Clean Water Act CAFO
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Overview of Clean Water Act CAFO Rule
I. What is this Rule?
Issuance of the final Clean Water Act (CWA) Concentrated Animal Feeding Operation (CAFO) rule, published in the Federal Register on November 20, 2008, completes a process the U.S. Environmental Protection Agency (“EPA”) set in motion in the late 1990’s to fundamentally reform and dramatically expand the federal regulation of livestock and poultry operations to protect water quality. Starting formally with a proposed rule in 2001, a final rule in 2003 that had portions overturned in federal court in 2005 (the “Waterkeeper decision”), and then subsequent proposed rulemakings in response to the court’s decision, the issuance of the final rule on November 20, 2008 is the culmination of a sustained, ten-year effort. While the November 20 rule implements changes to the 2003 CAFO rule in response to the Waterkeeper decision, many provisions of the 2003 CAFO rule were untouched by Waterkeeper and these remain in effect and are not changed by the new rulemaking.
The unchanged 2003 rule provisions, plus those issued on November 20 in response to Waterkeeper, constitute in total how EPA will implement the CWA’s prohibition against discharges of pollutants from livestock and poultry operations to the waters of the U.S. These regulations establish the National Pollution Discharge Elimination System (“NPDES”) permitting requirements for operations needing or wanting permits. The new rule also makes available “no discharge certification” criteria for those operations that do not need or want permits. Legal challenges to this final rule may yet take place, and so subsequent amendments to this final rule could be called for in the future.
II. Who is Covered by this Rule?
Essentially all animal feeding operations (“AFOs”) are covered by this rulemaking and the CWA’s prohibition against the discharge of pollutants to the waters of the U.S. AFOs over certain threshold sizes are considered “large CAFOs” and these CAFO rule requirements will in practice tend to be applied to them more commonly than for smaller operations. But in general, small, medium and large AFOs, if they are discharging manure or wastewater to waters of the U.S. are subject to CWA penalties. “Large” cattle CAFOs are defined by EPA as having 1000 head. “Cattle” includes but is not limited to heifers, steers, bulls and cow/calf pairs.
III. Who has to get a Permit?
The Waterkeeper decision stated that CAFOs that simply have a “potential to discharge” cannot be required to get a federal NPDES permit because the CWA regulates only actual discharges. As a result, the 2003 rule had to be modified to make it clear that only CAFO’s that “discharge or propose to discharge” are required to apply for an NPDES permit. The final rule calls for a case-by-case evaluation by the CAFO owner or operator as to whether the CAFO discharges or proposes to discharge from its production area or land application area. “Propose to discharge” means that a CAFO is “designed, constructed, operated or maintained in such a way that a discharge will occur.” While CAFOs that do not discharge nor intend to do so can apply for and receive an NPDES permit, it is the CAFO’s decision to make.
While the Waterkeeper decision may alleviate currently non-discharging CAFOs from the responsibility to get an NPDES permit, that decision does NOT relieve the unpermitted CAFO from the significant CWA liabilities if they discharge manure or wastewater into the waters of the U.S. at some point. Indeed, an unpermitted CAFO that has a discharge will be liable for the CWA’s penalties of up to $32,500 a day for discharging without a permit, plus a “second Duty to Apply” penalty of up to $32,500 per day for a violation described in the next paragraph.
Under EPA’s interpretation of the CWA, a CAFO that does not have an NPDES permit and does have a discharge is liable for more than just the discharge penalty under the CWA. The final rule establishes that an unpermitted discharging CAFO is also liable for a penalty for the failure to obtain an NPDES permit prior to the discharge. This latter penalty is referred to as the “second Duty to Apply” penalty which applies as soon as a CAFO proposes to discharge; and the discharging CAFO has the burden of establishing that it did not propose to discharge. According to EPA’s interpretation of the law and planned implementation of the rule, obtaining a permit is the only way for a CAFO to avoid these two penalties if the CAFO anticipates that it may have a discharge in the future. The first penalty would be imposed for the discharge itself; the second penalty would be imposed for each day the CAFO has not had a permit since the day the EPA determines that the CAFO discharged or proposed to discharge. There is a new provision, described below, in the final rule that allows a CAFO to avoid the second penalty if it voluntarily goes through a rigorous process to certify that it is a “no discharge” CAFO.
There is a question about whether EPA’s second “Duty to Apply” penalty is a fundamental misreading of the CWA and is an unlawful extension of the agency’s authority. Many animal agriculture groups believe that the CWA only authorizes sanctions for the discharge and not also for the failure to have a permit prior to a discharge. This issue may be litigated in the future.
IV. Agricultural Stormwater Exemption (ASE)
In the case of both permitted and unpermitted CAFOs, Waterkeeper did not relieve them from their responsibility to properly manage the application of manure or wastewater to land they control. As a result, under the CAFO rule all CAFOs (with or without an NPDES permit) that land apply manure or wastewater to land they control must do so in accordance with a nutrient management plan (NMP) containing EPA requirements that ensures nutrients are applied in accordance with “appropriate” agronomic and conservation practices in order to qualify for the Agricultural Stormwater Exemption (“ASE”) in the event a discharge reaches a water of the U.S. CAFOs also must use up to date soil and manure tests and they must document their use of all these practices in a recordkeeping system. CAFOs that use such an NMP, with associated records, will be exempt from being considered an illegal point source discharge under the CWA if runoff occurs during a precipitation event. CAFOs that do not have a nutrient management plan nor keep up-to-date records of their proper use of the plan could be liable for penalties described above.
CAFOs that have an NPDES permit will qualify for the ASE by following the NMP that they must submit with their permit application and which is reviewed by the public and approved for use by the permitting authority. Non-NPDES permitted CAFOs will need to have and use a similar NMP that meets these same ASE standards, and can do so either by getting an NMP that is comparable to that required under an NPDES permit, and keeping the appropriate records, or by practicing nutrient management in a manner that is otherwise deemed consistent with the practice standards in the NMP, as interpreted by the state. In this latter instance, full records also must be kept.
V. Permits Needed by February 27, 2009
The deadline for securing an NPDES permit for newly defined CAFOs, with an approved NMP, is February 27, 2009. The final rule states that CAFO’s that are discharging and need a permit, or that discharge in the future for whatever reason, should have their NPDES permit in hand by this date. Failure to do so could subject the discharging CAFO to CWA penalties described above.
Authorized states have up to one year to revise, as necessary, their NPDES regulations to adopt the requirements of the final rule, or two years if statutory changes are needed. States are not required to adopt the provisions for a no discharge certification in this time period.
The final rule also states that 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. Submission of a permit application does not equate to permit coverage: the CWA does not allow any CAFO to discharge without a permit regardless of whether a permit application has been submitted.
VI. No Discharge Certification
The final rule enables CAFOs to avoid the second “Duty to Apply” penalty in the event of a discharge by certifying based on an objective assessment that the CAFO operation does not discharge or propose to discharge. (A discharging CAFO would, however, still be liable for the first duty to apply penalty, i.e. discharging without a permit.)
A CAFO seeking the protections offered by a “no discharge certification” must (1) have an NMP that meets the same standards as an NPDES permit holder’s NMP; (2) conduct a study of the production area to show that it is designed, constructed, operated, and maintained so as not to discharge using Animal Waste Management (AWM) software, or equivalent software, and the Soil Plant Air Water (SPAW) hydrology tool, or an equivalent model; and (3) maintain documentation either onsite, at a nearby office, or where it can be made readily available.
The CAFO seeking the protections offered by a “no discharge certification” must submit a signed certification statement to the Director certifying that the CAFO has taken these steps and also provides some basic information about their operation. The signed certification makes the CAFO legally responsible for its representations to the Director. A CAFO’s no discharge certification is not subject to review by the permitting authority, and the permitting authority is not required to make the certification available for public review and hearings because the voluntary certification is not a permit requirement. Nor do they submit the annual NMP report that is required of the NPDES permit holder.
A CAFO that has a no discharge certification is presumed not to propose to discharge. Therefore, if a certified CAFO does discharge, the burden will be on the Director to establish that the CAFO proposed to discharge prior to the discharge in order to hold the CAFO liable for the second duty to apply penalty. (Recall that in a situation where an uncertified, unpermitted CAFO discharges, the burden is on the CAFO to establish that it did not propose to discharge.)
A CAFO that has a no discharge certification and has subsequently had a discharge may re-qualify its operation for a no discharge status by correcting the problem that caused the discharge.
A no discharge certification will expire five years after the effective date, unless the CAFO voluntarily withdraws the certification or it becomes invalid during the five year term. A certification can be renewed under certain circumstances.
VII. Nutrient Management Plans
Required contents of NMPs are listed in the 2003 CAFO rule. The Waterkeeper decision determined that all NMPs must be reviewed by the permitting authority; that the public must have adequate participation in the development, revision, and enforcement of the NMPs; and that the terms of the NMPs must be included as enforceable provisions in the permit.
A. CAFO Permit Application or Notice of Intent Requirements for NMPs
Applicants are required to submit to the permitting authority, as part of an individual permit application or Notice of Intent (NOI) to be covered under a general permit, an NMP developed in accordance with regulatory provisions detailed in the 2003 rule. The permitting authority must make the NMP available for public review, comment, and hearing. CAFO owners/operators are reminded that under the 2003 rule, CAFOs that transfer manure to persons outside of the CAFO operation must provide the recipient with the “most current nutrient analysis.”
B. Procedure for Permitting Authority Review and Public Participation Prior to Permit Coverage
After the permitting authority receives an application or an NOI from a CAFO, the permitting authority must review the application or NOI to ensure that it meets regulatory requirements, and for general permits, the requirements of the general permit. No specific timeframe for completion of this review is prescribed in the regulation. The permitting authority may obtain assistance and advice from technical experts, or tailor its review based on the development or certification of NMPs by State-certified nutrient management planners. The Director must provide for adequate opportunity for public review of both a CAFO’s NMP and the terms of the NMP to be incorporated into the permit prior to the CAFO obtaining permit approval.
When the permitting authority develops a draft general permit, it must provide the public with an opportunity to review the draft permit, submit comments, and request a hearing. A permit will be finalized after considering and responding to “significant” comments. Facilities may then submit an NOI seeking coverage under the final general permit. General permits for CAFOs must include terms of an NMP applicable to each specific CAFO authorized under the permit. The public must have an opportunity to review, comment, and hold a hearing on each CAFO-specific NMP and on the terms of the NMP to be incorporated into the permit. Thus, a second round of notice, comment, and hearing is necessary when providing coverage under a general permit. The Director has discretion as to how best to provide the public notification in the general permit context, and to establish an appropriate period of time for public review. The final rule does not restrict the ability of a permitting authority to provide notice of multiple NMPs at one time, but notice must be adequate, and the opportunity for comment must be meaningful. After consideration of public comments, the permitting authority may either grant coverage under the general permit, require the facility to seek coverage under an individual permit, or deny permit coverage.
For individual permits, the NMP will be submitted and reviewed as part of the permit application. If necessary, CAFOs are given the opportunity to modify the plan or provide additional information as requested. The Director must make a final decision after an opportunity for public comment and hearing. Procedures for public participation in the issuance of individual permits are already established in NPDES regulations that apply to all NPDES permit applicants. These regulations provide for a 30 day public notice period for proposed coverage under individual permits.
C. Identification of Terms of the NMP
The final rule establishes that the “terms” of the NMP “are the information, protocols, best management practices, and other conditions” identified in the CAFO’s NMP and determined by the permitting authority to be necessary to meet all of the measures required to be included in a CAFO’s NMP for both the production area and the land application area. In other words, terms of the NMP include whatever is contained in the NMP that is necessary to ensure compliance with § 122.42(e)(1) and, for large CAFOs, 40 CFR 412.4. Requirements in both of these sections of the regulation were included in the 2003 rule. Additional content of the NMP that is beyond the scope of compliance with these regulatory requirements would not be a term of the NMP. The 2008 final rule adds, however, three additional terms for CAFOs that land apply manure and wastewater. These terms include: 1. the fields available for land application (i.e. new fields must first be added to the NMP and the permit before they could be used by the CAFO for land application), 2. field-specific, crop specific rates of application, and 3. any timing limitations in the NMP that would make fields unavailable for land application at certain times or under certain conditions.
i. Rates of Application
The final rule requires the NMP to include “protocols to land apply manure, litter, or process wastewater in accordance with site-specific nutrient management practices that ensure appropriate agricultural utilization of the nutrients in the manure, litter, or process wastewater.” The rule allows for two alternative approaches for expressing rates of application: 1. the linear approach, 2. the narrative rate approach.
Under the linear approach, terms include maximum application rates for each year of permit coverage, for each crop identified in the NMP, in pounds per acre, per year, for each field to be used for land application, and other factors. The approach is considered “linear” because it is based on the use of only those crops included in planned crop rotations in the NMP; the amounts of nitrogen (N) and phosphorus (P) from manure, litter, and process wastewater to be land applied according to the planned schedule for land application (including source and method and timing of application); and the projected values for plant available N and P from other sources. Under this approach, a single set of field-specific rates of application would be established based on the predicted sequence of activities the CAFO plans to follow in implementing its NMP, and a CAFO would be required to follow the sequence identified in the NMP for each field, specific crop rotation, and each planned step for land application of nutrients. A CAFO must land apply nutrients in amounts that will result in the application of no more than the amounts of N and P specified for each field in the NMP, following the schedule and methods of application described in the NMP, taking into account annual manure test results required of large CAFOs, so as not to exceed the nutrient needs of the crops. Amounts of nutrients must be translated from pounds to tons or gallons. Any changes to the terms of the NMP would constitute a change in the terms of the permit, which would require a permit modification. Operators may provide themselves some flexibility by specifying more than one field-specific crop rotation plan in the NMP together with application rates for each alternative plan.
Under the narrative rate approach, rates of application can be expressed as a narrative rate that includes the total amount of plant available nutrients from all sources, combined with a specific, quantitative method for calculating the amount, in tons or gallons, of manure, litter, or process wastewater allowed to be land applied. Terms of the NMP include the maximum amounts of N and P (determined by the methodology set forth in the NMP) from all sources of nutrients for each crop or other field use identified in the NMP, in chemical forms determined to be acceptable to the Director, in pounds per acre, for each field. Other terms of the narrative rate approach include: 1. the outcome of the field specific assessment of the potential for N and P transport from each field (i.e. the phosphorus index), 2. the crop or crops to be planted in each field or any other uses such as pasture or fallow fields, 3. the realistic yield goal for each crop or use identified for each field, 4. the N and P recommendations from sources specified by the Director for each crop or use identified for each field, and 5. the methodology by which the NMP accounts for certain factors when calculating the amounts of manure, litter or process wastewater to be land applied. A CAFO using the narrative rate approach is required to apply in accordance with the resulting calculations that must be recalculated at least annually. Under this approach, rates of application can be changed without requiring the permit to be modified. The rule specifies factors that must be included in the methodology used by the CAFO. These factors are not terms of the permit, but the methodology is a term. Thus, the CAFO operator will be bound by the methodology and the way in which the factors must be accounted for in calculating the actual amount of nutrients to be land applied to each field. While the narrative rate approach requires CAFOs to project in their NMP the amount of manure, litter and process wastewater to be land applied, the projections are not terms of the NMP. The purpose of the projections is to give the permitting authority and the public an opportunity to review, prior to permit issuance, the adequacy of the CAFO’s methodology and the way the CAFO uses the methodology. In addition, crop rotations not included in the planned rotation in the NMP would be allowed. Calculations and the data from which they are derived are required to be included in the annual report for the previous 12 months.
D. Process for Incorporating Terms of the NMP into a General Permit
When a Director chooses to grant permit coverage to a CAFO, the Director must incorporate the relevant terms of the NMP into the general permit and inform the CAFO owner/operator and the public that coverage has been authorized and of the applicable terms and conditions of the permit. The Director is given the discretion to decide how to incorporate terms into the permit. For example, the Director could decide to attach the entire NMP and require compliance with the terms, or he could specifically identify each term in the permit. The rule provides some state discretion by allowing permitting authorities to determine which NMP provisions to include as terms of the permit, i.e. the rule specifies minimum terms in the permit, but states have the authority to adopt additional or more stringent requirements.
E. Changes to a Permitted CAFO’s NMP
CAFOs are required to notify the Director of all changes to the NMP, excluding the results of calculations using the linear or narrative rate approaches since these changes must be included in a CAFO’s annual report. The final rule lists changes to the NMP that would constitute “substantial” changes to the terms of a 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 in the maximum field specific rates of application or to the maximum amounts of N and P derived from all sources for each crop, as expressed in accordance with the linear or narrative rate approaches (for the narrative rate approach, this means any increase in the rate of application above the maximum rate determined by the methodology in the NMP); 3. addition of any crop not included in the terms of the CAFO’s NMP and corresponding field specific rates of application; 4. changes to the field specific components of the CAFO’s NMP, where such changes are likely to increase the risk of N and P transport from the field to waters of the US. The rule makes an exception to the first type of substantial change by allowing CAFOs to use additional land for application as long as the land is already included in the terms of another existing NMP incorporated into an existing NPDES permit, as long as nutrients are applied in accordance with the terms of the existing permit.
F. Process for Review of Changes to an NMP and for Modifying Terms of the NMP Incorporated into the Permit
When a CAFO’s NMP is revised, the operator must submit the revised NMP to the permitting authority and identify the changes from the previous version. Submission of the revised version is required to enable the Director to determine whether revisions to the CAFO’s NMP necessitate revisions to the terms, and if so, whether such changes are substantial or non-substantial. Non-substantial changes are not subject to public notice and comment before the permit is revised. If changes are non-substantial, the Director must notify the CAFO that the permit does not have to be modified. Upon such notification, the CAFO may implement the revised NMP.
If the Director determines that changes to the terms are substantial, the Director will 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. The Director must respond to all significant comments, and require revisions to the NMP if necessary. Once terms are incorporated, the owner/operator and the public must be notified. The Director may establish an appropriate period of time for the public to comment and request a hearing on the proposed substantial changes to the terms.
G. Annual Reporting Requirements
The final rule requires that all permitted CAFOs include in their annual report the actual crops planted and actual yields for each field, the actual N and P content of the manure, litter or process wastewater, and the amount of manure, litter or process wastewater applied to each field during the previous 12 months. This requirement ensures that the CAFO has been operating in compliance with the terms of its permit. A CAFO that uses the narrative rate approach for determining the manure application rate must include in its annual report the results of all soil testing and concurrent calculations to account for residual N and P 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, and the total amount of plant available N and P from all sources.
H. NMP Template
After considering comments, EPA decided not to utilize an NMP template. Instead, the USDA and EPA 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, known as the Manure Management Planner (MMP), would include the required elements of an NMP as well as the elements of a voluntary comprehensive nutrient management plan (CNMP). The MMP software, under development by a grant from EPA and USDA to Purdue University, is a computer program that will eventually be tailored to all individual state technical standards, requirements, and circumstances. At present, the program has been tailored to 34 states, and is available and ready for use in those states. The MMP software is strictly a voluntary tool. 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 the MMP can be found at: http://www.agry.purdue.edu/mmp/. EPA and USDA re 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.
VIII. Water Quality-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 can be required by states. For example, while agricultural stormwater discharges are allowed under the federal NPDES program, such discharges could be subject to additional state WQBEL requirements. Similarly, while the federal NPDES program allows for occasional discharges from a CAFO’s production area, a state may impose a more stringent WQBEL. Any additional requirements imposed by states would not be federally enforceable.
IX. BCT Limitations for Fecal Coliform
In response to the Second Circuit remand, the final rule affirmatively found that the best conventional pollutant control technology (BCT) limitations adopted in 2003 do, in fact, represent the BCT limitations for fecal coliform. In other words, no changes were made to the 2003 rule on this issue.
Under the revised CAFO rule producers have three primary options if they want to avoid potentially substantial CWA penalties: 1) get an NPDES permit with the associated NMP by February 27, 2009 that has been reviewed and commented on by the public and approved by the permitting authority, and comply with the terms of that permit and the NMP; 2) not get an NPDES permit, but operate their CAFO so as not to have a discharge under any circumstances, use a sound NMP for land application of manure that complies with the agricultural stormwater exemption requirements, demonstrates through modeling that the production area will not discharge, and certify in writing all of this to the permitting authority; or 3) not get an NPDES permit, operate the CAFO so as not to have a discharge under any circumstances, and use a sound nutrient management plan for the land application of manure that complies with the Agricultural Stormwater Exemption requirements.
Relative to the NMP required of producers that choose to seek a permit, there are two options: the linear approach and the narrative rate approach. The linear approach sets rates of nutrient application based on cropping plans that are fixed in the NMP. Any change in the crops grown, the addition of new fields, changes in animal numbers creating more manure for land application, will require that the NMP be resubmitted for further review and re-approval. The narrative rate approach requires the CAFO to specify in its NMP as a term of the permit the method by which it will calculate year-by-year the actual manure application rates for each field, using up-to-date field specific information, and consistent with sound agronomic use. As long as the producer follows this narrative rate approach, applying manure to those fields, crops, and conservation practices using, year-by-year, the method specified in the original NMP, no subsequent NMP review and approval of the manure application rate is needed.