New Clean Water Act Permitting Requirements for CAFOs

Ellen B. Steen
esteen@crowell.com

On Dec. 15, 2002, the U.S. Environmental Protection Agency (EPA) issued its much-anticipated final rule revising the Clean Water Act (CWA) National Pollution Discharge Elimination System (NPDES) regulations and effluent limitations guidelines (ELGs) for concentrated animal feeding operations (CAFOs). The CAFO rule establishes significant new requirements for CAFO owners and operators. Many operations that have never had federal NPDES permits must now obtain permits, develop and implement nutrient management plans that meet specific standards, keep detailed records of their compliance, and submit annual reports to the state or to EPA. Failure to comply with these permit conditions can trigger substantial penalties in enforcement actions by EPA, the state, or interested citizens.

This article summarizes several of the key elements of the new CAFO rule and how they change the prior regulations. A pre-publication copy of the new rule and preamble discussion, along with EPA brochures and other information, is available at <www.epa.gov/npdes/caforule>. In this article, specific page correspond to the page numbers in this pre-publication copy.

Overview of Key Changes in the Rule
EPA’s new CAFO rule establishes several fundamental changes to how animal feeding operations (AFOs) are regulated. First, the rule expands the number of AFOs that are deemed CAFOs and that must have NPDES permits. Second, the rule requires that all CAFO NPDES permits include requirements governing their nutrient management and land application of manure, litter, or process wastewater. Third, the ELG portions of the rule impose specific, more stringent permit conditions on certain “Large CAFOs” (i.e., those with more than 1,000 animal units or “AUs”) in the dairy, beef, swine, poultry, and veal sectors. These new ELG provisions identify specific additional land application, nutrient management, and recordkeeping requirements for these “Large CAFOs.” They also require that newly constructed large swine, poultry, and veal CAFOs meet a 100-year storm design standard, rather than the previous 25-year design standard.

Definition of CAFO
EPA’s original CAFO NPDES regulations (which were issued in 1976) generally defined CAFOs as AFOs that confine more than 1,000 AUs. Medium-sized operations (more than 300 AUs) and even smaller AFOs also were CAFOs if they met certain risk factors (e.g., allowing animals direct access to surface waters) or if they were “designated” on a case-by-case basis by EPA or the state. Under those prior regulations, however, operations that discharged only in the event of a 25-year, 24-hour storm were not CAFOs. See 40 C.F.R. Part 122.23, App. B (2002). As a result of this exclusion, most AFOs that met EPA’s 1,000 AU size threshold were not classified as CAFOs – and did not apply for NPDES permits.

In the revised regulations, EPA has eliminated the exclusion from the “CAFO” definition for operations that discharge only during a 25-year, 24-hour storm. Thus, for example, all operations that meet the size threshold for “Large CAFOs” are CAFOs, even if they are designed and operated to discharge only in the event of a 25-year, 24-hour storm. EPA has retained the previous size thresholds, although it expresses these as specific numbers for various types of animals, rather than in “animal units.” The new rule includes the same types of animals that the original CAFO rules covered, except that EPA has added coverage for swine nurseries and for dry litter chicken operations.

“Large CAFOs” are defined solely on the basis of size – with species-specific numbers that correspond to the previous 1,000 AU threshold (see Table 1).

“Medium CAFOs” are AFOs in the size ranges listed in Table 2 that either: (a) discharge pollutants through a man-made ditch or other device, or (b) discharge pollutants directly into (or whose animals come into direct contact with) an on-site stream running across the facility. Revised 122.23(b)(6).

Even smaller AFOs may become CAFOs by case-by-case designation if they have one or more of the Medium CAFO risk factors and are found (by EPA or the state) to be “substantial contributors” of pollutants to waters of the United States.

Under the new rules, an operation is a CAFO only if it meets the applicable size threshold for a single type of animal. For example, an operation with 700 mature dairy cattle is a Large CAFO, but an operation with 500 mature dairy cattle and 200 heifers is not. Once an operation is defined as a CAFO for one category of animal, however, the CAFO rule governs the handling of all manure, litter, or process wastewater from all animals at the operation. Preamble at 83.

CAFOs Must Obtain an NPDES Permit
The new rule expressly requires that all CAFOs obtain NPDES permit coverage unless they successfully demonstrate that they have “no potential to discharge” pollutants to navigable waters (waters that are subject to CWA jurisdiction). Revised § 122.23(a), (d), (f). The intent of these new provisions is to require that most CAFO operators obtain NPDES permits, even if they manage their operations to avoid any CWA discharge.

The owner or operator of the feeding operation has the duty to apply for an NPDES permit, regardless of who owns the animals. If the owner and operator are different, then it is the operator’s responsibility to apply. 40 C.F.R. § 122.21(b).

Permits will be issued by the state environmental protection agency if the state has been authorized by EPA to administer the NPDES program and has authority to issue permits to CAFOs under state law. Otherwise, operators must obtain permits from the EPA regional office. Currently, all states have authority to issue NPDES permits to CAFOs, with the exception of Alaska, Arizona, Idaho, Massachusetts, New Hampshire, New Mexico, and Oklahoma. See Preamble at 39.

The operator must apply for an individual permit unless a “general permit” is available from the permitting authority. Because of the large number of new permittees and the scarcity of permitting resources, it is likely that most permitting authorities will issue general permits. In those jurisdictions, operators typically will be required to submit a “notice of intent” to be covered by the general permit. Even where a general permit has been issued, however, permitting authorities retain the power to require that a producer apply for an individual permit.

The “No Potential to Discharge” Exception
There is only one exception to the requirement for CAFOs to obtain an NPDES permit. If the CAFO can demonstrate to the permitting authority that it has “no potential to discharge,” then an NPDES permit is not required. To qualify, the applicant must show that “there is no potential for any CAFO manure, litter or process wastewater to be added to waters of the United States under any circumstance or climatic condition.” Revised § 122.23(f). The applicant must make this showing for both its production area and any land application areas. In addition, the CAFO must not have had a discharge within the previous 5 years.

The regulations specify the minimum information for a “no potential to discharge” showing, but the permitting authority can require more. Revised § 122.23(f)(2). The request must be made prior to the deadline for applying for an NPDES permit. The permitting authority’s determination must be made on the administrative record and can be made only after public notice of the request. Even if a favorable decision is made, the permitting authority can reverse its determination based on changed circumstances or new information.

Regulation of Discharges from Land Application Areas
Unlike the original CAFO regulations, the new rules expressly assert regulatory authority over certain discharges from CAFO land application areas. The rule provides that “the discharge of manure, litter, or process wastewater to waters of the United States from a CAFO as a result of [land application] by the CAFO to land areas under its control is a discharge … subject to NPDES permit requirements, except where it is an agricultural storm water discharge as provided in [CWA § 502(14)].” Revised § 123.23(e) (emphasis added). The rule then provides that any such discharge is an exempt “agricultural storm water discharge” where the land application has been “in accordance with site specific nutrient management practices that ensure appropriate agricultural utilization of the nutrients … as specified in § 122.42(e).” Id. (emphasis added). Section 122.42(e) details the requirements for nutrient management plan, which are discussed below.

The rule is silent as to the consequences of failing to comply with the specified nutrient management practices. EPA’s preamble discussion, however, indicates that the agency at least intends to preserve the argument that storm water discharges violate the CWA if land application has not been in accordance with the nutrient management plan. Preamble at 97. According to the preamble, “where such practices have not been used, EPA believes it is reasonable to conclude that land application discharges of manure, litter, or process wastewater are not agricultural storm water but are discharges that Congress meant to subject to NPDES permitting requirements ….” The agency’s statements provide a strong incentive for CAFO operators to insulate themselves from potential liability by operating in accordance with their nutrient management plans. Failure to do so could expose operators to litigation over whether storm water runoff from their fields is an unlawful “discharge.”

Nutrient Management Plans for All CAFOs
EPA’s original CAFO regulations required simply that there be no discharge of process wastewater to navigable waters, except for rainfall-induced overflow from a facility designed and operated to discharge only in the event of a 25-year, 24-hour storm. See 40 C.F.R. Part 122, App. B, and § 412.13 (2002). The rules did not regulate land application.

The revised CAFO rules extend permit requirements to cover land application practices of all CAFOs. Any NPDES permit issued to a CAFO under the new rules must include a requirement to develop and implement a nutrient management plan. Revised § 122.42. Plans must be developed and implemented by Dec. 31, 2006. Id. Each plan must be designed to meet the following requirements.

• Ensure adequate manure storage;
• Ensure proper handling and disposal of mortalities;
• Ensure clean water is diverted from production area;
• Prevent direct animal contact with waters of the U.S.;
• Ensure chemicals are not disposed in manure or storm water storage system;
• Identify site-specific conservation practices to control runoff;
• Identify protocols for testing manure, litter, wastewater, and soil;
• Establish protocols for application to ensure appropriate plant uptake of nutrients; and
• Identify records to be maintained to document implementation of the above elements.

Recordkeeping
Every permitted CAFO must create and maintain certain records – and make those records available to the state or EPA on request. Revised § 122.42(e)(2). First, the CAFO must maintain and make available a copy of the nutrient management plan. In addition, the CAFO must maintain and make available all records that were identified by the CAFO in the nutrient management plan to document the implementation of the management practices specified in the plan (see above).

Annual Reporting
Every permitted CAFO must submit an annual report to the permitting authority. Revised § 122.42(e)(4). The report must include the following information.

• Number and type of all animals;
• Estimated total amount of manure, litter, and process wastewater generated in the last 12 months;
• Estimated total amount of manure, litter, and process wastewater transferred to others in the last 12 months;
• Number of acres covered by nutrient management plan;
• Number of acres under control of CAFO that were used for land application in the last 12 months;
• Description of all manure, litter, and process wastewater discharges from the production area in the last 12 months; and
• Statement of whether or not the nutrient management plan was prepared by a certified planner.

Permit Conditions for Large Dairy, Beef, Swine, Poultry, and Veal CAFOs
The ELG portions of the revised rule (to be codified in 40 C.F.R. Part 412) specify additional requirements that must be included in NPDES permits for so-called “Large CAFOs” in the dairy, beef, swine, poultry, and veal sectors. Medium-sized or smaller CAFOs (such as those that are designated as CAFOs on a case-by-case basis) are not subject to the ELG and will have permit conditions based on the “best professional judgment” of the permit writer.

For production areas at these Large CAFOs, there must be no discharge of manure, litter, or process wastewater pollutants into waters of the U.S., except that rainfall-induced overflow may be discharged if: (1) the production area is designed, constructed, operated, and maintained to contain all process wastewater plus the precipitation from a 25-year, 24-hour rainfall event, and (2) the production area is operated in accordance with specified best management practices (BMPs) and recordkeeping requirements. Revised § 412.31(a) and § 412.33(a). The only exception to this standard is for newly constructed Large CAFOs (“new sources”) in the swine, poultry, and veal sectors, which must meet a 100-year, 24-hour storm design standard, rather than the traditional 25-year, 24-hour standard. Revised § 412.46.

Production area BMPs include daily inspections of water lines (including drinking and cooling water lines), weekly inspections of storm water and runoff diversion devices, and weekly inspections of wastewater impoundments. Mandatory BMPs also include depth markers on open surface impoundments, corrective action to remedy any deficiencies found in inspections, and proper mortality handling. Revised § 412.37.

Production area recordkeeping requirements (set forth at Revised 412.37(b)-(c)) call for documentation of the following:

• Information in permit application;
• Records identified in nutrient management plan to document compliance;
• Required inspections in production area;
• Weekly readings of lagoon depth marker;
• Any corrective action to remedy deficiencies found in inspections;
• Explanation for delay for any corrective action not taken within 30 days;
• Mortality handling and disposal;
• Design and number of days capacity of manure/litter storage structures; and
• Description of any overflow.

For land application areas at all Large CAFOs in these sectors, the permittee must: (1) develop and implement land application BMPs, and (2) maintain land application records. See Revised §§ 412.31(b) (incorporated by reference into BAT and NSPS requirements for dairy, beef cattle, swine, poultry, and veal CAFOs).

Required BMPs for land application (which are described at revised 412.4) include the development and implementation of a site-specific nutrient management plan based on a “field-specific assessment of the potential for nitrogen and phosphorus transport from the field.” The nutrient management plan must require the following:

• Land application rates calculated to “minimize phosphorus and nitrogen transport from the field to surface waters in compliance with the technical standards for nutrient management established by the Director” (i.e., by the NPDES-authorized state or by EPA);
• Manure analysis at least once annually for nitrogen and phosphorus);
• Soil analysis at least once every five years for phosphorus;
• Setbacks of 100 feet from any downgradient surface waters or conduits to surface waters (such as tile line intake structures, sinkholes, or well heads) – or alternative setbacks based on a 35-foot vegetative buffer, field-specific conditions, or alternative conservation practices that provide at least as much protection as a 100-foot setback.

Land application recordkeeping requirements provide that Large CAFO operators must maintain on site a copy of the site-specific nutrient management plan, as well as documentation of the following:

• Records identified in nutrient management plan to document compliance;
• Expected crop yields;
• Dates of land application to each field;
• Weather conditions during, 24 hours before, and 24 hours after land application;
• Methods for manure and soil sampling and analysis;
• Results from manure and soil analysis;
• Calculations of total nitrogen and phosphorus to be applied to each field;
• Total amounts of nitrogen and phosphorus actually applied to each field;
• Method of land application; and
• Dates of land application equipment inspection.

Permit Application Deadlines
There are different application deadlines for different operations, depending largely on when and how the operation first comes within the definition of a “CAFO.” For existing operations that become newly defined as CAFOs on the effective date of the rule, the deadline is three years after the effective date of the rule, unless the permitting agency specifies an earlier deadline. Revised § 122.23(g)(2); Preamble at 124 and 128. This deadline applies, for example, to operations that met the 1,000 AU size threshold of the original CAFO regulations but also met the 25-year, 24-hour storm exemption from the definition of “CAFO.” Thus, if a large operation has been designed and operated to discharge only in the event of a 25-year, 24-hour storm, the rule allows up to three years to apply for permit coverage.

For operations that become newly defined as CAFOs after the effective date of the rule as a result of operational changes, there are alternative deadlines, depending on whether the change would have made the operation a “CAFO” under the original CAFO regulations. If the modified operation would not have been a CAFO under the original regulations (i.e., the operation meets the 25-year, 24-hour design standard), the deadline is the later of: (1) three years after the effective date of the rule, or (2) 90 days after the operation becomes defined as a CAFO. Revised § 122.23(g)(3)(ii)-(iii). This deadline applies, for example, to operations that expand their operations to meet the Large CAFO size threshold. However, if the operational change would have made the operation a “CAFO” even under the original regulatory definition, then the operation must comply with the shorter, 90-day deadline. Id. For example, if the operation is not designed and operated in accordance with the 25-year, 24-hour storm design standard, it must meet the 90-day deadline.

Newly constructed CAFOs – operations constructed at a new site, or that completely replace, or operate independently of, an existing operation at the same site – must apply for a permit at least 180 days prior to commencing operations (prior to populating the facility). See Revised § 122.23(g)(3)(i) and (g)(4). Newly designated CAFOs (i.e., designated substantial contributors of pollutants) must apply for a permit within 90 days of receiving notice of the designation. Revised § 122.23(g)(5).

Conclusion
The revised CAFO rules will usher in a new era for the federal regulation of livestock producers – dramatically expanding the number of operations that must obtain NPDES permits and increasing the potential for enforcement action and liability concerning producers’ compliance with NPDES requirements. To prepare for compliance with the new rules, producers should familiarize themselves with the rules’ requirements, identify which of their operations will require permits, and keep abreast of efforts by EPA regional offices and states to issue “general permits” for CAFOs under the new regulations.

Ms. Steen is a partner with Crowell & Moring LLP in Washington, D.C., and a vice-chair of the Agricultural Management Committee.