Regulatory Flexibility Act Section 610 Review of the

National Pollutant Discharge Elimination System (NPDES) Permit Regulation and Effluent 

Limitation Guidelines and Standards for Concentrated Animal Feeding Operations (CAFOs)

United States Environmental Protection Agency

Office of Water

June 3, 2014 

1 
Results of Section 610 Review of the National Pollutant Discharge Elimination System Regulations 

and Effluent Limitation Guidelines and Standards for Concentrated Animal Feeding Operations

Summary

The U.S. Environmental Protection Agency (EPA) completed its review of the 2003 National Pollutant 

Discharge Elimination System (NPDES) Permit Regulation and Effluent Limitation Guidelines (ELG)

and Standards for Concentrated Animal Feeding Operations (CAFOs) (the “2003 CAFO Rule”), 

pursuant to Section 610 of the Regulatory Flexibility Act (RFA). Section 610 of the RFA requires that 

an agency review, within 10 years of promulgation, each regulation that was determined to have, or will 

have, a significant economic impact on a substantial number of small entities. The EPA undertakes 

Section 610 reviews to determine whether a rule’s provisions as they relate to small entities should be 

continued unchanged, amended, or withdrawn. Upon completion of this review, the EPA has concluded 

that revisions or amendments to minimize economic impacts on small entities from the CAFO 

regulations are not warranted at this time.

The EPA promulgated the 2003 CAFO Rule on February 12, 2003.1 This rule expanded the number of 

operations covered by the CAFO regulations, required all CAFOs to seek NPDES permit coverage, and 

included requirements to address the land application of manure from CAFOs. There have been two 

revisions to the regulations since 2003, which were finalized in 2008 and 2012. These revisions were 

due to court decisions based on a legal challenge to the 2003 rulemaking, and then a challenge to the 

2008 rulemaking. 

The EPA initiated its Section 610 review of the 2003 CAFO Rule’s impact on small entities on October 

31, 2012.2

 The EPA solicited and considered comments on the following factors: (1) the continued need 

for the rule; (2) the nature of complaints or comments received from the public concerning the rule; 

(3) the complexity of the rule; (4) the extent to which the rule overlaps, duplicates, or conflicts with 

other federal, state, or local government rules; and (5) the degree to which technology, economic 

conditions, or other factors have changed in the area affected by the rule since promulgation. The public 

comment period was scheduled originally to end on December 31, 2012, but was extended to March 1, 

2013, in response to requests received for additional time to submit comments. 3

The EPA received 211 comment letters, which are available in the docket at www.regulations.gov, 

Docket ID number EPA-HQ-OW-2012-0813. Many comments received fell outside the scope of the 

review process required under Section 610 of the RFA for the 2003 CAFO Rule. Many of these 

comments discussed the 2008 or 2012 revisions to the CAFO regulations. Although the Section 610 

review only needs to address the 2003 CAFO Rule, the EPA exercised its discretion to consider relevant 

comments on the 2008 and 2012 regulation revisions. Much of the CAFO program’s implementation 

since 2003 has been affected by these revisions and/or the decisions of the Second Circuit Court of 

Appeals in Waterkeeper Alliance v. EPA,

4 and the Fifth Circuit Court of Appeals, in National Pork 

Producers Council v. EPA, 5 which led to those regulatory revisions. 

1

 68 Fed. Reg. 7,175. 

2

 77 Fed. Reg. 65,840. 

3 78 Fed. Reg. 277.

4 Waterkeeper Alliance et al. v. EPA, 399 F.3d 486 (2d Cir. 2005). 

5 National Pork Producers Council v. EPA, 635 F.3d 738 (5th Cir. 2011). 

2 

 
Pursuant to Section 610 of the RFA, the EPA reviewed the CAFO regulations to determine if they 

should be continued without change, or should be rescinded or amended to minimize adverse economic 

impacts on small entities. In promulgating the 2003 CAFO Rule, the EPA developed a Final Regulatory 

Flexibility Analysis and took several steps to minimize impacts on small businesses, including 

regulatory revisions designed to focus on the largest producers. The Agency provided a detailed 

assessment of economic impacts of the regulations on small businesses as part of the 2003 and 2008 

economic analyses and determined that the requirements were economically feasible for small 

businesses. In examining the burdens of the CAFO regulations on small entities during this Section 610 

review, the EPA also revisited the administrative burden analyses performed for the NPDES CAFO 

rulemakings since 2003, which showed that the overall burden on regulated facilities decreased. 

Upon completing this review, the Agency has concluded that there is a continued need for the CAFO 

regulations, and that the comments received did not demonstrate that revisions are necessary at this time 

to minimize impacts on small entities. The results of the Section 610 review of the 2003 CAFO Rule are 

presented in this report, which has been placed in the docket. 

3 
Discussion of Factors Required by Section 610 of the Regulatory Flexibility Act

1. Continued need for the rule. 

Many commenters supported a continued need for the rule and/or regulations. Some commenters called 

for increased regulation of CAFOs. Most of these comments referenced a need for clean water and many 

expressed concerns about increased manure production at CAFOs; bacteria and nutrients from farm 

runoff; and resulting risks to water quality (ground water, surface water, aquifers), air quality, and public 

health. Some commenters voiced concerns regarding bacterial resistance due to increased use of 

antibiotics at CAFOs. A commenter stated that CAFOs should not be allowed to generate more waste 

than can be absorbed by the land. A commenter referenced the EPA’s preamble to its 2003 CAFO Rule 

in noting that industry consolidation is leading to a greater concentration of nutrients on an inadequate 

land base, and that there is a trend toward increased reports of large discharges. Some commenters noted 

that the EPA has a responsibility to regulate pollution from CAFOs. One commenter stated that the 2003 

CAFO Rule is needed to ensure CAFO discharges meet the Clean Water Act (CWA) objectives and, in 

fact, it should be strengthened to fulfill the requirements of the CWA and address continued water 

quality impairments. 

Several commenters correlated weakened permitting requirements on CAFOs with negative economic 

impacts on other types of small farms and businesses. For example, a number of non-industry small 

business owners supported continued regulation of CAFOs, stating that their livelihoods depend on 

clean water resources and a clean environment, which they say are or would be adversely affected by 

manure production at CAFOs. Many non-regulated small businesses such as restaurants supported 

regulation of CAFOs because their businesses depend on clean crops; one mentioned it could not afford 

technology to irradiate produce contaminated with pathogens. Several commenters supported regulation 

of CAFOs due to potential negative impacts on surrounding property values. Some commenters stated 

that CAFOs need to be regulated, even if they are classified as “small businesses.” 

State commenters supported continuing regulation with specific enhancements, and suggested that the 

development of state programs that are more comprehensive than federal requirements was accelerated 

by the EPA’s establishment of the “federal floor.”

The EPA agrees with the general view of many commenters that there is a continued need for the 2003 

CAFO Rule, as revised in 2008 and 2012, to ensure protection of the nation’s water quality. The purpose 

of the CWA is “to restore and maintain the chemical, physical and biological integrity of the nation’s 

waters.”6 CWA Section 402(a) establishes the NPDES program to regulate the discharge of any 

pollutant from point sources into waters of the United States.7 As discussed in the preamble to the 2003 

CAFO Rule, the rule was promulgated to “ensure that CAFOs take appropriate actions to manage 

manure effectively in order to protect the nation’s water quality.”8

Since promulgation of the 2003 CAFO Rule, the EPA has found that research supports a continued need 

for the regulation of CAFOs. As discussed in the preamble to the 2011 Proposed NPDES CAFO 

Reporting Rule, “[d]espite more than 35 years of regulating CAFOs, reports of water quality impacts 

from large animal feeding operations persist.”9 In 2013 the EPA published a Literature Review of 

6

 33 U.S.C. 1251(a). 

7

 33 U.S.C. 1342(a). 

8

 68 Fed. Reg. 7,176. 

9

 76 Fed. Reg. 65,433. 

4 

 
Contaminants in Livestock and Poultry Manure and Implications for Water Quality, as part of the 

Agency’s ongoing efforts to better understand the environmental occurrence and potential water quality 

effects related to contaminants of emerging concern in animal manure.

10 Given the potential impacts 

from contaminants of emerging concern such as pathogens, viruses, antimicrobials, heavy metals, and 

hormones, effectively managing manure is critical to protecting water quality, the environment, and 

human health. 

Based on the U.S. Department of Agriculture’s (USDA’s) Census of Agriculture data and standard 

USDA methods, an estimated 2.2 billion head of livestock and poultry generated approximately 1.1 

billion tons of manure in 2007.11 CAFOs will commonly apply manure, litter, and process wastewater as 

fertilizer to crops on-site or transfer it to be applied to crops in other locations because they can provide 

value as fertilizer; however, manure can degrade the environment and surface water and ground water 

quality if it is not managed properly.12 When manure is over-applied to land, or applied to land before 

precipitation events, excess nutrients can run off and cause harmful aquatic plant growth (i.e., “algal 

blooms”) which can contribute to low dissolved oxygen, fish kills, or release of toxins that are harmful 

to human health.13 A continued trend toward fewer but larger operations has concentrated more manure 

nutrients, which, in some geographic areas, can exceed the amount of nutrients needed by the farmland 

around where that manure is produced.14 This trend has coincided with increased reports of large-scale 

discharges from CAFOs, as well as continued runoff that has contributed to the significant increase in 

nutrients and resulting impairment of many U.S. water bodies.15

Regulations requiring adequate storage of manure, litter, and process wastewater, including proper 

operation and maintenance of the storage facilities, are an important step in protecting water quality. 

Ensuring adequate storage capacity for manure enables operators to store manure during times of the 

year when no crops are growing and avoid applying manure on frozen or snow-covered ground, 

immediately before, during, or after precipitation events, or when the land is saturated.

16 Manure storage 

enables confined operations to better implement their nutrient management plans (NMPs) and apply 

manure to address crop needs.17 Storing manure for extended periods of time may also minimize 

pathogen loads and promote degradation or adsorption of antimicrobials and hormones.18

10 U.S. EPA, Literature Review of Contaminants in Livestock and Poultry Manure and Implications for 

Water Quality, EPA 820-R-13-002 v (2013), http://water.epa.gov/scitech/cec/upload/Literature-Reviewof-Contaminants-in-Livestock-and-Poultry-Manure-and-Implications-for-Water-Quality.pdf. 11 USDA, 2007 Census of Agriculture: United States Summary and State Data AC-07-A-51, Volume 1 

(2009), available at http://www.agcensus.usda.gov/Publications/2007/Full_Report/usv1.pdf. 12 76 Fed. Reg. 65,434. 

13 Id.

14 68 Fed. Reg. 7,180; Noel Gollenhon et al., USDA Economic Research Service, Confined Animal 

Production and Manure Nutrients, Agricultural Information Bulletin No. 771 (2001). 

15 68 Fed. Reg. 7,180. 

16 Z. Zhao et al., Hormones in Waste from Concentrated Animal Feeding Operations in D.S. Aga (ed.) 

Fate and Transport of Pharmaceuticals in the Environment and Water Treatment Systems, 1st ed. 291–

329 (2008). 

17 Id.

18 L. S. Shore et al., Relationship of Fertilization with Chicken Manure and Concentration of Estrogens 

in Small Streams in K. Steele (ed.) Animal Waste and the Land-Water Interface 152–162 (1995); L. S. 

Lee et al., Agricultural Contributions of Antimicrobials and Hormones on Soil and Water Quality, 93 

Adv Agron 1–68 (2007).

5 

 
The EPA acknowledges that water quality impacts from CAFOs may be due, in part, to inadequate 

compliance with existing regulations or due to limitations in CAFO permitting programs.

19 The Agency 

has determined that there is a continued need for regulation to protect the nation’s water quality. 

Although many commenters also supported a continued need for the rule, a number of commenters 

suggested that the EPA should improve specific aspects of the CAFO regulations. Such comments have 

been summarized in the sections that follow. 

2. Nature of complaints or comments received concerning the rule. 

In promulgating the CAFO regulations, the EPA considered impacts on small entities. The 

recordkeeping, reporting, and monitoring requirements of the CAFO regulations remain economically 

achievable and necessary to ensure protection of water quality and demonstrate compliance with 

technical requirements of the CAFO regulations. As discussed below, the Agency promulgated certain 

requirements in order to comply with court decisions, but attempted to afford owners and operators as 

much flexibility as possible by allowing for consideration of site-specific variations in the NPDES 

CAFO permits.

Court decisions since the 2003 CAFO Rule, in Waterkeeper Alliance v. EPA20 and National Pork 

Producers Council v. EPA21 led to revisions of the CAFO regulations in 2008 and 2012 that eliminated 

burdens for many CAFOs.

22 The 2011 decision by the U.S. Court of Appeals for the Fifth Circuit 

vacated the requirement that CAFOs that “discharge or propose to discharge” seek NPDES permit 

coverage and ruled instead that only those CAFOs that discharge need permits.23 The resulting projected 

decline in NPDES CAFO permittees was estimated to result in a reduction in administrative burden for 

CAFOs and state permitting authorities.24

In examining the burdens of the CAFO regulations on small entities during this review, the EPA 

revisited the administrative burden analyses performed for the NPDES CAFO rulemakings since 2003. 

In its 2013 Information Collection Request for Animal Sectors (analyses completed as part of meeting 

the requirements of the Paperwork Reduction Act and reviewed and approved by the Office of 

Management and Budget), the Agency analyzed the cost and impacts associated with recordkeeping, 

reporting, and monitoring requirements. The analyses showed that the overall burden on regulated 

facilities decreased because there was no substantive increase in technical requirements subsequent to 

the issuance of the 2003 CAFO Rule, and because the percentage of permitted entities declined based on 

the 2008 and 2012 revisions to the regulations.25

The EPA has organized comments received pertaining to this topic of the review under four main 

categories of issues, as outlined below: (1) programmatic, (2) economic, (3) technical, and (4) 

implementation.

19 76 Fed. Reg. 65,434. 

20 399 F.3d 486. 21 635 F.3d 738. 

22 40 CFR 122.23(b)(6), (b)(9), (c).

23 635 F.3d 738 at 756. 

24 U.S. EPA, Information Collection Request for Animal Sectors, OMB Control No. 2040-0250, 

EPA ICR No. 1989.08 23–38 (2013). 

25 Id. at 23. 

6 

 
• Programmatic Issues

Most commenters who discussed programmatic requirements of the CAFO regulations suggested that 

burdens associated with permit applications, recordkeeping, reporting, or public noticing should be 

decreased.

A state commented about the relevancy of some of the information required on NPDES permit 

application forms to permitted activities, and suggested that states could collect it under existing state 

authorities if needed. The EPA notes that permit applications are the primary mechanisms to ensure that 

NPDES permits are adequately protective of the requirements of the CWA, and permitting authorities 

need the information required under the NPDES CAFO regulations to implement CWA requirements.26

The EPA notes that in the administrative burden analysis performed by the Agency and approved by the 

Office of Management and Budget under the terms of the Paperwork Reduction Act, the EPA assumed 

that completing the NPDES CAFO permit application form would result in a 9-hour labor burden.27 This 

burden is comparatively minor because it occurs only every 5 years when the permit is renewed and it 

represents a small fraction of the overall compliance costs associated with implementing the manure 

storage, handling, and land application requirements called for elsewhere in the permitting regulations. 

Another commenter indicated that documenting weather conditions at the time of, and 24 hours before 

and after, land application of manure is overly burdensome and the data are likely to be inaccurate. The 

EPA requires this information because of its importance in determining whether manure has been 

applied in accordance with timing limitations set by the permitting authority outweighs the burden of 

documenting the information. Such regulatory requirements are reasonable and necessary for effective 

program implementation, given the direct relationship of precipitation to discharges from CAFOs that 

occur as a result of land application. 

Some commenters stated that requiring producers to document daily inspections of water lines is 

unnecessary because producers are already motivated to detect and fix water leaks and overflows in the 

production area daily, and recordkeeping of these normal activities is excessively burdensome and not 

beneficial. Another commenter stated more generally that the 2003 CAFO Rule’s daily and weekly 

recordkeeping requirements for NMPs are not manageable for most farmers. The EPA carefully 

considered the reporting requirements and analyzed the cost and impacts associated with these 

requirements. As stated in the preamble to the 2003 CAFO Rule: “Production area inspection data allow 

operators to actively manage and maintain their surface and liquid impoundments to ensure the 

structural integrity of the system and avoid catastrophic failure of such systems. These records also 

assist the CAFO operator to minimize discharges to the extent possible and demonstrate that any 

overflows that do occur are consistent with the proper operation and maintenance of storage structures to 

contain all process wastewater including the runoff from a 25-year, 24-hour rainfall event.”28 Based on 

the EPA’s analysis, the recordkeeping, reporting, and monitoring requirements of the CAFO regulations 

are economically achievable for the reasons discussed in the 2003 CAFO Rule and its supporting 

documents, and they continue to be necessary to ensure protection of water quality and demonstrate 

compliance with technical requirements of the CAFO regulations.

State commenters criticized the reporting, public notice, and recordkeeping requirements of the CAFO 

regulations that were revised in the 2008 CAFO Rule. Some commenters requested revisions to annual 

reporting requirements, including elimination of requirements for operators to report soil test results and 

26 Id. at 2. 

27 Id. at 26. 

28 68 Fed. Reg. 7,176 and 7,216. 

7 

 
data used in calculating manure application rates, in order to reduce burdens on states and producers and 

be consistent with other NPDES programs. The EPA notes that the Second Circuit Court of Appeals 

held that the terms of a CAFO’s NMP are effluent limitations subject to public review, consistent with 

the requirements of the CWA.

29 In order to comply with the Second Circuit’s holding while affording 

CAFO owners and operators maximum flexibility to make adjustments consistent with the terms of the 

NMP during the period of permit coverage, the EPA developed the narrative rate approach. As discussed 

in the preamble to the 2008 CAFO Rule, the annual reporting requirements of the CAFO regulations 

established in the 2008 CAFO Rule revisions are necessary to allow the flexibility afforded by the rule 

for CAFOs that land apply manure and wish to take advantage of the narrative rate approach. See, for 

example, 73 Fed. Reg. 70,449–70,450 regarding use of annual reports as a check on the narrative rate 

approach. The 2008 CAFO Rule added these annual reporting requirements as an essential step in 

implementing the narrative rate approach, so as to ensure public availability of information directly 

related to the terms of the NMP.

Several commenters stated that the public notice requirements for site-specific NMPs in the 2008 CAFO 

Rule is burdensome for producers and diminishes the benefits of general permits, which generally do not 

require facilities to undergo individual public notice processes. The EPA notes that for many types of 

permitted facilities, one of the benefits of using general permits to cover multiple facilities is a 

streamlined permit issuance process. However, the individual public notice requirements for the sitespecific terms of the NMP included in the general permitting process for CAFOs, as modified in the 

2008 CAFO Rule, were promulgated in response to the Second Circuit Court of Appeals decision in 

Waterkeeper Alliance v. EPA, which found that the terms of a CAFO’s NMP are effluent limitations 

subject to public review, as required by the CWA.30

A state commenter indicated that the complexity of nutrient management planning, recordkeeping, and 

reporting requirements, as well as increased public notice requirements in the 2008 CAFO Rule 

revisions are especially burdensome to small and medium animal feeding operations (AFOs), and are 

likely to cause those operations that voluntarily comply with a general permit to discontinue permit 

coverage, thereby reducing environmental protection. The EPA notes that small and medium AFOs are 

not required to apply for permits unless they are defined or designated as CAFOs, and that small and 

medium facilities may be defined or designated as CAFOs only if they discharge (and other specified 

criteria are satisfied). Moreover, small and medium CAFOs may, depending on circumstances, take 

steps to eliminate discharges and obviate the need for permits. The federal CAFO regulations do not 

impose requirements on small or medium AFOs that are not CAFOs. 

A state commenter recommended that that the process to make changes to NMPs should not prioritize 

public notification over technically sound NMP implementation. The commenter suggested that 

facilities should be allowed flexibility in how they meet the technical standards. The commenter 

suggested that states could require CAFOs to consult with certified planners prior to adjusting NMPs to 

ensure technical standards are met, and that certified planners should be viewed as a mechanism to both 

improve compliance by regulated entities and reduce burdens on states to review every NMP 

modification. The EPA notes that the CAFO regulations do not prioritize public notification over 

technically sound implementation. On the contrary, the CAFO regulations specify the many conditions 

that must be addressed to ensure technically sound implementation of an NMP. One purpose of the 

public notice process is to ensure that the terms of an NMP included in a permit will result in the NMP 

being implemented in a technically sound manner. Moreover, the regulations do not prohibit states from 

29 399 F.3d 486 at 502–503. 

30 Id.

8 

 
allowing or requiring the use of certified planners. In fact, the EPA strongly supports the use of certified 

planners in the development of NMPs and subsequent revisions to NMPs. Public notice of NMPs is 

consistent with the decision by the Second Circuit Court of Appeals, in Waterkeeper Alliance v. EPA, 

which found that the terms of a CAFO’s NMP are effluent limitations subject to public review, as 

required by the CWA.31 The EPA developed the narrative rate approach to allow CAFO operators 

maximum flexibility to anticipate adjustments that may be required during the course of implementing 

an NMP, and to make adjustments consistent with the terms of the NMP during the period of permit 

coverage, without the need for permit modification and a formal public notice process. 

A commenter supported flexibility for restricting land application of manure during winter months. The 

EPA notes that the regulations do not specifically address winter application; however, the regulations 

do require that manure, litter, and process wastewater be land applied in accordance with nutrient 

management practices that ensure appropriate agricultural utilization of manure nutrients. In applying 

this consideration, a number of states have prohibited or limited land application to frozen, saturated, or 

snow-covered ground or during winter months. 

A commenter suggested that all poultry operations be required to obtain permits, regardless of size or 

location. The EPA notes that the CAFO regulations apply to only CAFOs because the CWA defines 

CAFOs as point sources. Not all poultry operations are defined or designated as CAFOs. Moreover, the 

Fifth Circuit Court held in National Pork Producers Council v. EPA that only CAFOs that discharge 

must have NPDES permits.32

A commenter suggested that the CAFO regulations be tailored to specific types of animals or operations 

in order to minimize negative impacts on operations that were not intended to be addressed by the 

regulations. The EPA notes that the CAFO regulations are, in fact, tailored to different types of 

operations as well as to consideration of site-specific variations. For example, the regulations require 

development of site-specific NMPs and associated permit terms. In addition, the CAFO ELGs are 

sector-specific and are applicable based on the number and type (e.g., horses, ducks, dairy cattle, beef 

cattle, swine, and poultry) of animals produced. The EPA has no knowledge of negative economic 

impacts on unregulated facilities resulting from the CAFO regulations. Secondary impacts are not 

considered relevant within economic analyses for rules or the rule development process.

• Economic Issues

This section summarizes comments received regarding economic issues related to the rule.

A commenter stated that since elimination of the rule is not likely, the EPA should review the rule with 

consideration of the ability of agriculture operations to comply without going out of business. Another 

commenter did not challenge the need for regulation but generally stated that CAFOs are over-regulated 

and requested that the rule be revised with consideration for the economic impact of heavy regulation of 

small businesses. Some commenters suggested that the EPA should review or revise the rule with 

consideration for economic impacts on small businesses. Conversely, a commenter felt that the EPA has 

sufficiently minimized the impact of its CAFO rules on small businesses. The EPA provided a detailed 

assessment of economic impacts of the rule on small businesses as part of the 2003 and 2008 economic 

analyses and determined that the requirements were economically feasible for small businesses. None of 

the changes to the CWA CAFO regulations since 2003 involved revisions to the ELG requirements, nor 

have they required any new capital expenditures for permittees. Rather, the regulatory changes that the 

31 Id.

32 635 F.3d 738 at 751. 

9 

 
EPA finalized in response to litigation have yielded a net burden reduction to CAFO owners and 

operators, including small business owners and operators, since now only those operations with 

discharges are required to seek NPDES permit coverage. The EPA finds that the CAFO regulations have 

not had a direct economic impact on the vast majority of small- and medium-sized operations, as few 

medium AFOs have NPDES permits, and even fewer small AFOs have NPDES permit coverage.

Some commenters did not challenge the need for regulation or explicitly request eliminating it, but 

expressed general support for the EPA to review or revise the regulations with consideration for the 

economic impact of regulation of small businesses. The EPA did consider the economic impacts of the 

CAFO regulations on small entities as part of the 2003 and 2008 economic analyses, and reviewed such 

impacts as part of the Section 610 review.

A commenter stated that, by limiting the universe of operations required to apply for CAFO permits, the 

2008 and 2012 rules reduced the potential economic impact of the regulations on all CAFOs, including 

those that would be considered small entities. As noted above, the EPA has made the same 

determination.

A commenter stated that the 2003 CAFO Rule has resulted in a significant cost to the U.S. cattle feeding 

industry. The commenter stated that the number of smaller beef operations has declined since 2003, and 

further indicated that the CAFO regulations have exacerbated consolidation of small- and medium-sized 

operations, and that high costs of compliance have made it difficult to enter the industry or expand 

existing operations. The EPA notes that NPDES CAFO permits usually are issued only to cattle feedlots 

with more than 1,000 head of cattle. As previously noted, small and medium AFOs are not required to 

apply for permits unless they are defined or designated as CAFOs. Small and medium facilities may 

only be defined or designated as CAFOs if they discharge. Per a comparison with the Small Business 

Administration’s definitions of small entities, most medium and small CAFOs are small entities and 

some large CAFOs will be small entities as well. Broadly, CAFO ELG requirements apply to large 

CAFOs, and permitting authorities, which are mainly state agencies, will establish technology-based 

limitations and standards for small and medium CAFOs on the basis of best professional judgment.33

Based on USDA Census of Agriculture data, the EPA estimates that there are a total of 212,000 AFOs in 

the United States.34 Of the approximately 6,600 NPDES permits issued to CAFOs, the vast majority are 

held by large CAFOs. Few medium AFOs are permitted, and even fewer small AFOs have permit 

coverage. Thus, the EPA has determined that the CAFO regulations do not have a direct economic 

impact on the vast majority of small- and medium-sized operations or an impact on the industry as a 

whole. 

A commenter requested that permit fees for CAFOs be controlled. Permit fees are established by state 

permitting authorities, and not by the federal CAFO regulations. The EPA notes that it does not set state 

permit fees.

A commenter objected to the EPA’s position that dust particles, feathers, manure, and other materials 

blown from animal house ventilation exhaust fans, when mixed with precipitation, become process 

wastewater and a regulated discharge. The commenter stated that discharges associated with such 

emissions were not considered in the cost analyses conducted to support rule development, and were not 

specifically identified in the proposed or final rules. The commenter noted that the final 2003 CAFO 

33 U.S. EPA, Information Collection Request for Animal Sectors, OMB Control No. 2040-0250, EPA 

ICR No. 1989.08 23 (2013); 40 CFR 122.44(a)(1); 40 CFR 125.3. 

34 USDA, 2007 Census of Agriculture: United States Summary and State Data AC-07-A-51, Volume 1 

(2009), available at http://www.agcensus.usda.gov/Publications/2007/Full_Report/usv1.pdf. 

10

 
Rule explicitly rejected the use of the CWA to regulate air emissions. The EPA notes that the CWA 

prohibits the discharge of pollutants from a point source to waters of the United States, except as 

authorized by an NPDES permit.35 The EPA did not establish specific technology-based requirements 

for this source of wastewater pollution in the 2003 CAFO Rule, and therefore did not estimate the cost 

for controlling this source, but it is nevertheless a source of wastewater pollutants from CAFOs and 

permit limits may be established on a case-by-case basis.36 In exercising best professional judgment, the 

permit writer may take into account the specific circumstances of the CAFO structure and any 

environmental risks posed in considering limits that should be imposed. 

A few commenters requested that the EPA consider the economic impacts of continued regulation on 

small ranchers and other livestock and bird growers that depend on CAFOs to make a living. The EPA 

notes that secondary impacts are not considered relevant within economic analyses for rules or the rule 

development process. 

• Technical Issues

As noted above, the EPA promulgated certain requirements in order to comply with court decisions, but 

attempted to afford owners and operators flexibility. The Agency finds that technical burdens have been 

minimized for regulated small entities as much as possible. Some comments discussed below concerned 

substantial modifications to NMPs that are subject to public review. The NMP requirements established 

in 2008 were based on the decision of the Second Circuit Court of Appeals in the Waterkeeper Alliance 

v. EPA case.37 In general, the Agency believes that producers with well-designed NMPs should be able 

to implement the terms of their NMPs in a flexible manner, with minimal need for state oversight and 

public notice of adjustments made to accommodate changing circumstances at the CAFOs. The EPA 

also discusses comments below on other technical issues such as the ELG’s “no discharge” standard and 

runoff that is subject to it, and the definition of the production area. 

A state commenter recommended removing the 5-year crop rotation requirement and alternative crop 

requirements from the narrative rate approach outlined in the 2008 CAFO Rule, as long as a state has a 

process for calculating application rates. The EPA notes that, in Waterkeeper Alliance v. EPA, the Fifth 

Circuit Court of Appeals held that the terms of a CAFO’s NMP are effluent limitations subject to public 

review, and that these effluent limitations must be included as terms of the permit—even if the permit 

term is for 5 years, as required by the CWA.38 The EPA designed the regulatory requirements in the 

2008 CAFO Rule to allow permittees to implement the terms of the NMP over the entire course of a 5-

year permit term, unless the operator needs to make one of four types of substantial modifications to the 

NMP, in which case public review would be required. Thus, the EPA worked to minimize the number of 

instances when public review would be required. States may address NMP requirements on a short-term 

basis if they prefer to do so. In general, however, the narrative rate approach allows CAFO operators 

flexibility to anticipate adjustments that may be required during the course of implementing an NMP 

and to make adjustments consistent with the terms of the NMP during the period of permit coverage. A 

producer with a well-designed NMP should, in general, be able to implement the terms of the NMP in a 

flexible manner, with minimal need for public notice of adjustments made to accommodate changing 

circumstances at the CAFO.

35 33 U.S.C. 1251(a). 

36 33 U.S.C.1342(a)(1); 40 C.F.R. 125.3(c), (d). 

37 399 F.3d 486. 

38 Id. at 502. 

11

 
Commenters remarked on the procedures promulgated in the 2008 CAFO Rule for making changes to 

NMPs. A state commenter observed that additions of fields to land application areas should be reviewed 

by states, but should not be subject to public notice because the time involved in the public notice 

process creates risk for operators to miss seasonal windows for land application. The commenter 

suggested that the EPA could allow CAFOs to temporarily implement substantial changes for up to 180 

days prior to public notice, consistent with a provision proposed by the EPA in its 2006 proposed CAFO 

Rule, whereby there would be a temporary waiver of the approval period for certain substantial changes 

to NMPs. The EPA found that public comments on the proposed 2006 Rule were generally unsupportive 

of this proposal.39 As noted above, in Waterkeeper Alliance v. EPA, the Fifth Circuit Court of Appeals 

held that the terms of a CAFO’s site-specific NMP must be made available to the public for review.40 As 

discussed in the preamble to the 2008 CAFO Rule, the addition of new fields to the NMP is a substantial 

modification of the NMP, and must be subject to public review, consistent with the Waterkeeper

decision. 

A state commented that the review and public notice requirements for substantial changes to the terms of 

the NMP are administratively burdensome to both CAFO operators and the permitting authority, and can 

delay crop management decisions, causing operational and management challenges. The commenter 

added that changes to the permit term, “the outcome of a field risk assessment,” [sic] should not be 

considered a substantial change needing public notice if the risk assessment is determined using the 

Phosphorus Index (PI). The state explained that, even when the risk rating increases, the potential for 

phosphorus site runoff remains unchanged because application rates must be decreased when the PI 

increases. The state recommended that the permitting authority have flexibility in determining when 

subsequent revisions of NMPs need review and which of those revisions require public notice. As the 

EPA notes above, in Waterkeeper Alliance v. EPA, the Fifth Circuit Court of Appeals held that the terms 

of a CAFO’s site-specific NMP must be made available to the public for review.41 Following the 

Waterkeeper decision, the EPA issued the 2008 CAFO regulations, which require changes to the NMP 

to be reported to the state Director, in order for the Director to determine whether or not the changes 

require revising the terms of the NMP. Such changes can be implemented without public comment, 

unless the Director determines that the changes are substantial. The regulations require certain changes 

to be treated as substantial changes, thus requiring public notice and comment. The EPA notes that 

changes to “the outcome of the field-specific potential for nitrogen and phosphorus transport” do not, 

per se, constitute a substantial change needing public notice if the risk assessment is determined using 

the PI. Moreover, if the operator is following the requirements of the narrative rate approach, changes to 

the rate of application resulting from recalculations based on the most recent soil test data are not subject 

to the provisions for substantial changes.42 Thus, where the narrative rate approach is used for 

determining rates of application, changes in field-specific rates of application and concomitant changes 

to the PI ratings for those fields would not result in a substantial modification, so long as other extrinsic 

factors have not resulted in changes to “the maximum amounts of nitrogen and phosphorus derived from 

all sources for each crop.”

A commenter suggested that the ELG’s “no discharge” standard up to a certain size storm event is 

confusing and inconsistent with establishment of effluent limitations on actual discharges from other 

types of regulated industries. The commenter added that runoff from rainfall that occurs when the ELG 

is exceeded should be classified as stormwater and not subject to the CAFO “no discharge” 

39 73 Fed. Reg. 70,455. 

40 399 F.3d 486 at 502–503. 

41 Id.

42 40 CFR 122.42(e)(6). 

12

 
requirements. The EPA notes that effluent limitations for CAFOs are based on the nature of the 

activities associated with this unique industry. Effluent limitations in the form of best management 

practices, in conjunction with the prohibition of discharge (except as provided in the ELGs), are 

particularly suited to the regulation of CAFOs. For many CAFOs, controlling discharges to surface 

waters is largely associated with controlling runoff and controlling overflows from manure storage 

structures. For this reason, the EPA has determined that the use of numeric ELGs to control these 

discharges is generally infeasible. 

A state commenter suggested that the “support area,” including raw materials storage area, should not be 

subject to the regulations, in order to reduce burdens on operators associated with production area 

requirements. The EPA regulations define the entire production area as part of the CAFO. The 

production area includes the raw materials storage areas, which in turn includes feed silos, silage 

bunkers, and bedding materials storage. These areas must be managed to ensure that any wastewater 

generated is properly captured in order to meet the applicable ELGs. In the same way that releases and 

runoff of manure, litter, and process wastewater can cause adverse environmental impacts, releases of 

raw materials themselves can cause adverse effects.

• Implementation Issues

In general, the EPA did not receive relevant comments concerning implementation of the regulations for 

regulated small entities. Most comments regarding implementation were outside the scope of this 

review, such as concerning implementation of the regulations by state agencies.

State commenters requested that the EPA address differences in nutrient management planning 

requirements between CAFOs and non-CAFOs that receive manure from CAFOs. Some commenters 

thought the EPA should do this through rulemaking, and some thought the EPA should do this by 

highlighting best practices in states that have already addressed this concern. The EPA notes that the 

federal CAFO regulations do not include requirements for recipients of manure that are not CAFOs, but 

states may address recipients of CAFO-generated manure under non-NPDES state programs. The EPA 

recommends that states that have addressed concerns such as this share their experiences with other 

states that may be seeking to address this issue. To facilitate this information sharing, the Agency is 

developing a summary of state manure transfer programs and incentives, which the EPA will make 

publicly available. 

3. Complexity of the rule.

As discussed above, burdens from the 2003 CAFO Rule have been eliminated for many CAFOs in the 

2008 and 2012 revisions by virtue of the fact that they do not have to apply for permits if they do not 

discharge. A number of the comments addressed in the preceding discussion involved issues relating to 

the complexity of the CAFO regulations for those facilities that do discharge. This section does not 

repeat comments that have already been addressed in other sections of this report, but acknowledges that 

those concerns were raised by a number of commenters. This section summarizes the remaining 

comments that explicitly referred to complexity of the regulations, which generally indicated that the 

regulations are not too complex or unreasonable. 

Some commenters highlighted the fact that the regulatory burden for CAFO operators is less than for 

most other NPDES permittees because CAFOs are not required to conduct water quality monitoring and 

reporting, as is required of most other NPDES permittees. In addition, a commenter stated that 

modifications to the 2003 CAFO Rule have reduced the complexity of the regulations for most CAFOs, 

13
since only CAFOs that discharge are required to apply for permits and comply with the regulatory 

requirements. The EPA notes that the burden and complexity of the CAFO regulations have been 

reduced or eliminated for some small entities, as discussed above.

4. Extent to which the rule overlaps, duplicates, or conflicts with other federal, state, or local 

government rules.

The CAFO regulations are designed to support and complement the array of voluntary and other 

programs implemented by the USDA, the EPA, and the states. The EPA finds that the CAFO regulations 

accommodate differences in state-specific requirements and provide flexibility to allow state and local 

rules to be stronger than the federal CAFO regulations. In its 2013 renewal of the Information Collection 

Request for Animal Sectors, the EPA found that almost all of the information requested from 

respondents is required by statute or regulation and, in most cases, not available from other sources. The 

EPA examined requirements contained in the CWA and 40 CFR Parts 122, 123, 124, 125, 403, 501, and 

503, as well as consulted the EPA’s Inventory of Information Collection Requests, ICIS-NPDES, 

Government Information Locator Service, and USDA Census of Agriculture. Examination of these 

databases and discussions with other federal agencies did not identify any reporting requirements that 

duplicated existing requirements for CAFO facilities.

43

Several commenters indicated that the federal CAFO regulations are necessary because other regulatory 

programs or other portions of the CWA do not otherwise adequately address CAFOs. A commenter 

stated that the federal regulations are necessary because state permitting programs are inconsistent with 

each other; do not exist in all states; and, in the commenter’s view, do not meet CWA requirements on 

their own. The EPA notes that although state programs may be stronger in areas not addressed by the 

federal program, such programs often lack the opportunity for public involvement and oversight, as well 

as state oversight of nutrient management planning, that the CWA provides. The statutorily mandated 

transparency requirements that EPA has implemented in the CAFO regulations ensure that citizens are 

able to learn about and influence actions that affect their neighborhoods and the quality of their local 

water bodies and environment. 

Several commenters stated that the availability of federal and state (as well as industry) funding 

resources to assist CAFO operators in complying with the rule’s zero-discharge effluent limitation 

significantly reduces the economic burden on regulated entities. The EPA notes that the economic 

analysis the Agency performed for the 2003 CAFO Rule revisions included consideration of federal 

and/or state cost-share assistance and the effects of this assistance on the economic achievability of the 

revised regulations.

A state commenter voiced support for the discretion provided to state directors or regional 

administrators in designating medium or small AFOs as CAFOs because it allows states to consider the 

seriousness of a discharge from a medium or small AFO before designating an AFO as a CAFO. Some 

comments expressed support for the flexibility allowed for states to base their CAFO programs on 

regional variations such as weather and climate. Some commenters described specifically how certain 

state programs both overlap with and differ from federal regulations. These commenters supported the 

EPA continuing to provide states flexibility to implement state-specific requirements. Another state 

commenter expressed the opinion that many state animal agriculture programs are more robust, 

comprehensive, and protective of water quality, while not identically matching the current federal 

43 U.S. EPA, Information Collection Request for Animal Sectors, OMB Control No. 2040-0250, EPA 

ICR No. 1989.08 5 (2013).

14

 
regulations. The commenter suggested that the EPA consider allowing states to continue programs 

without having to change them to match the federal regulations. A commenter suggested that the EPA 

allow state and local rules to be stronger than the federal CAFO regulations. The EPA finds that the 

CAFO regulations provide the flexibility requested by these commenters, as the federal regulations 

accommodate differences in state-specific requirements. The EPA’s regulations ensure that “States are 

not precluded from omitting or modifying any [NPDES regulatory] provisions to impose more stringent 

requirements.”44 In addition, state technical standards are developed by each state to address the 

particular agricultural operations in that state. When federal regulations are modified, program revisions 

may be necessary to ensure that the state programs are consistent with federal law.45 The EPA generally 

works closely with state agencies to incorporate any new federal requirements as seamlessly as possible 

into existing state programs. If the state program modifications are substantial, the EPA provides the 

opportunity for public notice and comment.46

5. The degree to which technology, economic conditions, or other factors have changed in the 

area affected by the rule. 

Most commenters who spoke to the degree to which technology, economic conditions, or other factors 

have changed in the area affected by the rule, stated that the 2003 CAFO Rule’s impact on small entities 

either has not changed or has diminished based on changes in technology, economic conditions, or other 

factors.

A commenter stated that contraction of the livestock industry, including small livestock businesses, is 

due to market factors such as milk and hog prices, and not due to economic burden from the NPDES 

CAFO regulations. The commenter stated that CAFO operations have become larger since the EPA 

performed its initial analysis, such that fewer small businesses are affected by the rule. As discussed 

above, in promulgating these regulations, the Agency evaluated the risk that the regulations would cause 

businesses to fail and found that they would result in only a limited economic effect on the regulated 

community. 

Some commenters stated that the CAFO regulations have had diminished impacts on small businesses as 

a result of rule revisions that reduced the number of operations covered. 

A commenter stated that the fact that the EPA has not introduced new technology requirements, but 

rather, twice narrowed the scope of the 2003 CAFO Rule, supports a finding that CAFO regulations are 

not a burden on small entities. As noted above, the EPA agrees that the regulatory burden for CAFOs as 

a whole has declined since regulation changes have reduced the total number of facilities that need to 

apply for permits.

6. Comments outside the scope of the review. 

Comments or suggestions that pertained to the impact of the CAFO regulations on regulated small 

entities were within the scope of this review. Most of the comments pertaining to the impact of CAFO 

regulations on non-regulated or non-small entities (such as impacts on states, large regulated entities, or 

non-regulated small businesses) were outside the scope of this review. Some commenters also discussed 

44 40 CFR 123.25(a). 

45 40 CFR 123.62(a), (b). 

46 40 CFR 123.62(b).

15

 
suggestions for future or potential rulemaking (i.e., regarding prospective regulations, and not regarding 

regulations that currently exist). These comments were considered outside the scope of this review 

unless they pertained specifically to impacts on small regulated entities. Some of the topics raised in 

comments that were outside the scope of this review included: 

• the EPA’s authority under the CWA; 

• the frequency of CAFO rulemaking activity; 

• suggested revisions for future rulemaking (not directly tied to comments on the rule’s impact on 

small entities);

• NPDES regulations not related to CAFOs;

• burdens faced by states that regulate CAFOs;

• enforcement and compliance issues;

• environmental issues not associated with CAFO discharges covered by the CWA; and 

• complaints about specific existing or proposed CAFO facilities. 

Conclusion

After reviewing the CAFO regulations and the comments received for this RFA Section 610 review, the 

EPA has concluded that revisions to minimize the regulations’ economic impacts on small entities are 

not warranted at this time. The EPA finds a continued need for regulation of CAFOs, as promulgated in 

the 2003 CAFO Rule and amended in 2008 and 2012, to manage manure effectively in order to protect 

the nation’s water quality and human health. 

Based on economic analyses and cost analyses conducted by the EPA in the 2003 CAFO rulemaking, 

the Agency determined that the requirements were economically feasible for small businesses. The 

revisions to the CAFO regulations in 2008 and 2012 have further reduced the universe of CAFOs that 

must have NPDES permits and yielded a net reduction in burden to CAFO owners and operators, 

including small business owners and operators. 

In addition, the EPA has taken a number of measures to assist small entities including training, guidance 

and other materials, and support for states in their implementation of the CAFO regulations. The EPA 

will continue to evaluate the effectiveness of the CAFO regulations, consider ways to minimize burdens 

associated with implementation, and continue to work with states and assist small entities in ensuring the 

protection of the nation’s water quality.

16