved by the 
permitting authority. Further, EPA encourages operators to take 
advantage of the exception for substantial changes relating to the 
addition of new land application areas provided in Sec.  
122.42(e)(6)(iii)(A). Thus, EPA has not included the proposed 180-day 
temporary approval period in the final rule.
    Under this final rule, when a CAFO submits changes to an NMP to the 
permitting authority, the Director must determine whether the changes 
affect the terms of the NMP incorporated into the permit, and if so, 
whether such changes are substantial. Depending on this determination, 
the process and timing of modifying a permit will vary. A CAFO owner or 
operator must remain in compliance with his or her permit and, thus, 
should work closely with the permitting authority and should initiate 
this coordination as early as possible. EPA believes that permitting 
authorities will be sensitive to the needs of CAFOs to make a range of 
changes to NMPs from time to time and, as a result, will be diligent in 
reviewing and making determinations regarding such changes.
(g) Annual Reporting Requirements
    In the 2006 proposed rule, EPA discussed the use of annual reports 
to balance greater flexibility for CAFO operators in making cropping 
decisions with ensuring appropriate permitting authority and public 
oversight of permit compliance. The preamble solicited comment as to 
whether the annual report requirements should be modified to require 
all permitted CAFOs to submit information in their annual reports 
indicating how the CAFO achieved substantive compliance with the terms 
of the NMP as set forth in the permit. In the 2008 supplemental 
proposal, the Agency proposed additional annual reporting requirements 
for CAFOs that relate to the proposed provisions regarding the terms of 
the NMP.
    In this action, the Agency is establishing additional annual report 
requirements, in 40 CFR 122.42(e)(4)(viii), mandating all permitted 
CAFOs to include in their annual reports the actual crop(s) planted and 
actual yield(s) for each field, the actual nitrogen and phosphorus 
content of the manure, litter, and process wastewater, and the amount 
of manure, litter, or process wastewater applied to each field during 
the previous 12 months. The Agency believes that it is important for 
the permitting authority to obtain this information on an annual basis 
in order to ensure that the CAFO has been operating in compliance with 
the terms of its permit. The annual report will inform the Director and 
the public how the CAFO has operated, given the flexibility for the 
terms of the NMP incorporated into the permit.
    The Agency is also requiring CAFOs that follow the second 
(``narrative rate'') approach for describing rates of application in 
the NMP to submit as part of their annual report the results of all 
soil testing and concurrent calculations to account for residual 
nitrogen and phosphorus in the soil, all recalculations, and the new 
data from which they are derived. The CAFO is required to report the 
amounts of manure, litter, process wastewater and the amount of 
chemical fertilizer applied to each field during the preceding 12 
months. Together with the total amount of plant available nitrogen and 
phosphorus from all sources, the information that is required to be 
included in the annual report provides the information necessary to 
determine that the CAFO was adhering to the terms of its permit when 
calculating amounts of manure, litter, and process wastewater to apply.
    Many commenters supported the use of additional annual reporting 
requirements to address either non-substantial changes or all changes 
to the NMP. States also generally supported such an approach and sought 
flexibility regarding the content and use of the process to address 
other changes to the NMP. Another commenter noted that if CAFOs are 
allowed to provide alternative management scenarios in the original 
NMP, the CAFO must be required to submit documentation to the Director 
to specify which practices it is using from the ``menu'' of 
combinations in its NMP. This would allow the permitting authority and 
the public to know what practices the CAFO is actually implementing at 
any given time.
    Although EPA recognizes that NMPs may change throughout the period 
of permit coverage, as discussed above in section III.C.3(e), the 
annual report requirements are only appropriate for use in addressing 
implementation of existing NMP provisions and changes to the NMP 
contemplated through flexibilities built into the NMP during the 
initial planning process or subsequent modifications in accordance with 
40 CFR 122.42(e)(6). Because this rule requires the terms of the NMP to 
be incorporated as enforceable terms and conditions of the permit, an 
outcome of the Waterkeeper decision, changes to the terms of the NMP 
constitute changes to the permit and therefore must be processed 
according to Sec.  122.42(e)(6), as discussed above in section 
III.C.3(e).
    Some commenters expressed concern that CAFOs would be unable to 
complete more detailed reports and provide the information necessary to 
document changes to the NMP, and that some of the reporting 
requirements would be redundant. Some commenters also believed that 
reporting crop yields would be overly intrusive and would not be 
representative of the NMP effectiveness. In this rule, EPA has modified 
the content of the annual report to supplement the existing annual 
report requirements promulgated in 2003 so as to allow the public and 
the permitting authority to review whether the CAFO has implemented the 
NMP in accordance with the terms and conditions of its permit. This 
approach balances the recognized need to provide additional flexibility 
and the need for CAFOs to provide information concerning actual rates 
of application. The additional information required in this final rule 
is a limited burden on both the CAFO and the permitting authority that 
will provide public access

[[Page 70456]]

to information about NMP implementation throughout the period of permit 
coverage. For example, crop yield goals are a critical factor in 
developing rates of application. Other commenters expressed concern 
that facilities might overstate crop yields goals. As previously 
mentioned, by making information about actual crop yields public, both 
the Director and the public will have better information when 
evaluating NMPs for subsequent permit coverage.
(h) EPA Nutrient Management Plan Template
    As described in the 2006 proposed rule, EPA developed a draft 
template, made available in the rulemaking public record for public 
comments, which could be used as a voluntary tool to facilitate 
completion of the NMP by CAFO permit applicants, as well as to 
facilitate review by the permitting authority. As discussed in the 
proposed rule, EPA believed that such a template would help to 
systematically organize the information necessary to satisfy the NMP 
requirements in the regulation. Some commenters supported the concept 
of a voluntary NMP template and considered the draft template an 
excellent user-friendly model. Other commenters disagreed, stating that 
the detailed information required in the draft template would be 
quickly outdated. Other comments received on the NMP template include 
the following:
     A ``one size fits all'' template does not lend itself well 
to the different climates and terrains across the country, and use of 
the template should not be required by the regulation;
     The draft template lacked specific information to ensure 
that CAFOs are meeting technical standards and the ELGs;
     The draft template was too long and appeared to be more of 
an inspection checklist than a basic guideline;
     A concern that some States may actually adopt the 
template, once completed, as the required NMP format;
     The template could be a valuable tool to clearly 
differentiate between the terms of the NMP, for purposes of 
incorporation into the permit, and the background information;
     The template would be more beneficial if it is 
standardized through the use of a computer program which allows ease 
and flexibility in making changes to the NMP; and
     The template could be useful to an unpermitted CAFO to 
identify land application practices needed to qualify for the 
agricultural stormwater exemption.
    States generally agreed with the concept of using a consistent, 
stable template but wanted assurance that it is strictly a voluntary 
tool and can be modified to better address specific State requirements. 
Additionally, commenters stated that the draft template failed to 
address all of the regulatory requirements and should be modified 
accordingly by including additional technical portions. Other 
commenters suggested that a template would unnecessarily micromanage 
the structure or content of NMPs and that States should have the 
responsibility to define effective nutrient management strategies. 
Other commenters mentioned the need to keep the template flexible 
because NMPs are dynamic documents that change rapidly, and a plan that 
is too detailed will bind the producer to practices that, if altered, 
would require costly revisions and reviews. A few commenters also 
indicated that the format and sequence for providing information within 
the draft template was disjointed and inconsistent with the nutrient 
management planning process. Other State commenters did offer, however, 
that the template may be adequate for most public participation 
processes.
    After considering public comments, EPA, in coordination with USDA, 
has decided not to utilize the draft template. Instead, the two 
agencies have worked on the development of a planning tool that would 
generate a single document that meets the objectives of both agencies. 
The one document would include the required elements of an NMP as well 
as the elements of a voluntary comprehensive nutrient management plan 
(CNMP) developed in accordance with USDA technical guidance. A CNMP is 
a plan much like the NMP required by EPA's CAFO regulations. There are 
some minor differences between the scope of the two documents, such as 
a CNMP option to include feed management plans (which are not required 
for the NMP) and an NMP requirement to include chemical handling plans 
(which are not part of a CNMP). However, the EPA and USDA agree that 
there is no reason why one document could not suffice for both the CNMP 
and NMP by accommodating both agencies' requirements. To that end, EPA, 
in partnership with USDA, is in the process of coordinating the 
information necessary to complete an NMP as well as a CNMP and 
developing a software program that could integrate both sets of 
planning requirements, known as Manure Management Planner (MMP). Of 
course, even though both agencies would promote the use of a single 
tool, it would remain the CAFO operator's responsibility to provide 
that information to the Director in order to meet the requirements of 
this rule, inasmuch as USDA does not make facility-specific information 
available to other agencies or the public. EPA will encourage the use 
of the MMP to facilitate the development and review of NMPs under the 
NPDES permit program.
    The MMP software, under development by a grant from EPA and USDA to 
Purdue University, is a computer program that would provide permitting 
authorities and producers with a mix of programs, not currently 
available elsewhere, to assist in CNMP and/or NMP development. The 
objective of this effort is to accelerate the CNMP and NMP development 
process by integrating other software programs used to calculate manure 
application rates. Among these technologies are RUSLE II, the 
Phosphorus Index (PI), and other State-specific risk assessment tools 
used in CNMP and NMP development. In the longer term it is planned that 
additional integration will be achieved with planning, recordkeeping 
technologies and connectivity to the USDA Customer Service Toolkit. The 
MMP program incorporates field-specific data tables that allow the 
producer to list the type of crops planned, crop rotation by planting 
season, nutrients available for each crop based on previous manure 
applications, and the rate of application per crop. These data tables 
could provide permitting authorities with specific information that 
could be extracted as terms of the NMP that would be inserted into a 
permit. It also provides producers the flexibility to comply with the 
optional approach of calculating application rates as pounds of 
nutrients by developing tables with expanded crop contingency plans and 
related application rates. See section III.C.3(c) for detailed 
discussion of nutrient management plan terms.
    EPA and USDA anticipate that the MMP software can eventually be 
tailored to all individual State technical standards, requirements and 
circumstances. At present, the program has been tailored to 
approximately 34 States, and is available and ready for use in those 
States. EPA and USDA plan on updating and improving the MMP software 
and tailoring it to other States.
    When completed, the MMP software will be a user-friendly program 
available without charge. It is strictly a voluntary tool. There may be 
some situations at a livestock operation, such as varying terrains and 
unusual cropping sequences, which the MMP cannot

[[Page 70457]]

accommodate; thus the program may not, at present, be a good fit for 
all operators. Permitting authorities and producers may still choose to 
use an established State NMP software program or other technical 
standards methods to develop and implement their NMP. More information 
on MMP can be found at the Purdue University Web site, http://
www.agry.purdue.edu/mmp/.
    EPA and USDA are also developing a national nutrient management 
planning course that will cover how to develop, review, and implement 
an NMP and how to use the MMP software program.

D. Compliance Dates

    Following issuance of this rule, authorized States have up to one 
year to revise, as necessary, their NPDES regulations to adopt the 
requirements of this rule, or two years if statutory changes are 
needed, as provided in 40 CFR 123.62. States are not required to adopt 
the provisions for no discharge certification in this time period.
    As discussed above in section II.E, EPA has twice extended certain 
compliance dates originally established in the 2003 CAFO rule. 
Following the Second Circuit Court's decision in Waterkeeper Alliance 
et al. v. EPA, 399 F.3d 486 (2d Cir. 2005), the Agency extended dates 
for newly defined CAFOs to seek permit coverage and for all permitted 
CAFOs to develop and implement NMPs to July 31, 2007. 71 FR 6978 
(February 10, 2006) (hereinafter the ``2006 date change rule'').
    The 2006 proposed rule did not anticipate a need to revise the July 
31, 2007, compliance dates established by the 2006 date change rule. 
However, as a result of an array of public comment on the issues raised 
by the Waterkeeper decision, EPA was unable to complete this final rule 
prior to July 31, 2007. EPA published a second revision of the 
compliance dates on July 24, 2007, extending the dates from July 31, 
2007, to February 27, 2009. 72 FR 40,245 (July 24, 2007) (hereinafter 
the ``2007 date change rule''). The 2007 date change rule does not 
affect the applicable time for seeking permit coverage for existing 
facilities defined as CAFOs prior to the 2003 CAFO rule, nor does it 
apply to newly constructed CAFOs not subject to new source performance 
standards (NSPS) or to new source CAFOs subject to NSPS that discharge 
or propose to discharge. The February 27, 2009, compliance dates also 
do not affect the approximately 9,000 CAFOs currently covered under 
existing permits. Furthermore, for Large CAFOs that are new sources 
(i.e., those commencing construction after the effective date of the 
2003 CAFO rule) and are required to seek permit coverage under the 
revised duty to apply provision in this rule (40 CFR 122.23(d)(1)), the 
land application requirements at 40 CFR 412.4(c) apply immediately 
because new sources are subject to the NSPS under 40 CFR 412.35 and 
412.46, which do not include a delayed date for new sources to come 
into compliance with Sec.  412.4(c). The 2003 rule did not delay 
compliance with the land application requirements for new sources. See 
CWA section 306(e).
    EPA received comments on the 2006 proposed rule related to the July 
31, 2007, compliance dates in place at that time. The comments received 
generally focused on two issues: (1) That the permit application date 
did not allow enough time for States to revise their permitting 
programs, and (2) that the date did not allow CAFO operators sufficient 
time to develop permit applications and NMPs. Many commenters stated 
that it would not be possible for CAFOs to seek coverage under an NPDES 
permit by July 31, 2007, and that the deadline should be extended. A 
number of extension periods were suggested ranging from several months 
to up to two years after promulgation of the final rule. Rationales for 
extending the dates included the need to allow States to revise their 
programs to fully reflect CAFO regulations (which, in turn, allows 
CAFOs to know what requirements apply to them), limited technical 
assistance, and the need for adequate time to develop an NMP in the 
period between rule promulgation and the deadline for seeking permit 
coverage. Commenters asserted that CAFO owners and operators cannot 
know the precise requirements for NMPs, or the associated documentation 
and public participation requirements, until the rule is final. EPA 
promulgated the 2007 date change rule with these comments in mind.
    In the 2008 supplemental proposal (73 FR 12,336) EPA solicited 
comments on its intention to not extend the compliance deadlines beyond 
February 27, 2009. Some commenters stated that the deadline should be 
extended in order to allow States to adapt their existing programs. 
Others noted that more time would be needed for CAFO owners and 
operators to implement such complex rules and come into compliance. A 
number of extension periods were suggested ranging from several months 
to up to two years after promulgation of the final rule. Commenters 
were opposed to an extension of the deadlines; did not want to further 
delay the environmental benefits; and noted that an extension would 
provide a comparative advantage to those CAFOs that have not made 
capital improvements and promote interstate discrepancies that 
undermine the integrity of State CAFO programs.
    In this final rule, EPA is not extending the February 27, 2009, 
compliance deadlines. EPA believes that the time between publication of 
this final rule and February 27, 2009, is adequate for unpermitted 
CAFOs that discharge or propose to discharge to develop an NMP and seek 
permit coverage. EPA notes that most of the technical provisions of the 
2003 CAFO rule (e.g., the substantive NMP requirements) were unaffected 
by the Waterkeeper decision, and therefore CAFOs have already had the 
information they need to develop NMPs and have not needed to wait for 
further EPA action before doing so. In States where general permits 
have been issued and have not expired, eligible CAFOs may seek permit 
coverage under applicable existing general permits. Where general 
permits are not available, CAFOs may seek permit coverage by submitting 
an individual permit application. As mentioned above, 40 CFR 123.62(e) 
provides that States will have one year from the promulgation date of 
this final rule, or two years if statutory changes are needed, to adopt 
the requirements of this final rule. During this interim period, EPA 
expects States to issue permits that comply with all technical 
requirements of the 2003 rule that were unaffected by the Waterkeeper 
decision and, absent regulatory or statutory barriers, to provide for 
NMP submission, public review of NMPs, and incorporation of the NMP 
terms into the permit. EPA is committed to working with States to 
implement CAFO permitting requirements.
    The CWA does not allow any CAFO to discharge without a permit, 
regardless of whether a permit application has been submitted. EPA and 
States have a range of tools to help regulated entities come into 
compliance with new rules including outreach, compliance assistance, 
compliance incentives and compliance monitoring. For new rules EPA 
generally focuses on outreach initially. Where EPA becomes aware of 
particular instances of noncompliance, EPA may pursue appropriate 
enforcement. Since 2005, EPA has designated unpermitted CAFOs subject 
to the 1976 rule as an enforcement priority and continues to focus its 
efforts on those facilities. With respect to CAFOs subject to 
permitting as of February 27, 2009, EPA would take into consideration 
whether a permit application has been submitted and whether the entity 
is operating in

[[Page 70458]]

accordance with its NMP and all other applicable requirements of the 
2003 CAFO rule and this final rule.

E. Water Quality-Based Effluent Limitations

    Water quality-based effluent limitations (WQBELs) are one of two 
fundamental types of limitations imposed in NPDES permits. The other is 
technology-based effluent limitations. NPDES permits are required to 
contain technology-based limitations and, if the technology-based 
limitations are insufficient to meet applicable water quality 
standards, more stringent water quality-based effluent limitations 
(WQBELs). CWA section 301(b)(1)(C), 33 U.S.C. 1311(b)(1)(C); and 40 CFR 
122.44(d). While technology-based limitations are calculated taking 
into account the availability or effectiveness of treatment 
technologies and/or their associated costs, WQBELs are established 
without consideration of availability or effectiveness of treatment 
technologies or the costs that discharges would incur to meet such 
limits. Arkansas v. Oklahoma, 503 U.S. 91 (1992); Westvaco v. EPA, 899 
F.2d 1383 (4th Cir. 1990).
    The environmental petitioners challenged the 2003 rule as violating 
both the CWA and the Administrative Procedure Act by failing to 
promulgate WQBELs for CAFO discharges and by being ambiguous as to 
whether States may promulgate WQBELs for CAFO discharges. As explained 
in II.C.3 above, the Waterkeeper Court agreed in part with petitioners, 
and remanded the rule for clarification regarding the applicability of 
WQBELs for CAFO discharges that are not exempt as agricultural 
stormwater, to explain why EPA justified its decision not to promulgate 
WQBELs for discharges other than agricultural stormwater, and to 
clarify whether the CAFO rule bars States from requiring WQBELs for 
such discharges. Waterkeeper Alliance et al. v. EPA, 399 F.3d 486, 522-
524 (2d Cir. 2005).
    As EPA stated in the preamble to the 2006 proposed rule, the only 
issue that EPA addressed in the 2003 rule with respect to WQBELs was 
their applicability to agricultural stormwater discharges. EPA had 
explained in 2003 that, because agricultural stormwater discharges are 
not point source discharges, agricultural stormwater discharges cannot 
be subject to NPDES permit requirements, including either technology-
based limitations or WQBELs if technology-based limitations are 
insufficient to meet applicable water quality standards. The Second 
Circuit Court of Appeals agreed with EPA. However, the court seemed 
troubled by certain statements in the 2003 preamble that it thought 
might address how WQBELs apply to other CAFO discharges. The court 
therefore remanded the question of whether or not, and why, WQBELs are 
needed to assure attainment or maintenance of water quality standards 
as provided in section 302(a) of the CWA.
    In the preamble to the 2006 proposed rule, EPA responded to the 
remand by clarifying that discharges from CAFOs that are not exempt 
from CWA permitting requirements as agricultural stormwater discharges 
are subject to NPDES requirements, including WQBELs. EPA clarified the 
applicability of WQBELs both with respect to land application areas 
under the control of a CAFO and with respect to discharges from a 
CAFO's production area.
1. Discharges From Land Application Areas
    As explained in section III.B. above, under the 2003 rule, the 
agricultural stormwater discharge exemption applies only to 
precipitation-related discharges from land application areas under the 
control of the CAFO where application of manure, litter, or process 
wastewater is in accordance with appropriate nutrient management 
practices as specified in 40 CFR 122.42(e)(1)(vi)-(ix). Any other 
discharge from land application areas under the control of a CAFO is a 
point source discharge from the CAFO. 40 CFR 122.23(e). These point 
source discharges from land application areas are subject to NPDES 
permitting requirements, including WQBELs where necessary to meet 
applicable water quality standards.
    In most instances, a CAFO that meets technology-based permit limits 
requiring manure to be applied at appropriate agronomic rates will 
eliminate all or most dry weather discharges. If such discharges 
remain, the permit writer will determine the need for additional WQBELs 
to meet applicable water quality standards based on the circumstances 
of each particular case.
    Although EPA, in the 2003 rule preamble, encouraged States to 
address water quality protection issues in setting technical standards 
for appropriate land application practices (see Waterkeeper, 399 F.3d 
at 523, citing 68 FR 7198), EPA did not intend to change the basic 
regulatory scheme of the NPDES program. With respect to wet weather 
discharges, under 40 CFR 122.42(e)(1), the permit must already include 
effluent limitations defining the ``site-specific nutrient management 
practices'' required to be implemented under Sec.  122.23(e) in order 
for the remaining wet weather (``precipitation-related'') discharges to 
be ``agricultural stormwater discharges.'' As previously explained, 
agricultural stormwater discharges are exempt from the definition of 
``point source'' of section 502 of the CWA and are therefore not 
subject to permitting requirements under the CWA, including WQBELS. 
Thus, any precipitation-related discharge from land application areas 
remaining after compliance with the technology-based effluent 
limitations and permit conditions required pursuant to Sec.  
122.42(e)(1)(vi)-(ix) are exempt from CWA permitting requirements as 
agricultural stormwater, and these technology-based effluent 
limitations constitute the entirety of the federal NPDES permit 
requirements with respect to land application of manure, litter, and 
process wastewater. However, it is possible that a State may have 
additional requirements under its own State regulatory authorities that 
would go beyond the scope of the federal NPDES program. Thus, such 
agricultural stormwater discharges, though not subject to federal NPDES 
regulation, could be subject to additional State requirements, 
including additional requirements related to water quality. 33 U.S.C. 
1370 and 40 CFR 123.1 and 123.25. These requirements, however, would 
not be viewed as WQBELs as that term is used under the CWA. Nor would 
these State-law requirements be federally enforceable. 40 CFR 
123.1(i)(2).
2. Production Area Discharges
    EPA also explained in the preamble to the 2006 proposed rule that 
permit writers may require WQBELs in appropriate cases to further limit 
discharges from CAFO production areas. As EPA stated in the 2003 rule, 
the exclusion for agricultural stormwater does not apply to discharges 
from the CAFO production area. 40 CFR 122.23(e) and 68 FR 7198. Because 
the ELGs allow occasional overflow discharges from properly designed, 
operated, and maintained lagoons and storage ponds, the technology-
based limitations in the ELGs may not be as stringent as necessary to 
meet applicable water quality standards. In that case, a WQBEL would be 
appropriate. 40 CFR 122.44(d). For example, a facility subject to ELGs 
in 40 CFR part 412, subpart C is allowed to discharge from the 
production area, provided the production area is designed, constructed, 
operated, and maintained to contain all process wastewater plus any 
stormwater runoff resulting from the 25-year, 24-hour

[[Page 70459]]

storm. Thus, WQBELs would be necessary in a particular permit to 
further limit such discharges beyond the levels that are required under 
the CAFO ELGs, if necessary for the discharge to meet applicable water 
quality standards.
    In the preamble to the 2006 proposed rule, EPA indicated that for 
CAFOs in the swine and poultry sectors subject to New Source 
Performance Standards (NSPS) in part 412, subpart D, permits could not 
require WQBELs for production areas, because the NSPS already prohibit 
all production area discharges from these new sources. 71 FR 37,744, 
citing 40 CFR 412.46(a). Some commenters, however, urged EPA to 
reconsider its position given a possibility of a discharge even from 
CAFOs subject to a no discharge standard. Nothing in this rule limits 
the Director's authority to include any more stringent limitation than 
the NSPS in a CAFO's permit when necessary to meet applicable water 
quality standards pursuant to CWA section 301(b)(1)(C). Nonetheless, 
EPA continues to believe that WQBELs would not be needed for swine and 
poultry CAFOs subject to the no discharge NSPS. The provisions for 
implementing the NSPS BMP-based effluent limitation, based on advanced 
modeling, are meant to improve implementation of this provision by 
promoting up-front design, construction, operation, and maintenance to 
ensure that predictable discharges do not occur. Permitting authorities 
have full authority and responsibility to determine if the facility's 
demonstration is adequate. Therefore, as a practical matter, EPA finds 
it difficult to imagine circumstances in which such a limitation would 
be necessary for permitted CAFOs subject to this NSPS no discharge 
standard.

F. New Source Performance Standards for Subpart D Facilities

    This action responds to the Second Circuit's remand of certain 
aspects of the 2003 New Source Performance Standards (NSPS). First, EPA 
has deleted the remanded provisions that authorized two alternatives 
for compliance with the NSPS requirement for no discharge of manure, 
litter, or process wastewater into waters of the U.S. from the 
production area. Second, EPA is promulgating a new provision that would 
allow a CAFO using an open surface manure storage structure to request 
the NDPES permitting authority to establish site-specific effluent 
limitations for its NPDES permit that incorporate the NSPS no discharge 
requirement. These best management practices effluent limitations 
include design specifications and operational parameters and must be 
based on a technical evaluation of the adequacy of the CAFO's storage 
structure for achieving no discharge of manure, litter, or process 
wastewater into waters of the U.S. The new provision prescribes in 
detail the elements of that technical evaluation. A facility designed, 
constructed, operated, and maintained in accordance with these effluent 
limitations will meet the NSPS requirement for no discharge.
    This provision will have several positive ancillary effects. Some 
CAFOs may be reluctant to use innovative technologies that incorporate 
open storage as part of their manure management system in view of the 
no discharge requirements of Subpart D. This provision creates an 
incentive for the use of innovative technologies to meet the no 
discharge requirement by providing an up-front determination that the 
CAFO will meet the no discharge requirement prior to potentially 
expensive construction. Second, in the case of new source Subpart D 
CAFOs that do apply for a permit, this provision provides for an up-
front determination subject to public participation as part of the 
permitting proceeding, that the CAFO will meet the no discharge 
requirement. Finally, because facilities subject to no discharge of 
manure, litter, or process wastewater pollutants into waters of the 
U.S. may choose not to obtain a permit, and therefore are not eligible 
for upset and bypass defenses, the protection afforded by this 
provision provides an incentive for CAFOs to obtain a permit.
1. Background
    The 2003 CAFO rule established NSPS for swine, poultry, and veal 
calf CAFOs as ``no discharge of manure, litter, or process wastewater 
pollutants into waters of the U.S. from the production area.'' The rule 
provided two compliance alternatives that allowed a CAFO in these 
categories to meet this requirement by showing that either (1) its 
production area was designed, constructed, operated, and maintained to 
contain all manure, litter, or process wastewater, and precipitation 
from the 100-year, 24-hour storm, or (2) it would comply with 
``voluntary superior environmental performance standards'' based on 
innovative technologies. The ``voluntary superior environmental 
performance standards'' provision would allow a discharge from the 
production area if the discharge was accompanied by an equivalent or 
greater reduction in the quantity of pollutants released to other media 
(e.g., air emissions).
    The Second Circuit Court of Appeals remanded aspects of the NSPS to 
the Agency, holding that there was not adequate support in the record 
for the alternative standards. Specifically, the court directed EPA to 
clarify the statutory and evidentiary basis for allowing CAFOs to 
comply with a no discharge NSPS through either a production area 
containment structure or an alternate performance standard. With 
respect to the 100-year storm standard, the court noted that while 
certain studies showed that production area BMPs would have 
substantially prevented the production area discharges documented in 
the record, substantially preventing discharges is not the same as no 
discharge. With respect to the alternative performance standards, the 
court held that EPA had not justified its decision to allow compliance 
with the no discharge standard through an alternative standard that 
permits production area discharges so long as the aggregate pollution 
to all media is equivalent to or lower than that resulting from the 
baseline standards. The court further held that EPA did not provide 
adequate notice for either of these provisions under the CWA's public 
participation requirements. See 33 U.S.C. 1251(e) (public participation 
in the development, revision, and enforcement of any regulation, 
standard, effluent limitation, plan, or program established by the 
Administrator or any State under this Act shall be provided for, 
encouraged, and assisted by the Administrator and the States).
2. This Final Rule
    This final rule makes the following changes to the 2003 NSPS in 
subpart D. First, EPA is deleting 40 CFR 412.46(a)(1) that allowed 
subpart D CAFOs subject to NSPS to meet the no discharge standard 
through the use of a 100-year, 24-hour rain event containment 
structure. In a conforming change, EPA is also modifying 40 CFR 
412.37(a)(2) to remove the reference to such structures from Sec.  
412.37(a)(2). EPA is, however, retaining the requirement in Sec.  
412.37(a)(2) that all open surface liquid impoundments have a depth 
marker. The land application requirements for new sources remain 
unchanged.
    The record for the 2003 NSPS showed that new facilities routinely 
include systems and employ practices that result in no discharge of 
manure, litter, or process wastewater pollutants into waters of the 
U.S. from the production areas. Based on this information, EPA 
determined that a no discharge standard represented the best available

[[Page 70460]]

demonstrated control technology for new sources. EPA now recognizes 
that a system that is properly designed, constructed, operated, and 
maintained to contain precipitation from the 100-year, 24-hour event 
may still discharge as a result of multiple unusual and severe 
precipitation events. Given the record information, EPA now agrees that 
a system designed, constructed, operated, and maintained to contain 
precipitation from the 100-year, 24-hour storm event is not necessarily 
equivalent to no discharge and has consequently deleted this provision.
    Second, EPA is deleting 40 CFR 412.46(d) to remove the alternative 
voluntary superior performance NSPS for new swine, poultry, and veal 
calf sources in light of the Second Circuit Court of Appeals ruling.
    Third, EPA is promulgating a new provision that authorizes the 
permitting authority to develop a site-specific, no discharge NSPS for 
new CAFO's using open storage containment structures. Thus, this rule 
provides that the NPDES Program Director may establish no discharge 
best management practice effluent limitations based upon a site-
specific evaluation for an individual CAFO. CAFOs may request permit 
writers to establish no discharge best management practice effluent 
limitations on a case-by-case basis when the facility demonstrates 
through a rigorous modeling analysis that it has designed a containment 
system that will comply with the no discharge requirement. After such 
site-specific standards are established, a facility will be in 
compliance with the no discharge requirement if its containment system 
has complied with all of the specified site-specific design, 
construction, operation, and maintenance components of such a system 
demonstrated to meet the no discharge requirement.
3. EPA's Decision To Authorize Site-Specific, No Discharge Effluent 
Limitations
    In its 2006 proposal, EPA proposed an alternative no discharge 
requirement that would authorize the NPDES Program Director to 
establish no discharge, BMP effluent limitations based upon a site-
specific evaluation for an individual CAFO. A complete discussion of 
the proposal may be found at 71 FR 37,760-62. Such limitations would 
provide an alternate approach for CAFOs to meet the no discharge 
requirement through limitations designed to ensure no discharge of 
manure, litter, or process wastewater pollutants into waters of the 
U.S.
    Specifically, EPA proposed to authorize permit writers, upon 
request by a CAFO, to establish no discharge BMP effluent limitations 
on a case-by-case basis when a facility demonstrated through a rigorous 
modeling analysis that it could design, construct, operate, and 
maintain an open containment system that would comply with the no 
discharge requirement. When a facility complied with all of the site-
specific design, construction, operation, and maintenance components of 
such a system--all of which are conditions of its permit--the CAFO 
would be deemed to be in compliance with the no discharge requirement 
even in the event of an unanticipated discharge. EPA is promulgating 
the provision in essentially the same form as it was proposed.
    Commenters raised a number of concerns with this provision. 
Commenters asserted that the alternative provision creates an exception 
to the no discharge requirement. Some commenters viewed the modeling 
exercise as an ineffective substitute for meeting effluent limitations. 
Commenters also questioned the enforceability of the alternative 
provision if a new source would have a discharge.
    A number of reasons support EPA's decision to promulgate this 
provision and should allay commenters' concerns. First, the alternative 
provision requires a CAFO to demonstrate to the satisfaction of the 
permitting authority, after public notice and comment on the 
demonstration, that its open storage system is a no discharge system. 
In order for a new CAFO employing an open storage system to obtain no 
discharge BMP effluent limitations, the CAFO must demonstrate that the 
entirety of its operation including its production area, site-specific 
NMP and other best management practices are designed to ensure no 
discharge from the entire CAFO. Because this demonstration must be 
based on the use of a prescribed model and precipitation data for 100 
years, any showing of no discharge will necessarily account for a wide 
range of circumstances. Given the stringency of the required modeling 
exercise, described more fully below, a successful no discharge 
demonstration means that the site-specific limitations, in fact, are 
equivalent to a no discharge requirement. Moreover, because this 
demonstration will be subject to public participation requirements that 
apply to any permitting proceeding, commenters are assured that there 
will be an opportunity for public review of the assumptions used to 
support the no discharge conclusion. Further, the final determination 
will also be subject to judicial review as would be the case with any 
other final permit decision.
    Second, the argument that site-specific no discharge limitations 
are not true no discharge limitations reflects a fundamental 
misunderstanding on commenters' part. Commenters fail to recognize that 
the provision allowing site-specific, no discharge effluent limitations 
essentially places a CAFO with such limitations in the same position as 
a CAFO without such limitations. Commenters have apparently forgotten 
that, even in the absence of a provision like that promulgated today, 
permitted facilities that are subject to no discharge effluent 
limitations may discharge and not be subject to an enforcement action 
(or have a defense to any enforcement action) in certain uncontrollable 
and unforeseeable circumstances. The 2003 CAFO rule specifically 
provided for the availability of an upset/bypass defense from an 
enforcement action. See 40 CFR 412.47(a)(3) (``Provisions for upset/
bypass as provided in 40 CFR 122.41(m)-(n) apply to a new source 
subject to this provision.'').
    Thus, EPA NPDES regulations currently would provide a defense to an 
enforcement action, albeit in severely restricted circumstances, for 
discharges from any permitted new source CAFO. Under the 2003 rule, 
``no discharge'' for those facilities, in fact, means no discharge 
except in certain narrowly prescribed circumstances. The demonstration 
required under this rule to support the establishment of alternative 
site-specific no discharge limitations is designed to show that there 
will be no discharge from the CAFO except in exactly the circumstances 
provided in EPA's upset/bypass regulations and described under the 2003 
rule.
    Under EPA's regulations, an ``upset'' is defined as ``an 
unintentional and temporary noncompliance with technology based permit 
effluent limitations because of factors beyond the reasonable control 
of the permittee.'' 40 CFR 122.41(n). Under the regulations, the upset 
defense to an enforcement action would not be available to the extent 
that the noncompliance with permit conditions was due to operational 
error, an improperly designed treatment system, inadequate treatment 
system, improper maintenance or careless and improper operation. 40 CFR 
122.41(n)(1).
    This rule adopts requirements for an upfront demonstration that 
parallel the conditions under which an upset/bypass defense would be 
available in the event of a discharge from a no

[[Page 70461]]

discharge facility. It provides that, before a permit writer may 
establish site-specific limitations, the permittee must demonstrate 
through a rigorous modeling exercise that its open containment system 
would not discharge. Given the requirement for evaluation of the 
system's adequacy (size, operational practices, maintenance conditions 
and other factors) using precipitation data for 100 years, such an 
assessment would support the conclusion that any discharge that might 
occur results from ``factors beyond the reasonable control of the 
permittee,'' the conditions under which the upset/bypass defense would 
be available. Moreover, as noted, all of the design, construction, 
operation, and maintenance components evaluated for the site-specific 
permit become permit conditions. This similarly mirrors the provisions 
of the upset regulations which do provide for a defense only in the 
limited circumstances outlined in Sec.  122.41(n)(1), e.g., no 
operational error, improper design, or other factors as described 
above. As a consequence, this alternative NSPS provision requires an 
upfront determination that the CAFO would only discharge in 
circumstances that would parallel those for which an upset/bypass 
defense would be available.
    This final rule's new NSPS provision allowing site-specific BMP 
effluent limitations gives the CAFO complying with its permit 
conditions more certainty that its operations meet its CWA 
requirements. The permitting process has already established that the 
discharge is unintentional and beyond the reasonable control of the 
permittee. Therefore, in the extremely unlikely event of a discharge 
from a new source that is complying with a permit containing these 
site-specific no discharge effluent limitations, the CAFO would already 
have established in the permitting process an affirmative defense with 
respect to any discharge, and would not need to rely on Sec.  
122.41(n).
    Establishment of these no discharge, BMP effluent limitations 
represents a determination by the permit writer that the CAFO will not 
discharge. The only time a CAFO under this provision could potentially 
discharge would be in an extreme, rare event not reasonably foreseeable 
or under the reasonable control of CAFO as demonstrated in the 
permitting process and explained above.
    Fourth, while site-specific BMP effluent limitations provide 
greater certainty to CAFOs, they also provide the permitting authority 
and citizens more specific measures of compliance than is the case for 
CAFOs without such permit conditions. Unlike a CAFO that does not 
discharge or propose to discharge and therefore chooses not to seek 
permit coverage, a CAFO relying on site-specific BMP effluent 
limitations would have a permit and permit terms that include the 
design, construction, operation, and maintenance measures that formed 
the basis for the permitting authority's determination that the CAFO 
will meet no discharge. Because the elements demonstrating no discharge 
are permit conditions established in a process that provides for public 
participation and on-going oversight, use of this alternative should 
further ensure compliance with the no discharge requirements.
    So long as the facility complies with its BMP effluent limitations 
(and other terms of the permit such as monitoring or recordkeeping 
requirements), the CAFO will not be subject to enforcement action. EPA 
underscores for the regulated community that the protections afforded 
by this provision are only available through permits issued to new 
source CAFOs. EPA further wishes to emphasize that the more general 
upset and bypass regulations are only available to permitted CAFOs, and 
are otherwise unaffected by this NSPS provision.
    Finally, policy considerations support the Agency's adoption of an 
alternative no discharge approach. EPA encourages CAFOs to implement 
anaerobic digesters, multi-cell treatment lagoons, and nitrification/
denitrification technologies. In addition, EPA wants to encourage the 
development of innovative technologies for meeting the no discharge 
requirement. To do this, CAFOs want certainty that the technologies 
they develop and implement will comply with the CWA. EPA recognizes 
that the upset and bypass provisions do not provide certainty to the 
operator that any discharge will be excused. In particular, CAFOs 
operating innovative or advanced technologies may be reluctant to rely 
on the standard upset and bypass provisions. Under the regulation 
adopted here, an operator must demonstrate to the permitting 
authority's satisfaction, after public comment, that an innovative 
approach that includes an open storage system will be designed, 
constructed, operated, and maintained to achieve no discharge. This 
demonstration would mean that this CAFO would not discharge, except 
during an event beyond the CAFO's reasonable control; an event that 
could be excused under the normal upset provisions. Once this 
demonstration has been made, it makes sense to provide the CAFO with 
the certainty that would eliminate the need for the CAFO to go through 
the upset/bypass process in most circumstances.
    In addition, this approach is consistent with CWA section 101(f), 
requiring EPA to use efficient procedures for decision-making. Because 
of this provision, in the rare occurrence of a catastrophic event, this 
provision would relieve permitting authorities and CAFOs from the 
typical procedures necessary to meet the upset/bypass requirements.
4. Discussion of the New Provisions
    The CAFO NSPS provisions adopted today require an evaluation of the 
adequacy of the designed storage facility using the AWM (Animal Waste 
Management) tool and an evaluation of overall water budgets using SPAW 
(Soil Plant Air Water) Field and Pond Hydrology Tool, or equivalent 
analytic tools. EPA has concluded that 100 years of climate data is an 
ample time frame for simulation purposes and will support a reasonable 
finding that the system will not discharge. However, EPA is aware that 
100 years of continuous rainfall data may not be available for all 
CAFOs. Models can be run using actual rainfall data where available, 
and then simulated with a confidence interval analysis over a period of 
100 years.\6\
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    \6\ Some commenters confused the 100-year simulation analysis 
with the requirement in the 2003 final CAFO rule for a system 
designed to contain the precipitation associated with the 100-year, 
24-hour storm design event. Neither the proposed revisions nor these 
final requirements for new sources subject to subpart D refer to the 
100-year storm event.
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    AWM 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 thus determine the size of needed storage 
facilities. AWM accounts for wastewater, flush water, precipitation, 
runoff, and other additions to the waste stream. AWM can estimate 
storage facility sizes using either a defined storage period or by 
drawdown dates specified by the user. A monthly water and waste budget 
for each storage component is generated, in most cases allowing the 
CAFO to demonstrate no discharge from the entire production area. The 
procedures and calculations used in AWM are based on the USDA-NRCS 
Agricultural Waste Management Field Handbook.
    The SPAW model consists of two linked routines. The first routine 
develops field hydrologic budgets based upon daily climatic data, crop 
data, and hydraulic characteristics of the soil profile. The second 
routine utilizes the

[[Page 70462]]

climatic and hydrologic outputs of one or more farm fields as the input 
to hydrologic budgets for downstream ponds. These daily pond water 
budgets can be used to evaluate the performance, operation or 
reliability for many types of ponds such as liquid waste storage 
facilities. Water budget processes may be evaluated by making daily 
adjustments to crop canopy cover and antecedent soil moisture. For each 
user-specified soil profile and crop rotation, SPAW simulates possible 
runoff from fields as well as the irrigation water needs of fields 
receiving the manure storage effluent. Hydrologic groups are used by 
the model to rate soils for the potential to release excess water down 
grade.
    AWM tracks gross nutrients, but does not track the mass or 
concentration of nutrients. Further, the storage period or drawdown 
schedule is usually determined by the individual CAFO. Therefore, the 
CAFO's NMP must be used as an input to confirm both a water balance and 
a nutrient balance has been achieved by the CAFO. The NSPS provisions 
require that each CAFO use the SPAW tool to assess daily hydrologic 
budgets for each field. The complete modeling demonstration shows not 
only that the storage facility does not discharge, but also that there 
is no runoff of process wastewater from fields during land application 
activities consistent with the CAFO's NMP, which is necessary to ensure 
that the open containment system is operated in a way to meet the land 
application requirements of the rule. In EPA's view, the requirement to 
use the SPAW model (or an equivalent approved by the permitting 
authority) ensures CAFOs will rely on appropriate operational measures 
to achieve no discharge standards.
    The CAFO NSPS provisions require certain specified information 
regarding design, construction, operation, and maintenance of the 
system to be included in the CAFO's NMP under 40 CFR 122.42(e)(1). This 
includes the key user-defined inputs and model system parameters. CAFOs 
must submit a site-specific analysis to the Director. See 40 CFR 
412.46(a)(1). These site-specific design, construction, operation, and 
maintenance measures are enforceable requirements in the CAFO's permit. 
As long as the CAFO complies with these requirements, the CAFO 
presumptively meets the no discharge requirement. EPA has determined 
that the final rule revisions provide a clear and enforceable standard 
for the CAFO to achieve as well as providing assurance to the public 
that the proposed system complies with the no discharge requirement.
    Under these final amendments to the NSPS, the Director has the 
discretion to require additional information from a new source subpart 
D CAFO owner or operator to support site-specific BMP effluent 
limitations. The burden is on the CAFO to demonstrate that any proposed 
system it employs, including an open system, meets the new source 
standard. EPA expects CAFOs will utilize the most current version of 
AWM and SPAW when submitting their demonstration to the permitting 
authority. However, EPA is aware that other peer-reviewed models and 
programs have been or may be developed that could be determined to be 
equivalent to AWM and SPAW. Therefore the rule gives the Director the 
discretion to approve design software or procedures equivalent to AWM 
and SPAW. Once approved by the Director, the public still would have 
the opportunity to comment on the CAFO's submitted modeling and 
demonstration as discussed earlier.
    The information, design, and evaluation process required of all 
CAFOs wishing to avail themselves of this alternative is intended to 
allow CAFOs the flexibility to demonstrate compliance with the no 
discharge requirements for any type of open storage facility. As a 
practical consideration, EPA expects most CAFOs selecting this 
compliance alternative will submit designs for open manure storage 
structures accompanied by a narrow range of acceptable operation and 
management practices. However, for a given type of storage facility 
design (for example, an integrator with several company-owned CAFOs 
each designed and constructed in an essentially identical manner within 
the same county), EPA believes it is possible to conduct a series of 
assessments that together fully encompass the range of operational and 
management measures that would be used across multiple CAFOs with the 
specified storage facility design. In this case, SPAW could be run to 
validate a wide range of NMP and storage pond management scenarios (to 
continue the above example, the CAFOs all have the same sets of crops, 
soil types, land application equipment, etc.). This alternative does 
not change the requirement for a CAFO to develop a site-specific NMP. 
These final amendments authorize the permitting authority to determine 
that any CAFO using the specified facility type and submitting an NMP 
that falls within the pre-approved range of operational and management 
practices would not need to conduct an individualized assessment step 
(i.e., the validation using SPAW).
    The availability and use of such a geographical and categorical 
approach will require that the permit writer determine that a number of 
conditions are met. First, the assessment must fully account for all 
pertinent factors relevant to determination of the potential for 
discharge from an open storage system. The assessment must also include 
all parameters necessary to mirror properly the range of soil, plant, 
climatic, and hydrological conditions within the geographical area for 
which the assessment is intended to be representative. Second, the 
permittee must establish that the parameters reflected in the general 
assessment used to establish no discharge are, in fact, representative 
of those parameters for each CAFO. Finally, the assessment must reflect 
the operational and management practices to be employed by each CAFO at 
each individual site. As with the individual assessment, each CAFO must 
have a site-specific NMP that includes the operational and management 
measures utilized in the geographical assessment.
    EPA is eliminating the requirement to indicate the capacity for a 
100-year, 24-hour storm for new sources. EPA is maintaining the 
requirement to have a depth marker for all open storage structures. In 
EPA's view, a marker indicating the storage pond or containment depth 
can be an excellent means of displaying how much storage a CAFO has, 
whether it is time to pump down levels in the lagoon, pond, or other 
storage structure, or whether alternative management steps must be 
taken to prevent a full storage structure and potential overflow. 
Existing sources and new sources subject to subpart C continue to have 
the requirement for a depth marker that indicates the 25-year, 24-hour 
storm event. New sources subject to subpart D and using an open storage 
structure must use the depth marker to indicate the maximum volume of 
manure and process wastewater the structure is designed to contain.
    While one component of preventing discharge from an open system is 
to provide adequate storage of manure and wastewater during critical 
periods, ensuring adequate physical capacity is not sufficient. Rather, 
determining whether there is adequate storage is based on a site-
specific evaluation of the CAFO's entire waste handling system. 
Adequate storage has to be based on climate-specific variables that 
define the appropriate storage volume, but of equal importance are the 
nutrient management plan and other

[[Page 70463]]

management decisions that specify when and how the storage can be 
emptied. The link between adequate storage and land application 
practices is one of the most critical considerations in developing and 
implementing a site-specific nutrient management plan. For example, the 
amount of land available for application, the hydraulic limitations 
(ability of the land to handle additional water without the occurrence 
of runoff), geology, and soil properties of the available land base can 
play an important role. See Chapter 2 of EPA's technical guidance for 
CAFOs ``Managing Manure Nutrients at Concentrated Animal Feeding 
Operations'' (EPA-821-B-04-00) for more information. EPA expects these 
criteria preclude a CAFO from withdrawing manure and process wastewater 
from liquid storage structures and subsequently land applying process 
wastewater at inappropriate times. Given these considerations, EPA is 
establishing procedures for approval of site-specific management 
practices for open containment systems with the expectation that a 
system can be designed and operated to meet the no discharge standard. 
EPA has concluded that the design, construction, operation, and 
maintenance elements and the comprehensive analytical assessment are 
sufficient to achieve this objective.

G. BCT Limitations for Fecal Coliform

    In response to the Second Circuit remand, EPA is today 
affirmatively finding that the best conventional pollutant control 
technology (BCT) limitations it adopted in 2003 do, in fact, represent 
the best conventional control technology limitations for fecal 
coliform. After assessing various conventional pollutant removal 
technologies, EPA has determined that there are no available and 
economically achievable technologies that are cost reasonable that 
would result in greater removal of fecal coliform than the technologies 
on which EPA based the 2003 best practicable control technology 
currently available (BPT) and BCT effluent limitations guidelines 
(ELG).
    As EPA has explained, establishing BCT limitations begins by 
identifying technology options that provide additional conventional 
pollutant control beyond the level of control provided by BPT effluent 
limitations. Any such candidate technologies are then evaluated to 
determine if they meet the threshold CWA requirements of 
``availability'' and ``economic achievability.'' 51 FR 24,974, 24,976; 
July 9, 1986. A technology is economically achievable if its costs may 
be ``reasonably borne'' by the CAFOs. Waterkeeper Alliance et al. v. 
EPA, 399 F.3d 486, 516 (2d Cir. 2005). The Clean Water Act adds an 
additional evaluation step to the effluent limitations development 
process for conventional pollutants. ``In addition to the Clean Water 
Act requirement that effluent limitations be economically achievable, 
the cost associated with the BCT effluent limitations must also be 
`reasonable' in relation to the effluent pollutant reductions.'' 51 FR 
24,974. In determining this, the statute requires that EPA look at a 
number of factors including a comparison of the cost of effluent 
reductions for POTWs to that for direct dischargers using candidate BCT 
technologies. Thus, the statute requires that, not only must the costs 
of additional control be costs that CAFOs may reasonably bear 
(economically achievable), but the costs must also be reasonable 
relative to the costs for POTWs to achieve such conventional pollutant 
reductions.
    EPA evaluated 41 BCT candidate technologies for this rule and 
determined that all but two of them were either not available 
(technically feasible for all CAFOs in a subcategory) or not 
economically achievable. For the remaining two technologies, while 
their costs are high and EPA believes it likely that they are also not 
economically achievable, EPA was unable to conduct its traditional 
tests for economic achievability and thus has not determined in this 
rule whether or not they are economically achievable. However, EPA has 
determined that these two technologies, even if economically 
achievable, would not be cost reasonable, and has therefore rejected 
them as BCT technologies.
    As a result of this assessment, EPA has concluded that there are no 
available and economically achievable technologies that are cost 
reasonable that would provide greater fecal coliform removal than the 
BPT technology. How EPA performed this assessment and the results of 
that assessment supporting EPA's finding that the 2003 BPT/BCT 
limitations represent BCT technology for controlling fecal coliform is 
described in detail below.
1. The Waterkeeper Decision
    As previously noted, the Waterkeeper court remanded the 2003 CAFO 
rule's BCT standard for further clarification and analysis with regard 
to the appropriate BCT standard for pathogens.\7\ EPA's 2003 rule 
established non-numeric effluent limitations based on BPT and the best 
available technology economically achievable (BAT) as well as BCT 
limitations. In the 2003 CAFO rule, EPA established BPT effluent 
limitations guidelines for Large beef, dairy, and veal calf (Subpart 
C), swine and poultry (Subpart D) CAFOs.
---------------------------------------------------------------------------

    \7\ As the Second Circuit recognized, the CWA lists only one 
pathogen, fecal coliform, as a conventional pollutant for which BCT 
limitations are required. Waterkeeper, 399 F.3d at 518. Section 
304(a)(4) of the CWA provides that EPA may identify additional 
pollutants as conventional pollutants. EPA has identified only one 
additional pollutant, oil and grease as a conventional pollutant. 
Thus, the only pathogen subject to the Second Circuit remand is 
fecal coliform.
---------------------------------------------------------------------------

    At that time, EPA concluded that there were no available BCT 
technologies on which to base limits for conventional pollutants that 
were more stringent than the BPT limitations, and EPA therefore 
established BCT requirements equal to BPT limitations. EPA based this 
determination in part on the combined pollutant reductions (Table 7.2 
of 68 FR 7239), and in particular its evaluation of the reductions in 
discharges of the conventional pollutants (TSS, BOD, and fecal 
coliform) associated with the various technology options it considered. 
71 FR 37,763. EPA noted difficulties in quantifying the loadings and 
reductions in discharges of these pollutants--in particular, in 
assessing fecal coliform--and relied primarily on reductions in 
sediment discharges as a surrogate for reductions in TSS in reaching 
its BCT determination. EPA concluded that there were no technologically 
feasible candidate BCT technologies that would achieve greater TSS 
removals than the BPT requirements for either Subpart C or Subpart D 
facilities, and no economically achievable technologies for Subpart C 
facilities that would reduce discharges of BOD. Consequently, EPA found 
that there were no BCT technologies for establishing limits on 
conventional pollutants that would achieve greater removal than the BPT 
technology and established BCT requirements that were equal to BPT. 68 
FR 7224.
    While EPA's assessment of the effectiveness of various control 
options did attempt to measure pathogen reductions for the final rule, 
EPA did not establish any specific BPT or BCT limitations to control 
fecal coliform, a conventional pollutant and pathogen. The Waterkeeper 
court remanded the 2003 CAFO rule's BCT standard for further 
clarification and analysis because EPA had failed to make an 
affirmative finding that the BCT limitations it had adopted in fact 
represented the best conventional

[[Page 70464]]

pollutant control technology for reducing pathogens--specifically, 
fecal coliform. 399 F.3d at 519. EPA's final rule issued today responds 
to the court's remand.
    As EPA proposed, in this final rule EPA is affirmatively concluding 
that the current BCT limitations for conventional pollutants represent 
the best conventional control technology for fecal coliform and is 
establishing BCT limitations for fecal coliform that are equal to the 
current BPT/BCT limitations. These limitations prohibit the discharge 
of manure, litter, or process wastewater into waters of the U.S. from 
the production areas of CAFO except in limited circumstances. A 
discharge is allowed only if an existing, permitted CAFO has a properly 
designed, constructed, and operated storage structure with the capacity 
to contain all manure, litter, and process wastewater associated with 
the facility as well as the runoff and direct precipitation from a 25-
year, 24-hour rainfall event. See 40 CFR 412.31(a). The current rules 
also provide that a Large CAFO that land applies manure, litter, or 
process wastewater must do so in accordance with several BMPs: A 
nutrient management plan that includes the determination of application 
rates for manure, litter, and process wastewater; a field-specific 
assessment of the potential for nitrogen and phosphorus transport from 
the field to surface waters; manure and soil sampling; and setback 
requirements. See 40 CFR 412.4. EPA is not promulgating more stringent 
BCT limitations for fecal coliform because there is no available, 
achievable, and cost reasonable technology on which to base such 
limitations.
2. Background
    The CWA requires point sources to achieve effluent pollutant levels 
established by EPA that are attainable through progressively more 
stringent pollutant control technology. The CWA calls for technology-
based control in two stages. As originally enacted in 1972, the Act 
required existing point sources to comply in the first stage with EPA-
established limitations that are achievable by application of the 
``best practicable control technology currently available'' or ``BPT.'' 
These limitations control conventional, toxic, and nonconventional 
pollutants. EPA has typically based BPT limitations on the average 
pollutant removal performance of the best facilities examined by EPA. 
The 1972 Act also required existing point sources to comply in the 
second stage with EPA-established limitations that are achievable by 
the application of ``best available technology economically 
achievable,'' or ``BAT.'' In 1972, these limitations also controlled 
conventional, toxic and non-conventional pollutants.
    The 1977 amendments to the CWA replaced BAT for conventional 
pollutants with limitations that represent ``best conventional 
pollutant control technology'' or ``BCT.'' Section 304(a)(4) designates 
the following as conventional pollutants: Biochemical oxygen demand 
(BOD), total suspended solids (TSS), fecal coliform (FC), pH, and any 
additional pollutants defined by the Administrator as conventional. The 
Administrator designated oil and grease as an additional conventional 
pollutant, on July 30, 1979 (44 FR 44,501), but has listed no other 
pollutants for regulation as conventional pollutants.
    The decision to amend section 304(a) of the CWA to require 
achievement of BCT, rather than BAT, for control of conventional 
pollutants reflected two factors. The first was Congressional desire 
not to require ``treatment for treatment's sake'' and the second, 
Congress's view that BAT control of conventional pollutants might not 
be necessary to achieve the water quality goals of the Act. S.Rep. No. 
370 at 43, 1st Sess. 43 (1977), reprinted in Comm. on Env. and Public 
Works, 95th Cong., 2d Sess., A Legislative History of the Clean Water 
Act of 1977 at 676-77 (hereinafter ``Legislative History'').
    The CWA Amendments of 1977 that require EPA to determine BCT 
limitations also specify the factors to be taken into account in this 
determination of BCT. Section 304(b)(4)(B) provides that the factors to 
be assessed:

    [S]hall include consideration of the reasonableness of the 
relationship between costs of obtaining a reduction in effluents and 
the effluent reductions benefits derived, and a comparison of the 
cost and level of reduction of such pollutants from the discharge 
from publicly owned treatment works to the cost and level of 
reduction of such pollutants from a class or category of industrial 
sources. * * * 33 U.S.C. 1314(b)(4)(B).\8\
---------------------------------------------------------------------------

    \8\ As the Conference Report to the 1977 amendments explained:
    The cost test for conventional pollutants is a new test. It is 
expected to result in a determination of reasonableness which could 
be somewhat more than best practicable technology or could be 
somewhat less than best available technology for other conventional 
pollutants. The result of the cost test could be a 1984 requirement 
which is no more than that which would result from best practicable 
technology but also could result in effluent reductions equal to 
that required in the application of best available technology. Joint 
Explanatory Statement of the Committee of Conference, 95th Cong. 1st 
Sess., H.R. No. 95-830 at 85, Legislative History at 269.

    In the words of Senator Muskie, the Senate Floor Manager and 
---------------------------------------------------------------------------
leading sponsor of the amendments:

    The Administrator must determine whether or not the cost of 
achieving reductions of conventional effluent bears a reasonable 
relationship to the amount of effluent reduction achieved. In making 
this determination, the Administrator is to compare the costs of 
industrial effluent reduction to the cost of municipal waste 
treatment. Legislative History at 458.

    Accordingly, EPA developed a ``BCT Methodology'' to answer the 
question of whether it is ``cost-reasonable'' for industry to control 
two conventional pollutants, BOD (or oil and grease in the case of 
certain metals industries) and TSS, at a level more stringent than 
already required by BPT effluent limitations. EPA first explained its 
BCT methodology when it promulgated BCT effluent guidelines for 41 
industry subcategories (44 FR 50,732; August 29, 1979).\9\ The crux of 
the methodology was a comparison of the costs of removing the 
conventional pollutants BOD (or oil and grease) and TSS for a candidate 
BCT technology within a particular industry segment, to the costs of 
removal for an average-sized POTW.
---------------------------------------------------------------------------

    \9\ As noted above, the 1977 amendments established a second 
level of technology-based controls for conventional pollutants-BCT 
limitations. Accordingly, in 1979, pursuant to Congressional 
direction, EPA completed its review of then-existing BAT limitations 
for conventional pollutants to determine if they were more stringent 
than would be required by BCT technology. EPA limited its review to 
limitations for, and correspondingly developed its BCT methodology 
to address, only two categories of conventional pollutants: BOD (or 
oil and grease) and TSS. 44 FR 50,732-33. Noting the industries 
under consideration do not have fecal coliform discharges, EPA 
performed no analysis for fecal coliform.
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    A number of industries and industry associations challenged the 
regulation, and, in 1981, the U.S. Court of Appeals for the Fourth 
Circuit remanded it to the Agency, directing EPA to include an 
assessment of the cost-effectiveness of industry conventional pollutant 
removal in addition to the POTW test in its evaluation of cost 
reasonableness. American Paper Inst. v. EPA, 660 F. 2d 954 (4th Cir. 
1981). EPA proposed a revised BCT methodology in 1982 (47 FR 49,176) 
that addressed the industry cost-effectiveness test (the ``second'' 
test), again limited to the conventional pollutants BOD and TSS. EPA 
proposed to base the POTW benchmark on model plant costs in a 1984 
notice (49 FR 37,046). The final BCT methodology, promulgated as a rule 
in 1986 (51 FR 24,974), maintained the basic approach of the 1982 
proposed BCT methodology while also updating POTW removal cost with new 
POTW data. EPA again specifically noted that it had developed

[[Page 70465]]

its BCT methodology to evaluate more stringent BOD or TSS limits.
3. EPA's BCT Determination in the 2003 Rule
    As previously explained, EPA established BCT requirements equal to 
BPT in the 2003 CAFO rule (see 40 CFR 412.33 and 412.44). For its 
assessment of BCT limitations, EPA first considered whether there were 
any technically feasible technologies that would achieve greater 
conventional pollutants removals than the BPT limitations. Because of 
the difficulties in quantifying reductions of conventional pollutant 
discharges,\10\ EPA relied primarily on sediment discharges (as a 
surrogate for TSS) in evaluating potential BCT requirements. EPA 
identified no BCT technology option that achieves significantly greater 
TSS removals than the BPT requirements eventually promulgated in 2003 
with one exception. This option would have prohibited any discharge 
from swine and poultry CAFOs. Because this option was not an 
economically achievable one, EPA therefore concluded that there were no 
BCT technologies on which to base limits for conventional pollutants 
that were more stringent than BPT. EPA did note that if it had 
identified available and economically achievable technology options 
that achieve greater reductions of conventional pollutants than are 
achieved by BPT, then EPA would have evaluated these technologies 
applying EPA's two-part BCT cost test. 68 FR 7224.
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    \10\ For example, EPA could not easily assess fecal coliform 
loadings because they vary greatly depending on site 
characteristics. Further, quantifying discharges of other 
conventional pollutants is complicated by the challenge of 
distinguishing between CAFO and non-CAFO sources. 71 FR 37,763.
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    EPA also evaluated pathogen reductions associated with the 2003 BPT 
limitations. The BPT limitations prohibit dry weather discharges from 
land application areas, and the BPT land application requirements 
(including technical standards for timing, form, and rate of 
application, as well as the required vegetated buffer, setback, or 
equivalent practices) already minimize discharges from land application 
areas. The BPT production area requirements prohibit discharges, except 
for overflows from liquid storage structures that meet certain design 
and operational criteria. EPA used fecal coliform and fecal 
streptococcus as surrogates to estimate the pathogen reductions 
achieved by the CAFO rule requirements. EPA concluded that the BPT 
limitations would reduce these two pathogens by 2.7 x 1022 
colony forming units (CFU), or a 46 percent reduction over baseline 
pollutant loadings. See Chapter 12 of ``Development Document for the 
Final Revisions to the NPDES and the Effluent Guidelines for CAFOs'' 
EPA-821-R-03-001. Other pathogens would likely be reduced by a similar 
degree. EPA projected $0.3 to $3.4 million in improved shellfish 
harvests associated with reduced pathogen discharges from Large CAFOs. 
68 FR 7240.
4. This Rule
    As noted, EPA has determined that there are no technically feasible 
and economically achievable candidate technologies for fecal coliform 
removal that are cost reasonable and would achieve greater removals 
than the 2003 BPT limitations. The following discussion summarizes the 
basis for this final determination.
(a) EPA's Approach To Establishing BCT Limitations for Fecal Coliform
    As previously explained, the first step to establishing BCT 
limitations is to identify technology options that provide additional 
conventional pollutant control beyond the level of control provided by 
the application of BPT limitations and to evaluate these technologies 
for ``availability'' (including technical feasibility) and ``economic 
achievability.'' See 33 U.S.C. 1311(b)(2)(E). Out of 41 candidate 
technologies, EPA has identified no technologies that are both 
available and achievable for Subpart D facilities, and has identified 
only two available technologies that might be \11\ economically 
achievable for Subpart C facilities.
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    \11\ For Subpart C (beef cattle, heifer, and dairy) facilities, 
in the 2003 final CAFO rule, EPA rejected more stringent BAT options 
on availability, not economic achievability grounds. Thus, for this 
final rule, EPA had no comparison technology that it had already 
determined to be not economically achievable. Thus, while the two 
available technologies have high costs relative to BPT and are 
likely not economically achievable, EPA was not able to determine 
this using its traditional methodology or the analysis from the 2003 
rule.
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    The next step in determining BCT is to evaluate any candidate 
technology that is both technically feasible and economically 
achievable for cost reasonableness. Traditionally, EPA has evaluated 
candidate BCT technologies for cost-reasonableness using a two-part BCT 
cost test it developed for two conventional pollutants, BOD and TSS. 
The test is intended to assess whether there are cost-reasonable 
technologies that will achieve greater BOD and TSS removals than 
required by the BPT technology for an industry category by comparing 
the incremental cost-effectiveness of candidate BCT technologies with 
the incremental cost-effectiveness of BOD and TSS removals at POTWs 
through advanced secondary treatment as compared to secondary 
treatment. This test makes sense for BOD and TSS because advanced 
secondary treatment is specifically designed to remove additional BOD 
and TSS. However, it is not designed for additional fecal coliform 
removal, so the incremental cost-effectiveness of advanced secondary 
treatment in removing fecal coliform is not a good benchmark for use in 
evaluating candidate BCT technologies for fecal coliform removal.
    The methodology is appropriate for BOD and TSS because advanced 
secondary treatment is specific to the removal of BOD and TSS. Costs 
associated with upgrading a POTW from secondary to advanced secondary 
treatment were based on polymer addition to the activated sludge basin. 
The purpose of the polymer addition was to enhance removal of BOD and 
TSS in the secondary clarifier, and achieve final effluent 
concentrations of 20 mg/L BOD5 and 20 mg/L TSS. Therefore, the cost 
increment between secondary and advanced secondary treatment represents 
the incremental cost of removal of additional BOD and TSS at POTWs. 51 
FR 24,981.
    Unlike BOD and TSS, advanced secondary treatment is not designed to 
remove additional increments of fecal coliform beyond secondary 
treatment. When both secondary and advanced secondary treatment systems 
include disinfection, the total fecal coliform removal is nearly the 
same, over 99 percent. Secondary treatment by itself (without 
disinfection) also removes significant amounts of fecal coliform, 
although almost all POTWs include disinfection at some point in their 
treatment train. The polymer addition in advanced secondary treatment 
is not intended for additional fecal coliform removal since both 
secondary and advanced secondary POTWs use disinfection treatments to 
prevent fecal coliform releases to surface water. Therefore, because 
the object of the BCT cost test is to ensure that the costs of 
additional removals of conventional pollutants associated with BCT 
limitations do not exceed POTW conventional removal costs, 
distinguishing fecal coliform removals between advanced secondary 
treatment and secondary treatment is not relevant. Because advance 
secondary treatment is not intended to be more effective than secondary 
treatment at removing fecal coliform (and is not added for this 
purpose), it is not appropriate to apply

[[Page 70466]]

the same POTW cost test used for evaluating BOD and TSS BCT limitations 
to the evaluation of fecal coliform limitations.
    Given these circumstances, EPA recognized that if it were to use a 
similar numeric BCT cost test to evaluate fecal coliform removal for 
BCT, EPA would have to modify the traditional BCT cost test to address 
the issue that advanced secondary treatment at POTWs is not designed to 
remove fecal coliform. When the Agency promulgated the BCT methodology 
(including descriptions of how to apply the cost test), EPA envisioned 
the need for adjustments to the BCT cost test methodology in future 
rulemakings to account for lack of comparable data or other industry-
specific factors. 51 FR 24,974, 24,976. Moreover, section 304(b)(4)(B) 
authorizes EPA to consider other appropriate factors in establishing 
BCT.
    Accordingly, for the proposal, EPA suggested a modified BCT cost 
test. However, based on comments, EPA has identified a number of 
problems with the proposed test. These problems are discussed briefly 
here and described more fully in the Response to Comments Document 
prepared for this rule. First, although the revised test used a 
different cost-effectiveness calculation from the traditional test, it 
still relied indirectly on a comparison of the cost-effectiveness of 
BCT candidate technologies to the cost-effectiveness of advanced 
secondary treatment, even though, as just noted, advanced secondary 
treatment is not designed to remove fecal coliform. Second, the revised 
test did not compare the incremental cost-effectiveness of the 
candidate technologies to the incremental cost-effectiveness of fecal 
coliform removals at POTWs and therefore did not allow a comparison of 
``the cost and level of reduction of [fecal coliform] from the 
discharge from publicly owned treatment works to the cost and level of 
reduction of [fecal coliform] from * * * industry sources * * *'' as 
required by the statute. As a result, EPA has now determined that it 
cannot use the revised test to evaluate cost reasonableness.
    For this final rule, EPA also considered other possible approaches 
for evaluating cost reasonableness. One approach would have been to 
identify a technology that is used at POTWs specifically for fecal 
coliform removal and develop a test similar to the traditional cost 
test but based on this technology. EPA considered disinfection as one 
possible benchmark technology for fecal coliform removal, but 
determined that there is significant variability in the manner in which 
disinfection is used in combination with other technologies at 
different POTWs and it would thus be extremely difficult, both 
theoretically and logistically, to develop a revised benchmark based on 
this technology.
    Consequently, for the final rule, EPA has applied a simplified cost 
reasonableness test designed to specifically address fecal coliform. 
This approach is consistent with section 304(b)(4) of the CWA and is 
one EPA has used in the past. While the traditional cost test compares 
reductions from BCT candidate technologies to those of POTWs, EPA has, 
on occasion, rejected BCT technologies without comparing them to POTW 
performance, even for BOD and TSS. Thus, for example, where EPA lacked 
sufficient data to quantitatively evaluate BOD and TSS reductions under 
the traditional test, EPA rejected more stringent BCT limitations 
solely on the basis of an evaluation of the incremental costs of 
further reductions. See 51 FR 24,974, 24,991.
(b) EPA's Evaluation of Candidate Technologies for Technical 
Feasibility and Economic Achievability
    Based on its consideration of information submitted by commenters 
and its own analysis, EPA has determined that there are only two of 41 
candidate technologies that are technically feasible and may be 
economically achievable that provide greater removals of fecal coliform 
than the technologies selected as the basis for BPT limitations in the 
2003 rule. The discussion below provides the basis for this conclusion.
    In its evaluation of candidate BCT technologies, EPA reviewed data 
on different types of CAFO manure management systems. These systems 
employed treatment technologies, best management practices (BMPs) for 
pollution prevention, and management practices for the handling, 
storage, treatment, and land application of wastes. Sources of 
information included available technical literature, over 11,000 
comments submitted by industry and other public commenters, and 
insights gained from conducting over 116 site visits to CAFOs.
    In its search for candidate technologies, EPA initially reexamined 
the technology options it had considered for the 2003 rule because the 
Agency concluded that these might provide more fecal coliform 
reductions than the option selected for BPT limitations. EPA looked at 
technology Options 3, 5, 6 and 7 described in the proposal at 71 FR 
37,763 and the Technical Development Document. Options 3, 5, 6, and 7 
represented additional controls beyond the controls (e.g., nutrient-
based land application rates and production area discharges only under 
specified conditions). Option 3 would have required a reduction of 
discharges to ground water beneath the production area. Option 5 would 
require total containment of all manure and process wastewater by swine 
and poultry operations. Option 6 would require anaerobic digesters at 
swine and dairy facilities. Option 7 would require a national 
prohibition of manure application to frozen, snow-covered, or saturated 
ground.
    In addition to the four technologies reviewed for the 2003 final 
rule, EPA looked at an additional 37 technologies and systems 
identified either by EPA or commenters as candidate fecal coliform BCT 
technologies. At the outset of assessment for this rule, EPA rejected 
all of these technologies as the basis for BCT limitations for fecal 
coliform for Subpart D CAFOs because they were either not technically 
feasible for all Subpart D CAFOs, or were not economically achievable. 
Many of the rejected technologies were costlier than Option 5 which EPA 
in the 2003 final CAFO rule had earlier determined was not economically 
achievable for Subpart D (i.e., swine, poultry, and veal calf) 
facilities. The Waterkeeper court sustained the Agency's determination 
that CAFOs cannot reasonably bear the cost associated with Option 5. 
399 F.3d at 516. Option 5 would have cost Subpart D facilities $167 
million. See 68 FR 7218. Of the 19 technologies and systems approaches 
identified by commenters, none of the technologies costs less than $167 
million. The least costly of these technologies--gasification recycle, 
digester based systems, super soils composting, aerobic digestion, and 
ABS--cost 1.3 times the cost of Option 5. Other technologies reviewed 
cost as much as seven times the total national costs of Option 5. 
Having determined that the costs of Option 5 were unachievable for 
Subpart D facilities, EPA did not evaluate further those treatment 
technologies that had similar or greater total costs. After rejecting 
the economically unachievable technologies identified by commenters, 22 
technologies remained for further assessment with respect to technical 
feasibility. EPA found that none of these technologies were technically 
feasible for all CAFOs in Subpart D.
    For Subpart C facilities, EPA did not have a previously identified 
option that it had already determined to be economically unachievable 
against which to compare the costs of candidate

[[Page 70467]]

BCT technologies. To do an economic achievability analysis of candidate 
technologies for Subpart C, EPA would have had to conduct an analysis 
of the economic conditions of individual CAFOs in order to estimate 
potential closures and evaluate appropriate financial ratios, as it 
traditionally does for economic achievability analysis. EPA determined 
that conducting such an analysis was not practical, and eventually also 
determined that it was not necessary to do so to complete its 
evaluation of candidate BCT technologies for subpart D. Rather, EPA 
first evaluated the candidate technologies for technical feasibility, 
and on this basis, rejected 39 of the 41 technologies (the four options 
considered for the 2003 rule, 16 identified by EPA and 19 suggested by 
commenters) as the basis for BCT limitation for fecal coliform for 
Subpart C. The two remaining technologies were then evaluated directly 
for cost reasonableness, without considering economic achievability, as 
explained in section III.G.4(c) of this preamble.
    EPA explained the basis for its decisions with respect to 
feasibility of the other candidate technologies (for both Subparts C 
and D) in the proposed rule, and commenters have not provided any 
information that would lead the Agency to change its conclusions. 71 FR 
37,768-71.
    In addition, EPA specifically solicited comment on additional 
candidate technologies that might prove feasible and less costly than 
the technologies already evaluated for the proposal. EPA is aware of 
technologies that may, on a site-specific basis, be used to provide 
further reductions of conventional pollutants as compared to the 
technologies on which the 2003 BPT/BCT limitations were based. However, 
EPA's record shows these other technologies are not available 
engineering alternatives for most CAFOs, and they are therefore not 
feasible technology candidates. See Chapter 8 of the ``Development 
Document for the Final Revisions to the NPDES and the Effluent 
Guidelines for CAFOs'' and the docket accompanying this action for 
descriptions of these additional technologies.
    In response to its requests for additional information, EPA 
received no new data that support evaluation of additional candidate 
technologies or warrant revision to EPA's conclusions about the costs 
or performance of the candidate technologies EPA identified. 
Specifically, while some commenters recommended consideration of 
additional digester systems, the costs of the various digester systems 
do not vary sufficiently to warrant a detailed analysis of the costs of 
these technologies at every type of CAFO. To date, EPA has not 
identified less expensive, and consequently, economically achievable 
candidate technologies than those it had previously evaluated. 
Furthermore, EPA did not further evaluate the systems approach 
(combinations of one or more candidate technologies) recommended by 
some commenters because it would not reduce fecal coliform more than 
the 99 percent assumed by EPA \12\ in its analysis as the yardstick for 
performance of the candidate BCT technology. While not obtaining 
pollutant removals greater than those already considered by EPA, these 
systems would cost more than the cost of the individual technologies 
already reviewed. Therefore, EPA did not evaluate the suite of 
candidate technologies that performed comparably but were more 
expensive than the suite of technologies evaluated here. For the 
reasons described in Chapter 8 of the ``Development Document for the 
Final Revisions to the NPDES and the Effluent Guidelines for CAFOs'' 
and the proposal at 71 FR 37,765-8, EPA has determined that the 
candidate technologies it rejected are not technologically feasible and 
economically achievable for all CAFOs across a subcategory and thus not 
appropriate technologies for BCT limitations. The CWA does not 
authorize EPA to establish BCT limitations that are based on 
technologies that are not technologically feasible and economically 
achievable. Because only two technologies were both technically 
feasible and potentially economically achievable for Subpart C 
facilities (and none were for Subpart D facilities), EPA is only 
required to evaluate these two technologies further for cost 
reasonableness.
---------------------------------------------------------------------------

    \12\ In the proposed rule, as a simplifying assumption all 
technologies were expected to achieve a 99 percent reduction in 
fecal coliform. 71 FR 37,765 and 37,767.
---------------------------------------------------------------------------

(c) EPA's Evaluation of the Remaining Candidate Technologies for Cost 
Reasonableness
    The above assessment resulted in only two remaining candidate 
technologies (composting and constructed wetlands) that are potentially 
\13\ technically feasible and economically achievable for fecal 
coliform control for one subcategory, the Subpart C (beef and dairy) 
subcategory. As discussed above, EPA did not conduct a new analysis of 
economic achievability for these technologies at Subpart C facilities, 
although EPA notes the costs are high relative to the BPT technology 
(which EPA also determined to be BAT). Specifically, the cost of the 
BPT technology for Subpart C was $214 million per year, while the cost 
of composting was estimated to be $1.4 billion per year, and the cost 
of constructed wetlands was $2.9 billion. Thus, EPA expects that if it 
had conducted a formal economic achievability analysis, EPA would have 
determined that both of these technologies are not economically 
achievable.
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    \13\ EPA believes it is likely that some Subpart C facilities 
will have space constraints under either candidate technology. In 
this case the technology would not be feasible for all CAFOs in the 
subcategory. However, EPA lacks data regarding land availability and 
possible land constraints beyond an aggregate of data showing the 
average acres of cropland at Subpart C facilities. To the extent 
CAFOs can take the necessary amount of land out of crop production 
to provide the space to install construct wetlands or composting 
windrows, EPA does not have the data to estimate lost revenues 
associated with such losses of cropland. Therefore, EPA's estimated 
costs of such candidate technologies are potentially understated. 
Nonetheless, EPA analyzed cost reasonableness as if the technologies 
are feasible.
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    However, instead of evaluating these technologies with respect to 
economic achievability, EPA evaluated the cost reasonableness of the 
technologies using the simplified approach described above. In the 
past, EPA has adopted such an approach when it lacked a full data base 
to evaluate different BCT technologies. A simplified approach fits the 
circumstances here for two reasons. First, as noted, EPA has developed 
no standardized BCT cost test for fecal coliform. Second, EPA lacks the 
data to provide a comparison of incremental fecal coliform removals 
that is the basis for the BCT cost test for TSS and BOD.
    The annual operating costs for composting would be more than six 
times as much as the full BPT level of control at Subpart C facilities 
(see Chapter 4 and Table A-15 of the Final Cost Methodology, EPA-821-R-
03-004), while constructed wetlands would cost Subpart C facilities 
more than an order of magnitude (13) times the cost of the BPT level of 
control (see chapter 15 in the supplement to the TDD). EPA has 
determined that these costs are too high relative to the additional 
removals. EPA thus concludes that the incremental costs of the 
additional removals alone support a determination that these 
technologies are not cost reasonable.
    To further evaluate this conclusion, EPA conducted a modeling 
analysis of POTW removal costs for fecal coliform. As discussed above, 
the available data do not permit an empirical cost comparison between 
CAFO candidate

[[Page 70468]]

technologies and POTW fecal coliform performance. However, EPA was able 
to model POTW fecal coliform removal costs using reasonable 
approximating assumptions. EPA recognizes that the resulting 
calculation lacks the rigor of the determination of the 1986 POTW 
benchmark for TSS and BOD removal costs.\14\ What this assessment shows 
is that POTW average costs of removals of fecal coliform are very low 
(i.e., $0.33 per trillion CFU; see 71 FR 37,772). This is not 
surprising, given that most POTW permits require achievement of fecal 
coliform reduction near 99 percent.\15\ In contrast, the two 
technologies being evaluated for cost reasonableness (composting and 
constructed wetlands) have higher costs for fecal coliform removal 
($0.51 per trillion CFU for composting, and $1.02 per trillion CFU for 
constructed wetlands). (See supplement to Chapter 15 of the TDD, 
showing unit costs of NCSU technologies as provided by commenters, 
total national costs of employing such technologies at CAFOs, and a 
comparison of those costs to the BPT/BAT level of control.)
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    \14\ EPA made a number of assumptions for its calculations 
because it did not have the data to establish on a national basis 
the costs to POTWs of fecal coliform control. Thus, EPA's assessment 
used the cost of advanced secondary treatment as a proxy for the 
cost of additional technologies (e.g., filtration) that POTWs may 
employ to achieve high fecal coliform removals (98 percent) required 
by water quality standards of 200 colony forming units (CFU) per ml. 
This assumption may overstate the costs of such technologies, in 
which case the cost per trillion CFU removed would be lower.
    \15\ As described in the proposal, POTW influents are 
approximately 5 million CFU per 100 ml, and PCS data shows effluent 
concentrations of ~ 20 CFU per ml.
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    Even recognizing the necessary imprecision associated with EPA's 
calculations, EPA has determined that this limited POTW cost comparison 
further supports its determination that the costs of these two BCT 
candidate technologies are not cost reasonable, given the lack of hard 
data on which to base the determination. This is fully consistent with 
EPA's findings in the proposed rule that POTWs are very cost effective 
at fecal coliform removals. 71 FR 37,772. The assessment confirms what 
logic suggests: Given a POTW's requirement to virtually eliminate the 
extremely high fecal coliform discharges in its influent (basically raw 
sewage), POTWs, on a national basis, achieve fecal coliform removal on 
a cheaper basis than CAFOs.
    Finally, EPA notes that Congress intended the BCT level of control 
to be somewhere between the BPT and the BAT levels of control, as 
established in the statute. As noted in the conference report to the 
1977 amendments establishing BPT:

    ``The result of the cost test could be a 1984 requirement which 
is no more than that which would result from best practicable 
technology but also could result in effluent reductions equal to 
that required in the application of best available technology.'' 
Joint Explanatory Statement of the Committee of Conference, 95th 
Cong. 1st Sess., H.R. No. 95-830 at 85, Legislative History at 269.

    Thus, candidate technologies with costs between 6 and 13 times the 
costs of technologies that have already been determined to be BAT would 
not generally be appropriate as the basis for BCT.
5. Additional Comments on the Proposal
    The following discussion summarizes additional significant comments 
received by EPA on the proposed CAFO BCT determination for pathogens. 
For a complete response to the issues raised by commenters, see the 
Response to Comment Document.
    In calculating the BPT cost per unit of fecal coliform removal for 
its cost-reasonableness assessment, one commenter noted the cost was 
erroneously calculated in units of dollars per billion colony forming 
units (CFU); the units should have been dollars per trillion CFU in 
order for the test to be comparable and consistent with the remaining 
BCT cost calculations. EPA agrees with this comment and has corrected 
all calculations to dollars per trillion CFU.
    Some commenters correctly noted that as part of the BCT cost test 
for fecal coliform, EPA calculated the POTW and industry cost 
benchmarks as the difference in average costs of removing fecal 
coliform between secondary treatment and advanced secondary treatment 
rather than as the incremental cost for the upgrade. These commenters 
believed that such an approach was incorrect. As discussed above, EPA 
agrees and has not used the revised BCT cost test for this final rule. 
In regards to the BCT options that were selected for further analysis, 
some commenters believe that numerical limits are feasible for CAFOs 
and should have been selected for BCT. They would have liked to see EPA 
take a similar approach to CAFO waste that EPA has taken regarding 
human sewage sludge (i.e., setting numerical pathogen standards for 
use). Some commenters pointed to the ``sludge rule'' or ``biosolids'' 
program under 40 CFR part 503 as a possible basis for pathogen 
standards in the CAFO rule. EPA notes that the CWA statutory criteria 
for sewage sludge standards under section 405 of the Act are health and 
welfare-based. By contrast, CWA effluent limitations require 
consideration of different factors. However, the technologies used to 
meet the regulations in part 503 may, in some cases, be used by CAFOs. 
For these reasons, EPA included sewage sludge pollution reduction 
technologies such as composting and lime addition in the suite of BCT 
candidate technologies the Agency considered. In addition, some 
commenters criticized EPA's cost analysis for not including cost-share 
from federal sources such as EQIP, and for not including cost offsets 
from sale of treated manure. EPA considered both of these aspects in 
the cost analysis to the 2003 final CAFO rule, and was upheld on its 
economic analysis. 399 F.3d 486. In addition, EPA considered such cost 
offsets in a sensitivity analysis, and concluded that the cost offsets 
did not change EPA's fundamental conclusions regarding economic 
achievability and feasibility. See Chapter 14 of the TDD for more 
information.
    By contrast, other commenters found no fault or shortcomings in the 
EPA analysis of the technical feasibility of conventional technologies 
in determining BCT for pathogen removal. They agree that the candidate 
technologies examined by EPA present insurmountable challenges to many 
CAFOs that make them inappropriate as a basis for BCT. They found no 
fault with the cost data or analytical techniques used by EPA in the 
BCT cost test. These commenters also presented additional economic 
analysis of the candidate technologies that has been published in the 
``Phase 3'' report on the ``Development of Environmentally Superior 
Technologies'' per agreements between the North Carolina Attorney 
General and major pork producers in the State. These commenters note 
that the ``Phase 3'' economic analysis found that none of the 16 
technologies studied were economically feasible for existing swine 
operations in North Carolina, which is consistent with EPA's findings 
as discussed in detail above. These commenters also provided State 
records of CAFO violations and discharge data for the past three years 
to support their position that EPA has overstated the frequency of 
production area overflows. These additional data may be found in the 
record for this final action.

IV. Impact Analysis

A. Environmental Impacts

    When EPA issued the revised CAFO regulations on February 12, 2003, 
it estimated annual pollutant reductions

[[Page 70469]]

for the rule at 56 million pounds of phosphorus, 110 million pounds of 
nitrogen, and two billion pounds of sediment. This final, revised rule 
will not change these environmental benefits since the technical 
requirements for CAFOs that discharge are not affected and all CAFOs, 
whether covered by NPDES permits or not, still need to control nutrient 
releases from the production and land application areas in order to 
comply with the Clean Water Act. Under this rule, all CAFOs that do not 
apply for permits must be designed, constructed, operated, and 
maintained such that the CAFO does not discharge or propose to 
discharge. Therefore, as was true under the 2003 rule, all discharges 
from CAFOs (except precipitation-related discharges from land 
application areas under a CAFO's control that qualify as agricultural 
stormwater discharges) are required to be covered by NPDES permits. The 
overall magnitude of the benefits will increase compared to 2003 due to 
growth in the industry, but the analysis for this rule does not 
recalculate these effects since the increase is not due to changes in 
the CAFO regulations. EPA is assuming full compliance with the rule, 
which is standard Agency procedure when modeling impacts of a final 
rule.

B. Administrative Burden Impacts

    Since there is no change in technical requirements, changes in 
impacts on respondents are due exclusively to changes in the 
information collection burden. To determine the administrative burden 
for the Paperwork Reduction Act (PRA) analysis, the Agency first 
examined the two key permitting changes resulting from the Waterkeeper 
decision and how they would be implemented under the final regulations. 
These are the change in the duty to apply for CAFOs and the change to 
the nutrient management plan (NMP) related provisions for CAFO permits.
    The 2003 CAFO rule had a universal duty to apply requirement which 
required virtually all CAFOs to obtain NPDES permit coverage. The 
supporting analysis for the 2003 rule estimated that as a result of 
this requirement, approximately 15,500 CAFOs would ultimately receive 
NPDES permits. See the Technical Development Document for the 2003 
rule, Chapter 9.
    This final rule changes the duty to apply requirement so that only 
CAFOs that discharge or propose to discharge are required to seek NPDES 
coverage. To derive the number of CAFOs that could ultimately fall into 
this category, EPA first projected total industry size for 2008 based 
on both U.S. Department of Agriculture (USDA) Census of Agriculture 
statistics as well as Agency-based sector expertise. This exercise 
yielded an estimate of approximately 20,700 total CAFOs for 2008. EPA 
then combined the 2008 projections for each animal sector with 
information on standardized operational profiles to anticipate the 
number of facilities as of 2008 that might discharge. For example, when 
inclement weather precludes land application or dewatering activities, 
open lot type facilities such as beef lots and dairy operations are 
more likely to experience conditions that could result in a discharge 
due to the use of open on-site lagoons. Additionally, EPA assumed that 
all dairies generate wastewater from the production area and generally 
have uncovered on-site lagoons. Thus, for purposes of burden estimates, 
EPA assumed that all dairies and most beef feedlots would apply for 
permits.
    Even though the industry grew to roughly 20,700 CAFOs from 2002 to 
2008, the change in the duty to apply requirement is anticipated to 
reduce the number of facilities needing permit coverage to 
approximately 15,300 discharging CAFOs. Based on these updated figures, 
EPA estimates that approximately 25 percent of the total universe of 
CAFOs would not discharge and thus would not need NPDES coverage under 
this final rule. Although these facilities may not need to apply for 
permits, the administrative burden analysis performed by EPA under the 
PRA nonetheless accounts for the costs that unpermitted facilities will 
incur for the nutrient management planning that are necessary for 
demonstrating that the facility is land applying manure in such a way 
as to qualify for the agricultural stormwater exemption.
    These figures may overstate the numbers of CAFOs needing NPDES 
permits in that the estimates of the number of discharging facilities 
in each sector make conservative categorical assumptions about the 
likelihood of a discharge based on broad operational profiles and do 
not account for more subtle stratifications within specific operational 
categories. For instance, although most dairies generate wastewater 
from the production area and have on-site lagoons, there do, in fact, 
exist dairies designed to be no discharge operations.
    Based on the updated estimates of the CAFO universe, EPA's PRA 
analysis projects, as shown in Table 4.1, that CAFO operators and 
permitting authorities will collectively experience an increase in 
total annual administrative burden of approximately $0.5 million as a 
result of the EPA regulations to address the court decision. Although 
the PRA burden to CAFOs and permitting authorities declines as a result 
of the Waterkeeper court decision to limit permits only to discharging 
CAFOs, this burden reduction is offset by the new NMP-related 
requirements for permits and by the assumption, for purposes of this 
PRA analysis, that all unpermitted CAFOs will certify under the 
voluntary no discharge certification option. More specifically, CAFO 
operators will experience a $0.2 million reduction in net annual 
administrative burden. This net result is based on several offsetting 
changes. CAFOs that do not seek permit coverage under this final rule 
because they do not discharge or propose to discharge will save 
approximately $14 million annually in reduced permitting costs. 
However, even though fewer CAFOs will need to be covered by NPDES 
permits, permitted facilities as a group face an increase in annual 
administrative burden of $1.2 million per year due to the new NMP 
requirements.
    EPA's analysis of burden impacts to CAFOs also accounts for the 
burden that unpermitted facilities will incur in order to be able to 
qualify for the agricultural stormwater exemption--a cost category that 
EPA estimates will result in a burden on unpermitted facilities of 
$12.2 million annually. In addition, EPA estimates that the voluntary 
certification option for unpermitted CAFOs could add $0.4 million 
annually to the PRA burden for CAFOs. Although certification is 
voluntary, EPA elected to cost the PRA burden associated with this 
option so as to provide a complete accounting of all rule-related 
impacts. As noted above, the net result of these impacts is an 
administrative burden savings across all CAFO operators, permitted and 
unpermitted, of $0.2 million annually.
    Permitting authorities, on the other hand, are projected to 
experience a $0.7 million increase in annual administrative burden. 
Although the burden to issue permits declines by $4.2 million annually 
due to fewer facilities needing permits, this decline is more than 
offset by the added workload arising from the new NMP-related 
requirements. EPA estimates that States would face an additional PRA 
burden of $4.9 million annually specifically as a result of the new 
NMP-related requirements. In addition, States are projected to face a 
burden increment of up to $0.04 million annually to process the new 
certifications.
    EPA's estimate of PRA burden impacts changed from a reduction of 
$14.9 million annually for the 2006 proposed rule to an increase of 
$0.5

[[Page 70470]]

million annually in the final rule. This change is due principally to 
the Agency's decision, as discussed earlier in this section, to amend 
the PRA analysis to account for the burden incurred by unpermitted 
CAFOs for nutrient management planning, which is necessary for any 
unpermitted CAFO that land applies irrespective of whether the CAFO is 
certified under the voluntary no discharge certification option.
    The PRA burden analysis presented in this rule accounts both for 
growth in the industry and changes in labor rates since the 2003 rule 
was issued. In addition, the changes are based on annualized impacts 
and assume a permit term of five years as stipulated in the CWA. EPA 
submitted draft ICRs with the 2006 proposed rule and 2008 supplemental 
proposal, and did not receive any comments from the Office of 
Management and Budget (OMB). The documentation in the public record on 
the PRA analysis for this rulemaking discusses more fully the 
assumptions used to estimate the numbers of CAFOs needing permits and 
to project the associated administrative burden.

                                      Table 4.1--PRA Burden Impact Changes
                                  [Note: Numbers may not add due to rounding.]
----------------------------------------------------------------------------------------------------------------
                                                                 Total baseline
                                                                   PRA burden:    Total amended   Net change in
                                                                  based on 2003    PRA burden:      paperwork
                                                                    CAFO rule    based on final    burden (2003
                                                                  requirements        rule        rule compared
                                                                       \1\        requirements    to final rule)
----------------------------------------------------------------------------------------------------------------
CAFOs needing permits (2008)   ...............  ...............          20,685          15,281
 \2\.
CAFOs seeking agricultural     ...............  ...............             n/a           5,404
 stormwater exemption only
 (2008).
    Total CAFOs (2008).......  ...............  ...............          20,685          20,685
Annualized Costs \3\ (in $     CAFOs..........  Base NPDES                $54.0           $40.0          ($14.0)
 millions).                                      Permit.
                                                New NMP                     n/a            $1.2            $1.2
                                                 Provisions.
                                                Agricultural                n/a           $12.2           $12.2
                                                 Stormwater
                                                 Exemption.
                                                Certification..             n/a            $0.4            $0.4
                                                Total CAFO                $54.0           $53.8           ($0.2)
                                                 Burden.
                               Permitting       Base NPDES                $16.5           $12.2           ($4.2)
                                Authorities.     Permit.
                                                New NMP                     n/a            $4.9            $4.9
                                                 Provisions.
                                                Certification..             n/a           $0.04           $0.04
                                                Total Permit              $16.5           $17.1            $0.7
                                                 Authority
                                                 Burden.
                              ----------------------------------------------------------------------------------
                               All Respondents                            $70.5           $71.0            $0.5
----------------------------------------------------------------------------------------------------------------
\1\ 2003 baseline impacts adjusted to reflect current labor rates and growth in facilities.
\2\ Facility totals are annualized over 5 years in burden calcultions presented below to reflect CWA requirement
  for NPDES permit renewal every 5 years.
\3\ Annualized costs represent labor, capital and O&M costs.

C. Response to Public Comment on the Proposal

    The Agency received a variety of comments on the impacts analysis 
presented for the 2006 proposed rule and the 2008 supplemental 
proposal. Several commenters indicated that the Agency erred in 
assuming that the environmental benefits from the 2003 rule would be 
retained under the approach adopted in this final rule. The Agency 
stands by its position presented in the 2006 proposed rule, but has 
revised the burden analysis to reflect more fully that all unpermitted 
CAFOs do not discharge or propose to discharge and, therefore, must 
implement nutrient management practices to ensure that any discharge 
from the CAFO's land application area qualifies for the agricultural 
stormwater exemption. As a consequence, as indicated above, the annual 
burden reduction realized by CAFOs under the final revised rule is 
shown as approximately $0.2 million as opposed to the $15.4 million 
reduction projected for CAFOs in the 2006 proposed rule. This revised 
analysis also addresses specific comments suggesting that the Agency 
should recognize that operators without permits will continue to incur 
costs under the regulation in order to meet the burden of proof 
required to qualify for the agricultural stormwater exemption.
    Other commenters indicated that the impacts analysis underestimated 
the costs to CAFO operators of complying with the EPA regulations. 
Careful review of these statements makes clear that commenters with 
this viewpoint either did not account for the fact that the impacts 
analysis presented for this rulemaking is exclusively an assessment of 
the paperwork burden--not the overall compliance burden--faced by 
CAFOs, or did not fully consider that the costs shown represent average 
yearly (annualized) burden rather than total paperwork-related costs 
for a five-year CAFO NPDES permit.
    Other commenters provided specific information on nutrient 
management plan (NMP) development costs, which the Agency determined 
corroborated the original NMP cost estimates.
    One State commenter claimed that the Agency had underestimated 
costs to permitting authorities for managing the potential public 
hearings precipitated by the new requirements for public notice. This 
commenter projected that every public notice regarding NMPs would 
result in a public hearing. The Agency re-examined its assumptions 
regarding the incidence of public hearings, but did not find 
information to corroborate the commenter's projection either based on 
past NPDES public hearing patterns or based on expectations from other 
States regarding the number of hearings likely to be triggered by NMP-
related public notices. This assumption that public hearings would not 
be requested for every NMP is further confirmed by the experiences of 
States that currently require NMPs to be submitted as part of their 
permitting process.
    Several commenters indicated that they believed that the Agency had 
also

[[Page 70471]]

underestimated the cost to States of processing voluntary no discharge 
certifications. This final rule does not require permitting authority 
review of no discharge certifications. See discussion of certification 
submission in section III.A.3(c) of this preamble. The Agency notes 
that the cost analysis it performed to assess the paperwork burden 
associated with the final rule shows a net paperwork burden reduction 
to States on this aspect of the rule, since the 2003 rule required 
permits-which are more burdensome for permitting authorities to 
process-from all CAFOs.

V. Cross-Media Considerations and Pathogens

A. Cross-Media Approaches

    Since 2003, EPA and CAFO stakeholders have been interested in 
developing a framework to enable CAFOs to pursue superior environmental 
performance across all media. Today, some CAFOs voluntarily conduct 
whole-farm audits to evaluate releases of pollutants to all media 
through Environmental Management Systems (e.g., ISO 14001 
certification), self-assessment tools, EPA's performance track, and 
State-approved trade-offs in reducing discharges to water and emissions 
to air that accomplish the best overall level of protection given State 
and local conditions. The development of new and emerging technologies 
offers the potential to achieve equivalent or greater pollutant 
reductions relative to those achieved by the effluent guidelines and 
standards. Many of these are superior from a cross-media perspective, 
and EPA encourages superior cross-media solutions. These regulations 
regarding nutrient management plans may provide an opportunity for EPA 
to encourage cross-media approaches at CAFOs. For example, the nutrient 
value in the animal byproducts provides a valuable source of fertilizer 
for crops. However, inappropriate application can lead to preventable 
discharges to water and emissions to air. Optimal application 
technologies and rates reduce potential water quality and air quality 
standards violations.
    The fact that EPA has multiple efforts underway relating to 
livestock operations under several environmental statutes underscores 
the need to explore how to leverage existing regulatory authorities 
most effectively. For example, in addition to the regulations being 
finalized in this rulemaking, the Agency has recently undertaken a 
National Air Emissions Monitoring Study. EPA also proposed a rule that 
would exempt animal feeding operations from certain requirements 
relating to reporting of air releases under hazardous waste laws.
    EPA solicited comment in the 2006 proposed rule on the feasibility 
(including consideration of legal, technical, and implementation 
issues) of allowing flexibility in how facilities meet various 
programmatic requirements, for instance those of the Clean Air Act and 
the Clean Water Act (CWA), in order to achieve greater cross-media 
pollutant reductions. EPA received generalized support for this type of 
approach in the comments submitted in response. EPA will continue to 
explore cross-media considerations as it works together with CAFOs and 
stakeholders to build further experience on this issue.
    As an example of the Agency's work in this area, in October 2007, 
EPA awarded $8 million in federal grants for providing technical 
assistance to livestock operators, including animal feeding operations, 
for the prevention of water discharges and reduction of air emissions. 
More recently, EPA's Agricultural Advisor announced the establishment 
of the Farm, Ranch, and Rural Communities Federal Advisory Committee. 
One of the issues the committee will focus on will be identification 
and development of a comprehensive environmental strategy for livestock 
operations. EPA anticipates that the committee will offer timely 
observations on the opportunities and challenges of cross-media 
approaches to programs for addressing environmental concerns at 
livestock operations as its work progresses.

B. Pathogens and Animal Feeding Operations

    Although this final rule does not require any new best conventional 
pollutant control technology (BCT) effluent limitations specifically to 
control fecal coliform, EPA is continuing to assess environmental and 
human health concerns associated with the management of manure and 
wastewater at CAFOs. Pollutants most commonly associated with animal 
waste include nutrients (including ammonia), organic matter, solids, 
odorous compounds, and various pathogens. These pollutants, and others, 
can be released into the environment through discharge or runoff if 
manure and wastewater are not properly handled and managed. EPA is 
interested in recently initiated studies to assess potential impacts 
from pathogens in livestock manure, especially those which may pose 
unique risks such as Cryptosporidium and Giardia. These pathogens may 
be of concern if they make their way into drinking water sources (e.g., 
lakes, rivers, and streams) because of their stability in the natural 
environment and their resistance to the most commonly used drinking 
water disinfection procedure (i.e., chlorination). If proper treatment 
is not provided for these pathogens, they have the potential to cause 
adverse health impacts in exposed populations. While the Agency has a 
number of on-going efforts in these areas, research is still in its 
early stages. The absence of available information necessarily limits 
EPA's ability to act with respect to these potential concerns.
    EPA's Office of Research and Development (ORD) is actively working 
to identify sources of Cryptosporidium. In collaboration with the 
Centers for Disease Control (CDC), EPA Region 3, and the Potomac River 
Drinking Water Source Protection Partnership (DWSPP), ORD has initiated 
Cryptosporidium source tracking studies of the Potomac River Watershed. 
The primary objective of this project is to develop and implement a 
monitoring program for Cryptosporidium source tracking in order to 
identify the most significant sources of this parasite within the 
watershed. Once identified, appropriate source protection efforts, 
where available, may be mobilized and directed to the reduction of 
these sources' contributions. In addition, in 2005 EPA's Science to 
Achieve Results (STAR) program held a solicitation for proposals 
entitled, ``Development and Evaluation of Innovative Approaches for the 
Quantitative Assessment of Pathogens in Drinking Water,'' and has 
funded eleven research grants from this proposal involving the 
development and evaluation of innovative approaches to quantitatively 
detect microbial pathogens in drinking water, including Cryptosporidium 
and Giardia. The goal of the STAR research is to improve the suite of 
available detection methods for known and emerging microbial drinking 
water contaminants. EPA expects that this research will result in 
methods that will, among other things, allow determination of the 
presence and quantities of waterborne pathogens; present a protocol for 
preparing and processing water samples for application of the proposed 
approach; and where possible, allow comparison of the performance of 
the new detection methods with existing approved EPA methods for 
specific pathogens.
    ORD is also collaborating with the U.S. Department of Agriculture 
(USDA) in their research programs associated with Cryptosporidium. ORD 
scientists

[[Page 70472]]

participated in the USDA selection process for the National Research 
Initiative on Watershed Processes and Water Resources. Grants awarded 
under this program will explore the effects of a number of factors on 
Cryptosporidium mobility and contamination of waterways. These include 
the use of buffers and other best management practices for decreasing 
loadings of Cryptosporidium from land application of wastes and other 
soluble organic matter. EPA scientists have begun to review recently 
published research on Cryptosporidium and Giardia oocyst shedding. The 
research suggests that shedding is highest during early life stages of 
cattle and zoonotic forms and may greatly diminish as calves age. These 
factors have already led some veterinarians to recommend that farmers 
separate these high shedding young animals from older animals to 
decrease disease spread and economic losses among herds of cattle and 
dairy cows. The research also suggests that the separation may provide 
secondary environmental benefits by helping to prevent the release of 
Cryptosporidium into waterways. As part of their efforts to protect the 
New York City water supply, the New York State Department of 
Agriculture has recommended separation controls in their best 
management practice (BMP) guidance to dairy farmers. Other States, 
including California, are considering similar separation BMPs.
    EPA's ORD will continue to collaborate and assess the impacts that 
these and other research efforts may have on any future CAFO management 
recommendations.

VI. Statutory and Executive Order Reviews

A. Executive Order 12866: Regulatory Planning and Review

    Under Executive Order 12866 (58 FR 51,735; October 4, 1993), this 
action is a ``significant regulatory action.'' Accordingly, EPA 
submitted this action to the Office of Management and Budget (OMB) for 
review under Executive Order 12866 and any changes made in response to 
OMB recommendations have been documented in the docket for this action.
    In addition, EPA prepared an analysis of the potential costs and 
benefits associated with this action. This analysis is contained in 
section IV of this preamble above, entitled Impact Analysis. A copy of 
the supporting analysis is available in the docket for this action.

B. Paperwork Reduction Act

    The information collection requirements in this rule have been 
submitted for approval to the Office of Management and Budget (OMB) 
under the Paperwork Reduction Act, 44 U.S.C. 3501 et seq. The 
information collection requirements are not enforceable until OMB 
approves them. However, the Office of Management and Budget (OMB) has 
previously approved the information collection requirements contained 
in the existing regulations and has assigned OMB control number 2040-
0250. The Information Collection Request (ICR) document prepared by EPA 
was assigned EPA ICR No. 1989.06.
    The 2003 CAFO rule had a universal duty to apply requirement which 
required virtually all CAFOs to obtain NPDES permit coverage. This 
final revised rule changes the duty to apply requirement so that only 
CAFOs that discharge or propose to discharge must to seek NPDES 
coverage. EPA projects that CAFO operators and permitting authorities 
will collectively experience a reduction in total annual administrative 
burden of 25,500 hours as a result of the regulatory revisions to 
address the court decision. Labor burden is projected to undergo a net 
decrease compared to a net increase in administrative costs of $0.5 
million annually as discussed in Chapter IV. This difference arises 
from the fact that the PRA analysis performed for the final rule 
converts labor hour burden to labor costs using a higher wage rate for 
State permitting authorities than for CAFO operators.\16\ The higher 
wage rate for State permitting authorities causes the State labor cost 
increase to be large enough to offset the labor cost reduction 
experienced by CAFO operators once labor hours are converted to dollars 
in the PRA analysis of annual administrative impacts.
---------------------------------------------------------------------------

    \16\ Wage rates for the PRA analysis supporting this rulemaking 
were drawn from recent reports filed by the U.S. Department of 
Labor, Bureau of Labor Statistics. For further information please 
refer to the ICR prepared by EPA for the rulemaking, available in 
the record as EPA ICR No. 1989.06.
---------------------------------------------------------------------------

    More specifically, the estimated reduction in total annual 
administrative burden of 25,500 hours is based on a projected decrease 
in labor burden to CAFO operators of approximately 54,100 hours 
annually and a projected increase in labor burden to State permitting 
authorities of approximately 28,600 hours annually. For CAFOs, much of 
the labor burden decrease derives from the smaller number of facilities 
that will need permits, which results in an annual burden decrease of 
more than 703,000 labor hours. This burden reduction for CAFOs is 
offset by a concomitant increase of 603,200 labor hours annually at 
unpermitted facilities for activities necessary to meet the 
agricultural stormwater exemption, along with an increment of 33,100 
hours annually for permitted facilities to undertake the NMP-related 
activities and 12,600 hours annually for those CAFOs who elect to 
pursue the voluntary certification option.
    The annual labor burden increase for State permitting authorities 
of 28,600 hours includes an estimated annual reduction in labor burden 
of 93,000 hours due to the need to process fewer permits. However, for 
State permitting authorities this burden reduction is more than offset 
by an increment in annual labor burden of 120,700 hours to address the 
new NMP-related requirements combined with a relatively minor annual 
burden increase of 900 hours to handle the voluntary certifications.
    Additional details on the assumptions and parameters of the PRA 
analysis are available in the ICR document referenced above, which is 
available in the docket supporting this final rulemaking. Burden is 
defined at 5 CFR 1320.3(b).
    An agency may not conduct or sponsor, and a person is not required 
to respond to a collection of information unless it displays a 
currently valid OMB control number. The OMB control numbers for EPA's 
regulations in 40 CFR are listed in 40 CFR part 9.
    This final rule responds to OMB or public comments on the 
information collection requirements as discussed in the Impact Analysis 
(section IV) in this preamble.

C. Regulatory Flexibility Act

    The Regulatory Flexibility Act (RFA) generally requires an agency 
to prepare a regulatory flexibility analysis of any rule subject to 
notice and comment rulemaking requirements under the Administrative 
Procedure Act or any other statute unless the agency certifies that the 
rule will not have a significant economic impact on a substantial 
number of small entities. Small entities include small businesses, 
small organizations, and small governmental jurisdictions.
    For purposes of assessing the impacts of this rule on small 
entities, small entity is defined as: (1) A small business based on 
Small Business Administration (SBA) size standards at 13 CFR 121.201; 
(2) a small governmental jurisdiction that is a government of a city, 
county, town, school district, or special district with a population of 
less than 50,000; and (3) a small organization that is any

[[Page 70473]]

not-for-profit enterprise which is independently owned and operated and 
is not dominant in its field.
    After considering the economic impacts of this rule on small 
entities, I certify that this action will not have a significant 
adverse economic impact on a substantial number of small entities. This 
final rule does not change the substantive requirements for CAFO 
operators or increase the net paperwork burden faced by facilities 
compared to the burden imposed under the 2003 CAFO rule. Some CAFOs 
will face increased permitting costs due to the new NMP provisions, 
while others will face reduced costs due to the changes in the duty to 
apply. However, these paperwork cost changes are generally small and do 
not rise to the level of a significant adverse economic impact on a 
substantial number of operators. Additionally, this rule would not 
affect small governments as the permitting authorities are State or 
federal agencies.

D. Unfunded Mandates Reform Act

    Title II of the Unfunded Mandates Reform Act of 1995 (UMRA), Public 
Law 104-4, establishes requirements for federal agencies to assess the 
effects of their regulatory actions on State, local, and tribal 
governments and the private sector. Under section 202 of UMRA, EPA 
generally must prepare a written statement, including a cost-benefit 
analysis, for proposed and final rules with ``federal mandates'' that 
may result in expenditures to State, local, and tribal governments, in 
the aggregate, or to the private sector, of $100 million or more in any 
one year. Before promulgating an EPA rule for which a written statement 
is needed, section 205 of the UMRA generally requires EPA to identify 
and consider a reasonable number of regulatory alternatives and adopt 
the least costly, most cost-effective, or least burdensome alternative 
that achieves the objectives of the rule. The provisions of section 205 
do not apply when they are inconsistent with applicable law. Moreover, 
section 205 allows EPA to adopt an alternative other than the least 
costly, most cost-effective, or least burdensome alternative if the 
Administrator publishes with the final rule an explanation why that 
alternative was not adopted. Before EPA establishes any regulatory 
requirements that may significantly or uniquely affect small 
governments, including tribal governments, it must have developed under 
section 203 of the UMRA a small government agency plan. The plan must 
provide for notifying potentially affected small governments, enabling 
officials of affected small governments to have meaningful and timely 
input in the development of EPA regulatory proposals with significant 
federal intergovernmental mandates, and informing, educating, and 
advising small governments on compliance with the regulatory 
requirements.
    EPA has determined that this rule does not contain a federal 
mandate that may result in expenditures of $100 million or more for 
State, local, and tribal governments, in the aggregate, or the private 
sector in any one year. The revised administrative burden EPA 
calculated for the final rule constitutes a reduction of roughly 25,500 
labor hours annually compared to the administrative burden estimated 
for the 2003 CAFO rule. This burden reduction reflects a decrease in 
annual labor burden of 54,100 hours for CAFO operators and an annual 
labor burden increase to State permitting authorities of 28,600 hours. 
In addition, this rulemaking is in response to a federal court decision 
and is necessary to assure compliance with applicable law. Thus, this 
rule is not subject to the requirements of sections 202 and 205 of the 
UMRA.
    EPA has determined that this rule contains no regulatory 
requirements that might significantly or uniquely affect small 
governments. There are no local or Tribal governments authorized to 
implement the NPDES permit program and the Agency is unaware of any 
local or Tribal governments who are owners or operators of CAFOs. Thus 
this rule is not subject to the requirements of section 203 of UMRA.

E. Executive Order 13132: Federalism

    Executive Order 13132, entitled ``Federalism'' (64 FR 43,255; 
August 10, 1999), requires EPA to develop an accountable process to 
ensure ``meaningful and timely input by State and local officials in 
the development of regulatory policies that have federalism 
implications.'' ``Policies that have federalism implications'' is 
defined in the Executive Order to include regulations that have 
``substantial direct effects on the States, on the relationship between 
the national government and the States, or on the distribution of power 
and responsibilities among the various levels of government.''
    This final rule does not have federalism implications. It will not 
have substantial direct effects on the States, on the relationship 
between the national government and the States, or on the distribution 
of power and responsibilities among the various levels of government, 
as specified in Executive Order 13132. EPA estimates that the average 
annual impact on all authorized States together is a cost increase of 
$0.7 million. EPA does not consider an annual impact of this magnitude 
on States to be a substantial effect. In addition, EPA does not expect 
this rule to have any impact on local governments. EPA also considered 
flexibility as an important factor when developing this regulation.
    Further, the revised regulations will not alter the basic State-
federal scheme established in the CWA under which EPA authorizes States 
to carry out the NPDES permitting program. EPA expects the revised 
regulations to have little effect on the relationship between, or the 
distribution of power and responsibilities among, the federal and State 
governments. Thus, Executive Order 13132 does not apply to this rule.
    In the spirit of Executive Order 13132, and consistent with EPA 
policy to promote communications between EPA and State and local 
governments, EPA specifically solicited comment on the proposed rule 
from State and local officials. In addition, through a variety of 
meetings with State associations during the rulemaking process, States 
have been informed about the issues related to addressing the court's 
decisions. States provided input during these meetings. State concerns 
generally focused on the process for incorporating NMPs into permits 
and the related public review process, and also on guidance related to 
what constitutes a discharge from a CAFO given that the proposed rule 
would have required only those operations that discharge or propose to 
discharge to apply for a permit. These concerns have been addressed in 
such a way as to provide flexibility and accountability in the new 
permit application requirements and review processes promulgated in 
this rule.

F. Executive Order 13175: Consultation and Coordination With Indian 
Tribal Governments

    Executive Order 13175, entitled, ``Consultation and Coordination 
with Indian Tribal Governments'' (65 FR 67,249; November 9, 2000), 
requires EPA to develop an accountable process to ensure ``meaningful 
and timely input by tribal officials in the development of regulatory 
policies that have tribal implications.''
    This rule does not have tribal implications. There are currently no 
tribal governments authorized for the NPDES program. This rulemaking 
provides increased opportunity for the public and tribal governments to 
comment on specific CAFOs' applications for permit coverage. It will 
not have substantial direct effects on

[[Page 70474]]

tribal governments, on the relationship between the federal government 
and Indian tribes, or on the distribution of power and responsibilities 
between the federal government and Indian tribes, as specified in 
Executive Order 13175. Thus, Executive Order 13175 does not apply to 
this rule.
    In the spirit of Executive Order 13175, and consistent with EPA 
policy to promote communications between EPA and tribal governments, 
EPA specifically solicited comment on the proposed rule from tribal 
officials.

G. Executive Order 13045: Protection of Children From Environmental 
Health and Safety Risks

    Executive Order 13045 ``Protection of Children from Environmental 
Health Risks and Safety Risks'' (62 FR 19,885; April 23, 1997) applies 
to any rule that: (1) Is determined to be ``economically significant'' 
as defined under Executive Order 12866, and (2) concerns an 
environmental health or safety risk that EPA has reason to believe may 
have a disproportionate effect on children. If the regulatory action 
meets both criteria, the Agency must evaluate the environmental health 
or safety effects of the planned rule on children, and explain why the 
planned regulation is preferable to other potentially effective and 
reasonably feasible alternatives considered by the Agency.
    This final rule is not subject to Executive Order 13045 because it 
is not economically significant as defined in Executive Order 12866, 
and because the Agency does not have reason to believe the 
environmental health or safety risks addressed by this action present a 
disproportionate risk to children. The benefits analysis performed for 
the 2003 CAFO rule determined that the rule would result in certain 
significant benefits to children's health. (Please refer to the 
Benefits Analysis in the record for the 2003 CAFO final rule.) This 
action does not affect the environmental benefits of the 2003 CAFO 
rule.

H. Executive Order 13211: Actions Concerning Regulations That 
Significantly Affect Energy Supply, Distribution, or Use

    This rule is not a ``significant energy action'' as defined in 
Executive Order 13211, ``Actions Concerning Regulations That 
Significantly Affect Energy Supply, Distribution, or Use'' (66 FR 
28,355; May 22, 2001) because it is not likely to have a significant 
adverse effect on the supply, distribution, or use of energy. EPA has 
concluded that this rule is not likely to have any adverse energy 
effects since CAFOs in general do not figure significantly in the 
energy market, and the regulatory revisions finalized in this rule are 
not likely to change existing energy generation or consumption profiles 
for CAFOs.

I. National Technology Transfer and Advancement Act

    Section 12(d) of the National Technology Transfer and Advancement 
Act of 1995 (``NTTAA''), Public Law 104-113, 12(d) (15 U.S.C. 272 note) 
directs EPA to use voluntary consensus standards in its regulatory 
activities unless to do so would be inconsistent with applicable law or 
otherwise impractical. Voluntary consensus standards are technical 
standards (e.g., materials specifications, test methods, sampling 
procedures, and business practices) that are developed or adopted by 
voluntary consensus standards bodies. The NTTAA directs EPA to provide 
Congress, through OMB, explanations when the Agency decides not to use 
available and applicable voluntary consensus standards.
    This final rule does not change the technical requirements for land 
application from those of the 2003 rule. Production area requirements 
are the same for existing sources and for new sources as in the 2003 
rule. The no discharge production area requirements for new sources in 
this rulemaking, however, now include an option for complying with the 
requirement through the development of site-specific design, operation 
and maintenance permit conditions that will ensure no discharge from 
the site. However, the specific no discharge conditions applicable to a 
specific operator choosing this option for compliance will be 
determined by the permitting authority on a site-specific BPJ basis. 
EPA encourages the use by permitting authorities of voluntary consensus 
standards, such as those that may be developed by USDA, in establishing 
the site-specific technical requirements in CAFO permits when the 
permittee demonstrates that these standards are consistent with the 
achievement of no discharge from a specific CAFO.
    This rule for new source requires that CAFOs complying with the no 
discharge requirement through the development of site-specific design, 
maintenance and operation standards must use prescribed technical 
standards in demonstrating that a specific CAFO's design, operation and 
maintenance will be consistent with no discharge from its production 
area. (In certain circumstances, a CAFO may use either equivalent 
evaluation and simulation procedures or technical standards developed 
for a class of specific facilities within a specified geographical area 
if approved by its permitting authority), EPA has not required the use 
of any particular voluntary consensus standards in this rule. The use, 
however, of voluntary consensus standards such as those that may be 
developed by USDA for the required demonstration that site-specific 
design, maintenance and operational requirements for CAFOs to comply 
with the no discharge standard is encouraged. The decisions as to what 
specific best management practices and technologies must be applied at 
individual animal feeding operations are left to the State or EPA in 
the exercise of their NPDES authority.

J. Congressional Review Act

    The Congressional Review Act, 5 U.S.C. 801 et seq., as added by the 
Small Business Regulatory Enforcement Fairness Act of 1996, generally 
provides that before a rule may take effect, the agency promulgating 
the rule must submit a rule report, which includes a copy of the rule, 
to each House of the Congress and to the Comptroller General of the 
United States. EPA will submit a report containing this rule and other 
required information to the U.S. Senate, the U.S. House of 
Representatives, and the Comptroller General of the United States prior 
to publication of the rule in the Federal Register. A major rule cannot 
take effect until 60 days after it is published in the Federal 
Register. This action is not a ``major rule'' as defined by 5 U.S.C. 
804(2). This rule will become effective December 22, 2008.
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BILLING CODE 6560-50-C

List of Subjects

40 CFR Part 9

    Environmental protection, Reporting and recordkeeping requirements.

40 CFR Part 122

    Administrative practice and procedure, confidential business 
information, hazardous substances, reporting and recordkeeping 
requirements, water pollution control.

40 CFR Part 412

    Environmental protection, feedlots, livestock, waste treatment and 
disposal, water pollution control.

    Dated: October 31, 2008.
Stephen L. Johnson,
Administrator.

0
For the reasons set out in the preamble, chapter I of Title 40 of the 
Code of Federal Regulations is to be amended as follows:

PART 9--OMB APPROVALS UNDER THE PAPERWORK REDUCTION ACT

0
1. The authority citation for part 9 continues to read as follows:

    Authority: 7 U.S.C. 135 et seq., 136-136y; 15 U.S.C. 2001, 2003, 
2005, 2006, 2601-2671; 21 U.S.C. 331j, 346a, 348; 31 U.S.C. 9701; 33 
U.S.C. 1251 et seq., 1311, 1313d, 1314, 1318, 1321, 1326, 1330, 
1342, 1344, 1345(d) and (e), 1361; Executive Order 11735, 38 FR 
21243, 3 CFR, 1971-1975 Comp. p. 973; 42 U.S.C. 241, 242b, 243, 246, 
300f, 300g-1, 300g-2, 300g-3, 300g-4, 300g-5, 300g-6, 300j-1, 300j-
2, 300j-3, 300j-4, 300j-9, 1857 et seq., 6901-6992k, 7401-7671q, 
7542, 9601-9657, 11023, 11048.

0
2. In Sec.  9.1 the table is amended by adding entries in numerical 
order under the indicated heading to read as follows:

Sec.  9.1  OMB approvals under the Paperwork Reduction Act.

* * * * *

------------------------------------------------------------------------
                                                             OMB control
                      40 CFR citation                            No.
------------------------------------------------------------------------

                               * * * * *
EPA Administered Permit Programs: The National Pollutant Discharge
 Elimination System

                                * * * * *
122.21(i)..................................................    2040-0250

                                * * * * *
122.23 (d), (e), (h).......................................    2040-0250

                                * * * * *
------------------------------------------------------------------------

PART 122--EPA ADMINISTERED PERMIT PROGRAMS: THE NATIONAL POLLUTANT 
DISCHARGE ELIMINATION SYSTEM

0
3. The authority citation for part 122 continues to read as follows:

    Authority: The Clean Water Act, 33 U.S.C. 1251 et seq.

0
4. Section 122.21 is amended by revising the last sentence in paragraph 
(a)(1), and revising paragraph (i)(1)(x), to read as follows:

Sec.  122.21  Application for a permit (applicable to State programs, 
see Sec.  123.25).

    (a) * * *
    (1) * * * The requirements for concentrated animal feeding 
operations are described in Sec.  122.23(d).
* * * * *
    (i) * * *
    (1) * * *
    (x) A nutrient management plan that at a minimum satisfies the 
requirements specified in Sec.  122.42(e), including, for all CAFOs 
subject to 40 CFR part 412, subpart C or subpart D, the requirements of 
40 CFR 412.4(c), as applicable.
* * * * *

0
5. Section 122.23 is amended as follows:
0
a. By revising paragraph (a).
0
b. By revising paragraphs (d)(1) and (d)(2).
0
c. By adding paragraphs (e)(1) and (e)(2).
0
d. By revising paragraph (f).
0
e. By revising paragraph (g).
0
f. By revising paragraph (h).
0
g. By adding paragraph (i).
0
h. By adding paragraph (j).

Sec.  122.23  Concentrated animal feeding operations (applicable to 
State NPDES programs, see Sec.  123.25).

    (a) Scope. Concentrated animal feeding operations (CAFOs), as 
defined in paragraph (b) of this section or designated in accordance 
with paragraph (c) of this section, are point sources, subject to NPDES 
permitting requirements as provided in this section. Once an animal 
feeding operation is defined as a CAFO for at least one type of animal, 
the NPDES requirements for CAFOs apply with respect to all animals in 
confinement at the operation and all manure, litter, and process 
wastewater generated by those animals or the production of those 
animals, regardless of the type of animal.
* * * * *
    (d) * * *
    (1) Permit Requirement. The owner or operator of a CAFO must seek 
coverage under an NPDES permit if the CAFO discharges or proposes to 
discharge. A

[[Page 70481]]

CAFO proposes to discharge if it is designed, constructed, operated, or 
maintained such that a discharge will occur. Specifically, the CAFO 
owner or operator must either apply for an individual NPDES permit or 
submit a notice of intent for coverage under an NPDES general permit. 
If the Director has not made a general permit available to the CAFO, 
the CAFO owner or operator must submit an application for an individual 
permit to the Director.
    (2) Information to submit with permit application or notice of 
intent. An application for an individual permit must include the 
information specified in Sec.  122.21. A notice of intent for a general 
permit must include the information specified in Sec. Sec.  122.21 and 
122.28.
* * * * *
    (e) * * *
    (1) For unpermitted Large CAFOs, a precipitation-related discharge 
of manure, litter, or process wastewater from land areas under the 
control of a CAFO shall be considered an agricultural stormwater 
discharge only where the manure, litter, or process wastewater has been 
land 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) through (ix).
    (2) Unpermitted Large CAFOs must maintain documentation specified 
in Sec.  122.42(e)(1)(ix) either on site or at a nearby office, or 
otherwise make such documentation readily available to the Director or 
Regional Administrator upon request.
    (f) When must the owner or operator of a CAFO seek coverage under 
an NPDES permit? Any CAFO that is required to seek permit coverage 
under paragraph (d)(1) of this section must seek coverage when the CAFO 
proposes to discharge, unless a later deadline is specified below.
    (1) Operations defined as CAFOs prior to April 14, 2003. For 
operations defined as CAFOs under regulations that were in effect prior 
to April 14, 2003, the owner or operator must have or seek to obtain 
coverage under an NPDES permit as of April 14, 2003, and comply with 
all applicable NPDES requirements, including the duty to maintain 
permit coverage in accordance with paragraph (g) of this section.
    (2) Operations defined as CAFOs as of April 14, 2003, that were not 
defined as CAFOs prior to that date. For all operations defined as 
CAFOs as of April 14, 2003, that were not defined as CAFOs prior to 
that date, the owner or operator of the CAFO must seek to obtain 
coverage under an NPDES permit by February 27, 2009.
    (3) Operations that become defined as CAFOs after April 14, 2003, 
but which are not new sources. For a newly constructed CAFO and for an 
AFO that makes changes to its operations that result in its becoming 
defined as a CAFO for the first time after April 14, 2003, but is not a 
new source, the owner or operator must seek to obtain coverage under an 
NPDES permit, as follows:
    (i) For newly constructed operations not subject to effluent 
limitations guidelines, 180 days prior to the time CAFO commences 
operation;
    (ii) For other operations (e.g., resulting from an increase in the 
number of animals), as soon as possible, but no later than 90 days 
after becoming defined as a CAFO; or
    (iii) If an operational change that makes the operation a CAFO 
would not have made it a CAFO prior to April 14, 2003, the operation 
has until February 27, 2009, or 90 days after becoming defined as a 
CAFO, whichever is later.
    (4) New sources. The owner or operator of a new source must seek to 
obtain coverage under a permit at least 180 days prior to the time that 
the CAFO commences operation.
    (5) Operations that are designated as CAFOs. For operations 
designated as a CAFO in accordance with paragraph (c) of this section, 
the owner or operator must seek to obtain coverage under a permit no 
later than 90 days after receiving notice of the designation.
    (g) Duty to Maintain Permit Coverage. No later than 180 days before 
the expiration of the permit, or as provided by the Director, any 
permitted CAFO must submit an application to renew its permit, in 
accordance with Sec.  122.21(d), unless the CAFO will not discharge or 
propose to discharge upon expiration of the permit.
    (h) Procedures for CAFOs seeking coverage under a general permit. 
(1) CAFO owners or operators must submit a notice of intent when 
seeking authorization to discharge under a general permit in accordance 
with Sec.  122.28(b). The Director must review notices of intent 
submitted by CAFO owners or operators to ensure that the notice of 
intent includes the information required by Sec.  122.21(i)(1), 
including a nutrient management plan that meets the requirements of 
Sec.  122.42(e) and applicable effluent limitations and standards, 
including those specified in 40 CFR part 412. When additional 
information is necessary to complete the notice of intent or clarify, 
modify, or supplement previously submitted material, the Director may 
request such information from the owner or operator. If the Director 
makes a preliminary determination that the notice of intent meets the 
requirements of Sec. Sec.  122.21(i)(1) and 122.42(e), the Director 
must notify the public of the Director's proposal to grant coverage 
under the permit to the CAFO and make available for public review and 
comment the notice of intent submitted by the CAFO, including the 
CAFO's nutrient management plan, and the draft terms of the nutrient 
management plan to be incorporated into the permit. The process for 
submitting public comments and hearing requests, and the hearing 
process if a request for a hearing is granted, must follow the 
procedures applicable to draft permits set forth in 40 CFR 124.11 
through 124.13. The Director may establish, either by regulation or in 
the general permit, an appropriate period of time for the public to 
comment and request a hearing that differs from the time period 
specified in 40 CFR 124.10. The Director must respond to significant 
comments received during the comment period, as provided in 40 CFR 
124.17, and, if necessary, require the CAFO owner or operator to revise 
the nutrient management plan in order to be granted permit coverage. 
When the Director authorizes coverage for the CAFO owner or operator 
under the general permit, the terms of the nutrient management plan 
shall become incorporated as terms and conditions of the permit for the 
CAFO. The Director shall notify the CAFO owner or operator and inform 
the public that coverage has been authorized and of the terms of the 
nutrient management plan incorporated as terms and conditions of the 
permit applicable to the CAFO.
    (2) For EPA-issued permits only. The Regional Administrator shall 
notify each person who has submitted written comments on the proposal 
to grant coverage and the draft terms of the nutrient management plan 
or requested notice of the final permit decision. Such notification 
shall include notice that coverage has been authorized and of the terms 
of the nutrient management plan incorporated as terms and conditions of 
the permit applicable to the CAFO.
    (3) Nothing in this paragraph (h) shall affect the authority of the 
Director to require an individual permit under Sec.  122.28(b)(3).
    (i) No Discharge Certification Option. (1) The owner or operator of 
a CAFO that meets the eligibility criteria in paragraph (i)(2) of this 
section may certify to the Director that the CAFO does not discharge or 
propose to discharge. A CAFO owner or operator who certifies that the 
CAFO does not

[[Page 70482]]

discharge or propose to discharge is not required to seek coverage 
under an NPDES permit pursuant to paragraph (d)(1) of this section, 
provided that the CAFO is designed, constructed, operated, and 
maintained in accordance with the requirements of paragraphs (i)(2) and 
(3) of this section, and subject to the limitations in paragraph (i)(4) 
of this section.
    (2) Eligibility Criteria. In order to certify that a CAFO does not 
discharge or propose to discharge, the owner or operator of a CAFO must 
document, based on an objective assessment of the conditions at the 
CAFO, that the CAFO is designed, constructed, operated, and maintained 
in a manner such that the CAFO will not discharge, as follows:
    (i) The CAFO's production area is designed, constructed, operated, 
and maintained so as not to discharge. The CAFO must maintain 
documentation that demonstrates that:
    (A) Any open manure storage structures are designed, constructed, 
operated, and maintained to achieve no discharge based on a technical 
evaluation in accordance with the elements of the technical evaluation 
set forth in 40 CFR 412.46(a)(1)(i) through (viii);
    (B) Any part of the CAFO's production area that is not addressed by 
paragraph (i)(2)(i)(A) of this section is designed, constructed, 
operated, and maintained such that there will be no discharge of 
manure, litter, or process wastewater; and
    (C) The CAFO implements the additional measures set forth in 40 CFR 
412.37(a) and (b);
    (ii) The CAFO has developed and is implementing an up-to-date 
nutrient management plan to ensure no discharge from the CAFO, 
including from all land application areas under the control of the 
CAFO, that addresses, at a minimum, the following:
    (A) The elements of Sec.  122.42(e)(1)(i) through (ix) and 40 CFR 
412.37(c); and
    (B) All site-specific operation and maintenance practices necessary 
to ensure no discharge, including any practices or conditions 
established by a technical evaluation pursuant to paragraph 
(i)(2)(i)(A) of this section; and
    (iii) The CAFO must maintain documentation required by this 
paragraph either on site or at a nearby office, or otherwise make such 
documentation readily available to the Director or Regional 
Administrator upon request.
    (3) Submission to the Director. In order to certify that a CAFO 
does not discharge or propose to discharge, the CAFO owner or operator 
must complete and submit to the Director, by certified mail or 
equivalent method of documentation, a certification that includes, at a 
minimum, the following information:
    (i) The legal name, address and phone number of the CAFO owner or 
operator (see Sec.  122.21(b));
    (ii) The CAFO name and address, the county name and the latitude 
and longitude where the CAFO is located;
    (iii) A statement that describes the basis for the CAFO's 
certification that it satisfies the eligibility requirements identified 
in paragraph (i)(2) of this section; and
    (iv) The following certification statement: ``I certify under 
penalty of law that I am the owner or operator of a concentrated animal 
feeding operation (CAFO), identified as [Name of CAFO], and that said 
CAFO meets the requirements of 40 CFR 122.23(i). I have read and 
understand the eligibility requirements of 40 CFR 122.23(i)(2) for 
certifying that a CAFO does not discharge or propose to discharge and 
further certify that this CAFO satisfies the eligibility requirements. 
As part of this certification, I am including the information required 
by 40 CFR 122.23(i)(3). I also understand the conditions set forth in 
40 CFR 122.23(i)(4), (5) and (6) regarding loss and withdrawal of 
certification. I certify under penalty of law that this document and 
all other documents required for this certification were prepared under 
my direction or supervision and that qualified personnel properly 
gathered and evaluated the information submitted. Based upon my inquiry 
of the person or persons directly involved in gathering and evaluating 
the information, the information submitted is to the best of my 
knowledge and belief true, accurate and complete. I am aware there are 
significant penalties for submitting false information, including the 
possibility of fine and imprisonment for knowing violations.''; and
    (v) The certification must be signed in accordance with the 
signatory requirements of 40 CFR 122.22.
    (4) Term of Certification. A certification that meets the 
requirements of paragraphs (i)(2) and (i)(3) of this section 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. Certification will remain in effect for five years or until 
the certification is no longer valid or is withdrawn, whichever occurs 
first. A certification is no longer valid when a discharge has occurred 
or when the CAFO ceases to meet the eligibility criteria in paragraph 
(i)(2) of this section.
    (5) Withdrawal of Certification. (i) At any time, a CAFO may 
withdraw its certification by notifying the Director by certified mail 
or equivalent method of documentation. A certification is withdrawn on 
the date the notification is submitted to the Director. The CAFO does 
not need to specify any reason for the withdrawal in its notification 
to the Director.
    (ii) If a certification becomes invalid in accordance with 
paragraph (i)(4) of this section, the CAFO must withdraw its 
certification within three days of the date on which the CAFO becomes 
aware that the certification is invalid. Once a CAFO's certification is 
no longer valid, the CAFO is subject to the requirement in paragraph 
(d)(1) of this section to seek permit coverage if it discharges or 
proposes to discharge.
    (6) Recertification. A previously certified CAFO that does not 
discharge or propose to discharge may recertify in accordance with 
paragraph (i) of this section, except that where the CAFO has 
discharged, the CAFO may only recertify if the following additional 
conditions are met:
    (i) The CAFO had a valid certification at the time of the 
discharge;
    (ii) The owner or operator satisfies the eligibility criteria of 
paragraph (i)(2) of this section, including any necessary modifications 
to the CAFO's design, construction, operation, and/or maintenance to 
permanently address the cause of the discharge and ensure that no 
discharge from this cause occurs in the future;
    (iii) The CAFO has not previously recertified after a discharge 
from the same cause;
    (iv) The owner or operator submits to the Director for review the 
following documentation: 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 in addition to 
submitting a certification in accordance with paragraph (i)(3) of this 
section; and
    (v) Notwithstanding paragraph (i)(4) of this section, a 
recertification that meets the requirements of paragraphs (i)(6)(iii) 
and (i)(6)(iv) of this section shall only become effective 30 days from 
the date of submission of the recertification documentation.
    (j) Effect of certification. (1) An unpermitted CAFO certified in 
accordance with paragraph (i) of this section is presumed not to 
propose to discharge. If such a CAFO does discharge, it is not in 
violation of the requirement that CAFOs that propose to discharge seek 
permit coverage pursuant

[[Page 70483]]

to paragraphs (d)(1) and (f) of this section, with respect to that 
discharge. In all instances, the discharge of a pollutant without a 
permit is a violation of the Clean Water Act section 301(a) prohibition 
against unauthorized discharges from point sources.
    (2) In any enforcement proceeding for failure to seek permit 
coverage under paragraphs (d)(1) or (f) of this section that is related 
to a discharge from an unpermitted CAFO, the burden is on the CAFO to 
establish that it did not propose to discharge prior to the discharge 
when the CAFO either did not submit certification documentation as 
provided in paragraph (i)(3) or (i)(6)(iv) of this section within at 
least five years prior to the discharge, or withdrew its certification 
in accordance with paragraph (i)(5) of this section. Design, 
construction, operation, and maintenance in accordance with the 
criteria of paragraph (i)(2) of this section satisfies this burden.

0
6. Section 122.28 is amended by adding a new paragraph (b)(2)(vii), to 
read as follows:

Sec.  122.28  General permits (applicable to State NPDES programs, see 
Sec.  123.25).

* * * * *
    (b) * * *
    (2) * * *
    (vii) A CAFO owner or operator may be authorized to discharge under 
a general permit only in accordance with the process described in Sec.  
122.23(h).
* * * * *

0
7. Section 122.42 is amended as follows:
0
a. By revising paragraph (e) introductory text and paragraph (e)(1) 
introductory text.
0
b. By removing the period at the end of paragraph (e)(4)(vii) and 
adding in its place ``; and''.
0
c. By adding paragraph (e)(4)(viii).
0
d. By adding paragraphs (e)(5) and (e)(6).

Sec.  122.42  Additional conditions applicable to specified categories 
of NPDES permits (applicable to State NPDES programs, see Sec.  
123.25).

* * * * *
    (e) Concentrated animal feeding operations (CAFOs). Any permit 
issued to a CAFO must include the requirements in paragraphs (e)(1) 
through (e)(6) of this section.
    (1) Requirement to implement a nutrient management plan. Any permit 
issued to a CAFO must include a requirement to implement a nutrient 
management plan that, at a minimum, contains best management practices 
necessary to meet the requirements of this paragraph and applicable 
effluent limitations and standards, including those specified in 40 CFR 
part 412. The nutrient management plan must, to the extent applicable:
* * * * *
    (4) * * *
    (viii) The actual crop(s) planted and actual yield(s) for each 
field, the actual nitrogen and phosphorus content of the manure, 
litter, and process wastewater, the results of calculations conducted 
in accordance with paragraphs (e)(5)(i)(B) and (e)(5)(ii)(D) of this 
section, and the amount of manure, litter, and process wastewater 
applied to each field during the previous 12 months; and, for any CAFO 
that implements a nutrient management plan that addresses rates of 
application in accordance with paragraph (e)(5)(ii) of this section, 
the results of any soil testing for nitrogen and phosphorus taken 
during the preceding 12 months, the data used in calculations conducted 
in accordance with paragraph (e)(5)(ii)(D) of this section, and the 
amount of any supplemental fertilizer applied during the previous 12 
months.
    (5) Terms of the nutrient management plan. Any permit issued to a 
CAFO must require compliance with the terms of the CAFO's site-specific 
nutrient management plan. The terms of the nutrient management plan are 
the information, protocols, best management practices, and other 
conditions in the nutrient management plan determined by the Director 
to be necessary to meet the requirements of paragraph (e)(1) of this 
section. The terms of the nutrient management plan, with respect to 
protocols for land application of manure, litter, or process wastewater 
required by paragraph (e)(1)(viii) of this section and, as applicable, 
40 CFR 412.4(c), must include the fields available for land 
application; field-specific rates of application properly developed, as 
specified in paragraphs (e)(5)(i) through (ii) of this section, to 
ensure appropriate agricultural utilization of the nutrients in the 
manure, litter, or process wastewater; and any timing limitations 
identified in the nutrient management plan concerning land application 
on the fields available for land application. The terms must address 
rates of application using one of the following two approaches, unless 
the Director specifies that only one of these approaches may be used:
    (i) Linear approach. An approach that expresses rates of 
application as pounds of nitrogen and phosphorus, according to the 
following specifications:
    (A) The terms include maximum application rates from manure, 
litter, and process wastewater for each year of permit coverage, for 
each crop identified in the nutrient management plan, in chemical forms 
determined to be acceptable to the Director, in pounds per acre, per 
year, for each field to be used for land application, and certain 
factors necessary to determine such rates. At a minimum, the factors 
that are terms must include: The outcome of the field-specific 
assessment of the potential for nitrogen and phosphorus transport from 
each field; the crops to be planted in each field or any other uses of 
a field such as pasture or fallow fields; the realistic yield goal for 
each crop or use identified for each field; the nitrogen and phosphorus 
recommendations from sources specified by the Director for each crop or 
use identified for each field; credits for all nitrogen in the field 
that will be plant available; consideration of multi-year phosphorus 
application; and accounting for all other additions of plant available 
nitrogen and phosphorus to the field. In addition, the terms include 
the form and source of manure, litter, and process wastewater to be 
land-applied; the timing and method of land application; and the 
methodology by which the nutrient management plan accounts for the 
amount of nitrogen and phosphorus in the manure, litter, and process 
wastewater to be applied.
    (B) Large CAFOs that use this approach must calculate the maximum 
amount of manure, litter, and process wastewater to be land applied at 
least once each year using the results of the most recent 
representative manure, litter, and process wastewater tests for 
nitrogen and phosphorus taken within 12 months of the date of land 
application; or
    (ii) Narrative rate approach. An approach that expresses rates of 
application as a narrative rate of application that results in the 
amount, in tons or gallons, of manure, litter, and process wastewater 
to be land applied, according to the following specifications:
    (A) The terms include maximum amounts of nitrogen and phosphorus 
derived from all sources of nutrients, for each crop identified in the 
nutrient management plan, in chemical forms determined to be acceptable 
to the Director, in pounds per acre, for each field, and certain 
factors necessary to determine such amounts. At a minimum, the factors 
that are terms must include: the outcome of the field-specific 
assessment of the potential for nitrogen and phosphorus transport from 
each field; the crops to be planted in each field or any other uses 
such as pasture or fallow fields (including

[[Page 70484]]

alternative crops identified in accordance with paragraph (e)(5)(ii)(B) 
of this section); the realistic yield goal for each crop or use 
identified for each field; and the nitrogen and phosphorus 
recommendations from sources specified by the Director for each crop or 
use identified for each field. In addition, the terms include the 
methodology by which the nutrient management plan accounts for the 
following factors when calculating the amounts of manure, litter, and 
process wastewater to be land applied: Results of soil tests conducted 
in accordance with protocols identified in the nutrient management 
plan, as required by paragraph (e)(1)(vii) of this section; credits for 
all nitrogen in the field that will be plant available; the amount of 
nitrogen and phosphorus in the manure, litter, and process wastewater 
to be applied; consideration of multi-year phosphorus application; 
accounting for all other additions of plant available nitrogen and 
phosphorus to the field; the form and source of manure, litter, and 
process wastewater; the timing and method of land application; and 
volatilization of nitrogen and mineralization of organic nitrogen.
    (B) The terms of the nutrient management plan include alternative 
crops identified in the CAFO's nutrient management plan that are not in 
the planned crop rotation. Where a CAFO includes alternative crops in 
its nutrient management plan, the crops must be listed by field, in 
addition to the crops identified in the planned crop rotation for that 
field, and the nutrient management plan must include realistic crop 
yield goals and the nitrogen and phosphorus recommendations from 
sources specified by the Director for each crop. Maximum amounts of 
nitrogen and phosphorus from all sources of nutrients and the amounts 
of manure, litter, and process wastewater to be applied must be 
determined in accordance with the methodology described in paragraph 
(e)(5)(ii)(A) of this section.
    (C) For CAFOs using this approach, the following projections must 
be included in the nutrient management plan submitted to the Director, 
but are not terms of the nutrient management plan: The CAFO's planned 
crop rotations for each field for the period of permit coverage; the 
projected amount of manure, litter, or process wastewater to be 
applied; projected credits for all nitrogen in the field that will be 
plant available; consideration of multi-year phosphorus application; 
accounting for all other additions of plant available nitrogen and 
phosphorus to the field; and the predicted form, source, and method of 
application of manure, litter, and process wastewater for each crop. 
Timing of application for each field, insofar as it concerns the 
calculation of rates of application, is not a term of the nutrient 
management plan.
    (D) CAFOs that use this approach must calculate maximum amounts of 
manure, litter, and process wastewater to be land applied at least once 
each year using the methodology required in paragraph (e)(5)(ii)(A) of 
this section before land applying manure, litter, and process 
wastewater and must rely on the following data:
    (1) A field-specific determination of soil levels of nitrogen and 
phosphorus, including, for nitrogen, a concurrent determination of 
nitrogen that will be plant available consistent with the methodology 
required by paragraph (e)(5)(ii)(A) of this section, and for 
phosphorus, the results of the most recent soil test conducted in 
accordance with soil testing requirements approved by the Director; and
    (2) The results of most recent representative manure, litter, and 
process wastewater tests for nitrogen and phosphorus taken within 12 
months of the date of land application, in order to determine the 
amount of nitrogen and phosphorus in the manure, litter, and process 
wastewater to be applied.
    (6) Changes to a nutrient management plan. Any permit issued to a 
CAFO must require the following procedures to apply when a CAFO owner 
or operator makes changes to the CAFO's nutrient management plan 
previously submitted to the Director:
    (i) The CAFO owner or operator must provide the Director with the 
most current version of the CAFO's nutrient management plan and 
identify changes from the previous version, except that the results of 
calculations made in accordance with the requirements of paragraphs 
(e)(5)(i)(B) and (e)(5)(ii)(D) of this section are not subject to the 
requirements of paragraph (e)(6) of this section.
    (ii) The Director must review the revised nutrient management plan 
to ensure that it meets the requirements of this section and applicable 
effluent limitations and standards, including those specified in 40 CFR 
part 412, and must determine whether the changes to the nutrient 
management plan necessitate revision to the terms of the nutrient 
management plan incorporated into the permit issued to the CAFO. If 
revision to the terms of the nutrient management plan is not necessary, 
the Director must notify the CAFO owner or operator and upon such 
notification the CAFO may implement the revised nutrient management 
plan. If revision to the terms of the nutrient management plan is 
necessary, the Director must determine whether such changes are 
substantial changes as described in paragraph (e)(6)(iii) of this 
section.
    (A) If the Director determines that the changes to the terms of the 
nutrient management plan are not substantial, the Director must make 
the revised nutrient management plan publicly available and include it 
in the permit record, revise the terms of the nutrient management plan 
incorporated into the permit, and notify the owner or operator and 
inform the public of any changes to the terms of the nutrient 
management plan that are incorporated into the permit.
    (B) If the Director determines that the changes to the terms of the 
nutrient management plan are substantial, the Director must notify the 
public and make the proposed changes and the information submitted by 
the CAFO owner or operator available for public review and comment. The 
process for public comments, hearing requests, and the hearing process 
if a hearing is held must follow the procedures applicable to draft 
permits set forth in 40 CFR 124.11 through 124.13. The Director may 
establish, either by regulation or in the CAFO's permit, an appropriate 
period of time for the public to comment and request a hearing on the 
proposed changes that differs from the time period specified in 40 CFR 
124.10. The Director must respond to all significant comments received 
during the comment period as provided in 40 CFR 124.17, and require the 
CAFO owner or operator to further revise the nutrient management plan 
if necessary, in order to approve the revision to the terms of the 
nutrient management plan incorporated into the CAFO's permit. Once the 
Director incorporates the revised terms of the nutrient management plan 
into the permit, the Director must notify the owner or operator and 
inform the public of the final decision concerning revisions to the 
terms and conditions of the permit.
    (iii) Substantial changes to the terms of a nutrient management 
plan incorporated as terms and conditions of a permit include, but are 
not limited to:
    (A) Addition of new land application areas not previously included 
in the CAFO's nutrient management plan. Except that if the land 
application area that is being added to the nutrient management plan is 
covered by terms of a nutrient management plan incorporated into an 
existing NPDES permit in accordance with the requirements of paragraph 
(e)(5) of this section, and the CAFO owner or operator applies manure, 
litter, or

[[Page 70485]]

process wastewater on the newly added land application area in 
accordance with the existing field-specific permit terms applicable to 
the newly added land application area, such addition of new land would 
be a change to the new CAFO owner or operator's nutrient management 
plan but not a substantial change for purposes of this section;
    (B) Any changes to the field-specific maximum annual rates for land 
application, as set forth in paragraphs (e)(5)(i) of this section, and 
to the maximum amounts of nitrogen and phosphorus derived from all 
sources for each crop, as set forth in paragraph (e)(5)(ii) of this 
section;
    (C) Addition of any crop or other uses not included in the terms of 
the CAFO's nutrient management plan and corresponding field-specific 
rates of application expressed in accordance with paragraph (e)(5) of 
this section; and
    (D) Changes to site-specific components of the CAFO's nutrient 
management plan, where such changes are likely to increase the risk of 
nitrogen and phosphorus transport to waters of the U.S.
    (iv) For EPA-issued permits only. Upon incorporation of the revised 
terms of the nutrient management plan into the permit, 40 CFR 124.19 
specifies procedures for appeal of the permit decision. In addition to 
the procedures specified at 40 CFR 124.19, a person must have submitted 
comments or participated in the public hearing in order to appeal the 
permit decision.

0
8. Section 122.62 is amended by adding paragraph (a)(17) to read as 
follows:

Sec.  122.62  Modification or revocation and reissuance of permits 
(applicable to State programs, see Sec.  123.25)

* * * * *
    (a) * * *
    (17) Nutrient Management Plans. The incorporation of the terms of a 
CAFO's nutrient management plan into the terms and conditions of a 
general permit when a CAFO obtains coverage under a general permit in 
accordance with Sec. Sec.  122.23(h) and 122.28 is not a cause for 
modification pursuant to the requirements of this section.
* * * * *

0
9. Section 122.63 is amended by adding paragraph (h) to read as 
follows:

Sec.  122.63  Minor modification of permits.

* * * * *
    (h) Incorporate changes to the terms of a CAFO's nutrient 
management plan that have been revised in accordance with the 
requirements of Sec.  122.42(e)(6).

PART 412--CONCENTRATED ANIMAL FEEDING OPERATIONS (CAFO) POINT 
SOURCE CATEGORY

0
10. The authority citation for part 412 continues to read as follows:

    Authority: 33 U.S.C. 1311, 1314, 1316, 1317, 1318, 1342, and 
1361.

0
11. Section 412.37 is amended by revising paragraph (a)(2) to read as 
follows:

Sec.  412.37  Additional measures.

    (a) * * *
    (2) Depth marker. All open surface liquid impoundments must have a 
depth marker which clearly indicates the minimum capacity necessary to 
contain the runoff and direct precipitation of the 25-year, 24-hour 
rainfall event. In the case of new sources subject to effluent 
limitations established pursuant to Sec.  412.46(a)(1) of this part, 
all open surface manure storage structures associated with such sources 
must include a depth marker which clearly indicates the minimum 
capacity necessary to contain the maximum runoff and direct 
precipitation associated with the design storm used in sizing the 
impoundment for no discharge.

0
12. Section 412.46 is amended by revising paragraphs (a)(1), (d), and 
(e) to read as follows:

Sec.  412.46  New source performance standards (NSPS).

* * * * *
    (a) * * *
    (1) Any CAFO subject to this subpart may request that the Director 
establish NPDES permit best management practice effluent limitations 
designed to ensure no discharge of manure, litter, or process 
wastewater based upon a site-specific evaluation of the CAFO's open 
surface manure storage structure. The NPDES permit best management 
practice effluent limitations must address the CAFO's entire production 
area. In the case of any CAFO using an open surface manure storage 
structure for which the Director establishes such effluent limitations, 
``no discharge of manure, litter, or process wastewater pollutants,'' 
as used in this section, means that the storage structure is designed, 
operated, and maintained in accordance with best management practices 
established by the Director on a site-specific basis after a technical 
evaluation of the storage structure. The technical evaluation must 
address the following elements:
    (i) Information to be used in the design of the open manure storage 
structure including, but not limited to, the following: minimum storage 
periods for rainy seasons, additional minimum capacity for chronic 
rainfalls, applicable technical standards that prohibit or otherwise 
limit land application to frozen, saturated, or snow-covered ground, 
planned emptying and dewatering schedules consistent with the CAFO's 
Nutrient Management Plan, additional storage capacity for manure 
intended to be transferred to another recipient at a later time, and 
any other factors that would affect the sizing of the open manure 
storage structure.
    (ii) The design of the open manure storage structure as determined 
by the most recent version of the National Resource Conservation 
Service's Animal Waste Management (AWM) software. CAFOs may use 
equivalent design software or procedures as approved by the Director.
    (iii) All inputs used in the open manure storage structure design 
including actual climate data for the previous 30 years consisting of 
historical average monthly precipitation and evaporation values, the 
number and types of animals, anticipated animal sizes or weights, any 
added water and bedding, any other process wastewater, and the size and 
condition of outside areas exposed to rainfall and contributing runoff 
to the open manure storage structure.
    (iv) The planned minimum period of storage in months including, but 
not limited to, the factors for designing an open manure storage 
structure listed in paragraph (a)(1)(i) of this section. Alternatively 
the CAFO may determine the minimum period of storage by specifying 
times the storage pond will be emptied consistent with the CAFO's 
Nutrient Management Plan.
    (v) Site-specific predicted design specifications including 
dimensions of the storage facility, daily manure and wastewater 
additions, the size and characteristics of the land application areas, 
and the total calculated storage period in months.
    (vi) An evaluation of the adequacy of the designed manure storage 
structure using the most recent version of the Soil Plant Air Water 
(SPAW) Hydrology Tool. The evaluation must include all inputs to SPAW 
including but not limited to daily precipitation, temperature, and 
evaporation data for the previous 100 years, user-specified soil 
profiles representative of the CAFO's land application areas, planned 
crop rotations consistent with the CAFO's Nutrient Management Plan, and 
the final modeled result of no overflows from the designed open manure 
storage structure. For those CAFOs where 100 years of local weather 
data for the CAFO's location is not available, CAFOs

[[Page 70486]]

may use a simulation with a confidence interval analysis conducted over 
a period of 100 years. The Director may approve equivalent evaluation 
and simulation procedures.
    (vii) The Director may waive the requirement of (a)(1)(vi) for a 
site-specific evaluation of the designed manure storage structure and 
instead authorize a CAFO to use a technical evaluation developed for a 
class of specific facilities within a specified geographical area.
    (viii) Waste management and storage facilities designed, 
constructed, operated, and maintained consistent with the analysis 
conducted in paragraphs (a)(1)(i) through (a)(1)(vii) of this section 
and operated in accordance with the additional measures and records 
required by Sec.  412.47(a) and (b), will fulfill the requirements of 
this section.
    (ix) The Director has the discretion to request additional 
information to support a request for effluent limitations based on a 
site-specific open surface manure storage structure.
* * * * *
    (d) Any source subject to this subpart that commenced discharging 
after April 14, 1993, and prior to April 14, 2003, which was a new 
source subject to the standards specified in Sec.  412.15, revised as 
of July 1, 2002, must continue to achieve those standards for the 
applicable time period specified in 40 CFR 122.29(d)(1). Thereafter, 
the source must achieve the standards specified in Sec.  412.43(a) and 
(b).
    (e) Any source subject to this subpart that commenced discharging 
after April 14, 2003, and prior to January 20, 2009, which was a new 
source subject to the standards specified in Sec.  412.46(a) through 
(d) in the July 1, 2008, edition of 40 CFR part 439, must continue to 
achieve those standards for the applicable time period specified in 40 
CFR 122.29(d)(1).

 [FR Doc. E8-26620 Filed 11-19-08; 8:45 am]

BILLING CODE 6560-50-P