# Revised National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitation Guidelines for Concentrated Animal Feeding Operations in Response to Waterkeeper Decision > Briefs, arguments, decisions, and more. URL: https://www.frixlaw.com/law-library/documents/fr%3A06-5773 ## Record - **Collection:** Federal Register - **Document type:** Proposed Rule - **Published:** June 30, 2006 - **Citation:** 71 FR 37744 ## Text ENVIRONMENTAL PROTECTION AGENCY 40 CFR Parts 122 and 412 [EPA-HQ-OW-2005-0037; FRL-8189-7] RIN 2040-AE80 Revised National Pollutant Discharge Elimination System Permit Regulation and Effluent Limitation Guidelines for Concentrated Animal Feeding Operations in Response to Waterkeeper Decision AGENCY: Environmental Protection Agency (EPA). ACTION: Proposed rule. SUMMARY: EPA is proposing to revise 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 Second Circuit Court of Appeals in Waterkeeper Alliance et al. v. EPA, 399 F.3d 486 (2nd Cir. 2005). This proposed rule responds to the court order while furthering the statutory goal of restoring and maintaining the nation's water quality and effectively ensuring that CAFOs properly manage manure generated by their operations. This proposal would revise several aspects of EPA's current regulations governing discharges from CAFOs. First, EPA proposes to require only the owners and operators of those CAFOs that discharge or propose to discharge to seek coverage under a permit. Second, EPA proposes to require CAFOs seeking coverage under a permit to submit their nutrient management plan (NMP) with their application for an individual permit or notice of intent to be authorized under a general permit. Permitting authorities would be required to review the plan 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 conditions. Third, this action proposes to authorize permit writers, upon request by a CAFO, to establish best management, zero discharge effluent limitations when the facility demonstrates that it has designed an open containment system that will comply with the no discharge requirements. This proposed rule also responds to the court's remand orders regarding water-quality based effluent limitations (WQBELs) and pathogens. EPA proposes to clarify that WQBELs are available in permits with respect to production area discharges and non-precipitation related discharges from land application, but are statutorily unavailable in permits for Large CAFOs with respect to precipitation related land application discharges because the only allowable discharge from a land application area is due to agricultural storm water which is by statute exempt from permitting requirements. Finally, EPA proposes to clarify its selection of BCT technologies for pathogens (fecal coliform), and reaffirm its decision to set the BCT limitations for fecal coliform to be equal to the BPT limits established in the 2003 CAFO rule. DATES: Comments on this proposed action must be received on or before August 14, 2006. ADDRESSES: Submit your comments, identified by Docket ID No. EPA-HQ-OW-2005-0037 by one of the following methods: (1) http://www.regulations.gov: Follow the on-line instructions for submitting comments. (2) E-mail: ow-docket@epa.gov, Attention Docket ID No. EPA-HQ-OW-2005-0037. (3) Mail: Send the original and three copies of your comments to: Water Docket, Environmental Protection Agency, Mail code 4203M, 1200 Pennsylvania Ave., NW., Washington, DC 20460, Attention Docket ID No. OW-2005-0037. (4) Hand Delivery: Deliver your comments to: EPA Docket Center, EPA West, Room B102, 1301 Constitution Avenue, NW., Washington, DC, Attention Docket ID No. OW-2005-0037. Such deliveries are only accepted during the Docket's normal hours of operation and special arrangements should be made for deliveries of boxed information. Instructions: Direct your comments to Docket ID No. EPA-HQ-OW-2005-0037. EPA's policy is that all comments received will be included in the public docket without change and may be made available online at www.regulations.gov, including any personal information provided, unless the comment includes information claimed to be Confidential Business Information (CBI) or other information whose disclosure is restricted by statute. Do not submit information that you consider to be CBI or otherwise protected through www.regulations.gov or e-mail. The www.regulations.gov Web site is an “anonymous access” system, which means EPA will not know your identity or contact information unless you provide it in the body of your comment. If you send an e-mail comment directly to EPA without going through www.regulations.gov, your e-mail address will be automatically captured and included as part of the comment that is placed in the public docket and made available on the Internet. If you submit an electronic comment, EPA recommends that you include your name and other contact information in the body of your comment and with any disk or CD-ROM you submit. If EPA cannot read your comment due to technical difficulties and cannot contact you for clarification, EPA may not be able to consider your comment. Electronic files should avoid the use of special characters, any form of encryption, and be free of any defects or viruses. For additional information about EPA's public docket visit the EPA Docket Center homepage at http://www.epa.gov/epahome/dockets.htm. Docket: All documents in the docket are listed in the www.regulations.gov index. Although listed in the index, some information is not publicly available, e.g. , 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, Room B102, 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. FOR FURTHER INFORMATION CONTACT: For additional information contact Kawana Cohen, Water Permits Division, Office of Wastewater Management (4203M), Environmental Protection Agency, 1200 Pennsylvania Ave., NW., Washington, DC 20460; telephone number: (202) 564-2345, e-mail address: cohen.kawana@epa.gov or 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. What Should I Consider as I Prepare My Comments for EPA? 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 1. Issues Upheld by the Court 2. Issues Vacated by the Court 3. Issues Remanded by the Court D. What Requirements Still Apply to CAFOs? E. Status of EPA's Response to the Waterkeeper Decision III. This Proposal A. Duty to Apply for a Permit B. Nutrient Management Plans C. Remand Concerning Water Quality Based Effluent Limitations D. New Source Performance Standards for Subpart D Facilities E. Remand Concerning Pathogens for BCT IV. Impact Analysis V. Cross Media Approaches 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 I. General Information A. Does This Action Apply to Me? This action applies to concentrated animal feeding operations (CAFOs) as defined in section 502(14) of the Clean Water Act and in the NPDES regulations at 40 CFR 122.23. The following table provides a list of standard industrial codes for operations covered under this revised rule. Table 1.—Entities Potentially Regulated by this Rule Category Examples of regulated entities North American industry code (NAIC) Standarial industrial classification code Federal, State, and Local Government: Industry Operators of animal production operations that meet the definition of a CAFO Beef cattle feedlots (including veal) 112112 0211 Beef cattle ranching and farming 112111 0212 Hogs 11221 0213 Sheep 1241, 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 112390 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 40 CFR 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. What Should I Consider as I Prepare My Comments for EPA? 1. Submitting Confidential Business Information. Do not submit this information to EPA through www.regulations.gov or e-mail. Clearly mark the part or all of the information that you claim to be CBI. For CBI information in a disk or CD-ROM that you mail to EPA, mark the outside of the disk or CD-ROM as CBI and then identify electronically within the disk or CD-ROM the specific information that is claimed as CBI. In addition to one complete version of the comment that includes information claimed as CBI, a copy of the comment that does not contain the information claimed as CBI must be submitted for inclusion in the public docket. Information so marked will not be disclosed except in accordance with procedures set forth in 40 CFR Part 2. 2. Tips for Preparing Your Comments. It will be helpful if you follow these guidelines as you prepare your written comments: i. Identify the rulemaking by docket number and other identifying information (subject heading, Federal Register date and page number). ii. Follow directions—The Agency may ask you to respond to specific questions or organize comments by referencing a Code of Federal Regulations (CFR) part or section number. iii. Explain why you agree or disagree; suggest alternatives and substitute language for your requested changes. iv. Describe any assumptions and provide any technical information and/or data that you used. v. If you estimate potential costs or burdens, explain how you arrived at your estimate in sufficient detail to allow for it to be reproduced. vi. Provide specific examples to illustrate your concerns, and suggest alternatives. vii. Explain your views as clearly as possible. viii. Make sure to submit your comments by the comment period deadline identified. II. Background A. The Clean Water Act Congress passed 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” (33 U.S.C. 1251(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. 33 U.S.C. 1342. 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's regulation of wastewater and manure from CAFOs dates to 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 11458). 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) (“the 2003 CAFO rule”). The 2003 CAFO rule required the owners or operators of all CAFOs 1 to seek coverage under an NPDES permit. 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 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 (2nd Cir. 2005). The court's decision, which applies nationally, 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 proposed 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 proposing to revise any of these provisions and is not soliciting comment on them. (a) Land Application Regulatory Framework and Interpretation of “Agricultural Storm Water” The Waterkeeper court upheld EPA's authority to regulate, through NPDES permits, the discharge of manure, litter, and process wastewater that CAFOs apply to crop or forage land. 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. Waterkeeper Alliance et al. v. EPA , 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, and 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). Waterkeeper Alliance et al. v. EPA , 399 F.3d at 508-09. (b) Effluent Guidelines —Identification of best available technologies. The court rejected the environmental organizations' claim that when EPA chose the pollution control technologies on which to base effluent guidelines for CAFOs, the Agency did not meet its duty to identify the single CAFO with the best-performing technology. 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, and on those bases, EPA had adequately justified its selection of “best available technologies” on which to base the regulations. —Groundwater controls. 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 were beyond the scope of the ELGs promulgated in the rule. 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. —Economic methodologies. 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. 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 the 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, which the Agency had based on a presumption that most CAFOs have at least a 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 but found that the Agency lacked statutory authority to do so. (b) Nutrient Management Plans The environmental organizations argued that the 2003 CAFO rule was unlawful because: (1) The rule empowered permitting authorities to issue permits without any meaningful review of a CAFO's NMP, (2) the rule failed to require that the terms of the nutrient management plan be included in the NPDES permit, and (3) the permitting approach established by the rule violated the Clean Water Act'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 Large CAFO's discharges comply with these CWA provisions. In addition, the court found that by not making the NMPs part of the permit and available to the public for review, the 2003 CAFO rule violated public participation requirements in sections 101(e) and 402 of the Act. The court also found that the terms of the NMPs themselves are “effluent limitations” as that term is defined in the Act and therefore must be made part of the permit and enforceable as required under CWA sections 301 and 402. 3. Issues Remanded by the Court The Waterkeeper court also remanded other aspects of the CAFO rule to EPA “for further clarification and analysis,” as follows: (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.” (b) New Source Performance Standards—100-Year Storm Standard The 2003 CAFO rule set the new source performance standards (NSPS) for swine, poultry, and veal CAFOs at a level of zero 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, process wastewater, and precipitation from the 100-year, 24-hour storm, or (2) it would comply with “voluntary superior environmental performance standards” based on innovative technologies, 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 with respect to 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. (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 technology. The court remanded this issue to EPA to make such a finding based on the BAT/BPT technologies EPA studied or to establish specific BCT limitations for pathogens based on some other technology. 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 not addressed in or affected by today's proposal, except to provide background information. EPA has not reconsidered its initial decision regarding these provisions and is not soliciting comment on them. 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 directly 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 AFO, including small AFOs, 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 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 directly 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). Although the Waterkeeper decision invalidated the duty to apply provision promulgated in the CAFO regulations at 40 CFR 122.23(d), there remains in the NPDES regulations a different duty to apply provision, at 40 CFR 122.21(a), that applies to point sources in general, including CAFOs. While the CAFO provision in § 122.23(d) would have required all CAFOs to apply for a permit, § 122.21(a) requires only a person who “discharges or proposes to discharge pollutants” to apply. The Waterkeeper decision did not invalidate § 122.21(a), nor is this provision's continued application to CAFOs inconsistent with the decision in Waterkeeper . Therefore, under § 122.21(a), CAFOs currently are required to apply for an NPDES permit if they discharge or propose to discharge pollutants other than agricultural stormwater, which is not a point source discharge. It should also be noted that the definitions of both “Medium CAFO” and “Small CAFO” in the regulations include only those facilities that have an actual discharge. Thus, under § 122.21(a), all Medium and Small CAFOs must apply for a permit. Nutrient management planning requirements for permitted CAFOs established in the 2003 CAFO rule also were unaffected by the court's ruling. All permitted CAFOs 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, and wastewater management, including compliance with the ELGs. Permitted CAFOs must comply with all applicable recordkeeping and reporting requirements, including those specified in 40 CFR 122.42(e). ELG requirements for existing Large CAFOs also are unaffected by the court decision, with the exception of changes to the NMP compliance dates and BCT. ELG requirements ensure the appropriate storage of manure, litter, and process wastewater and proper land application practices. They vary depending upon the types 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, New Source requirements for beef and dairy operations 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)). E. Status of EPA's Response to the Waterkeeper Decision In addition to the changes made through this proposed rule, EPA extended certain deadlines in the NPDES permitting requirements and ELGs in a separate rulemaking in order to allow the Agency adequate time to complete this rulemaking in response to the Waterkeeper decision in advance of those deadlines. (71 FR 6978). That 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 have nutrient management plans developed and implemented. EPA extended the date by which operations defined as CAFOs as of April 14, 2003, who were not defined as CAFOs prior to that date, must 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, must seek NPDES permit coverage, from April 13, 2006, to July 31, 2007. Finally, EPA extended the deadline by which CAFOs are 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 NMPs must be developed and implemented as specified in the 2003 CAFO rule. III. This Proposal This proposed rule is in response to the Second Circuit Court's vacature and remand orders. EPA intends to make only those changes necessary to address the court's decision. 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 coverage under an NPDES permit unless the Director determined that the CAFO has no potential to discharge. The breadth of this duty to apply was based on EPA's presumption that most CAFOs have a potential to discharge pollutants into waters of the United States. Therefore, all CAFOs were required to apply for a permit, except where the Director determined a 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, 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 downslope from waters of the United States, 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 to apply for an NPDES permit. The court held that the Clean Water Act 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 Clean Water Act. 3. This Proposal To address the court's decision on the duty to apply, EPA is proposing changes to the 2003 CAFO rule in two areas: • Revising the requirement that all CAFOs apply for an NPDES permit; and • Eliminating the procedures for a no potential to discharge determination. EPA also seeks to clarify how unpermitted CAFOs may meet the agricultural stormwater exemption when they land apply manure, litter, or process wastewater. (a) Requirement That All CAFOs With a Discharge Seek Permit Coverage EPA is proposing to delete 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 (40 CFR 122.21(a)(1) and 40 CFR 122.23(a) and (d)(1)). Today's proposed rule would replace the “duty to apply” requirement of the 2003 rule with a requirement that all CAFOs that “discharge or propose to discharge” must seek coverage under an NPDES permit. This proposed change would address the Waterkeeper court's ruling and would hold CAFO owners and operators to the same “duty to apply” requirement as already exists for point sources under 40 CFR 122.21(a)(1). The result of this proposed revision is that only owners and operators of those CAFOs that discharge or propose to discharge would be required to seek coverage under an NPDES permit. This revised duty to apply applies to all owners and operators that discharge or propose to discharge, regardless of the volume or duration of the discharge except for discharges of agricultural stormwater ( see below). A facility may seek permit coverage in one of two ways, by submitting an application for an individual permit or by submitting a notice of intent to be covered by a general permit that has been issued by the permitting authority. Generally, under this proposal, it would be the CAFO's responsibility to decide whether or not to seek permit coverage based on whether they discharge or propose to discharge. This is how the NPDES program operates for other point sources. Any CAFO that discharged or proposed to discharge and failed to obtain an NPDES permit would be in violation of the NPDES regulatory requirement to seek coverage under an NPDES permit. A facility with an actual discharge would also be in violation of the CWA prohibition against discharging without an NPDES permit (33 U.S.C. 1311(a)). Any discharge from a CAFO, even one that is unplanned or accidental, is illegal unless it is authorized by the terms of a permit. Many CAFOs have conditions that may result in a discharge. For example, manure structures that are improperly designed or, for other reasons, have insufficient capacity ( e.g. , due to facility expansion) may discharge. In addition, discharges can occur from a properly designed containment structure that is improperly operated and maintained or as a result of precipitation that exceeds the operating capacity of the structure. In the absence of an actual discharge or proposed discharge, CAFOs with such conditions are not required under the terms of today's proposed rule to obtain an NPDES permit. However, the owner or operator of a CAFO that fails to obtain an NPDES permit and has a discharge is subject to State or federal enforcement, as well as liability from citizen suits under CWA Section 505(a). Because discharges are prohibited from unpermitted CAFOs, NPDES permit coverage reduces CAFO operator risk and provides certainty to CAFO operators regarding activities and actions that are necessary to comply with the Clean Water Act. Compliance with the permit is deemed compliance with the CWA and thus acts as a shield against EPA enforcement or citizen suits under CWA Section 402(k). Furthermore, under the 2003 rule, most CAFO NPDES permits will incorporate ELG provisions that allow for discharge when precipitation causes an overflow from a structure that is properly designed, constructed, operated, and maintained, in accordance with the applicable design standards. Finally, upset provisions can protect permittees from legal liability when emergencies or natural disasters cause discharges beyond the permittee's reasonable control, as provided in § 122.41(n). This protection is not available to unpermitted CAFOs. There are many factors a CAFO owner or operator should consider in determining whether to seek permit coverage. For example, if the CAFO is in a flood plain, subject to high annual precipitation, or subject to lengthy rainy seasons, it is likely to have a discharge if the CAFO drains to a water of the United States. Other factors likely to result in a discharge include runoff from open feed bunkers, field storage, or other stockpiles exposed to precipitation; lagoons that are not sufficiently pumped down for the upcoming winter season; holding of process wastewater for summer irrigation that precludes adequate capacity for chronic rainfalls; and inadequate containment due to unavailability of land for manure, litter, or process wastewater application due to timing constraints associated with, for example, saturated ground or imminent rain. In addition, a discharge may occur from land application due to improper maintenance or operation of manure handling equipment that may lead to spills, and application of manure, litter or process wastewater to land in such a way that it does not qualify for the agricultural stormwater exemption (see below). EPA recognizes that some CAFOs have a higher likelihood of actually discharging due to certain geographic and physiographic conditions. In order to guide CAFOs in making a decision on whether or not to seek permit coverage, EPA suggests that Large CAFOs falling into one or more of these categories should consider seeking permit coverage (this list is not intended to be exhaustive): 1. Where a CAFO is located in close proximity to waters of the United States with land classified in USDA Land Use Capability Classes III through VIII 2 ; 2 Land capability classification is a system of grouping soils primarily on the basis of their capability to produce common cultivated crops and pasture plants without deteriorating over a long period of time. Soil survey map units contained in United States Department of Agriculture (USDA) soil surveys typically are assigned a land capability classification. The eight classes are defined as follows: Class 1 soils have slight limitations that restrict their use; Class 2 soils have moderate limitations that reduce the choice of plants or require moderate conservation practices; Class 3 soils have severe limitations that reduce the choice of plants or require special conservation practices, or both; Class 4 soils have very severe limitations that restrict the choice of plants or require very careful management, or both; Class 5 soils have little or no hazard of erosion but have other limitations, impractical to remove, that limit their use mainly to pasture, range, forestland, or wildlife food and cover; Class 6 soils have severe limitations that make them generally unsuited to cultivation and that limit their use mainly to pasture, range, forestland, or wildlife food and cover; Class 7 soils have very severe limitations that make them unsuited to cultivation and that restrict their use mainly to grazing, forestland, or wildlife; and Class 8 soils and miscellaneous areas (areas dominated by disturbed soil) have limitations that preclude their use for plant production and limit their use to recreation, wildlife, or water supply or for esthetic purposes. 2. Where the CAFO's production area is not designed and operated for zero discharge, including where the containment structure is not designed or maintained to contain all manure, litter, process wastewater, precipitation and runoff that may accumulate during periods when the facility is unable to land apply in accordance with a nutrient management plan; 3. Where a CAFO that land applies does not have or is not implementing nutrient management planning that is designed to ensure that any land application runoff qualifies for the agricultural stormwater exemption; and 4. Where the CAFO has had a discharge in the past and has not corrected the factors that caused the discharge to occur. EPA seeks comment on the completeness and accuracy of the above list of situations where a discharge may occur to further assist CAFOs in their decisions regarding whether or not to seek permit coverage. EPA also solicits comment on its proposal to replace the duty to apply provision promulgated in the 2003 CAFO rule with the narrower duty to apply provision described above. (b) “No Potential to Discharge” Determination EPA is proposing to delete 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). Such a designation would be irrelevant because the proposed rule requires only those CAFOs that discharge or propose to discharge to seek coverage under a permit. (c) Agricultural Storm Water 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 permit requirements, unless the discharge is agricultural stormwater, which is excluded from the meaning of the term “point source” under 33 U.S.C. 1362(14). As described in the preamble to the 2003 rule, EPA recognized that manure, litter, or process wastewater applied in accordance with practices designed to ensure appropriate agricultural utilization of nutrients fulfills an important agricultural purpose, namely the fertilization of crops, while reducing the potential for a subsequent discharge of pollutants to waters of the U.S. However, EPA also recognized that some runoff may occur during rainfall events even when a CAFO applies manure, litter, or process wastewater in accordance with practices designed to ensure appropriate agricultural utilization of nutrients. EPA believed that the potential for runoff and water quality impairments would be minimized where a CAFO implemented a site-specific NMP in conformance with 40 CFR 122.42(e)(1)(vi)-(ix) and, for Large CAFOs, the additional management practices required in 40 CFR 412.4(c). In the 2003 rule, EPA promulgated a definition of agricultural stormwater that included compliance with 40 CFR 122.42(e)(1)(vi-ix). The referenced regulatory text includes requirements for edge-of-field buffers, testing of manure and soil, land application at agronomic rates, and record keeping. While not explicitly included in the definition, Large CAFOs were also required under the effluent guidelines to comply with technical standards established by the Director, in accordance with 40 CFR 412.4(c). These more specific limitations implemented the general requirements at 40 CFR 122.42(e)(1)(vi-ix), and because all CAFOs with a potential to discharge were required to obtain permits, virtually all Large CAFOs were required to comply with them. Under today's proposed rulemaking, Large CAFOs that have only agricultural stormwater discharges from their land application area, and no other discharges or proposed discharges from their production or land application areas, would no longer be required to seek permit coverage. (See 40 CFR 122.23(e).) However, precipitation-related discharges from CAFO land application areas would be considered agricultural stormwater only where the CAFO land applies in accordance with nutrient management practices that meet the requirements of 40 CFR 122.42(e)(1)(vi)-(ix). EPA believes that, in order for the owner or operator of a CAFO to qualify for the statutory agricultural stormwater exemption, manure, litter, and process wastewater must be applied in compliance with technical standards that are, in significant part, intended to ensure the appropriate agricultural utilization of the nutrients contained in the manure, litter, and process wastewater. The Second Circuit upheld EPA's definition of agricultural stormwater, and EPA is not proposing to change the definition at this time, or requesting comment on such a change. However, EPA is considering requiring explicitly that Large CAFOs that are not permitted because they do not discharge or propose to discharge comply with the technical standards for land application established by the Director (in addition to meeting the requirements of 40 CFR 122.42(e)(1)(vi-ix)) in order for runoff from their fields to be considered agricultural stormwater (which is exempt from permitting requirements). Even if EPA does not adopt this requirement explicitly, EPA believes that unpermitted Large CAFOs should incorporate the technical standards established by the Director into their NMPs. EPA also recommends that small or medium AFOs use nutrient management practices consistent with 40 CFR 122.42(e)(1)(vi-ix) and comply with the applicable technical standards in their land application of manure, litter, or process wastewater. EPA requests comment on this issue. Unpermitted CAFOs that land apply manure, litter, or process wastewater must document that they are land applying in accordance with the requirements described above in order to qualify for the statutory exclusion for agricultural stormwater. (See 40 CFR 122.42(e)(1)(ix).) The documentation required includes both the nutrient planning and the additional recordkeeping necessary to demonstrate that the CAFO properly land applied manure, litter, or process wastewater in accordance with 40 CFR 122.42(e)(1)(vi)-(ix), including the technical standards used to translate these requirements into specific land application rates and practices. EPA believes that an appropriate approach to planning and documenting such practices is by preparing a comprehensive nutrient management plan in accordance with guidance provided by USDA and the appropriate technical standards. Whatever form the documentation takes, it must be maintained on site. This documentation is crucial in determining whether the CAFO is land applying manure, litter, or process wastewater in a manner that ensures the appropriate agricultural utilization of nutrients and, as a result, is not illegally discharging pollutants from land application areas. B. Nutrient Management Plans 1. Provisions in the 2003 CAFO Rule Affected by the Court Decision (a) Requirement to Develop and Implement a Nutrient Management Plan Under the 2003 CAFO rule, NPDES permits for all CAFOs must include a requirement for the permittee to develop and implement a nutrient management plan. At a minimum, the NMP must include BMPs and procedures necessary to achieve effluent limitations and standards. The plan must, to the extent applicable, include the minimum elements established at 40 CFR 122.42(e)(1)(i)-(ix). For Large CAFOs in the cattle, swine, poultry, and veal subcategories, the NMP must also meet the more detailed requirements in the Part 412 effluent limitations guidelines. For Small and Medium CAFOs, or other operations not otherwise subject to Part 412 requirements for land application, the required elements of a nutrient management plan would be further specified in the permit based on the best professional judgment (BPJ) of the permitting authority. The Second Circuit's decision did not affect these provisions and EPA is not revisiting them or soliciting comments. (b) Due Dates for Developing and Implementing Nutrient Management Plans The 2003 CAFO rule required all CAFOs to develop and implement an NMP by December 31, 2006, except that CAFOs seeking to obtain coverage under a permit subsequent to that date were required to have an NMP developed and implemented upon the date of permit coverage. This timing was consistent with the dates for the implementation of the ELG, which required existing Large CAFOs to implement the land application requirements at 40 CFR 412.4(c) by December 31, 2006. (Following the court decision these dates were extended to July 31, 2007, to give EPA time to complete the current rulemaking ( see Section II.E).) As discussed in the preamble to the 2003 CAFO rule, EPA believed that these dates were reasonable given that operations would have had three and a half years from the time the 2003 rule was issued to conduct the necessary planning and construction to implement an NMP. For Large CAFOs that are new sources ( i.e. , those commencing construction after the effective date of the 2003 CAFO rule), the land application requirements at 40 CFR 412.4(c) apply immediately. EPA concluded that this timeframe also allowed States to update their NPDES programs and issue permits to reflect the NMP requirements of the 2003 CAFO rule and provided flexibility for permit authorities to establish permit schedules based on specific circumstances, including prioritization of nutrient management plan development and implementation based on site-specific water quality risks and the availability of technical expertise for development of NMPs. 2. Summary of the Second Circuit Court of Appeals Decision on Nutrient Management Plans As previously discussed, the Second Circuit Court of Appeals found that the terms of the NMPs were effluent limitations and vacated the 2003 CAFO rule insofar as the rule allowed permitting authorities to issue NPDES permits to CAFOs without: reviewing the terms of the nutrient management plans, providing for adequate public participation in the development, revision, and enforcement of the nutrient management plans, and including the terms of the nutrient management plan in the permit. The decision did not affect the required contents of nutrient management plans established at 40 CFR 122.42(e)(1) and 40 CFR 412.4(c)(1) in the 2003 CAFO rule. The Second Circuit court decision did not vacate any NPDES permits issued pursuant to the 2003 CAFO rule. Therefore, such permits already issued to CAFOs by States or EPA prior to June 27, 2005 (the effective date of the court's decision), are not directly affected by the court decision and the nutrient management plan requirements in those permits remain in effect until and unless the permits are modified, revoked and reissued, or terminated in accordance with State regulations. 3. This Proposal To address the court's decision, EPA is proposing regulatory revisions to the 2003 CAFO rule and other provisions of the NPDES regulations to provide for: • Receipt and review of the nutrient management plan by the permitting authority prior to issuing an individual permit or granting coverage under a general permit; • Procedures to provide opportunity for adequate public participation prior to issuing an individual permit or granting coverage under a general permit; and • Incorporation of the terms of the nutrient management plan into the NPDES permit. In proposing these revisions, EPA has devoted particular attention to the process for issuance of general permits, because most CAFOs are expected to be covered by general permits and, for those that will be permitted under individual permits, the individual permitting process already allows for review of NMPs by the permitting authority, public review of an NMP as part of the individual permit application process, and incorporation of the terms of the NMP into the individual permit consistent with the CWA. Further, EPA proposes a process to address changes to the NMP once permit coverage is granted, for both individual and general permits. To effectuate these changes, EPA is proposing regulatory revisions to 40 CFR 122.21, 122.23, 122.28, 122.42, 122.62, and 122.63. In addition, in a separate rulemaking 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. (71 FR 6978.) The preamble discussion that follows is divided into six sections to separately address each of the following issues: • CAFO permit application and notice of intent requirements; • Procedures for permitting authority review; • Procedures for public review and comment; • Incorporation of nutrient management plan terms in NPDES permits; • Changes to nutrient management plans; and • Required dates to seek coverage under a permit and submit an NMP. (a) CAFO Permit Application or Notice of Intent Requirements for Nutrient Management Plans In order to satisfy the court's requirements that the terms of a nutrient management plan must be publicly reviewed and incorporated into the permit, EPA is proposing to revise 40 CFR 122.21(i)(1)(x) to require the applicant to submit, as part of its permit application or notice of intent (NOI), a nutrient management plan developed in accordance with the provisions of 40 CFR 122.42(e)(1) and 40 CFR 412.4(c)(1), as applicable. Although this proposed change would be codified in the section of the regulations applicable to individual permit applications (40 CFR 122.21(i)(1)), it would also apply to notices of intent to be covered by a general permit, because 40 CFR 122.28(b)(2)(ii), the regulation governing notices of intent for general permits, incorporates the requirements of 40 CFR 122.21(i)(1) by reference. EPA Application Form 2B will also be revised to reflect these changes. The revised form is provided as Appendix A to this notice. This approach is consistent with the decision of the Second Circuit Court of Appeals, which left undisturbed the basic substantive requirements for nutrient management plans in the 2003 CAFO rule. The proposed revisions would not change the required contents of the NMP, but would now require CAFOs to submit the plan with the application or the notice of intent rather than only at the request of the Director. The permitting authority would then make the nutrient management plan available for review prior to developing an individual permit or providing coverage under an NPDES general permit. (b) Procedures for Permitting Authority Review Once the permitting authority receives an application or an NOI from a CAFO seeking permit coverage, it would be the responsibility of the permitting authority to review the application or NOI to ensure that the nutrient management plan meets the requirements of 40 CFR 122.42(e)(1) and, for Large CAFOs, the applicable requirements of 40 CFR 412.4(c). As part of that process, the Director would review the NMP for completeness and sufficiency. EPA believes that this review process responds to the Waterkeeper decision by providing for permitting authority review of the NMP. For individual permits, the NMP would be submitted and reviewed as part of the permit application. The decision-making procedures in 40 CFR Part 124 continue to apply to the Director's review of the application, which now would include the NMP. Part 124 requires review of the completeness and sufficiency of the permit, includes an opportunity for the CAFO to modify the plan or provide additional information to the permitting authority, and provides for a final decision by the Director after an opportunity for public comment and a public hearing. While the review process for NMPs in individual permits is already established in existing NPDES regulations, there are gaps in the requirements for general permitting of CAFOs that EPA proposes to fill in order to address the Second Circuit Court decision. Specifically, EPA is proposing new regulatory provisions to establish permitting authority review of NMPs for CAFO general permits. These procedures are in the proposed new Paragraph (d) to be added to 40 CFR 122.28. Proposed 40 CFR 122.28(d) would require the Director to review the NMP submitted with the NOI and to take appropriate steps to ensure that the NMP meets the requirements of the regulations. If upon review the permitting authority determines that additional information is necessary to complete the notice of intent or clarify, modify, or supplement previously submitted material, the Director would notify the CAFO owner or operator and request the appropriate information be provided. When the NOI is complete the permitting authority would notify the public of its receipt and of the terms of the nutrient management plan proposed to be incorporated into the existing general permit as terms and conditions applicable to that CAFO. Following an opportunity for public comment and public hearing, the permitting authority would decide whether to authorize coverage under the general permit and incorporate the terms of the NMP into the general permit for that CAFO. EPA is considering the use of a template which could be used as a voluntary tool to facilitate completion of the NMP by CAFO applicants, as well as to facilitate review by the permitting authority. Such a template would help to systematically organize the information necessary to satisfy the NMP requirements in the regulation. The template could, for example, be used as a form, that when completed by the operator, and approved by the permitting authority, could suffice as the NMP itself. Alternatively, it could also be used as a checklist that the operator and/or permitting authority could use to organize the information in the NMP and to assist in assessing its adequacy ( see Section III.B.3.d, below). It would be up to the permitting authority's discretion as to how to incorporate the terms of the NMP into the permit and permitting authorities might need to tailor any template to their permit process and technical requirements, including the technical standards established by the Director. EPA has developed a draft template for public review that is intended to be user friendly. It follows the requirements for an NMP identified in 40 CFR 122.42(e) relating to: manure storage; management of animal mortalities; diversion of clean water; prevention of direct contact of animals with waters of the US; chemical handling; site-specific conservation practices; protocols for testing manure, litter, process wastewater and soil; protocols for land application; and recordkeeping. This draft template is in the public record for this rulemaking at www.regulations.gov under docket # EPA-HQ-OW-2005-0037 and is also available on the EPA Web site at www.epa.gov. EPA is interested in receiving feedback on the form and content of the template. (c) Procedures for Public Participation Prior to Permit Coverage As noted above, the regulatory procedures for public participation in the issuance of individual permits are already established. ( See generally, 40 CFR Part 124.) Because the NMP would be part of the individual permit application, it would be subject to existing regulations requiring public participation, including the requirement for public notice (40 CFR 124.10) and the opportunity for the public to provide comments and request a public hearing (40 CFR 124.11). Because of the proposed regulatory change requiring nutrient management plans to be submitted with the permit application ( see discussion at II.B.3.i.; 40 CFR 122.21 and 122.28), the public would have access to the nutrient management plan prior to permit issuance and would also have full opportunity to comment on the adequacy of the plan and on the nutrient management terms and conditions of the draft NPDES permit developed for the specific CAFO facility. EPA believes that this process responds to the court's decision. The general permit issuance process differs from the individual permitting process discussed above in the way in which a permit is developed and the means by which individual facilities obtain coverage under the permit. A general permit is developed by the permitting authority to cover multiple facilities without the need to receive individual permit applications from facilities in advance of the development of the permit. Once the draft general permit is developed, the public (including potential future permittees) is provided the opportunity to review the permit, submit comments, and request a hearing. After considering any comments submitted, the permitting authority then finalizes the general permit. Once the final general permit is issued, facilities may submit a notice of intent (NOI) seeking coverage under the permit. Typically, the permitting authority then grants coverage, without the need for further public notice and comment, or requires the facility to seek coverage under an individual permit. Following the Waterkeeper decision, general permits for CAFOs must be modified, once issued, to include the terms of an NMP applicable to a specific CAFO. Moreover, Waterkeeper requires that the public have an opportunity to comment on the incorporation of NMP requirements into the permit. Thus, a second round of public notice and comment is necessary when providing coverage for CAFOs under a general permit. There is no provision in the existing regulations that explicitly addresses incorporation of site-specific requirements into a general permit when a CAFO seeks coverage or any additional public process for such incorporation. Today, in proposed 40 CFR 122.28(d), EPA proposes to establish new procedures applicable to the general permitting process that would allow the incorporation of the site-specific NMPs into CAFO general permits and provide an opportunity for public review of a CAFO's NOI (including the entire NMP) before the CAFO receives coverage under a general permit. The proposed procedures would also allow the public to review and comment on those terms of the nutrient management plan to be incorporated into the permit, and to request a public hearing before a CAFO receives coverage under a general permit. The discussion that follows describes the process for public participation that EPA is proposing. Further discussion of incorporation of the terms of the NMP into the general permit is provided below in section III.B.3.d of this preamble. The proposed § 122.28(d) would provide specific procedures for public participation. The proposed rule would require that, for each facility submitting a completed NOI, the permitting authority must notify the public of the following: (1) That it has received a complete NOI; (2) that the permitting authority is proposing to allow coverage under the general permit; and (3) that the nutrient management plan is available for public review, along with the terms of the nutrient management plan proposed to be incorporated into the permit by the permitting authority. Today's proposed rule would allow the permitting authority discretion as to how best to provide such public notification in the general permit context. For example, public notification could be provided on the permitting authority's web page or through other electronic means. Another alternative would be to use the notice or fact sheet for the general permit to establish a procedure allowing any person to request notice by mail or electronically of the receipt of an NOI, the permitting authority's proposed action, and the terms of the nutrient management plan proposed to be incorporated into the permit. EPA believes that these are appropriate ways to balance the competing concerns of providing adequate notification to the public, providing flexibility to the permitting authority, and ensuring the practicality of general permits. The permitting authority should describe the process to be used to give the public notice of and comment opportunities on site-specific NMPs in the draft and final general permit to ensure meaningful public participation. EPA solicits comment on the methodology for providing public notice. Under today's proposal, the Director would also have discretion to establish an appropriate period of time for public review of the NOI and proposed permit conditions incorporating the terms of the NMP into the permit. For example, the Director might establish a period of 30 days, depending upon a variety of factors. Factors to consider might include the number of NOIs being publicly noticed at any one time, the complexity of the material made available for public review, expected level of public interest based on prior notices of CAFOs seeking coverage, the relative availability of NOIs to the public (e.g., on the internet), the opportunity for the public to extend the comment period for one or more facilities, and whether individuals can request and receive individual notification of CAFOs seeking coverage in a timely fashion. Because this proposal would not mandate a 30-day public notice period as currently required in 40 CFR 124.10, EPA would require that the Director establish a time frame for public review by regulation or propose the time frame for public notice in the draft general permit and include it as a provision in the final permit. This would allow the public and other interested parties an opportunity to comment on the sufficiency of the time allotted for public notice. EPA solicits comment on this approach, as well as on fixed minimum time frames for public review, such as 7 days, 15 days, 21 days, and 30 days. The Director would also have to provide an opportunity for the public to request a hearing. EPA further proposes that the procedures for requesting and holding a hearing on the terms of the NMP to be incorporated into the general permit would be the same as those for draft individual permits, which are provided in §§ 124.11 through 124.13. When granting permit coverage, the permitting authority would be required to respond to all significant public comments. EPA believes that the proposed processes will provide adequate notice to affected States. CWA section 402(b)(3) provides that the Administrator, in approving State programs, shall make sure adequate authority exists to ensure notice to “any other State the waters of which may be affected” and Section 402(b)(5) provides that the Administrator must insure that any State “whose waters may be affected by the issuance of a permit may submit written recommendations to the permitting State” and that if those recommendations are rejected that the permitting State notify the affected State in writing of the reasons for the rejection. Although today's proposal does not include provisions specifically intended to address these requirements, EPA believes that the public notice provisions are sufficient to notify affected States. Additionally, the permitting authority's response to all significant comments would include responses to comments from affected States. EPA solicits comment from States and other interested parties as to whether this approach is adequate or whether there are specific requirements for review by affected States that should be added to this proposal. The proposed rule seeks to balance several competing concerns in crafting the public participation procedures for general permitting of CAFOs. First, EPA believes that the proposed rule would maintain the utility of a general permit program as a resource-efficient method by which to authorize multiple dischargers under an NPDES permit while meeting the court's directive to “provide for adequate public participation” in the development of site-specific effluent limitations. Waterkeeper Alliance et al. v. EPA, 399 F.3d at 524. Second, EPA believes the proposed rule would provide sufficient flexibility for State permitting authorities to adopt their own procedures while ensuring they meet the public participation requirements of the Clean Water Act. EPA is attempting to implement the Second Circuit decision in a way that would not have the effect of eliminating the use of general permits for CAFOs. Because of the large number of CAFOs that may seek permit coverage, the Agency considers it appropriate to develop procedures that would allow and encourage permitting authorities to continue the use of NPDES general permits as a means for applying Clean Water Act limitations and standards to CAFOs on a timely basis. Of course, the Director may always require a facility to apply for an individual permit instead of allowing coverage under a general permit (even after coverage under a general permit has been granted) under already existing regulations. EPA seeks comment on the approach taken in today's proposal concerning public participation in the general permitting process. Specifically, the Agency is interested in comment as to whether the procedures strike an appropriate balance between the above mentioned competing concerns. (d) Incorporation of Nutrient Management Plan Terms in NPDES Permits EPA is proposing to modify the language of 40 CFR 122.42(e)(1) to require that any individual or general permit issued to a CAFO contain the terms of the NMP. In the 2003 CAFO rule, the Agency finalized regulations that required each CAFO permit to include requirements to develop and implement a nutrient management plan that met the conditions specified in 40 CFR 122.42(e)(1)(i)-(ix) and, for Large CAFOs, that also fulfilled the requirements of 40 CFR 412.4(c). The Second Circuit decision did not affect these requirements and EPA is not revisiting its decision with respect to the contents of the nutrient management plan. The NMP must continue to include the elements in 40 CFR 122.42(e)(1)(i) through (x) and the elements required by the effluent limitation guideline at 40 CFR 412.4(c), where applicable. However, the proposal would ensure that the terms of the NMP become terms and conditions of the permit, as required by the Second Circuit. The Waterkeeper decision requires the permitting authority to include the terms of a CAFO's nutrient management plan in the NPDES permit issued to the CAFO. The court's opinion appeared to distinguish between the “nutrient management plan,” which must be submitted by the CAFO to the permitting authority for review (as discussed above), and the “terms” of the nutrient management plan, which must be incorporated into the permit following the public review process described above. In light of the court's opinion, EPA is proposing to require the permitting authority to incorporate the terms of the NMP into the permit as enforceable terms and conditions of the permit. At a minimum, the terms of the NMP must meet the requirements specified in 40 CFR 122.42(e)(1)(i)-(ix) and 412.4(c) (for Large CAFOs, as applicable). Thus, the terms of the NMP would need to ensure, for example, adequate storage of manure, litter, and process wastewater, proper management of mortalities, and diversion of clean water. The terms of the NMP would identify site-specific conservation practices to be implemented by the CAFO and establish site-specific requirements for proper land application of manure, litter, and process wastewater, including application rates. EPA expects that a submitted NMP, as a whole, will include data, calculations, and other information that provide a basis for the terms of the NMP and any other planning decisions encompassed in an NMP. The data, calculations, and additional information are generally analogous to both the information contained in a permit application and the assumptions, calculations, and other determinations typically provided as part of the fact sheet that is prepared for every draft NPDES permit. On the other hand, the terms of the NMP are the sort of requirements normally found as terms and conditions in a permit. In other words, whereas a fact sheet (or, in this case, the supplemental information provided in the NMP) contains the information that forms the basis of the requirements included in a permit, the permit itself contains the actual requirements applicable to the permitted facility. A complete NMP contains both the requirements applicable to the facility (“the terms of the NMP”) and the background information (assumptions, data, calculations, etc.) which provide the basis for those requirements. This relationship is well illustrated when considering rates of application for land applying manure, which, for Large CAFOs, must be developed consistent with technical standards for nutrient management established by the Director in accordance with 40 CFR 123.36. These technical standards typically require application rates to be calculated using the Phosphorous Index or its equivalent established by the State. The calculations in turn are derived from data from fields where land application is to occur and predictions for nutrient utilization based upon crops to be planted in those fields. In preparing an NMP, a CAFO would include both the data necessary to determine the application rates in accordance with the applicable technical standards and the calculations it used to determine those rates. EPA believes that it is appropriate to allow the permitting authority discretion as to how to incorporate the terms of an NMP that meets the regulatory requirements of 40 CFR 122.42(e) and 412.4 into the permit. For example, the permitting authority could simply attach the whole NMP to the permit and require implementation of the terms of the NMP as a condition of the permit. Alternatively, the permitting authority could identify and extract the terms of the NMP from the larger document and incorporate only the extracted terms into the permit. Another possibility is that the software used by some nutrient management planners to develop NMPs could be modified to generate a separate form that would clearly identify the terms of the NMP when generating the whole NMP report. As mentioned above, the Agency is considering the use of a model or template for identification of the terms of the NMP. The Agency solicits comment on these various approaches to identify the terms of the NMP that would be included in the permit. EPA also seeks comments on a modified approach as an alternative to the process described above for incorporating nutrient management terms and conditions into general permits. It is premised on EPA's recognition that some NMP requirements may be broadly applicable to all of the CAFOs covered by a general permit. Under this approach there would be three possible categories of permit conditions. The first category would include permit conditions that can be established in the general permit itself so as to apply to all CAFOs seeking coverage under that permit. The second category would allow for flexibility in some broadly applicable requirements. Conditions falling into this category would lend themselves to a default requirement set by the permitting authority, with the option for facilities to substitute alternative measures in their NMPs that are equivalent or more effective in achieving the same objective. In such instances, of course, it would be necessary for the permitting authority to review the NMP submitted by each CAFO that chooses such alternative measures to determine whether the selected measures satisfy the relevant regulatory requirement(s). The third category would include those requirements for which a broadly applicable condition in the general permit would not be possible because they are of necessity facility-specific. A prime example of this third category is the requirement for field-specific rates of application. Under this alternative approach, for the first category of conditions, the permitting authority would have the discretion to incorporate some NMP requirements into the terms and conditions of the general permit itself so they are applicable to all CAFOs covered by the permit. Examples of requirements that might lend themselves to the first category include, 40 CFR 122.42(e)(1)(iii) (diversion of clean water), (iv) (prevent contact of confined animals with waters of the United States), and (v) (proper disposal of chemicals), and 40 CFR 412.37(a)(4) (mortality management)). During the comment period on the draft general permit, the public would have the opportunity to comment and request a hearing on the broadly applicable nutrient management terms and conditions proposed by the permitting authority. If after notice and comment the permitting authority included these conditions in the final permit, the permitting authority would be free to focus greater attention on those terms of a facility's nutrient management plan that were actually site-specific ( i.e. , those conditions in the second and third categories, described below, specified in the facility's NMP). Of course, the public would still have the opportunity to review each CAFO's nutrient management plan (as well as the terms of the NMP that would be included in the general permit) to ensure that the plan complied with all conditions of the general permit. EPA seeks comment on the feasibility of utilizing this approach under a general permit. For the second category of permit conditions in this modified approach, the permitting authority might establish broadly-applicable permit terms that could be implemented through specific NMP measures, while allowing for flexibility as previously noted. For example, the permitting authority could set a minimum requirement for adequate storage of manure (40 CFR 122.42(e)(1)(i)) by specifying the number of days of storage capacity for each facility type. In such an instance, a facility wishing to take an alternative approach would need to describe, for example, the alternative measures it would take that would justify a shorter period of storage capacity. Other broadly applicable requirements that so many qualifiers could lend themselves to site-specific alternatives might include permit conditions requiring conservation practices to reduce soil erosion from land application areas to the tolerable rate (“T”) as a standard to ensure adequate conservation practices, as required by 40 CFR 122.42(e)(1)(vi), or requiring CAFOs to address the timing of land application (40 CFR 412.4(c)(2)(i)) in part by prohibiting surface application of manure on frozen or snow-covered land that is upslope from waters of the United States. EPA solicits comment on such an approach, the sort of measures that might lend themselves to such an approach, and the sort of alternative measures that might qualify as site-specific substitutions. Under this alternative methodology for establishing some terms of the NMP, the permitting authority would still need to identify the third category of facility-specific terms of the nutrient management plan to be incorporated into the permit. For example, the permitting authority would need to identify the manure, litter, and process wastewater application rates in each CAFO's nutrient management plan on a site-specific basis and incorporate those rates as terms and conditions of the permit before the permitting authority could authorize coverage of the CAFO under the permit. The public would have the opportunity to review and comment and request a hearing on these site-specific terms and conditions, as well as on the NMP's adequacy to satisfy any generally applicable permit requirements, as provided by the procedures in today's proposal. EPA believes the alternative described above has the potential to speed the pace at which unpermitted CAFOs receive authorization under general permits while being consistent with the Second Circuit decision. In seeking comments, EPA specifically asks States to comment on the possible workload burden associated with the procedures proposed today as well as the alternative described immediately above. For either approach discussed above, EPA is proposing that the permitting authority would be required to respond to all significant comments received during the comment period. As necessary, the Director would require a CAFO owner or operator to make revisions to the CAFO's NMP in order to address issues raised during the review process. Once the Director determines that the process for the development of a CAFO's NMP has been completed, the Director must make a final decision whether to grant permit coverage to the CAFO under the general permit. If coverage is granted, the Director must incorporate the relevant terms of the NMP into the general permit and inform the CAFO owner or operator of the terms of the NMP that have been incorporated as permit conditions. Under today's proposal, incorporation of the terms of a particular CAFO's NMP into a general permit would not be a permit modification subject to 40 CFR 122.62. Rather, EPA views this as an extension of the CAFO general permitting process itself. As discussed above, EPA intends the process proposed in 40 CFR 122.28(d)(1) to generally parallel the procedures in 40 CFR Part 124. A person who objects to the incorporation of the terms of an individual CAFO's NMP into a general permit could appeal the permit decision to the Environmental Appeals Board pursuant to 40 CFR 124.19, when EPA is the permitting authority. EPA seeks comment on today's proposed process for incorporation of the terms of a CAFO's NMP into NPDES permits. EPA specifically seeks comment from States on the workload implications of requiring the permitting authority to respond to all significant comments on each individual CAFO's NOI (including the NMP) and the terms of the NMP to be incorporated into the permit. (e) Changes to Nutrient Management Plans When a CAFO obtains coverage under an NPDES permit, as proposed in today's notice, it would be the CAFO's responsibility to implement the terms and conditions of the nutrient management plan as incorporated into the permit, as of the date of permit coverage. Because agricultural operations sometimes modify their nutrient management and farming practices as a normal part of their operations, and because such alterations may require changes to NMPs after a permit is issued, EPA is proposing a permit revision process to specifically address these circumstances. The Agency does not, however, believe that such a process is necessary for all operating changes at a CAFO. Most routine changes at a facility should not require changes to the NMP itself because of the way NMPs are developed. Nutrient management plans are dynamic documents and are developed to accommodate routine variations, for example changes resulting from anticipated crop rotation or climatic variability inherent in agricultural operations, as well as changes in numbers of animals and volume of manure, litter or process wastewater resulting from normal fluctuations or a facility's planned expansion. Nevertheless, as discussed in the preamble to the 2003 CAFO rule, changes to a nutrient management plan will be necessary under some circumstances; for example, when there is a substantial increase in the number of animals, or a major change in the CAFO's cropping program not anticipated in the original NMP. EPA encourages CAFO operators to develop, at the outset, NMPs that thoughtfully anticipate, to the extent feasible, all contingencies and changes in operations that may occur over the term of the permit. The NMP should provide information on possible crop rotations or other alterations in cropping patterns with accompanying field-specific calculations for manure, litter, and process wastewater application rates based on realistic crop yield goals, soil characteristics, weather, and other site-specific field conditions. In this way, the public will have the opportunity to review all anticipated operational scenarios and associated field-specific manure, litter, and process wastewater application rates, including the calculation on which these rates were based. In this manner, NMPs and associated permit conditions can address most year-to-year changes in nutrient management practices during the term of the permit and greatly reduce the need for NMP and associated permit modifications as a range of potential operational scenarios will have already been accounted for. For example, the NMP could specify: (1) The maximum amount of manure that the CAFO may apply to land application areas under its control, based on its total available land application area and the capacity of its waste storage and treatment facilities, as well as manure and soil test results; (2) the maximum amount of manure that may be transferred to other persons (see § 122.42(e)(3)) by the CAFO, given limitations on available markets, the cost of transporting wastes, etc.; (3) a complete inventory of all of the fields under the CAFO's control that might receive manure, with the associated acreage, soil types, soil tests and testing protocols, setbacks, and other soil conservation measures; (4) a list of all of the crops the CAFO may wish to grow on each of those fields, with a matrix of the associated realistic yield expectations and land application rates consistent with the various field conditions; and/or (5) plans to address contingencies ( e.g. , a spill or especially heavy rainfall event), including consultation with the permitting authority as appropriate. The NMP should indicate calculations necessary to determine rates of application for the array of crops most likely to be planted in accordance with the cropping system utilized by the CAFO operator, including likely fallback scenarios. For Large CAFOs, the land application rates must comply with the ELG requirements of 40 CFR 412.4. The NMP may also identify other crops that could be planted and other fields that might be utilized for land application, thus allowing the CAFO to utilize a mix of fields and crops different from the most likely or preferred combinations. Nevertheless, the NMP should reasonably forecast the practices most likely to be utilized by the CAFO. EPA solicits comment on the degree of flexibility that should be allowed in NMPs. Greater flexibility would minimize the need for subsequent permit revisions, but will also increase the up-front work load, both for the permittee and for the permitting authority, and provide the permitting authority and the public with less certainty as to which practices the CAFO will actually utilize. Even when a CAFO owner or operator develops an NMP that encompasses a significant degree of flexibility, it nevertheless may be necessary to revise the NMP during a CAFO's term of permit coverage. EPA believes that, due to the issues associated with agricultural operations and the variables associated with nutrient management planning, including seasonal variations, weather, soil and slope variation, and availability of feed, seed, and other resources, it is necessary to provide flexibility in the best management practice requirements for CAFOs beyond that typically available for other permit conditions. Consistent with this objective, EPA is proposing to establish specific protocols to allow changes to an NMP after permit coverage has been granted. EPA is proposing formal public notice and comment procedures that the permitting authority would be required to follow for permit modification when a CAFO is seeking to make substantial changes to its NMP. EPA is proposing that substantial changes would include, but are not limited to: (1) Changes that could result in an increase in runoff of manure, litter, or process wastewater from the facility; (2) an increase in the rate of nutrients from manure, litter, or process wastewater applied to the land application area that is significant in relation to technical standards established by the Director; (3) a significant change in the nutrient balance at the CAFO caused by: (i) An increase in the ratio of animals, manure, litter, or process wastewater to the available land application acreage or storage capacity; (ii) changes in the CAFO's procedures for handling, storage, treatment, or land application of manure, litter, or process wastewater; (iii) a significant increase in the number of animals; or (iv) a significant reduction of manure, litter, or process wastewater hauled off site when there is no equivalent decrease in the amount of manure, litter, or process wastewater produced; and (4) the addition of land application areas not previously included in the nutrient management plan. Specific examples of such changes would include changes to the method of land application from injection to surface application, changes in timing from spring to late fall or winter application, and installation of new drainage systems that would increase runoff from land application fields. The proposed new paragraph 40 CFR 122.42(e)(5)(iv) identifies what would constitute substantial changes to the facility's NMP that would trigger this process for permit revisions. For these types of changes, EPA is proposing to create new procedures in 40 CFR 122.42(e)(5) to allow CAFOs to change their nutrient management plans after the Director has incorporated the terms of the NMP into the permit. These procedures, which would be available to CAFOs operating under both individual and general permits, would be nearly identical to those for CAFOs seeking coverage in the first place. The Agency believes that such a process satisfies the need for the permitting authority and the public to have ample opportunity to review and comment on changes to a facility's NMP, while allowing the CAFO the flexibility it needs. In addition, there may be changes at a facility that were not contemplated in the currently applicable NMP that do not require substantial changes to the terms of the NMP in the permit. In these instances, while a revised NMP would need to be submitted to the Director, the Director should not need to seek public comment on the revised NMP. Such changes might include, for example, changes in cropping patterns not anticipated in the original NMP where they are managed consistent with the original plan and properly documented. In such instances, today's proposal would require the CAFO owner or operator to provide the revised NMP, along with appropriate documentation to reflect changed conditions, to the permitting authority. The better the documentation of the terms in the NMP, including calculations, the easier it will be for a permitted facility to demonstrate that changes in its nutrient management practices are non-substantial modifications of its NMP. Today's proposal (see proposed 40 CFR 122.42(e)(5)) would require that, whenever a CAFO makes any change to its NMP, the owner or operator would provide the Director with the revised NMP and identify the changes from the previous version submitted to the permitting authority. The Director would then review the changes to ensure that the NMP still meets the requirements of 40 CFR 122.42(e)(1)(i) through (x) and, for Large CAFOs, 40 CFR 412.4(c) and technical standards developed by the Director. If the changes are not substantial, the Director would simply modify the permit as necessary and notify the public of such modification (and not seek public comment). If the changes are substantial, the nutrient management plan would be revised using procedures similar to those proposed for the initial incorporation of an NMP into a general permit. Thus, today's proposed rule would require the Director to notify the public of substantial changes, and provide an opportunity for public notice and comment. Moreover, the appeals process would be the same as that for incorporation of NMPs into a general permit. EPA solicits comment on the approach proposed to deal with NMP revisions, as well as on the conditions concerning what constitutes a substantial change to an NMP. Because the process in 40 CFR 122.42(e)(5) would allow for public review of changes to the terms of nutrient management plans and the underlying data and calculations, EPA proposes that the incorporation of changes to the permit through this process would be treated as a minor permit modification, under § 122.63(h), and not require additional review. EPA considered requiring any change to the NMP to be considered a permit modification requiring procedures under § 122.62, but rejected this option as it would significantly burden permitting authorities and CAFO operators' ability to make necessary and timely minor changes to NMPs as discussed above. For substantial changes, the Agency also proposes to expressly allow the facility, at the Director's discretion, to proceed in implementing the change for up to 180 days before completion of public review and permitting authority approval, so long as the change is not likely to result in increased runoff of manure, litter or process wastewater from the facility. Given the importance of timing in farming, EPA recognizes that CAFOs may be unable to delay the implementation of a substantial change to their nutrient management plan to allow for public review and still implement the change in a timely fashion. EPA believes that it would be reasonable to allow the Director to temporarily allow substantial changes so long as certain conditions are met. First, the approval would be temporary, allowing the CAFO to implement the changes for only 180 days. Second, the facility would need to provide to the Director documentation to demonstrate that the change would not result in increased runoff of manure, litter, or process wastewater from the facility. Third, the Director would have to review the documentation and conclude that the changes would not result in increased runoff of manure, litter, or process wastewater from the facility. Finally, the Director would have to include such expedited decisions with the permit in the public record and notify the public of its decision. Moreover, by the end of the 180 day period, these changes would need to undergo the public review procedures required for all substantial changes and be incorporated into the CAFO's permit by the Director. Changes EPA intends to encompass within this provision include the addition of new fields for land application where the Director determines that such additional or replacement fields have equivalent phosphorous ratings (based on the Phosphorous Index, for example) for nutrient uptake as the fields they are supplementing or replacing, whichever may be the case. EPA is interested in commenters' views concerning this proposed provision. EPA specifically solicits comment on whether a change that would result in increased rates of land application of manure, litter, or process wastewater in addition to those changes likely to result in increased runoff, should also be precluded from expedited implementation during the 180 day period. EPA is also interested in taking comment on an approach that might allow greater flexibility for CAFO operators in making cropping decisions while assuring permitting authorities and the public that they are complying substantively with the terms of the NMP as incorporated into the permit, even if the CAFO modifies its practices somewhat from those articulated in the NMP and the permit. Under this approach, the Agency would modify the annual report requirements for permitted CAFOs in 40 CFR 122.42(e)(4) to require all CAFOs to submit information with the annual report indicating how the CAFO achieved substantive compliance with the terms of the NMP as set forth in the permit. If the CAFO implemented any cropping options not included in the calculations provided in the NMP, the CAFO would document the procedures and nutrient management practices utilized, including crops grown and fields planted, together with nutrient management calculations that governed its land application practices for the prior calendar year, and explain how the modified cropping options as implemented continued to comply with the substantive terms of the NMP incorporated into the permit. Under this option, EPA would include guidance in either rule or preamble text on which types of deviations from the NMP would be allowed, and what would be required to demonstrate in the annual report that these deviations substantively complied with the permit terms. The Agency solicits comment on whether such an approach would be practical and the extent to which it could allow greater flexibility for CAFOs to meet the NMP requirements incorporated into their permits, while still ensuring appropriate permitting authority and public oversight of permit compliance. (f) Required Dates In a separate rulemaking, EPA revised the dates in the 2003 CAFO rule by which CAFOs were required to develop and implement their NMPs. (71 FR 6978.) The 2003 CAFO rule required newly defined CAFOs to seek coverage under an NPDES permit by February 13, 2006, but required the development and implementation of a nutrient management plan by December 31, 2006. This would have conflicted with today's proposal that CAFOs submit their NMPs with their permit applications or notices of intent, as required by the Second Circuit Court's decision. The new rule requires CAFO owners and operators to submit their NMPs at the time of the permit application by extending the deadline for both to July 31, 2007. EPA extended these deadlines in a separate rulemaking so as to provide the Agency sufficient time to develop the regulatory revisions proposed in this rulemaking that more broadly respond to the Waterkeeper decision. C. Remand Concerning Water Quality Based Effluent Limitations Water quality-based effluent limitations (WQBELs) are one of two fundamental types of limitations imposed in NPDES permits. The other is technology-based limitations. Technology-based limitations are required in all NPDES permits, unless the permit writer imposes more stringent WQBELs in the permit where necessary to ensure that water quality standards are attained in the receiving waters. (See CWA Section 301(b)(1)(c), 33 U.S.C. 1311(b)(1)(c), and 40 CFR 122.44(d).) Where WQBELs are necessary, the permit writer establishes them without consideration of the availability or effectiveness of treatment technologies or the costs that dischargers would incur to meet those water quality-based limits. ( See Arkansas v. Oklahoma , 112 S.Ct. 1046, 1054 (1992); Westvaco v. EPA , 899 F.2d 1383 (4th Cir. 1990).) The environmental petitioners claimed that the 2003 CAFO rule violated both the Clean Water Act and the Administrative Procedure Act because it failed to promulgate WQBELs for CAFO discharges and also barred States from doing so. The Second Circuit agreed in part with this claim, as described in Section II.D.3 above, and remanded this issue to EPA for further clarification. The terms of the 2003 CAFO rule itself do not contain any requirements concerning WQBELs, but EPA addressed the subject of WQBELs in the preamble. In fact, there was only one WQBELs issue that EPA addressed or intended to address in the preamble—whether WQBELs can be imposed for land application discharges of agricultural stormwater—and on that issue, the court expressly agreed with EPA's discussion. What appears to have troubled the court were certain statements in the preamble that the court thought might also address how WQBELs apply to other types of discharges. EPA therefore offers the following clarification. 1. The Application of WQBELs to CAFO Discharges Under the 2003 CAFO Rule How WQBELs apply to a CAFO's land application runoff is different from how they apply to discharges from a CAFO's production areas, as explained below. (a) Land Application Discharges In the 2003 rule, to determine how WQBELs apply to land application discharges at CAFOs, EPA first had to consider the statutory exclusion for agricultural stormwater. In the Clean Water Act, the definition of “point source” specifically includes CAFOs but excludes agricultural stormwater discharges. ( See CWA Section 502(14).) In the 2003 CAFO rule, EPA interpreted how this exclusion applies to discharges from land application at CAFOs. EPA found that where a CAFO applies manure, litter, or process wastewater to its fields, the resulting discharges from those fields are regulated by the Clean Water Act as point source discharges except where they qualify as agricultural stormwater. EPA determined that land application discharges qualify as agricultural stormwater only where 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). ( See 40 CFR 122.23(e).) Where a CAFO has not followed such practices, EPA concluded that any resulting precipitation-related discharge was not intended by Congress to be excluded from the Act as agricultural stormwater and is therefore subject to NPDES requirements. The land application requirements of the 2003 CAFO rule reflected this interpretation by EPA of the agricultural stormwater exclusion in the Act. EPA found that where a CAFO follows these practices, any and all precipitation-related discharges of manure, litter, or process wastewater that occur from land application fields would be covered by the agricultural stormwater exclusion and would thus be considered nonpoint source runoff. (68 FR 7198.) In other words, a CAFO that follows the requirements in the 2003 rule eliminates all precipitation-related point source discharges from its land application fields. While physically there may still be some runoff from the fields related to precipitation, the CAFO has no discharge of regulated precipitation-related runoff, since any remaining precipitation runoff is agricultural stormwater. Because the CAFO effluent guidelines—the technology-based regulations —already prohibit all precipitation-related land application discharges that are subject to regulation, EPA noted in the 2003 rule that it is not possible for a CAFO permit writer to add any other permit limitations on these discharges that are more stringent than the CAFO effluent guidelines, including any water quality-based limitations. ( See 68 FR at 7198.) Only discharges of agricultural stormwater, which are nonpoint source discharges, remain. The Second Circuit agreed that the rule “does not present a problem to the extent that [it] fails to promulgate—and bars States from promulgating—WQBELs for any ‘agricultural stormwater discharge’ * * * Agricultural storm water discharges are, after all, statutorily exempt from any effluent limitations, including WQBELs, because they are non-point source discharges.” Waterkeeper, 399 F.3d at 522. It should be noted that the key point of this discussion—that water quality-based effluent limits are not available to limit land application discharges that are agricultural stormwater—involves, in the first instance, only precipitation-related land application discharges, since only precipitation-related discharges can be agricultural stormwater. Water quality-based effluent limits are available to the permit writer to limit any non-precipitation related ( i.e. , dry-weather) discharges that occur at land application areas to levels that are more stringent than the technology-based limitations (effluent guidelines), and EPA never intended to indicate otherwise. As EPA stated in the 2003 rule, “any dry weather discharge of manure or process wastewater resulting from its application to land area under the control of a CAFO would not be considered an agricultural stormwater discharge and would thus be subject to Clean Water Act requirements.” 68 FR 7198. To be sure, in most instances, a CAFO's requirement to meet technology-based permit limits that require manure to be applied at appropriate agronomic rates should itself eliminate all or most dry weather discharges. Nevertheless, if such discharges remain, the need for additional water quality-based effluent limits to control them will be determined by the permit writer based on the circumstances of each particular case. (b) Production Area Discharges In contrast to precipitation-related land application discharges, under the 2003 rule, WQBELs can be applied by permit writers in appropriate cases to further limit discharges from CAFO production areas (except for new source CAFOs in the swine and poultry sectors, as discussed below). WQBELs can be imposed on these production area discharges, where appropriate, because the effluent guidelines do not, by themselves, prohibit all “regulatable” discharges from the production area. The effluent guidelines allow occasional overflow discharges from properly designed, operated, and maintained lagoons and storage ponds. It is possible that WQBELs might be necessary in a particular permit to further limit these discharges beyond the levels that are authorized under the CAFO effluent guidelines. It should also be noted that the exclusion for agricultural stormwater does not apply to discharges from the CAFO production area, as EPA stated in the 2003 rule. ( See 40 CFR 122.23(e) and 68 FR 7198). Thus, the agricultural stormwater exclusion does not serve to limit how WQBELs may be imposed to control production area discharges. For new source CAFOs in the swine and poultry sectors, however, no WQBELs can be imposed in permits for the production areas. This is because the effluent guidelines already prohibit all production area discharges from these new sources. ( See 40 CFR 412.46(a).) 2. Discussion The Second Circuit expressed two concerns with EPA's discussion of how WQBELs apply at CAFOs. First, the court found that it was “unclear * * * why the CAFO Rule exempts discharges other than agricultural storm water discharges from WQBELs.” (See 399 F.3d at 522.) EPA had indicated its intention, the court found, “not to promulgate any WQBELs whatsoever.” As an initial matter, WQBELs for CAFOs are derived, where appropriate, on a case-by-case basis for individual permits, not promulgated in EPA regulations. EPA never intended to “promulgate” any WQBELs in the 2003 rule, but simply to discuss how WQBELs might apply once a CAFO applied for a permit. Specifically, the court was concerned by EPA's preamble statement that “EPA does not expect that water quality-based effluent limitations will be established for CAFO discharges resulting from the land application of manure, litter, or process wastewater.” 399 F.3d at 522, citing 68 FR 7207. The court may have been concerned that EPA was exempting from the application of WQBELs not only agricultural stormwater discharges from CAFO land application areas (which the court agreed are not subject to WQBELs) but also any other discharges from land application areas or even production areas. (See 399 F.3d at 522 (“EPA has * * * only justified its determination not to impose WQBELs * * * only insofar as agricultural stormwater discharges are concerned * * * The EPA has not attempted, in any way, to explain its failure to promulgate WQBELs for CAFO discharges other than agricultural stormwater discharges * * *”).) This was not EPA's intent. EPA intended only to affirm that where the precipitation-related discharge from land application areas has been limited to only agricultural stormwater, WQBELs are not available as further limitations on those discharges. Based on its understanding, the court directed EPA “to explain whether or not, and why, WQBELs are needed to assure that CAFO discharges will not ‘interfere with the attainment or maintenance of that water quality in a specific portion of the navigable waters which shall assure protection of public health, public water supplies, agricultural and industrial uses, and the protection and propagation of a balanced population of shellfish, fish and wildlife, and allow recreational activities in and on the water,’ ” citing 33 U.S.C. 1312(a). 399 F.3d at 523. In response, EPA clarifies that WQBELs are not available for permits with respect to precipitation-related land application discharges for CAFOs. However, water quality-based effluent limits can be included in permits as necessary with respect to non-precipitation-related land application discharges and with respect to production area discharges, as discussed above. For example, with respect to production area discharges, under the effluent guidelines, a CAFO may be subject to a permit requirement that allows production area discharges only if the CAFO designs and operates its lagoon or pond to contain all process wastewater plus any storm water runoff resulting from the 25-year, 24-hour storm. But water quality considerations may lead the permit writer to impose a more stringent permit requirement such as allowing discharges only if the lagoon or pond is designed and operated to contain water from an even bigger storm. The court's second concern was that the 2003 rule preamble was “ambiguous about whether States may promulgate WQBELs for discharges other than agricultural stormwater discharges.” 399 F.3d at 523. The court directed EPA to explain this issue more clearly on remand. In response, the reasoning described above applies to State-issued as well as EPA-issued NPDES permits. Permit writers in NPDES-authorized States can include WQBELs as necessary with respect to non-precipitation-related land application discharges and with respect to production area discharges. There are two additional considerations, however, with respect to State-issued permits. First, the effluent guidelines require CAFOs to limit their land application of wastes to levels that comport with State technical standards for manure management. In the 2003 rule preamble, EPA encouraged States to address water quality protection issues in setting those technical standards for appropriate land application practices. ( See 399 F.3d at 523, citing 68 FR 7198). Thus, although the effluent guidelines are by their nature technology-based, EPA encouraged the States to address water quality concerns in setting their technical standards for manure management. But this does not change the basic regulatory scheme under which, once those technology-based standards are applied in a permit, the only remaining precipitation-related runoff is agricultural stormwater, for which water quality-based effluent limitations are not available. Second, it is possible that a State can have additional requirements under its own State regulatory authorities that would go beyond the requirements of the federal NPDES program. Thus, where the only runoff from a CAFO's land application area is agricultural stormwater, that remaining runoff, though not subject to further NPDES regulation, could be subject to additional State requirements that are broader in scope, including additional requirements related to water quality. 33 U.S.C. 1370 and 40 CFR 123.1 and 123.25. These requirements, however, would not be federally enforceable. D. New Source Performance Standards for Subpart D Facilities 1. Provisions in the 2003 CAFO Rule (a) 100-Year, 24-Hour Rainfall Event Design Standards The Clean Water Act requires EPA to promulgate New Source Performance Standards (NSPS) for new, as opposed to already existing, sources of pollution. ( See 33 U.S.C. 1316.) The Act provides that these standards must “reflect the greatest degree of effluent reduction which the Administrator determines to be achievable through application of the best available demonstrated control technology, processes, operating methods, or other alternatives, including, where practicable, a standard permitting no discharge of pollutants.” 33 U.S.C. 1316(a)(1). The Act further requires that EPA “take into consideration the cost of achieving such effluent reduction, and any non-water quality, environmental impact and energy requirements.” 33 U.S.C. 1316(b)(1)(B). EPA is given considerable discretion to weigh and balance the various factors required by statute to set NSPS. Riverkeeper, Inc. v. EPA, 358 F. 3d 174, 195 (2d Cir. 2004). The 2003 CAFO rule effluent guidelines for new Subpart D (swine, poultry, and veal) operations prohibit the discharge of any pollutants from CAFO production areas. It is common for new poultry, veal, and swine operations to confine the animals so that they are never exposed to rainfall or storm water runoff. In addition, many new operations employ manure handling systems that greatly reduce or eliminate the use of water as a conveyance or handling mechanism for the manure, and typically contain manure in covered or indoor facilities. ( See 68 FR 7219 and Chapter 8 of the “Technical Development Document for the Final Revisions to the National Pollutant Discharge Elimination System Regulation and the Effluent Guidelines for Concentrated Animal Feeding Operations” (EPA-821-R-03-001) or “TDD” for more information.) Based on these technologies, EPA determined that a no discharge standard was technologically feasible. EPA recognized that CAFOs may use different technologies to meet the no discharge standard and that these technologies may have slightly different vulnerabilities to extreme weather events. Therefore, the 2003 CAFO rule would have allowed CAFOs to meet the no discharge standard by using waste management and storage facilities designed, constructed, operated, and maintained to contain all manure and process wastewater including the runoff and precipitation from a 100-year, 24-hour rainfall event. 3 The 100-year, 24-hour rainfall event is a statistical event defined as the amount of rainfall that has a one percent chance of being exceeded in a 24-hour period in any given year. Thus, a facility that was adequate to contain both the process wastewater generated at the facility and the runoff and precipitation from the 100-year event would not discharge in circumstances resulting in runoff and precipitation less than that produced in the 100-year event, when properly operated and maintained. EPA provided the 100-year, 24-hour rainfall event criteria to provide clarity to the regulated community about how to design, operate and maintain their manure handling systems to achieve the no discharge standard. 3 All storage structures must be operated in accordance with the additional measures specified in the regulations at 40 CFR 412.37(a) and (b). (b) Superior Alternative Performance Standards The 2003 CAFO rule also allows existing CAFOs in Subparts C and D, and new beef, dairy, and heifer CAFOs to voluntarily participate in the Voluntary Alternative Performance Standards program. The alternative performance provisions allow CAFOs to request that the Director establish alternate permit effluent limitations in place of the 25-year, 24-hour storm standard that would otherwise apply. This provision enables CAFOs to implement new technologies and management practices that perform as well as or better than the baseline effluent guidelines at reducing pollutant discharges to surface waters from the production area. To demonstrate that an alternative control technology would achieve equivalent or better pollutant reductions than the baseline effluent guidelines, the CAFO must submit a technical analysis, which first calculates the pollutant discharges based on the site-specific modeled performance of a system designed to comply with the baseline effluent guidelines and then demonstrates that the proposed alternate limitations would result in equal or lower discharges. The minimum specific components of the technical analysis were included in the ELGs at 40 CFR 412.31(a)(2). For new Large swine, poultry, and veal CAFOs (new sources under Subpart D), the 2003 rule had a similar provision for alternative permit limitations—the “Voluntary Superior Environmental Performance Standards” provision. This NSPS provision empowered permitting authorities to establish site-specific alternative performance standards that allow production area discharges, so long as such discharges were accompanied by reductions of pollutant discharges to other media. ( See 40 CFR 412.46(d).) Specifically, the quantity of pollutants discharged from the production area had to be accompanied by an equivalent or greater reduction in the quantity of pollutants released to other media from the production area ( e.g. , air emissions from housing and storage), the land application areas for all manure, litter, and process wastewater at on-site and off-site locations, or both. The Director was given the discretion to request supporting information to supplement such a request. 2. Summary of the Second Circuit Court Decision Concerning Remanded Issues The Second Circuit Court of Appeals remanded several elements of the 2003 CAFO rule related to new sources. Specifically, the court directed EPA to clarify the statutory and evidentiary basis for allowing subpart D CAFOs to comply with the NSPS requirements by either the 100-year storm standard or the alternative performance standards. With respect to the 100-year storm standard, the Court noted that while certain studies showed that the production area BMPs adopted by the 2003 CAFO rule would have substantially prevented the production area discharges documented in the record, the court explicitly stated that substantially preventing discharges is not the same as prohibiting them outright. With respect to the alternative performance standards, the court held that EPA had not justified its decision to allow compliance with the no discharge standard through an alternative standard permitting production area discharges so long as the aggregate pollution to all media is equivalent to or lower than that resulting from the baseline standards. The court further held that EPA did not provide adequate notice for either of these provisions under the Clean Water Act's public participation requirements. ( See 33 U.S.C. 1251(e) (“Public participation in the development, revision, and enforcement of any regulation, standard, effluent limitation, plan, or program established by the Administrator or any State under this Act shall be provided for, encouraged, and assisted by the Administrator and the States”).) 3. This Proposal (a) 100-Year Storm Containment Structure EPA has reconsidered the NSPS in light of the Second Circuit decision. As a result of its review, EPA is proposing to delete 40 CFR 412.46(a)(1), the provision allowing CAFOs to meet the no discharge standard through the use of a 100-year, 24-hour rain event containment structure. If EPA adopts this change, all discharge of manure, litter, and process wastewater would be prohibited from the production area for new source swine, poultry, and veal calf operations. The land application requirements would remain unchanged. Regulatory language implementing the proposed change may be found in today's proposed rule text. As part of this approach, EPA also proposes to modify Section 412.37(a)(2) by removing the requirement that all surface liquid impoundments at new sources have a depth marker indicating the minimum capacity to contain the runoff and direct precipitation from a 100-year, 24-hour rain event. The removal of the 100-year storm containment structure provision for new sources makes this provision irrelevant. Although the Agency proposes to delete the 100-year, 24-hour depth marker requirement, EPA recognizes that a marker indicating depth can be an excellent means of displaying how much storage a CAFO has, and whether it is time to pump down levels in the lagoon or pond. EPA believes depth markers are a useful tool to help with the management of any facility, and proposes to maintain, in 412.37(a), the depth marker requirement in the rule, even though EPA removed the 100-year, 24 hour rainfall specification. EPA solicits comment on this provision of the ELGs. Additionally, EPA is proposing an alternative that would authorize the NPDES Program Director to establish no discharge best management practice effluent limitations based upon a site-specific evaluation for an individual CAFO. Compliance with such limitations would provide an alternate approach for CAFOs to meet the zero discharge requirement. Specifically, EPA is proposing to authorize permit writers, upon request by a CAFO, to establish best management, zero discharge effluent limitations on a case-by-case basis when a facility demonstrates through a rigorous modeling analysis that it has designed an open containment system that will comply with the no discharge requirements. If a facility has complied with all of the specified site-specific design, construction, operation, and maintenance components of such a system demonstrated to meet the zero discharge requirement, it would be deemed to be in compliance with the no discharge requirement even in the event of an unanticipated discharge. EPA continues to recognize that CAFOs m [Text truncated at 120,000 characters. The full text is on the page linked above.] --- Source: Frix Law Library, https://www.frixlaw.com/law-library/documents/fr%3A06-5773. Public record. Not legal advice.