inherent in agricultural operations such as anticipated changes in crop
rotation, as well as changes in numbers of animals and volume of
manure, litter, or process wastewater resulting from normal
fluctuations or a facility's planned expansion. Typically, an NMP is
developed to accommodate, for example, normal fluctuations in herd or
flock size, capacity for manure, litter, and process wastewater
storage, the fields available for land application and their capacity
for nutrient applications. Moreover, as discussed in this preamble, EPA
would encourage operators to develop an NMP that includes reasonably
predictable alternatives that a CAFO may implement during the period of
permit coverage. However, unanticipated changes to a nutrient
management plan may nevertheless be necessary.
    The final rule includes 40 CFR 122.42(e)(6), which requires a CAFO
to notify the Director of changes to the CAFO's NMP. Section
122.42(e)(6) excludes the results of calculations made in accordance
with 40 CFR 122.42(e)(5)(i)(B) and 122.42(e)(5)(ii)(D) from the
requirements of paragraph (e)(6). The results of these calculations,
which are required of Large CAFOs using the linear approach and all
CAFOs using the narrative rate approach, must be reported in the CAFO's
annual report. Thus, there is no need to provide this information
pursuant to the requirements of paragraph (e)(6).
    In the 2006 proposed rule, EPA proposed a process that CAFOs and
the permitting authority would need to follow when a CAFO makes changes
to its NMP. The proposal also included criteria for determining when a
change to a CAFO's NMP should be considered a substantial change. In
the 2008 supplemental notice, the Agency solicited comment on several
modifications to the 2006 proposal including a list of changes to the
NMP that would constitute a substantial change.
    In this final rule, EPA is including a list of changes to the NMP
that would constitute a substantial change to the terms of a facility's
NMP, thus triggering public notice and permit modification. Substantial
changes include: (1) Addition of new land application areas not
previously included in the CAFO's NMP; (2) any changes to the maximum
field-specific annual rates of application or to the maximum amounts of
nitrogen and phosphorus derived from all sources for each crop, as
expressed in accordance with, respectively, the linear approach or the
narrative rate approach; (3) addition of any crop not included in the
terms of the CAFO's NMP and corresponding field-specific rates of
application; and (4) changes to field-specific components of the CAFO's
NMP, where such changes are likely to increase the risk of nitrogen and
phosphorus transport from the field to waters of the U.S.
    This final rule also makes one exception to the first type of
substantial change (a land application area being

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

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

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

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

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

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

D. Compliance Dates

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

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

E. Water Quality-Based Effluent Limitations

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

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

F. New Source Performance Standards for Subpart D Facilities

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

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

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

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

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

G. BCT Limitations for Fecal Coliform

    In response to the Second Circuit remand, EPA is today
affirmatively finding that the best conventional pollutant control
technology (BCT) limitations it adopted in 2003 do, in fact, represent
the best conventional control technology limitations for fecal
coliform. After assessing various conventional pollutant removal
technologies, EPA has determined that there are no available and
economically achievable technologies that are cost reasonable that
would result in greater removal of fecal coliform than the technologies
on which EPA based the 2003 best practicable control technology
currently available (BPT) and BCT effluent limitations guidelines
(ELG).
    As EPA has explained, establishing BCT limitations begins by
identifying technology options that provide additional conventional
pollutant control beyond the level of control provided by BPT effluent
limitations. Any such candidate technologies are then evaluated to
determine if they meet the threshold CWA requirements of
``availability'' and ``economic achievability.'' 51 FR 24,974, 24,976;
July 9, 1986. A technology is economically achievable if its costs may
be ``reasonably borne'' by the CAFOs. Waterkeeper Alliance et al. v.
EPA, 399 F.3d 486, 516 (2d Cir. 2005). The Clean Water Act adds an
additional evaluation step to the effluent limitations development
process for conventional pollutants. ``In addition to the Clean Water
Act requirement that effluent limitations be economically achievable,
the cost associated with the BCT effluent limitations must also be
`reasonable' in relation to the effluent pollutant reductions.'' 51 FR
24,974. In determining this, the statute requires that EPA look at a
number of factors including a comparison of the cost of effluent
reductions for POTWs to that for direct dischargers using candidate BCT
technologies. Thus, the statute requires that, not only must the costs
of additional control be costs that CAFOs may reasonably bear
(economically achievable), but the costs must also be reasonable
relative to the costs for POTWs to achieve such conventional pollutant
reductions.
    EPA evaluated 41 BCT candidate technologies for this rule and
determined that all but two of them were either not available
(technically feasible for all CAFOs in a subcategory) or not
economically achievable. For the remaining two technologies, while
their costs are high and EPA believes it likely that they are also not
economically achievable, EPA was unable to conduct its traditional
tests for economic achievability and thus has not determined in this
rule whether or not they are economically achievable. However, EPA has
determined that these two technologies, even if economically
achievable, would not be cost reasonable, and has therefore rejected
them as BCT technologies.
    As a result of this assessment, EPA has concluded that there are no
available and economically achievable technologies that are cost
reasonable that would provide greater fecal coliform removal than the
BPT technology. How EPA performed this assessment and the results of
that assessment supporting EPA's finding that the 2003 BPT/BCT
limitations represent BCT technology for controlling fecal coliform is
described in detail below.
1. The Waterkeeper Decision
    As previously noted, the Waterkeeper court remanded the 2003 CAFO
rule's BCT standard for further clarification and analysis with regard
to the appropriate BCT standard for pathogens.\7\ EPA's 2003 rule
established non-numeric effluent limitations based on BPT and the best
available technology economically achievable (BAT) as well as BCT
limitations. In the 2003 CAFO rule, EPA established BPT effluent
limitations guidelines for Large beef, dairy, and veal calf (Subpart
C), swine and poultry (Subpart D) CAFOs.
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    \7\ As the Second Circuit recognized, the CWA lists only one
pathogen, fecal coliform, as a conventional pollutant for which BCT
limitations are required. Waterkeeper, 399 F.3d at 518. Section
304(a)(4) of the CWA provides that EPA may identify additional
pollutants as conventional pollutants. EPA has identified only one
additional pollutant, oil and grease as a conventional pollutant.
Thus, the only pathogen subject to the Second Circuit remand is
fecal coliform.
---------------------------------------------------------------------------

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

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

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

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

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

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