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

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.

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.

Table 1.1—Operations Potentially Regulated by this Rule

Category

Examples of regulated entities

North American Industry Classification System (NAICS)

Standard Industrial Classification (SIC)

Industry

Operators of animal production operations that meet the definition of a CAFO:

Beef cattle feedlots (including veal calves)

112112

0211

Beef cattle ranching and farming

112111

0212

Hogs

11221

0213

Sheep and Goats

11241, 11242

0214

General livestock except dairy and poultry

11299

0219

Dairy farms

11212

0241

Broilers, fryers, and roaster chickens

11232

0251

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

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 § 122.23. If you have questions regarding the applicability of this action to a particular entity, consult the person listed in the preceding

FOR FURTHER INFORMATION CONTACT

section.

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

1.

Docket.

EPA has established an official public docket for this action under Docket ID No. EPA-HQ-OW-2005-0037. The official public docket consists of the documents specifically referenced in this action, any public comments received, and other information related to this action. Although listed in the index, some information is not publicly available,

e.g.

, Confidential Business Information (CBI) or other information whose disclosure is restricted by statute. Certain other material, such as copyrighted material, will be publicly available only in hard copy. Publicly available docket materials are available either electronically in

www.regulations.gov

or in hard copy at the Water Docket in the EPA Docket Center, EPA West, 1301 Constitution Ave., NW., Washington, DC. The Public Reading Room is open from 8:30 a.m. to 4:30 p.m., Monday through Friday, excluding legal holidays. The telephone number for the Public Reading Room is (202) 566-1744, and the telephone number for the Water Docket is (202) 566-2426.

2.

Electronic Access

. This

Federal Register

document and key supporting documents are also electronically available on the Internet at

http://www.epa.gov/npdes/agriculture

.

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

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

D. What Is the Comment Response Document?

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

II. Background

A. The Clean Water Act

Congress enacted the Federal Water Pollution Control Act (1972), also known as the Clean Water Act (CWA), to “restore and maintain the chemical, physical, and biological integrity of the nation's waters” (CWA section 101(a)). Among the core provisions, the CWA establishes the NPDES permit program to authorize and regulate the discharge of pollutants from point sources to waters of the U.S. (CWA section 402). Section 502(14) of the CWA specifically includes CAFOs in the definition of the term “point source.” Section 502(12) defines the term “discharge of a pollutant” to mean “

any

addition of any pollutant to navigable waters from any point source” (emphasis added). EPA has issued comprehensive regulations that implement the NPDES program at 40 CFR part 122. The Act also provides for the development of technology-based and water quality-based effluent limitations that are imposed through NPDES permits to control the discharge of pollutants from point sources. CWA sections 301(a) and (b).

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

EPA began regulating discharges of wastewater and manure from CAFOs in the 1970s. EPA initially issued national effluent limitations guidelines and standards for feedlots on February 14, 1974 (39 FR 5704), and NPDES CAFO regulations on March 18, 1976 (41 FR 11,458).

In February 2003, EPA issued revisions to these regulations that focused on the 5% of the nation's animal feeding operations (AFOs) that presented the highest risk of impairing water quality and public health (68 FR 7176-7274; February 12, 2003) (“the 2003 CAFO rule”). The 2003 CAFO rule required the owners or operators of all CAFOs

1

to seek coverage under an NPDES permit, unless they demonstrated no potential to discharge.

A number of CAFO industry organizations (American Farm Bureau Federation, National Pork Producers Council, National Chicken Council, and National Turkey Federation (NTF), although NTF later withdrew its petition) and several environmental groups (Waterkeeper Alliance, Natural Resources Defense Council, Sierra Club, and American Littoral Society) filed petitions for judicial review of certain aspects of the 2003 CAFO rule. This case was brought before the U.S. Court of Appeals for the Second Circuit. On February 28, 2005, the court ruled on these petitions and upheld most provisions of the 2003 rule but vacated and remanded others.

Waterkeeper Alliance, et al.

v.

EPA

, 399 F.3d 486 (2d Cir. 2005). The court's decision is described in detail below.

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.

The revisions to the 2003 CAFO rule being published today relate directly to the changes required by the court's decision and continue to maintain the focus on regulating discharges from the universe of high-risk AFOs.

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

The Second Circuit's decision in

Waterkeeper

upheld certain challenged provisions of the 2003 rule and vacated or remanded others, as follows.

1. Issues Upheld by the Court

This section discusses provisions of the 2003 CAFO rule that were challenged by either industry or environmental petitioners, but were upheld by the

Waterkeeper

Court and therefore remain unchanged. EPA is not revising any of these provisions and did not solicit comment on them.

(a) Land Application Regulatory Framework and Interpretation of “Agricultural Stormwater”

The

Waterkeeper

Court upheld EPA's authority to regulate, through NPDES permits, the discharge of manure, litter, or process wastewater that a CAFO applies to its land application area. The court rejected the industry petitioners' claim that land application runoff must be channelized before it can be considered to be a point source discharge subject to permitting. The court noted that the CWA expressly defines the term “point source” to include “any * * * concentrated animal feeding operation * * * from which pollutants are or may be discharged,” and found that the Act “not only permits, but demands” that land application discharges be construed as discharges “from” a CAFO. 399 F.3d at 510.

The

Waterkeeper

Court also upheld EPA's determination in the 2003 CAFO rule that precipitation-related discharges of manure, litter, or process wastewater from land application areas under the control of a CAFO qualify as “agricultural stormwater” only where the CAFO has applied the manure in accordance with nutrient management practices that ensure “appropriate agricultural utilization” of the manure, litter, or process wastewater nutrients. EPA's interpretation of the Act in this regard was reasonable, the court found, in light of Congressional intent in excluding agricultural stormwater from the meaning of the term “point source” and given the precedent set in an earlier Second Circuit case,

Concerned Area Residents for the Environment

v.

Southview Farm

, 34 F.3d 114 (2d Cir. 1994). 399 F.3d at 508-09.

(b) Effluent Guidelines

The court rejected the environmental organizations' claim that EPA, in developing best available technology effluent limitations guidelines, had failed to consider the single best performing CAFO and adopt limitations that reflected its performance. The court found that EPA had collected extensive data on the waste management systems at CAFOs and had considered approximately 11,000 public comments on the proposed CAFO rule. The court determined that EPA had either adopted as the basis for its limitations the best performing technology or declined to do so for permissible reasons. 399 F.3d at 513.

The court upheld EPA's decision in the 2003 rule relating to groundwater controls. In the 2003 rule, EPA stated that the Agency believed that requirements limiting the discharge of pollutants to surface water via groundwater that has a direct hydrologic connection to surface water should be addressed on a site-specific basis. The Agency also stated that nothing in the 2003 rule was to be construed to expand, diminish, or otherwise affect the jurisdiction of the CWA over discharges to surface water via groundwater that has a direct hydrologic connection to surface water. 399 F.3d at 514-15.

The court upheld the analytic methodologies that EPA used for determining whether the technology-based permit requirements for CAFOs set in the 2003 rule would be economically achievable by the industry as a whole. 399 F.3d at 515-18.

2. Issues Vacated by the Court

The following are the elements of the 2003 rule that the

Waterkeeper

Court found to be unlawful and therefore vacated.

(a) Duty To Apply

The CAFO industry organizations argued that EPA exceeded its statutory authority by requiring all CAFOs to either apply for NPDES permits or demonstrate that they have no potential to discharge. The court agreed with the CAFO industry petitioners on this issue and therefore vacated the “duty to apply” provision of the 2003 CAFO rule.

The court found that the duty to apply, based on the potential to discharge, was invalid because the CWA subjects only actual discharges to permitting requirements rather than potential discharges. The court acknowledged EPA's policy considerations for seeking to impose a duty to apply based on the potential to discharge but found that the Agency lacked statutory authority to do so. 399 F.3d at 505.

(b) Nutrient Management Plans (NMPs)

The court concluded that the 2003 CAFO rule impermissibly: (1) Empowered permitting authorities to issue permits without any meaningful review of a CAFO's NMP, (2) failed to require that the terms of the nutrient management plan be included as effluent limitations in the NPDES permit, and (3) violated the CWA's public participation requirements. The court agreed with the environmental petitioners on these three issues.

The court relied on provisions of the Act that authorize point source discharges only where NPDES permits “ensure that every discharge of pollutants will comply with all applicable effluent limitations and standards,” citing CWA sections 402(a)(1), (a)(2), and (b). Because the 2003 CAFO rule did not provide for permitting authority review of a CAFO's nutrient management plan before the permit was issued, the court found that the rule did not ensure that each CAFO's discharges comply with these CWA provisions. The court also found that the terms of the NMP themselves are “effluent limitations” as that term is defined in the Act and therefore must be made part of the permit and be enforceable as required under CWA sections 301 and 402. The court also held that as effluent limitations, those terms must be made available for public review. 399 F.3d at 499-502.

3. Issues Remanded by the Court

The

Waterkeeper

Court also remanded other aspects of the CAFO rule to EPA “for further clarification and analysis.”

(a) Water Quality-Based Effluent Limits

The court agreed with EPA that agricultural stormwater is excluded from the meaning of the term “point source” and therefore is not subject to water quality-based effluent limitations in permits. However, the court directed EPA to “clarify the statutory and evidentiary basis for failing to promulgate water quality-based effluent limitations for discharges other than agricultural stormwater discharges as that term is defined in 40 CFR 122.23(e),” and to “clarify whether States may develop water quality-based effluent limitations on their own.” 399 F.3d at 524.

(b) New Source Performance Standards—100-Year Storm Standard

The 2003 CAFO rule set new source performance standards (NSPS) for swine, poultry, and veal calf CAFOs at no discharge. A CAFO in these categories could fulfill this requirement by showing that either (1) its production area was designed to contain all manure, litter, or process wastewater, and precipitation from a 100-year, 24-hour storm, or (2) it would comply with “voluntary superior environmental performance standards” based on innovative technologies, under which a discharge from the production area would be allowed if it was accompanied by an equivalent or greater reduction in the quantity of pollutants released to other media (

e.g.

, air emissions). The court found that EPA had neither justified in the record nor provided an adequate opportunity for public comment for either of these provisions. As a result, the court remanded these provisions to EPA to clarify, via a process that adequately involves the public, the statutory and evidentiary basis for them. 399 F.3d at 520-21.

(c) BCT Effluent Guidelines for Pathogens

The court held that the 2003 CAFO rule violated the CWA because EPA had not made an affirmative finding that the BCT-based Effluent Limitations Guidelines (ELGs),

i.e.

, the “best conventional technology” guidelines for conventional pollutants such as fecal coliform, do in fact represent BCT for pathogens. The court remanded this issue to EPA for such a finding. 399 F.3d at 519.

D. What Requirements Still Apply to CAFOs?

The

Waterkeeper

decision either upheld or did not address most provisions of the 2003 CAFO rule. This section describes certain key portions of the rule that were not challenged in

Waterkeeper

. These unchallenged provisions are addressed in this final rule only to provide background information and are not in any way reopened or affected by this rulemaking.

The definitions provided in 40 CFR 122.23(b) of the 2003 CAFO rule remain in effect and are unchanged. First, an operation must be defined as an animal feeding operation (AFO) before it can be defined as a concentrated animal feeding operation (CAFO). 40 CFR 122.23. The term “animal feeding operation” is defined by EPA regulation as a “lot or facility” where animals “have been, are or will be stabled or confined and fed or maintained for a total of 45 days or more in any 12 month period and crops, vegetation, forage growth, or post harvest residues are not sustained in the normal growing season over any portion of the lot or facility.”

Whether an AFO is a CAFO depends primarily on the number of animals confined, which is also unchanged. Large CAFOs are AFOs that confine more than the threshold number of animals detailed in 40 CFR 122.23(b)(4). Medium CAFOs confine fewer animals than Large CAFOs and also: (1) Discharge pollutants into waters of the U.S. through a man-made ditch, flushing system, or other similar man-made device; or (2) discharge pollutants into waters of the U.S. which originate outside of and pass over, across, or through the facility or otherwise come into direct contact with the confined animals. 40 CFR 122.23(b)(6)(ii). The NPDES permitting authority also may, on a case-by-case basis, designate any medium or small AFO, as a CAFO after conducting an on-site inspection and finding that the facility “is a significant contributor of pollutants to waters of the United States.” 40 CFR 122.23(c). The permitting authority may not exercise its authority to designate a small AFO as a CAFO unless pollutants are discharged into waters of the U.S. through a man-made ditch, flushing system, or other similar man-made device, or are discharged into waters of the U.S. which originate outside of the facility and pass over, across, or through the facility or otherwise come into direct contact with the animals confined in the operation. 40 CFR 122.23(c)(3).

As previously described, the court upheld EPA's definition of “agricultural stormwater discharge” in relation to discharges from land application areas under the control of a CAFO in 40 CFR 122.23(e). Discharges of manure, litter, or process wastewater from land application areas under the control of a CAFO are discharges from the CAFO (i.e., point source discharges) unless they are agricultural stormwater discharges, which are exempt from permit requirements. Section 122.23(e) provides that precipitation-related discharges of manure, litter, or process wastewater from a CAFO's land application areas are agricultural stormwater discharges, provided that “the manure, litter, or process wastewater has been applied in accordance with site-specific nutrient management practices that ensure appropriate agricultural utilization of the nutrients in the manure, litter, or process wastewater, as specified in § 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 § 122.42(e).

The court ruling also did not affect the ELG requirements for Large CAFOs, with the exception of new source performance standards (NSPS) for swine, poultry, and veal calf operations. ELG requirements ensure the appropriate storage of manure, litter, and process wastewater and proper land application practices. They vary depending upon the type of animals confined: Subpart A for horses and sheep; subpart B for ducks; subpart C for dairy cattle, heifers, steers, and bulls; and subpart D for swine, poultry, and veal calves. 40 CFR part 412. Additionally, NSPS for beef and dairy operations were not affected by the decision and remain unchanged (40 CFR 412.35).

Permitted small and medium CAFOs are not subject to the ELGs specified in part 412. Rather, they must comply with technology-based requirements developed by the permitting authority on a case-by-case basis (

i.e.

, best professional judgment (BPJ)), pursuant to CWA section 402(a)(1)(B) and as defined in 40 CFR 125.3(c)(2) and (d).

E. EPA's Response to the Waterkeeper Decision

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

CAFO's in response to the

Waterkeeper

decision. 71 FR 37,744. In summary, EPA proposed to require only owners or operators of those CAFOs that discharge or propose to discharge to seek authorization to discharge under a permit. Second, EPA proposed to require CAFOs seeking authorization to discharge under individual permits to submit their NMPs with their permit applications or, under general permits, with their notices of intent. Permitting authorities would be required to review the NMP and provide the public with an opportunity for meaningful public review and comment. Permitting authorities would also be required to incorporate terms of the NMP as NPDES permit requirements. Additionally, EPA proposed a process for modifying a CAFO's NPDES permit to incorporate changes to the NMP during the permit term by designating permit modifications in accordance with that process to be “minor modifications of permits” under 40 CFR 122.63. The 2006 proposed rule also addressed the remand of issues for further clarification and analysis. These issues concerned clarifications regarding the applicability of water quality-based effluent limitations (WQBELs) to CAFO discharges; NSPS for swine, poultry, and veal CAFOs; and BCT effluent limitations guidelines for fecal coliform.

A March 7, 2008,

Federal Register

notice supplemented the 2006 proposed rule by proposing additional options considered by EPA for inclusion in this final rule in response to the Second Circuit's decision in the

Waterkeeper

decision. In that notice, EPA proposed a voluntary option for a CAFO to certify that the CAFO does not discharge or propose to discharge based on an objective assessment of the CAFO's design, construction, operation, and maintenance. EPA also proposed a framework for identifying the terms of the NMP and three alternative approaches for addressing rates of application of manure, litter, and process wastewater when identifying terms of the NMP to be included in the permit. In the 2008 supplemental proposal, EPA sought comment only on the issues presented in the 2008 supplemental proposal.

In addition to the changes made through this rulemaking, EPA extended certain deadlines in the NPDES permitting requirements and ELGs in two separate rulemakings in order to allow the Agency adequate time to complete this rulemaking in response to the

Waterkeeper

decision, in advance of those deadlines. The principal purpose of these rulemakings was to provide additional time for the Agency to complete this final rule. Neither of these date extension rules addressed any of the substantive issues addressed in this final rule or promulgated any provisions in response to the

Waterkeeper

decision. The first rule revised dates established in the 2003 CAFO rule by which facilities newly defined as CAFOs were required to seek permit coverage and by which all CAFOs were required to develop and implement nutrient management plans. 71 FR 6978-84 (February 10, 2006). EPA extended the date by which operations defined as CAFOs as of April 14, 2003, that were not defined as CAFOs prior to that date, were required to seek NPDES permit coverage, from February 13, 2006, to July 31, 2007. EPA also amended the date by which operations that become defined as CAFOs after April 14, 2003, due to operational changes that would not have made them a CAFO prior to April 14, 2003, and that are not new sources, were required to seek NPDES permit coverage, from April 13, 2006, to July 31, 2007. Finally, EPA extended the deadline by which CAFOs were required to develop and implement nutrient management plans, from December 31, 2006, to July 31, 2007. That rulemaking revised all references to the date by which CAFOs must develop and implement NMPs as specified in the 2003 CAFO rule.

As a result of the extensive array of public comments on the issues raised by the

Waterkeeper

decision, EPA was unable to complete this final rule prior to July 31, 2007. Thus, EPA published a second revision of the compliance dates on July 24, 2007, extending the dates from July 31, 2007, to February 27, 2009. The preamble to the second date change rule explained EPA's belief that the February 27, 2009, deadlines were appropriate because they would provide additional time for States, the regulated community, and other stakeholders to adjust to the new regulatory requirements.

See

72 FR 40,245-50. In the 2008 supplemental rule, EPA requested comment on further extending the compliance deadline. For additional discussion of compliance dates, see section III.D of this preamble.

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

Waterkeeper

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

A. Duty To Apply for a Permit

1. Provisions in the 2003 CAFO Rule

(a) Duty To Apply

The 2003 CAFO rule required all CAFOs to seek authorization to discharge under an NPDES permit unless the Director,

i.e.

, the permitting authority, determined that the CAFO had no potential to discharge.

(b) “No Potential To Discharge” Determination

The 2003 CAFO rule included a process for CAFOs to seek a “no potential to discharge” determination by the Director. Where the Director determined, based on information supplied by the CAFO operator, that a CAFO had no potential to discharge manure, litter, or process wastewater to waters of the U.S., the CAFO operator had no duty to apply for a permit, unless circumstances at the facility changed such that the facility would have the potential to discharge. Examples of facilities that possibly would have qualified for this exemption included facilities in very arid areas, facilities that are down slope from waters of the U.S., and facilities with completely enclosed operations.

2. Summary of the Second Circuit Court Decision

The Second Circuit Court of Appeals vacated the provision that required all CAFO owners or operators with a potential to discharge to apply for an NPDES permit. The court held that the Clean Water Act (CWA) authorizes EPA to require permits for the actual discharge of pollutants, but not for mere potential discharges. Because the 2003 CAFO rule imposed an obligation on all CAFOs to either apply for an NPDES permit or affirmatively demonstrate that they have no potential to discharge, the court ruled that it exceeded EPA's authority under the CWA.

Waterkeeper Alliance et al.

v.

EPA

, 399 F.3d 486, 506 (2d Cir. 2005).

3. This Final Rule

To address the court's decision on the duty to apply, EPA is revising the 2003 CAFO rule in three ways:

• Deleting the requirement that all CAFOs apply for an NPDES permit to provide instead that all CAFOs that “discharge or propose to discharge” have a duty to apply when they propose to discharge;

• Eliminating the procedures for a no potential to discharge determination; and

• Establishing a voluntary option for unpermitted CAFOs to certify that they

do not discharge or propose to discharge.

(a) Duty To Seek Permit Coverage

EPA proposed to replace the “duty to apply” requirement adopted in the 2003 rule, which states that all CAFO owners or operators must seek coverage under an NPDES permit unless they demonstrate “no potential to discharge” (40 CFR 122.21(a)(1) and 40 CFR 122.23(a) and 40 CFR 122.23(d)(1)) with a modified “duty to apply” provision. The 2006 proposed rule would have required that all CAFOs that “discharge or propose to discharge” seek coverage under an NPDES permit, which is the same language that applies generally to point sources under longstanding NPDES regulations at § 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 § 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 § 122.23(d)(1) duty to apply. Section 122.23(j)(2) also clarifies how a CAFO may satisfy the burden of establishing that it did not propose to discharge.

Under section 301(a) of the CWA, only those CAFO discharges authorized by an NPDES permit (or otherwise authorized by the statute), regardless of the volume or duration of the discharge, are allowed. Any discharge from a CAFO, even one that is unplanned or accidental, is illegal unless it is authorized by the terms of a permit or is agricultural stormwater. While EPA recognizes that not every discharge indicates that the CAFO will discharge in the future, an operator should certainly consider any unplanned or accidental discharge that may have occurred in the past in deciding whether to seek permit coverage. CAFO operators must objectively assess whether a discharge from the CAFO, including from the production area or land application areas under the control of the CAFO, is occurring or will occur for purposes of determining whether to obtain permit coverage.

It is well established that “discharge” is not limited to continuous discharges of pollutants from a point source to waters of the U.S., but also includes intermittent and sporadic discharges. “Intermittent or sporadic violations do not cease to be ongoing until the date when there is no real likelihood of repetition.”

Chesapeake Bay Foundation

v.

Gwaltney of Smithfield

, 890 F.2d 690, 693 (4th Cir. 1989). Such intermittent, sporadic, even occasional, discharges may in fact be the norm for many CAFOs, but they are nonetheless “discharges” under the CWA and are prohibited unless authorized under the terms of an NPDES permit. CAFOs that have had such intermittent or sporadic discharges in the past would generally be expected to have such discharges in the future, and therefore be expected to obtain a permit, unless they have modified their design, construction, operation, or maintenance in such a way as to prevent all discharges from occurring.

EPA received a number of comments concerning past discharges. Some commenters asserted that a prior discharge is not, by itself, a sufficient basis for requiring a permit and observed that it is quite possible that a CAFO may have eliminated the cause of the discharge. EPA agrees that not every past discharge from a CAFO necessarily triggers a duty to apply for a permit; however, a past discharge may indicate that the CAFO discharges or proposes to discharge if the conditions that gave rise to the discharge have not changed or been corrected. See,

e.g., Gwaltney of Smithfield. Ltd.

v.

Chesapeake Bay Foundation,

484 U.S. 49, 57 (1987) (“a reasonable likelihood that a past polluter will continue to pollute in the future” is a continuous or intermittent violation);

American Canoe Ass'n

v.

Murphy Farms, Inc.,

412 F.3d. 536 (4th Cir. 2005) (CWA violation continues where corrective measures are insufficient to eliminate real likelihood of repeated discharges). The same rationale that led the courts in these cases to conclude that the point sources in question were discharging in violation of the CWA underlies the final rule's requirement that CAFOs must seek permit coverage when they discharge or propose to discharge (

i.e.

, are designed, constructed, operated, or maintained such that a discharge will occur). Sections 122.23(d)(1) and (f).

An uncorrected past discharge is not the only indicator that operators should consider in assessing whether the CAFO discharges or proposes to discharge. Other key factors the operator should consider include the proximity of the production area to waters of the U.S., whether the CAFO is upslope from waters of the U.S., and climatic conditions. Similarly, the type of waste storage system, storage capacity, quality

of construction, and presence and extent of built-in safeguards are important factors. Standard operating procedures and level of maintenance are also critical factors for the operator to consider when assessing whether a CAFO discharges or proposes to discharge. Such considerations contributed to EPA's decision to include in this final rule an option for unpermitted CAFOs to certify that they do not discharge or propose to discharge by meeting the criteria in 40 CFR 122.23(i)(2), discussed in detail below. EPA encourages unpermitted CAFOs that choose not to certify to consider the set of criteria for certification eligibility when deciding whether to seek permit coverage, and this final rule provides in § 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 § 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 § 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 § 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 § 122.23(d)(1) and may choose to take advantage of the voluntary no discharge certification.

Some commenters on the 2006 proposed rule requested that EPA specifically state in the regulation that facilities designed to the 25-year, 24-hour design standard have not “proposed” to discharge. One commenter questioned whether existing operations should be required to obtain permit coverage if they have installed structures and production area BMPs using Natural Resources Conservation Service (NRCS) standards and if they have been operating without discharging. The commenter indicated that “since EPA is requiring that a zero discharge standard be met only for certain new CAFOs and not existing CAFOs, it is unreasonable to expect all existing animal operations that do not otherwise come under a permit to meet a zero discharge standard.”

EPA disagrees that CAFOs designed for the 25-year, 24-hour storm should be categorically excluded from the requirement to apply for a permit simply based on their design standard. EPA also believes that it is reasonable to expect unpermitted CAFOs to meet a zero discharge standard. The CWA is very clear that point source discharges from CAFOs are illegal unless the operator has applied for and obtained an NPDES permit. Thus, “zero discharge” is the only standard to which EPA can

hold unpermitted CAFOs under the CWA. Large storms and chronic rainfall events do occur and production areas built to the 25-year, 24-hour storm design standard can and do discharge during precipitation events. Under the CWA, as previously discussed, a violation of the prohibition against discharging without a permit occurs even if the discharge was not planned or intended. Conversely, in the event of a discharge from a permitted CAFO, the discharge will not violate the CWA if the CAFO is in compliance with its permit.

EPA notes that design is only one aspect for a CAFO to consider when assessing whether or not to apply for a permit. Construction, operation, and maintenance are equally important components of a CAFO's operation and can make the difference between a CAFO that discharges and one that does not. With regard to the commenter's question about the applicability of NRCS standards, a CAFO's decision as to whether to seek permit coverage should be based on an objective assessment of conditions at the operation, including, but not limited to, the manure storage design standard. EPA notes that whether or not a CAFO is designed according to NRCS standards may be an important component of the objective evaluation it undertakes to assess whether it is designed, constructed, operated, or maintained such that a discharge will occur. A CAFO that does not discharge or propose to discharge is not required to seek permit coverage under § 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

§ 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 § 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 § 122.23(f) because the paragraph codified as § 122.23(f) in the 2003 rule is being removed. See section III.A.3(b) of this preamble. Revised § 122.23(f) is consistent with the revised duty to apply requirement in § 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 § 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 § 122.23(f) simply conforms to the requirements of § 122.23(d)(1).

EPA is making corresponding revisions to the regulatory text requiring CAFOs to maintain permit coverage. Due to the fact that § 122.23(f) as codified in 2003 is being removed, EPA is recodifying 40 CFR 122.23(h), “Duty to Maintain Permit Coverage,” as § 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 § 122.23(g) excludes CAFOs that will not discharge or propose to discharge upon expiration of the permit from the requirement to reapply 180 days in advance of permit expiration.

(b) “No Potential To Discharge” Determination

In this final rule, EPA is deleting the regulatory provisions adopted in the 2003 CAFO rule allowing CAFOs to demonstrate that they have no potential to discharge and authorizing the Director to make such a determination. 40 CFR 122.23(d)(2) and 122.23(f). Because EPA is not requiring CAFOs to seek permit coverage based merely on potential to discharge, this provision is no longer relevant to determining whether or not a facility needs to seek permit coverage. This final rule is

unchanged from the 2006 proposed rule in this respect.

Overall, most commenters supported eliminating the “no potential to discharge” provisions in the CAFO regulations, noting that it is no longer necessary because only CAFOs that discharge or propose to discharge must apply for permits. One State observed that the “no potential to discharge” criteria could still be useful to CAFOs in determining whether they need to apply for a permit. While these criteria may continue to be useful to CAFO owners and operators for that purpose, EPA is eliminating these provisions from 40 CFR 122.23 of the regulations.

(c) Voluntary No Discharge Certification

In this final rule, the Agency is adopting a new provision that allows CAFOs to voluntarily certify that the CAFO does not discharge or propose to discharge. As discussed above, EPA received several hundred comments on the 2006 proposed rule related to how a CAFO operator would decide whether to seek permit coverage under a revised rule that requires CAFOs that discharge or propose to discharge to apply for a permit or submit a Notice of Intent for coverage under a general permit. Several commenters were particularly concerned with the consequences for an unpermitted CAFO that has an “accidental discharge” because they understood EPA's proposal to mean that a CAFO that does not apply for a permit and subsequently has a discharge of pollutants to waters of the U.S. would be liable for two violations, one associated with the discharge itself and another violation for failing to apply for a permit for authority to discharge. In response to these comments, in the 2008 supplemental proposal, EPA requested public comment on an option that would allow a CAFO that determines, based on an objective assessment, that it does not discharge or propose to discharge to certify to the permitting authority that it is designed, constructed, operated, and maintained not to discharge. In the unlikely event that a properly certified CAFO discharges (which would constitute a violation of section 301(a) of the CWA), the CAFO would not be liable for failing to apply for a permit prior to the discharge in accordance with the permit application requirements of 40 CFR 122.23(d)(1) and (f).

EPA received many comments on the proposed voluntary certification option. Commenters were divided, with some generally supportive and others generally opposed to the concept of a voluntary certification option for unpermitted CAFOs. Those in favor stated that certification would assist CAFOs that do not discharge or propose to discharge by providing a structured process for CAFOs to notify the permitting authority that they are not required to seek permit coverage. Some commenters opposed to certification believe the Agency's record supports a regulatory presumption that all CAFOs discharge, and, therefore, the no discharge certification process is a further departure from the decision of the

Waterkeeper

court. The majority of State permitting authorities commenting on the 2008 supplemental proposal were opposed to the certification option, as proposed.

In this final rule, EPA has addressed both the decision from the

Waterkeeper

court that CAFOs with only a potential to discharge are not subject to NPDES permitting requirements and the concerns expressed by commenters that some CAFOs may be uncertain as to whether they discharge or propose to discharge. In the NPDES program, the first step is for a point source to decide whether it needs to seek permit coverage. Generally, the question of whether a point source needs permit coverage is easily answered; indeed other point sources are typically designed to discharge to waters of the U.S. After careful consideration of the comments and in light of the unique characteristics of CAFOs among point sources, EPA has concluded that providing a voluntary option for unpermitted CAFOs to certify to the Director that the CAFO does not discharge or propose to discharge based on an objective assessment of the CAFO's design, construction, operation, and maintenance is reasonable and appropriate for CAFOs. However, in response to comments received on the proposed certification option, EPA is clarifying several aspects of the process, eligibility requirements, and effect of certification as discussed below. The Agency is also making several changes to the proposed option to ensure that certification will be properly implemented.

Under this final rule, and as proposed in the 2008 supplemental proposal, a CAFO operator may certify that the CAFO does not discharge or propose to discharge by signing and submitting a certification statement to the Director. The objective assessment necessary for the CAFO to qualify for certification takes into account the CAFO's production area design and construction and its operating and maintenance procedures and practices as described in its nutrient management plan (NMP) in accordance with the eligibility criteria, described in detail below. The certification option established by this rule does not change the requirement that CAFOs that propose to discharge must seek permit coverage when they propose to discharge pursuant to § 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 § 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 § 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 § 122.23(i) is presumed not to propose to discharge. A CAFO that is “certified in accordance with

§ 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 § 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 § 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 § 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 § 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 § 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 § 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 § 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 § 122.23(i); or (2) to operate without a permit and without certifying. The purpose of certification is to provide a voluntary mechanism for the CAFO to establish in advance that it does not discharge or propose to discharge. As previously discussed, a CAFO that operates without a permit must be designed, constructed, operated, and maintained such that no discharge will occur, because any discharge (other than agricultural stormwater) is prohibited from unpermitted CAFOs pursuant to CWA section 301(a), while permitted CAFOs are allowed to discharge under specified conditions and may also have defenses for upset and bypass. NPDES permit coverage reduces CAFO operator risk and provides certainty to CAFO operators regarding activities and actions that are necessary to comply with the CWA. In contrast, certified CAFOs are not allowed to discharge under any conditions (other than discharges of agricultural stormwater), and are liable for any unpermitted discharge pursuant to CWA 301(a), but they will not additionally be held liable for a violation of the duty to apply, provided their certification is valid and still in effect at the time of discharge. EPA strongly recommends that all CAFOs that have any doubt about their ability to operate under all circumstances without discharging seek to obtain NPDES permit coverage, and believes it is in their interest to do so. However, in accordance with the

Waterkeeper

decision, EPA is requiring CAFOs to seek permit coverage only if they discharge or propose to discharge.

The final rule provisions for certification eligibility and submission, and conditions for a valid certification are discussed in detail below.

(i) Certification Eligibility Criteria

EPA is establishing specific eligibility criteria for CAFO certification at 40 CFR 122.23(i)(2). Meeting these criteria establishes that the CAFO does not “discharge or propose to discharge” for purposes of 40 CFR 122.23(d)(1), for as long as the certification is valid. Eligibility for certification means meeting the criteria described below at the time certification is established and continuing to meet the eligibility criteria throughout the period of certification as new information or situations arise. The three criteria are as follows: (1) An objective evaluation which shows that the CAFO's production area is designed, constructed, operated, and maintained so as not to discharge, (2) development and implementation of an NMP to ensure no discharge (other than agricultural stormwater discharges) that, at a minimum, addresses the elements set forth in 40 CFR 122.42(e)(1) and 40 CFR 412.37(c), including operation and maintenance practices for the production area and land application areas under the control of the CAFO, and (3) maintenance of the documentation required for certification either on site, at a nearby office, or where it can be made readily available to the permitting authority upon request. A statement that describes the basis for the CAFO's certification that it satisfies these eligibility criteria must be submitted to the Director, but there is no requirement for permitting authority review in order for the certification to be valid.

The first two criteria concern the existing physical and operational conditions at the CAFO. In addition, meeting these criteria includes making proper accommodations during the certification period to address changes to the operation. For example, if an increase in animals will cause the CAFO to exceed the existing storage capacity for precipitation, manure and process

wastewater required for no discharge, in order to remain certified, the CAFO must remedy the storage capacity problem prior to bringing the additional animals to the operation. Operation and maintenance practices may need to be modified to accommodate changes to the CAFO. For example, a reduction in fields available for land application would trigger the need to reevaluate the adequacy of manure storage and handling protocols. The third eligibility criterion requires a certified CAFO to maintain records needed to support the basis for the certification throughout the duration of the certification, such as monitoring and inspection records, records of maintenance and repairs, and land application records, including updated documentation to match current conditions and circumstances at the CAFO. Certified CAFOs, like any other permitted or unpermitted CAFO, may be asked to send information to the permitting authority that is relevant to implementation of the CWA, or inspected by EPA or authorized State inspectors. During an inspection the certified CAFO could be required to produce the documentation showing that it meets the eligibility criteria, including that the CAFO has been and is being operated and maintained in accordance with an NMP that has been updated as necessary.

Commenters offered numerous perspectives on the proposed eligibility criteria. Some commenters asserted that the proposed criteria were too extensive, stringent, and complex, and therefore would make it unlikely that self-certifying CAFOs could accurately demonstrate their eligibility. These commenters indicated that, as proposed, the eligibility criteria would be expensive to implement and, thus, would serve as a disincentive for a CAFO to choose to certify. In response to these comments, EPA emphasizes that certification is voluntary, and CAFOs may choose not to certify. As noted above, EPA believes that it is generally in an operator's best interest to obtain permit coverage. However, EPA has provided the certification option for CAFOs that choose not to seek permit coverage but would like to establish up front that they do not discharge or propose to discharge. The final rule contains stringent eligibility criteria because in light of the CWA prohibition against unpermitted discharges, the eligibility criteria for certification must establish that the CAFO does not discharge or propose to discharge. Only CAFOs that establish eligibility and meet all of the certification provisions in 40 CFR 122.23(i)(2)-(3) will receive the benefit of certification, which is that a validly certified CAFO that discharges will not be in violation of the requirement to apply for a permit pursuant to § 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 § 122.23(d)(1), a CAFO that has discharged in the past would generally be expected to discharge in the future, and therefore be expected to obtain a permit, unless it has modified the design, construction, operation or maintenance in such a way as to prevent any discharges from occurring.

The first eligibility criterion for valid certification covers the design, construction, operation, and maintenance of the CAFO's production area. As proposed, 40 CFR 122.23(i)(2)(i) of this final rule requires the CAFO to demonstrate that the CAFO's production area is designed, constructed, operated, and maintained so as not to discharge. Due to the variations in production area design based on the type of containment system used at the operation, EPA proposed and is finalizing today a rule with two parts for the first eligibility criterion: the first for open manure storage structures and the second for any part of the production area not considered to be open containment.

Consistent with the 2008 supplemental proposal, under the final rule, any CAFO with an open manure storage structure seeking to certify that it does not discharge or propose to discharge is required to perform a technical evaluation under 40 CFR 122.23(i)(2)(i)(A). To demonstrate that the CAFO meets the production area requirement for certification, this evaluation must be conducted in accordance with the elements of the technical evaluation required for open storage new source swine, poultry and veal calf operations seeking to demonstrate no discharge under 40 CFR 412.46(a)(1)(i)-(viii), as revised by this action. EPA clarifies that, although this provision references the new source performance standard (NSPS) for swine, poultry and veal calf operations, this eligibility criterion applies to any unpermitted CAFO with open manure storage seeking to certify that it does not discharge or propose to discharge, not just new sources in the swine, poultry and veal calf sectors with open storage.

Elsewhere in this final rule, EPA is revising the provisions at 40 CFR 412.46(a)(1) to allow such new sources with open containment to meet the no discharge requirement for their NPDES permit using best management practices based in part on a rigorous site-specific technical evaluation that includes use of the most recent versions of the Animal Waste Management (AWM) software, or equivalent software, and the Soil Plant Air Water (SPAW) Hydrology Tool, or an equivalent model. For a discussion of the technical evaluation and the AWM and SPAW modeling tools, see section III.F of this preamble.

Several commenters expressed the need for evaluation criteria specific to beef cattle feedlots, based on their belief that reliance on swine, poultry, and veal calf new source provisions is inappropriate for all animal sectors. As described in more detail in Section III.F of this preamble, AWM software is a planning and design tool for animal feeding operations that can be used to estimate the production of manure, bedding, and process water and determine the size of storage facilities necessary to meet no discharge. AWM (CCE version 2.3.0) currently provides manure characteristics for eight animal types with the ability to modify these characteristics and add animal types as necessary. The field and pond hydrologic analyses conducted with the SPAW model are not specific to any animal species. Therefore beef and dairy

operators can use the AWM and SPAW tools to establish the appropriate design, construction, operation and maintenance of their facility to meet the no discharge requirement of certification.

EPA also received comments seeking clarification regarding how the technical evaluation for new source swine, poultry and veal calf operations can apply to existing facilities given that EPA stated in the preamble to the 2003 CAFO rule that the no discharge performance standard was not economically achievable for existing facilities. While EPA has determined that the no discharge performance standard was not appropriate to require for existing facilities on a national basis (

see

68 FR 7218), EPA acknowledges that there are existing CAFOs that could meet the standard. Existing CAFOs that feel it is not economically achievable to meet a no-discharge standard always have the option of applying for a permit.

In order to meet the second part of the first eligibility criterion, the final rule requires, in 40 CFR 122.23(i)(2)(i)(B), that any certifying CAFO must demonstrate that all of its production area, as defined at 40 CFR 122.23(b)(8), not just open containment structures, is designed, constructed, operated, and maintained such that there will be no discharge of manure, litter, process wastewater, or raw materials, such as feed, to surface waters. For a CAFO without open containment, this provision requires a demonstration of no discharge from the entire production area. For a CAFO that has an open containment structure, this provision requires a demonstration that the remainder of the production area (other than the open containment structure subject to the demonstration in § 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 § 122.23(i)(2)(i)(A); however, the demonstration in § 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 § 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 § 122.23(i)(2)(i), which includes the measures set forth in § 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 § 122.42(e)(1) and 40 CFR 412.37(c), and all site-specific operation and maintenance practices necessary to ensure that the CAFO will not discharge. The NMP must include provisions regarding nutrient management in the production area as well as in all land application areas under the control of the CAFO where the CAFO will land-apply manure. Because operation and maintenance practices and procedures are critical to discharge prevention, implementation of an NMP is an essential component of any CAFO's efforts to ensure that it will not discharge from its production or land application areas. Furthermore, in order for any certified CAFO that land applies to ensure that the only discharges from the land application areas are non-point source agricultural stormwater discharges, the CAFO would, at a minimum, need to land apply in accordance with practices that ensure appropriate agricultural utilization of nutrients, including conservation practices and agronomic rates of application. For detailed discussion of unpermitted CAFOs and the agricultural stormwater exemption, see section III.B of this preamble.

EPA received comments indicating that the final rule should establish a link between a facility's open storage structure design and the land application practices outlined in a CAFO's NMP. In the 2008 supplemental proposal, EPA intended that the CAFO's NMP would reflect any operation and maintenance practices related to and assumed in the technical evaluation performed for open containment structures. To clarify this intent, 40 CFR 122.23(i)(2)(ii)(B) of this final rule states that the operation and maintenance practices required to be part of the NMP must include “any practices or conditions established by a technical evaluation pursuant to paragraph (i)(2)(i)(A),” the provision applicable to CAFOs with open containment. For example, an existing facility may develop an NMP and then use AWM and the SPAW model to evaluate the adequacy of the designed storage facility and overall water budgets for the operation, respectively, which will rely upon inputs from the CAFO's NMP such as the number and type of animals, soil profiles and planned crop rotations. In such a scenario, the CAFO may learn from the technical evaluation that more frequent lagoon drawdowns are necessary in order to achieve no discharge. To be eligible for certification under the final rule, the CAFO's NMP

would then need to be revised to include the adjusted operation and maintenance practices resulting from the technical evaluation. It is these changed operation and maintenance practices that EPA is referring to in the § 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 § 122.42(e)(1) and § 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 § 122.22, signing the certification signifies that the signer is certifying that the certification was prepared under his/her direction or supervision in accordance with a system designed to assure that qualified personnel properly gathered and evaluated the information submitted and that based on the responsible official's inquiry of the person or persons who manage the system, or those persons directly responsible for gathering the

information, the information submitted is, to the best of their knowledge and belief, true, accurate and complete.

This final rule makes no changes to the existing regulations concerning how CAFOs may make Confidential Business Information (CBI) claims with respect to information they must submit to the permitting authority and how those claims will be evaluated. A facility may make a claim of confidentiality under the existing regulations at 40 CFR part 2, subpart B.

The third item the Agency is requiring for submission to the Director, as listed above, is a statement describing the basis for the CAFO's certification that it is designed, constructed, operated, and maintained in accordance with the certification eligibility criteria. EPA's expectation for what this description should include is unchanged from the 2008 supplemental proposal. In the preamble to the 2008 supplemental proposal, EPA requested public comment on whether the scope and type of information included in the description of eligibility submitted to the Director should include: (1) The type and number of animals; (2) the type and capacity of manure and wastewater storage and/or containment; (3) storm size used as the basis for containment design; (4) whether the CAFO consulted with a professional engineer or technical service provider (TSP); (5) identification of the documents maintained on site in accordance with the eligibility criteria; and (6) any technical standards, tools (

e.g.

, RUSLE and Phosphorus Index) and formulas used to calculate application rates of manure, litter, and process wastewater.

Commenters expressed differing viewpoints as to what documentation must be provided to the Director for the no discharge certification. Some commenters felt that the 2008 supplemental proposal would have required the submission of too much information, and that CAFOs should only be required to submit a list of the documents created to establish a facility's eligibility. Some of these stated that submission of any facility design or operation specifics is superfluous given that there is no review by the permitting authority. In contrast, other commenters believed that the extent of documentation to be submitted to the Director was insufficient to establish that a facility is designed, operated, and maintained in a way to ensure that it is not discharging. Specifically, these commenters desired that submissions include all documents associated with meeting the eligibility criteria for certification.

After consideration of these comments, EPA believes that the list of information presented in the preamble to the supplemental proposal balances the need of the Director to be informed of critical aspects of the certified CAFO's operation with the fact that the certification is not subject to review by the Director in order to become effective. It is reasonable that the description of the CAFO's basis for certification be submitted as part of the certification, including the type of information listed above, as proposed in the supplemental proposal. EPA also recognizes that depending on site-specific conditions at a particular facility, certain information may not be necessary (

e.g.

, an operation with no land application areas would not need to provide information about application rates of manure, litter, and process wastewater). Furthermore, if the Director is concerned that a CAFO that discharges or proposes to discharge has submitted a certification, the Director has the authority to request additional information from the CAFO, as discussed below.

The authority given to the permitting authority under section 308 of the CWA to conduct inspections at operations is not affected by this rule. Section 308 authorizes, among other things, EPA to require owners or operators of point sources to establish records, conduct monitoring activities and inspections, and make reports, to enable the permitting authority to determine whether there is any violation of any prohibition, or any requirement established under section 308, 402, or 504 of the CWA. Therefore, any CAFO, whether it is certified, permitted, or neither, may be subject to an information gathering request or inspection, at the Director's discretion and for any of the reasons provided by section 308 of the CWA. 33 U.S.C. 1318.

Under this final rule, 40 CFR 122.23(i)(4), a “certification that meets the requirements of paragraphs (i)(2) and (i)(3) * * * shall become effective on the date it is submitted, unless the Director establishes an effective date of up to 30 days after the date of submission.” A certification is effective if the CAFO meets the eligibility criteria in § 122.23(i)(2) and submits the signed certification statement and other required information in accordance with § 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 § 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 § 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 § 122.23(i)(2)-(3) will go into effect on day 30 regardless of any activities that take place during the 30-day period, so long as the CAFO maintains eligibility throughout that period. Similarly, because the certification is not subject to permitting authority review and approval, inaction on the part of the permitting authority at any time during or after the 30 days does not indicate that the CAFO either has or has not met the eligibility and submission requirements. An effective date that is no more than 30 days after submission provides sufficient time for the permitting authority to receive the certification and have an exchange with

the CAFO, but it does not constitute an unreasonable delay for the CAFO to obtain a valid certification. Given these underlying principles, EPA has determined that it is appropriate to allow the Director discretion to establish an effective date that is up to, but not more than, 30 days after submission.

EPA received comments concerning the submission process for no discharge certifications. Numerous commenters expressed concerns with the lack of any explicit requirement for Director review and approval of certifications. Some commenters asserted that the lack of review and public participation under the 2008 supplemental proposal violates the CWA and the

Waterkeeper

decision, and that without such review, certification provides no assurance of “no discharge” and creates an impermissible permitting structure based on self-regulation. Other commenters indicated that Director review of key documentation is necessary to ensure that a facility's certification meets applicable criteria. Some commenters requested that the documents necessary to meet the eligibility criteria also be subject to review by the Director and that approval of the no discharge certification be made contingent on such review.

EPA does not agree that the lack of a requirement for Director review is contrary to the CWA or the

Waterkeeper

decision. The voluntary certification option is available only to CAFOs that do not discharge or propose to discharge and, therefore, are not required to seek NPDES permit coverage. Neither the CWA nor the

Waterkeeper

decision requires a permitting authority to review no discharge certifications or to subject such information to public participation. Under the CWA, such requirements apply only to the permitting process. In addition, EPA emphasizes that certification is not a substitute for a permit. Rather, a valid certification simply allows an unpermitted CAFO that is designed, constructed, operated, and maintained not to discharge to establish and document that it does not discharge or propose to discharge, in exchange for the assurance provided by a no discharge certification that it is not subject to the regulatory requirement to seek permit coverage in 40 CFR 122.23(d)(1) and (f). It is the CAFO's choice and responsibility to establish and maintain a valid certification or lose the benefits afforded by the certification. Furthermore, as mentioned above, the final rule allows the permitting authority to establish an effective date for certification of up to 30 days after the date of submission by the CAFO. Allowing States the discretion to delay the effective date of certification addresses some comments from States expressing uncertainty about the role of the permitting authority in the certification process.

(iii) Limitations on Certification

This rule includes several limitations on certification related to the term of a certification, withdrawal of certification, and recertification after a certification becomes invalid.

Consistent with the 2008 supplemental proposal, under this final rule, a no discharge certification will expire five years after the effective date, unless the CAFO voluntarily withdraws the certification or the certification becomes invalid (

i.e.

, the CAFO has either discharged or ceases to be designed, constructed, operated, and maintained in accordance with certification eligibility criteria) during the five-year term.

See

40 CFR 122.23(i)(4). Some commenters agreed with the proposed five-year term of certification, because the limited term of certification would ensure that the CAFO reevaluates eligibility. Other commenters contended that facilities should recertify on a more frequent basis, either annually or triennially, to ensure more frequent reevaluation of their certification. A number of commenters did not believe that a term of certification should be prescribed; several of these commenters maintained that if a facility remains in compliance with the certification criteria and does not make any significant changes in operation, the certification should remain valid indefinitely.

After considering the comments regarding the appropriate term for certification, EPA has concluded that the proposed five-year term is appropriate. At the end of this term the certification can be renewed, if desired by the CAFO. Since CAFOs commonly alter their operations over time, it is reasonable for the CAFO to periodically reevaluate and update its certification submission. In addition, renewal every five years does not create an undue burden on the CAFO or the permitting authority because CAFOs that have not had major changes in operations may be able to use much of the same documentation as prepared previously, and permitting authorities are not required to review and approve the certification. A shorter term for certification, such as one or three years, is not necessary because a properly certified CAFO needs to evaluate the facility at regular intervals as part of the inspection and recordkeeping requirements. Thus, a five-year term is reasonable.

Under 40 CFR 122.23(i)(5) a CAFO may withdraw its certification at any time by notifying the Director, by certified mail or equivalent method of documentation, that it is withdrawing its certification. The certification is effectively withdrawn on the date the notification is submitted to the Director. If a CAFO's certification becomes invalid as provided in § 122.23(i)(4), discussed below, § 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

§ 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 § 122.23(i)(4) the situations that cause a certification to become invalid. First, in the unlikely event of a discharge from a properly certified CAFO, the

certification would cease to be valid and would no longer be in effect. Second, should a CAFO fail to continue to meet any of the eligibility criteria, the CAFO's certification would no longer be valid. Circumstances that could result in the certification becoming invalid include, for example, an increase in animals that exceeds the capacity of the production area for manure storage and handling or a loss of land application areas such that the assumptions in the NMP concerning land application would no longer be appropriate, if the CAFO's operations, NMP and certification documentation were not revised to address these changed circumstances. EPA emphasizes that failure by a certified CAFO to continue to meet the eligibility requirements in 40 CFR 122.23(i)(2) is not, in and of itself, a violation of any regulatory requirement because certification is strictly voluntary. For example, failure to implement the measures set forth in 40 CFR 412.37(a)-(b), which are required for no discharge certification eligibility under 40 CFR 122.23(i)(2)(i), is not a violation of § 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 § 122.23(i)(2). The provisions applicable to the recertification submission and effective date would be the same as for any certification.

See

§ 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 § 122.23(i)(2) to discharge. Furthermore, EPA maintains its position, stated in the preamble to the 2008 supplemental proposal, that the Agency generally considers a recurring discharge as evidence that a CAFO is not eligible for certification or recertification and needs to seek permit coverage. However, given the possibility of a discharge from a properly certified CAFO, albeit remote, EPA believes it is necessary for the final rule to include provisions specifically for a CAFO seeking to recertify after a discharge.

In response to comments, EPA has established specific criteria in this final rule that limit a CAFO's ability to recertify after a discharge to those situations where (1) the certification was valid at the time of the discharge, meaning the CAFO continued to be designed, constructed, operated, and maintained for no discharge in accordance with all provisions of the NMP and any operation and maintenance plans included in the certification; (2) the operator has made any necessary changes to the CAFO's design, construction, operation and maintenance to permanently address the cause of the discharge and ensure that no discharge from this cause occurs in the future; and (3) the CAFO has not previously recertified after a discharge from the same cause. The first criterion limits the availability of recertification after a discharge by excluding CAFOs that discharge after allowing the certification to lapse. EPA believes that a CAFO that certifies under penalty of law that it is and will continue to be designed, constructed, operated, and maintained so as not to discharge, that then fails to satisfy this criterion and subsequently discharges, should not be given the opportunity to once again obtain the benefits of a no discharge certification. The second criterion ensures that a CAFO will only recertify after it has carefully evaluated the cause of the discharge and taken whatever action is necessary to ensure that a discharge from the same cause will not occur again. Finally, the third criterion constrains a CAFO from engaging in a cycle of recertifying after multiple discharges from the same cause. The voluntary certification option established in this rule is not intended to be a mechanism for discharging CAFOs to avoid obtaining permit coverage, a concern cited by several commenters who opposed the certification option. On the contrary, EPA is providing the certification option to allow CAFOs that meet the eligibility criteria to establish up front that they do not discharge or propose to discharge.

The final rule provides that the CAFO's recertification will not become effective until 30 days from the date of submission. The operator is also required to submit the following information for review by the Director: A description of the discharge, including the date, time, cause, duration and approximate volume of the discharge, and a detailed explanation of the steps taken by the CAFO to permanently address the cause of the discharge. This 30-day review period provides an opportunity for the Director to consider the circumstances leading to the discharge, any actions taken by the CAFO to permanently address the cause of the discharge, and any other relevant

compliance information regarding the facility. EPA encourages State permitting authorities to take advantage of this opportunity to consider such information. As is true for the general certification process described above, when a CAFO seeks to recertify after a discharge, the Director has the authority to collect additional information from the CAFO, assess whether the criteria in this rule are satisfied, and provide feedback to the CAFO if he/she believes that the CAFO has not met the recertification criteria. For example, the 30-day review period will allow the Director to assess whether or not the CAFO has previously recertified after a discharge from the same cause. However, as with the initial certification, the Director is not required to take any action for a certification to become effective at the end of the 30-day review period and inaction does not indicate that the CAFO has met the recertification criteria. After considering public comments on the 2008 supplemental proposal regarding recertification after a discharge, EPA has determined that this 30-day review period is reasonable and prudent to allow the Director to review situations where a previously certified CAFO has had an actual discharge.

Overall, the limited conditions under which a CAFO can recertify following a discharge, the description of the discharge submitted to the permitting authority, and the required 30-day review period prior to the recertification becoming effective, provide an opportunity for the Director to determine whether the CAFO discharges or proposes to discharge and must seek coverage under an NPDES permit. For example, as provided in 40 CFR 122.28(b)(2)(vi), the Director has the authority to direct that the CAFO be covered under a general permit if one is available.

EPA believes the final rule provisions covering recertification after a discharge provide an appropriate balance of the flexibility offered by voluntary certification and the need for scrutiny of previously certified CAFOs that have discharged. Additionally, under the final rule, any previously certified CAFO that discharges or proposes to discharge is subject to the permit application requirements of 40 CFR 122.23(d)(1) and (f), and therefore must apply when the CAFO proposes to discharge. A CAFO that has permanently addressed the cause of the discharge such that the CAFO does not “discharge or propose to discharge” is not required to seek permit coverage regardless of whether it recertifies. For further discussion of the effects of a past discharge on a CAFO's permit application requirements, see the duty to apply discussion at section III.A.3(a) of this preamble.

B. Agricultural Stormwater Exemption

1. Provisions in the 2003 CAFO Rule

The discharge of manure, litter, or process wastewater from a land application area under the control of a CAFO is a discharge subject to NPDES permitting requirements, unless the discharge is an “agricultural stormwater discharge,” which is excluded from the meaning of the term “point source” under 33 U.S.C. 1362(14). In the 2003 CAFO rule, EPA differentiated between discharges from land application areas under the control of the CAFO that are point source discharges and those that are “agricultural stormwater discharges” exempt from NPDES permit requirements.

In the 2003 rule, EPA promulgated a definition of agricultural stormwater for CAFO land application areas that referenced 40 CFR 122.42(e)(1)(vi)-(ix). The referenced regulatory text includes requirements for edge-of-field buffers or equivalent measures, testing of manure and soil, land application at site-specific agronomic rates, and recordkeeping. While not explicitly included in the definition of agricultural stormwater, technical standards established by the Director, in accordance with effluent limitations guidelines (ELGs) in 40 CFR 412.4(c) applied to Large CAFOs' nutrient management plans for land application. These more specific limitations implemented the general requirements at § 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 § 122.42(e)(1)(iv)-(ix)” in § 122.23(e) include land application rates and other practices determined in compliance with technical standards.

The 2003 rule at § 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 § 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

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 § 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 § 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 § 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 § 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 § 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 § 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 § 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 § 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 § 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 § 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

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 § 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 § 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 § 122.23(e)(1). This is not a new concept, as one of the requirements specified in § 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 § 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 § 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 § 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 § 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

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 § 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 § 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 § 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 § 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

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 § 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 § 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 § 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 § 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 § 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

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 § 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

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