rwilkins on PROD1PC63 with RULES_2

Thursday, 

November 20, 2008 

Part II 

Environmental 

Protection Agency 

40 CFR Parts 9, 122, and 412 

Revised National Pollutant Discharge 

Elimination System Permit Regulation and 

Effluent Limitations Guidelines for 

Concentrated Animal Feeding Operations 

in Response to the Waterkeeper Decision; 

Final Rule 

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70418 Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 

ENVIRONMENTAL PROTECTION 

AGENCY 

40 CFR Parts 9, 122, and 412 

[EPA–HQ–OW–2005–0037; FRL–8738–9] 

RIN 2040–AE80 

Revised National Pollutant Discharge 

Elimination System Permit Regulation 

and Effluent Limitations Guidelines for 

Concentrated Animal Feeding 

Operations in Response to the 

Waterkeeper Decision 

AGENCY: Environmental Protection 


Agency (EPA). 


ACTION: Final rule. 


SUMMARY: Under the Federal Water 

Pollution Control Act (Clean Water Act 

or CWA), EPA is revising the National 

Pollutant Discharge Elimination System 

(NPDES) permitting requirements and 

Effluent Limitations Guidelines and 

Standards (ELGs) for concentrated 

animal feeding operations (CAFOs) in 

response to the order issued by the U.S. 

Court of Appeals for the Second Circuit 

in Waterkeeper Alliance et al. v. EPA, 

399 F.3d 486 (2d Cir. 2005). This final 

rule responds to the court order while 

furthering the statutory goal of restoring 

and maintaining the nation’s water 

quality by ensuring that CAFOs 

properly manage manure generated by 

their operations. 

This final rule revises several aspects 

of EPA’s current regulations governing 

discharges from CAFOs. EPA is 

modifying the requirement to apply for 

a permit by specifying that an owner or 

operator of a CAFO that discharges or 

proposes to discharge must apply for an 

NPDES permit. The final rule also 

includes an option for an unpermitted 

CAFO to certify to the permitting 

authority that the CAFO does not 

discharge or propose to discharge. In 

addition, EPA is clarifying how the 

agricultural stormwater discharge 

exemption criteria are interpreted for 

unpermitted Large CAFOs. EPA is also 

requiring CAFOs seeking permit 

coverage to submit their nutrient 

management plans (NMPs) with their 

applications for individual permits or 

notices of intent to be authorized under 

general permits. Permitting authorities 

are required to review the NMPs and 

provide the public with an opportunity 

for meaningful public review and 

comment. Permitting authorities are also 

required to incorporate terms of NMPs 

as NPDES permit conditions. 

Additionally, this action removes the 

provision that allowed CAFOs to use a 

100-year, 24-hour containment structure 

to fulfill the no discharge requirement 

for new source swine, poultry, and veal 

calf operations. Instead, this action 

authorizes permit writers, upon request 

by swine, poultry, and veal calf CAFOs 

that are new sources, to establish best 

management practice no discharge 

effluent limitations when the facility 

demonstrates that it has designed an 

open containment system that will 

comply with the no discharge 

requirements. 

This final rule also responds to the 

court’s remand orders regarding water 

quality-based effluent limitations 

(WQBELs) and pathogens. EPA is 

clarifying that WQBELs may be required 

in permits with respect to production 

area discharges and discharges from 

land application areas that are not 

exempt as agricultural stormwater. 

Finally, EPA is making the finding that 

the best conventional technology (BCT) 

limitations established in 2003 also 

apply to fecal coliform. 

DATES: These final regulations are 

effective December 22, 2008. For 

judicial review purposes, this final rule 

is promulgated as of 1 p.m. Eastern 

Daylight Time, on December 4, 2008, as 

provided in 40 CFR 23.2. 

ADDRESSES: The record for this 

rulemaking is available for inspection 

and copying at the Water Docket, 

located at the EPA Docket Center (EPA/ 

DC), EPA West 1301 Constitution Ave., 

NW., Washington, DC 20004. The record 

is also available via EPA Dockets at 

http://www.regulations.gov under 

docket number OW–2005–0037. The 

rule and key supporting documents are 

also available electronically on the 

Internet at http://www.epa.gov/npdes/ 

caforule. 

FOR FURTHER INFORMATION CONTACT: For 

additional information contact Rebecca 

Roose, Water Permits Division, Office of 

Wastewater Management (4203M), 

Environmental Protection Agency, 1200 

Pennsylvania Ave., NW., Washington, 

DC 20460, telephone number: (202) 

564–0758, e-mail address: 

roose.rebecca@epa.gov. For additional 

information specific to New Source 

Performance Standards and BCT 

Limitations contact Paul Shriner, 

Engineering and Analysis Division, 

Office of Science and Technology 

(4303T), Environmental Protection 

Agency, 1200 Pennsylvania Ave., NW., 

Washington, DC 20460, telephone 

number: (202) 566–1076, e-mail address: 

shriner.paul@epa.gov. 

SUPPLEMENTARY INFORMATION: 

I. General Information 

A. Does This Action Apply to Me? 

B. How Can I Get Copies of This Document 

and Other Related Information? 

C. Under What Legal Authority Is this 


Final Rule Issued? 


D. What Is the Comment Response 


Document? 


II. Background 

A. The Clean Water Act 

B. History of Actions To Address CAFOs 

Under the NPDES Permitting Program 

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

the Second Circuit 

D. What Requirements Still Apply to 


CAFOs? 


E. EPA’s Response to the Waterkeeper 


Decision 


III. The Final Rule: Revisions to the 2003 

CAFO Rule in Response to Waterkeeper 

A. Duty to Apply for a Permit 

B. Agricultural Stormwater Exemption 

C. Nutrient Management Plans 

D. Compliance Dates 

E. Water Quality-Based Effluent 


Limitations 


F. New Source Performance Standards for 

Subpart D Facilities 

G. BCT Limitations for Fecal Coliform 

IV. Impact Analysis 

A. Environmental Impacts 

B. Administrative Burden Impacts 

C. Response to Public Comment on the 

Proposal 

V. Cross-Media Considerations and 

Pathogens 

A. Cross-Media Approaches 

B. Pathogens and Animal Feeding 


Operations 


VI. Statutory and Executive Order Reviews 

A. Executive Order 12866: Regulatory 


Planning and Review 


B. Paperwork Reduction Act 

C. Regulatory Flexibility Act 

D. Unfunded Mandates Reform Act 

E. Executive Order 13132: Federalism 

F. Executive Order 13175: Consultation 

and Coordination With Indian Tribal 

Governments 

G. Executive Order 13045: Protection of 

Children From Environmental Health 

and Safety Risks 

H. Executive Order 13211: Actions 


Concerning Regulations That 


Significantly Affect Energy Supply, 


Distribution, or Use 


I. National Technology Transfer and 


Advancement Act 


J. Congressional Review Act 

I. General Information 

A. Does This Action Apply to Me? 

This action applies to concentrated 

animal feeding operations (CAFOs) as 

specified in section 502(14) of the Clean 

Water Act (CWA), 33 U.S.C. 1362(14) 

and defined in the NPDES regulations at 

40 CFR 122.23. Table 1.1 provides a list 

of standard industrial codes for 

operations potentially regulated under 

this revised rule. The rule also applies 

to States and Tribes with authorized 

NPDES Programs. 

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Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 70419 

TABLE 1.1—OPERATIONS POTENTIALLY REGULATED BY THIS RULE 

Category Examples of regulated entities 

North American 

Industry Classification System 

(NAICS) 

Standard Industrial Classification 

(SIC) 

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

Beef cattle feedlots (including veal calves) ......................................................... 112112 0211 

Beef cattle ranching and farming ......................................................................... 112111 0212 

Hogs ..................................................................................................................... 11221 0213 

Sheep and Goats ................................................................................................. 11241, 11242 0214 

General livestock except dairy and poultry .......................................................... 11299 0219 

Dairy farms ........................................................................................................... 11212 0241 

Broilers, fryers, and roaster chickens .................................................................. 11232 0251 

Chicken eggs ....................................................................................................... 11231 0252 

Turkey and turkey eggs ....................................................................................... 11233 0253 

Poultry hatcheries ................................................................................................ 11234 0254 

Poultry and eggs .................................................................................................. 11239 0259 

Ducks ................................................................................................................... 11239 0259 

Horses and other equines .................................................................................... 11292 0272 

This table is not intended to be 

exhaustive, but rather provides a guide 

for readers regarding entities likely to be 

regulated by this action. This table lists 

the types of entities that EPA is now 

aware could potentially be regulated by 

this action. Other types of entities not 

listed in the table could also be 

regulated. To determine whether your 

facility is regulated under this 

rulemaking, you should carefully 

examine the applicability criteria in 

§ 122.23. If you have questions 

regarding the applicability of this action 

to a particular entity, consult the person 

listed in the preceding FOR FURTHER 

INFORMATION CONTACT section. 

B. How Can I Get Copies of This 

Document and Other Related 

Information? 

1. Docket. EPA has established an 

official public docket for this action 

under Docket ID No. EPA–HQ–OW– 

2005–0037. The official public docket 

consists of the documents specifically 

referenced in this action, any public 

comments received, and other 

information related to this action. 

Although listed in the index, some 

information is not publicly available, 

e.g., Confidential Business Information 

(CBI) or other information whose 

disclosure is restricted by statute. 

Certain other material, such as 

copyrighted material, will be publicly 

available only in hard copy. Publicly 

available docket materials are available 

either electronically in 

www.regulations.gov or in hard copy at 

the Water Docket in the EPA Docket 

Center, EPA West, 1301 Constitution 

Ave., NW., Washington, DC. The Public 

Reading Room is open from 8:30 a.m. to 

4:30 p.m., Monday through Friday, 

excluding legal holidays. The telephone 

number for the Public Reading Room is 

(202) 566–1744, and the telephone 

number for the Water Docket is (202) 

566–2426. 

2. Electronic Access. This Federal 

Register document and key supporting 

documents are also electronically 

available on the Internet at http:// 

www.epa.gov/npdes/agriculture. 

C. Under What Legal Authority Is This 

Final Rule Issued? 

This final rule is issued under the 

authority of sections 101, 301, 304, 306, 

308, 402, and 501 of the CWA. 33 U.S.C. 

1251, 1311, 1314, 1316, 1317, 1318, 

1342, and 1361. 

D. What Is the Comment Response 

Document? 

EPA received a large number of 

comments on the 2006 proposed rule 

(71 FR 37,744–87; June 20, 2006) and 

the 2008 supplemental proposal (73 FR 

12,321–40; March 7, 2008). EPA 

evaluated all of the comments submitted 

and prepared a Comment Response 

Document containing both the 

comments received and the Agency’s 

responses to those comments. The 

Comment Response Document 

complements and supplements this 

preamble by providing more detailed 

explanations of EPA’s final action. The 

Comment Response Document is 

available in the Docket. 

II. Background 

A. The Clean Water Act 

Congress enacted the Federal Water 

Pollution Control Act (1972), also 

known as the Clean Water Act (CWA), 

to ‘‘restore and maintain the chemical, 

physical, and biological integrity of the 

nation’s waters’’ (CWA section 101(a)). 

Among the core provisions, the CWA 

establishes the NPDES permit program 

to authorize and regulate the discharge 

of pollutants from point sources to 

waters of the U.S. (CWA section 402). 

Section 502(14) of the CWA specifically 

includes CAFOs in the definition of the 

term ‘‘point source.’’ Section 502(12) 

defines the term ‘‘discharge of a 

pollutant’’ to mean ‘‘any addition of any 

pollutant to navigable waters from any 

point source’’ (emphasis added). EPA 

has issued comprehensive regulations 

that implement the NPDES program at 

40 CFR part 122. The Act also provides 

for the development of technologybased and water quality-based effluent 

limitations that are imposed through 

NPDES permits to control the discharge 

of pollutants from point sources. CWA 

sections 301(a) and (b). 

B. History of Actions To Address CAFOs 

Under the NPDES Permitting Program 

EPA began regulating discharges of 

wastewater and manure from CAFOs in 

the 1970s. EPA initially issued national 

effluent limitations guidelines and 

standards for feedlots on February 14, 

1974 (39 FR 5704), and NPDES CAFO 

regulations on March 18, 1976 (41 FR 

11,458). 

In February 2003, EPA issued 

revisions to these regulations that 

focused on the 5% of the nation’s 

animal feeding operations (AFOs) that 

presented the highest risk of impairing 

water quality and public health (68 FR 

7176–7274; February 12, 2003) (‘‘the 

2003 CAFO rule’’). The 2003 CAFO rule 

required the owners or operators of all 

CAFOs1 to seek coverage under an 

NPDES permit, unless they 

demonstrated no potential to discharge. 

1 The Clean Water Act regulates the conduct of 

persons, which includes the owners and operators 

of CAFOs, rather than the facilities or their 

discharges. To improve readability in this preamble, 

reference is made to ‘‘CAFOs’’ as well as ‘‘owners’’ 

and ‘‘operators’’ of CAFOs. No change in meaning 

is intended. 

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70420 Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 

A number of CAFO industry 

organizations (American Farm Bureau 

Federation, National Pork Producers 

Council, National Chicken Council, and 

National Turkey Federation (NTF), 

although NTF later withdrew its 

petition) and several environmental 

groups (Waterkeeper Alliance, Natural 

Resources Defense Council, Sierra Club, 

and American Littoral Society) filed 

petitions for judicial review of certain 

aspects of the 2003 CAFO rule. This 

case was brought before the U.S. Court 

of Appeals for the Second Circuit. On 

February 28, 2005, the court ruled on 

these petitions and upheld most 

provisions of the 2003 rule but vacated 

and remanded others. Waterkeeper 

Alliance, et al. v. EPA, 399 F.3d 486 (2d 

Cir. 2005). The court’s decision is 

described in detail below. 

The revisions to the 2003 CAFO rule 

being published today relate directly to 

the changes required by the court’s 

decision and continue to maintain the 

focus on regulating discharges from the 

universe of high-risk AFOs. 

C. Ruling by the U.S. Court of Appeals 

for the Second Circuit 

The Second Circuit’s decision in 

Waterkeeper upheld certain challenged 

provisions of the 2003 rule and vacated 

or remanded others, as follows. 

1. Issues Upheld by the Court 

This section discusses provisions of 

the 2003 CAFO rule that were 

challenged by either industry or 

environmental petitioners, but were 

upheld by the Waterkeeper Court and 

therefore remain unchanged. EPA is not 

revising any of these provisions and did 

not solicit comment on them. 

(a) Land Application Regulatory 

Framework and Interpretation of 

‘‘Agricultural Stormwater’’ 

The Waterkeeper Court upheld EPA’s 

authority to regulate, through NPDES 

permits, the discharge of manure, litter, 

or process wastewater that a CAFO 

applies to its land application area. The 

court rejected the industry petitioners’ 

claim that land application runoff must 

be channelized before it can be 

considered to be a point source 

discharge subject to permitting. The 

court noted that the CWA expressly 

defines the term ‘‘point source’’ to 

include ‘‘any * * * concentrated 

animal feeding operation * * * from 

which pollutants are or may be 

discharged,’’ and found that the Act 

‘‘not only permits, but demands’’ that 

land application discharges be 

construed as discharges ‘‘from’’ a CAFO. 

399 F.3d at 510. 

The Waterkeeper Court also upheld 

EPA’s determination in the 2003 CAFO 

rule that precipitation-related 

discharges of manure, litter, or process 

wastewater from land application areas 

under the control of a CAFO qualify as 

‘‘agricultural stormwater’’ only where 

the CAFO has applied the manure in 

accordance with nutrient management 

practices that ensure ‘‘appropriate 

agricultural utilization’’ of the manure, 

litter, or process wastewater nutrients. 

EPA’s interpretation of the Act in this 

regard was reasonable, the court found, 

in light of Congressional intent in 

excluding agricultural stormwater from 

the meaning of the term ‘‘point source’’ 

and given the precedent set in an earlier 

Second Circuit case, Concerned Area 

Residents for the Environment v. 

Southview Farm, 34 F.3d 114 (2d Cir. 

1994). 399 F.3d at 508–09. 

(b) Effluent Guidelines 

The court rejected the environmental 

organizations’ claim that EPA, in 

developing best available technology 

effluent limitations guidelines, had 

failed to consider the single best 

performing CAFO and adopt limitations 

that reflected its performance. The court 

found that EPA had collected extensive 

data on the waste management systems 

at CAFOs and had considered 

approximately 11,000 public comments 

on the proposed CAFO rule. The court 

determined that EPA had either adopted 

as the basis for its limitations the best 

performing technology or declined to do 

so for permissible reasons. 399 F.3d at 

513. 

The court upheld EPA’s decision in 

the 2003 rule relating to groundwater 

controls. In the 2003 rule, EPA stated 

that the Agency believed that 

requirements limiting the discharge of 

pollutants to surface water via 

groundwater that has a direct hydrologic 

connection to surface water should be 

addressed on a site-specific basis. The 

Agency also stated that nothing in the 

2003 rule was to be construed to 

expand, diminish, or otherwise affect 

the jurisdiction of the CWA over 

discharges to surface water via 

groundwater that has a direct hydrologic 

connection to surface water. 399 F.3d at 

514–15. 

The court upheld the analytic 

methodologies that EPA used for 

determining whether the technologybased permit requirements for CAFOs 

set in the 2003 rule would be 

economically achievable by the industry 

as a whole. 399 F.3d at 515–18. 

2. Issues Vacated by the Court 

The following are the elements of the 

2003 rule that the Waterkeeper Court 

found to be unlawful and therefore 

vacated. 

(a) Duty To Apply 

The CAFO industry organizations 

argued that EPA exceeded its statutory 

authority by requiring all CAFOs to 

either apply for NPDES permits or 

demonstrate that they have no potential 

to discharge. The court agreed with the 

CAFO industry petitioners on this issue 

and therefore vacated the ‘‘duty to 

apply’’ provision of the 2003 CAFO 

rule. 

The court found that the duty to 

apply, based on the potential to 

discharge, was invalid because the CWA 

subjects only actual discharges to 

permitting requirements rather than 

potential discharges. The court 

acknowledged EPA’s policy 

considerations for seeking to impose a 

duty to apply based on the potential to 

discharge but found that the Agency 

lacked statutory authority to do so. 399 

F.3d at 505. 

(b) Nutrient Management Plans (NMPs) 

The court concluded that the 2003 

CAFO rule impermissibly: (1) 

Empowered permitting authorities to 

issue permits without any meaningful 

review of a CAFO’s NMP, (2) failed to 

require that the terms of the nutrient 

management plan be included as 

effluent limitations in the NPDES 

permit, and (3) violated the CWA’s 

public participation requirements. The 

court agreed with the environmental 

petitioners on these three issues. 

The court relied on provisions of the 

Act that authorize point source 

discharges only where NPDES permits 

‘‘ensure that every discharge of 

pollutants will comply with all 

applicable effluent limitations and 

standards,’’ citing CWA sections 

402(a)(1), (a)(2), and (b). Because the 

2003 CAFO rule did not provide for 

permitting authority review of a CAFO’s 

nutrient management plan before the 

permit was issued, the court found that 

the rule did not ensure that each 

CAFO’s discharges comply with these 

CWA provisions. The court also found 

that the terms of the NMP themselves 

are ‘‘effluent limitations’’ as that term is 

defined in the Act and therefore must be 

made part of the permit and be 

enforceable as required under CWA 

sections 301 and 402. The court also 

held that as effluent limitations, those 

terms must be made available for public 

review. 399 F.3d at 499–502. 

3. Issues Remanded by the Court 

The Waterkeeper Court also remanded 

other aspects of the CAFO rule to EPA 

‘‘for further clarification and analysis.’’ 

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Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 70421 

(a) Water Quality-Based Effluent Limits 

The court agreed with EPA that 

agricultural stormwater is excluded 

from the meaning of the term ‘‘point 

source’’ and therefore is not subject to 

water quality-based effluent limitations 

in permits. However, the court directed 

EPA to ‘‘clarify the statutory and 

evidentiary basis for failing to 

promulgate water quality-based effluent 

limitations for discharges other than 

agricultural stormwater discharges as 

that term is defined in 40 CFR 

122.23(e),’’ and to ‘‘clarify whether 

States may develop water quality-based 

effluent limitations on their own.’’ 399 

F.3d at 524. 

(b) New Source Performance 

Standards—100-Year Storm Standard 

The 2003 CAFO rule set new source 

performance standards (NSPS) for 

swine, poultry, and veal calf CAFOs at 

no discharge. A CAFO in these 

categories could fulfill this requirement 

by showing that either (1) its production 

area was designed to contain all 

manure, litter, or process wastewater, 

and precipitation from a 100-year, 24-

hour storm, or (2) it would comply with 

‘‘voluntary superior environmental 

performance standards’’ based on 

innovative technologies, under which a 

discharge from the production area 

would be allowed if it was accompanied 

by an equivalent or greater reduction in 

the quantity of pollutants released to 

other media (e.g., air emissions). The 

court found that EPA had neither 

justified in the record nor provided an 

adequate opportunity for public 

comment for either of these provisions. 

As a result, the court remanded these 

provisions to EPA to clarify, via a 

process that adequately involves the 

public, the statutory and evidentiary 

basis for them. 399 F.3d at 520–21. 

(c) BCT Effluent Guidelines for 

Pathogens 

The court held that the 2003 CAFO 

rule violated the CWA because EPA had 

not made an affirmative finding that the 

BCT-based Effluent Limitations 

Guidelines (ELGs), i.e., the ‘‘best 

conventional technology’’ guidelines for 

conventional pollutants such as fecal 

coliform, do in fact represent BCT for 

pathogens. The court remanded this 

issue to EPA for such a finding. 399 

F.3d at 519. 

D. What Requirements Still Apply to 

CAFOs? 

The Waterkeeper decision either 

upheld or did not address most 

provisions of the 2003 CAFO rule. This 

section describes certain key portions of 

the rule that were not challenged in 

Waterkeeper. These unchallenged 

provisions are addressed in this final 

rule only to provide background 

information and are not in any way 

reopened or affected by this rulemaking. 

The definitions provided in 40 CFR 

122.23(b) of the 2003 CAFO rule remain 

in effect and are unchanged. First, an 

operation must be defined as an animal 

feeding operation (AFO) before it can be 

defined as a concentrated animal 

feeding operation (CAFO). 40 CFR 

122.23. The term ‘‘animal feeding 

operation’’ is defined by EPA regulation 

as a ‘‘lot or facility’’ where animals 

‘‘have been, are or will be stabled or 

confined and fed or maintained for a 

total of 45 days or more in any 12 month 

period and crops, vegetation, forage 

growth, or post harvest residues are not 

sustained in the normal growing season 

over any portion of the lot or facility.’’ 

Whether an AFO is a CAFO depends 

primarily on the number of animals 

confined, which is also unchanged. 

Large CAFOs are AFOs that confine 

more than the threshold number of 

animals detailed in 40 CFR 122.23(b)(4). 

Medium CAFOs confine fewer animals 

than Large CAFOs and also: (1) 

Discharge pollutants into waters of the 

U.S. through a man-made ditch, 

flushing system, or other similar manmade device; or (2) discharge pollutants 

into waters of the U.S. which originate 

outside of and pass over, across, or 

through the facility or otherwise come 

into direct contact with the confined 

animals. 40 CFR 122.23(b)(6)(ii). The 

NPDES permitting authority also may, 

on a case-by-case basis, designate any 

medium or small AFO, as a CAFO after 

conducting an on-site inspection and 

finding that the facility ‘‘is a significant 

contributor of pollutants to waters of the 

United States.’’ 40 CFR 122.23(c). The 

permitting authority may not exercise 

its authority to designate a small AFO 

as a CAFO unless pollutants are 

discharged into waters of the U.S. 

through a man-made ditch, flushing 

system, or other similar man-made 

device, or are discharged into waters of 

the U.S. which originate outside of the 

facility and pass over, across, or through 

the facility or otherwise come into 

direct contact with the animals confined 

in the operation. 40 CFR 122.23(c)(3). 

As previously described, the court 

upheld EPA’s definition of ‘‘agricultural 

stormwater discharge’’ in relation to 

discharges from land application areas 

under the control of a CAFO in 40 CFR 

122.23(e). Discharges of manure, litter, 

or process wastewater from land 

application areas under the control of a 

CAFO are discharges from the CAFO 

(i.e., point source discharges) unless 

they are agricultural stormwater 

discharges, which are exempt from 

permit requirements. Section 122.23(e) 

provides that precipitation-related 

discharges of manure, litter, or process 

wastewater from a CAFO’s land 

application areas are agricultural 

stormwater discharges, provided that 

‘‘the manure, litter, or process 

wastewater has been applied in 

accordance with site-specific nutrient 

management practices that ensure 

appropriate agricultural utilization of 

the nutrients in the manure, litter, or 

process wastewater, as specified in 

§ 122.42(e)(1)(vi)–(ix).’’ 

The court ruling also did not affect 

the nutrient management planning 

requirements for permitted CAFOs 

established in the 2003 CAFO rule. All 

CAFOs that apply for permits must 

develop and implement an NMP that 

meets the requirements of 40 CFR 

122.42(e) and, for Large CAFOs subject 

to 40 CFR part 412, subpart C or D, 40 

CFR 412.4. The NMP identifies the 

necessary actions to ensure that runoff 

is eliminated or minimized through 

proper and effective manure, litter, or 

process wastewater management, 

including compliance with the ELGs as 

applicable. Permitted CAFOs must 

comply with all applicable 

recordkeeping and reporting 

requirements, including those specified 

in § 122.42(e). 

The court ruling also did not affect 

the ELG requirements for Large CAFOs, 

with the exception of new source 

performance standards (NSPS) for 

swine, poultry, and veal calf operations. 

ELG requirements ensure the 

appropriate storage of manure, litter, 

and process wastewater and proper land 

application practices. They vary 

depending upon the type of animals 

confined: Subpart A for horses and 

sheep; subpart B for ducks; subpart C for 

dairy cattle, heifers, steers, and bulls; 

and subpart D for swine, poultry, and 

veal calves. 40 CFR part 412. 

Additionally, NSPS for beef and dairy 

operations were not affected by the 

decision and remain unchanged (40 CFR 

412.35). 

Permitted small and medium CAFOs 

are not subject to the ELGs specified in 

part 412. Rather, they must comply with 

technology-based requirements 

developed by the permitting authority 

on a case-by-case basis (i.e., best 

professional judgment (BPJ)), pursuant 

to CWA section 402(a)(1)(B) and as 

defined in 40 CFR 125.3(c)(2) and (d). 

E. EPA’s Response to the Waterkeeper 

Decision 

On June 30, 2006, EPA published a 

proposed rule to revise the Agency’s 

regulations governing discharges from 

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70422 Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 

CAFO’s in response to the Waterkeeper 

decision. 71 FR 37,744. In summary, 

EPA proposed to require only owners or 

operators of those CAFOs that discharge 

or propose to discharge to seek 

authorization to discharge under a 

permit. Second, EPA proposed to 

require CAFOs seeking authorization to 

discharge under individual permits to 

submit their NMPs with their permit 

applications or, under general permits, 

with their notices of intent. Permitting 

authorities would be required to review 

the NMP and provide the public with an 

opportunity for meaningful public 

review and comment. Permitting 

authorities would also be required to 

incorporate terms of the NMP as NPDES 

permit requirements. Additionally, EPA 

proposed a process for modifying a 

CAFO’s NPDES permit to incorporate 

changes to the NMP during the permit 

term by designating permit 

modifications in accordance with that 

process to be ‘‘minor modifications of 

permits’’ under 40 CFR 122.63. The 

2006 proposed rule also addressed the 

remand of issues for further clarification 

and analysis. These issues concerned 

clarifications regarding the applicability 

of water quality-based effluent 

limitations (WQBELs) to CAFO 

discharges; NSPS for swine, poultry, 

and veal CAFOs; and BCT effluent 

limitations guidelines for fecal coliform. 

A March 7, 2008, Federal Register 

notice supplemented the 2006 proposed 

rule by proposing additional options 

considered by EPA for inclusion in this 

final rule in response to the Second 

Circuit’s decision in the Waterkeeper 

decision. In that notice, EPA proposed 

a voluntary option for a CAFO to certify 

that the CAFO does not discharge or 

propose to discharge based on an 

objective assessment of the CAFO’s 

design, construction, operation, and 

maintenance. EPA also proposed a 

framework for identifying the terms of 

the NMP and three alternative 

approaches for addressing rates of 

application of manure, litter, and 

process wastewater when identifying 

terms of the NMP to be included in the 

permit. In the 2008 supplemental 

proposal, EPA sought comment only on 

the issues presented in the 2008 

supplemental proposal. 

In addition to the changes made 

through this rulemaking, EPA extended 

certain deadlines in the NPDES 

permitting requirements and ELGs in 

two separate rulemakings in order to 

allow the Agency adequate time to 

complete this rulemaking in response to 

the Waterkeeper decision, in advance of 

those deadlines. The principal purpose 

of these rulemakings was to provide 

additional time for the Agency to 

complete this final rule. Neither of these 

date extension rules addressed any of 

the substantive issues addressed in this 

final rule or promulgated any provisions 

in response to the Waterkeeper decision. 

The first rule revised dates established 

in the 2003 CAFO rule by which 

facilities newly defined as CAFOs were 

required to seek permit coverage and by 

which all CAFOs were required to 

develop and implement nutrient 

management plans. 71 FR 6978–84 

(February 10, 2006). EPA extended the 

date by which operations defined as 

CAFOs as of April 14, 2003, that were 

not defined as CAFOs prior to that date, 

were required to seek NPDES permit 

coverage, from February 13, 2006, to 

July 31, 2007. EPA also amended the 

date by which operations that become 

defined as CAFOs after April 14, 2003, 

due to operational changes that would 

not have made them a CAFO prior to 

April 14, 2003, and that are not new 

sources, were required to seek NPDES 

permit coverage, from April 13, 2006, to 

July 31, 2007. Finally, EPA extended the 

deadline by which CAFOs were 

required to develop and implement 

nutrient management plans, from 

December 31, 2006, to July 31, 2007. 

That rulemaking revised all references 

to the date by which CAFOs must 

develop and implement NMPs as 

specified in the 2003 CAFO rule. 

As a result of the extensive array of 

public comments on the issues raised by 

the Waterkeeper decision, EPA was 

unable to complete this final rule prior 

to July 31, 2007. Thus, EPA published 

a second revision of the compliance 

dates on July 24, 2007, extending the 

dates from July 31, 2007, to February 27, 

2009. The preamble to the second date 

change rule explained EPA’s belief that 

the February 27, 2009, deadlines were 

appropriate because they would provide 

additional time for States, the regulated 

community, and other stakeholders to 

adjust to the new regulatory 

requirements. See 72 FR 40,245–50. In 

the 2008 supplemental rule, EPA 

requested comment on further 

extending the compliance deadline. For 

additional discussion of compliance 

dates, see section III.D of this preamble. 

III. The Final Rule: Revisions to the 

2003 CAFO Rule in Response to 

Waterkeeper 

This final rule responds to the Second 

Circuit Court’s vacature and remand 

orders. 

A. Duty To Apply for a Permit 

1. Provisions in the 2003 CAFO Rule 

(a) Duty To Apply 

The 2003 CAFO rule required all 

CAFOs to seek authorization to 

discharge under an NPDES permit 

unless the Director, i.e., the permitting 

authority, determined that the CAFO 

had no potential to discharge. 

(b) ‘‘No Potential To Discharge’’ 

Determination 

The 2003 CAFO rule included a 

process for CAFOs to seek a ‘‘no 

potential to discharge’’ determination by 

the Director. Where the Director 

determined, based on information 

supplied by the CAFO operator, that a 

CAFO had no potential to discharge 

manure, litter, or process wastewater to 

waters of the U.S., the CAFO operator 

had no duty to apply for a permit, 

unless circumstances at the facility 

changed such that the facility would 

have the potential to discharge. 

Examples of facilities that possibly 

would have qualified for this exemption 

included facilities in very arid areas, 

facilities that are down slope from 

waters of the U.S., and facilities with 

completely enclosed operations. 

2. Summary of the Second Circuit Court 

Decision 

The Second Circuit Court of Appeals 

vacated the provision that required all 

CAFO owners or operators with a 

potential to discharge to apply for an 

NPDES permit. The court held that the 

Clean Water Act (CWA) authorizes EPA 

to require permits for the actual 

discharge of pollutants, but not for mere 

potential discharges. Because the 2003 

CAFO rule imposed an obligation on all 

CAFOs to either apply for an NPDES 

permit or affirmatively demonstrate that 

they have no potential to discharge, the 

court ruled that it exceeded EPA’s 

authority under the CWA. Waterkeeper 

Alliance et al. v. EPA, 399 F.3d 486, 506 

(2d Cir. 2005). 

3. This Final Rule 

To address the court’s decision on the 

duty to apply, EPA is revising the 2003 

CAFO rule in three ways: 

• Deleting the requirement that all 

CAFOs apply for an NPDES permit to 

provide instead that all CAFOs that 

‘‘discharge or propose to discharge’’ 

have a duty to apply when they propose 

to discharge; 

• Eliminating the procedures for a no 

potential to discharge determination; 

and 

• Establishing a voluntary option for 

unpermitted CAFOs to certify that they 

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do not discharge or propose to 

discharge. 

(a) Duty To Seek Permit Coverage 

EPA proposed to replace the ‘‘duty to 

apply’’ requirement adopted in the 2003 

rule, which states that all CAFO owners 

or operators must seek coverage under 

an NPDES permit unless they 

demonstrate ‘‘no potential to discharge’’ 

(40 CFR 122.21(a)(1) and 40 CFR 

122.23(a) and 40 CFR 122.23(d)(1)) with 

a modified ‘‘duty to apply’’ provision. 

The 2006 proposed rule would have 

required that all CAFOs that ‘‘discharge 

or propose to discharge’’ seek coverage 

under an NPDES permit, which is the 

same language that applies generally to 

point sources under longstanding 

NPDES regulations at § 122.21(a)(1). 

This rule adopts the approach in the 

2006 proposed rule by replacing the 

‘‘duty to apply’’ requirement of the 2003 

rule with a requirement that a CAFO 

that ‘‘discharges or proposes to 

discharge’’ must seek authorization to 

discharge under an NPDES permit. 

Because a number of commenters 

misunderstood, or were confused by, 

the term ‘‘propose to discharge,’’ EPA is 

providing additional clarification in this 

rule and preamble on how operators 

should evaluate whether they discharge 

or propose to discharge. While 

commenters generally agreed that the 

changes proposed by EPA were 

consistent with the Second Circuit 

decision, some commenters thought that 

‘‘propose to discharge’’ and ‘‘potential 

to discharge’’ were not sufficiently 

distinguishable, and that ‘‘proposed’’ 

discharges could be understood as 

contrary to the Waterkeeper court’s 

holding that only ‘‘actual’’ discharges 

are subject to CWA requirements. 

EPA disagrees with these 

commenters. Including a duty to apply 

for CAFOs that ‘‘propose to discharge’’ 

is not the same as requiring a permit for 

CAFOs with only a ‘‘potential to 

discharge.’’ Unlike the 2003 rule, which 

categorically required a permit for any 

CAFO with a ‘‘potential to discharge,’’ 

this final rule calls for a case-by-case 

evaluation by the CAFO owner or 

operator as to whether the CAFO 

discharges or proposes to discharge 

from its production area or land 

application area based on actual design, 

construction, operation, and 

maintenance. ‘‘Potential’’ connotes the 

possibility that there might—as opposed 

to will—be a discharge, which, as the 

Waterkeeper court held, is not sufficient 

under the CWA to trigger NPDES 

permitting requirements. In contrast to 

the 2003 rule, this rule requires a caseby-case assessment by each CAFO to 

determine whether the CAFO in 

question, due to its individual 

attributes, discharges or proposes to 

discharge. Therefore, revised 

§ 122.23(d)(1) requires only CAFOs that 

actually discharge to seek permit 

coverage and clarifies that a CAFO 

proposes to discharge if based on an 

objective assessment it is designed, 

constructed, operated, or maintained 

such that a discharge will occur, not 

simply such that it might occur. 

Consistent with the Waterkeeper 

decision, CAFOs that are required to 

seek permit coverage must do so when 

they propose to discharge. (See below 

for discussion of the provision relating 

to when a CAFO must seek permit 

coverage, 40 CFR 122.23(f).) Thus, it is 

the responsibility of the CAFO owner or 

operator to seek authorization to 

discharge at the time they propose to 

discharge. A CAFO that discharges 

without a permit is in violation of the 

CWA section 301(a) prohibition on such 

discharges and additionally has the 

burden of establishing that it did not 

propose to discharge prior to the 

discharge (unless the permitting 

authority has a current, complete 

certification from that CAFO as 

provided by 40 CFR 122.23(j)(2), 

discussed below). If it is determined 

that it did, in fact, propose to discharge 

prior to the discharge (that is, it was 

designed, constructed, operated, or 

maintained such that a discharge would 

occur), it is also in violation of the 

§ 122.23(d)(1) duty to apply. Section 

122.23(j)(2) also clarifies how a CAFO 

may satisfy the burden of establishing 

that it did not propose to discharge. 

Under section 301(a) of the CWA, 

only those CAFO discharges authorized 

by an NPDES permit (or otherwise 

authorized by the statute), regardless of 

the volume or duration of the discharge, 

are allowed. Any discharge from a 

CAFO, even one that is unplanned or 

accidental, is illegal unless it is 

authorized by the terms of a permit or 

is agricultural stormwater. While EPA 

recognizes that not every discharge 

indicates that the CAFO will discharge 

in the future, an operator should 

certainly consider any unplanned or 

accidental discharge that may have 

occurred in the past in deciding 

whether to seek permit coverage. CAFO 

operators must objectively assess 

whether a discharge from the CAFO, 

including from the production area or 

land application areas under the control 

of the CAFO, is occurring or will occur 

for purposes of determining whether to 

obtain permit coverage. 

It is well established that ‘‘discharge’’ 

is not limited to continuous discharges 

of pollutants from a point source to 

waters of the U.S., but also includes 

intermittent and sporadic discharges. 

‘‘Intermittent or sporadic violations do 

not cease to be ongoing until the date 

when there is no real likelihood of 

repetition.’’ Chesapeake Bay 

Foundation v. Gwaltney of Smithfield, 

890 F.2d 690, 693 (4th Cir. 1989). Such 

intermittent, sporadic, even occasional, 

discharges may in fact be the norm for 

many CAFOs, but they are nonetheless 

‘‘discharges’’ under the CWA and are 

prohibited unless authorized under the 

terms of an NPDES permit. CAFOs that 

have had such intermittent or sporadic 

discharges in the past would generally 

be expected to have such discharges in 

the future, and therefore be expected to 

obtain a permit, unless they have 

modified their design, construction, 

operation, or maintenance in such a way 

as to prevent all discharges from 

occurring. 

EPA received a number of comments 

concerning past discharges. Some 

commenters asserted that a prior 

discharge is not, by itself, a sufficient 

basis for requiring a permit and 

observed that it is quite possible that a 

CAFO may have eliminated the cause of 

the discharge. EPA agrees that not every 

past discharge from a CAFO necessarily 

triggers a duty to apply for a permit; 

however, a past discharge may indicate 

that the CAFO discharges or proposes to 

discharge if the conditions that gave rise 

to the discharge have not changed or 

been corrected. See, e.g., Gwaltney of 

Smithfield. Ltd. v. Chesapeake Bay 

Foundation, 484 U.S. 49, 57 (1987) (‘‘a 

reasonable likelihood that a past 

polluter will continue to pollute in the 

future’’ is a continuous or intermittent 

violation); American Canoe Ass’n v. 

Murphy Farms, Inc., 412 F.3d. 536 (4th 

Cir. 2005) (CWA violation continues 

where corrective measures are 

insufficient to eliminate real likelihood 

of repeated discharges). The same 

rationale that led the courts in these 

cases to conclude that the point sources 

in question were discharging in 

violation of the CWA underlies the final 

rule’s requirement that CAFOs must 

seek permit coverage when they 

discharge or propose to discharge (i.e., 

are designed, constructed, operated, or 

maintained such that a discharge will 

occur). Sections 122.23(d)(1) and (f). 

An uncorrected past discharge is not 

the only indicator that operators should 

consider in assessing whether the CAFO 

discharges or proposes to discharge. 

Other key factors the operator should 

consider include the proximity of the 

production area to waters of the U.S., 

whether the CAFO is upslope from 

waters of the U.S., and climatic 

conditions. Similarly, the type of waste 

storage system, storage capacity, quality 

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of construction, and presence and extent 

of built-in safeguards are important 

factors. Standard operating procedures 

and level of maintenance are also 

critical factors for the operator to 

consider when assessing whether a 

CAFO discharges or proposes to 

discharge. Such considerations 

contributed to EPA’s decision to include 

in this final rule an option for 

unpermitted CAFOs to certify that they 

do not discharge or propose to discharge 

by meeting the criteria in 40 CFR 

122.23(i)(2), discussed in detail below. 

EPA encourages unpermitted CAFOs 

that choose not to certify to consider the 

set of criteria for certification eligibility 

when deciding whether to seek permit 

coverage, and this final rule provides in 

§ 122.23(j)(2) that these same criteria 

may be used to establish that a CAFO 

did not propose to discharge prior to a 

discharge occurring. 

As a result of the revisions to 40 CFR 

122.23(d) and (f), only CAFOs that 

discharge or propose to discharge are 

required to seek permit coverage, and a 

CAFO that proposes to discharge must 

seek coverage as soon as it proposes to 

discharge in order to avoid having 

unpermitted discharges. In the event of 

a discharge from an unpermitted CAFO, 

the CAFO operator would be in 

violation of the CWA prohibition 

against discharging without a permit. 

Under this final rule, if the CAFO 

proposed to discharge prior to the 

discharge, the CAFO would also be in 

violation of the requirement in 

§ 122.23(d)(1) and (f), implementing 

sections 308 and 402 of the CWA, that 

CAFOs seek permit coverage when they 

propose to discharge. 

In revised § 122.23(d)(1), EPA is 

clarifying that ‘‘a CAFO proposes to 

discharge if it is designed, constructed, 

operated, or maintained such that a 

discharge will occur.’’ EPA intends that 

the CAFO operator should make an 

objective assessment of the operation to 

determine whether the CAFO will 

discharge. Such an objective assessment 

would take into account not only the 

characteristics of the manmade aspects 

of the CAFO itself, but climatic, 

hydrological, topographical, and other 

characteristics beyond the operator’s 

control that impact whether the CAFO 

will discharge, given the design, 

construction, operation and 

maintenance of the CAFO. 

To assist CAFO operators in making 

this objective assessment and to provide 

assurance for CAFOs deciding not to 

seek permit coverage that they are not 

required to obtain permit coverage, EPA 

is finalizing a voluntary certification 

option, proposed in the 2008 

supplemental proposal. This option 

provides a means for a CAFO to certify 

that it does not discharge or propose to 

discharge. The voluntary certification 

provisions are discussed below in 

section III.A.3(c) of this preamble. 

This rule is consistent with the 

Waterkeeper decision because the duty 

to apply for a permit only arises when 

a CAFO discharges or proposes to 

discharge, that is, when it discharges or 

is designed, constructed, operated, or 

maintained such that a discharge will 

occur. It is also consistent with 

Chesapeake Bay Foundation v. 

Gwaltney of Smithfield, discussed 

above, which found a violation under 

the CWA where it is reasonably likely 

that a discharge will occur due to 

existing circumstances. This rule 

derives from sections 402(a)(3) and 308 

of the CWA, 33 U.S.C. 1342(a)(3), 1318. 

Under section 402(a)(3), EPA is required 

to establish a permit program that, 

among other things, ensures compliance 

with all applicable requirements of 

sections 301 (requirements for 

establishing technology-based and water 

quality-based effluent limitations), 306 

(requirements for establishing new 

source performance standards), 308 

(requirements relating to inspections, 

monitoring and entry, including 

requests for information to determine 

compliance status or support 

development of effluent limitations) and 

402 (NPDES permits). 

Section 301(a) prohibits the discharge 

of pollutants, except in compliance with 

specific provisions in the CWA. 

Particularly relevant to CAFOs, section 

301(b) provides that ‘‘there shall be 

achieved’’ effluent limitations 

controlling pollutants discharged from 

point sources. Section 308(a) provides 

EPA broad authority to require the 

owner or operator of any point source 

(including CAFOs) to provide 

information necessary to develop 

effluent limitations, to ‘‘carry out’’ 

section 402, and to ‘‘carry out’’ the 

objectives of the Act, which are set forth 

in CWA section 101(a). Under section 

501(a) EPA is authorized to prescribe 

‘‘such regulations as are necessary to 

carry out’’ its functions under the CWA. 

Any permit program established to carry 

out section 402 must, of necessity, 

require point sources that discharge or 

propose to discharge to submit 

information to allow the permitting 

authority to determine prior to issuance 

of a permit what effluent limitations 

should apply to a discharger and be 

included in its permit (including 

providing the public and any other 

affected State notice and opportunity for 

public comment, as required by section 

402(b)(3)). It is therefore reasonable for 

EPA to require those CAFOs that 

discharge or propose to discharge to 

apply for NPDES permit coverage. 

Some commenters on the 2006 

proposed rule opposed regulating 

entities that ‘‘propose’’ to discharge, or 

alternatively, suggested that EPA should 

clarify that ‘‘propose’’ means ‘‘intend’’ 

or ‘‘plan.’’ While EPA acknowledges 

that ‘‘propose’’ to discharge could be 

understood to mean ‘‘intend’’ or ‘‘plan’’ 

to discharge, under this final rule 

‘‘propose to discharge’’ means that the 

CAFO is designed, constructed, 

operated, or maintained such that it will 

discharge. This is consistent with the 

Waterkeeper decision because a mere 

‘‘potential’’ to discharge is not sufficient 

to trigger the revised duty to apply. 

Accordingly, as previously discussed, 

revised § 122.23(d)(1) clarifies that ‘‘a 

CAFO proposes to discharge if it is 

designed, constructed, operated, or 

maintained such that a discharge will 

occur.’’ The CAFO’s decision as to 

whether to apply for a permit should be 

based on an objective assessment of 

conditions at that operation. As 

discussed below, under this final rule, 

a CAFO that is not designed, 

constructed, operated, or maintained in 

a manner such that the CAFO does or 

will discharge is not required to seek 

permit coverage under § 122.23(d)(1) 

and may choose to take advantage of the 

voluntary no discharge certification. 

Some commenters on the 2006 

proposed rule requested that EPA 

specifically state in the regulation that 

facilities designed to the 25-year, 24-

hour design standard have not 

‘‘proposed’’ to discharge. One 

commenter questioned whether existing 

operations should be required to obtain 

permit coverage if they have installed 

structures and production area BMPs 

using Natural Resources Conservation 

Service (NRCS) standards and if they 

have been operating without 

discharging. The commenter indicated 

that ‘‘since EPA is requiring that a zero 

discharge standard be met only for 

certain new CAFOs and not existing 

CAFOs, it is unreasonable to expect all 

existing animal operations that do not 

otherwise come under a permit to meet 

a zero discharge standard.’’ 

EPA disagrees that CAFOs designed 

for the 25-year, 24-hour storm should be 

categorically excluded from the 

requirement to apply for a permit 

simply based on their design standard. 

EPA also believes that it is reasonable to 

expect unpermitted CAFOs to meet a 

zero discharge standard. The CWA is 

very clear that point source discharges 

from CAFOs are illegal unless the 

operator has applied for and obtained an 

NPDES permit. Thus, ‘‘zero discharge’’ 

is the only standard to which EPA can 

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hold unpermitted CAFOs under the 

CWA. Large storms and chronic rainfall 

events do occur and production areas 

built to the 25-year, 24-hour storm 

design standard can and do discharge 

during precipitation events. Under the 

CWA, as previously discussed, a 

violation of the prohibition against 

discharging without a permit occurs 

even if the discharge was not planned 

or intended. Conversely, in the event of 

a discharge from a permitted CAFO, the 

discharge will not violate the CWA if 

the CAFO is in compliance with its 

permit. 

EPA notes that design is only one 

aspect for a CAFO to consider when 

assessing whether or not to apply for a 

permit. Construction, operation, and 

maintenance are equally important 

components of a CAFO’s operation and 

can make the difference between a 

CAFO that discharges and one that does 

not. With regard to the commenter’s 

question about the applicability of 

NRCS standards, a CAFO’s decision as 

to whether to seek permit coverage 

should be based on an objective 

assessment of conditions at the 

operation, including, but not limited to, 

the manure storage design standard. 

EPA notes that whether or not a CAFO 

is designed according to NRCS 

standards may be an important 

component of the objective evaluation it 

undertakes to assess whether it is 

designed, constructed, operated, or 

maintained such that a discharge will 

occur. A CAFO that does not discharge 

or propose to discharge is not required 

to seek permit coverage under 

§ 122.23(d)(1) and may be eligible for no 

discharge certification under 40 CFR 

122.23(i). 

CAFO NPDES permit requirements 

include, but are not limited to, best 

management practices (BMPs) to 

eliminate discharges from the 

production area under most 

circumstances and to ensure appropriate 

agricultural utilization of nutrients in 

manure, litter, and process wastewater 

that is applied to land under the CAFO’s 

control. EPA expects that an 

unpermitted CAFO would also need to 

implement BMPs in order to ensure that 

it does not discharge or propose to 

discharge. However, in many, if not 

most, cases the BMPs called for will be 

more rigorous than those required for 

permitted CAFOs, because the operator 

of an unpermitted CAFO is never 

authorized to discharge under CWA 

section 301(a). Permitted CAFOs have 

greater flexibility because, in addition to 

being authorized to discharge under the 

circumstances prescribed by the permit, 

other discharges can be excused when 

the conditions contained in EPA’s upset 

and/or bypass regulations are met. See 

40 CFR 122.41(m) and (n). 

In contrast to commenters who 

believe that some non-discharging 

CAFOs will needlessly go through the 

permitting process, other commenters 

expressed concern that some CAFOs 

that should have permits will not seek 

needed permit coverage. They 

contended that many CAFOs are 

currently discharging without a permit 

and objected to having CAFOs make the 

determination themselves as to whether 

or not they discharge or propose to 

discharge, as such an approach would, 

in their view, establish a self-permitting 

scheme. These commenters further 

contended that the administrative 

record from the 2003 rule supports the 

presumption that all Large CAFOs 

actually discharge and, therefore, such 

CAFOs should be required to obtain a 

permit. 

EPA does not agree that the rule 

establishes a self-permitting scheme. As 

is the case with all point sources, it is 

up to the operator to determine whether 

or not to apply for a permit in the first 

instance, by assessing whether the point 

source (CAFO) discharges or proposes to 

discharge. Point sources that do not 

discharge or propose to discharge are 

not subject to CWA permitting 

requirements. See § 122.21(a)(1). 

Regarding the administrative record for 

the 2003 rule, that rule established a 

duty to apply for all CAFOs unless the 

CAFO could demonstrate to the 

satisfaction of the permitting authority 

that it had no ‘‘potential to discharge.’’ 

That provision was vacated by the 

Second Circuit, which noted that EPA 

did not argue that the administrative 

record supported a regulatory 

presumption that all Large CAFOs 

actually discharge. 399 F.3d at 506, 

n.22. Thus, consistent with the 

Waterkeeper decision, EPA is 

promulgating a rule which requires 

those CAFOs that discharge or propose 

to discharge, but not CAFOs with a mere 

‘‘potential’’ to discharge, to seek permit 

coverage on a case-by-case basis. With 

regard to the comments that EPA should 

establish a categorical presumption that 

all Large CAFOs discharge, the Agency 

is evaluating various options for 

exploring the nature of discharges from 

Large CAFOs. 

Finally, this rule revises the 

regulatory provisions for when a CAFO 

must seek permit coverage and the duty 

to maintain permit coverage for CAFOs. 

The final rule clarifies that those CAFOs 

that are required under § 122.23(d)(1) to 

seek permit coverage must do so ‘‘when 

the CAFO proposes to discharge,’’ 

unless a later deadline, such as February 

27, 2009, is specified for the specific 

category of operation. EPA is 

recodifying 40 CFR 122.23(g) as 

§ 122.23(f) because the paragraph 

codified as § 122.23(f) in the 2003 rule 

is being removed. See section III.A.3(b) 

of this preamble. Revised § 122.23(f) is 

consistent with the revised duty to 

apply requirement in § 122.23(d)(1) and 

EPA’s authority under sections 301, 308 

and 402 of the CWA to require CAFOs 

that actually discharge to seek permit 

coverage. None of the specific 

timeframes for the various categories of 

CAFOs in paragraphs (1)–(5) of 

§ 122.23(f), as amended by the 2007 date 

change rule (72 FR 40,245), is affected 

by this rule. The revised language in the 

introductory paragraph of § 122.23(f) 

simply conforms to the requirements of 

§ 122.23(d)(1). 

EPA is making corresponding 

revisions to the regulatory text requiring 

CAFOs to maintain permit coverage. 

Due to the fact that § 122.23(f) as 

codified in 2003 is being removed, EPA 

is recodifying 40 CFR 122.23(h), ‘‘Duty 

to Maintain Permit Coverage,’’ as 

§ 122.23(g). See section III.A.3(b) of this 

preamble. Also, in the 2006 proposed 

rule, EPA proposed to revise this 

provision to address the Waterkeeper 

court’s decision vacating the 

requirement for all CAFOs to seek 

permit coverage unless they obtained a 

no potential to discharge determination. 

See 71 FR 37,785. In this final rule (as 

in the proposed rule), a CAFO would 

not need to reapply based solely on the 

fact of having had a permit, if the permit 

had been terminated in accordance with 

the NPDES provisions at 40 CFR 

122.64(b). Since a CAFO that terminated 

permit coverage is no longer a permitted 

CAFO, it is not subject to the duty to 

maintain permit coverage provision. 

Consistent with the requirement that 

only CAFOs that discharge or propose to 

discharge seek NPDES permit coverage, 

new § 122.23(g) excludes CAFOs that 

will not discharge or propose to 

discharge upon expiration of the permit 

from the requirement to reapply 180 

days in advance of permit expiration. 

(b) ‘‘No Potential To Discharge’’ 

Determination 

In this final rule, EPA is deleting the 

regulatory provisions adopted in the 

2003 CAFO rule allowing CAFOs to 

demonstrate that they have no potential 

to discharge and authorizing the 

Director to make such a determination. 

40 CFR 122.23(d)(2) and 122.23(f). 

Because EPA is not requiring CAFOs to 

seek permit coverage based merely on 

potential to discharge, this provision is 

no longer relevant to determining 

whether or not a facility needs to seek 

permit coverage. This final rule is 

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unchanged from the 2006 proposed rule 

in this respect. 

Overall, most commenters supported 

eliminating the ‘‘no potential to 

discharge’’ provisions in the CAFO 

regulations, noting that it is no longer 

necessary because only CAFOs that 

discharge or propose to discharge must 

apply for permits. One State observed 

that the ‘‘no potential to discharge’’ 

criteria could still be useful to CAFOs 

in determining whether they need to 

apply for a permit. While these criteria 

may continue to be useful to CAFO 

owners and operators for that purpose, 

EPA is eliminating these provisions 

from 40 CFR 122.23 of the regulations. 

(c) Voluntary No Discharge Certification 

In this final rule, the Agency is 

adopting a new provision that allows 

CAFOs to voluntarily certify that the 

CAFO does not discharge or propose to 

discharge. As discussed above, EPA 

received several hundred comments on 

the 2006 proposed rule related to how 

a CAFO operator would decide whether 

to seek permit coverage under a revised 

rule that requires CAFOs that discharge 

or propose to discharge to apply for a 

permit or submit a Notice of Intent for 

coverage under a general permit. Several 

commenters were particularly 

concerned with the consequences for an 

unpermitted CAFO that has an 

‘‘accidental discharge’’ because they 

understood EPA’s proposal to mean that 

a CAFO that does not apply for a permit 

and subsequently has a discharge of 

pollutants to waters of the U.S. would 

be liable for two violations, one 

associated with the discharge itself and 

another violation for failing to apply for 

a permit for authority to discharge. In 

response to these comments, in the 2008 

supplemental proposal, EPA requested 

public comment on an option that 

would allow a CAFO that determines, 

based on an objective assessment, that it 

does not discharge or propose to 

discharge to certify to the permitting 

authority that it is designed, 

constructed, operated, and maintained 

not to discharge. In the unlikely event 

that a properly certified CAFO 

discharges (which would constitute a 

violation of section 301(a) of the CWA), 

the CAFO would not be liable for failing 

to apply for a permit prior to the 

discharge in accordance with the permit 

application requirements of 40 CFR 

122.23(d)(1) and (f). 

EPA received many comments on the 

proposed voluntary certification option. 

Commenters were divided, with some 

generally supportive and others 

generally opposed to the concept of a 

voluntary certification option for 

unpermitted CAFOs. Those in favor 

stated that certification would assist 

CAFOs that do not discharge or propose 

to discharge by providing a structured 

process for CAFOs to notify the 

permitting authority that they are not 

required to seek permit coverage. Some 

commenters opposed to certification 

believe the Agency’s record supports a 

regulatory presumption that all CAFOs 

discharge, and, therefore, the no 

discharge certification process is a 

further departure from the decision of 

the Waterkeeper court. The majority of 

State permitting authorities commenting 

on the 2008 supplemental proposal 

were opposed to the certification option, 

as proposed. 

In this final rule, EPA has addressed 

both the decision from the Waterkeeper 

court that CAFOs with only a potential 

to discharge are not subject to NPDES 

permitting requirements and the 

concerns expressed by commenters that 

some CAFOs may be uncertain as to 

whether they discharge or propose to 

discharge. In the NPDES program, the 

first step is for a point source to decide 

whether it needs to seek permit 

coverage. Generally, the question of 

whether a point source needs permit 

coverage is easily answered; indeed 

other point sources are typically 

designed to discharge to waters of the 

U.S. After careful consideration of the 

comments and in light of the unique 

characteristics of CAFOs among point 

sources, EPA has concluded that 

providing a voluntary option for 

unpermitted CAFOs to certify to the 

Director that the CAFO does not 

discharge or propose to discharge based 

on an objective assessment of the 

CAFO’s design, construction, operation, 

and maintenance is reasonable and 

appropriate for CAFOs. However, in 

response to comments received on the 

proposed certification option, EPA is 

clarifying several aspects of the process, 

eligibility requirements, and effect of 

certification as discussed below. The 

Agency is also making several changes 

to the proposed option to ensure that 

certification will be properly 

implemented. 

Under this final rule, and as proposed 

in the 2008 supplemental proposal, a 

CAFO operator may certify that the 

CAFO does not discharge or propose to 

discharge by signing and submitting a 

certification statement to the Director. 

The objective assessment necessary for 

the CAFO to qualify for certification 

takes into account the CAFO’s 

production area design and construction 

and its operating and maintenance 

procedures and practices as described in 

its nutrient management plan (NMP) in 

accordance with the eligibility criteria, 

described in detail below. The 

certification option established by this 

rule does not change the requirement 

that CAFOs that propose to discharge 

must seek permit coverage when they 

propose to discharge pursuant to 

§ 122.23(f). It does, however, provide a 

structured process for CAFOs that wish 

to certify to establish by objective means 

that they do not discharge or propose to 

discharge. EPA believes that such a 

structured process is helpful to CAFOs 

as they decide whether to seek permit 

coverage. A CAFO’s no discharge 

certification is not subject to review by 

the permitting authority in order for it 

to become effective and the permitting 

authority is not required to make the 

certification available to the public for 

comment because the certification is not 

a permit application for which review is 

required under section 402 of the CWA. 

EPA wishes to emphasize that 

submission of a no discharge 

certification is voluntary and the 

process for obtaining a certification has 

been developed with that underlying 

principle in mind. 

As explained in detail above, under 

§ 122.23(d)(1) a CAFO that does not 

discharge or propose to discharge is not 

required to apply for an NPDES permit. 

A certification in accordance with this 

final rule documents the CAFO 

operator’s basis for making an informed 

decision not to seek permit coverage 

because the CAFO does not discharge or 

propose to discharge. A CAFO that 

certifies in accordance with the 

requirements of this final rule, 

discussed in detail below, is properly 

certified so long as the CAFO maintains 

its eligibility. EPA believes that 

providing a properly certified CAFO 

assurance that it is not required by 

§ 122.23(d)(1) to seek permit coverage is 

reasonable and justified. The threshold 

question regarding which CAFOs are 

required to seek permit coverage— 

whether the CAFO discharges or 

proposes to discharge—is the same for 

all CAFOs. A CAFO that does not 

discharge or propose to discharge can 

choose to certify or not. Certification in 

accordance with the requirements of 40 

CFR 122.23(i) requires a CAFO owner or 

operator to undertake and document a 

rigorous analysis of the operation’s 

structure and design, and to be 

committed to operation and 

maintenance protocols designed to 

ensure no discharge, discussed in detail 

below. 

EPA is adding subsection (j) 40 CFR 

122.23 to clarify the effect of 

certification. As provided in new 

paragraph (j)(1), a CAFO certified in 

accordance with § 122.23(i) is presumed 

not to propose to discharge. A CAFO 

that is ‘‘certified in accordance with 

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§ 122.23(i)’’ has submitted a complete 

certification that is in effect pursuant to 

40 CFR 122.23(i)(4). In the unlikely 

event that such a CAFO does discharge, 

it will not be in violation of the 

requirement that CAFOs that propose to 

discharge seek permit coverage pursuant 

to § 122.23(d)(1) and (f), with respect to 

that discharge, provided the CAFO 

maintained its certification by 

continuing to be designed, constructed, 

operated, and maintained in accordance 

with the eligibility criteria in 40 CFR 

122.23(i)(2). This is because meeting the 

eligibility criteria at the time of the 

discharge establishes that the CAFO did 

not propose to discharge. If a certified 

CAFO does discharge, and the Director 

believes that the CAFO’s certification 

was invalid at the time of the discharge 

(i.e., not in accordance with the 

eligibility criteria in § 122.23(i)(2)), the 

presumption means that, in any 

enforcement action alleging failure to 

seek permit coverage prior to the 

discharge, the burden is on the Director 

to establish that the CAFO ‘‘proposed to 

discharge’’ prior to the discharge. EPA 

notes that any unpermitted discharge 

from a properly certified CAFO is still 

a violation of CWA section 301(a) and 

terminates the certification pursuant to 

§ 122.23(i)(4). Moreover, if subsequent 

to the discharge event the CAFO is 

designed, constructed, operated, or 

maintained such that a discharge will 

occur, it must seek permit coverage 

under § 122.23(d)(1) and (f). For 

additional discussion of past discharges 

from unpermitted CAFOs see section 

III.C.3(a) of this preamble. 

To further clarify the effect of 

voluntary certification, EPA is also 

including in the final rule a provision 

specifically related to uncertified 

CAFOs. As provided in 40 CFR 

122.23(j)(2) of this final rule, in any 

enforcement proceeding for failure to 

seek permit coverage under 

§ 122.23(d)(1) or (f) that is associated 

with a discharge from an unpermitted 

CAFO that has not submitted 

certification documentation as provided 

in 40 CFR 122.23(i)(3) or 40 CFR 

122.23(i)(6)(iv), the CAFO would have 

the burden to establish that it did not 

propose to discharge prior to the 

discharge. Also, a CAFO that had 

submitted a certification more than five 

years prior to the discharge (and not 

recertified within the past five years) or 

that had withdrawn its certification 

pursuant to 40 CFR 122.23(i)(5) prior to 

the discharge would also have the 

burden to establish that it did not 

propose to discharge. EPA’s intent is to 

clarify that when an unpermitted CAFO 

discharges and the permitting authority 

does not have a current, signed 

certification from that CAFO, it is the 

CAFO’s responsibility to show that it 

was not required to have applied for 

permit coverage (i.e., did not propose to 

discharge) prior to the discharge. 

Section 122.23(j)(2) provides that the 

CAFO can satisfy this burden by 

establishing that at the time of the 

discharge the CAFO’s design, 

construction, operation, and 

maintenance were all in accordance 

with the certification eligibility criteria 

of § 122.23(i)(2). 

Unlike the 2003 rule that required all 

CAFOs to seek permit coverage in order 

to operate unless they obtained a 

determination of ‘‘no potential to 

discharge,’’ the certification provision is 

entirely voluntary. The requirement for 

a CAFO to apply for a permit is 

triggered if a CAFO discharges or 

proposes to discharge, regardless of 

whether it has certified or not. Any 

CAFO operator’s decision as to whether 

to seek permit coverage should be made 

based on an objective assessment of the 

CAFO’s design, construction, operation, 

and maintenance, in contrast to the 

2003 rule, which required the operator 

either to seek permit coverage or prove 

to the satisfaction of the Director that 

the CAFO had no potential to discharge. 

Therefore, under § 122.23(d)(1) and (i), 

the operator must evaluate based on 

such an objective assessment whether it 

discharges or proposes to discharge. If it 

does it must seek and obtain permit 

coverage; if it does not it may operate 

without a permit and decide either (1) 

to certify under the provisions at 

§ 122.23(i); or (2) to operate without a 

permit and without certifying. The 

purpose of certification is to provide a 

voluntary mechanism for the CAFO to 

establish in advance that it does not 

discharge or propose to discharge. As 

previously discussed, a CAFO that 

operates without a permit must be 

designed, constructed, operated, and 

maintained such that no discharge will 

occur, because any discharge (other than 

agricultural stormwater) is prohibited 

from unpermitted CAFOs pursuant to 

CWA section 301(a), while permitted 

CAFOs are allowed to discharge under 

specified conditions and may also have 

defenses for upset and bypass. NPDES 

permit coverage reduces CAFO operator 

risk and provides certainty to CAFO 

operators regarding activities and 

actions that are necessary to comply 

with the CWA. In contrast, certified 

CAFOs are not allowed to discharge 

under any conditions (other than 

discharges of agricultural stormwater), 

and are liable for any unpermitted 

discharge pursuant to CWA 301(a), but 

they will not additionally be held liable 

for a violation of the duty to apply, 

provided their certification is valid and 

still in effect at the time of discharge. 

EPA strongly recommends that all 

CAFOs that have any doubt about their 

ability to operate under all 

circumstances without discharging seek 

to obtain NPDES permit coverage, and 

believes it is in their interest to do so. 

However, in accordance with the 

Waterkeeper decision, EPA is requiring 

CAFOs to seek permit coverage only if 

they discharge or propose to discharge. 

The final rule provisions for 

certification eligibility and submission, 

and conditions for a valid certification 

are discussed in detail below. 

(i) Certification Eligibility Criteria 

EPA is establishing specific eligibility 

criteria for CAFO certification at 40 CFR 

122.23(i)(2). Meeting these criteria 

establishes that the CAFO does not 

‘‘discharge or propose to discharge’’ for 

purposes of 40 CFR 122.23(d)(1), for as 

long as the certification is valid. 

Eligibility for certification means 

meeting the criteria described below at 

the time certification is established and 

continuing to meet the eligibility criteria 

throughout the period of certification as 

new information or situations arise. The 

three criteria are as follows: (1) An 

objective evaluation which shows that 

the CAFO’s production area is designed, 

constructed, operated, and maintained 

so as not to discharge, (2) development 

and implementation of an NMP to 

ensure no discharge (other than 

agricultural stormwater discharges) that, 

at a minimum, addresses the elements 

set forth in 40 CFR 122.42(e)(1) and 40 

CFR 412.37(c), including operation and 

maintenance practices for the 

production area and land application 

areas under the control of the CAFO, 

and (3) maintenance of the 

documentation required for certification 

either on site, at a nearby office, or 

where it can be made readily available 

to the permitting authority upon 

request. A statement that describes the 

basis for the CAFO’s certification that it 

satisfies these eligibility criteria must be 

submitted to the Director, but there is no 

requirement for permitting authority 

review in order for the certification to be 

valid. 

The first two criteria concern the 

existing physical and operational 

conditions at the CAFO. In addition, 

meeting these criteria includes making 

proper accommodations during the 

certification period to address changes 

to the operation. For example, if an 

increase in animals will cause the CAFO 

to exceed the existing storage capacity 

for precipitation, manure and process 

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wastewater required for no discharge, in 

order to remain certified, the CAFO 

must remedy the storage capacity 

problem prior to bringing the additional 

animals to the operation. Operation and 

maintenance practices may need to be 

modified to accommodate changes to 

the CAFO. For example, a reduction in 

fields available for land application 

would trigger the need to reevaluate the 

adequacy of manure storage and 

handling protocols. The third eligibility 

criterion requires a certified CAFO to 

maintain records needed to support the 

basis for the certification throughout the 

duration of the certification, such as 

monitoring and inspection records, 

records of maintenance and repairs, and 

land application records, including 

updated documentation to match 

current conditions and circumstances at 

the CAFO. Certified CAFOs, like any 

other permitted or unpermitted CAFO, 

may be asked to send information to the 

permitting authority that is relevant to 

implementation of the CWA, or 

inspected by EPA or authorized State 

inspectors. During an inspection the 

certified CAFO could be required to 

produce the documentation showing 

that it meets the eligibility criteria, 

including that the CAFO has been and 

is being operated and maintained in 

accordance with an NMP that has been 

updated as necessary. 

Commenters offered numerous 

perspectives on the proposed eligibility 

criteria. Some commenters asserted that 

the proposed criteria were too extensive, 

stringent, and complex, and therefore 

would make it unlikely that selfcertifying CAFOs could accurately 

demonstrate their eligibility. These 

commenters indicated that, as proposed, 

the eligibility criteria would be 

expensive to implement and, thus, 

would serve as a disincentive for a 

CAFO to choose to certify. In response 

to these comments, EPA emphasizes 

that certification is voluntary, and 

CAFOs may choose not to certify. As 

noted above, EPA believes that it is 

generally in an operator’s best interest to 

obtain permit coverage. However, EPA 

has provided the certification option for 

CAFOs that choose not to seek permit 

coverage but would like to establish up 

front that they do not discharge or 

propose to discharge. The final rule 

contains stringent eligibility criteria 

because in light of the CWA prohibition 

against unpermitted discharges, the 

eligibility criteria for certification must 

establish that the CAFO does not 

discharge or propose to discharge. Only 

CAFOs that establish eligibility and 

meet all of the certification provisions 

in 40 CFR 122.23(i)(2)–(3) will receive 

the benefit of certification, which is that 

a validly certified CAFO that discharges 

will not be in violation of the 

requirement to apply for a permit 

pursuant to § 122.23(d)(1) and 40 CFR 

122.23(f). As EPA is clarifying in 40 CFR 

122.23(j), without a certification, an 

unpermitted CAFO that discharges has 

the burden of establishing that it did not 

propose to discharge in an enforcement 

action arising from a discharge from the 

CAFO. 

In contrast, other commenters 

indicated that the proposed criteria do 

not ensure that a certified CAFO will 

not discharge and, therefore, additional 

requirements and procedures should be 

imposed for certification eligibility. In 

response to these comments, the 

certification eligibility criteria in this 

final rule have been modified from the 

2008 supplemental proposal in order to 

clarify what EPA expects of a certified 

CAFO. The final rule clarifies that the 

CAFO’s NMP must include any 

operation and maintenance practices 

that are established by the technical 

evaluation of production area open 

storage structures as necessary to ensure 

no discharge. Also, EPA reminds 

unpermitted CAFOs considering 

certification that many site-specific 

factors, such as location and the 

facility’s discharge history, must be 

taken into account when demonstrating 

certification eligibility in accordance 

with this final rule. A CAFO in close 

proximity to waters of the U.S. or a 

conduit to waters of the U.S. may need 

to take additional protective measures 

for design, construction, operation and 

maintenance in order to be able to 

demonstrate that it will not discharge. A 

CAFO operator who intends to establish 

eligibility for certification should be 

mindful that, as stated above in the 

discussion of revised § 122.23(d)(1), a 

CAFO that has discharged in the past 

would generally be expected to 

discharge in the future, and therefore be 

expected to obtain a permit, unless it 

has modified the design, construction, 

operation or maintenance in such a way 

as to prevent any discharges from 

occurring. 

The first eligibility criterion for valid 

certification covers the design, 

construction, operation, and 

maintenance of the CAFO’s production 

area. As proposed, 40 CFR 122.23(i)(2)(i) 

of this final rule requires the CAFO to 

demonstrate that the CAFO’s production 

area is designed, constructed, operated, 

and maintained so as not to discharge. 

Due to the variations in production area 

design based on the type of containment 

system used at the operation, EPA 

proposed and is finalizing today a rule 

with two parts for the first eligibility 

criterion: the first for open manure 

storage structures and the second for 

any part of the production area not 

considered to be open containment. 

Consistent with the 2008 

supplemental proposal, under the final 

rule, any CAFO with an open manure 

storage structure seeking to certify that 

it does not discharge or propose to 

discharge is required to perform a 

technical evaluation under 40 CFR 

122.23(i)(2)(i)(A). To demonstrate that 

the CAFO meets the production area 

requirement for certification, this 

evaluation must be conducted in 

accordance with the elements of the 

technical evaluation required for open 

storage new source swine, poultry and 

veal calf operations seeking to 

demonstrate no discharge under 40 CFR 

412.46(a)(1)(i)–(viii), as revised by this 

action. EPA clarifies that, although this 

provision references the new source 

performance standard (NSPS) for swine, 

poultry and veal calf operations, this 

eligibility criterion applies to any 

unpermitted CAFO with open manure 

storage seeking to certify that it does not 

discharge or propose to discharge, not 

just new sources in the swine, poultry 

and veal calf sectors with open storage. 

Elsewhere in this final rule, EPA is 

revising the provisions at 40 CFR 

412.46(a)(1) to allow such new sources 

with open containment to meet the no 

discharge requirement for their NPDES 

permit using best management practices 

based in part on a rigorous site-specific 

technical evaluation that includes use of 

the most recent versions of the Animal 

Waste Management (AWM) software, or 

equivalent software, and the Soil Plant 

Air Water (SPAW) Hydrology Tool, or 

an equivalent model. For a discussion of 

the technical evaluation and the AWM 

and SPAW modeling tools, see section 

III.F of this preamble. 

Several commenters expressed the 

need for evaluation criteria specific to 

beef cattle feedlots, based on their belief 

that reliance on swine, poultry, and veal 

calf new source provisions is 

inappropriate for all animal sectors. As 

described in more detail in Section III.F 

of this preamble, AWM software is a 

planning and design tool for animal 

feeding operations that can be used to 

estimate the production of manure, 

bedding, and process water and 

determine the size of storage facilities 

necessary to meet no discharge. AWM 

(CCE version 2.3.0) currently provides 

manure characteristics for eight animal 

types with the ability to modify these 

characteristics and add animal types as 

necessary. The field and pond 

hydrologic analyses conducted with the 

SPAW model are not specific to any 

animal species. Therefore beef and dairy 

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operators can use the AWM and SPAW 

tools to establish the appropriate design, 

construction, operation and 

maintenance of their facility to meet the 

no discharge requirement of 

certification. 

EPA also received comments seeking 

clarification regarding how the technical 

evaluation for new source swine, 

poultry and veal calf operations can 

apply to existing facilities given that 

EPA stated in the preamble to the 2003 

CAFO rule that the no discharge 

performance standard was not 

economically achievable for existing 

facilities. While EPA has determined 

that the no discharge performance 

standard was not appropriate to require 

for existing facilities on a national basis 

(see 68 FR 7218), EPA acknowledges 

that there are existing CAFOs that could 

meet the standard. Existing CAFOs that 

feel it is not economically achievable to 

meet a no-discharge standard always 

have the option of applying for a permit. 

In order to meet the second part of the 

first eligibility criterion, the final rule 

requires, in 40 CFR 122.23(i)(2)(i)(B), 

that any certifying CAFO must 

demonstrate that all of its production 

area, as defined at 40 CFR 122.23(b)(8), 

not just open containment structures, is 

designed, constructed, operated, and 

maintained such that there will be no 

discharge of manure, litter, process 

wastewater, or raw materials, such as 

feed, to surface waters. For a CAFO 

without open containment, this 

provision requires a demonstration of 

no discharge from the entire production 

area. For a CAFO that has an open 

containment structure, this provision 

requires a demonstration that the 

remainder of the production area (other 

than the open containment structure 

subject to the demonstration in 

§ 122.23(i)(2)(i)(A)), also will not 

discharge. Because of the special risk of 

discharge from open manure storage 

structures, greater specificity is 

provided regarding the elements of the 

demonstration in § 122.23(i)(2)(i)(A); 

however, the demonstration in 

§ 122.23(i)(2)(i)(B) must be technically 

sound and must be adequate to 

demonstrate that the production area is 

designed, constructed, operated, and 

maintained for no discharge. This 

demonstration must be based on an 

evaluation of site-specific 

characteristics, including, among others, 

the amount of manure generated during 

the storage period, the size of the storage 

structure, control measures to ensure 

diversion of clean water, and seasonal 

restrictions on land application. The 

preamble to the 2003 rule provides 

additional information regarding 

production area design for total 

containment and closed manure storage 

systems, such as lagoon covers, 

underhouse pit storage systems, and 

stockpile storage sheds. See 68 FR 7176, 

7219–20. Some CAFOs may have a 

combination of open manure storage 

structures and covered structures, while 

others will house all animals and store 

all manure, feed and by-products under 

cover. In either case, all parts of the 

production area must be included in the 

demonstrations required under 

§ 122.23(i)(2)(i)(A) and (B). 

In addition, as proposed under 40 

CFR 122.23(i)(2)(i)(C), this final rule 

requires any certified unpermitted 

CAFO to implement the measures set 

forth in 40 CFR 412.37(a) and (b) for the 

production area. These additional 

measures pertain to operation and 

maintenance and include provisions for 

visual inspections, depth markers for all 

open surface liquid impoundments, 

corrective action, mortality handling 

and recordkeeping. This final rule also 

requires these measures for permitted 

new swine, poultry and veal calf 

operations to meet a no discharge 

standard. Since both these permitted 

new source operations and unpermitted 

certified CAFOs need to ensure no 

discharge from the production area 

under the permit and certification 

requirements, respectively, it is 

appropriate to rely, in part, on those 

provisions to establish eligibility criteria 

for no discharge certification. The 

documents that are necessary to satisfy 

the first eligibility criterion, which 

addresses the CAFO’s design, 

construction, operation, and 

maintenance of the entire production 

area, include design documentation and 

all recordkeeping and operation and 

maintenance planning necessary to 

address the elements of § 122.23(i)(2)(i), 

which includes the measures set forth in 

§ 412.37(a) and (b). 

In the preamble to the 2008 

supplemental proposal, EPA requested 

comment on whether a recordkeeping 

checklist for use by certified CAFOs 

would be a useful tool. EPA suggested 

the possibility of making such a 

checklist available to all CAFO 

operators. Commenters generally 

supported the concept of a 

recordkeeping checklist that could be 

used by certified CAFOs, since the 

checklist could be used to document 

‘‘expectations for risk management.’’ 

Commenters added that the checklist 

should be developed in concert with the 

States. EPA plans to work with States to 

develop a checklist and consider 

whether State-specific checklists would 

also be appropriate. 

The second eligibility criterion 

requires the CAFO to have developed 

and be implementing an NMP that 

addresses, at a minimum, the elements 

set forth in § 122.42(e)(1) and 40 CFR 

412.37(c), and all site-specific operation 

and maintenance practices necessary to 

ensure that the CAFO will not 

discharge. The NMP must include 

provisions regarding nutrient 

management in the production area as 

well as in all land application areas 

under the control of the CAFO where 

the CAFO will land-apply manure. 

Because operation and maintenance 

practices and procedures are critical to 

discharge prevention, implementation 

of an NMP is an essential component of 

any CAFO’s efforts to ensure that it will 

not discharge from its production or 

land application areas. Furthermore, in 

order for any certified CAFO that land 

applies to ensure that the only 

discharges from the land application 

areas are non-point source agricultural 

stormwater discharges, the CAFO 

would, at a minimum, need to land 

apply in accordance with practices that 

ensure appropriate agricultural 

utilization of nutrients, including 

conservation practices and agronomic 

rates of application. For detailed 

discussion of unpermitted CAFOs and 

the agricultural stormwater exemption, 

see section III.B of this preamble. 

EPA received comments indicating 

that the final rule should establish a link 

between a facility’s open storage 

structure design and the land 

application practices outlined in a 

CAFO’s NMP. In the 2008 supplemental 

proposal, EPA intended that the CAFO’s 

NMP would reflect any operation and 

maintenance practices related to and 

assumed in the technical evaluation 

performed for open containment 

structures. To clarify this intent, 40 CFR 

122.23(i)(2)(ii)(B) of this final rule states 

that the operation and maintenance 

practices required to be part of the NMP 

must include ‘‘any practices or 

conditions established by a technical 

evaluation pursuant to paragraph 

(i)(2)(i)(A),’’ the provision applicable to 

CAFOs with open containment. For 

example, an existing facility may 

develop an NMP and then use AWM 

and the SPAW model to evaluate the 

adequacy of the designed storage facility 

and overall water budgets for the 

operation, respectively, which will rely 

upon inputs from the CAFO’s NMP such 

as the number and type of animals, soil 

profiles and planned crop rotations. In 

such a scenario, the CAFO may learn 

from the technical evaluation that more 

frequent lagoon drawdowns are 

necessary in order to achieve no 

discharge. To be eligible for certification 

under the final rule, the CAFO’s NMP 

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would then need to be revised to 

include the adjusted operation and 

maintenance practices resulting from 

the technical evaluation. It is these 

changed operation and maintenance 

practices that EPA is referring to in the 

§ 122.23(i)(2)(ii)(B) requirement for the 

NMP to address ‘‘any practices or 

conditions established by’’ the technical 

evaluation required for CAFOs with 

open containment structures under the 

first eligibility criteria. 

Commenters requested that EPA 

define what criteria can be used to meet 

the NMP eligibility requirement (e.g., 

whether a comprehensive nutrient 

management plan (CNMP) would 

suffice). As EPA stated in the 2008 

supplemental proposal, a CAFO may 

rely upon a CNMP 2 for purposes of 

certification eligibility, so long as the 

minimum NMP requirements of 

§ 122.42(e)(1) and § 412.37(c) are met by 

the CAFO’s plan, including all 

necessary operation and maintenance 

protocols.3 

As discussed below, 40 CFR 

122.23(i)(4) requires the certified CAFO 

to at all times be designed, constructed, 

operated, and maintained such that it 

meets the eligibility criteria to establish 

that the operation does not discharge or 

propose to discharge. Thus, to maintain 

a valid certification, a certified CAFO 

must update its NMP if any of the 

design specifications, practices, or other 

NMP provisions change over time. For 

example, if a certified CAFO operator 

decides to land-apply manure on a field 

that is not included in the NMP, the 

CAFO will need to calculate rates of 

application in accordance with the 

protocols for land application consistent 

with 40 CFR 122.42(e)(1)(viii) and revise 

the NMP to include the new field and 

the corresponding application rates and 

any other land application practices for 

the field in accordance with the 

protocols. Furthermore, since the 

eligibility criteria require the certified 

CAFO to implement the ‘‘up-to-date’’ 

NMP, the CAFO would then need to 

land apply in accordance with the 

application rates and other practices 

incorporated into the NMP for that field. 

2 Technical Guidance for Developing 

Comprehensive Nutrient Management Plans, USDA 

Natural Resources Conservation Service (2003), 

available at http://policy.nrcs.usda.gov/ 

viewerFS.aspx?id=3073. 

3 It is common for an operation to have one or 

more operation and maintenance plans in order to 

properly implement a number of NRCS 

conservation practice standards simultaneously. 

Also, to the extent that the necessary operation and 

maintenance requirements to implement any 

provision of the NMP are not included in the NMP 

itself, those requirements need to be implemented 

and included in an operation and maintenance plan 

to be maintained on site or at a nearby location. 

In the 2008 supplemental proposal, 

EPA stated that it would encourage 

CAFOs seeking certification to consult 

with qualified third-party professionals, 

but did not propose to require such 

consultation. Some commenters 

supported EPA’s position, while others 

believe that a third-party validation of 

the certification by an NRCS-certified 

technical service provider and 

professional engineer should be a 

required element of the eligibility 

criteria. Commenters expressed 

concerns that many CAFOs do not have 

the requisite knowledge to make 

technically sound determinations 

regarding how to meet the eligibility 

criteria for certification. EPA continues 

to believe that it is appropriate that the 

third-party consultation be 

recommended but not required because 

certification is voluntary and it is the 

CAFO owner or operator who must 

certify to the operation’s eligibility. 

Because a CAFO’s certification will not 

be approved by the permitting authority, 

it is up to the CAFO operator to be 

certain that the certification is valid in 

order to benefit from the presumption 

that it does not propose to discharge. 

Therefore, EPA recommends 

consultation with a qualified thirdparty. As stated in the preamble to the 

2008 supplemental proposal, any 

professional consulted by the CAFO 

should have the requisite training, 

experience and expertise to conduct 

and/or substantively review the 

required analyses, and to advise the 

owner or operator as to whether the 

CAFO is, in fact, designed, constructed, 

operated, and maintained such that it 

will not discharge. 

The third eligibility criterion for 

certification established by this final 

rule, 40 CFR 122.23(i)(2)(iii), requires 

that the CAFO maintain the 

documentation required by the first two 

criteria ‘‘either on site or at a nearby 

office, or otherwise make such 

documentation readily available to the 

Director or Regional Administrator upon 

request.’’ The 2008 supplemental 

proposal included a regulatory 

requirement that the NMP and other 

documentation of eligibility be 

maintained by the CAFO ‘‘on site.’’ 

Many commenters expressed the need 

for the final rule to include regulatory 

language allowing all documentation of 

the certification eligibility criteria to be 

held on-site or made readily available 

upon request. These commenters were 

primarily concerned that a requirement 

to maintain the documentation on site 

would be unreasonably burdensome on 

facilities that have multiple production 

sites with one central office. EPA agrees 

that the documentation necessary to 

demonstrate certification eligibility, 

including the CAFO’s site-specific NMP, 

should be maintained either on site or 

at a nearby office, or otherwise made 

readily available to the permitting 

authority upon request. The final rule 

established today includes this revision 

to the proposed language, which is also 

consistent with the provision 

established today applicable to the 

agricultural stormwater discharge 

exemption for unpermitted CAFOs, 

discussed in section III.B of this 

preamble. EPA recommends that 

operators maintain the necessary 

documentation on-site to ensure proper 

implementation of all operation and 

maintenance procedures. 

(ii) Submitting the Certification 

Under the certification option 

promulgated by this action, a CAFO 

seeking to certify that it does not 

discharge or propose to discharge is 

required to submit the certification to 

the permitting authority. Under 40 CFR 

122.23(i)(3), the submission to the 

Director must include: (1) The CAFO 

owner or operator’s name, address and 

phone number; (2) information 

regarding the CAFO’s location, 

including latitude and longitude; (3) a 

description of the basis for the CAFO’s 

certification that it satisfies the 

eligibility requirements of 40 CFR 

122.23(i)(2); (4) the certification 

statement set forth in 40 CFR 

122.23(i)(3)(iv); and (5) an official 

signature that meets the signatory 

requirements of 40 CFR 122.22. 

The signed certification makes the 

CAFO legally responsible for its 

representations to the Director regarding 

the design, construction, operation, and 

maintenance of the CAFO. As EPA 

noted in the preamble to the 2008 

supplemental proposal, the language 

regarding legal liability for making a 

false statement under the certification 

option is consistent with language in 40 

CFR 122.26(g) which applies to facilities 

seeking to obtain a ‘‘no exposure’’ 

exclusion from the requirement for an 

industrial stormwater discharge permit. 

EPA clarifies that under the applicable 

signatory requirements in § 122.22, 

signing the certification signifies that 

the signer is certifying that the 

certification was prepared under his/her 

direction or supervision in accordance 

with a system designed to assure that 

qualified personnel properly gathered 

and evaluated the information 

submitted and that based on the 

responsible official’s inquiry of the 

person or persons who manage the 

system, or those persons directly 

responsible for gathering the 

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information, the information submitted 

is, to the best of their knowledge and 

belief, true, accurate and complete. 

This final rule makes no changes to 

the existing regulations concerning how 

CAFOs may make Confidential Business 

Information (CBI) claims with respect to 

information they must submit to the 

permitting authority and how those 

claims will be evaluated. A facility may 

make a claim of confidentiality under 

the existing regulations at 40 CFR part 

2, subpart B. 

The third item the Agency is requiring 

for submission to the Director, as listed 

above, is a statement describing the 

basis for the CAFO’s certification that it 

is designed, constructed, operated, and 

maintained in accordance with the 

certification eligibility criteria. EPA’s 

expectation for what this description 

should include is unchanged from the 

2008 supplemental proposal. In the 

preamble to the 2008 supplemental 

proposal, EPA requested public 

comment on whether the scope and type 

of information included in the 

description of eligibility submitted to 

the Director should include: (1) The 

type and number of animals; (2) the type 

and capacity of manure and wastewater 

storage and/or containment; (3) storm 

size used as the basis for containment 

design; (4) whether the CAFO consulted 

with a professional engineer or 

technical service provider (TSP); (5) 

identification of the documents 

maintained on site in accordance with 

the eligibility criteria; and (6) any 

technical standards, tools (e.g. , RUSLE 

and Phosphorus Index) and formulas 

used to calculate application rates of 

manure, litter, and process wastewater. 

Commenters expressed differing 

viewpoints as to what documentation 

must be provided to the Director for the 

no discharge certification. Some 

commenters felt that the 2008 

supplemental proposal would have 

required the submission of too much 

information, and that CAFOs should 

only be required to submit a list of the 

documents created to establish a 

facility’s eligibility. Some of these stated 

that submission of any facility design or 

operation specifics is superfluous given 

that there is no review by the permitting 

authority. In contrast, other commenters 

believed that the extent of 

documentation to be submitted to the 

Director was insufficient to establish 

that a facility is designed, operated, and 

maintained in a way to ensure that it is 

not discharging. Specifically, these 

commenters desired that submissions 

include all documents associated with 

meeting the eligibility criteria for 

certification. 

After consideration of these 

comments, EPA believes that the list of 

information presented in the preamble 

to the supplemental proposal balances 

the need of the Director to be informed 

of critical aspects of the certified 

CAFO’s operation with the fact that the 

certification is not subject to review by 

the Director in order to become 

effective. It is reasonable that the 

description of the CAFO’s basis for 

certification be submitted as part of the 

certification, including the type of 

information listed above, as proposed in 

the supplemental proposal. EPA also 

recognizes that depending on sitespecific conditions at a particular 

facility, certain information may not be 

necessary (e.g. , an operation with no 

land application areas would not need 

to provide information about 

application rates of manure, litter, and 

process wastewater). Furthermore, if the 

Director is concerned that a CAFO that 

discharges or proposes to discharge has 

submitted a certification, the Director 

has the authority to request additional 

information from the CAFO, as 

discussed below. 

The authority given to the permitting 

authority under section 308 of the CWA 

to conduct inspections at operations is 

not affected by this rule. Section 308 

authorizes, among other things, EPA to 

require owners or operators of point 

sources to establish records, conduct 

monitoring activities and inspections, 

and make reports, to enable the 

permitting authority to determine 

whether there is any violation of any 

prohibition, or any requirement 

established under section 308, 402, or 

504 of the CWA. Therefore, any CAFO, 

whether it is certified, permitted, or 

neither, may be subject to an 

information gathering request or 

inspection, at the Director’s discretion 

and for any of the reasons provided by 

section 308 of the CWA. 33 U.S.C. 1318. 

Under this final rule, 40 CFR 

122.23(i)(4), a ‘‘certification that meets 

the requirements of paragraphs (i)(2) 

and (i)(3) * * * shall become effective 

on the date it is submitted, unless the 

Director establishes an effective date of 

up to 30 days after the date of 

submission.’’ A certification is effective 

if the CAFO meets the eligibility criteria 

in § 122.23(i)(2) and submits the signed 

certification statement and other 

required information in accordance with 

§ 122.23(i)(3). This rule also requires the 

use of certified mail or an equivalent 

method of documentation for 

identifying the date of submission, 

consistent with the supplemental 

proposal, in order to notify the Director 

that the CAFO has chosen to self-certify. 

EPA notes that under the final 

provision, the Director may, but is not 

required to, establish that certifications 

will become effective after a specified 

number of days, not to exceed 30 days, 

following submission of the certification 

if the Director deems such action 

appropriate, as discussed below. 

Regardless of whether the permitting 

authority chooses to establish an 

effective date in accordance with 

§ 122.23(i)(4), a certification becomes 

effective (either on the date it is 

submitted or on the date established by 

the Director) without acceptance or 

approval by the permitting authority. A 

decision by the permitting authority to 

delay the effective date would allow the 

permitting authority to become aware of 

the CAFO’s certification prior to it going 

into effect. A delayed effective date of 

up to 30 days could provide the 

opportunity for the permitting authority 

and the CAFO to have a focused 

exchange of information before the 

certification becomes effective. For 

example, as a result of such an exchange 

the CAFO may choose to consider 

making revisions to its certification to 

be assured it has submitted a 

certification that meets all the 

requirements of § 122.23(i)(2) and (3). 

Also, such an exchange could provide 

an opportunity for the CAFO to obtain 

additional information about 

maintaining a valid certification after it 

goes into effect. The permitting 

authority can also request information 

from an unpermitted CAFO, as provided 

in section 308 of the CWA, and provide 

feedback to the CAFO operator if the 

Director believes that the CAFO has not 

met the certification requirements. 

EPA emphasizes that the final rule 

does not require Director review of the 

certification. Therefore, if, for example, 

the permitting authority establishes that 

certifications in that State will become 

effective 30 days after submission, a 

certification from a CAFO that has met 

the eligibility and submission 

requirements in § 122.23(i)(2)–(3) will 

go into effect on day 30 regardless of 

any activities that take place during the 

30-day period, so long as the CAFO 

maintains eligibility throughout that 

period. Similarly, because the 

certification is not subject to permitting 

authority review and approval, inaction 

on the part of the permitting authority 

at any time during or after the 30 days 

does not indicate that the CAFO either 

has or has not met the eligibility and 

submission requirements. An effective 

date that is no more than 30 days after 

submission provides sufficient time for 

the permitting authority to receive the 

certification and have an exchange with 

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the CAFO, but it does not constitute an 

unreasonable delay for the CAFO to 

obtain a valid certification. Given these 

underlying principles, EPA has 

determined that it is appropriate to 

allow the Director discretion to establish 

an effective date that is up to, but not 

more than, 30 days after submission. 

EPA received comments concerning 

the submission process for no discharge 

certifications. Numerous commenters 

expressed concerns with the lack of any 

explicit requirement for Director review 

and approval of certifications. Some 

commenters asserted that the lack of 

review and public participation under 

the 2008 supplemental proposal violates 

the CWA and the Waterkeeper decision, 

and that without such review, 

certification provides no assurance of 

‘‘no discharge’’ and creates an 

impermissible permitting structure 

based on self-regulation. Other 

commenters indicated that Director 

review of key documentation is 

necessary to ensure that a facility’s 

certification meets applicable criteria. 

Some commenters requested that the 

documents necessary to meet the 

eligibility criteria also be subject to 

review by the Director and that approval 

of the no discharge certification be made 

contingent on such review. 

EPA does not agree that the lack of a 

requirement for Director review is 

contrary to the CWA or the Waterkeeper 

decision. The voluntary certification 

option is available only to CAFOs that 

do not discharge or propose to discharge 

and, therefore, are not required to seek 

NPDES permit coverage. Neither the 

CWA nor the Waterkeeper decision 

requires a permitting authority to review 

no discharge certifications or to subject 

such information to public 

participation. Under the CWA, such 

requirements apply only to the 

permitting process. In addition, EPA 

emphasizes that certification is not a 

substitute for a permit. Rather, a valid 

certification simply allows an 

unpermitted CAFO that is designed, 

constructed, operated, and maintained 

not to discharge to establish and 

document that it does not discharge or 

propose to discharge, in exchange for 

the assurance provided by a no 

discharge certification that it is not 

subject to the regulatory requirement to 

seek permit coverage in 40 CFR 

122.23(d)(1) and (f). It is the CAFO’s 

choice and responsibility to establish 

and maintain a valid certification or lose 

the benefits afforded by the certification. 

Furthermore, as mentioned above, the 

final rule allows the permitting 

authority to establish an effective date 

for certification of up to 30 days after 

the date of submission by the CAFO. 

Allowing States the discretion to delay 

the effective date of certification 

addresses some comments from States 

expressing uncertainty about the role of 

the permitting authority in the 

certification process. 

(iii) Limitations on Certification 

This rule includes several limitations 

on certification related to the term of a 

certification, withdrawal of certification, 

and recertification after a certification 

becomes invalid. 

Consistent with the 2008 

supplemental proposal, under this final 

rule, a no discharge certification will 

expire five years after the effective date, 

unless the CAFO voluntarily withdraws 

the certification or the certification 

becomes invalid (i.e., the CAFO has 

either discharged or ceases to be 

designed, constructed, operated, and 

maintained in accordance with 

certification eligibility criteria) during 

the five-year term. See 40 CFR 

122.23(i)(4). Some commenters agreed 

with the proposed five-year term of 

certification, because the limited term of 

certification would ensure that the 

CAFO reevaluates eligibility. Other 

commenters contended that facilities 

should recertify on a more frequent 

basis, either annually or triennially, to 

ensure more frequent reevaluation of 

their certification. A number of 

commenters did not believe that a term 

of certification should be prescribed; 

several of these commenters maintained 

that if a facility remains in compliance 

with the certification criteria and does 

not make any significant changes in 

operation, the certification should 

remain valid indefinitely. 

After considering the comments 

regarding the appropriate term for 

certification, EPA has concluded that 

the proposed five-year term is 

appropriate. At the end of this term the 

certification can be renewed, if desired 

by the CAFO. Since CAFOs commonly 

alter their operations over time, it is 

reasonable for the CAFO to periodically 

reevaluate and update its certification 

submission. In addition, renewal every 

five years does not create an undue 

burden on the CAFO or the permitting 

authority because CAFOs that have not 

had major changes in operations may be 

able to use much of the same 

documentation as prepared previously, 

and permitting authorities are not 

required to review and approve the 

certification. A shorter term for 

certification, such as one or three years, 

is not necessary because a properly 

certified CAFO needs to evaluate the 

facility at regular intervals as part of the 

inspection and recordkeeping 

requirements. Thus, a five-year term is 

reasonable. 

Under 40 CFR 122.23(i)(5) a CAFO 

may withdraw its certification at any 

time by notifying the Director, by 

certified mail or equivalent method of 

documentation, that it is withdrawing 

its certification. The certification is 

effectively withdrawn on the date the 

notification is submitted to the Director. 

If a CAFO’s certification becomes 

invalid as provided in § 122.23(i)(4), 

discussed below, § 122.23(i)(5) requires 

the CAFO operator to withdraw its 

certification within three days of the 

date on which the CAFO becomes aware 

that the no discharge certification is 

invalid. As proposed, this final rule 

does not require the CAFO operator to 

notify the Director of the reason for 

withdrawing the certification because 

certification is voluntary. 

EPA received a number of comments 

concerning the withdrawal of 

certification. These comments generally 

focused on the need for a certified 

CAFO to provide more information 

regarding its actions leading to the 

withdrawal. Some commenters observed 

that in order to withdraw certification, 

CAFOs should have to submit the 

reasons for such withdrawal to the 

Director. EPA believes it is reasonable 

for a CAFO to be able to withdrawal its 

voluntary certification at any time 

without additional explanation. The 

decision to certify is voluntary, and 

thus, it is appropriate to allow a CAFO 

to decide to withdraw its certification 

for any reason with no further 

explanation. However, certain situations 

require the CAFO to withdraw its 

certification. This final rule requires 

that a CAFO withdraw its certification 

by notifying the Director in the event 

that the certification is no longer valid, 

either because of a discharge or because 

the CAFO ceases to meet the eligibility 

criteria. See § 122.23(i)(4) and (5). 

Notifying the Director that a CAFO is 

withdrawing its certification provides 

the information necessary for the 

Director to maintain an up-to-date 

record of certified CAFOs. A CAFO that 

fails to withdraw its certification within 

three days of becoming aware that the 

certification is invalid would be in 

violation of this regulatory requirement. 

EPA believes these provisions 

appropriately balance the voluntary 

nature of certification with the value to 

the Director of maintaining accurate 

records of the universe of certified 

CAFOs. 

This final rule describes in 

§ 122.23(i)(4) the situations that cause a 

certification to become invalid. First, in 

the unlikely event of a discharge from 

a properly certified CAFO, the 

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certification would cease to be valid and 

would no longer be in effect. Second, 

should a CAFO fail to continue to meet 

any of the eligibility criteria, the CAFO’s 

certification would no longer be valid. 

Circumstances that could result in the 

certification becoming invalid include, 

for example, an increase in animals that 

exceeds the capacity of the production 

area for manure storage and handling or 

a loss of land application areas such that 

the assumptions in the NMP concerning 

land application would no longer be 

appropriate, if the CAFO’s operations, 

NMP and certification documentation 

were not revised to address these 

changed circumstances. EPA 

emphasizes that failure by a certified 

CAFO to continue to meet the eligibility 

requirements in 40 CFR 122.23(i)(2) is 

not, in and of itself, a violation of any 

regulatory requirement because 

certification is strictly voluntary. For 

example, failure to implement the 

measures set forth in 40 CFR 412.37(a)– 

(b), which are required for no discharge 

certification eligibility under 40 CFR 

122.23(i)(2)(i), is not a violation of 

§ 412.37(a)–(b) but renders the 

certification invalid. However, failure to 

withdraw a certification that has 

become invalid is a violation of the 

requirement to do so. 

As explained in the 2008 

supplemental proposal, once a 

certification ceases to be valid, the 

operator cannot rely on it if a 

subsequent enforcement action is 

brought for a violation of the duty to 

apply for a permit that is triggered after 

the certification becomes invalid. In 

other words, once a CAFO’s certification 

becomes invalid, the CAFO is in the 

same position as any other unpermitted 

and uncertified CAFO. After 

withdrawing the invalid certification, 

the operator may be interested in 

seeking to recertify that the CAFO does 

not discharge or propose to discharge or, 

if the CAFO does discharge or propose 

to discharge, the CAFO is required to 

seek permit coverage, as stated in 40 

CFR 122.23(i)(5)(ii). 

In the 2008 supplemental proposal, 

EPA proposed to allow a previously 

certified CAFO to recertify by revising 

its operations to address the deficiency 

that led to the invalid certification and 

submitting a new certification 

statement. Under the proposal, if the 

certification was rendered invalid by a 

discharge, in order to recertify a CAFO 

would have to submit to the Director the 

information required under 40 CFR 

122.23(i)(3) and additional information 

describing the discharge and the steps 

taken by the CAFO to permanently 

address the cause of the discharge. As 

proposed, such a recertification 

submission, like the initial submission, 

would not be subject to review. 

Under this final rule, if a CAFO’s 

certification becomes invalid due to a 

failure to meet the eligibility criteria, as 

opposed to because of a discharge, and 

the CAFO wishes to recertify, the owner 

or operator would need to make the 

changes necessary to establish eligibility 

under § 122.23(i)(2). The provisions 

applicable to the recertification 

submission and effective date would be 

the same as for any certification. See 

§ 122.23(i)(3) and (4). If the CAFO 

wishes to recertify after a discharge has 

occurred, the CAFO would need to meet 

the additional requirements of 40 CFR 

122.23(i)(6), discussed in detail below. 

Commenters expressed several 

viewpoints with regard to the proposed 

provisions for recertification after a 

discharge. Some commenters supported 

the recertification process as proposed. 

These commenters generally recognized 

that CAFOs may encounter unusual 

circumstances that result in a discharge 

and that it is appropriate to allow for 

recertification once the conditions that 

resulted in the discharge are addressed. 

Certain other commenters argued that 

subsequent to a discharge any 

recertification should be reviewed by 

the permitting authority and open to 

public comment to ensure a rigorous 

assessment of whether recertification is 

appropriate. Some commenters asserted 

that recertification after a discharge 

should not be allowed at all under the 

CAFO regulations. Furthermore, some 

commenters believe it would be 

inequitable for unpermitted CAFOs to 

discharge and recertify if other 

discharging operators are required to 

seek permit coverage. Several of these 

commenters asserted that any CAFO 

that discharges should be required to 

obtain an NPDES permit. 

EPA emphasizes that it will be highly 

unlikely for a CAFO that is designed, 

constructed, operated, and maintained 

in accordance with the eligibility 

criteria in § 122.23(i)(2) to discharge. 

Furthermore, EPA maintains its 

position, stated in the preamble to the 

2008 supplemental proposal, that the 

Agency generally considers a recurring 

discharge as evidence that a CAFO is 

not eligible for certification or 

recertification and needs to seek permit 

coverage. However, given the possibility 

of a discharge from a properly certified 

CAFO, albeit remote, EPA believes it is 

necessary for the final rule to include 

provisions specifically for a CAFO 

seeking to recertify after a discharge. 

In response to comments, EPA has 

established specific criteria in this final 

rule that limit a CAFO’s ability to 

recertify after a discharge to those 

situations where (1) the certification 

was valid at the time of the discharge, 

meaning the CAFO continued to be 

designed, constructed, operated, and 

maintained for no discharge in 

accordance with all provisions of the 

NMP and any operation and 

maintenance plans included in the 

certification; (2) the operator has made 

any necessary changes to the CAFO’s 

design, construction, operation and 

maintenance to permanently address the 

cause of the discharge and ensure that 

no discharge from this cause occurs in 

the future; and (3) the CAFO has not 

previously recertified after a discharge 

from the same cause. The first criterion 

limits the availability of recertification 

after a discharge by excluding CAFOs 

that discharge after allowing the 

certification to lapse. EPA believes that 

a CAFO that certifies under penalty of 

law that it is and will continue to be 

designed, constructed, operated, and 

maintained so as not to discharge, that 

then fails to satisfy this criterion and 

subsequently discharges, should not be 

given the opportunity to once again 

obtain the benefits of a no discharge 

certification. The second criterion 

ensures that a CAFO will only recertify 

after it has carefully evaluated the cause 

of the discharge and taken whatever 

action is necessary to ensure that a 

discharge from the same cause will not 

occur again. Finally, the third criterion 

constrains a CAFO from engaging in a 

cycle of recertifying after multiple 

discharges from the same cause. The 

voluntary certification option 

established in this rule is not intended 

to be a mechanism for discharging 

CAFOs to avoid obtaining permit 

coverage, a concern cited by several 

commenters who opposed the 

certification option. On the contrary, 

EPA is providing the certification option 

to allow CAFOs that meet the eligibility 

criteria to establish up front that they do 

not discharge or propose to discharge. 

The final rule provides that the 

CAFO’s recertification will not become 

effective until 30 days from the date of 

submission. The operator is also 

required to submit the following 

information for review by the Director: 

A description of the discharge, 

including the date, time, cause, duration 

and approximate volume of the 

discharge, and a detailed explanation of 

the steps taken by the CAFO to 

permanently address the cause of the 

discharge. This 30-day review period 

provides an opportunity for the Director 

to consider the circumstances leading to 

the discharge, any actions taken by the 

CAFO to permanently address the cause 

of the discharge, and any other relevant 

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compliance information regarding the 

facility. EPA encourages State 

permitting authorities to take advantage 

of this opportunity to consider such 

information. As is true for the general 

certification process described above, 

when a CAFO seeks to recertify after a 

discharge, the Director has the authority 

to collect additional information from 

the CAFO, assess whether the criteria in 

this rule are satisfied, and provide 

feedback to the CAFO if he/she believes 

that the CAFO has not met the 

recertification criteria. For example, the 

30-day review period will allow the 

Director to assess whether or not the 

CAFO has previously recertified after a 

discharge from the same cause. 

However, as with the initial 

certification, the Director is not required 

to take any action for a certification to 

become effective at the end of the 30-

day review period and inaction does not 

indicate that the CAFO has met the 

recertification criteria. After considering 

public comments on the 2008 

supplemental proposal regarding 

recertification after a discharge, EPA has 

determined that this 30-day review 

period is reasonable and prudent to 

allow the Director to review situations 

where a previously certified CAFO has 

had an actual discharge. 

Overall, the limited conditions under 

which a CAFO can recertify following a 

discharge, the description of the 

discharge submitted to the permitting 

authority, and the required 30-day 

review period prior to the recertification 

becoming effective, provide an 

opportunity for the Director to 

determine whether the CAFO discharges 

or proposes to discharge and must seek 

coverage under an NPDES permit. For 

example, as provided in 40 CFR 

122.28(b)(2)(vi), the Director has the 

authority to direct that the CAFO be 

covered under a general permit if one is 

available. 

EPA believes the final rule provisions 

covering recertification after a discharge 

provide an appropriate balance of the 

flexibility offered by voluntary 

certification and the need for scrutiny of 

previously certified CAFOs that have 

discharged. Additionally, under the 

final rule, any previously certified 

CAFO that discharges or proposes to 

discharge is subject to the permit 

application requirements of 40 CFR 

122.23(d)(1) and (f), and therefore must 

apply when the CAFO proposes to 

discharge. A CAFO that has 

permanently addressed the cause of the 

discharge such that the CAFO does not 

‘‘discharge or propose to discharge’’ is 

not required to seek permit coverage 

regardless of whether it recertifies. For 

further discussion of the effects of a past 

discharge on a CAFO’s permit 

application requirements, see the duty 

to apply discussion at section III.A.3(a) 

of this preamble. 

B. Agricultural Stormwater Exemption 

1. Provisions in the 2003 CAFO Rule 

The discharge of manure, litter, or 

process wastewater from a land 

application area under the control of a 

CAFO is a discharge subject to NPDES 

permitting requirements, unless the 

discharge is an ‘‘agricultural stormwater 

discharge,’’ which is excluded from the 

meaning of the term ‘‘point source’’ 

under 33 U.S.C. 1362(14). In the 2003 

CAFO rule, EPA differentiated between 

discharges from land application areas 

under the control of the CAFO that are 

point source discharges and those that 

are ‘‘agricultural stormwater discharges’’ 

exempt from NPDES permit 

requirements. 

In the 2003 rule, EPA promulgated a 

definition of agricultural stormwater for 

CAFO land application areas that 

referenced 40 CFR 122.42(e)(1)(vi)–(ix). 

The referenced regulatory text includes 

requirements for edge-of-field buffers or 

equivalent measures, testing of manure 

and soil, land application at site-specific 

agronomic rates, and recordkeeping. 

While not explicitly included in the 

definition of agricultural stormwater, 

technical standards established by the 

Director, in accordance with effluent 

limitations guidelines (ELGs) in 40 CFR 

412.4(c) applied to Large CAFOs’ 

nutrient management plans for land 

application. These more specific 

limitations implemented the general 

requirements at § 122.42(e)(1)(vi)–(ix), 

and because the 2003 rule required all 

CAFOs with a potential to discharge to 

obtain permits, virtually all Large 

CAFOs were required to comply with 

them. 

2. Summary of the Second Circuit Court 

Decision 

The Second Circuit upheld EPA’s 

definition of agricultural stormwater 

established by the 2003 rule. In 

addition, ELG requirements of 40 CFR 

412.4(c) concerning land application for 

Large CAFOs were not challenged. The 

court did not, however, specifically 

address the applicability of these 

requirements to unpermitted Large 

CAFOs seeking to claim the agricultural 

stormwater exemption for land 

application discharges, in light of its 

vacature of the duty to apply for all 

Large CAFOs. Waterkeeper Alliance et 

al. v. EPA, 399 F.3d 486 (2d Cir. 2005). 

3. This Final Rule 

As a result of the regulatory revisions 

being made by this action in response to 

the Waterkeeper decision, which held 

that EPA does not have authority to 

require facilities with solely a potential 

to discharge to obtain permits, Large 

CAFOs are not required to seek NPDES 

permit coverage unless they discharge 

or propose to discharge. For those Large 

CAFOs that obtain NPDES permit 

coverage, provisions for determining 

whether precipitation-related discharges 

from their land application areas qualify 

for the agricultural stormwater 

exemption were promulgated in the 

2003 rule and codified at 40 CFR 

122.23(e). As explained above, under 

the 2003 rule, Large CAFO NPDES 

permits must require the development 

and implementation of nutrient 

management plans for land application 

in accordance with the ELG in 40 CFR 

part 412. Nutrient management plans for 

land application in accordance with 40 

CFR 412.4(c) include application rates 

and other practices for manure, litter, 

and process wastewater developed in 

compliance with technical standards, as 

well as other requirements. These land 

application requirements are then 

incorporated into the permit pursuant to 

40 CFR 122.42(e)(1). Therefore, for 

permitted Large CAFOs that land apply 

manure, litter, or process wastewater, 

‘‘site-specific nutrient management 

practices * * * as specified in 

§ 122.42(e)(1)(iv)–(ix)’’ in § 122.23(e) 

include land application rates and other 

practices determined in compliance 

with technical standards. 

The 2003 rule at § 122.23(e) specifies 

how Large CAFOs that have NPDES 

permits qualify for the agricultural 

stormwater exemption. Specifically, 

under the existing regulation, the permit 

must set forth the site-specific nutrient 

management practices that ensure 

appropriate agricultural utilization of 

nutrients as specified in 40 CFR 

122.42(e)(1)(vi)–(ix) in order for 

precipitation-related discharges from 

such land application areas to be 

exempt agricultural stormwater 

discharges. EPA did not propose to 

amend the existing agricultural 

stormwater discharge exemption 

provision in § 122.23(e), nor has EPA 

otherwise reopened the provision. 

In this rule, however, EPA is adopting 

a new regulatory provision clarifying 

what constitutes agricultural stormwater 

for unpermitted Large CAFOs. The 

Waterkeeper court held that Large 

CAFOs with a mere potential to 

discharge were not required to obtain 

permits. Because the existing 

regulations could be construed as 

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applying only to Large CAFOs with 

NPDES permits, EPA explained in the 

preamble to the 2006 proposed rule that 

a CAFO with no discharges other than 

precipitation-related discharges from its 

land application areas would not be 

considered to ‘‘discharge’’ if it applies 

manure, litter, or process wastewater to 

land under its control in accordance 

with nutrient management practices that 

ensure appropriate agricultural 

utilization of the nutrients in the 

manure, litter, or process wastewater as 

specified § 122.42(e)(1)(vi)–(ix). The 

Agency also expressly stated in its 2006 

proposal that, for unpermitted Large 

CAFOs to qualify for the statutory 

agricultural stormwater exemption, 

manure, litter, and process wastewater 

must be applied in compliance with 

technical standards, noting that 

technical standards are, in significant 

part, intended to ensure the appropriate 

agricultural utilization of the nutrients 

contained in the manure, litter, or 

process wastewater. 71 FR 37,750. EPA 

also requested comment on whether to 

codify language to require that 

unpermitted Large CAFOs that land 

apply manure, litter, or process 

wastewater must comply with the 

technical standards established by the 

Director in order to qualify for the 

agricultural stormwater discharge 

exemption for precipitation-related 

discharges from land application areas 

under their control. 

In the preamble to the 2006 proposed 

rule, EPA also discussed the reference to 

the documentation requirement found 

in 40 CFR 122.42(e)(1)(ix). EPA noted 

that documentation is a crucial element 

for determining whether a CAFO is land 

applying manure, litter, or process 

wastewater in a manner that ensures the 

appropriate agricultural utilization of 

nutrients such that any runoff from land 

application areas under a CAFO’s 

control consists only of exempt 

agricultural stormwater discharges. 71 

FR 37,750. 

The provision established in this rule 

at § 122.23(e)(1) clarifies that in order 

for unpermitted Large CAFOs to have 

their precipitation-related discharges 

qualify as agricultural stormwater 

discharges, they must land apply 

manure, litter, or process wastewater 

‘‘in accordance with site-specific 

nutrient management practices that 

ensure appropriate agricultural 

utilization of the nutrients in the 

manure, litter, or process wastewater, as 

specified in § 122.42(e)(1)(vi)–(ix).’’ This 

interpretation of the statutory 

agricultural stormwater exemption was 

upheld by the Second Circuit in the 

Waterkeeper decision. In addition, the 

new provision established at 40 CFR 

122.23(e)(2) requires unpermitted Large 

CAFOs to have nutrient management 

planning documentation on site, at a 

nearby office, or otherwise make it 

readily available upon request to 

support assertions that the only 

discharges from their land application 

areas are precipitation-related 

discharges that qualify for the 

agricultural stormwater exemption. As 

noted above, EPA has not reopened any 

aspect of the 2003 CAFO rule applicable 

to permitted CAFOs. Rather, the new 

provisions clarify how the agricultural 

stormwater exemption applies to Large 

CAFOs that do not have an NPDES 

permit. This is not a new requirement 

for unpermitted CAFOs, but rather a 

clarification of EPA’s existing 

interpretation of the agricultural 

stormwater exemption in CWA section 

502(14). 

EPA is modifying the interpretation 

articulated by EPA in the 2006 proposal 

of how technical standards apply to 

unpermitted CAFOs seeking to have 

their precipitation-related discharges 

from land application areas qualify for 

the agricultural stormwater exemption. 

Under this final rule, a precipitationrelated discharge from land application 

areas under the control of an 

unpermitted Large CAFO constitutes an 

agricultural stormwater discharge where 

the CAFO has land applied manure, 

litter, or process wastewater in 

accordance with site-specific nutrient 

management practices that ensure 

appropriate agricultural utilization of 

the nutrients in the manure, litter, or 

process wastewater, as specified in 

§ 122.42(e)(1)(vi)–(ix). Nutrient 

management practices and rates of 

application satisfy the requirements of 

40 CFR122.42(e)(1)(viii) when they are 

in accordance with technical standards 

established by the Director. The form, 

source, amount, timing, and method of 

application of nutrients are essential 

components of the protocols for land 

application of manure, litter, or process 

wastewater specified in 

§ 122.42(e)(1)(viii). As explained below, 

CAFOs that land apply using nutrient 

management practices based on 

standards other than the technical 

standards established by the Director 

would have to demonstrate that such 

practices ensure the appropriate 

agricultural utilization of the nutrients 

in the manure, litter, or process 

wastewater as specified in 

§ 122.42(e)(1)(viii). 

Technical standards established by 

the Director provide an objective basis 

for determining when precipitationrelated discharges from land application 

areas are exempt from NPDES permit 

requirements. Such technical standards 

are reviewed and determined by the 

permitting authority to provide a 

technically sound framework for 

establishing rates of application that 

generally would satisfy the 

requirements of § 122.42(e)(1)(viii). 

Such technical standards specify the 

method or methods for determining 

whether land application rates are to be 

based on nitrogen or phosphorus, or 

whether existing nutrient loads in the 

soil preclude land application, and also 

address the form, source, amount, 

timing, and method of application on 

each field to achieve realistic 

production goals while minimizing 

movement of nitrogen and phosphorus 

to surface waters. Thus, technical 

standards provide an objective and 

reliable framework for developing rates 

of application and other practices for 

each field, taking into account a range 

of critical factors. For purposes of 

§ 122.42(e)(1)(viii), rates of application 

developed using technical standards 

must encompass and include all of the 

factors discussed above. 

Because the technical standards 

established by the Director represent the 

permitting authority’s judgment as to 

practices that ensure appropriate 

agricultural utilization of nutrients, as 

discussed above, they provide a sound 

basis for determining and documenting 

that a precipitation-related discharge 

from land application areas will meet 

the requirements of § 122.42(e)(1)(viii). 

If a facility chooses to take a different 

approach and follow other standards, 

the facility would need to demonstrate 

not only that its practices accorded with 

such alternative standards, but also that 

the standards provided a reliable, 

technically valid basis for meeting the 

terms of § 122.42(e)(1)(viii). While 

technical standards established by the 

Director would have undergone careful 

review by the Director to determine 

their validity for purposes of applying 

the agricultural stormwater exemption, 

there may not have been a comparable 

review in place for alternative 

standards. Thus, the CAFO may have to 

demonstrate both the appropriateness of 

alternative standards and that its 

practices conformed to them in order for 

its discharges to qualify for the 

agricultural stormwater exemption. 

EPA recognizes that there may be 

other standards that are developed 

besides those established by the Director 

that may also provide guidance to 

producers regarding appropriate 

agronomic nutrient management 

practices and the development of rates 

of application. Under this rule, owners 

and operators of unpermitted CAFOs are 

not precluded from relying on such 

other standards. However, while other 

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standards may provide useful guidance, 

in the absence of being reviewed and 

established by the Director, it is the 

CAFO’s responsibility to demonstrate 

that such alternative standards do, in 

fact, ‘‘ensure appropriate agricultural 

utilization of the nutrients in the 

manure, litter, or process wastewater,’’ 

as required by § 122.42(e)(1)(viii). 

In determining whether a CAFO’s 

site-specific nutrient management 

practices do ‘‘ensure appropriate 

utilization of the nutrients’’ in the land 

applied manure, litter, or process 

wastewater, EPA will evaluate an 

unpermitted CAFO’s nutrient 

management practices using the 

technical standards established by the 

Director as a baseline and expects the 

same of authorized States. As discussed, 

EPA considers the technical standards 

established by the Director to be a sound 

measure for determining whether the 

form, source, amount, timing, and 

method of application meet the 

requirements of § 122.42(e)(1)(viii). 

As noted above, in order for an 

unpermitted Large CAFO without an 

NPDES permit to establish that the only 

precipitation-related discharges from its 

land application areas are agricultural 

stormwater discharges, it must have 

documentation showing that its nutrient 

management practices are in accordance 

with § 122.23(e)(1). This is not a new 

concept, as one of the requirements 

specified in § 122.23(e) promulgated in 

the 2003 rule is to maintain 

documentation as required by 40 CFR 

122.42(e)(1)(ix). Section 122.42(e)(1)(ix) 

requires specific records to be 

maintained to document the 

implementation of the elements of 

§ 122.42(e)(1)(vi)–(viii). As stated in the 

preamble to the 2006 proposed rule, the 

necessary documentation includes both 

the nutrient management planning 

documents and the additional 

recordkeeping that demonstrates the 

actual nutrient management practices 

that have been implemented. See 71 FR 

37,750. Such documentation is essential 

for determining whether precipitationrelated discharges from a land 

application area are agricultural 

stormwater discharges or point source 

discharges. 

It is reasonable and appropriate that 

unpermitted CAFOs be required to 

demonstrate that their nutrient 

management practices, including rates 

of application, meet the regulatory 

definition of agricultural stormwater 

promulgated in 2003, and to do so 

means maintaining documentation of 

their nutrient management practices. 

Without adequate documentation, it 

would be difficult, if not impossible, to 

know whether such precipitationrelated discharges are unpermitted point 

source discharges or are exempt 

agricultural stormwater discharges. 

Because unpermitted CAFOs are not 

subject to the place and time 

recordkeeping requirements of 

§ 122.42(e)(2), EPA is in this rule 

requiring that unpermitted CAFOs that 

land apply manure, litter, or process 

wastewater maintain on site or at a 

nearby office, or otherwise make 

available upon request documentation 

showing that precipitation-related 

discharges from their land application 

areas are agricultural stormwater 

discharges. The requirement for 

documentation is referenced in 

§ 122.42(e)(1)(ix), and is authorized by 

section 308(a) of the CWA. Section 

308(a) gives EPA authority to require 

any point source to establish and 

maintain records for determining 

whether ‘‘any person is in violation’’ of 

a prohibition, including the section 

301(a) prohibition against point source 

discharges unless authorized under an 

NPDES permit. Section 308(a)(4) 

authorizes EPA to require records, 

reports, and other information when 

required to carry out provisions of the 

CWA, including sections 301 and 402. 

The inclusion of this requirement for 

unpermitted CAFOs to keep the 

documentation on site or to make it 

readily available upon request is for the 

purpose of giving States and EPA a basis 

for determining whether the CAFO’s 

land application discharges are within 

the statutory exemption for agricultural 

stormwater. EPA expects that, in 

general, CAFOs will maintain their 

nutrient management plans for land 

application on site because they set out 

the protocols that must be followed in 

practice. Documentation of the sitespecific nutrient management practices 

that is not produceable to an inspector 

at the time of a permitting authority’s 

inspection would not be considered to 

be made ‘‘readily available’’ and, 

further, would raise questions as to 

whether it is actually being properly 

used by the CAFO. 

EPA received comments in support of 

its position that a facility need not have 

an NPDES permit in order for 

precipitation-related discharges from 

land application areas to be deemed 

agricultural stormwater discharges. 

Other commenters disagreed for a 

variety of reasons. First, commenters 

asserted that the proposal was 

inconsistent with the approach EPA 

established in the 2003 rule. Second, 

some commenters argued that allowing 

the CAFO owner or operator to 

determine whether its nutrient 

management practices meet the 

requirements of the rule creates a 

similar ‘‘impermissible self-regulatory 

permitting scheme’’ as that struck down 

by the Second Circuit Court of Appeals 

in the Waterkeeper decision. They 

argued that these nutrient management 

practices must be subject to review and 

consideration by the permitting 

authority and the public. 

EPA does not agree that only CAFOs 

with NPDES permits should be allowed 

to claim that discharges from their land 

application areas are agricultural 

stormwater discharges. The question is 

whether a precipitation-related 

discharge from a CAFO’s land 

application area is exempt from 

permitting requirements as an 

‘‘agricultural stormwater discharge’’ or 

whether it is a point source discharge 

that requires a permit. As the Court of 

Appeals for the Second Circuit 

reiterated in the Waterkeeper decision, 

‘‘a discharge from an area under the 

control of a CAFO can be considered 

either a CAFO discharge that is subject 

to regulation or an agricultural 

stormwater discharge that is not subject 

to regulation.’’ 399 F.3d 486 at 508 

(citing Concerned Area Residents for the 

Environment v. Southview Farms, 34 

F.3d 114 (2d Cir. 1994)). The assessment 

of whether a discharge is exempt as 

agricultural stormwater or a point 

source discharge subject to permitting 

requirements is not part of the 

permitting process, but rather precedes 

it. 

For the same reason, EPA does not 

agree that a self-regulatory regime is 

created by allowing unpermitted CAFOs 

to claim that precipitation-related 

discharges from their land application 

areas are exempt if they land apply 

manure, litter, or process wastewater in 

accordance with appropriate nutrient 

management practices as required by 

§ 122.23(e). In the context of the 

agricultural stormwater discharge 

exemption, nutrient management 

practices are not effluent limitations, 

which can only be established and 

enforced through NPDES permits. 

NPDES permits are authorized by 

section 402 of the CWA for the 

‘‘discharge of any pollutant’’ under the 

terms of that section, including 

compliance with effluent limitations. 

Section 502(12) defines ‘‘discharge of a 

pollutant’’ and ‘‘discharge of pollutants’’ 

as ‘‘the addition of any pollutant * * * 

from any point source.’’ The definition 

of ‘‘point source’’ in section 502(14) 

expressly excludes ‘‘agricultural 

stormwater discharges and return flows 

from irrigated agriculture.’’ Therefore, 

NPDES permits are necessary for point 

source discharges, but not for 

agricultural stormwater discharges. 

Consequently, the site-specific nutrient 

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management practices that a CAFO 

must implement in order for 

precipitation-related discharges from 

areas under the CAFO’s control to be 

considered agricultural stormwater 

discharges are not effluent limitations. 

Rather, they are preconditions for 

determining whether the agricultural 

stormwater exemption applies for 

discharges from land application areas 

under the CAFO’s control. Because the 

site-specific nutrient management 

practices are not effluent limitations, 

they are not subject to the requirements 

in section 402 for public review and 

comment. However, persons who 

believe that an unpermitted Large 

CAFO’s nutrient management practices 

are not sufficient to qualify for the 

agricultural stormwater exemption are 

free to bring citizen suits under CWA 

section 505 alleging that the CAFO is 

discharging without a permit. 

The Waterkeeper court upheld EPA’s 

construction of the definition of point 

source as articulated in § 122.23(e) as 

reasonable. In this rule, EPA has not in 

any way reopened this provision of the 

2003 rule. Nor is EPA changing any 

aspect of § 122.23(e) with respect to 

what is required in order for 

precipitation-related discharges from 

land under the control of a CAFO where 

manure, litter, or process wastewater is 

applied to qualify as ‘‘agricultural 

stormwater discharges.’’ The approach 

taken in this rule is simply to describe 

how a CAFO without an NPDES permit 

may come within the scope of the 

existing language in § 122.23(e). 

C. Nutrient Management Plans 

1. Provisions in the 2003 CAFO Rule 

Under the 2003 CAFO rule, an NPDES 

permit issued to a CAFO must include 

a requirement for the permittee to 

develop and implement a nutrient 

management plan (NMP). At a 

minimum, the NMP is required to 

include best management practices 

(BMPs) and procedures necessary to 

achieve effluent limitations and 

standards, to the extent applicable, 

including the minimum requirements of 

40 CFR 122.42(e)(1)(i)–(ix). Effluent 

limitations for Large CAFOs are set forth 

in the effluent limitations guidelines 

(ELG) in 40 CFR part 412, which contain 

specific NMP requirements applicable 

to both the production area and the land 

application areas under the control of 

Large CAFOs in the cattle, swine, 

poultry, and veal calf subcategories. For 

small and medium CAFOs, and other 

operations not subject to 40 CFR part 

412 requirements, effluent limitations, 

including those applicable to land 

application areas, are established on the 

basis of the best professional judgment 

(BPJ) of the permitting authority 

pursuant to CWA section 402(a)(1)(B) 

and defined in 40 CFR 125.3(c)(2). 

2. Summary of the Second Circuit Court 

Decision 

The U.S. Court of Appeals for the 

Second Circuit found that the terms of 

an NMP are effluent limitations and 

vacated the 2003 CAFO rule insofar as 

the rule allowed permitting authorities 

to issue NPDES permits to CAFOs 

without (1) reviewing the terms of the 

NMPs; (2) providing for adequate public 

participation in the development, 

revision, and enforcement of the 

nutrient management plans; and (3) 

including the terms of the NMP in the 

permit. Waterkeeper Alliance et al. v. 

EPA, 399 F.3d 486, 498–504 (2d Cir. 

2005). The decision did not affect the 

substantive requirements for NMPs 

established at 40 CFR 122.42(e)(1) and 

412.4(c) in the 2003 CAFO rule. 

3. This Final Rule 

To address the court’s decision, EPA 

is revising the 2003 CAFO rule and 

other provisions of the NPDES 

regulations to provide for: 

• Receipt and review of the NMP by 

the permitting authority prior to issuing 

an individual permit or granting 

coverage under a general permit; 

• Adequate public participation prior 

to issuing an individual permit or 

granting coverage under a general 

permit; 

• Incorporation of the terms of the 

NMP into the NPDES permit; and 

• The process to address changes to 

the NMP once permit coverage is 

granted, for both individual and general 

permits. 

The individual permitting process 

already allows for review of NMPs by 

the permitting authority and the public, 

and incorporation of the terms of the 

NMP into the individual permit 

consistent with the CWA. This is not the 

case, however, for general permits. 

Given that fact, in promulgating these 

revisions, EPA is devoting particular 

attention to the process for issuance of 

general permits. Furthermore, EPA 

expects most CAFOs to be covered by 

general permits. 

To effectuate these changes, EPA is 

revising 40 CFR 122.21, 122.23, 122.28, 

122.42, 122.62, and 122.63. As 

mentioned above, EPA extended the 

deadlines set in the 2003 CAFO rule for 

NMP development and implementation, 

as well as for newly defined CAFOs to 

seek permit coverage in separate 

rulemakings. 71 FR 6978 (February 10, 

2006); 72 FR 40,245 (July 24, 2007). 

The preamble discussion that follows 

is divided into eight sections to 

separately address each of the following 

issues: 

• CAFO permit application or notice 

of intent requirements; 

• Procedures for permitting authority 

review and public participation prior to 

permit coverage; 

• Identification of terms of the NMP; 

• Process for incorporating terms of 

the NMP into a general permit; 

• Changes to a permitted CAFO’s 

NMP; 

• Process for review of changes to an 

NMP and for modifying terms of the 

NMP incorporated into the permit; 

• Annual reporting requirements; and 

• EPA nutrient management plan 

template. 

(a) CAFO Permit Application or Notice 

of Intent Requirements for Nutrient 

Management Plans 

EPA is revising 40 CFR 122.21(i)(1)(x) 

to require the applicant to submit, as 

part of its permit application or notice 

of intent (NOI) to be covered by a 

general permit, an NMP developed in 

accordance with the provisions of 40 

CFR 122.42(e) and, for Large CAFOs 

subject to subparts C or D of 40 CFR part 

412, the requirements of 40 CFR 

412.4(c), as applicable. Although this 

change is codified in the section of the 

regulations applicable to individual 

permit applications (40 CFR 

122.21(i)(1)), it also applies to NOIs, 

because the regulation governing NOIs 

(40 CFR 122.28(b)(2)(ii)) crossreferences the requirements of 

§ 122.21(i)(1). EPA revised Application 

Form 2B to reflect these changes, and 

the revised form is provided as 

Appendix A of this notice. 

The final rule adopts the approach 

that EPA proposed. This approach is 

consistent with the Waterkeeper 

decision, which left undisturbed the 

substantive requirements for nutrient 

management plans in the 2003 CAFO 

rule but held that such plans must be 

submitted to the permitting authority for 

public review prior to permit coverage. 

These revisions do not change the 

required contents of the NMP, but add 

a requirement for CAFOs to submit their 

NMP as part of their application for an 

individual permit or NOI to be covered 

under a general permit. This differs 

from the requirements of the 2003 rule, 

which required that NMPs be submitted 

only at the request of the Director. 

In the 2006 proposed rule, EPA 

proposed requiring an applicant to 

submit, as part of its permit application 

or NOI, an NMP developed in 

accordance with the provisions of 40 

CFR 122.42(e)(1) and if applicable, 40 

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CFR 412.4(c)(1). The permitting 

authority would then make the NMP 

available for review prior to issuing an 

individual permit or providing coverage 

under an NPDES general permit. 

Many commenters supported the 

proposed requirements to submit NMPs 

with the initial permit application or 

NOI. One State commented that a CAFO 

should be allowed to submit the NOI 

information in batches so that the 

permitting authority could begin 

processing the NOI before a facility has 

completed its NMP to prevent delays in 

the review and approval process. The 

commenter added that authorization to 

discharge under the permit could not be 

granted until the permitting authority 

had received, processed, and reviewed 

all required NOI and NMP information 

according to the regulations. 

Nothing in this rule prohibits 

permitting authorities from accepting 

permit application information in 

batches, provided that the application 

information and submission process 

satisfies all applicable requirements. For 

example, existing NPDES regulations 

address, in relevant part, the effective 

date of an application and the 

processing of a permit. See 40 CFR 

124.3. EPA recognizes that early 

communication between the owner or 

operator of a CAFO and the permitting 

authority can help facilitate the 

permitting process, and EPA encourages 

CAFOs to work closely with their 

permitting authorities. 

EPA received some comments 

suggesting that the Director issue a 

general permit that defines the terms of 

the NMP and details BMP options for a 

range of possible conditions combined 

with a requirement for the CAFO to 

submit a summarized NMP. The 

summarized NMP would include sitespecific facility information needed to 

apply the management approach 

prescribed by the general permit. One 

State recommended that, for general 

permits, CAFOs submit a ‘‘universal 

NMP’’ with their NOI that contains 

decision-making tools used by 

producers to determine application 

rates, dates, and methods rather than 

including site-specific information in 

the permit. This would allow for the 

public to comment on a generic 

‘‘universal NMP’’ and would reduce the 

number of comments that the State 

regulatory agencies would need to 

review and consider if comments were 

provided for each individual NMP 

submitted for a general permit. 

EPA weighed these comments in 

deciding what information needed to be 

submitted to the Director for review to 

comport with the CWA requirements 

cited by the Waterkeeper Court. The 

final rule requires any CAFO seeking 

coverage under a general permit to 

submit with the NOI an NMP that meets 

the requirements of § 122.42(e) and 

applicable effluent limitations and 

standards. EPA did not identify any 

other specific regulatory alternatives 

that substantially reduce burden while 

still providing for meaningful 

permitting authority and public review 

of site-specific NMPs prior to permit 

coverage. Thus, EPA is promulgating an 

approach that is consistent with the 

Waterkeeper decision and the NPDES 

CAFO permit program requirements, 

while continuing to allow for the use of 

general permits for CAFOs. 

EPA also received a comment that 

production and land application areas 

should have separate permitting 

requirements such that a facility that 

does not land apply would not need to 

submit an NMP that addresses its land 

application area. EPA is not revising the 

NMP requirements established in the 

2003 CAFO rule that added land 

application requirements for permitted 

CAFOs. Under the NPDES regulations 

established in the 2003 rule, permits 

issued to CAFOs apply to the entire 

facility, including land application 

areas. Furthermore, the NMP provisions 

address discharges that can originate 

either from production areas or from 

land application areas. Thus, NMPs 

have been designed to be 

comprehensive documents required of 

all permitted CAFOs. The NMP 

provisions at § 122.42(e)(1) must be 

included in a CAFO’s NMP ‘‘to the 

extent applicable.’’ Thus, if a facility 

does not land apply manure, litter, or 

process wastewater, the land 

application provisions of the regulation 

would not be applicable. CAFOs should 

note, however, that even facilities that 

do not land apply manure, litter, or 

process wastewater, but transfer all 

manure, litter, or process wastewater to 

other persons, are required by 40 CFR 

122.42(e)(3) to provide the ‘‘most 

current nutrient analysis’’ to the 

recipient. 

Although EPA is not revising the 

substantive requirements of paragraph 

(e)(1) in this rule, EPA is modifying the 

introductory paragraph to conform to 

the procedural requirements 

promulgated in this rule. Because this 

rule requires an NMP to be submitted as 

part of the CAFO’s permit application or 

NOI, EPA is removing, from paragraph 

(e)(1), the permit condition for 

development of an NMP once permit 

coverage is granted. EPA is thus revising 

§ 122.42(e)(1) simply to require that any 

individual or general NPDES permit 

issued to a CAFO require the 

implementation of an NMP that 

contains best management practices 

(BMPs) as specified in 40 CFR 

122.42(e)(1)(i)–(ix) and the applicable 

effluent limitations and standards. 

Applicable effluent limitations include, 

for Large CAFOs, the requirements of 40 

CFR part 412, and for other CAFOs BAT 

requirements set on a best professional 

judgment (BPJ) basis. 

EPA notes that the definition of 

‘‘BMPs’’ in the NPDES regulations (40 

CFR 122.2) is very broad and includes 

both practices and procedures to be 

implemented by a permittee. For this 

reason, EPA is also changing the phrase 

in the introductory paragraph of 

§ 122.42(e)(1) concerning the contents of 

an NMP from ‘‘best management 

practices and procedures’’ to simply 

reference ‘‘best management practices’’ 

without intending any change in the 

actual scope of what must be included 

in an NMP. 

(b) Procedures for Permitting Authority 

Review and Public Participation Prior to 

Permit Coverage 

This rule promulgates 40 CFR 

122.23(h), which provides new general 

permit procedures for CAFO general 

permits. The provisions of § 122.23(h) 

supplement the general permitting 

requirements of 40 CFR 122.28 with 

specific provisions for review and 

incorporation of CAFO NMPs into 

general permits for CAFOs. These 

provisions implement the decision of 

the Waterkeeper courts concerning 

public review of NMPs and 

incorporation of the terms of the NMP 

into CAFO permits, specifically for 

CAFOs seeking authorization under a 

general permit. 

After the permitting authority receives 

an application or an NOI from a CAFO, 

it is the permitting authority’s 

responsibility to review the application 

or NOI to ensure that it meets the 

requirements of the regulations, and for 

general permits, the requirements of the 

general permit. This includes 

determining whether the nutrient 

management plan meets the 

requirements of 40 CFR 122.42(e)(1) 

and, for Large CAFOs subject to 40 CFR 

412 subpart C or D, the applicable 

requirements of 40 CFR 412.4(c). As part 

of that process, the Director must review 

the NMP for both completeness and 

sufficiency, as required by the 

Waterkeeper decision. Also, because the 

Waterkeeper decision requires terms of 

the NMP to be incorporated as permit 

terms, the Director must provide for 

adequate public participation in the 

process of establishing permit terms 

based on each CAFO’s NMP. 

The general permit issuance process 

and the individual permitting process 

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differ in how a permit is developed and 

the means by which individual facilities 

obtain authorization to discharge. A 

general permit covers multiple facilities, 

and is made available to facilities 

seeking permit coverage after it is 

finalized. When the permitting authority 

develops a draft general permit, it must 

provide the public (including potential 

future permittees) an opportunity to 

review the permit, submit comments, 

and request a hearing. After considering 

comments submitted, the permitting 

authority then finalizes the general 

permit. Facilities may then submit an 

NOI seeking coverage under the final 

general permit. Typically, the 

permitting authority may then, without 

the need for further public notice and 

comment, either grant coverage under 

the general permit, require the facility to 

seek coverage under an individual 

permit, or deny permit coverage. 

Existing regulations establish a right for 

any interested person to petition the 

Director to require a facility authorized 

under a general permit to apply for an 

individual permit. See 40 CFR 

122.28(b)(3). 

For individual permits, the NMP will 

be submitted and reviewed as part of the 

permit application. The decisionmaking procedures in 40 CFR part 124 

apply to the Director’s review of the 

application, which includes the NMP. 

Part 124 requires review of the 

completeness and sufficiency of the 

permit application, includes an 

opportunity for the CAFO to modify the 

plan or provide additional information 

to the permitting authority, and requires 

a final decision by the Director after an 

opportunity for the public to comment 

and request a hearing. 

Although a review process for data 

submitted by applicants, including 

NMPs, is already provided for in 

existing NPDES regulations that address 

issuance of individual permits, such a 

process has not previously been 

expressly available in the regulations for 

CAFO general permits. Following the 

Waterkeeper decision, general permits 

for CAFOs must include the terms of an 

NMP applicable to each specific CAFO 

authorized under the permit. Moreover, 

Waterkeeper requires that the public 

have an opportunity to review each 

CAFO-specific NMP and comment on 

terms of the NMP to be incorporated 

into the permit. Thus, a second round 

of public notice and comment is 

necessary when providing coverage for 

CAFOs under a general permit. To fill 

these gaps and address the Waterkeeper 

decision, this rule creates new 

provisions at § 122.23(h) that establish a 

process for permitting authority and 

public review of NMPs for CAFO 

general permits. 

(i) Permitting Authority Review of 

Nutrient Management Plans 

As discussed above, the Waterkeeper 

court held that NMPs must be reviewed 

by the permitting authority before 

permit coverage is issued to any CAFO. 

Waterkeeper, 399 F.3d at 498–502. The 

process for permitting authority review 

of NMPs for CAFOs seeking coverage 

under a general permit is established by 

this final rule at 40 CFR 122.23(h)(1). 

Section 122.23(h) requires the Director 

to review the NOI submitted by a CAFO 

owner or operator to ensure that the NOI 

includes the information required by 40 

CFR 122.21(i)(1), including an NMP that 

meets the requirements of 40 CFR 

122.42(e) and applicable effluent 

limitations and standards, including 

those specified in 40 CFR part 412. 

Section 122.23(h)(1) also provides that 

if, upon review, the permitting authority 

determines that additional information 

is necessary to complete the NOI or 

clarify, modify, or supplement 

previously submitted material, the 

Director will notify the CAFO owner or 

operator and request that the 

appropriate information be provided. 

When the NOI is complete, the Director 

must then proceed with the public 

notification process required by this 

rule and discussed below. 

In the 2006 proposed rule, EPA 

proposed a new regulatory provision to 

establish permitting authority review of 

NMPs for general permits. This 

provision would require the Director to 

review the NMP submitted with the NOI 

and to take appropriate steps to ensure 

that the NMP meets the applicable 

requirements of 40 CFR 122.42(e)(1) 

and, for Large CAFOs, 40 CFR 412.4(c). 

Upon review of the NMP, the permitting 

authority would request from the CAFO 

owner or operator any additional 

information needed to complete the NOI 

or clarify, modify, or supplement the 

submitted material. The permitting 

authority would then notify the public 

of its receipt of a complete NOI and of 

the terms of the NMP proposed to be 

incorporated into the general permit. 

After allowing time for public comment 

and a public hearing, if needed, the 

permitting authority would decide 

whether to authorize coverage under the 

general permit. 

Many commenters disagreed with the 

proposed modified general permit 

process that would add permitting 

authority review of the NMP. The 

primary concern was that the permitting 

authorities may have insufficient 

resources to review all NMPs, which 

could limit the usefulness of general 

permits. To address this concern, a 

number of commenters suggested 

variations on the proposed process. 

These suggestions are addressed in more 

detail below under the corresponding 

discussion for the respective stage of the 

general permitting process. 

The Waterkeeper decision held that 

permitting authorities must review the 

permit application and the NMP to 

ensure that all applicable requirements 

have been met. The court made no 

distinction between individual or 

general permits with regard to this 

requirement. Because existing 

regulations do not provide for a review 

process that addresses the submission 

and review of NMPs for inclusion in a 

general permit, and given that EPA 

expects many CAFOs to be permitted 

under general permits, EPA is adopting 

provisions at § 122.23(h) that provide 

for permitting authority review of the 

CAFO NOI and NMP, as well as 

opportunity for the public to comment 

and request a hearing on the NOI, NMP, 

and the terms of the NMP to be 

incorporated into the permit. 

The procedure for review and notice 

of CAFO NOIs and NMPs will impose 

some increased burden on permitting 

authorities and will add steps to the 

process of administering a general 

permit. However, EPA has worked to 

adapt these new requirements to a twostage review process that comports with 

the Waterkeeper decision and the CWA 

and adds some flexibility to the parallel 

NPDES permit procedure regulations of 

40 CFR part 124. 

Commenters stated that EPA should 

establish a correlation between the 

timing of the application process and 

permit coverage. These commenters 

wanted the regulation to automatically 

authorize discharges within 60 days 

from the date of application/NOI 

submission unless the permitting 

authority denied permit coverage within 

that period, even if the public review 

process was incomplete. They took the 

view that CAFOs should not be 

penalized by a review process that 

could vary in length based on factors 

out of the control of the CAFO. 

Similarly, some commenters stated that 

EPA’s final regulation should provide a 

clearly defined process with a limited 

length of time for permitting authority 

review. Suggestions for a time limit 

ranged from 30 to 60 days. 

To provide permitting authorities 

flexibility to review NMPs of varying 

complexity, this action does not require 

a specific timeframe for completion of 

the permitting authority review process. 

This approach is consistent with the 

existing NPDES regulations in part 124 

for other industries, which similarly do 

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not specify a timeframe for automatic 

authorization to discharge or for the 

completion of the permitting authority 

and public review processes. 

Commenters expressed concern over 

the additional workload that reviewing 

individual NMPs would create, and 

suggested alternatives to reduce 

permitting authority workload, 

including: Submission of a ‘‘universal 

NMP’’ with permit applications for use 

in determining application rates, timing, 

and methods rather than including sitespecific information in the permit; and 

combining a detailed, clear general 

permit with the submission of a 

summarized NMP for review. 

In developing the 2006 proposed rule 

EPA evaluated alternative approaches 

for reducing operator and permitting 

authority workload. For example, EPA 

considered the use of an NMP template 

as a voluntary tool to facilitate 

completion and review of the NMP by 

CAFO applicants and permitting 

authorities, respectively. 71 FR 37,752. 

Such a template could serve as one of 

many tools available to support CAFO 

permitting and reduce permitting 

authority workloads. See preamble 

section III.C.3(h) for a discussion of the 

template. EPA also plans to develop 

additional tools and guidance to reduce 

the burden on both the CAFO operator 

and the permitting authority to meet the 

requirements of the NPDES regulations. 

For example, EPA is developing a 

training course that focuses on 

development and review of NMPs to 

comport with this final rule. EPA plans 

to first make the course available to 

State and federal permitting authorities 

in 2009. 

Another possible approach for 

minimizing permitting authority 

resource expenditures is utilizing a 

third-party for NMP review. A few 

commenters noted that having 

permitting authority staff review NMPs 

that have already been prepared by a 

State-certified planner is duplicative 

and unnecessary. Commenters believe 

that, due to their extensive training, 

certified planners are in the best 

position to review and certify NMPs 

coupled with appropriate public agency 

oversight. This is one State commenter’s 

established NMP review process. 

Commenters noted that, in some States, 

another State agency (typically the State 

agricultural agency) reviews and 

approves NMPs. A State commenter 

asserted that the final rule would meet 

the intent of the Waterkeeper decision if 

it allowed NMP review by qualified 

professionals meeting educational and 

technical training requirements as set 

forth by the Director. Such professionals 

should be properly trained and subject 

to a quality assurance protocol. One 

commenter asserted that this flexibility 

is imperative for effective State 

programs. 

The permitting authority is 

responsible for reviewing NMPs and for 

ensuring that the terms of the NMP meet 

the applicable requirements of the 

NPDES process. There is no reason, 

however, why a State cannot obtain 

assistance and advice from technical 

experts, or tailor its review based on the 

development or certification of NMPs by 

State-certified nutrient management 

planners. However, it is the permitting 

authorities’ responsibility to ensure that 

comments are properly addressed and 

the final permit terms are incorporated. 

Regarding the increased workload 

permitting authorities may experience 

due to review of NMPs, EPA notes that 

30 out of the 44 States that regulate 

CAFOs currently require NMPs to be 

submitted with a CAFO’s request for 

NPDES permit application coverage. 

Further, 28 of these States allow for 

public review of these NMPs. Thus, 

even though EPA did not specifically 

require this in the 2003 CAFO rule, such 

a review process already exists for many 

State regulatory authorities. 

(ii) Public Review of Nutrient 

Management Plans 

In the Waterkeeper decision, the 

Second Circuit held that ‘‘The CAFO 

rule deprives the public of the 

opportunity for the sort of participation 

that the Act guarantees because the Rule 

effectively shields the nutrient 

management plans [NMPs] from public 

scrutiny and comment.’’ 399 F.3d at 

503. This rule responds to the 

Waterkeeper decision by establishing 

public participation requirements that 

ensure adequate opportunity for public 

review of both a CAFO’s NMP and the 

terms of the NMP to be incorporated 

into the permit prior to the CAFO 

obtaining authorization to discharge 

under the permit. 

As previously discussed, procedures 

for public participation in the issuance 

of individual permits are already 

established in the NPDES regulations. 

See 40 CFR part 124. Because this rule 

requires CAFOs to submit their NMP as 

part of their permit application (see 

discussion at section III.C.3(a) of this 

preamble; 40 CFR 122.21 and 122.23)), 

the public will have access to the NMP 

prior to permit issuance and will also 

have full opportunity to comment on 

the adequacy of the plan and on the 

nutrient management terms in the draft 

NPDES permit developed for the 

specific CAFO facility. This individual 

permit process addresses the court’s 

decision in this respect. 

To preserve the option of general 

permits for CAFOs and to conform to 

the Waterkeeper decision which 

requires the terms of each CAFO’s NMP 

to be incorporated into the CAFO’s 

permit, this rule establishes new 

provisions, at 40 CFR 122.23(h), that 

require the permitting authority to allow 

public review of both the NMP and the 

terms of the NMP to be included in a 

general permit. 

In § 122.23(h), the rule establishes 

new general permitting procedures for 

CAFOs that require permitting 

authorities to incorporate the terms of 

site-specific NMPs, which must be 

submitted with the NOI, into CAFO 

general permits when authorizing 

coverage under a general permit. These 

procedures require the Director to notify 

the public that the permitting authority 

is proposing to grant coverage for a 

facility under the general permit and 

make available for public review and 

comment the CAFO’s NOI (including its 

NMP) and the draft terms of the NMP to 

be incorporated into the permit. The 

public will also have an opportunity to 

request a hearing on this information 

before the CAFO is authorized to 

discharge under the general permit. 

After making a preliminary 

determination that the NOI meets the 

requirements of 40 CFR 122.21(i)(1) and 

122.42(e), the Director has discretion as 

to how best to provide the requisite 

public notification in the general permit 

context. For example, public 

notification may be provided on the 

permitting authority’s Web page or 

through other electronic means. Another 

alternative is to use the notice or fact 

sheet for the general permit to establish 

a procedure allowing any person to 

request notice by mail or electronically 

of the receipt of an NOI, the permitting 

authority’s proposed action, and the 

terms of the NMP proposed to be 

incorporated into the permit. These are 

appropriate ways to balance the 

competing concerns of providing 

adequate notification to the public, 

providing flexibility to the permitting 

authority, and ensuring the practicality 

of general permits. 

Under this rule, the Director also has 

discretion to establish an appropriate 

period of time for public review of the 

NOI and draft terms of the NMP 

proposed to be incorporated into the 

permit. Under 40 CFR 122.23(h)(1), the 

Director may establish by regulation or 

in the general permit an appropriate 

period of time for the public to 

comment and request a hearing. This 

differs from the specifications in 40 CFR 

124.10, which sets a 30-day public 

notice period for proposed coverage 

under individual permits. Having the 

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Director set the time period for public 

review by regulation or in the general 

permit process will allow the public and 

other interested parties an opportunity 

to comment on the sufficiency of that 

time period. Factors the permitting 

authority might consider when 

establishing an appropriate time period 

include the number of NOIs being 

publicly noticed at any one time, the 

complexity of the material made 

available for public review, the expected 

level of public interest based on prior 

notices of CAFOs seeking coverage, the 

opportunity for the public to request an 

extension of the comment period for one 

or more facilities, and whether 

individuals can request and receive 

individual notification of CAFOs 

seeking authorization to discharge 

under the permit in a timely fashion. 

As mentioned above, the Director 

must also provide an opportunity for the 

public to request a hearing. The 

procedures for requesting and holding a 

hearing on the terms of the NMP to be 

incorporated into the general permit are 

the same as those for draft individual 

permits, which are provided in 40 CFR 

124.11 through 40 CFR 124.13. When 

granting permit coverage, the Director 

must respond to all significant 

comments received during the comment 

period as provided in 40 CFR 124.17, 

and if necessary, require the CAFO 

owner or operator to revise their NMP. 

Additionally, under the procedures 

promulgated in § 122.23(h)(1) of this 

rule, if after the public notice period 

and the conclusion of any hearings, the 

Director decides to authorize discharge 

under the permit, the permitting 

authority must notify the CAFO and 

inform the public. Such notification is 

necessary to ensure that the applicant 

and interested individuals are aware of 

the Director’s final decision on granting 

authorization to discharge under the 

general permit and incorporating sitespecific NMP terms into the general 

permit. Furthermore, the provision 

provides notification equivalent to that 

required when CAFOs are issued 

coverage under individual permits 

consistent with this rule revision. 

EPA is promulgating 40 CFR 

122.23(h)(2), which establishes 

additional procedures for EPA-issued 

permits. Paragraph (h)(2) requires the 

EPA Regional Administrator to notify 

each person who has submitted written 

comments on the proposal to grant 

permit coverage and the draft terms of 

the NMP of the final permit decision. A 

person affected by the general permit 

can either challenge the general permit 

in court, or apply for an individual 

permit as authorized in 40 CFR 122.28. 

The public notice process described 

above also includes providing notice to 

other affected States, as required by the 

CWA. Section 402(b)(3) of the CWA 

provides that the Administrator, in 

approving a State program, shall make 

sure the State has adequate authority to 

ensure notice to ‘‘any other State the 

waters of which may be affected.’’ 

Section 402(b)(5) provides that the 

Administrator must ensure that any 

State ‘‘whose waters may be affected by 

the issuance of a permit may submit 

written recommendations to the 

permitting State,’’ and that if those 

recommendations are rejected, the 

permitting State must notify the affected 

State in writing of the reasons for the 

rejection. The public notice provisions 

in this rule provide notification to 

affected States as well as to the public 

in general. Additionally, the permitting 

authority’s response to all significant 

comments will include responses to 

comments from affected States. 

This rule balances several competing 

concerns regarding public participation 

procedures for general permitting of 

CAFOs. First, the final rule maintains 

the utility of a general permit program 

as a resource-efficient method by which 

to authorize multiple CAFOs under an 

NPDES permit while meeting the 

Second Circuit’s directive to ‘‘provide 

for adequate public participation’’ in the 

development of site-specific effluent 

limitations. Waterkeeper, 399 F.3d at 

524. Second, the final rule provides 

sufficient flexibility for State permitting 

authorities to adopt their own 

procedures while ensuring that they 

meet the public participation 

requirements of the CWA. Because of 

the large number of CAFOs that may 

seek permit coverage, the Agency 

considers it appropriate to have 

procedures that allow and encourage 

permitting authorities to continue the 

use of NPDES general permits as a 

means for applying CWA limitations 

and standards to CAFOs on a timely 

basis. Of course, existing regulations 

give the Director authority to require a 

facility to apply for an individual permit 

instead of allowing coverage under a 

general permit (even after coverage 

under a general permit has been 

granted). The Director may thus choose 

not to issue a general permit for CAFOs, 

but instead to require all CAFOs seeking 

permit coverage to obtain coverage 

under individual permits. 

The 2006 proposed rule included 

procedures for public review of NOIs 

and draft terms of the NMP substantially 

the same as the procedures promulgated 

today in § 122.23(h). EPA solicited 

comment on the proposal to give the 

Director discretion regarding the means 

of public notification and the length of 

the public notice period, and also on the 

possibility of fixed minimum time 

frames for public review. The Agency 

also specifically sought comment on 

whether the proposed public 

participation process achieved an 

appropriate balance between the 

competing interests of maintaining the 

utility of general permits for CAFOs and 

providing adequate public review of 

permit terms. 

Several commenters expressed 

concern that public review of the NMP 

would eliminate the use of general 

permits, noting that States have limited 

resources for accommodating a public 

review process. Several commenters 

stated that the proposed process 

provided inadequate opportunity for 

public input. Some believed that the 

proposed public participation process is 

inconsistent with the general permitting 

approach and that only individual 

permits are appropriate for CAFOs since 

the terms of the NMP constitute sitespecific effluent guidelines. Others felt 

that the public participation process 

needed to begin before the development 

of the NMP to provide an opportunity 

for comment on the specific best 

management practices (BMPs) to be 

included in the plan. 

The procedures for public 

participation in this final rule preserve 

the availability of general permits for 

CAFOs. As discussed above, the 

changes to the CAFO general permit 

process made in this rule are necessary 

to meet the requirements of the 

Waterkeeper decision. In addition, EPA 

has provided flexibility where it could 

with regard to how a permitting 

authority provides public notice and 

makes key information available. 

Further, the rule provides permitting 

authorities with flexibility to establish 

an appropriate time period for public 

review. Finally, the rule does not 

change any of the existing regulations 

that allow a permitting authority to 

require an individual permit when 

appropriate. Overall, the final rule 

maintains the utility of a CAFO general 

permit program as a resource-efficient 

method for authorizing multiple CAFOs 

under an NPDES permit while meeting 

the court’s directive to ‘‘provide for 

adequate public participation’’ in the 

development of site-specific effluent 

limitations. 

One commenter stated that public 

access to the entire NMP will strongly 

compel operators to risk noncompliance 

by operating without authorization 

under a permit. Some commenters were 

concerned that sensitive information 

will be made available to the public. 

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EPA understands the sensitivity of 

some information that may be contained 

in a CAFO’s NMP. However, public 

availability and permitting authority 

review of a CAFO’s NMP is not a new 

practice; rather, it is one that is 

currently employed in many State 

NPDES CAFO programs. As stated 

above, 30 of the 44 States that permit 

CAFOs request that NMPs be submitted 

as part of their permit application 

process. In most of those States the 

permitting authority conducts a 

comprehensive technical review of the 

NMPs prior to granting authorization to 

discharge under the permit. These 

NMPs have already been publicly 

available in these States for some time. 

Moreover, most of these States provide 

notice to the public of the availability of 

these plans and seek public review, 

with some conducting public meetings 

as well. Any information submitted to 

the permitting authority as part of a 

permit application or NOI must be made 

available for public review and 

comment, unless it is confidential 

business information (CBI). See 40 CFR 

122.7. 

EPA disagrees with commenters who 

believe that the permitting process 

provides inadequate opportunity for 

public input or that such opportunity 

should arise earlier in the process. The 

final rule provides ample opportunity 

for the public to comment on the terms 

and conditions of the general permit, 

including for each permitted CAFO, the 

opportunity to comment on permit 

coverage and the terms of the NMP. This 

rule requires that the public have access 

to the NOI and the NMP when 

reviewing and commenting on BMPs 

and other terms of the NMP to be 

incorporated as enforceable conditions 

of the permit. 

Several commenters supported 

permitting authority discretion on the 

method of providing public notice of the 

opportunity to comment on an NMP or 

request a hearing. One commenter 

stated that EPA should allow 

applications to be processed jointly so 

that the permitting authority could 

provide notice to the public of multiple 

NMPs at the same time. Another 

commenter supported web-based or 

other electronic notice. One commenter 

suggested that the general permit fact 

sheet be utilized to establish a 

procedure allowing any person to 

request notice by mail or electronically 

of the receipt of an NOI, the permitting 

authority’s proposed action, and the 

terms of the NMP proposed to be 

incorporated into the permit. Such an 

approach would provide flexibility to 

the permitting authority and reduce the 

number of notices that must be 

published. 

As stated above, this rule allows the 

permitting authority discretion as to 

how best to provide such public 

notification in the general permit 

context. For example, public 

notification may be provided on the 

permitting authority’s Web page or 

through other electronic means. The 

final rule does not restrict the ability of 

a permitting authority to provide notice 

of multiple NMPs at one time provided 

the all applicable procedural and 

substantive permitting requirements are 

satisfied. However, notice must be 

adequate, and the opportunity to 

comment must be meaningful. 

Some commenters expressed that EPA 

should require a minimum of 30 days 

for public review and that the 2006 

proposed rule provided permitting 

authorities too much discretion. Others 

stated that the public participation 

process should be limited, with many 

suggesting no more than 30 days for an 

initial submission. In addition, 

commenters requested that EPA limit 

the circumstances under which the 

comment period could be extended. 

EPA believes that the decision as to how 

much time should be allowed for public 

participation is best decided by the 

Director for reasons discussed above, 

including that the public will have an 

opportunity to comment on the length 

of the public notice period when 

reviewing either the draft regulations or 

draft general permit. 

EPA also received comments 

suggesting that EPA specify that each 

facility would be subject to only one 

public hearing on a draft permit; that 

the decision to hold a public hearing on 

a draft permit and NMP should be based 

on a finding of a significant degree of 

public interest and limited to issues 

germane to permitting; and that public 

review of a general permit be limited to 

the terms of the NMP that are 

incorporated into the permit. Several 

commenters were concerned that 

without some limitations, the public 

review process could be misused. This 

rule specifies that permitting authorities 

follow the procedures set forth in 

§ 124.11–124.13. These protocols are 

well established for NPDES permits and 

allow the Director to weigh the relevant 

circumstances in addressing each of the 

issues raised by commenters. 

State commenters were generally 

supportive of EPA’s proposed approach 

and the flexibility it allows for 

permitting authorities in the general 

permit process. In particular, these 

commenters said that establishing 

timeframes for public review should be 

left to the permitting authority. 

One State suggested that the public 

participation aspects of the 2006 

proposed rule be limited to only new 

Large CAFOs and that NMP terms for 

previously authorized Large CAFOs be 

made available as part of a modified 

annual reporting requirement. The 

public participation requirements in 

this final rule are applicable to all CAFO 

NPDES permits. The Waterkeeper 

decision did not distinguish between 

new facilities seeking permit coverage 

for the first time and existing facilities 

seeking permit reissuance for purposes 

of public participation in reviewing 

CAFO NMPs. Such a distinction would 

not make sense given that the Second 

Circuit found that the terms of NMPs are 

effluent limits that must be included in 

the permit and presented for public 

review and comment. Providing the 

NMP terms to the public only in an 

annual report would not address the 

Waterkeeper requirement that the 

permitting authority must provide for 

public notice and the opportunity to 

comment on the NMP terms and that the 

NMP terms must be enforceable. 

EPA regulations applicable to State 

NPDES programs specify that where 

notice and opportunity for comment 

must be provided, a permitting 

authority must respond to significant 

public comments (§ 124.17). Several 

commenters said EPA should 

specifically narrow what constitutes a 

significant comment warranting a 

response by the permitting authority. 

Their general position was that 

comments must have a technical or 

scientific basis, or address errors, 

omissions, or misrepresentations in 

order to be considered significant. Some 

said that comments should be limited 

only to issues under the purview of the 

CWA, and generalized grievances about 

the operation or location should be 

identified as insignificant and not 

warrant any response by the permitting 

authority. Other commenters, namely 

State agencies, identified the need to 

provide the permitting authority with 

flexibility for determining which 

comments are significant and warrant a 

response. They also indicated that the 

permitting authority will have limited 

resources for responding to all 

comments on a draft permit and NMP. 

EPA intends that this final rule be 

consistent with existing regulatory 

provisions addressing public 

participation in the NPDES program and 

believes that it provides a reasonable 

amount of discretion and flexibility for 

permitting authorities to determine and 

respond to those comments deemed to 

be significant. 

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(c) Identification of Terms of the NMP 

In the Waterkeeper decision, the 

Second Circuit held that because the 

terms of the NMP constitute effluent 

limitations, the CAFO Rule, ‘‘by failing 

to require that the terms of the nutrient 

management plans be included in 

NPDES permits—violates the CWA and 

is otherwise arbitrary and capricious in 

violation of the Administrative 

Procedure Act.’’ 399 F.3d at 502. 

To respond to the Waterkeeper 

decision, the Agency is promulgating 40 

CFR 122.42(e)(5) in order to specify the 

minimum terms of the nutrient 

management plan (NMP) that must be 

enforceable requirements of a CAFO’s 

NPDES permit. As discussed in the 

preambles to both the 2006 proposed 

rule and 2008 supplemental proposal, 

EPA is not revisiting the decisions the 

Agency made in 2003 with respect to 

the contents of the nutrient management 

plan because the Waterkeeper decision 

did not affect these requirements. This 

rule requires that, based on the 

provisions promulgated in 2003 that 

define nutrient management plans (40 

CFR 122.42(e)(1) and 412.4(c)), the 

‘‘terms’’ of the nutrient management 

plan become terms and conditions of 

the permit, as required by the Second 

Circuit decision. 

The Waterkeeper court clearly 

indicated that the terms of the NMP 

must be included in the permit and that 

the terms must include ‘‘waste 

application rates’’ developed by Large 

CAFOs pursuant to their NMPs. 399 

F.3d at 502. Paragraph (e)(5) includes 

two alternative approaches for 

specifying terms of the NMP with 

respect to rates of application, which are 

needed to satisfy the requirement that 

the NMP include ‘‘protocols to land 

apply manure, litter, or process 

wastewater * * * that ensure 

appropriate agricultural utilization of 

the nutrients.’’ 40 CFR 122.42(e)(1)(viii). 

For Large CAFOs, use of either of these 

alternative approaches also satisfies the 

requirements set forth in 40 CFR 412.4 

(i) Background 

In the 2006 proposed rule and 2008 

supplemental proposal, EPA discussed 

how the ‘‘terms’’ of a CAFO’s NMP 

could be identified so as to address the 

nine minimum required elements in 40 

CFR 122.42(e)(1)(i)–(ix)) and 412.4(c) 

(for Large CAFOs, as applicable). 

The 2006 proposed rule preamble 

identified a number of factors that are 

necessary to the development of an 

NMP and discussed the need to allow a 

CAFO some flexibility in managing its 

operation. 71 FR 37,753–55. With 

respect to portions of the NMP that 

would be incorporated as permit terms, 

the Agency also proposed regulatory 

language for accommodating changes to 

the NMP that involve changes to the 

terms during the permit period. 71 FR 

37,756. 

EPA received many comments on the 

NMP issues highlighted in the 2006 

proposed rule preamble concerning the 

complexity associated with nutrient 

management planning, particularly with 

respect to land application, and seeking 

clarification of what constitutes the 

terms of the NMP. In particular, 

commenters sought clarification for 

terms regarding rates of application, 

given the complexity of factors used to 

determine rates of application and the 

dynamics associated with such factors. 

In light of these concerns, EPA in 

March 2008, issued a supplemental 

proposal that proposed what elements 

of the NMP would be terms of the NMP 

that would be required to be included 

as enforceable terms of a CAFO’s 

NPDES permit. EPA received many 

comments on the supplemental 

proposal that identified the need for 

some further revisions to EPA’s 

proposed approach concerning the 

terms of the NMP. 

(ii) Terms of the NMP To Be Included 

in the Permit 

In this final rule, EPA is promulgating 

40 CFR 122.42(e)(5) to identify the 

minimum terms of an NMP to be 

included in a CAFO’s NPDES permit as 

enforceable requirements of the permit. 

Paragraph (e)(5) establishes that any 

permit issued to a CAFO must require 

the CAFO to comply with the terms of 

the CAFO’s site-specific nutrient 

management plan. 

Paragraph (e)(5) states that the terms 

of the NMP ‘‘are the information, 

protocols, best management practices, 

and other conditions’’ identified in a 

CAFO’s nutrient management plan and 

determined by the permitting authority 

to be necessary to meet the requirements 

of 40 CFR 122.42(e)(1). For Large CAFOs 

subject to the land application 

requirements of the effluent limitations 

guideline, the terms would include the 

best management practices necessary to 

meet the requirements of 40 CFR 

412.4(c) in addition to the requirements 

of 40 CFR part 122. This requirement is 

thus broadly applicable to all of the 

measures required to be included in a 

CAFO’s NMP. EPA believes that this 

clarification should address the 

concerns of some commenters that the 

proposed terms of the NMP were 

limited to land application requirements 

only. 

The ‘‘information, protocols, best 

management practices, and other 

conditions’’ that constitute the terms of 

a CAFO’s NMP include what the CAFO 

operator would be required to do to 

properly implement its NMP and 

determinative conditions upon which 

such actions are based. For example, 

both the structural design capacity 

necessary to satisfy the storage 

requirement of 40 CFR 122.42(e)(1)(i) 

and the associated operational and 

maintenance conditions necessary to 

ensure adequate storage, would be 

considered terms of the NMP. Likewise, 

the terms of the NMP would need to 

ensure, for example, proper 

management of mortalities and 

diversion of clean water. However, the 

number of animals confined would not 

necessarily need to be a term of the 

NMP because a CAFO operator would 

be required to properly operate and 

maintain the CAFO’s storage facilities 

regardless of the number of animals or 

the volume of manure, litter, or process 

wastewater generated. 

Some commenters asserted that the 

entire NMP should be included in or 

expressly referenced by the permit and 

that all the elements of a CAFO’s NMP 

must be included in a CAFO’s NPDES 

permit so as to ensure that the permit 

requires the CAFO to comply with every 

discharge reduction or prevention 

measure in its NMP. These commenters 

disagreed with EPA’s interpretation of 

Waterkeeper and felt that the 2006 

proposed rule put forth a more narrow 

meaning of the word ‘‘terms’’ than 

intended by the court. They also felt 

that the proposed rule provided the 

permitting authority too much 

discretion for determining what 

constitutes the ‘‘terms’’ of the NMP. 

The Agency agrees that the 

enforceable terms of the NMP must be 

clear so as to provide notice, both to the 

operator and to the public, about what 

is enforceable and to ensure compliance 

with the discharge reduction and 

prevention measures in the NMP. 

However, EPA does not agree that the 

all of the information in the NMP 

constitutes enforceable terms. By 

establishing the information, protocols, 

best management practices, and other 

conditions or activities necessary to 

meet the requirements of 40 CFR part 

122 and part 412, this rule ensures that 

effluent limitations in the permit will be 

fully implemented, consistent with the 

NPDES regulations, the effluent 

guidelines, and the Waterkeeper 

decision. In addition, this approach 

preserves NMPs as comprehensive 

management tools used to guide a wide 

range of practices regarding nutrient 

production, storage, and use. Regarding 

the degree of discretion afforded to the 

Director, the requirements of this final 

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rule concerning terms of the NMP and 

the opportunity for public review of the 

full NMP together with the draft terms 

of the NMP to be incorporated into the 

permit provides a check on the exercise 

of that discretion. 

Moreover, whether the NMP has been 

properly developed, whether the 

information in the NMP is accurate, and 

whether calculations are correct and 

consistent with applicable requirements 

are issues which are properly addressed 

when the NMP is reviewed by the 

Director and by the public. This is 

analogous to the types of calculations 

and data submitted in a permit 

application and found in the fact sheet 

that accompanies a draft NPDES permit 

for other types of permitted point 

sources. 

Other commenters observed that 

NMPs do not fit well in this regulatory 

context due to their design and the way 

in which they have been used by CAFO 

operators. Rather, they asserted that 

NMPs are developed to guide 

management decisions regarding 

nutrients and, by necessity, must remain 

flexible to address the many conditions 

that affect nutrient generation and 

management. 

The final rule allows for the 

incorporation of the key NMP terms in 

a regulatory context without 

overburdening the permitting process or 

completely recasting the NMP itself. As 

discussed above, the terms of the NMP 

include whatever is contained in the 

NMP that is necessary to ensure 

compliance with § 122.42(e)(1) and, for 

Large CAFOs, 40 CFR 412.4. Additional 

content of the NMP that is beyond the 

scope of compliance with those 

regulatory requirements would not be a 

term of the NMP. 

Some commenters on the 2006 

proposed rule urged EPA to provide 

greater clarity, guidance, and certainty 

in the final rule on the meaning and 

significance of the distinction between 

the NMP and the ‘‘terms’’ of the NMP. 

As proposed in the 2008 supplemental 

proposal, the final rule establishes more 

specific requirements for terms of the 

NMP applicable to CAFOs that land 

apply manure, litter, and process 

wastewater than were included in the 

proposed rule. For such CAFOs, 

paragraph (e)(5) includes as terms the 

fields available for land application, 

field-specific rates of application, and 

timing limitations for land application. 

As stated above, with respect to land 

application, the terms of every NMP 

must include the fields the CAFO plans 

to use for land application. The sitespecific elements of the NMP can only 

be properly represented in the NMP by 

the inclusion of field-specific 

information that must be made available 

for review by the Director and for public 

review in determining, for example, the 

appropriate conservation practices and 

rates of application to be included in the 

plan and, ultimately, in the permit. 

Compliance with the permit during the 

period of coverage would require any 

new fields (i.e., fields not addressed 

specifically in the terms of the permit) 

to first be added to the NMP and the 

permit, in accordance with the 

requirements of 40 CFR 122.42(e)(6), 

discussed below, before they could be 

used by the CAFO for land application. 

Similarly, as discussed in greater detail 

below, field-specific, crop-specific 

application rates would be terms of the 

NMP, as would certain factors needed to 

determine the rates. However, 

background information that is fixed 

and unchangeable, such as actual 

historic yields used in the development 

of an NMP, while important for 

determining rates of application, would 

not need to be terms of the NMP. Such 

information is also relevant and 

important for public review of the draft 

permit, in order to ascertain that the 

terms relating to rates of application are 

correct and enforceable. In other words, 

this is an example of information 

necessary for the development of the 

NMP, but is not relevant for compliance 

or enforcement purposes. 

Finally, the terms of the NMP must 

include any timing limitations in the 

NMP that would make fields 

unavailable for land application at 

certain times or under certain 

conditions.4 Insofar as the NMP 

includes such limitations, the resulting 

limitations are terms of the NMP and 

thus enforceable. 

(iii) Rates of Application 

40 CFR 122.42(e)(1)(viii) requires the 

nutrient management plan to include 

‘‘protocols to land apply manure, litter, 

or process wastewater in accordance 

with site-specific nutrient management 

practices that ensure appropriate 

agricultural utilization of the nutrients 

in the manure, litter, or process 

wastewater.’’ As EPA noted in the 2006 

proposed rule, the Waterkeeper court 

focused on rates of application as 

perhaps the most important term of the 

NMP, in particular the provisions of the 

effluent limitations guidelines in 40 

4 There are two types of ‘‘timing’’ referred to in 

this rule regarding land application. One type 

relates specifically to rates of application, i.e., the 

availability of nutrients for crop uptake based on 

the timing (and method) of application. There are 

also timing limitations, such as restrictions on 

applying under certain conditions, such as on 

saturated or frozen fields, or at certain times of the 

year. The latter types of timing restrictions are the 

subject of this paragraph. 

CFR 412.4(c), and emphasized their sitespecific nature. 71 FR 37,753. In the 

2008 supplemental notice, the Agency 

proposed regulatory requirements to 

ensure that legally-enforceable fieldand crop-specific application rates are 

included in the permit as part of the 

protocols for land application required 

to be in the NMP under 

§ 122.42(e)(1)(viii). 

This rule promulgates two alternative 

approaches for expressing the terms of 

the nutrient management plan with 

respect to rates of application. 40 CFR 

122.42(2)(5)(i)–(ii). Each approach 

provides a means by which a CAFO may 

articulate in its NMP annual maximum 

rates of application of manure, litter, 

and process wastewater by field and 

crop for each year of permit coverage 

and identify the minimum required 

terms of the NMP specific to that 

approach. One approach expresses fieldspecific maximum rates of application 

in terms of the amount of nitrogen and 

phosphorus from manure, litter, and 

process wastewater allowed to be 

applied. This is called the ‘‘linear 

approach.’’ The other approach 

expresses the field-specific rate of 

application as a narrative rate 

prescribing how to calculate the amount 

of manure, litter, and process 

wastewater allowed to be applied. This 

is called the ‘‘narrative rate approach.’’ 

Each of the approaches requires the 

CAFO operator to develop an NMP that 

projects for each field and for each year 

of permit coverage the crops to be 

planted, crop rotation, crop nutrient 

needs, expected yield, amount of 

nitrogen and phosphorus to be land 

applied, and projected amounts of 

manure, litter, and process wastewater 

to be applied. However, each approach 

is different in identifying which of these 

projections would be required to be 

‘‘terms of the NMP.’’ In neither 

approach is the projected amount of 

manure, litter, and process wastewater 

to be land applied a term of the permit 

because these projected amounts must 

be adjusted at least once a year. 

Several commenters suggested that 

the NMP and permitting authority 

review of the NMP should focus on how 

agronomic rates are developed in the 

NMP rather than the specific rate 

determined in the NMP, based on the 

difficulty of developing accurate 

application rates for a five-year term and 

because agency review of specific 

application rates for each field would be 

too burdensome. As discussed above 

and in the 2006 proposed rule, the 

Waterkeeper court focused on rates of 

application as perhaps the most 

important term of the NMP and 

emphasized their site-specific nature. 

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To comply with the decision of the 

Waterkeeper court with regard to the 

terms of the NMP and to allow 

flexibility both for CAFO operators to 

develop NMPs in a manner appropriate 

for a particular operation as well as for 

States to develop regionally-appropriate 

program requirements that meet the 

needs of a particular agency, EPA in this 

final rule is providing two alternatives 

for expressing rates and determining the 

associated terms of the NMP. 

Rates of application are field-specific 

and are designed to ensure that crops 

receive sufficient nutrients to meet yield 

goals, while minimizing the amounts of 

nutrients that could be transported from 

the field. The discussion that follows 

summarizes the basic process for 

establishing rates of application in an 

NMP, in light of the comments received 

in the 2008 supplemental proposal, as 

an introduction to the specific 

discussion of the two approaches 

promulgated in this final rule. 

To develop appropriate land 

application rates for each field where 

land application will occur, CAFOs 

must identify the crops to be planted 

and the planned crop rotations, or other 

uses, and the nitrogen and phosphorus 

needs of these crops or other uses. The 

NMP also must identify the realistic 

yield expected from the crop or crops 

planted in the field, in order to calculate 

the proper amount of nutrients to apply. 

A crop’s nutrient needs are generally 

determined in accordance with the 

nutrient recommendations for a given 

crop (or other planting, such as forage 

or pasture) and the per acre realistic 

yield goal for that crop. The State land 

grant university typically provides these 

values or the formulas for calculating 

these values. The realistic yield goal can 

also be based on historic field-specific 

yield data. 

Because a CAFO operator could plant 

more than one crop on a field in a given 

year, the plant available amount of 

nitrogen and phosphorus needs to be 

calculated with reference to the nutrient 

needs of all the crops to be planted on 

such field in a given year in order to be 

accurate. This includes accounting for 

other field uses, such as pasture and 

cover crops. 

A properly developed NMP must also 

evaluate the condition of the fields to be 

used for land application. A fieldspecific assessment based on soil test 

nutrient levels and other factors 

required by the technical standards 

established by the Director provides 

information needed to determine 

whether land application of manure is 

appropriate for a site. The capacity of 

the field for manure, litter, or process 

wastewater application generally 

depends on the capacity of the soil to 

retain phosphorus. The phrase 

‘‘outcome of the field-specific 

assessment of the potential for nitrogen 

and phosphorus transport from each 

field,’’ as used in this rule, reflects the 

terminology typically associated with 

the use of the phosphorus index, which 

is one of three field-specific risk 

assessment methods discussed in NRCS 

conservation practice standard 590. 

However, in this final rule, EPA is using 

this phrase to reflect the results of 

whichever method is required by the 

technical standards established by the 

Director, including the soil test 

phosphorus method and the phosphorus 

threshold method. 

One commenter suggested that, for 

some States, it may be appropriate to 

require that the field-specific 

assessment of the potential for nitrogen 

and phosphorus transport be conducted 

on an annual basis. EPA recognizes that 

some States require, for example, use of 

a phosphorus index that factors into the 

calculated risk rating the amount of 

manure applied to the field in the 

previous year. EPA agrees that, for these 

States, it would be appropriate to 

require recalculation of the phosphorus 

index on an annual basis and 

anticipates that such States would 

include the appropriate requirements in 

technical standards, permits, or other 

requirements applicable to CAFOs. 

Furthermore, EPA encourages CAFO 

operators to reevaluate field-specific 

assessments of the potential for nitrogen 

and phosphorus transport as frequently 

as necessary to ensure minimization of 

nutrient transport from each field. 

Ultimately, the purpose of the fieldspecific assessment of the potential for 

nitrogen and phosphorus transport is to 

determine the appropriate limiting 

nutrient for developing land application 

rates, i.e., whether phosphorus or 

nitrogen limits the amount of manure, 

litter, or process wastewater that can be 

applied and the degree to which the 

limiting nutrient restricts land 

application, or whether land application 

is to be avoided altogether. State 

technical standards typically allow 

nitrogen-based application rates on 

fields with a low phosphorus risk rating. 

For fields that have a moderate to very 

high phosphorus risk rating, State 

technical standards generally limit the 

amount of phosphorus that may be 

added to a field. 

In determining rates of application 

where phosphorus is the limiting 

nutrient, the amount of phosphorus that 

may be land applied is based on the 

annual phosphorus removal rate for 

each crop or other field use. In deciding 

how much manure may be land applied, 

the amount of plant available 

phosphorus already in the field is not 

deducted because State technical 

standards identify the rate of 

application based on the crop removal 

rate. Because soil levels tend to change 

incrementally, depending on the 

buffering capacity of the soil, and 

because a phosphorus-based application 

rate doesn’t reduce the amount of 

phosphorus already in soil, phosphorusbased rates of application may remain 

relatively constant for a period of 

several years or longer, so long as the 

outcome of the assessment of 

phosphorus transport does not change 

during that time. However, any multiyear phosphorus application must be 

done in accordance with State technical 

standards. 

In determining rates of application 

where nitrogen is the limiting nutrient, 

the NMP must consider the total amount 

of plant available nitrogen for each crop 

from residual nitrogen already in the 

field and the nitrogen added for a 

particular field. Residual nitrogen is the 

nitrogen that remains from prior 

applications of manure, litter, process 

wastewater, or chemical fertilizer, or 

from other sources such as crop residues 

and nitrogen fixing legumes. The 

addition of nitrogen to a field includes 

application of chemical fertilizer as well 

as application of manure, litter, or 

process wastewater and other materials 

such as biosolids. 

Crediting for all residual nitrogen in 

the field that will be plant available, as 

a result of prior additions (e.g., crop 

residue, legume credits, and previous 

manure applications), should be done in 

accordance with the directions provided 

in the technical standards established 

by the Director (required for all 

permitted Large CAFOs). Since organic 

forms of nitrogen typically become plant 

available when they are converted to 

inorganic forms, such as nitrate and 

ammonium, crediting generally 

identifies the amount of organic 

nitrogen likely to be converted to 

inorganic forms that will be plant 

available. Credits are calculated using 

soil test results included in the NMP 

and projected applications of nitrogen 

from manure, litter, and process 

wastewater during intervening years, as 

well as other additions, including from 

crops (e.g., where crops are plowed 

under or residues are left on the field or 

where nitrogen-fixing legumes are 

grown), and other sources of nitrogen 

remaining on the field that would be 

plant available during the next growing 

season. 

EPA expects a complete NMP also to 

account for any other additions of plant 

available nutrients during the crop year, 

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such as chemical fertilizer, irrigation 

water (groundwater may have 

measurable concentrations of nutrients), 

and biosolids, where applied. 

The forms of nitrogen and phosphorus 

to be factored into calculations for rates 

of application are generally identified in 

the technical standards established by 

the Director or in other documentation 

referenced in the State’s technical 

standards. Typically, the amount of 

plant available phosphorus is 

determined based on the amount of 

various forms of phosphate added to or 

present in the soil and the amount of 

organic phosphorus that will mineralize 

during the growing season. The amount 

of plant available nitrogen is based on 

the amount of inorganic nitrogen (e.g., 

nitrate and ammonium-nitrogen) added 

to or present in the soil and the amount 

of organic nitrogen that will mineralize 

during the growing season. The amount 

of plant available nitrogen also depends 

on losses due to volatilization, which is 

calculated using the nitrogen 

volatilization rate associated with the 

source of nutrients and the timing and 

method of land application. As 

previously discussed, it is the forms of 

nitrogen and phosphorus that will be 

available to a given crop that are most 

relevant in determining rates of 

application. In this final rule, the 

appropriate forms of nitrogen and 

phosphorus to be factored into these 

calculations must be expressed in 

chemical forms determined to be 

acceptable by the Director, such as in 

the permit or in the technical standards 

established by the Director. 

As discussed above, the NMP must 

include calculations projecting for the 

length of the permit term the amount of 

manure, litter, or process wastewater, in 

tons or gallons, to be land applied in 

order to meet, but not exceed, crop 

nutrient needs (after considering 

residual nutrients and other additions of 

nutrients and results of the most recent 

manure test) based on the outcome of 

the field-specific assessment of the 

potential for nitrogen and phosphorus 

transport, i.e., whether application rates 

will be limited by nitrogen or 

phosphorus. These calculations must 

also take into account, with respect to 

each crop to be grown or other 

agricultural use, the source and form of 

nutrients to be land applied; the method 

of application of manure, litter, and 

process wastewater; and the timing of 

when application will occur. Although 

a properly developed NMP addresses all 

of these factors, some operators may 

have multiple sources of manure, litter, 

or process wastewater and may need to 

make the determination as to which 

source to draw from for land application 

to a particular field in a given year at 

some point in time after the NMP has 

been developed. The method of 

application depends on the source and 

form of manure, litter, or process 

wastewater; the location of a particular 

field and the equipment available for 

such field; the soil nutrient status; and 

the crop to be planted. For example, 

wastewater could be spray-irrigated, 

otherwise surface applied, or injected, 

whereas poultry litter is most likely to 

be surface applied by a manure 

spreader. 

Whereas one CAFO operator may 

wish to follow the planned sequence of 

steps for planting crops and applying 

manure, litter, and process wastewater 

described in the NMP submitted to the 

Director, another operator may want or 

need to vary from that linear sequence 

of events, due to choices made in the 

course of normal operations, or in 

response to events or circumstances 

beyond the CAFO’s control, such as 

weather, crop failure, or market 

conditions. EPA has addressed this 

concern in this final rule by including 

two alternative approaches for 

determining the terms of an NMP, as 

discussed below. 

As indicated above, EPA is 

promulgating two approaches for 

defining the terms of an NMP for rates 

of application, rather than the three 

approaches that were proposed in the 

2008 supplemental notice. While a 

number of commenters encouraged EPA 

to include all three proposed 

approaches in the final rule to allow 

operators the greatest number of 

alternative options, many commenters 

were critical of the matrix approach. 

Some commenters suggested EPA 

should finalize only the narrative rate 

approach because they felt that the 

linear and matrix approaches were too 

inflexible to be useful. Others suggested 

that the inclusion of three approaches 

would create a program that is too 

complicated for permittees, permitting 

authorities, and the public. One 

commenter stated that the matrix 

approach fails to fully address the 

complexity of the decision-making 

process facing the CAFO operator. 

Several industry commenters found the 

matrix approach to be less flexible than 

necessary and overly burdensome. 

Environmental group commenters found 

the matrix approach to be too rigid to 

ensure protection of water quality and 

not inclusive of critical information. In 

reviewing the comments, EPA agrees 

that the matrix approach does not 

adequately address the complexity of 

the nutrient management decisions to be 

made by the CAFO operator and that it 

could result in over-application of 

manure, litter, or process wastewater. In 

addition, EPA agrees that having three 

approaches to identifying terms of the 

NMP with respect to application rates is 

unduly complicated and would be 

unnecessarily burdensome. Moreover, 

EPA believes that the improvements and 

clarifications to the linear and narrative 

rate approaches promulgated in this 

final rule make inclusion of the matrix 

approach unnecessary. In considering 

comments that criticized the inability of 

the matrix approach, as proposed, to 

more directly address the complex 

dynamics relating application rates to 

crop needs, EPA would have needed to 

make adjustments that would have 

made the matrix approach either more 

like the linear approach or more like the 

narrative rate approach. As a result, and 

in consideration of comments stating 

that including three approaches is 

unnecessary and burdensome, EPA has 

decided to eliminate the matrix 

approach as an option for identifying 

the terms of the NMP for rates of 

application. 

Some industry commenters indicated 

that CAFOs should be allowed to choose 

from either approach as long as they 

maintain the same approach for the fiveyear permit term while another industry 

commenter stated that CAFOs should be 

allowed to switch approaches during 

the permit term. This final rule does not 

address the possibility of switching 

approaches during a permit term. It is 

up to the discretion of the Director 

whether such a change would be 

allowed. However, because each 

approach differs in what are the terms 

of the permit, switching approaches 

during the permit term would require a 

permit modification to include the 

terms of the NMP associated with the 

selected approach into the permit. 

Under both of the approaches, the 

terms of the NMP are required to 

include specific factors used for the 

development of rates of application. 

These include: 

• The outcome of the field-specific 

assessment of the potential for nitrogen 

and phosphorus transport from each 

field; 

• The crop or crops to be planted in 

each field or any other uses such as 

pasture or fallow fields;

• The realistic yield goal for each 

crop or use identified for each field; and

• The nitrogen and phosphorus 

recommendations from sources 

specified by the Director for each crop 

or use identified for each field. 

Both of the approaches account for 

other information necessary for 

determining the amount of manure, 

litter, and process wastewater to be land 

applied. This information relates to: (1) 

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Credits for residual nitrogen available in 

each successive year during the five 

year term of the permit; (2) 

consideration of any multi-year 

phosphorus application; (3) accounting 

for additions of commercial fertilizer 

and other additions of nitrogen and 

phosphorus during each successive 

year; (4) the form (liquid, solid) and 

source (e.g., lagoon, compost, process 

wastewater) of the material to be land 

applied; (5) nitrogen and phosphorus 

content of the manure, litter, or process 

wastewater; (6) timing of application; 

and (7) method of application (e.g., 

spreading, spray, injection). However, 

the two approaches differ in the way 

they incorporate this information in 

expressing the rates of application as 

terms of the NMP. The following 

sections of the preamble describe the 

two approaches and how each approach 

accounts for this information. 

(A) Linear Approach—Rates Expressed 

in Pounds of Nitrogen and Phosphorus 

From Manure, Litter, and Process 

Wastewater 

The first approach (see 40 CFR 

122.42(e)(5)(i)) allows the CAFO to 

express rates of application as pounds of 

nitrogen and phosphorus from manure 

or litter, and process wastewater. The 

terms of the NMP include maximum 

application rates for each year of permit 

coverage, for each crop identified in the 

NMP, in pounds per acre, per year, for 

each field to be used for land 

application. In addition, the terms of the 

NMP include the following factors: 

• The outcome of the field-specific 

assessment of the potential for nitrogen 

and phosphorus transport from each 

field; 

• The crop or crops to be planted in 

each field or any other uses such as 

pasture or fallow fields; 

• The realistic yield goal for each 

crop or use identified for each field; 

• The nitrogen and phosphorus 

recommendations from sources 

specified by the Director for each crop 

or use identified for each field; 

• Credits for all nitrogen in the field 

that will be plant available; 

• Consideration of multi-year 

phosphorus application; 

• Accounting for all other additions 

of plant available nitrogen and 

phosphorus to the field; 

• The form and source of manure, 

litter, and process wastewater to be land 

applied; and 

• The timing and method of land 

application. 

The terms also include the 

methodology by which the NMP 

accounts for the amount of nitrogen and 

phosphorus in the manure, litter, and 

process wastewater to be applied. 

This approach is considered a 

‘‘linear’’ approach because it is based on 

the use of only those crops included in 

the planned crop rotations in the NMP; 

the amounts of nitrogen and phosphorus 

from manure, litter, and process 

wastewater to be land applied according 

to the planned schedule for land 

application (including source and 

method and timing of application); and 

the projected values for plant available 

nitrogen and phosphorus from other 

sources. Under this approach, a single 

set of field-specific rates of application 

would be established, based on the 

predicted sequence of activities the 

CAFO plans to follow in implementing 

its NMP, and a CAFO would be required 

to follow the sequence identified in the 

NMP for each field-specific crop 

rotation and each planned step for land 

application of manure, litter, or process 

wastewater. 

Under this linear approach, a CAFO 

must land apply manure, litter, and 

process wastewater in amounts that will 

result in application of no more than the 

amounts of nitrogen and phosphorus 

from manure, litter, and process 

wastewater specified for each field in 

the NMP, following the schedule and 

the methods of application described in 

the NMP. When applying manure, litter, 

and process wastewater, CAFOs will 

need to take into account manure test 

results, including for Large CAFOs the 

annual manure test results required by 

the 2003 final rule, so as to not exceed 

the nutrient needs of the crops. Medium 

and small CAFOs must apply manure, 

litter, and process wastewater consistent 

with Best Professional Judgment (BPJ)-

based requirements established in the 

permit for accounting for the nutrient 

content of the manure. Large CAFOs 

using the linear approach must calculate 

the maximum amount of manure, litter, 

and process wastewater to be land 

applied at least once each year using the 

results of the most recent representative 

manure, litter, and process wastewater 

tests for nitrogen and phosphorus taken 

within 12 months of the date of land 

application. 

The methodology used for translating 

the amounts of nutrients in pounds into 

the amount of manure, litter, and 

process wastewater to be land applied, 

in tons or gallons, is a term in the linear 

approach. This includes incorporation 

of manure test results in determining 

such rates. 

The final rule differs from the 

proposed linear approach with respect 

to the expression of the rates of 

application. EPA proposed that 

application rates in the linear approach 

be expressed in terms of tons or gallons 

of manure, litter, and process 

wastewater. Several commenters stated 

that the application rate under the linear 

approach should be expressed in terms 

of pounds of nitrogen and phosphorus 

rather than tons and gallons of manure 

and wastewater. The commenters felt 

that this approach would more 

accurately account for the actual 

nutrient content of the manure and 

wastewater being applied. EPA agrees 

with the commenters and has changed 

the linear approach accordingly to 

address this concern. The key advantage 

of this change is that it ensures that the 

results of manure testing, which for 

Large CAFOs is required to be done 

annually, are used in determining the 

actual amount of manure, litter, and 

process wastewater to be applied. EPA 

believes that expressing the rate in 

terms of pounds of nitrogen and 

phosphorus from manure, litter, and 

process wastewater provides greater 

environmental protection by requiring 

operators to adjust the actual amount of 

manure, litter, and process wastewater 

applied based on the most current 

manure nutrient test results. 

The utility of this approach, 

nevertheless, hinges on the CAFO 

making accurate predictions in the NMP 

that are not disrupted by changes to the 

CAFO’s operation or by circumstances 

beyond the control of the CAFO 

operator. Any changes to the terms of 

the NMP would constitute a change to 

the terms of the permit, which would 

require a permit modification. See 

discussion in section III.C.3(e) of this 

preamble, ‘‘Changes to a Permitted 

CAFO’s Nutrient Management Plan.’’ 

For example, any change to the planned 

crop sequence, such as the addition of 

a second crop to a field, requires a 

permit modification. 

On the other hand, the advantage of 

this approach is its relative simplicity 

for CAFOs with predictable crops and 

land application. The linear approach 

would be particularly suitable for 

operations that consistently plant one 

crop or two crops in rotation on the 

same fields, using the same source and 

form of manure, litter, or process 

wastewater, and that land apply on a 

regular annual schedule using the same 

application method(s). 

EPA notes that even under the linear 

approach, operators may provide 

themselves some flexibility by 

specifying more than one field-specific 

crop rotation plan in the NMP, with 

application rates of nitrogen or 

phosphorus specified for each 

alternative plan for inclusion in the 

permit. This might be practical for 

operators who are reasonably confident 

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that they will follow one of two or three 

potential crop rotations. EPA is 

promulgating the other approach for 

operators seeking a greater degree of 

flexibility. 

(B) Narrative Rate Approach—Rates 

Derived From Total Amounts of Plant 

Available Nitrogen and Phosphorus 

This final rule includes a second 

approach that would allow rates of 

application to be expressed as a 

narrative rate that includes the total 

amount of plant available nutrients from 

all sources combined with a specific, 

quantitative method for calculating the 

amount, in tons or gallons, of manure, 

litter, and process wastewater allowed 

to be land applied. (See 40 CFR 

122.42(e)(5)(ii).) Unlike the linear 

approach, in this quantitative narrative 

rate approach, the terms of the NMP 

include the maximum amounts of 

nitrogen and phosphorus from all 

sources of nutrients for each crop or 

other field use identified in the NMP, in 

chemical forms determined to be 

acceptable to the Director, in pounds 

per acre, for each field. 

As required at 40 CFR 

122.42(e)(5)(ii)(A), the narrative rate 

approach also includes as terms the 

following four factors: 

• The outcome of the field-specific 

assessment of the potential for nitrogen 

and phosphorus transport from each 

field; 

• The crop or crops to be planted in 

each field or any other uses such as 

pasture or fallow fields; 

• The realistic yield goal for each 

crop or use identified for each field; and 

• The nitrogen and phosphorus 

recommendations from sources 

specified by the Director for each crop 

or use identified for each field. 

In addition, this narrative rate 

approach includes as a term of the NMP 

the methodology by which the NMP 

accounts for certain factors when 

calculating the amounts of manure, 

litter, and process wastewater to be land 

applied. A CAFO using the narrative 

rate approach is required to apply in 

accordance with the resulting 

calculations. This final rule requires the 

methodology in NMPs developed using 

this approach to account for the 

following factors: 

• Results of soil tests conducted in 

accordance with protocols identified in 

the nutrient management plan, as 

required by 40 CFR 122.42 (e)(1)(vii); 

• Credits for all nitrogen in the field 

that will be plant available; 

• The amount of nitrogen and 

phosphorus in the manure, litter, and 

process wastewater to be applied; 

• Consideration of multi-year 

phosphorus application;

• All other additions of plant 

available nitrogen and phosphorus to 

the field; 

• The form and source of manure, 

litter, and process wastewater;

• The timing and method of land 

application; and

• Volatilization of nitrogen and 

mineralization of organic nitrogen. 

The factors listed above are not 

themselves required to be terms in the 

narrative rate approach, but the 

methodology used to account for them 

in the CAFO’s permit is a term. Thus, 

the CAFO operator will be bound by the 

methodology and the way in which 

these factors must be accounted for in 

calculating the actual amount of 

manure, litter, or process wastewater 

allowed to be applied to the field. The 

terms of the NMP under this approach 

do not include the amount of nitrogen 

and phosphorus in the manure, litter, or 

process wastewater allowed to be landapplied as set forth in the NMP, but they 

do include the methodology prescribed 

in the NMP for calculating these 

amounts. And while the terms of the 

NMP do not include the predicted 

source, form, timing, and method of 

application of manure, litter, or process 

wastewater set forth in the NMP, they 

include the methodology that accounts 

for these factors in determining the 

amount of manure, litter, or process 

wastewater allowed to be applied. This 

allows the actual inputs and results for 

these factors to be something other than 

what was projected in the NMP during 

the period of permit coverage, using the 

methodology, while ensuring that the 

CAFO meets the requirements of 40 CFR 

122.42(e)(1) and, for Large CAFOs, 40 

CFR 412.4, by applying in accordance 

with the methodology and other terms 

of the NMP. 

This approach requires that the CAFO 

apply manure, litter, or process 

wastewater according to the results of 

this calculated amount. For example, if 

the NMP projected an amount of 

manure to be applied based on 

incorporation of solid manure, the 

operator could apply process 

wastewater from the lagoon by spraying 

the field instead. In this example, the 

methodology must account for factors of 

form, source, and method of application 

such that these inputs and results can be 

other than what was projected in the 

NMP and the amount of manure 

allowed to be applied will be 

predictably and accurately calculated. 

In other words, the methodology and 

requirement that application be in 

accordance with the rate calculated 

using that methodology are enforceable 

term that must be complied with at the 

time of determining how much, from 

which source, in what form is allowed 

to be applied to the field using which 

method of application. 

40 CFR 122.42(e)(5)(ii)(C) clarifies 

that the amount of manure, litter, and 

process wastewater to be applied as 

projected in the NMP submitted with 

the permit application or NOI is not a 

term of the NMP under the narrative 

rate approach. As explained above, the 

amount of manure, litter, and process 

wastewater is to be calculated using the 

methodology included in the NMP and 

based on actual amounts of plant 

available nitrogen and phosphorus from 

all sources at the time of land 

application. Other projections that must 

be included in the NMP but are not 

terms are the CAFO’s planned crop 

rotations for each field; credits for all 

nitrogen in the field that will be plant 

available; consideration of multi-year 

phosphorus application; accounting for 

all other additions of plant available 

nitrogen and phosphorus to the field; 

the predicted form, source, and method 

of application of manure, litter, and 

process wastewater for each crop; and 

the timing of application for each field, 

insofar as it concerns the calculation of 

rates of application (permitting 

authorities may establish in permits or 

technical standards for nutrient 

management land application timing 

restrictions, such as prohibitions on 

land application to frozen or saturated 

ground, that would be permit terms).5 

As specified at 40 CFR 

122.42(e)(5)(ii)(B), NMPs for which 

terms are identified using the narrative 

rate approach may also include 

alternative crops not included in the 

planned rotation in the NMP, so long as 

the NMP includes for each crop realistic 

yield goals, nitrogen and phosphorus 

recommendations from sources 

specified by the Director, and maximum 

amounts of nitrogen and phosphorus 

from all sources. The terms and factors 

associated with alternative crops would 

be the same as the terms and factors 

required for the crops included in the 

planned rotation in the NMP. 

EPA received several comments on 

the proposed terms and factors for the 

narrative rate approach. Commenters 

requested that EPA refer only to ‘‘plant 

available’’ nutrients in the narrative rate 

approach. Some confusion may have 

been caused by EPA’s reference in the 

preamble to the 2008 supplemental 

proposal to the ‘‘maximum amount of 

total nitrogen and phosphorus’’ with 

regard to expression of the application 

rate under the narrative approach. This 

5 See footnote 4. 

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language was intended to refer to the 

total amounts of nitrogen and 

phosphorus, rather than referring to a 

specific chemical form (‘‘total nitrogen’’ 

or ‘‘total phosphorus’’). This has been 

corrected in this final rule and preamble 

by removing the word ‘‘total.’’ The final 

rule refers to plant available forms of 

nutrients with regard to determining 

credits for nitrogen in the field and 

accounting for all other additions of 

plant available nitrogen and phosphorus 

to the field. Otherwise, the rule requires 

expression of application rates in 

chemical forms determined to be 

acceptable to the Director, such as 

indicated in the technical standards 

established by the Director, or in the 

permit. 

One commenter suggested that crop 

yields be included as a factor under the 

narrative rate approach and that yield 

goals should be adjusted for operations 

that consistently fail to meet them. This 

final rule includes realistic yield goals 

as a term under both approaches. 

Realistic yield goals will be included in 

the NMP and, therefore, will be subject 

to review by the permitting authority 

and the public. In addition, States may 

establish in their technical standards 

criteria for deriving realistic yield goals 

including criteria for adjusting yield 

goals based on actual crop yields. EPA 

believes that this is sufficient to ensure 

that the yield goals used to calculate 

application rates in NMPs are 

appropriate. Upon subsequent permit 

issuance, the public will have the 

opportunity to review yield goals in 

light of actual yields reported by the 

CAFO in its annual reports (see 40 CFR 

122.42(e)(4)(viii)). 

The narrative rate approach would 

eliminate certain issues associated with 

a five-year planning cycle previously 

discussed in connection with the linear 

approach presented above. A key 

difference of the narrative rate 

approach, is that it would require 

application rates for manure, litter, and 

process wastewater to be recalculated at 

least annually using the methodology 

specified in the NMP (40 CFR 

122.42(e)(5)(ii)(D)). Unlike the linear 

approach, the narrative rate approach 

allows CAFOs that may need to adjust 

their rates of application of manure, 

litter, and process wastewater due to 

changes in soil levels of nitrogen and 

phosphorus to do so without requiring 

the permit to be modified. Therefore, it 

is important to ensure that the actual 

changes in soil levels of plant available 

nitrogen and phosphorus are taken into 

account, rather than relying on five-year 

projections of fluctuations provided in 

the NMP. 

The narrative rate approach requires 

an annual determination of soil levels of 

nitrogen and phosphorus. For nitrogen, 

the annual determination must include 

a concurrent calculation of nitrogen that 

will be plant available consistent with 

the methodology specified in the NMP. 

As described above, this methodology 

must account for the factors that would 

affect soil nitrogen levels on an annual 

basis such as the form and timing of 

previous land application(s); the actual 

amount of nitrogen in the manure, litter, 

and process wastewater previously 

applied; and volatilization and 

mineralization rates for nitrogen. For 

phosphorus, the annual determination 

must include the results of the most 

recent soil test conducted in accordance 

with sampling requirements approved 

by the Director. As in the case of other 

technical determinations to be made by 

the Director as part of this final rule, the 

Director’s determination concerning 

sampling requirements may be made in 

the technical standards established by 

the Director, in the permit, or by an 

equivalent determination made 

elsewhere. Many States require 

sampling to be done every two or three 

years, for most conditions. Some require 

more frequent sampling generally, and 

others require more frequent sampling 

at higher concentrations of soil test 

phosphorus. If sampling is conducted 

more frequently than required by the 

Director, then the determination must 

be based on the results of the most 

recent test. 

EPA proposed that CAFOs using the 

narrative rate approach would be 

required to test soils annually for 

nutrient content and that these data be 

used in recalculating the amount of 

manure, litter, and process wastewater 

to apply annually. Many commenters 

opposed annual soil testing for 

phosphorus. These commenters stated 

that annual testing is inconsistent with 

State land grant university guidance, is 

unnecessary because phosphorus levels 

in the soil do not change significantly 

from year to year and that such testing 

would be cost-prohibitive for many 

operations. A number of commenters 

suggested alternative testing frequencies 

ranging from three to five years. Several 

commenters suggested that annual 

phosphorus testing be required only 

where the soil phosphorus level is 

already high or previous applications 

have exceeded the crop phosphorus 

removal rate (such as where manure is 

applied at a nitrogen-based rate). A few 

commenters asked EPA to clarify that 

annual soil testing only applies to fields 

that will receive manure in the year the 

testing is performed. One commenter 

indicated that, under certain 

circumstances, manure nutrient testing 

should be required more frequently than 

annually. Although the supplemental 

proposal did not specifically propose to 

require annual soil nitrogen testing, 

several commenters indicated that such 

testing should not be required, citing 

limitations in accuracy and 

effectiveness of the testing methods 

currently available. EPA agrees with 

commenters that, in a number of States, 

annual soil testing for phosphorus has 

been determined to be unnecessary. 

EPA recognizes that soil test 

requirements vary from State to State, 

and may include testing for nitrogen as 

well as phosphorus. Based on these 

responses from a range of commenters 

and the various suggested alternatives, 

EPA has replaced the proposed annual 

soil testing requirement for the narrative 

rate approach with the requirement that 

an annual determination of soil nutrient 

levels be based on current data and 

calculations as described above to 

support ‘‘real time’’ calculation of 

appropriate application rates. This final 

rule does not specify a minimum 

frequency for soil phosphorus testing, 

but instead requires CAFOs to include 

the results of the most recent soil tests 

for phosphorus conducted in 

accordance with soil testing 

requirements approved by the Director. 

The annual recalculation of the 

amount of manure, litter, and process 

wastewater allowed to be applied must 

also rely on the results of the most 

recent representative manure, litter, and 

process wastewater tests taken within 

12 months of the date of land 

application. These data along with the 

annual determination of soil levels of 

nitrogen and phosphorus must be used 

to calculate, in real time, the amount of 

manure, litter, and process wastewater 

to be applied to supply the remaining 

nitrogen and phosphorus needed for the 

actual crop being planted on the field. 

Commenters requested that the narrative 

rate approach express application rates 

in terms of pounds of nutrients rather 

than tons of manure to allow 

appropriate utilization of nutrients in 

manure whose nutrient content varies 

over time. In practice, the narrative rate 

approach requires that amounts of 

manure, litter, and process wastewater 

to be land applied be calculated first in 

pounds of nutrients and then translated 

into tons or gallons of manure, litter, 

and process wastewater using current 

manure nutrient analyses. The 

information presented to the public in 

the CAFO’s NMP will include the 

projected amounts for the planned crop 

rotation, in tons or gallons of manure, 

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litter, or process wastewater, since this 

is the endpoint of the calculation of the 

amount to be applied. As discussed 

above, these projected amounts are not 

themselves terms, since they will need 

to be recalculated each year based on 

updated information. 

One commenter suggested that EPA 

specify that manure tests and plant 

tissue tests also be used in the annual 

rate recalculation. As described above, 

this final rule does require 

consideration of recent manure test 

results in annual application rate 

recalculations. Plant tissue testing may 

be an effective tool for determining 

nitrogen deficiencies (and the need for 

supplemental nitrogen application), as 

well as for determining excess nitrogen. 

However, plant tissue tests are typically 

taken after manure applications have 

been made on a field and thus are 

unavailable at the time the operator is 

determining rates of application. A 

CAFO’s NMP may include plant tissue 

testing as part of the CAFO’s 

methodology so long as it is done 

consistently with State technical 

standards. 

In addition to accounting for the crop 

and field information, the methodology 

for the annual recalculation of the 

amount of manure, litter, and process 

wastewater to apply must account for a 

number of other variables, including the 

form and source of the manure, litter, 

and process wastewater and the timing 

and method of application, as described 

above. The operator may not apply more 

than the maximum amount of nitrogen 

and phosphorus calculated using the 

methodology. 

Under this approach, the NMP will 

include planned crop rotations for each 

field and corresponding projected 

amounts, in tons or gallons, of manure, 

litter, and process wastewater to be 

applied, including all of the calculations 

for determining such projected amounts, 

for the period of permit coverage. This 

will give the permitting authority and 

the public an opportunity to review, 

prior to permit issuance, the adequacy 

of the CAFO’s methodology and the way 

the CAFO uses the methodology to 

calculate the appropriate amount of 

manure, litter, and process wastewater 

to be applied, based on the operator’s 

planned crop rotation at the time of 

permit issuance. Again, these planned 

crop rotations and projected amounts 

are not terms, as they will need to be 

recalculated each year based on updated 

information; however these projections 

will allow the public to see how the 

methodology (which is a term) is 

applied to a projected set of facts to 

calculate the amounts to be land 

applied. 

Several commenters expressed 

concerns about the enforceability of the 

narrative rate approach, citing the lack 

of an objective rate and public 

availability of supporting information 

used to calculate the rate. The narrative 

rate approach requires the CAFO to 

recalculate the amount projected in the 

NMP of manure, litter, and process 

wastewater to be land applied, using the 

methodology in the NMP, at least once 

a year, throughout the period of permit 

coverage. In recalculating these 

amounts, a CAFO will be required to 

use concurrent calculations of credits 

for all plant available nitrogen in the 

field and the results of the most recent 

soil tests for phosphorus in the field. 

The CAFO will then calculate the 

maximum amount of nitrogen and 

phosphorus from manure, litter, and 

process wastewater allowed to be 

applied, as a portion of the total amount 

of nitrogen and phosphorus from all 

sources, using the methodology in the 

NMP. Under the narrative rate 

approach, the CAFO must use the 

methodology specified in the NMP 

(which is a term) to account for the 

amount of nitrogen and phosphorus in 

the manure, litter, and process 

wastewater to be applied when 

calculating the maximum amount of 

manure, litter, and process wastewater 

allowed to be applied. To ensure that 

such recalculations are made available 

to the Director and the public, the 

recalculations and the new data from 

which they are derived are required to 

be reported in the CAFO’s annual report 

for the previous twelve months. In other 

words, the rate of application would be 

an objective, enforceable rate, because 

the permit will specify the methodology 

required for calculating the amount of 

manure, litter, and process wastewater 

allowed to be applied, certain values or 

sources of information required to be 

used in the methodology, and will limit 

the total amount of nitrogen and 

phosphorus from all sources for each 

crop. Failure to comply with the rate 

established under the permit would be 

a violation of the permit, and the 

Director and the public will be able to 

determine whether the rate was 

complied with from the annual report. 

Most commenters who commented on 

the narrative rate approach were 

supportive of the approach in terms of 

its degree of flexibility. Some 

commenters suggested that it should be 

the only approach adopted in the final 

rule. EPA believes that the flexibility of 

the narrative rate approach will reduce 

the burden on permitting authorities 

and CAFO operators by decreasing the 

number of substantial changes to the 

permit which require public notice and 

comment, arising from changes to the 

CAFO’s crop rotations, while ensuring 

that all effluent limitations applicable to 

a permitted CAFO are incorporated as 

terms of the permit, as required by the 

Waterkeeper decision. 

As many commenters on the 2006 

proposed rule pointed out and EPA 

recognizes, there may be changes in 

field conditions or practices at a CAFO, 

including, for example, those that alter 

the projected levels of plant available 

nitrogen and phosphorus in the soil or 

in the manure over the period of permit 

coverage. Such changes introduce some 

uncertainty in setting application rates 

for five years as enforceable terms of the 

permit. The narrative rate approach is 

designed to accommodate these 

concerns by allowing a CAFO to 

compensate for changes in soil levels of 

plant available nutrients, in manure 

nutrient content, or in the timing and 

method of application, by adjusting the 

application rates accordingly without 

the need for a permit modification. 

However, the operator will be limited to 

the total crop-specific amount of 

nitrogen and phosphorus from all 

sources and will have to adhere to a 

methodology that establishes the way in 

which such rates are to be calculated. 

Thus, in the second and later years of 

the permit term, this approach will 

provide an accurate and verifiable 

means of achieving realistic production 

goals while minimizing transport of 

phosphorus and nitrogen from the field. 

This will help CAFOs avoid the 

possibility of over-application of 

nitrogen or phosphorus because of 

increased levels of nutrients in the soil, 

compared to what was projected at the 

time of permit issuance, and, 

conversely, the possibility of failing to 

meet crop agronomic needs due to 

under-application of nitrogen or 

phosphorus. 

(d) Process for Incorporating Terms of 

the Nutrient Management Plan Into a 

General Permit 

The Agency is also promulgating 

procedural requirements for 

incorporating the terms of the NMP into 

an NPDES general permit, in new 

paragraph 40 CFR 122.23(h)(1). 

Once the processes for publicly 

reviewing the NMP and the terms of the 

NMP have been completed, the Director 

must address all significant comments 

raised and make a final decision 

whether to grant coverage under a 

general permit. As necessary, the 

Director will require a CAFO owner or 

operator to revise their NMP to address 

issues raised during the review process. 

Once the Director determines that the 

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process for the development of a 

CAFO’s NMP is complete, the Director 

must make the final decision whether to 

grant permit coverage to the CAFO 

under the general permit. If coverage is 

granted, the Director must incorporate 

the relevant terms of the NMP into the 

general permit (as described later) and 

inform the CAFO owner or operator and 

the public that coverage has been 

authorized and of the applicable terms 

and conditions of the permit. Once a 

CAFO obtains authorization to 

discharge under an NPDES permit, the 

CAFO must implement the terms and 

conditions of the nutrient management 

plan as incorporated into the permit, as 

of the date of permit coverage 

authorization. 

The preamble to the 2006 proposed 

rule discussed and requested comment 

on approaches for the Director to 

identify the terms of the NMP to be 

incorporated into the permit. These 

options ranged from attaching the entire 

NMP to the permit to identifying 

specific elements to be included in the 

permit as terms. Based on comments 

received on the proposed rule, EPA is 

specifying certain elements of NMPs 

with respect to land application as 

‘‘terms of the NMP’’ that must be 

incorporated into the permit. EPA is 

not, however, requiring a single 

approach whereby the terms are made 

part of the permit, leaving to the 

Director the discretion to decide 

whether, for example, to attach the 

entire NMP to the permit and require 

compliance with the terms of the NMP 

or to specify the terms of the NMP and 

specifically identify each of them in the 

permit. Under this final rule, 

incorporation of the terms of a 

particular CAFO’s NMP into a general 

permit is not a permit modification 

subject to 40 CFR 122.62. Rather, it is 

an extension of the CAFO general 

permitting process itself. As discussed 

above, EPA intends the process 

proposed in 40 CFR 122.23(h) to 

generally parallel the procedures in 40 

CFR part 124. 

Commenters supported an approach 

allowing a permitting authority to 

incorporate the entire NMP as a 

condition of the permit without 

distinguishing between the NMP and 

the ‘‘terms’’ of the NMP. Some 

supported attaching an NMP to the 

permit or general permit and requiring 

that the CAFO implement that NMP as 

a permit condition. As discussed above, 

this rule requires that a permit include 

the terms of a site-specific NMP. 

However, EPA is not prescribing the 

manner in which this incorporation 

takes place. The permitting authority 

may satisfy this requirement by 

incorporating a CAFO’s NMP by 

reference into the permit or as described 

in the preamble to the 2006 proposed 

rule, the permitting authority may 

extract the terms of the NMP and attach 

them to the permit. Either way, the 

terms of the NMP are enforceable terms 

of the NPDES permit. 

Other commenters sought greater 

State discretion in implementing NMP 

requirements as permit conditions. 

These commenters recognized the 

importance of implementing the NMP 

provisions but did not want this rule to 

interfere with effective existing State 

approaches. In addition, these 

commenters wanted to preserve the 

administrative advantages of using 

general permits. 

This rule provides some State 

discretion by allowing permitting 

authorities to determine which NMP 

provisions to include as terms of the 

permit. The rule specifies what must be 

included at a minimum in the permit as 

terms of the NMP. However, States have 

the authority to adopt additional or 

more stringent requirements, under 

CWA section 510. 

(e) Changes to a Permitted CAFO’s 

Nutrient Management Plan 

It is well understood that agricultural 

operations modify their nutrient 

management and farming practices 

during the normal course of their 

operations. Such alterations may require 

changes to a permitted CAFO’s NMP 

during the period of permit coverage. 

As discussed in the preamble to the 

2006 proposed rule, the permit does not 

need to be modified for all operating 

changes. Because of the way NMPs are 

developed and the flexibility provided 

by the two options for developing the 

terms of the nutrient management plan 

at 40 CFR 122.42(e)(5), most routine 

changes at a facility should not require 

changes to the NMP itself. For example, 

a CAFO using the narrative rate 

approach would not ordinarily need to 

change its NMP when it makes changes 

to factors that are not themselves terms 

but are accounted for in the 

methodology. To minimize the need for 

revision, nutrient management plans 

should anticipate and accommodate 

routine variations inherent in 

agricultural operations such as 

anticipated changes in crop rotation, as 

well as changes in numbers of animals 

and volume of manure, litter, or process 

wastewater resulting from normal 

fluctuations or a facility’s planned 

expansion. Typically, an NMP is 

developed to accommodate, for 

example, normal fluctuations in herd or 

flock size, capacity for manure, litter, 

and process wastewater storage, the 

fields available for land application and 

their capacity for nutrient applications. 

Moreover, as discussed in this 

preamble, EPA would encourage 

operators to develop an NMP that 

includes reasonably predictable 

alternatives that a CAFO may 

implement during the period of permit 

coverage. However, unanticipated 

changes to a nutrient management plan 

may nevertheless be necessary. 

The final rule includes 40 CFR 

122.42(e)(6), which requires a CAFO to 

notify the Director of changes to the 

CAFO’s NMP. Section 122.42(e)(6) 

excludes the results of calculations 

made in accordance with 40 CFR 

122.42(e)(5)(i)(B) and 122.42(e)(5)(ii)(D) 

from the requirements of paragraph 

(e)(6). The results of these calculations, 

which are required of Large CAFOs 

using the linear approach and all 

CAFOs using the narrative rate 

approach, must be reported in the 

CAFO’s annual report. Thus, there is no 

need to provide this information 

pursuant to the requirements of 

paragraph (e)(6). 

In the 2006 proposed rule, EPA 

proposed a process that CAFOs and the 

permitting authority would need to 

follow when a CAFO makes changes to 

its NMP. The proposal also included 

criteria for determining when a change 

to a CAFO’s NMP should be considered 

a substantial change. In the 2008 

supplemental notice, the Agency 

solicited comment on several 

modifications to the 2006 proposal 

including a list of changes to the NMP 

that would constitute a substantial 

change. 

In this final rule, EPA is including a 

list of changes to the NMP that would 

constitute a substantial change to the 

terms of a facility’s NMP, thus triggering 

public notice and permit modification. 

Substantial changes include: (1) 

Addition of new land application areas 

not previously included in the CAFO’s 

NMP; (2) any changes to the maximum 

field-specific annual rates of application 

or to the maximum amounts of nitrogen 

and phosphorus derived from all 

sources for each crop, as expressed in 

accordance with, respectively, the linear 

approach or the narrative rate approach; 

(3) addition of any crop not included in 

the terms of the CAFO’s NMP and 

corresponding field-specific rates of 

application; and (4) changes to fieldspecific components of the CAFO’s 

NMP, where such changes are likely to 

increase the risk of nitrogen and 

phosphorus transport from the field to 

waters of the U.S. 

This final rule also makes one 

exception to the first type of substantial 

change (a land application area being 

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added to the nutrient management 

plan), where such additional land is 

already included in the terms of another 

existing NMP incorporated into an 

existing NPDES permit. If, under the 

revised NMP, the CAFO owner or 

operator applies manure, litter, or 

process wastewater on such land 

application area in accordance with the 

existing field-specific terms of the 

existing permit, such addition of new 

land would not be a substantial change 

to the terms of the CAFO owner or 

operator’s NMP. 

EPA received a number of comments 

on the list of substantial changes in the 

2006 proposed rule and 2008 

supplemental proposal. One commenter 

encouraged EPA to state that substantial 

changes under the narrative rate 

approach only occur when the CAFO 

changes the system used to determine 

maximum allowable application rates. 

EPA agrees that changes in the 

methodology may be substantial 

changes to the terms of the NMP if they 

result in changes to the maximum rates 

of application or maximum amounts of 

nitrogen and phosphorus derived from 

all sources for each crop or if they result 

in changes likely to increase the risk of 

nutrient transport to waters of the U.S. 

However, EPA does not agree that there 

are no other changes that are substantial 

changes under the narrative rate 

approach. EPA believes that the four 

substantial changes identified in this 

final rule are appropriate for both of the 

approaches for determining rates of 

application. For example, proper 

implementation of the narrative rate 

approach depends on identification of 

the fields to be used for land 

application, so use of a new field for 

land application that had not been 

previously covered in the facility’s (or 

another facility’s) permit terms would 

constitute a substantial change. In 

addition, under the narrative rate 

approach a change to the field-specific 

maximum amounts of nitrogen and 

phosphorus derived from all sources is 

a substantial change to the NMP, 

because it defines the upper bounds on 

nutrient additions. 

Some commenters suggested that EPA 

expand the list of substantial changes to 

include changes such as the maximum 

number of animals allowed for the 

CAFO site; production area changes that 

alter the volume and composition of 

waste; using soil, manure, plant tissue 

test results to refine the NMP; and 

changes in the status of the receiving 

waterbodies. With regard to the number 

of animals confined and the volume of 

waste generated, EPA has stated that the 

number of animals confined at a CAFO 

would not necessarily be a term of the 

NMP because a CAFO operator is 

required to properly operate and 

maintain the CAFO’s storage facilities 

regardless of the number of animals or 

the volume of manure, litter, or process 

wastewater generated. For the same 

reasons, EPA believes that changes to 

these factors will not necessarily trigger 

substantial change to a CAFO’s permit, 

although accommodating an increase in 

the number of animals or volume of 

manure could lead to changes to the 

NMP that would constitute substantial 

changes to terms of the NMP (and the 

permit). With regard to the use of soil 

and manure tests, both approaches 

discussed above for expressing land 

application rates in NMPs and 

associated terms allow for consideration 

of manure testing on an annual basis; 

and the narrative rate approach also 

requires consideration of the most 

recent soil test results. Finally, NPDES 

permits for all types of dischargers, 

including CAFOs, typically include 

reopener provisions under which the 

Director may revise the permit during 

the permit term based on factors such as 

changes to the status of the receiving 

water body. EPA believes that such 

standard NPDES provisions are 

sufficient to allow permit revisions 

necessary to support the criteria and 

standards established for receiving 

waters. 

The Agency believes that the list of 

substantial changes included in this 

final rule address changes that most 

directly affect fundamental components 

of the NMP that relate to the land 

application of manure, litter, and 

process wastewater, which was a 

primary focus of the Waterkeeper 

decision. First, by identifying the 

addition of new land application areas 

not originally included in the terms of 

the NMP as a substantial change, the 

Agency makes clear that the fields to be 

used for land application must be 

permit terms, as all permitted CAFOs 

that land apply manure, litter, and 

process wastewater are required to do so 

at field-specific agronomic rates. The 

identification of land application areas 

in the NMP is essential for determining 

the effluent limitations applicable to a 

particular CAFO, which the 

Waterkeeper decision required be made 

available for public review and 

comment and incorporated into the 

permit. Thus, the public must have an 

opportunity to comment on the fields 

planned for land application during 

both the initial permit issuance phase 

and any subsequent permit modification 

phase. The exception for the addition of 

new fields already covered by an 

existing NPDES permit is consistent 

with the Waterkeeper decision because 

the rates of application for those land 

application areas will have already been 

publicly reviewed, approved, and 

incorporated into a permit as required 

by Waterkeeper. 

Some commenters supported the 

addition of new land application areas 

as a substantial change. They also 

commented that adding or reducing 

land application areas would require a 

recalculation of the application rate. 

Some commenters were concerned that 

the addition of new land application 

areas as a substantial change is 

counterproductive, severely limits 

flexibility for producers to plan, does 

not add water quality benefit, 

discourages producers from adding land 

to their NMP and will hinder a CAFO’s 

ability to quickly add more fields to the 

NMP. These commenters suggested the 

addition of land application areas can 

be addressed by requiring producers to 

submit this information with their 

annual reports. Some commenters also 

suggested granting States the flexibility 

to define when and what types of land 

application area additions would be 

considered a substantial change. Some 

commenters suggested that only the loss 

of land application areas should be 

treated as a major modification which 

requires public participation. As 

discussed above, under Waterkeeper, 

the public must have opportunity to 

review the fields planned for land 

application during both the initial 

permit issuance phase and any 

subsequent permit modification phase 

in order to determine whether fieldspecific rates of application have been 

properly developed. For this reason, the 

addition of new land application areas 

not already addressed under an existing 

NMP and permit must be considered a 

substantial change and made available 

for public review. 

The second substantial change is any 

change to the field-specific maximum 

rates of application. The Waterkeeper 

decision makes clear the importance of 

these rates as terms of the NMP. Some 

commenters indicated this change 

should not apply to NMPs developed 

using the narrative approach, since the 

appropriate application rate should be 

calculated using the approved 

methodology. This final rule clarifies 

that, for the narrative rate approach, a 

substantial change is triggered by a 

change in the field-specific maximum 

amount of nitrogen and phosphorus 

derived from all sources. 

The third substantial change is the 

addition to the NMP of crops or other 

uses not previously included in the 

CAFO’s NMP, together with the 

corresponding maximum field-specific 

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rates of application for those crops or 

other uses. Because rates of application 

are based on the yield goals for each 

specific crop, any crops or other uses 

newly added to the plan will require 

corresponding newly calculated rates of 

application. In addition, because the 

maximum rates of application must be 

made available to the public for review 

prior to incorporation as terms of the 

permit, consistent with Waterkeeper, 

the addition of new crops or other uses 

and their corresponding rates of 

application is considered a substantial 

change. 

Finally, any change to site-specific 

components of the CAFO’s nutrient 

management plan that is likely to 

increase the risk of nitrogen and 

phosphorus transport to waters of the 

U.S. is a substantial change. The Agency 

recognizes a number of changes as 

potentially triggering this requirement, 

including the following examples: (1) 

Alternate timing of land application that 

would diminish the potential for plant 

nutrient uptake; (2) methods of land 

application not provided for in the NMP 

calculation of amount of manure, litter, 

and process wastewater to be applied; 

(3) changes to conservation practices; 

and (4) changes in the CAFO’s 

procedures for handling, storage, or 

treatment of manure, litter, and process 

wastewater. The actual crop planted, 

timing and method of land application, 

crop uptake, and conservation practices 

utilized with respect to the land 

application areas are all key factors that 

affect nitrogen and phosphorus runoff 

from the land application area. Changes 

to any of the planning considerations 

listed above can directly (and 

measurably) alter the outcome of the 

decisions made in an NMP and the 

efficacy of that plan in ensuring 

appropriate agricultural utilization of 

those nutrients that are land applied. 

An advantage of the narrative rate 

approach is that it reduces the 

likelihood that changes to a CAFO’s 

operation would result in a substantial 

change to the terms of the CAFO’s NMP. 

For example, a change to the method or 

timing of application would be a 

substantial change to the terms of the 

NMP for CAFOs using the linear 

approach if the Director determines that 

it is likely to increase the risk of 

nutrient transport to surface waters. For 

a CAFO using the narrative rate 

approach, a change in the method or 

timing of application would not be a 

change to the terms of the NMP, and 

therefore not a substantial change, so 

long as the methodology in the NMP 

(itself a permit term) accounts for the 

change in method or timing. 

Because changes to the NMP could 

result in a change to a permit term, the 

2006 proposed rule provided that 

whenever a CAFO makes any change to 

its NMP, the owner or operator would 

be required to provide the Director with 

the revised NMP and identify the 

changes from the previous version 

submitted. Of course, any change to the 

CAFO’s implementation of its NMP that 

does not constitute a change to the NMP 

itself would not be submitted to the 

Director. For example, for CAFOs 

following the narrative rate approach, 

any change in crop rotation or 

substitution of crops in a given rotation 

with alternative crops identified in the 

NMP for a given field would not be a 

change and thus would not need to be 

submitted to the Director prior to 

implementation. 

Some commenters felt that substantial 

changes could be addressed by making 

those changes part of the annual report. 

For example, some commenters 

recommended that CAFOs using the 

narrative rate approach be required to 

include information associated with the 

addition of new crops in their annual 

reports. The annual report does not 

provide sufficient public notice for 

making changes to the terms of the 

NPDES permit. Those procedures are 

detailed below. 

(f) Process for Review of Changes to an 

NMP and for Modifying Terms of the 

NMP Incorporated Into the Permit 

When a permitted CAFO operator 

revises its NMP, this rule requires the 

CAFO operator to submit the revised 

NMP to the permitting authority for 

review and for the permitting authority 

to incorporate any revised terms of the 

NMP into the permit. This rule includes 

provisions that enable the Director to 

determine whether revisions to the 

CAFO’s NMP necessitate revisions to 

the terms of the NMP incorporated into 

the permit, and if so, whether such 

changes are substantial or nonsubstantial. This rule identifies several 

specific types of changes that must be 

considered substantial changes to the 

NMP, and this preamble provides 

further guidance for distinguishing 

between substantial and non-substantial 

changes. This final rule also establishes 

a streamlined process for formal public 

notice and comment that the permitting 

authority must follow for permit 

modification when a CAFO is seeking to 

make substantial changes to the terms of 

its NMP. Non-substantial changes to the 

terms of the NMP are not subject to 

public notice and comment before the 

permit is revised. Finally, this rule 

establishes provisions for incorporating 

both substantial and non-substantial 

revisions to terms of the NMP into the 

permit as a minor permit modification. 

These procedures apply to all permitted 

CAFOs, regardless of whether they are 

covered under an individual permit or 

under a general permit. These 

procedures are discussed in greater 

detail, below. 

As mentioned above, this final rule 

requires that whenever a CAFO makes 

any change to its NMP (see discussion 

in section III.C.3(e) of this preamble, 

‘‘Changes to a Permitted CAFO’s 

Nutrient Management Plan’’), the owner 

or operator must provide the Director 

with the revised NMP and identify the 

changes from the previous version 

submitted to the permitting authority. 

See 40 CFR 122.42(e)(6)(i). 40 CFR 

122.24(e)(6)(ii) requires the Director to 

then review the revised plan to ensure 

that it still meets the requirements of 40 

CFR 122.42(e) and applicable effluent 

limitations and standards, including 

those specified in 40 CFR part 412. This 

rule also requires the Director to 

determine whether the changes 

necessitate revision to the terms of the 

NMP that were incorporated into the 

permit issued to the CAFO. If not, the 

Director must notify the CAFO that the 

permit does not need to be modified. 

Upon such notification the CAFO may 

implement the revised nutrient 

management plan. 

If, on the other hand, the Director 

determines that the changes to the NMP 

do require that the terms of the NMP 

that were incorporated into the permit 

be revised, the Director must next 

decide whether or not the change is 

substantial. The Director will evaluate 

the change based on the provisions in 

§ 122.42(e)(6)(iii) discussed above. 

Pursuant to 40 CFR 122.42(e)(6)(ii)(A), 

for non-substantial changes, the Director 

must make the revised nutrient 

management plan publicly available and 

include it in the permit record, revise 

the terms of the nutrient management 

plan incorporated into the permit, and 

notify the owner or operator and inform 

the public of any changes to the terms 

of the nutrient management plan that 

are incorporated into the permit. Upon 

such notification the CAFO may 

implement the revised nutrient 

management plan. 

If the changes to the terms of the NMP 

are substantial, the Director will also 

modify the permit as necessary by 

incorporating revised terms of the NMP, 

but only after the public has had the 

opportunity to review and comment on 

the NMP changes pursuant to the 

requirements of 40 CFR 

122.24(e)(6)(ii)(B). The process for 

public comments, hearing requests, and 

the hearing process if a hearing is 

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granted must follow the procedures for 

draft permits set forth in 40 CFR 

124.11–13. The Director must respond 

to all significant comments received 

during the comment period as provided 

in 40 CFR 124.17, and require the CAFO 

owner or operator to further revise the 

nutrient management plan if necessary. 

Once the Director incorporates the 

revised terms of the nutrient 

management plan into the permit, the 

Director must notify the owner or 

operator and inform the public. A 

permit modification to revise the terms 

of the NMP incorporated into the permit 

may be appealed in the same manner as 

the initial final permit decision. 

The Director may establish by 

regulation, or in the general permit for 

CAFOs authorized under a general 

permit, an appropriate period of time for 

the public to comment and request a 

hearing on the proposed substantial 

changes to the terms of the nutrient 

management plan incorporated into the 

permit that differs from the time period 

specified in 40 CFR 124.10. EPA is 

providing this discretion to the Director 

to allow CAFOs to implement revised 

nutrient management practices in 

accordance with growing seasons and 

other time sensitive circumstances. As 

is stated above in section III.C.3(b) of 

this preamble regarding public review of 

NMPs during the general permit 

process, the public will have an 

opportunity to comment on the 

sufficiency of the time period when the 

Director proposes it, either in the 

regulations or general permit. 

Because the process in 

§ 122.42(e)(6)(ii) allows for public 

review of substantial changes to the 

terms of nutrient management plans and 

the underlying data and calculations, 

the incorporation of changes to the 

permit through this process will be 

treated as a minor permit modification, 

under 40 CFR 122.63(h), and not require 

additional review. EPA considered 

requiring that any change to the NMP be 

considered a permit modification 

subject to procedures under 40 CFR 

122.62, but rejected this interpretation 

as it would significantly limit 

permitting authorities and CAFO 

operators’ ability to make necessary and 

timely minor changes to NMPs as 

discussed above. 

Commenters identified several issues 

associated with the proposed process for 

making substantial changes to NMPs. 

Several commenters indicated that the 

need for the permitting authority to 

review, provide public notice and 

comment, and approve substantial 

changes to NMPs will likely result in 

significant delays which will impact the 

operational ability of many CAFOs to 

make timely nutrient management 

decisions. Some commenters suggested 

that the process for making such 

changes be streamlined or time-limited. 

Other commenters requested that EPA 

provide flexibility to accommodate 

existing State criteria and procedures for 

determining and addressing substantial 

changes. Some State commenters 

indicated that they already have 

effective procedures in place. Some 

commenters simply asserted that the 

State Director should have discretion 

whether or not to require a permit 

modification. 

The NPDES regulations at § 122.62 

specifically require that any change to 

permit terms and conditions requires 

permit modification to be subject to 

public review and comment procedures, 

unless it falls under a minor 

modification listed at 40 CFR 122.63. In 

this rule, EPA has accounted for the 

frequent operational changes unique to 

CAFOs which are not typical for other 

NPDES-regulated industries. This 

tailoring is an effort to balance 

environmental protection with the 

burden to CAFOs and permitting 

authorities as well as the need to allow 

other operational changes that would 

not trigger the substantial modification 

requirements. 

The process in this rule for making 

changes to NMPs and incorporating 

such changes in permits is necessary as 

a result of the Waterkeeper decision, 

which held that terms of the NMP are 

effluent limitations and that the CWA 

requires that the terms of each NMP be 

incorporated into a corresponding 

permit and be subject to public notice 

and comment and permitting authority 

review. Within this context, EPA has 

worked to streamline the process to the 

extent possible. This includes 

promulgating a process for revising 

NMPs that delineates what are 

substantial changes to the terms of the 

NMP and allows non-substantial 

changes to proceed in an expedited 

manner. It also includes provisions that 

allow a CAFO to develop NMPs with 

operational contingencies to minimize 

the number of substantial changes that 

must be made. As explained herein, the 

process and criteria in 40 CFR 

122.42(e)(6) are reasonable and 

necessary to provide permitting 

authorities an effective mechanism to 

maintain linkage between the NMP and 

the permit in a manner consistent with 

the Waterkeeper decision. 

Commenters suggested changes to the 

process in the 2006 proposed rule. 

Several commenters requested that EPA 

approve certain substantial changes as 

long as the CAFO continues to comply 

with all applicable technical 

requirements. Such substantial changes 

could include adding a new and 

substantially different field or 

increasing the animal headcount so as to 

exceed the previously identified 

‘‘maximum’’ amount of manure in the 

NMP. In addition, one commenter 

recommended that the permitting 

authority inspect the CAFO before 

allowing any substantial changes to the 

NMP. 

The final rule does not expressly 

provide that a permitting authority can 

pre-approve certain substantial changes, 

unless they are specified in an NMP that 

encompasses normal fluctuations or 

variations, because the Waterkeeper 

decision dictates that NMPs must be 

subject to permitting authority review 

and the terms of the NMP available for 

public comment. In addition, EPA does 

not believe an inspection is needed 

prior to allowing any substantial change 

to an NMP. Apart from the burden this 

would entail, EPA expects that selfreported information is credible and 

notes that there are significant penalties 

for submitting false or misleading 

information. 

Many commenters supported the 

proposal that non-substantial changes 

would require only that the CAFO 

submit a revised NMP and that the 

permitting authority would notify the 

public of the change without allowing 

for public comment. Commenters 

encouraged EPA to clarify that, upon 

submission, the CAFO may proceed to 

implement such changes if the CAFO 

believes they are non-substantial. Many 

commenters stated that there is a need 

to ensure that CAFOs can quickly make 

changes to NMPs. One commenter 

recommended that EPA allow CAFOs to 

accumulate minor changes and submit 

them as a group when renewing their 

permit. Another commenter suggested 

that any changes incurred during a 

given year be reported in an annual 

NMP update form. EPA decided that, 

because the terms of the NMP are 

enforceable terms and conditions of the 

permit, CAFOs must submit changes to 

the NMP to the permitting authority and 

receive approval before a change is 

made, not annually or at the beginning 

of each new permit cycle. 

Commenters were generally 

unsupportive of the proposed 180-day 

temporary approval period for 

implementation of certain substantial 

changes. Numerous commenters stated 

that this would not be helpful to CAFO 

owners because they would be hesitant 

to invest significant amounts of money 

to make substantial changes based only 

on a temporary approval, since final 

approval would remain subject to an 

uncertain regulatory status. Others 

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requested clarification regarding what 

happens if a change is implemented and 

then not approved. Some of these 

commenters suggested as an alternative 

that EPA require the permitting 

authority to process the applications in 

fewer than 45 days, and then allow 

seven days of public review. 

Another commenter stated that the 

temporary approval period is 

inadequate because 180 days is longer 

than the crop growing season. This 

commenter observed that the temporary 

approval would allow CAFOs to change 

their entire land application patterns for 

an entire crop season without having 

public comment and review by the 

permitting agency. This commenter 

suggested that CAFOs plan in advance 

for any substantial changes and that 

only if the substantial changes are the 

result of unforeseen circumstances 

outside the control of the CAFO, should 

it be allowed temporary approval. 

Based on comments, EPA reevaluated 

the usefulness of the 180-day temporary 

approval. In light of the comments, EPA 

recognizes that such an approach may 

be problematic for both industry and 

permitting authorities. Some industry 

commenters stated that the 180-day 

grace period would be meaningless 

because no operator would employ 

expensive changes without knowing if 

they would be approved. States 

commented that any permit 

modification must be approved before it 

is implemented. There is no 

requirement precluding operators from 

purchasing new land; rather, practices 

on the land cannot be employed until 

approved by the permitting authority. 

Further, EPA encourages operators to 

take advantage of the exception for 

substantial changes relating to the 

addition of new land application areas 

provided in § 122.42(e)(6)(iii)(A). Thus, 

EPA has not included the proposed 180-

day temporary approval period in the 

final rule. 

Under this final rule, when a CAFO 

submits changes to an NMP to the 

permitting authority, the Director must 

determine whether the changes affect 

the terms of the NMP incorporated into 

the permit, and if so, whether such 

changes are substantial. Depending on 

this determination, the process and 

timing of modifying a permit will vary. 

A CAFO owner or operator must remain 

in compliance with his or her permit 

and, thus, should work closely with the 

permitting authority and should initiate 

this coordination as early as possible. 

EPA believes that permitting authorities 

will be sensitive to the needs of CAFOs 

to make a range of changes to NMPs 

from time to time and, as a result, will 

be diligent in reviewing and making 

determinations regarding such changes. 

(g) Annual Reporting Requirements 

In the 2006 proposed rule, EPA 

discussed the use of annual reports to 

balance greater flexibility for CAFO 

operators in making cropping decisions 

with ensuring appropriate permitting 

authority and public oversight of permit 

compliance. The preamble solicited 

comment as to whether the annual 

report requirements should be modified 

to require all permitted CAFOs to 

submit information in their annual 

reports indicating how the CAFO 

achieved substantive compliance with 

the terms of the NMP as set forth in the 

permit. In the 2008 supplemental 

proposal, the Agency proposed 

additional annual reporting 

requirements for CAFOs that relate to 

the proposed provisions regarding the 

terms of the NMP. 

In this action, the Agency is 

establishing additional annual report 

requirements, in 40 CFR 

122.42(e)(4)(viii), mandating all 

permitted CAFOs to include in their 

annual reports the actual crop(s) planted 

and actual yield(s) for each field, the 

actual nitrogen and phosphorus content 

of the manure, litter, and process 

wastewater, and the amount of manure, 

litter, or process wastewater applied to 

each field during the previous 12 

months. The Agency believes that it is 

important for the permitting authority to 

obtain this information on an annual 

basis in order to ensure that the CAFO 

has been operating in compliance with 

the terms of its permit. The annual 

report will inform the Director and the 

public how the CAFO has operated, 

given the flexibility for the terms of the 

NMP incorporated into the permit. 

The Agency is also requiring CAFOs 

that follow the second (‘‘narrative rate’’) 

approach for describing rates of 

application in the NMP to submit as 

part of their annual report the results of 

all soil testing and concurrent 

calculations to account for residual 

nitrogen and phosphorus in the soil, all 

recalculations, and the new data from 

which they are derived. The CAFO is 

required to report the amounts of 

manure, litter, process wastewater and 

the amount of chemical fertilizer 

applied to each field during the 

preceding 12 months. Together with the 

total amount of plant available nitrogen 

and phosphorus from all sources, the 

information that is required to be 

included in the annual report provides 

the information necessary to determine 

that the CAFO was adhering to the 

terms of its permit when calculating 

amounts of manure, litter, and process 

wastewater to apply. 

Many commenters supported the use 

of additional annual reporting 

requirements to address either nonsubstantial changes or all changes to the 

NMP. States also generally supported 

such an approach and sought flexibility 

regarding the content and use of the 

process to address other changes to the 

NMP. Another commenter noted that if 

CAFOs are allowed to provide 

alternative management scenarios in the 

original NMP, the CAFO must be 

required to submit documentation to the 

Director to specify which practices it is 

using from the ‘‘menu’’ of combinations 

in its NMP. This would allow the 

permitting authority and the public to 

know what practices the CAFO is 

actually implementing at any given 

time. 

Although EPA recognizes that NMPs 

may change throughout the period of 

permit coverage, as discussed above in 

section III.C.3(e), the annual report 

requirements are only appropriate for 

use in addressing implementation of 

existing NMP provisions and changes to 

the NMP contemplated through 

flexibilities built into the NMP during 

the initial planning process or 

subsequent modifications in accordance 

with 40 CFR 122.42(e)(6). Because this 

rule requires the terms of the NMP to be 

incorporated as enforceable terms and 

conditions of the permit, an outcome of 

the Waterkeeper decision, changes to 

the terms of the NMP constitute changes 

to the permit and therefore must be 

processed according to § 122.42(e)(6), as 

discussed above in section III.C.3(e). 

Some commenters expressed concern 

that CAFOs would be unable to 

complete more detailed reports and 

provide the information necessary to 

document changes to the NMP, and that 

some of the reporting requirements 

would be redundant. Some commenters 

also believed that reporting crop yields 

would be overly intrusive and would 

not be representative of the NMP 

effectiveness. In this rule, EPA has 

modified the content of the annual 

report to supplement the existing 

annual report requirements promulgated 

in 2003 so as to allow the public and the 

permitting authority to review whether 

the CAFO has implemented the NMP in 

accordance with the terms and 

conditions of its permit. This approach 

balances the recognized need to provide 

additional flexibility and the need for 

CAFOs to provide information 

concerning actual rates of application. 

The additional information required in 

this final rule is a limited burden on 

both the CAFO and the permitting 

authority that will provide public access 

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to information about NMP 

implementation throughout the period 

of permit coverage. For example, crop 

yield goals are a critical factor in 

developing rates of application. Other 

commenters expressed concern that 

facilities might overstate crop yields 

goals. As previously mentioned, by 

making information about actual crop 

yields public, both the Director and the 

public will have better information 

when evaluating NMPs for subsequent 

permit coverage. 

(h) EPA Nutrient Management Plan 

Template 

As described in the 2006 proposed 

rule, EPA developed a draft template, 

made available in the rulemaking public 

record for public comments, which 

could be used as a voluntary tool to 

facilitate completion of the NMP by 

CAFO permit applicants, as well as to 

facilitate review by the permitting 

authority. As discussed in the proposed 

rule, EPA believed that such a template 

would help to systematically organize 

the information necessary to satisfy the 

NMP requirements in the regulation. 

Some commenters supported the 

concept of a voluntary NMP template 

and considered the draft template an 

excellent user-friendly model. Other 

commenters disagreed, stating that the 

detailed information required in the 

draft template would be quickly 

outdated. Other comments received on 

the NMP template include the 

following: 

• A ‘‘one size fits all’’ template does 

not lend itself well to the different 

climates and terrains across the country, 

and use of the template should not be 

required by the regulation; 

• The draft template lacked specific 

information to ensure that CAFOs are 

meeting technical standards and the 

ELGs; 

• The draft template was too long and 

appeared to be more of an inspection 

checklist than a basic guideline; 

• A concern that some States may 

actually adopt the template, once 

completed, as the required NMP format; 

• The template could be a valuable 

tool to clearly differentiate between the 

terms of the NMP, for purposes of 

incorporation into the permit, and the 

background information; 

• The template would be more 

beneficial if it is standardized through 

the use of a computer program which 

allows ease and flexibility in making 

changes to the NMP; and 

• The template could be useful to an 

unpermitted CAFO to identify land 

application practices needed to qualify 

for the agricultural stormwater 

exemption. 

States generally agreed with the 

concept of using a consistent, stable 

template but wanted assurance that it is 

strictly a voluntary tool and can be 

modified to better address specific State 

requirements. Additionally, commenters 

stated that the draft template failed to 

address all of the regulatory 

requirements and should be modified 

accordingly by including additional 

technical portions. Other commenters 

suggested that a template would 

unnecessarily micromanage the 

structure or content of NMPs and that 

States should have the responsibility to 

define effective nutrient management 

strategies. Other commenters mentioned 

the need to keep the template flexible 

because NMPs are dynamic documents 

that change rapidly, and a plan that is 

too detailed will bind the producer to 

practices that, if altered, would require 

costly revisions and reviews. A few 

commenters also indicated that the 

format and sequence for providing 

information within the draft template 

was disjointed and inconsistent with the 

nutrient management planning process. 

Other State commenters did offer, 

however, that the template may be 

adequate for most public participation 

processes. 

After considering public comments, 

EPA, in coordination with USDA, has 

decided not to utilize the draft template. 

Instead, the two agencies have worked 

on the development of a planning tool 

that would generate a single document 

that meets the objectives of both 

agencies. The one document would 

include the required elements of an 

NMP as well as the elements of a 

voluntary comprehensive nutrient 

management plan (CNMP) developed in 

accordance with USDA technical 

guidance. A CNMP is a plan much like 

the NMP required by EPA’s CAFO 

regulations. There are some minor 

differences between the scope of the two 

documents, such as a CNMP option to 

include feed management plans (which 

are not required for the NMP) and an 

NMP requirement to include chemical 

handling plans (which are not part of a 

CNMP). However, the EPA and USDA 

agree that there is no reason why one 

document could not suffice for both the 

CNMP and NMP by accommodating 

both agencies’ requirements. To that 

end, EPA, in partnership with USDA, is 

in the process of coordinating the 

information necessary to complete an 

NMP as well as a CNMP and developing 

a software program that could integrate 

both sets of planning requirements, 

known as Manure Management Planner 

(MMP). Of course, even though both 

agencies would promote the use of a 

single tool, it would remain the CAFO 

operator’s responsibility to provide that 

information to the Director in order to 

meet the requirements of this rule, 

inasmuch as USDA does not make 

facility-specific information available to 

other agencies or the public. EPA will 

encourage the use of the MMP to 

facilitate the development and review of 

NMPs under the NPDES permit 

program. 

The MMP software, under 

development by a grant from EPA and 

USDA to Purdue University, is a 

computer program that would provide 

permitting authorities and producers 

with a mix of programs, not currently 

available elsewhere, to assist in CNMP 

and/or NMP development. The objective 

of this effort is to accelerate the CNMP 

and NMP development process by 

integrating other software programs 

used to calculate manure application 

rates. Among these technologies are 

RUSLE II, the Phosphorus Index (PI), 

and other State-specific risk assessment 

tools used in CNMP and NMP 

development. In the longer term it is 

planned that additional integration will 

be achieved with planning, 

recordkeeping technologies and 

connectivity to the USDA Customer 

Service Toolkit. The MMP program 

incorporates field-specific data tables 

that allow the producer to list the type 

of crops planned, crop rotation by 

planting season, nutrients available for 

each crop based on previous manure 

applications, and the rate of application 

per crop. These data tables could 

provide permitting authorities with 

specific information that could be 

extracted as terms of the NMP that 

would be inserted into a permit. It also 

provides producers the flexibility to 

comply with the optional approach of 

calculating application rates as pounds 

of nutrients by developing tables with 

expanded crop contingency plans and 

related application rates. See section 

III.C.3(c) for detailed discussion of 

nutrient management plan terms. 

EPA and USDA anticipate that the 

MMP software can eventually be 

tailored to all individual State technical 

standards, requirements and 

circumstances. At present, the program 

has been tailored to approximately 34 

States, and is available and ready for use 

in those States. EPA and USDA plan on 

updating and improving the MMP 

software and tailoring it to other States. 

When completed, the MMP software 

will be a user-friendly program available 

without charge. It is strictly a voluntary 

tool. There may be some situations at a 

livestock operation, such as varying 

terrains and unusual cropping 

sequences, which the MMP cannot 

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accommodate; thus the program may 

not, at present, be a good fit for all 

operators. Permitting authorities and 

producers may still choose to use an 

established State NMP software program 

or other technical standards methods to 

develop and implement their NMP. 

More information on MMP can be found 

at the Purdue University Web site, 

http://www.agry.purdue.edu/mmp/. 

EPA and USDA are also developing a 

national nutrient management planning 

course that will cover how to develop, 

review, and implement an NMP and 

how to use the MMP software program. 

D. Compliance Dates 

Following issuance of this rule, 

authorized States have up to one year to 

revise, as necessary, their NPDES 

regulations to adopt the requirements of 

this rule, or two years if statutory 

changes are needed, as provided in 40 

CFR 123.62. States are not required to 

adopt the provisions for no discharge 

certification in this time period. 

As discussed above in section II.E, 

EPA has twice extended certain 

compliance dates originally established 

in the 2003 CAFO rule. Following the 

Second Circuit Court’s decision in 

Waterkeeper Alliance et al. v. EPA, 399 

F.3d 486 (2d Cir. 2005), the Agency 

extended dates for newly defined 

CAFOs to seek permit coverage and for 

all permitted CAFOs to develop and 

implement NMPs to July 31, 2007. 71 

FR 6978 (February 10, 2006) (hereinafter 

the ‘‘2006 date change rule’’). 

The 2006 proposed rule did not 

anticipate a need to revise the July 31, 

2007, compliance dates established by 

the 2006 date change rule. However, as 

a result of an array of public comment 

on the issues raised by the Waterkeeper 

decision, EPA was unable to complete 

this final rule prior to July 31, 2007. 

EPA published a second revision of the 

compliance dates on July 24, 2007, 

extending the dates from July 31, 2007, 

to February 27, 2009. 72 FR 40,245 (July 

24, 2007) (hereinafter the ‘‘2007 date 

change rule’’). The 2007 date change 

rule does not affect the applicable time 

for seeking permit coverage for existing 

facilities defined as CAFOs prior to the 

2003 CAFO rule, nor does it apply to 

newly constructed CAFOs not subject to 

new source performance standards 

(NSPS) or to new source CAFOs subject 

to NSPS that discharge or propose to 

discharge. The February 27, 2009, 

compliance dates also do not affect the 

approximately 9,000 CAFOs currently 

covered under existing permits. 

Furthermore, for Large CAFOs that are 

new sources (i.e., those commencing 

construction after the effective date of 

the 2003 CAFO rule) and are required to 

seek permit coverage under the revised 

duty to apply provision in this rule (40 

CFR 122.23(d)(1)), the land application 

requirements at 40 CFR 412.4(c) apply 

immediately because new sources are 

subject to the NSPS under 40 CFR 

412.35 and 412.46, which do not 

include a delayed date for new sources 

to come into compliance with § 412.4(c). 

The 2003 rule did not delay compliance 

with the land application requirements 

for new sources. See CWA section 

306(e). 

EPA received comments on the 2006 

proposed rule related to the July 31, 

2007, compliance dates in place at that 

time. The comments received generally 

focused on two issues: (1) That the 

permit application date did not allow 

enough time for States to revise their 

permitting programs, and (2) that the 

date did not allow CAFO operators 

sufficient time to develop permit 

applications and NMPs. Many 

commenters stated that it would not be 

possible for CAFOs to seek coverage 

under an NPDES permit by July 31, 

2007, and that the deadline should be 

extended. A number of extension 

periods were suggested ranging from 

several months to up to two years after 

promulgation of the final rule. 

Rationales for extending the dates 

included the need to allow States to 

revise their programs to fully reflect 

CAFO regulations (which, in turn, 

allows CAFOs to know what 

requirements apply to them), limited 

technical assistance, and the need for 

adequate time to develop an NMP in the 

period between rule promulgation and 

the deadline for seeking permit 

coverage. Commenters asserted that 

CAFO owners and operators cannot 

know the precise requirements for 

NMPs, or the associated documentation 

and public participation requirements, 

until the rule is final. EPA promulgated 

the 2007 date change rule with these 

comments in mind. 

In the 2008 supplemental proposal 

(73 FR 12,336) EPA solicited comments 

on its intention to not extend the 

compliance deadlines beyond February 

27, 2009. Some commenters stated that 

the deadline should be extended in 

order to allow States to adapt their 

existing programs. Others noted that 

more time would be needed for CAFO 

owners and operators to implement 

such complex rules and come into 

compliance. A number of extension 

periods were suggested ranging from 

several months to up to two years after 

promulgation of the final rule. 

Commenters were opposed to an 

extension of the deadlines; did not want 

to further delay the environmental 

benefits; and noted that an extension 

would provide a comparative advantage 

to those CAFOs that have not made 

capital improvements and promote 

interstate discrepancies that undermine 

the integrity of State CAFO programs. 

In this final rule, EPA is not extending 

the February 27, 2009, compliance 

deadlines. EPA believes that the time 

between publication of this final rule 

and February 27, 2009, is adequate for 

unpermitted CAFOs that discharge or 

propose to discharge to develop an NMP 

and seek permit coverage. EPA notes 

that most of the technical provisions of 

the 2003 CAFO rule (e.g., the 

substantive NMP requirements) were 

unaffected by the Waterkeeper decision, 

and therefore CAFOs have already had 

the information they need to develop 

NMPs and have not needed to wait for 

further EPA action before doing so. In 

States where general permits have been 

issued and have not expired, eligible 

CAFOs may seek permit coverage under 

applicable existing general permits. 

Where general permits are not available, 

CAFOs may seek permit coverage by 

submitting an individual permit 

application. As mentioned above, 40 

CFR 123.62(e) provides that States will 

have one year from the promulgation 

date of this final rule, or two years if 

statutory changes are needed, to adopt 

the requirements of this final rule. 

During this interim period, EPA expects 

States to issue permits that comply with 

all technical requirements of the 2003 

rule that were unaffected by the 

Waterkeeper decision and, absent 

regulatory or statutory barriers, to 

provide for NMP submission, public 

review of NMPs, and incorporation of 

the NMP terms into the permit. EPA is 

committed to working with States to 

implement CAFO permitting 

requirements. 

The CWA does not allow any CAFO 

to discharge without a permit, 

regardless of whether a permit 

application has been submitted. EPA 

and States have a range of tools to help 

regulated entities come into compliance 

with new rules including outreach, 

compliance assistance, compliance 

incentives and compliance monitoring. 

For new rules EPA generally focuses on 

outreach initially. Where EPA becomes 

aware of particular instances of 

noncompliance, EPA may pursue 

appropriate enforcement. Since 2005, 

EPA has designated unpermitted CAFOs 

subject to the 1976 rule as an 

enforcement priority and continues to 

focus its efforts on those facilities. With 

respect to CAFOs subject to permitting 

as of February 27, 2009, EPA would take 

into consideration whether a permit 

application has been submitted and 

whether the entity is operating in 

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accordance with its NMP and all other 

applicable requirements of the 2003 

CAFO rule and this final rule. 

E. Water Quality-Based Effluent 

Limitations 

Water quality-based effluent 

limitations (WQBELs) are one of two 

fundamental types of limitations 

imposed in NPDES permits. The other is 

technology-based effluent limitations. 

NPDES permits are required to contain 

technology-based limitations and, if the 

technology-based limitations are 

insufficient to meet applicable water 

quality standards, more stringent water 

quality-based effluent limitations 

(WQBELs). CWA section 301(b)(1)(C), 

33 U.S.C. 1311(b)(1)(C); and 40 CFR 

122.44(d). While technology-based 

limitations are calculated taking into 

account the availability or effectiveness 

of treatment technologies and/or their 

associated costs, WQBELs are 

established without consideration of 

availability or effectiveness of treatment 

technologies or the costs that discharges 

would incur to meet such limits. 

Arkansas v. Oklahoma, 503 U.S. 91 

(1992); Westvaco v. EPA, 899 F.2d 1383 

(4th Cir. 1990). 

The environmental petitioners 

challenged the 2003 rule as violating 

both the CWA and the Administrative 

Procedure Act by failing to promulgate 

WQBELs for CAFO discharges and by 

being ambiguous as to whether States 

may promulgate WQBELs for CAFO 

discharges. As explained in II.C.3 above, 

the Waterkeeper Court agreed in part 

with petitioners, and remanded the rule 

for clarification regarding the 

applicability of WQBELs for CAFO 

discharges that are not exempt as 

agricultural stormwater, to explain why 

EPA justified its decision not to 

promulgate WQBELs for discharges 

other than agricultural stormwater, and 

to clarify whether the CAFO rule bars 

States from requiring WQBELs for such 

discharges. Waterkeeper Alliance et al. 

v. EPA, 399 F.3d 486, 522–524 (2d Cir. 

2005). 

As EPA stated in the preamble to the 

2006 proposed rule, the only issue that 

EPA addressed in the 2003 rule with 

respect to WQBELs was their 

applicability to agricultural stormwater 

discharges. EPA had explained in 2003 

that, because agricultural stormwater 

discharges are not point source 

discharges, agricultural stormwater 

discharges cannot be subject to NPDES 

permit requirements, including either 

technology-based limitations or 

WQBELs if technology-based limitations 

are insufficient to meet applicable water 

quality standards. The Second Circuit 

Court of Appeals agreed with EPA. 

However, the court seemed troubled by 

certain statements in the 2003 preamble 

that it thought might address how 

WQBELs apply to other CAFO 

discharges. The court therefore 

remanded the question of whether or 

not, and why, WQBELs are needed to 

assure attainment or maintenance of 

water quality standards as provided in 

section 302(a) of the CWA. 

In the preamble to the 2006 proposed 

rule, EPA responded to the remand by 

clarifying that discharges from CAFOs 

that are not exempt from CWA 

permitting requirements as agricultural 

stormwater discharges are subject to 

NPDES requirements, including 

WQBELs. EPA clarified the applicability 

of WQBELs both with respect to land 

application areas under the control of a 

CAFO and with respect to discharges 

from a CAFO’s production area. 

1. Discharges From Land Application 

Areas 

As explained in section III.B. above, 

under the 2003 rule, the agricultural 

stormwater discharge exemption applies 

only to precipitation-related discharges 

from land application areas under the 

control of the CAFO where application 

of manure, litter, or process wastewater 

is in accordance with appropriate 

nutrient management practices as 

specified in 40 CFR 122.42(e)(1)(vi)–(ix). 

Any other discharge from land 

application areas under the control of a 

CAFO is a point source discharge from 

the CAFO. 40 CFR 122.23(e). These 

point source discharges from land 

application areas are subject to NPDES 

permitting requirements, including 

WQBELs where necessary to meet 

applicable water quality standards. 

In most instances, a CAFO that meets 

technology-based permit limits 

requiring manure to be applied at 

appropriate agronomic rates will 

eliminate all or most dry weather 

discharges. If such discharges remain, 

the permit writer will determine the 

need for additional WQBELs to meet 

applicable water quality standards 

based on the circumstances of each 

particular case. 

Although EPA, in the 2003 rule 

preamble, encouraged States to address 

water quality protection issues in setting 

technical standards for appropriate land 

application practices (see Waterkeeper, 

399 F.3d at 523, citing 68 FR 7198), EPA 

did not intend to change the basic 

regulatory scheme of the NPDES 

program. With respect to wet weather 

discharges, under 40 CFR 122.42(e)(1), 

the permit must already include effluent 

limitations defining the ‘‘site-specific 

nutrient management practices’’ 

required to be implemented under 

§ 122.23(e) in order for the remaining 

wet weather (‘‘precipitation-related’’) 

discharges to be ‘‘agricultural 

stormwater discharges.’’ As previously 

explained, agricultural stormwater 

discharges are exempt from the 

definition of ‘‘point source’’ of section 

502 of the CWA and are therefore not 

subject to permitting requirements 

under the CWA, including WQBELS. 

Thus, any precipitation-related 

discharge from land application areas 

remaining after compliance with the 

technology-based effluent limitations 

and permit conditions required 

pursuant to § 122.42(e)(1)(vi)–(ix) are 

exempt from CWA permitting 

requirements as agricultural stormwater, 

and these technology-based effluent 

limitations constitute the entirety of the 

federal NPDES permit requirements 

with respect to land application of 

manure, litter, and process wastewater. 

However, it is possible that a State may 

have additional requirements under its 

own State regulatory authorities that 

would go beyond the scope of the 

federal NPDES program. Thus, such 

agricultural stormwater discharges, 

though not subject to federal NPDES 

regulation, could be subject to 

additional State requirements, including 

additional requirements related to water 

quality. 33 U.S.C. 1370 and 40 CFR 

123.1 and 123.25. These requirements, 

however, would not be viewed as 

WQBELs as that term is used under the 

CWA. Nor would these State-law 

requirements be federally enforceable. 

40 CFR 123.1(i)(2). 

2. Production Area Discharges 

EPA also explained in the preamble to 

the 2006 proposed rule that permit 

writers may require WQBELs in 

appropriate cases to further limit 

discharges from CAFO production areas. 

As EPA stated in the 2003 rule, the 

exclusion for agricultural stormwater 

does not apply to discharges from the 

CAFO production area. 40 CFR 

122.23(e) and 68 FR 7198. Because the 

ELGs allow occasional overflow 

discharges from properly designed, 

operated, and maintained lagoons and 

storage ponds, the technology-based 

limitations in the ELGs may not be as 

stringent as necessary to meet 

applicable water quality standards. In 

that case, a WQBEL would be 

appropriate. 40 CFR 122.44(d). For 

example, a facility subject to ELGs in 40 

CFR part 412, subpart C is allowed to 

discharge from the production area, 

provided the production area is 

designed, constructed, operated, and 

maintained to contain all process 

wastewater plus any stormwater runoff 

resulting from the 25-year, 24-hour 

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storm. Thus, WQBELs would be 

necessary in a particular permit to 

further limit such discharges beyond the 

levels that are required under the CAFO 

ELGs, if necessary for the discharge to 

meet applicable water quality standards. 

In the preamble to the 2006 proposed 

rule, EPA indicated that for CAFOs in 

the swine and poultry sectors subject to 

New Source Performance Standards 

(NSPS) in part 412, subpart D, permits 

could not require WQBELs for 

production areas, because the NSPS 

already prohibit all production area 

discharges from these new sources. 71 

FR 37,744, citing 40 CFR 412.46(a). 

Some commenters, however, urged EPA 

to reconsider its position given a 

possibility of a discharge even from 

CAFOs subject to a no discharge 

standard. Nothing in this rule limits the 

Director’s authority to include any more 

stringent limitation than the NSPS in a 

CAFO’s permit when necessary to meet 

applicable water quality standards 

pursuant to CWA section 301(b)(1)(C). 

Nonetheless, EPA continues to believe 

that WQBELs would not be needed for 

swine and poultry CAFOs subject to the 

no discharge NSPS. The provisions for 

implementing the NSPS BMP-based 

effluent limitation, based on advanced 

modeling, are meant to improve 

implementation of this provision by 

promoting up-front design, 

construction, operation, and 

maintenance to ensure that predictable 

discharges do not occur. Permitting 

authorities have full authority and 

responsibility to determine if the 

facility’s demonstration is adequate. 

Therefore, as a practical matter, EPA 

finds it difficult to imagine 

circumstances in which such a 

limitation would be necessary for 

permitted CAFOs subject to this NSPS 

no discharge standard. 

F. New Source Performance Standards 

for Subpart D Facilities 

This action responds to the Second 

Circuit’s remand of certain aspects of 

the 2003 New Source Performance 

Standards (NSPS). First, EPA has 

deleted the remanded provisions that 

authorized two alternatives for 

compliance with the NSPS requirement 

for no discharge of manure, litter, or 

process wastewater into waters of the 

U.S. from the production area. Second, 

EPA is promulgating a new provision 

that would allow a CAFO using an open 

surface manure storage structure to 

request the NDPES permitting authority 

to establish site-specific effluent 

limitations for its NPDES permit that 

incorporate the NSPS no discharge 

requirement. These best management 

practices effluent limitations include 

design specifications and operational 

parameters and must be based on a 

technical evaluation of the adequacy of 

the CAFO’s storage structure for 

achieving no discharge of manure, litter, 

or process wastewater into waters of the 

U.S. The new provision prescribes in 

detail the elements of that technical 

evaluation. A facility designed, 

constructed, operated, and maintained 

in accordance with these effluent 

limitations will meet the NSPS 

requirement for no discharge. 

This provision will have several 

positive ancillary effects. Some CAFOs 

may be reluctant to use innovative 

technologies that incorporate open 

storage as part of their manure 

management system in view of the no 

discharge requirements of Subpart D. 

This provision creates an incentive for 

the use of innovative technologies to 

meet the no discharge requirement by 

providing an up-front determination 

that the CAFO will meet the no 

discharge requirement prior to 

potentially expensive construction. 

Second, in the case of new source 

Subpart D CAFOs that do apply for a 

permit, this provision provides for an 

up-front determination subject to public 

participation as part of the permitting 

proceeding, that the CAFO will meet the 

no discharge requirement. Finally, 

because facilities subject to no discharge 

of manure, litter, or process wastewater 

pollutants into waters of the U.S. may 

choose not to obtain a permit, and 

therefore are not eligible for upset and 

bypass defenses, the protection afforded 

by this provision provides an incentive 

for CAFOs to obtain a permit. 

1. Background 

The 2003 CAFO rule established 

NSPS for swine, poultry, and veal calf 

CAFOs as ‘‘no discharge of manure, 

litter, or process wastewater pollutants 

into waters of the U.S. from the 

production area.’’ The rule provided 

two compliance alternatives that 

allowed a CAFO in these categories to 

meet this requirement by showing that 

either (1) its production area was 

designed, constructed, operated, and 

maintained to contain all manure, litter, 

or process wastewater, and precipitation 

from the 100-year, 24-hour storm, or (2) 

it would comply with ‘‘voluntary 

superior environmental performance 

standards’’ based on innovative 

technologies. The ‘‘voluntary superior 

environmental performance standards’’ 

provision would allow a discharge from 

the production area if the discharge was 

accompanied by an equivalent or greater 

reduction in the quantity of pollutants 

released to other media (e.g., air 

emissions). 

The Second Circuit Court of Appeals 

remanded aspects of the NSPS to the 

Agency, holding that there was not 

adequate support in the record for the 

alternative standards. Specifically, the 

court directed EPA to clarify the 

statutory and evidentiary basis for 

allowing CAFOs to comply with a no 

discharge NSPS through either a 

production area containment structure 

or an alternate performance standard. 

With respect to the 100-year storm 

standard, the court noted that while 

certain studies showed that production 

area BMPs would have substantially 

prevented the production area 

discharges documented in the record, 

substantially preventing discharges is 

not the same as no discharge. With 

respect to the alternative performance 

standards, the court held that EPA had 

not justified its decision to allow 

compliance with the no discharge 

standard through an alternative 

standard that permits production area 

discharges so long as the aggregate 

pollution to all media is equivalent to or 

lower than that resulting from the 

baseline standards. The court further 

held that EPA did not provide adequate 

notice for either of these provisions 

under the CWA’s public participation 

requirements. See 33 U.S.C. 1251(e) 

(public participation in the 

development, revision, and enforcement 

of any regulation, standard, effluent 

limitation, plan, or program established 

by the Administrator or any State under 

this Act shall be provided for, 

encouraged, and assisted by the 

Administrator and the States). 

2. This Final Rule 

This final rule makes the following 

changes to the 2003 NSPS in subpart D. 

First, EPA is deleting 40 CFR 

412.46(a)(1) that allowed subpart D 

CAFOs subject to NSPS to meet the no 

discharge standard through the use of a 

100-year, 24-hour rain event 

containment structure. In a conforming 

change, EPA is also modifying 40 CFR 

412.37(a)(2) to remove the reference to 

such structures from § 412.37(a)(2). EPA 

is, however, retaining the requirement 

in § 412.37(a)(2) that all open surface 

liquid impoundments have a depth 

marker. The land application 

requirements for new sources remain 

unchanged. 

The record for the 2003 NSPS showed 

that new facilities routinely include 

systems and employ practices that result 

in no discharge of manure, litter, or 

process wastewater pollutants into 

waters of the U.S. from the production 

areas. Based on this information, EPA 

determined that a no discharge standard 

represented the best available 

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demonstrated control technology for 

new sources. EPA now recognizes that 

a system that is properly designed, 

constructed, operated, and maintained 

to contain precipitation from the 100-

year, 24-hour event may still discharge 

as a result of multiple unusual and 

severe precipitation events. Given the 

record information, EPA now agrees that 

a system designed, constructed, 

operated, and maintained to contain 

precipitation from the 100-year, 24-hour 

storm event is not necessarily 

equivalent to no discharge and has 

consequently deleted this provision. 

Second, EPA is deleting 40 CFR 

412.46(d) to remove the alternative 

voluntary superior performance NSPS 

for new swine, poultry, and veal calf 

sources in light of the Second Circuit 

Court of Appeals ruling. 

Third, EPA is promulgating a new 

provision that authorizes the permitting 

authority to develop a site-specific, no 

discharge NSPS for new CAFO’s using 

open storage containment structures. 

Thus, this rule provides that the NPDES 

Program Director may establish no 

discharge best management practice 

effluent limitations based upon a sitespecific evaluation for an individual 

CAFO. CAFOs may request permit 

writers to establish no discharge best 

management practice effluent 

limitations on a case-by-case basis when 

the facility demonstrates through a 

rigorous modeling analysis that it has 

designed a containment system that will 

comply with the no discharge 

requirement. After such site-specific 

standards are established, a facility will 

be in compliance with the no discharge 

requirement if its containment system 

has complied with all of the specified 

site-specific design, construction, 

operation, and maintenance 

components of such a system 

demonstrated to meet the no discharge 

requirement. 

3. EPA’s Decision To Authorize SiteSpecific, No Discharge Effluent 

Limitations 

In its 2006 proposal, EPA proposed an 

alternative no discharge requirement 

that would authorize the NPDES 

Program Director to establish no 

discharge, BMP effluent limitations 

based upon a site-specific evaluation for 

an individual CAFO. A complete 

discussion of the proposal may be found 

at 71 FR 37,760–62. Such limitations 

would provide an alternate approach for 

CAFOs to meet the no discharge 

requirement through limitations 

designed to ensure no discharge of 

manure, litter, or process wastewater 

pollutants into waters of the U.S. 

Specifically, EPA proposed to 

authorize permit writers, upon request 

by a CAFO, to establish no discharge 

BMP effluent limitations on a case-bycase basis when a facility demonstrated 

through a rigorous modeling analysis 

that it could design, construct, operate, 

and maintain an open containment 

system that would comply with the no 

discharge requirement. When a facility 

complied with all of the site-specific 

design, construction, operation, and 

maintenance components of such a 

system—all of which are conditions of 

its permit—the CAFO would be deemed 

to be in compliance with the no 

discharge requirement even in the event 

of an unanticipated discharge. EPA is 

promulgating the provision in 

essentially the same form as it was 

proposed. 

Commenters raised a number of 

concerns with this provision. 

Commenters asserted that the 

alternative provision creates an 

exception to the no discharge 

requirement. Some commenters viewed 

the modeling exercise as an ineffective 

substitute for meeting effluent 

limitations. Commenters also 

questioned the enforceability of the 

alternative provision if a new source 

would have a discharge. 

A number of reasons support EPA’s 

decision to promulgate this provision 

and should allay commenters’ concerns. 

First, the alternative provision requires 

a CAFO to demonstrate to the 

satisfaction of the permitting authority, 

after public notice and comment on the 

demonstration, that its open storage 

system is a no discharge system. In 

order for a new CAFO employing an 

open storage system to obtain no 

discharge BMP effluent limitations, the 

CAFO must demonstrate that the 

entirety of its operation including its 

production area, site-specific NMP and 

other best management practices are 

designed to ensure no discharge from 

the entire CAFO. Because this 

demonstration must be based on the use 

of a prescribed model and precipitation 

data for 100 years, any showing of no 

discharge will necessarily account for a 

wide range of circumstances. Given the 

stringency of the required modeling 

exercise, described more fully below, a 

successful no discharge demonstration 

means that the site-specific limitations, 

in fact, are equivalent to a no discharge 

requirement. Moreover, because this 

demonstration will be subject to public 

participation requirements that apply to 

any permitting proceeding, commenters 

are assured that there will be an 

opportunity for public review of the 

assumptions used to support the no 

discharge conclusion. Further, the final 

determination will also be subject to 

judicial review as would be the case 

with any other final permit decision. 

Second, the argument that sitespecific no discharge limitations are not 

true no discharge limitations reflects a 

fundamental misunderstanding on 

commenters’ part. Commenters fail to 

recognize that the provision allowing 

site-specific, no discharge effluent 

limitations essentially places a CAFO 

with such limitations in the same 

position as a CAFO without such 

limitations. Commenters have 

apparently forgotten that, even in the 

absence of a provision like that 

promulgated today, permitted facilities 

that are subject to no discharge effluent 

limitations may discharge and not be 

subject to an enforcement action (or 

have a defense to any enforcement 

action) in certain uncontrollable and 

unforeseeable circumstances. The 2003 

CAFO rule specifically provided for the 

availability of an upset/bypass defense 

from an enforcement action. See 40 CFR 

412.47(a)(3) (‘‘Provisions for upset/ 

bypass as provided in 40 CFR 

122.41(m)–(n) apply to a new source 

subject to this provision.’’). 

Thus, EPA NPDES regulations 

currently would provide a defense to an 

enforcement action, albeit in severely 

restricted circumstances, for discharges 

from any permitted new source CAFO. 

Under the 2003 rule, ‘‘no discharge’’ for 

those facilities, in fact, means no 

discharge except in certain narrowly 

prescribed circumstances. The 

demonstration required under this rule 

to support the establishment of 

alternative site-specific no discharge 

limitations is designed to show that 

there will be no discharge from the 

CAFO except in exactly the 

circumstances provided in EPA’s upset/ 

bypass regulations and described under 

the 2003 rule. 

Under EPA’s regulations, an ‘‘upset’’ 

is defined as ‘‘an unintentional and 

temporary noncompliance with 

technology based permit effluent 

limitations because of factors beyond 

the reasonable control of the permittee.’’ 

40 CFR 122.41(n). Under the 

regulations, the upset defense to an 

enforcement action would not be 

available to the extent that the 

noncompliance with permit conditions 

was due to operational error, an 

improperly designed treatment system, 

inadequate treatment system, improper 

maintenance or careless and improper 

operation. 40 CFR 122.41(n)(1). 

This rule adopts requirements for an 

upfront demonstration that parallel the 

conditions under which an upset/ 

bypass defense would be available in 

the event of a discharge from a no 

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discharge facility. It provides that, 

before a permit writer may establish 

site-specific limitations, the permittee 

must demonstrate through a rigorous 

modeling exercise that its open 

containment system would not 

discharge. Given the requirement for 

evaluation of the system’s adequacy 

(size, operational practices, 

maintenance conditions and other 

factors) using precipitation data for 100 

years, such an assessment would 

support the conclusion that any 

discharge that might occur results from 

‘‘factors beyond the reasonable control 

of the permittee,’’ the conditions under 

which the upset/bypass defense would 

be available. Moreover, as noted, all of 

the design, construction, operation, and 

maintenance components evaluated for 

the site-specific permit become permit 

conditions. This similarly mirrors the 

provisions of the upset regulations 

which do provide for a defense only in 

the limited circumstances outlined in 

§ 122.41(n)(1), e.g., no operational error, 

improper design, or other factors as 

described above. As a consequence, this 

alternative NSPS provision requires an 

upfront determination that the CAFO 

would only discharge in circumstances 

that would parallel those for which an 

upset/bypass defense would be 

available. 

This final rule’s new NSPS provision 

allowing site-specific BMP effluent 

limitations gives the CAFO complying 

with its permit conditions more 

certainty that its operations meet its 

CWA requirements. The permitting 

process has already established that the 

discharge is unintentional and beyond 

the reasonable control of the permittee. 

Therefore, in the extremely unlikely 

event of a discharge from a new source 

that is complying with a permit 

containing these site-specific no 

discharge effluent limitations, the CAFO 

would already have established in the 

permitting process an affirmative 

defense with respect to any discharge, 

and would not need to rely on 

§ 122.41(n). 

Establishment of these no discharge, 

BMP effluent limitations represents a 

determination by the permit writer that 

the CAFO will not discharge. The only 

time a CAFO under this provision could 

potentially discharge would be in an 

extreme, rare event not reasonably 

foreseeable or under the reasonable 

control of CAFO as demonstrated in the 

permitting process and explained above. 

Fourth, while site-specific BMP 

effluent limitations provide greater 

certainty to CAFOs, they also provide 

the permitting authority and citizens 

more specific measures of compliance 

than is the case for CAFOs without such 

permit conditions. Unlike a CAFO that 

does not discharge or propose to 

discharge and therefore chooses not to 

seek permit coverage, a CAFO relying 

on site-specific BMP effluent limitations 

would have a permit and permit terms 

that include the design, construction, 

operation, and maintenance measures 

that formed the basis for the permitting 

authority’s determination that the CAFO 

will meet no discharge. Because the 

elements demonstrating no discharge 

are permit conditions established in a 

process that provides for public 

participation and on-going oversight, 

use of this alternative should further 

ensure compliance with the no 

discharge requirements. 

So long as the facility complies with 

its BMP effluent limitations (and other 

terms of the permit such as monitoring 

or recordkeeping requirements), the 

CAFO will not be subject to 

enforcement action. EPA underscores 

for the regulated community that the 

protections afforded by this provision 

are only available through permits 

issued to new source CAFOs. EPA 

further wishes to emphasize that the 

more general upset and bypass 

regulations are only available to 

permitted CAFOs, and are otherwise 

unaffected by this NSPS provision. 

Finally, policy considerations support 

the Agency’s adoption of an alternative 

no discharge approach. EPA encourages 

CAFOs to implement anaerobic 

digesters, multi-cell treatment lagoons, 

and nitrification/denitrification 

technologies. In addition, EPA wants to 

encourage the development of 

innovative technologies for meeting the 

no discharge requirement. To do this, 

CAFOs want certainty that the 

technologies they develop and 

implement will comply with the CWA. 

EPA recognizes that the upset and 

bypass provisions do not provide 

certainty to the operator that any 

discharge will be excused. In particular, 

CAFOs operating innovative or 

advanced technologies may be reluctant 

to rely on the standard upset and bypass 

provisions. Under the regulation 

adopted here, an operator must 

demonstrate to the permitting 

authority’s satisfaction, after public 

comment, that an innovative approach 

that includes an open storage system 

will be designed, constructed, operated, 

and maintained to achieve no discharge. 

This demonstration would mean that 

this CAFO would not discharge, except 

during an event beyond the CAFO’s 

reasonable control; an event that could 

be excused under the normal upset 

provisions. Once this demonstration has 

been made, it makes sense to provide 

the CAFO with the certainty that would 

eliminate the need for the CAFO to go 

through the upset/bypass process in 

most circumstances. 

In addition, this approach is 

consistent with CWA section 101(f), 

requiring EPA to use efficient 

procedures for decision-making. 

Because of this provision, in the rare 

occurrence of a catastrophic event, this 

provision would relieve permitting 

authorities and CAFOs from the typical 

procedures necessary to meet the upset/ 

bypass requirements. 

4. Discussion of the New Provisions 

The CAFO NSPS provisions adopted 

today require an evaluation of the 

adequacy of the designed storage facility 

using the AWM (Animal Waste 

Management) tool and an evaluation of 

overall water budgets using SPAW (Soil 

Plant Air Water) Field and Pond 

Hydrology Tool, or equivalent analytic 

tools. EPA has concluded that 100 years 

of climate data is an ample time frame 

for simulation purposes and will 

support a reasonable finding that the 

system will not discharge. However, 

EPA is aware that 100 years of 

continuous rainfall data may not be 

available for all CAFOs. Models can be 

run using actual rainfall data where 

available, and then simulated with a 

confidence interval analysis over a 

period of 100 years.6 

AWM is a planning and design tool 

for animal feeding operations that can 

be used to estimate the production of 

manure, bedding, and process water, 

and thus determine the size of needed 

storage facilities. AWM accounts for 

wastewater, flush water, precipitation, 

runoff, and other additions to the waste 

stream. AWM can estimate storage 

facility sizes using either a defined 

storage period or by drawdown dates 

specified by the user. A monthly water 

and waste budget for each storage 

component is generated, in most cases 

allowing the CAFO to demonstrate no 

discharge from the entire production 

area. The procedures and calculations 

used in AWM are based on the USDA– 

NRCS Agricultural Waste Management 

Field Handbook. 

The SPAW model consists of two 

linked routines. The first routine 

develops field hydrologic budgets based 

upon daily climatic data, crop data, and 

hydraulic characteristics of the soil 

profile. The second routine utilizes the 

6 Some commenters confused the 100-year 

simulation analysis with the requirement in the 

2003 final CAFO rule for a system designed to 

contain the precipitation associated with the 100-

year, 24-hour storm design event. Neither the 

proposed revisions nor these final requirements for 

new sources subject to subpart D refer to the 100-

year storm event. 

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climatic and hydrologic outputs of one 

or more farm fields as the input to 

hydrologic budgets for downstream 

ponds. These daily pond water budgets 

can be used to evaluate the 

performance, operation or reliability for 

many types of ponds such as liquid 

waste storage facilities. Water budget 

processes may be evaluated by making 

daily adjustments to crop canopy cover 

and antecedent soil moisture. For each 

user-specified soil profile and crop 

rotation, SPAW simulates possible 

runoff from fields as well as the 

irrigation water needs of fields receiving 

the manure storage effluent. Hydrologic 

groups are used by the model to rate 

soils for the potential to release excess 

water down grade. 

AWM tracks gross nutrients, but does 

not track the mass or concentration of 

nutrients. Further, the storage period or 

drawdown schedule is usually 

determined by the individual CAFO. 

Therefore, the CAFO’s NMP must be 

used as an input to confirm both a water 

balance and a nutrient balance has been 

achieved by the CAFO. The NSPS 

provisions require that each CAFO use 

the SPAW tool to assess daily 

hydrologic budgets for each field. The 

complete modeling demonstration 

shows not only that the storage facility 

does not discharge, but also that there 

is no runoff of process wastewater from 

fields during land application activities 

consistent with the CAFO’s NMP, which 

is necessary to ensure that the open 

containment system is operated in a 

way to meet the land application 

requirements of the rule. In EPA’s view, 

the requirement to use the SPAW model 

(or an equivalent approved by the 

permitting authority) ensures CAFOs 

will rely on appropriate operational 

measures to achieve no discharge 

standards. 

The CAFO NSPS provisions require 

certain specified information regarding 

design, construction, operation, and 

maintenance of the system to be 

included in the CAFO’s NMP under 40 

CFR 122.42(e)(1). This includes the key 

user-defined inputs and model system 

parameters. CAFOs must submit a sitespecific analysis to the Director. See 40 

CFR 412.46(a)(1). These site-specific 

design, construction, operation, and 

maintenance measures are enforceable 

requirements in the CAFO’s permit. As 

long as the CAFO complies with these 

requirements, the CAFO presumptively 

meets the no discharge requirement. 

EPA has determined that the final rule 

revisions provide a clear and 

enforceable standard for the CAFO to 

achieve as well as providing assurance 

to the public that the proposed system 

complies with the no discharge 

requirement. 

Under these final amendments to the 

NSPS, the Director has the discretion to 

require additional information from a 

new source subpart D CAFO owner or 

operator to support site-specific BMP 

effluent limitations. The burden is on 

the CAFO to demonstrate that any 

proposed system it employs, including 

an open system, meets the new source 

standard. EPA expects CAFOs will 

utilize the most current version of AWM 

and SPAW when submitting their 

demonstration to the permitting 

authority. However, EPA is aware that 

other peer-reviewed models and 

programs have been or may be 

developed that could be determined to 

be equivalent to AWM and SPAW. 

Therefore the rule gives the Director the 

discretion to approve design software or 

procedures equivalent to AWM and 

SPAW. Once approved by the Director, 

the public still would have the 

opportunity to comment on the CAFO’s 

submitted modeling and demonstration 

as discussed earlier. 

The information, design, and 

evaluation process required of all 

CAFOs wishing to avail themselves of 

this alternative is intended to allow 

CAFOs the flexibility to demonstrate 

compliance with the no discharge 

requirements for any type of open 

storage facility. As a practical 

consideration, EPA expects most CAFOs 

selecting this compliance alternative 

will submit designs for open manure 

storage structures accompanied by a 

narrow range of acceptable operation 

and management practices. However, 

for a given type of storage facility design 

(for example, an integrator with several 

company-owned CAFOs each designed 

and constructed in an essentially 

identical manner within the same 

county), EPA believes it is possible to 

conduct a series of assessments that 

together fully encompass the range of 

operational and management measures 

that would be used across multiple 

CAFOs with the specified storage 

facility design. In this case, SPAW could 

be run to validate a wide range of NMP 

and storage pond management scenarios 

(to continue the above example, the 

CAFOs all have the same sets of crops, 

soil types, land application equipment, 

etc.). This alternative does not change 

the requirement for a CAFO to develop 

a site-specific NMP. These final 

amendments authorize the permitting 

authority to determine that any CAFO 

using the specified facility type and 

submitting an NMP that falls within the 

pre-approved range of operational and 

management practices would not need 

to conduct an individualized 

assessment step (i.e., the validation 

using SPAW). 

The availability and use of such a 

geographical and categorical approach 

will require that the permit writer 

determine that a number of conditions 

are met. First, the assessment must fully 

account for all pertinent factors relevant 

to determination of the potential for 

discharge from an open storage system. 

The assessment must also include all 

parameters necessary to mirror properly 

the range of soil, plant, climatic, and 

hydrological conditions within the 

geographical area for which the 

assessment is intended to be 

representative. Second, the permittee 

must establish that the parameters 

reflected in the general assessment used 

to establish no discharge are, in fact, 

representative of those parameters for 

each CAFO. Finally, the assessment 

must reflect the operational and 

management practices to be employed 

by each CAFO at each individual site. 

As with the individual assessment, each 

CAFO must have a site-specific NMP 

that includes the operational and 

management measures utilized in the 

geographical assessment. 

EPA is eliminating the requirement to 

indicate the capacity for a 100-year, 24-

hour storm for new sources. EPA is 

maintaining the requirement to have a 

depth marker for all open storage 

structures. In EPA’s view, a marker 

indicating the storage pond or 

containment depth can be an excellent 

means of displaying how much storage 

a CAFO has, whether it is time to pump 

down levels in the lagoon, pond, or 

other storage structure, or whether 

alternative management steps must be 

taken to prevent a full storage structure 

and potential overflow. Existing sources 

and new sources subject to subpart C 

continue to have the requirement for a 

depth marker that indicates the 25-year, 

24-hour storm event. New sources 

subject to subpart D and using an open 

storage structure must use the depth 

marker to indicate the maximum 

volume of manure and process 

wastewater the structure is designed to 

contain. 

While one component of preventing 

discharge from an open system is to 

provide adequate storage of manure and 

wastewater during critical periods, 

ensuring adequate physical capacity is 

not sufficient. Rather, determining 

whether there is adequate storage is 

based on a site-specific evaluation of the 

CAFO’s entire waste handling system. 

Adequate storage has to be based on 

climate-specific variables that define the 

appropriate storage volume, but of equal 

importance are the nutrient 

management plan and other 

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management decisions that specify 

when and how the storage can be 

emptied. The link between adequate 

storage and land application practices is 

one of the most critical considerations 

in developing and implementing a sitespecific nutrient management plan. For 

example, the amount of land available 

for application, the hydraulic 

limitations (ability of the land to handle 

additional water without the occurrence 

of runoff), geology, and soil properties 

of the available land base can play an 

important role. See Chapter 2 of EPA’s 

technical guidance for CAFOs 

‘‘Managing Manure Nutrients at 

Concentrated Animal Feeding 

Operations’’ (EPA–821–B–04–00) for 

more information. EPA expects these 

criteria preclude a CAFO from 

withdrawing manure and process 

wastewater from liquid storage 

structures and subsequently land 

applying process wastewater at 

inappropriate times. Given these 

considerations, EPA is establishing 

procedures for approval of site-specific 

management practices for open 

containment systems with the 

expectation that a system can be 

designed and operated to meet the no 

discharge standard. EPA has concluded 

that the design, construction, operation, 

and maintenance elements and the 

comprehensive analytical assessment 

are sufficient to achieve this objective. 

G. BCT Limitations for Fecal Coliform 

In response to the Second Circuit 

remand, EPA is today affirmatively 

finding that the best conventional 

pollutant control technology (BCT) 

limitations it adopted in 2003 do, in 

fact, represent the best conventional 

control technology limitations for fecal 

coliform. After assessing various 

conventional pollutant removal 

technologies, EPA has determined that 

there are no available and economically 

achievable technologies that are cost 

reasonable that would result in greater 

removal of fecal coliform than the 

technologies on which EPA based the 

2003 best practicable control technology 

currently available (BPT) and BCT 

effluent limitations guidelines (ELG). 

As EPA has explained, establishing 

BCT limitations begins by identifying 

technology options that provide 

additional conventional pollutant 

control beyond the level of control 

provided by BPT effluent limitations. 

Any such candidate technologies are 

then evaluated to determine if they meet 

the threshold CWA requirements of 

‘‘availability’’ and ‘‘economic 

achievability.’’ 51 FR 24,974, 24,976; 

July 9, 1986. A technology is 

economically achievable if its costs may 

be ‘‘reasonably borne’’ by the CAFOs. 

Waterkeeper Alliance et al. v. EPA, 399 

F.3d 486, 516 (2d Cir. 2005). The Clean 

Water Act adds an additional evaluation 

step to the effluent limitations 

development process for conventional 

pollutants. ‘‘In addition to the Clean 

Water Act requirement that effluent 

limitations be economically achievable, 

the cost associated with the BCT 

effluent limitations must also be 

‘reasonable’ in relation to the effluent 

pollutant reductions.’’ 51 FR 24,974. In 

determining this, the statute requires 

that EPA look at a number of factors 

including a comparison of the cost of 

effluent reductions for POTWs to that 

for direct dischargers using candidate 

BCT technologies. Thus, the statute 

requires that, not only must the costs of 

additional control be costs that CAFOs 

may reasonably bear (economically 

achievable), but the costs must also be 

reasonable relative to the costs for 

POTWs to achieve such conventional 

pollutant reductions. 

EPA evaluated 41 BCT candidate 

technologies for this rule and 

determined that all but two of them 

were either not available (technically 

feasible for all CAFOs in a subcategory) 

or not economically achievable. For the 

remaining two technologies, while their 

costs are high and EPA believes it likely 

that they are also not economically 

achievable, EPA was unable to conduct 

its traditional tests for economic 

achievability and thus has not 

determined in this rule whether or not 

they are economically achievable. 

However, EPA has determined that 

these two technologies, even if 

economically achievable, would not be 

cost reasonable, and has therefore 

rejected them as BCT technologies. 

As a result of this assessment, EPA 

has concluded that there are no 

available and economically achievable 

technologies that are cost reasonable 

that would provide greater fecal 

coliform removal than the BPT 

technology. How EPA performed this 

assessment and the results of that 

assessment supporting EPA’s finding 

that the 2003 BPT/BCT limitations 

represent BCT technology for 

controlling fecal coliform is described in 

detail below. 

1. The Waterkeeper Decision 

As previously noted, the Waterkeeper 

court remanded the 2003 CAFO rule’s 

BCT standard for further clarification 

and analysis with regard to the 

appropriate BCT standard for 

pathogens.7 EPA’s 2003 rule established 

7 As the Second Circuit recognized, the CWA lists 

only one pathogen, fecal coliform, as a conventional 

non-numeric effluent limitations based 

on BPT and the best available 

technology economically achievable 

(BAT) as well as BCT limitations. In the 

2003 CAFO rule, EPA established BPT 

effluent limitations guidelines for Large 

beef, dairy, and veal calf (Subpart C), 

swine and poultry (Subpart D) CAFOs. 

At that time, EPA concluded that 

there were no available BCT 

technologies on which to base limits for 

conventional pollutants that were more 

stringent than the BPT limitations, and 

EPA therefore established BCT 

requirements equal to BPT limitations. 

EPA based this determination in part on 

the combined pollutant reductions 

(Table 7.2 of 68 FR 7239), and in 

particular its evaluation of the 

reductions in discharges of the 

conventional pollutants (TSS, BOD, and 

fecal coliform) associated with the 

various technology options it 

considered. 71 FR 37,763. EPA noted 

difficulties in quantifying the loadings 

and reductions in discharges of these 

pollutants—in particular, in assessing 

fecal coliform—and relied primarily on 

reductions in sediment discharges as a 

surrogate for reductions in TSS in 

reaching its BCT determination. EPA 

concluded that there were no 

technologically feasible candidate BCT 

technologies that would achieve greater 

TSS removals than the BPT 

requirements for either Subpart C or 

Subpart D facilities, and no 

economically achievable technologies 

for Subpart C facilities that would 

reduce discharges of BOD. 

Consequently, EPA found that there 

were no BCT technologies for 

establishing limits on conventional 

pollutants that would achieve greater 

removal than the BPT technology and 

established BCT requirements that were 

equal to BPT. 68 FR 7224. 

While EPA’s assessment of the 

effectiveness of various control options 

did attempt to measure pathogen 

reductions for the final rule, EPA did 

not establish any specific BPT or BCT 

limitations to control fecal coliform, a 

conventional pollutant and pathogen. 

The Waterkeeper court remanded the 

2003 CAFO rule’s BCT standard for 

further clarification and analysis 

because EPA had failed to make an 

affirmative finding that the BCT 

limitations it had adopted in fact 

represented the best conventional 

pollutant for which BCT limitations are required. 

Waterkeeper, 399 F.3d at 518. Section 304(a)(4) of 

the CWA provides that EPA may identify additional 

pollutants as conventional pollutants. EPA has 

identified only one additional pollutant, oil and 

grease as a conventional pollutant. Thus, the only 

pathogen subject to the Second Circuit remand is 

fecal coliform. 

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pollutant control technology for 

reducing pathogens—specifically, fecal 

coliform. 399 F.3d at 519. EPA’s final 

rule issued today responds to the court’s 

remand. 

As EPA proposed, in this final rule 

EPA is affirmatively concluding that the 

current BCT limitations for 

conventional pollutants represent the 

best conventional control technology for 

fecal coliform and is establishing BCT 

limitations for fecal coliform that are 

equal to the current BPT/BCT 

limitations. These limitations prohibit 

the discharge of manure, litter, or 

process wastewater into waters of the 

U.S. from the production areas of CAFO 

except in limited circumstances. A 

discharge is allowed only if an existing, 

permitted CAFO has a properly 

designed, constructed, and operated 

storage structure with the capacity to 

contain all manure, litter, and process 

wastewater associated with the facility 

as well as the runoff and direct 

precipitation from a 25-year, 24-hour 

rainfall event. See 40 CFR 412.31(a). 

The current rules also provide that a 

Large CAFO that land applies manure, 

litter, or process wastewater must do so 

in accordance with several BMPs: A 

nutrient management plan that includes 

the determination of application rates 

for manure, litter, and process 

wastewater; a field-specific assessment 

of the potential for nitrogen and 

phosphorus transport from the field to 

surface waters; manure and soil 

sampling; and setback requirements. See 

40 CFR 412.4. EPA is not promulgating 

more stringent BCT limitations for fecal 

coliform because there is no available, 

achievable, and cost reasonable 

technology on which to base such 

limitations. 

2. Background 

The CWA requires point sources to 

achieve effluent pollutant levels 

established by EPA that are attainable 

through progressively more stringent 

pollutant control technology. The CWA 

calls for technology-based control in 

two stages. As originally enacted in 

1972, the Act required existing point 

sources to comply in the first stage with 

EPA-established limitations that are 

achievable by application of the ‘‘best 

practicable control technology currently 

available’’ or ‘‘BPT.’’ These limitations 

control conventional, toxic, and 

nonconventional pollutants. EPA has 

typically based BPT limitations on the 

average pollutant removal performance 

of the best facilities examined by EPA. 

The 1972 Act also required existing 

point sources to comply in the second 

stage with EPA-established limitations 

that are achievable by the application of 

‘‘best available technology economically 

achievable,’’ or ‘‘BAT.’’ In 1972, these 

limitations also controlled conventional, 

toxic and non-conventional pollutants. 

The 1977 amendments to the CWA 

replaced BAT for conventional 

pollutants with limitations that 

represent ‘‘best conventional pollutant 

control technology’’ or ‘‘BCT.’’ Section 

304(a)(4) designates the following as 

conventional pollutants: Biochemical 

oxygen demand (BOD), total suspended 

solids (TSS), fecal coliform (FC), pH, 

and any additional pollutants defined 

by the Administrator as conventional. 

The Administrator designated oil and 

grease as an additional conventional 

pollutant, on July 30, 1979 (44 FR 

44,501), but has listed no other 

pollutants for regulation as conventional 

pollutants. 

The decision to amend section 304(a) 

of the CWA to require achievement of 

BCT, rather than BAT, for control of 

conventional pollutants reflected two 

factors. The first was Congressional 

desire not to require ‘‘treatment for 

treatment’s sake’’ and the second, 

Congress’s view that BAT control of 

conventional pollutants might not be 

necessary to achieve the water quality 

goals of the Act. S.Rep. No. 370 at 43, 

1st Sess. 43 (1977), reprinted in Comm. 

on Env. and Public Works, 95th Cong., 

2d Sess., A Legislative History of the 

Clean Water Act of 1977 at 676–77 

(hereinafter ‘‘Legislative History’’). 

The CWA Amendments of 1977 that 

require EPA to determine BCT 

limitations also specify the factors to be 

taken into account in this determination 

of BCT. Section 304(b)(4)(B) provides 

that the factors to be assessed: 

[S]hall include consideration of the 

reasonableness of the relationship between 

costs of obtaining a reduction in effluents 

and the effluent reductions benefits derived, 

and a comparison of the cost and level of 

reduction of such pollutants from the 

discharge from publicly owned treatment 

works to the cost and level of reduction of 

such pollutants from a class or category of 

industrial sources. * * * 33 U.S.C. 

1314(b)(4)(B).8 

8 As the Conference Report to the 1977 

amendments explained: 

The cost test for conventional pollutants is a new 

test. It is expected to result in a determination of 

reasonableness which could be somewhat more 

than best practicable technology or could be 

somewhat less than best available technology for 

other conventional pollutants. The result of the cost 

test could be a 1984 requirement which is no more 

than that which would result from best practicable 

technology but also could result in effluent 

reductions equal to that required in the application 

of best available technology. Joint Explanatory 

Statement of the Committee of Conference, 95th 

Cong. 1st Sess., H.R. No. 95–830 at 85, Legislative 

History at 269. 

In the words of Senator Muskie, the 

Senate Floor Manager and leading 

sponsor of the amendments: 

The Administrator must determine 

whether or not the cost of achieving 

reductions of conventional effluent bears a 

reasonable relationship to the amount of 

effluent reduction achieved. In making this 

determination, the Administrator is to 

compare the costs of industrial effluent 

reduction to the cost of municipal waste 

treatment. Legislative History at 458. 

Accordingly, EPA developed a ‘‘BCT 

Methodology’’ to answer the question of 

whether it is ‘‘cost-reasonable’’ for 

industry to control two conventional 

pollutants, BOD (or oil and grease in the 

case of certain metals industries) and 

TSS, at a level more stringent than 

already required by BPT effluent 

limitations. EPA first explained its BCT 

methodology when it promulgated BCT 

effluent guidelines for 41 industry 

subcategories (44 FR 50,732; August 29, 

1979).9 The crux of the methodology 

was a comparison of the costs of 

removing the conventional pollutants 

BOD (or oil and grease) and TSS for a 

candidate BCT technology within a 

particular industry segment, to the costs 

of removal for an average-sized POTW. 

A number of industries and industry 

associations challenged the regulation, 

and, in 1981, the U.S. Court of Appeals 

for the Fourth Circuit remanded it to the 

Agency, directing EPA to include an 

assessment of the cost-effectiveness of 

industry conventional pollutant removal 

in addition to the POTW test in its 

evaluation of cost reasonableness. 

American Paper Inst. v. EPA, 660 F. 2d 

954 (4th Cir. 1981). EPA proposed a 

revised BCT methodology in 1982 (47 

FR 49,176) that addressed the industry 

cost-effectiveness test (the ‘‘second’’ 

test), again limited to the conventional 

pollutants BOD and TSS. EPA proposed 

to base the POTW benchmark on model 

plant costs in a 1984 notice (49 FR 

37,046). The final BCT methodology, 

promulgated as a rule in 1986 (51 FR 

24,974), maintained the basic approach 

of the 1982 proposed BCT methodology 

while also updating POTW removal cost 

with new POTW data. EPA again 

specifically noted that it had developed 

9 As noted above, the 1977 amendments 

established a second level of technology-based 

controls for conventional pollutants-BCT 

limitations. Accordingly, in 1979, pursuant to 

Congressional direction, EPA completed its review 

of then-existing BAT limitations for conventional 

pollutants to determine if they were more stringent 

than would be required by BCT technology. EPA 

limited its review to limitations for, and 

correspondingly developed its BCT methodology to 

address, only two categories of conventional 

pollutants: BOD (or oil and grease) and TSS. 44 FR 

50,732–33. Noting the industries under 

consideration do not have fecal coliform discharges, 

EPA performed no analysis for fecal coliform. 

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its BCT methodology to evaluate more 

stringent BOD or TSS limits. 

3. EPA’s BCT Determination in the 2003 

Rule 

As previously explained, EPA 

established BCT requirements equal to 

BPT in the 2003 CAFO rule (see 40 CFR 

412.33 and 412.44). For its assessment 

of BCT limitations, EPA first considered 

whether there were any technically 

feasible technologies that would achieve 

greater conventional pollutants 

removals than the BPT limitations. 

Because of the difficulties in quantifying 

reductions of conventional pollutant 

discharges,10 EPA relied primarily on 

sediment discharges (as a surrogate for 

TSS) in evaluating potential BCT 

requirements. EPA identified no BCT 

technology option that achieves 

significantly greater TSS removals than 

the BPT requirements eventually 

promulgated in 2003 with one 

exception. This option would have 

prohibited any discharge from swine 

and poultry CAFOs. Because this option 

was not an economically achievable 

one, EPA therefore concluded that there 

were no BCT technologies on which to 

base limits for conventional pollutants 

that were more stringent than BPT. EPA 

did note that if it had identified 

available and economically achievable 

technology options that achieve greater 

reductions of conventional pollutants 

than are achieved by BPT, then EPA 

would have evaluated these 

technologies applying EPA’s two-part 

BCT cost test. 68 FR 7224. 

EPA also evaluated pathogen 

reductions associated with the 2003 

BPT limitations. The BPT limitations 

prohibit dry weather discharges from 

land application areas, and the BPT 

land application requirements 

(including technical standards for 

timing, form, and rate of application, as 

well as the required vegetated buffer, 

setback, or equivalent practices) already 

minimize discharges from land 

application areas. The BPT production 

area requirements prohibit discharges, 

except for overflows from liquid storage 

structures that meet certain design and 

operational criteria. EPA used fecal 

coliform and fecal streptococcus as 

surrogates to estimate the pathogen 

reductions achieved by the CAFO rule 

requirements. EPA concluded that the 

BPT limitations would reduce these two 

pathogens by 2.7 x 1022 colony forming 

10 For example, EPA could not easily assess fecal 

coliform loadings because they vary greatly 

depending on site characteristics. Further, 

quantifying discharges of other conventional 

pollutants is complicated by the challenge of 

distinguishing between CAFO and non-CAFO 

sources. 71 FR 37,763. 

units (CFU), or a 46 percent reduction 

over baseline pollutant loadings. See 

Chapter 12 of ‘‘Development Document 

for the Final Revisions to the NPDES 

and the Effluent Guidelines for CAFOs’’ 

EPA–821–R–03–001. Other pathogens 

would likely be reduced by a similar 

degree. EPA projected $0.3 to $3.4 

million in improved shellfish harvests 

associated with reduced pathogen 

discharges from Large CAFOs. 68 FR 

7240. 

4. This Rule 

As noted, EPA has determined that 

there are no technically feasible and 

economically achievable candidate 

technologies for fecal coliform removal 

that are cost reasonable and would 

achieve greater removals than the 2003 

BPT limitations. The following 

discussion summarizes the basis for this 

final determination. 

(a) EPA’s Approach To Establishing BCT 

Limitations for Fecal Coliform 

As previously explained, the first step 

to establishing BCT limitations is to 

identify technology options that provide 

additional conventional pollutant 

control beyond the level of control 

provided by the application of BPT 

limitations and to evaluate these 

technologies for ‘‘availability’’ 

(including technical feasibility) and 

‘‘economic achievability.’’ See 33 U.S.C. 

1311(b)(2)(E). Out of 41 candidate 

technologies, EPA has identified no 

technologies that are both available and 

achievable for Subpart D facilities, and 

has identified only two available 

technologies that might be 11 

economically achievable for Subpart C 

facilities. 

The next step in determining BCT is 

to evaluate any candidate technology 

that is both technically feasible and 

economically achievable for cost 

reasonableness. Traditionally, EPA has 

evaluated candidate BCT technologies 

for cost-reasonableness using a two-part 

BCT cost test it developed for two 

conventional pollutants, BOD and TSS. 

The test is intended to assess whether 

there are cost-reasonable technologies 

that will achieve greater BOD and TSS 

removals than required by the BPT 

technology for an industry category by 

comparing the incremental cost11 For Subpart C (beef cattle, heifer, and dairy) 

facilities, in the 2003 final CAFO rule, EPA rejected 

more stringent BAT options on availability, not 

economic achievability grounds. Thus, for this final 

rule, EPA had no comparison technology that it had 

already determined to be not economically 

achievable. Thus, while the two available 

technologies have high costs relative to BPT and are 

likely not economically achievable, EPA was not 

able to determine this using its traditional 

methodology or the analysis from the 2003 rule. 

effectiveness of candidate BCT 

technologies with the incremental costeffectiveness of BOD and TSS removals 

at POTWs through advanced secondary 

treatment as compared to secondary 

treatment. This test makes sense for 

BOD and TSS because advanced 

secondary treatment is specifically 

designed to remove additional BOD and 

TSS. However, it is not designed for 

additional fecal coliform removal, so the 

incremental cost-effectiveness of 

advanced secondary treatment in 

removing fecal coliform is not a good 

benchmark for use in evaluating 

candidate BCT technologies for fecal 

coliform removal. 

The methodology is appropriate for 

BOD and TSS because advanced 

secondary treatment is specific to the 

removal of BOD and TSS. Costs 

associated with upgrading a POTW from 

secondary to advanced secondary 

treatment were based on polymer 

addition to the activated sludge basin. 

The purpose of the polymer addition 

was to enhance removal of BOD and 

TSS in the secondary clarifier, and 

achieve final effluent concentrations of 

20 mg/L BOD5 and 20 mg/L TSS. 

Therefore, the cost increment between 

secondary and advanced secondary 

treatment represents the incremental 

cost of removal of additional BOD and 

TSS at POTWs. 51 FR 24,981. 

Unlike BOD and TSS, advanced 

secondary treatment is not designed to 

remove additional increments of fecal 

coliform beyond secondary treatment. 

When both secondary and advanced 

secondary treatment systems include 

disinfection, the total fecal coliform 

removal is nearly the same, over 99 

percent. Secondary treatment by itself 

(without disinfection) also removes 

significant amounts of fecal coliform, 

although almost all POTWs include 

disinfection at some point in their 

treatment train. The polymer addition in 

advanced secondary treatment is not 

intended for additional fecal coliform 

removal since both secondary and 

advanced secondary POTWs use 

disinfection treatments to prevent fecal 

coliform releases to surface water. 

Therefore, because the object of the BCT 

cost test is to ensure that the costs of 

additional removals of conventional 

pollutants associated with BCT 

limitations do not exceed POTW 

conventional removal costs, 

distinguishing fecal coliform removals 

between advanced secondary treatment 

and secondary treatment is not relevant. 

Because advance secondary treatment is 

not intended to be more effective than 

secondary treatment at removing fecal 

coliform (and is not added for this 

purpose), it is not appropriate to apply 

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70466 Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 

the same POTW cost test used for 

evaluating BOD and TSS BCT 

limitations to the evaluation of fecal 

coliform limitations. 

Given these circumstances, EPA 

recognized that if it were to use a 

similar numeric BCT cost test to 

evaluate fecal coliform removal for BCT, 

EPA would have to modify the 

traditional BCT cost test to address the 

issue that advanced secondary treatment 

at POTWs is not designed to remove 

fecal coliform. When the Agency 

promulgated the BCT methodology 

(including descriptions of how to apply 

the cost test), EPA envisioned the need 

for adjustments to the BCT cost test 

methodology in future rulemakings to 

account for lack of comparable data or 

other industry-specific factors. 51 FR 

24,974, 24,976. Moreover, section 

304(b)(4)(B) authorizes EPA to consider 

other appropriate factors in establishing 

BCT. 

Accordingly, for the proposal, EPA 

suggested a modified BCT cost test. 

However, based on comments, EPA has 

identified a number of problems with 

the proposed test. These problems are 

discussed briefly here and described 

more fully in the Response to Comments 

Document prepared for this rule. First, 

although the revised test used a 

different cost-effectiveness calculation 

from the traditional test, it still relied 

indirectly on a comparison of the costeffectiveness of BCT candidate 

technologies to the cost-effectiveness of 

advanced secondary treatment, even 

though, as just noted, advanced 

secondary treatment is not designed to 

remove fecal coliform. Second, the 

revised test did not compare the 

incremental cost-effectiveness of the 

candidate technologies to the 

incremental cost-effectiveness of fecal 

coliform removals at POTWs and 

therefore did not allow a comparison of 

‘‘the cost and level of reduction of [fecal 

coliform] from the discharge from 

publicly owned treatment works to the 

cost and level of reduction of [fecal 

coliform] from * * * industry sources 

* * *’’ as required by the statute. As a 

result, EPA has now determined that it 

cannot use the revised test to evaluate 

cost reasonableness. 

For this final rule, EPA also 

considered other possible approaches 

for evaluating cost reasonableness. One 

approach would have been to identify a 

technology that is used at POTWs 

specifically for fecal coliform removal 

and develop a test similar to the 

traditional cost test but based on this 

technology. EPA considered 

disinfection as one possible benchmark 

technology for fecal coliform removal, 

but determined that there is significant 

variability in the manner in which 

disinfection is used in combination with 

other technologies at different POTWs 

and it would thus be extremely difficult, 

both theoretically and logistically, to 

develop a revised benchmark based on 

this technology. 

Consequently, for the final rule, EPA 

has applied a simplified cost 

reasonableness test designed to 

specifically address fecal coliform. This 

approach is consistent with section 

304(b)(4) of the CWA and is one EPA 

has used in the past. While the 

traditional cost test compares reductions 

from BCT candidate technologies to 

those of POTWs, EPA has, on occasion, 

rejected BCT technologies without 

comparing them to POTW performance, 

even for BOD and TSS. Thus, for 

example, where EPA lacked sufficient 

data to quantitatively evaluate BOD and 

TSS reductions under the traditional 

test, EPA rejected more stringent BCT 

limitations solely on the basis of an 

evaluation of the incremental costs of 

further reductions. See 51 FR 24,974, 

24,991. 

(b) EPA’s Evaluation of Candidate 

Technologies for Technical Feasibility 

and Economic Achievability 

Based on its consideration of 

information submitted by commenters 

and its own analysis, EPA has 

determined that there are only two of 41 

candidate technologies that are 

technically feasible and may be 

economically achievable that provide 

greater removals of fecal coliform than 

the technologies selected as the basis for 

BPT limitations in the 2003 rule. The 

discussion below provides the basis for 

this conclusion. 

In its evaluation of candidate BCT 

technologies, EPA reviewed data on 

different types of CAFO manure 

management systems. These systems 

employed treatment technologies, best 

management practices (BMPs) for 

pollution prevention, and management 

practices for the handling, storage, 

treatment, and land application of 

wastes. Sources of information included 

available technical literature, over 

11,000 comments submitted by industry 

and other public commenters, and 

insights gained from conducting over 

116 site visits to CAFOs. 

In its search for candidate 

technologies, EPA initially reexamined 

the technology options it had 

considered for the 2003 rule because the 

Agency concluded that these might 

provide more fecal coliform reductions 

than the option selected for BPT 

limitations. EPA looked at technology 

Options 3, 5, 6 and 7 described in the 

proposal at 71 FR 37,763 and the 

Technical Development Document. 

Options 3, 5, 6, and 7 represented 

additional controls beyond the controls 

(e.g., nutrient-based land application 

rates and production area discharges 

only under specified conditions). 

Option 3 would have required a 

reduction of discharges to ground water 

beneath the production area. Option 5 

would require total containment of all 

manure and process wastewater by 

swine and poultry operations. Option 6 

would require anaerobic digesters at 

swine and dairy facilities. Option 7 

would require a national prohibition of 

manure application to frozen, snowcovered, or saturated ground. 

In addition to the four technologies 

reviewed for the 2003 final rule, EPA 

looked at an additional 37 technologies 

and systems identified either by EPA or 

commenters as candidate fecal coliform 

BCT technologies. At the outset of 

assessment for this rule, EPA rejected all 

of these technologies as the basis for 

BCT limitations for fecal coliform for 

Subpart D CAFOs because they were 

either not technically feasible for all 

Subpart D CAFOs, or were not 

economically achievable. Many of the 

rejected technologies were costlier than 

Option 5 which EPA in the 2003 final 

CAFO rule had earlier determined was 

not economically achievable for Subpart 

D (i.e., swine, poultry, and veal calf) 

facilities. The Waterkeeper court 

sustained the Agency’s determination 

that CAFOs cannot reasonably bear the 

cost associated with Option 5. 399 F.3d 

at 516. Option 5 would have cost 

Subpart D facilities $167 million. See 68 

FR 7218. Of the 19 technologies and 

systems approaches identified by 

commenters, none of the technologies 

costs less than $167 million. The least 

costly of these technologies— 

gasification recycle, digester based 

systems, super soils composting, aerobic 

digestion, and ABS—cost 1.3 times the 

cost of Option 5. Other technologies 

reviewed cost as much as seven times 

the total national costs of Option 5. 

Having determined that the costs of 

Option 5 were unachievable for Subpart 

D facilities, EPA did not evaluate further 

those treatment technologies that had 

similar or greater total costs. After 

rejecting the economically unachievable 

technologies identified by commenters, 

22 technologies remained for further 

assessment with respect to technical 

feasibility. EPA found that none of these 

technologies were technically feasible 

for all CAFOs in Subpart D. 

For Subpart C facilities, EPA did not 

have a previously identified option that 

it had already determined to be 

economically unachievable against 

which to compare the costs of candidate 

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BCT technologies. To do an economic 

achievability analysis of candidate 

technologies for Subpart C, EPA would 

have had to conduct an analysis of the 

economic conditions of individual 

CAFOs in order to estimate potential 

closures and evaluate appropriate 

financial ratios, as it traditionally does 

for economic achievability analysis. 

EPA determined that conducting such 

an analysis was not practical, and 

eventually also determined that it was 

not necessary to do so to complete its 

evaluation of candidate BCT 

technologies for subpart D. Rather, EPA 

first evaluated the candidate 

technologies for technical feasibility, 

and on this basis, rejected 39 of the 41 

technologies (the four options 

considered for the 2003 rule, 16 

identified by EPA and 19 suggested by 

commenters) as the basis for BCT 

limitation for fecal coliform for Subpart 

C. The two remaining technologies were 

then evaluated directly for cost 

reasonableness, without considering 

economic achievability, as explained in 

section III.G.4(c) of this preamble. 

EPA explained the basis for its 

decisions with respect to feasibility of 

the other candidate technologies (for 

both Subparts C and D) in the proposed 

rule, and commenters have not provided 

any information that would lead the 

Agency to change its conclusions. 71 FR 

37,768–71. 

In addition, EPA specifically solicited 

comment on additional candidate 

technologies that might prove feasible 

and less costly than the technologies 

already evaluated for the proposal. EPA 

is aware of technologies that may, on a 

site-specific basis, be used to provide 

further reductions of conventional 

pollutants as compared to the 

technologies on which the 2003 BPT/ 

BCT limitations were based. However, 

EPA’s record shows these other 

technologies are not available 

engineering alternatives for most 

CAFOs, and they are therefore not 

feasible technology candidates. See 

Chapter 8 of the ‘‘Development 

Document for the Final Revisions to the 

NPDES and the Effluent Guidelines for 

CAFOs’’ and the docket accompanying 

this action for descriptions of these 

additional technologies. 

In response to its requests for 

additional information, EPA received no 

new data that support evaluation of 

additional candidate technologies or 

warrant revision to EPA’s conclusions 

about the costs or performance of the 

candidate technologies EPA identified. 

Specifically, while some commenters 

recommended consideration of 

additional digester systems, the costs of 

the various digester systems do not vary 

sufficiently to warrant a detailed 

analysis of the costs of these 

technologies at every type of CAFO. To 

date, EPA has not identified less 

expensive, and consequently, 

economically achievable candidate 

technologies than those it had 

previously evaluated. Furthermore, EPA 

did not further evaluate the systems 

approach (combinations of one or more 

candidate technologies) recommended 

by some commenters because it would 

not reduce fecal coliform more than the 

99 percent assumed by EPA 12 in its 

analysis as the yardstick for 

performance of the candidate BCT 

technology. While not obtaining 

pollutant removals greater than those 

already considered by EPA, these 

systems would cost more than the cost 

of the individual technologies already 

reviewed. Therefore, EPA did not 

evaluate the suite of candidate 

technologies that performed comparably 

but were more expensive than the suite 

of technologies evaluated here. For the 

reasons described in Chapter 8 of the 

‘‘Development Document for the Final 

Revisions to the NPDES and the Effluent 

Guidelines for CAFOs’’ and the proposal 

at 71 FR 37,765–8, EPA has determined 

that the candidate technologies it 

rejected are not technologically feasible 

and economically achievable for all 

CAFOs across a subcategory and thus 

not appropriate technologies for BCT 

limitations. The CWA does not 

authorize EPA to establish BCT 

limitations that are based on 

technologies that are not technologically 

feasible and economically achievable. 

Because only two technologies were 

both technically feasible and potentially 

economically achievable for Subpart C 

facilities (and none were for Subpart D 

facilities), EPA is only required to 

evaluate these two technologies further 

for cost reasonableness. 

(c) EPA’s Evaluation of the Remaining 

Candidate Technologies for Cost 

Reasonableness 

The above assessment resulted in only 

two remaining candidate technologies 

(composting and constructed wetlands) 

that are potentially 13 technically 

12 In the proposed rule, as a simplifying 

assumption all technologies were expected to 

achieve a 99 percent reduction in fecal coliform. 71 

FR 37,765 and 37,767. 

13 EPA believes it is likely that some Subpart C 

facilities will have space constraints under either 

candidate technology. In this case the technology 

would not be feasible for all CAFOs in the 

subcategory. However, EPA lacks data regarding 

land availability and possible land constraints 

beyond an aggregate of data showing the average 

acres of cropland at Subpart C facilities. To the 

extent CAFOs can take the necessary amount of 

land out of crop production to provide the space 

feasible and economically achievable for 

fecal coliform control for one 

subcategory, the Subpart C (beef and 

dairy) subcategory. As discussed above, 

EPA did not conduct a new analysis of 

economic achievability for these 

technologies at Subpart C facilities, 

although EPA notes the costs are high 

relative to the BPT technology (which 

EPA also determined to be BAT). 

Specifically, the cost of the BPT 

technology for Subpart C was $214 

million per year, while the cost of 

composting was estimated to be $1.4 

billion per year, and the cost of 

constructed wetlands was $2.9 billion. 

Thus, EPA expects that if it had 

conducted a formal economic 

achievability analysis, EPA would have 

determined that both of these 

technologies are not economically 

achievable. 

However, instead of evaluating these 

technologies with respect to economic 

achievability, EPA evaluated the cost 

reasonableness of the technologies using 

the simplified approach described 

above. In the past, EPA has adopted 

such an approach when it lacked a full 

data base to evaluate different BCT 

technologies. A simplified approach fits 

the circumstances here for two reasons. 

First, as noted, EPA has developed no 

standardized BCT cost test for fecal 

coliform. Second, EPA lacks the data to 

provide a comparison of incremental 

fecal coliform removals that is the basis 

for the BCT cost test for TSS and BOD. 

The annual operating costs for 

composting would be more than six 

times as much as the full BPT level of 

control at Subpart C facilities (see 

Chapter 4 and Table A–15 of the Final 

Cost Methodology, EPA–821–R–03– 

004), while constructed wetlands would 

cost Subpart C facilities more than an 

order of magnitude (13) times the cost 

of the BPT level of control (see chapter 

15 in the supplement to the TDD). EPA 

has determined that these costs are too 

high relative to the additional removals. 

EPA thus concludes that the 

incremental costs of the additional 

removals alone support a determination 

that these technologies are not cost 

reasonable. 

To further evaluate this conclusion, 

EPA conducted a modeling analysis of 

POTW removal costs for fecal coliform. 

As discussed above, the available data 

do not permit an empirical cost 

comparison between CAFO candidate 

to install construct wetlands or composting 

windrows, EPA does not have the data to estimate 

lost revenues associated with such losses of 

cropland. Therefore, EPA’s estimated costs of such 

candidate technologies are potentially understated. 

Nonetheless, EPA analyzed cost reasonableness as 

if the technologies are feasible. 

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technologies and POTW fecal coliform 

performance. However, EPA was able to 

model POTW fecal coliform removal 

costs using reasonable approximating 

assumptions. EPA recognizes that the 

resulting calculation lacks the rigor of 

the determination of the 1986 POTW 

benchmark for TSS and BOD removal 

costs.14 What this assessment shows is 

that POTW average costs of removals of 

fecal coliform are very low (i.e., $0.33 

per trillion CFU; see 71 FR 37,772). This 

is not surprising, given that most POTW 

permits require achievement of fecal 

coliform reduction near 99 percent.15 In 

contrast, the two technologies being 

evaluated for cost reasonableness 

(composting and constructed wetlands) 

have higher costs for fecal coliform 

removal ($0.51 per trillion CFU for 

composting, and $1.02 per trillion CFU 

for constructed wetlands). (See 

supplement to Chapter 15 of the TDD, 

showing unit costs of NCSU 

technologies as provided by 

commenters, total national costs of 

employing such technologies at CAFOs, 

and a comparison of those costs to the 

BPT/BAT level of control.) 

Even recognizing the necessary 

imprecision associated with EPA’s 

calculations, EPA has determined that 

this limited POTW cost comparison 

further supports its determination that 

the costs of these two BCT candidate 

technologies are not cost reasonable, 

given the lack of hard data on which to 

base the determination. This is fully 

consistent with EPA’s findings in the 

proposed rule that POTWs are very cost 

effective at fecal coliform removals. 71 

FR 37,772. The assessment confirms 

what logic suggests: Given a POTW’s 

requirement to virtually eliminate the 

extremely high fecal coliform discharges 

in its influent (basically raw sewage), 

POTWs, on a national basis, achieve 

fecal coliform removal on a cheaper 

basis than CAFOs. 

Finally, EPA notes that Congress 

intended the BCT level of control to be 

somewhere between the BPT and the 

BAT levels of control, as established in 

the statute. As noted in the conference 

14 EPA made a number of assumptions for its 

calculations because it did not have the data to 

establish on a national basis the costs to POTWs of 

fecal coliform control. Thus, EPA’s assessment used 

the cost of advanced secondary treatment as a proxy 

for the cost of additional technologies (e.g., 

filtration) that POTWs may employ to achieve high 

fecal coliform removals (98 percent) required by 

water quality standards of 200 colony forming units 

(CFU) per ml. This assumption may overstate the 

costs of such technologies, in which case the cost 

per trillion CFU removed would be lower. 

15 As described in the proposal, POTW influents 

are approximately 5 million CFU per 100 ml, and 

PCS data shows effluent concentrations of ∼ 20 CFU 

per ml. 

report to the 1977 amendments 

establishing BPT: 

‘‘The result of the cost test could be a 1984 

requirement which is no more than that 

which would result from best practicable 

technology but also could result in effluent 

reductions equal to that required in the 

application of best available technology.’’ 

Joint Explanatory Statement of the 

Committee of Conference, 95th Cong. 1st 

Sess., H.R. No. 95–830 at 85, Legislative 

History at 269. 

Thus, candidate technologies with 

costs between 6 and 13 times the costs 

of technologies that have already been 

determined to be BAT would not 

generally be appropriate as the basis for 

BCT. 

5. Additional Comments on the 

Proposal 

The following discussion summarizes 

additional significant comments 

received by EPA on the proposed CAFO 

BCT determination for pathogens. For a 

complete response to the issues raised 

by commenters, see the Response to 

Comment Document. 

In calculating the BPT cost per unit of 

fecal coliform removal for its costreasonableness assessment, one 

commenter noted the cost was 

erroneously calculated in units of 

dollars per billion colony forming units 

(CFU); the units should have been 

dollars per trillion CFU in order for the 

test to be comparable and consistent 

with the remaining BCT cost 

calculations. EPA agrees with this 

comment and has corrected all 

calculations to dollars per trillion CFU. 

Some commenters correctly noted 

that as part of the BCT cost test for fecal 

coliform, EPA calculated the POTW and 

industry cost benchmarks as the 

difference in average costs of removing 

fecal coliform between secondary 

treatment and advanced secondary 

treatment rather than as the incremental 

cost for the upgrade. These commenters 

believed that such an approach was 

incorrect. As discussed above, EPA 

agrees and has not used the revised BCT 

cost test for this final rule. In regards to 

the BCT options that were selected for 

further analysis, some commenters 

believe that numerical limits are feasible 

for CAFOs and should have been 

selected for BCT. They would have 

liked to see EPA take a similar approach 

to CAFO waste that EPA has taken 

regarding human sewage sludge (i.e., 

setting numerical pathogen standards 

for use). Some commenters pointed to 

the ‘‘sludge rule’’ or ‘‘biosolids’’ 

program under 40 CFR part 503 as a 

possible basis for pathogen standards in 

the CAFO rule. EPA notes that the CWA 

statutory criteria for sewage sludge 

standards under section 405 of the Act 

are health and welfare-based. By 

contrast, CWA effluent limitations 

require consideration of different 

factors. However, the technologies used 

to meet the regulations in part 503 may, 

in some cases, be used by CAFOs. For 

these reasons, EPA included sewage 

sludge pollution reduction technologies 

such as composting and lime addition 

in the suite of BCT candidate 

technologies the Agency considered. In 

addition, some commenters criticized 

EPA’s cost analysis for not including 

cost-share from federal sources such as 

EQIP, and for not including cost offsets 

from sale of treated manure. EPA 

considered both of these aspects in the 

cost analysis to the 2003 final CAFO 

rule, and was upheld on its economic 

analysis. 399 F.3d 486. In addition, EPA 

considered such cost offsets in a 

sensitivity analysis, and concluded that 

the cost offsets did not change EPA’s 

fundamental conclusions regarding 

economic achievability and feasibility. 

See Chapter 14 of the TDD for more 

information. 

By contrast, other commenters found 

no fault or shortcomings in the EPA 

analysis of the technical feasibility of 

conventional technologies in 

determining BCT for pathogen removal. 

They agree that the candidate 

technologies examined by EPA present 

insurmountable challenges to many 

CAFOs that make them inappropriate as 

a basis for BCT. They found no fault 

with the cost data or analytical 

techniques used by EPA in the BCT cost 

test. These commenters also presented 

additional economic analysis of the 

candidate technologies that has been 

published in the ‘‘Phase 3’’ report on the 

‘‘Development of Environmentally 

Superior Technologies’’ per agreements 

between the North Carolina Attorney 

General and major pork producers in the 

State. These commenters note that the 

‘‘Phase 3’’ economic analysis found that 

none of the 16 technologies studied 

were economically feasible for existing 

swine operations in North Carolina, 

which is consistent with EPA’s findings 

as discussed in detail above. These 

commenters also provided State records 

of CAFO violations and discharge data 

for the past three years to support their 

position that EPA has overstated the 

frequency of production area overflows. 

These additional data may be found in 

the record for this final action. 

IV. Impact Analysis 

A. Environmental Impacts 

When EPA issued the revised CAFO 

regulations on February 12, 2003, it 

estimated annual pollutant reductions 

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for the rule at 56 million pounds of 

phosphorus, 110 million pounds of 

nitrogen, and two billion pounds of 

sediment. This final, revised rule will 

not change these environmental benefits 

since the technical requirements for 

CAFOs that discharge are not affected 

and all CAFOs, whether covered by 

NPDES permits or not, still need to 

control nutrient releases from the 

production and land application areas 

in order to comply with the Clean Water 

Act. Under this rule, all CAFOs that do 

not apply for permits must be designed, 

constructed, operated, and maintained 

such that the CAFO does not discharge 

or propose to discharge. Therefore, as 

was true under the 2003 rule, all 

discharges from CAFOs (except 

precipitation-related discharges from 

land application areas under a CAFO’s 

control that qualify as agricultural 

stormwater discharges) are required to 

be covered by NPDES permits. The 

overall magnitude of the benefits will 

increase compared to 2003 due to 

growth in the industry, but the analysis 

for this rule does not recalculate these 

effects since the increase is not due to 

changes in the CAFO regulations. EPA 

is assuming full compliance with the 

rule, which is standard Agency 

procedure when modeling impacts of a 

final rule. 

B. Administrative Burden Impacts 

Since there is no change in technical 

requirements, changes in impacts on 

respondents are due exclusively to 

changes in the information collection 

burden. To determine the administrative 

burden for the Paperwork Reduction Act 

(PRA) analysis, the Agency first 

examined the two key permitting 

changes resulting from the Waterkeeper 

decision and how they would be 

implemented under the final 

regulations. These are the change in the 

duty to apply for CAFOs and the change 

to the nutrient management plan (NMP) 

related provisions for CAFO permits. 

The 2003 CAFO rule had a universal 

duty to apply requirement which 

required virtually all CAFOs to obtain 

NPDES permit coverage. The supporting 

analysis for the 2003 rule estimated that 

as a result of this requirement, 

approximately 15,500 CAFOs would 

ultimately receive NPDES permits. See 

the Technical Development Document 

for the 2003 rule, Chapter 9. 

This final rule changes the duty to 

apply requirement so that only CAFOs 

that discharge or propose to discharge 

are required to seek NPDES coverage. To 

derive the number of CAFOs that could 

ultimately fall into this category, EPA 

first projected total industry size for 

2008 based on both U.S. Department of 

Agriculture (USDA) Census of 

Agriculture statistics as well as Agencybased sector expertise. This exercise 

yielded an estimate of approximately 

20,700 total CAFOs for 2008. EPA then 

combined the 2008 projections for each 

animal sector with information on 

standardized operational profiles to 

anticipate the number of facilities as of 

2008 that might discharge. For example, 

when inclement weather precludes land 

application or dewatering activities, 

open lot type facilities such as beef lots 

and dairy operations are more likely to 

experience conditions that could result 

in a discharge due to the use of open onsite lagoons. Additionally, EPA assumed 

that all dairies generate wastewater from 

the production area and generally have 

uncovered on-site lagoons. Thus, for 

purposes of burden estimates, EPA 

assumed that all dairies and most beef 

feedlots would apply for permits. 

Even though the industry grew to 

roughly 20,700 CAFOs from 2002 to 

2008, the change in the duty to apply 

requirement is anticipated to reduce the 

number of facilities needing permit 

coverage to approximately 15,300 

discharging CAFOs. Based on these 

updated figures, EPA estimates that 

approximately 25 percent of the total 

universe of CAFOs would not discharge 

and thus would not need NPDES 

coverage under this final rule. Although 

these facilities may not need to apply 

for permits, the administrative burden 

analysis performed by EPA under the 

PRA nonetheless accounts for the costs 

that unpermitted facilities will incur for 

the nutrient management planning that 

are necessary for demonstrating that the 

facility is land applying manure in such 

a way as to qualify for the agricultural 

stormwater exemption. 

These figures may overstate the 

numbers of CAFOs needing NPDES 

permits in that the estimates of the 

number of discharging facilities in each 

sector make conservative categorical 

assumptions about the likelihood of a 

discharge based on broad operational 

profiles and do not account for more 

subtle stratifications within specific 

operational categories. For instance, 

although most dairies generate 

wastewater from the production area 

and have on-site lagoons, there do, in 

fact, exist dairies designed to be no 

discharge operations. 

Based on the updated estimates of the 

CAFO universe, EPA’s PRA analysis 

projects, as shown in Table 4.1, that 

CAFO operators and permitting 

authorities will collectively experience 

an increase in total annual 

administrative burden of approximately 

$0.5 million as a result of the EPA 

regulations to address the court 

decision. Although the PRA burden to 

CAFOs and permitting authorities 

declines as a result of the Waterkeeper 

court decision to limit permits only to 

discharging CAFOs, this burden 

reduction is offset by the new NMPrelated requirements for permits and by 

the assumption, for purposes of this 

PRA analysis, that all unpermitted 

CAFOs will certify under the voluntary 

no discharge certification option. More 

specifically, CAFO operators will 

experience a $0.2 million reduction in 

net annual administrative burden. This 

net result is based on several offsetting 

changes. CAFOs that do not seek permit 

coverage under this final rule because 

they do not discharge or propose to 

discharge will save approximately $14 

million annually in reduced permitting 

costs. However, even though fewer 

CAFOs will need to be covered by 

NPDES permits, permitted facilities as a 

group face an increase in annual 

administrative burden of $1.2 million 

per year due to the new NMP 

requirements. 

EPA’s analysis of burden impacts to 

CAFOs also accounts for the burden that 

unpermitted facilities will incur in 

order to be able to qualify for the 

agricultural stormwater exemption—a 

cost category that EPA estimates will 

result in a burden on unpermitted 

facilities of $12.2 million annually. In 

addition, EPA estimates that the 

voluntary certification option for 

unpermitted CAFOs could add $0.4 

million annually to the PRA burden for 

CAFOs. Although certification is 

voluntary, EPA elected to cost the PRA 

burden associated with this option so as 

to provide a complete accounting of all 

rule-related impacts. As noted above, 

the net result of these impacts is an 

administrative burden savings across all 

CAFO operators, permitted and 

unpermitted, of $0.2 million annually. 

Permitting authorities, on the other 

hand, are projected to experience a $0.7 

million increase in annual 

administrative burden. Although the 

burden to issue permits declines by $4.2 

million annually due to fewer facilities 

needing permits, this decline is more 

than offset by the added workload 

arising from the new NMP-related 

requirements. EPA estimates that States 

would face an additional PRA burden of 

$4.9 million annually specifically as a 

result of the new NMP-related 

requirements. In addition, States are 

projected to face a burden increment of 

up to $0.04 million annually to process 

the new certifications. 

EPA’s estimate of PRA burden 

impacts changed from a reduction of 

$14.9 million annually for the 2006 

proposed rule to an increase of $0.5 

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70470 Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 

million annually in the final rule. This voluntary no discharge certification with the 2006 proposed rule and 2008 

change is due principally to the option. supplemental proposal, and did not 

Agency’s decision, as discussed earlier The PRA burden analysis presented in receive any comments from the Office of 

in this section, to amend the PRA this rule accounts both for growth in the Management and Budget (OMB). The 

analysis to account for the burden industry and changes in labor rates documentation in the public record on 

incurred by unpermitted CAFOs for since the 2003 rule was issued. In the PRA analysis for this rulemaking 

nutrient management planning, which addition, the changes are based on discusses more fully the assumptions 

is necessary for any unpermitted CAFO annualized impacts and assume a used to estimate the numbers of CAFOs 

that land applies irrespective of whether permit term of five years as stipulated needing permits and to project the 

the CAFO is certified under the in the CWA. EPA submitted draft ICRs associated administrative burden. 

TABLE 4.1—PRA BURDEN IMPACT CHANGES 

[Note: Numbers may not add due to rounding.] 

Total baseline Total amended Net change in 

PRA burden: PRA burden: paperwork burbased on 2003 based on final den (2003 rule 

CAFO rule rule require- compared to 

requirements 1 ments final rule) 

CAFOs needing permits 

(2008) 2. 

CAFOs seeking agricultural stormwater exemption only (2008). 

Total CAFOs (2008) 

Annualized Costs 3 (in $ 

millions). 

........................................ 

........................................ 

........................................ 

CAFOs ........................... 

Permitting Authorities .... 

............................................................ 

............................................................ 

............................................................ 

Base NPDES Permit ......................... 

New NMP Provisions ........................ 

Agricultural Stormwater Exemption ... 

Certification ........................................ 

Total CAFO Burden ........................... 

Base NPDES Permit ......................... 

New NMP Provisions ........................ 

Certification ........................................ 

Total Permit Authority Burden ........... 

20,685 

n/a 

20,685 

$54.0 

n/a 

n/a 

n/a 

$54.0 

$16.5 

n/a 

n/a 

$16.5 

15,281 

5,404 

20,685 

$40.0 

$1.2 

$12.2 

$0.4 

$53.8 

$12.2 

$4.9 

$0.04 

$17.1 

($14.0 ) 

$1.2 

$12.2 

$0.4 

($0.2 ) 

($4.2 ) 

$4.9 

$0.04 

$0.7 

All Respondents ............................................................................ $70.5 $71.0 $0.5 

1 2003 baseline impacts adjusted to reflect current labor rates and growth in facilities. 


2 Facility totals are annualized over 5 years in burden calcultions presented below to reflect CWA requirement for NPDES permit renewal every 


5 years. 
 3 Annualized costs represent labor, capital and O&M costs. 


C. Response to Public Comment on the 

Proposal 

The Agency received a variety of 

comments on the impacts analysis 

presented for the 2006 proposed rule 

and the 2008 supplemental proposal. 

Several commenters indicated that the 

Agency erred in assuming that the 

environmental benefits from the 2003 

rule would be retained under the 

approach adopted in this final rule. The 

Agency stands by its position presented 

in the 2006 proposed rule, but has 

revised the burden analysis to reflect 

more fully that all unpermitted CAFOs 

do not discharge or propose to discharge 

and, therefore, must implement nutrient 

management practices to ensure that 

any discharge from the CAFO’s land 

application area qualifies for the 

agricultural stormwater exemption. As a 

consequence, as indicated above, the 

annual burden reduction realized by 

CAFOs under the final revised rule is 

shown as approximately $0.2 million as 

opposed to the $15.4 million reduction 

projected for CAFOs in the 2006 

proposed rule. This revised analysis 

also addresses specific comments 

suggesting that the Agency should 

recognize that operators without permits 

will continue to incur costs under the 

regulation in order to meet the burden 

of proof required to qualify for the 

agricultural stormwater exemption. 

Other commenters indicated that the 

impacts analysis underestimated the 

costs to CAFO operators of complying 

with the EPA regulations. Careful 

review of these statements makes clear 

that commenters with this viewpoint 

either did not account for the fact that 

the impacts analysis presented for this 

rulemaking is exclusively an assessment 

of the paperwork burden—not the 

overall compliance burden—faced by 

CAFOs, or did not fully consider that 

the costs shown represent average 

yearly (annualized) burden rather than 

total paperwork-related costs for a fiveyear CAFO NPDES permit. 

Other commenters provided specific 

information on nutrient management 

plan (NMP) development costs, which 

the Agency determined corroborated the 

original NMP cost estimates. 

One State commenter claimed that the 

Agency had underestimated costs to 

permitting authorities for managing the 

potential public hearings precipitated 

by the new requirements for public 

notice. This commenter projected that 

every public notice regarding NMPs 

would result in a public hearing. The 

Agency re-examined its assumptions 

regarding the incidence of public 

hearings, but did not find information to 

corroborate the commenter’s projection 

either based on past NPDES public 

hearing patterns or based on 

expectations from other States regarding 

the number of hearings likely to be 

triggered by NMP-related public notices. 

This assumption that public hearings 

would not be requested for every NMP 

is further confirmed by the experiences 

of States that currently require NMPs to 

be submitted as part of their permitting 

process. 

Several commenters indicated that 

they believed that the Agency had also 

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underestimated the cost to States of 

processing voluntary no discharge 

certifications. This final rule does not 

require permitting authority review of 

no discharge certifications. See 

discussion of certification submission in 

section III.A.3(c) of this preamble. The 

Agency notes that the cost analysis it 

performed to assess the paperwork 

burden associated with the final rule 

shows a net paperwork burden 

reduction to States on this aspect of the 

rule, since the 2003 rule required 

permits-which are more burdensome for 

permitting authorities to process-from 

all CAFOs. 

V. Cross-Media Considerations and 

Pathogens 

A. Cross-Media Approaches 

Since 2003, EPA and CAFO 

stakeholders have been interested in 

developing a framework to enable 

CAFOs to pursue superior 

environmental performance across all 

media. Today, some CAFOs voluntarily 

conduct whole-farm audits to evaluate 

releases of pollutants to all media 

through Environmental Management 

Systems (e.g., ISO 14001 certification), 

self-assessment tools, EPA’s 

performance track, and State-approved 

trade-offs in reducing discharges to 

water and emissions to air that 

accomplish the best overall level of 

protection given State and local 

conditions. The development of new 

and emerging technologies offers the 

potential to achieve equivalent or 

greater pollutant reductions relative to 

those achieved by the effluent 

guidelines and standards. Many of these 

are superior from a cross-media 

perspective, and EPA encourages 

superior cross-media solutions. These 

regulations regarding nutrient 

management plans may provide an 

opportunity for EPA to encourage crossmedia approaches at CAFOs. For 

example, the nutrient value in the 

animal byproducts provides a valuable 

source of fertilizer for crops. However, 

inappropriate application can lead to 

preventable discharges to water and 

emissions to air. Optimal application 

technologies and rates reduce potential 

water quality and air quality standards 

violations. 

The fact that EPA has multiple efforts 

underway relating to livestock 

operations under several environmental 

statutes underscores the need to explore 

how to leverage existing regulatory 

authorities most effectively. For 

example, in addition to the regulations 

being finalized in this rulemaking, the 

Agency has recently undertaken a 

National Air Emissions Monitoring 

Study. EPA also proposed a rule that 

would exempt animal feeding 

operations from certain requirements 

relating to reporting of air releases 

under hazardous waste laws. 

EPA solicited comment in the 2006 

proposed rule on the feasibility 

(including consideration of legal, 

technical, and implementation issues) of 

allowing flexibility in how facilities 

meet various programmatic 

requirements, for instance those of the 

Clean Air Act and the Clean Water Act 

(CWA), in order to achieve greater crossmedia pollutant reductions. EPA 

received generalized support for this 

type of approach in the comments 

submitted in response. EPA will 

continue to explore cross-media 

considerations as it works together with 

CAFOs and stakeholders to build further 

experience on this issue. 

As an example of the Agency’s work 

in this area, in October 2007, EPA 

awarded $8 million in federal grants for 

providing technical assistance to 

livestock operators, including animal 

feeding operations, for the prevention of 

water discharges and reduction of air 

emissions. More recently, EPA’s 

Agricultural Advisor announced the 

establishment of the Farm, Ranch, and 

Rural Communities Federal Advisory 

Committee. One of the issues the 

committee will focus on will be 

identification and development of a 

comprehensive environmental strategy 

for livestock operations. EPA anticipates 

that the committee will offer timely 

observations on the opportunities and 

challenges of cross-media approaches to 

programs for addressing environmental 

concerns at livestock operations as its 

work progresses. 

B. Pathogens and Animal Feeding 

Operations 

Although this final rule does not 

require any new best conventional 

pollutant control technology (BCT) 

effluent limitations specifically to 

control fecal coliform, EPA is 

continuing to assess environmental and 

human health concerns associated with 

the management of manure and 

wastewater at CAFOs. Pollutants most 

commonly associated with animal waste 

include nutrients (including ammonia), 

organic matter, solids, odorous 

compounds, and various pathogens. 

These pollutants, and others, can be 

released into the environment through 

discharge or runoff if manure and 

wastewater are not properly handled 

and managed. EPA is interested in 

recently initiated studies to assess 

potential impacts from pathogens in 

livestock manure, especially those 

which may pose unique risks such as 

Cryptosporidium and Giardia. These 

pathogens may be of concern if they 

make their way into drinking water 

sources (e.g., lakes, rivers, and streams) 

because of their stability in the natural 

environment and their resistance to the 

most commonly used drinking water 

disinfection procedure (i.e., 

chlorination). If proper treatment is not 

provided for these pathogens, they have 

the potential to cause adverse health 

impacts in exposed populations. While 

the Agency has a number of on-going 

efforts in these areas, research is still in 

its early stages. The absence of available 

information necessarily limits EPA’s 

ability to act with respect to these 

potential concerns. 

EPA’s Office of Research and 

Development (ORD) is actively working 

to identify sources of Cryptosporidium. 

In collaboration with the Centers for 

Disease Control (CDC), EPA Region 3, 

and the Potomac River Drinking Water 

Source Protection Partnership (DWSPP), 

ORD has initiated Cryptosporidium 

source tracking studies of the Potomac 

River Watershed. The primary objective 

of this project is to develop and 

implement a monitoring program for 

Cryptosporidium source tracking in 

order to identify the most significant 

sources of this parasite within the 

watershed. Once identified, appropriate 

source protection efforts, where 

available, may be mobilized and 

directed to the reduction of these 

sources’ contributions. In addition, in 

2005 EPA’s Science to Achieve Results 

(STAR) program held a solicitation for 

proposals entitled, ‘‘Development and 

Evaluation of Innovative Approaches for 

the Quantitative Assessment of 

Pathogens in Drinking Water,’’ and has 

funded eleven research grants from this 

proposal involving the development and 

evaluation of innovative approaches to 

quantitatively detect microbial 

pathogens in drinking water, including 

Cryptosporidium and Giardia. The goal 

of the STAR research is to improve the 

suite of available detection methods for 

known and emerging microbial drinking 

water contaminants. EPA expects that 

this research will result in methods that 

will, among other things, allow 

determination of the presence and 

quantities of waterborne pathogens; 

present a protocol for preparing and 

processing water samples for 

application of the proposed approach; 

and where possible, allow comparison 

of the performance of the new detection 

methods with existing approved EPA 

methods for specific pathogens. 

ORD is also collaborating with the 

U.S. Department of Agriculture (USDA) 

in their research programs associated 

with Cryptosporidium. ORD scientists 

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participated in the USDA selection 

process for the National Research 

Initiative on Watershed Processes and 

Water Resources. Grants awarded under 

this program will explore the effects of 

a number of factors on Cryptosporidium 

mobility and contamination of 

waterways. These include the use of 

buffers and other best management 

practices for decreasing loadings of 

Cryptosporidium from land application 

of wastes and other soluble organic 

matter. EPA scientists have begun to 

review recently published research on 

Cryptosporidium and Giardia oocyst 

shedding. The research suggests that 

shedding is highest during early life 

stages of cattle and zoonotic forms and 

may greatly diminish as calves age. 

These factors have already led some 

veterinarians to recommend that farmers 

separate these high shedding young 

animals from older animals to decrease 

disease spread and economic losses 

among herds of cattle and dairy cows. 

The research also suggests that the 

separation may provide secondary 

environmental benefits by helping to 

prevent the release of Cryptosporidium 

into waterways. As part of their efforts 

to protect the New York City water 

supply, the New York State Department 

of Agriculture has recommended 

separation controls in their best 

management practice (BMP) guidance to 

dairy farmers. Other States, including 

California, are considering similar 

separation BMPs. 

EPA’s ORD will continue to 

collaborate and assess the impacts that 

these and other research efforts may 

have on any future CAFO management 

recommendations. 

VI. Statutory and Executive Order 

Reviews 

A. Executive Order 12866: Regulatory 

Planning and Review 

Under Executive Order 12866 (58 FR 

51,735; October 4, 1993), this action is 

a ‘‘significant regulatory action.’’ 

Accordingly, EPA submitted this action 

to the Office of Management and Budget 

(OMB) for review under Executive 

Order 12866 and any changes made in 

response to OMB recommendations 

have been documented in the docket for 

this action. 

In addition, EPA prepared an analysis 

of the potential costs and benefits 

associated with this action. This 

analysis is contained in section IV of 

this preamble above, entitled Impact 

Analysis. A copy of the supporting 

analysis is available in the docket for 

this action. 

B. Paperwork Reduction Act 

The information collection 

requirements in this rule have been 

submitted for approval to the Office of 

Management and Budget (OMB) under 

the Paperwork Reduction Act, 44 U.S.C. 

3501 et seq. The information collection 

requirements are not enforceable until 

OMB approves them. However, the 

Office of Management and Budget 

(OMB) has previously approved the 

information collection requirements 

contained in the existing regulations 

and has assigned OMB control number 

2040–0250. The Information Collection 

Request (ICR) document prepared by 

EPA was assigned EPA ICR No. 1989.06. 

The 2003 CAFO rule had a universal 

duty to apply requirement which 

required virtually all CAFOs to obtain 

NPDES permit coverage. This final 

revised rule changes the duty to apply 

requirement so that only CAFOs that 

discharge or propose to discharge must 

to seek NPDES coverage. EPA projects 

that CAFO operators and permitting 

authorities will collectively experience 

a reduction in total annual 

administrative burden of 25,500 hours 

as a result of the regulatory revisions to 

address the court decision. Labor 

burden is projected to undergo a net 

decrease compared to a net increase in 

administrative costs of $0.5 million 

annually as discussed in Chapter IV. 

This difference arises from the fact that 

the PRA analysis performed for the final 

rule converts labor hour burden to labor 

costs using a higher wage rate for State 

permitting authorities than for CAFO 

operators.16 The higher wage rate for 

State permitting authorities causes the 

State labor cost increase to be large 

enough to offset the labor cost reduction 

experienced by CAFO operators once 

labor hours are converted to dollars in 

the PRA analysis of annual 

administrative impacts. 

More specifically, the estimated 

reduction in total annual administrative 

burden of 25,500 hours is based on a 

projected decrease in labor burden to 

CAFO operators of approximately 

54,100 hours annually and a projected 

increase in labor burden to State 

permitting authorities of approximately 

28,600 hours annually. For CAFOs, 

much of the labor burden decrease 

derives from the smaller number of 

facilities that will need permits, which 

results in an annual burden decrease of 

more than 703,000 labor hours. This 

16 Wage rates for the PRA analysis supporting this 

rulemaking were drawn from recent reports filed by 

the U.S. Department of Labor, Bureau of Labor 

Statistics. For further information please refer to the 

ICR prepared by EPA for the rulemaking, available 

in the record as EPA ICR No. 1989.06. 

burden reduction for CAFOs is offset by 

a concomitant increase of 603,200 labor 

hours annually at unpermitted facilities 

for activities necessary to meet the 

agricultural stormwater exemption, 

along with an increment of 33,100 hours 

annually for permitted facilities to 

undertake the NMP-related activities 

and 12,600 hours annually for those 

CAFOs who elect to pursue the 

voluntary certification option. 

The annual labor burden increase for 

State permitting authorities of 28,600 

hours includes an estimated annual 

reduction in labor burden of 93,000 

hours due to the need to process fewer 

permits. However, for State permitting 

authorities this burden reduction is 

more than offset by an increment in 

annual labor burden of 120,700 hours to 

address the new NMP-related 

requirements combined with a relatively 

minor annual burden increase of 900 

hours to handle the voluntary 

certifications. 

Additional details on the assumptions 

and parameters of the PRA analysis are 

available in the ICR document 

referenced above, which is available in 

the docket supporting this final 

rulemaking. Burden is defined at 5 CFR 

1320.3(b). 

An agency may not conduct or 

sponsor, and a person is not required to 

respond to a collection of information 

unless it displays a currently valid OMB 

control number. The OMB control 

numbers for EPA’s regulations in 40 

CFR are listed in 40 CFR part 9. 

This final rule responds to OMB or 

public comments on the information 

collection requirements as discussed in 

the Impact Analysis (section IV) in this 

preamble. 

C. Regulatory Flexibility Act 

The Regulatory Flexibility Act (RFA) 

generally requires an agency to prepare 

a regulatory flexibility analysis of any 

rule subject to notice and comment 

rulemaking requirements under the 

Administrative Procedure Act or any 

other statute unless the agency certifies 

that the rule will not have a significant 

economic impact on a substantial 

number of small entities. Small entities 

include small businesses, small 

organizations, and small governmental 

jurisdictions. 

For purposes of assessing the impacts 

of this rule on small entities, small 

entity is defined as: (1) A small business 

based on Small Business Administration 

(SBA) size standards at 13 CFR 121.201; 

(2) a small governmental jurisdiction 

that is a government of a city, county, 

town, school district, or special district 

with a population of less than 50,000; 

and (3) a small organization that is any 

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not-for-profit enterprise which is 

independently owned and operated and 

is not dominant in its field. 

After considering the economic 

impacts of this rule on small entities, I 

certify that this action will not have a 

significant adverse economic impact on 

a substantial number of small entities. 

This final rule does not change the 

substantive requirements for CAFO 

operators or increase the net paperwork 

burden faced by facilities compared to 

the burden imposed under the 2003 

CAFO rule. Some CAFOs will face 

increased permitting costs due to the 

new NMP provisions, while others will 

face reduced costs due to the changes in 

the duty to apply. However, these 

paperwork cost changes are generally 

small and do not rise to the level of a 

significant adverse economic impact on 

a substantial number of operators. 

Additionally, this rule would not affect 

small governments as the permitting 

authorities are State or federal agencies. 

D. Unfunded Mandates Reform Act 

Title II of the Unfunded Mandates 

Reform Act of 1995 (UMRA), Public 

Law 104–4, establishes requirements for 

federal agencies to assess the effects of 

their regulatory actions on State, local, 

and tribal governments and the private 

sector. Under section 202 of UMRA, 

EPA generally must prepare a written 

statement, including a cost-benefit 

analysis, for proposed and final rules 

with ‘‘federal mandates’’ that may result 

in expenditures to State, local, and 

tribal governments, in the aggregate, or 

to the private sector, of $100 million or 

more in any one year. Before 

promulgating an EPA rule for which a 

written statement is needed, section 205 

of the UMRA generally requires EPA to 

identify and consider a reasonable 

number of regulatory alternatives and 

adopt the least costly, most costeffective, or least burdensome 

alternative that achieves the objectives 

of the rule. The provisions of section 

205 do not apply when they are 

inconsistent with applicable law. 

Moreover, section 205 allows EPA to 

adopt an alternative other than the least 

costly, most cost-effective, or least 

burdensome alternative if the 

Administrator publishes with the final 

rule an explanation why that alternative 

was not adopted. Before EPA establishes 

any regulatory requirements that may 

significantly or uniquely affect small 

governments, including tribal 

governments, it must have developed 

under section 203 of the UMRA a small 

government agency plan. The plan must 

provide for notifying potentially 

affected small governments, enabling 

officials of affected small governments 

to have meaningful and timely input in 

the development of EPA regulatory 

proposals with significant federal 

intergovernmental mandates, and 

informing, educating, and advising 

small governments on compliance with 

the regulatory requirements. 

EPA has determined that this rule 

does not contain a federal mandate that 

may result in expenditures of $100 

million or more for State, local, and 

tribal governments, in the aggregate, or 

the private sector in any one year. The 

revised administrative burden EPA 

calculated for the final rule constitutes 

a reduction of roughly 25,500 labor 

hours annually compared to the 

administrative burden estimated for the 

2003 CAFO rule. This burden reduction 

reflects a decrease in annual labor 

burden of 54,100 hours for CAFO 

operators and an annual labor burden 

increase to State permitting authorities 

of 28,600 hours. In addition, this 

rulemaking is in response to a federal 

court decision and is necessary to assure 

compliance with applicable law. Thus, 

this rule is not subject to the 

requirements of sections 202 and 205 of 

the UMRA. 

EPA has determined that this rule 

contains no regulatory requirements that 

might significantly or uniquely affect 

small governments. There are no local 

or Tribal governments authorized to 

implement the NPDES permit program 

and the Agency is unaware of any local 

or Tribal governments who are owners 

or operators of CAFOs. Thus this rule is 

not subject to the requirements of 

section 203 of UMRA. 

E. Executive Order 13132: Federalism 

Executive Order 13132, entitled 

‘‘Federalism’’ (64 FR 43,255; August 10, 

1999), requires EPA to develop an 

accountable process to ensure 

‘‘meaningful and timely input by State 

and local officials in the development of 

regulatory policies that have federalism 

implications.’’ ‘‘Policies that have 

federalism implications’’ is defined in 

the Executive Order to include 

regulations that have ‘‘substantial direct 

effects on the States, on the relationship 

between the national government and 

the States, or on the distribution of 

power and responsibilities among the 

various levels of government.’’ 

This final rule does not have 

federalism implications. It will not have 

substantial direct effects on the States, 

on the relationship between the national 

government and the States, or on the 

distribution of power and 

responsibilities among the various 

levels of government, as specified in 

Executive Order 13132. EPA estimates 

that the average annual impact on all 

authorized States together is a cost 

increase of $0.7 million. EPA does not 

consider an annual impact of this 

magnitude on States to be a substantial 

effect. In addition, EPA does not expect 

this rule to have any impact on local 

governments. EPA also considered 

flexibility as an important factor when 

developing this regulation. 

Further, the revised regulations will 

not alter the basic State-federal scheme 

established in the CWA under which 

EPA authorizes States to carry out the 

NPDES permitting program. EPA 

expects the revised regulations to have 

little effect on the relationship between, 

or the distribution of power and 

responsibilities among, the federal and 

State governments. Thus, Executive 

Order 13132 does not apply to this rule. 

In the spirit of Executive Order 13132, 

and consistent with EPA policy to 

promote communications between EPA 

and State and local governments, EPA 

specifically solicited comment on the 

proposed rule from State and local 

officials. In addition, through a variety 

of meetings with State associations 

during the rulemaking process, States 

have been informed about the issues 

related to addressing the court’s 

decisions. States provided input during 

these meetings. State concerns generally 

focused on the process for incorporating 

NMPs into permits and the related 

public review process, and also on 

guidance related to what constitutes a 

discharge from a CAFO given that the 

proposed rule would have required only 

those operations that discharge or 

propose to discharge to apply for a 

permit. These concerns have been 

addressed in such a way as to provide 

flexibility and accountability in the new 

permit application requirements and 

review processes promulgated in this 

rule. 

F. Executive Order 13175: Consultation 

and Coordination With Indian Tribal 

Governments 

Executive Order 13175, entitled, 

‘‘Consultation and Coordination with 

Indian Tribal Governments’’ (65 FR 

67,249; November 9, 2000), requires 

EPA to develop an accountable process 

to ensure ‘‘meaningful and timely input 

by tribal officials in the development of 

regulatory policies that have tribal 

implications.’’ 

This rule does not have tribal 

implications. There are currently no 

tribal governments authorized for the 

NPDES program. This rulemaking 

provides increased opportunity for the 

public and tribal governments to 

comment on specific CAFOs’ 

applications for permit coverage. It will 

not have substantial direct effects on 

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tribal governments, on the relationship 

between the federal government and 

Indian tribes, or on the distribution of 

power and responsibilities between the 

federal government and Indian tribes, as 

specified in Executive Order 13175. 

Thus, Executive Order 13175 does not 

apply to this rule. 

In the spirit of Executive Order 13175, 

and consistent with EPA policy to 

promote communications between EPA 

and tribal governments, EPA 

specifically solicited comment on the 

proposed rule from tribal officials. 

G. Executive Order 13045: Protection of 

Children From Environmental Health 

and Safety Risks 

Executive Order 13045 ‘‘Protection of 

Children from Environmental Health 

Risks and Safety Risks’’ (62 FR 19,885; 

April 23, 1997) applies to any rule that: 

(1) Is determined to be ‘‘economically 

significant’’ as defined under Executive 

Order 12866, and (2) concerns an 

environmental health or safety risk that 

EPA has reason to believe may have a 

disproportionate effect on children. If 

the regulatory action meets both criteria, 

the Agency must evaluate the 

environmental health or safety effects of 

the planned rule on children, and 

explain why the planned regulation is 

preferable to other potentially effective 

and reasonably feasible alternatives 

considered by the Agency. 

This final rule is not subject to 

Executive Order 13045 because it is not 

economically significant as defined in 

Executive Order 12866, and because the 

Agency does not have reason to believe 

the environmental health or safety risks 

addressed by this action present a 

disproportionate risk to children. The 

benefits analysis performed for the 2003 

CAFO rule determined that the rule 

would result in certain significant 

benefits to children’s health. (Please 

refer to the Benefits Analysis in the 

record for the 2003 CAFO final rule.) 

This action does not affect the 

environmental benefits of the 2003 

CAFO rule. 

H. Executive Order 13211: Actions 

Concerning Regulations That 

Significantly Affect Energy Supply, 

Distribution, or Use 

This rule is not a ‘‘significant energy 

action’’ as defined in Executive Order 

13211, ‘‘Actions Concerning Regulations 

That Significantly Affect Energy Supply, 

Distribution, or Use’’ (66 FR 28,355; 

May 22, 2001) because it is not likely to 

have a significant adverse effect on the 

supply, distribution, or use of energy. 

EPA has concluded that this rule is not 

likely to have any adverse energy effects 

since CAFOs in general do not figure 

significantly in the energy market, and 

the regulatory revisions finalized in this 

rule are not likely to change existing 

energy generation or consumption 

profiles for CAFOs. 

I. National Technology Transfer and 

Advancement Act 

Section 12(d) of the National 

Technology Transfer and Advancement 

Act of 1995 (‘‘NTTAA’’), Public Law 

104–113, 12(d) (15 U.S.C. 272 note) 

directs EPA to use voluntary consensus 

standards in its regulatory activities 

unless to do so would be inconsistent 

with applicable law or otherwise 

impractical. Voluntary consensus 

standards are technical standards (e.g., 

materials specifications, test methods, 

sampling procedures, and business 

practices) that are developed or adopted 

by voluntary consensus standards 

bodies. The NTTAA directs EPA to 

provide Congress, through OMB, 

explanations when the Agency decides 

not to use available and applicable 

voluntary consensus standards. 

This final rule does not change the 

technical requirements for land 

application from those of the 2003 rule. 

Production area requirements are the 

same for existing sources and for new 

sources as in the 2003 rule. The no 

discharge production area requirements 

for new sources in this rulemaking, 

however, now include an option for 

complying with the requirement 

through the development of site-specific 

design, operation and maintenance 

permit conditions that will ensure no 

discharge from the site. However, the 

specific no discharge conditions 

applicable to a specific operator 

choosing this option for compliance will 

be determined by the permitting 

authority on a site-specific BPJ basis. 

EPA encourages the use by permitting 

authorities of voluntary consensus 

standards, such as those that may be 

developed by USDA, in establishing the 

site-specific technical requirements in 

CAFO permits when the permittee 

demonstrates that these standards are 

consistent with the achievement of no 

discharge from a specific CAFO. 

This rule for new source requires that 

CAFOs complying with the no discharge 

requirement through the development of 

site-specific design, maintenance and 

operation standards must use prescribed 

technical standards in demonstrating 

that a specific CAFO’s design, operation 

and maintenance will be consistent with 

no discharge from its production area. 

(In certain circumstances, a CAFO may 

use either equivalent evaluation and 

simulation procedures or technical 

standards developed for a class of 

specific facilities within a specified 

geographical area if approved by its 

permitting authority), EPA has not 

required the use of any particular 

voluntary consensus standards in this 

rule. The use, however, of voluntary 

consensus standards such as those that 

may be developed by USDA for the 

required demonstration that site-specific 

design, maintenance and operational 

requirements for CAFOs to comply with 

the no discharge standard is 

encouraged. The decisions as to what 

specific best management practices and 

technologies must be applied at 

individual animal feeding operations 

are left to the State or EPA in the 

exercise of their NPDES authority. 

J. Congressional Review Act 

The Congressional Review Act, 5 

U.S.C. 801 et seq., as added by the Small 

Business Regulatory Enforcement 

Fairness Act of 1996, generally provides 

that before a rule may take effect, the 

agency promulgating the rule must 

submit a rule report, which includes a 

copy of the rule, to each House of the 

Congress and to the Comptroller General 

of the United States. EPA will submit a 

report containing this rule and other 

required information to the U.S. Senate, 

the U.S. House of Representatives, and 

the Comptroller General of the United 

States prior to publication of the rule in 

the Federal Register. A major rule 

cannot take effect until 60 days after it 

is published in the Federal Register. 

This action is not a ‘‘major rule’’ as 

defined by 5 U.S.C. 804(2). This rule 

will become effective December 22, 

2008. 

BILLING CODE 6560–50–P 

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BILLING CODE 6560–50–C 

List of Subjects 

40 CFR Part 9 

Environmental protection, Reporting 

and recordkeeping requirements. 

40 CFR Part 122 

Administrative practice and 

procedure, confidential business 

information, hazardous substances, 

reporting and recordkeeping 

requirements, water pollution control. 

40 CFR Part 412 

Environmental protection, feedlots, 

livestock, waste treatment and disposal, 

water pollution control. 

Dated: October 31, 2008. 

Stephen L. Johnson, 

Administrator. 

■ For the reasons set out in the 

preamble, chapter I of Title 40 of the 

Code of Federal Regulations is to be 

amended as follows: 

PART 9—OMB APPROVALS UNDER 

THE PAPERWORK REDUCTION ACT 

■ 1. The authority citation for part 9 

continues to read as follows: 

Authority: 7 U.S.C. 135 et seq., 136–136y; 

15 U.S.C. 2001, 2003, 2005, 2006, 2601–2671; 

21 U.S.C. 331j, 346a, 348; 31 U.S.C. 9701; 33 

U.S.C. 1251 et seq., 1311, 1313d, 1314, 1318, 

1321, 1326, 1330, 1342, 1344, 1345(d) and 

(e), 1361; Executive Order 11735, 38 FR 

21243, 3 CFR, 1971–1975 Comp. p. 973; 42 

U.S.C. 241, 242b, 243, 246, 300f, 300g–1, 

300g–2, 300g–3, 300g–4, 300g–5, 300g–6, 

300j–1, 300j–2, 300j–3, 300j–4, 300j–9, 1857 

et seq., 6901–6992k, 7401–7671q, 7542, 

9601–9657, 11023, 11048. 

■ 2. In § 9.1 the table is amended by 

adding entries in numerical order under 

the indicated heading to read as follows: 

§ 9.1 OMB approvals under the Paperwork 

Reduction Act. 

* * * * * 

OMB control 40 CFR citation No. 

* * * * * 

EPA Administered Permit Programs: The 

National Pollutant Discharge Elimination 

System 

* * * * * 

122.21(i) .................................... 2040–0250 

* * * * * 

122.23 (d), (e), (h) .................... 2040–0250 

* * * * * 

PART 122—EPA ADMINISTERED 

PERMIT PROGRAMS: THE NATIONAL 

POLLUTANT DISCHARGE 

ELIMINATION SYSTEM 

■ 3. The authority citation for part 122 

continues to read as follows: 

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

1251 et seq. 

■ 4. Section 122.21 is amended by 

revising the last sentence in paragraph 

(a)(1), and revising paragraph (i)(1)(x), to 

read as follows: 

§ 122.21 Application for a permit 

(applicable to State programs, see § 123.25). 

(a) * * * 

(1) * * * The requirements for 

concentrated animal feeding operations 

are described in § 122.23(d). 

* * * * * 

(i) * * * 

(1) * * * 

(x) A nutrient management plan that 

at a minimum satisfies the requirements 

specified in § 122.42(e), including, for 

all CAFOs subject to 40 CFR part 412, 

subpart C or subpart D, the requirements 

of 40 CFR 412.4(c), as applicable. 

* * * * * 

■ 5. Section 122.23 is amended as 

follows: 

■ a. By revising paragraph (a). 

■ b. By revising paragraphs (d)(1) and 

(d)(2). 

■ c. By adding paragraphs (e)(1) and 

(e)(2). 

■ d. By revising paragraph (f). 

■ e. By revising paragraph (g). 

■ f. By revising paragraph (h). 

■ g. By adding paragraph (i). 

■ h. By adding paragraph (j). 

§ 122.23 Concentrated animal feeding 

operations (applicable to State NPDES 

programs, see § 123.25). 

(a) Scope. Concentrated animal 

feeding operations (CAFOs), as defined 

in paragraph (b) of this section or 

designated in accordance with 

paragraph (c) of this section, are point 

sources, subject to NPDES permitting 

requirements as provided in this 

section. Once an animal feeding 

operation is defined as a CAFO for at 

least one type of animal, the NPDES 

requirements for CAFOs apply with 

respect to all animals in confinement at 

the operation and all manure, litter, and 

process wastewater generated by those 

animals or the production of those 

animals, regardless of the type of 

animal. 

* * * * * 

(d) * * * 

(1) Permit Requirement. The owner or 

operator of a CAFO must seek coverage 

under an NPDES permit if the CAFO 

discharges or proposes to discharge. A 

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CAFO proposes to discharge if it is 

designed, constructed, operated, or 

maintained such that a discharge will 

occur. Specifically, the CAFO owner or 

operator must either apply for an 

individual NPDES permit or submit a 

notice of intent for coverage under an 

NPDES general permit. If the Director 

has not made a general permit available 

to the CAFO, the CAFO owner or 

operator must submit an application for 

an individual permit to the Director. 

(2) Information to submit with permit 

application or notice of intent. An 

application for an individual permit 

must include the information specified 

in § 122.21. A notice of intent for a 

general permit must include the 

information specified in §§ 122.21 and 

122.28. 

* * * * * 

(e) * * * 

(1) For unpermitted Large CAFOs, a 

precipitation-related discharge of 

manure, litter, or process wastewater 

from land areas under the control of a 

CAFO shall be considered an 

agricultural stormwater discharge only 

where the manure, litter, or process 

wastewater has been land applied in 

accordance with site-specific nutrient 

management practices that ensure 

appropriate agricultural utilization of 

the nutrients in the manure, litter, or 

process wastewater, as specified in 

§ 122.42(e)(1)(vi) through (ix). 

(2) Unpermitted Large CAFOs must 

maintain documentation specified in 

§ 122.42(e)(1)(ix) either on site or at a 

nearby office, or otherwise make such 

documentation readily available to the 

Director or Regional Administrator upon 

request. 

(f) When must the owner or operator 

of a CAFO seek coverage under an 

NPDES permit? Any CAFO that is 

required to seek permit coverage under 

paragraph (d)(1) of this section must 

seek coverage when the CAFO proposes 

to discharge, unless a later deadline is 

specified below. 

(1) Operations defined as CAFOs prior 

to April 14, 2003. For operations 

defined as CAFOs under regulations 

that were in effect prior to April 14, 

2003, the owner or operator must have 

or seek to obtain coverage under an 

NPDES permit as of April 14, 2003, and 

comply with all applicable NPDES 

requirements, including the duty to 

maintain permit coverage in accordance 

with paragraph (g) of this section. 

(2) Operations defined as CAFOs as of 

April 14, 2003, that were not defined as 

CAFOs prior to that date. For all 

operations defined as CAFOs as of April 

14, 2003, that were not defined as 

CAFOs prior to that date, the owner or 

operator of the CAFO must seek to 

obtain coverage under an NPDES permit 

by February 27, 2009. 

(3) Operations that become defined as 

CAFOs after April 14, 2003, but which 

are not new sources. For a newly 

constructed CAFO and for an AFO that 

makes changes to its operations that 

result in its becoming defined as a 

CAFO for the first time after April 14, 

2003, but is not a new source, the owner 

or operator must seek to obtain coverage 

under an NPDES permit, as follows: 

(i) For newly constructed operations 

not subject to effluent limitations 

guidelines, 180 days prior to the time 

CAFO commences operation; 

(ii) For other operations (e.g., 

resulting from an increase in the 

number of animals), as soon as possible, 

but no later than 90 days after becoming 

defined as a CAFO; or 

(iii) If an operational change that 

makes the operation a CAFO would not 

have made it a CAFO prior to April 14, 

2003, the operation has until February 

27, 2009, or 90 days after becoming 

defined as a CAFO, whichever is later. 

(4) New sources. The owner or 

operator of a new source must seek to 

obtain coverage under a permit at least 

180 days prior to the time that the 

CAFO commences operation. 

(5) Operations that are designated as 

CAFOs. For operations designated as a 

CAFO in accordance with paragraph (c) 

of this section, the owner or operator 

must seek to obtain coverage under a 

permit no later than 90 days after 

receiving notice of the designation. 

(g) Duty to Maintain Permit Coverage. 

No later than 180 days before the 

expiration of the permit, or as provided 

by the Director, any permitted CAFO 

must submit an application to renew its 

permit, in accordance with § 122.21(d), 

unless the CAFO will not discharge or 

propose to discharge upon expiration of 

the permit. 

(h) Procedures for CAFOs seeking 

coverage under a general permit. (1) 

CAFO owners or operators must submit 

a notice of intent when seeking 

authorization to discharge under a 

general permit in accordance with 

§ 122.28(b). The Director must review 

notices of intent submitted by CAFO 

owners or operators to ensure that the 

notice of intent includes the information 

required by § 122.21(i)(1), including a 

nutrient management plan that meets 

the requirements of § 122.42(e) and 

applicable effluent limitations and 

standards, including those specified in 

40 CFR part 412. When additional 

information is necessary to complete the 

notice of intent or clarify, modify, or 

supplement previously submitted 

material, the Director may request such 

information from the owner or operator. 

If the Director makes a preliminary 

determination that the notice of intent 

meets the requirements of 

§§ 122.21(i)(1) and 122.42(e), the 

Director must notify the public of the 

Director’s proposal to grant coverage 

under the permit to the CAFO and make 

available for public review and 

comment the notice of intent submitted 

by the CAFO, including the CAFO’s 

nutrient management plan, and the draft 

terms of the nutrient management plan 

to be incorporated into the permit. The 

process for submitting public comments 

and hearing requests, and the hearing 

process if a request for a hearing is 

granted, must follow the procedures 

applicable to draft permits set forth in 

40 CFR 124.11 through 124.13. The 

Director may establish, either by 

regulation or in the general permit, an 

appropriate period of time for the public 

to comment and request a hearing that 

differs from the time period specified in 

40 CFR 124.10. The Director must 

respond to significant comments 

received during the comment period, as 

provided in 40 CFR 124.17, and, if 

necessary, require the CAFO owner or 

operator to revise the nutrient 

management plan in order to be granted 

permit coverage. When the Director 

authorizes coverage for the CAFO owner 

or operator under the general permit, 

the terms of the nutrient management 

plan shall become incorporated as terms 

and conditions of the permit for the 

CAFO. The Director shall notify the 

CAFO owner or operator and inform the 

public that coverage has been 

authorized and of the terms of the 

nutrient management plan incorporated 

as terms and conditions of the permit 

applicable to the CAFO. 

(2) For EPA-issued permits only. The 

Regional Administrator shall notify each 

person who has submitted written 

comments on the proposal to grant 

coverage and the draft terms of the 

nutrient management plan or requested 

notice of the final permit decision. Such 

notification shall include notice that 

coverage has been authorized and of the 

terms of the nutrient management plan 

incorporated as terms and conditions of 

the permit applicable to the CAFO. 

(3) Nothing in this paragraph (h) shall 

affect the authority of the Director to 

require an individual permit under 

§ 122.28(b)(3). 

(i) No Discharge Certification Option. 

(1) The owner or operator of a CAFO 

that meets the eligibility criteria in 

paragraph (i)(2) of this section may 

certify to the Director that the CAFO 

does not discharge or propose to 

discharge. A CAFO owner or operator 

who certifies that the CAFO does not 

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70482 Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 

discharge or propose to discharge is not 

required to seek coverage under an 

NPDES permit pursuant to paragraph 

(d)(1) of this section, provided that the 

CAFO is designed, constructed, 

operated, and maintained in accordance 

with the requirements of paragraphs 

(i)(2) and (3) of this section, and subject 

to the limitations in paragraph (i)(4) of 

this section. 

(2) Eligibility Criteria. In order to 

certify that a CAFO does not discharge 

or propose to discharge, the owner or 

operator of a CAFO must document, 

based on an objective assessment of the 

conditions at the CAFO, that the CAFO 

is designed, constructed, operated, and 

maintained in a manner such that the 

CAFO will not discharge, as follows: 

(i) The CAFO’s production area is 

designed, constructed, operated, and 

maintained so as not to discharge. The 

CAFO must maintain documentation 

that demonstrates that: 

(A) Any open manure storage 

structures are designed, constructed, 

operated, and maintained to achieve no 

discharge based on a technical 

evaluation in accordance with the 

elements of the technical evaluation set 

forth in 40 CFR 412.46(a)(1)(i) through 

(viii); 

(B) Any part of the CAFO’s 

production area that is not addressed by 

paragraph (i)(2)(i)(A) of this section is 

designed, constructed, operated, and 

maintained such that there will be no 

discharge of manure, litter, or process 

wastewater; and 

(C) The CAFO implements the 

additional measures set forth in 40 CFR 

412.37(a) and (b); 

(ii) The CAFO has developed and is 

implementing an up-to-date nutrient 

management plan to ensure no 

discharge from the CAFO, including 

from all land application areas under 

the control of the CAFO, that addresses, 

at a minimum, the following: 

(A) The elements of § 122.42(e)(1)(i) 

through (ix) and 40 CFR 412.37(c); and 

(B) All site-specific operation and 

maintenance practices necessary to 

ensure no discharge, including any 

practices or conditions established by a 

technical evaluation pursuant to 

paragraph (i)(2)(i)(A) of this section; and 

(iii) The CAFO must maintain 

documentation required by this 

paragraph either on site or at a nearby 

office, or otherwise make such 

documentation readily available to the 

Director or Regional Administrator upon 

request. 

(3) Submission to the Director. In 

order to certify that a CAFO does not 

discharge or propose to discharge, the 

CAFO owner or operator must complete 

and submit to the Director, by certified 

mail or equivalent method of 

documentation, a certification that 

includes, at a minimum, the following 

information: 

(i) The legal name, address and phone 

number of the CAFO owner or operator 

(see § 122.21(b)); 

(ii) The CAFO name and address, the 

county name and the latitude and 

longitude where the CAFO is located; 

(iii) A statement that describes the 

basis for the CAFO’s certification that it 

satisfies the eligibility requirements 

identified in paragraph (i)(2) of this 

section; and 

(iv) The following certification 

statement: ‘‘I certify under penalty of 

law that I am the owner or operator of 

a concentrated animal feeding operation 

(CAFO), identified as [Name of CAFO], 

and that said CAFO meets the 

requirements of 40 CFR 122.23(i). I have 

read and understand the eligibility 

requirements of 40 CFR 122.23(i)(2) for 

certifying that a CAFO does not 

discharge or propose to discharge and 

further certify that this CAFO satisfies 

the eligibility requirements. As part of 

this certification, I am including the 

information required by 40 CFR 

122.23(i)(3). I also understand the 

conditions set forth in 40 CFR 

122.23(i)(4), (5) and (6) regarding loss 

and withdrawal of certification. I certify 

under penalty of law that this document 

and all other documents required for 

this certification were prepared under 

my direction or supervision and that 

qualified personnel properly gathered 

and evaluated the information 

submitted. Based upon my inquiry of 

the person or persons directly involved 

in gathering and evaluating the 

information, the information submitted 

is to the best of my knowledge and 

belief true, accurate and complete. I am 

aware there are significant penalties for 

submitting false information, including 

the possibility of fine and imprisonment 

for knowing violations.’’; and 

(v) The certification must be signed in 

accordance with the signatory 

requirements of 40 CFR 122.22. 

(4) Term of Certification. A 

certification that meets the requirements 

of paragraphs (i)(2) and (i)(3) of this 

section shall become effective on the 

date it is submitted, unless the Director 

establishes an effective date of up to 30 

days after the date of submission. 

Certification will remain in effect for 

five years or until the certification is no 

longer valid or is withdrawn, whichever 

occurs first. A certification is no longer 

valid when a discharge has occurred or 

when the CAFO ceases to meet the 

eligibility criteria in paragraph (i)(2) of 

this section. 

(5) Withdrawal of Certification. (i) At 

any time, a CAFO may withdraw its 

certification by notifying the Director by 

certified mail or equivalent method of 

documentation. A certification is 

withdrawn on the date the notification 

is submitted to the Director. The CAFO 

does not need to specify any reason for 

the withdrawal in its notification to the 

Director. 

(ii) If a certification becomes invalid 

in accordance with paragraph (i)(4) of 

this section, the CAFO must withdraw 

its certification within three days of the 

date on which the CAFO becomes aware 

that the certification is invalid. Once a 

CAFO’s certification is no longer valid, 

the CAFO is subject to the requirement 

in paragraph (d)(1) of this section to 

seek permit coverage if it discharges or 

proposes to discharge. 

(6) Recertification. A previously 

certified CAFO that does not discharge 

or propose to discharge may recertify in 

accordance with paragraph (i) of this 

section, except that where the CAFO has 

discharged, the CAFO may only 

recertify if the following additional 

conditions are met: 

(i) The CAFO had a valid certification 

at the time of the discharge; 

(ii) The owner or operator satisfies the 

eligibility criteria of paragraph (i)(2) of 

this section, including any necessary 

modifications to the CAFO’s design, 

construction, operation, and/or 

maintenance to permanently address the 

cause of the discharge and ensure that 

no discharge from this cause occurs in 

the future; 

(iii) The CAFO has not previously 

recertified after a discharge from the 

same cause; 

(iv) The owner or operator submits to 

the Director for review the following 

documentation: a description of the 

discharge, including the date, time, 

cause, duration, and approximate 

volume of the discharge, and a detailed 

explanation of the steps taken by the 

CAFO to permanently address the cause 

of the discharge in addition to 

submitting a certification in accordance 

with paragraph (i)(3) of this section; and 

(v) Notwithstanding paragraph (i)(4) 

of this section, a recertification that 

meets the requirements of paragraphs 

(i)(6)(iii) and (i)(6)(iv) of this section 

shall only become effective 30 days 

from the date of submission of the 

recertification documentation. 

(j) Effect of certification. (1) An 

unpermitted CAFO certified in 

accordance with paragraph (i) of this 

section is presumed not to propose to 

discharge. If such a CAFO does 

discharge, it is not in violation of the 

requirement that CAFOs that propose to 

discharge seek permit coverage pursuant 

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Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 70483 

to paragraphs (d)(1) and (f) of this 

section, with respect to that discharge. 

In all instances, the discharge of a 

pollutant without a permit is a violation 

of the Clean Water Act section 301(a) 

prohibition against unauthorized 

discharges from point sources. 

(2) In any enforcement proceeding for 

failure to seek permit coverage under 

paragraphs (d)(1) or (f) of this section 

that is related to a discharge from an 

unpermitted CAFO, the burden is on the 

CAFO to establish that it did not 

propose to discharge prior to the 

discharge when the CAFO either did not 

submit certification documentation as 

provided in paragraph (i)(3) or (i)(6)(iv) 

of this section within at least five years 

prior to the discharge, or withdrew its 

certification in accordance with 

paragraph (i)(5) of this section. Design, 

construction, operation, and 

maintenance in accordance with the 

criteria of paragraph (i)(2) of this section 

satisfies this burden. 

■ 6. Section 122.28 is amended by 

adding a new paragraph (b)(2)(vii), to 

read as follows: 

§ 122.28 General permits (applicable to 

State NPDES programs, see § 123.25). 

* * * * * 

(b) * * * 

(2) * * * 

(vii) A CAFO owner or operator may 

be authorized to discharge under a 

general permit only in accordance with 

the process described in § 122.23(h). 

* * * * * 

■ 7. Section 122.42 is amended as 

follows: 

■ a. By revising paragraph (e) 

introductory text and paragraph (e)(1) 

introductory text. 

■ b. By removing the period at the end 

of paragraph (e)(4)(vii) and adding in its 

place ‘‘; and’’. 

■ c. By adding paragraph (e)(4)(viii). 

■ d. By adding paragraphs (e)(5) and 

(e)(6). 

§ 122.42 Additional conditions applicable 

to specified categories of NPDES permits 

(applicable to State NPDES programs, see 

§ 123.25). 

* * * * * 

(e) Concentrated animal feeding 

operations (CAFOs). Any permit issued 

to a CAFO must include the 

requirements in paragraphs (e)(1) 

through (e)(6) of this section. 

(1) Requirement to implement a 

nutrient management plan. Any permit 

issued to a CAFO must include a 

requirement to implement a nutrient 

management plan that, at a minimum, 

contains best management practices 

necessary to meet the requirements of 

this paragraph and applicable effluent 

limitations and standards, including 

those specified in 40 CFR part 412. The 

nutrient management plan must, to the 

extent applicable: 

* * * * * 

(4) * * * 

(viii) The actual crop(s) planted and 

actual yield(s) for each field, the actual 

nitrogen and phosphorus content of the 

manure, litter, and process wastewater, 

the results of calculations conducted in 

accordance with paragraphs (e)(5)(i)(B) 

and (e)(5)(ii)(D) of this section, and the 

amount of manure, litter, and process 

wastewater applied to each field during 

the previous 12 months; and, for any 

CAFO that implements a nutrient 

management plan that addresses rates of 

application in accordance with 

paragraph (e)(5)(ii) of this section, the 

results of any soil testing for nitrogen 

and phosphorus taken during the 

preceding 12 months, the data used in 

calculations conducted in accordance 

with paragraph (e)(5)(ii)(D) of this 

section, and the amount of any 

supplemental fertilizer applied during 

the previous 12 months. 

(5) Terms of the nutrient management 

plan. Any permit issued to a CAFO 

must require compliance with the terms 

of the CAFO’s site-specific nutrient 

management plan. The terms of the 

nutrient management plan are the 

information, protocols, best 

management practices, and other 

conditions in the nutrient management 

plan determined by the Director to be 

necessary to meet the requirements of 

paragraph (e)(1) of this section. The 

terms of the nutrient management plan, 

with respect to protocols for land 

application of manure, litter, or process 

wastewater required by paragraph 

(e)(1)(viii) of this section and, as 

applicable, 40 CFR 412.4(c), must 

include the fields available for land 

application; field-specific rates of 

application properly developed, as 

specified in paragraphs (e)(5)(i) through 

(ii) of this section, to ensure appropriate 

agricultural utilization of the nutrients 

in the manure, litter, or process 

wastewater; and any timing limitations 

identified in the nutrient management 

plan concerning land application on the 

fields available for land application. The 

terms must address rates of application 

using one of the following two 

approaches, unless the Director 

specifies that only one of these 

approaches may be used: 

(i) Linear approach. An approach that 

expresses rates of application as pounds 

of nitrogen and phosphorus, according 

to the following specifications: 

(A) The terms include maximum 

application rates from manure, litter, 

and process wastewater for each year of 

permit coverage, for each crop identified 

in the nutrient management plan, in 

chemical forms determined to be 

acceptable to the Director, in pounds 

per acre, per year, for each field to be 

used for land application, and certain 

factors necessary to determine such 

rates. At a minimum, the factors that are 

terms must include: The outcome of the 

field-specific assessment of the potential 

for nitrogen and phosphorus transport 

from each field; the crops to be planted 

in each field or any other uses of a field 

such as pasture or fallow fields; the 

realistic yield goal for each crop or use 

identified for each field; the nitrogen 

and phosphorus recommendations from 

sources specified by the Director for 

each crop or use identified for each 

field; credits for all nitrogen in the field 

that will be plant available; 

consideration of multi-year phosphorus 

application; and accounting for all other 

additions of plant available nitrogen and 

phosphorus to the field. In addition, the 

terms include the form and source of 

manure, litter, and process wastewater 

to be land-applied; the timing and 

method of land application; and the 

methodology by which the nutrient 

management plan accounts for the 

amount of nitrogen and phosphorus in 

the manure, litter, and process 

wastewater to be applied. 

(B) Large CAFOs that use this 

approach must calculate the maximum 

amount of manure, litter, and process 

wastewater to be land applied at least 

once each year using the results of the 

most recent representative manure, 

litter, and process wastewater tests for 

nitrogen and phosphorus taken within 

12 months of the date of land 

application; or 

(ii) Narrative rate approach. An 

approach that expresses rates of 

application as a narrative rate of 

application that results in the amount, 

in tons or gallons, of manure, litter, and 

process wastewater to be land applied, 

according to the following 

specifications: 

(A) The terms include maximum 

amounts of nitrogen and phosphorus 

derived from all sources of nutrients, for 

each crop identified in the nutrient 

management plan, in chemical forms 

determined to be acceptable to the 

Director, in pounds per acre, for each 

field, and certain factors necessary to 

determine such amounts. At a 

minimum, the factors that are terms 

must include: the outcome of the fieldspecific assessment of the potential for 

nitrogen and phosphorus transport from 

each field; the crops to be planted in 

each field or any other uses such as 

pasture or fallow fields (including 

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70484 Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 

alternative crops identified in 

accordance with paragraph (e)(5)(ii)(B) 

of this section); the realistic yield goal 

for each crop or use identified for each 

field; and the nitrogen and phosphorus 

recommendations from sources 

specified by the Director for each crop 

or use identified for each field. In 

addition, the terms include the 

methodology by which the nutrient 

management plan accounts for the 

following factors when calculating the 

amounts of manure, litter, and process 

wastewater to be land applied: Results 

of soil tests conducted in accordance 

with protocols identified in the nutrient 

management plan, as required by 

paragraph (e)(1)(vii) of this section; 

credits for all nitrogen in the field that 

will be plant available; the amount of 

nitrogen and phosphorus in the manure, 

litter, and process wastewater to be 

applied; consideration of multi-year 

phosphorus application; accounting for 

all other additions of plant available 

nitrogen and phosphorus to the field; 

the form and source of manure, litter, 

and process wastewater; the timing and 

method of land application; and 

volatilization of nitrogen and 

mineralization of organic nitrogen. 

(B) The terms of the nutrient 

management plan include alternative 

crops identified in the CAFO’s nutrient 

management plan that are not in the 

planned crop rotation. Where a CAFO 

includes alternative crops in its nutrient 

management plan, the crops must be 

listed by field, in addition to the crops 

identified in the planned crop rotation 

for that field, and the nutrient 

management plan must include realistic 

crop yield goals and the nitrogen and 

phosphorus recommendations from 

sources specified by the Director for 

each crop. Maximum amounts of 

nitrogen and phosphorus from all 

sources of nutrients and the amounts of 

manure, litter, and process wastewater 

to be applied must be determined in 

accordance with the methodology 

described in paragraph (e)(5)(ii)(A) of 

this section. 

(C) For CAFOs using this approach, 

the following projections must be 

included in the nutrient management 

plan submitted to the Director, but are 

not terms of the nutrient management 

plan: The CAFO’s planned crop 

rotations for each field for the period of 

permit coverage; the projected amount 

of manure, litter, or process wastewater 

to be applied; projected credits for all 

nitrogen in the field that will be plant 

available; consideration of multi-year 

phosphorus application; accounting for 

all other additions of plant available 

nitrogen and phosphorus to the field; 

and the predicted form, source, and 

method of application of manure, litter, 

and process wastewater for each crop. 

Timing of application for each field, 

insofar as it concerns the calculation of 

rates of application, is not a term of the 

nutrient management plan. 

(D) CAFOs that use this approach 

must calculate maximum amounts of 

manure, litter, and process wastewater 

to be land applied at least once each 

year using the methodology required in 

paragraph (e)(5)(ii)(A) of this section 

before land applying manure, litter, and 

process wastewater and must rely on the 

following data: 

(1) A field-specific determination of 

soil levels of nitrogen and phosphorus, 

including, for nitrogen, a concurrent 

determination of nitrogen that will be 

plant available consistent with the 

methodology required by paragraph 

(e)(5)(ii)(A) of this section, and for 

phosphorus, the results of the most 

recent soil test conducted in accordance 

with soil testing requirements approved 

by the Director; and 

(2) The results of most recent 

representative manure, litter, and 

process wastewater tests for nitrogen 

and phosphorus taken within 12 months 

of the date of land application, in order 

to determine the amount of nitrogen and 

phosphorus in the manure, litter, and 

process wastewater to be applied. 

(6) Changes to a nutrient management 

plan. Any permit issued to a CAFO 

must require the following procedures 

to apply when a CAFO owner or 

operator makes changes to the CAFO’s 

nutrient management plan previously 

submitted to the Director: 

(i) The CAFO owner or operator must 

provide the Director with the most 

current version of the CAFO’s nutrient 

management plan and identify changes 

from the previous version, except that 

the results of calculations made in 

accordance with the requirements of 

paragraphs (e)(5)(i)(B) and (e)(5)(ii)(D) of 

this section are not subject to the 

requirements of paragraph (e)(6) of this 

section. 

(ii) The Director must review the 

revised nutrient management plan to 

ensure that it meets the requirements of 

this section and applicable effluent 

limitations and standards, including 

those specified in 40 CFR part 412, and 

must determine whether the changes to 

the nutrient management plan 

necessitate revision to the terms of the 

nutrient management plan incorporated 

into the permit issued to the CAFO. If 

revision to the terms of the nutrient 

management plan is not necessary, the 

Director must notify the CAFO owner or 

operator and upon such notification the 

CAFO may implement the revised 

nutrient management plan. If revision to 

the terms of the nutrient management 

plan is necessary, the Director must 

determine whether such changes are 

substantial changes as described in 

paragraph (e)(6)(iii) of this section. 

(A) If the Director determines that the 

changes to the terms of the nutrient 

management plan are not substantial, 

the Director must make the revised 

nutrient management plan publicly 

available and include it in the permit 

record, revise the terms of the nutrient 

management plan incorporated into the 

permit, and notify the owner or operator 

and inform the public of any changes to 

the terms of the nutrient management 

plan that are incorporated into the 

permit. 

(B) If the Director determines that the 

changes to the terms of the nutrient 

management plan are substantial, the 

Director must notify the public and 

make the proposed changes and the 

information submitted by the CAFO 

owner or operator available for public 

review and comment. The process for 

public comments, hearing requests, and 

the hearing process if a hearing is held 

must follow the procedures applicable 

to draft permits set forth in 40 CFR 

124.11 through 124.13. The Director 

may establish, either by regulation or in 

the CAFO’s permit, an appropriate 

period of time for the public to 

comment and request a hearing on the 

proposed changes that differs from the 

time period specified in 40 CFR 124.10. 

The Director must respond to all 

significant comments received during 

the comment period as provided in 40 

CFR 124.17, and require the CAFO 

owner or operator to further revise the 

nutrient management plan if necessary, 

in order to approve the revision to the 

terms of the nutrient management plan 

incorporated into the CAFO’s permit. 

Once the Director incorporates the 

revised terms of the nutrient 

management plan into the permit, the 

Director must notify the owner or 

operator and inform the public of the 

final decision concerning revisions to 

the terms and conditions of the permit. 

(iii) Substantial changes to the terms 

of a nutrient management plan 

incorporated as terms and conditions of 

a permit include, but are not limited to: 

(A) Addition of new land application 

areas not previously included in the 

CAFO’s nutrient management plan. 

Except that if the land application area 

that is being added to the nutrient 

management plan is covered by terms of 

a nutrient management plan 

incorporated into an existing NPDES 

permit in accordance with the 

requirements of paragraph (e)(5) of this 

section, and the CAFO owner or 

operator applies manure, litter, or 

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Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 70485 

process wastewater on the newly added 

land application area in accordance 

with the existing field-specific permit 

terms applicable to the newly added 

land application area, such addition of 

new land would be a change to the new 

CAFO owner or operator’s nutrient 

management plan but not a substantial 

change for purposes of this section; 

(B) Any changes to the field-specific 

maximum annual rates for land 

application, as set forth in paragraphs 

(e)(5)(i) of this section, and to the 

maximum amounts of nitrogen and 

phosphorus derived from all sources for 

each crop, as set forth in paragraph 

(e)(5)(ii) of this section; 

(C) Addition of any crop or other uses 

not included in the terms of the CAFO’s 

nutrient management plan and 

corresponding field-specific rates of 

application expressed in accordance 

with paragraph (e)(5) of this section; and 

(D) Changes to site-specific 

components of the CAFO’s nutrient 

management plan, where such changes 

are likely to increase the risk of nitrogen 

and phosphorus transport to waters of 

the U.S. 

(iv) For EPA-issued permits only. 

Upon incorporation of the revised terms 

of the nutrient management plan into 

the permit, 40 CFR 124.19 specifies 

procedures for appeal of the permit 

decision. In addition to the procedures 

specified at 40 CFR 124.19, a person 

must have submitted comments or 

participated in the public hearing in 

order to appeal the permit decision. 

■ 8. Section 122.62 is amended by 

adding paragraph (a)(17) to read as 

follows: 

§ 122.62 Modification or revocation and 

reissuance of permits (applicable to State 

programs, see § 123.25) 

* * * * * 

(a) * * * 

(17) Nutrient Management Plans. The 

incorporation of the terms of a CAFO’s 

nutrient management plan into the 

terms and conditions of a general permit 

when a CAFO obtains coverage under a 

general permit in accordance with 

§§ 122.23(h) and 122.28 is not a cause 

for modification pursuant to the 

requirements of this section. 

* * * * * 

■ 9. Section 122.63 is amended by 

adding paragraph (h) to read as follows: 

§ 122.63 Minor modification of permits. 

* * * * * 

(h) Incorporate changes to the terms of 

a CAFO’s nutrient management plan 

that have been revised in accordance 

with the requirements of § 122.42(e)(6). 

PART 412—CONCENTRATED ANIMAL 

FEEDING OPERATIONS (CAFO) POINT 

SOURCE CATEGORY 

■ 10. The authority citation for part 412 

continues to read as follows: 

Authority: 33 U.S.C. 1311, 1314, 1316, 

1317, 1318, 1342, and 1361. 

■ 11. Section 412.37 is amended by 

revising paragraph (a)(2) to read as 

follows: 

§ 412.37 Additional measures. 

(a) * * * 

(2) Depth marker. All open surface 

liquid impoundments must have a 

depth marker which clearly indicates 

the minimum capacity necessary to 

contain the runoff and direct 

precipitation of the 25-year, 24-hour 

rainfall event. In the case of new sources 

subject to effluent limitations 

established pursuant to § 412.46(a)(1) of 

this part, all open surface manure 

storage structures associated with such 

sources must include a depth marker 

which clearly indicates the minimum 

capacity necessary to contain the 

maximum runoff and direct 

precipitation associated with the design 

storm used in sizing the impoundment 

for no discharge. 

■ 12. Section 412.46 is amended by 

revising paragraphs (a)(1), (d), and (e) to 

read as follows: 

§ 412.46 New source performance 

standards (NSPS). 

* * * * * 

(a) * * * 

(1) Any CAFO subject to this subpart 

may request that the Director establish 

NPDES permit best management 

practice effluent limitations designed to 

ensure no discharge of manure, litter, or 

process wastewater based upon a sitespecific evaluation of the CAFO’s open 

surface manure storage structure. The 

NPDES permit best management 

practice effluent limitations must 

address the CAFO’s entire production 

area. In the case of any CAFO using an 

open surface manure storage structure 

for which the Director establishes such 

effluent limitations, ‘‘no discharge of 

manure, litter, or process wastewater 

pollutants,’’ as used in this section, 

means that the storage structure is 

designed, operated, and maintained in 

accordance with best management 

practices established by the Director on 

a site-specific basis after a technical 

evaluation of the storage structure. The 

technical evaluation must address the 

following elements: 

(i) Information to be used in the 

design of the open manure storage 

structure including, but not limited to, 

the following: minimum storage periods 

for rainy seasons, additional minimum 

capacity for chronic rainfalls, applicable 

technical standards that prohibit or 

otherwise limit land application to 

frozen, saturated, or snow-covered 

ground, planned emptying and 

dewatering schedules consistent with 

the CAFO’s Nutrient Management Plan, 

additional storage capacity for manure 

intended to be transferred to another 

recipient at a later time, and any other 

factors that would affect the sizing of 

the open manure storage structure. 

(ii) The design of the open manure 

storage structure as determined by the 

most recent version of the National 

Resource Conservation Service’s Animal 

Waste Management (AWM) software. 

CAFOs may use equivalent design 

software or procedures as approved by 

the Director. 

(iii) All inputs used in the open 

manure storage structure design 

including actual climate data for the 

previous 30 years consisting of 

historical average monthly precipitation 

and evaporation values, the number and 

types of animals, anticipated animal 

sizes or weights, any added water and 

bedding, any other process wastewater, 

and the size and condition of outside 

areas exposed to rainfall and 

contributing runoff to the open manure 

storage structure. 

(iv) The planned minimum period of 

storage in months including, but not 

limited to, the factors for designing an 

open manure storage structure listed in 

paragraph (a)(1)(i) of this section. 

Alternatively the CAFO may determine 

the minimum period of storage by 

specifying times the storage pond will 

be emptied consistent with the CAFO’s 

Nutrient Management Plan. 

(v) Site-specific predicted design 

specifications including dimensions of 

the storage facility, daily manure and 

wastewater additions, the size and 

characteristics of the land application 

areas, and the total calculated storage 

period in months. 

(vi) An evaluation of the adequacy of 

the designed manure storage structure 

using the most recent version of the Soil 

Plant Air Water (SPAW) Hydrology 

Tool. The evaluation must include all 

inputs to SPAW including but not 

limited to daily precipitation, 

temperature, and evaporation data for 

the previous 100 years, user-specified 

soil profiles representative of the 

CAFO’s land application areas, planned 

crop rotations consistent with the 

CAFO’s Nutrient Management Plan, and 

the final modeled result of no overflows 

from the designed open manure storage 

structure. For those CAFOs where 100 

years of local weather data for the 

CAFO’s location is not available, CAFOs 

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70486 Federal Register / Vol. 73, No. 225 / Thursday, November 20, 2008 / Rules and Regulations 

may use a simulation with a confidence 

interval analysis conducted over a 

period of 100 years. The Director may 

approve equivalent evaluation and 

simulation procedures. 

(vii) The Director may waive the 

requirement of (a)(1)(vi) for a sitespecific evaluation of the designed 

manure storage structure and instead 

authorize a CAFO to use a technical 

evaluation developed for a class of 

specific facilities within a specified 

geographical area. 

(viii) Waste management and storage 

facilities designed, constructed, 

operated, and maintained consistent 

with the analysis conducted in 

paragraphs (a)(1)(i) through (a)(1)(vii) of 

this section and operated in accordance 

with the additional measures and 

records required by § 412.47(a) and (b), 

will fulfill the requirements of this 

section. 

(ix) The Director has the discretion to 

request additional information to 

support a request for effluent limitations 

based on a site-specific open surface 

manure storage structure. 

* * * * * 

(d) Any source subject to this subpart 

that commenced discharging after April 

14, 1993, and prior to April 14, 2003, 

which was a new source subject to the 

standards specified in § 412.15, revised 

as of July 1, 2002, must continue to 

achieve those standards for the 

applicable time period specified in 40 

CFR 122.29(d)(1). Thereafter, the source 

must achieve the standards specified in 

§ 412.43(a) and (b). 

(e) Any source subject to this subpart 

that commenced discharging after April 

14, 2003, and prior to January 20, 2009, 

which was a new source subject to the 

standards specified in § 412.46(a) 

through (d) in the July 1, 2008, edition 

of 40 CFR part 439, must continue to 

achieve those standards for the 

applicable time period specified in 40 

CFR 122.29(d)(1). 

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

BILLING CODE 6560–50–P